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On the theory of the proton free induction decay and Hahn echo in polymer systems: The role of intermolecular magnetic dipole-dipole interactions and the modified Anderson-Weiss approximation
NASA Astrophysics Data System (ADS)
The influence of the intermolecular magnetic dipole-dipole interaction on the free induction decay (FID) as well as on the Hahn-echo of proton spins in polymer melts is investigated. It is shown that for isotropic models of polymer dynamics, when polymer segment displacements do not correlate with an initial chain conformation, the influence of the intermolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing more rapidly with evolution time than the corresponding influence of the intramolecular magnetic dipole-dipole interactions. On the other hand, the situation is inverted for the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing faster with time than the contribution from intermolecular interactions. A simple expression for the relative mean squared displacements of polymer segments from different chains is obtained from the intermolecular contribution to the FID. A modified Anderson-Weiss approximation, taking into account flip-flop transitions between different spins, is proposed and on that basis, the conditions for extracting the relative intermolecular mean squared displacements of polymer segments from the intermolecular contribution to the proton FID is established. Systematic investigations of intermolecular contributions, which were considered as an unimportant factor for FID and Hahn echo in polymer systems by most previous works, actually cannot be considered as negligible and opens a new dimension for obtaining information about polymer dynamics in the millisecond regime.
Fatkullin, N.; Gubaidullin, A.; Mattea, C.; Stapf, S.
Dipole-dipole interaction in optical cavities
At the most fundamental level of quantum electrodynamics, there is no such thing as two-body interactions between atoms. The potentials that describe these interactions are effective potentials resulting from a series of approximations whose validity depends on the precise situation at hand. Considering a one-dimensional geometry for simplicity, we discuss under which conditions the familiar form of the near-resonant dipole-dipole interaction is valid, paying particular attention to the effects of interatomic propagation of light, and to what extent it can be modified in the tailored electromagnetic environments provided by optical resonators. We find that once the atoms have established that they are inside a resonator, the dipole-dipole potential may or may not remain a useful concept, depending upon the strength of the atom-field interaction. In the weak-coupling regime, one finds a two-body dipole-dipole interaction that can be enhanced or inhibited by varying the atom-field detuning. In the strong-coupling regime, by contrast, the two-body dipole-dipole potential ceases to be meaningful.
Goldstein, E. V.; Meystre, P.
Alternating 2,6-/3,5-substituted pyridine-acetylene macrocycles: ?-stacking self-assemblies enhanced by intermolecular dipole-dipole interaction.
Macrocyclic compounds consisting of three 2,6-pyridylene and three 3,5-pyridylene units linked by acetylene bonds were synthesized by a Sonogashira reaction. The X-ray structures showed ?-stacked pairs of two macrocycles, in which a 2,6-pyridylene unit of the one molecule overlaps a 3,5-pyridylene of the other molecule because of dipole-dipole interaction. Atomic force microscope (AFM) measurements revealed fibril structures indicating the stacking of the rigid planar macrocycles. Hydrogen-bonding ability of the macrocyclic inside was demonstrated by the addition of octyl ?-D-glucopyranoside. PMID:24446734
Abe, Hajime; Ohtani, Kohei; Suzuki, Daiki; Chida, Yusuke; Shimada, Yuta; Matsumoto, Shinya; Inouye, Masahiko
Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions
We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-?-carotene (?-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute ?-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of ?-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of ?-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of ?-carotene with the vibrations of a proximate solvent molecule through solute-solvent dipole-dipole and dipole-quadrupole interactions. It is shown that the infrared active modes arise from the dipole-dipole interaction, whereas Raman active modes from the dipole-quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 �.
Shimada, Rintaro; Hamaguchi, Hiro-o.
Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions.
We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-?-carotene (?-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute ?-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of ?-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of ?-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of ?-carotene with the vibrations of a proximate solvent molecule through solute-solvent dipole-dipole and dipole-quadrupole interactions. It is shown that the infrared active modes arise from the dipole-dipole interaction, whereas Raman active modes from the dipole-quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10��. PMID:24880300
Shimada, Rintaro; Hamaguchi, Hiro-O
Vortices in fermion droplets with repulsive dipole-dipole interactions
Vortices are found in a fermion system with repulsive dipole-dipole interactions, trapped by a rotating quasi-two-dimensional harmonic oscillator potential. Such systems have much in common with electrons in quantum dots, where rotation is induced via an external magnetic field. In contrast to the Coulomb interactions between electrons, the (externally tunable) anisotropy of the dipole-dipole interaction breaks the rotational symmetry of the Hamiltonian. This may cause the otherwise rotationally symmetric exact wave function to reveal its internal structure more directly.
Eriksson, G.; Cremon, J. C.; Manninen, M.; Reimann, S. M.
Dipole-dipole interactions in solution mixtures probed by two-dimensional synchronous spectroscopy based on orthogonal sample design scheme.
Two-dimensional (2D) synchronous spectroscopy together with a new approach called "Orthogonal Sample Design Scheme" was used to study the dipole-dipole interactions in two representative ternary chemical systems (N,N-dimethyllformamide (DMF)/CH3COOC2H5/CCl4 and C60/CH3COOC2H5/CCl4). For the first system, dipole-dipole interactions among carbonyl groups from DMF and CH3COOC2H5 are characterized by using the cross peak in 2D Fourier Transform Infrared Radiation (FT-IR) spectroscopy. For the second system, intermolecular interaction among ?-? transition from C60 and vibration transition from the carbonyl band of ethyl acetate is probed by using 2D spectra. The experimental results demonstrate that "Orthogonal Sample Design Scheme" can effectively remove interfering part that is not relevant to intermolecular interaction. Additional procedures are carried out to preclude the possibilities of producing interfering cross peaks by other reasons, such as experimental errors. Dipole-dipole interactions that manifest in the form of deviation from the Beer-Lambert law generate distinct cross peaks visualized in the resultant 2D synchronous spectra of the two chemical systems. This work demonstrates that 2D synchronous spectra coupled with orthogonal sample design scheme provide us an applicable experimental approach to probing and characterizing dipole-dipole interactions in complex molecular systems. PMID:24582337
Li, Hui-zhen; Tao, Dong-liang; Qi, Jian; Wu, Jin-guang; Xu, Yi-zhuang; Noda, Isao
Fazovye perekhody metall-diehlektrik v strukturakh s dipol'-dipol'nym vzaimodejstviem. (Metal-insulator phase transitions in the systems with dipole-dipole interaction).
National Technical Information Service (NTIS)
An approach to metal-insulator phase transitions (MIPT) concerning with dipole-dipole interaction in systems has been introduced. Along with dipole states owing to local structural distortions there localized electrons states are considered in Hamiltonian...
O. A. Plaksin V. A. Stepanov
Geometrical Simplification of the Dipole-Dipole Interaction Formula
ERIC Educational Resources Information Center
Many students meet dipole-dipole potential energy quite early on when they are taught electrostatics or magnetostatics and it is also a very popular formula, featured in encyclopedias. We show that by a simple rewriting of the formula it becomes apparent that, for example, by reorienting the two dipoles, their attraction can become exactly twice�
Kocbach, Ladislav; Lubbad, Suhail
Giant Skyrmions Stabilized by Dipole-Dipole Interactions in Thin Ferromagnetic Films
Microsoft Academic Search
Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion
Ezawa; Motohiko
Geometrical simplification of the dipole-dipole interaction formula
Many students meet dipole-dipole potential energy quite early on when they are taught electrostatics or magnetostatics and it is also a very popular formula, featured in encyclopedias. We show that by a simple rewriting of the formula it becomes apparent that, for example, by reorienting the two dipoles, their attraction can become exactly twice as large. The physical facts are naturally known, but the transformation presented seems to underline the geometrical features in a rather unexpected way. The consequence of the features discussed is the so-called magic angle which appears in many applications. The present discussion contributes to an easier introduction of this feature. We also discuss the possibility of designing educational toys and try to suggest why this formula has not been written down frequently before this work. A similar transformation is also possible for the field of a single dipole. In this case we found one such formula on the Web, but we could not find any published detailed discussion for this case either.
Resonant dipole-dipole interaction in confined and strong-coupling dielectric geometries
Using the electromagnetic response function of an electric dipole located within a dielectric geometry, we derive the mathematical equivalence between the classical response and quantum mechanical resonant dipole-dipole interaction between two quantum objects (atoms, quantum dots, etc). Cooperative spontaneous emission likewise emerges from this equivalence. We introduce a practical numerical technique using finite difference time domain for calculating both dipole-dipole interaction and collective spontaneous emission in confined dielectric structures, where strong light-matter coupling might arise. This method is capable of obtaining resonant dipole-dipole interaction over a wide range of frequencies in a single run. Our method recaptures the results of quantum mechanical second order perturbation theory for weak light-matter coupling. In strong coupling situations such as near a photonic band edge, second order Rayleigh-Schr�dinger perturbation theory leads to divergences, and instead Brillouin-Wigner perturbation theory is required. This is equivalent to the use of a variational wavefunction to describe the exciton transfer between initial and final states. We introduce a system of coupled classical oscillators, that describes resonant dipole-dipole interaction and vacuum Rabi splitting in the strong-coupling regime, and that provides an effective numerical scheme based on the finite difference time domain method. This includes the effects of quantum entanglement and the correlation of quantum fluctuations. We discuss the crossover to Forster energy transfer when quantum correlations between the dipoles are damped by strong environmental interactions.
El-Ganainy, Ramy; John, Sajeev
Magnetic Field of a Dipole and the Dipole-Dipole Interaction
With a data-acquisition system and sensors commercially available, it is easy to determine magnetic fields produced by permanent magnets and to study the dipole-dipole interaction for different separations and angular positions of the magnets. For sufficiently large distances, the results confirm the 1/R[superscript 3] law for the magnetic field�
Kraftmakher, Yaakov
Dipole-dipole interactions in optical lattices do not follow an inverse cube power law
We study the effective dipole-dipole interactions in ultracold quantum gases on optical lattices as a function of asymmetry in confinement along the principal axes of the lattice. In particular, we study the matrix elements of the dipole-dipole interaction in the basis of lowest band Wannier functions which serve as a set of low-energy states for many-body physics on the lattice. We demonstrate that, for shallow lattices in quasi-reduced dimensional scenarios, the effective interaction between dipoles in an optical lattice is non-algebraic in the inter-particle separation at short to medium distance on the lattice scale and has a long-range power-law tail, in contrast to the pure power-law behavior of the dipole-dipole interaction in free space. The modifications to the free-space interaction can be sizable; we identify differences of up to 36% from the free-space interaction at the nearest-neighbor distance in quasi-one-dimensional arrangements. The interaction difference depends essentially on asymmetry in confinement, due to the d-wave anisotropy of the dipole-dipole interaction. Our results do not depend on statistics, applying to both dipolar Bose-Einstein condensates and degenerate Fermi gases. Using matrix product state simulations, we demonstrate that use of the correct lattice dipolar interaction leads to significant deviations from many-body predictions using the free-space interaction. Our results are relevant to up and coming experiments with ultracold heteronuclear molecules, Rydberg atoms and strongly magnetic atoms in optical lattices.
Wall, M. L.; Carr, L. D.
Observation of dipole-dipole interaction in a degenerate quantum gas.
We have investigated the expansion of a Bose-Einstein condensate of strongly magnetic chromium atoms. The long-range and anisotropic magnetic dipole-dipole interaction leads to an anisotropic deformation of the expanding chromium condensate which depends on the orientation of the atomic dipole moments. Our measurements are consistent with the theory of dipolar quantum gases and show that a chromium condensate is an excellent model system to study dipolar interactions in such gases. PMID:16241705
Stuhler, J; Griesmaier, A; Koch, T; Fattori, M; Pfau, T; Giovanazzi, S; Pedri, P; Santos, L
Observation of Dipole-Dipole Interaction in a Degenerate Quantum Gas
SciTech Connect
We have investigated the expansion of a Bose-Einstein condensate of strongly magnetic chromium atoms. The long-range and anisotropic magnetic dipole-dipole interaction leads to an anisotropic deformation of the expanding chromium condensate which depends on the orientation of the atomic dipole moments. Our measurements are consistent with the theory of dipolar quantum gases and show that a chromium condensate is an excellent model system to study dipolar interactions in such gases.
Stuhler, J.; Griesmaier, A.; Koch, T.; Fattori, M.; Pfau, T. [5. Physikalisches Institut, Universitaet Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); Giovanazzi, S. [Physikalisches Institut, Universitaet Tuebingen, Auf der Morgenstelle 14, 72076 Tuebingen (Germany); Pedri, P.; Santos, L. [Institut fuer Theoretische Physik III, Universitaet Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany)
Controlling the dipole-dipole interactions between terbium(III) phthalocyaninato triple-decker moieties through spatial control using a fused phthalocyaninato ligand.
Using a fused phthalocyaninato ligand to control the spatial arrangement of Tb(III) moieties in Tb(III) single-molecule magnets (SMMs), we could control the dipole-dipole interactions in the molecules and prepared the first tetranuclear Tb(III) SMM complex. [Tb(obPc)2]Tb(Fused-Pc)Tb[Tb(obPc)2] (abbreviated as [Tb4]; obPc = 2,3,9,10,16,17,23,24-octabutoxyphthalocyaninato, Fused-Pc = bis{7(2),8(2),12(2),13(2),17(2),18(2)-hexabutoxytribenzo[g,l,q]-5,10,15,20-tetraazaporphirino}[b,e]benzenato). In direct-current magnetic susceptibility measurements, ferromagnetic interactions among the four Tb(3+) ions were observed. In [Tb4], there are two kinds of magnetic dipole-dipole interactions. One is strong interactions in the triple-decker moieties, which dominate the magnetic relaxations, and the other is the weak one through the fused phthalocyaninato (Pc) ligand linking the two triple-decker complexes. In other words, [Tb4] can be described as a weakly ferromagnetically coupled dimer of triple-decker Tb2(obPc)3 complexes with strong dipole-dipole interactions in the triple-decker moieties and weak ones through the fused phthalocyaninato ligand linking the two triple-decker complexes. For [Tb4], dual magnetic relaxation processes were observed similar to other dinuclear Tb(III)Pc complexes. The relaxation processes are due to the anisotropic centers. This is clear evidence that the magnetic relaxation mechanism depends heavily on the dipole-dipole (f-f) interactions between the Tb(3+) ions in the systems. Through a better understanding of the magnetic dipole-dipole interactions obtained in these studies, we have developed a new strategy for preparing Tb(III) SMMs. Our work shows that the SMM properties can be fine-tuned by introducing weak intermolecular magnetic interactions in a controlled SMM spatial arrangement. PMID:24224522
Morita, Takaumi; Katoh, Keiichi; Breedlove, Brian K; Yamashita, Masahiro
Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion radius. The radius is controllable by the external magnetic field. It is intriguing that a Skyrmion may have already been observed as a magnetic domain. A salient feature is that a single Skyrmion can be created or destroyed experimentally. An analysis is made also on Skyrmions in chiral magnets.
Ezawa, Motohiko [Department of Applied Physics, University of Tokyo, Hongo 7-3-1, 113-8656 (Japan)
Giant Skyrmions stabilized by dipole-dipole interactions in thin ferromagnetic films.
Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion radius. The radius is controllable by the external magnetic field. It is intriguing that a Skyrmion may have already been observed as a magnetic domain. A salient feature is that a single Skyrmion can be created or destroyed experimentally. An analysis is made also on Skyrmions in chiral magnets. PMID:21231193
Ezawa, Motohiko
Absolute absorption on the rubidium D1 line including resonant dipole-dipole interactions
Here we report on measurements of the absolute absorption spectra of dense rubidium vapour on the D1 line in the weak-probe regime for temperatures up to 170 �C and number densities up to 3 � 1014 cm-3. In such vapours, modifications to the homogeneous linewidth of optical transitions arise due to dipole-dipole interactions between identical atoms, in superpositions of the
Lee Weller; Robert J. Bettles; Paul Siddons; Charles S. Adams; Ifan G. Hughes
Geometrically Frustrated Systems with Long Range Dipole-Dipole Interactions
Crystalline structures with elementary corner-shared triangular or tetrahedral geometrical units are the common template for producing high magnetic frustration. Examples include Heisenberg spins residing on lattice sites of kagom�, pyrochlore and garnet lattices. Another example is that of ``spin ice'' with Ising spins interacting via nearest-neighbor ferromagnetic exchange. All these systems share a simple common property: mean-field theory (e.g. gaussian
Michel Gingras
Effects of dipole-dipole interaction between cigar-shaped BECs of cold alkali atoms: towards inverse-squared interactions.
We show that the dipole-dipole coupling between Wannier modes in cigar-shaped Bose-Einstein condensates (BECs) is significantly enhanced while the short-range coupling is strongly suppressed. As a result, the dipole-dipole interaction can become the dominant interaction between ultracold alkali Bose atoms. In the long length limit of a cigar-shaped BEC, the resulting effective one-dimensional models possess an effective inverse squared interacting potential, the Calogero-Sutherland potential, which plays a fundamental role in many fields of contemporary physics; but its direct experimental realization has been a challenge for a long time. We propose to realize the Calogero-Sutherland model in ultracold alkali Bose atoms and study the effects of the dipole-dipole interaction. PMID:25001313
Yu, Yue; Luo, Zhuxi; Wang, Ziqiang
A path integral approach to the full Dicke model with dipole-dipole interaction
We consider the full Dicke spin-boson model composed by a single bosonic mode and an ensemble of N identical two-level atoms with different couplings for the resonant and anti-resonant interaction terms, and incorporate a dipole-dipole interaction between the atoms. Assuming that the system is in thermal equilibrium with a reservoir at temperature ?-1, we compute the free energy in the thermodynamic limit N ? ? in the saddle-point approximation to the path integral and determine the critical temperature for the super-radiant phase transition. In the zero temperature limit, we recover the critical coupling of the quantum phase transition, presented in the literature.
Aparicio Alcalde, M.; Stephany, J.; Svaiter, N. F.
Investigation on the dipole-dipole interactions between tetramethylurea and acetonitrile by two-dimensional asynchronous spectroscopy
Double Asynchronous Orthogonal Sample Design scheme (DAOSD) proposed in our previous work is used to probe dipole-dipole interaction between Cdbnd O and Ctbnd N groups in tetramethylurea/CD3CN systems. The results indicate that the carbonyl band of tetramethylurea undergoes a red shift and the absorptivity of the carbonyl band of tetramethylurea and ?Ctbnd N of CD3CN decreases under intermolecular interaction. Then the interaction between tetramethylurea and CH3CN was also detected. Besides Cdbnd O and Ctbnd N groups, the spectral behavior of a combination band (?CH3 + ?Csbnd C) of CH3CN was also investigated. The spectral behavior is somewhat similar to the TMU/CD3CN system. However, a noticeable feature is observed on the relationship between ?Ctbnd N band at 2254 cm-1 and the ?CH3 + ?Csbnd C band at 2292 cm-1 of CH3CN: no cross peak was observed at (2254, 2292) in the 2D asynchronous spectrum. Mathematical analysis indicates that absence of the cross peak can occur only when the variation of the absorptivity of ?Ctbnd N and that of ?CH3 + ?Csbnd C band are in the same proportion. Thus, the DAOSD approach reveals an unexpected relationship on the spectral behavior of the ?Ctbnd N and ?CH3 + ?Csbnd C band under intermolecular interaction.
Bi, Quan; Chen, Jing; Li, Xiaopei; Shi, Jia-jia; Wang, Xiaomin; Zhang, Jin; Gao, Danqing; Zhai, Yanjun; Zhao, Ying; Weng, Shifu; Xu, Yizhuang; Noda, Isao; Wu, Jinguang
Dipole-dipole interaction between cold Rydberg atoms in RF fields
Already for some time, dipole-dipole interaction between cold Rydberg atoms is promising as application in quantum information. This promise drives the research on this interaction. In this context we report two aspects: 1) Coherence. When a quantum-mechanical state energetically shifts under the influence of some external perturbation, the effect of a periodic perturbation will show up as side bands. When this shift is linear (e.g. a dipole in an electric field) the population of this side band is described by Bessel-functions. Here we treat the situation that the shift of the state is quadratic under an external perturbation (a polarizable state in an electric field). Now not only the population of the sidebands is a (known but complicated) function of the perturbation, but also the energy of the state and its sidebands is no longer constant. Both the energy and the population of the sidebands are probed by introduction a second state, which is insensitive for the perturbation and that is weakly couple to the first state. This weak coupling is dipole-dipole interaction between two Rydberg atoms. This coupling leads to an avoided crossing between the externally perturbed and the unperturbed states. This particular realization allows for an alternative interpretation of the population of sidebands, in particular of the minima, in terms of St�ckelberg oscillations. These oscillations are measured in the sidebands of the resonant interaction between Rb 49s and 41d states with 49p and 42p states and are used to obtain information about the coherent nature of the interaction. 2) Surfaces. In addition we report on the effect of a conducting surface nearby a Rydberg atoms. This issue is particularly relevant in case the conducting surface is an atom chip. The Rydberg atoms are probed by means of electromagnetically induced transparency (EIT) induced in Rb 5s-5p-Rydberg ladder schemes.
van Linden van den Heuvell, H. B.
Three-body bound states in dipole-dipole interacting Rydberg atoms.
We show that the dipole-dipole interaction between three identical Rydberg atoms can give rise to bound trimer states. The microscopic origin of these states is fundamentally different from Efimov physics. Two stable trimer configurations exist where the atoms form the vertices of an equilateral triangle in a plane perpendicular to a static electric field. The triangle edge length typically exceeds R?2 ?m, and each configuration is twofold degenerate due to Kramers degeneracy. The depth of the potential wells and the triangle edge length can be controlled by external parameters. We establish the Borromean nature of the trimer states, analyze the quantum dynamics in the potential wells, and describe methods for their production and detection. PMID:24476267
Kiffner, Martin; Li, Wenhui; Jaksch, Dieter
Geometric Measure of Nonlocality and Quantum Discord of Two Charge Qubits with Phase Decoherence and Dipole-Dipole Interaction
The effects of both phase decoherence and dipole-dipole interaction on quantum correlations of superconducting (SC) charge qubits, placed in a single-mode SC-cavity, are investigated. When the initial qubit-states are unentangled, measurement-induced nonlocality (MIN), geometric quantum discord (GQD) and quantum entanglement (QE) have different evolutions. They remain at stationary nonzero values with phase decoherence. These stationary correlations clearly appear with the photon number of Fock state. The quantum correlations can be enhanced by dipole-dipole interaction that can weaken the phase decoherence effect. When the initial states of charge qubits are entangled, the appearance of the stationary correlations can be accelerated by the photon number. The correlations can be also increased by the dipole-dipole interaction. These increases can be weaken by the photon number. The photon number also leads to sudden death and sudden birth for QE while MIN periodically reaches its maximum values, but GQD decays continuously with respect to time until it tends to be zero. When the states of the qubits have no entanglement nor entanglement sudden death, MIN and GQD keep nonzero values. The steady-state of correlations is calculated. It is found that these correlations depend on the initial states, the photon number and the dipole-dipole interaction.
Mohamed, Abdel-Baset A.
The nature of the broadening of EPR lines as determined by dipole-dipole interaction in magnetically diluted systems
The effect of dipole-dipole interactions between spins, as modified by their random rotations, on the nature of the EPR line broadening is discussed. The spins are divided into two groups. The spins are sufficiently far removed from the isolated spin (for which the rotation velocity is comparable or greater l:han the broadening produced by the spins in question) and provide
G. M. Zhidomirov; K. M. Salikhov; A. M. Raitsimring; Yu. D. Tsvetkov
Analysis of a quantum logic device based on dipole-dipole interactions of optically trapped Rydberg atoms
We present a detailed analysis and design of a neutral atom quantum logic device based on atoms in optical traps interacting via dipole-dipole coupling of Rydberg states. The dominant physical mechanisms leading to decoherence and loss of fidelity are enumerated. Our results support the feasibility of performing single- and two-qubit gates at MHz rates with decoherence probability and fidelity errors
M. Saffman; T. G. Walker
Characterization of Stable Kinetic Equilibria of Rigid, Dipolar Rod Ensembles for Coupled Dipole-Dipole and Maier-Saupe Potentials.
We study equilibria of the Smoluchowski equation for rigid, dipolar rod ensembles where the intermolecular potential couples the dipole-dipole interaction and the Maier-Saupe interaction. We thereby extend previous analytical results for the decoupled cas...
H. Wang H. Zhou M. G. Forest Q. Wang
The Range and Shielding of Dipole-Dipole Interactions in Phospholipid Bilayers
PubMed Central
In molecular dynamics simulations of lipid bilayers, the structure is sensitive to the precise treatment of electrostatics. The dipole-dipole interactions between headgroup dipoles are not long-ranged, but the area per lipid and, through it, other properties of the bilayer are very sensitive to the detailed balance between the perpendicular and in-plane components of the headgroup dipoles. This is affected by the detailed properties of the cutoff scheme or if long-range interactions are included by Ewald or particle-mesh Ewald techniques. Interaction between the in-plane components of the headgroup dipoles is attractive and decays as the inverse sixth power of distance. The interaction is screened by the square of a dielectric permittivity close to the value for water. Interaction between the components perpendicular to the membrane plane is repulsive and decays as the inverse third power of distance. These interactions are screened by a dielectric permittivity of the order 10. Thus, despite the perpendicular components being much smaller in magnitude than the in-plane components, they will dominate the interaction energies at large distances.
Wohlert, Jakob; Edholm, Olle
Contribution of dipole-dipole interactions to the stability of the collagen triple helix
Unveiling sequence�stability and structure�stability relationships is a major goal of protein chemistry and structural biology. Despite the enormous efforts devoted, answers to these issues remain elusive. In principle, collagen represents an ideal system for such investigations due to its simplified sequence and regular structure. However, the definition of the molecular basis of collagen triple helix stability has hitherto proved to be a difficult task. Particularly puzzling is the decoding of the mechanism of triple helix stabilization/destabilization induced by imino acids. Although the propensity-based model, which correlates the propensities of the individual imino acids with the structural requirements of the triple helix, is able to explicate most of the experimental data, it is unable to predict the rather high stability of peptides embedding Gly�Hyp�Hyp triplets. Starting from the available X-ray structures of this polypeptide, we carried out an extensive quantum chemistry analysis of the mutual interactions established by hydroxyproline residues located at the X and Y positions of the Gly�X�Y motif. Our data clearly indicate that the opposing rings of these residues establish significant van der Waals and dipole�dipole interactions that play an important role in triple helix stabilization. These findings suggest that triple helix stabilization can be achieved by distinct structural mechanisms. The interplay of these subtle but recurrent effects dictates the overall stability of this widespread structural motif.
Improta, Roberto; Berisio, Rita; Vitagliano, Luigi
Teaching Ion-Ion, Ion-Dipole, and Dipole-Dipole Interactions
Discusses how electrostatic interactions can be taught quantitatively through Coulomb's Law at a variety of points in a chemistry curriculum. Each type of interaction is shown at both the intramolecular and the inter-"molecular" levels. (MR)
Yoder, Claude H.
Tailored electronic structure and optical properties of conjugated systems through aggregates and dipole-dipole interactions.
A series of PPVO (p-phenylene vinylene oligomer) derivatives with functional groups of varying electronegativity were synthesized via the Horner-Wadsworth-Emmons reaction. Subtle changes in the end group functionality significantly impact the molecular electronic and optical properties of the PPVOs, resulting in broadly tunable and efficient UV absorption and photoluminescence spectra. Of particular interest is the NO2-substituted PPVO which exhibits photoluminescence color ranging from the blue to the red, thus encompassing the entire visible spectrum. Our experimental study and electronic structure calculations suggest that the formation of aggregates and strong dipole-dipole solute-solvent interactions are responsible for the observed strong solvatochromism. Experimental and theoretical results for the NH2-, H-, and NO2-substituted PPVOs suggest that the stabilization of ground or excited state dipoles leads to the blue or red shift of the optical spectra. The electroluminescence (EL) spectra of H-, COOH-, and NO2-PPVO have maxima at 487, 518, and 587 nm, respectively, in the OLED device. This trend in the EL spectra is in excellent agreement with the end group-dependent PL spectra of the PPVO thin-films. PMID:23607446
Park, Young Il; Kuo, Cheng-Yu; Martinez, Jennifer S; Park, Young-Shin; Postupna, Olena; Zhugayevych, Andriy; Kim, Seungho; Park, Jongwook; Tretiak, Sergei; Wang, Hsing-Lin
We present a detailed analysis and design of a neutral atom quantum logic device based on atoms in optical traps interacting via dipole-dipole coupling of Rydberg states. The dominant physical mechanisms leading to decoherence and loss of fidelity are enumerated. Our results support the feasibility of performing single- and two-qubit gates at MHz rates with decoherence probability and fidelity errors at the level of 10{sup -3} for each operation. Current limitations and possible approaches to further improvement of the device are discussed.
Saffman, M.; Walker, T.G. [Department of Physics, University of Wisconsin, 1150 University Avenue, Madison, Wisconsin 53706 (United States)
Effects of dipole-dipole interaction on the transmitted spectrum of two-level atoms trapped in an optical cavity
The transmission spectrum of two dipole-coupled atoms interacting with a single-mode optical cavity in the strong coupling regime is investigated theoretically for the lower and higher excitation cases. The dressed states containing the dipole-dipole interaction (DDI) are obtained by transforming the two-atom system into an effective single-atom system. We find that the DDI can enhance the effects resulting from the positive atom-cavity detunings but weakens them for the negative detuning cases for the lower excitation, which causes the spectrum to exhibit two asymmetric peaks with shifted heights and positions. For the higher excitation cases, the DDI augments the atomic saturation and leads to the deforming of the spectrum. Furthermore, the large DDI can cause the atom and the cavity to decouple, producing a singlet of the normal-mode spectrum.
Zhang, Yu-Qing; Tan, Lei; Barker, Peter
Freezing-Out of Tunneling Motion of OH- in NaCl Crystal Due to Dipole-Dipole Interaction
It is noticed that the dipole-dipole interactions between pairs of off-center impurity ions in alkali halide crystals effectively freeze out the tunneling motions of the individual ions and this can be optically detected. The concentration dependence of the infrared absorption line shape of NaCl: OH observed by Wedding-Klein and Nanba et al. (the O-H stretching band) is explained from this point of view. The so-called B band is assigned as due to the stretching mode excitation of the frozen pairs of dipoles. A fairly good fit to the observed spectra is obtained by the virial expansion theory for the line shape function applied to the six-state hopping model with the tunneling parameter of 1 cm-1 hc and with the magnitude of the dipole moment of 3.3 Debye.
Kayanuma, Yosuke; Tanaka, Satoshi
Vertical Liquid Crystal Orientation on Amorphous Tantalum Pentoxide Surfaces Depending on Anisotropic Dipole--Dipole Interaction via Ion Beam Irradiation
We achieved vertically aligned (VA) liquid crystals (LCs) on amorphous tantalum pentoxide (Ta2O5) alignment films deposited by radio frequency (rf) magnetron sputtering using ion beam (IB) irradiation. By analyzing measurements by X-ray photoelectron spectroscopy (XPS), we confirmed the bond breaking, as detected from the O 1s spectra, which caused an isotropic dipole--dipole interaction between the LC molecules and the Ta2O5 alignment film to uniformly align the vertical LC molecular orientation as a function of IB energy density. Moreover, by examining the electro-optical (EO) characteristics of the Ta2O5 surfaces compared with those of the polyimide (PI) alignment layer, we confirmed that Ta2O5 has a low threshold voltage and a low power consumption when used as an LC alignment layer.
Lee, Jong-Jin; Kim, Hyung-Jun; Kang, Young-Gu; Kim, Young-Hwan; Park, Hong-Gyu; Kim, Byoung-Yong; Seo, Dae-Shik
Bright solitons in the one-dimensional discrete Gross-Pitaevskii equation with dipole-dipole interactions
A model of the Bose-Einstein condensate of dipolar atoms, confined in a combination of a cigar-shaped trap and deep optical lattice acting in the axial direction, is introduced, taking into regard the dipole-dipole (DD) and contact interactions. The model is based on the discrete nonlinear Schr�dinger equation with an additional nonlocal term accounting for the DD interactions. The existence and stability of fundamental unstaggered solitons are studied for attractive and repulsive signs of both the local and nonlocal interactions. The DD forces strongly affect the shape and stability of on-site and intersite discrete solitons. The corresponding existence and stability regions in the parametric space are summarized in the form of diagrams, which feature a multiple stability exchange between the on-site and intersite families; in the limit of the dominating DD attraction, the on-site solitons are stable, while their intersite counterparts are not. We also demonstrate that the DD interactions reduce the Peierls-Nabarro barrier and enhance the mobility of the discrete solitons.
Gligori?, Goran; Maluckov, Aleksandra; Had�ievski, Ljup?o; Malomed, Boris A.
Heat Capacity, Susceptibility, and Critical Temperature of Erbium Phosphate as Predicted by Dipole-Dipole Interactions.
In this paper the authors compute the heat capacity and susceptibility of erbium phosphate above the critical temperature, assuming that the interaction between the spins is purely dipolar. They also obtain, using the same assumption, the ground-state ene...
P. H. E. Meijer B. V. Kessler
Analytical representation of half-width for molecular ro-vibrational lines in the case of dipole-dipole and dipole-quadrupole interactions
The analytical formula for half-width of molecular ro-vibrational lines is obtained for the case of dipole�dipole and dipole�quadrupole interactions. This formula depends on the variable parameters, which have to be determined by fitting to experimental half-widths or to half-widths calculated by semi-classical methods. The application of the analytical formula to the H2O�H2O, NH3�NH3, DCl�HCl and CO�H2O systems is discussed.
V. I. Starikov
Single-molecule magnets ``without'' intermolecular interactions
Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).
Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.
Two-dimensional array of particles originating from dipole-dipole interaction as evidenced by potential curve measurements at vertical oil/water interfaces.
We propose a new method to evaluate the interaction potential energy between the particles adsorbed at an oil/water interface as a function of interparticle distance. The method is based on the measurement of the interparticle distance at a vertical oil/water interface, at which the gravitational force is naturally applied to compress the particle monolayer in the in-plane direction. We verified the method by examining whether we obtained the same potential curve upon varying the gravitational acceleration by tilting the interface. The present method is applicable in the force range from ?0.1 to ?100 pN, determined by the effective weight of the particles at the interface. The method gives a rather simple procedure to estimate a long range interaction among the particles adsorbed at oil/water interfaces. We applied this method to polystyrene particles at the decane/aqueous surfactant solution interface, and obtained the interparticle potential curves. All the potential curves obtained by the present method indicated that the interparticle repulsion is due to the electrical dipole-dipole interaction based on the negative charge of the particles. The mechanism of the dipole-dipole interaction is further discussed on the basis of the effects of surfactants. PMID:25005863
Sakka, Tetsuo; Kozawa, Daichi; Tsuchiya, Kiyoto; Sugiman, Nao; Oye, Gisle; Fukami, Kazuhiro; Nishi, Naoya; Ogata, Yukio H
An exact analytical solution for the evolution of a dipole-dipole interacting system under spherical diffusion in magnetic resonance experiments
A model system consisting of an isotropic ensemble of spin pairs, where dipole-dipole interaction is assumed to be effective only within each pair, is considered. The ideal segment connecting the spins in a couple has a fixed length but is free to rotate following a diffusion dynamics. This allows the free induction decay (FID) to be derived non-perturbatively by solving the appropriate Dyson equation associated to the problem. Motional narrowing can be described analytically in terms of only two parameters, i.e. the coupling constant of the interaction hamiltonian, b, and the orientational diffusion coefficient D. Salient features of the transverse correlation function thus obtained are discussed, and a comparison with numerical simulations performed with the software SPINEVOLUTION is presented. Interpreting b and D as effective parameters describing multiple interactions of a single spin with its neighbors in a real system, the analysis of published experimental data on poly(ethyl acrylate) has been carried out. It is found that for temperatures higher than and not too close to the glass transition, the results are the same as those found within the Anderson-Weiss approach by assuming a single time exponential decay of the average dipole-dipole interaction. On the other hand, as D tends to zero, FID oscillations characteristic of a rigid lattice show up.
Sturniolo, Simone; Pieruccini, Marco
Spin exchange and magnetic dipole-dipole interactions leading to the magnetic superstructures of MAs2O6 (M = Mn, Co, Ni).
The three isostructural magnetic oxides MAs2O6 (M = Mn, Co, Ni) containing high-spin M(2+) ions undergo a long-range antiferromagnetic ordering below 30 K, but their ordered magnetic structures are not identical. While CoAs2O6 and NiAs2O6 adopt the commensurate superstructure of q1 = (0, 0, 1/2), MnAs2O6 has the incommensurate superstructure of q2 = (0.055, 0.389, 0.136). The cause for this difference was examined by calculating their spin exchange and magnetic dipole-dipole interaction energies. In CoAs2O6 and NiAs2O6, the strongest M-O���O-M spin exchange, J1, dominates over other exchanges, hence leading to the q1 superstructure. For MnAs2O6, the spin exchanges are not a deciding factor leading to its magnetic superstructure, being all weak and comparable in strengths, but the magnetic dipole-dipole interactions are. PMID:24601528
Koo, Hyun-Joo; Whangbo, Myung-Hwan
Determination of Nanocrystal Size Distribution in Magnetic Multicore Particles Including Dipole-Dipole Interactions and Magnetic Anisotropy: a Monte Carlo Study
A correct estimate of the size distribution (i.e., median diameter D and geometric standard deviation ?) of the magnetic nanocrystals (MNCs) embedded in magnetic multicore particles is a necessity in most applications relying on the magnetic response of these particles. In this paper we use a Monte Carlo method to simulate the equilibrium magnetization of two types of multicore particles: (I) MNCs fused in a random compact cluster, and (II) MNCs distributed on the surface of a large carrier sphere. The simulated magnetization data are then fitted using a common method based on a Langevin equation weighted with a size distribution function. Finally, the fitting parameters Dm and ?m are compared to the real parameters Dp and ?p used to generate the MNCs. Our results show that fitting magnetization data with a Langevin model that neglects magnetic anisotropy and dipole-dipole interactions leads to an erroneous estimate of the size distribution of the MNCs in multicore particles. The magnitude of the error depends on the particle morphology, number of MNCs contained in the particle and magnetic properties of the MNCs.
Schaller, Vincent; Wahnstr�m, G�ran; Sanz-Velasco, Anke; Enoksson, Peter; Johansson, Christer
Optical control of excitons in a pair of quantum dots coupled by the dipole-dipole interaction.
We demonstrate coherent nonlinear-optical control of excitons in a pair of quantum dots (QDs) coupled via dipolar interaction. The single-exciton population in the first QD is controlled by resonant picosecond excitation, giving rise to Rabi oscillations. As a result, the exciton transition in the second QD is spectrally shifted and concomitant Rabi oscillations are observed. We identify coupling between permanent excitonic dipole moments as the dominant interaction mechanism, whereas quasiresonant (F�rster) energy transfer is weak. Such control schemes based on dipolar interaction are a prerequisite for realizing scalable quantum logic gates. PMID:15904035
Unold, Thomas; Mueller, Kerstin; Lienau, Christoph; Elsaesser, Thomas; Wieck, Andreas D
Role of charge transfer, dipole-dipole interactions, and electrostatics in Fermi-level pinning at a molecular heterojunction on a metal surface
Recently, Niederhausen [Phys. Rev. BPRBMDO0163-182910.1103/PhysRevB.86.081411 86, 081411(R) (2012)] have reported on the energy level alignment of C60 adsorbed on a bilayer ?-sexithiophene (6T) film on Ag(111). The possibility of charge transfer from the metal to the C60 through the bilayer 6T as discussed by the authors may have a strong impact on understanding the energy level alignment (ELA) at organic-organic (O-O) heterojunctions grown on electrodes. In this paper, we aim at a comprehensive picture of the ELA at O-O interfaces on a metal. We carry out a detailed investigation of the same pair of materials on Ag(111) as employed previously, however, with varying 6T interlayer thickness. The results allow unambiguous identification of integer charge transfer towards a fraction of the C60 molecules as the mechanism leading to the formation of interface dipoles. Varying the 6T interlayer thickness also reveals the dependence of the observed features on the C60-metal distance. This dependence is quantitatively addressed by electrostatic considerations involving a metal-to-overlayer charge transfer. From this, we demonstrate the important role of dipole-dipole interaction potentials in the molecular layer and electric fields resulting from interface dipole formation for the energy level alignment. These findings provide a deeper understanding of the fundamental mechanisms that establish electronic equilibrium at molecular heterojunctions and will aid the prediction of an accurate energy level alignment at device relevant heterojunctions, e.g. in organic opto-electronic devices.
Amsalem, P.; Niederhausen, J.; Wilke, A.; Heimel, G.; Schlesinger, R.; Winkler, S.; Vollmer, A.; Rabe, J. P.; Koch, N.
VES dipole--dipole filter coefficients
The conversion of sampled Schlumberger and dipole-dipole vertical electrical sounding (VES) apparent resistivity values into raised kernel function values is an important step in the interpretation of these data. This conversion involves the convolution of the sampled values, uniformly spaced on a log distance scale, with a set of filter coefficients. For Schlumberger and dipole-dipole configurations, these coefficients can be
Douglas C. Nyman; M. Landisman
Pulsed Electric Current Dipole/Dipole Interference.
A time-domain analysis of electromagnetic, pulsed electric current dipole/dipole interference is presented. The emitting and suscepting dipoles may be either 'electric dipoles' (short segments of electric current carrying wire) or 'magnetic dipoles' (smal...
D. Quak A. T. de Hoop
Magnetic sponge phenomena associated with interchain dipole-dipole interactions in a series of ferrimagnetic chain compounds doped with minor diamagnetic species.
The donor/acceptor ionic chain (i.e., the D(+)A(-) chain) [Ru2(2-MeO-4-ClPhCO2)4(BTDA-TCNQ)]�2.5(benzene) (1; 2-MeO-4-ClPhCO2(-) = 2-methoxy-4-chlorobenzoate; BTDA-TCNQ = bis(1,2,5-thiadiazolo)tetracyanoquinodimethane) is a ferrimagnetic chain with S = 3/2 from [Ru2(II,III)](+) (i.e., D(+)) and S = 1/2 from BTDA-TCNQ(�-) (i.e., A(-)), with J ? -100 K, in which long-range antiferromagnetic ordering at TN = 11 K occurs because interchain antiferromagnetic interactions are critical. Compound 1 undergoes a reversible crystal-to-crystal structural transformation with the elimination/absorption of the crystallization solvent to form the dried compound [Ru2(2-MeO-4-ClPhCO2)4(BTDA-TCNQ)] (1'), which has a higher TN (14 K). This change is clearly caused by the shortening of the interchain distances because the exchange coupling parameter for the chain is the same in both 1 and 1'. The chain compounds in 1 can be doped with minor diamagnetic [Rh2(II,II)] species, [{(Ru2)(1-x)(Rh2)(x)(2-MeO-4-ClPhCO2)4}(BTDA-TCNQ)]�2.5(benzene) (x = 0.03 for Rh-3%; x = 0.05 for Rh-5%; x = 0.16 for Rh-16%), which shifts the TN to lower temperatures, the magnitude of the shift being dependent on the doping ratio x (TN = 5.9 K for Rh-3%, TN = 3.7 K for Rh-5%, and TN was not observed above 1.8 K for Rh-16%). Drying a doped compound increased its TN, as was found for 1': TN = 9.9 K for Rh-3%', TN = 9.2 K for Rh-5%', and TN was not observed above 1.8 K for Rh-16%'. TN had a linear relationship with the doping ratio x of the [Rh2] species in both the fresh and dried compounds. The TN linear relationship is associated with the magnitude of the effective magnetic dipole (i.e., the average correlation length) in the chains caused by the [Rh2] defects as well as naturally generated defects in the synthetic process and with the interchain distances affected by the crystal-to-crystal transformations. These results demonstrate that slightly modifying the short-range correlation lengths, which changes the magnetic dipole magnitudes, strongly affects the bulk antiferromagnetic transition, with key dipole-dipole interactions, in low-dimensional anisotropic systems. PMID:24750071
Nishio, Masaki; Miyasaka, Hitoshi
Perturbation analyses of intermolecular interactions
Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the ? state and PPII (polyproline II) + ? states) for larger cutoff length, the separation between the PPII state and the ? state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.
Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.
A basic program to transform continuous polar dipole-dipole resistivity soundings to half-Schlumberger soundings
USGS Publications Warehouse
An interactive HP 9845B BASIC program transforms continuous polar dipole-dipole resistivity soundings to half-Schlumberger soundings. The program features graphic presentation of the field dipole-dipole data as well as the transformed half-Schlumberger data. An example of the transformation and its effectiveness in smoothing "high-frequency" noise is given. ?? 1990.
Zerilli, A.; Bisdorf, R. J.
Rydberg-wave-packet evolution in a frozen gas of dipole-dipole-coupled atoms
We have studied the evolution of Rydberg wave packets in the presence of interatomic dipole-dipole interactions in a frozen Rb gas. Rb atoms in a magneto-optical trap (MOT) are first laser excited to ns Rydberg eigenstates. A picosecond THz pulse further excites them into coherent superposition states involving the initial-level and neighboring np states. A second, identical, time-delayed THz pulse probes the wave-packet dynamics. As the wave packets evolve they are influenced by dipole-dipole interactions, predominantly pairwise excitation-exchange processes of the form |s >|p>?|p>|s>. The coherent electronic evolution of the ensemble dephases due to the variation in dipole-dipole coupling strength between atom pairs in the MOT. The experimental results are in good agreement with numerical calculations that simulate the interactions between nearest neighbors in a frozen gas.
Zhou, Tao; Li, Sha; Jones, R. R.
Dipole�dipole induced global motion of Rydberg-dressed atom clouds
We consider two clouds of ground-state alkali atoms in two distinct hyperfine ground states. Each level is far off-resonantly coupled to a Rydberg state, which leads to dressed ground states with a weak admixture of the Rydberg state properties. Due to this admixture, for a proper choice of the Rydberg states, the atoms experience resonant dipole�dipole interactions that induce mechanical forces acting on all atoms within both clouds. This behaviour is in contrast to the dynamics predicted for bare dipole�dipole interactions between Rydberg superatoms, where only a single atom per cloud is subject to dipole�dipole induced motion (M�bius et al 2013 Phys. Rev. A 88 012716).
Genkin, M.; W�ster, S.; M�bius, S.; Eisfeld, A.; Rost, J. M.
Power-law relaxation decay in two-dimensional arrays of magnetic dots interacting by long-range dipole-dipole interactions
The magnetic relaxation of two-dimensional arrays of dipolar coupled magnetic dots has been measured and simulated. Arrays (50�50) with perpendicular magnetized Co dots (2 ?m�2 ?m) were patterned using a high resolution Ga+ focused ion beam irradiation. Magnetic domain pattern and time relaxation of the dot arrays were investigated using Faraday magneto-optical microscopy. For arrays designed with high irradiation doses (>=0.5 nC/cm), the magnetic relaxation of the array proceeds by the magnetization reversal of individual dots and follows a power-law time decay. The long-range character of the dipolar interaction is found to be responsible for magnetic relaxation with a power-law decay. Monte Carlo simulations, based on a modified Ising Hamiltonian, reproduce this time dependence, and show that the power law is not a consequence of either the finite size or the boundary of the arrays, and it is independent of the shape of dots as well.
Sampaio, L. C.; Hyndman, R.; de Menezes, F. S.; Jamet, J. P.; Meyer, P.; Gierak, J.; Chappert, C.; Mathet, V.; Ferr�, J.
Resonant Dipole-Dipole Collisions of Rydberg Atoms in a Magneto-Optical Trap
I present a study of resonant energy transfer via a dipole-dipole interaction between alkali atoms in Rydberg states. We have studied such interactions between atoms prepared in a magneto-optical trap (MOT). In binary collisions the atomic density plays no role in the collision dynamics, however, using laser cooling and trapping techniques we have been able to enter a new regime
W. R. Anderson
Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect
This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN)4] layers to form a solid of formula unit T(ImD)2[Ni(CN)4]. These hybrid inorganic-organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN)4] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole-dipole and quadrupole-quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2-300 K temperature range. The samples containing Co and Ni are characterized by presence of spin-orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands ?-? interaction was detected.
Gonz�lez, M.; Lemus-Santana, A. A.; Rodr�guez-Hern�ndez, J.; Aguirre-Velez, C. I.; Knobel, M.; Reguera, E.
Dipole-Dipole Induced Forces in the Reaction of Alkali Metal Atoms with Polar Molecules,
The title reaction is shown to be dominated by a relatively large dipole-dipole induced interaction at distances of 4-5 Angstroms. The cone of nonreaction and orientation dependence of the reactive scattering cross section are estimated from this potentia...
Y. R. Luo S. W. Benson
Orthogonal Intermolecular Interactions of CO molecules on a one-dimensional substrate.
By low-temperature scanning tunneling microscopy, we study CO molecule chemisorption on a quasi-one-dimensional Cu(110)-(2�1)-O surface. Atom-resolved images reveal how the interaction of CO with the surface Cu-O- chains gives rise to orthogonal attractive and repulsive intermolecular interactions. First-principles calculations show that CO molecules induce unprecedented lifting of the host Cu atoms by 1 � from the Cu-O- chains, enabling the Cu-CO unit to tilt by 45� from the surface normal. Contrary to the behavior of CO on metal surfaces, this structural distortion enables unprecedented, orthogonal, short-range intermolecular dipole-dipole attraction and long-range, surface-mediated repulsion. These interactions lead to self-assembly into molecular nanograting structures consisting of arrays of single-molecule-wide CO rows. The origin of the novel behavior of CO molecules in the electronic and geometrical properties of the quasi-one-dimensional substrate suggests that similar molecule-molecule and molecule-substrate interactions could play an important role at catalytic sites on reactive surfaces. PMID:22404595
Feng, Min; Lin, Chungwei; Zhao, Jin; Petek, Hrvoje
Comment on ``Low-temperature ordered states of RBa2Cu3O7-? due to dipole-dipole and exchange interactions''
In a recent paper Misra and Felsteiner calculate the low-temperature ordered states of certain RBa2Cu3O7-? compounds, using the Luttinger-Tisza method. Based on the results of these calculations the authors conclude that dipolar interactions alone can account for all the observed orderings of these materials. However, the calculations and the conclusions drawn from these calculations are based on assumptions that we believe are inconsistent with many crystal electric field measurements in the RBa2Cu3O7-? compounds.
Whitehead, J. P.; de'bell, K.; Noakes, D. R.
Dipole-dipole broadening of Rb ns-np microwave transitions
The dipole-dipole broadening of ns-np microwave transitions of cold Rb Rydberg atoms in a magneto-optical trap has been recorded for 28{<=}n{<=}51. Since the electric dipole transition matrix elements scale as n{sup 2}, a broadening rate scaling as n{sup 4} is expected and a broadening rate of 8.2x10{sup -15}n{sup 4} MHz cm{sup 3} is observed. The observed broadening is smaller than expected from a classical picture due to the spin-orbit interaction in the np atoms. The broadened resonances are asymmetric and cusp shaped, and their line shapes can be reproduced by a diatomic model which takes into account the dipole-dipole interaction, including the spin-orbit interaction, the strengths of the allowed microwave transitions, and the distribution of the atomic spacings in the trap.
Park, Hyunwook; Tanner, P. J.; Claessens, B. J.; Shuman, E. S.; Gallagher, T. F. [Department of Physics, University of Virginia, Charlottesville, Virginia 22904-0714 (United States)
Light amplification related to collective atomic recoil affected by dipole-dipole collision
We have studied a collective atomic recoil laser (CARL) including atomic dipole-dipole (D-D) collisions. The results simulated under some sets of parametric conditions reveal that this interatomic interaction plays a negative role in the laser process due to its noncoherent characteristic for the collective atomic recoil motions, which greatly reduces the spatial orderliness of the atomic density distribution necessary for the laser operation.
Zhang, L.; Yang, G. J.; He, Z. H.
Intermolecular interactions and photoprocesses in molecular systems
Influence of intermolecular interactions on the electronic states and spectral and luminescent properties of bimolecular systems is analyzed. It is demonstrated that the spatial structure of single-electron states (molecular orbitals) must be analyzed in the initial stage of quantum-chemical study of this influence. The assumption that the overlap of molecular orbitals in contact complexes can be neglected is incorrect and leads to false conclusions about photophysics of such complexes.
Artyukhov, V. Ya.; Mayer, G. V.
Reduced intermolecular interaction in organic ultrathin films
Submonolayer sensitivity was achieved using in situ ellipsometry to monitor the evolution of the dielectric function of tris(8-hydroxyquinoline)-aluminum(III) (Alq3) layers from submonolayer coverage to thick bulklike layers. The Alq3 layers were deposited under ultrahigh vacuum conditions onto hydrogen passivated silicon. The characteristic vacuum-ultraviolet (VUV) absorption lines of Alq3 were detected using synchrotron radiation as light source. In such ultrathin films the absorption lines corresponding to molecular transitions of the Alq3 are found to be spectrally blueshifted with respect to bulklike layers. We attribute the shift to the effect of reduced intermolecular interaction in the submonolayer regime.
Gordan, O. D.; Himcinschi, C.; Zahn, D. R. T.; Cobet, C.; Esser, N.; Braun, W.
Interactions in dendronized polymers: intramolecular dominates intermolecular.
In an attempt to relate atomistic information to the rheological response of a large dendritic object, interand intramolecular hydrogen bonds and p,p-interactions have been characterized in a dendronized polymer (DP) that consists of a polymethylmethacrylate backbone with tree-like branches of generation four (PG4) and contains both amide and aromatic groups. Extensive atomistic molecular dynamics simulations have been carried out on (i) an isolated PG4 chain and (ii) ten dimers formed by two PG4 chains associated with different degrees of interpenetration. Results indicate that the amount of nitrogen atoms involved in hydrogen bonding is ~11% while ~15% of aromatic groups participate in p,pinteractions. Furthermore, in both cases intramolecular interactions clearly dominate over intermolecular ones, while exhibiting markedly different behaviors. Specifically, the amount of intramolecular hydrogen bonds increases when the interpenetration of the two chains decreases, whereas intramolecular p,pinteractions remain practically insensitive to the amount of interpenetration. In contrast, the strength of the corresponding two types of intermolecular interactions decreases with interpenetration. Although the influence of complexation on the density and cross-sectional radius is relatively small, interpenetration affects significantly the molecular length of the DP. These results support the idea of treating DPs as long colloidal molecules. PMID:24983117
C�rdova-Mateo, Esther; Bertran, Oscar; Zhang, Baozhong; Vlassopoulos, Dimitris; Pasquino, Rossana; Schl�ter, A Dieter; Kr�ger, Martin; Alem�n, Carlos
Quantitative analysis of long-range interactions between adsorbed dipolar molecules on Cu(111).
Highly dispersed superstructures of a dipolar iridium complex are formed on a Cu(111) surface. We show that the dilute superstructures with density-controlled intermolecular separations are stabilized by the strong and long-range repulsive intermolecular interactions. The repulsive intermolecular interactions are quantitatively evaluated by using low-temperature scanning tunneling microscopy, which are characterized by the surface-enhanced dipole-dipole interactions. PMID:17677711
Yokoyama, Takashi; Takahashi, Tomonori; Shinozaki, Kazuteru; Okamoto, Masakuni
Intermolecular Interactions Between Uracil and Reactive Species
We have investigated intermolecular interactions between uracil (U) and each of the fluoride ion, superoxide anion, and the hydroxyl radical. Computational study of these new systems presents several challenges, most importantly is the choice of the proper level of theory and the appropriate size of the basis set. Our investigations on the U-F- complex showed that the MP2 and density functional method (DFT) with aug-cc-pVDZ and aug-cc-pVTZ basis sets provide results that are consistent with those obtained with highly correlated methods for H{_2}O-F-. This suggests that these levels of calculations are suitable for exploring the structures and the potential energy surfaces of the U-O{_2}- and U-OH complexes. Our preliminary results show that each of the F- and the superoxide ions forms a very strong hydrogen bond with a specific hydrogen atom in the uracil ring. Also, results suggest that proton transfer occurs between the bonding site in uracil and each of the F- and O{_2}- ions. On the other hand, preliminary results show that the OH radical chemically reacts with the uracil molecule. Discussion of details of calculations and results will be presented.
Ren, Sijin; Fawzy, Wafaa M.
The interactions in solution between purine or pyrimidine bases and polybenzenoid aromatic hydrocarbons probably consist in a vertical, stacking-type physical association. By molecular orbital calculations the role of the Van der Waals-London intermolecular forces in these interactions is determined. The electrostatic dipole-dipole forces are negligible, the polarization (or induction) dipole-induced dipole forces are contributory, but most important are the dispersion (or fluctuation) forces. This loose, physical type of interaction should not show any specificity with respect to the carcinogenic activity of the hydrocarbons. PMID:14250326
Characterization of stable kinetic equilibria of rigid, dipolar rod ensembles for coupled dipole dipole and Maier Saupe potentials
We study equilibria of the Smoluchowski equation for rigid, dipolar rod ensembles where the intermolecular potential couples the dipole-dipole interaction and the Maier-Saupe interaction. We thereby extend previous analytical results for the decoupled case of the dipolar potential only (Fatkullin and Slastikov 2005 Nonlinearity 18 2565-80 Ji et al Phys. Fluids at press; Wang et al 2005 Commun. Math. Sci. 3 605-20) or the Maier-Saupe potential only (Constantin et al 2004 Arch. Ration. Mech. Anal. 174 365-84 Constantin et al 2004 Discrete Contin. Dyn. Syst. 11 101-12 Constantin and Vukadinovic 2005 Nonlinearity 18 441-3 Constantin 2005 Commun. Math. Sci. 3 531-44 Fatkullin and Slastikov 2005 Commun. Math. Sci. 3 21-6 Liu et al 2005 Commun. Math. Sci. 3 201-18 Luo et al 2005 Nonlinearity 18 379-89 Zhou et al 2005 Nonlinearity 18 2815-25 Zhou and Wang Commun. Math. Sci. at press), and prove certain numerical observations for equilibria of coupled potentials (Ji et al Phys. Fluids at press). We first derive stability conditions, on the magnitude of the polarity vector (the first moment of the orientational probability distribution function) and on the direction of the polarity. We then prove that all stable equilibria of rigid, dipolar rod dispersions are either isotropic or prolate uniaxial. In particular, all stable anisotropic equilibrium distributions admit the following remarkable symmetry: the peak axis of orientation is aligned with both the polarity vector (first moment) and the distinguished director of the uniaxial second moment tensor. The stability is essential in establishing the axisymmetry. To demonstrate that the stability is indeed required, we show that there exist unstable non-axisymmetric equilibria.
Zhou, Hong; Wang, Hongyun; Wang, Qi; Forest, M. Gregory
Influence of intermolecular interactions on the sign of d TC/d p in critical solutions
Results of studies on variations of the critical temperature ( TC) due to the action of high hydrostatic pressure ( p) are presented. Studies were conducted in three series of critical solutions composed of a dipole component (nitrobenzene, o-nitroluene, 1-nitropropane) and a non-dipole solvent ( n-alkanes). For solutions containing nitrobenzene and o-nitrotoluene the sign and value of d TC/d p depend on the length of the molecule of n-alkane. Additional studies on dipole-dipole interactions between molecules of the dipole components by means of the nonlinear dielectric effect indicate their important influence on d TC/d p.
Urbanowicz, P.; Rzoska, S. J.; Paluch, M.; Sawicki, B.; Szulc, A.; Zio?o, J.
Learning about Intermolecular Interactions from the Cambridge Structural Database
A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the�
Battle, Gary M.; Allen, Frank H.
Qualitative change of character of dispersive interaction with intermolecular distance.
The dispersive interaction between molecules results from Coulomb-correlated fluctuations of electrons and for large intermolecular distances it can be related to the molecular polarizabilities as in London's theory (F. London, Trans. Faraday Soc. 33, 8-26 (1937)). Here, we investigate the interaction between molecules with anisotropic polarizabilities at arbitrary distances using symmetry adapted perturbation theory, which allows us to analyze the different parts of the intermolecular potential separately. Whereas at large distances, in accordance with London's theory, there is no way to describe the dispersive interaction by a sum over pairwise isotropic atom-centered energy terms, at short distances such a description becomes possible. This surprising result has consequences for the development of molecular mechanics force fields, supports the dispersion energy terms applied in dispersion corrected density functional theory, and indicates that there is a qualitative change in electron correlation with distance. Apparently, at short distances intermolecular electron correlation is less influenced by intramolecular electron delocalization. PMID:23901956
Haslmayr, Johannes; Renger, Thomas
Qualitative change of character of dispersive interaction with intermolecular distance
The dispersive interaction between molecules results from Coulomb-correlated fluctuations of electrons and for large intermolecular distances it can be related to the molecular polarizabilities as in London's theory (F. London, Trans. Faraday Soc. 33, 8-26 (1937)). Here, we investigate the interaction between molecules with anisotropic polarizabilities at arbitrary distances using symmetry adapted perturbation theory, which allows us to analyze the different parts of the intermolecular potential separately. Whereas at large distances, in accordance with London's theory, there is no way to describe the dispersive interaction by a sum over pairwise isotropic atom-centered energy terms, at short distances such a description becomes possible. This surprising result has consequences for the development of molecular mechanics force fields, supports the dispersion energy terms applied in dispersion corrected density functional theory, and indicates that there is a qualitative change in electron correlation with distance. Apparently, at short distances intermolecular electron correlation is less influenced by intramolecular electron delocalization.
Intermolecular forces: a solution to dispersion interactions.
London dispersion forces have been cited as an important factor in protein folding, drug�receptor interactions, and catalyst selectivities. However, careful analysis of a model system finds that the dispersion interactions are only minor contributors to the formation of complexes in solution. PMID:24256859
Shimizu, Ken D
Dipole-Dipole Dispersion Forces for Small, Intermediate and Large Distances.
An improved expression is obtained for the dipole-dipole London dispersion force between closed shell atoms for small, intermediate and large distances compared with their linear dimensions. (Atomindex citation 18:086946)
J. C. Antonio
Direct observation of intermolecular interactions mediated by hydrogen bonding.
Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N-H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions. PMID:25053321
De Marco, Luigi; Th�mer, Martin; Reppert, Mike; Tokmakoff, Andrei
Intermolecular interactions of 4-pyrrolidino pyridine: a simulation study
Simulations of intermolecular interaction by the AM1 method have been performed. The hydrogen bonding complex between and 4-pyrrolidino pyridine (PP) and water molecules with 1: n complexes have been considered to investigate possible stable complex configurations and to calculate the stable interaction energy. These calculations confirm the influence of water molecules on twisting of the pyrrolidino group in ground state. The excited state simulation predicts that the energy minimized geometry of the PP molecule takes an almost sandwich like structure, confirming the formation of an intramolecular exciplex in the gas phase as well as in nonpolar or in weakly polar solvents in line with the experimental findings.
Ranjan Bangal, Prakriti; Chakravorti, Sankar
Effects of aromatic trifluoromethylation, fluorination, and methylation on intermolecular ?-? interactions.
Marcus theory states that the rate of charge transfer is directly proportional to the amount of intermolecular orbital overlap. Theoretically optimizing the electronic coupling through the orientation and distance which both can increase the frontier orbital overlap between molecules is an attractive route to potentially provide theoretical insight for discovering new high performance semiconductor materials. To investigate how these parameters qualitatively affect charge transfer of model systems, unconstrained dimer optimizations with MP2 and dispersion-corrected DFT methods were used to probe the ?-? interactions of methylated, fluorinated, and trifluoromethylated benzene, pyridine, and bipyridine dimers. These systems can serve as simplified models representing weak noncovalent interactions in organic semiconductor materials. Enhanced intermolecular interaction energies, reduced ?-? distances, and more favorable cofacial orientations were found with the trifluoromethylated dimers compared to fluorinated and methylated dimers studied. Similar effects were found with donor-acceptor pairs that represent organic p-n heterojunction systems. These enhanced ?-? interactions are likely caused by increased molecular quadrupole moment and dispersion interaction associated with trifluoromethylation. This computational study illustrates the strong potential of trifluoromethylation and, possibly perfluoroalkylation of acenes and heteroacenes, leading qualitatively to enhanced electron transfer through better ?-? stacked structures, making them viable candidates for use as n-type organic semiconductor materials. The findings also provide insight for fundamental interactions between drug molecules that include fluorinated and trimethylfluorinated aromatics binding to protein receptors. PMID:23906416
Mottishaw, Jeffery D; Sun, Haoran
Intermolecular interactions and the thermodynamic properties of supercritical fluids.
The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of ? = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids. PMID:23697423
Yigzawe, Tesfaye M; Sadus, Richard J
Intermolecular interactions and the thermodynamic properties of supercritical fluids
The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of ? = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.
Yigzawe, Tesfaye M.; Sadus, Richard J.
Intermolecular interactions in phase transitions in petroleum disperse systems
Atmospheric resids were obtained from paraffinic-naphthenic base Mangyshlak crude, aromatic, high-resin Arlan crude, and mixed West Siberian crudes and their physicochemical properties were determined along with their permittivities and electric conductivities as functions of temperature. For the Arlan and West Siberian resids the temperature dependence of viscosity in the state of a molecular solution was expressed by the Frenkel-Eyring equation. Values were determined for the effective activation energy of viscous flow. The temperature intervals of phase transitions were established, the structure types in the bound-dispersed state were identified, and the intermolecular interaction intensities in the three resids were assessed.
Merezhko, Yu.I.; Nesterov, A.N.; Syunyaev, Z.I.; Saidakhmedov, I.M.
Intermolecular interactions in molecular systems: pros and cons
For applications as diverse as molecular electronics and nonlinear optics, organic molecular systems have long been vaunted as ideal candidates due to their low cost and the tailorability of their physical properties through well explored organic chemistry. Indeed, examples of porphyrins and systematically structured oligomers show how the properties of these systems can be finely tuned leading to simple structure-property relationships. In most cases, however, these finely tuned properties are lost in the solid state, and even at moderate concentrations in solution, as illustrated for the liquid crystal forming materials, hexabenzocoronenes. Not only are structure property relationships lost, but the optical properties, in particular fluorescence efficiency, are greatly suppressed. In polymers, which are structurally less defined, such aggregration effects can be both interchain and intrachain and have been seen to depend on the backbone isomerism. Raman spectroscopy has been shown to be a valuable probe of the purity of the backbone isomerisation and thus of the inhibition of interchain interaction. The use of nanospacers has been also explored for the local inhibition of intermolecular interaction. In particular, carbon nanotubes are shown to selectively interact with organic polymers in order to reduce the polymer-polymer interaction and so enhance fluorescence in the solid state. Minimisation of the interaction between molecules in order to preserve the as designed properties is a further challenge to molecular science. In fullerenes in the solid state, however, it appears that interaction between excited state species enhances both the electronic and optical properties of the material. The insulating, weakly optically active crystalline material becomes highly fluorescent and highly conducting under high intensity illumination. The origin of the nonlinear process is proposed to be an optically induced insulator to metal transition as a result of the increased interaction of neighbouring excited states. It is proposed that while in many molecular systems intermolecular can be detrimental, they do potentially offer a further design parameter to the molecular scientist.
Byrne, Hugh J.
Phospholipid head-group conformations; intermolecular interactions and cholesterol effects.
The predominant orientation of the phosphorylcholine polar head group in phosphatidylcholine and sphingomyelin bilayers and cholesterol perturbations of that orientation have been identified by exploiting the 31P (1H) nuclear Overhauser effect (NOE) in the 31P NMR spectra of phospholipid bilayers. In pure egg phosphatidylcholine bilayers, a NOE of 40% is observed. The magnitude of the NOE has been measured as a function of continuous-wave proton-decoupler frequency in order to identify the proton source of the NOE. In pure egg phosphatidylcholine bilayers, the maximum NOE occurs at the N-methyl proton resonance position of the choline moiety. In a modified phosphatidylcholine in which all the N-methyl protons were replaced by deuterium, the NOE arose from methylene protons next to the phosphate. In mixed systems of phosphatidylcholine and phosphatidylethanolamine, and phosphatidylcholine and diphosphatidylglycerol, both phospholipid resonances attained maximum NOE at the position of the N-methyl proton resonance of phosphatidylcholine. An analogous result was obtained with pure sphingomyelin. These results are explained by orienting the phosphorylcholine portion of the molecule parallel to the surface of the bilayer so that the positively charged N-methyl moiety is located close to the negatively charged phosphate on a neighboring phospholipid in an intermolecular interaction. Addition of cholesterol is shown to disrupt the intermolecular interaction in phosphatidylcholine bilayers. PMID:911759
Yeagle, P L; Hutton, W C; Huang, C; Martin, R B
Interpretation of Dipole-Dipole Resistivity Monitoring Data at Cerro Prieto.
Repetitive dipole-dipole resistivity data have been taken on a yearly basis at Cerro Prieto since 1978. Stations along a single profile line extending from the Cucapa Mountains to the center of the Mexicali Valley and passing over the present production z...
M. J. Wilt N. E. Goldstein
Direct measurement of dipole-dipole/CSA cross-correlated relaxation by a constant-time experiment.
Relaxation rates in NMR are usually measured by intensity modulation as a function of a relaxation delay during which the relaxation mechanism of interest is effective. Other mechanisms are often suppressed during the relaxation delay by pulse sequences which eliminate their effects, or cancel their effects when two data sets with appropriate combinations of relaxation rate effects are added. Cross-correlated relaxation (CCR) involving dipole-dipole and CSA interactions differ from auto-correlated relaxation (ACR) in that the signs of contributions can be changed by inverting the state of one spin involved in the dipole-dipole interaction. This property has been exploited previously using CPMG sequences to refocus CCR while ACR evolves. Here we report a new pulse scheme that instead eliminates intensity modulation by ACR and thus allows direct measurement of CCR. The sequence uses a constant time relaxation period for which the contribution of ACR does not change. An inversion pulse is applied at various points in the sequence to effect a decay that depends on CCR only. A 2-D experiment is also described in which chemical shift evolution in the indirect dimension can share the same constant period. This improves sensitivity by avoiding the addition of a separate indirect dimension acquisition time. We illustrate the measurement of residue specific CCR rates on the non-myristoylated yeast ARF1 protein and compare the results to those obtained following the conventional method of measuring the decay rates of the slow and fast-relaxing (15)N doublets. The performances of the two methods are also quantitatively evaluated by simulation. The analysis shows that the shared constant-time CCR (SCT-CCR) method significantly improves sensitivity. PMID:18406649
Liu, Yizhou; Prestegard, James H
Direct measurement of dipole dipole/CSA cross-correlated relaxation by a constant-time experiment
Relaxation rates in NMR are usually measured by intensity modulation as a function of a relaxation delay during which the relaxation mechanism of interest is effective. Other mechanisms are often suppressed during the relaxation delay by pulse sequences which eliminate their effects, or cancel their effects when two data sets with appropriate combinations of relaxation rate effects are added. Cross-correlated relaxation (CCR) involving dipole-dipole and CSA interactions differ from auto-correlated relaxation (ACR) in that the signs of contributions can be changed by inverting the state of one spin involved in the dipole-dipole interaction. This property has been exploited previously using CPMG sequences to refocus CCR while ACR evolves. Here we report a new pulse scheme that instead eliminates intensity modulation by ACR and thus allows direct measurement of CCR. The sequence uses a constant time relaxation period for which the contribution of ACR does not change. An inversion pulse is applied at various points in the sequence to effect a decay that depends on CCR only. A 2-D experiment is also described in which chemical shift evolution in the indirect dimension can share the same constant period. This improves sensitivity by avoiding the addition of a separate indirect dimension acquisition time. We illustrate the measurement of residue specific CCR rates on the non-myristoylated yeast ARF1 protein and compare the results to those obtained following the conventional method of measuring the decay rates of the slow and fast-relaxing 15N doublets. The performances of the two methods are also quantitatively evaluated by simulation. The analysis shows that the shared constant-time CCR (SCT-CCR) method significantly improves sensitivity.
Liu, Yizhou; Prestegard, James H.
Very strong metal ligand aromatic cation-? interactions in transition metal complexes: intermolecular interaction in tetraphenylborate salts
Strong intermolecular interactions between ligands in cationic metal complexes and aromatic rings of tetraphenylborate anion, so-called metal ligand aromatic cation-? (MLAC?) interactions, were found by screening Cambridge Structural Database. Distances between phenyl ring and ligand are shorter in these structures than in previously reported MLAC? interactions by 0.2 �.
Milo� K. Mil?i?; Zoran D. Tomi?; Sne�ana D. Zari?
Intermolecular interactions, nucleation, and thermodynamics of crystallization of hemoglobin C.
The mutated hemoglobin HbC (beta 6 Glu-->Lys), in the oxygenated (R) liganded state, forms crystals inside red blood cells of patients with CC and SC diseases. Static and dynamic light scattering characterization of the interactions between the R-state (CO) HbC, HbA, and HbS molecules in low-ionic-strength solutions showed that electrostatics is unimportant and that the interactions are dominated by the specific binding of solutions' ions to the proteins. Microscopic observations and determinations of the nucleation statistics showed that the crystals of HbC nucleate and grow by the attachment of native molecules from the solution and that concurrent amorphous phases, spherulites, and microfibers are not building blocks for the crystal. Using a novel miniaturized light-scintillation technique, we quantified a strong retrograde solubility dependence on temperature. Thermodynamic analyses of HbC crystallization yielded a high positive enthalpy of 155 kJ mol(-1), i.e., the specific interactions favor HbC molecules in the solute state. Then, HbC crystallization is only possible because of the huge entropy gain of 610 J mol(-1) K(-1), likely stemming from the release of up to 10 water molecules per protein intermolecular contact-hydrophobic interaction. Thus, the higher crystallization propensity of R-state HbC is attributable to increased hydrophobicity resulting from the conformational changes that accompany the HbC beta 6 mutation.
Vekilov, Peter G; Feeling-Taylor, Angela R; Petsev, Dimiter N; Galkin, Oleg; Nagel, Ronald L; Hirsch, Rhoda Elison
Intermolecular interactions in electron transfer through stretched helical peptides.
The helical peptide Cys-Ala-Lys-(Glu-Ala-Ala-Ala-Lys)(2)-Ala-NH-(CH(2))(2)-SH has been organized forming a self-assembled monolayer on gold (0.602 peptides per nm(2)), its conductance behavior under stretching conditions being studied using scanning tunnelling microscopy and current sensing atomic force microscopy. The helical conformation of the peptide has been found to play a fundamental role in the conductance. Moreover, variation of the current upon molecular stretching indicates that peptides can be significantly elongated before the conductance drops to zero, the critical elongation being 1.22 � 0.47 nm. Molecular dynamics simulations of a single peptide in the free state and of a variable number of peptides tethered to a gold surface (i.e. densities ranging from 0.026 to 1.295 peptides per nm(2)) have indicated that the helical conformation is intrinsically favored in solvated environments while in desolvated environments it is retained because of the fundamental role played by peptide-peptide intermolecular interactions. The structure obtained for the system with 24 tethered peptides, with a density of 0.634 peptides per nm(2) closest to the experimental one, is in excellent agreement with experimental observations. On the other hand, simulations in which a single molecule is submitted to different compression and stretching processes while the rest remain in the equilibrium have been used to mimic the variation of the tip-substrate distance in experimental measures. Results allowed us to identify the existence, and in some cases coexistence, of intermolecular and intramolecular ionic ladders, suggesting that peptide-mediated electron transfer occurs through the hopping mechanism. Finally, quantum mechanical calculations have been used to investigate the variation of the electronic structure upon compression and stretching deformations. PMID:22735160
L�pez-P�rez, Daniel E; Revilla-L�pez, Guillermo; Jacquemin, Denis; Zanuy, David; Palys, Barbara; Sek, Slawomir; Alem�n, Carlos
Determination of structural characteristics of all-organic radical liquid crystals based on analysis of the dipole-dipole broadened EPR spectra.
The angular dependences of g-value and line width of EPR spectra of paramagnetic all-organic liquid crystalline (LC) materials were measured for the quantitative characterization of the nematic, cholesteric, and smectic C phases. The detailed molecular alignment in mesophases was determined by means of numerical spectra simulation focusing on spin exchange and dipole-dipole magnetic interactions of neighboring molecules. The obtained structural data indicate that the spin polarization mechanism between neighboring molecules rather than the direct through-space interactions between paramagnetic centers is responsible for the specific magnetic properties of the studied LC materials. PMID:24479531
Vorobiev, A Kh; Chumakova, N A; Pomogailo, D A; Uchida, Y; Suzuki, K; Noda, Y; Tamura, R
Generalized Donkor model with induced dipole-dipole forbidden transitions using Maple
The idea of this work was to generalize the Donkor model (Quantum Information and Computation IX, edited by Eric Donkor, Andrew R. Pirich, Howard E. Brandt, Proc. of SPIE Vol. 8057) about the application of induced dipole-dipole forbidden transitions to quantum computation. Using computer algebra we were able to reproduce the original Donkor model. Then we applied some modifications to this model and obtained the respective solutions. It is expected that this model has applications for quantum computation.
Jaramillo Correa, Camilo
The 13C Dipole-dipole Relaxation and Pseudorotation of Cyclododecanone
C dipole-dipole relaxation time of the carbon atoms of macrocyclic ketone, cyclododecanone, have been determined at various temperatures in 15.0 MHz in CDC1. T1 measurements of the methylene bridges were conducted with inversion recovery method and the measured NOE values at similar conditions gave the T 1 of the particular carbon moiety. The linear relationship between the inverse of absolute
�akil Erk
Electronic Structure Theory for Radicaloid Systems and Intermolecular Interactions
A radical molecule contains one or more electrons that are unpaired. A radicaloid may be defined as a molecule in which there are that are partially unpaired. As a result, the electronic structure of the radicaloid can be quite complicated for a variety of reasons. For a singlet biradicaloid, the singlet and triplet wavefunction can be quite close energetically which can lead to problems when trying to describe the system with a single determinant. The simplest solution to this problem is to allow the wavefunction to break spin-symmetry in order to get a lower energy. Unfortunately this action can lead to wavefunctions that are no longer eigenfunctions of the < S2> operator. In the second chapter we investigate a distannyne which has a biradicaloid resonance structure. By examining the orbital Hessian, it is discovered that the spin-symmetric solution is a saddle-point in wavefunction space and is structurally different than the spin-polarized solution. We then increase the complexity of the model system and see that the spin-symmetric solution is only a minimum for the exact experimental system and not for a simplified model system in which bulky organic substituents are replaced by simpler phenyl groups. Therefore, the breaking of spin-symmetry is absolutely critical in the small model systems and the full substituents play a non-trivial role. However, the breaking of the spin-symmetry can have consequences for physical quantities when correlated methods are used. At the point of spin polarization or unrestriction the orbital Hessian will have one eigenvalue which is zero. Since the relaxed density matrix in correlated methods like Second-Order Mo ller-Plesset theory (MP2) depend on the inverse of the Hessian, at the unrestriction point this quantity will be undefined. Some unphysical artifacts are identified as a direct consequence of this fact. First, discontinuities in first order molecular properties such as the dipole moment are seen at the geometries associated with unrestriction. Second, the relaxed density matrix itself fails to be N-representable, with natural orbital occupation numbers less than zero and greater than one. Therefore, it is desirable to use a method that is not dependent on the inverse of the Hessian like orbital optimized MP2 (O2). Another system which requires the use of orbital optimization is a neutral soliton on a polyacetylene chain. In this system, the Hartree-Fock reference suffers from severe spin-polarization making the wavefunction physically unreasonable unless a very sophisticated treatment of electron correlation is used to correct this problem. Originally, it was found that computationally expensive methods like CCSD(T) and CASSCF could adequately describe small model chain but not the full system. The O2 method is found to be an dramatic improvement over traditional MP2 which can be feasibly applied to polyenyl chains long enough to characterize the soliton. It is also discovered that density functionals are generally inadequate in describing the half-width of the soliton. Finally, the last chapter takes a slightly different perspective and focuses on the addition of correlation energy to a successful energy decomposition analysis based on absolutely localized molecular orbitals. It is discovered that the resulting new method can adequately describe systems with dispersive intermolecular interactions and large amounts of charge transfer. This scheme is then applied to the water dimer systems and it is found that all of the intermolecular interactions similar in size with the electrostatic interaction being the largest and the dispersive interaction being the smallest. This method is also contrasted with other EDA schemes.
Kurlancheek, Westin
Femtosecond Fourier-transform spectroscopy of low-frequency intermolecular motions in weakly interacting liquids.
Recent work on the subject of solvation dynamics has concentrated on understanding the ultrafast dynamics of intermolecular interactions in strongly interacting, polar, and hydrogen-bonding solvents. In general, investigations into the effects of solvatio...
E. W. Castner Y. J. Chang J. S. Melinger D. McMorrow
Determining the parameters of the potential of intermolecular interaction by the Zeno line
The method of determination of intermolecular interaction potential parameters by the Zeno line is proposed. The intermolecular interaction of ethane, propane, ethylene, and propylene is described using a model of site-site interactions and Karr-Konowalow potential. It is shown that the parameters of intermolecular interaction for this potential can be determined from a small number of experimental data in the single-phase area. It is noted that the final parameters allow us to describe the thermodynamic properties over a broad range of gas and liquid states with precision acceptable for practical use.
Anashkin, I. P.; Klinov, A. V.
Femtosecond Fourier-transform spectroscopy of low-frequency intermolecular motions in weakly interacting liquids
Recent work on the subject of solvation dynamics has concentrated on understanding the ultrafast dynamics of intermolecular interactions in strongly interacting, polar, and hydrogen-bonding solvents. In general, investigations into the effects of solvation dynamics on chemical reactions have concentrated on the highly polar liquids because it is in these solvents that the largest spectroscopic changes with solvent relaxation are observed. In these very polar liquids, however, the intermolecular dynamics are very complex, consisting of contributions from reorientational diffusion, inertially limited rotations, intermolecular vibrations involving both reorientational (librational) and translational degrees of freedom, and interaction-induced collisional effects. The role of collisional interaction-induced effects in shaping the intermolecular dynamics of molecular liquids has been a subject of considerable discussion. Molecular dynamics simulations have suggested that collisional effects can have a significant role in shaping the femtosecond dynamics and nonlinear-optical properties of molecular liquids. However, for anisotropic molecules, it is difficult to separate experimentally the collisional effects from other phenomena. In this paper the authors examine the intermolecular dynamics of the weakly interacting liquid carbon tetrachloride (CCl{sub 4}). Because carbon tetrachloride is a spherical top molecule (belonging to the T{sub d} point group), its intermolecular light-scattering spectrum is purely interaction-induced. By studying this purely collision-induced feature in CCl{sub 4}, the authors hope to gain insight on the lowest-frequency intermolecular vibrational behavior of more complex systems.
Castner, E.W. Jr.; Chang, Y.J. [Brookhaven National Lab., Upton, NY (United States); Melinger, J.S.; McMorrow, D. [Naval Research Lab., Washington, DC (US)
Intermolecular Embraces and Intermolecular Energies
Control of the assembly of molecules in the crystalline state requires management of all possible intermolecular interactions, and their energies. Any one molecule is surrounded by and interacts with parts of the surface of several others, and it is the balance of all the intermolecular interaction energies that determines the lattice enthalpy, and therefore the product structure. In this context
Ian Dance
Joint inversion of Wenner and dipole-dipole data to study a gasoline-contaminated soil
The goal of this work was to study a contaminated soil due to a gasoline spill produced by fissures in a concrete purge chamber located along a gas transmission line. A monitoring well drilled 16 m down gradient from the purge chamber revealed the presence of a gasoline layer of 0.5 m thick at 1.5 m depth, floating on top of the water table. A second well, drilled 30 m away from the first well, and in the same direction, did not show any evidence of contamination. To investigate this problem, a geoelectrical survey was conducted, combining dipole-dipole and Wenner arrays. First, four dipole-dipole profiles in a direction perpendicular to the longitudinal axis joining the wells were carried out. The electrical tomographies obtained from the 2D inversion of the data showed that the contaminated region was characterized by a resistive plume located at a depth between 1 to 2 m and had lateral extent of about 6-8 m. The longitudinal extension was less than 20 m, since the last profile located 30 m farther from the chamber did not show this kind of anomaly. To better determine the longitudinal extension, we performed a dipole-dipole profile along a line in this direction. The inverse model confirmed that the extension of the contaminated section was about 16 m. To complete the study of the deeper layer, we carried out Wenner soundings. The results of the inversion process indicated that to a depth of 20 m the soil was very conductive, because of the presence of clays as the main constituents, which confine the contaminant within this impermeable surrounding. To improve the inverse model, we performed a joint inversion of dipole-dipole and Wenner data. Analysis of the depth of penetration showed that it increased to 25 m and comparing the resulting model with the ones obtained from each array separately, we concluded that the joint inversion improves the depth obtained by the survey, while maintaining the shallow lateral resolution.
de la Vega, Mat�as; Osella, Ana; Lascano, Eugenia
Influence of medium chirality on electric dipole-dipole resonance energy transfer
Electric dipole-dipole resonance energy transfer taking place between two chromophores in an absorptive and dispersive chiral medium is studied. Quantized electromagnetic field operators in this environment are first obtained from the time-harmonic Maxwell equations and the Drude-Born-Fedorov equations. Second-order time-dependent perturbation theory and the Fermi Golden rule are used to calculate the transfer rate. A complicated dependence on the permittivity, permeability and chirality admittance of the medium is found. In the near-zone, the rate is amplified in a medium with negligible absorption comprised of one enantiomer relative to that in a racemic mixture.
Rodriguez, Justo J.; Salam, A.
Computer-graphics studies of dipole-dipole collisions - Evidence for neutral collision complexes.
NASA Technical Reports Server (NTRS)
Extension of three-dimensional computer-graphics studies of orientation-dependent forces to multiple reflection behavior in dipole-dipole collisions. The collision pairs DCl-DCl and HCl-HCl are studied for rotational temperatures of 25, 77, and 300 K and translational temperatures of 77 and 300 K. The probability of a multiple reflection collision is a very sensitive inverse function of hard-core reflection distance for fixed temperatures. A brief comparison of the results is made with two-dimensional results of Clarke and Smith (1970) for CHF3-CHF3.
Dugan, J. V., Jr.; Palmer, R. W.
Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals
The symmetry-adapted perturbation theory (SAPT) that has the ability in decomposition of the total interaction energy into\\u000a physically meaningful components is used to provide a more fundamental understanding of intermolecular forces. This work was\\u000a motivated by the difficulty of standard SAPT in computing the intermolecular interactions for large energetic dimer systems.\\u000a SAPT based on Kohn-Sham orbitals (SAPT(DFT)) proves computationally efficient
Huajie Song; Heming Xiao; Haishan Dong
Long-term dipole-dipole resistivity monitoring at the Cerro Prieto geothermal field
Dipole-dipole resistivity measurements for the combined purposes of reservoir delineation and reservoir monitoring were first made at Cerro Prieto in 1978 and have continued on approximately an annual basis since then. Two 20 km-long dipole-dipole lines with permanently emplaced electrodes at 1-km spacings were established over the field area. Resistivity remeasurements have been made on one line at 6- to 18-month intervals using a 25 kW generator capable of up to 80A output and a microprocessor-controlled signal-averaging receiver. This high-power, low-noise system provides highly accurate measurements even at large transmitter receiver separations. Standard error calculations for collected data indicate errors less than 5% for all points. Results from four years of monitoring (1979-1983) indicate a 5% average annual increase in apparent resistivity over the present production area, and larger decreases in apparent resistivity in the region to the east. The increase in resistivity in the production zone is most likely due to dilution of reservoir fluids with fresher water, as evidenced by a drop in chloride content of produced waters. The area of decreasing resistivity east of the reservoir is associated with a steeply dipping conductive body, a zone of higher thermal gradients and an increase in shale thickness in the section. Decreasing resistivity in this area may be caused by an influx of high temperature, saline water from depths of 3/sup +/ km through a sandy gap in the shales.
Wilt, M.; Goldstein, N.E.; Sasaki, Y.
Characterization of intermolecular interaction between two substances when one substance does not possess any characteristic peak
We explore whether it is possible to use 2D correlation spectrum to characterize intermolecular interactions between two solutes dissolved in the same solution when one substance does not possesses any characteristic peak. We demonstrate that the interaction can be manifested by characteristic cross peaks in 2D asynchronous correlated spectrum. The above cross peaks reflect the subtle spectral variations on the characteristic peak of another solute under intermolecular interaction. On the other hand, 2D synchronous spectrum is not suitable to characterize intermolecular interaction since the cross peaks contain irremovable interfering parts. The terbium-chloride/benzamide/methanol system is used to demonstrate that this approach is applicable in the real chemical system.
Li, Xiaopei; Fan, Xiaokun; Huang, Kun; Liu, Huizhou; Zhao, Ying; Wei, Yongju; Liu, Cuige; Xu, Yizhuang; Noda, Isao; Wu, Jinguang
Modulation of the intermolecular interaction of myoglobin by removal of the heme.
Toward understanding intermolecular interactions governing self-association of proteins, the present study investigated a model protein, myoglobin, using a small-angle X-ray scattering technique. It has been known that removal of the heme makes myoglobin aggregation-prone. The interparticle interferences of the holomyoglobin and the apomyoglobin were compared in terms of the structure factor. Analysis of the structure factor using a model potential of Derjaguin-Laudau-Verwey-Overbeek (DLVO) suggests that the intermolecular interaction potential of apomyoglobin is more attractive than that of holomyoglobin at short range from the protein molecule. PMID:24121340
Imamura, Hiroshi; Morita, Takeshi; Sumi, Tomonari; Isogai, Yasuhiro; Kato, Minoru; Nishikawa, Keiko
Intermolecular interactions of the malate synthase of Paracoccidioides spp
Background The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands. Results The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software. Conclusion These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell.
Intermolecular interaction potentials of the methane dimer from the local density approximation
The intermolecular interaction potentials of methane (CH{sub 4}) dimer are calculated within the density functional theory in the local density approximation (LDA). It is found that the calculated potentials have minima when the intermolecular distance of CH{sub 4} dimer is about 7.0 a.u., which is in good agreement with the experiment. The depth of the potential is 0.017 eV. The results obtained by our LDA calculations seem to agree well with those obtained by MP2, MP3, and CCSD from the Moeller-Plesset and coupled cluster methods by Tsuzuki et al. and with the experimental data.
Chen Xiangrong [Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065 (China); International Centre for Materials Physics, Chinese Academy of Sciences, Shenyang 110016 (China); Institute of Physics, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8571 (Japan); Bai Yulin [Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065 (China); Department of Science and Technology of Eelectronic Information, Yibin University, Yibin 644000 (China); Zhu Jun; Yang Xiangdong [Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065 (China)
Probing Weak Intermolecular Interactions by Using the Invariom Approach: A Comparative Study of s-Tetrazine.
A comparative study of chemical bonding peculiarities in 1,2,4,5-tetrazine was carried out to test the performance of a recently developed invariom approach against a conventional charge density analysis of high-resolution X-ray diffraction data and quantum chemical calculations within the plane-wave functional theory. The amazing similarity between the intermolecular features thus obtained for this van der Waals crystal showed the invariom approximation to now emerge as a fast and convenient way towards reliable description of weak intermolecular interactions. PMID:24737643
Nelyubina, Yulia V; Korlyukov, Alexander A; Lyssenko, Konstantin A
Problem-Based Learning in 9th Grade Chemistry Class: �Intermolecular Forces�
This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students� understanding\\u000a of intermolecular forces (dipole�dipole forces, London dispersion forces and hydrogen bonding). The student�s alternate conceptions\\u000a about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight 9th grade students were stratified\\u000a by cognitive levels and then randomly assigned to experimental (PBL,
Leman Tarhan; Hulya Ayar-Kayali; Raziye Ozturk Urek; Burcin Acar
Vibrational spectroscopy on intermolecular interactions in solutions and at interfaces
In recent years, considerable progress has been made in the areas of molecular recognition and surface analysis. These fields meet in the field of sensor development, where the interaction\\u000abetween molecules and a suitably modified surface is of utmost importance. Vibrational\\u000aspectroscopy is quite useful in these areas of research, as it may reveal the processes taking place\\u000aat a
Johannes Wilhelmus Maria Nissink
Potential functions for describing intermolecular interactions in cyanoacetylene clusters
Potential functions for describing interactions between cyanoacetylene molecules based on ab initio determined molecular properties and IMPT calculations are proposed. Electrostatic interactions are described by a multipole expansion on atoms and midbond points; dispersion is expressed by a London-type function of atomic polarizabilities and induction is considered via a series of polarizabilities distributed over the atoms. The repulsion contribution was determined by using a test-particle model involving a helium atom as probe particle. Two functions based on two basis sets of different size, viz. 6-311G** and 5S4P2D/3S2P, were used. Cyanoacetylene dimer exhibits two minima corresponding to a linear and an antiparallel configuration, respectively. The proposed functions accurately reproduce the characteristics of the dimer minima as derived from ab initio calculations at the M�ller-Plesset (MP2) level. In addition, they can describe cooperativeness in larger clusters; specifically, the dipole moment and interaction energy per molecule increase with increasing number of constituent units in the cluster. The behavior observed is similar to previously reported findings for HCN clusters.
Cabaleiro-Lago, Enrique M.; R�os, Miguel A.
Mass spectrometry tools for analysis of intermolecular interactions.
The small quantities of protein required for mass spectrometry (MS) make it a powerful tool to detect binding (protein-protein, protein-small molecule, etc.) of proteins that are difficult to express in large quantities, as is the case for many intrinsically disordered proteins. Chemical cross-linking, proteolysis, and MS analysis, combined, are a powerful tool for the identification of binding domains. Here, we present a traditional approach to determine protein-protein interaction binding sites using heavy water ((18)O) as a label. This technique is relatively inexpensive and can be performed on any mass spectrometer without specialized software. PMID:22821539
Auclair, Jared R; Somasundaran, Mohan; Green, Karin M; Evans, James E; Schiffer, Celia A; Ringe, Dagmar; Petsko, Gregory A; Agar, Jeffrey N
Intermolecular interactions in the bilirubin-cholate-silica system
Bilirubin-cholate interactions in aqueous solutions were studied. The constants of binding of bilirubin with taurocholate dimers and taurodeoxycholate trimers were calculated. The adsorption of bilirubin and cholates on the surface of highly dispersed silica was studied. It was shown that taurine-conjugated cholates are poorly adsorbed from micellar solutions on the silica surface, the specific amount of bilirubin adsorbed decreases with increasing concentration of cholates in the solution, the affinity of free bilirubin for the silica surface is independent of the nature of the cholic acid, and that the affinity of cholate-bilirubin complexes for the silica surface is lower than the affinity of free bilirubin.
Vlasova, N. N.; Golovkova, L. P.; Severinovskaya, O. V.
Intermolecular interactions between cucurbit[7]uril and pilocarpine.
The interactions between cucurbit[7]uril (CB7) macrocycles and pilocarpine (PIL) were investigated in aqueous solution by using (1)H NMR and circular dichroism (CD) spectroscopic techniques. The characterizations of the freeze-drying solid complex were conducted by electrospray ionization mass spectroscopy (ESI-MS), Fourier transform-infrared spectroscopy (FT-IR), thermogravimetry, and differential scanning calorimetry (DSC) techniques. The DSC and thermogravimetry confirmed the production of a thermally stable solid complex. The NMR, CD and ESI-MS measurements confirmed asymmetric induction during the complexation reaction, in which the ?-lactone ring of PIL (not the imidazole nucleus) has been fully encapsulated within the cavity of CB7. The stability of the drug has significantly enhanced as evidenced by the high-performance liquid chromatographic (HPLC) method. The results are discussed in the context of utilizing non-conventional supramolecular host-guest approaches to enhance the chemical stability in aqueous media of hydrophilic PIL drugs as model compounds. The non-classical stereospecific interactions between CB7 and PIL drugs are also highlighted. PMID:24239578
Saleh, Na'il; Al-Handawi, Marieh B; Al-Kaabi, Leena; Ali, Liaquat; Salman Ashraf, S; Thiemann, Thies; Al-Hindawi, Bassam; Meetani, Mohammed
Empirical intermolecular potential from depolarized interaction-induced light scattering spectra for tetrafluoromethane
Depolarized interaction-induced light scattering spectra of tetrafluoromethane in the frequency range 2�150cm?1 at 294.5 K and 0.91 mol\\/l with the interaction pressure virial coefficient and viscosity have been used for deriving the empirical multiparameter Morse�Morse�Morse�Spline�van der Waals (M3SV), Lennard-Jones, Kihara, and exp-6 intermolecular potentials. The line shape at relatively low frequencies is determined largely by the effect of bound and
Mohamed Sayed Abdel Kader
Atom depth analysis delineates mechanisms of protein intermolecular interactions
Highlights: �3D atom depth analysis is proposed to identify different layers in protein structures. �Amino acid contents for each layers have been analyzed for a large protein dataset. �Charged amino acids in the most external layer are present at very different extents. �Atom depth indexes of K residues reflect their side chains flexibility. �Mobile surface charges can be responsible for long range protein�protein recognition. -- Abstract: The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein�protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein�protein functional interactions.
Alocci, Davide, E-mail: firstname.lastname@example.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy)] [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Bernini, Andrea, E-mail: firstname.lastname@example.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy)] [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Niccolai, Neri, E-mail: firstname.lastname@example.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy) [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena (Italy)
Surface dipole of F4TCNQ films: Collective charge transfer and dipole-dipole repulsion in submonolayers
A charge transfer (CT) model is introduced for strong acceptors like A = F4TCNQ that are ionized on surfaces at low coverage {\\\\theta}. Each A forms a CT dimer with a surface state S. Dipole-dipole repulsion grows as {\\\\theta}^(3\\/2) up to {\\\\theta} = 1 in a full monolayer. Electron transfer {\\\\rho}({\\\\theta}) within dimers is found self-consistently and decreases with increasing
Zolt�n G. Soos; Benjamin J. Topham
Surface dipole of F4TCNQ films: Collective charge transfer and dipole�dipole repulsion in submonolayers
A charge transfer (CT) model is introduced for strong acceptors like A=F4TCNQ that are ionized on surfaces at low coverage ?. Each A forms a CT dimer with a surface state S. Dipole�dipole repulsion grows as ?3\\/2 up to ?=1 in a full monolayer. Electron transfer ?(?) within dimers is found self-consistently and decreases with increasing coverage. The surface dipole
Distinguishability and chiral stability in solution: effects of decoherence and intermolecular interactions.
We examine the effect of decoherence and intermolecular interactions (chiral discrimination energies) on the chiral stability and the distinguishability of initially pure versus mixed states in an open chiral system. Under a two-level approximation for a system, intermolecular interactions are introduced by a mean-field theory, and interaction between a system and an environment is modeled by a continuous measurement of a population difference between the two chiral states. The resultant equations are explored for various parameters, with emphasis on the combined effects of the initial condition of the system, the chiral discrimination energies, and the decoherence in determining: the distinguishability as measured by a population difference between the initially pure and mixed states, and the decoherence process; the chiral stability as measured by the purity decay; and the stationary state of the system at times long relative to the time scales of the system dynamics and of the environmental effects. PMID:24880262
Han, Heekyung; Wardlaw, David M; Frolov, Alexei M
Cation-? interactions: accurate intermolecular potential from symmetry-adapted perturbation theory.
Symmetry-adapted perturbation theory (SAPT) is used to decompose the total intermolecular interaction energy between the ammonium cation and a benzene molecule into four physically motivated individual contributions: electrostatics, exchange, dispersion, and induction. Based on this rigorous decomposition, it is shown unambiguously that both the electrostatic and the induction energy components contribute almost equally to the attractive forces stabilizing the dimer with a nonnegligible contribution coming from the dispersion term. A polarizable potential model for the interaction of ammonium cation with benzene is parametrized by fitting these four energy components separately using the functional forms of the AMOEBA force field augmented with the missing charge penetration energy term calculated as a sum over pairwise electrostatic energies between spherical atoms. It is shown that the proposed model is able to produce accurate intermolecular interaction energies as compared to ab initio results, thus avoiding error compensation to a large extent. PMID:23924321
Ansorg, Kay; Tafipolsky, Maxim; Engels, Bernd
Structure features and intermolecular interaction investigation in long-chain aliphatic compounds by IR spectroscopy methods
The results of the structure features and intermolecular interaction investigations in long-chain aliphatic compounds (LCAC) by JR spectroscopy (experiment, the theory), differential thermal analysis, polarizing microscopy, and X-ray methods have been generalized. The objects for the researches have been the carboxylic acids derivatives (alkyl- and alkyloxybenzoic, alkylcyclohexanecarboxylic and their completely or partially fluoroalkyl substituted), 4-n-alkyl-4'- cyanobiphenyls, 4-n-alkiloxy-4' -cyanobiphenyls n-n' -butyloxybenzoate of cholesterol. The results of investigations have been proved by the data of the infra-red spectrum LCAC modeling taking into consideration conformational mobility of molecules and intermolecular specific interaction (H-bond). Both factors become apparent in JR spectra and determine LCAC structure features. It is established, that the conformational mobility of molecules.
Babkov, L. M.; Vedyaeva, E. S.; Trukhachev, S. V.
Nonlinear optical properties of highly conjugated push�pull porphyrin aggregates: Role of intermolecular interaction
We present a quantum-chemical analysis of porphyrin aggregates performed to provide insight into the intermolecular interactions and the relationship between their structural and collective non-linear optical properties. The first hyperpolarizabilities are evaluated for monomer and aggregates of a series of push�pull porphyrins, whose synthesis and hyperpolarizabilities are reported recently in literature [T.G. Zhang, Y. Zhao, I. Asselberghs, A. Persoons, K.
Paresh Chandra Ray; Jerzy Leszczynski
Intermolecular interactions between a Ru complex and organic dyes in cosensitized solar cells: a computational study.
Intermolecular interactions in cyclometalated Ru complex dye (FT89) dimers, carbazole organic dye (MK-45 and MK-111) dimers, FT89-MK-45 complexes, and FT89-MK-111 complexes were investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT) to elucidate the improvement mechanism of dye-sensitized solar cell (DSSC) performance due to cosensitization with FT89 and MK dyes. All of the dimers and complexes form intermolecular cyclic hydrogen bonds via the carboxyl groups. The FT89 dimer and complexes with the TiO2Na model system promote intermolecular interactions with I2via the NCS ligand of the FT89 monomer. The computational results verify that MK-111 behaves not only as a sensitizer but also inhibits FT89 aggregation by effectively serving as a coadsorbent similar to deoxycholic acid (DCA) in the dye solution, suppressing recombination of the injected electrons in TiO2 with I2, improving DSSC performance. PMID:24968132
Kusama, Hitoshi; Funaki, Takashi; Koumura, Nagatoshi; Sayama, Kazuhiro
Interplay between molecular conformation and intermolecular interactions in conformational polymorphism: a molecular perspective from electronic calculations of tolfenamic acid.
Tolfenamic acid exhibits conformational polymorphism. The molecules in its two commonly occurred crystal structures form similar hydrogen-bonded dimers but differ in conformation. The conformational variance was analyzed by electronic calculation methods with the aim to unravel intrinsic connection between the conformational flexibility and intermolecular interactions in the polymorphs. The study was conducted mainly by conceptual density functional theory (DFT) and natural bond orbital (NBO) analysis. It is found that the conformational polymorphism is resulted from the energy competition between intramolecular ?-conjugation and intermolecular hydrogen bonding. By adapting conformation that departs from being the most energetically stable, tolfenamic acid molecules can strengthen the intermolecular hydrogen-bonding interactions in the crystals. The study illustrates how the molecule's electronic properties are influenced by conformational variation and, inherently, how the intermolecular interactions become regulated. Moreover, understanding molecular interaction and crystal packing necessitates electronic structure calculation and analysis, which can be further facilitated by utilizing DFT and NBO concepts. PMID:21570454
Mattei, Alessandra; Li, Tonglei
Competition between intermolecular and substrate interactions in a multicomponent lattice gas model
Recent experiments have shown that acridine-9-carboxylic acid (ACA) molecules form a dense phase consisting of chain-like structures on Ag(111) with alternating orientations along the chain direction that permit the formation of strong hydrogen bonds. Despite the anisotropy in intermolecular interactions that leads to chain formation, molecular boundaries along and normal to the chair direction have very similar thermodynamic properties and fluctuations. We introduce a multicomponent lattice gas model where molecules with different orientations are treated as different species with different intermolecular interactions as well as different interactions with the substrate. This a generalization of the familiar Blume-Emery-Griffiths model of a binary lattice gas but in a region of parameter space not usually explored. We argue that the novel domain shapes, boundary fluctuations and phase densities seen in experiment arise from a competition between favorable anisotropic pair interactions in the chain phase and less favorable substrate interactions due to the different orientations. Detailed results of Monte Carlo simulations of this model and analytic work using mean field and pair approximation theories will be presented.
Liu, Qiang; Weeks, John
Intermolecular Interactions between Eosin Y and Caffeine Using 1H-NMR Spectroscopy
DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC) from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB), and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1) and the analyte (caffeine) that is responsible for the fluorescence and color changes observed in the actual array. Using 1H-NMR, 1H-COSY, and 1H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed.
Okuom, Macduff O.; Wilson, Mark V.; Jackson, Abby; Holmes, Andrea E.
Intermolecular interactions in binary system of 1-methylimidazole with methanol: A volumetric and theoretical investigation
The Letter demonstrates an experimental and computational investigation of intermolecular interactions in binary system of 1-methylimidazole (MeIm) with methanol. The densities of binary system were measured at T = 288.15-323.15 K, and the values of excess molar volumes were obtained as a function of composition at each temperature. The experimental results indicate the formation of strong cross-associated complex in the binary system. Meanwhile, the nature of hydrogen bond of the associated complexes was explored based on theoretical calculations. In addition, the changes of thermodynamic properties from the monomers to cross-associated complex were also investigated.
Guo, Chang; Fang, Hui; Huang, Rong-Yi; Xu, Heng; Wu, Gen-Hua; Ye, Shi-Yong
Structure and intermolecular interactions of glipizide from laboratory X-ray powder diffraction.
The crystal structure of glipizide, used as a major treatment of type-2 diabetes, has been determined ab initio using variable-temperature laboratory X-ray powder diffraction combined with a direct-space Monte Carlo/simulated annealing methodology. The strengths of the intermolecular interactions (van der Waals, pi-pi stacking, hydrogen bonding and steric interlock) were quantitatively estimated using the thermal expansion data, which were collected in the same set of experiments as those used to determine the structure. PMID:16306678
Burley, Jonathan C
Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.
The ribosome is a very large complex that consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, intermolecular interactions in the Escherichia coli 70S ribosome are investigated by coarse-grained (CG) analysis. CG models are defined to preserve dynamic domains in RNAs and proteins and to capture functional motions in the ribosome, and then the CG sites are connected by harmonic springs, and spring constants are obtained by matching the computed fluctuations to those of an all-atom molecular dynamics (MD) simulation. Those spring constants indicate how strong the interactions are between the ribosomal components, and they are in good agreement with various experimental data. Nearly all the bridges between the small and large ribosomal subunits are indicated by CG interactions with large spring constants. The head of the small subunit is very mobile because it has minimal CG interactions with the rest of the subunit; however, a large number of small subunit proteins bind to maintain the internal structure of the head. The results show a clear connection between the intermolecular interactions and the structural and functional properties of the ribosome because of the reduced complexity in domain-based CG models. The present approach also provides a useful strategy to map interactions between molecules within large biomolecular complexes since it is not straightforward to investigate these by either atomistic MD simulations or residue-based elastic network models. PMID:21910449
Zhang, Zhiyong; Sanbonmatsu, Karissa Y; Voth, Gregory A
Ab-initio study of intermolecular interaction and structure of liquid cyclopentasilane
We report on an ab initio calculation study of intermolecular interactions between cyclopentasilane (CPS) molecules in liquid CPS. Our calculations show that the Sisbnd H bonds that are oriented toward the center of the ring of a CPS molecule play a significant role in the interaction between CPS molecules. This interaction results in the formation of special bonds between CPS molecules, which resemble hydrogen bonds. These hydrogen bonds cause a red shift of IR absorption peaks corresponding to the Sisbnd H stretch vibration. The formation of hydrogen bonds in the liquid phase of CPS was further confirmed by ab-initio molecular dynamics simulations. The analysis of pair correlation functions has shown a significant contribution of hydrogen bonds to the structure of the CPS liquid system.
Lam, Pham Tien; Sugiyama, Ayumu; Masuda, Takashi; Shimoda, Tatsuya; Otsuka, Nobuo; Chi, Dam Hieu
The effect of intermolecular interactions on the charge transport properties of thiazole/thiophene-based oligomers with trifluoromethylphenyl.
A fundamental understanding of the relationship between intermolecular interactions and transport properties in organic semiconducting materials is significant for their potential applications as electronic device element. Carrier transport properties of thiazole/thiophene-based oligomers with trifluoromethylphenyl groups 1, 2, and 3, in which the type and strength of the intermolecular interactions are different, were investigated within the framework of band model. The results show that ?-? stacking interactions are mainly responsible for the hole transport, while hydrogen bonding interactions have a great influence on the electron transport. The specific transport mechanism could be explained by analyzing the density of states (DOS) and ? point wave functions. PMID:24863342
Liu, Ling; Yang, Guochun; Tang, Xiaodan; Geng, Yun; Wu, Yong; Su, Zhongmin
The effects of P-T changes on intermolecular interactions in crystal structure of iodoform
The structural transition at different pressures of a halogen and hydrogen bonded molecular structure (iodoform, CHI3) is described. The pressures analyzed up to sample decomposition are 0.85 GPa (P1RT) and 2.15 GPa (P2RT); also room conditions (P0RT) and low temperature (106 K, P0LT) structures have been reported for comparison. The observed disorder-order phase transition, from P63/m to P63 space group, can be rationalized by the intermolecular interaction analysis. The shortening of the distances among iodoform planes, observed during the compression and the temperature decreasing, determines an ordering of molecular dipoles in a parallel arrangement: this phase transition causes a shortening of I⋯I halogen bondings. The BSSE corrected cohesive energies have been calculated for all structures at DFT/B3LYP level of theory using a periodic boundary condition code and the Grimme dispersion correction. Hirshfeld surfaces and electrostatic potential mapped on charge density isosurfaces have been computed and their features have been analyzed, in order to better understand the halogen intermolecular interactions that control the structural modification of iodoform crystal.
Bertolotti, Federica; Curetti, Nadia; Benna, Piera; Gervasio, Giuliana
Kinetics of Intermolecular Interaction during Protein Folding of Reduced Cytochrome c
Kinetics of intermolecular interaction between reduced cytochrome c (Cyt c) protein and solvent during the protein-refolding process is studied by monitoring the time dependence of apparent diffusion coefficient (D) using the pulsed-laser-induced transient grating technique. The refolding was triggered by photoinduced reduction of unfolded Fe(III) Cyt c in 3.5 M guanidine hydrochloride (GdnHCl) solution and the change in the diffusion coefficient was monitored in time domain. The relationship between D and the protein conformations under equilibrium condition were investigated at various GdnHCl concentrations using a photolabeling reagent. The time dependence of the observed transient grating signal was analyzed using these data and two models: a continuous change model of the intermolecular interaction and a two-state model. It was found that the TG signals in various time ranges can be consistently reproduced well by the two-state model. The dynamics of D is expressed well by a single exponential function with a rate constant of 22 � 7 s?1 in a whole time range. The folding process of Cyt c is discussed based on these observations.
Nishida, Shinpei; Nada, Tomokazu; Terazima, Masahide
Depolarized interaction-induced light scattering spectra of tetrafluoromethane in the frequency range 2-150 cm-1 at 294.5 K and 0.91 mol/l with the interaction pressure virial coefficient and viscosity have been used for deriving the empirical multiparameter Morse-Morse-Morse-Spline-van der Waals (M3SV), Lennard-Jones, Kihara, and exp-6 intermolecular potentials. The line shape at relatively low frequencies is determined largely by the effect of bound and free transitions. At intermediate frequencies it is sensitive to both the attractive part of the potential and the short-range part of the polarizability anisotropy. The high frequency wings are discussed in terms of the collision-induced rotational Raman effect and estimates for the dipole-quadrupole and dipole-octopole polarizabilities A and E, respectively, are obtained. Absolute zeroth and second moments have been measured and compared with theoretical calculations using these models of the intermolecular potentials. The results show that M3SV is the most accurate potential yet reported for this system.
Kader, Mohamed Sayed Abdel
Intermolecular vibrational coherence in bacteriochlorophyll a with clustered polar solvent molecules.
We show that resonant impulsive excitation of the Qy absorption band of bacteriochlorophyll a (BChl) launches a rapidly damped (gamma < 200 fs) ground-state coherent wave-packet motion that arises from intermolecular modes with clustered solvent molecules. Femtosecond pump-probe, dynamic-absorption signals were obtained at room temperature with BChl solutions in pyridine, acetone, and 1-propanol. The vibrational coherence observed in the 0-800-fs regime is modeled in the time domain by two (or three, in the case of 1-propanol) modulation components with asymmetric, inhomogeneously broadened line shapes and frequencies in the 100-200-cm(-1) range. The mean frequency of the vibrational coherence exhibits at least a quadratic dependence on the dipole moment of the solvent molecules and a y-intercept in the 100-cm(-1) regime. This trend is modeled by an expression for the natural frequency of a "6-12" potential composed of attractive terms from van der Waals forces and a repulsive term from the exchange (Pauli exclusion) force. The model suggests that comparable contributions to the potential are provided by the dipole-dipole and London dispersion interactions. These results support the hypothesis that the low-frequency vibrational modes in the 100-cm(-1) regime that are coupled to the light-driven charge-separation reactions in the reaction center from purple bacteria are derived from intermolecular vibrational modes between the chromophores and the surrounding protein medium. PMID:17034248
Shelly, Katherine R; Golovich, Elizabeth C; Beck, Warren F
Application of atomic force microscopy for characteristics of single intermolecular interactions.
Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions. PMID:23379527
Safenkova, I V; Zherdev, A V; Dzantievf, B B
Nonlinear optical properties of highly conjugated push pull porphyrin aggregates: Role of intermolecular interaction
We present a quantum-chemical analysis of porphyrin aggregates performed to provide insight into the intermolecular interactions and the relationship between their structural and collective non-linear optical properties. The first hyperpolarizabilities are evaluated for monomer and aggregates of a series of push-pull porphyrins, whose synthesis and hyperpolarizabilities are reported recently in literature [T.G. Zhang, Y. Zhao, I. Asselberghs, A. Persoons, K. Clays, M.J. Therien, J. Am. Chem. Soc. 127 (2005) 9710]. The molecular geometries are obtained via B3LYP/6-31G (d, p) level optimization including SCRF/PCM approach, while the dynamic NLO properties are calculated with the ZINDO/CV method including solvent effects. It has been observed that the first hyperpolarizability changes tremendously as monomer undergoes aggregation and the magnitude of first hyperpolarizabilities are highly dependent on the nature of aggregates. Importance of our results on the design of electro-optic materials has been discussed.
Ray, Paresh Chandra; Leszczynski, Jerzy
Manifestation of structure and intermolecular interactions of biologically active brassinosteroids in infrared spectra
We have analyzed the IR spectra obtained for steroidal phytohormones 24-epibrassinolide, 24-epicastasterone, 28-homobrassinolide, and 28-homocastasterone. The characteristic frequencies of the stretching vibrations of the hydrocarbon groups CH3, CH2, and CH and also the C=O groups in the spectra of brassinolides are higher than in the spectra of castasterones, which makes it possible to identify them from the IR spectra. Study of the spectra of these brassinosteroids in different media (pressed samples in KBr, films, solutions in CHCl3 and CDCl3) allowed us to establish the presence of intermolecular interactions in which C=O and OH groups, OH-OH groups participate, and also the possible formation of intramolecular hydrogen bonds between the OH groups of the molecules.
Borisevich, N. A.; Skornyakov, I. V.; Khripach, V. A.; Tolstorozhev, G. B.; Zhabinskii, V. N.
Range-separated density-functional theory with random phase approximation applied to noncovalent intermolecular interactions
Range-separated methods combining a short-range density functional with long-range random phase approximations (RPAs) with or without exchange response kernel are tested on rare-gas dimers and the S22 benchmark set of weakly interacting complexes of Jure?ka et al. [Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The methods are also compared to full-range RPA approaches. Both range separation and inclusion of the Hartree-Fock exchange kernel largely improve the accuracy of intermolecular interaction energies. The best results are obtained with the method called RSH+RPAx, which yields interaction energies for the S22 set with an estimated mean absolute error of about 0.5-0.6 kcal/mol, corresponding to a mean absolute percentage error of about 7%-9% depending on the reference interaction energies used. In particular, the RSH+RPAx method is found to be overall more accurate than the range-separated method based on long-range second-order M�ller-Plesset (MP2) perturbation theory (RSH+MP2).
Zhu, Wuming; Toulouse, Julien; Savin, Andreas; �ngy�n, J�nos G.
Structural changes of CFTR R region upon phosphorylation: a plastic platform for intramolecular and intermolecular interactions.
Chloride channel gating and trafficking of the cystic fibrosis transmembrane conductance regulator (CFTR) are regulated by phosphorylation. Intrinsically disordered segments of the protein are responsible for phospho-regulation, particularly the regulatory (R) region that is a target for several kinases and phosphatases. The R region remains disordered following phosphorylation, with different phosphorylation states sampling various conformations. Recent studies have demonstrated the crucial role that intramolecular and intermolecular interactions of the R region play in CFTR regulation. Different partners compete for the same binding segment, with the R region containing multiple overlapping binding elements. The non-phosphorylated R region interacts with the nucleotide binding domains and inhibits channel activity by blocking heterodimerization. Phosphorylation shifts the equilibrium such that the R region is excluded from the dimer interface, facilitating gating and processing by stimulating R region interactions with other domains and proteins. The dynamic conformational sampling and transient binding of the R region to multiple partners enables complex control of CFTR channel activity and trafficking. PMID:23826884
Bozoky, Zoltan; Krzeminski, Mickael; Chong, P Andrew; Forman-Kay, Julie D
Intermolecular interaction of prednisolone with bovine serum albumin: Spectroscopic and molecular docking methods
The intermolecular interaction of prednisolone with bovine serum albumin (BSA) was studied using fluorescence, circular dichroism (CD) and molecular docking methods. The experimental results showed that the fluorescence quenching of the BSA at 338 nm by prednisolone resulted from the formation of prednisolone-BSA complex. The number of binding sites (n) for prednisolone binding on BSA was approximately equal to 1. Base on the sign and magnitude of the enthalpy and entropy changes (?H0 = -149.6 kJ mol-1 and ?S0 = -370.7 J mol-1 K-1) and the results of molecular docking, it could be suggested that the interaction forces were mainly Van der Waals and hydrogen bonding interactions. Moreover, in the binding process of BSA with prednisolone, prednisolone molecule can be inserted into the hydrophobic cavity of subdomain IIIA (site II) of BSA. The distance between prednisolone and Trp residue of BSA was calculated as 2.264 nm according to Forster's non-radiative energy transfer theory.
Shi, Jie-hua; Zhu, Ying-Yao; Wang, Jing; Chen, Jun; Shen, Ya-Jing
Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: theory and applications to intermolecular interactions involving radicals.
Radical-closed shell and radical-radical intermolecular interactions are less well-understood than those between closed shell species. With the objective of gaining additional insight, this work reports a generalization of the absolutely localized molecular orbital (ALMO) energy decomposition analysis (EDA) to open shell fragments, described by self-consistent field methods, such as standard density functional theory. The ALMO-EDA variationally partitions an intermolecular interaction energy into three separate contributions; frozen orbital interactions, polarization, and charge transfer. The first examples involve comparison of the interactions of alkanes and alkyl radicals (methyl radical, methane, tertiary butyl radical, and isobutane) with sodium, potassium, hydronium, and ammonium cations. A second series of examples involve benzene cation interacting with a series of nucleophiles in both on-top and side-on geometries. The ALMO-EDA yields a variety of interesting insights into the relative roles of its component contributions as the interacting partners and their geometries are changed. PMID:23574220
Horn, Paul R; Sundstrom, Eric Jon; Baker, Thomas A; Head-Gordon, Martin
Calculation of the energies of interatomic and intermolecular van der Waals interactions in terms of variational perturbation theory
A new quantum mechanical method is suggested for calculating separate contributions to the energies of interatomic and intermolecular\\u000a van der Waals interactions. The method involves the multipole expansion of the electrostatic potential of two interacting\\u000a charge systems, which is treated as a perturbation. Equations for the induction and dispersion contributions are obtained\\u000a by varying the second-order correction to the interaction
Yu. B. Malykhanov; V. V. Glazkov
Intermolecular interactions in binary mixtures of 2-Chloroethanol with 2-Dimethylaminoethanol and 2-Diethylaminoethanol at different temperatures
The ultrasonic velocity (u) and density (?) of binary mixtures of 2-Chloroethanol (2-CletOH) with 2-Dimethylaminoethanol (DMAE) and 2-Diethylaminoethanol (DEAE) have been measured over the entire concentration range at temperatures 293.15, 303.15 and 313.15 K. The ultrasonic velocity and density data are used to estimate adiabatic compressibility (?S), intermolecular free length (Lf), molar sound velocity (R), molar compressibility (B) and specific acoustic impedance (Z) along with excess values of ultrasonic velocity (uE), adiabatic compressibility (?SE), intermolecular free length (LfE), acoustic impedance (ZE) and molar volume (VmE). The infrared spectra of both of the systems, 2-CletOH + DMAE and 2-CletOH + DEAE, have also been recorded at room temperature (298.15 K). The observed variations of these parameters, with concentration and temperature, are discussed in terms of the intermolecular interactions between the unlike molecules of the binary mixtures.
Pandey, Puneet Kumar; Awasthi, Anjali; Awasthi, Aashees
Donor-Acceptor Interactions at Interfaces
The free energy change per unit area on separating an interface (the work of adhesion, WA) is composed of a variety of interactions: where superscripts are d for London dispersion forces, h for hydrogen-bonding, ab for acid-base interaction, p for dipole-dipole interaction, and i for induced dipole-dipole interaction. The work of cohesion can be similarly separated into components of surface
Frederick M. Fowkes
Vibrational dynamics, intermolecular interactions, and compound formation in GeH4-H2 under pressure
Optical microscopy, spectroscopic and x-ray diffraction studies at high-pressure are used to investigate intermolecular interactions in binary mixtures of germane (GeH4)+hydrogen (H2). The measurements reveal the formation of a new molecular compound, with the approximate stoichiometry GeH4(H2)2, when the constituents are compressed above 7.5 GPa. Raman and infrared spectroscopic measurements show multiple H2 vibrons substantially softened from bulk solid hydrogen. With increasing pressure, the frequencies of several Raman and infrared H2 vibrons decrease, indicating anomalous attractive interaction for closed-shell, nonpolar molecules. Synchrotron powder x-ray diffraction measurements show that the compound has a structure based on face-centered cubic (fcc) with GeH4 molecules occupying fcc sites and H2 molecules likely distributed between Oh and Td sites. Above ca. 17 GPa, GeH4 molecules in the compound become unstable with respect to decomposition products (Ge+H2), however, the compound can be preserved metastably to ca. 27 GPa for time-scales of the order of several hours.
Strobel, Timothy A.; Chen, Xiao-Jia; Somayazulu, Maddury; Hemley, Russell J.
Vibrational dynamics, intermolecular interactions, and compound formation in GeH4-H2 under pressure.
Optical microscopy, spectroscopic and x-ray diffraction studies at high-pressure are used to investigate intermolecular interactions in binary mixtures of germane (GeH(4)) + hydrogen (H(2)). The measurements reveal the formation of a new molecular compound, with the approximate stoichiometry GeH(4)(H(2))(2), when the constituents are compressed above 7.5 GPa. Raman and infrared spectroscopic measurements show multiple H(2) vibrons substantially softened from bulk solid hydrogen. With increasing pressure, the frequencies of several Raman and infrared H(2) vibrons decrease, indicating anomalous attractive interaction for closed-shell, nonpolar molecules. Synchrotron powder x-ray diffraction measurements show that the compound has a structure based on face-centered cubic (fcc) with GeH(4) molecules occupying fcc sites and H(2) molecules likely distributed between O(h) and T(d) sites. Above ca. 17 GPa, GeH(4) molecules in the compound become unstable with respect to decomposition products (Ge + H(2)), however, the compound can be preserved metastably to ca. 27 GPa for time-scales of the order of several hours. PMID:21033810
Strobel, Timothy A; Chen, Xiao-Jia; Somayazulu, Maddury; Hemley, Russell J
Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential
We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order M�ller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.
Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D., E-mail: email@example.com [Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan (China)
Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin
The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic ?-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 � resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 ?-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.
Yogesha, SD; Sharff, A; Bricogne, G; Izard, T
Development of an intermolecular potential function for interactions in formamide clusters based on ab initio calculations
A potential function for describing interactions between formamide molecules is proposed. The function was developed from ab initio computed molecular properties and intermolecular perturbation theory (IMPT) calculations for formamide dimer involving the 6-311G** basis set. It consists of an electrostatic term that is a function of multipoles distributed over the atoms, an exponential repulsion term obtained by fitting results for the dimer, an induction contribution that is a function of atomic polarizabilities, and a dispersion term based on a London expression that is also dependent on atomic polarizabilities. The results obtained by applying the proposed function to formamide dimer are similar to those found at the MP2/6-311G** level; the function allows one to identify five structures corresponding to as many energy minima. Application of the function to larger clusters revealed that the most attractive minima correspond to planar structures, the most common structural pattern among which is that of the global minimum for the dimer. Based on cooperativeness data for the larger clusters, chained structures seemingly form stronger hydrogen bonds due to increased cooperativeness in interactions between molecules, which may account for the tendency of condensed phases of formamide to adopt open structures.
Sensitivity of predicted gas hydrate occupancies on treatment of intermolecular interactions.
The sensitivity of gas hydrate occupancies predicted on the basis of van der Waals-Platteeuw theory is investigated, as a function of the intermolecular guest-water interaction potential model, and of the number of water molecules taken into account. Simple analytical correction terms that account for the interactions with the water molecules beyond the cutoff distance are introduced, and shown to improve significantly the convergence rate, and hence the efficiency of the computation of the Langmuir constants. The predicted cage occupancies in pure methane and pure carbon dioxide clathrates, calculated using different recent guest-water pair potentials models derived from ab initio calculations, can vary significantly depending on the model. That sensitivity becomes especially strong in the case of multiple guest clathrates. It is shown that the abundances of coenclathrated molecules in multiple guest clathrate hydrates potentially formed on the surface of Mars can vary by more than two orders of magnitude depending on the model. These results underline the strong need for experimental data on pure and multiple guest clathrate hydrates, in particular in the temperature and pressure range that are relevant in extreme environment conditions, to discriminate among the theoretical models. PMID:20232974
Thomas, Caroline; Picaud, Sylvain; Ballenegger, Vincent; Mousis, Olivier
Insights into the AIEE of 1,8-Naphthalimides (NPIs): Inverse Effects of Intermolecular Interactions in Solution and Aggregates.
Systematic structural perturbation has been used to fine-tune and understand the luminescence properties of three new 1,8-naphthalimides (NPIs) in solution and aggregates. The NPIs show blue emission in the solution state and their fluorescence quantum yields are dependent upon their molecular rigidity. In concentrated solutions of the NPIs, intermolecular interactions were found to quench the fluorescence due to the formation of excimers. In contrast, upon aggregation (in THF/H2 O mixtures), the NPIs show aggregation-induced emission enhancement (AIEE). The NPIs also show moderately high solid-state emission quantum yields (ca. 10-12.7?%). The AIEE behaviour of the NPIs depends on their molecular rigidity and the nature of their intermolecular interactions. The NPIs 1-3 show different extents of intermolecular (?-? and C?H???O) interactions in their solid-state crystal structures depending on their substituents. Detailed photophysical, computational and structural investigations suggest that an optimal balance of structural flexibility and intermolecular communication is necessary for achieving AIEE characteristics in these NPIs. PMID:24848578
Mukherjee, Sanjoy; Thilagar, Pakkirisamy
Intermolecular Interactions within the Abundant DEAD-box Protein Dhh1 Regulate Its Activity in Vivo*
Dhh1 is a highly conserved DEAD-box protein that has been implicated in many processes involved in mRNA regulation. At least some functions of Dhh1 may be carried out in cytoplasmic foci called processing bodies (P-bodies). Dhh1 was identified initially as a putative RNA helicase based solely on the presence of conserved helicase motifs found in the superfamily 2 (Sf2) of DEXD/H-box proteins. Although initial mutagenesis studies revealed that the signature DEAD-box motif is required for Dhh1 function in vivo, enzymatic (ATPase or helicase) or ATP binding activities of Dhh1 or those of any its many higher eukaryotic orthologues have not been described. Here we provide the first characterization of the biochemical activities of Dhh1. Dhh1 has weaker RNA-dependent ATPase activity than other well characterized DEAD-box helicases. We provide evidence that intermolecular interactions between the N- and C-terminal RecA-like helicase domains restrict its ATPase activity; mutation of residues mediating these interactions enhanced ATP hydrolysis. Interestingly, the interdomain interaction mutant displayed enhanced mRNA turnover, RNA binding, and recruitment into cytoplasmic foci in vivo compared with wild type Dhh1. Also, we demonstrate that the ATPase activity of Dhh1 is not required for it to be recruited into cytoplasmic foci, but it regulates its association with RNA in vivo. We hypothesize that the activity of Dhh1 is restricted by interdomain interactions, which can be regulated by cellular factors to impart stringent control over this very abundant RNA helicase.
Dutta, Arnob; Zheng, Suting; Jain, Deepti; Cameron, Craig E.; Reese, Joseph C.
Intermolecular C-H���O and C-H���X interactions in substituted spiroacenaphthylene structures.
In the three spiroacenaphthylene structures 5''-[(E)-2,3-dichlorobenzylidene]-7'-(2,3-dichlorophenyl)-1''-methyldispiro[acenaphthylene-1,5'-pyrrolo[1,2-c][1,3]thiazole-6',3''-piperidine]-2,4''-dione, C(35)H(26)Cl(4)N(2)O(2)S, (I), 5''-[(E)-4-fluorobenzylidene]-7'-(4-fluorophenyl)-1''-methyldispiro[acenaphthylene-1,5'-pyrrolo[1,2-c][1,3]thiazole-6',3''-piperidine]-2,4''-dione, C(35)H(28)F(2)N(2)O(2)S, (II), and 5''-[(E)-4-bromobenzylidene]-7'-(4-bromophenyl)-1''-methyldispiro[acenaphthylene-1,5'-pyrrolo[1,2-c][1,3]thiazole-6',3''-piperidine]-2,4''-dione, C(35)H(28)Br(2)N(2)O(2)S, (III), the substituted aryl groups are 2,3-dichloro-, 4-fluoro- and 4-bromophenyl, respectively. The six-membered piperidine ring in all three structures adopts a half-chair conformation, the thiazolidine ring adopts a slightly twisted envelope and the pyrrolidine ring an envelope conformation; in each case, the C atom linking the rings is the flap atom. In all three structures, weak intramolecular C-H���O interactions are present. The crystal packing is stabilized through a number of intermolecular C-H���O and C-H���X interactions, where X = Cl in (I) and F or S in (II), and C-H���O interactions are observed predominantly in (III). In all three structures, molecules are linked through centrosymmetric ring motifs, further tailored through a relay of C-H���X [Cl in (I), Br in (II) and O in (III)] interactions. PMID:22763692
Suresh, J; Vishnupriya, R; Sivakumar, S; Kumar, R Ranjith; Athimoolam, S
Theoretical study of intermolecular magnetic interaction of chromium(V)-nitrido complex self-assembly with tetradentate Schiff base ligand
A theoretical study of the intermolecular magnetic interaction of [CrN(salpn)] is discussed based on DFT calculations. The close contact between the 2p orbitals on the axial nitrogen and other 3d orbitals besides the 3d xy orbital on the adjacent chromium is effective for ferromagnetic coupling. The magnetic interaction is rationally explained by the significantly large spin polarization of the axial nitrogen.
Matsuoka, Naoki; Yoshioka, Naoki
Intermolecular interactions and solvent diffusion in ordered nanostructures formed by self-assembly of block copolymers
Hydrogels formed by Poloxamer poly(ethylene oxide)-poly(propylene oxide) (PEO-PPO) block copolymers find various pharmaceutical and biomedical applications. A variety of ordered structures can be exhibited by Poloxamer block copolymers in selective solvents such as water, for example, micellar cubic phase, hexagonal phase, lamellar phase, etc. We are interested in the thermodynamic and transport properties of water in such hydrogels that have an ordered (lyotropic liquid crystalline) structure. We have investigated the time evolution of water loss from Poloxamer gel films under a driving force of known water vapor pressure in the air in contact with the film. The experimental data on the drying process have been fitted to the diffusion equation for water in the film, under a boundary condition that includes the water concentration in the gel at infinite time; the water diffusion coefficient and other parameters have thus been obtained. The water chemical potential and osmotic pressure in the gel have been obtained from osmotic stress measurements. The osmotic pressure (force), together with data on the corresponding lyotropic liquid crystal spacing (distance) that we obtained from Small Angle X-Ray Scattering (SAXS) measurements, have been analyzed to provide information on the prevailing intermolecular (inter-assembly) forces in the gel. The forces in the gel reveal interactions that occur at two levels, that of the PEO coil and that of the PEO segment.
Gu, Zhiyong
Nonlinear optical properties of zwitterionic merocyanine aggregates: role of intermolecular interaction and solvent polarity.
We present a time-dependent quantum-chemical analysis on merocyanine aggregates to understand the insight of the intermolecular interactions and to find the relationship between structural and collective nonlinear optical properties. The first hyperpolarizabilities are evaluated for monomer and aggregates of a series of zwitterionic merocyanine dyes, whose synthesis and formation of H and J type aggregates in solvents are reported recently in the literature (J. Am. Chem. Soc. 2002, 124, 9431). The molecular geometries are obtained via B3LYP/6-31G (hybrid density-functional theory) optimization including PCM approach, while the dynamic NLO properties are calculated with the TD-DFT/SOS and ZINDO/CV method including solvent effects. It has been observed that the first hyperpolarizability changes tremendously as monomers undergo aggregation, and the magnitude of first hyperpolarizabilities highly depends on the nature of the aggregates. It is found that solvents play a remarkable role on the structure and first hyperpolarizabilities of merocyanine monomers and aggregates. Changing the solvent from low to high dielectric causes not only an increase in magnitude of beta but also a change in sign, therefore passing through zero at intermediate dielectric. The importance of our results on the design of electrooptic materials have been discussed. PMID:16332017
Sainudeen, Zuhail; Ray, Paresh Chandra
Intermolecular vs molecule-substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)
Summary The competition between intermolecular interactions and long-range lateral variations in the substrate�adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moir� structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results.
Roos, Michael; Uhl, Benedikt; Kunzel, Daniela; Hoster, Harry E; Gross, Axel
Optimized spin-component scaled second-order M�ller-Plesset perturbation theory for intermolecular interaction energies
The optimal set of scaling parameters that minimize the error between spin-component scaled (SCS-MP2) and scaled opposite spin (SOS-MP2) theories and CCSD(T) in computing intermolecular binding energies were determined using multivariate linear least squares analysis. Counterpoise corrected intermolecular binding energies among a diverse test set of hydrogen bonded, dispersion, and mixed complexes (S22 training set) were obtained using RI-MP2 theory and the cc-pVXZ (X = D, T, and Q) and the extrapolated cc-pV(XY)Z (XY = D ? T, T ? Q) atomic orbital basis set series. Optimization of the opposite spin-component scaling parameter yielded the SOS(MI)-MP2 model, with the ability to outperform RI-MP2 theory in obtaining accurate intermolecular binding energies among dispersion complexes with only fourth-order computational effort. At the extrapolated cc-pV(DT)Z and cc-pV(TQ)Z levels, for example, intermolecular binding energies among dispersion complexes were computed with RMS errors of 1.00 kcal/mol and 0.87 kcal/mol, respectively, thereby allowing for accurate treatment of prohibitively large molecular systems at a fraction of the computational cost associated with standard RI-MP2 calculations. With both spin-component scaling parameters optimized, the resultant model, SCS(MI)-MP2, emerged as a highly accurate methodology that simultaneously corrects the MP2 errors associated with hydrogen bonded and dispersion complexes. Computations at the extrapolated SCS(MI)-MP2/cc-pV(DT)Z level yielded RMS errors of 0.31 kcal/mol, and therefore represented a computationally efficient method for obtaining intermolecular binding energies with quadruple-? accuracy. With scaling parameters that are essentially inverted with respect to their original recommended values, namely, cOS = 0.40 and cSS = 1.29, intermolecular binding energies computed at the SCS(MI)-MP2/cc-pV(TQ)Z level of theory were found to be within 0.25 kcal/mol of the highest level CCSD(T) benchmarks available to date. Surprisingly, it was found that scaling only the same spin-component of the MP2 energy (SSS(MI)-MP2) leads to significant decreases in the errors associated with MP2 theory in computing intermolecular binding energies. These findings, coupled with the earlier work on SOS-MP2 theory, strongly suggest that the MP2 description of bond energies contains a systematically underestimated opposite spin-component and a simultaneously overestimated same spin-component, while the reverse appears generally true for intermolecular interactions.
Distasio, Robert A., Jr.; Head-Gordon, Martin
Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry
The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated with the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.
Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan; Overgaard, Jacob; Koutsantonis, George A.; Spackman, Mark A.; Iversen, Bo B. (Aarhus); (UWA); (UC)
Quantum phase transitions for two coupled cavities with dipole-interaction atoms
We investigate the quantum phase transitions for two weakly coupled atom-cavity sites. The interatomic dipole-dipole interaction is considered. Our numerical results show that the dipole-dipole interaction is a crucial parameter for the quantum phase transition. For small atom-cavity detuning, the ''superfluid'' becomes more and more obvious with the increase of the dipole-dipole interaction. In addition, the strong dipole-dipole interaction can lead the atomic excitation to be suppressed completely, and only the photonic excitation exists for the ground states. When the atom-cavity detuning is comparable with the dipole-dipole interaction, the dipole-dipole interaction enlarges the positive detunings, which is in favor of exhibiting superfluid photonic states. While for the negative detuning, the dipole-dipole interaction will reduce it, and contribute to the formation of the polaritonic insulator states. The cases for extended models have also been briefly analyzed. We also discuss how to find these novel phenomena in future experiments.
Tan Lei [Institute of Theoretical Physics, Lanzhou University, Lanzhou 730000 (China); Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Zhang Yuqing [Institute of Theoretical Physics, Lanzhou University, Lanzhou 730000 (China); Liu Wuming [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)
Molecular packing and intermolecular interactions in two structural polymorphs of N-palmitoylethanolamine, a type 2 cannabinoid receptor agonist
The molecular structure, packing properties, and intermolecular interactions of two structural polymorphs of N-palmitoylethanolamine (NPEA) have been determined by single-crystal X-ray diffraction. Polymorphs a and b crystal- lized in monoclinic space group P21\\/c and orthorhombic space group Pbca, respectively. In both polymorphs, NPEA molecules are organized in a tail-to-tail manner, resembling a bilayer membrane. Although the molecular packing in polymorph
Ravi Kanth Kamlekar; Musti J. Swamy
Intermolecular interaction potentials of methane and ethylene dimers calculated with the M�ller�Plesset, coupled cluster and density functional methods
Intermolecular interaction potentials of methane and ethylene dimers were calculated by the Hartree�Fock, M�ller�Plesset, coupled cluster and density functional methods. The CCSD(T) electron correlation energies were close to the MP4(SDTQ) ones. The MP2 and MP3 energies were not largely different from the MP4(SDTQ) ones. On the other hand the CCSD and MP4(SDQ) methods largely underestimated the electron correlation energies. Dispersion
Seiji Tsuzuki; Tadafumi Uchimaru; Kazutoshi Tanabe
On the resource evaluation of marine gas hydrate deposits using sea-floor transient electric dipole-dipole methods
Methane hydrates are solid, nonstoichiometric mixtures of water and the gas methane. The depth extent and stability of the hydrate zone is governed by the phase diagram for mixtures of methane and hydrate and determined by ambient pressures and temperatures. The base of the hydrate zone is a phase boundary between solid hydrate and free gas and water. It stands out on seismic sections as a bright reflection. The diffuse upper boundary is not as well marked so that the total mass of hydrate is not determined easily by seismic alone. The addition of electrical data, collected with a seafloor transient electric dipole-dipole system, can aid in the evaluation of the resource. Two exploration scenarios are investigated through numerical modeling. In the first, a very simple example illustrating some of the fundamental characteristics of the electrical response, most of the properties of the section including the probable, regional thickness of the hydrate zone (200 m) are assumed known from seismic and spot drilling. In the second example, less information is assumed available a priori and the complementary electrical survey is required to find both the thickness and the hydrate content in a hydrate zone about 200 m thick beneath the sea floor containing 20 and 40% hydrate in the available pore space, respectively. A linear eigenfunction analysis reveals that for these two models, the total mass of hydrate, the product of hydrate content and thickness, may be estimated to an accuracy of about 3{epsilon}% given measurements of traveltime to an accuracy of {epsilon}% over a range of separations from 100 to 1300 m. Based on these data, the author suggests that the value of {epsilon} may be of the order of 3%.
Edwards, R.N. [Univ. of Toronto, Ontario (Canada). Dept. of Physics] [Univ. of Toronto, Ontario (Canada). Dept. of Physics
Intermolecular electronic interactions in the primary charge separation in bacterial photosynthesis
In this paper the intermolecular overlap approximation is used to calculate the relative magnitudes of the electronic transfer integrals between the excited singlet state (¹P*) of the bacteriochlorophyll dimer (P) and the accessory bacteriochlorophyll (B) and between B⁻ and bacteriopheopytin (H), along the L and M subunits of the reaction center (RC) of Rps. viridis. The ratio of the electron-transfer
M. Plato; K. Moebius; M. E. Michel-Beyerle; M. Bixon; Joshua. Jortner
EPA Science Inventory
Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) provide a significant inc...
The Interaction of Paramagnetic Relaxation Reagents with Intra- and Intermolecular Hydrogen Bonded Phenols.
Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) ...
T. A. Holak G. C. Levy
Structural elucidation and contribution of intermolecular interactions in O-hydroxy acyl aromatics: Insights from X-ray and Hirshfeld surface analysis
An O-hydroxy acyl aromatics, namely 1,1?,1?-(2,4,6-trihydroxybenzene-1,3,5-triyl) triethanone (1) was synthesized and characterized by spectroscopic and single crystal X-ray structural studies with a detailed scrutiny of visualizing and exploring intermolecular interactions in molecular crystals through Hirshfeld surface. The crystal packing of (1) exhibits intermolecular ?�? stacking interactions to generate a one-dimensional parallel stacked ribbon propagating along (0 0 1) direction. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D fingerprint plots have been used to scrutinize molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.
Seth, Saikat Kumar
Fluorescence Study of Intermolecular Interactions in Diluted Aqueous Solutions of Some Cationic Amphiphilic Polysaccharides
The intermolecular hydrophobic association in diluted aqueous solutions of some cationic amphiphilic polysaccharides was investigated using fluorescence techniques. Dextran and dextran carrying N-alkyl-N,N-dimethyl-N(2-hydroxypropylene) ammonium chloride groups as side chains were single labeled with pyrene or naphthalene. The intensity of the pyrene excimer peak and the ratio I3\\/I1 determined from the fluorescence emission spectra of pyrene-labeled amphiphilic polymer increased with increasing
Marieta Nichifor; Magdalena Cristina Stanciu; Bogdan C. Simionescu
Adsorption induced surface-stress sensing signal originating from both vertical interface effects and intermolecular lateral interactions.
This research investigates the origin of specific molecule-adsorption induced surface-stress for micro/nano-cantilever bio/chemical sensors. Systematic discussion is presented on the contribution from types of molecule interactions to the generated surface-stress sensing signal. With the main arguments verified by our micro-cantilever sensing experiments, the origin of the adsorption induced surface-stress is, for the first time, clearly categorized into interface vertical effects and lateral interactions, which helps to comprehensively understand the surface-stress generation and overall to optimize the sensing performance of micro-cantilever chemo-mechanical sensors. The key findings of this research are that, vertically at the molecule adsorption surface, interfacial energy change and charge redistribution are the main origins of the generated surface-stress. More importantly, intermolecular lateral interactions may make a more significant contribution to the nano-mechanical surface-stress response. Compared with other lateral interactions like van der Waals force and the electrostatic coulombic effect, intermolecular hydrogen-bond intensity and steric factor easily cause much greater disparity in surface-stress. PMID:22010113
Yang, Tiantian; Li, Xinxin; Chen, Ying; Lee, Dong-Weon; Zuo, Guomin
Cooperativity of anion⋯? and ?⋯? interactions regulates the self-assembly of a series of carbene proligands: Towards quantitative analysis of intermolecular interactions with Hirshfeld surface
The cooperative effect of weak non-covalent forces between anions and electron deficient aromatics by ?⋯? stacking of a series of carbene proligands (1-3) have been thoroughly explored by crystallographic studies. Structural analysis revealed that the anion⋯? and ?⋯? interactions along with intermolecular hydrogen bonding mutually cooperate to facilitate the assembling of the supramolecular framework. The ?⋯? and corresponding anion⋯? interactions have been investigated in the title carbene proligands despite their association with counter ions. The presence of the anion in the vicinity of the ?-system leads to the formation of anion⋯?/?⋯?/?⋯anion network for an inductive stabilization of the assemblies. To assess the dimensionality of the supramolecular framework consolidated by cooperative anion⋯?/?⋯? interactions and hydrogen bonding, different substituent effects in the carbene backbone have been considered to tune these interactions. These facts show that the supramolecular framework based on these cooperative weak forces may be robust enough for application in molecular recognition. The investigation of close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented in order to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within each crystal.
Samanta, Tapastaru; Dey, Lingaraj; Dinda, Joydev; Chattopadhyay, Shyamal Kumar; Seth, Saikat Kumar
Functional organotrimethoxysilane derivative with strong intermolecular pi-pi interaction: one-pot grafting reaction on oxidized silicon substrates.
Although the fabrication of self-assembled monolayers (SAMs) on an oxidized silicon substrate with special functionality is an important topic for various applications, it is still very difficult to obtain a densely grafted monolayer. With a newly synthesized organotrimethoxysilane containing a 1-cyano-1,2-bisbiphenyl-ethylene (CNMBE) moiety which provides a strong pi-pi intermolecular interaction, an SAM of well-ordered structure is readily obtained by a one-pot grafting reaction under mild conditions. The aggregation process of the CNMBE moiety, which induced a close packing of organosilane on the substrate, was visually monitored by the fluorescence of the monolayer grafted on quartz. PMID:16893203
Nam, Haehyun; Granier, Michel; Boury, Bruno; Park, Soo Young
Copper(II) complexes with chiral reduced Schiff bases: Helical self-assembly via intermolecular C�H?O interactions
Copper(II) complexes having the general formula [Cu(Ln)2] with the N,O-donor reduced Schiff bases N-(2-hydroxy-5-X-benzyl)-(R)-?-methylbenzylamine and N-(2-hydroxy-5-X-benzyl)-(S)-?-methylbenzylamine (X=Cl and Br) (HLn) are described. These chiral complexes crystallize in the noncentrosymmetric P212121 (X=Cl) and P21 (X=Br) space groups. In each case, self-assembly via intermolecular C�H?O interaction leads to a supramolecular helical superstructure.
Vamsee Krishna Muppidi; Sunirban Das; Pallepogu Raghavaiah; Samudranil Pal
Analysis of intermolecular interaction of poly(N-isopropylacrylamide) solution with attenuated total reflectance terahertz spectroscopy
The terahertz attenuated total reflectance spectra of Poly(N-isopropylacrylamide) (P-NIPAAm) solutions were measured in the range of 26.5-47.3 �C. The phase-change in P-NIPAAm was observed via the temperature dependence of the spectra. The collapse of hydrogen bonds in solution was confirmed by the decrease in the signal intensities around 62 cm-1, which corresponds to fast dielectric relaxation by rotation and collision of molecules, and around 166 cm-1, which corresponds to the stretching mode of the intermolecular vibration of water molecules.
Naito, H.; Ogawa, Y.; Hoshina, H.; Sultana, S.; Kondo, N.
Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis
The ribosome is a very large complex, which consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, inter-molecular interactions in the E. coli 70S ribosome are investigated by coarse-grained (CG) analysis. CG models are defined to preserve dynamic domains in RNAs and proteins, and capture functional motions in the ribosome, then the CG sites are connected by harmonic springs and spring constants are obtained by matching the computed fluctuations to those of an all-atom molecular dynamics (MD) simulation. Those spring constants indicate how strong the interactions are between the ribosomal components, which are in good agreement with various experimental data. Nearly all of bridges between the small and large ribosomal subunits are indicated by CG interactions with large spring constants. The head of the small subunit is very mobile because it has the minimal CG interactions with the rest of the subunit; However, a large number of small subunit proteins bind to maintain the internal structure of the head. The results show a clear connection between the inter-molecular interactions and the structural and functional properties of the ribosome because of the reduced complexity in domain-based CG models. The present approach also provides a useful strategy to map interactions between molecules within large biomolecular complexes since it is not straightforward to investigate these by either atomistic MD simulations or residue-based elastic network models.
Zhang, Zhiyong; Sanbonmatsu, Karissa Y.; Voth, Gregory A.
The effects of intra- and inter-molecular interactions on the photophysics of platinum(II) complexes
Square planar platinum(II) complexes have been the subject of intense study for several years due to their many unique properties and potential applications. Exploiting the emission of these complexes allows for a wide range of applications as spectroscopic probes and anticancer reagents. Manipulation of both intra-molecular and inter-molecular interactions allows one to tune the photophysical properties of compounds with great precision. Chapter one of this thesis will introduce the critical role of platinum(II) in medicinal chemistry and basic photophysics of platinum(II) complexes. Chapter two describes the synthesis and studies of a series of novel expanded framework polypyridine platinum(II) complexes that employ a little-explored method of intra-molecular modification. The majority of the compounds exhibit improved photophysics over the parent compound [Pt(trpy)Cl]+. Chapter three summarizes a body of work conducted by McMillin group members over the past several years and describes the synthesis and characterization of the missing members of the series. These complexes involving 4'-substituted trpy ligands, exhibit very impressive photophysics and utilize a well-recognized approach to intra-molecular modification. Chapter four describes the solid state photophysical properties of compounds synthesized by the Lu group. These compounds provide excellent examples of classic intermolecular interaction in Pt(II) compounds and MMLCT emission.
Hight, Lauren M.
Structure and intermolecular interactions in selected binary solutions studied by X-ray methods
The results of X-ray structural studies of liquid chloroanisole C6H4OCH3Cl and 10% solutions of chloroanisole in 1,4-dimethylbenzene C8H10 are presented. It is the first paper on an X-ray diffraction study of the liquid solutions of chloroanisole. The X-ray measurements were made at 293 K for the scattering angle range 2? varying from 6� to 120�. Averaged scattered X-ray angular distributions I�(S) were determined. The angular distributions of the intensity of X-ray scattered by 10% solutions of chloroanisole in 1,4-dimethylbenzene were compared to the angular distributions obtained for liquid ortho-, meta- and para-chloroanisole. The differential radial distribution functions of electron density 4?r?j,knK[?k(r)-?0] were numerically found using the Fourier analysis from a modified Warren, Krutter and Morningstar equation. To the maxima of DRDFs, interatomic and intermolecular distances were assigned. The use of short-wave radiation from an X-ray tube with a molybdenum anode permitted determination of the spheres of intermolecular ordering in the studied liquids and their solutions. The experimental results were used to plot models of the most highly probable mutual disposition of the molecules in liquid chloroanisole and their solutions. The benzene rings of two molecules are situated in parallel plane what results in antiparallel setting of the dipole moments of the chloroanisole molecules. X-ray structural analysis was applied to determine the packing coefficients of chloroanisole molecules. The results obtained in this paper confirm the specific structural properties of the solutions studied.
Drozdowski, Henryk; Romaniuk, Anna; B?aszczak, Zdzis?aw
Intermolecular Interactions Between Proteins and Individual Poly(ethylene oxide) Chains Measured via High-Resolution Force Spectroscopy
The noncovalent adsorption of biofluid proteins onto biomaterial surface coatings, such as poly(ethylene oxide) (PEO), is known to be a primary determining factor of biocompatibility. The molecular mechanisms and precise details of the nanoscale forces acting between proteins and synthetic surface polymers are complex and poorly understood. We have directly measured the intermolecular interaction forces in aqueous buffer solution between individual end-grafted PEO chains and a probe tip covalently bound with human serum albumin (HSA) using high-resolution force spectroscopy. Long-range adhesion is frequently observed between the HSA probe tip and the PEO chain on retraction, which is strong enough to allow stretching of the individual PEO chains (Fadhesion=0.125nN�0.22nN, Dadhesion=246nm�148nm). Statistical analysis, comparison to a variety of control experiments, and theoretical modeling enable us to interpret these experimental results in terms of electrostatic, hydrogen, and steric interactions.
Ortiz, Christine; Rixman, Monica
Intermolecular interactions in methyl formate-ethanol mixtures at 303-313 K according to ultrasonic data
Density (?), viscosity (?), and ultrasonic velocity ( U) have been measured for a binary mixture composed of methyl formate and ethanol at 303, 308, and 313 K. The adiabatic compressibility (?), acoustic impedance (Z), free length ( L f ), free volume ( V f ), internal pressure (? i ), viscous relaxation time (?), and Gibbs free energy (? G) were calculated from the experimental data. The excess values of these parameters (? E , Z E , L {/f E }, V {/f E }, ? {/i E }, ? E , and ? G E ) have also been calculated using the determined parameters and interpreted in terms of molecular interactions. The deviations in the sign and values of these excess parameters from the ideal mixing reveal the nature of intermolecular interactions between components of the mixture.
Elangovan, S.; Mullainathan, S.
A method based on the DAOSD approach to estimate the variation of the peak position and bandwidth caused by intermolecular interactions
Subtle spectral variations caused by intermolecular interactions, which are hardly observed in the original one-dimensional spectra or the second derivative spectra, can be distinctly visualized via spectral patterns in two-dimensional spectra generated by using double asynchronous orthogonal sample designed scheme (DAOSD). If intermolecular interaction only brings about band-shift on a characteristic peak, a pair of cross peaks appears in the corresponding near diagonal region. If intermolecular interaction induces variation of bandwidth only, a cluster of cross peaks forms a diamond pattern in the near diagonal region. In both cases, the variation of peak position or bandwidth can be deduced quantitatively from the pattern of cross peaks. If intermolecular interaction causes variations on both peak position and bandwidth, four cross peaks form a butterfly pattern. In this case, however, it is not straightforward to estimate the variation of peak position and bandwidth directly from the patterns of the cross peaks. In this paper, we propose an algorithm to estimate the variations of peak position and bandwidth of a characteristic peak caused by intermolecular interactions. The validity of this approach was confirmed by computer simulation on several model systems.
Bi, Quan; Chen, Jing; Li, Xiaopei; Shi, Jia-Jia; Guo, Ran; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang
Identification of molecular crystals capable of undergoing an acyl-transfer reaction based on intermolecular interactions in the crystal lattice.
Investigation of the intermolecular acyl-transfer reactivity in molecular crystals of myo-inositol orthoester derivatives and its correlation with crystal structures enabled us to identify the essential parameters to support efficient acyl-transfer reactions in crystals: 1)?the favorable geometry of the nucleophile (-OH) and the electrophile (C-O) and 2)?the molecular assembly, reinforced by C-H???? interactions, which supports a domino-type reaction in crystals. These parameters were used to identify another reactive crystal through a data-mining study of the Cambridge Structural Database. A 2:1 co-crystal of 2,3-naphthalene diol and its di-p-methylbenzoate was selected as a potentially reactive crystal and its reactivity was tested by heating the co-crystals in the presence of solid sodium carbonate. A facile intermolecular p-toluoyl group transfer was observed as predicted. The successful identification of reactive crystals opens up a new method for the detection of molecular crystals capable of exhibiting acyl-transfer reactivity. PMID:23934729
Tamboli, Majid I; Krishnaswamy, Shobhana; Gonnade, Rajesh G; Shashidhar, Mysore S
In this paper the intermolecular overlap approximation is used to calculate the relative magnitudes of the electronic transfer integrals between the excited singlet state ({sup 1}P*) of the bacteriochlorophyll dimer (P) and the accessory bacteriochlorophyll (B) and between B{sup {minus}} and bacteriopheopytin (H), along the L and M subunits of the reaction center (RC) of Rps. viridis. The ratio of the electron-transfer integrals for B{sub L}{sup {minus}}H{sub L}{sup {minus}}B{sub L}H{sub L}{minus} and for B{sub M}{sup {minus}}H{sub M}{minus}B{sub M}H{sub M}{sup {minus}} was calculated to be 2.1 {plus minus} 0.5, which together with the value of 2.8 {plus minus} 0.7 for the ratio of the transfer integrals for {sup 1}P*B{sub L}-P{sup +}B{sub L}- and for {sup 1}P*B{sub M}-P{sup +}B{sub M}- results in the electronic contribution of 33 {plus minus} 16 to the ratio k{sub L}/k{sub m} of the rate constants k{sub L} and k{sub M} for the primary charge separation across the L and M branches of the RC, respectively. The asymmetry of the electronic coupling terms, which originates from the combination of the asymmetry in the charge distribution of {sup 1}P* and of structural asymmetry of the P-M and B-H arrangements across the L and M subunits, provides a major contribution to the unidirectionality of the charge separation in bacterial photosynthesis. A significant contribution to the transfer integrals between adjacent pigments originates from nearby methyl groups through hyperconjugation. The ratio 6 {plus minus} 2 of the transfer integrals for {sup 1}P*B{sub L}-P{sup +}B{sub L}- and for B{sub L}-H{sub L}-B{sub L}H{sub L}- was utilized to estimate the energetic parameters required to ensure the dominance of the superexchange mediated unistep electron transfer {sup 1}P*BH {yields} P{sup +}BH{sup {minus}} over the thermally activated {sup 1}P*B {yields} P{sup +}B{sup {minus}} process. 31 refs., 6 figs., 2 tabs.
Plato, M.; Moebius, K.; Michel-Beyerle, M.E.; Bixon, M.; Jortner, J. (Freie Universitaet Berlin (West Germany))
The role of intermolecular interactions: studies on model systems for bacterial biofilms
The mechanical stability of biofilms and other microbial aggregates is of great importance for both the maintenance of biofilm processes and the removal of undesired biofilms. The binding forces are weak interactions such as London dispersion forces, electrostatic interactions and hydrogen bonds. In a first attempt to rank their contribution, the viscosity of solutions of extracellular polymeric substances (EPS) from
Christian Mayer; Ralf Moritz; Carolin Kirschner; Werner Borchard; Ralf Maibaum; Jost Wingender; Hans-Curt Flemming
Theoretical study of intermolecular interactions in meso-tetraphenylporphyrin diacid dimer (H4TPPCl2)2.
The intermolecular interactions between two meso-tetraphenylporphyrin diacid H(4)TPPCl(2) monomers are investigated by density functional theory with the PBE1PBE functional and 6-31G* basis set. Structures of five stable isomers of (H(4)TPPCl(2))(2) are determined. It is found that the interaction (IMHB-1) of Cl with ortho H atoms in two phenyl groups of H(4)TPPCl(2) is unique in that it is the strongest interaction between two H(4)TPPCl(2) monomers. Natural bond orbital analysis is carried out to explain the subtle differences of hydrogen bondings in these isomers. To understand the interactions of water molecule with H(4)TPPCl(2) and (H(4)TPPCl(2))(2), structures of H(4)TPPCl(2) x H(2)O and nine isomers of (H(4)TPPCl(2))(2) x H(2)O are also determined. The binding energy of H(4)TPPCl(2) x H(2)O is 36.47 kJ mol(-1), less than that of the most stable structure of (H(4)TPPCl(2))(2) dimers, 41.59 kJ mol(-1). The dimers containing the special IMHB-1 interactions may be the elementary building blocks for the aggregation of H(4)TPPCl(2), which is supported by the crystal structure of H(4)TPPCl(2).H(2)O x 2CH(3)CN. Thus, study of the interactions between two or a small number of gas molecules can provide important information for understanding the main interactions and stable structures in related condensed-phase systems. PMID:19325989
Ma, Yan-Ping; He, Sheng-Gui; Ding, Xun-Lei; Wang, Zhe-Chen; Xue, Wei; Shi, Qiang
Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions.
Intrinsically disordered proteins play crucial roles in regulatory processes and often function as protein interaction hubs. Here, we present a detailed characterization of a full-length disordered hub protein region involved in multiple dynamic complexes. We performed NMR, CD, and fluorescence binding studies on the nonphosphorylated and highly PKA-phosphorylated human cystic fibrosis transmembrane conductance regulator (CFTR) regulatory region, a ?200-residue disordered segment involved in phosphorylation-dependent regulation of channel trafficking and gating. Our data provide evidence for dynamic, phosphorylation-dependent, multisite interactions of various segments of the regulatory region for its intra- and intermolecular partners, including the CFTR nucleotide binding domains 1 and 2, a 42-residue peptide from the C terminus of CFTR, the SLC26A3 sulphate transporter and antisigma factor antagonist (STAS) domain, and 14-3-3?. Because of its large number of binding partners, multivalent binding of individually weak sites facilitates rapid exchange between free and bound states to allow the regulatory region to engage with different partners and generate a graded or rheostat-like response to phosphorylation. Our results enrich the understanding of how disordered binding segments interact with multiple targets. We present structural models consistent with our data that illustrate this dynamic aspect of phospho-regulation of CFTR by the disordered regulatory region. PMID:24191035
Bozoky, Zoltan; Krzeminski, Mickael; Muhandiram, Ranjith; Birtley, James R; Al-Zahrani, Ateeq; Thomas, Philip J; Frizzell, Raymond A; Ford, Robert C; Forman-Kay, Julie D
Characterization of intermolecular interaction between cyanidin-3-glucoside and bovine serum albumin: Spectroscopic and molecular docking methods.
The intermolecular interaction between cyanidin-3-glucoside (Cy-3-G) and bovine serum albumin (BSA) was investigated using fluorescence, circular dichroism and molecular docking methods. The experimental results revealed that the fluorescence quenching of BSA at 338?nm by Cy-3-G resulted from the formation of Cy-3-G-BSA complex. The number of binding sites (n) for Cy-3-G binding on BSA was approximately equal to 1. The experimental and molecular docking results revealed that after binding Cy-3-G to BSA, Cy-3-G is closer to the Tyr residue than the Trp residue, the secondary structure of BSA almost not change, the binding process of Cy-3-G with BSA is spontaneous, and Cy-3-G can be inserted into the hydrophobic cavity of BSA (site II') in the binding process of Cy-3-G with BSA. Moreover, based on the sign and magnitude of the enthalpy and entropy changes (?H(0) ?=?- 29.64?kcal/mol and ?S(0) ?=?- 69.51?cal/mol?K) and the molecular docking results, it can be suggested that the main interaction forces of Cy-3-G with BSA are Van der Waals and hydrogen bonding interactions. Copyright � 2013 John Wiley & Sons, Ltd. PMID:24123897
Shi, Jie-Hua; Wang, Jing; Zhu, Ying-Yao; Chen, Jun
plasma desorption mass spectrometry of quinolinium salts and method of estimation of their intermolecular interactions with phospholipids
Using plasma desorption mass spectrometry, the fragmentation of 1-phenyl-2(p-aminostyryl)quinolinium and 1-phenyl-2(p-aminostyryl)benzo(f)quinolinium derivatives, with various substituents at the amino nitrogen, was studied. With plasma desorption ionization, the fragmentation features of the compounds studied are mainly determined by the nature of the N',N'' substituents. The behaviour of some quinolinium derivatives in the presence of lecithin, a basic component of the phospholipid fraction of cell membranes, was investigated. For the benzo(f)quinolinium derivative, the analysis of changes in the mass spectra indicates a strong interaction between these substances, leading to the formation of a molecular complex stabilized by the interactions of the negatively charged phosphate group of lecithin with the quinolinium quaternary nitrogen and the lecithin quaternary nitrogen with the benzene part of the aminophenyl fragment. The effect of the third aromatic ring of the benzoquinolinium system on complex stabilization is discussed. For the benzoquinolinium derivative with lecithin, the changes in the mass spectrometric fragmentation pattern of the molecule can be used as a sensitive and informative method for the characterization of intermolecular interactions which may result in molecular complex formation.
Andrievsky, Grigory V.; Lisnyak, Yury V.; Klochkov, Vladimir K.; Volyansky, Yury L.; Malaya, Lubov T.
The role of intermolecular interactions: studies on model systems for bacterial biofilms.
The mechanical stability of biofilms and other microbial aggregates is of great importance for both the maintenance of biofilm processes and the removal of undesired biofilms. The binding forces are weak interactions such as London dispersion forces, electrostatic interactions and hydrogen bonds. In a first attempt to rank their contribution, the viscosity of solutions of extracellular polymeric substances (EPS) from a mucoid strain of Pseudomonas aeruginosa is measured. In order to distinguish the binding forces, substances are chosen which individually address the different types of bonds. Polyacrylic acid is identified as a suitable model system for EPS when molecular interactions are studied. Electrostatic interactions and hydrogen bonds are found to be the dominating forces among macromolecules within the biofilm. PMID:10520951
Mayer, C; Moritz, R; Kirschner, C; Borchard, W; Maibaum, R; Wingender, J; Flemming, H C
First-order intermolecular interaction energies from Kohn�Sham orbitals
It is investigated whether similar to Brueckner orbitals also Kohn�Sham monomer orbitals from current density functional approaches reliably reproduce electron correlation effects on first-order Coulomb and exchange dimer interaction energies. While the Coulomb energy is potentially exact, i.e., exact, if the monomers exact exchange-correlation potential were known, this is not true for the exchange interaction energy. Considering He2,Ne2,Ar2, NeAr, NeHF,
Andreas He�elmann; Georg Jansen
The Role of Intermolecular Interactions in the Electro-Optical Kerr Effect in Liquid Alkanes
The electro-optical Kerr effect of n-alkanes from C5 to C16 was investigated in gas phase, liquid phase, and solution. The values of the Kerr constants in gas phase are noticeably distinguishable from those in liquids, where the molecules interact by the London dispersion forces. Both the energy of the dispersion interaction and the difference in the Kerr constants in liquid
O. V. Prezhdo; L. Switek; V. V. Zubkova; V. V. Prezhdo
Theory of elastic interaction between colloidal particles in the nematic cell in the presence of the external electric or magnetic field
The Green function method developed in Ref.[S. B. Chernyshuk and B. I. Lev, Phys. Rev. E \\\\textbf{81}, 041707 (2010)] is used to describe elastic interactions between axially symmetric colloidal particles in the nematic cell in the presence of the external electric or magnetic field. General formulas for dipole-dipole, dipole-quadrupole and quadrupole-quadrupole interactions in the homeotropic and planar nematic cells with
S. B. Chernyshuk; O. M. Tovkach; B. I. Lev
The Experimental Charge-Density Approach in the Evaluation of Intermolecular Interactions. Application of a New Module of the XD Programming Package to Several Solids Including a Pentapeptide
A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, l-asparagine monohydrate and the pentapeptide Boc-Gln- d-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol).
Yu. A. Abramov; Anatoliy Volkov; G. Wu; P. Coppens
Abramov, Yu A.; Volkov, Anatoliy; Wu, G; Coppens, P
Theory of Two-Step Magnetic Ordering Phenomena in a Geometrically Frustrated Heisenberg Pyrochlore Antiferromagnet with Long Range Dipolar Interactions
A model for a Heisenberg antiferromagnet on a pyrochlore lattice with\\u000aexchange and dipole-dipole interactions is studied via mean-field theory. In\\u000atreating the dipoles by use of the Ewald method, a soft (critical) mode with a\\u000aunique ordering wave vector is selected for all strengths of the dipole-dipole\\u000acoupling. For weak dipoles a partially ordered, three sublattice spin structure\\u000a(P
Matthew Enjalran; Michel J. P. Gingras
Further analysis and comparative study of intermolecular interactions using dimers from the S22 database
Accurate MP2 and CCSD(T) complete basis set (CBS) interaction energy curves (14 points for each curve) have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory (DFT) and force field models. The magnitude and the effect of the basis set
Laszlo Fusti Molnar; Xiao He; Bing Wang; Kenneth M. Merz
Investigating Intermolecular Interactions via Scanning Tunneling Microscopy: An Experiment for the Physical Chemistry Laboratory
A scanning tunneling microscope (STM) project designed as a module for the undergraduate physical chemistry laboratory is described. The effects of van der Waals interactions on the condensed-phase structure are examined by the analysis of the pattern of the monolayer structures.
Pullman, David; Peterson, Karen I.
Accurate MP2 and CCSD(T) complete basis set (CBS) interaction energy curves (14 points for each curve) have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory (DFT) and force field models. The magnitude and the effect of the basis set superposition error (BSSE) were carefully investigated. We found that going up to aug-cc-pVDZ and aug-cc-pVTZ basis sets is enough to obtain accurate CBS MP2 energies when BSSE corrected values are used but aug-cc-pVTZ and aug-cc-pVQZ basis sets are needed when the BSSE uncorrected total energies are used in CBS extrapolations. MP2 interaction energies with smaller basis sets such as 6-31G* are found to have very little dispersion energy and that the true source of dispersion attributed attractive interactions is almost entirely due to BSSE. MP2 and CCSD(T) CBS interaction energies are found to be very close to one another if aromatic systems are not involved. Comparative analyses have been performed with semiempirical and ab initio methods utilizing the moderate in size but affordable 6-31G* basis set both of which can be readily applied to macromolecular systems. The new M06-2X and M06-L DFT functionals were found to be more accurate than all methods tested herein. Interaction energy curves using the SG1 grid showed discontinuities for several of the dimer systems but this problem disappeared when finer DFT numerical grids were used.
Molnar, Laszlo Fusti; He, Xiao; Wang, Bing; Merz, Kenneth M.
Weak carbonyl-methyl intermolecular interactions in acetone clusters explored by IR plus VUV spectroscopy
Size-selected IR-VUV spectroscopy is employed to detect vibrational characteristics in the region 2850 � 3550 cm-1 of neutral acetone and its clusters (CH3COCH3)n (n = 1-4). Features around 3440 cm-1 in the spectra of acetone monomer and its clusters are assigned to the carbonyl stretch (CO) overtone. These features red-shift from 3455 to 3433 cm-1 as the size of the clusters increases from the monomer to the tetramer. Based on calculations, the experimental IR spectra in the Cdbnd O overtone region suggest that the dominant structures for the acetone trimer and tetramer should be cyclic in the supersonic expansion sample. This study also suggests that the carbonyl groups interact with the methyl groups in the acetone clusters. These weak interactions are further confirmed by the use of deuterium substitution.
Guan, Jiwen; Hu, Yongjun; Xie, Min; Bernstein, Elliot R.
Exploring intermolecular interactions of a substrate binding protein using a riboswitch-based sensor.
The study of biological transporters can be hampered by a dearth of methodology for tracking their activity within cells. Here, we present a means of monitoring the function of transport machinery within bacteria, exploiting a genetically encoded riboswitch-based sensor to detect the accumulation of the substrate in the cytoplasm. This method was used to investigate the model ABC transporter BtuC2D2F, which permits vitamin B12 uptake in Escherichia coli. We exploited the wealth of structural data available for this transporter to probe the functional and mechanistic importance of key residues of the substrate binding protein BtuF that are predicted to support its interaction with its substrate or with the BtuC channel-forming subunits. Our results reveal molecular interaction requirements for substrate binding proteins and demonstrate the utility of riboswitch-based sensors in the study of biological transport. PMID:24290881
Fowler, Casey C; Sugiman-Marangos, Seiji; Junop, Murray S; Brown, Eric D; Li, Yingfu
Intermolecular Interaction between a Synthetic Pseudoceramide and a Sterol-Combined Fatty Acid
To better understand the phase behavior of a pseudoceramide (SLE), a potential skin moisturizer and\\/or a drug carrier, we investigated the lipid�lipid interaction between SLE and a sterol-combined fatty acid (CEOS), which has a sterol ring and a carboxyl group in a molecule. X-ray analysis showed that a hexagonal packing (4.15 � spacing) and a liquid-like packing (4.5 � spacing)
Hiromoto Mizushima; Jun-ichi Fukasawa; Toshiyuki Suzuki
Can Water Clusters Ionize HCl under the Conditions of Arctic Stratosphere? 1. Intermolecular Interactions
Pseudopotential model was constructed to simulate the H3O+(H2O)nCl� clusters at room and stratosphere temperatures using the Monte Carlo method. Numerical values of interaction parameters were restored from the experimental data on the free energy and entropy of vapor nucleation on ions in the combination with the data of quantum chemical calculations of the optimal configurations of HCl(H2O)n clusters. The stability
S. V. Shevkunov
The electro-optical Kerr effect of n-alkanes from C5 to C16 was investigated in gas phase, liquid phase, and solution. The values of the Kerr constants in gas phase are noticeably distinguishable from those in liquids, where the molecules interact by the London dispersion forces. Both the energy of the dispersion interaction and the difference in the Kerr constants in liquid and gas phase grow with molecular size, indicating the key influence of the interaction on the magnitude of the Kerr effect. Several orientation and molecular-statistical theories of electro-optical Kerr effect were applied to model the change in electro-optical Kerr effect due to the dispersion force. Most theories show significant divergence compared to the experimental data. It is argued that the decisive contribution to electro-optical Kerr effect in liquids and the deviations between the experiment and theory arise due to local liquid structures that collectively orient in the external electric field.
Prezhdo, O. V.; Switek, L.; Zubkova, V. V.; Prezhdo, V. V.
Synthesis, crystal structures and intermolecular interactions of two Mn(II) complexes with 4,4?-bipy and methyl benzoates
Two manganese complexes containing 4,4'-bipyridine and methyl benzoate as ligands have been prepared and crystallized by solvent evaporation method in DMF. The single crystal X-ray crystallographic analyses reveal that the complexes crystallize in monoclinic system. Crystal of 1 [Mn2(4,4'-bipy)2 (o-MBA)4]n has space group of P21/c with unit cell parameters of a = 17.508 (�), b = 11.6229 (�), c = 27.983 (�), ? = 128.123�, V = 4.4797 nm3, empirical formula: C52H44Mn2N4O8, Mr = 962.79, Z = 4, Dc = 1.428 g/cm3, ? = 0.625 mm-1, and F(000) = 1992. The crystal of 2 [Mn (4,4'-bipy)(m-MBA)2]n belongs to space group C2/c with a = 16.079 (�), b = 11.652 (�), c = 24.887 (�), ? = 92.02�, V = 4.660 nm3, empirical formula: C26H22MnN2O4, Mr = 481.40, Z = 8, Dc = 1.372 g/cm3, ? = 1.179 mm-1, F(000) = 1992. The weak interactions in structures are observed from the X-ray crystallographic data. These include the Csbnd H⋯O hydrogen bonds, ?-? stacking and Csbnd H⋯? interactions found in 1. The different strength of intermolecular interaction in the structures is reflected on their different thermal stability of the two complexes measured by thermal gravimetric analysis and the 2D-IR correlation spectroscopy. The study of weak interactions is meaningful to provide supporting data for potential application in molecular biology.
Xin-Jian, Wu; Yi-Ping, Chen; Ze-Min, Xia; Su-Zhi, Ge; Feng, Chai; Ling-Yan, Zhao; Jian-Zhong, Chen
Potential Intra- and Intermolecular Interactions involving the Unique-5? Region of the HIV-1 5?-UTR
The 5?-untranslated region (5?-UTR) of the human immunodeficiency virus type-1 (HIV-1) genome regulates multiple RNA-dependent functions during viral replication and has been proposed to adopt multiple secondary structures. Recent phylogenetic studies identified base pair complementarity between residues of the unique 5? element and those near the gag start codon (gagAUG) that is conserved among evolutionarily distant retroviruses, suggesting a potential long-range RNA-RNA interaction. However, nucleotide accessibility studies led to conflicting conclusions about the presence of such interactions in virions and in infected cells. Here we show that an 11-nucleotide oligo-RNA spanning residues 105-115 of the 5?-UTR (U5) readily binds to oligoribonucleotides containing the gag start codon (AUG), disrupting a pre-existing stem loop and forming a heteroduplex stabilized by 11 Watson Crick base pairs (Kd = 0.47 � 0.16 ?M). Addition of the HIV-1 nucleocapsid protein (NC), the transacting viral factor required for genome packaging, disrupts the heteroduplex by binding tightly to U5 (Kd = 122 � 10 nM). The structure of the NC:U5 complex, determined by NMR, exhibits features similar to those observed in NC complexes with HIV-1 stem loop RNAs, including the insertion of guanosine nucleobases to hydrophobic clefts on the surface of the zinc fingers and a 3?-to-5? orientation of the RNA relative to protein. Our findings indicate that the previously proposed long-range U5-gagAUG interaction is feasible, and suggest a potential NC-dependent mechanism for modulating the structure of the 5?-UTR.
Spriggs, Shardell; Garyu, Lianko; Connor, Ryan; Summers, Michael F.
Closed-shell ring coupled cluster doubles theory with range separation applied on weak intermolecular interactions
We explore different variants of the random phase approximation to the correlation energy derived from closed-shell ring-diagram approximations to coupled cluster doubles theory. We implement these variants in range-separated density-functional theory, i.e., by combining the long-range random phase approximations with short-range density-functional approximations. We perform tests on the rare-gas dimers He2, Ne2, and Ar2, and on the weakly interacting molecular complexes of the S22 set of Jure?ka et al. [P. Jure?ka, J. �poner, J. ?ern�, and P. Hobza, Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The two best variants correspond to the ones originally proposed by Szabo and Ostlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977)]. With range separation, they reach mean absolute errors on the equilibrium interaction energies of the S22 set of about 0.4 kcal/mol, corresponding to mean absolute percentage errors of about 4%, with the aug-cc-pVDZ basis set.
Toulouse, Julien; Zhu, Wuming; Savin, Andreas; Jansen, Georg; �ngy�n, J�nos G.
Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues
Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.
Leszczynski, Jerzy [Computational Center for Molecular Structure and Interactions, Jackson, MS; Sponer, Judit [Academy of Sciences of the Czech Republic; Sponer, Jiri [Academy of Sciences of the Czech Republic; Sumpter, Bobby G [ORNL; Fuentes-Cabrera, Miguel A [ORNL; Vazquez-Mayagoitia, Alvaro [ORNL
Intermolecular C�H⋯O interactions in cyclopentanone: An inelastic neutron scattering study
The inelastic neutron scattering (INS) spectra of cyclopentanone were obtained for pure and 50% CCl4 solution forms. Spectra are compared with infrared and Raman data, and with DFT calculated eigenvectors. This exercise aims to find spectroscopic evidence in the neutron spectra for the presence of C�H⋯O hydrogen bonds. These are weak interactions with an energy of ca. ?6 kJ mol?1 as predicted by DFT. The neutron spectra show narrow and sharp bands which allows for an assignment of the vibrational modes. The simulated neutron spectrum of C�H⋯O bonded cyclopentanone dimers matches the experimental spectrum of the pure compound, whereas the monomer simulation monomer matches the experimental spectrum of the diluted solution, meaning that such interaction can be probed by INS. Assignment of the 95 cm?1 band to the ?H⋯O anti-translational mode, being supported by DFT results and in agreement with previous literature data, is considered and discussed.
Vaz, Pedro D.; Nolasco, Mariela M.; Ribeiro-Claro, Paulo J. A.
Intermolecular Interactions between Poly(propylene-imine) Dendrimers: Small-Angle Neutron Scattering
SANS has been applied for structural investigations of amine-terminated poly(propylene-imine) dendrimer (Astramol^TM) solutions. By increasing the concentration, a single broad peak appears in the scattering curves centred at a wavevector Q-max, which shifted towards wider angles. Q-max scales as ?^0.55 with an exponent larger than that of a packing argument (?^1/3). By increasing ?, the intensity at Q=AE0, decreases progressively, due to the inter-dendrimer correlations while at large Q the curves collapse to a single curve. By adding acid (HCl), the dendrimers become charged. The electrostatic repulsion dominates and correlation peaks were observed in the intensities, indicating a spatial arrangement of the molecules in the acidified medium due to the interaction potential. The peak position from acidified dendrimer solutions remains unchanged whereas its intensity is increased indicating that the system has a liquid-like ordering. These interactions can be screened by adding an excess of acid or salt (NaCl).
Ramzi, A.; Scherrenberg, R.; Brackman, J.; Joosten, J.; Mortensen, K.
Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.
Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (?B97X, ?B97, LC-?PBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ?B97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ?B97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ?B97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. � 2012 Wiley Periodicals, Inc. PMID:22949382
Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang
Visualization and sensing of intermolecular interactions with two-color fluorescent probes.
We developed a new generic fluorescence sensing technology based on the change of relative intensities between two well-separated emission bands of the novel functional 3-hydroxychromone (3HC) dyes. A greatly enhanced self-calibrating wavelength-ratiometric response is obtained to all major types of non-covalent interactions that can be used in sensing--to polarity, hydrogen bonding ability and to local electrostatic fields. This technology may find a broad range of applications--from homogeneous assays in solutions to microarrays, microfluidic devices, nanosensors and whole cell imaging systems. It allows transforming micelles or phospholipid vesicles into nanosensor devices. In cellular research a high sensitivity to membrane potentials can be obtained and the membrane changes during apoptosis detected. PMID:16643906
Demchenko, Alexander P
Interaction of red blood cells with a polarized electrode: evidence of long-range intermolecular forces.
We have investigated the electrostatic interaction of glutaraldehyde-fixed human red cells with a polarizable electrode carrying a defined surface charge density which can be varied continuously through a wide range. Cells in a dilute salt solution are unable to adhere to the electrode at high negative charge, but at lower negative charge densities they are reversibly adherent and can be forced off by increasing the negative polarization. Near zero electrode charge they become irreversibly stuck to the electrode and cannot be evicted even at maximum electrode polarization. Calculation of the electrostatic repulsive force using measured charge densities indicates the existence of an attractive force which may be acting over several hundred angstroms.
Gingell, D; Fornes, J A
Carbon dioxide clathrate hydrates: selective role of intermolecular interactions and action of the SDS catalyst.
The ability of a single sodium dodecyl sulfate (SDS) molecule to promote the formation of CO2 clathrate hydrates in water (as it does for methane) has been investigated at the microscopic level. For this purpose, the components of the related force field were carefully formulated and assembled following the procedure previously adopted for methane. The properties of the whole system (as well as those of its components) were analyzed by carrying out extended molecular dynamics calculations. Contrary to what happens for methane, the calculations singled out the propensity of CO2 (pure) water clusters to form clathrate hydrate-like structures and the disappearance of such propensity when a single SDS molecule is added to the clusters. This feature was found to be due to the strong interaction of carbon dioxide with the additive that makes the SDS molecule lose its shape together with its ability to drive water molecules to form a suitable cage. PMID:23635031
Albert�, M; Pirani, F; Lagan�, A
Fabrication and Intermolecular Interactions of Silk Fibroin/Hydroxybutyl Chitosan Blended Nanofibers
The native extracellular matrix (ECM) is composed of a cross-linked porous network of multifibril collagens and glycosaminoglycans. Nanofibrous scaffolds of silk fibroin (SF) and hydroxybutyl chitosan (HBC) blends were fabricated using 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and trifluoroacetic acid (TFA) as solvents to biomimic the native ECM via electrospinning. Scanning electronic microscope (SEM) showed that relatively uniform nanofibers could be obtained when 12% SF was blended with 6% HBC at the weight ratio of 50:50. Meanwhile, the average nanofibrous diameter increased when the content of HBC in SF/HBC blends was raised from 20% to 100%. Fourier transform infrared spectra (FTIR) and 13C nuclear magnetic resonance (NMR) showed SF and HBC molecules existed in hydrogen bonding interactions but HBC did not induce conformation of SF transforming from random coil form to ?-sheet structure. X-ray diffraction (XRD) confirmed the different structure of SF/HBC blended nanofibers from both SF and HBC. Thermogravimetry-Differential thermogravimetry (TG-DTG) results demonstrated that the thermal stability of SF/HBC blend nanofibrous scaffolds was improved. The results indicated that the rearrangement of HBC and SF molecular chain formed a new structure due to stronger hydrogen bonding between SF and HBC. These electrospun SF/HBC blended nanofibers may provide an ideal tissue engineering scaffold and wound dressing.
Zhang, Kui-Hua; Yu, Qiao-Zhen; Mo, Xiu-Mei
Radiative recombination of trapped excitons in Alq3 films: Importance of intermolecular interactions
We investigate the light emission of optically excited tris(8-hydroxyquinolinato) aluminum (Alq3) films by temperature-dependent, time-integrated, as well as time-resolved photoluminescence (PL) at various photon densities. The Alq3 films are deposited on Si (001) substrate using organic molecular beam deposition. At high excitation densities, the PL efficiency decreases when the temperature is reduced from 170 to 15 K. At low laser intensities, the PL efficiency is nearly temperature independent. The observed PL quenching at high-excitation densities is assigned to singlet-singlet annihilation revealing a low-temperature bimolecular quenching coefficient that is more than two orders of magnitude higher than previously reported at room temperature. The observed strong bimolecular interaction at low temperature is attributed to an enhanced local (microscopic) density of captured excitons in extended traps. The reduction of the exciton annihilation with increasing temperature is assigned to a thermally activated occupation of nonquenchable localized exciton states. Above 190 K, the PL efficiency starts to decrease independently from the excitation level which is ascribed to a thermally activated detrapping of excitons and subsequent migration to nonradiative centers outside the traps. A coupled-rate equation model, including bimolecular quenching, thermally activated occupation of nonquenchable states, and detrapping of excitons at higher temperatures, supports these interpretations.
Ajward, A. M.; Wang, X.; Wickremasinghe, N.; DeSilva, L. A. A.; Wagner, H. P.
Intermolecular interactions as controlling factor for water sorption into polymer membranes.
A multidisciplinary approach was used for delineating the mechanisms controlling water sorption into modified block co-poly-(ether/amide) (PEBAX) membranes. In particular, incorporation of aromatic sulfonamide (KET) into the polymer matrix led to a nonlinear increase of water sorption in the membrane. The modification in sorption was accompanied by a nonlinear behavior in membrane surface energies. Infrared analysis revealed a different availability and accessibility of free polar groups supporting the formation of hydrogen bonding as a function of modifier concentration. A combination of both experimental and theoretical procedures was used to analyze the molecular processes of water sorption on PEBAX membranes. Molecular dynamics (MD) and quantum chemical (QC) calculations demonstrated that the formation of KET-KET dimers in the polymeric matrix led to a decrease in the interaction energy between water and modifiers. In addition, no variations in the dipole moments of water-dimer structures were found in comparison to a single KET and water-KET molecule. The formation of water-dimer complexes at higher concentration of modifier decreases the number of the dipole moment, thus preventing the polarization of polymer chains. PMID:17608518
Gugliuzza, A; Luca, G De; Tocci, E; Lorenzo, L De; Drioli, E
To better understand the phase behavior of a pseudoceramide (SLE), a potential skin moisturizer and/or a drug carrier, we investigated the lipid-lipid interaction between SLE and a sterol-combined fatty acid (CEOS), which has a sterol ring and a carboxyl group in a molecule. X-ray analysis showed that a hexagonal packing (4.15 A spacing) and a liquid-like packing (4.5 A spacing) coexisted within the hydrocarbon chains of the SLE/CEOS (1/1 mole) lipid mixture. The structural characteristics were very similar to those of the SLE/stearic acid/cholesterol (1/1/1 mole) system, which was in a stable lamellar alpha-phase. However, in the SLE/stearic acid (1/1 mole) system, there was only a strong hexagonal reflection in the wide-angle X-ray profile. The melting enthalpy (23.9 kJ mol-1) and entropy (75.0 J mol-1 K-1) of the SLE/CEOS system were also smaller than those (DeltaHm = 43.9 kJ mol-1, DeltaSm = 131.6 J mol-1 K-1) of the SLE/stearic acid system. The X-ray data along with the DSC results suggested that the sterol ring of CEOS molecule contributed to the enhancement of molecular motion or the decrease in the molecular packing of lipids. A strong hydrogen bond between the carboxyl group of CEOS and the amide group of SLE molecule was also considered to be important for the formation of the stable alpha-phase, as suggested by FT-IR spectroscopy. Further, in the presence of water, the three artificial SC lipids, SLE/CEOS (1/1 mole), SLE/stearic acid/cholesterol (1/1/1 mole), and SLE/stearic acid (1/1 mole), were all capable of forming lamellar structures. Copyright 1997 Academic Press. Copyright 1997Academic Press PMID:9441616
Mizushima; Fukasawa; Suzuki
Intermolecular interactions as actors in energy-transfer processes in lanthanide complexes with 2,2'-bipyridine.
A series of lanthanide complexes [LnCl(x)(bpy)(y)(H(2)O)(z)]Cl(3-x)(H(2)O)(n)(EtOH)(m) (Ln = Eu, Gd, Tb; x = 1, 2; y = 1, 2; z = 2-4) with different numbers of 2,2'-bipyridine (bpy), chloride ions, and water molecules in the inner coordination sphere were synthesized and investigated with the aim of relating their molecular geometry and crystal packing to the efficiency of ligand-to-metal energy transfer. In conjunction to the rotation of the pyridine rings upon coordination to the Ln ion, the high flexibility displayed by bpy ligands leads to rather unexpected bending of these rings with respect to the central bond, owing to intermolecular interactions such as Cl...pi and pi-stacking ones. Deciphering the luminescence properties of the Eu and Tb complexes needs to take into account both the composition of the inner coordination sphere and the peculiarities of the crystal packing. For instance, in addition to the classical ligand --> Eu charge-transfer state (LMCT), another charge-transfer state induced by pi-stacking interactions (SICT) could be identified. These two states, located between the singlet and triplet states of the bpy ligand(s), provide relays facilitating the energy migration from the singlet to the triplet states and eventually to the excited Eu states, improving the overall ligand-to-Eu energy transfer. Another point is the involvement of the inner-sphere water molecules in H-bonding with chloride ions, which considerably lowers their luminescence quenching ability, so that the adducts remain highly luminescent. For instance, the terbium chloride with two bpy ligands is an efficient near-UV to green light converter, with an overall quantum yield equal to 37% despite the coordinated water molecules. The interpretations given are substantiated by DFT and TD-DFT theoretical calculations of the complexes and ligand assemblies. PMID:19522489
Puntus, Lada N; Lyssenko, Konstantin A; Pekareva, Irina S; B�nzli, Jean-Claude G
Conformations, conformational preferences, and conformational exchange of N'-substituted N-acylguanidines: intermolecular interactions hold the key.
Guanidine and acylguanidine groups are crucial structural features of numerous biologically active compounds. Depending on the biological target, acylguanidines may be considered as considerably less basic bioisosteres of guanidines with improved pharmacokinetics and pharmacodynamics, as recently reported for N'-monoalkylated N-acylguanidines as ligands of G-protein-coupled receptors (GPCRs). The molecular basis for enhanced ligand-receptor interactions of acylguanidines is far from being understood. So far, only a few and contradictory results about their conformational preferences have been reported. In this study, the conformations, conformational preferences, and conformational exchange of four unprotonated and seven protonated monoalkylated acylguanidines with up to six anions and with bisphosphonate tweezers are investigated by NMR. Furthermore, the effects of the acceptor properties in acylguanidine salts, of microsolvation by dimethylsulfoxide, and of varying acyl and alkyl substituents are studied. Throughout the whole study, exclusively two out of eight possible acylguanidine conformations were detected, independent of the compound, the anion, or the solvent used. For the first time, it is shown that the strength and number of intermolecular interactions with anions, solvent molecules, or biomimetic receptors decide the conformational preferences and exchange rates. One recently presented and two new crystal structures resemble the conformational preferences observed in solution. Thus, consistent conformational trends are found throughout the structurally diverse compound pool, including two potent GPCR ligands, different anions, and receptors. The presented results may contribute to a better understanding of the mechanism of action at the molecular level and to the prediction and rational design of these biologically active compounds. PMID:20698689
Kleinmaier, Roland; Keller, Max; Igel, Patrick; Buschauer, Armin; Gschwind, Ruth M
Cooperative Assembly of Pyrene-Functionalized Donor/Acceptor Blend for Ordered Nanomorphology by Intermolecular Noncovalent ?-? Interactions.
A facile approach to develop the stable and well-defined bulk heterojunction (BHJ) nanomorphology has been demonstrated. Novel pyrene (Py)-functionalized diblock copolymers poly(3-hexylthiophene)-block-poly[3-(10-(pyren-1-yloxy)decyloxy)thiophene] (P3HT-b-P3TPy), and pyrene-functionalized fullerene [6,6]-phenyl-C61-butyric acid 1-pyrene butyl ester (PCBPy), were successfully synthesized. The ?-? interactions of Py mesogens interdigitated between the functionalized fullerene and P3TPy segment can allow for the cooperative assembly of P3HT-b-P3TPy and PCBPy. The orientation of the Py mesogens also can further enhance the molecular arrangement. Compared with the as-cast and thermal annealing, solvent annealing can promote cooperative assembly of P3HT-b-P3TPy:PCBPy undergoing the slow film growth. Note that the assembly microstructure strongly depends on the molar ratio of P3HT and P3TPy with Py mesogens. Low loading of P3TPy block in the copolymers blends keeps the same behavior to the P3HT, whereas relatively high loading of Py mesogens favors the better intermolecular ?-? stacking interactions between P3HT-b-P3TPy and PCBPy. As a result, the P3HT-b-P3TPy(3/1) forms the orientated nanowires with PCBPy in bulk heterojunction, and the average domain size is estimated to be 10-20 nm, which is desirable for enlarge surface area for donor/acceptor interfaces and give a bicontinuous pathway for efficient electron transfer. Furthermore, the cooperative assembly between P3HT-b-P3TPy and PCBPy is found to effectively suppress the PCBPy macrophase separation, and stabilize the blend morphology. PMID:24884074
Chen, Lie; Peng, Siwan; Chen, Yiwang
Measurement of Homonuclear Cross-Correlation Cross-Relaxation Rates along an Effective Field: Application to Dipole Dipole Cross-Correlation
We describe three new schemes to explore homonuclear cross-correlation contributions to relaxation along an effective field tilted by an angle ? from the static magnetic field direction. Their key feature is to detect, during the evolution time t1, multiquantum transverse coherences whose frequencies are characteristic of the multispin order produced by cross-correlation processes. This makes it possible to obtain in-phase magnetization in both dimensions. The three schemes correspond to the combination of two evolutions due either to static Jcoupling in the transverse plane or to cross-correlation cross-relaxation along an effective field. This combination allows the conversion of one-spin order into multispin order and the reverse. If only cross-correlation cross-relaxation transfers are involved, there is no restriction on the coupling network. The quantitative exploitation of the results to obtain structural information from cross-correlation-induced relaxation rates requires a normalization coefficient which is provided by the simultaneous monitoring of one-spin coherence. These ideas have been tested experimentally in the case of dipole-dipole cross-correlation on a sample of cyclosporin. Buildup curves at various angles ? are described which yield information on the internal dynamics.
Desvaux, Herv�
Static and frequency-dependent dipole-dipole polarizabilities of all closed-shell atoms up to radium: a four-component relativistic DFT study.
We test the performance of four-component relativistic density functional theory by calculating the static and frequency-dependent electric dipole-dipole polarizabilities of all (ground-state) closed-shell atoms up to Ra. We consider 12 nonrelativistic functionals, including three asymptotically shape-corrected functionals, by using two smooth interpolation schemes introduced by the Baerends group: the gradient-regulated asymptotic connection (GRAC) procedure and the statistical averaging of (model) orbital potentials (SAOP). Basis sets of doubly augmented triple-zeta quality are used. The results are compared to experimental data or to accurate ab initio results. The reference static electric dipole polarizability of palladium has been obtained by finite-field calculations using the coupled-cluster singles, doubles, and perturbative triples method within this work. The best overall performance is obtained using hybrid functionals and their GRAC shape-corrected versions. The performance of SAOP is among the best for nonhybrid functionals for Group 18 atoms but its precision degrades when considering the full set of atoms. In general, we find that conclusions based on results obtained for the rare-gas atoms are not necessarily representative of the complete set of atoms. GRAC cannot be used with effective core potentials since the asymptotic correction is switched on in the core region. PMID:18224633
Bast, Radovan; Hesselmann, Andreas; Sa?ek, Pawe?; Helgaker, Trygve; Saue, Trond
Clarification of isomeric structures and the effect of intermolecular interactions in blue-emitting aluminum complex Alq3 using first-principles 27Al NMR calculations
We have performed structure analysis of the blue-emitting aluminum complex Alq3 using 27Al NMR and gauge-including projector-augmented wave calculations. The results clearly show that 27Al NMR spectra are insensitive to intermolecular interactions, thus providing a means of carrying out precise intramolecular structure determination. The key determinant of the blue-shifted emission of Alq3 is the facial isomerization.
Suzuki, Furitsu; Nishiyama, Yusuke; Kaji, Hironori
Exploring the inter-molecular interactions in amyloid-? protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
Aggregation of amyloid-? (A?) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between A? protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in A?17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the A?17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the A?17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of A? as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between A? monomers in A?17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of A? aggregation.
Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan
Molecular-beam study of the ammonia-noble gas systems: Characterization of the isotropic interaction and insights into the nature of the intermolecular potential
We report new high resolution molecular beam experiments aimed at characterizing the intermolecular interaction in the NH3-Ng (Ng = He, Ne, Ar, Kr, Xe) weakly bound complexes. Integral cross section data are obtained over a sufficiently wide velocity range and with rotationally hot NH3 molecules to produce (except for the NH3-He case) a well resolved ``glory'' quantum interference pattern. Data analysis, carried out by employing a recently proposed potential model, allows unique information on the absolute scale of the intermolecular interaction to be obtained both at long range and at the equilibrium distance. An extensive and internally consistent comparison with the behavior of the corresponding Kr-Ng systems is exploited in order to identify those cases where an interaction component due to charge transfer effects provides an appreciable intermolecular bond stabilization that is clearly distinct from and must be added to the standard van der Waals plus induction picture. The results of the present investigation extend the phenomenology of perturbative charge transfer effects in gas phase complexes involving hydrogenated molecules.
Pirani, Fernando; Roncaratti, Luiz F.; Belpassi, Leonardo; Tarantelli, Francesco; Cappelletti, D.
The dipole-dipole dispersion forces between spherical atoms from the Callen-Welton linear response theory
The dispersion interaction energy between spherical atoms is derived on the basis of linear response theory, by evaluation of the cross terms of the response to a long-wavelength electric field applied to each other atom, in the spirit of the Lifshitz theory. Then the correlation energy of the corresponding fluctuations is evaluated by application of the Hellmann-Feynman theorem. The self-consistency is easily introduced in this scheme, leading to a general expression of the interaction energy in terms of the poles of the linear response function of the whole system, related to those of the separated constituents. This is shown to be approximately equivalent to the variation of the zero-point energy of each independent oscillator, according to a generalization of London's formula for oscillating dipoles.
Battezzati, M.
The dispersion interaction energy between spherical atoms is derived on the basis of linear response theory, by evaluation of the cross terms of the response to a long-wavelength electric field applied to each other atom, in the spirit of the Lifshitz theory. Then the correlation energy of the corresponding fluctuations is evaluated by application of the Hellmann-Feynman theorem. The self-consistency
M. Battezzati
Intermolecular interactions in the mechanism of skeletal muscle sarcoplasmic reticulum Ca(2+)-ATPase (SERCA1): evidence for a triprotomer.
Native membrane sarcoplasmic reticulum (SR) Ca(2+)-ATPase isolated from skeletal muscle (SERCA1) exhibits oligomeric kinetic behavior [Mahaney, J. E., Thomas, D. D., and Froehlich, J. P. (2004) Biochemistry 43, 4400-4416]. In the present study we used quenched-flow mixing, electron paramagnetic resonance (EPR), and chemical cross-linking to probe for intermolecular interactions at physiological (0.1 M) and high (0.4 M) KCl. Exposure of SR membranes to water- and lipid-soluble cross-linking reagents revealed a mixture of SERCA1 oligomeric species consisting mainly of dimers and trimers. Titration of iodoacetamide spin-labeled SERCA1 with AMPPCP in the presence of 10 microM Ca(2+) and 0.1 M KCl revealed high- (K(D) = 45 microM) and low-affinity (K(D) = 315 microM) nucleotide binding sites in a 2:1 ratio, respectively. Raising the [KCl] to 0.4 M increased the fraction of weak binding sites and lowered the K(D) of the high-affinity component (20 microM). Phosphorylation by 10 microM ATP at 21 degrees C and 0.1 M KCl produced an early burst of P(i) production without a corresponding decline in the steady-state phosphoenzyme (EP) level. The steady-state EP level was twice as large as the P(i) burst and received equal contributions from E1P and E2P. Chasing the phosphoenzyme at 0.4 M KCl and 2 degrees C with ADP revealed a biphasic time course of E1P formation with a slow phase that matched the kinetics of the transient EPR signal from the spin-labeled Ca(2+)-ATPase. The absence of a fast component in the EPR signal excludes E1P as its source. Instead, it arises from a slow, KCl-dependent transformation at the start of the cycle which controls the formation of downstream intermediates with an increased mole fraction of rotationally restricted probes. We modeled this behavior with a SERCA1 trimer in which the formation of E1P/E2/E2P from E1ATP/E2P/E1P results from concerted transformations in the subunits coupling phosphorylation (E1ATP --> E1P + ADP) to dephosphorylation (E2P --> E2 + P(i)) and the conversion of E1P to E2P. PMID:19046074
Mahaney, James E; Thomas, David D; Farrance, Iain K; Froehlich, Jeffrey P
Nonresonant and resonant mode-specific intermolecular vibrational energy transfers in electrolyte aqueous solutions.
The donor/acceptor energy mismatch and vibrational coupling strength dependences of interionic vibrational energy transfer kinetics in electrolyte aqueous solutions were investigated with ultrafast multiple-dimensional vibrational spectroscopy. An analytical equation derived from the Fermi's Golden rule that correlates molecular structural parameters and vibrational energy transfer kinetics was found to be able to describe the intermolecular mode specific vibrational energy transfer. Under the assumption of the dipole-dipole approximation, the distance between anions in the aqueous solutions was obtained from the vibrational energy transfer measurements, confirmed with measurements on the corresponding crystalline samples. The result demonstrates that the mode-specific vibrational energy transfer method holds promise as an angstrom molecular ruler. PMID:21916443
Bian, Hongtao; Chen, Hailong; Li, Jiebo; Wen, Xiewen; Zheng, Junrong
Orthogonal Interactions of CO Molecules on a One-Dimensional Substrate
We investigate the chemisorption structure of CO molecules on the quasi-one-dimensional Cu(110)-(2�1)-O surface by low-temperature scanning tunneling microscopy and density functional theory. Contrary to flat metal surfaces, where CO molecules adsorb in an upright geometry and interact through repulsive intermolecular interactions, we find the most stable adsorption structure of single CO molecules to be at Cu atoms of substrate Cu�O� chains with the Cu�CO unit bent by?�45� in two equivalent structures at low coverages. At higher coverages, CO molecules combine in the same structure into highly ordered single-molecule-wide rows perpendicular to the substrate chains in an approximately 8 �1 full monolayer structure. Firstprinciples calculations attribute the unprecedented chemisorption behavior of CO molecules to lifting of the host Cu atoms by 1 � from the surface Cu�O� chains, in order to optimize the bonding and reduce the repulsive interactions with the substrate. This structural distortion enables short-range intermolecular dipole�dipole attraction and creates orthogonal long-range surface-mediated repulsion leading to unusual self-assembly of CO molecules into coherent nanometer scale molecular grating structures.
Feng, Min; Cabrera-Sanfelix, Pepa; Lin, Chungwei; Arnau, Andres; Sanchez-Portal, Daniel; Zhao, Jin; Echenique, P. M.; Petek, Hrvoje
Effects of intermolecular interaction on the energy distribution of valance electronic states of a carbazole-based material in amorphous thin films
Effects of intermolecular interactions on the occupied electronic structure of amorphous solid of a carbazole-based material were investigated under an assumption that the organic solid consists of randomly oriented assemblies of dimers. The electronic energy states were calculated on the ensemble of large number of random dimers, of which geometries are relaxed using semiempirical van der Waals density functional theory. Intermolecular interactions result in splitting of energy level, and further disorders occur by aggregation of randomly orientated molecules. As a result, frontier occupied energy states can be represented by a superposition of Gaussian distributions, including (i) a main distribution with full width at half maximum of 80-110 meV, depending on the methods of relaxation and (ii) shoulders separated from the center of the main distribution with a value as large as 150 meV. A possible origin for the appearance of these shoulders was ascribed to the presence of molecular assemblies consisting of more tightly bound dimers compared with the others.
Kwon, Soonnam; Wee, Kyung-Ryang; Kim, Jeong Won; Pac, Chyongjin; Kang, Sang Ook
The magnetic relaxation of two-dimensional arrays of dipolar coupled magnetic dots has been measured and simulated. Arrays (50�50) with perpendicular magnetized Co dots (2 mum�2 mum) were patterned using a high resolution Ga+ focused ion beam irradiation. Magnetic domain pattern and time relaxation of the dot arrays were investigated using Faraday magneto-optical microscopy. For arrays designed with high irradiation doses
L. C. Sampaio; R. Hyndman; F. S. de Menezes; J. P. Jamet; P. Meyer; J. Gierak; C. Chappert; V. Mathet; J. Ferr�
Nuclear spin relaxation driven by intermolecular dipolar interactions: the role of solute-solvent pair correlations in the modeling of spectral density functions.
Nuclear spin relaxation provides useful information related to the dynamics of molecular systems. When relaxation is driven by intermolecular dipolar interactions, the relevant spectral density functions (SDFs) also have significant contributions, in principle, from distant spins all over the dynamic range typically probed by NMR experiments such as NOESY. In this work, we investigate the intermolecular dipolar spin relaxation as driven by the relative diffusion of solvent and solute molecules taking place under a central force field, and we examine the relevant implications for (preferential) solvation studies. For this purpose, we evaluate the SDFs by employing a numerical approach based on spatial discretization of the time-propagation equation, and we supply an analytical solution for the simplest case of a steplike mean-field potential. Several situations related to different solute-solvent pair correlation functions are examined in terms of static/dynamic effects and relaxation modes, and some conclusions are drawn about the interpretation of NOE measurements. While we confirm previous results concerning the spoiling effect of long-range spins (Halle, B. J. Chem. Phys. 2003, 119, 12372), we also show that SDFs are sufficiently sensitive to pair correlation functions that useful, yet rather complicated, inferences can be made on the nature of the solvation shell. PMID:16539513
Frezzato, Diego; Rastrelli, Federico; Bagno, Alessandro
Studies on tolfenamic acid-chitosan intermolecular interactions: effect of pH, polymer concentration and molecular weight.
Solid-state properties of tolfenamic acid (TA) and its complexes with chitosan (CT) have been studied. Effect of medium pH, molecular weight of polymer and its different concentrations on these TA-CT complexes were studied in detail. Low and medium molecular weight CT have been used in different ratios at pH ranging from 4 to 6 and freeze-drying technique has been employed to modify the appearance of crystalline TA. Physical properties of the formed complexes have been studied by employing X-ray diffraction, differential scanning calorimetry and scanning electron microscopy; chemical structure has been studied using Fourier transform infrared spectroscopy. The results showed that both forms of the polymer exhibited complete conversion in 1:8 ratio at pH 4, 1:4 at pH 5 and 1:1 at pH 6 indicating a marked effect of pH on drug-polymer complexation. The percent crystallinity calculations indicated low molecular weight CT slightly more effective than the other form. No changes in the complexes have been observed during the 12 week storage under controlled conditions. Both forms of CT at different pH values indicated retardation of recrystallization in TA during cooling of the melt from 1:1 ratios exhibiting formation of strong intermolecular hydrogen bonding between the drug and the polymer. PMID:23620261
Ahmed, Sofia; Sheraz, Muhammad Ali; Rehman, Ihtesham Ur
Nonlinear theory of laser-induced dipolar interactions in arbitrary geometry
Polarizable dipoles, such as atoms, molecules, or nanoparticles, subject to laser radiation may attract or repel each other. We derive a general formalism in which such laser-induced dipole-dipole interactions (LIDDIs) in any geometry and for any laser strength are described in terms of the resonant dipole-dipole interaction (RDDI) between dipoles dressed by the laser. This approach provides a simple route towards the analysis of LIDDI in a general geometry. Our general results reveal LIDDI effects due to nonlinear dipolar response to the laser, previously unaccounted for. The origin of these nonlinear effects is discussed. Our general formalism is illustrated for LIDDI between atoms in a cavity.
Shahmoon, Ephraim; Kurizki, Gershon
A surface plasmon resonance study of the intermolecular interaction between Escherichia coli topoisomerase I and pBAD/Thio supercoiled plasmid DNA.
To date, the bacterial DNA topoisomerases are one of the major target biomolecules for the discovery of new antibacterial drugs. DNA topoisomerase regulates the topological state of DNA, which is very important for replication, transcription and recombination. The relaxation of negatively supercoiled DNA is catalyzed by bacterial DNA topoisomerase I (topoI) and this reaction requires Mg(2+). In this report, we first quantitatively studied the intermolecular interactions between Escherichia coli topoisomerase I (EctopoI) and pBAD/Thio supercoiled plasmid DNA using surface plasmon resonance (SPR) technique. The equilibrium dissociation constant (Kd) for EctopoI-pBAD/Thio interactions was determined to be about 8 nM. We then studied the effect of Mg(2+) on the catalysis of EctopoI-pBAD/Thio reaction. A slightly higher equilibrium dissociation constant (~15 nM) was obtained for Mg(2+) coordinated EctopoI (Mg(2+)EctopoI)-pBAD/Thio interactions. In addition, we observed a larger dissociation rate constant (kd) for Mg(2+)EctopoI-pBAD/Thio interactions (~0.043 s(-1)), compared to EctopoI-pBAD/Thio interactions (~0.017 s(-1)). These results suggest that enzyme turnover during plasmid DNA relaxation is enhanced due to the presence of Mg(2+) and furthers the understanding of importance of the Mg(2+) ion for bacterial topoisomerase I catalytic activity. PMID:24530905
Tiwari, Purushottam Babu; Annamalai, Thirunavukkarasu; Cheng, Bokun; Narula, Gagandeep; Wang, Xuewen; Tse-Dinh, Yuk-Ching; He, Jin; Darici, Yesim
In-vitro anti-proliferative and anti-oxidant activity of galangin, fisetin and quercetin: Role of localization and intermolecular interaction in model membrane.
Flavonols are an important class of naturally occurring molecules and are known for their pharmacological activity. The activity is associated with the ability of flavonols to influence membrane-dependent processes. We have investigated the in-vitro anti-proliferative and anti-oxidant activity of galangin (GLN), fisetin (FTN) and quercetin (QTN), which possess variable number of phenolic hydroxyl groups. An attempt has been made to correlate the biological activity of these molecules with their interaction and localization in dipalmitoyl phosphatidyl choline (DPPC) bilayers, using differential dcanning calorimetry (DSC) and nuclear magnetic resonance (NMR) methods. Results indicate that GLN interacts to the alkyl chains of the lipid bilayer involving hydrophobic interactions. FTN and QTN interact with head region and sn-1-glycero region involving hydrogen bonding. Ring current induced chemical shifts of lipid protons, due to intermolecular interaction indicate that GLN acquires a parallel orientation with respect to the bilayer normal whereas FTN and QTN resume a mixed orientation. The membrane binding constants of these molecules are in the order GLN�>�QTN�>�FTN. It has been shown that the number and position of hydroxyl groups in these molecules play an important role in membrane binding and thereby in biological activity. PMID:24727463
Sinha, Ragini; Srivastava, Sudha; Joshi, Akshada; Joshi, Urmila J; Govil, Girjesh
Intermolecular interactions and high dielectric energy storage density in poly(vinylidene fluoride-hexafluoropropylene)/poly(vinylidene fluoride) blend thin films
Homogeneous poly(vinylidene fluoride-hexafluoropropylene) and poly (vinylidene fluoride) (P(VDF-HFP)/PVDF) blend films were prepared via a chemical solution approach, followed by quenching, annealing, and hot pressing. The intermolecular interactions of the blends were investigated through atomic simulation. Higher melting temperature, higher crystallinity, larger elastic modulus, and improved breakdown strength (>850 MV/m) were observed in the optimized polymer blends, in comparison with either of the two constituent polymers, PVDF or P(VDF-HFP). In addition, the P(VDF-HFP)/PVDF blend film also showed larger dielectric constant. As a result, an extremely high energy density of 30.1 J/cm3 was achieved in P(VDF-HFP)/PVDF (50:50 by weight) blend films.
Rahimabady, Mojtaba; Yao, Kui; Arabnejad, Saeid; Lu, Li; Shim, Victor P. W.; Cheong Wun Chet, Davy
Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).
Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125
Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, J�lio C�sar; Sfor�a, Maur�cio Lu�s; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, J�rg
Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)
Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth.
da Silva, Julio Cesar; Sforca, Mauricio Luis; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jorg
A programmable optimization environment using the GAMESS-US and MERLIN/MCL packages. Applications on intermolecular interaction energies
The Merlin/MCL optimization environment and the GAMESS-US package were combined so as to offer an extended and efficient quantum chemistry optimization system, capable of implementing complex optimization strategies for generic molecular modeling problems. A communication and data exchange interface was established between the two packages exploiting all Merlin features such as multiple optimizers, box constraints, user extensions and a high level programming language. An important feature of the interface is its ability to perform dimer computations by eliminating the basis set superposition error using the counterpoise (CP) method of Boys and Bernardi. Furthermore it offers CP-corrected geometry optimizations using analytic derivatives. The unified optimization environment was applied to construct portions of the intermolecular potential energy surface of the weakly bound H-bonded complex C 6H 6-H 2O by utilizing the high level Merlin Control Language. The H-bonded dimer HF-H 2O was also studied by CP-corrected geometry optimization. The ab initio electronic structure energies were calculated using the 6-31G ** basis set at the Restricted Hartree-Fock and second-order Moller-Plesset levels, while all geometry optimizations were carried out using a quasi-Newton algorithm provided by Merlin. Program summaryTitle of program: MERGAM Catalogue identifier:ADYB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYB_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The program is designed for machines running the UNIX operating system. It has been tested on the following architectures: IA32 (Linux with gcc/g77 v.3.2.3), AMD64 (Linux with the Portland group compilers v.6.0), SUN64 (SunOS 5.8 with the Sun Workshop compilers v.5.2) and SGI64 (IRIX 6.5 with the MIPSpro compilers v.7.4) Installations: University of Ioannina, Greece Operating systems or monitors under which the program has been tested: UNIX Programming language used: ANSI C, ANSI Fortran-77 No. of lines in distributed program, including test data, etc.:11 282 No. of bytes in distributed program, including test data, etc.: 49 458 Distribution format: tar.gz Memory required to execute with typical data: Memory requirements mainly depend on the selection of a GAMESS-US basis set and the number of atoms No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: no Nature of physical problem: Multidimensional geometry optimization is of great importance in any ab initio calculation since it usually is one of the most CPU-intensive tasks, especially on large molecular systems. For example, the geometric and energetic description of van der Waals and weakly bound H-bonded complexes requires the construction of related important portions of the multidimensional intermolecular potential energy surface (IPES). So the various held views about the nature of these bonds can be quantitatively tested. Method of solution: The Merlin/MCL optimization environment was interconnected with the GAMESS-US package to facilitate geometry optimization in quantum chemistry problems. The important portions of the IPES require the capability to program optimization strategies. The Merlin/MCL environment was used for the implementation of such strategies. In this work, a CP-corrected geometry optimization was performed on the HF-H 2O complex and an MCL program was developed to study portions of the potential energy surface of the C 6H 6-H 2O complex. Restrictions on the complexity of the problem: The Merlin optimization environment and the GAMESS-US package must be installed. The MERGAM interface requires GAMESS-US input files that have been constructed in Cartesian coordinates. This restriction occurs from a design-time requirement to not allow reorientation of atomic coordinates; this rule holds always true when applying the COORD = UNIQUE keyword in a GAMESS-US input file. Typical running time: It depends on the size of
Kalatzis, Fanis G.; Papageorgiou, Dimitrios G.; Demetropoulos, Ioannis N.
Tailored donor-acceptor polymers with an a-d1-a-d2 structure: controlling intermolecular interactions to enable enhanced polymer photovoltaic devices.
Extensive efforts have been made to develop novel conjugated polymers that give improved performance in organic photovoltaic devices. The use of polymers based on alternating electron-donating and electron-accepting units not only allows the frontier molecular orbitals to be tuned to maximize the open-circuit voltage of the devices but also controls the optical band gap to increase the number of photons absorbed and thus modifies the other critical device parameter-the short circuit current. In fact, varying the nonchromophoric components of a polymer is often secondary to the efforts to adjust the intermolecular aggregates and improve the charge-carrier mobility. Here, we introduce an approach to polymer synthesis that facilitates simultaneous control over both the structural and electronic properties of the polymers. Through the use of a tailored multicomponent acceptor-donor-acceptor (A-D-A) intermediate, polymers with the unique structure A-D1-A-D2 can be prepared. This approach enables variations in the donor fragment substituents such that control over both the polymer regiochemistry and solubility is possible. This control results in improved intermolecular ?-stacking interactions and therefore enhanced charge-carrier mobility. Solar cells using the A-D1-A-D2 structural polymer show short-circuit current densities that are twice that of the simple, random analogue while still maintaining an identical open-circuit voltage. The key finding of this work is that polymers with an A-D1-A-D2 structure offer significant performance benefits over both regioregular and random A-D polymers. The chemical synthesis approach that enables the preparation of A-D1-A-D2 polymers therefore represents a promising new route to materials for high-efficiency organic photovoltaic devices. PMID:24697300
Qin, Tianshi; Zajaczkowski, Wojciech; Pisula, Wojciech; Baumgarten, Martin; Chen, Ming; Gao, Mei; Wilson, Gerry; Easton, Christopher D; M�llen, Klaus; Watkins, Scott E
Multidimensional frameworks assembled from silver(I) coordination polymers containing flexible bis(thioquinolyl) ligands: role of the intra- and intermolecular aromatic stacking interactions.
The two flexible multidentate ligands 1,3-bis(8-thioquinolyl)propane (C3TQ) and 1,4-bis(8-thioquinolyl)butane (C4TQ) were reacted with AgX (X = CF(3)SO(3)(-) or ClO(4)(-)) to give four new complexes: ([Ag(C3TQ)](ClO(4)))(n)() 1, ([Ag(C3TQ)](CF(3)SO(3)))(n)() 2, ([Ag(2)(C4TQ)(CF(3)SO(3))(CH(3)CN)](CF(3)SO(3)))(n)() 3, and ([Ag(C4TQ)](ClO(4)))(n)() 4. All complexes have been characterized by elemental analysis, IR, and (1)H NMR spectroscopy. Single-crystal X-ray analysis showed that chain structures form for all complexes in which the quinoline rings interact via various intra- (1) or intermolecular (2, 3, and 4) pi-pi aromatic stacking interactions, which in the latter cases results in multidimensional structures. Additional weak interactions, such as Ag.O and Ag.S contacts and C-H.O hydrogen bonding, are also present and help form stable, crystalline materials. It was found that the (CH(2))(n) spacers (n = 3 or 4) affect the orientation of the two terminal quinolyl rings, thereby significantly influencing the specific framework structure that forms. If the same ligand is used, on the other hand, then the different counteranions have the greatest effect on the final structure. PMID:12793810
Chen, Chun-Long; Su, Cheng-Yong; Cai, Yue-Peng; Zhang, Hua-Xin; Xu, An-Wu; Kang, Bei-Sheng; Zur Loye, Hans-Conrad
The experimental charge-density approach in the evaluation of intermolecular interactions. Application of a new module of the XD programming package to several solids including a pentapeptide.
A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, L-asparagine monohydrate and the pentapeptide Boc-Gln-D-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol). The electrostatic interactions are evaluated with the atom-centered distributed multipoles from KRMM (kappa'-restricted multipole model) refinements, using the Buckingham expression for non-overlapping charge densities. Results for p-nitroaniline are compared with Hartree-Fock (HF), density functional (DFT) and Moller-Plesset (MP2) supermolecular calculations and with HF and DFT periodic calculations. The HF and DFT methods fail to predict the stability of the p-nitroaniline crystal but the results of the experimental charge-density approach (ECDA) are in good agreement with both MP2 interaction energies and the experimental lattice energy. ECDA results for L-asparagine monohydrate compare well with those from DFT supermolecular and periodic HF calculations. The disorder of the terminal group in the pentapeptide, which persists at the experimental temperature of 20 K, corresponds to an energy difference of only 0.35 kJ mol(-1), which is too small to be reproduced with current methods. PMID:11058845
Abramov, Y A; Volkov, A; Wu, G; Coppens, P
Relationship between molecular weight of poly(ethylene)glycol and intermolecular interaction of Taka-amylase A monomers
Dynamic and static light scattering investigations of Taka-amylase A (TAA) protein monomers were done using solutions containing poly(ethylene)glycol (PEG) with molecular weights of 1500, 4000, 8000, and 20 000. The anomalies observed in a previous study using a weight of 8000, in which the hydrodynamic TAA monomer radius at a zero protein concentration and the molecular weight of the monomers decreased when the PEG concentration was increased, were observed for all four weights. These anomalies became more pronounced as the PEG molecular weight was increased. The overall interaction parameter did not move further in the direction of the attractive force despite an increase in the PEG concentration from 6% to 12.5% for the PEG 8000 and 20 000 solutions. This was due to the change in the relative contributions of the static structure factor (direct interaction) and the hydrodynamic interaction factor (indirect interaction) against the overall interaction parameter. For the PEG 1500 and 4000 solutions, the change in the overall interaction parameter with an increase in the PEG concentration was controlled by changing the static structure factor. For the PEG 8000 and 20 000 solutions, a change in the hydrodynamic interaction factor with an increase in the PEG concentration offset the change in the static structure factor, unexpectedly resulting in the overall interaction parameter being independent of the PEG concentration. This suggests that the scale and density of a PEG network structure, which are thought to be the origin of the observed anomalies, change nonlinearly with the PEG molecular weight.
Onuma, Kazuo; Furubayashi, Naoki; Shibata, Fujiko; Kobayashi, Yoshiko; Kaito, Sachiko; Ohnishi, Yuki; Inaka, Koji
Solvent dependence of the first hyperpolarizability of p-nitroanilines: Differences between nonspecific dipole-dipole interactions and solute-solvent H-bonds
In this paper, the influence of solvents on the first hyperpolarizability beta of nonlinear optical (NLO) molecules is studied at 25 �C for solutions of p-nitroaniline and N,N-dimethyl paranitroaniline in some 50 solvents belonging to different classes. The hyperpolarizabilities deduced from measured hyper-Rayleigh scattering are the relative ones with as reference that of paranitroaniline in 1,4-dioxane. Taking for the latter
Fran�ois L. Huyskens; Pierre L. Huyskens; Andr� P. Persoons
Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly.
Coat protein (CP) and RNA3 from Prunus necrotic ringspot virus (PNRSV-rose), the most prevalent virus infecting rose in India, were characterized and regions in the coat protein important for self-interaction, during dimer formation were identified. The sequence analysis of CP and partial RNA 3 revealed that the rose isolate of PNRSV in India belongs to PV-32 group of PNRSV isolates. Apart from the already established group specific features of PV-32 group member's additional group-specific and host specific features were also identified. Presence of methionine at position 90 in the amino acid sequence alignment of PNRSV CP gene (belonging to PV-32 group) was identified as the specific conserved feature for the rose isolates of PNRSV. As protein-protein interaction plays a vital role in the infection process, an attempt was made to identify the portions of PNRSV CP responsible for self-interaction using yeast two-hybrid system. It was found (after analysis of the deletion clones) that the C-terminal region of PNRSV CP (amino acids 153-226) plays a vital role in this interaction during dimer formation. N-terminal of PNRSV CP is previously known to be involved in CP-RNA interactions, but our results also suggested that N-terminal of PNRSV CP represented by amino acids 1-77 also interacts with C-terminal (amino acids 153-226) in yeast two-hybrid system, suggesting its probable involvement in the CP-CP interaction. PMID:24426281
Kulshrestha, Saurabh; Hallan, Vipin; Sharma, Anshul; Seth, Chandrika Attri; Chauhan, Anjali; Zaidi, Aijaz Asghar
Intermolecular interactions in albumin-sulfoxide-water systems at low temperatures, investigated by means of fluorescence quenching
The effect of low temperatures on the interaction in human serum albumin (HSA)-diethyl sulfoxife (DESO)-dipropyl sulfoxide (DPSO)-water systems is investigated by means of fluorescence spectroscopy (intrinsic protein fluorescence, three-dimensional excitation/emission matrix (3D EEM)). The Stern-Volmer constants of HSA quenching are calculated for these systems. The structural changes occurring in these systems are characterized using 3D EEM profiles of HSA. It is shown that the HSA structural changes depend not only on the direct interaction of protein with sulfoxides but on structural changes in the solvent as well.
Grigoryan, K. R.; Shilajyan, H. A.
Revealing the nature of intermolecular interaction and configurational preference of the nonpolar molecular dimers (H?)?, (N?)?, and (H?)(N?).
Understanding the nature of noncovalent interactions between nonpolar small molecules is not only theoretically interesting but also important for practical purposes. The interaction mechanism of three prototype dimers (H?)?, (N?)?, and (H?)(N?) are investigated by state-of-the-art quantum chemistry calculations and energy decomposition analysis. It is shown that their configuration preferences are essentially controlled by the electrostatic component rather than the dispersion effect though the monomers have zero dipole moment. These configuration preferences can also be fairly well and conveniently interpreted by visually examining the electrostatic potential map. PMID:24178898
Lu, Tian; Chen, Feiwu
Crystal habits of cubic insulin from porcine pancreas and evaluation of intermolecular interactions by macrobond and EET analyses
Experimental and theoretical investigations of the crystal growth of cubic insulin from porcine pancreas were carried out. Three different crystal habits, cube, cube and dodecahedron, and rhombic dodecahedron forms, were obtained. Judging from the results of macroseeding, the most stable of these forms would be the rhombic dodecahedron surrounded by {110} faces. Molecular interactions in the crystal were evaluated by
Masanori Ootaki; Shigeru Endo; Yoko Sugawara; Takuya Takahashi
Study on the intermolecular interactions of alkylcobaloxime complexes (RCo(dmgH) 2L, dmgH=dimethylglyoxime, R=alkyl, L=H 2O or pyridine)
A series of alkylcobaloxime complexes, [RCo(dmgH) 2L, where dmgH=dimethylglyoxime, R=alkyl, L=neutral monodentate axial ligand], i.e. (EtO 2C) 2C(Me)CH 2Co(dmgH) 2H 2O( 1), n-C 5H 11Co(dmgH) 2H 2O( 2), Br(CH 2) 4Co(dmgH) 2py( 3) and Br(CH 2) 4Co(dmgH) 2H 2O( 4), have been synthesized and characterized. Analysis and comparison of their crystal packing structures with that of our previous reported complexes, COOCH 3(CH 2) 2Co(dmgH) 2H 2O( 5) and c-C 6H 11Co(dmgH) 2H 2O( 6), disclose that one-dimensional ribbon-like zigzag hydrogen bonded networks in 1, 2 and 4 are sustained and controlled by self-assembly between dimethylglyoxime and coordinated water through O-H⋯O - interactions. And the further formation of different types of hydrogen bond linkages with the variation of the axial groups leads to creation of special 2D or 3D architectures. However, the crystal packing structure of 5 and 6 are absolutely different from 1, 2 and 4 due to conformational isomerism effect. Additionally, different types of the protons attachment at O-H⋯O - bridge are observed in 3 and 4, respectively, which is favorable to the intermolecular interactions.
Zhang, Xin; Song, Xin-Yi; Li, Yi-Zhi; Chen, Hui-Lan
Accurate Calculations of Intermolecular Interaction Energies Using Explicitly Correlated Coupled Cluster Wave Functions and a Dispersion-Weighted MP2 Method
Explicitly correlated coupled-cluster calculations of intermolecular interaction energies for the S22 benchmark set of Jure?ka, \\vsponer, ?ern�, and Hobza (Chem. Phys. Phys. Chem. 2006, 8, 1985) are presented. Results obtained with the recently proposed CCSD(T)-F12a method and augmented double-? basis sets are found to be in very close agreement with basis set extrapolated conventional CCSD(T) results. Furthermore, we propose a dispersion-weighted MP2 (DW-MP2) approximation that combines the good accuracy of MP2 for complexes with predominately electrostatic bonding and SCS-MP2 for dispersion-dominated ones. The MP2-F12 and SCS-MP2-F12 correlation energies are weighted by a switching function that depends on the relative HF and correlation contributions to the interaction energy. For the S22 set, this yields a mean absolute deviation of 0.2 kcal/mol from the CCSD(T)-F12a results. The method, which allows obtaining accurate results at low cost, is also tested for a number of dimers that are not in the training set.
Marchetti, Oliver; Werner, Hans-Joachim
Experimental and theoretical investigations of the crystal growth of cubic insulin from porcine pancreas were carried out. Three different crystal habits, cube, cube and dodecahedron, and rhombic dodecahedron forms, were obtained. Judging from the results of macroseeding, the most stable of these forms would be the rhombic dodecahedron surrounded by {1 1 0} faces. Molecular interactions in the crystal were evaluated by the macrobond analysis and electrostatic energy of transfer (EET) analysis. The calculated surface energy of {1 1 0} was lower than {1 0 0} by around 40%, which was consistent with the experimental results. Atomic EET supported the macrobond analysis, where the number of hydrogen bonds was primarily evaluated. At the same time, it was suggested that the parameters of the interaction energies of electrically neutral pairs would be smaller than those of charged pairs. The contribution from the bound water molecules to the crystal stabilization was discussed.
Ootaki, Masanori; Endo, Shigeru; Sugawara, Yoko; Takahashi, Takuya
Nanoscale Intermolecular Interactions between Human Serum Albumin and Low Grafting Density Surfaces of Poly(ethylene oxide)
The net nanoscale interaction between a probe tip covalently bound with the blood plasma protein human serum albumin (HSA) and a surface of end-grafted poly(ethylene oxide) (PEO) mushrooms (Mn 50K, Flory radius RF 9 nm, contour length Lcontour 393 nm) was measured directly on approach (loading) and retract (unloading) in aqueous buffer solution using the technique of high-resolution force spectroscopy
M. A. Rixman; D. Dean; C. Ortiz
Regulation of De Novo-Initiated RNA Synthesis in Hepatitis C Virus RNA-Dependent RNA Polymerase by Intermolecular Interactions?
The hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) has been proposed to change conformations in association with RNA synthesis and to interact with cellular proteins. In vitro, the RdRp can initiate de novo from the ends of single-stranded RNA or extend a primed RNA template. The interactions between the ?1 loop and thumb domain in NS5B are required for de novo initiation, although it is unclear whether these interactions are within an NS5B monomer or are part of a higher-order NS5B oligomeric complex. This work seeks to address how polymerase conformation and/or oligomerization affects de novo initiation. We have shown that an increasing enzyme concentration increases de novo initiation by the genotype 1b and 2a RdRps while primer extension reactions are not affected or inhibited under similar conditions. Initiation-defective mutants of the HCV polymerase can increase de novo initiation by the wild-type (WT) polymerase. GTP was also found to stimulate de novo initiation. Our results support a model in which the de novo initiation-competent conformation of the RdRp is stimulated by oligomeric contacts between individual subunits. Using electron microscopy and single-molecule reconstruction, we attempted to visualize the low-resolution conformations of a dimer of a de novo initiation-competent HCV RdRp.
Chinnaswamy, S.; Murali, A.; Li, P.; Fujisaki, K.; Kao, C. C.
Basis sets for the evaluation of van der Waals complex interaction energies: Ne-N2 intermolecular potential and microwave spectrum.
In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 �, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto. PMID:24375320
Baranowska-??czkowska, Angelika; Fern�ndez, Berta
Problem-Based Learning in 9th Grade Chemistry Class: `Intermolecular Forces'
This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students� understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student�s alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight 9th grade students were stratified by cognitive levels and then randomly assigned to experimental (PBL, 40 students) and control (lecture-style teaching, 38 students) groups. Following a preparatory lesson where activation and remediation of existing knowledge occur, a pre-test was given, and no significant difference was found between the two groups of students ( p > .05). After the instruction was completed, a post-test and also a questionnaire related to the quality of the problem, the teacher�s role and group functioning were administered. Results from the post-test of both groups ( p < .05) and questionnaire showed that PBL is affective on students� achievement, remedying formation of alternate conceptions and also social skills.
Tarhan, Leman; Ayar-Kayali, Hulya; Urek, Raziye Ozturk; Acar, Burcin
Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study.
An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin??/?)max = 1.1?�(-1)] measured at 100?(2)?K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the ?-electron cloud. PMID:24892603
Rajalakshmi, Gnanasekaran; Hathwar, Venkatesha R; Kumaradhas, Poomani
Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf(3+).
This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n](m+)(H2O)? clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average [Formula: see text] in the range 2.43-2.48 �, whereas the fourth one is closer to 9 with [Formula: see text] = 2.54 �. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination. PMID:24907987
Galbis, Elsa; Hern�ndez-Cobos, Jorge; Pappalardo, Rafael R; Marcos, Enrique S�nchez
Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf3+
This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H2O)n]m+(H2O)? clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R_{{Cf-O}} in the range 2.43-2.48 �, whereas the fourth one is closer to 9 with R_{{Cf-O}} = 2.54 �. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.
Galbis, Elsa; Hern�ndez-Cobos, Jorge; Pappalardo, Rafael R.; Marcos, Enrique S�nchez
On the existence of Fr�hlich's long-range interactions in dipolar chains
A chain of N identical polarizable molecules interacting via dipole-dipole forces is investigated. A careful mathematical analysis results in a proof of the existence of long-range forces analogous to those described by Fr�hlich for two giant dipoles which is a special case in our model. The energy spectrum is more complicated and depends on the structure constants of the system.
J. A. Tuszynski
Theory of elastic interaction between arbitrary colloidal particles in confined nematic liquid crystals
We develop the method proposed by Chernyshuk and Lev [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 81, 041701 (2010)] for theoretical investigation of elastic interactions between colloidal particles of arbitrary shape and chirality (polar as well as azimuthal anchoring) in the confined nematic liquid crystal (NLC). General expressions for six different types of multipole elastic interactions are obtained in the confined NLC: monopole-monopole (Coulomb type), monopole-dipole, monopole-quadrupole, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. The obtained formulas remain valid in the presence of the external electric or magnetic fields. The exact equations are found for all multipole coefficients for the weak anchoring case. For the strong anchoring coupling, the connection between the symmetry of the shape or director and multipole coefficients is obtained, which enables us to predict which multipole coefficients vanish and which remain nonzero. The particles with azimuthal helicoid anchoring are considered as an example. Dipole-dipole interactions between helicoid cylinders and cones are found in the confined NLC. In addition, the banana-shaped particles in homeotropic and planar nematic cells are considered. It is found that the dipole-dipole interaction between banana-shaped particles differs greatly from the dipole-dipole interaction between the axially symmetrical particles in the nematic cell. There is a crossover from attraction to repulsion between banana particles along some directions in nematic cells. It is shown that monopoles do not �feel� the type of nematic cell: monopole-monopole interaction turns out to be the same in homeotropic and planar nematic cells and converges to the Coulomb law as thickness increases, L??.
Tovkach, O. M.; Chernyshuk, S. B.; Lev, B. I.
Preparation and characterization of co-amorphous Ritonavir-Indomethacin systems by solvent evaporation technique: Improved dissolution behavior and physical stability without evidence of intermolecular interactions.
The aim of this study was to stabilize the amorphous form of Ritonavir (RTV) a BCS class-II drug with known amorphous stabilizing small molecule Indomethacin (IND) by co-amorphous technology. The co-amorphous samples were prepared by solvent evaporation technique in the molar ratios RTV:IND (2:1), RTV:IND (1:1), RTV:IND (1:2) and their amorphous nature was confirmed by XRPD, DSC and FT-IR. Physical stability studies were carried out at temp 25�C and 40�C for maximum up to 90days under dry conditions. Solubility and dissolution testing were carried out to investigate the dissolution advantage of prepared co-amorphous systems. The amorphous mixtures of all tested molar ratios were found to become amorphous after solvent evaporation. The same was confirmed by detecting halo pattern in diffractograms of co-amorphous mixtures. The Tg values of all three systems were found to be more than 40�C, the highest being 51.88�C for RTV:IND (2:1) system. Theoretical Tg values were calculated by Gordon-Taylor equation. Insignificant deviation of theoretical Tg values from that of practical one, corroborated by FT-IR studies showed no evidence of intermolecular interactions between RTV and IND. Almost 3-folds increase in the solubility for both amorphous RTV and IND was found as compared to their respective crystalline counterparts. The study demonstrated significant increase in the dissolution rate as well as increase in the total amount of drug dissolved for amorphous RTV, however it failed to demonstrate any significant improvement in the dissolution behavior of IND. PMID:24878386
Dengale, Swapnil J; Ranjan, Om Prakash; Hussen, Syed Sajjad; Krishna, B S M; Musmade, Prashant B; Gautham Shenoy, G; Bhat, Krishnamurthy
FT-IR study on interactions between medroxyprogesterone acetate and solvent in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems
The intermolecular interactions between medroxyprogesterone acetate (MPA) and CHCl3 and CCl4 solvent in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems have been studied by Fourier transform infrared spectroscopy (FT-IR). The experimental results showed that there are hydrogen bonding interactions between oxygen atoms of all carbonyl groups in MPA and hydrogen atom of CHCl3 so as to form 1:3 complex of MPA with CHCl3 and produce three new absorption bands at 1728.9-1736.1, 1712.7-1717.4 and 1661.9-1673.8 cm-1, respectively. And, 1:1 complex of MPA with CCl4 is formed in CCl4/cyclo-C6H12 binary solvent as a result of hydrogen bonding interaction between C3 carbonyl group and empty d-orbital in chlorine atom of CCl4 leading to producing new absorption band at 1673.2-1674.2 cm-1. However, all free carbonyl and associated carbonyl stretching vibrations of MPA in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems shift to lower wavenumbers with the increasing of volume fraction of CHCl3 and CCl4 in binary solvent systems owing to the dipole-dipole interaction and the dipole-induced dipole interaction between MPA and solvents.
Shi, Jie-hua; Fan, Chun-hui
New Type of Dual Solid-State Thermochromism: Modulation of Intramolecular Charge Transfer by Intermolecular ?-? Interactions, Kinetic Trapping of the Aci-Nitro Group, and Reversible Molecular Locking
When heated above room temperature, some crystalline polymorphs of the 1,3-bis(hydroxyalkylamino)-4,6-dinitrobenzenes (BDBn, n = 2-5), bis(hydroxyalkyl) analogues of the intramolecular charge-transfer molecule 1,3-diamino-4,6-dinitrobenzene, exhibit "dual" thermochromism: gradual color change from yellow to orange at lower temperatures, and sharp color change from orange to red at higher temperatures. These two thermochromic changes are related to different solid-state processes. When allowed to cool to room temperature, the yellow color of the thermochromic molecules with different alkyl length (n) is recovered with unexpectedly different kinetics, the order of the respective rate constants ranging from 10-7-10-6 s-1 for BDB2 to about 0.1 s-1 in the case of BDB3. The thermochromic mechanism and the reasons behind the different kinetics were clarified on the basis of detailed crystallographic characterization, kinetic thermoanalysis, and spectroscopic study of eight crystalline forms (seven polymorphs and one solvate). It was found that the polymorphism is due to the possibility of "locking" and "unlocking" of the alkyl arms by formation of a strong intramolecular hydrogen bond between the hydroxyl groups at their hydroxyl termini. The locking of BDB2, with shortest alkyl arms, is reversible and it can be controlled thermally; either of the two conformations can be obtained in the solid state by proper thermal treatment. By use of high temperature in situ single crystal X-ray diffraction analysis of BDB3, direct evidence was obtained that the gradual thermochromic change is related to increased distance and weakened ?-? interactions between the stacked benzene rings: the lattice expands preferably in the stacking direction, causing enhanced oscillator strength and red shift of the absorption edge of the intramolecular charge transfer transition. The second, sharp thermochromic change had been assigned previously to solid-solid phase transition triggered by intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular ?-? interactions and thermal intramolecular proton transfer to aromatic nitro group.
Naumov, Pan?e; Lee, Sang Cheol; Ishizawa, Nobuo; Jeong, Young Gyu; Chung, Ihn Hee; Fukuzumi, Shunichi
Temperature-dependent van der Waals atom-surface interaction
The van der Waals (vW) long-range atom-surface interaction is often described as a dipole-dipole interaction, originating in the coupling between the quantum dipole fluctuations of an atom and the instantaneously induced fluctuations in the electrostatic image. Due to the finite light velocity, this atom-surface interaction is better understood in the more general frame of the Casimir-Polder theory. Recently, it was
P. C. de Souza Segundo; P. Ballin; T. P. de Silans; I. Maurin; A. Laliotis; S. Saltiel; M.-P. Gorza; M. Ducloy; D. Bloch; D. de Sousa Meneses; P. Echegut
Microwave control of the interaction between two optical photons
A microwave field is used to control the interaction between pairs of optical photons stored in highly excited collective states (Rydberg polaritons). We show that strong dipole-dipole interactions induced by the microwave field destroy the coherence of polariton modes with more than one Rydberg excitation. Consequently, single-polariton modes, which correspond to single stored photons, are preferentially retrieved from the sample. Measurements of the photon statistics of the retrieved light field also reveal nontrivial propagation dynamics of the interacting polaritons.
Maxwell, D.; Szwer, D. J.; Paredes-Barato, D.; Busche, H.; Pritchard, J. D.; Gauguet, A.; Jones, M. P. A.; Adams, C. S.
Intermolecular potential functions from spectroscopic properties of weakly bound complexes
The goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of
John S. Muenter
Critical Behaviour of Heisenberg Ferromagnets with Dipolar Interactions and Uniaxial Anisotropy
In any real magnetic system, weak anisotropic long-range dipole-dipole interactions are invariably present besides crystal-field interactions and dominant isotropic short-range Heisenberg interactions (in insulating systems) or isotropic long-range Ruderman-Kittel-Kasuya-Yosida (RKKY) interactions (in metallic systems) that couple the localized magnetic moments. In many magnetic systems, the dominant interactions normally sustain long-range magnetic order and govern the ground state and finite-temperature magnetic
S. N. Kaul
Thermal diffusion factors and intermolecular potentials for noble gas-SF sub 6 systems
Experimental thermal diffusion factors for equimolar mixtures of He-, Ne-, Ar-, Kr-, and Xe-SF{sub 6} have been measured in the temperature range from 225 to 500 K. The data were obtained in a 20-tube trennschaukel, or swing separator.'' The systems containing the four lighter noble gases all exhibited a normal'' thermal diffusion factor, {alpha}{sub T}, that is concentration of the heavy species, SF{sub 6}, in the cold region of the apparatus and increase of {alpha}{sub T} with temperature. Xe-SF{sub 6}, the system with the smallest mass difference, exhibited abnormal'' behavior. The spherically symmetric Pack potentials were used to calculate the thermal diffusion factor with reasonable success. Recently published dipole-dipole dispersion coefficients were used to construct intermolecular potentials of the Hartree-Fock-Dispersion functional form with individually damped attractive terms. The potentials, when tested against the available transport and thermodynamic data, improved the fit to experiment in almost all cases. 35 refs., 7 figs., 2 tabs.
Taylor, W.L.; Hurly, J.J. (EG and G Mound Applied Technologies, Miamisburg, OH (USA) Cincinnati Univ., OH (USA). Dept. of Chemistry) [EG and G Mound Applied Technologies, Miamisburg, OH (USA) Cincinnati Univ., OH (USA). Dept. of Chemistry
C-NOT gate based on ultracold Rydberg atom interactions
The Rydberg states of neutral atoms are strongly polarisable and possess long lifetimes because of high energies which can lead to strong and long range dipole-dipole interactions. The energy levels corresponding to these states are shifted because of dipole-dipole interactions and can be used to block transitions of more than one excitation in the Rydberg regime. This reputed Rydberg blockade is obtained when the excitation is shifted out of resonance by these interactions. Electromagnetically induced transparency (EIT) is sensitive to a small detuning. At large distances, up to several micrometers, the interactions can interrupt the EIT consequence. Herein we investigate a novel scheme based on EIT and Rydberg blockade and performed a simulation of a controlled-NOT (C-NOT) quantum gate which is critical for quantum computation by using neutral atoms.
Rashid, Muhammad; Maarten, Hoogerland; Yasir, Jamil
How resonance assists hydrogen bonding interactions: an energy decomposition analysis.
Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. PMID:17143867
Beck, John Frederick; Mo, Yirong
Intermolecular interactions involving C-H bonds, 3, Structure and energetics of the interaction between CH{sub 4} and CN{sup {minus}}
On the basis of SCF and single reference MP2 calculations, the full potential energy surface of the interaction between CH{sub 4} and CN{sup {minus}} was studied using extended basis sets of up to near Hartree-Fock limit quality. Colinear arrangements C-N{sup {minus}}{hor_ellipsis}H-CH{sub 3} and N-C{sup {minus}}{hor_ellipsis}H-CH{sub 3} are found to be the only two energy minima. The binding energies of these two structures are calculated to be 2.5 and 2.1 kcal/mol, respectively, at the MP2 level. The full vibrational analyses of two structures show a red shift of about 30 cm{sup {minus}1} for the v{sub s} C-H stretching.
Novoa, J.J.; Whangbo, Myung-Hwan [North Carolina State Univ., Raleigh, NC (United States). Dept. of Chemistry; Williams, J.M. [Argonne National Lab., IL (United States)
Investigation of Rydberg Atomic Interaction via Collisional Loss
We present a detailed theoretically analysis of the time evolution of ultracold Rydberg atom number and effective lifetime as functions of the various parameters. We derive simple analytical formula from the existing theoretical model to estimate the strength of the Rydberg atom interaction from collisional loss rate. And estimate the strength of the dipole--dipole and van der Waals interaction from the evaluation of our recent experimental results using the present formula.
Feng, Zhi-Gang; Zhao, Jian-Ming; Jia, Suo-Tang; Zheng, Wan-Hua
On the Probability of Intermolecular Energy Transfer in Polar Molecules.
An expression is developed for the probability of intermolecular energy transfer P in polar molecules for particular orientations on the basis of the Lennard-Jones-dipole-quadrupole interaction energy. The temperature dependence of P is briefly discussed....
H. K. Shin
Bose-Einstein condensation of trapped atoms with dipole interactions
The path-integral Monte Carlo method is used to simulate dilute trapped Bose gases and to investigate the equilibrium properties at finite temperatures. The quantum particles have a long-range dipole-dipole interaction and a short-range s-wave interaction. Using an anisotropic pseudopotential for the long-range dipolar interaction and a hard-sphere potential for the short-range s-wave interaction, we calculate the energetics and structural properties as a function of temperature and the number of particles. Also, in order to determine the effects of dipole-dipole forces and the influence of the trapping field on the dipolar condensate, we use two cylindrically symmetric harmonic confinements (a cigar-shaped trap and a disk-shaped trap). We find that the net effect of dipole-dipole interactions is governed by the trapping geometry. For a cigar-shaped trap, the net contribution of dipolar interactions is attractive and the shrinking of the density profiles is observed. For a disk-shaped trap, the net effect of long-range dipolar forces is repulsive and the density profiles expand.
Nho, Kwangsik; Landau, D.P. [Center for Simulational Physics, University of Georgia, Athens, Georgia 30602 (United States)
Studies on Non-Covalent Interaction of Coumarin Attached Pyrimidine and 1-Methyl Indole 1,2,3 Triazole Analogues with Intermolecular Telomeric G-Quadruplex DNA Using ESI-MS and Spectroscopy.
In the present study, electrospray ionization mass spectrometry (ESI-MS) and spectroscopy have been used to evaluate the non-covalent interaction, stoichiometry, and selectivity of two synthetic coumarin-attached nucleoside and non-nucleoside 1,2,3-triazoles, namely, (1-(5-(hydroxymethyl)-4-(4-((2-oxo-2H-chromen-4-yloxy)methyl)-1H-1,2,3-triazol-1-yl)tetrahydro-furan-2-yl)5-methyl pyrimidine-2,4(1H,3H)-dione (Tr1) and 4-((1-((-1-methyl-1H-indol-2-yl)methyl)-1H-1,2,3-triazol-4-yl)methoxy)-2H-chromen-2-one (Tr2) with two different human telomeric intermolecular G-quadruplex DNA structures formed by d(T2AG3) and d(T2AG3)2 sequences. ESI-MS studies indicate that Tr1 specifically interacts with four-stranded intermolecular parallel quadruplex complex, whereas Tr2 interacts with two hairpin as well as four-stranded intermolecular parallel quadruplex complexes. UV-Visible spectroscopic studies suggest that Tr1 and Tr2 interact with G-quadruplex structure and unwind them. Job plots show that stoichiometry of ligand:quadruplex DNA is 1:1. Circular dichroism (CD) studies of G-quadruplex DNA and Tr1/Tr2 ligands manifest that they unfold DNA on interaction. Fluorescence studies demonstrate that ligand molecules intercalate between the two stacks of quadruplex DNA and non-radiative energy transfer occurs between the excited ligand molecules (donor) and quadruplex DNA (acceptor), resulting in enhancement of fluorescence emission intensity. Thus, these studies suggest that nucleoside and non-nucleoside ligands efficiently interact with d(T2AG3) and d(T2AG3)2 G-quadruplex DNA but the interaction is not alike with all kinds of quadruplex DNA, this is probably due to the variation in the pharmacophores and structure of the ligand molecules. PMID:24972013
Raju, G; Srinivas, R; Reddy, M Damoder; Reddy, Ch Raji; Nagesh, N
Desensitization of metastable intermolecular composites
A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.
Busse, James R. (South Fork, CO); Dye, Robert C. (Los Alamos, NM); Foley, Timothy J. (Los Alamos, NM); Higa, Kelvin T. (Ridgecrest, CA); Jorgensen, Betty S. (Jemez Springs, NM); Sanders, Victor E. (White Rock, NM); Son, Steven F. (Los Alamos, NM)
Molecular structure, spectral studies, intra and intermolecular interactions analyses in a novel ethyl 4-[3-(2-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate and its dimer: A combined DFT and AIM approach
A newly synthesized chalcone, Ethyl 4-[3-(2-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate (ECPADMPC) has been characterized by 1H NMR, 13C NMR, UV-Vis, FT-IR, Mass spectroscopy and elemental analysis. Quantum chemical calculations have been performed by DFT level of theory using B3LYP functional and 6-31G(d,p) as basis set. The time dependent density functional theory (TD-DFT) is used to find the various electronic transitions within molecule. A combined theoretical and experimental wavenumber analysis confirms the existence of dimer. Topological parameters-electron density (?BCP), Laplacian of electron density (?2?BCP), energetic parameters-kinetic electron energy density (GBCP), potential electron density (VBCP) and the total electron energy density (HBCP) at the bond critical points (BCP) have been analyzed by 'Atoms in molecules' AIM theory in detail. The intermolecular hydrogen bond energy of dimer is calculated as -12.3 kcal/mol using AIM calculations. AIM ellipticity analysis is carried out to confirm the presence of resonance assisted intermolecular hydrogen bonds in stabilization of dimer. The analysis clearly depicts the presence of different kind of interactions in dimer. This dimer may work as model system to understand the H-bonding interaction in biomolecules. The local reactivity descriptor analysis is performed to find the reactive sites within molecule.
Singh, R. N.; Baboo, Vikas; Rawat, Poonam; Kumar, Amit; Verma, Divya
Characterization the effects of structure and energetics of intermolecular interactions on the oligomerization of peptides in aqueous 2, 2, 2-trifluoroethanol via circular dichroism and nuclear magnetic resonance spectroscopy.
Intermolecular interactions are of fundamental importance to fully comprehend a wide range of protein behaviors such as oligomerization, folding and recognition. Two peptides, NPY([18-36]) and NPY([15-29]), segmented from human neuropeptide Y (hNPY), were synthesized in this work to study the interaction between species. Information about intermolecular interactions was extracted from their oligomerizing behaviors. The results from CD and NMR showed that the addition of 2, 2, 2-trifluoroethanol (TFE) induces a stable helix in each peptides and an extended helix in NPY([18-36]), formed between residues 30-36. Pulsed field gradient NMR data revealed that NPY([15-29]) forms a larger oligomer at lower temperatures and continuously dissociates into the monomeric form with increasing temperature. NPY([18-36]) was also found to undergo an enhanced interaction with TFE and a more favorable self-association at higher temperatures. We characterized the changes of oligomerized states with respect to temperature to infer the effects of entropy and interaction energy on the association-dissociation equilibrium. As shown by NPY([15-29]), deletion of helical secondary structure or residues from the C-terminal segment may disrupt the solvation by TFE and results in entropy increase as the oligomer dissociates. Unlike that in NPY([15-29]), the extended helix in NPY([18-36]) improves the binding of TFE, and as a result, entropy is gained via the transfer of the TFE cluster from the interface between monomeric peptides into the bulk solvent. This observation suggests that the oligomerized state may be modulated by the entropy and energetics contributed by helical segments in the oligomerization process. PMID:22311423
Lee, Chang-Shin; Tung, Wei-Cheng; Luo, Wan-Chi
Long-range and frustrated spin-spin interactions in crystals of cold polar molecules
We describe a simple scheme for the implementation and control of effective spin-spin interactions in self-assembled crystals of cold polar molecules. In our scheme, spin states are encoded in two long-lived rotational states of the molecules and coupled via state-dependent dipole-dipole forces to the lattice vibrations. We show that, by choosing an appropriate time-dependent modulation of the induced dipole moments, the resulting phonon-mediated interactions compete with the direct dipole-dipole coupling and lead to long-range and tunable spin-spin interaction patterns. We illustrate how this technique can be used for the generation of multiparticle entangled spin states and the implementation of spin models with long-range and frustrated interactions, which exhibit nontrivial phases of magnetic ordering.
Zhou, Y. L. [College of Science, National University of Defense Technology, Changsha, 410073 (China); Ortner, M. [Institute for Theoretical Physics, University of Innsbruck, AT-6020 Innsbruck (Austria); Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, AT-6020 Innsbruck (Austria); Rabl, P. [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, AT-6020 Innsbruck (Austria)
Cold gases with anisotropic interactions
A cold gas of particles with anisotropic interactions of a general form, due to a polarizing field, is studied. Special cases are atoms or molecules with dipole-dipole or quadrupole-quadrupole interactions. It is shown that the angular dependence of an observable on the direction of the polarizing field is largely determined by symmetry. For a gas in a confined quasi-two-dimensional geometry, the effective interaction is calculated in a general form. Some examples of dipole and quadrupole gases are considered. It is concluded that when anisotropic forces are studied in a general manner, one can obtain simpler results and better understanding for some problems.
Pikovski, Alexander
Long-range interactions between ultracold atoms and molecules including atomic spin-orbit
We investigate theoretically the long-range electrostatic interactions between a ground-state homonuclear alkali-metal dimer and an excited alkali-metal atom taking into account its fine-structure. The interaction involves the combination of first-order quadrupole-quadrupole and second-order dipole-dipole effects. Depending on the considered species, the atomic spin-orbit may be comparable to the atom-molecule electrostatic energy and to the dimer rotational structure. Here we extend
Maxence Lepers; Olivier Dulieu
Phase Diagram for a Magnetic Thin Film with Dipolar Interactions and Magnetic Surface Anisotropy
The phase diagram of a model thin film with long-range dipole-dipole interactions and magnetic surface anisotropy is determined as a function of temperature and the surface anisotropy. We show that the model studied here exhibits a reorientation transition in the absence of an exchange interaction. Further we show that, unexpectedly, the transition is from an in-plane phase to an out-of-plane
A. B. MacIsaac; J. P. Whitehead; K. de'Bell; P. H. Poole
Crystallographic studies on substituted m-terphenyls: identification of weak [CH3���I] interactions
Crystallographic studies of 2,6-bis(2,4,6-trimethylphenyl)-4-methyliodobenzene 1 and 2,6-diphenyl-4-methyliodobenzene 2 were performed and in both cases [CH3���I] interactions were identified. Theoretical calculation of the dipole moment of 1 and the partial charges of the iodine and methyl hydrogens were performed. These charges, although small, suggest that they are large enough to encourage the formation of weak dipole-dipole interactions in the absence of
Diane A. Dickie; Deepa Abeysekera; Iain D. McKenzie; Hilary A. Jenkins; Jason A. C. Clyburne
Intermolecular Forces: A Jigsaw Activity
NSDL National Science Digital Library
This jigsaw activity is designed as a cooperative learning activity used to introduce the idea of intermolecular forces. Intermolecular forces are the types of attractive forces that occur between molecules in a solid, liquid, or gas. Each force causes different physical properties of matter. Each member of the group will become an expert on one type of force and then teach the rest of the group.
Edu., Boise S.
Vortex lattices in planar Bose-Einstein condensates with dipolar interactions.
In this Letter, we investigate the effects of dipole-dipole interactions on the vortex lattices in fast rotating Bose-Einstein condensates. For single planar condensate, we show that the triangular lattice structure will be unfavorable when the s-wave interaction is attractive and exceeds a critical value. It will first change to a square lattice, and then become more and more flat with the increase of s-wave attraction, until the collapse of the condensate. For an array of coupled planar condensates, we discuss how the dipole-dipole interactions between neighboring condensates compete with quantum tunneling processes, which affects the relative displacement of two neighboring vortex lattices and leads to the loss of phase coherence between different condensates. PMID:16384039
Zhang, Jian; Zhai, Hui
Vortex Lattices in Planar Bose-Einstein Condensates with Dipolar Interactions
In this Letter, we investigate the effects of dipole-dipole interactions on the vortex lattices in fast rotating Bose-Einstein condensates. For single planar condensate, we show that the triangular lattice structure will be unfavorable when the s-wave interaction is attractive and exceeds a critical value. It will first change to a square lattice, and then become more and more flat with the increase of s-wave attraction, until the collapse of the condensate. For an array of coupled planar condensates, we discuss how the dipole-dipole interactions between neighboring condensates compete with quantum tunneling processes, which affects the relative displacement of two neighboring vortex lattices and leads to the loss of phase coherence between different condensates.
Zhang Jian; Zhai Hui [Center for Advanced Study, Tsinghua University, Beijing 100084 (China)
Resonance interaction induced by metal surfaces catalyzes atom-pair breakage
We present the theory for retarded resonance interaction between two identical atoms at arbitrary positions near a metal surface. The dipole-dipole resonance interaction force that binds isotropically excited atom pairs together in free space may turn repulsive close to an ideal (totally reflecting) metal surface. On the other hand, close to an infinitely permeable surface it may turn more attractive. We illustrate numerically how the dipole-dipole resonance interaction between two oxygen atoms near a metal surface may provide a repulsive energy of the same order of magnitude as the ground-state binding energy of an oxygen molecule. As a complement we also present results from density-functional theory.
Bostr�m, Mathias; Persson, Clas; Ninham, Barry W.; Norman, Patrick; Sernelius, Bo E.
Competing intermolecular interactions in the high-temperature solid phases of even saturated carboxylic acids (C10H19O2H to C20H39O2H).
Structural knowledge of the high-temperature phases of saturated carboxylic acids (C(n)H(2n-1)O(2)H) from C(6)H(11)O(2)H to C(23)H(45)O(2)H is now complete. Crystal structures of the high-temperature phases of even acids from decanoic (C(10)H(19)O(2)H) to eicosanoic (C(20)H(39)O(2)H) are reported. The crystal structures of the six compounds were determined from powder X-ray diffraction data following direct space methods and refined by the Rietveld method combined with force field geometry optimization. The combination proved to be a valuable approach to obtain structures that are chemically sensible and in close agreement with the powder pattern. At the end of the process solid-state DFT calculations were applied to improve the overall accuracy of the system but in this case DFT did not render better structures. The high-temperature solid phases of even carboxylic acids are all P2(1)/c with Z=4, the molecules are united into dimers via strong hydrogen bonds. Two major types of interactions govern the crystal packing of carboxylic acids, hydrogen bonds and van der Waals interactions. A survey of the intermolecular interactions has revealed that hydrogen bonds are the dominant interaction for acids with less than 23 carbon atoms in the alkyl chain while van der Waals interactions dominate the packing for acids with more than 23 carbon atoms. PMID:19862782
Moreno-Calvo, Evelyn; Gbabode, Gabin; Cordobilla, Raquel; Calvet, Teresa; Cuevas-Diarte, Miquel Angel; Negrier, Philippe; Mondieig, Denise
Effect of dipolar interactions on optical nonlinearity of two-dimensional nanocomposites
In this work, we calculate the contribution of dipole-dipole interactions to the optical nonlinearity of the two-dimensional random ensemble of nanoparticles that possess a set of exciton levels, for example, quantum dots. The analytical expressions for the contributions in the cases of TM- and TE-polarized light waves propagating along the plane are obtained. It is shown that the optical nonlinearity, caused by the dipole-dipole interactions in the planar ensemble of the nanoparticles, is several times smaller than the similar nonlinearity of the bulk nanocomposite. This type of optical nonlinearity is expected to be observed at timescales much larger than the quantum dot exciton rise time. The proposed method may be applied to various types of nanocomposite shape.
Panov, Andrey V.
Non-metal-to-metal transition driven by van der Waals forces in an interacting polaronic gas
Using path integrals and the theory of polarizable fluids, we develop a model treating non-degenerate interacting Fr�hlich polarons at low densities and temperatures. Starting from the dilute regime, we show that at strong electron-phonon coupling, the collective properties of polarons are mainly governed by the London dispersion forces, i.e. induced dipole-dipole van der Waals interactions. At a critical density, these
P. Qu�merais; G. N. Chuev
Intra- and Intermolecular Regulatory Interactions in Upf1, the RNA Helicase Central to Nonsense-Mediated mRNA Decay in Yeast
RNA helicases are involved in almost every aspect of RNA metabolism, yet very little is known about the regulation of this class of enzymes. In Saccharomyces cerevisiae, the stability and translational fidelity of nonsense-containing mRNAs are controlled by the group I RNA helicase Upf1 and the proteins it interacts with, Upf2 and Upf3. Combining the yeast two-hybrid system with genetic analysis, we show here that the cysteine- and histidine-rich (CH) domain and the RNA helicase domain of yeast Upf1 can engage in two new types of molecular interactions: an intramolecular interaction between these two domains and self-association of each of these domains. Multiple observations indicate that these molecular interactions are crucial for Upf1 regulation. First, coexpression of the CH domain and the RNA helicase domain in trans can reconstitute Upf1 function in both promoting nonsense-mediated mRNA decay (NMD) and preventing nonsense suppression. Second, mutations that disrupt Upf1 intramolecular interaction cause loss of Upf1 function. These mutations weaken Upf2 interaction and, surprisingly, promote Upf1 self-association. Third, the genetic defects resulting from deficiency in Upf1 intramolecular interaction or RNA binding are suppressed by expression of Upf2. Collectively, these data reveal a set of sequential molecular interactions and their roles in regulating Upf1 function during activation of NMD and suggest that cis intramolecular interaction and trans self-association may be general mechanisms for regulation of RNA helicase functions.
Ganesan, Robin
Exciton�Exciton Interaction in CdWO Under Resonant Excitation by Intense Femtosecond Laser Pulses
Using time-resolved luminescence spectroscopy, excitation density effects were investigated under conditions of resonant creation of excitons by femtosecond laser pulses in CdWO4 scintillator at room temperature. It was revealed that the decay kinetics of intrinsic emission becomes accelerated and deviates from the exponential law in the initial stage due to the Fo?rster dipole-dipole interaction of self-trapped excitons. It is shown
V. Nagirnyi; S. Dolgov; R. Grigonis; M. Kirm; L. L. Nagornaya; F. Savikhin; V. Sirutkaitis; S. Vielhauer; A. Vasil'ev
Spin Ice Behavior in Ising Pyrochlore Magnets with Long Range Dipole Interactions
Recent experiments suggest that the Ising pyrochlore magnets Ho_2Ti_2O7 and Dy_2Ti_2O7 display qualitative properties of the ferromagnetic nearest neighbor spin ice model proposed by Harris et al., Phys. Rev. Lett. 79, 2554 (1997). The manifestation of spin ice behavior in these systems, despite the energetic constraints introduced by the strength and the long range nature of dipole-dipole interactions, remains difficult
Michel Gingras; Roger Melko; Byron den Hertog
Ground-State Properties of a Homogeneous 2d System of Bosons with Dipolar Interactions
The ground-state phase properties of a two-dimensional Bose system with dipole-dipole interactions is studied by means of quantum Monte Carlo techniques. Limitations of mean-field theory in a two-dimensional geometry are discussed. A quantum phase transition from gas to solid is found. The crystal is tested for the existence of a supersolid in the vicinity of the phase transition. The mesoscopic
G. E. Astrakharchik; J. Boronat; J. Casulleras; I. L. Kurbakov; Yu. E. Lozovik
n??* Interactions of Amides and Thioamides: Implications for Protein Stability
Carbonyl�carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n??* donor�acceptor interaction with an energy of at least 0.27 kcal/mol. The n??* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor�acceptor orbital interactions rather than dipole�dipole interactions.
Newberry, Robert W.; VanVeller, Brett; Guzei, Ilia A.; Raines, Ronald T.
Application of charge density methods to a protein model compound: Calculation of Coulombic intermolecular interaction energies from the experimental charge density
A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6�31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2�3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.
Li, Xue; Wu, Guang; Abramov, Yuriy A.; Volkov, Anatoliy V.; Coppens, Philip
Application of charge density methods to a protein model compound: calculation of Coulombic intermolecular interaction energies from the experimental charge density.
A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6-31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2-3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules. PMID:12221293
Li, Xue; Wu, Guang; Abramov, Yuriy A; Volkov, Anatoliy V; Coppens, Philip
Characterization of the Structure and Intermolecular Interactions between the Connexin 32 Carboxyl-terminal Domain and the Protein Partners Synapse-associated Protein 97 and Calmodulin*
In Schwann cells, connexin 32 (Cx32) can oligomerize to form intracellular gap junction channels facilitating a shorter pathway for metabolite diffusion across the layers of the myelin sheath. The mechanisms of Cx32 intracellular channel regulation have not been clearly defined. However, Ca2+, pH, and the phosphorylation state can regulate Cx32 gap junction channels, in addition to the direct interaction of protein partners with the carboxyl-terminal (CT) domain. In this study, we used different biophysical methods to determine the structure and characterize the interaction of the Cx32CT domain with the protein partners synapse-associated protein 97 (SAP97) and calmodulin (CaM). Our results revealed that the Cx32CT is an intrinsically disordered protein that becomes ?-helical upon binding CaM. We identified the GUK domain as the minimal SAP97 region necessary for the Cx32CT interaction. The Cx32CT residues affected by the binding of CaM and the SAP97 GUK domain were determined as well as the dissociation constants for these interactions. We characterized three Cx32CT Charcot-Marie-Tooth disease mutants (R219H, R230C, and F235C) and identified that whereas they all formed functional channels, they all showed reduced binding affinity for SAP97 and CaM. Additionally, we report that in RT4-D6P2T rat schwannoma cells, Cx32 is differentially phosphorylated and exists in a complex with SAP97 and CaM. Our studies support the importance of protein-protein interactions in the regulation of Cx32 gap junction channels and myelin homeostasis.
Stauch, Kelly; Kieken, Fabien; Sorgen, Paul
A new insight into the mechanism of intermolecular forces
A generalized version of the response theory within molecular quantum electrodynamics is used to determine intermolecular interaction energies. The method brings into focus the important role of the energy density associated with the electric field. It is first applied to obtain the well-known London R-6 potential to illustrate the powerful nature of the method. For this case the appropriate energy density is entirely electrostatic. A straightforward generalization that includes contributions from dynamic fields leads to the fully retarded dispersion force. An extension of this approach to calculate intermolecular interactions involving molecules in excited states is given and a new power law with an R-2 dependence is predicted.
Power, E. A.; Thirunamachandran, T.
Redetermined structure of diphenyl-phospho-nimidotriphenyl-phospho-rane: location of the hydrogen atoms and analysis of the inter-molecular inter-actions
The title compound, C30H25NOP2, is a bulky phosphazene derivative. Its previous crystal structure [Cameron et al. (1979 ?). Acta Cryst. B35, 1373�1377] is confirmed and its H atoms have been located in the present study. The formal P=N double bond is about 0.05?� shorter than the P�N single bond and the large P=N�P bond angle reflects the steric strain in the mol�ecule. An intra�molecular C�H?O inter�action occurs. In the crystal, short C�H?O contacts connect the mol�ecules into chains propagating in [011], which are cross-linked via C�H?? inter�actions, generating a three-dimensional network. Aromatic ?�? stacking also occurs [shortest centroid�centroid separation = 3.6012?(11)?�].
Betz, Richard; Gerber, Thomas; Hosten, Eric; Schalekamp, Henk
Intermolecular weak interactions in HTeXH dimers (X=O, S, Se, Te): hydrogen bonds, chalcogen-chalcogen contacts and chiral discrimination.
A theoretical study of the HTeXH (X=O, S, Se and Te) monomers and homodimers was carried out by means of second-order M�ller-Plesset perturbation theory (MP2) computational methods. In the case of monomers, the isomerization energy from HTeXH to H(2) Te=X and H(2) X=Te (X=O, S, Se, and Te) and the rotational transition-state barriers were obtained. Due to the chiral nature of these compounds, homo and heterochiral dimers were found. The electron density of the complexes was characterized with the atoms-in-molecules (AIM) methodology, finding a large variety of interactions. The charge transfer within the dimers was analyzed by means of natural bond orbitals (NBO). The density functional theory-symmetry adapted perturbation theory (DFT-SAPT) method was used to compute the components of the interaction energies. Hydrogen bonds and chalcogen-chalcogen interactions were characterized and their influence analyzed concerning the stability and chiral discrimination of the dimers. PMID:22253208
S�nchez-Sanz, Goar; Trujillo, Cristina; Alkorta, Ibon; Elguero, Jos�
Center motions of nonoverlapping condensates coupled by long-range dipolar interaction in bilayer and multilayer stacks
We investigate the effect of anisotropic and long-range dipole-dipole interaction (DDI) on the center motions of nonoverlapping Bose-Einstein condensates in bilayer and multilayer stacks. In the bilayer, it is shown analytically that while DDI plays no role in the in-phase modes of center motions of condensates, out-of-phase mode frequency ({sub o}) depends crucially on the strength of DDI (a{sub d}).
Chao-Chun Huang; Wen-Chin Wu
We investigate the effect of anisotropic and long-range dipole-dipole interaction (DDI) on the center motions of nonoverlapping Bose-Einstein condensates in bilayer and multilayer stacks. In the bilayer, it is shown analytically that while DDI plays no role in the in-phase modes of center motions of condensates, out-of-phase mode frequency (omegao) depends crucially on the strength of DDI (ad). At the
Intramolecular and intermolecular ion�dipole interactions in sodium lauryl ether sulfates (SLES) self-aggregation and mixed micellization with Triton X-100
Micellization of a series of sodium lauryl ether sulfate (SLES), C12H25(OCH2CH2)xOSO3Na, where x=1 (CS130), 2 (CS230), and 3 (CS330) and their interaction with Triton X-100 in aqueous media were investigated by fluorescence quenching of (Ru(bipy)32+, 2Cl?) by 9-methylanthracene, conductivity, and surface tension measurements at room temperature. A similar critical micelle concentration (CMC) value of 0.80mM was found for the three
Mohamed Aoudia; Thurayia Al-Maamari; Fathiya Al-Salmi
The effect of dipolar interaction on the magnetic isotope effect
A multi-channel kinetic description is used to study the magnetic isotope effect (MIE) in zero magnetic field. The maximal isotope effect is equal to the number of channels, two for the hyperfine interaction but four for the electron spin dipole-dipole interaction of the intermediate radical pair. Quantum mechanical calculations agree with these conclusion and show that large MIE may be obtained even in the presence of a strong exchange interaction. The observed magnesium isotope effect on the rate of enzymatic synthesis of adenosine triphosphate (ATP) is approximately 3 implying that the dipolar interaction is responsible for the effect. Our calculations provide support for the proposed mechanism.
Pedersen, J. Boiden; Mojaza, Matin; Lukzen, Nikita N.
Anomalous behavior of spin systems with dipolar interactions.
We study the properties of spin systems realized by cold polar molecules interacting via dipole-dipole interactions in two dimensions. Using a spin wave theory, that allows for the full treatment of the characteristic long-distance tail of the dipolar interaction, we find several anomalous features in the ground state correlations and the spin wave excitation spectrum, which are absent in their counterparts with short-range interaction. The most striking consequence is the existence of true long-range order at finite temperature for a two-dimensional phase with a broken U(1) symmetry. PMID:23030175
Peter, D; M�ller, S; Wessel, S; B�chler, H P
Intermolecular potentials from shock structure experiments. [for monatomic gases
Ground-state intermolecular interaction potentials determined from shock structure experiments with four monatomic gases are reported. These potentials are assessed for self-consistency, using the law of corresponding states, and their suitability for engineering applications in rarefied gas dynamics is discussed.
Sturtevant, B.; Steinhilper, E. A.
Effect of intermolecular hydrogen bonding and proton transfer on fluorescence of salicylic acid
Effects of intermolecular interactions, in particular the influence of intermolecular hydrogen bonds formed by salicylic acid (SA) as a proton donor with proton acceptors of different strength, on fluorescence spectra of SA in non-aqueous solutions have been investigated. Infrared spectra of studied systems have been analyzed in order to elucidate the ground state structure of the complexes formed. It has
G. S. Denisov; N. S. Golubev; V. M. Schreiber; Sh. S. Shajakhmedov; A. V. Shurukhina
Intermolecular potentials for hexafluoride gases
Second virial coefficient and viscosity data were used to evaluate intermolecular potential functions proposed in the literature for SF{sub 6}, UF{sub 6}, and WF{sub 6}. It was found that none of the potentials could predict the properties simultaneously. By suitable adjustment of the repulsive wall, we constructed an inverse power (n{minus}7) potential which correlates second virial coefficient and viscosity data at the same time. The best integer repulsive exponent for SF{sub 6} was found to be n = 40, while that for UF{sub 6} and WF{sub 6} was n = 46. 41 refs., 10 figs., 11 tabs.
Aziz, R.A. (Waterloo Univ., ON (Canada). Dept. of Physics); Taylor, W.L. (EG and G Mound Applied Technologies, Miamisburg, OH (USA))
?-Stacking, C-H/?, and halogen bonding interactions in bromobenzene and mixed bromobenzene-benzene clusters.
Noncovalent interactions play an important role in many chemical and biochemical processes. Building upon our recent study of the homoclusters of chlorobenzene, where ?-? stacking and CH/? interactions were identified as the most important binding motifs, in this work we present a study of bromobenzene (PhBr) and mixed bromobenzene-benzene clusters. Electronic spectra in the region of the PhBr monomer S0-S1 (??*) transition were obtained using resonant two-photon ionization (R2PI) methods combined with time-of-flight mass analysis. As previously found for related systems, the PhBr cluster spectra show a broad feature whose center is red-shifted from the monomer absorption, and electronic structure calculations indicate the presence of multiple isomers and Franck-Condon activity in low-frequency intermolecular modes. Calculations at the M06-2X/aug-cc-pVDZ level find in total eight minimum energy structures for the PhBr dimer: four ?-stacked structures differing in the relative orientation of the Br atoms (denoted D1-D4), one T-shaped structure (D5), and three halogen bonded structures (D6-D8). The calculated binding energies of these complexes, corrected for basis set superposition error (BSSE) and zero-point energy (ZPE), are in the range of -6 to -24 kJ/mol. Time-dependent density functional theory (TDDFT) calculations predict that these isomers absorb over a range that is roughly consistent with the breadth of the experimental spectrum. To examine the influence of dipole-dipole interaction, R2PI spectra were also obtained for the mixed PhBr���benzene dimer, where the spectral congestion is reduced and clear vibrational structure is observed. This structure is well-simulated by Franck-Condon calculations that incorporate the lowest frequency intermolecular modes. Calculations find four minimum energy structures for the mixed dimer and predict that the binding energy of the global minimum is reduced by ~30% relative to the global minimum PhBr dimer structure. PMID:23978255
Reid, Scott A; Nyambo, Silver; Muzangwa, Lloyd; Uhler, Brandon
Quantum chemical investigation of the intra- and intermolecular proton transfer reactions and hydrogen bonding interactions in 4-amino-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione.
The intramolecular thione-thiol tautomerism and intermolecular double proton transfer reaction of the hydrogen-bonded thione and thiol dimers in the title triazole compound were studied at the B3LYP level of theory using 6-311++G(d,p) basis function. The influence of the solvent on the single and double proton transfer reactions was examined in three solvents (chloroform, methanol and water) using the polarizable continuum model (PCM) approximation. The computational results show that the thione tautomer is the most stable isomer with a very high tautomeric energy barrier both in the gas phase and in solution phase, indicating a quite disfavored process. The solvent effect is found to be sizable with increasing polarity. In the double proton transfer reaction, the thione dimer is found to be more stable than thiol dimer both in the gas phase and in solution phase. The energetic and thermodynamic parameters of the double proton transfer process show that the double proton exchange from thione dimer to thiol dimer is thermodynamically unfavored. However, the exchange from thiol dimer to thione dimer for the gas phase and water phase seems to be feasible with a low barrier height and with a negative value in enthalpy and free energy changes. In addition, the hydrogen bonding interactions were analyzed in the gas phase regarding their geometries and energies. It is found that all complex formations are enthalpically favored, and the stability of the H-bonds comes in the order of S1-H2���N2>N2-H2���S1>N3-H3B���O1. Finally, non-linear optical properties were carried out at the same calculation level in the gas phase. PMID:22940855
�zdemir, Nam?k
In any real magnetic system, weak anisotropic long-range dipole-dipole interactions are invariably present besides crystal-field\\u000a interactions and dominant isotropic short-range Heisenberg interactions (in insulating systems) or isotropic long-range Ruderman�Kittel�Kasuya�Yosida\\u000a (RKKY) interactions (in metallic systems) that couple the localized magnetic moments. In many magnetic systems, the dominant\\u000a interactions normally sustain long-range magnetic order and govern the ground state and finite-temperature magnetic
Spin radical enhanced magnetocapacitance effect in intermolecular excited states.
This article reports the magnetocapacitance effect (MFC) based on both pristine polymer MEH-PPV and its composite system doped with spin radicals (6R-BDTSCSB). We observed that a photoexcitation leads to a significant positive MFC in the pristine MEH-PPV. Moreover, we found that a low doping of spin radicals in polymer MEH-PPV causes a significant change on the MFC signal: an amplitude increase and a line-shape narrowing under light illumination at room temperature. However, no MFC signal was observed under dark conditions in either the pristine MEH-PPV or the radical-doped MEH-PPV. Furthermore, the magnitude increase and line-shape narrowing caused by the doped spin radicals are very similar to the phenomena induced by increasing the photoexcitation intensity. Our studies suggest that the MFC is essentially originated from the intermolecular excited states, namely, intermolecular electron-hole pairs, generated by a photoexcitation in the MEH-PPV. More importantly, by comparing the effects of spin radicals and electrically polar molecules on the MFC magnitude and line shape, we concluded that the doped spin radicals can have the spin interaction with intermolecular excited states and consequently affect the internal spin-exchange interaction within intermolecular excited states in the development of MFC. Clearly, our experimental results indicate that dispersing spin radicals forms a convenient method to enhance the magnetocapacitance effect in organic semiconducting materials. PMID:24144347
Zang, Huidong; Wang, Jianguo; Li, Mingxing; He, Lei; Liu, Zitong; Zhang, Deqing; Hu, Bin
Morphology and the Strength of Intermolecular Contact in Protein Crystals
The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.
Matsuura, Yoshiki; Chernov, Alexander A.
Desensitization and recovery of metastable intermolecular composites
Intermolecular dynamics in crystalline iron octaethylporphyrin (FeOEP).
The new technique of nuclear resonance vibrational spectroscopy (NRVS) has increased the range and quality of dynamical data from Fe-containing molecules that when combined with Raman and infrared spectroscopies impose stricter constraints on normal mode simulations, especially at lower frequencies. Going beyond the usual single molecule approximation, a classical normal-mode analysis that includes intermolecular coupling and the full crystalline symmetry is found to produce a better fit with fewer free parameters for the heme compound iron octaethylporphyrin (FeOEP), using NRVS data from polycrystalline material. Off-diagonal force constants were completely unnecessary, indicating that their role in previous single molecule fits was just to emulate intermolecular coupling. Sound velocities deduced from the calculated phonon dispersion curves are compared to NRVS measurements to further constrain the intermolecular force constants. The NRVS data by themselves are insufficient to rigorously determine all unknown force constants for molecules of this size, but the improved crystal model fit indicates the necessity of including intermolecular interactions for normal-mode analyses. PMID:18793016
Starovoitova, Valeriia; Wyllie, Graeme R A; Scheidt, W Robert; Sturhahn, Wolfgang; Alp, E Ercan; Durbin, Stephen M
Conformations and intermolecular interactions pattern in solid chloroxylenol and triclosan (API of anti-infective agents and drugs). A (35) Cl NQR, (1) H-(14) ?N NQDR, X-ray and DFT/QTAIM study.
Two antibacterial and antifungal agents, chloroxylenol (4-chloro-3,5-dimethyl-phenol) and triclosan (5-chloro-2-(2',4'-dichlorophenoxy)-phenol), were studied experimentally in solid state with an X-ray, (35) Cl-nuclear quadrupole resonance (NQR) and (17) O-nuclear quadrupole double resonance (NQDR) spectroscopies and, theoretically, with the density functional theory/quantum theory of atoms in molecules (DFT/QTAIM). The crystallographic structure of triclosan, which crystallises in space group P3(1) with one molecule in the asymmetric unit [a?=?12.64100(10), b?=?12.64100(10), c = 6.71630(10) �], was solved with an X-ray and refined to a final R-factor of 2.81% at room temperature. The NQR frequencies of (35) Cl and (17) O were detected with the help of the density functional theory (DFT) assigned to particular chlorine and oxygen sites in the molecules of both compounds. The NQR frequencies at (35) Cl sites in chloroxylenol and triclosan were found to be more differentiated than frequencies at the (17) O site. The former better describes the substituent withdrawing effects connected to ?-electron delocalization within the benzene rings and the influence of temperature; whereas, those at the (17) O site provide more information on O-H bond and intermolecular interactions pattern. The conformation adopted by diphenyl ether of triclosan in solid state was found to be typical of diphenyl ethers, but the opposite to those adopted when it was bound to different inhibitors. According to an X-ray study, temperature had no effect on the conformation of the diphenyl ring of triclosan, which was the same at 90?K and at room temperature (RT). The scattering of NQR frequencies reproduced by the DFT under assumption of the X-ray data at 90?K and RT is found to be a good indicator of the quality of resolution of the crystallographic structure. Copyright � 2012 John Wiley & Sons, Ltd. PMID:22354770
Latosi?ska, J N; Latosi?ska, M; Tomczak, M A; Seliger, J; Zagar, V; Maurin, J K
Intermolecular domain docking in the hairpin ribozyme
The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodynamics and kinetics of the docking process using constructs in which loop A and loop B reside on separate molecules. Using a novel CD difference assay to isolate the effects of metal ions linked to domain docking, we find the intermolecular docking process to be driven by sub-millimolar concentrations of the exchange-inert Co(NH3)63+. RNA self-cleavage requires binding of lower-affinity ions with greater apparent cooperativity than the docking process itself, implying that, even in the absence of direct coordination to RNA, metal ions play a catalytic role in hairpin ribozyme function beyond simply driving loop-loop docking. Surface plasmon resonance assays reveal remarkably slow molecular association, given the relatively tight loop-loop interaction. This observation is consistent with a �double conformational capture� model in which only collisions between loop A and loop B molecules that are simultaneously in minor, docking-competent conformations are productive for binding.
Sumita, Minako; White, Neil A.; Julien, Kristine R.; Hoogstraten, Charles G.
Direct evidence of three-body interactions in a cold {sup 85}Rb Rydberg gas
Cold Rydberg atoms trapped in a magneto-optical trap (MOT) are not isolated and they interact through dipole-dipole and multipole-multipole interactions. First-order dipole-dipole interactions and van der Waals interactions between two atoms have been intensively studied. However, the facts that the first-order dipole-dipole interactions and van der Waals interactions show the same size of broadening [A. Reinhard, K. C. Younge, T. C. Liebisch, B. Knuffman, P. R. Berman, and G. Raithel, Phys. Rev. Lett. 100, 233201 (2008)] and there are transitions between two dimer states [S. M. Farooqi, D. Tong, S. Krishnan, J. Stanojevic, Y. P. Zhang, J. R. Ensher, A. S. Estrin, C. Boisseau, R. Cote, E. E. Eyler, and P. L. Gould, Phys. Rev. Lett. 91, 183002 (2003); K. R. Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. A 76, 011403(R) (2007)] cannot be explained by the two-atom picture. The purpose of this article is to show the few-body nature of a dense cold Rydberg gas by studying the molecular-state microwave spectra. Specifically, three-body energy levels have been calculated. Moreover, the transition from three-body energy levels to two-body coupled molecular energy levels and to isolated atomic energy levels as a function of the internuclear spacing is studied. Finally, single-body, two-body, and three-body interaction regions are estimated according to the experimental data. The results reported here provides useful information for plasma formation, further cooling, and superfluid formation.
Han Jianing [Department of Physics, University of Virginia, Charlottesville, Virginia 22904 (United States)
Intramolecular chalcogen-tin interactions in [(o-MeE-C6H4)CH2]2SnPh2-nCln; E = S, O, CH2, n = 0, 1, 2 and intermolecular chlorine-tin interactions in the meta and para-methoxy isomers
Organotin(IV) compounds of the type [(o-MeE-C6H4)CH2]2SnPh2-nCln were synthesized, E = O, n = 0 (1), n = 1 (2), n = 2 (3), E = S, n = 0 (4), n = 1 (5), n = 2 (6) and E = CH2, n = 0 (7), n = 1 (8), n = 2 (9). The dichloro compounds 3 and 6 have been investigated by single crystal X-ray diffraction and exhibit bi-capped tetrahedral geometry at the tin atom as a consequence of significant intramolecular Sn?O (3) and Sn?S (6) secondary bonding, in monomolecular units. Compound 3 when crystallized from a hexane/thf solvent mixture shows two different conformers, 3? and 3?, in the crystal structure, 3? has two equivalent Sn?O interactions, while 3? has two non-equivalent Sn?O interactions. Upon recrystallization of 3 from hexane only a single structural form is observed, 3?. The Sn?E distances in 3?, 3?, and 6 are 71.3; 73.5, 72.9; and 76.3% of the ?vdW radii, respectively. The meta and para-substituted isomers of 3 (10, 11) exhibit a distortion at the tin atom due to self-association via intermolecular Sn?Cl interactions resulting in polymeric structures. 119Sn NMR spectroscopy suggests that the intramolecular Sn?E interactions persist in solution for the dichloride compounds 3 and 6.
Vargas-Pineda, Diana Gabriela; Guardado, Tanya; Cervantes-Lee, Francisco; Metta-Magana, Alejandro J.
Tunable high-temperature thermodynamics of weakly interacting dipolar gases
We consider dilute gases of dipolar bosons or fermions in the high-temperature limit in a spherically symmetric harmonic trapping potential. We examine the system using a virial expansion up to second order in the fugacity. Using the Born approximation and assuming purely dipolar interactions, we find that the second-order virial coefficient for both bosons and fermions depends quadratically on the dipole length and is negative at high temperatures, indicating that to lowest order in the dipole-dipole interactions the dipolar single-component quantum gases are repulsive. If the s-wave scattering length for the bosonic system is tunable and its absolute value is made small, then the s-wave interactions dominate and the dipolar gas behaves like a weakly interacting Bose gas with isotropic s-wave interactions. If the generalized scattering lengths for the fermionic system are tunable, then the dipole length can enter linearly in the virial equation of state, enhancing the dipole-dipole effects in the thermodynamic observables.
Daily, K. M.; Blume, D.
The role of directed van der Waals bonded interactions in the determination of the structures of molecular arsenate solids
On the basis of his famous electrostatic theorem, Feynman (1939) showed that it is not the fluctuating dipole- dipole interactions among neighboring molecules that lead to van der Waals forces, but rather it is the net attraction of the nuclei for the distorted electron density, ED, accumulated between the nuclei of bonded atoms that accounts for the van der Waals R-7 forces. Bader and his coworkers (1990) have since concluded that the distortions in the internuclear region arise by dint of the formation of local maxima and minima of the Laplacian distribution, L(r) = ?2?(r), with the formation of van der Waals bond paths associated with the maxima and minima. The maxima are ascribed to Lewis base domains where the ED is locally charge concentrated, CC, whereas the minima are ascribed to Lewis acid domains where the ED is locally charge depleted, CD. For the As2O3 molecular crystals arsenolite, claudetite I and claudetite II, AsO2 and the As- metalloid, arsenolamprite, the ED of the constituent molecules were found to adopt a configuration where the Lewis acid and base domains of molecules are aligned and connected by As-O, O-O and As-As van der Waals intermolecular bond paths. Despite the relative weakness of the van der Waals bonded interactions relative to the intramolecular As-O bonded interactions, the interactions are concluded to serve as mainstays for the individual molecules in each of the molecular solids. Intermolecular As-O bond paths between the bonded atoms connect Lewis base CC and Lewis acid CD domains whereas the O-O and As-As paths connect Lewis base-pair CC-CC domains and Lewis acid pair CD-CD domains, respectively, give rise to sets of directed van der Waals bond paths. The alignment of the bond paths, like any other bond path, results in the periodic structures adopted by the molecules in the arsenates. The cubic structure adopted by arsenolite polymorph can be understood in terms of sets of As-O and O-O directed bond paths that radiate from the tetrahedral faces of its constituent molecules, serving as face-to-face Fischer key-lock mainstays in forming a periodic tetrahedral array of molecules. The arrangements of the As atoms in the claudetite polymorphs of As2O3 and those in the As metalloid arsenolamprite are similar. The arrangement of the molecules in the thiosulfides realgar, AsS, alancranite, AsS, ?-dimorphite, As4S3 and uzonite, As4S5 can also be understood in terms of the Lewis domains and the van der Waals bond paths that radiate from the faces of the constituient molecules. Like the two clausetite polymorphs, arsenolamprite is a molecular solid bound by relatively weak intermolecular van der Waals bonded interactions. The bond critical point and local energy density properties of the intermolecular As-As interactions in arsenolamprite are comparable with those in claudetite I. As such, the structure of claudetite I can be viewed in large part as a stuffed derivative of the arsenolamprite structure with O atoms between pairs of As atoms comprising the layers of the structure.
Gibbs, G. V.; Wallace, A. F.; Cox, D. F.; Dove, P. M.; Downs, R. T.; Ross, N. L.; Rosso, K. M.
Intermolecular potential energy surface of the water-carbon dioxide complex
A complete intermolecular potential energy surface (PES) of the H2O-CO2 complex has been constructed using a large scale ab initio calculations. This PES was sampled at 23 000 points of a five dimensional configuration space of the intermolecular coordinates. The interaction energy was calculated using the second order M�ller-Plesset perturbation method in conjunction with the standard aug-cc-pVTZ basis set supplemented
Jan Makarewicz
Anisotropic and Long-Range Vortex Interactions in Two-Dimensional Dipolar Bose Gases
We perform a theoretical study into how dipole-dipole interactions modify the properties of superfluid vortices within the context of a two-dimensional atomic Bose gas of co-oriented dipoles. The reduced density at a vortex acts like a giant antidipole, changing the density profile and generating an effective dipolar potential centred at the vortex core whose most slowly decaying terms go as 1/?2 and ln?(?)/?3. These effects modify the vortex-vortex interaction which, in particular, becomes anisotropic for dipoles polarized in the plane. Striking modifications to vortex-vortex dynamics are demonstrated, i.e., anisotropic corotation dynamics and the suppression of vortex annihilation.
Mulkerin, B. C.; van Bijnen, R. M. W.; O'Dell, D. H. J.; Martin, A. M.; Parker, N. G.
Interactions between Rydberg-dressed atoms
We examine interactions between atoms continuously and coherently driven between the ground state and a Rydberg state, producing 'Rydberg-dressed atoms'. Because of the large dipolar coupling between two Rydberg atoms, a small admixture of Rydberg character into a ground state can produce an atom with a dipole moment of a few debye, the appropriate size to observe interesting dipolar physics effects in cold atom systems. We have calculated the interaction energies for atoms that interact via the dipole-dipole interaction and find that because of blockade effects, the R dependent two-atom interaction terms are limited in size and can be R independent up until the dipolar energy is equal to the detuning. This produces R dependent interactions different from the expected 1/R{sup 3} dipolar form that have no direct analogy in condensed-matter physics and could lead to interesting quantum phases in trapped Rydberg systems.
Johnson, J. E.; Rolston, S. L. [Joint Quantum Institute, Department of Physics, University of Maryland (United States) and National Institute of Standards and Technology, College Park, Maryland 20742-4111 (United States)
Interparticle interactions in magnetic core/shell nanoarchitectures
Magnetic and M�ssbauer measurements are reported on single-crystalline monodispersed ?-Fe2O3 nanoparticles of 12.5 nm diameter, coated with multiple silica and mesoporous silica layers of various thicknesses. The high crystallinity and monodispersity of the samples allow resolution of the tetrahedral (A) and octahedral [B] iron sites of the spinel structure of maghemite. The precisely tuned silica coating thickness offers controlled, homogeneous magnetic dilution with the sample magnetic volume fraction ranging from 1 to 0.002, leading to various degrees of interparticle dipole-dipole interaction strength. Analysis of the zero-field-cooled magnetization data shows that dipole-dipole interactions increase the superparamagnetic energy barrier. The relevant magnetic parameters, for both the individual particles (Keff) and the particle assemblies (Uint) , are determined within the framework of weak and strong dipolar-interaction models. At low temperatures, the steepness of the magnetic hyperfine field reduction with increasing temperature in the strongly interacting particle assemblies is examined within the context of the collective magnetic-excitations model.
Papaefthymiou, Georgia C.; Devlin, Eamonn; Simopoulos, Athanassios; Yi, Dong Kee; Riduan, Siti Nurhanna; Lee, Su Seong; Ying, Jackie Y.
Interaction between two spherical particles in a nematic liquid crystal
We numerically investigate the interaction between two spherical particles in a nematic liquid crystal mediated by elastic distortions in the orientational order. We pay attention to the cases where two particles with equal radii R0 impose rigid normal anchoring on their surfaces and carry a pointlike topological defect referred to as a hyperbolic hedgehog. To describe the geometry of our system, we use bispherical coordinates, which prove useful in the implementation of boundary conditions at the particle surfaces and at infinity. We adopt the Landau de Gennes continuum theory in terms of a second-rank tensor order parameter Qij for the description of the orientational order of a nematic liquid crystal. We also utilize an adaptive mesh refinement scheme that has proven to be an efficient way of dealing with topological defects whose core size is much smaller than the particle size. When the two �dipoles,� composed of a particle and a hyperbolic hedgehog, are in parallel directions, the two-particle interaction potential is attractive for large interparticle distances D and proportional to D-3 as expected from the form of the dipole-dipole interaction, until the well-defined potential minimum at D?2.46 R0 is reached. For the antiparallel configuration with no hedgehogs between the two particles, the interaction potential is repulsive and behaves as D-2 for D?10 R0 , which is stronger than the dipole-dipole repulsion ( � D-3 ) expected theoretically as an asymptotic behavior for large D .
Fukuda, Jun-Ichi; Stark, Holger; Yoneya, Makoto; Yokoyama, Hiroshi
Rh-Catalyzed Intermolecular Reactions of Cyclic ?-Diazocarbonyl Compounds with Selectivity Over Tertiary C-H Bond Migration
Intermolecular Rh-catalyzed reactions of cyclic ?-diazocarbonyl compounds with chemoselectivity over ?-hydride elimination are described. These methods represent the first general intermolecular reactions of Rh-carbenoids that are selective over tertiary ?-C?H bond migration. Successful transformations include cyclopropanation, cyclopropenation, and various X�H insertion reactions with a broad scope of substrates. We propose that the intermolecular approach of substrates to carbenes from acyclic diazo precursors may be relatively slow due to a steric interaction with the ester function, which is perpendicular to the ?-system of the carbene. For carbenes derived from 5- and 6-membered cyclic ?-diazocarbonyls, it is proposed that the carbene is constrained to be more conjugated with the carbonyl, thereby relieving the steric interaction for intermolecular reactions, and accelerating the rate of intermolecular reactivity relative to intramolecular ?-hydride migration. However, attempts to use ?-diazo-?-ethylcaprolactone in intermolecular cyclopropanation with styrene were unsuccessful. It is proposed that the conformational flexibility of the 7-membered ring allows the carbonyl to be oriented perpendicular to Rh-carbene. The significant intermolecular interaction between the carbonyl and approaching substrate is in agreement with the poor ability of ?-diazo-?-ethylcaprolactone to participate in intermolecular cyclopropanation reactions. DFT calculations provide support for the mechanistic proposals that are described.
DeAngelis, Andrew; Dmitrenko, Olga; Fox, Joseph M.
Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity
This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine ?-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 � 0.2) � 105 M-1] is similar to the value for the PA [(3.8 � 0.1) � 105 M-1]; Ka for 3-OHPA [(1.1 � 0.3) � 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 � 0.2) � 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.
Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.
Energetics of intermolecular hydrogen bonds in a hydrophobic protein cavity.
This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the ?7 charge state) of complexes of bovine ?-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)(7�) ions, compared with that of the (Lg + PA)(7�) ion, it is concluded that the �OH groups of the X-OHPA ligands participate in strong (5 � 11 kcal mol(�1)) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the �OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the �OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 � 0.2) � 10(5) M(�1)] is similar to the value for the PA [(3.8 � 0.1) � 10(5) M(�1)]; Ka for 3-OHPA [(1.1 � 0.3) � 10(6) M(�1)] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 � 0.2) � 10(4) M(�1)] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand �OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds. PMID:24658798
Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N; Schnier, Paul D; Klassen, John S
1H-13C hetero-nuclear dipole-dipole couplings of methyl groups in stationary and magic angle spinning solid-state NMR experiments of peptides and proteins
13C NMR of isotopically labeled methyl groups has the potential to combine spectroscopic simplicity with ease of labeling for protein NMR studies. However, in most high resolution separated local field experiments, such as polarization inversion spin exchange at the magic angle (PISEMA), that are used to measure 1H�13C hetero-nuclear dipolar couplings, the four-spin system of the methyl group presents complications. In this study, the properties of the 1H�13C hetero-nuclear dipolar interactions of 13C-labeled methyl groups are revealed through solid-state NMR experiments on a range of samples, including single crystals, stationary powders, and magic angle spinning of powders, of 13C3 labeled alanine alone and incorporated into a protein. The spectral simplifications resulting from proton detected local field (PDLF) experiments are shown to enhance resolution and simplify the interpretation of results on single crystals, magnetically aligned samples, and powders. The complementarity of stationary sample and magic angle spinning (MAS) measurements of dipolar couplings is demonstrated by applying polarization inversion spin exchange at the magic angle and magic angle spinning (PISEMAMAS) to unoriented samples.
Wu, Chin H.; Das, Bibhuti B.; Opella, Stanley J.
Inelastic x-ray scattering of dense solid oxygen: Evidence for intermolecular bonding
The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O2 molecules interact predominantly through the half-filled 1?g* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1?g* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O2 molecules at the transition to the ?-phase. The ?-phase, which consists of (O2)4 clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O2)4 clusters develop upon compression of the ?-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.
Meng, Yue; Eng, Peter J.; Tse, John S.; Shaw, Dawn M.; Hu, Michael Y.; Shu, Jinfu; Gramsch, Stephen A.; Kao, Chichang; Hemley, Russell J.; Mao, Ho-kwang
Theory of elastic interaction of colloidal particles in nematic liquid crystals near one wall and in the nematic cell
We apply the method developed [Chernyshuk and Lev, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 81, 041701 (2010)] for theoretical investigation of colloidal elastic interactions between axially symmetric particles in the confined nematic liquid crystal near one wall and in the nematic cell with thickness L. Both cases of homeotropic and planar director orientations are considered. Particularly, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions of the one particle with the wall and within the nematic cell are found as well as corresponding two particle elastic interactions. A set of results has been predicted: The effective power of repulsion between two dipole particles at height h near the homeotropic wall is reduced gradually from inverse 3 to 5 with an increase of dimensionless distance r/h; near the planar wall, the effect of dipole-dipole isotropic attraction is predicted for large distances r>rdd=4.76h; maps of attraction and repulsion zones are crucially changed for all interactions near the planar wall and in the planar cell; and one dipole particle in the homeotropic nematic cell was found to be shifted by the distance ?eq from the center of the cell. The proposed theory fits very well with experimental data for the confinement effect of elastic interaction between spheres in the homeotropic cell [Vilfan , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.101.237801 101, 237801 (2008)] in the range 1-1000 kT. The influence of the K24 and K13 terms as well as connection with other theoretical approaches are discussed.
Chernyshuk, S. B.; Lev, B. I.
Quantum phases of a dipolar Bose-Einstein condensate in an optical lattice with three-body interaction
We investigate the quantum phases of a dipolar Bose-Einstein condensate (BEC) in an optical lattice based on the extended Bose-Hubbard model taking into account the three-body scattering. Accordingly, the phase diagrams from the superfluid state to the Mott-insulator state for such BEC systems are obtained and analyzed, employing both the mean-field approach and the functional-integral method. In particular, we explore the combined effects of three-body interaction and dipole-dipole interaction on the insulating lobes in detail. The experimental scenario is also discussed.
Zhou Kezhao; Liang Zhaoxin; Zhang Zhidong [Shenyang National Laboratory for Materials Science, Institute of Metal Research, and International Centre for Materials Physics, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016 (China)
Using path integrals and the theory of polarizable fluids, we develop a model treating non-degenerate interacting Fr�hlich polarons at low densities and temperatures. Starting from the dilute regime, we show that at strong electron-phonon coupling, the collective properties of polarons are mainly governed by the London dispersion forces, i.e. induced dipole-dipole van der Waals interactions. At a critical density, these forces provoke a non-metal-to-metal transition by means of a polarization catastrophe and a mechanical instability, which results in a polaron dissociation.
Qu�merais, P.; Chuev, G. N.
Electromagnetic interaction of split-ring resonators: The role of separation and relative orientation.
Extinction cross-section spectra of split-ring-resonator dimers have been measured at near-infrared frequencies with a sensitive spatial modulation technique. The resonance frequency of the dimer's coupled mode as well as its extinction cross-section and its quality factor depend on the relative orientation and separation of the two split-ring resonators. The findings can be interpreted in terms of electric and magnetic dipole-dipole interaction. Numerical calculations based on a Discontinuous Galerkin Time-Domain approach are in good agreement with the experiments and support our physical interpretation. PMID:20389678
Feth, Nils; K�nig, Michael; Husnik, Martin; Stannigel, Kai; Niegemann, Jens; Busch, Kurt; Wegener, Martin; Linden, Stefan
Intermolecular Forces and Solvent Effects. III
The shifts of frequency of two vibration bands of carbon dioxide in different solvents have been measured. The results cannot be explained satisfactorily in terms of the simple model of an oscillator in a continuous dielectric medium, but suggest that intermolecular forces are dominant. In non-polar solvents dispersion forces appear to account very well for the observed shifts, and attempts
C. Heald; H. W. Thompson
An improved intermolecular potential for sulfur hexafluoride
Second virial coefficient data and viscosity were used to evaluate effective isotropic intermolecular potential functions proposed in the literature for sulfur hexafluoride. It was found that none of the potentials could predict the properties simultaneously. We have constructed a Morse--Morse--Spline--van der Waals (MMSV) potential which satisfactorily correlates second virial coefficient and viscosity data at the same time.
Aziz, R.A.; Slaman, M.J. (Department of Physics, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1 (US)); Taylor, W.L.; Hurly, J.J. (EG G Mound Applied Technologies, Inc., Miamisburg, Ohio 45343 (US) Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221 (US))
Catalytic intermolecular alkene oxyamination with nitrenes.
The Rh(II) -catalyzed intermolecular addition of nitrenes to aromatic and aliphatic alkenes provides vicinal amino alcohols with yields of up to 95?% and complete regioselectivity. This 1,2-oxyamination reaction involves the formation of an aziridine intermediate that undergoes in situ ring opening. The latter is induced by the Rh-bound nitrene that behaves as a Lewis acid. PMID:24939636
Dequirez, Geoffroy; Ciesielski, Jennifer; Retailleau, Pascal; Dauban, Philippe
Thermodynamic curvature for attractive and repulsive intermolecular forces.
The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential. PMID:24125229
May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George
Thermodynamic curvature for attractive and repulsive intermolecular forces
The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential.
Interaction potential for indium phosphide: a molecular dynamics and first-principles study of the elastic constants, generalized stacking fault and surface energies.
Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two-�and three-body terms that represent atomic-size effects, charge-charge, charge-dipole and dipole-dipole interactions as well as covalent bond bending and stretching. Predictions are made for the elastic constants as a function of density and temperature, the generalized stacking fault energy and the low-index surface energies. PMID:21817375
Branicio, Paulo Sergio; Rino, Jos� Pedro; Gan, Chee Kwan; Tsuzuki, H�lio
Intermolecular Michael Reactions: A Computational Investigation
Computational studies have suggested that ?3-lithium enolates in which the cation is partially bound to both carbon and oxygen may be important reactive intermediates. DFT calculations are used to demonstrate that explicitly solvated acetone enolates are largely O-bound. With this premise in mind, the stereochemical course of intermolecular Michael additions is examined. The results are generally consistent with what is observed experimentally and the model advanced by Heathcock and coworkers.
Kwan, Eugene E.; Evans, David A.
Copper-catalyzed intermolecular aminoazidation of alkenes.
Copper-catalyzed intermolecular aminoazidation of alkenes is described. This novel methodology provides an efficient approach to vicinal amino azides which can easily be transformed into other valuable amine derivatives. The commercially available N-fluorobenzenesulfonimide (NFSI) is used as a nitrogen-radical precursor and TMSN3 as the N3 source. Yields are moderate to excellent, and for internal alkenes aminoazidation occurs with excellent diastereoselectivity. PMID:24588747
Zhang, Bo; Studer, Armido
Iron-catalyzed intermolecular hydroamination of styrenes.
An iron-catalyzed formal hydroamination of alkenes has been developed. It features O-benzoyl-N,N-dialkylhydroxylamines as the electrophilic nitrogen source and cyclopentylmagnesium bromide as the reducing agent for intermolecular hydroamination of styrene and derivatives with good yield and excellent Markovnikov regioselectivity. The reaction presumably proceeds through the iron-catalyzed hydrometalation of styrene followed by electrophilic amination with the electrophilic O-benzoylhydroxylamine. PMID:24983840
Huehls, C Bryan; Lin, Aijun; Yang, Jiong
Intermolecular diatomic energies of a hydrogen dimer with non-Born-Oppenheimer nuclear and electron wave packets
We have developed an efficient theoretical framework of a non-Born-Oppenheimer (non-BO) nuclear and electron wave packet (NWP and EWP) method and applied it to intra- and intermolecular energies of a hydrogen dimer. The energy surface functions were derived at low computational cost. In contrast with the ordinary BO nuclear quantization on a given energy surface that reduces the effective barrier, non-trivial non-BO interactions between the EWPs and NWPs resulted in increases of intermolecular rotational and translational barriers. A direct comparison demonstrated that the non-BO effect on the intermolecular energy is significant.
Hyeon-Deuk, Kim; Ando, Koji
Effects of intermolecular interactions, in particular the influence of intermolecular hydrogen bonds formed by salicylic acid (SA) as a proton donor with proton acceptors of different strength, on fluorescence spectra of SA in non-aqueous solutions have been investigated. Infrared spectra of studied systems have been analyzed in order to elucidate the ground state structure of the complexes formed. It has been found that at the room temperature in dilute solutions in non-polar or slightly polar aprotic solvents, where the SA molecule is not involved in intermolecular hydrogen bonding, the position of the main (blue) fluorescence component is determined by the excited state intramolecular proton transfer (ESIPT) in the lowest singlet excited state S 1. With increasing proton acceptor ability of the environment, when formation of weak or middle strength intermolecular H-bonds is possible, the emission band shifts gradually to lower frequency, the quantum yield falls and poorly resolved doublet structure becomes more pronounced, especially in the solvents containing heavy bromine atoms. As a possible reason for these effects, coupling between the S 1 and closely lying triplet term is considered. With the strongest proton acceptors like aliphatic amines, intermolecular proton transfer with ionic pair formation in the ground state and double (intra- and intermolecular) proton transfer in the excited state take place, resulting in a blue shift of the emission band. Similar emission is typical for the SA anion in aqueous solutions. The p Ka value of SA in S 1 state has been found to be 3.1. Such a small value can be explained taking into account the ESIPT reaction following the excitation. The SA complex with pyridine exhibits emission spectrum containing both molecular-like and anion-like bands with relative intensities strongly dependent on the temperature and solvent properties. The most probable origin of this dual emission is the molecular-ionic tautomerism caused by the existence of two potential minima and reversible intermolecular proton transfer in the excited state.
Denisov, G. S.; Golubev, N. S.; Schreiber, V. M.; Shajakhmedov, Sh. S.; Shurukhina, A. V.
He-, Ne-, and Ar-phosgene intermolecular potential energy surfaces.
Using the CCSD(T) model, we evaluated the intermolecular potential energy surfaces of the He-, Ne-, and Ar-phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and double augmented (Ne and Ar complexes) correlation-consistent polarized valence triple-? basis sets extended with a set of 3s3p2d1f1g midbond functions. These basis sets were selected after systematic basis set studies carried out at geometries close to those of the surface minima. The He-, Ne-, and Ar-phosgene surfaces were found to have absolute minima of -72.1, -140.4, and -326.6 cm(-1) at distances between the rare-gas atom and the phosgene center of mass of 3.184, 3.254, and 3.516 �, respectively. The potentials were further used in the evaluation of rovibrational states and the rotational constants of the complexes, providing valuable results for future experimental investigations. Comparing our results to those previously available for other phosgene complexes, we suggest that the results for Cl2-phosgene should be revised. PMID:23617631
Munteanu, Cristian R; Henriksen, Christian; Felker, Peter M; Fern�ndez, Berta
Theoretically inspired nano-engineering of complex photonic media
The macroscopic electro-optic activity of organic materials is linearly related to molecular first hyperpolarizability of individual chromophores, chromophore number density, and the acentric order parameter describing chromophore order. When strong chromophore-chromophore intermolecular electrostatic interactions (e.g., dipole-dipole interactions) are present, the latter two quantities are not independent. In previous publications, we have demonstrated how electro-optic activity can be systematically improved by
Larry Dalton; Yi Liao; Philip Sullivan; Bruce Robinson
Quantum Hall effects in fast-rotating Fermi gases with anisotropic dipolar interaction
We investigate fast rotating quasi-two-dimensional dipolar Fermi gases in the quantum Hall regime. By tuning the direction of the dipole moments with respect to the z axis, the dipole-dipole interaction becomes anisotropic in the x-y plane. For a soft confining potential we find that, as we tilt the angle of the dipole moments, the system evolves from a {nu}=1/3 Laughlin state with dipoles being polarized along the z axis to a series of ground states characterized by distinct mean total angular momentum, and finally to an anisotropic integer quantum Hall state. During the transition from the fractional regime to the integer regime, we find that the density profile of the system exhibits crystal-like structures. We map out the ground states as a function of the tilt angle and the confining potential, revealing the competition of the isotropic confining potential and both the isotropic and anisotropic components of the dipole-dipole interaction.
Qiu, R.-Z.; Yi, S. [Key Laboratory of Frontiers in Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190 (China); Kou, Su-Peng [Department of Physics, Beijing Normal University, Beijing 100875 (China); Hu, Z.-X. [Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Wan Xin [Zhejiang Institute of Modern Physics, Zhejiang University, Hangzhou 310027 (China)
Limits on Exotic Long-Range Spin-Spin Interactions of Electrons
We surrounded a rotating torsion pendulum containing 9.8�1022 polarized electrons by 2 or 4 stationary sources, each with a net spin of 6.0�1024 polarized electrons. Multiple source configurations gave sensitivity to hypothetical dipole-dipole, spin-dot-spin, and spin-cross-spin exchange interactions mediated by bosons with masses up to 20?eV. For bosons with masses ?0.1?eV our null results for the dipole-dipole, spin-dot-spin, and spin-cross-spin forces imply 1? upper limits on (gPe)2/(?c), (gAe)2/(?c) and (gVegAe)/(?c) of 2.2�10-16, 3.8�10-40, and 1.2�10-28, respectively. We also constrain, for the first time, any possible linear combination of static spin-spin interactions. In this case our upper limits relax to 5.6�10-16, 9.8�10-40, and 1.2�10-28, respectively.
Heckel, B. R.; Terrano, W. A.; Adelberger, E. G.
Digital communication through intermolecular fluorescence modulation.
[see reaction]. Ultraminiaturized processors incorporating molecular components can be developed only after devising efficient strategies to communicate signals at the molecular level. We have demonstrated that a three-state molecular switch responds to ultraviolet light, visible light, and H+, attenuating the emission intensity of a fluorescent probe. Intermolecular communication is responsible for the transduction of three input signals into a single optical output. The behavior of the communicating ensemble of molecules corresponds to that of a logic circuit incorporating seven gates. PMID:11405723
Raymo, F M; Giordani, S
Intermolecular hybridization governs molecular electrical doping.
Current models for molecular electrical doping of organic semiconductors are found to be at odds with other well-established concepts in that field, like polaron formation. Addressing these inconsistencies for prototypical systems, we present experimental and theoretical evidence for intermolecular hybridization of organic semiconductor and dopant frontier molecular orbitals. Common doping-related observations are attributed to this phenomenon, and controlling the degree of hybridization emerges as a strategy for overcoming the present limitations in the yield of doping-induced charge carriers. PMID:22400758
Salzmann, Ingo; Heimel, Georg; Duhm, Steffen; Oehzelt, Martin; Pingel, Patrick; George, Benjamin M; Schnegg, Alexander; Lips, Klaus; Blum, Ralf-Peter; Vollmer, Antje; Koch, Norbert
Intermolecularly Hydrogen-Bonded Dimeric Helices. Tripyrrindiones
A rare and unusual class of tripyrrolic compounds, violet-colored tripyrrin-1,14-diones, can be prepared easily and in moderately high yields from base (piperidine)-catalyzed condensation of 3-pyrrolin-2-ones with 2,5-diformylpyrroles. Dipyrrinones adopt the all syn-Z conformation leading to helical, lock-washer like structures, which form dimers that are held together by intermolecular hydrogen bonds in nonpolar solvents and in the crystal. Strong bathochromic spectral shifts of the tripyrrindione ?480 nm long wavelength UV-visible absorption band are seen with added base: DBU, 615 nm; TFA, 573 nm; and Zn (OAc)2, 586 nm.
Roth, Steven D.; Shkindel, Tetyana; Lightner, David A.
Inter-molecular correlations in liquid Se2Br2
The structure of molecular liquid Se2Br2 was analyzed by means of reverse Monte Carlo structural modeling, using a calculation based on high-energy x-ray diffraction data. It was found that, between the optical isomers of L and D types, the number of L-D neighboring molecular pairs increases, while that of the L-L and D-D pairs decreases with increasing temperature. From this temperature dependence and from the relaxation mode analysis of quasi-elastic neutron scattering spectra, it is reasonable to assume that the presence of L-D pairs relates to genuine inter-molecular interactions while the L-L and D-D pairs appear due to geometrical packing of the gauche-shaped molecules.
Shimakura, Hironori; Kawakita, Yukinobu; Ohara, Koji; Pusztai, L�szl�; Wakisaka, Yuiko; Takeda, Shin'ichi
Quantum phases of strongly interacting Rydberg atoms in triangular lattices
We present a theoretical study on the system of laser-driven strongly interacting Rydberg atoms trapped in a two-dimensional triangular lattice, in which the dipole-dipole interactions between Rydberg states result in exotic quantum phases. By using the mean-field theory, we investigate the steady state solutions and analyze their dynamical stabilities. We find that in the strong-interaction limit, the dynamics of the system is chaotic and exhibits random oscillations under appropriate laser detunings. The Lyapunov exponent criterion is introduced to confirm the existence of this chaotic behavior. In addition, we present a full quantum calculation based on a six-atom model, and find that the system exhibits some biantiferromagnetic properties in every triangular cell when the one-photon detuning is exactly resonant or blue shifted.
Qian, Jing; Zhou, Lu; Zhang, Weiping
Genome-wide expression profiling and mutagenesis studies reveal that lipopolysaccharide responsiveness appears to be absolutely dependent on TLR4 and MD-2 expression and is dependent upon intermolecular ionic interactions.
Lipid A (a hexaacylated 1,4' bisphosphate) is a potent immune stimulant for TLR4/MD-2. Upon lipid A ligation, the TLR4/MD-2 complex dimerizes and initiates signal transduction. Historically, studies also suggested the existence of TLR4/MD-2-independent LPS signaling. In this article, we define the role of TLR4 and MD-2 in LPS signaling by using genome-wide expression profiling in TLR4- and MD-2-deficient macrophages after stimulation with peptidoglycan-free LPS and synthetic Escherichia coli lipid A. Of the 1396 genes significantly induced or repressed by any one of the treatments in the wild-type macrophages, none was present in the TLR4- or MD-2-deficient macrophages, confirming that the TLR4/MD-2 complex is the only receptor for endotoxin and that both are required for responses to LPS. Using a molecular genetics approach, we investigated the mechanism of TLR4/MD-2 activation by combining the known crystal structure of TLR4/MD-2 with computer modeling. According to our murine TLR4/MD-2-activation model, the two phosphates on lipid A were predicted to interact extensively with the two positively charged patches on mouse TLR4. When either positive patch was abolished by mutagenesis into Ala, the responses to LPS and lipid A were nearly abrogated. However, the MyD88-dependent and -independent pathways were impaired to the same extent, indicating that the adjuvant activity of monophosphorylated lipid A most likely arises from its decreased potential to induce an active receptor complex and not more downstream signaling events. Hence, we concluded that ionic interactions between lipid A and TLR4 are essential for optimal LPS receptor activation. PMID:21865549
Meng, Jianmin; Gong, Mei; Bj�rkbacka, Harry; Golenbock, Douglas T
Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)
Muenter, J.S.
Intermolecular and intramolecular V --> V transfer in the vibrational predissociation of some polyatomic van der Waals molecules
In this paper we present a theoretical study of vibrational predissociation (VP) on the ground state potential surface of van der Waals complexes consisting of polyatomic molecules. The intermolecular interaction was represented by separate contributions of atom�atom interactions, which were expressed in terms of Morse potentials. The VP process was handled utilizing the distorted wave approximation to describe a zero-order
J. A. Beswick; Joshua Jortner
Strongly interacting photons in hollow-core waveguides
Hollow-core photonic-crystal waveguides filled with cold atoms can support giant optical nonlinearities through nondispersive propagation of light tightly confined in the transverse direction. Here we explore electromagnetically induced transparency is such structures, considering a pair of counterpropagating weak quantum fields in the medium of coherently driven atoms in the ladder configuration. Strong dipole-dipole interactions between optically excited, polarized Rydberg states of the atoms translate into a large dispersive interaction between the two fields. This can be used to attain a spatially homogeneous conditional phase shift of {pi} for two single-photon pulses, realizing a deterministic photonic phase gate, or to implement a quantum nondemolition measurement of the photon number in the signal pulse by a coherent probe, thereby achieving a heralded source of single- or few-photon pulses.
Shahmoon, Ephraim; Kurizki, Gershon [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel); Fleischhauer, Michael [Department of Physics and Research Center OPTIMAS, Technische Universitaet Kaiserslautern, DE-67663 Kaiserslautern (Germany); Petrosyan, David [Department of Physics and Research Center OPTIMAS, Technische Universitaet Kaiserslautern, DE-67663 Kaiserslautern (Germany); Institute of Electronic Structure and Laser, FORTH, GR-71110 Heraklion, Crete (Greece)
Hollow-core photonic-crystal waveguides filled with cold atoms can support giant optical nonlinearities through nondispersive propagation of light tightly confined in the transverse direction. Here we explore electromagnetically induced transparency is such structures, considering a pair of counterpropagating weak quantum fields in the medium of coherently driven atoms in the ladder configuration. Strong dipole-dipole interactions between optically excited, polarized Rydberg states of the atoms translate into a large dispersive interaction between the two fields. This can be used to attain a spatially homogeneous conditional phase shift of ? for two single-photon pulses, realizing a deterministic photonic phase gate, or to implement a quantum nondemolition measurement of the photon number in the signal pulse by a coherent probe, thereby achieving a heralded source of single- or few-photon pulses.
Shahmoon, Ephraim; Kurizki, Gershon; Fleischhauer, Michael; Petrosyan, David
Spectroscopic studies on the intermolecular charge transfer interaction of Fe(II)- and Fe(III)-phthalocyanines with 2,3,5,6-tetrachloro-1,4-benzoquinone and its application in colorimetric sensing of amino acids and amines
The interactions of Fe IIPc and Fe IIIPc with ?-acceptor 2,3,5,6-tetrachloro-1,4-benzoquinone ( p-chloranil, p-CHL) have been investigated spectroscopically (UV/vis and FT-IR) and spectrofluorimetrically at three different temperatures. The stoichiometry of the complexes was found to be 1:1. The results of electronic spectral studies indicated that the formation constant for Fe IIPc- p-CHL system is found to be higher than that for Fe IIIPc- p-CHL system. This observation is well supported by the results of fluorescence quenching studies and the association constants calculated for Fe IIPc- p-CHL system is 4.2 � 10 3 mol L -1 and that for Fe IIIPc- p-CHL system is 2.2 � 10 3 mol L -1. The data are discussed in terms of physico-chemical parameters viz. molar extinction coefficient, oscillator strength, dipole moment, ionization potential, dissociation energy and thermodynamic parameters. The results indicated that the formation of ?-? CT complex is spontaneous and endothermic. Preliminary studies indicated that the CT complex can effectively be used as a colorimetric agent for sensing amino acids and amines.
Balraj, Chellamuthu; Elango, Kuppanagounder P.
Spectroscopic studies on the intermolecular charge transfer interaction of Fe(II)- and Fe(III)-phthalocyanines with 2,3,5,6-tetrachloro-1,4-benzoquinone and its application in colorimetric sensing of amino acids and amines.
The interactions of Fe(II)Pc and Fe(III)Pc with ?-acceptor 2,3,5,6-tetrachloro-1,4-benzoquinone (p-chloranil, p-CHL) have been investigated spectroscopically (UV/vis and FT-IR) and spectrofluorimetrically at three different temperatures. The stoichiometry of the complexes was found to be 1:1. The results of electronic spectral studies indicated that the formation constant for Fe(II)Pc-p-CHL system is found to be higher than that for Fe(III)Pc-p-CHL system. This observation is well supported by the results of fluorescence quenching studies and the association constants calculated for Fe(II)Pc-p-CHL system is 4.2 � 10(3) mol L(-1) and that for Fe(III)Pc-p-CHL system is 2.2 � 10(3) mol L(-1). The data are discussed in terms of physico-chemical parameters viz. molar extinction coefficient, oscillator strength, dipole moment, ionization potential, dissociation energy and thermodynamic parameters. The results indicated that the formation of ?-? CT complex is spontaneous and endothermic. Preliminary studies indicated that the CT complex can effectively be used as a colorimetric agent for sensing amino acids and amines. PMID:22074888
Balraj, Chellamuthu; Elango, Kuppanagounder P
Structure, vibrational spectra and DFT characterization of the intra- and inter-molecular interactions in 2-hydroxy-5-methylpyridine-3-carboxylic acid--normal modes of the eight-membered HB ring.
Fourier transform IR and Raman spectra, XRD studies and DFT quantum chemical calculations have been used to characterize the structural and vibrational properties of 2-hydroxy-5-methylpyridine-3-carboxylic acid. In the unit-cell of this compound two molecules related by the inversion center interact via OH?N hydrogen bonds. The double hydrogen bridge system is spaced parallel to the (102) crystallographic plane forming eight-membered arrangement characteristic for pyridine derivatives. The six-membered ring is the second characteristic unit formed via the intramolecular OH?O hydrogen bond. The geometry optimization of the monomer and dimer have been performed applying the Gaussian03 program package. All calculations were performed in the B3LYP/6-31G(d,p) basis set using the XRD data as input parameters. The relation between the molecular and crystal structures has been discussed in terms of the hydrogen bonds formed in the unit cell. The vibrations of the dimer have been discussed in terms of the resonance inside the system built of five rings coupled via hydrogen bonds. PMID:24184924
Godlewska, P; Ja?czak, J; Kucharska, E; Hanuza, J; Lorenc, J; Michalski, J; Dymi?ska, L; W?gli?ski, Z
Theory of elastic interaction between colloidal particles in a nematic cell in the presence of an external electric or magnetic field.
The Green's function method developed previously [S. B. Chernyshuk and B. I. Lev, Phys. Rev. E 81, 041701 (2010)] is used to describe elastic interactions between axially symmetric colloidal particles in a nematic cell in the presence of an external electric or magnetic field. Formulas for dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions in the homeotropic and planar nematic cells with parallel and perpendicular field orientations are obtained. A set of predictions has been made: (1) The deconfinement effect for dipole particles in the homeotropic nematic cell when an electric field is approaching its Freedericksz threshold value E?E(t). This means cancellation of the confinement effect found in [M. Vilfan et al., Phys. Rev. Lett. 101, 237801 (2008)] near the Freedericksz transition. In the planar nematic cell this deconfinement effect exists for both dipole and quadrupole particles and depends on the field orientation as well as on the sign of dielectric anisotropy ??. (2) The effect of tunable stabilization of the particles is predicted. The equilibrium distance between two particles, which are attracted along the electric field parallel to the planes of a homeotropic nematic cell with ??<0, depends on the strength of the field. (3) Attraction and repulsion zones for all elastic interactions are changed dramatically under the action of the external field. PMID:22400582
Chernyshuk, S B; Tovkach, O M; Lev, B I
Higher-order electric multipole contributions to retarded non-additive three-body dispersion interaction energies between atoms: equilateral triangle and collinear configurations.
The theory of molecular quantum electrodynamics (QED) is used to calculate higher electric multipole contributions to the dispersion energy shift between three atoms or molecules arranged in a straight line or in an equilateral triangle configuration. As in two-body potentials, three-body dispersion interactions are viewed in the QED formalism to arise from exchange of virtual photons between coupled pairs of particles. By employing an interaction Hamiltonian that is quadratic in the electric displacement field means that third-order perturbation theory can be used to yield the energy shift for a particular combination of electric multipole polarizable species, with only six time-ordered diagrams needing to be summed over. Specific potentials evaluated include dipole-dipole-quadrupole (DDQ), dipole-quadrupole-quadrupole (DQQ), and dipole-dipole-octupole (DDO) terms. For the geometries of interest, near-zone limiting forms are found to exhibit an R(-11) dependence on separation distance for the DDQ interaction, and an R(-13) behaviour for DQQ and DDO shifts, agreeing with an earlier semi-classical computation. Retardation weakens the potential in each case by R(-1) in the far-zone. It is found that by decomposing the octupole moment into its irreducible components of weights-1 and -3 that the former contribution to the DDO potential may be taken to be a higher-order correction to the leading triple dipole energy shift. PMID:24387355
Salam, A
Unravelling the effect of interparticle interactions and surface spin canting in ?-Fe2O3@SiO2 superparamagnetic nanoparticles
The present study investigates the magnetic properties of spherical monodispersed maghemite (?-Fe2O3) nanoparticles coated with multiple silica (SiO2) layers of different thicknesses, forming core-shell multifunctional nanomaterials. This study was performed using a combination of local probe techniques (M�ssbauer spectrometry) and magnetization measurements. At room temperature, both techniques confirm the superparamagnetic state of the samples, even after being coated with the SiO2 shells. The zero-field-cooling-field-cooling magnetization curves of the silica-coated ?-Fe2O3 nanomaterials with different shell thicknesses allow the evaluation of the intensity of the interparticle dipole-dipole interactions. We estimate the interparticle energy within the framework of dipolar interaction models and relate it with the hyperfine parameters. We further observe that this dipole-dipole interaction increases the superparamagnetic energy barrier, which largely depends on the interparticle distance. Finally, we consider the effect of spin canting at the surface (``dead layer'') of uncoated ?-Fe2O3 nanoparticles manifested by a layer of ~0.5(1) nm.
Pereira, Andr� M.; Pereira, Clara; Silva, Ana S.; Schmool, David S.; Freire, Cristina; Gren�che, Jean-Marc; Ara�jo, Joa~O. P.
The role of intermolecular interactions in the assemblies of Fe{sup II} and Co{sup II} tetrakis-isothiocyanatometalates with tris(1,10-phenanthroline)-Ru{sup II}: Crystal structures of two dual-metal assemblies featuring octahedral cationic and tetrahedral anionic modules
Two new dual-metal assemblies: 2[Ru(phen){sub 3}]{sup 2+}.[Fe(SCN){sub 4}]{sup 2-}.2SCN{sup -}.4H{sub 2}O 1 and [Ru(phen){sub 3}]{sup 2+}.[Co(SCN){sub 4}]{sup 2-}2, (phen:1,10-phenanthroline), have been prepared and their structures were characterized by X-ray diffraction. In 1, the cationic octahedral enantiomers are arranged with a {lambda}{delta}{lambda}{delta}{lambda} sequence supported by {pi}-{pi} stacking and the anionic inorganic tetrahedral units are oriented between these stacks by interacting with the nearby water molecules through strong O-H...O and O-H...S hydrogen bonds. In 2, homochiral double helices in the b-direction are revealed, with tetrakis-isothiocyanate Co{sup II} anions arranged in the crystal to furnish one-dimensional (1D)-helical chains with S...S intermolecular interactions at 3.512(2) and 3.966(2) A supporting [Ru(phen){sub 3}]{sup 2+}{lambda}- and {delta}-helices with Ru...Ru shortest distance of 8.676(7) A. In both 1 and 2, the supramolecular assembly is maintained by C-H...S hydrogen bonds extending between the phenanthroline aromatic carbons in the cationic nodes and the sulphur atoms of the isothiocyanates anions. Analysis of S...S interactions in isothiocyanate containing compounds using Cambridge structural database (CSD) showed an angle dependence categorizing these interactions into 'type-I' and 'type-II'. - Graphical abstract: Side projection in 2 showing the crankshaft caused by S...S interactions in [Co(NCS){sub 4}]{sup 2-} in-between [Ru{sup II}(phen){sub 3}]{sup 2+} helices. Only isothiocyanates arms of [Co(NCS){sub 4}]{sup 2-} that are part of S...S interactions are shown and [Ru{sup II}(phen){sub 3}]{sup 2+} are presented as polyhedra.
Ghazzali, Mohamed [Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)], E-mail: email@example.com; Langer, Vratislav; Ohrstroem, Lars [Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)
The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O{sub 2} molecules interact predominantly through the half-filled 1{pi}{sub g}* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1{pi}{sub g}* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O{sub 2} molecules at the transition to the {epsilon}-phase. The {epsilon}-phase, which consists of (O{sub 2}){sub 4} clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O{sub 2}){sub 4} clusters develop upon compression of the {epsilon}-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.
Meng, Yue; Eng, Peter J.; Tse, John S.; Shaw, Dawn M.; Hu, Michael Y.; Shu, Jinfu; Gramsch, Stephen A.; Kao, Chichang; Hemley, Russell J.; Mao, Ho-kwang (CIW); (UC); (Saskatchewan); (BNL)
Vibrational nano-spectroscopic imaging correlating structure with intermolecular coupling and dynamics
Molecular self-assembly, the function of biomembranes and the performance of organic solar cells rely on nanoscale molecular interactions. Understanding and control of such materials have been impeded by difficulties in imaging their properties with the desired nanometre spatial resolution, attomolar sensitivity and intermolecular spectroscopic specificity. Here we implement vibrational scattering-scanning near-field optical microscopy with high spectral precision to investigate the structure�function relationship in nano-phase separated block copolymers. A vibrational resonance is used as a sensitive reporter of the local chemical environment and we image, with few nanometre spatial resolution and 0.2?cm?1 spectral precision, solvatochromic Stark shifts and line broadening correlated with molecular-scale morphologies. We discriminate local variations in electric fields between nano-domains with quantitative agreement with dielectric continuum models. This ability to directly resolve nanoscale morphology and associated intermolecular interactions can form a basis for the systematic control of functionality in multicomponent soft matter systems.
Pollard, Benjamin; Muller, Eric A.; Hinrichs, Karsten; Raschke, Markus B.
Nonlinear Dynamics of Bose-Einstein Condensates with Long-Range Interactions
The motto of this paper is: Let's face Bose-Einstein condensation through nonlinear dynamics. We do this by choosing variational forms of the condensate wave functions (of given symmetry classes), which convert the Bose-Einstein condensates via the time-dependent Gross-Pitaevskii equation into Hamiltonian systems that can be studied using the methods of nonlinear dynamics. We consider in particular cold quantum gases where long-range interactions between the neutral atoms are present, in addition to the conventional short-range contact interaction, viz. gravity-like interactions, and dipole-dipole interactions. The results obtained serve as a useful guide in the search for nonlinear dynamics effects in numerically exact quantum calculations for Bose-Einstein condensates. A main result is the prediction of the existence of stable islands as well as chaotic regions for excited states of dipolar condensates, which could be checked experimentally.
Wunner, G.; Cartarius, H.; Fabcic, T.; Koeberle, P.; Main, J.; Schwidder, T. [Institut fuer Theoretische Physik 1, Universitaet Stuttgart, 70550 Stuttgart (Germany)
Mechanisms of interaction between polycyclic aromatic hydrocarbons and dissolved organic matters.
Binding of phenanthrene and fluorene to a number of humic and fulvic substances isolated from various sources as well as a commercially available humic acid, was investigated using a fluorescence quenching approach. The observed fluorescence quenching indicated by linear Stern-Volmer plots and high bimolecular quenching rate constant was induced by a static interaction process. A significant correlation of binding constants with aromaticity and polarity of dissolved organic matter (DOM) was observed. It is hypothesized that the binding of polycyclic aromatic hydrocarbons (PAHs) by DOM is due to both ?-? interactions and hydrophobic interactions. In addition, energy transfer from PAHs to DOM occurs because of the significant overlap between the absorbance spectra of DOM and emission spectra of PAHs. Thus, dipole-dipole interaction may also play an important role in the binding mechanism between PAHs and DOM. PMID:24117086
Wang, Huan Bo; Zhang, Yu Jun
Intermolecular repulsive�dispersive potentials explain properties of impurity spectra in soft solids
Behavior of optical impurity spectra in van der Waals glasses is rationalized with the aid of a two-particle Lennard�Jones model of intermolecular interactions. Simple mathematical manipulations with the 6�12 potential yield inhomogeneous distribution functions (IDFs) of zero phonon lines (ZPLs) at different compressions, and the expressions for wavelength dependent pressure shift coefficients of ZPLs (or holes), local phonon frequencies, and
Indrek Renge; Margus R�tsep; Arvi Freiberg
Intermolecular Alignment in ?2-Microglobulin Amyloid Fibrils
The deposition of amyloid-like fibrils, composed primarily of the 99-residue protein ?2-microglobulin (?2m), is one of the characteristic symptoms of dialysis-related amyloidosis. Fibrils formed in vitro at low pH and low salt concentration share many properties with the disease related fibrils and have been extensively studied by a number of biochemical and biophysical methods. These fibrils contain a significant ?-sheet core and have a complex cryoEM electron density profile. Here, we investigate the intrasheet arrangement of the fibrils by means of 15N?13C MAS NMR correlation spectroscopy. We utilize a fibril sample grown from a 50:50 mixture of 15N,12C- and 14N,13C-labeled ?2m monomers, the latter prepared using 2-13C glycerol as the carbon source. Together with the use of ZF-TEDOR mixing, this sample allowed us to observe intermolecular 15N?13C backbone-to-backbone contacts with excellent resolution and good sensitivity. The results are consistent with a parallel, in-register arrangement of the protein subunits in the fibrils and suggest that a significant structural reorganization occurs from the native to the fibril state.
Intermolecular alignment in ?2-microglobulin amyloid fibrils.
The deposition of amyloid-like fibrils, composed primarily of the 99-residue protein ?2-microglobulin (?2m), is one of the characteristic symptoms of dialysis-related amyloidosis. Fibrils formed in vitro at low pH and low salt concentration share many properties with the disease related fibrils and have been extensively studied by a number of biochemical and biophysical methods. These fibrils contain a significant ?-sheet core and have a complex cryoEM electron density profile. Here, we investigate the intrasheet arrangement of the fibrils by means of (15)N-(13)C MAS NMR correlation spectroscopy. We utilize a fibril sample grown from a 50:50 mixture of (15)N,(12)C- and (14)N,(13)C-labeled ?2m monomers, the latter prepared using 2-(13)C glycerol as the carbon source. Together with the use of ZF-TEDOR mixing, this sample allowed us to observe intermolecular (15)N-(13)C backbone-to-backbone contacts with excellent resolution and good sensitivity. The results are consistent with a parallel, in-register arrangement of the protein subunits in the fibrils and suggest that a significant structural reorganization occurs from the native to the fibril state. PMID:21077676
Debelouchina, Galia T; Platt, Geoffrey W; Bayro, Marvin J; Radford, Sheena E; Griffin, Robert G
Propagation studies of metastable intermolecular composites (MIC).
Thermite materials are attractive energetic materials because the reactions are highly exothermic, have high energy densities, and high temperatures of combustion. However, the application of thermite materials has been limited because of the relative slow release of energy compared to other energetic materials. Engineered nano-scale composite energetic materials, such as Al/MoO{sub 3}, show promise for additional energetic material applications because they can react very rapidly. The composite material studied in this work consists of tailored, ultra-fine grain (30-200 nm diameter) aluminum particles that dramatically increase energy release rates of these thermite materials. These reactant clusters of fuel and oxidizer particles are in nearly atomic scale proximity to each other but are constrained from reaction until triggered. Despite the growing importance of nano-scale energetic materials, even the most basic combustion characteristics of these materials have not been thoroughly studied. This paper reports initial studies of the ignition and combustion of metastable intermolecular composites (MIC) materials. The goals were lo obtain an improved understanding of flame propagation mechanisms and combustion behaviors associated with nano-structured energetic materials. Information on issues such as reaction rate and behavior as a function of composition (mixture ratio), initial static charge, and particle size are essential and will allow scientists to design applications incorporating the benefits of these compounds. The materials have been characterized, specifically focusing on particle size, shape, distribution and morphology.
Son, S. F. (Steven F.); Busse, J. R. (James R.); Asay, B. W. (Blaine W.); Peterson, P. D. (Paul D.); Mang, J. T. (Joseph T.); Bockmon, B. (Bryan); Pantoya, M. (Michelle)
Functional Molecular Materials: Modelling Structure, Optical Properties, Intermolecular Interactions.
In the past few years we have investigated structural, electric and photo-physical properties of several molecular systems forming the building blocks of functional molecular materials, and we paid increasing attention to the effects that condensed phase and structured environments can have on the properties of the material. Here we present an overview of our most recent achievements concerning the modelling of properties of several classes of organic functional molecules. The results presented comprise the prediction of optical properties of 2D and 3D carbon rich materials (models for defected graphite, hetero-fullerenes), studies on reactivity, dynamics and aggregation of polyphenylene dendrimers including their ability to encapsulate gas molecules, predictions of photo-physical properties of molecular switches, linear, non-linear electric responses and optical properties of polar chromophores and dyes for organic electric memory devices.
Negri, Fabrizia
Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins
A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and ?-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S2 band of ?-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available.
Renge, I.; van Grondelle, R.; Dekker, J. P.
Intermolecular interaction in plant oils from refractive and density measurements
Refractive indices n and density ? of three plant oils (Anise, Nigelle, and Juniper berries) have been measured in the temperature range of 10-60�C. The model of the effective electric field E' acting on a molecule in the material, E' = E + x4? P, with the unlimited value of the coefficient of polarization input x has been applied to the analysis of the results obtained. The value x of the oils studied have been found to be in the range of 0.193-0.269, which is smaller than a similar value for water ( x water > 0.3), known as a strong polar liquid.
Andriyevsky, B.; Andriyevska, L.; Piecuch, T.
1H NMR Relaxation Investigation of Inhibitors Interacting with Torpedo californica Acetylcholinesterase
Two naphthyridines interacting with Torpedo californica acetylcholinesterase (AChE) were investigated. 1H NMR spectra were recorded and nonselective, selective, and double-selective spin-lattice relaxation rates were measured. The enhancement of selective relaxation rates could be titrated by different ligand concentrations at constant AChE (yielding 0.22 and 1.53 mM for the dissociation constants) and was providing evidence of a diverse mode of interaction. The double-selective relaxation rates were used to evaluate the motional correlation times of bound ligands at 34.9 and 36.5 ns at 300 K. Selective relaxation rates of bound inhibitors could be interpreted also in terms of dipole-dipole interactions with protons in the enzyme active site.
Delfini, Maurizio; Gianferri, Raffaella; Dubbini, Veronica; Manetti, Cesare; Gaggelli, Elena; Valensin, Gianni
The interaction of colloidal particles with weak homeotropic anchoring energy in homogeneous nematic liquid crystal cells.
We have investigated interactions of colloidal particles with weak homeotropic anchoring energy in homogeneous nematic liquid crystal cells. Particle-wall and inter-particle interactions were observed experimentally and analyzed using typical dipole-dipole and quadrupole-quadrupole interactions, including substrate effects as the image charges. Both experimental results matched well with the calculated results for the effective particle radius reflecting the weak anchoring. The effective radius is reduced by the amount of extrapolation length than the actual particle radius. The effective radii of polyethylene micro-particles were reduced to a coefficient ? (0.78 ? ? ? 0.52) times the actual radius with anchoring coefficients in the range of 3.8 � 10(-6) to 1.4 � 10(-6) J m(-2). The anchoring energy of the particles is, therefore, a key component for explaining liquid crystal colloidal systems. PMID:24647470
Kim, Sung-Jo; Kim, Jong-Hyun
Photochemistry of intermolecular C-H bond activation reactions.
Goals at the onset were to obtain photophysical and photochemical data on transition-metal organometallic complexes which undergo light-induced intermolecular C-H bond activation reactions with hydrocarbon substrates. The complexes included these of rhodi...
A. J. Lees
Magnetic interactions in silica coated nanoporous assemblies of CoFe2O4 nanoparticles with cubic magnetic anisotropy.
Magnetic interactions in silica coated spherical nanoporous assemblies of CoFe(2)O(4) nanoparticles have been investigated by low temperature field dependent remanent magnetization (M(DCD) and M(IRM)) and magnetization relaxation measurements. The synthesis procedure leads to the formation of spherical aggregates of about 50-60 nm in diameter composed of hexagonal shaped nanocrystals with shared edges. The negative deviation from the non-interacting case in the Henkel plot indicates the predominance of dipole-dipole interactions favouring the demagnetized state, although the presence of exchange interactions in the porous system cannot be excluded. The activation volume, derived from time dependent magnetization measurements, turns out to be comparable with the particle physical volume, thus indicating, in agreement with static and dynamic irreversible magnetization measurements, that the magnetization reversal actually involves individual crystals. PMID:20622300
Laureti, S; Varvaro, G; Testa, A M; Fiorani, D; Agostinelli, E; Piccaluga, G; Musinu, A; Ardu, A; Peddis, D
Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest�host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the �VAS� model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site�site ab initio intermolecular potentials) as ??(w)(0) = 1206 � 2 J/mol and ?H(w)(0) = 1260 � 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234
Velaga, Srinath C; Anderson, Brian J
Nanostructure van der Waals interaction between a quantum well and a quantum dot atom
We examine the van der Waals interaction between mobile plasma electrons in a narrow quantum well nanostructure and a quantum dot atom. This formulation of the van der Waals interaction exhibits it to second order as the correlation energy (self-energy) of the dot-atom electrons mediated by the image potential arising from the dynamic, nonlocal and spatially inhomogeneous polarization of the quantum well plasma electrons. This image potential of the quantum-well plasma is, in turn, determined by the dynamic, nonlocal, inhomogeneous screening function of the quantum well, which involves the space time matrix inversion of its spatially inhomogeneous, nonlocal and time-dependent dielectric function. The latter matrix inversion is carried out exactly, in closed form, and the van der Waals energy is evaluated in the electrostatic limit to dipole dipole terms.
Morgenstern Horing, Norman J.
Multipole expansion of the electrostatic interaction between charged colloids at interfaces
The general form of the electrostatic potential around an arbitrarily charged colloid at a flat interface between a dielectric and a screening phase (such as air and water, respectively) is analyzed in terms of a multipole expansion. The leading term is isotropic in the interfacial plane and varies with d-3 where d is the in-plane distance from the colloid. The effective interaction potential between two arbitrarily charged colloids is likewise isotropic and proportional to d-3 , thus generalizing the dipole-dipole repulsion first found for point charges at water interfaces. Anisotropic attractive interaction terms can arise only for higher powers d-n with n?4 . The relevance of these findings for recent experiments is discussed.
Dom�nguez, A.; Frydel, D.; Oettel, M.
Using Voronoi tessellations to assess nanoparticle-nanoparticle interactions and ordering in monolayer films formed through electrophoretic deposition.
Monolayers of iron oxide nanoparticles of two different sizes, 9.6 nm and 16.5 nm, were fabricated through electrophoretic deposition. The arrangements of nanoparticles within the films were analyzed using the technique of Voronoi tessellations. These analyses indicated that the films possessed equivalent degrees of ordering, and that the films were uniform over centimeter length scales. Precise measurements of the interparticle spacing were obtained, and the magnitudes of magnetic dipole interactions were calculated. The dipole-dipole interaction among the larger nanoparticles was 14 times larger than that of the smaller nanoparticles, indicating that magnetic coupling interactions could not have been the lone source of ordering in the system. PMID:22908936
Krejci, Alex J; Thomas, Colin G W; Mandal, Jyotirmoy; Gonzalo-Juan, Isabel; He, Weidong; Stillwell, Ryan L; Park, Ju-Hyun; Prasai, Dhiraj; Volkov, Vyacheslav; Bolotin, Kirill I; Dickerson, James H
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.
A unified coarse-grained model of three major classes of biological molecules-proteins, nucleic acids, and polysaccharides-has been developed. It is based on the observations that the repeated units of biopolymers (peptide groups, nucleic acid bases, sugar rings) are highly polar and their charge distributions can be represented crudely as point multipoles. The model is an extension of the united residue (UNRES) coarse-grained model of proteins developed previously in our laboratory. The respective force fields are defined as the potentials of mean force of biomacromolecules immersed in water, where all degrees of freedom not considered in the model have been averaged out. Reducing the representation to one center per polar interaction site leads to the representation of average site-site interactions as mean-field dipole-dipole interactions. Further expansion of the potentials of mean force of biopolymer chains into Kubo's cluster-cumulant series leads to the appearance of mean-field dipole-dipole interactions, averaged in the context of local interactions within a biopolymer unit. These mean-field interactions account for the formation of regular structures encountered in biomacromolecules, e.g., ?-helices and ?-sheets in proteins, double helices in nucleic acids, and helicoidally packed structures in polysaccharides, which enables us to use a greatly reduced number of interacting sites without sacrificing the ability to reproduce the correct architecture. This reduction results in an extension of the simulation timescale by more than four orders of magnitude compared to the all-atom representation. Examples of the performance of the model are presented. PMID:25024008
Liwo, Adam; Baranowski, Maciej; Czaplewski, Cezary; Go?a?, Ewa; He, Yi; Jagie?a, Dawid; Krupa, Pawe?; Maciejczyk, Maciej; Makowski, Mariusz; Mozolewska, Magdalena A; Niadzvedtski, Andrei; O?dziej, Stanis?aw; Scheraga, Harold A; Sieradzan, Adam K; Slusarz, Rafa?; Wirecki, Tomasz; Yin, Yanping; Zaborowski, Bart?omiej
Comparison of interionic/intermolecular vibrational dynamics between ionic liquids and concentrated electrolyte solutions
In this study, we have compared the interionic/intermolecular vibrational dynamics of ionic liquids (ILs) and concentrated electrolyte solutions measured by femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. A typical anion in ILs, bis(trifluoromethanesulfonyl)amide ([NTf2]-), has been chosen as the anion for the sample ILs and concentrated electrolyte solutions. ILs used in this study are 1-butyl-3-methylimidazolium, 1-butylpyridinium, N-butyl-N,N,N-triethylammonium, and 1-butyl-1-methylpyrrolidinium with [NTf2]-. Li[NTf2] solutions (~3.3 M) of water, methanol, propylene carbonate, and poly(ethylene glycol) have been selected as control samples. Kerr transients of the ILs and electrolyte solutions show intra- and interionic/intermolecular vibrational dynamics followed by slow picosecond overdamped relaxation. Fourier transform Kerr spectra have shown a difference in the relative intensities of intraionic vibrational bands of [NTf2]- (280-350 cm-1) between the ILs and electrolyte solutions. The origin of the difference is attributed to the change in the conformational equilibrium between cisoid and transoid forms of [NTf2]-, which is caused by a favorable stabilization of dipolar cisoid form due to Li+ and dipolar solvent molecules in the electrolyte solutions. Low-frequency Kerr spectra (0-200 cm-1) exhibit unique features with the variation of cation and solvent species. The aromatic ILs have a prominent high-frequency librational motion at about 100 cm-1 in contrast to the case for the nonaromatic ones. The common structure of the spectra observed at about 20 cm-1 likely comes from an interionic motion of [NTf2]-. The nonaromatic ILs allow a fair comparison with the electrolyte solutions of propylene carbonate and poly(ethylene glycol) because of the structural similarities. The comparison based on the first moment of the interionic/intermolecular vibrational spectrum suggests the stronger interionic/intermolecular interaction in the concentrated electrolyte solutions than the ILs.
Fujisawa, Tomotsumi; Nishikawa, Keiko; Shirota, Hideaki
Comparison of interionic/intermolecular vibrational dynamics between ionic liquids and concentrated electrolyte solutions.
In this study, we have compared the interionic/intermolecular vibrational dynamics of ionic liquids (ILs) and concentrated electrolyte solutions measured by femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. A typical anion in ILs, bis(trifluoromethanesulfonyl)amide ([NTf(2)](-)), has been chosen as the anion for the sample ILs and concentrated electrolyte solutions. ILs used in this study are 1-butyl-3-methylimidazolium, 1-butylpyridinium, N-butyl-N,N,N-triethylammonium, and 1-butyl-1-methylpyrrolidinium with [NTf(2)](-). Li[NTf(2)] solutions (approximately 3.3 M) of water, methanol, propylene carbonate, and poly(ethylene glycol) have been selected as control samples. Kerr transients of the ILs and electrolyte solutions show intra- and interionic/intermolecular vibrational dynamics followed by slow picosecond overdamped relaxation. Fourier transform Kerr spectra have shown a difference in the relative intensities of intraionic vibrational bands of [NTf(2)](-) (280-350 cm(-1)) between the ILs and electrolyte solutions. The origin of the difference is attributed to the change in the conformational equilibrium between cisoid and transoid forms of [NTf(2)](-), which is caused by a favorable stabilization of dipolar cisoid form due to Li(+) and dipolar solvent molecules in the electrolyte solutions. Low-frequency Kerr spectra (0-200 cm(-1)) exhibit unique features with the variation of cation and solvent species. The aromatic ILs have a prominent high-frequency librational motion at about 100 cm(-1) in contrast to the case for the nonaromatic ones. The common structure of the spectra observed at about 20 cm(-1) likely comes from an interionic motion of [NTf(2)](-). The nonaromatic ILs allow a fair comparison with the electrolyte solutions of propylene carbonate and poly(ethylene glycol) because of the structural similarities. The comparison based on the first moment of the interionic/intermolecular vibrational spectrum suggests the stronger interionic/intermolecular interaction in the concentrated electrolyte solutions than the ILs. PMID:20059091
Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR
We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range 13C-13C correlation spectra and a third based on the identification of intermolecular interactions in 13C-15N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3), that efficient 13C-13C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The 13C-13C experiments are corroborated by 15N-13C correlation spectrum obtained from a mixed [15N,12C]/[14N,13C] sample which directly quantifies interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular 15N-13C constraints present in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total the experiments provide 111 intermolecular 13C-13C and 15N-13C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril.
Bayro, Marvin J.; Debelouchina, Galia T.; Eddy, Matthew T.; Birkett, Neil R.; MacPhee, Catherine E.; Rosay, Melanie; Maas, Werner E.; Dobson, Christopher M.
Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR.
We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range (13)C-(13)C correlation spectra and the third based on the identification of intermolecular interactions in (13)C-(15)N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3 or PI3K-SH3), that efficient (13)C-(13)C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The (13)C-(13)C experiments are corroborated by (15)N-(13)C correlation spectra obtained from a mixed [(15)N,(12)C]/[(14)N,(13)C] sample which directly quantify interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular (15)N-(13)C constraints detectable in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total, the experiments provide 111 intermolecular (13)C-(13)C and (15)N-(13)C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril. PMID:21774549
Bayro, Marvin J; Debelouchina, Galia T; Eddy, Matthew T; Birkett, Neil R; MacPhee, Catherine E; Rosay, Melanie; Maas, Werner E; Dobson, Christopher M; Griffin, Robert G
Role of long-range intermolecular forces in the formation of inorganic nanoparticle clusters.
An understanding of the role played by intermolecular forces in terms of the electron density distribution is fundamental to the understanding of the self-assembly of molecules in the formation of a molecular crystal. Using ab initio methods capable of describing both short-range intramolecular interactions and long-range London dispersion interactions arising from electron correlation, analyses of inorganic dimers of As(4)S(4) and As(4)O(6) molecules cut from the structures of realgar and arsenolite, respectively, reveal that the molecules adopt a configuration that closely matches that observed for the crystal. Decomposition of the interaction energies using symmetry-adapted perturbation theory reveals that both model dimers feature significant stabilization from electrostatic forces as anticipated by a Lewis acid/Lewis base picture of the interaction. London dispersion forces also contribute significantly to the interaction, although they play a greater role in the realgar structure near equilibrium than in arsenolite. PMID:21939256
Gibbs, G V; Crawford, T D; Wallace, A F; Cox, D F; Parrish, R M; Hohenstein, E G; Sherrill, C D
A specific intermolecular association between the regulatory domains of a tec family kinase 1 1 Edited by P. Wright
Interleukin-2 tyrosine kinase (Itk), is a T-cell specific tyrosine kinase of the Tec family. We have examined a novel intermolecular interaction between the SH3 and SH2 domains of Itk. In addition to the interaction between the isolated domains, we have found that the dual SH3\\/SH2 domain-containing fragment of Itk self-associates in a specific manner in solution. Tec family members contain
Kristine N Brazin; D. Bruce Fulton; Amy H Andreotti
Dielectric spectra broadening as a signature for dipole-matrix interaction. III. Water in adenosine monophosphate/adenosine-5'-triphosphate solutions
In this, the third part of our series on the dielectric spectrum symmetrical broadening of water, we consider the nucleotide aqueous solutions. Where in Parts I [E. Levy et al., J. Chem. Phys. 136, 114502 (2012)] and II [E. Levy et al., J. Chem. Phys. 136, 114503 (2012)], the dipole-dipole or ion-dipole interaction had a dominant feature, now the interplay between these two types of dipole-matrix interactions will be considered. We present the results of high frequency dielectric measurements of different concentrations of adenosine monophosphate/adenosine-5'-triphosphate aqueous solutions. We observed the Cole-Cole broadening of the main relaxation peak of the solvent in the solutions. Moreover, depending on the nucleotide concentration, we observed both types of dipole-matrix interaction. The 3D trajectory approach (described in detail in Part I) is applied in order to highlight the differences between the two types of interaction.
Puzenko, Alexander; Levy, Evgeniya; Shendrik, Andrey; Talary, Mark S.; Caduff, Andreas; Feldman, Yuri
The fluorobenzene-argon S(1) excited-state intermolecular potential energy surface.
We evaluate the first excited-state (S1) intermolecular potential energy surface for the fluorobenzene-Ar van der Waals complex using the coupled cluster method and the augmented correlation-consistent polarized valence double-zeta basis set extended with a set of 3s3p2d1f1g midbond functions. To calculate the S(1) interaction energies, we use ground-state interaction energies evaluated with the same basis set and the coupled cluster singles and doubles (CCSD) including connected triple excitations [CCSD(T)] model and interaction and excitation energies evaluated at the CCSD level. The surface minima are characterized by the Ar atom located above and below the fluorobenzene ring at a distance of 3.5060 A with respect to the fluorobenzene center of mass and at an angle of 5.89 degrees with respect to the axis perpendicular to the fluorobenzene plane. The corresponding interaction energy is -425.226 cm(-1). The surface is used in the evaluation of the intermolecular level structure of the complex, and the results are compared to the experimental data available and to those found in previous theoretical papers on ground-state potentials for similar complexes. PMID:17658771
Faj�n, Jos� Luis Cagide; Capelo, Silvia Bouz�n; Fernandez, Berta; Felker, Peter M
Effective Intermolecular Pair Potentials in Nonpolar Media
Using third-order perturbation theory, effective London dispersion forces between two molecules in a medium are evaluated. The reduction in the pair interaction is calculated for spherical and polymeric bodies at various separations. For nearest neighbors in pure liquids, pair potentials decrease by 1.8% in helium, and 32% in carbon tetrachloride. The contribution to the total energy of the liquid is
NEIL R. KESTNERt
Van der Waals interactions in density functional theory by combining the quantum harmonic oscillator-model with localized Wannier functions
We present a new scheme to include the van der Waals (vdW) interactions in approximated Density Functional Theory (DFT) by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique. With respect to the recently developed DFT/vdW-WF2 method, also based on Wannier Functions, the new approach is more general, being no longer restricted to the case of well separated interacting fragments. Moreover, it includes higher than pairwise energy contributions, coming from the dipole-dipole coupling among quantum oscillators. The method is successfully applied to the popular S22 molecular database, and also to extended systems, namely graphite and H2 adsorbed on the Cu(111) metal surface (in this case metal screening effects are taken into account). The results are also compared with those obtained by other vdW-corrected DFT schemes.
Silvestrelli, Pier Luigi
The ground-state phase properties of a two-dimensional Bose system with dipole-dipole interactions is studied by means of quantum Monte Carlo techniques. Limitations of mean-field theory in a two-dimensional geometry are discussed. A quantum phase transition from gas to solid is found. The crystal is tested for the existence of a supersolid in the vicinity of the phase transition. The mesoscopic analogue of the off-diagonal long-range order is shown in the one-body density matrix in a finite-size crystal. A non-zero superfluid fraction is found in a finite-size crystal, the signal increasing dramatically in presence of vacancies.
Astrakharchik, G. E.; Boronat, J.; Casulleras, J.; Kurbakov, I. L.; Lozovik, Yu. E.
Interaction effects on the magneto-optical response of magnetoplasmonic dimers
The effect that dipole-dipole interactions have on the magneto-optical (MO) properties of magnetoplasmonic dimers is theoretically studied. The specific plasmonic versus magnetoplasmonic nature of the dimer's metallic components and their specific location within the dimer play a crucial role in the determination of these properties. We find that it is possible to generate an induced MO activity in a purely plasmonic component, even larger than that of the MO one, therefore dominating the overall MO spectral dependence of the system. Adequate stacking of these components may allow one to obtain, for specific spectral regions, larger MO activities in systems with a reduced amount of MO metal and therefore with lower optical losses. Theoretical results are contrasted and confirmed with experiments for selected structures.
de Sousa, N.; Froufe-P�rez, L. S.; Armelles, G.; Cebollada, A.; Gonz�lez, M. U.; Garc�a, F.; Meneses-Rodr�guez, D.; Garc�a-Mart�n, A.
Cross-Correlated 19F Relaxation Measurements for the Study of Fluorinated Ligand-Receptor Interactions
Fluorine is often used in drug-design efforts to enhance the pharmacokinetic properties of biologically active compounds. Additionally fluorine nuclei ( 19F) have properties that are well suited to current pharmaceutical NMR screening programs. Together, these considerations have motivated our interest in the utility of fluorine relaxation parameters to study ligand-receptor interactions. Here, we investigate the potential for cross-correlated relaxation effects between the 19F anisotropic chemical-shift and 19F- 1H dipole-dipole relaxation mechanisms to help pinpoint and quantify exchange processes. Methods are proposed and demonstrated in which the magnitude ratio of the transverse cross-correlation rate constant ? xy and the fluorine transverse relaxation rate constant, R2, help estimate the exchange rate constant for ligand-binding equilibria. These exchange rate constants provide estimates of the ligand dissociation rate constants koff and can thus provide a means for rank-ordering the binding affinities of ligands identified in pharmaceutical screens.
Peng, Jeffrey W.
Intermolecular potential for binding of protonated peptide ions with perfluorinated hydrocarbon surfaces.
An analytic potential energy function was developed to model both short-range and long-range interactions between protonated peptide ions and perfluorinated hydrocarbon chains. The potential function is defined as a sum of two-body potentials of the Buckingham form. The parameters of the two-body potentials were obtained by fits to intermolecular potential energy curves (IPECs) calculated for CF4, which represents the F and C atoms of a perfluoroalkane chain, interacting with small molecules chosen as representatives of the main functional groups and atoms present in protonated peptide ions: specifically, CH4, NH3, NH4(+), and HCOOH. The IPECs were calculated at the MP2/aug-cc-pVTZ level of theory, with basis set superposition error (BSSE) corrections. Good fits were obtained for an energy range extending up to about 400 kcal/mol. It is shown that the pair potentials derived from the NH3/CF4 and HCOOH/CF4 fits reproduce acceptably well the intermolecular interactions in HCONH2/CF4, which indicates that the parameters obtained for the amine and carbonyl atoms may be transferable to the corresponding atoms of the amide group. The derived potential energy function may be used in chemical dynamics simulations of collisions of peptide-H(+) ions with perfluorinated hydrocarbon surfaces. PMID:24779856
Pratihar, Subha; Kohale, Swapnil C; V�zquez, Saulo A; Hase, William L
Curcumin amorphous solid dispersions: the influence of intra and intermolecular bonding on physical stability.
We have investigated the physical stability of amorphous curcumin dispersions and the role of curcumin-polymer intermolecular interactions in delaying crystallization. Curcumin is an interesting model compound as it forms both intra and intermolecular hydrogen bonds in the crystal. A structurally diverse set of amorphous dispersion polymers was investigated; poly(vinylpyrrolidone), Eudragit E100, carboxymethyl cellulose acetate butyrate, hydroxypropyl methyl cellulose (HPMC) and HPMC-acetate succinate. Mid-infrared spectroscopy was used to determine and quantify the extent of curcumin-polymer interactions. Physical stability under different environmental conditions was monitored by powder X-ray diffraction. Curcumin chemical stability was monitored by UV-Vis spectroscopy. Isolation of stable amorphous curcumin was difficult in the absence of polymers. Polymers proved to be effective curcumin crystallization inhibitors enabling the production of amorphous solid dispersions; however, the polymers showed very different abilities to inhibit crystallization during long-term storage. Curcumin intramolecular hydrogen bonding reduced the extent of its hydrogen bonding with polymers; hence most polymers were not highly effective crystallization inhibitors. Overall, polymers proved to be crystallization inhibitors, but inhibition was limited due to the intramolecular hydrogen bonding in curcumin, which leads to a decrease in the ability of the polymers to interact at a molecular level. PMID:24192454
Wegiel, Lindsay A; Zhao, Yuhong; Mauer, Lisa J; Edgar, Kevin J; Taylor, Lynne S
Chiral Br�nsted acid catalyzed enantioselective intermolecular allylic aminations.
This paper describes an enantioselective intermolecular allylic amination catalyzed by a chiral Br�nsted acid via a possible chiral contact ion pair intermediate. A variety of symmetrical or unsymmetrical allylic alcohols can be smoothly aminated to afford the desired products in moderate to high yields with good enantioselectivities and/or regioselectivities. PMID:24872122
Zhuang, Minyang; Du, Haifeng
Hydrogen-hydrogen intermolecular structure of polyethylene in the melt
Three polyethylene samples, which differed in their degree of deuteration, were studied in neutron diffraction isotopic substitution (NDIS) experiments at 428 K. These results were complemented at small wavevectors by small angle neutron measurements. The intermolecular hydrogen-hydrogen (HH) structure function, hHH(Q), was obtained without recourse to intramolecular structure models, as demonstrated in a prior report. The PE experimental results are compared to computer simulation results for the alkanes C100 at 509 K and C44 at 350, 400, and 450 K. The small temperature dependence of the HH intermolecular radial distribution functions, gHH(r) for C44 indicates that the differences observed between the PE, C100, and C44 (450 K) results are, for the most part, not due to just temperature differences. It is shown that the string model, an analytic result from an integral equation theory of polymers (PRISM), can account approximately for the overall shape of the gHH(r) functions, and that this overall shape is dependent on the radius of gyration of the molecule. Further analysis shows that there are two other contributions to gHH(r), both of which are independent of chain length to first order. The first is due to chain-chain packing, and the second is due to local HH intermolecular correlations. These results are significant because they demonstrate that hHH(Q) is a useful function for studying intermolecular polymer structure, which has been shown to underpin phase behavior in polyolefin blends.
Londono, J. D.; Annis, B. K.; Habenschuss, A.; Smith, G. D.; Borodin, O.; Tso, C.; Hsieh, E. T.; Soper, A. K.
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