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670435d751558a15ef66d508 | 15 | The work of Xi et al. shows how two-point extrapolations of the CCSD(T) energy can be much more accurate than previously expected if one optimizes the parameters for each pair of basis sets. Here we build on this outstanding work by showing that this higher accuracy can be obtained at even lower cost by choosing the diffuse basis functions more efficiently. Since jul and jun basis sets have less functions than aug, there is a significant reduction in the cost of the calculations. Our first finding is that the jul results are almost the same as the aug results. Our second finding is that jun basis set have either a minimal reduction in accuracy or even an improved accuracy as compared to aug basis sets; since there is a huge reduction in computational cost, we recommend using jun basis sets for CBS calculations with the parameters optimized here rather than using aug basis sets. |
6193820e2bf8a90552de4f1a | 0 | The improvement of high-energy-density batteries is a major focus in current research owing to consumer demand for sophisticated electronic gadgets and the everincreasing demand for electric vehicles. Conventional Liion batteries cannot satisfy present demand, whereas allsolid-state batteries(ASSB) could be suitable because of favorable factors such as high volumetric and gravimetric energy density, safety, and long life cycle. Fast ion conducting (FIC) solids form an integral part of ASSB and are a leading topic of current research . Significant efforts have been devoted over the last three decades to the advancement of Li + ion conducting materials . Recently, sodium ion conductors have been reported to be promising for energy storage applications because the Na ion has a very similar intercalation chemistry to the Li ion and, in some cases, the Na ionic radius is more suitable for stabilizing fast ion conducting frameworks because of its larger size compared with the Li ionic radius. Thus, the development of sodium ion conducting ASSB working at ambient temperatures is gaining renewed attention. |
6193820e2bf8a90552de4f1a | 1 | Recently, a unique class of heterostructures known as honeycomb layered oxides has gained attention as highenergy-density electrodes and electrolyte materials for their rich crystal chemistry that provides high cationic conduction and high voltages using Na and K ions . The general formula of this series of materials is A 2 M 2 DO 6 , A 3 M 2 DO 6 or A 4 M DO 6 , where M can be divalent or trivalent transition metal atoms such as Cr, Mn, Fe, Co, Ni, Cu, or some combination thereof; D rep- * [email protected] resents pentavalent or hexavalent metal atoms such as Sb, Te, or Bi; and A can be alkali metal atoms such as Li, Na, or K . The structure in general consists of an array of parallel transition metal slabs with a distinct honeycomb arrangement of multiple M atoms surrounding D atoms in a layered framework of interposed A alkali atoms. Specifically, the tellurates in honeycomb layered oxides have been reported to produce the highest voltages (over 4V) to date . Thus, a thorough study on the cationic diffusion mechanism in honeycomb layered oxides based on tellurate (Na 2 LiFeTeO 6 ) presents an ideal platform for maximizing the cationic conduction. |
6193820e2bf8a90552de4f1a | 2 | Atomistic details are valuable for better understanding and development of FIC solids . Molecular dynamics (MD) simulation has emerged as one of the first simulation methods for its ability to elucidate the underlying mechanisms at atomic level , as a complement to experimental probes, which are often difficult to implements. Silver iodide , β-alumina , and Na 1+x Zr 2 Si x P 3-x O 12 (NASICON) (0 ≤ x ≤ 3) are classic examples that show how MD studies predicted the experimental results. The technique has been successfully applied to a variety of oxide ion conductors as well . Recently, we developed an inter-atomic potential model for a family of fast ion conductors-A 2 M 2 TeO 6 (A = Li, Na, or K ; M = Ni, Zn, Co, or Mg) -to perform MD studies that represent the structural and dynamical properties reported in the experiments and present several interesting behaviors such as energy-driven or entropy-driven diffusion depending on the concentration of the mobile ions. Our previous work on A 2 Ni 2 TeO 6 (A = Li, Na, or K) showed how cationic distribution and the energy landscape vary with increasing inter-layer distance. The study also showed that ionic conductivity increases exponentially with increasing inter-layer distance. Moreover, the simulated cationic path in Na 2 Ni 2 TeO 6 has been experimentally confirmed . Accurately depicting microscopic physicochemical properties of materials that are beyond experimental reach requires the use of reliable potential parameters that can effectively reproduce the structural and transport properties determined by experiment. In this context, first-principles MD (FPMD) simulation, which reproduce forces on atoms precisely from electronic structure, plays a major role. However, FPMD is computationally extremely expensive and cannot deal with larger system sizes. Therefore, achieving accurate diffusion behavior is difficult because of low statistical accuracy. Thus, we rely on force-field-based MD simulations. |
6193820e2bf8a90552de4f1a | 3 | The present MD simulations are motivated by the recent experimental studies by Nalbandyan et al. , who synthesized a fast Na + -conducting solid (0.04 S/cm at 573 K comparable with the β-alumina ) of the formula Na 2 LiFeTeO 6 . The material is isostructural with heterovalence analogs of A 2 M 2 TeO 6 (A = Na, K ; M = Ni, Zn, Co, and Mg), consisting of edge-sharing LiO 6 , FeO 6 and TeO 6 octahedral brucite-like layers spanning the ab-plane, in which Te alternates with Li or Fe. The brucite-like octahedral layers are not identical along the c-axis, unlike the structure A 2 Ni 2 TeO 6 (A = Na, K), where the Na + ions occupy the inter-layer. The present study provides full inter-atomic potentials and fresh insights on ion transport. |
6193820e2bf8a90552de4f1a | 4 | To illustrate the local octahedral ordering, a crystal structural illustration of Na 2 LiFeTeO 6 is furnished in figure 1. As shown, the Na + ions are interspersed between metal slabs consisting of Li, Fe, and Te in an octahedral coordination environment with oxygen atoms. Despite the immense potential envisioned in the experimental study, details theoretical explorations of honeycomb layered materials, such as surrounding of the various mesoscopic mechanisms engendering their remarkable electrochemical performance still remain unexplored. Specifically, local octahedral inter-layer influencing on ionic conductivity are unclear, as the inter-layer distance is determined by existing elements in the framework octahedral layer and by mobile ions within the framework inter-layer. |
6193820e2bf8a90552de4f1a | 5 | The Na 2 LiFeTeO 6 structure consists of several polyhedral inter-layers with sandwiching Na + ions, as shown in Figure reported by Nalbandyan et al. . The top and the bottom of the adjacent framework inter-layers are not identical, unlike the other materials, A 2 Ni 2 TeO 6 (A = Na, and K). The LiO 6 , FeO 6 , and TeO 6 octahedra are arranged in a honeycomb fashion inside the framework layer. The octahedral inter-layers are stabilized along the c-axis by Van der Waals forces and by interactions me- diated via the Na atoms occupying the inter-layers. To understand octahedral ordering, an octahedral density pattern of Na 2 LiFeTeO 6 along the y-direction from MD simulation is shown in Figure , in which the FeO 6 octahedra are located on the top and the bottom along the c-axis. The Na + ion density pattern in the conduction plane is significantly influenced by the local octahedral sequences, most importantly where the inter-layer distance is small (∼ 3.5 Å). The octahedral density pattern from MD simulation follows same ordering as reported in X-ray structure. The inter-layer octahedral density are found to be a slightly off particularly at high temperatures because of thermal oscillation that leads to polyhedral layer-sliding. Furthermore, the average cell parameters of Na Herein, we want to emphasize that most of the cases the Li-atoms are consider to be mobile; in this case they form immobile framework. In contrast, the loose coordination to the framework polyhedral inter-layer allocates several cationic sub-lattices in the conduction layer for facile cationic conduction, as identified in the reported experimental structure. The facile Na + ion diffusion is reflected in the plot of the mean square displacements (MSD) against time (figure ). The closely packed framework octahedral layers parallel to the ab-plane restrict the Na + ion diffusion along the c-axis direction of the cell, as reflected in the inset of Figure (b) (less than 0.04 Å2 ). Therefore, cationic mobility appears to be restricted within the sublattices oriented parallel to the ab-plane, affirming the diffusion to be highly anisotropic (or layer diffusion), as also observed in the previous studies . |
6193820e2bf8a90552de4f1a | 6 | The Na + ion conductivity, σ, is calculated from the diffusion coefficient, D (the slope of the MSD near the diffusive region), according to Eq. 4. Calculation of the conductivity is also possible using the Green-Kubo relation instead of the Nernst-Einstein eq. 3. In principle, both approaches are equivalent. However, the correlation function involved in the Green-Kubo formula shows Inset shows the MSD of Na + ions along the c-axis direction (MSD-z) at 600 K. These results demonstrate that the framework atoms are immobile and the Na + ions are restricted along the ab-plane, rendering the diffusion to be highly anisotropic. |
6193820e2bf8a90552de4f1a | 7 | a slow decay or what is referred to as long-time tail that includes large fluctuations in the calculated electrical conductivity at long times . The plot of the logarithm of σT versus the inverse temperature (1000/T ) is displayed in Figure . The simulated result displays a straight line indicating Arrhenius behavior, whereas the experimental result shows a deviation from linearity at high temperature, possibly because of a phase transition. The activation energy can be calculated from the slope of the straight line according to Eq. 3. The activation energy of Na 2 LiFeTeO 6 is found to be 0.54 ± 0.02 eV from the MD simulation, whereas 0.48 eV is reported from the experimental study . Therefore, we conclude that the present MD simulation model successfully represents the structural (framework octahedral orientation and radial distribution functions) and dynamical properties of Na 2 LiFeTeO 6 with reasonable experimental agreement. |
6193820e2bf8a90552de4f1a | 8 | Herein, our focus is on the atomistic origin of high ionic conductivity in Na 2 LiFeTeO 6 . We calculated the threedimensional isosurface population density along with the polyhedral framework, as shown in Figures ) and (b) for understanding of Na + ion transport path. The Na + ion density lies inside the octahedral framework layer, which is also reflected in the MSD plot of the Na + ions along the z-direction. For further clarity of the Na + ions' diffusion paths, the two-dimensional population density (the number of ions per unit area) pattern and the average potential energy of the Na + ions in the conduc- The average potential energy of the individual cations is calculated using Eq. 6 (detailed in the METHODOL-OGY section IV) and projected onto a 2D grid in the ab-plane. Both the projected population density and the average potential energy are also replicated in 2×2 unit cells in the conduction plane for continuity, as shown in Figures ) and (d). The high density areas and their local environment-the octahedral centers and the Na sites-are indicated on top of the density and energy patterns. There are five high-density maxima in the population density profile, whereas there are four available Na + ions per unit cell per inter-layer. Therefore, the Na + ions can occupy the high-density maxima and can diffuse as well through the available vacant sites; as a result, the occupancy at each high-density area has to be less than unity. The occupancy at each maximaum density site was calculated using Bader charge analysis code, which was principlly developed for electron density analysis . Herein, the iso-surface density of Na + ion was used instead of charge density. The occupancy at S1 and S2 are close to unity, whereas close to half occupancy is identified at S3. For cationic channel connectivity, two types of ring connectivity are observed, as marked by circles: ring 1 (sky blue circle) consists of three high-density maxima, whereas ring 2 (orange circle) is formed by two maxima. The sites are marked S1, S2, and S3, as shown in Figure (c). Among the three high-density sites, S1 and S3 find good agreement with the reported crystallographic sites, whereas site S2 deviates from any reported crystallographic site. Furthermore, the sites S2 and S3 are located inside the circles formed by the framework octahedral centers, whereas site S1 is identified on the side of a triangle. None of the Na sites are found on top of the octahedral center because of strong repulsion between the top and bottom octahedra and the Na + ions. |
6193820e2bf8a90552de4f1a | 9 | The high-density population maxima are indicated on top of the potential energy profile in Figure , which reveals a different behavior than the population profile; the potential energy minima do not match with the population maxima. Rather, the high densities are found around the potential energy minima, possibly because of the entropic effect. For instance, two potential energy minima per layer per unit cell are identified, whereas four Na + ions are available. Thus, the sodium ions cannot occupy the energetically favorable sharp potential energy regions (-2.4 eV), but rather occupy the sites which are greater in number and therefore higher in entropy. The difference between the effects of energy and entropy can be linked through Eq. 8, in which entropy plays a significant role. Specifically, particles usually avoid energetically favorable sharp potential energy minima with low entropy, whereas they prefer a relatively higher energy basin which has high entropy. This scenario can be understood by implementing a simulation which places fewer Na + ions in a conducting layer (detailed in the METHODOLOGY section IV). The Na + ion density pattern and the potential energy profile are shown in Figure in the supplementary information for the under-loaded conduction plane. In the potential energy profile, the locations of the potential energy minima are almost unchanged, whereas the population density pattern changes significantly. Only one type of ring exists, consisting of four high-density maxima. The highest population densities are identified exactly at the potential minima. In this case, the smaller number of Na + ions contributes to a lower entropy, resulting in an energy-driven population distribution. The entropy contribution is even lower if the number of Na + ions in the conduction layer is reduced even further, as shown in Figure , where all population density maxima and potential minima coincide exactly in the conduction plane, implying a minimal entropic contribution. For a quantitative estimation of the intra-and interring free energy barrier heights that determine the Na + ion diffusion mechanism, the one-dimensional free energy distributions among the high-density population maxima are shown in Figure . The free energies were calculated by counting the population density distributions inside a rectangle connecting two high-density areas (with a width of 1.0 Å) as indicated in Figure and projected along a straight line connecting two sites using Eq. 9. Figure captures the free energy minima and maxima for inter and intra-ring cases, distinctly, as reflected in Figure . The pairs of site distances and corresponding free energy barriers of Na + ion hopping are listed in Table II. The inter-ring free energy barriers are higher than the intra-ring free energy barriers, which is also reflected in Figure . Thus, the intra-ring mechanism is more favorable than the inter-ring mechanism. However, both mechanisms are responsible for the long-range Na + ion diffusion. A direct ring mechanism is also revealed by randomly tracking a Na + ion over simulation time, as displayed in Figure , where the high-density Na sites (S1, S2, and S3) are also marked. The Na + ions diffuse through both the inter-ring and intra-ring pathways, as evident in the free energy barriers and the population density profiles. |
6193820e2bf8a90552de4f1a | 10 | Both the population density profile and the free energy profile indicate that the Na + ion is trapped for a while within the ring. Therefore, the estimation of the trapping time of the Na + ions provides a valuable insight into Na + ion diffusion. Thus, the self-van Hove correlation function is calculated (Figure The free energy distribution is calculated using Eq. 8. Two different (intra-ring and inter-ring) free energy distributions are displayed. |
6193820e2bf8a90552de4f1a | 11 | in their respective lattice sites, whereas the other peaks signify the Na + ions hopping to the neighboring sites. The residence time (the time taken before the second peak arises) of Na + ions at the lattice sites is observed to be roughly 10 ∼ 15 ps. However, the third peak appears after a significantly longer time (∼ 100 ps), because the Na + ions become trapped inside the ring. Furthermore, the trapping time of Na + ions inside the ring is also found in a log-log plot of the Na + ions' MSD, as shown in Figure (b), which shows a caging of about 100 ps (roughly until the point at which the log-log MSD follows straight-line behavior) with an MSD value of about 4 Å2 before moving to the diffusive region. Interestingly, this 4 Å2 is close to a value of d 2 /2, where d is the approximate diameter of a ring (∼ 3 Å). Therefore, the log-log MSD plot also supports the ring mechanism of the diffusion of the Na + ions. The above behavior is also confirmed in the underloaded Na plane for case 1, as displayed in Figure in the supplementary information. In this case, the Na + ion also shows trapping inside a ring consisting of four high-density maxima, as revealed in Figure in the Supplementary Information. The corresponding self-van Hove correlation function also reflects a trapping time of about 50 ∼ 60 ps in Figure (a). The same time duration is also identified in the log-log MSD plot in Figure . |
6193820e2bf8a90552de4f1a | 12 | For further clarity of the Na + ion hopping mechanism, the coordination number of the Na + ion is analyzed. The first peak at 3 Å in Figure (a) indicates that if one S3 site is occupied, the nearest S3 site has to remain vacant (the nearest S3-S3 distance is 2.25 Å). The above scenario can be explained using a schematic diagram, as shown in The most likely distribution of Na + ions invokes the occupation of two sites of a ring, leaving one site vacant to avoid strong Na-Na repulsion, as there are six Na sites and four Na + ions per layer per unit cell. Thus, the Na + ions can show a circular motion inside the ring, or they can move out from the ring. When one Na + ion moves out from a ring, another Na + ion should enter from a neighboring ring to maintain local charge The self-van Hove correlation function, Gs(r, t ), as a function of radial distance (r) and time (t ) for Na 2 LiFeTeO 6 at 600 K from NVE-MD simulations, shown on a logarithmic scale for better visualization. Several high-intensity regions (marked as 1st, 2nd, and 3rd) indicate the Na + ion occupancy while hopping from one site to another site occurs. Time-scales of just before grow the 2nd and 3rd peaks are also mentioned. (b) A log-log plot of MSD for identifying the ion trapping in a ring. A dotted red line is added to distinguish the caging and diffusive regions. |
6193820e2bf8a90552de4f1a | 13 | A refined set of inter-atomic models represents the structural and transport properties of honeycomb layered oxides in Na 2 LiFeTeO 6 , in excellent agreement with the experimental results. This potential model can be leveraged to garner distinct atomistic insights such as the entropic contribution in cationic distribution and the ring-like cationic diffusion from the population density profile, the free energy barrier, the self-van Hove correlation, and the log-log MSD plot. Therefore, an MD simulation provides a new avenue to test the ion dynamics of various honeycomb layered oxides. Particularly, the entropic contribution and the distinct ring-like feature that controls fast ion transport in solids is interesting in applications beyond honeycomb layered oxides. |
6193820e2bf8a90552de4f1a | 14 | To carry out an MD simulation, the reported Vashishta-Rahman form of interatomic potential is employed. This method is becoming popular recently, as it describes structural and dynamical properties of a series of honeycomb layered oxides, namely Na 2 M 2 TeO 6 (M = Ni, Zn, Co and Mg), as well as NASICONs. A Na-Na = 0 eV, A Na-Li = 80000 eV, A Na-Fe = 27000 eV, A Na-Te = 7000 eV, n Na-Na = n Na-Li = n Na-Fe = n Na-Te = 11 a The value used from the reported literature . |
6193820e2bf8a90552de4f1a | 15 | where q i represents the charge and σi the ionic radius of the i-th atom. The parameters A ij , P ij and C ij describe the overlap-repulsion energy of the electron clouds, the average charge dipole interactions, and the dispersion constant between the ion pairs i and j, respectively. The Vashishta-Rahman potential has a softer overlap repulsion (1/r n , where n = 11, 9, or 7 for cation-cation, cationanion, and anion-anion pairs, respectively), particularly between the anion-anion pairs. The inter-atomic parameters used in this study are listed in Table . Some of the parameters have already been reported . The parameters that are unavailable in the literature were determined using empirical fitting to attain the experimentally reported bond lengths (Li-O, Fe-O, and O-O) of Na 2 LiFeTeO 6 . The details of the empirical fitting methods are as follows: The non-identical brucite-like octahedral framework along the c-axis is retained by refining the Li-Na, Fe-Na, and Te-Na pairs and the Na-O parameters were refined to represent the conductivity. |
6193820e2bf8a90552de4f1a | 16 | The empirically fitted set of parameters listed in Table III were used to carry out a series of MD simulations in the temperature range of 400 K to 600 K with 25 K intervals, and zero atmospheric pressure. The Parrinello-Rahman isobaric-isothermal (NPT) MD method , which allows for changes in the simulation box sizes while keeping angles fixed, was used. The temperatures and pressure in the system were controlled using thermostating and barostating techniques, whereby some dynamic variables are coupled with particle velocities and simulation box dimensions. Simulations commenced from the reported X-ray diffraction structures wherein the simulation supercell was constructed by 7 × 4 × 3 unit cells comprising 3696 atoms in an orthorhombic symme-try following P2 1 2 1 2 1 (No. ). Several partially occupied crystallographic sites were identified in the Na conduction plane. In MD simulations, we placed the Na + ions at the crystallographically reported highest occupied sites (Na2 and Na5) to avoid strong cation-cation repulsion. For clarity, all reported crystallographically distinct sites (Na1, Na2, Na3, Na4, Na5, and Na6) in the layered frameworks of Na 2 LiFeTeO 6 are shown in Figure . The inter-layer interaction is usually weaker in nature; thus, inter-layer sliding is expected unless the initial configuration is not set properly. To avoid inter-layer sliding, we performed a constrained MD simulation for 500 ps for each temperature case; the framework atoms (Li, Fe, and Te) were frozen at the crystallographic sites and the other atoms were allowed to move. Finally, we lifted the former constraint and performed the usual MD simulation. A time step of 2 fs was applied to the velocity Verlet algorithm to solve Newton equations of motion. A typical run-time of 6 ns or longer was used with trajectory samples stored at intervals of 200 fs for detailed analyses. To guarantee the thermodynamic convergence properties, a few longer run-time simulations of 100 ns were performed separately. Periodic boundary conditions in all three directions and the Ewald summation technique for the convergence of long-range Coulombic interactions were applied using the LAMMPS software package . A cut-off distance of 13 Å was used for both the short-range interactions and the short-range part of the Ewald summation. Micro-canonical MD (NVE-MD) simulations were further performed at 600 K using the final structure obtained from NPT-MD simulations. |
6193820e2bf8a90552de4f1a | 17 | Furthermore, to understand the entropy effect in the presence of a larger number of Na + -ions, we performed a few constrained MD simulations with a different number of Na + ions in each layer. For instance, there are four Na + -ions in each layer in each unit cell. Here, we performed two distinct NPT-MD simulations with alternative Na + -ion densities as follows: |
6193820e2bf8a90552de4f1a | 18 | Finally, an FPMD simulation was performed based on Density Functional Theory (DFT) using the Vienna Ab Initio Simulation Package (VASP) to compare the structure with that obtained using the force-field-based MD simulation. We performed FPMD simulations in an NPT ensemble, in which temperature and pressure were controlled using Langevin thermostating and barostating techniques. The plane-wave basis sets and projectoraugmented-wave pseudopotentials were used under periodic boundary conditions. An energy cutoff of 320 eV was used; integrals over the Brillouin zone were performed only at the Γ-point. The simulated super-cell consisted of 2× 1× 1 unit cells with a total of 88 atoms. The FPMD simulation was performed at 800 K for 1-ps equilibration and 2-ps sampling with a time step of 1 fs. |
6193820e2bf8a90552de4f1a | 19 | where N denotes the total number of mobile atoms in the system, r j (t) is the position vector of the j th ion at time t, t is the time difference, and the angular bracket indicates the average over several points in time. The factor four appeared in the denominator of eq. 2b is because of two-dimensional diffusion, whereas it is six for the three-dimensional case. The diffusion coefficient, D, depends on the temperature (T ) according to the Arrhenius equation, |
6193820e2bf8a90552de4f1a | 20 | where p represents the population density function (the occupancy) of the cations, p max is the maximum value of the population density function, ∆V is the difference in potential energy of the individual cations (eq. ( )), and ∆S is the difference in entropy (the relative entropy). Finally, we calculated the "self" part of the self-van Hove correlation function, G S (r, t ), to understand the Na + ion hopping mechanism using the formula , |
63c14932553889a2f17f8147 | 0 | Cubane was first theorized to exist by Thorpe and Beesley 1 over 100 years ago and consists of eight nominally sp -hybridized carbon atoms bonded together to produce a highly strained cubic structure. Cubane is not only interesting because of its peculiarity as a hydrocarbon Platonic solid, but it is also a useful bioisostere for the benzene ring due to its similar size and shape (Scheme 1A). Therefore the 1,4-substitution pattern of a cubane molecule could replace a para-substituted phenyl ring in a molecule and potentially offer improved properties including a departure from "flat-land". Furthermore, there are other uses for cubane and its derivatives such as its ability to rearrange into cunenes, its utilization in explosives and its incorporation into polymers. The first successful synthesis of cubane was accomplished by Eaton and Cole 10 to give dimethyl cubane-1,4-dicarboxylate 1 in 8 steps with a 12% overall yield from cyclopentenone. Subsequent routes by and Tsanaktsidis 12 allowed for cyclopentanone to be used as starting material at comparable synthetic efficiency and overall yield. Further optimizations of Tsanaktsidis's route by Linclau and co-workers allowed for the synthesis of decagram quantities of 1 in overall yields of between 33-40%. Despite extensive work, current synthetic routes to 1 rely upon the synthesis of key building block dibromo-dione 2 from cyclopentanone in 5 steps (Scheme 1B). |
63c14932553889a2f17f8147 | 1 | Dione 2 can then undergo an intramolecular photochemical [2+2] cycloaddition, which is promoted by the use of either a high-powered Hg lamp or a UV-B lamp (λexc = 311 nm) under acidic conditions and has been successfully scaled-up using continuous flow photochemistry. After being refluxed in water to hydrolyse any methyl ketals, 3 can then be transformed into the cubane scaffold using a Favorskii rearrangement to give cubane-1,4-dicarboxylic acid 4, which is then esterified and isolated as 1. Scheme 1. (A) Body diagonals of cubane and benzene. (B) Overall synthesis for dimethyl cubane-1,4-dicarboxylate. |
63c14932553889a2f17f8147 | 2 | While these synthetic routes have been refined over decades and can now be scaledup to efficiently produce large quantities of 1, the key [2+2] cycloaddition step still requires the use of UV-B lamps and specialist glassware. With this in mind, we set out to identify and optimize alternative conditions that would allow for lower energy light to be used. Two different strategies to achieve this were considered: the use of Lewis |
63c14932553889a2f17f8147 | 3 | Initial exploration focused on the use of Lewis acids to shift the absorption spectra of 2 closer to the visible region. This has been demonstrated previously for simpler α,ßunsaturated ketones by Bach and coworkers 14 using oxazaborolidine-based catalysts for enantioselective reactions and boron trichloride in the racemic version, which achieved bathochromic shifts of nearly 70 nm. To test if this was possible for 2, UV-vis absorption spectra were obtained in the presence and absence of BCl3 (Figure ). |
63c14932553889a2f17f8147 | 4 | Without BCl3, 2 shows a band with a peak maximum, λabs, of 250 nm. Pleasingly, in the presence of BCl3 a new band appears at λabs of 300 nm and with a tail into the visible region. However, attempts at direct photoexcitation of 2 in the presence of boron trichloride with a 370 nm LED showed no reactivity and only returned unreacted starting material. Therefore, even though the Lewis acid does shift the absorption of 2 as hypothesized, this strategy did not prove productive, and investigation turned to the use of a photocatalytic DET reaction. ). The most accurate methodology used was at the BLYP/6-31G(d,p) level of theory, which predicted an ET of 62. Based on these calculations, a solution of 2 and 25 mol% of benzophenone in MeCN was irradiated with a 390 nm LED over 24 h (Table , entry 1). Pleasingly, partial conversion to the desired product (3) was observed using our standard photoreactor (see ESI). Increasing the catalyst loading gave increased product conversion over the same period but fell short of complete conversion to 3 (Table , entries 2-3). To achieve full conversion, an alternative reaction set-up that involved direct irradiation rather than the use of a photoreactor (see ESI) was employed that provided more intense irradiation (Table , entry 4-6). At this point, control reactions were carried out to confirm the necessity of benzophenone. When using the photoreactor in the absence of benzophenone, no conversion to the desired product was observed, which is consistent with our previous attempts with BCl3 (Table , entry 7). However, upon direct irradiation, a modest conversion to 3 was observed in the absence of benzophenone (Table , entry 8). This suggests that if the light is sufficiently intense, then photoirradiation at 390 nm should promote the [2+2] cycloaddition via direct excitation of 2, albeit much less efficiently. To obtain useful quantities of 3 the reaction was scaled up to a 0.5 mmol scale. Similar results were observed, with full conversion to 3 requiring 0.5 equivalents of benzophenone (Table , entries 9-11). Further increase in scale to a 1.0 mmol reaction could also be achieved using the same conditions and an NMR yield of 93% was observed (Table , entry 12). 1.0 50 100 (93) d a Conditions: 2, benzophenone, MeCN (0.1 M), N2, LED (λexc = 390 nm), rt. b From crude 1 H NMR. c Reaction performed in a photoreactor (see Figure ). d1 H NMR yield using 1,3,5-trimethoxybenzene as the internal standard. |
63c14932553889a2f17f8147 | 5 | Linclau and co-workers reported that crude 3 could only be subjected to the Favorskii rearrangement conditions after being refluxed in water to hydrolyse any methyl ketals present. As our method avoids the formation of any methyl ketals, crude 3 could undergo the desired Favorskii rearrangement without the water hydrolysis step to give crude 4. To allow for facile purification, 4 was then converted to the methyl ester using an acidic methanol solution to give the final compound 1 in 20% yield over three steps from 2. Although this represents a lower overall yield than the 54% achieved by Linclau and coworkers, considering the high conversion and NMR yield for the formation of 3 through [2+2] cycloaddition we hypothesise this is due to difficulties in precipitating 4 on a much smaller scale. Having completed the synthesis of 1, our attention turned to the photocatalytic functionalization of cubane using cubane carboxylic acid 5 as a convenient cubyl radical precursor. First, 5 was synthesised via hydrolysis of 1 in 50% yield, with 44% of the unreacted diester being recovered (Scheme 3A). Then, 5 was subjected to a photocatalytic decarboxylation procedure known to work efficiently with other tertiary carboxylic acids such as 1-adamantylcarboxyclic acid; 18 however, only trace amounts of the desired product, 6, was observed (Scheme 3B). |
63c14932553889a2f17f8147 | 6 | In summary, we have developed a synthetic route to dimethyl cubane-1,4-dicarboxylate where the key photochemical [2+2] cycloaddition is catalysed by the cheap and widely available photosensitizer benzophenone to give near quantitative yields of the desired product 3 from dione 2. This allowed for the use of much lower energy light (λexc = 390 nm) than previous direct excitation methods that required a high-power Hg lamp or UV-B irradiation. Issues involving scale-up should be remedied using flow chemistry to allow for the photocatalysed [2+2] cycloaddition to be performed on a much larger scale. Finally, attempts at photocatalytic decarboxylation of 5 were attempted using conditions known to work for tertiary carboxylic acids; however, these were unsuccessful, with further work towards the photocatalytic functionalization of cubane derivatives ongoing. |
655337036e0ec7777fe7d9c4 | 0 | In undergraduate courses of Chemistry, quantum mechanics of one-dimensional systems occupy a prominent position. Quantum states of a particle in a one-dimensional potential well, rigid rotator on a plane, harmonic oscillator, etc. are taught to demonstrate the techniques of arriving at solutions of the Schrodinger equation (SE) posed as a boundary value problem, emphasizing at the same time the importance of all mathematical conditions imposed on the wavefunctions. It is almost mandatory in all such courses to venture a little beyond and discuss quantum mechanics of the hydrogen atom in three dimensions. The bound energy levels and wave functions of the hydrogen atom are key to the development of general ideas and understanding of the level structures of heavier atoms. The (SE) for H-atom in 3D is not separable in Cartesian system of coordinates. The standard textbook recipe has been to transform the energy eigenvalue equation from Cartesian (x, y, z) to spherical polar coordinates (r, θ, ϕ) and separate the angular and the radial parts Rnl(r) of the wave equation which are then analytically solved. The former turns out to be the spherical harmonics [Y l m (θ, ϕ)] while the latter takes the form of the associated Laguerre polynomials. The total wave function inversion symmetric. Its signature, the parity, is a 'good' quantum number and the hydrogenic levels alternately belong to even and odd parity. We note, however, that V (r ⃗) is singular at the origin (|r| ⃗⃗⃗⃗⃗ = 0). The role of the singularity, if any, in shaping the radial wavefunctions is usually bypassed or underemphasized at the introductory level of the undergraduate courses in Chemistry. But several issues do come up and require careful handling while discussing the behavior of Ψ, in the neighborhood of |r ⃗| = 0. Whatever be the 'parity', the allowed quantum states have (2l + 1) fold degeneracy (the m-degeneracy, the magnetic quantum number 'm' taking integer values from -l to l in steps of 1) arising from the rotational symmetry of the hydrogen atom. There is also an extra l-degeneracy (e.g., 2s, 2p) not connected with the rotational symmetry. It has been often called an accidental degeneracy, the origin of which is a dynamical symmetry. The hydrogenic energy levels turn out to be dependent only on the principal quantum number ( Enlm = -R n 2 , n = 1, 2, 3,...) revealing the l and m degeneracies referred to. |
655337036e0ec7777fe7d9c4 | 1 | . It has inversion symmetry just as V (r ⃗) has in 3 dimensions. The singularity at the origin (x = 0), although reminiscent of the singularity at r = 0 in the 3-D hydrogen atom, is more problematic as it separates the available coordinate space into two regions ( x > 0 and x < 0 ). The 'enigma' of the hydrogen atom in one dimension originates from this singularity at x = 0. (iv) What kind of spectrum (vis-à-vis the 3-D hydrogen spectrum) can be anticipated? |
655337036e0ec7777fe7d9c4 | 2 | The one-dimensional hydrogen atom has been a controversial problem with a fairly long history, but its importance in understanding how the calculus of quantum mechanics operates in singular potentials, can hardly be overestimated. In this article, we briefly trace the history of hydrogen atom in one dimension and elucidate how the standard Frobenius method (a generalized series expansion method) can be applied to this system vitiated as it is, by the singularity at the origin. As expected, the conditions that the wave function 𝛹(𝑥) must be single valued and continuous with continuous first derivative, 𝛹 remaining finite everywhere (including the singular point) and vanishing at the outer boundaries' (𝑥 = ±∞) play a key role in shaping the energy eigenfunctions and the corresponding energy eigenvalues. |
655337036e0ec7777fe7d9c4 | 3 | The one-dimensional hydrogen atom has been at the center of controversies and debate ever since Loudon (1952) published his theoretical work on the system. Since then, it has been debated if the system has an infinite or a finite energy ground state, whether there are energy degeneracies, violating the one-D non-degeneracy theorem, whether the states are localized (symmetry broken) on either side of the singularity (x = 0) or delocalized across the origin, and are parity eigenstates as well. There is no unequivocal or concrete experimental evidence on the existence of the hydrogen atom in one dimension and its spectral signatures; but there have been several attempts to define limiting experimental conditions (e.g., high magnetic field) which may lead to the realization of the one-dimensional H-atom and recording of its spectrum. Calculations of Landau & Lipshitz, which dealt with giving an estimate of the strength of such magnetic field, emphasize that the highest available magnetic fields in the laboratory is almost negligible compared to the range of the magnetic field strength required to approach the condition for the realization of the one-D H-atom. Some experiments on quasi-one-D polymer chains, which resembles the system of the one-D H-atom, reported optical absorption spectra with the dominance of the ground state. There are other such examples, such as semiconductor quantum wires and carbon nanotubes, , which reported various forms of the absorption spectra. However, these results are inadequate to characterize the exact experimental form of the absorption spectrum of one-D H-atom, as the conditions for its realization are still elusive. Thus, the one-D H-atom has largely remained a theoretical problem to test various theoretical techniques of handling quantum mechanical problems of the present kind. The result of all these investigations do not seem to have converged to a generally accepted conclusion about the nature of quantum states supported by the 1-D Coulomb potential, or their number. More significantly, the spectral signature of the 1-D H-atom, if it exists, is not yet known. Among the theoretical investigations, the series expansion method, Fourier transform method, Supersymmetric method and insertion of cut-off potential to the one-D potential function method , infinite number of discrete quantum states with exactly the same energy levels as found in the 3-D hydrogen atom, the reduction in the dimension (from 3 to 1) notwithstanding. However, these results are confined to research journals and reviews and are not easily accessible or comprehensible to chemists or students of chemistry, who could ultimately play a crucial role in the eventual experimental realization of the 1-D H-atom, if it exists. It is primarily this objective, that has guided us in exploring the problem and writing this article. |
655337036e0ec7777fe7d9c4 | 4 | which severely limits the classically accessible region around r = 0. This region around r = 0 is, however, accessible to a quantum particle via tunnelling. The wave function χ in this region however, decreases rapidly according to the power law (χ~r l ), the damping being stronger for higher l values. For l = 0 there is no centrifugal barrier and the electron (s electron) can therefore approach the nucleus infinitesimally closely. |
655337036e0ec7777fe7d9c4 | 5 | where, f(ξ) is a function that needs to be determined. Substituting equation ( Ψ 0 also infinite. The choice α = 1, however, does not lead to a blow up. The correct form of Ψ(ξ) from ξ = 0 to ∞, that keeps Ψ(ξ) finite at or near ξ = 0 and also makes it vanish at the right boundary (ξ ~ ∞) is therefore ψ(ξ) = e -ξ 2 ξ g(ξ) , where g(ξ) may be chosen as a power series in ξ. |
655337036e0ec7777fe7d9c4 | 6 | a n , n = 1,2,3, … (ξ > 0) 4. 1.12 In order that the infinite series generated by the recursion relation (4.1.12) does not diverge but truncates at a finite number of terms converting it into a polynomial of degree 'n', the energy E of which β is a function must have such values that: |
655337036e0ec7777fe7d9c4 | 7 | The quantum states supported by the one-dimensional Coulomb potential are linked to their energies. The corresponding wavefunctions Ψ n (ξ) (n = 1,2,3) are easily found to be: The ground state wave function ψ 1 (ξ) (ξ < 0) is found to be localized on the left of the origin and has the energy |
655337036e0ec7777fe7d9c4 | 8 | N being the normalization constant. The profile of Ψ 1 (-) (x) is displayed in figure . Thus, the 1-D H-atom has a finite energy bound ground state having odd parity as opposed to the ground state of H-atom in 3 dimensions, which is of even parity. It is not a nodeless ground state as expected in a 1-D system, but is definitely non-degenerate. The singularity at the origin has thus stamped its signature on the wave function for the ground state. Are there excited bound states as well with definite parity? Are they degenerate? We analyze these issues in the section that follows. |
655337036e0ec7777fe7d9c4 | 9 | The procedure adopted to calculate the ground state wave-function (n = 1) and energy (E1) can be extended to higher values of n (n = 2, 3, … etc) as well. The left (x < 0) and right (x > 0) localized components of the eigenfunctions of the energy operator for n = 2 and n = 3 (the first and the second excited states of the system) are reported in Table along with their respective energy eigenvalues. Ψ nL and Ψ nR can be seen to have the same energy eigenvalue |
655337036e0ec7777fe7d9c4 | 10 | 2n 2 a 0 for a particular value of n. They are degenerate but lack parity and are therefore physically unacceptable as eigenfunctions in an inversion symmetric potential. However, their symmetric and antisymmetric combinations (Ψ n (+) and Ψ n ) have even and odd parity, respectively in each case. They are physically acceptable, although apparently degenerate in energy as displayed in Table . |
655337036e0ec7777fe7d9c4 | 11 | The left (x < 0) and the right (x > 0) components of Ψ n (x) (n = 2,3) Ψ n (+) and Ψ n (-) (n = 2, 3) have clear parity labels, but other mathematical restrictions on the wavefunctions must now be considered. Ψ n (+) and Ψ n (-) (n > 1) clearly vanish at x = ±∞ and are finite at all the interior points. They are also continuous at all points including x = 0, and linearly independent. We may, however reject the even parity eigenfunctions (Ψ n (+) , n > 1) and accept only the odd parity eigenfunctions (Ψ n , n > 1) on the mathematical ground that the first derivative of Ψ n (-) (x) is continuous at x = 0 (the singular point) while the first derivative of Ψ n (+) (x) may not so be. This fact can be demonstrated in a slightly roundabout way. Let us consider the SE for the one-D H-atom for the quantum state Ψ n (-) (n > 1): |
655337036e0ec7777fe7d9c4 | 12 | Ψ 2 (-) (x) and Ψ 3 (-) (x) are displayed in the figure (a) and 3(b). The still higher states can be calculated similarly. The odd parity of all the bound states suggests that the transition moment integral mediated by the electric dipole moment operator ⅆ = ex vanishes in, |
655337036e0ec7777fe7d9c4 | 13 | The transition moment integrals mediated by the electric quadrupole moment operator ex 2 may, however, be nonzero (See Appendix II for further details). The spectrum of the one-D H-atom is, therefore expected to be dominated by electric quadrupole transitions while the spectrum of 3-D Hydrogen atom is essentially electric dipole driven spectrum. Experimental spectral data alone can confirm this prediction, which is unavailable at this moment. |
6744808ef9980725cfd26c0e | 0 | Fused aromatic networks (FANs), the network polymers consisting of fully fused aromatic rings, have been intensively studied due to their unique structural, optical, and electronic properties. 1 While many types of two-dimensional (2D) FANs have been reported, 3D FANs have not been well studied due to the difficulty of constructing 3D networks with fused aromatic structures. To date, several examples of 3D FANs have been synthesized using nonplanar conjugated units and their structural features, thermal stability, porosity, and semiconductor properties have been studied. The 3D FANs with saddle-shaped cyclooctatetraene derivatives as nonplanar conjugated units exhibited physical and chemical stability, permanent porosity, high surface area, and semiconductor properties. 2 Triptycenes were also used as nonplanar conjugated units to form 3D FANs that exhibited high gas adsorption properties and thermal stability. Considering the high stability and electronic properties, phthalocyanines and their analogues are useful π-conjugated units. Phthalocyanine-based polymers have been studied for many years. Based on band structure calculations, 1D and 2D fully fused polymers were predicted to exhibit electrical conductivity. The synthesis of 2D phthalocyanine polymers was carried out both on metal surfaces and in solution. 6 However, only a few examples of 3D polymers have been reported. The 3D frameworks containing phthalocyanines reported so far were not conjugated because they were linked by sp 3 carbon or boron atoms. 7 An electrically neutral, spiro-linked phthalocyanine-containing 3D polymer was synthesized by Later in 2017, Kimura and co-workers reported the synthesis of a spiro-conjugated 3D polymer using spirobifluorenes. To synthesize 3D FANs containing phthalocyanine analogues, we devised a strategy of using tetrapyrazinoporphyrazine (TPyzPz) and bending it with bulky substituents. TPyzPz is an analogue in which the benzene rings of phthalocyanine are replaced with pyrazine rings, and 2D FANs based on TPyzPz units have been synthesized (Fig. ). 10 Since the introduction of bulky substituents distorts phthalocyanines to be saddleshaped structures, we assumed that 2D and 3D FANs can be synthesized from tetracyanodihydrodipyrazinopyrazines (TCDP) depending on the size of the substituents (Fig. ). Herein, we report the synthesis of Zn TPyzPz FANs bearing 1-ethylpropyl and 2,4,6-trimethylphenyl (mesityl) groups. The crystallinity of the obtained solids was investigated by X-ray diffraction and the progress of the polymerization reaction was confirmed by using IR, solid-state C NMR, and diffuse reflectance spectroscopy. The thermal stability and porosity of the polymers were also measured by thermogravimetric analysis and adsorptiondesorption experiments, respectively. First, the structures of Zn TPyzPz dimers were optimized by density functional theory (DFT) calculations to investigate the influence of the substituent size on polymer networks. For the calculation, B3LYP method was used and LANL2DZ and 6-31G (d) basis sets were applied for Zn and other atoms, respectively (Fig. ). As shown in Fig. , the dimer having 1-ethylpropyl groups (DiEtPr) adopts a planar structure. On the other hand, the optimized structures of the dimers having mesityl and 3,5-di-tbutylphenyl groups (DiMes and DiBuPh) are nonplanar in which the TPyzPz are distorted to be saddle-shaped structures. The bent angles of DiMes and DiBuPh are 145.3° and 123.3°, respectively, indicating that the bent angles increase with the substituent size caused by the steric repulsion of substituents. The dimer structure of DiMes was then extended to a 3D periodic structure and structural relaxation was performed by Quantum Espresso to obtain the framework structure with diaf topology (See Fig. for details). 12 These calculations indicate that the TPyzPz polymers with bulky substituents hinder the formation of 2D sheet and result in a 3D network structure. |
6744808ef9980725cfd26c0e | 1 | Monomers 3a-c were prepared according to reported procedures with modifications (Fig. ). The SNAr reactions of dichlorodicyanopyrazine 1 with corresponding alkyl-and arylamines were carried out to produce monoaminated products 2a-c. Dimerization of 2a-c using triethylamine was performed in refluxing N,N-dimethylformamide (DMF) to obtain desired monomers 3a-c. The monomers 3a-c were identified by 1 H and 13 C NMR spectroscopy, mass spectrometry, and X-ray crystallography (see SI for details). With three monomers in hand, we investigated the polymerization reactions. As shown in Fig. , polymer 4a was synthesized by the cyclotetramerization of the dicyanopyrazine moieties of monomer 3a in the presence of anhydrous zinc chloride (0.5 equiv.), n-pentanol, and a catalytic amount of triethylamine in N,N-dimethylacetamide (DMAc). The mixture was heated without stirring and the solution turned dark green as the reaction progressed. Polymer 4a was obtained as an insoluble black solid and thoroughly washed with organic solvent and water. The use of diphenyl ether instead of DMAc as solvent afforded a brittle solid. In the reaction conditions using 1,8-diazabicyclo [5.4.0]-7-undecene as a base, no insoluble solid product was obtained. The optimized procedure using DMAc and triethylamine was also applied to 3b and 3c, and as a result, an insoluble black solid (polymer 4b) was obtained from 3b whereas no solid was formed from 3c. These results indicate that 3a and 3b were polymerized to form highly crosslinked polymers. As described in Fig. , the oligomers of 3a cannot form a planar 2D sheet, suggesting the formation of 3D structures. On the other hand, no polymer was obtained from 3c. Considering that the electronic effects of the mesityl and 3,5-di-tert-butylphenyl groups are comparable, the size of the substituent causes a significant difference in the reactivity of polymerization. The formation of TPyzPz structure was confirmed by the cyclotetramerization of 2,3-dicyanopyrazine under the reaction conditions using zinc chloride, n-pentanol and triethylamine in DMAc to obtain compound 5 in 70% isolated yield (Fig. ). To confirm the polymer structures in detail, a series of analyses were performed including Fourier transform infrared (FT-IR) spectroscopy, solid-state C nuclear magnetic resonance (NMR) spectroscopy, energy dispersive spectroscopy (EDS), and Powder X-ray diffraction (PXRD) measurement. FT-IR measurements of 4a, 4b and their monomers (3a, 3b) were performed in air using an attenuated total reflectance method. Because the C≡N stretching peak at about 2230 cm -1 observed in the FT-IR spectra of monomers 3a and 3b disappeared in those of polymers 4a and 4b, it is inferred that the cyano groups were consumed (Fig. ). Solid-state 13 C NMR spectra of 4a and 4b using the cross polarization magic angle spinning with total suppression of sidebands (CP-MAS TOSS) method are shown in Fig. and, respectively. In the spectrum of 4a, aliphatic and aromatic signals derived from mesityl groups and TPyzPz moieties were observed. Signals attributed to DMAc were also observed at 160-170 ppm and 25-40 ppm. The spectrum of 4b shows the signals corresponding to 1-ethylpropyl, TPyzPz, and DMAc. For 4b, a small signal at 115 ppm was observed, which could be unreacted cyano groups. The EDS of 4a and 4b were performed using a Schottky emission scanning electron microscope. As shown in Fig. and S12, C, N, and Zn elements are distributed throughout the surface of the solids. PXRD results of 4a and 4b supported the formation of partially ordered polymers (See SI for details). Thermogravimetric analysis was performed to investigate the thermal stability of polymers 4a and 4b. Before the measurement, polymers were soaked in diethyl ether and dried under vacuum. The weight loss derived from decomposition of 4b was observed at around 300 °C, whereas no decomposition of 4a was observed up to 500 °C (Fig. ). These differences in thermal stability are probably due to the 2D and 3D network structures. |
6744808ef9980725cfd26c0e | 2 | In order to gain insight into the photophysical properties of 4a and 4b, diffuse reflectance spectroscopies were carried out. Each polymer was dispersed to 1w% in magnesium oxide as dispersant and ground for 30 min prior to the measurements. The diffuse reflectance spectra of 4a and 4b are shown in Fig. with the absorption spectrum of 5 in dimethyl sulfoxide (DMSO) solution as a reference. Both spectra show two broad peaks that can be assigned as Soret bands (4a: 436 nm, 4b: 430 nm) and Q bands (4a: 667 nm, 4b: 664 nm). In comparison to the absorption spectrum of 5 (soret: 335 nm, Q: 634 nm) in DMSO, the Soret and Q bands of 4a were red-shifted by 101 and 33 nm (6.91 × 10 3 and 7.80 × 10 2 cm -1 ), respectively, indicating the extension of π-conjugation through polymerization. Similar results were observed for 4b (6.59 × 10 3 cm -1 for soret band and 7.13 × 10 2 cm -1 for Q band). |
6744808ef9980725cfd26c0e | 3 | Adsorption-desorption experiments were carried out to investigate the porous properties of 4a and 4b. As shown in Fig. , 4a and 4b showed adsorption behavior for CO2. These results show the porous properties of 4a and 4b. The BET surface and Langmuir surface area of 4a calculated from CO2 adsorption are 581 and 576 m 2 •g -1 , respectively, are slightly larger than those of 4b (386 and 446 m 2 •g -1 ). |
6744808ef9980725cfd26c0e | 4 | Monomers 3a-3c were prepared from dichlorodicyanopyrazine and aryl-or alkylamines in two steps. Polymerization of monomers 3a and 3b afforded insoluble black solids 4a and 4b, while no solid was obtained from 3c indicating that 3,5-di-tert-butylphenyl groups were too bulky to polymerize. The consumption of cyano groups and the formation of Zn TPyzPz moieties were confirmed by IR spectra and solid-state 13 C NMR spectra. The formation of partially ordered polymers was supported by PXRD measurements. Differences in thermal stability, possibly due to the 2D and 3D network structures, were observed in TG-DTA measurements. The extension of π-conjugation through polymerization and the porous properties of the 4a and 4b were confirmed by diffuse reflectance spectroscopies and adsorption-desorption measurements, respectively. This work demonstrated the novel strategy for the synthesis of 3D FANs to create optically unique and porous organic materials. |
670819a112ff75c3a1130890 | 0 | phosphoanhydride bonds. 2 PolyP plays diverse roles in both prokaryotic and eukaryotic cells. For example, it is involved in energy storage, molecular chaperoning, regulating apoptosis, hemostatis and thrombosis, 6 bone mineralization and proinflammatory functions, and oxidative stress response. 8 Moreover, polyP has been linked to cognitive performance as well as neurodegenerative conditions such as Parkinson's disease, Alzheimer's disease, and amyotrophic lateral sclerosis. Short-chain polyPs are found in parasites such as Trypanosoma cruzi, Trypanosoma brucei, and Leishmania major where they are important for parasite metabolism. Besides its biological roles, polyP is also important in biotechnological applications such as e.g. ATP regeneration systems using polyP kinases. Furthermore, the ability of microorganisms to accumulate polyP is used to remove phosphates from wastewater. Given the diverse areas in which polyP plays an important role, there is a significant demand for simple chemical sensors that enable the detection of polyP, ideally with selectivity regarding chain length. For biological applications, such detection would benefit from selectivity over other abundant condensed phosphates, such as e.g. ATP. Currently, there is only a very limited number of colorimetric and fluorescent probes available to visualise polyPs. The use of 4ʹ,6-diamidino-2-phenylindole (DAPI), a yellow fluorescent compound in complex with polyP, is the most popular approach, owing to its significant fluorescence shift when binding to polyP. In addition to DAPI, toluidine blue has also been used for the detection of polyPs. However, literature reports that only polyPs with a chain length longer than 15 units are detected by DAPI and toluidine blue. 1 Also, some interferences with other phosphate containing molecules have been reported. |
670819a112ff75c3a1130890 | 1 | For example, characteristic yellow fluorescence is also emitted from DAPI-inositol phosphate complexes. As an alternative to DAPI-polyP emission, Pavlov's group reported fluorescent benzimidazolinium dyes, but these also require longer chain polyPs. Thus, currently the detection of polyPs with fluorescent sensors is not covering polyPs with comparatively short-chains in the single digit range. |
670819a112ff75c3a1130890 | 2 | Selective fluorescent sensors of important (condensed) phosphates, such as Pi and pyrophosphate (PPi), have been developed using different strategies, including hydrogen bonding interaction, coordination chemistry, displacement assay/decomplexation, and aggregation-induced emission/quenching. The choice of using an ESIPT-based strategy is promising due to its current success in detection of numerous environmentally and biologically significant analytes. 18a, 19 However, achieving selective detection of polyP over PPi and other anions like nucleotides is not a trivial task. Moreover, the sensor should rapidly respond in an aqueous environment. This adds a solubility problem, as a majority of the known ESIPT based fluorescence sensors are only sparingly soluble in aqueous solution, which limits their widespread applicability. 20 Herein, we report the first chemoselective, reversible, water-soluble, short chain inorganic polyP sensors that work in an aqueous environment and rely on the ESIPT mechanism providing large Stokes-shifts for diverse applications. |
670819a112ff75c3a1130890 | 3 | Ligand designing and synthesis: The ESIPT phenomenon is linked to the presence of an intramolecular hydrogen bond, usually between a proton donor (-OH/-NH) and a proton acceptor (-C=O/heterocyclic N). The fluorophore 2-hydroxy phenyl benzoxazole and its derivatives could provide on-off switching properties of the ESIPT signal through metal complexation, leading to metal induced fluorescence quenching. Decomplexation of the metal through the analyte would then lead to recovery of the ESIPT signal. Provided the decomplexation can be selective, as previously shown in disassembly strategies, e.g. by the Zelder group for PPi, one could design a polyphosphate responsive ESIPT sensor. To confer solubility in aqueous medium, a charged group, such as a sulfonate, would be beneficial. Based on the above considerations, fluorophore 4 was synthesized in four steps starting from 3-chloro-2-hydroxybenzaldehyde (Scheme 2). |
670819a112ff75c3a1130890 | 4 | Condensation of aniline with 3-chloro-2-hydroxybenzaldehyde afforded imine 1. The imine intermediate 1 was refluxed with conc. H2SO4 to introduce a sulfonate group at the 5 position in 84% yield. Treatment with Na2CO3 gave the sodium salt 3 in 58% yield. Afterwards, condensation of 3 with 2-aminophenol followed by in situ cyclization afforded the ESIPT fluorophore 4 in 41% yield (Scheme 2). Another ESIPT fluorophore 5 was synthesized in two steps in 52% yield (Scheme 2). These two fluorophores with slightly modulated photophysical properties served as basis for our follow-up studies. |
670819a112ff75c3a1130890 | 5 | The main challenge for designing fluorescence sensors for negatively charged species is that its hydration tendency reduces the sensors' ability to interact with the target analyte. One potential solution to surmount this challenge involves the employment of a displacement strategy, where initially the fluorescent probe is complexed to a metal ion that quenches the fluorescence (metal-ion-induced fluorescence quenching). Then, decomplexation of the metal ion by the negatively charged analyte leads to a restored ESIPT fluorophore. Copper complexes have been used for Pi and PPi sensing, 25 however no other condensed phosphate chains have been examined with related complexes. |
670819a112ff75c3a1130890 | 6 | To generate a metal quenched ESIPT-OFF probe 6, we reacted probe 4 with 0.5 equiv. of CuCl2 at room temperature (61% yield). The formation of this complex in a 2:1 stoichiometry was confirmed by HRMS data (Fig. ). Furthermore, we confirmed the correct stoichiometry by changes in photophysical properties and Job's plot analysis (see next section). While the Cl substituent in 6 was mainly installed to enable further potential modifications, we also generated a non-chlorinated version to study and compare the impact of substitution on the photophysical properties and selectivity regarding different anions. An identical complexation of 5 with Cu 2+ in a 2:1 stoichiometry was conducted, resulting in complex 7. |
670819a112ff75c3a1130890 | 7 | Photophysical studies of the fluorophores in the presence of Cu 2+ : Spectrophotometric titration was used to examine the UV-Vis absorption spectrum of ligand 4 in 10 mM HEPES buffer solution at pH 7.4 (Fig. ). A prominent band with an absorption peak at 368 nm was visible. With increasing addition of Cu 2+ (from 0.1-0.5 equiv.) the absorption maximum at 368 nm increased, and adding more equivalents did not elicit additional changes indicating a 2:1 complexation with Cu 2+ . further changes, suggesting that 4 is complexed with Cu 2+ in a 2:1 stoichiometric ratio. Further, the 2 : 1 stoichiometry was confirmed by a Job's plot (Fig. ) and the HRMS data for 6 and 7 (Fig. and S8, respectively). |
670819a112ff75c3a1130890 | 8 | Initially, we therefore looked into the decomplexation of the sensor with polyP8, which is currently the longest monodisperse polyP available by synthesis. Also shorter polyphosphates are accessible in monodisperse form through chemical synthesis (see SI section 12). 26 Addition of polyP8 to complex 6 (in 10 mM HEPES buffer at pH = 7.4) led to a gradual decrease of the absorption peaks at 288 nm, 300 nm and 356 nm (Fig. ). In case of complex 7, the absorption peaks at 254 nm, 284 nm and 351 nm also decreased while absorption increased at 317 nm with increasing polyP8 concentration (Fig. ). Interestingly, the decrease in absorption intensities was much higher with non-chlorinated 7 compared to chlorinated 6. The structures of complexes 6 and 7 are tentatively assigned to be square planar, but we could not obtain crystal structures of the compounds. The very different behaviour might be a result of distortions of the geometry based on steric constraints potentially exerted by the chlorine atom. |
670819a112ff75c3a1130890 | 9 | Both complexes were further studied regarding their ESIPT-ON state upon titration. PolyP8 sensing of weakly emissive 6 was investigated by using fluorescence spectroscopy. Upon addition of polyP8 sodium salt into a solution of 6 (2.5 μM in 10 mM HEPES buffer at pH = 7.4), the fluorescence emission intensity (λex= 254 nm) centred at λem=434 nm was progressively enhanced within 2 minutes of polyP8 addition. An eightfold enhancement in the fluorescence intensity was observed when 10 equiv. of polyP8 were added (Fig. ). We attribute these significant changes in the spectral properties to the removal of Cu 2+ from the ligand's coordination sphere by polyP8, releasing the ESIPT fluorophore characterized by its large Stokes shift. During excitation at 254 nm, we observed a polyP8 concentration-dependent fluorescence increase at 434 nm (Fig. ). The titration resulted in a sigmoidal curve, by using nonlinear regression analysis of the polyP8 induced emission data. Notably, the fluorescence intensity did not decrease with time (Fig. ), demonstrating stability of the released fluorophore. To determine the complexation stoichiometry between 6 and polyP8, Job's plot analysis was conducted on the basis of the emission intensity at 434 nm (Fig. ). The result suggested that a 1:2 stoichiometry was found between 6 and polyP8, while [6] + [polyP8] = 5 µM was maintained throughout the experiment. Probe 7 (5 µM concentration) behaved in a similar way and showed ESIPT-ON under titration with polyP8 (excitation at 250 nm, emission at 430 nm; see Fig. ). Selectivity studies of the probes towards polyP over other phosphates: Given the excellent ESIPT-ON properties of the sensors in response to polyP8, we were now interested in profiling the selectivity of 6 and 7 with respect to other condensed phosphates. Both probes 6 and 7 were incubated with a wide range of biologically relevant (condensed) phosphates, like monophosphate (Pi), pyrophosphate (PPi), several abundant nucleotides such as ATP, AMP, ADP, GTP, GMP and GDP under the same conditions of 10 mM HEPES at pH = 7.4 with 2 minutes of incubation time. |
670819a112ff75c3a1130890 | 10 | The emission intensities elicited by all these analytes were measured. Fig. shows that the decomplexation and resulting ESIPT fluorescence of 6 reached a maximum in presence of polyP8 as compared to other tested anions. Both sensors 6 and 7 had a similar selectivity profile regarding anions. However, the emission intensity was higher for the released ESIPT fluorophore 4, enabling its application at twofold lower concentrations. Fluorescence quantum yields for 4 and 5 were determined to be 0.33 and 0.16 respectively (experimental details in the SI), directly explaining the higher sensitivity of 6 in the assays. The limit of detection (LOD) of polyP8 with 6 and 7 were found to be 97 nM and 110 nM, respectively (details in SI section 9). Both sensors did not respond to phosphate (Pi) and monophosphate esters, such as GMP or AMP. In contrast, both sensors did respond to pyrophosphate (PPi), but the increment in fluorescence gain is small in both cases. Diphosphate esters like e.g. ADP and GDP also elicited a response, but reduced when compared to free PPi. Nucleoside triphosphates like ATP or GTP also released some of the fluorophore, but by far the largest increment of ca. 8-fold was achieved with polyP8 in both cases. Consequently, sensors 6 and 7 represent the first selective short-chain polyP sensors that work in an aqueous environment based on an ESIPT-ON mechanism (Fig. ). Next, we investigated the dependence of the signal of sensors 6 and 7 on polyP chain lengths using several synthetic standards and commercial polydisperse references. Interestingly, we observed that with increasing chain length the signal intensity increased, reaching a plateau around polyP8, when incubated under the same conditions (10 mM HEPES, pH = 7.4). Figure depicts this trend in fluorescence intensity gain from monophosphate to pyrophosphate to polyP8 (10 equivalents of each different polyP with 6 or 7). We also examined the fluorescence response of probes 6 and 7 towards different cyclic metaphosphates like cyP3, cyP4 and cyP8. 29 cyP4 and cyP8 showed a considerable fluorescence response, unlike cyP3. Yet, linear polyP8 still elicited a 1.5 times higher response as compared to its cyclic analogue cyP8 (Fig. ). |
670819a112ff75c3a1130890 | 11 | We also profiled longer polyphosphate chains, which are commercially available. These are polydisperse mixtures of different chain length and so it is difficult to obtain their real concentration. Usually, the phosphate content in thus indicated in terms of Pi monomers after digestion with exopolyphosphatase (PPX). 1 After increasing the concentration of the longer chain polyPs (polyP14 -polyP700) to 125 µM for 6 and 250 µM for 7 (in terms of Pi residues), we observed a trend of reduced response from both sensors 6 and 7 with increasing chain length from polyP14 (7-fold increase) to polyP130 and polyP700 (4-fold increase), indicating that our sensors are most responsive to short-chain polyP with an average chain length of around 8. (Fig. ). |
670819a112ff75c3a1130890 | 12 | Addition of Cu 2+ into a solution of 4 leads to a quench of fluorescence at 434 nm due to the formation of 6. The fluorescence was recovered by the addition of polyP8 into the solution of 6, leading to the release of 4. Five alternating additions of Cu 2+ and polyP8 showed interconversion of 4 to 6 and back, which indicates that 4 can be used as a reversible fluorescent 'turn-off-turnon' probe for Cu 2+ and polyP8 (Fig. ). The concentration of Cu 2+ and polyP8 had to be adjusted in each cycle to obtain reversibility (see details in SI section 4). |
670819a112ff75c3a1130890 | 13 | respectively (Scheme 4). Using this rationale, we investigated the application of the more sensitive probe 6, due to its higher quantum yield, towards monitoring polyP digestion by PPX. PPX (2.9 mg/mL, 40 mM Tris-acetate, 10 mM Mg(OAc)2, 30 mM NH4OAc, 0.2 mM EDTA at pH= 8) was added to an aqueous solution of polyphosphates of varying chain length (2-10 mM, for polydisperse polyphosphates the concentration is based on Pi units) and incubated at 37 0 C for 21 hr. The enzyme reaction mixture as well as the control (no PPX) were added separately to a solution of 2.5 µM of 6 (in 10 mM HEPES buffer at pH= 7.4), and the ensuing fluorescence intensity at 434 nm was measured as the mean of three replicates in a 96 well-plate (details in SI section 5). When the control mixture (only polyP8, no PPX) was incubated with probe 6, a clear increase in emission was observed. However, no significant increase in the emission intensity was observed when incubated with the PPX reaction mixture, because of the digestion of polyP8 by PPX to 6 Pi units and one PPi (Fig. a,b). PolyP digestion was also monitored for polydisperse polyphosphates (polyP22, polyP60, and polyP130). A significant decrease in fluorescence emission after digestion was observed (Fig. ). It is apparent that for polyP8 the difference of emission between control and PPX digestion is lower than that obtained for longer polyPs. This can be rationalized by the fact that digestion of polyP8 results in a higher PPi:Pi ratio as compared to the digestion of longer chain-length polyPs that release less PPi overall. Since the sensor shows no response to Pi, but a small response to PPi, the larger difference can be rationalised. |
664f0bb7418a5379b0133a8e | 0 | Since its inception, click chemistry has been established as a powerful approach for molecule synthesis. Strategies within click chemistry include several widely used reactions such as the (hetero-)Diels-Alder, 1,2 alkene hydrothiolation, and an array of amide-bond forming chemistries. However, by virtue of the access to alkyne and azide precursors and the formation of a single 1,4-disubstituted triazole product, the copper-catalysed azide-alkyne cycloaddition (CuAAC) remains the archetypal click reaction (Scheme 1). Scheme 1. The CuAAC reaction and installation of functional groups for product diversification. The reaction has shown applicability on small and large scale, as well as under flow conditions, and extensive scope across a range of benign solvent conditions. In addition, the CuAAC reaction uses inexpensive Cu catalysts, 11 is insensitive towards oxygen and water, and consistently delivers high yields and (where relevant) enantioselectivities. As such, the reaction has been used extensively throughout drug discovery, chemical biology, and materials science. Orthogonal alkyne reactivity can also be observed under certain systems. The reaction typically uses a Cu(II) pre-catalyst, which is converted to a mechanistically-required Cu(I) species in situ through the addition of a reductant (e.g., sodium ascorbate, NaAsc), or via Glaser-Hay alkyne homocoupling. The mild and accessible nature of the CuAAC reaction has allowed the use of azide or alkyne components that bear functional groups for subsequent product diversification (Scheme 1). For example, protected alkynylboron reagents can be employed, such as N-methyliminodiacetic acid (MIDA), potassium trifluoroborates, and others. Similarly, organosilicon reagents have proven useful in various Cu-and Pd-catalysed C-X bond forming strategies, including widespread use across several CuAAC methodologies. Germanium-based functional groups have recently emerged as highly useful components for transition metal-catalysed crosscouplings. Schoenebeck and co-workers have shown that Gebased compounds are versatile reagents for chemoselective cross-coupling processes for the formation of a variety of C-C and C-X bonds. Importantly, these transformations can take place in the presence of borylated functional groups, allowing orthogonal cross-coupling, whilst also offering excellent stability compared to boron-based reagents. Based on their utility and stability, germanium units could therefore be useful within CuAAC reactions and offer potential as functional handles for downstream elaboration of CuAAC products. To date, the use of germanyl alkynes in (3+2) cycloadditions has been limited to a small number of Huisgen (non-Cu-catalysed) reactions. Here we report the development of germanyl alkynes as CuAAC components, with exploration of their scope and downstream diversification. We undertook an exploratory survey of CuAAC reaction conditions using benzyl azide and triethylgermanyl acetylene (see ESI). The most effective conditions were found to be based on the classical combination of CuSO4/NaAsc, with optimisation (see ESI) delivering the general conditions shown in Scheme 2. These afforded clean conversion to the desired triazole products (1-21) without any observable degermylation or other side reactions that could be anticipated based on transmetalation to Cu. The generality of the CuAAC process was explored using a range of azides (Scheme 2a), with variation of the germanyl alkyne motif (Scheme 2b), and with variation of both components (Scheme 2c). In general, the CuAAC process worked effectively, tolerating the functional groups for which the CuAAC is wellknown -in all cases the remaining mass balance was the germanyl acetylene, suggesting sluggish CuAAC reactivity compared to other alkynes, which typically require much shorter reaction times. Extending the reaction time provided higher conversion to the product (14). Yields were observed to be greater for aryl azides (e.g., 4 vs. 6). Heterocycles such as pyridine (1), pyrimidine (10), phenothiazine (11), and chromene (12) were tolerated. Benzylic azides were accommodated including those bearing nitro (2), iodo (3), and boronic ester groups (5, 21). Strained rings were effective including cubane (18) and bicyclopentane (20). While 18 and 20 were isolated in lower yield, no evidence of ring opening was observed and the starting material could be recovered in each case, consistent with observations by MacMillan. Variation of the steric and electronic parameters of the germanyl acetylene was straightforward (14-17; Scheme 2b). Several limitations were observed (Scheme 2d): benzyl azides displaying an arylboronic acid and MIDA ester (22 and 23) gave no reaction, side reactions were observed with a dialkynyl germane (24), and the product derived from azide 25 was unstable to purification. |
664f0bb7418a5379b0133a8e | 1 | To further demonstrate the compatibility and utility of germanyl alkynes in CuAAC reactions, we applied the CuAAC process to more challenging substrates. Using fluorophore-and cholesterol-derived azides, coupling with the triethyl germanyl alkyne delivered the expected products 26 and 27, respectively, in good yield, enabling possible downstream diversification of these functional of relevance to chemical biology (Scheme 3a). The utility of the germanyl triazole products was then assessed by subsequent derivatisation of exemplar compounds 15 and 21 (Scheme 3b). Chemoselective Suzuki-Miyaura cross-coupling of the BPin moiety in 21 was straightforward, giving 28 in excellent yield. Similarly, cross-coupling of the GeEt3 moiety in 15 under conditions developed by Schoenebeck and coworkers gave 29. Bromodegermanylation using NBS employing conditions from Schoenebeck gave bromotriazoles 30 and 31 in moderate to excellent yield. These could then undergo Suzuki-Miyaura cross-coupling to give 32 or chemoselective Negishi coupling to give 33. Finally, BPin 21 could be oxidised to the phenol derivative 34 or cross-coupled with piperidine under Chan-Lam conditions to give the aniline derivative 35 in good yield. In summary, we have demonstrated the first application of germanyl alkynes in CuAAC chemistry. These reagents are generally compatible but seem to be less reactive than other classes of alkyne. The germanyl alkyne CuAAC is applicable to functional group-rich molecules, opening opportunities for downstream diversification by chemoselective functionalisation strategies. The germanyl group installed in the triazole products can be used as a reactive handle for further diversification including cross-coupling reactions. |
659bf0c29138d231617324ed | 0 | For decades it was thought that two-dimensional crystals were not possible, until the successful preparation of monolayer graphene with mechanical exfoliation proved that two-dimensional planar crystal structures could be isolated. These layers are not only stable but also exhibit remarkable physical and chemical properties not found in their parent materials. For example, the thermal conductivity of suspended monolayer graphene is as high as 5,000 W/mK as measured by Raman spectroscopy, a value much higher than that of bulk diamond or graphite. Similarly, at room temperature, the carrier mobility in graphene can also reach much higher values of up to 15,000 cm 2 V -1 s -1 and is less dependent on temperature than in its bulk counterpart. Because of these outstanding properties, graphene can be used in high-speed electronics, optical devices, chemical sensors, energy production and storage, and DNA sequencing among many other fields. |
659bf0c29138d231617324ed | 1 | The successful preparation of graphene led to a growing number of other two-dimensional materials being reported. Similar to graphene, transition metal dichalcogenides (TMDs) have been studied for some time, with the structure of TMDs first reported by Linus and colleagues as early as 1923. By the 1960s, about 60 TMDs materials had been reported, of which at least 40 exhibit layered structures, for example MoS2, MoSe2, WS2 and WSe2, among others. These layered crystals not only have a thickness comparable to that of graphene, but additionally have an intrinsic band gap, which gives them the potential to be used in a new generation of small, low energy-consuming transistor materials. The semiconductor industry is driven by the continued reduction in transistor size, with Moore's law stating that the number of transistors that can fit on an integrated circuit doubles approximately every eighteen months. These days, the state-ofthe-art silicon-based transistor has all but reached its fundamental limit and, to further break through the gate length of silicon-based field-effect transistors, materials that can achieve smaller sizes than silicon are sought. Two-dimensional (2D) materials have an inherent advantage for transistor applications because they are intrinsically stable at atomic thicknesses and still have robust and well-characterized electrostatic properties. In a study by Xie et al. it was noted that in field effect transistors prepared from MoS2, channel lengths of down to 4 nm could be reliably achieved; owing to the planar confinement of the 2D material effectively |
659bf0c29138d231617324ed | 2 | Please do not adjust margins Please do not adjust margins suppressing short channel effects. By comparison, the minimum channel length that can be achieved in state-of-the-art silicon-based transistors is around 5 nm, which is difficult to reduce further without the device failing. Thus, it is expected that TMDs will be able to enable further reduction in transistor size beyond the intrinsic limit of silicon. There are also other 2D materials that have been successfully exfoliated from their parent materials apart from TMDs, such as phosphole, arsenene, hexagonal boron nitride and C3N4, which have crystal structures similar to that of graphene. In general, these two-dimensional materials have great potential for applications in sensors, batteries, transistors and many other fields, as shown in the Figure . Therefore, there is strong motivation to explore new two-dimensional materials and as such, an expansion of the tools used by researchers to identify and understand 2D materials is desirable for the research community. |
659bf0c29138d231617324ed | 3 | The varied nature of 2D materials has defied facile classification thus far owing to the numerous atomic structures and the myriad arrangements with which bonded layers may nestle together. However, the poor bonding in the interlayer direction should always be observable in the electronic band structure of the material; see for example the band structures of the archetypal 2D materials WSe2, MoS2, WS2 and MoSe2 in Figure . The curvature of the bands is known to correlate with degree of bonding and each of these materials has a noticeable contraction to flat bands in the specific path of the Brillouin zone that corresponds to the interlayer crystallographic direction. This band curvature is often quantified or expressed as conductivity effective mass; with positive (p-type) charge effective mass arising from the curvature in the occupied valence bands and negative (n-type) charge effective mass arising from the curvature of the unoccupied conduction bands. These days, publicly available codes and open-source software exist that can calculate the conductivity effective mass automatically and indeed have already been deployed on repositories of many thousands of materials. In this paper we assess whether such automated analysis can recover the likelihood of 2-dimensional nature of a material based on the conductivity effective masses arising from the band structure by calculating the exfoliation energy of the two thousand stable materials reported to have the most anisotropic conductivity effective mass tensors. |
659bf0c29138d231617324ed | 4 | There are two publicly available repositories that form the basis of this work. First is the database of information on conductivity effective mass for 22,976 materials published by Ricci et al. The second is the structures and values of energy above convex hull from the Materials Project database. We use the energy above convex hull as a metric of thermodynamic stability for the first screening criterion. Then, we cross-reference the remaining stable materials with their corresponding values of conductivity effective masses of carriers in three crystallographic directions from the repository of Ricci et al. Next, we eliminate any materials containing F-block elements due to their scarcity. Finally, we select |
659bf0c29138d231617324ed | 5 | Please do not adjust margins Please do not adjust margins the one thousand materials each of p-type and n-type that have the largest standard deviation of effective mass. For these materials, we automatically construct slabs and calculate their exfoliation energy with density functional theory (DFT). Ultimately, we explore the relationship between exfoliation energy and standard deviation of the effective mass. A schematic of the screening workflow of this paper is shown in Figure . |
659bf0c29138d231617324ed | 6 | The DFT calculations were performed using the Vienna Ab Initio Simulation Package (VASP) version 5.4.4, which uses the Projector Augmented Wave (PAW) method for modelling core and valence electrons. The Perdew-Burke-Enzerhof (PBE) exchange correlational functional of the Generalized Gradient Approximation (GGA) was chosen. For the long-range, non-local interactions that give rise to the van der Waals force, the D-3 method correction proposed by Grimme was used to describe the van der Waals interaction where indicated in this work. All of the VASP input files were automatically generated using pymatgen "io.vasp.sets" module, 41 however the magnetic moment of atoms and the spin polarization effect were not considered to allow for convergence of structural relaxation of slab calculations containing surface terminations. |
659bf0c29138d231617324ed | 7 | The data of the conductivity effective masses was obtained from the work of Ricci et al, which is based on the Boltzmann transport theory. The BoltzTraP software was used to calculate the conductivity, Seebeck coefficient, effective masses and other transport properties of the materials. BoltzTrap uses the relaxation time approximation and the k-point interpolation method based on a Fourier expansion to calculate conductivity effective mass, which is dependent on temperature T and doping level. In this work, the data we used were found at a temperature of 300 K and a doping concentration of 10 18 cm -3 . |
659bf0c29138d231617324ed | 8 | To create the slab structures for high-throughput ab initio calculations, we developed a python code with the help of the pymatgen toolkit to expand the relaxed crystal cell along the axis in which the effective mass has its largest value, so that the unit cell length is not less than 15 angstroms. Then, the code adds a fake atom incrementally throughout the lattice space and collects the distance from that atom to its closest other atom (so-called nearest neighbour distance). After doing this 1,600 times across the unit cell, the code reports back the position of the fake atom that gives the maximum nearest neighbour distance. Once the coordinates of fake atom have been determined, the code will pull the crystallographic cell apart by 10 angstroms (to ensure that the periodic boundaries of the cell don't allow the surfaces to interact with themselves) along the high-effective mass axis. A summary of this process and example slab construct can be seen in Figure . Please do not adjust margins Please do not adjust margins All of these slabs were subject to static calculations to obtain internal energy without ionic relaxation at the PBE or PBE+vdW level of theory. The exfoliation energy could then be obtained by the formula: |
659bf0c29138d231617324ed | 9 | The left side of the equation Ef is the exfoliation energy, Eslab on the right is the energy from the slab structure and Esuper is the energy of supercell. S is the surface area of structure after relaxation. Practically the exfoliation energy reflects the relative ease of separating atomic layers of a material. |
659bf0c29138d231617324ed | 10 | Since, the inverse of the effective mass is the second-order partial derivative of the energy on the k-point in the energy band diagram dividing the square of the Planck constant; the effective mass reflects the degree of dispersity or bending of the electronic energy band. When the value of the effective mass is very large, it indicates that the band is flat and barely diverges at that point in the Brillouin zone, akin to the features of the band structures shown in Figure . Conversely, if the effective mass value is low, there should be high dispersion of the bands in that region of the Brillouin zone. We posit therefor that a 2-dimensional material should exhibit a relatively high conductivity effective mass in the inter-layer direction of a 2D crystal and a relatively low effective mass in the two bonded crystallographic directions. Overall, this behaviour should be possible to capture and quantify in the single value of standard deviation for the conductivity effective mass tensor. |
659bf0c29138d231617324ed | 11 | Firstly, we identify the materials from the Materials Project that present with an energy above convex hull of 0 eV. These materials IDs are then cross-referenced with the publicly available database of calculated conductivity effective mass values of Ricci et al. While the known examples of 2D materials have band contraction in the conduction band (see Figure ), it may not necessarily be the case for all 2D materials. As a result, we consider datasets for both p-and n-type effective mass in parallel. |
659bf0c29138d231617324ed | 12 | Among the screening candidates identified to be on the convex hull, 3,938 n-type materials show their standard deviation of effective mass less than one, which indicates that most stable materials are electronically isotropic, as is perhaps to be expected. By comparison however, the maximum standard deviation of effective mass for n-type materials reaches an outlandish 1,910,154. Such a huge standard deviation as this is meaningless and arises as an artifact from the effective mass. Because the derivative of a perfectly flat band is infinite, there is no upper limit to the value that can be presented by the standard deviation. What exactly is a high enough effective mass for the band to be considered flat is entirely arbitrary and so a heuristic approach is still needed. As examples for comparison, we include experimentally reported values of effective mass in Table . We include more details on the effective mass at a, b and c crystallographic directions for the selected 1,000 p-type and 1,000 n-type materials in the supplementary materials (see Figures and ). |
659bf0c29138d231617324ed | 13 | Next, we identify both the 1,000 materials with the highest effect mass standard deviation for n-type doping and 1,000 of the highest for p-type doping. For these 2,000 materials we automatically create slab simulations and calculate exfoliation energies for each. We do this for two levels of DFT: PBE and PBE with van der Waals corrections (PBE+vdW); meaning a total of four thousand data points. These are plotted as four separate panels in Figure by taking the logarithm of the exfoliation energy against a truncated standard deviation of conductivity effective mass. Figure and 5b show the results obtained for n-type materials at the PBE and PBE+vdW functional levels, respectively. And Figure and are the results obtained for p-type materials at the PBE and PBE+vdW functional levels, respectively. Detailed information on the structure of these materials and related information, as well as the structures that did not converge during the calculations, can be found in the supplementary materials (see Figures ). |
659bf0c29138d231617324ed | 14 | From Figure , we can see that the distribution characteristics of the p-type and the n-type material scatters are very similar, the data points are mainly concentrated in the lower left corner and a few isolated points are distributed up the middle area of the graphs. This relationship shows the expected behaviour posited at the start of this paper -that as the standard deviation of conductivity effective mass approaches zero the exfoliation energy rises rapidly-indeed the exfoliation energy appears to increase |
659bf0c29138d231617324ed | 15 | Please do not adjust margins exponentially. The subplot on the right indicates that most materials have a small exfoliation energy, even though we selected those with the highest standard of effective mass from all stable compounds. This observation is to be expected given that of the many thousands of known materials, only a few dozen twodimensional materials have been successfully prepared experimentally. The subplot underneath each panel shows similarly that most materials have a relatively low standard deviation of effective mass. From this we can infer that a material with a standard deviation of effective mass of more than 100, for example, is already exceptional relative to almost all known cases (see Figure for the interval distribution of the conductivity effective mass for each of the 1,000 materials datasets). |
659bf0c29138d231617324ed | 16 | We also confirm this behaviour with the effect of van der Waals interaction included for the exfoliation energy calculations for both n-type and p-type materials (images b and d in Figure ). The effect of the vdW corrections serves to raise the exfoliation energy values higher than those obtained using the PBE functional, which is to be expected given that the instantaneous dipoles create forces of attraction and therefor make materials harder to pull apart. The nature of the relationship between exfoliation energy and effective mass standard deviation remains unchanged at this higher level of theory. This is a fortuitous result as it benefits the community to be able to screen for 2D materials at as rapid a level of theory as possible. However, we note that when the van der Waals interaction is not considered, there are several materials that show negative values for the exfoliation energy (see Figure in the SI for the specific cases). This should not be possible, as negative exfoliation energies imply that the structure of the material is unstable prior to layer separation, even though we screened for only thermodynamically stable materials. The expected positive respectively. Information about all these materials can be found in Table . |
659bf0c29138d231617324ed | 17 | Please do not adjust margins Please do not adjust margins exfoliation energies are obtained when the total energy of the structure is calculated considering van der Waals interactions, however. As such, we encourage other researchers to include van der Waals corrections in any future studies involving the calculation of exfoliation energies. We note that there is a discrepancy between the values of standard deviation of charge effective mass for the p-and n-type datasets, observable in Figure . Whereas the smallest standard deviation for the n-type results is 5.14, the smallest value for the ptype results is 31.1. This indicates that sampling the conduction band can give a broader range of values across the same set of materials than does the valence band and is perhaps therefore a more suitable resource for use in future screening. Once again, this observation is somewhat intuitive and relatable to fundamental materials physics in that higher energy bands in general are less likely to be strongly bonding when compared to lower energy bands due to the shielding effects of the deeper, core states of the material. With less strong bonding, the bands are likely to be relatively flatter and hence give rise to a greater standard deviation for the charge effective mass tensor. |
659bf0c29138d231617324ed | 18 | As a whole, we believe there is a clear relationship between the two properties considered in this work. However, there are multiple outliers in the data which we investigate further. From the datasets represented in Figure For the n-type materials, Figure (from the top left section of Figure ) is K4Ta2S11 which presents an atomic structure that immediately appears not amenable to exfoliation. The anions and cations are reasonably interspersed throughout the structure and there is a high density of bonds present. This is to be expected given the compound's position high on the graph, as pulling apart oppositely charged ions and breaking bonds is certain to lead to a high exfoliation energy. It is also in line with the premise of the paper; since the material is to the left of the graph it has a relatively isotropic charge effective mass tensor yielding one of the lowest standard deviations of effective mass. Figure shows the material BCl3 that immediately seems quite amenable to exfoliation and unsurprisingly presents in the lower quadrant of the graph for exfoliation energy. Interestingly this material was extracted as being relatively isotropic in effective mass tensor. We believe that perhaps this can be explained by an interaction between cations and anions in the interlayer direction. It can be seen that the oppositely charged ions almost eclipse one another when viewed along the c axis, and so are likely to have electrostatic interactions that can give rise to some degree of dispersion of the electronic bands. Finally, Figure shows ScBrO a material that has both a low exfoliation energy and high standard deviation of effective mass. When contrasted with BCl3, it can be seen that this material does not have potential anion-cation interactions between the layers, instead the structure is composed of anion terminated bonded layers, similar to MoS2, MoSe2, WS2 and WSe2 and we predict to be ScBrO to be an unequivocal two-dimensional material. To the knowledge of the authors, this is the first time this compound has been highlighted as a two-dimensional material. |
659bf0c29138d231617324ed | 19 | Figure , e and f are p-type materials selected from the top left, bottom left and bottom right of Figure , respectively. Figure shows the compound KRb2YF6, which, like K4Ta2S11 has a high density of bonds and interspersed oppositely charged anions that explain the high exfoliation energy. Figure shows the compound TlF3, which does appear to be possible to separate into constituent layers. Like BCl3, TlF3 has potential interactions between the cations and anions, visible as long bonds in the centre of the unit cell in this case. We believe this explains how the material (like BCl3) exhibits both a relatively isotropic effective mass tensor and a relatively low exfoliation energy. Finally, we again end with a material that has both a high standard deviation of effective mass and a low exfoliation energy in TiBrN. Again, like ScBrO, we believe this material is highly likely to be an inherent 2D material as it has a bonded layer structure, and these bonded layers are terminated in anions as in the case of the archetypal 2D materials. Please do not adjust margins Please do not adjust margins These two sets of sample materials, whose information is summarized in Table , lends confidence to our initial premise, that the conductivity effective mass tensor can provide a summary of chemical structure and the likeliness of manifesting a layered nature. Based on our results it seems that n-type and p-type conductivity effective mass sampling perform equally well in estimating 2D nature. Furthermore, we remind the reader that our slabs were constructed without human intervention. We believe these results also corroborate our simplistic automated exfoliation approach. |
659bf0c29138d231617324ed | 20 | Returning to the material TlF3 (Figure ), its ease of exfoliation is perhaps surprising as at first glance there is no obvious layered sub-structure (only upon closer inspection are the elongated bonds noticeable: 2.42 vs 2.15 angstroms). This observation suggests that significant lattice gaps in the atomic structure are not necessary for a material to have a small exfoliation energy. Even if a bulk material does not exhibit layered structure, it may have the potential to be stripped down into a two-dimensional layer. In fact, non-van der Waals layered materials have been successfully exfoliated recently in experiment. Ilmenene, for example, has been exfoliated from the naturally occurring titanite ore ilmenite (FeTiO3) by employing liquid phase exfoliation in a dimethylformamide solvent by ultrasonic bath sonication. Similarly, a new two-dimensional material 'hematene' has been successfully obtained from the natural iron ore hematite (α-Fe2O3), by means of liquid exfoliation. Finally, In the work of Ma et al. they report successful exfoliate of stable monolayer wurtzite semi-conductors from bulk materials that are non-vdW material and show isotropic in three crystallographic directions. This is a fascinating and surprising new avenue of research in the field of 2D materials, and it is hoped that the tools and data presented in this work can be brought to bear in understanding this new phenomenon in future work. |
659bf0c29138d231617324ed | 21 | It should also be noted that theoretical tools for the calculation of charge mobilities are continuously improving in both accuracy and efficiency. Density functional perturbation theory combined with Wannier interpolation can yield highly accurate predictions of electron mobility and conductivity in semiconductors and does not rely on the constant relaxation time approximation for example, unlike the BoltzTrap method. New open-source tools have also been released recently lending such advanced techniques to highthroughput screening, which could provide an even better basis for large-scale analysis projects such as this in the future. Finally, we highlight that according to our data WS2 -one of the archetypal 2-dimensional materials -has very small standard deviation of conductivity effective mass for both p-type and n-type sampling and has a small exfoliation energy (see Table ) and does have anion terminated bonded layers in its crystal structure. The atomic structures of the four archetypal 2D materials are shown in Figure . This places one of the most important 2D materials outside of the premise of our paper. Together with the several outliers that can be seen in Figure , we conclude that while the conductivity effective mass tensor can be instructive in the field, 1 the relationship between it and exfoliation energy is not absolute in applicability. On the other hand, we do find that the conductivity effective mass tensor is very useful in predicting the crystallographic direction along which a material can be exfoliated. The code used in this work was designed according to this principle. |
659bf0c29138d231617324ed | 22 | We found that the conductivity effective mass tensor was able to reliably provide the crystallographic direction along which a material could be exfoliated in conjunction with an automated script, an example of which we release with this article for free use. Such a simplistic approach, which requires no human intervention, can significantly facilitate materials screening for technologically relevant applications. |
659bf0c29138d231617324ed | 23 | Subsequently, we calculated the exfoliation energy of one thousand p-type materials and one thousand n-type materials that have highest standard deviation of effective mass and compared them at the PBE and PBE+vdW level. We find that the use of a vdW correction is highly recommended for any calculation of accurate exfoliation energy, successfully erasing aberrant results that arose at the PBE level. By knowing the exfoliation energy and conductivity effective mass we were able to predict physiological and structural features of a range of materials. Not least among which, we were able to identify at least one material that to our knowledge has not been considered as a two-dimensional material previously but that exhibits the physical hallmarks of such compounds. We provide the full dataset of our results in the SI (Tables and) and encourage the reader to explore further, bearing in mind that there are known exceptions to the proposed relationship (specifically WS2 in this case). |
65d39af766c13817290035c1 | 0 | Laboratory automation has been identified as a key strategy for increasing the rate at which new discoveries are made in chemistry and materials science. Automation serves two central purposes: 1) to increase the experimental throughput via continuous and/or parallel execution of otherwise repetitive, manual tasks, and 2) to foster more standardized and reproducible results. While the history of automation in chemistry traces back to the mid-20 th century, recent years have seen a "renaissance" of automation in both academic and industrial laboratories. Advances in robotics and engineering have enabled the automation of increasingly challenging laboratory operations such as thin-film fabrication, sample handling under inert gas, or dosing of powders, gels and slurries. Integrating such automated modules into larger workflows has demonstrated the potential to tackle increasingly complex scientific challenges in an automated fashion. This surge in automated experimentation has produced a growing market of instruments, particularly platform solutions consisting of multiple experimental modules. Arguably, the most prominent such systems have come from companies such as Chemspeed Technologies and Unchained Labs, and have shown the enormous potential to enable highly complex discovery workflows across various fields in chemistry and materials science. Examples include the discovery of battery electrolytes, new catalysts, organic laser materials, polymer formulations, or stereoselective synthesis. The current phase in the evolution of automated laboratories involves the transition from static, predefined automation workflows to modular and flexible labs where decisions about the next experimental steps are adaptively made in real time (Fig. ). Particularly with recent strides in data-driven design and machine learning, this has the potential to optimize the use of automated resources, and thereby accelerate scientific discoveries. Especially against the background of modularity and adaptive decision making, the availability of open software interfaces (application programming interfaces, APIs) for automated platforms are essential for the seamless incorporation into flexible, customizable workflows. At the same time, such dynamic APIs are often not provided by instrument manufacturers, whose software tends to follow a workflow-and instrument-centric philosophy. In fact, available APIs are often constrained to the configuration and post-run evaluation of static workflows. This presents a major barrier to integrating further instruments into the workflow, or to making adaptive data-driven decisions in real time. |
65d39af766c13817290035c1 | 1 | To address these gaps, we introduce Chemspyd, an open-source Python API specifically designed for Chemspeed platforms. This API enables real-time, adaptive control of Chemspeed instruments, empowering researchers to seamlessly integrate these robotic platforms into custom workflows and automated or self-driving laboratories (SDLs). We use three experimental case studies to demonstrate how Chemspyd can be used for experiments in the chemical and materials sciences. Most importantly, Chemspyd is designed as a modular and expandable open-source project, and can therefore serve as a blueprint for the development of similar interfaces that meet the evolving demands of modern, flexible, and customizable automated laboratories. |
65d39af766c13817290035c1 | 2 | Chemspyd's architecture is guided by three core design principles: 1) dynamic and fine-grained control over the robot's actions; 2) easy installation and usage with existing Chemspeed setups; 3) modular, extendable open-source architecture, facilitating continuous development by the community, and enabling effortless integration with experiment planning and scheduling workflows. Because of 2) and 3), Chemspyd comes as a lightweight Python package that dynamically interacts with Chemspeed's proprietary AutoSuite software. |
65d39af766c13817290035c1 | 3 | Chemspyd is organized following object-oriented design principles and is structured into two main classes: the Controller and the Executor. Whereas the Executor handles the communication with the instrument's control software (for details, vide infra), the Controller provides a standardized, public API for users to develop customizable, adaptive workflows in Python. For this purpose, it houses an extensive catalog of elementary actions that encompass a wide range of the functionalities that the Chemspeed robotic platforms offer. These elementary actions enable dynamic and fine-grained control over the action space. A full list of elementary actions is provided in the Supplementary Information, as well as the detailed package documentation. Chemspyd communicates with AutoSuite through the Executor, which read and writes shared CSV files, providing a standardized means of communication that is human-readable and supported by both Python and AutoSuite (Figure ). This enables bidirectional communication between AutoSuite (and thereby, the Chemspeed robotic platform) and Chemspyd, containing the instrument status, execution commands and parameters, instrument return values, and general metadata. A full description of the communication protocol is provided in the Supplementary Information. |
65d39af766c13817290035c1 | 4 | To enable dynamic control on the Chemspeed side, we created a dedicated AutoSuite application file, referred to as the Manager, that listens for command files, and executes actions based on the provided keywords and parameters. Each elementary Controller method has an execution counterpart in the Manager. As a result, Chemspyd allows users to perform individual actions (helpful during development and troubleshooting) or perform different routines without needing to restart the platform. |
65d39af766c13817290035c1 | 5 | Beyond the fine-grained control over elementary actions, we developed Chemspyd to contain a series of optional tools to assist with operation safety, accurate resource management, and standardized data collection. These safety checks include, for example, a simulation mode for testing software before deployment in a "digital-twin"-like scenario. In addition, operations or workflows can be validated prior to execution to ensure that liquids or solids can be added or removed from the specified wells. At a higher level, Chemspyd's resource management features also allow users to ensure that wells won't be overfilled or depleted by accident. The herefore required attributes of each well (type, volume, ...) are automatically extracted from the instrument configuration, avoiding manual input by the user (see section "Installation and Usage" for further details). |
65d39af766c13817290035c1 | 6 | To streamline workflow development and enhance convenience for the user, we have organized common experimental routines within the routines sub-package. Examples of such routines include the priming of syringe pumps, evacuate-backfill cycles (i.e., "Schlenk cycles"), filtration and collection steps, and injection to on-deck HPLC ports. Notably, the routines sub-package provides a framework for implementing further custom experimental routines, highlighting the modular, open-source nature of Chemspyd, and fostering continued active development by the community. |
65d39af766c13817290035c1 | 7 | The Chemspyd Python package can be installed from the PyPI repository (Figure ). The source code repository can be accessed at its GitLab page under the Apache 2.0 license, and provides extensive documentation, including installation instructions, usage guides and tutorial examples. Once installed, Chemspyd code can be written entirely in Python (versions ≥ 3.9), and, thus, enables users to developed and test their code on any platform. |
65d39af766c13817290035c1 | 8 | The process of setting up Chemspyd on any local platform involves two stages: 1) creating a custom, local Manager and 2) extracting the platform's hardware configuration. In the first stage, users should create a new Manager application file in AutoSuite whose instrument configuration matches that of their platform. All pre-defined commands, which are provided as part of Chemspyd (see package documentation for further details) should be copied into this application file. Second, for extracting the hardware configuration from the Manager and making it accessible to Chemspyd, we provide an automated solution to ease the installation process. For this purpose, Chempyd interacts with AutoSuite's .NET API. For user convenience, this process is fully wrapped in the chemspyd.autosuite.get_config() function (Figure , see package documentation for further details). As a result, the installation of Chemspyd is largely automated, and does not require a tedious configuration procedure, but is designed for the seamless integration with existing robotic setups. Should the API not be accessible, the resulting configuration file can also be created manually. Once the Python package and the corresponding AutoSuite Manager have been properly set up, executing Chempyd code on a Chemspeed platform requires the following two steps: (1) start the Manager in AutoSuite, (2) execute one or multiple Chemspyd scripts, an example of which is shown in Figure . |
65d39af766c13817290035c1 | 9 | In order to showcase the different features of Chemspyd, we demonstrate a set of experiments from inorganic and organic chemistry as possible use cases of the software in automated laboratories. All experiments were performed on the Chemspeed SWING XL robot available in our laboratory at the Matter Lab at the University of Toronto. |
65d39af766c13817290035c1 | 10 | As a first use case, we performed a systematic evaluation of reaction conditions for the formation of silver nanoprisms. The size distribution of the nanoprismsand thereby, their absorption properties are determined by the stoichiometric ratios of the silver source (AgNO3), the reductive component (NaBH4), the oxidative component (H2O2), the buffer (sodium citrate) and the silver concentration mediator (KBr). We selected a representative set of conditions from this five-dimensional continuous parameter space through Latin hypercube sampling. Using Chemspyd, we were able to quickly write the execution code, simply looping over all hypercube samples, and the required liquid transfer and stirring operations were performed automatically. Optical absorption measurements were carried out on our spectroscopic characterization platform. The resulting dataset of spectroscopic properties of the obtained nanoprisms is shown in Figure . |
65d39af766c13817290035c1 | 11 | Our second use case targeted the screening of experimental conditions for the Buchwald-Hartwig coupling reaction, one of the most prominent reaction classes in organic and medicinal chemistry. Specifically, we created a combinatorial dataset by varying three categorical parameters, namely the palladium precursor, ligand, and base. Exploiting our platform's capacity to perform reactions under an inert gas atmosphere, all synthesis (inertization, reagent addition, temperature control, vortex stirring), workup (filtration) and analysis (injection to an HPLC) were encoded in Chemspyd, and run without manual intervention. Notably, the modular design of Chemspyd was crucial for the softwarelevel integration with our group's HPLC-MS instrument and its Python control code. Relative yields (with respect to an internal standard) for each reaction are visualized in the heatmap in Figure . |
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