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62ab247f1fdc34fd493beda4 | 10.26434/chemrxiv-2022-3njq6 | Metallaphotoredox-Catalyzed Decarboxylative sp3–sp3 Cou-pling with Iso(thio)chroman and Tetrahydroisoquinoline Cores | A mild and direct strategy for the 1-alkylation of isochroman, isothiochroman and tetrahydroisoquinoline cores has been achieved through the combination of photoredox and nickel catalysis. The resulting motifs are commonly found in bioac-tive compounds and natural products, but accessibility has to date been limited to scaffolds containing electron-rich aro-matic rings. The approach reported here, using an easily syn-thesized carboxylic acid building block in a cross-coupling manifold, enables rapid access to diverse scaffolds with broad functional group tolerance on a gram scale. | Paul King; Peter Rutledge; Matthew Todd | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab247f1fdc34fd493beda4/original/metallaphotoredox-catalyzed-decarboxylative-sp3-sp3-cou-pling-with-iso-thio-chroman-and-tetrahydroisoquinoline-cores.pdf |
64ef38673fdae147fa21f741 | 10.26434/chemrxiv-2023-b86zb | Origins and importance of intragranular cracking in layered lithium transition metal oxide cathodes | Li-ion batteries have a pivotal role in the transition towards electric transportation. Ni-rich layered transition metal oxide (LTMO) cathode materials promise high specific capacity and lower cost but exhibit faster degradation compared to lower Ni alternatives. Here, we employ high resolution electron microscopy and spectroscopies to investigate the nanoscale origins and impact on performance of intragranular cracking (within primary crystals) in Ni-rich LTMOs. We find that intragranular cracking is widespread in charged specimens early in cycle life, but uncommon in discharged samples even after cycling. The distribution of intragranular cracking is highly inhomogeneous. We conclude that intragranular cracking is caused by local stresses that can have several independent sources: neighbouring particle anisotropic expansion/contraction, Li- and TM-inhomogeneities at the primary and secondary particle levels and interfacing of electrochemically active and inactive phases. Our results suggest that intragranular cracks can manifest at different points of life of the cathode and can potentially lead to capacity fade and impedance rise of LTMO cathodes through plane gliding and particle detachment that lead to exposure of new surfaces to the electrolyte and loss of electrical contact. | Jędrzej Morzy; Wesley Dose; Per Erik Vullum; May Ching Lai; Amoghavarsha Mahadevegowda; Michael De Volder; Caterina Ducati | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ef38673fdae147fa21f741/original/origins-and-importance-of-intragranular-cracking-in-layered-lithium-transition-metal-oxide-cathodes.pdf |
6682c911c9c6a5c07ae94206 | 10.26434/chemrxiv-2024-gh8fz-v3 | Transforming Aryl-Tetrazines into Bioorthogonal Scissors for Systematic Cleavage of trans-Cyclooctenes | Bioorthogonal bond-cleavage reactions have emerged as a powerful tool for precise spatiotemporal control of (bio)molecular function in the biological context. Among these chemistries, the tetrazine-triggered elimination of cleavable trans-cyclooctenes (click-to-release) stands out due to high reaction rates, versatility, and selectivity. Despite an increasing understanding of the underlying mechanisms, application of this reaction remains limited by the cumulative performance trade-offs (i.e., click kinetics, release kinetics, release yield) of existing tools. Efficient release has been restricted to tetrazine scaffolds with comparatively low click reactivity, while highly reactive aryl-tetrazines give only minimal release. By introducing hydroxyl groups onto phenyl- and pyridyl-tetrazine scaffolds, we have developed a new class of ‘bioorthogonal scissors’ with unique chemical performance. We demonstrate that hydroxyaryl-tetrazines achieve near-quantitative release upon accelerated click reaction with cleavable trans-cyclooctenes, as exemplified by click-triggered activation of a caged prodrug, intramitochondrial cleavage of a fluorogenic probe (turn-on) in live cells, and rapid intracellular bioorthogonal disassembly (turn-off) of a ligand-dye conjugate. | Martin Wilkovitsch; Walter Kuba; Patrick Keppel; Barbara Sohr; Andreas Löffler; Stefan Kronister; Andres Fernandez del Castillo; Marion Goldeck; Rastislav Dzijak; Michal Rahm; Milan Vrabel; Dennis Svatunek; Jonathan Carlson; Hannes Mikula | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6682c911c9c6a5c07ae94206/original/transforming-aryl-tetrazines-into-bioorthogonal-scissors-for-systematic-cleavage-of-trans-cyclooctenes.pdf |
641333aedab08ad68f36e4ce | 10.26434/chemrxiv-2023-qnstd | Structural Characterization and Reactivity of a Room Temperature-Stable, Antiaromatic Cyclopentadienyl Cation Salt | The singlet states of cyclopentadienyl (Cp) cations are considered as true prototypes of an antiaromatic system. Due to their high reactivity, their isolation in the solid state as a salt has so far failed. We present here the synthesis of the first room temperature-stable Cp cation salt Cp(C6F5)5Sb3F16 (1·Sb3F16) by single electron oxidation of the corresponding Cp radical Cp(C6F5)5∙ (2) with either an excess of XeF2 and SbF5·SO2 or by hydroxide abstraction from Cp(C6F5)5OH (D) with SbF5·SO2 in hexafluorobenzene. 1·Sb3F16 was characterized by sc-XRD, SQUID, UV-vis, and EPR spectroscopy. Although the aromatic triplet state of the Cp(C6F5)5 cation 1 is energetically favored in the gas phase according to quantum chemical calculations, the coordination of the cation by either Sb3F16⁻ (1a·Sb3F16) or C6F6 (1b·Sb3F16) in the crystal lattice stabilizes the antiaromatic singlet state, which is present in the solid state. The calculated hydride and fluoride ion affinities of 1 are higher than those of the tritylium cation C(C6F5)3+. In addition, results from reactions of 1·Sb3F16 with CO, which most likely yields the corresponding carbonyl complex, and 2 with selected model substrates (Cp2Fe, (Ph3C∙)2, and Cp*Al) are presented. | Yannick Schulte; Christoph Wölper; Susanne M. Rupf; Moritz Malischewski; Gebhard Haberhauer; Stephan Schulz | Organic Chemistry; Organic Compounds and Functional Groups; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641333aedab08ad68f36e4ce/original/structural-characterization-and-reactivity-of-a-room-temperature-stable-antiaromatic-cyclopentadienyl-cation-salt.pdf |
67c860defa469535b90d10b2 | 10.26434/chemrxiv-2024-lrh78-v2 | Determination of the experimental minimal formula of metal-organic frameworks | Metal-organic frameworks have emerged as one of the most promising classes of materials in the last decade with potential applications in many domains of science. However, the determination of their precise chemical composition has often been overlooked, although it is crucial for many advanced applications such as catalysis or drug delivery. Here, we propose a rigorous yet simple method for the accurate determination of a MOF’s minimal formula. By integrating quantitative NMR and UV-Vis spectroscopy data alongside TGA analysis, we construct the complete minimal formula of several MOFs: MOF-808(Zr), UiO-66(Zr), MOF-5(Zn), and MIL-125(Ti). We show the critical influence of the MOF digestion method and the NMR measurement parameters on the accuracy of the minimal formula. Furthermore, we provide a quantitative method for determining the amount of residual chloride that originates from metal precursors used in MOF synthesis, which has been often ignored in minimal formula determination. In order to help improve the reproducibility and accuracy of MOF applications, we introduce the concept of the experimental molar mass that can deviate significantly from the idealized molar mass. Although the determination of the MOF experimental minimal formula is often perceived as a complex and tedious task, the general methodology presented here is straightforward and can be achieved with very simple equations and procedures. It is easily generalized to new MOFs and even amorphous coordination networks such as Al-BDC. | Jikson Pulparayil Mathew; Charlotte Simms; David E. Salazar Marcano; Evert Dhaene; Tatjana N. Parac-Vogt; Jonathan De Roo | Physical Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Ligands (Organomet.); Spectroscopy (Organomet.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c860defa469535b90d10b2/original/determination-of-the-experimental-minimal-formula-of-metal-organic-frameworks.pdf |
66023d9066c1381729d17e4a | 10.26434/chemrxiv-2023-7k37p-v2 | Alcohols as substrates in transition metal-catalyzed arylation, alkylation and related reactions | Alcohols are abundant and attractive feedstock molecules for organic synthesis. Many methods for their functionalization require them to first be converted into a more activated derivative, while recent years have seen a vast increase in the number of complexity-building transformations that directly harness unprotected alcohols. This review discusses how transition metal catalysis can be used towards this goal. These transformations are broadly classified into three categories. Etherifications, characterized by derivatization of the O–H bond, represent classical reactivity that has been modernized to include mild reactions conditions, diverse reaction partners, and high selectivities. Deoxygenative functionalizations, representing derivatization of the C–O bond, enable the alcohol to act as a leaving group towards the formation of new C–C bonds. Lastly, chain functionalization reactions are described, wherein the alcohol group acts as a mediator in formal C–H functionalization reactions of the alkyl backbone. Each of these three classes of transformation will be discussed in context of intermolecular alkylation, arylation, and related reactions, illustrating how catalysis can enable alcohols to be directly harnessed for organic synthesis. | Adam Cook; Stephen Newman | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66023d9066c1381729d17e4a/original/alcohols-as-substrates-in-transition-metal-catalyzed-arylation-alkylation-and-related-reactions.pdf |
63ed43291d2d1840638f9981 | 10.26434/chemrxiv-2022-gg4kr-v3 | Weighted multivariate curve resolution – alternating least squares based on sample relevance | Alternating least squares, within the multivariate curve resolution framework has seen a lot of practical applications and shows its distinction with its relatively simple and flexible implementation. However, the limitations of least squares should be considered carefully when deviating from the standard assumed data structure. Within this work we highlight the effects of noise in the presence of minor components, and we propose a novel weighting scheme within the weighted multivariate curve-resolution-alternating least squares framework, to resolve it. Two simulated and one Raman imaging case is investigated, by comparing the novel methodology against standard multivariate curve resolution-alternating least squares and essential spectral pixel selection. A trade-off is observed between current methods, while the novel weighting scheme demonstrates a balance, where the benefits of the previous two methods are retained. | Mohamad Ahmad; Raffaele Vitale; Marina Cocchi; Cyril Ruckebusch | Analytical Chemistry; Analytical Chemistry - General; Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ed43291d2d1840638f9981/original/weighted-multivariate-curve-resolution-alternating-least-squares-based-on-sample-relevance.pdf |
64c1c76ece23211b209c9220 | 10.26434/chemrxiv-2023-f5gb0 | Directed Crystallization of a Nanoscale Quasi-1D van der Waals Topological Insulator | Anisotropy often yields unexpected structures and properties in the solid state. In van der Waals (vdW) solids comprised of 1D or quasi-1D (q-1D) chains, anisotropy in both intra- and inter-chain directions results in an abundance of packing motifs and altered physical states. Q-1D vdW solids with topologically protected states are most sought after due to their potential as building blocks for quantum and spintronic devices. Yet, access to such facet- and edge-specific states is limited by the stochastic nature of micromechanical exfoliation. Here, we demonstrate that Bi4I4, a q-1D vdW topological insulator, can be crystallized from the vapor phase either into nanowires or quasi-2D nanosheets. We find that gold nanoparticles (Au NPs) on the growth substrate, in conjunction with the anisotropic structure of Bi4I4, direct the dimensionality of Bi4I4 nanostructures. Systematic variation of Au NP diameters, Bi:I precursor ratios, and growth-deposition temperatures reveal that Au NPs generally act as nucleation sites for vapor-solid growth of nanowires. Post-synthesis analyses of 20 nm Au NPs show that the 1:1 ratio of Bi to I within the Au NPs uniquely triggers the vapor-liquid-solid growth of [001]-oriented nanosheets from laterally-ordered [Bi4I4]n chains along the [100] direction. We rationalize the bimodal growth pathways and the morphologically distinct nanostructures based on crystallization habits of the nanostructures, Bi:I ratios in the Au NPs post-synthesis, and orientation of stereochemically active Bi lone pairs between adjacent chains. We anticipate that these pathways are adaptable to other halide- and chalcogen-based 1D vdW nanocrystals with diverse physical and quantum properties. | Steven Allison; Dmitri Leo Cordova; Maham Hasib; Toshihiro Aoki; Maxx Arguilla | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c1c76ece23211b209c9220/original/directed-crystallization-of-a-nanoscale-quasi-1d-van-der-waals-topological-insulator.pdf |
60c74164bb8c1a49cb3d9f1d | 10.26434/chemrxiv.8024135.v1 | Time-Dependent Long-Range Corrected Density-Functional Tight-Binding Method Combined with the Polarizable Continuum Model | In this study, excited-state free energies and geometries were efficiently evaluated using a linear-response time-dependent long-range corrected density-functional tight-binding method integrated with the polarizable continuum model (TD-LC-DFTB/PCM). Although the LC-DFTB method required the evaluation of the exchange-type term, which was moderately computationally expensive, a single evaluation of the excited-state gradient for a system consisting of more than 1000 atoms in a vacuum was completed within 30 minutes using one CPU core. Benchmark calculations were conducted for 3-hydroxy avone, which exhibits dual emission: the absorption and enol-form emission wavelengths calculated by TD-LC-DFTB/PCM agreed well with those predicted based on density functional theory using a long-range corrected functional; however, there was a large error in the predicted keto-form emission wavelength. Further benchmark calculations for more than 20 molecules indicated that the conventional TD-DFTB method underestimated the absorption and 0-0 transition energies compared with those which were measured experimentally while the TD-LC-DFTB method systematically overestimated these metrics. Nevertheless, the agreement of the results of the TD-LC-DFTB method with those obtained by the CAM-B3LYP method demonstrates the potential of the TD-LC-DFTB/PCM method. Moreover, changing the range-separation parameter to 0.15 minimized this deviation.<br /> | Yoshio Nishimoto | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74164bb8c1a49cb3d9f1d/original/time-dependent-long-range-corrected-density-functional-tight-binding-method-combined-with-the-polarizable-continuum-model.pdf |
60c7553d4c89193051ad4654 | 10.26434/chemrxiv.14054783.v1 | N-Ammonium Ylide Mediators for Selective Electrochemical C–H Oxidation | <p>The site-specific oxidation of strong C(sp3)-H bonds is of uncontested utility in organic</p><p>synthesis. From simplifying access to metabolites and late-stage diversification of lead compounds</p><p>to truncating retrosynthetic plans, there is a growing need for new reagents and methods for</p><p>achieving such a transformation in both academic and industrial circles. One main drawback of</p><p>current chemical reagents is the lack of diversity with regards to structure and reactivity that</p><p>prevent a combinatorial approach for rapid screening to be employed. In that regard, directed</p><p>evolution still holds the greatest promise for achieving complex C–H oxidations in a variety of</p><p>complex settings. Herein we present a rationally designed platform that provides a step towards</p><p>this challenge using N-ammonium ylides as electrochemically driven oxidants for site-specific,</p><p>chemoselective C(sp3)–H oxidation. By taking a first-principles approach guided by computation,</p><p>these new mediators were identified and rapidly expanded into a library using ubiquitous building</p><p>blocks and trivial synthesis techniques. The ylide-based approach to C–H oxidation exhibits</p><p>tunable selectivity that is often exclusive to this class of oxidants and can be applied to real world</p><p>problems in the agricultural and pharmaceutical sectors.</p> | Masato Saito; Yu Kawamata; Michael Meanwell; Rafael Navratil; Debora Chiodi; Ethan Carlson; Pengfei Hu; Longrui Chen; Sagar Udyavara; Cian Kingston; Mayank Tanwar; Sameer Tyagi; Bruce Mckillican; Moses Gichinga; Michael A. Schmidt; Martin Eastgate; Max Lamberto; Chi He; Tianhua Tang; Christian A. Malapit; Matthew S. Sigman; Shelley D. Minteer; Matthew Neurock; Phil Baran | Organic Synthesis and Reactions; Electrocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7553d4c89193051ad4654/original/n-ammonium-ylide-mediators-for-selective-electrochemical-c-h-oxidation.pdf |
64bb6ffcae3d1a7b0d238827 | 10.26434/chemrxiv-2023-n6972 | Spin-Selective Oxygen Evolution Reaction in Chiral Iron Oxide Nanoparticles: Synergistic Impact of Inherent Magnetic Moment and Chirality | Electron spin polarization is identified as a promising avenue for enhancing the oxygen evolution reaction (OER), the bottleneck that limits the energy efficiency of water-splitting. Here, we report that both ferrimagnetic (f-Fe3O4) and superparamagnetic iron oxide (s-Fe3O4) catalysts can exhibit external magnetic field (Hext) induced OER enhancement, and the activity is proportional to their intrinsic magnetic moment. Additionally, chirality induced spin selectivity (CISS) effect was utilized in synergy with Hext to get a maximum enhancement of up to 89% improvement in current density (at 1.8 V vs. RHE) with a low onset potential of 270 mV in s-Fe3O4 catalysts. Spin polarization and the resultant spin selectivity suppresses the production of H2O2 and promote the formation of ground state triplet O2 during OER. Furthermore, the design of chiral s-Fe3O4 with synergistic spin potential effect demonstrates a high spin polarization of ~42%, as measured using conductive Atomic Force Microscopy (c-AFM) measurements. | Aruna N Nair; Sara E Fernandez, ; Mariana Marcos; Daniel Rascon Romo; Srinivasa Rao Singamaneni; Dino Villagran; Sreeprasad Sreenivasan | Physical Chemistry; Materials Science; Catalysis; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bb6ffcae3d1a7b0d238827/original/spin-selective-oxygen-evolution-reaction-in-chiral-iron-oxide-nanoparticles-synergistic-impact-of-inherent-magnetic-moment-and-chirality.pdf |
60c74274567dfe6cf8ec3f57 | 10.26434/chemrxiv.8299406.v1 | Operando Visualization of Morphological Dynamics in All-Solid-State Batteries | <div>
<div>
<div>
<p>All-solid-state batteries are considered as attractive options for next-generation energy storage
owing to the favourable properties (unit transference number and thermal stabilities) of solid
electrolytes. However, there are also serious concerns about mechanical deformation of solid
electrolytes leading to the degradation of the battery performance. Therefore, understanding
the mechanism underlying the electro-mechanical properties in SSBs are essentially important.
Here, we show three-dimensional and time-resolved measurements of an all-solid-state cell
using synchrotron radiation x-ray tomographic microscopy. We could clearly observe the
gradient of the electrochemical reaction and the morphological evolution in the composite
layer. Volume expansion/compression of the active material (Sn) was strongly oriented along
the thickness of the electrode. While this results in significant deformation (cracking) in the
solid electrolyte region, we also find organized cracking patterns depending on the particle
size and their arrangements. This study based on operando visualization therefore opens the
door towards rational design of particles and electrode morphology for all-solid-state batteries. </p>
</div>
</div>
</div> | Xiaohan Wu; Juliette Billaud; Iwan Jerjen; Federica Marone; Yuya Ishihara; Masaki Adachi; Yoshitaka Adachi; Claire Villevieille; Yuki Kato | Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74274567dfe6cf8ec3f57/original/operando-visualization-of-morphological-dynamics-in-all-solid-state-batteries.pdf |
6406e376cc600523a3c9c165 | 10.26434/chemrxiv-2023-wvbd3 | Biexciton-Like Auger Blinking in Strongly Confined CsPbBr3 Perovskite Quantum Dots | Single perovskite quantum dots (QDs) are notorious for their poor stability. As a result, surface defects will be generated and this will lead to trion formation that reduces fluorescence intensity, setting barriers to exploring the intrinsic exciton dynamics and the applications of perovskite QDs in single-photon sources. Here we demonstrate that strongly confined CsPbBr3 perovskite QDs (SCPQDs) embedded in a matrix formed by phenethylammonium bromide exhibit suppressed trion formation and remain photostable under intense photoexcitation. The increased surface passivation and stability enables the study of multi-exciton interactions in SCPQDs. We found that, in well-passivated SCPQDs, increasing excitation rates leads to weak fluorescence intensity fluctuations accompanied by an unusual spectral blueshift in the photoluminescence. We attribute this to a biexciton-like Auger interaction between excitons and trapped excitons formed by surface lattice elastic distortions. This hypothesis is corroborated by the unique repulsive biexciton interaction in SCPQDs. Our study provides insights into the fundamental multi-exciton interactions in SCPQDs and will advance the development of quantum light sources based on perovskite QDs. | Chenjia Mi; Matthew Atteberry; Varun Mapara; Lamia Hidayatova; Gavin Gee; Wai Tak Yip; Madalina Furis; Binbin Weng; Yitong Dong | Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Materials; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6406e376cc600523a3c9c165/original/biexciton-like-auger-blinking-in-strongly-confined-cs-pb-br3-perovskite-quantum-dots.pdf |
667fcfd8c9c6a5c07abc0c79 | 10.26434/chemrxiv-2024-s8z45 | Ab Initio Multiple Spawning nonadiabatic dynamics with different CASPT2 flavors: A fully open-source PySpawn/OpenMolcas interface | We introduce an interface between PySpawn, a simulation package to run ab initio multiple spawning (AIMS) nonadiabatic dynamics, and OpenMolcas, a software package to perform multiconfigurational perturbations theory (CASPT2) electronic structure calculations. Our interface allows us to exploit all the functionalities of the two codes: the modular and efficient Python implementation of the AIMS algorithm and the extensive analysis tools offered by PySpawn, with the cutting-edge implementation of CASPT2 equations in OpenMolcas, including the recently introduced analytical gradients and different flavors. Both are fully open-source and free of charge, making the following implementation unique in the current plethora of software for nonadiabatic dynamics. This represents an important step towards a wider application of AIMS-based nonadiabatic dynamics combined with high-accuracy excited-state calculations. The importance and the need for such an implementation are demonstrated by application to the ultrafast relaxation of fulvene from S1 to S0 , which is drastically affected by the potential energy surface on which the nuclear wavepacket is propagated. Additionally, the decay is influenced by the CASPT2 flavor adopted, posing interesting questions in the choice of one over the other and opening the door to deeper studies on the effect of CASPT2 formulations in nonadiabatic dynamics. | Lea Ibele; Arshad Memhood; Benjamin G. Levine; Davide Avagliano | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667fcfd8c9c6a5c07abc0c79/original/ab-initio-multiple-spawning-nonadiabatic-dynamics-with-different-caspt2-flavors-a-fully-open-source-py-spawn-open-molcas-interface.pdf |
658406f266c1381729b57cc8 | 10.26434/chemrxiv-2023-218lq | CIME4R: Exploring iterative, AI-guided chemical reaction optimization campaigns in their parameter space | Chemical reaction optimization (RO) is an iterative process that results in large and high-dimensional datasets. Current tools only allow for limited analysis and understanding of parameter spaces, making it hard for scientists to review or follow changes throughout the process. With the recent emergence of using artificial intelligence (AI) models to aid RO, another level of complexity was added. It is critical to assess the quality of a model’s prediction and understand its decision to aid human-AI collaboration and trust calibration. To that regard, we propose CIME4R—an open-source interactive web application for analyzing RO data and AI predictions. CIME4R supports users in (i) comprehending a reaction parameter space, (ii) investigating how the RO process developed over iterations, (iii) identifying critical factors of a reaction, and (iv) understanding model predictions. This aids users in making informed decisions during the RO process and helps them review an RO process in retrospect, especially in the realm of AI-guided RO. CIME4R aids decision-making through the interaction between humans and AI by combining the strengths of expert experience and high computational precision. We developed and tested CIME4R together with
domain experts and verified its usefulness with three case studies. With CIME4R the experts were able to produce valuable insights from past RO campaigns and
make informed decisions on which experiments to perform next. We believe that CIME4R is the beginning of an open-source community project that improves the workflow of scientists working in the reaction optimization domain. | Christina Humer; Rachel Nicholls; Henry Heberle; Moritz Heckmann; Michael Pühringer; Thomas Wolf; Maximilian Lübbesmeyer; Julian Heinrich; Julius Hillenbrand; Giulio Volpin; Marc Streit | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658406f266c1381729b57cc8/original/cime4r-exploring-iterative-ai-guided-chemical-reaction-optimization-campaigns-in-their-parameter-space.pdf |
60c740a0bb8c1a55e73d9e00 | 10.26434/chemrxiv.7767194.v1 | A Solution to Chemical Pseudaminylation via Development of a Bimodal Glycosyl Donor to Enable Highly Stereocontrolled α- and β-Glycosylation | Bacterial pseudaminic acids (Pse)
are present on the surface of many pathogenic
bacteria. Herein, we report a robust methodology for the stereocontrolled
chemical glycosylation of
pseudaminic acid to afford both α- (axial) and β- (equatorial) glycosides reliably
with complete stereoselectivity, using a common glycosyl donor (7<i>N-</i>Cbz/5<i>N</i>-azido Pse thioglycoside) simply by changing the reaction
conditions (DCM-DMF, -40 <sup>o</sup>C and
DCM/MeCN, -78 <sup>o</sup>C, respectively). Examples of such bimodal
selectivity are both sparse and highly sought-after in carbohydrate chemistry.
This method enables efficient access to pseudaminylated molecules, which will
open up various opportunities in chemical glycobiology research of bacterial
pseudaminic acids and carbohydrate-based antibacterial vaccine development. | Ruohan Wei; Han Liu; Arthur Tang; Richard Payne; Xuechen Li | Bioorganic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a0bb8c1a55e73d9e00/original/a-solution-to-chemical-pseudaminylation-via-development-of-a-bimodal-glycosyl-donor-to-enable-highly-stereocontrolled-and-glycosylation.pdf |
60c745954c8919daabad2a01 | 10.26434/chemrxiv.10060253.v1 | Reimagining Third Phase Formation as the Miscibility Gap of a Molecular Solution | Liquid/liquid phase transitions are inherent to multicomponent solutions, which often contain a diversity of intermolecular interactions between their molecular constituents. In one such example, a phase transition is observed in liquid/liquid extraction where the nonpolar organic phase separates into two phases under sufficiently high metal and acid extraction by the amphiphilic extractant molecule. This deleterious phenomenon, known as third phase formation, complicates processing and limits efficiency. While empirically well documented, the molecular origin of this phenomenon is not understood. The prevailing conceptualization of the organic phase treats it as a microemulsion where extractant molecules form reverse micelles that contain the extracted aqueous solutes in their polar cores. Yet recent studies indicate that a microemulsion paradigm is insufficient to describe molecular aggregation in some solvent extraction systems, implying that an alternative description of aggregation, and explanation for third phase formation, is needed. In this study, we demonstrate that the formation of a third phase is consistent with crossing the liquid-liquid miscibility gap for a molecular solution rather than a Winsor II to Winsor III transition as presumed in the microemulsion paradigm. This insight is provided by using a graph theoretic methodology, generalizable to other complex multicomponent molecular solutions, to identify the onset of phase splitting. This approach uses connectivity obtained from molecular dynamics simulation to correlate the molecular-scale association of extractants and extracted solutes to the solution phase behavior using percolation theory. The method is applied to investigate a solvent extraction system relevant to ore purification and used nuclear fuel recycling: tri-n-butyl phosphate/uranyl nitrate/water/nitric acid/n-dodecane. In analogy to a molecular solution, immediately preceding the liquid-liquid coexistence curve from the single phase region, the metal-ligand complexes percolate. This demonstrates that describing this solution with microemulsion chemistry is neither applicable nor broadly required to explain third phase formation. Additionally, the method developed herein can predict third phase formation phase boundaries from simulation for this and potentially other solvent extraction systems. | Michael Servis; David T. Wu; Jenife Shafer; Aurora Clark | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745954c8919daabad2a01/original/reimagining-third-phase-formation-as-the-miscibility-gap-of-a-molecular-solution.pdf |
61a8deb063557c5af49415b3 | 10.26434/chemrxiv-2021-0ccx8 | Atomistic molecular dynamics insights on water local structure and dynamics on different surfaces of zeolitic-imidazolate frameworks | Most of chemistry in nanoporous materials with small pore sizes and windows is known to occur on the surface which is in immediate contact with substrate/solvent, rather than inside pores and channels. Here, we report the results of our comprehensive atomistic molecular dynamics simulations on deciphering the intermolecular hydrogen bond network of water on outer surface of a nanoparticle model of ZIF-8 vs. inner surfaces of its pristine crystalline bulk model. Using a finite ~5.1 nm nanoparticle model with edges containing under--coordinated Zn2+ metal sites we show that water exposed to the surface of the nanoparticle exhibits both interfacial and bulk-like characters. Furthermore, we illustrate that as water content increases larger droplets are formed with water molecules starting to diffuse into the nanopores. While the confined water in the crystalline bulk simulations is pushed to the vacant pores due to hydrophobic inner surfaces, the outer surface water molecules form chemical bonds with under--coordinated Zn2+ metal sites which act as nucleation sites for the water droplets to form and hence making the surface hydrophilic.
By adapting a similar mechanism to the dangling linker defect formation mechanism, we probe the tendency of the outer surface of ZIF-8 nanoparticles to water attack and hydrolysis. Results presented in this work are useful in designing more robust materials for applications in humid environments. | Mohammad R. Momeni; Dil K. Limbu; Sara Abdelhamid; Shaina Pearson; Farnaz A. Shakib | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a8deb063557c5af49415b3/original/atomistic-molecular-dynamics-insights-on-water-local-structure-and-dynamics-on-different-surfaces-of-zeolitic-imidazolate-frameworks.pdf |
60c747c0469df41b4cf43892 | 10.26434/chemrxiv.11760414.v1 | DNA Microviscosity Converts Ruthenium Polypyridyl Complexes to Effective Photosensitizers | <div>
<div>
<div>
<p>A unique radiative decay engineering strategy using DNA microviscosity for the
generation of ruthenium polypyridyl complex (RPCs) mediated singlet oxygen for selective
damage of DNA and killing cancer cells is reported. This investigation also demonstarte the
effect of light-driven RPCs on bacterial growth arrest, through DNA nick, and differential
localization in cancer and non-cancer cells. Moreover, upon binding with DNA, RPCs
experience high local microviscosity, which causes significant enhancement of the excited
state lifetime and thus generates singlet oxygen. The visible-light-triggered singlet-oxygen
efficiently produce nick in DNA and inhibits bacterial growth. RPCs also localize inside the
nucleus of the cancer cell and in the vicinity of the nuclear membrane of non-cancerous cells,
confirmed by live-cell confocal microscopy. The results provide a facile platform for the novel
antibiotic intended discovery combined with cancer therapy.
</p>
</div>
</div>
</div> | Prashant Kumar; Falguni Chandra; Paltan Laha; Srikanta Patra; Apurba Koner | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c0469df41b4cf43892/original/dna-microviscosity-converts-ruthenium-polypyridyl-complexes-to-effective-photosensitizers.pdf |
65e8f798e9ebbb4db918a09f | 10.26434/chemrxiv-2024-sj081 | Pd(COD)(DQ): A Stable, Versatile, and Monometallic Palladium(0) Source for Organometallic Synthesis and Catalysis | Pd(COD)(DQ) (COD=1,5-cyclooctadiene, DQ=duroquinone) is a robust, air-stable, and well-defined 18-electron Pd(0)–olefin complex first synthesized by Sakai et al. in 1983. Herein, we describe an operationally convenient synthetic procedure to prepare this complex on decagram scale; we show that it undergoes facile ligand exchange with phosphines, N-heterocyclic carbenes, and other catalytically important ancillary ligands to give stable organometallic products; and we demonstrate its catalytic competence in numerous useful reactions in organic synthesis. We anticipate that the pronounced stability of Pd(COD)(DQ) and its favorable handling properties will allow it to find use as a convenient Pd(0) source in academic and industrial research labs. | Wen-Ji He; Wen-Zhuo Qin; Shenghua Yang; Senjie Ma; Nana Kim; Johnathan Schultz; Maximilian Palkowitz; Chi He; Anqi Ma; Michael Schmidt; Milan Gembicky; Steven Wisniewski; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Coordination Chemistry (Organomet.); Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e8f798e9ebbb4db918a09f/original/pd-cod-dq-a-stable-versatile-and-monometallic-palladium-0-source-for-organometallic-synthesis-and-catalysis.pdf |
6622329721291e5d1d28d995 | 10.26434/chemrxiv-2024-3n05d | Dynamic correlation driven paramagnetic insulating state and optical properties of the cathode material rhombohedral LiNiO2 at room temperature | Inspired by the experimental finding of a paramagnetic insulating state in rhom- bohedral LiNiO2, a lithium-ion battery cathode of great interest, we calculate the electronic, magnetic, and optical properties of LiNiO2 employing a range of single- particle and many-body methods. Within density-functional theory (DFT) using the generalised-gradient approximation (GGA), meta-GGA, and hybrid functionals we obtain a ferromagnetic half-metallic ground state for rhombohedral LiNiO2, as has been seen previously. Self-consistent GW calculations including self-interaction corrections beyond DFT of various flavours show an electronic band gap albeit with a small quasi-particle peak at the Fermi energy. Moving beyond this, room temperature state-of- the-art dynamical mean-field theory (DMFT) calculations on rhombohedral LiNiO2 show for the first time a gap of combined Mott and charge-transfer character. The paramagnetic insulating state has a band gap of ∼0.6 eV, in excellent agreement with experiments and is in sharp contrast to DFT calculations that require the presence of an extra structural symmetry breaking in the form of Jahn-Teller distortions to open a gap. We observe Ni to be in a +2 state in a d8L configuration, with a charge-transfer ligand hole on O p, and identify the ligand hole state from the DMFT DOS. We further show that whereas DFT shows the presence of an unphysical metallic Drude peak in optical absorption spectra, DMFT calculations capture the correct form of the optical absorption spectra, and have an excellent match with the calculated band gap as well. Our results clarify that at room temperature, it is the charge transfer gap with a Mott character that causes rhombohedral LiNiO2’s insulating nature; a structural distortion is not required. | Hrishit Banerjee; Markus Aichhorn; Clare P. Grey; Andrew J. Morris | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6622329721291e5d1d28d995/original/dynamic-correlation-driven-paramagnetic-insulating-state-and-optical-properties-of-the-cathode-material-rhombohedral-li-ni-o2-at-room-temperature.pdf |
630741a20187d9eb20a0a0ab | 10.26434/chemrxiv-2022-1jtms | From LUVs to GUVs - how to cover micrometer-sized pores with membranes | Pore-spanning membranes (PSMs) are a versatile tool to investigate membrane-confined processes in a bottom-up approach. Pore sizes in the micrometer range are most suited to visualize PSMs using fluorescence microscopy. However, the preparation of these PSMs relies on the spreading of giant unilamellar vesicles (GUVs). GUV production faces several limitations. Thus, alternative ways to generate PSMs starting from large or small unilamellar vesicles that are more reproducibly prepared, are highly desirable. Here we describe a method to produce PSMs obtained from large unilamellar vesicles making use of droplet-stabilized GUVs generated in a microfluidic device. We analyzed the lipid diffusion in the free-standing and supported parts of the PSMs using z-scan fluorescence correlation spectroscopy and fluorescence recovery after photobleaching experiments in combination with finite element simulations. Employing atomic force indentation experiments, we also investigated the mechanical properties of the PSMs. Both, lipid diffusion constants and lateral membrane tension were compared to those obtained on PSMs derived from electroformed GUVs, which are known to be solvent- and detergent-free, under otherwise identical conditions. Our results demonstrate that the lipid diffusion, as well as the mechanical properties of the resulting PSMs, are almost unaffected by the GUV formation procedure but depend on the chosen substrate. With the new method in hand, we were then able to reconstitute the syntaxin-1A transmembrane domain in microfluidic GUVs and PSMs, which was visualized by fluorescence microscopy. | Kristina Kramer; Merve Sari; Kathrin Schulze; Hendrik Flegel; Miriam Stehr; Ingo Mey; Andreas Janshoff ; Claudia Steinem | Biological and Medicinal Chemistry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630741a20187d9eb20a0a0ab/original/from-lu-vs-to-gu-vs-how-to-cover-micrometer-sized-pores-with-membranes.pdf |
6453ccaa1ca6101a45c6ad7c | 10.26434/chemrxiv-2023-tgc4v-v2 | From waste to energy - Photocatalytic anaerobic degradation of microplastics to generate hydrogen | Microplastics are very prominent pollutants in our environment, and the reduction of microplastics waste is a major responsibility for our society. Here, microplastics are used as hydrogen source to generate the green energy carrier hydrogen from anaerobic photocatalysis. Using P25 TiO2 as typical photocatalyst, we show that as used model microplastics can act as solid sources for hydrogen. The highest hydrogen evolution rate was observed when LDPE or PET were used, leading to stable hydrogen evolution for several hours. | Morten Weiss; Roland Marschall | Catalysis; Energy; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6453ccaa1ca6101a45c6ad7c/original/from-waste-to-energy-photocatalytic-anaerobic-degradation-of-microplastics-to-generate-hydrogen.pdf |
66e81cf051558a15ef23fdae | 10.26434/chemrxiv-2024-991vw | Ligand Non-Innocence and Proton Channel Promote Cobalt-Catalyzed Electrochemical CO2 Reduction with Predominant CO Selectivity | Enzymes and heterogenous catalysts for CO2 reduction reactions (CO2RR) use secondary interactions between metal sites and protein-derived coordination spheres to control the precise transfer of protons and electrons to minimize overpotential and maximize selectivity over the competitive hydrogen evolution reaction. We now report a molecular cobalt (II) complex [1-Co]2+ that uses a similar strategy under homogenous condition through the use of a redox non-innocent ligand, Hbbpya, containing two 2,2′-bipyridine chelating groups linked by a -NH moiety. By acting as a structural anchor to form a hydrogen-bonded network of four phenol groups, the -NH group enables efficient binding and protonation of CO2 at a cobalt center to form CO under electrocatalytic conditions at a moderate overpotential and with high selectivity. Methylation of the -NH group in [2-Co]2+ results in a loss of CO2RR selectivity and increased production of hydrogen. The complexes [1-Co]2+ and [2-Co]2+, and their one and two electron-reduced counterparts are extensively characterized by X-ray diffraction, cyclic voltammetry, electron paramagnetic resonance and density functional theoretical calculations. The electronic structure of the catalytically active doubly-reduced [1-Co]0 and [2-Co]0 can be best described as containing a cobalt(I) center and a mono reduced ligand system. Most importantly, in stoichiometric reactions, due to the presence of an efficient proton relay, [1-Co]0 performs fast two-electron reduction of CO2 to form [1-Co]2+ and CO, thereby, avoiding the formation of the high-energy CO2 radical anion, reminiscent of the CO2RR mechanism proposed in NiFe-carbon monoxide dehydrogenase. In contrast, a one-electron chemistry prevails in reactions of [2-Co]0 and CO2. | Ayan Bera; Sarah Bimmermann; Dibya Jyoti Barman; Leon Gerndt; Thomas Lohmiller; Kaltum Abdiaziz; Maylis Orio; Alexander Schnegg; Kara L. Bren; Dennis G. H. Hetterscheid; Michael Römelt; Ulf-Peter Apfel; Kallol Ray | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e81cf051558a15ef23fdae/original/ligand-non-innocence-and-proton-channel-promote-cobalt-catalyzed-electrochemical-co2-reduction-with-predominant-co-selectivity.pdf |
6741bcba7be152b1d0780aef | 10.26434/chemrxiv-2024-fj3gp | Microneedles loaded with lipid nanocarriers for local treatment of vulvovaginal candidiasis | Vaginal yeast infections, such as vulvovaginal candidiasis (VVC), affect nearly three out of four women worldwide. Re-occurrence is frequent and requires repeated treatments with oral, antifungal medications at high doses. Prolonged treatments contribute to development of resistant fungal strains and the risk of systemic adverse effects. Vaginal drug delivery can overcome several of the disadvantages associated with oral drug administration. However, current dosage forms, such as vaginal creams and gels, are rapidly expelled from the vaginal tract and require daily dosing to assure therapeutic outcome, thus jeopardizing patient compliance. Therefore, we developed rapidly dissolving microneedle arrays for local, vaginal delivery of antifungal drugs. Clotrimazole, a poorly water-soluble antifungal agent, was formulated in lipid-based nanocarriers (LNCs) and incorporated in the tips of microneedles. The antifungal activity was then tested against the most common VVC fungal strains, C. albicans and C. glabrata, using an in vitro disk diffusion assay and an explant model from bovine vaginal tissue. Antifungal activity increased when the LNCs were incorporated in the microneedles. Notably, the LNC-loaded microneedles inhibited fungal growth at a 10-fold lower drug dose than a commercial clotrimazole cream. Finally, a device prototype was manufactured, based on an intravaginal ring with multiple microneedle arrays on its surface. Local vaginal drug delivery using such microneedle-based devices could enable more effective treatment strategies for VVC. | Paarkavi Udayakumar; Nataša Škalko-Basnet; Cristhian Fernando Salas Cotaquispe; Lisa Myrseth Hemmingsen; Georgios Sotiriou; Juan Du; Alexandra Teleki | Materials Science; Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6741bcba7be152b1d0780aef/original/microneedles-loaded-with-lipid-nanocarriers-for-local-treatment-of-vulvovaginal-candidiasis.pdf |
60c75391469df49da6f44db3 | 10.26434/chemrxiv.13440206.v2 | A Computational Binding Affinity Estimation Protocol with Maximum Utilization of Experimental Data : A Case Study for Adenosine Receptor | Estimating binding affinity between a target protein and the ligand is a crucial step in the drug discovery process. In computer aided drug design (CADD), the problem can be divided into two steps, finding the correct binding pose and estimating binding free energy. In this study, a new binding affinity estimation protocol, which uses molecular docking and binding affinity estimation with Molecular Dynamics (MD) simulation and maximizes the use of available experimental data, is suggested. Docking with a custom scoring function was used to find a better initial binding pose and Linear Interaction Energy (LIE) method with an optimized coefficient was used to estimate the binding affinity. The protocol has been validated with an external validation set and applied to five modafinil and its derivatives to set the order of binding affinity to Adenosine A2A receptors (ADORA2A, A2aR), which is a membrane protein, for a case study. This protocol could be time efficient and useful for computational drug discovery where limited experimental data is available. | Il Kwon Cho; Sung Hyun Moon; Kwang-Hui Cho | Chemoinformatics | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75391469df49da6f44db3/original/a-computational-binding-affinity-estimation-protocol-with-maximum-utilization-of-experimental-data-a-case-study-for-adenosine-receptor.pdf |
60c75351ee301c02d3c7adaa | 10.26434/chemrxiv.13416881.v1 | A New Twist on an ‘Old’ Ligand: A [Mn16] Double Square Wheel and a [Mn10] Contorted Wheel | Ligand design remains key to the synthesis of coordination compounds possessing specific topologies,
nuclearities and symmetries that direct targeted physical properties. N,O-chelates based on ethanolamine
have been particularly prolific in constructing a variety of paramagnetic 3d transition metal complexes with
fascinating magnetic properties. Here, we show that combining three ethanolamine moieties within the same
organic framework in the form of the ligand 1,3,5-tri(2-hydroxyethyl)-1,3,5-triazacyclohexane (LH3) leads to
the formation of two highly unusual Mn wheels. Reaction of Mn(NO3)2·6H2O with LH3 in basic methanolic
solutions leads to the formation of [MnIII
12MnII
4(µ3-O)6(µ-OH)4(µ3-OMe)2(µOMe)2(L)4(LH)2(H2O)10](NO3)6(OH)2 (1) and [MnIII
10(µ3-O)4(µ-OH)4(µ-OMe)4(L)4(H2O)4](NO3)2 (2); the only
difference in the synthesis being the ratio of metal:ligand employed. The structure of the former describes
two offset [MnIII
6MnII
2] square wheels, linked through a common centre, and the latter a single [MnIII
10] wheel
twisted at its centre, such that the top half is orientated perpendicular to the bottom half. In both cases the
L
3-
/LH2-
ligands dictate the orientation of the Jahn-Teller axes of the MnIII ions which lie perpendicular to the
triazacyclohexane plane. Direct current magnetic susceptibility and magnetisation data reveal the presence
of competing exchange interactions in 1 and strong antiferromagnetic interactions in 2. Given the simplicity
of the reactions employed and the paucity of previous work, the formation of these two compounds suggests
that LH3 will prove to be a profitable ligand for the synthesis of a multitude of novel 3d transition metal
complexes | Euan Brechin; Constantinos J. Milios; Thomais Tziotzi; Marco Coletta; Mark Gray; Scott Dalgarno; Giulia Lorusso; Marco Evangelisti; Cameron Campbell | Coordination Chemistry (Inorg.); Ligands (Inorg.); Magnetism; Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75351ee301c02d3c7adaa/original/a-new-twist-on-an-old-ligand-a-mn16-double-square-wheel-and-a-mn10-contorted-wheel.pdf |
6668d303409abc03452ef1da | 10.26434/chemrxiv-2024-zfjp6 | Interrogating Explicit Solvent Effects on the Mechanism and
Site-Selectivity of Aryl Halide Oxidative Addition to L2Pd(0) | We report a study of solvent effects on the rate, selectivity, and mechanism of (hetero)aryl (pseudo)halide oxidative addition to Pd(PCy3)2 as an exemplar of L2Pd(0) species. First, 2-chloro-3-aminopyridine is observed to undergo faster oxidative addition in toluene compared to more polar solvents, which is not consistent with the trend we observe with many other 2-halopyridines. We attribute this to solvent basicity hydrogen-bonding between solvent and substrate. Greater hydrogen-bond donation from the substrate leads to a more electron-rich aromatic system, and therefore slower oxidative addition. We demonstrate how this affects rate and site-selectivity for hydrogen-bond donating substrates. Second, electron-deficient multihalogenated pyridines exhibit improved site-selectivity in polar solvents, which we attribute to different C–X sites undergoing oxidative addition by two different mechanisms. The C–X site that favours the more polar nucleophilic displacement transition state is preferred over the site that favours a less-polar 3-centered transition state. Finally, (hetero)aryl triflates consistently undergo faster oxidative addition in more polar solvents, which we attribute to highly polar nucleophilic displacement transition states. This leads to improved site-selectivity for C–OTf oxidative addition, even in the presence of highly reactive 2-pyridyl halides. | Jingru Lu; Holly Celuszak; Irina Paci; David Leitch | Physical Chemistry; Organic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6668d303409abc03452ef1da/original/interrogating-explicit-solvent-effects-on-the-mechanism-and-site-selectivity-of-aryl-halide-oxidative-addition-to-l2pd-0.pdf |
60c74d9fee301c031ec7a2ff | 10.26434/chemrxiv.12642779.v1 | Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I) | <div><div><div><p>Chemoselective ligation reactions, such as native chemical ligation (NCL),
enable the assembly of synthetic peptides into proteins. However, the scope of proteins
accessible to total chemical synthesis is limited by ligation efficiency. Sterically hindered
thioesters and poorly soluble peptides can undergo incomplete ligations, leading to
challenging purifications with low yields. This work describes a new method, ClickAssisted NCL (CAN), which overcomes these barriers. In CAN, peptides are modified
with traceless “helping hand” lysine linkers that enable addition of dibenzocyclooctyne
(DBCO) and azide handles for strain-promoted alkyne-azide cycloaddition (SPAAC)
reactions. This cycloaddition templates the peptides to increase their effective
concentration and greatly accelerate ligation kinetics. After ligation, mild hydroxylamine
treatment tracelessly removes the linkers to afford the native ligated peptide. Although
DBCO is incompatible with standard Fmoc solid-phase peptide synthesis (SPPS) due to
an acid-mediated rearrangement that occurs during peptide cleavage, we demonstrate
that copper(I) protects DBCO from this side reaction, enabling direct production of
DBCO-containing synthetic peptides. Excitingly, low concentrations of triazole-linked
model peptides reacted ~1,200-fold faster than predicted for non-templated control
ligations, which also accumulated many side products due to the long reaction time.
Using the E. coli ribosomal subunit L32 as a model protein, we further demonstrate that
the SPAAC, ligation, desulfurization, and linker cleavage steps can be performed in a
one-pot fashion. CAN will be useful for overcoming ligation challenges to expand the
reach of chemical protein synthesis.</p></div></div></div> | Patrick Erickson; James Fulcher; Michael Kay | Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d9fee301c031ec7a2ff/original/traceless-click-assisted-native-chemical-ligation-enabled-by-protecting-dibenzocyclooctyne-from-acid-mediated-rearrangement-with-copper-i.pdf |
66fea39c51558a15eff3f07f | 10.26434/chemrxiv-2024-1fk8r | Hydrogels with Tethered Transcription Circuit Elements for Chemical Communication and Collective Computation | Tissues, robots, and other distributed systems must make decisions about information originating from and then orchestrate responses at different physical locations. Cell-cell communication processes are essential for morphogenesis, immune response, and wound healing. Devising methods for programming analogous distributed behaviors in synthetic materials, such as multi-scale pattern formation or self-assembly, remains a challenge. Here, we devise a design principle for distributed chemical computing and construct a library of transcription circuit elements, termed tethered genelets (TGs), that implement this design principle within networks of 50-micron hydrogel nodes (HNs). TGs exhibit digital behavior in the form of a "distance-response curve" - they switch off in response to signals emanating from an HN within a specific distance but are unaffected by faraway signals. Computational studies show that this property allows HN networks to reliably propagate information without attenuation and to program specific spatiotemporal patterns such as pulses and oscillations with tunable frequencies. In experiments, we verify that TGs send and receive signals as designed and validate the function and modularity of a library of 15 TGs circuit elements. The resulting design principle and library of molecules now provide a means of programming a diverse range of distributed chemical behaviors, allowing for distributed communication and dynamics in soft robots, responsive surfaces, and other bio-materials. | Kuan-Lin Chen; Joshua Cole; Cheng-Hung Chou; Samuel W. Schaffter; Pepijn Moerman; Moshe Rubanov; Keren Sneh; Rebecca Schulman | Biological and Medicinal Chemistry; Chemical Biology; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fea39c51558a15eff3f07f/original/hydrogels-with-tethered-transcription-circuit-elements-for-chemical-communication-and-collective-computation.pdf |
67a2f2f881d2151a023672dc | 10.26434/chemrxiv-2025-vdjb1-v2 | Visible-Light Photocatalysis Using CsPbX3 Perovskite Nanocrystals for Organic Transformations | The increasing interest in efficient organic synthesis by applying solar radiation has propelled a surge in the demand for introducing new types of photocatalysts in synthetic toolboxes. During the last few decades, tremendous efforts have been invested in developing low-cost, non-toxic, stable, and potent photocatalysts. In this perspective, Cesium Lead Halide perovskite (CsPbX3) nanocrystal has emerged as a brand new photocatalyst, creating a renaissance in pioneering organic photochemistry with its enchanting optoelectronic features. Due to their unique band structure, tunable bandgap, and near unity quantum yield, these highly fluorescent nanocrystals are exceptional candidates to catalyze numerous fundamental organic transformations by absorbing energy from ultraviolet to visible regions. Also, anion metathesis, long average excited state lifetime, tunable morphology, and photo-generated charge carriers, make them capable of a broader range of organic substrate activation in bench-stable conditions. These nanocrystals are well known for their superb power conversion efficiency (PCE) of solar radiation which reached up to 26.3% in the last few years, and its potential has already surpassed everyone’s expectations in multiple fields like photovoltaics, photoelectronics, lasers, scintillators, etc. But, its use in photo organic chemistry just started and we believe this typical promising material is going to fetch a new era in the field of organic photocatalysis. This comprehensive review systematically summarizes the development made over CsPbX3 perovskite catalysis in the last few years by assembling pieces of literature on perovskite-based organic reactions. And also, explores the intricacies of the underlying mechanistic cycles and discusses limitations with future scope of exploration | Pravat Nayek; Buddhadeb Pal; Prasenjit Mal | Organic Chemistry; Photochemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a2f2f881d2151a023672dc/original/visible-light-photocatalysis-using-cs-pb-x3-perovskite-nanocrystals-for-organic-transformations.pdf |
6650dc8491aefa6ce1e73b74 | 10.26434/chemrxiv-2024-rv4w0 | Accessing Five- and Seven-Membered Phosphorus-Based Heterocycles via Cycloaddition Reactions of Azophosphines | Heterocycles containing both phosphorus and nitrogen have seen increasing use in recent years in luminescent materials, coordination chemistry and building blocks for inorganic polymers, yet their chemistry is currently dominated by five- and six-memberd derivatives. Seven-membered P/N heterocycles are comparatively scarce and lack general, high yielding syntheses. We explore the synthesis and characterisation of 1,2,5-diazaphosphepines from azophosphines. The mechanism has been probed in detail with both computational and experimental studies supporting a stepwise mechanism to form a five-membered ring, and subsequent ring expansion to the diazaphosphepine. Regioselective synthesis of five- and seven-membered rings is possible using asymmetric alkynes. The Lewis acidic borane B(C6F5)3 could either catalyse the formation of the seven-membered ring (iPr derivative) or trap out a key intermediate via a frustrated Lewis pair (FLP) mechanism (tBu derivative). | Ethan Calder; Louise Male; Andrew Jupp | Inorganic Chemistry; Catalysis; Frustrated Lewis Pairs; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6650dc8491aefa6ce1e73b74/original/accessing-five-and-seven-membered-phosphorus-based-heterocycles-via-cycloaddition-reactions-of-azophosphines.pdf |
644987ff83fa35f8f64c3d5e | 10.26434/chemrxiv-2023-ftt1v | Levels of symmetry adapted perturbation theory (SAPT). II. Convergence of interaction energy components | Symmetry adapted perturbation theory (SAPT) is a valuable theoretical technique use- ful in quantifying intermolecular interaction energies in terms of four physically meaningful components: electrostatics, exchange-repulsion, induction, and London dispersion. We present a systematic analysis of the convergence of SAPT total and component energies with respect to level of theory and basis set using an extended database of 4567 dimer geometries. Our analysis supports the use of SAPT0/aug-cc-pVDZ over previously recommended sSAPT0/jun-cc-pVDZ as an economical level of SAPT. Our previous recommendations of SAPT2+/aug-cc-pVDZ and SAPT2+(3)δMP2/aug-cc-pVTZ as medium and high cost variants, respectively, remain unchanged. However, SAPT0/aug-cc-pVDZ and SAPT2+/aug-cc-pVDZ total interaction energies on average rely on error cancellations, so their use in parameterizing SAPT-based force fields and intermolecular potentials should be used with caution. SAPT2+(3)δMP2/aug-cc-pVTZ does show quantitatively accurate component energies, making it the preferred choice for all applications when feasible. Lastly, we introduce a focal point technique which approaches the accuracy of SAPT2+(3)δMP2/aug-cc-pVTZ with a significantly reduced cost. | Jeffrey Schriber; Daniel Cheney; C. David Sherrill | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644987ff83fa35f8f64c3d5e/original/levels-of-symmetry-adapted-perturbation-theory-sapt-ii-convergence-of-interaction-energy-components.pdf |
62787cf5a42e9c1128399283 | 10.26434/chemrxiv-2022-zk09d | Y2Ti2O5S2 – a promising n-type oxysulphide for thermoelectric applications | Thermoelectric materials offer an unambiguous solution to the ever-increasing global demand for energy by harnessing the Seebeck effect to convert waste heat to electrical energy. Mixed-anion materials are ideal candidate thermoelectric materials due to their thermal stability and potential for “phonon-glass, electron-crystal” behaviour. In this study, we use density-functional theory (DFT) calculations to investigate Y2Ti2O5S2, a cation-deficient Ruddlesten-Popper system, as a potential thermoelectric. We use hybrid DFT to calculate the electronic structure and band alignment, which indicate a preference for n-type doping with highly anisotropic in-plane and the out-of-plane charge-carrier mobilities as a result of the anisotropy in the crystal structure. We compute phonon spectra and calculate the lattice thermal conductivity within the single-mode relaxation-time approximation using lifetimes obtained by considering three-phonon interactions. We also calculate the transport properties using the momentum relaxation-time approximation to solve the electronic Boltzmann transport equations. The predicted transport properties and lattice thermal conductivity suggest a maximum in-plane ZT of 1.18 at 1000 K with a carrier concentration of 2.37 × 1020 cm−3. Finally, we discuss further the origins of the low lattice thermal conductivity, in particular exploring the possibility of nanostructuring to lower the phonon mean free path, reduce the thermal conductivity, and further enhance the ZT. Given the experimentally-evidenced high thermal stability and the favourable band alignment found in this work, Y2Ti2O5S2 has the potential to be a promising high-temperature n-type thermoelectric.
| Katarina Brlec; Kieran B. Spooner; Jonathan M. Skelton; David O. Scanlon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62787cf5a42e9c1128399283/original/y2ti2o5s2-a-promising-n-type-oxysulphide-for-thermoelectric-applications.pdf |
652bf05245aaa5fdbb0fd3b4 | 10.26434/chemrxiv-2023-v4xq7 | One-pot Synthesis of a Visible-light Responsive Carbon Nitride/TiO2 Heterointerface Material for Photoelectrocatalytic Applications | The rapid integration of green, clean, and renewable technologies in a circular economy requires stable, abundant, and visible-light responsive absorbers. The ideal solar energy harness and conversion process uses a single material that fulfills photon absorption, exciton dissociation, carrier migration, and surface activity requirements. Heterojunctions enable multiple charge pathways, inhibiting recombination while promoting charge transfer across the heterointerface. This study pinpoints the synergy of combining titanium dioxide (TiO2) anatase with carbon nitride (CN) to create a hybrid TiO2(90%)-CN(10%) heterointerface through a one-pot thermal step. The composite outperforms TiO2 and CN references in four individual photo and photoelectrocatalytic reactions.
In benzylamine photooxidation, the TiO2(90%)-CN(10%) composite achieved a four-fold increase with 51% conversion at 625 nm (red light). In photocatalytic hydrogen production, Pt/TiO2-CN outperformed references by 1.9-fold and 1.6-fold, yielding 319 and 148 μmol h-1 g-1 at 465 and 410 nm (blue and violet lights). Photoelectrochemical characterization using 410 nm filter performed 23% of the full-spectrum measurement. The composite displayed unprecedented TiO2 photosensitization under visible-light, attributed to improved charge transfer, prolonged lifetimes, and the multiple charge carrier pathways.
| Ingrid F. Silva; Carolina Pulignani; Jokotadeola Odutola; Alexey Galushchinskiy ; Ivo F. Texeira ; Mark Isaacs ; Camilo A. Mesa; Ernesto Scoppola; Albert These; Bolortuya Badamdorj; Miguel Ángel Muñoz-Márquez; Ivo Zizak ; Robert Palgrave; Nadezda V. Tarakina ; Sixto Gimenez ; Christoph Brabec; Julien Bachmann ; Emiliano Cortes; Nikolai Tkachenko ; Oleksandr Savateev ; Pablo Jiménez-Calvo | Physical Chemistry; Energy; Interfaces; Photochemistry (Physical Chem.); Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652bf05245aaa5fdbb0fd3b4/original/one-pot-synthesis-of-a-visible-light-responsive-carbon-nitride-ti-o2-heterointerface-material-for-photoelectrocatalytic-applications.pdf |
60c73e9cbb8c1aa9b63d994f | 10.26434/chemrxiv.7072577.v1 | Theoretical and Experimental Evaluation of the Effect of Fluorinated Substituent on the Topological Landscape and Thermodynamic Stability of Zeolitic Imidazolate Framework Polymorphs | By combining mechanochemical synthesis and calorimetry with theoretical calculations, we demonstrate that dispersion-corrected periodic density functional theory (DFT) can accurately survey the topological landscape and predict relative energies of polymorphs for a previously inaccessible fluorine-substituted zeolitic imidazolate framework (ZIF). Experimental screening confirmed two out of three theoretically anticipated polymorphs, and the calorimetric measurements provided an excellent match to theoretically calculated energetic difference between them.<br /> | Mihails Arhangelskis; Athanassis Katsenis; Novendra Novendra; Zamirbek Akimbekov; Dayaker Gandrath; Joseph Marrett; Ghada Ayoub; Andrew Morris; Omar Farha; Tomislav Friscic; Alexandra Navrotsky | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9cbb8c1aa9b63d994f/original/theoretical-and-experimental-evaluation-of-the-effect-of-fluorinated-substituent-on-the-topological-landscape-and-thermodynamic-stability-of-zeolitic-imidazolate-framework-polymorphs.pdf |
63d39ca11a1ead1841b9a1a7 | 10.26434/chemrxiv-2023-ks8vp | Chemically Inspired Convolutional Neural Network using Electronic Structure Representation | In recent years, a development of appropriate crystal representations for accurate prediction of inorganic crystal properties has been considered as one of the essential tasks to accelerate materials discovery through high-throughput virtual screening (HTVS). However, many of them were developed aiming to predict properties of the given structures, although property predictions of ground state structures using unrelaxed structures as inputs are much more important in practical HTVS. To tackle this challenge, we develop a chemically inspired convolutional neural network based on convolution block attention modules using density of states of unrelaxed initial structures (IS-DOS) as inputs. Our model, Electronic Structure Network (ESNet), achieved the highest accuracy for predicting formation energy, proving that IS-DOS is appropriate input for the property prediction and the attention module is capable of properly featurizing DOS signals by capturing contributions of each spin and orbital state. In addition, we statistically evaluated a stability screening performance of ESNet, measuring computational cost and capability of materials discovery simultaneously. We found that ESNet outperformed previously reported models and various models with different types of input features and architectures. Indeed, ESNet successfully discovered 926 stable materials from 15,318 unrelaxed structures with 82 % reduced computational cost compared to the complete DFT validation. | Dong Hyeon Mok; Daeun Shin; Jonggeol Na; Seoin Back | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d39ca11a1ead1841b9a1a7/original/chemically-inspired-convolutional-neural-network-using-electronic-structure-representation.pdf |
6401f35737e01856dc159a87 | 10.26434/chemrxiv-2023-q3sd8 | Click-electrochemistry for the rapid labeling of virus, bacteria and cell surfaces | The remodeling of microorganism surfaces with biomolecules is a powerful tool to study the role of membrane receptors in chemical biology and to develop drug delivery systems in gene therapy using viral vectors and cell-based therapies. Methods for direct covalent ligation of these surfaces remain poorly reported, and mostly based on metabolic engineering for bacteria and cells functionalization. In the latter case, a tagged precursor must first be enzymatically metabolized and delivered to the outer cell membrane to become available for chemo-selective labeling. While effective, a faster method avoiding the bio-incorporation step would be highly complementary. This would also need to be compatible with organisms showing poor levels of precursor assimilation or lacking the metabolic function. Here, we used N-methylluminol (NML), a fully tyrosine-selective protein anchoring group after one-electron oxidation, to label the surface of viruses, living bacteria and cells. The functionalization was performed electrochemically and in situ by applying a 750 mV vs Ag/AgCl electric potential to aqueous buffered solutions of tagged NML containing the viruses, bacteria or cells. The electro-coupling was performed with NML anchors bearing a bioorthogonal azide, biotin, or carbohydrate (mannose and N-acetyl galactosamine) handles. The broad applicability of the click-electrochemistry method was explored on recombinant adeno-associated viruses (rAAV2), E. coli (Gram-) and S. epidermis (Gram+) bacterial strains, and HEK293 and HeLa eukaryotic cell lines. Surface electro-conjugation was achieved in minutes to yield functionalized rAAV2 that conserved both structural integrity and infectivity properties, and living bacteria and cell lines that were still alive and able to divide. As NML activation immediately stops if there is no current, the method offers reproducible temporal control on the degree of surface functionalization. Thus, click-electrochemistry should significantly expand the scope of bioconjugation methods. | Sébastien Depienne; Mohammed Bouzelha; Emmanuelle Courtois; Karine Pavageau; Pierre-Alban Lalys; Maia Marchand; Dimitri Alvarez-Dorta; Steven Nedellec; Laura Marin-Fernandez; Cyrille Grandjean; Mohammed Boujtita; David Deniaud; Mathieu Mével; sebastien gouin | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6401f35737e01856dc159a87/original/click-electrochemistry-for-the-rapid-labeling-of-virus-bacteria-and-cell-surfaces.pdf |
60c753ccee301c43f4c7ae7d | 10.26434/chemrxiv.13546634.v1 | High-Throughput Screening Single-Atom Alloy for Electroreduction of Dinitrogen to Ammonia | <p></p><p>Exploring electrocatalyst with high activity,
selectivity and stability is essential for development of applicable
electrocatalytic ammonia synthesis technology. By performing density functional
theory calculations, we systematically investigated a series of transition-metal
doped Au-based single atom alloys (SAAs) as promising electrocatalysts for
nitrogen reduction reaction (NRR). For Au-based electrocatalyst, the first
hydrogenation step (*N<sub>2</sub>→*NNH) normally determines the limiting
potential of the overall reaction process. Compared with pristine Au(111) surface, introducing single atom can significantly
enhance the binding strength of N<sub>2</sub>, leading to decreased energy barrier
of the key step, i.e., ΔG(*N<sub>2</sub>→*NNH). According to
simulation results, three descriptors were proposed to describe ΔG(*N<sub>2</sub>→*NNH), including
ΔG(*NNH), <i>d</i>-band center, and
. Eight doped elements (Ti, V, Nb, Ru, Ta, Os, W, and Mo)
were initially screened out with limiting potential ranging from -0.75V to
-0.30 V. Particularly, Mo- and W-doped systems possess the best activity with
limiting potentials of -0.30 V, respectively. Then the intrinsic
relationship between structure and the potential performance was further
analyzed by using
machine-learning. The selectivity, feasibility, stability of these candidates
were also evaluated, confirming that SAA containing Mo, Ru ,Ta, and W could be outstanding NRR electrocatalysts. This
work not only broadens the understating of SAA application in electrocatalysis,
but also devotes to the discovery of novel NRR electrocatalysts.</p><br /><p></p> | Guokui Zheng; Ziqi Tian; Xingwang Zhang; Liang Chen; Xu Qian; YanLe Li | Theory - Computational; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753ccee301c43f4c7ae7d/original/high-throughput-screening-single-atom-alloy-for-electroreduction-of-dinitrogen-to-ammonia.pdf |
64501eeb0d87b493e39c655c | 10.26434/chemrxiv-2023-0xbh5 | Active, selective, and stable single-component
precatalysts for asymmetric allylic alkylation | The stereoselective construction of new carbon-element bonds is a crucial aspect of organic synthesis. Among the many strategies developed to date, palladium-catalysed asymmetric allylic alkylation is commonly used to access chiral molecules in natural product and active pharmaceutical ingredient synthesis. The use of modular Trost-type ligands and phosphinooxazoline (PHOX) ligands results in generally high stereoselectivity for a wide range of transformations. However, these reactions nearly always require relatively high catalyst loadings (5-10 mol%), reaction-specific catalyst preactivation protocols, and excess chiral ligand to ensure high yield and selectivity. Here we report the isolation and catalytic evaluation of a series of chiral palladium(0) single-component precatalysts that are active for a variety of asymmetric allylic alkylation reactions. The four Trost-type precatalysts in this work are the first characterized examples of stable, isolable Pd complexes with the diphosphines coordinated in the desired κ2-P,P fashion. All of the palladium(0) complexes are stable for >12 months when stored under nitrogen, and can be handled as solids and even in solution under air for hours without decomposition. A catalytic evaluation of these single-component precatalysts across 9 distinct asymmetric allylic alkylation reactions reveals excellent performance in terms of reactivity, selectivity, practicality, and minimizing palladium and chiral ligand loading. This enables both small-scale multivariate screening studies and preparative scale synthesis of key chiral building blocks, exemplified with the unprecedented enantioselective allylation of hydantoins. The optimized reaction achieves high yield and enantioselectivity with only 0.2 mol% of catalyst (turnover number of 465). These precatalysts will enable development of more efficient and robust asymmetric allylic alkylation reactions toward complex target molecules. | Jingjun Huang; Thomas Keenan; Francois Richard; Jingru Lu; Sarah Jenny; Alexandre Jean; Stellios Arseniyadis; David Leitch | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64501eeb0d87b493e39c655c/original/active-selective-and-stable-single-component-precatalysts-for-asymmetric-allylic-alkylation.pdf |
641cda7c62fecd2a835588e8 | 10.26434/chemrxiv-2023-zwkhm | Polytypes and twins in new boron-rich chalcogenides B6S and B6Se synthesized at high pressure | Microstructure of new boron-rich chalcogenides, orthorhombic B6X (X = S, Se) synthesized at high pressures and high temperatures, has been studied by high-resolution transmission electron microscopy. Two twins systems have been found along planes (101) and (002). Apart from numerous twins on the (101) plane, two types of polytypes were found: ABAB in both chalcogenides and AB1CD1AB1CD1 in B6Se. It has been shown that shear bands in B6S and cracks in both materials lie in planes {011}. | Boris A. Kulnitskiy; Vladimir D. Blank; Tatyana A. Gordeeva; Vladimir L. Solozhenko | Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641cda7c62fecd2a835588e8/original/polytypes-and-twins-in-new-boron-rich-chalcogenides-b6s-and-b6se-synthesized-at-high-pressure.pdf |
62eafa91a05ea133c1920f70 | 10.26434/chemrxiv-2022-js7k7 | Synthetic duocarmycins: structural evolution from SAR to prodrugs and ADCs - a searchable structure/function database | Synthetic analogues of the DNA-alkylating cytotoxins of the duocarmycin class have been extensively investigated in the past 40 years, driven by their high potency, their unusual mechanism of bioactivity, and the beautiful modularity of their structure-activity relationship (SAR). This minireview analyses how the molecular designs of synthetic duocarmycins have evolved: from (1) early SAR studies, through to modern applications for directed cancer therapy as (2) prodrugs and (3) antibody-drug conjugates in late-stage clinical development. Analysing 583 primary research articles and patents from 1978-2022, we distill out a searchable A0-format "Minard map" poster of ca. 200 key structure/function-tuning steps tracing chemical developments across these three key areas. This structure-based overview showcases the ingenious approaches to tune and target bioactivity, that continue to drive development of the elegant and powerful duocarmycin platform.
| Jan Felber; Oliver Thorn-Seshold | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Education; Chemical Education - General; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eafa91a05ea133c1920f70/original/synthetic-duocarmycins-structural-evolution-from-sar-to-prodrugs-and-ad-cs-a-searchable-structure-function-database.pdf |
6340a106e61502499b364494 | 10.26434/chemrxiv-2022-60dt1 | On the rational design of mesoporous silica humidity sensors | Mesoporous silica is commonly used as matrix for humidity sensors, which operate on the principle of relative humidity-dependent water uptake and read-out by resistive or capacitive means. Although numerous studies have been dedicated to improving the sensing performance, in particular with conductive additives, the effect of pore structure on sensing behaviour has not been systematically investigated so far. Herein, we showcase the effects of pore size and porosity on resistive sensing behaviour in the 0.5-85% relative humidity (RH) range. We employed evaporation-induced self-assembly (EISA) in combination with sol-gel chemistry to fabricate well-defined mesoporous silica thin films with high degree of structural control. Material architectures with pore sizes of 3 to 15 nm and porosities of 40 to 70% were rationally designed by using structure directing agents (SDAs) with increasing molecular weight and tuning the silica to SDA ratio. We found that a combination of pore size of 15 nm and 70% porosity showcases a particularly high sensitivity (~104 times change in resistance) in the measured range, with quick response and recovery times of 3 and 9 seconds, respectively. Across the various sensors, we identified a clear correlation between the pore size and the linear RH sensing range. Sensors with larger mesopores (~15 nm) exhibited higher sensitivity and linear response in the 65 to 85% RH range than sensors with smaller pores (<8 nm). Additionally, increasing the porosity while retaining the pore size, yields better overall sensitivity across the range. Our findings may serve as guidelines for developing broad spectrum high-performance mesoporous sensors and for sensors specifically engineered for optimal operation in specific RH ranges. | Máté Füredi; Alberto Alvarez-Fernandez; Maximiliano Jara Fornerod; Bálint Fodor; Stefan Guldin | Materials Science; Analytical Chemistry; Nanoscience; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6340a106e61502499b364494/original/on-the-rational-design-of-mesoporous-silica-humidity-sensors.pdf |
60c73e964c89196b5cad1deb | 10.26434/chemrxiv.7013009.v1 | Chemistry Education Fostering Creativity in the Digital Era | Renewing undergraduate
education in the chemical sciences to foster creativity using research,
visualization and connectivity resources has substantial benefits, but requires
changes in the curriculum and teaching methodology as well as in conventional university teaching and academic
human resource policies. | Mario Pagliaro | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e964c89196b5cad1deb/original/chemistry-education-fostering-creativity-in-the-digital-era.pdf |
60c755d1bdbb8914f9a3a8f0 | 10.26434/chemrxiv.14156918.v1 | Disrupters of the Thymidylate Synthase Homodimer Accelerate Its Proteasomal Degradation and Inhibit Cancer Growth. | <p>Drugs that target human thymidylate synthase (hTS) are widely used in anti-cancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces its over-expression and the development of drug resistance. We thus pursued an alternative strategy that led to the discovery of TS-dimer disrupters that bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. We performed a structural, spectroscopic and kinetic investigation of the effects of these small molecules and<b></b>the best one, <b>E7, </b>accelerates the proteasomal degradation of hTS in cancer cells. <b>E7</b> showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, <b>E7 </b>breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.</p> | Costantino Luca; Stefania Ferrari; Matteo Santucci; Outi M. Salo-Ahen; Carosati Emanuele; Silvia Franchini; Lauriola Angela; Cecilia Pozzi; Gaetano Marverti; Matteo Trande; Gozzi Gaia; Puneet Saxena; Giuseppe Cannazza; Lorena Losi; Daniela Cardinale; Alberto Venturelli; Antonio Quotadamo; Pasquale Linciano; Remo Guerrini; Salvatore Pacifico; Rosaria Luciani; Filippo Genovese; Henrich Stefan; Alboni Silvia; Nuno Santarem; Anabela Cordeiro-da-Silva; Elisa Giovannetti; Godefridus Peters; Paolo Pinton; Alessandro Rimessi; Gabriele Cruciani; Robert Stroud; Rebecca Wade; Stefano Mangani; Domenico D'Arca; Glauco Ponterini; Maria Paola Costi | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755d1bdbb8914f9a3a8f0/original/disrupters-of-the-thymidylate-synthase-homodimer-accelerate-its-proteasomal-degradation-and-inhibit-cancer-growth.pdf |
64738aa84f8b1884b76c052d | 10.26434/chemrxiv-2023-0nzgm | Modelling the effects of E/Z photoisomerization of a cyclocurcumin analogue on the properties of cellular lipid membranes | The use of photosensitive molecules capable of isomerizing under light stimuli, and thus induce perturbation in biological systems, is becoming increasingly popular for potential light-activated chemotherapeutic purposes. We recently show that a cyclocurcumin derivative (CCBu), may be suitable for light-activated chemotherapy and may constitute a valuable alternative to traditional photodynamic therapy, due to its oxygen-independent mechanism of action, which allows the treatment of hypoxic solid tumors. In particular, we have shown that the E/Z photoisomerization of CCBu correlates with strong perturbations of model lipid bilayers1. In this work, we perform all-atom classical molecular dynamics for a more complex bilayer, whose composition is, thus, much closer to eukaryotic outer cell membranes. We have evidenced important differences in the interaction pathway between CCBu and the complex lipid bilayer as compared to previous models, concerning both the membrane penetration capacity and the isomerization-induced perturbations. While, we confirm that structural perturbations of the lipid membrane are induced by isomerization, we also show how the use of a simplified membrane model can result in an oversimplification of the system and hinders key physical and biological phenomena. Although, CCBu derivative may be considered as suitable candidate for light-activated chemotherapy, we also underline how the inclusion of bulkier substituents, inducing larger perturbations upon photoisomerization, may enhanced its efficiency. | Anastasiia Delova ; Raul Losantos; Jéremy Pecourneau ; Maxime Mourer; Andreea Pasc; Antonio Monari | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64738aa84f8b1884b76c052d/original/modelling-the-effects-of-e-z-photoisomerization-of-a-cyclocurcumin-analogue-on-the-properties-of-cellular-lipid-membranes.pdf |
67c07589fa469535b92bc5bf | 10.26434/chemrxiv-2025-mcm8g | Ion Sensing based on Frequency-Dependent Physico-Chemical Processes at Electrode/Electrolyte Interfaces | Ions are fundamental to solid-liquid-phase processes, whether as essential components or contaminants, making precise and real-time monitoring necessary. Electrochemical sensors have been identified as promising tools, particularly for field-deployable applications. However, conventional electrochemical sensing is inherently restricted to species that participate in redox reactions and are often single use, limiting its scope. In this study, electrochemical impedance spectroscopy (EIS) is presented as a promising alternative for ion detection, utilizing physico-chemical interactions at the electrode/electrolyte interface. A first-principles model was developed to describe the impedance behavior of electrochemical interfaces, demonstrating how ion-specific interfacial processes influence electrochemical response. Based on this framework, an extensive EIS dataset was compiled, and an AI-assisted model was trained to predict electrolyte composition with high accuracy, achieving detection limits in the parts-per-billion (ppb) range. The findings indicate that EIS has significant potential as a complementary method for ion sensing, providing a novel perspective on selectivity and sensitivity beyond traditional electrochemical approaches. It is anticipated that this work will serve as a foundation for more advanced models of impedance behavior and EIS interpretation, as well as for the development of next-generation impedance-based sensors with broader applicability in complex environments, including biological fluids and industrial liquids. | Amir Mohseni Armaki; Yaqi Guo; Majid Ahmadi; Roan Streefland; Patrick S. Bäuerlein; Arjan Mol; Sidhant Kumar; Peyman Taheri | Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY 4.0 | CHEMRXIV | 2025-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c07589fa469535b92bc5bf/original/ion-sensing-based-on-frequency-dependent-physico-chemical-processes-at-electrode-electrolyte-interfaces.pdf |
6336b42ce615027d3d2c26a9 | 10.26434/chemrxiv-2022-6whfn | Dephosphorization of Nitric Acid Solutions from the Leaching of Monazite Ferrous Ores under Hydrothermal Conditions | The precipitation of phosphoric acid from nitric acid solutions in the presence of iron(3+) oxides and hydroxyoxides under hydrothermal conditions was studied. It was shown that the dephosphorization process proceeds with the formation of iron(3+) hydroxyphosphate (giniite) Fe5(PO4)4(OH)3∙2H2O. The most efficient and fast process is implemented at temperatures of 180-200 °C and above. It was found that the content of phosphoric acid in the solution as a result can be reduced to 10-3 mol/l and below. Lanthanide, uranium, and thorium nitrates are stable under conditions of hydrothermal dephosphorization of solutions, in contrast to iron(3+) nitrates decomposing to hematite and nitric acid. The features of the studied hydrothermal process were used to increase the efficiency of direct nitric acid leaching of monazite iron-bearing ores of the Chuktukon rare metal deposit. | Dmitry Kuzmin; Natalia Gudkova; Marina Leskiv; Anna Kuzmina; Vladimir Kuzmin | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery | CC BY NC 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6336b42ce615027d3d2c26a9/original/dephosphorization-of-nitric-acid-solutions-from-the-leaching-of-monazite-ferrous-ores-under-hydrothermal-conditions.pdf |
62e0d5e8cf6612ae24b6c28c | 10.26434/chemrxiv-2022-6wvxm | Systematic studies of graphite intercalation compounds with various intercalants using a first-principles calculation | Graphite intercalation compounds (GICs) are formed by inserting various atoms and molecules between the layers of graphite. Among these GICs, five structures have been reported wherein a single atom M was intercalated into graphite with chemical formulae MC6 and MC8 and different stacking orders. The formation energies of the GICs with these crystal structures and various intercalants (M) were investigated using first-principles calculation. Consequently, the formation energies of all the GICs reported to be synthesized were negative, indicating a good agreement with the experimental results. Our study also provides insights into the relative stability required for synthesizing GICs. Furthermore, we determined the negative formation energies of GICs for M =Sc, Y, Fr, and Ra, which are yet to be reported. | Teruyasu Mizoguchi; Naoto Kawaguchi; Kiyou Shibata | Theoretical and Computational Chemistry; Inorganic Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e0d5e8cf6612ae24b6c28c/original/systematic-studies-of-graphite-intercalation-compounds-with-various-intercalants-using-a-first-principles-calculation.pdf |
60c75586702a9bbf5518c710 | 10.26434/chemrxiv.10316819.v4 | The Thermodynamic Way of Assessing Reversible Metal Hydride Volume Expansion: Getting a Grip on Metal Hydride Formation Overpotential | <p>The relative volume expansion of reversible metal hydride crystals upon formation is determined by means of the van’t Hoff reaction entropy and STP ideal gas parameters, the development of this approach leads to a general method for calculating metal hydride single-crystal density. These results allow highlighting the pressure requirement to hydride phase formation, shown by the example of Ti-NaAlH<sub>4</sub>.</p> | Roland Hermann Pawelke | Alloys; Catalysts; Fuels - Materials; Hydrogen Storage Materials; Nanostructured Materials - Materials; Chemical Education - General; Environmental Science; Space Chemistry; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Main Group Chemistry (Inorg.); Reaction (Inorg.); Solid State Chemistry; Theory - Inorganic; Computational Chemistry and Modeling; Theory - Computational; Reaction Engineering; Thermodynamics (Chem. Eng.); Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Energy Storage; Fuels - Energy Science; Fuel Cells; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75586702a9bbf5518c710/original/the-thermodynamic-way-of-assessing-reversible-metal-hydride-volume-expansion-getting-a-grip-on-metal-hydride-formation-overpotential.pdf |
67da789281d2151a02f8f292 | 10.26434/chemrxiv-2024-706kv-v3 | The Critical Helping Hand of Water: Theory Shows the Way to Obtain Elusive, Granular Information about Kinetic Asymmetry Driven Systems | Kinetic asymmetry is crucial in chemical systems where the selective synthesis of one product over another, or the accelera-tion of specific reaction(s) is necessary. However, obtaining precise information with current experimental methods about the behavior of such systems as a function of time, substrate concentration and other relevant factors, is not possible. Com-putational chemistry provides a powerful means to address this problem. The current study unveils a two-pronged computa-tional approach: (i) full quantum chemical studies with density functional theory (DFT), followed by (ii) stochastic simula-tions with a validated Gillespie algorithm (GA) (using representative model systems where necessary), to study the behavior of a kinetic asymmetry driven unidirectional molecular motor (1-phenylpyrrole2,2′-dicarboxylic acid) (Na-ture 2022, 604 (7904), 80–85). Our approach allows us to understand what is really taking place in the system, underlining the crucial role played by water molecules in facilitating the rotation of the motor. It is seen that water lubricates the motion by increasing the rotation rate constant of the final step by, remarkably, more than ten orders of magnitude! These insights further serve to explain the efficient rotation of the very recently reported gel-embedded molecular motor (Na-ture 2025, 637 (8046), 594–600), providing an upper limit for the allowed rotation barrier in such systems, and thus also casts light into the functioning of bio-molecular motors. The current work therefore provides a template for carefully and properly studying a wide variety of important, kinetic asymmetry driven systems in the future. | Priyam Bajpai; Shrivatsa Thulasiram; Kumar Vanka | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67da789281d2151a02f8f292/original/the-critical-helping-hand-of-water-theory-shows-the-way-to-obtain-elusive-granular-information-about-kinetic-asymmetry-driven-systems.pdf |
6477527a4f8b1884b7990d54 | 10.26434/chemrxiv-2023-sh4p8-v3 | Chiral and Conductive Viologen-based Supramolecular Gels Exhibiting Tunable Charge-Transfer Properties | Redox-active conductive supramolecular gels involving highly ordered chiral assemblies of small organic molecules are very promising soft materials for many applications ranging from catalysis to electronics. However, combining all these properties in the same material has so far remained a difficult task. We now report the synthesis and detailed structural, rheological and electrical characterizations of supramolecular gels obtained by self-assembly of a dicationic low molecular weight gelator incorporating a redox-active 4,4’-bipyridinium unit. These molecules have been shown to self-assemble in pentanol to form chiral hollow core-shell cylinders eventually yielding dendritic clusters inducing gelation. We also showed that the optical, rheological and electrical properties of the gels can be tuned by addition of ionic additives. Careful control of the formation of charge-transfer complexes between viologens and iodides have led to a robust, transparent, conductive and chiral gel. The gelation process and the structure/properties of the gel have been thoroughly investigated by UV-Vis and ECD spectroscopy, rheology, bright-field microscopy, SAXS, AFM, electrochemical and impedance measurements. | Vivien Andrieux; Thomas Gibaud; Julien Bauland; Thibaut Divoux; Sébastien Manneville; Stéphan Guy; Amina Bensalah-Ledoux; Laure Guy; Floris Chevallier; Denis Frath; Christophe Bucher | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6477527a4f8b1884b7990d54/original/chiral-and-conductive-viologen-based-supramolecular-gels-exhibiting-tunable-charge-transfer-properties.pdf |
63a54b99b9c5f6ea28dd17c9 | 10.26434/chemrxiv-2022-g2x18-v2 | A Simple and Precise Detection of the Adulteration of Olive Oil with Hazelnut Oil Using Lawesson’s Reagent | Adulteration of olive oil, particularly with hazelnut oil and/or other less expensive vegetable oils, is among the most encountered ways of defrauding the consumers, which makes the detection of these oils in olive oil an important subject. Off the vegetable oil, the hazelnut oil shows the highest resemblance with olive oil in terms of the lipid profile. Therefore, the profile analysis of the lipidic compounds (fatty acids, sterols, tocols etc.) using common analytical techniques such as High Performance Liquid Chromatography (HPLC), Gas Chromatography with Flame Ionization Detector (GC-FID), etc. does not allow the detection of the hazelnut oil adulteration in olive oil. This study presents a simple and precise method for the detection of hazelnut oil in olive oil through the reaction of Lawesson’s reagent (LR) with 5-methylhept-2-en-4-one (filbertone), known as the specific flavor compound in hazelnut oil and does not exist in other vegetable oils. The reaction produces a non-volatile and stable compound which can be identified by HPLC/UV-Vis system with a sensitivity up to 3.0% (w/w). This is a highly satisfactory limit for the detection of adulteration of olive oil to hazelnut oil. Application of the proposed method is not limited with olive oil and can be applied to other oils as well. | Erdal Ertas; İlknur Demirtaş | Agriculture and Food Chemistry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a54b99b9c5f6ea28dd17c9/original/a-simple-and-precise-detection-of-the-adulteration-of-olive-oil-with-hazelnut-oil-using-lawesson-s-reagent.pdf |
66820c355101a2ffa8f6b716 | 10.26434/chemrxiv-2024-m1q43 | Multi-Objective Synthesis Optimization and Kinetics of
a Sustainable Terpolymer | The properties of polymers are primarily influenced by their monomer constituents, functional groups, and their mode of linkages. Copolymers, synthesized from multiple monomers, offer unique material properties compared to their homopolymers. Optimizing the synthesis of terpolymers is a complex and labor-intensive task due to variations in monomer reactivity and their compositional shifts throughout the polymerization process. The present work focuses on polymerization of styrene, myrcene, and dibutyl itaconate (DBI) with the goal of achieving a high glass transition temperature (T_g) in the resulting terpolymer. While the copolymerization of pairwise combinations of styrene, myrcene, and DBI have been previously investigated, the terpolymerization of all three at once remains unexplored. Terpolymers with monomers like styrene would provide high glass transition temperatures as the resultant polymers exhibit a rigid glassy state at ambient temperatures. Conversely, minimizing styrene incorporation also reduces reliance on petrochemical-derived monomer sources for terpolymer synthesis, thus enhancing the sustainability of terpolymer usage. To balance the objectives of maximizing T_g while minimizing styrene incorporation, we employ multi-objective Bayesian Optimization to efficiently sample in a design space comprising 5 experimental parameters. We perform two iterations of optimization for a total of 89 terpolymers, reporting terpolymers with a T_g above ambient temperature while retaining less than 50% styrene incorporation. This underscores the potential for exploring and utilizing renewable monomers such as myrcene and DBI, to foster sustainability in polymer synthesis. Additionally, the dataset enables the calculation of ternary reactivity ratios using a system of Ordinary Differential Equations based on the Terminal Model, providing valuable insights into the reactivity of monomers in complex ternary systems compared to binary copolymer systems. This approach reveals the nuanced kinetics of terpolymerization, further informing the synthesis of polymers with desired properties. | Jin Da Tan; Andre KY Low; Shannon RY Thoi; Sze Yu Tan; Wenguang Zhao; Yee-Fun Lim; Qianxiao Li; Saif A Khan; Balamurugan Ramalingam; Kedar Hippalgaonkar | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Polymer blends; Polymerization kinetics; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66820c355101a2ffa8f6b716/original/multi-objective-synthesis-optimization-and-kinetics-of-a-sustainable-terpolymer.pdf |
644f3f6880f4b75b53683480 | 10.26434/chemrxiv-2023-9r9w1 | Harnessing Sulfur(VI) Fluoride Exchange Click Chemistry and Photocatalysis for Deaminative Benzylic Arylation | While among the most common functional handles present in organic molecules, amines are a widely underutilized linchpin for C–C bond formation. To facilitate C–N bond cleavage, large activating groups are typically used but result in the generation of stoichiometric amounts of organic waste. Herein, we report an atom-economic activation of benzylic primary amines relying on the Sulfur Fluoride Exchange (SuFEx) click chemistry and the aza-Ramberg-Bäcklund reaction. This two-step sequence allows the efficient generation of 1,2-dialkyldiazenes from primary amines via loss of SO2. Excitation of the diazenes with blue light and an Ir photocatalyst affords radical pairs upon expulsion of N2, which can be coaxed into the formation of C(sp3)–C(sp2) bonds upon diffusion and capture by a Ni catalyst. This unique arylative strategy relying on a trace-less click approach was harnessed in a variety of examples and its mechanism was investigated. | Deepta Chattapadhyay; Akin Aydogan; Katarzyna Doktor; Arunava Maity; Jiun Wei Wu; Quentin Michaudel | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Photocatalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f3f6880f4b75b53683480/original/harnessing-sulfur-vi-fluoride-exchange-click-chemistry-and-photocatalysis-for-deaminative-benzylic-arylation.pdf |
67af823181d2151a02728b5b | 10.26434/chemrxiv-2025-sqpbn | Towards an understanding of the mode of action of arsenic(III) on the fungus Neofusicoccum parvum fungus: Identification of target proteins | Before it was banned, sodium arsenite was the unique fungicide able to control fungi associated with grapevine trunk diseases. However, its mode of action has not been fully elucidated yet. This study focuses on the identification of arsenic(III)-binding proteins using an arsenic-based fluorescent probe and an arsenic-based affinity chromatography. To the best of our knowledge, this is the first comparative study of these techniques to demonstrate their complementarity. Mainly cysteine-rich proteins were identified, the majority of which are involved in the infection process, in particular in plant cell wall degradation, host-pathogen interaction, adhesion and pathogenicity. These proteins could therefore be relevant targets for the development of new ways of grapevine trunk disease control. | Andréa ENGEL; Florence FERRARI; Maude MEYER; Jean-Marc STRUB; Martin SPICHTY; Christophe BERTSCH; Christine SCHAEFFER; Céline TARNUS; Sébastien ALBRECHT; Mary-Lorène GODDARD | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af823181d2151a02728b5b/original/towards-an-understanding-of-the-mode-of-action-of-arsenic-iii-on-the-fungus-neofusicoccum-parvum-fungus-identification-of-target-proteins.pdf |
60c74479702a9b440d18a849 | 10.26434/chemrxiv.9821468.v1 | Carbon Dioxide Hydrogenation to Formic Acid With an Extremely Efficient Base-Free Homogeneous Catalytic System | We present a highly efficient catalytic system to transform carbon dioxide to formic acid under base-free conditions. Our system employs a vbasic ionic liquid as a buffer for the producty. Our results show an exceptionally active catalyst with unprecedentedly high turnover numbers and frequency. | Andreas Weilhard; Stephen Argent; Victor Sans | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479702a9b440d18a849/original/carbon-dioxide-hydrogenation-to-formic-acid-with-an-extremely-efficient-base-free-homogeneous-catalytic-system.pdf |
6743e0d37be152b1d0a897fd | 10.26434/chemrxiv-2024-znh0f | Accelerated development of gas diffusion electrodes for CO2 electrolyzers | Here we present a high-throughput flexible automation system, AdaCarbon, to accelerate the development of gas diffusion electrodes (GDEs) for CO2 electrolysis. AdaCarbon consists of a team of seven robots with automated modules for GDE fabrication and characterization and an automated test cell (ATC) that performs zero-gap CO2 electrolysis. We use this platform to fabricate and test 90 GDEs (30 unique GDEs in triplicate) with varied compositions of Cu-Ag metal and Nafion-Sustainion ionomer bilayers with the goal of increasing the yield of ethylene produced at the current density of 200 mA cm–2. We show GDEs with higher Cu and Nafion ionomer content increased ethylene selectivity 5 to 9%. We also demonstrate that AdaCarbon accelerates the workflow for making and testing GDEs by a factor of three compared to a manual workflow. | Abhishek Soni; Siwei Ma; Karry Ocean; Kevan Dettelbach; Daniel Lin; Connor Rupnow; Mehrdad Mokhtari; Christopher Waizenegger; Giuseppe Crescenzo; Curtis Berlinguette | Materials Science; Inorganic Chemistry; Catalysis; Electrochemistry; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6743e0d37be152b1d0a897fd/original/accelerated-development-of-gas-diffusion-electrodes-for-co2-electrolyzers.pdf |
655254302c3c11ed715178e5 | 10.26434/chemrxiv-2023-0f7tx | Supramolecular umpolung: converting electron-rich resorcin[4]arenes into potent CH-bonding anion receptors and transporters | CH-hydrogen bonding anion receptors constitute an emerging class of anion sensors and transporters which, owing to their proteolytic and pH resistance, have great potential for biological applications. However, CH groups, being weak hydrogen bond donors, require additional enhancement of their binding properties. In this work, we demonstrate a new enhancement strategy that relies on the generation of large dipole moments by a combination of electron-donating and electron-withdrawing substituents. More specifically, the substitution of electron-rich resorcin[4]arenes with electron-withdrawing nitro groups in the upper rim induces a dipole moment of 15.8 D and concentrates electrostatic potential at the lower rim, leading to strong CH···anion binding at this remote site. As a result, tetranitroresorcin[4]arenes, available in just two synthetic steps, acquire high affinities towards halides (Ka(Cl-) = 1.36 × 105 M-1 in THF), remarkable tolerance to water, and selective chloride transport activity (EC50 = 0.012 mol%). A pivotal role of the seemingly innocent alkyl chains surrounding the binding site in making the receptors resistant to competitive aqueous/organic solvent mixtures and enabling anion transport is also demonstrated. | Esma R. Abdurakhmanova; Debashis Mondal; Hanna Jędrzejewska; Piotr Cmoch; Oksana Danylyuk; Michał J. Chmielewski; Agnieszka Szumna | Physical Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.); Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655254302c3c11ed715178e5/original/supramolecular-umpolung-converting-electron-rich-resorcin-4-arenes-into-potent-ch-bonding-anion-receptors-and-transporters.pdf |
622ab2a4bbeaf30c2704acad | 10.26434/chemrxiv-2022-ghw8h | A General and Modular Access to Enantioenriched α Trifluoromethyl Ketones via Nickel-Catalyzed Reductive Cross-Coupling | The development of new catalytic enantioselective access to CF3-containing stereogenicity is of great interest for the expediting discovery of lead compounds yet remains challenging. We devised a general and modular approach to facilely access enantioenriched α-CF3 ketones via nickel-catalyzed reductive cross-coupling of readily available acid chlorides and racemic α-CF3 alkyl bromides in an enantioconvergent fashion under mild conditions. This protocol featured neighboring directing group-free, high chemoselectivity, excellent functional group tolerance, facile scale-up, and notable amenability to straightforward downstream elaboration toward molecule complexity, thus constituting a reliable, direct, practical, and efficient synthetic alternative to furnish enantiopure α-CF3 carbonyls. Interestingly, an appropriate choice of the phosphine ligand as co-ligand plays an important role in high efficiency and asymmetric induction. Mechanistic studies suggest a radical chain pathway. | Liang-An Chen; Dengkai Lin; Yongzhi Chen; Zhan Dong; Pan Pei; Haiting Ji; Lanzhu Tai | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622ab2a4bbeaf30c2704acad/original/a-general-and-modular-access-to-enantioenriched-trifluoromethyl-ketones-via-nickel-catalyzed-reductive-cross-coupling.pdf |
65e80fab9138d23161c5ac93 | 10.26434/chemrxiv-2024-jg5z3 | Advanced Insulin Synthesis by One-pot/stepwise Disulfide Bond Formation Enabled by Acid-activated S-Protected Cysteine Sulfoxide in the Presence of Chloride Anion | An advanced insulin synthesis is presented that utilizes one-pot/stepwise disulfide bond formation enabled by acid-activated S-protected cysteine sulfoxides in the presence of chloride anion. S-chlorocysteine generated from cysteine sulfoxides reacts with an S-protected cysteine to afford S-sulfenylsulfonium cation, which then furnishes the disulfide or reversely returns to the starting materials depending on the S-protection employed and the reaction conditions. Use of S-acetamidomethyl cysteine (Cys(Acm)) and its sulfoxide (Cys(Acm)(O)) selectively give the disulfide under weak acid conditions in the presence of MgCl2 even if S-p-methoxybenzyl cysteine (Cys(MBzl)) and its sulfoxide (Cys(MBzl)(O)) are also present. In contrast, the S-MBzl pair yields the disulfide under more acidic conditions in the presence of a chloride anion source. These reaction conditions allowed a one-pot insulin synthesis. Additionally, lipidated insulin was prepared by a one-pot disulfide-bonding/lipidation sequence. | Kota Hidaka; Daishiro Kobayashi; Junya Hayashi; Masaya Denda; Akira Otaka | Organic Chemistry; Bioorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e80fab9138d23161c5ac93/original/advanced-insulin-synthesis-by-one-pot-stepwise-disulfide-bond-formation-enabled-by-acid-activated-s-protected-cysteine-sulfoxide-in-the-presence-of-chloride-anion.pdf |
60c74d310f50db7661396fa1 | 10.26434/chemrxiv.12462062.v2 | Shear-Induced Microporous Nanocomposite Epoxy Thermosets (MiNET) | <p>To
create microporous nanocomposite epoxy thermosets (MiNET), a mixing pathway is
demonstrated in which a bicontinuous emulsion gel (bijel) like viscous fluid is
kinetically trapped by high shear mixing of immiscible liquids, surfactant, and
nanoparticles. The MiNETs are prepared from common ingredients, that are widely
employed in industry, including epoxy resin, vegetable oil, epoxidized soybean
oil, and different types of nanoparticles such as silica, activated carbon,
alumina, and zinc oxide. MiNETs prepared by the presented route are processed at
ambient conditions and exhibit low shrinkage (less than 2%). Furthermore, they are
suitable to erect macro- to microscale structures with high precision and
various porosity. The interconnected porous architecture of MiNET is even preserved
in microscale features and thus ensures the mass transport in microstructures. With
facile processability and tunability of pore sizes in a wide range (~100 nm to
few microns), the proposed route overcomes the two major roadblocks – difficulty
in fabrication and large domain size (on the order of 5µm or larger) – of bijel-like
materials to apply in catalysis, energy storage, and molecular encapsulation. </p> | Molla Hasan; Yogin Patel; Arielle R. Gamboa; Michael Grzenda; Valeria Saro-Cortes; Vivek Mhatre; Jonathan Singer | Composites | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d310f50db7661396fa1/original/shear-induced-microporous-nanocomposite-epoxy-thermosets-mi-net.pdf |
670c866212ff75c3a156f8ea | 10.26434/chemrxiv-2024-w3ld0-v2 | Molecular Quantum Chemical Data Sets and Databases for Machine Learning Potentials | The field of computational chemistry is increasingly leveraging machine learning (ML) potentials to predict molecular properties with high accuracy and efficiency, providing a viable alternative to traditional quantum mechanical (QM) methods, which are often computationally intensive. Central to the success of ML models is the quality and comprehensiveness of the data sets on which they are trained. Quantum chemistry data sets and databases, comprising extensive information on molecular structures, energies, forces, and other properties derived from QM calculations, are crucial for developing robust and generalizable ML potentials. In this review, we provide an overview of the current landscape of quantum chemical data sets and databases. We examine key characteristics and functionalities of prominent resources, including the types of information they store, the level of electronic structure theory employed, the diversity of chemical space covered, and the methodologies used for data creation. Additionally, an updatable resource is provided to track new data sets and databases at https://github.com/Arif-PhyChem/datasets_and_databases_4_MLPs. Looking forward, we discuss the challenges associated with the rapid growth of quantum chemical data sets and databases, emphasizing the need for updatable and accessible resources to ensure the long-term utility of them. We also address the importance of data format standardization and the ongoing efforts to align with the FAIR principles to enhance data interoperability and reusability. Drawing inspiration from established materials databases, we advocate for the development of user-friendly and sustainable platforms for these data sets and databases. | Arif Ullah; Yuxinxin Chen; Pavlo O. Dral | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c866212ff75c3a156f8ea/original/molecular-quantum-chemical-data-sets-and-databases-for-machine-learning-potentials.pdf |
60c74e50ee301c2a45c7a4a5 | 10.26434/chemrxiv.12735377.v1 | Rapid Mechanochemical Synthesis of Amides with Uronium-Based Coupling Reagents, a Method for Hexa-amidation of Biotin[6]uril | <p>Solid-state reactions using
mechanochemical activation have emerged as solvent-free atom-efficient
strategies for sustainable chemistry. Herein we report a new mechanochemical approach
for the amide coupling of carboxylic acids and amines, mediated by combination
of (1-сyano-2-ethoxy-2-oxoethylidenaminooxy)dimethylaminomorpholinocarbenium
hexafluorophosphate (COMU) or <i>N</i>,<i>N</i>,<i>N</i>′,<i>N</i>′-tetramethylchloroformamidinium
hexafluorophosphate (TCFH) and K<sub>2</sub>HPO<sub>4</sub>. The method
delivers a range of amides in high 70–96% yields and fast reaction rates. The
reaction protocol is mild, maintains the integrity of the adjacent to carbonyl
stereocenters, and streamlines isolation procedure for solid amide products. Minimal
waste is generated due to the absence of bulk solvent. We show that K<sub>2</sub>HPO<sub>4</sub>
plays a dual role, acting as a base and a precursor of reactive acyl phosphate species.
Amide bonds from hindered carboxylic acids and low-nucleophilic amines can be
assembled within 90 min by using TCFH in combination with K<sub>2</sub>HPO<sub>4</sub>
or <i>N</i>-methylimidazole. The developed mechanochemical liquid-assisted
amidation protocols were successfully applied to the challenging couplings of all
six carboxylate functions of biotin[6]uril macrocycle with phenylalanine methyl
ester, resulting in an 80% yield of highly pure hexa-amide-biotin[6]uril. In
addition, fast and high-yielding synthesis of peptides and versatile amide
compounds can be performed in a safe and environmentally benign manner, as
verified by green metrics.<b></b></p> | Tatsiana Dalidovich; Kamini A. Mishra; Tatsiana Shalima; Marina Kudrjašova; Dzmitry Kananovich; Riina Aav | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e50ee301c2a45c7a4a5/original/rapid-mechanochemical-synthesis-of-amides-with-uronium-based-coupling-reagents-a-method-for-hexa-amidation-of-biotin-6-uril.pdf |
62a1675a804dbe75f63f8ec1 | 10.26434/chemrxiv-2022-tqv76-v2 | Reconstruction of lossless molecular representations, SMILES and SELFIES, from fingerprints | SMILES is the most dominant molecular representation used in AI-based chemical applications, but it has innate limitations associated with its internal structure.
Here, we exploit the idea that a set of structural fingerprints can be used as efficient alternatives to unique molecular representations. For this purpose, we trained neural-machine-translation based models that translate a set of various structural fingerprints to conventional text-based molecular representations, i.e., SMILES and SELFIES. The assessment of their conversion efficiency showed that our models successfully reconstructed molecules and achieved a high level of accuracy. Therefore, our approach brings structural fingerprints into play as strong representational tools in chemical natural language processing applications by restoring the connectivity information that is lost during fingerprint transformation. This comprehensive study addressed the major limitation of structural fingerprints, which precludes their implementation in NLP models. Our findings would facilitate the development of text or fingerprint-based chemoinformatic models for generative and translational tasks. | Umit Volkan Ucak; Islambek Ashyrmamatov; Juyong Lee | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a1675a804dbe75f63f8ec1/original/reconstruction-of-lossless-molecular-representations-smiles-and-selfies-from-fingerprints.pdf |
60c742b6469df45574f43036 | 10.26434/chemrxiv.8217266.v2 | Toward Real-Time Monitoring and Control of Single Nanoparticle Properties with a Microbubble Resonator Spectrometer | <p></p><p></p><p>Optical
microresonators have widespread application at the frontiers of nanophotonic
technology, driven by their ability to confine light to the nanoscale and
enhance light-matter interactions. Microresonators form the heart of a new
method for single-particle photothermal absorption spectroscopy, whereby the
microresonators act as microscale thermometers to detect the heat dissipated by
optically pumped, non-luminescent nanoscopic targets. However, translation of
this technology to chemically dynamic systems requires a platform that is
mechanically stable, solution compatible, and visibly transparent. We report
microbubble absorption spectrometers as a new and versatile platform that meets
these requirements. Microbubbles integrate a two-port microfluidic device within
a Whispering Gallery Mode (WGM) microresonator, allowing for the facile
exchange of chemical reagents within the resonator’s interior while maintaining
a solution-free environment on its exterior. We first leverage these qualities to
investigate the photo-activated etching of single gold nanorods by ferric
chloride, providing a new method for rapid acquisition of spatial and
morphological information about nanoparticles as they undergo chemical
reactions. We then demonstrate the ability to control nanorod orientation within
a microbubble through optically exerted torque, a new route toward the
construction of hybrid photonic-plasmonic systems. Critically, the reported
platform advances microresonator spectrometer technology by permitting
room-temperature, aqueous experimental conditions, opening a regime of time-resolved
single-particle experiments on non-emissive, nanoscale analytes engaged in
catalytically and biologically relevant chemical dynamics.</p><p></p><p></p> | Levi Hogan; Erik Horak; Jonathan Ward; Kassandra Knapper; Síle Nic Chormaic; Randall Goldsmith | Nanodevices; Plasmonic and Photonic Structures and Devices; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b6469df45574f43036/original/toward-real-time-monitoring-and-control-of-single-nanoparticle-properties-with-a-microbubble-resonator-spectrometer.pdf |
6655527491aefa6ce127a86b | 10.26434/chemrxiv-2024-kn0jg | Characterization of a monoclonal antibody by native and denaturing top-down mass spectrometry | Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methods – namely higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociation – in their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points towards disulfide bonds as the primary reason behind the largely overlapping dissociation patterns. | Ryan Oates; Linda Lieu; Kristina Srzentić; Eugen Damoc; Luca Fornelli | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6655527491aefa6ce127a86b/original/characterization-of-a-monoclonal-antibody-by-native-and-denaturing-top-down-mass-spectrometry.pdf |
62c58cf9c79aca2081532f39 | 10.26434/chemrxiv-2022-56w2r | Long Story Short: Donor Set Symmetry in Eu(DOTA) Crystals Determines the Electronic Structure | Lanthanide complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid DOTA have been studied in great detail due to their use as MRI contrast agents. Since the first report from Desreux in 1980, the Ln.DOTA complexes of gadolium(III) in particular have been thouroughly investigated. The forms of the nine-coordinated [Ln(DOTA)(H2O)]- complexes are well known, and the ligand backbone has been used extensively to create functional MRI contrast agents, luminescent probes, and as a model system for studying the properties of lanthanide(III) ions. In solution, the photophysical properties have been mapped, but as the structures are not known, direct structure property relationships have not been created. Here, the electronic properties of two Eu.DOTA compounds (1 and 2) and a Eu.DOTA-like compound (3) were studied using single-crystal luminescence spectroscopy. The donor set in the three compounds is identical (4N 4O 1O), and using the symmetry deviation value σideal it was shown that the coordination geomtry is close to identical. Nevertheless, the electronic properties evaluted using the luminescece spectrum was found to differ significantly between the three compounds. The magnitude of the crystal field splitting was found not to scale with the symmetry of the coordination geometry. It was concluded that the donor set dictates the splitting, yet the structure-property relationships governing the electronic properties of europium(III) ions still elude us. | Maria Storm Thomsen; Helene O B Andersen; Thomas Just Sørensen | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides | CC BY NC 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c58cf9c79aca2081532f39/original/long-story-short-donor-set-symmetry-in-eu-dota-crystals-determines-the-electronic-structure.pdf |
60c74f380f50db8096397378 | 10.26434/chemrxiv.9823625.v6 | Forcing or Forced Exertions in Amalgamation of Nanoparticles and Particles inside the Solution | The study of forcing or
forced exertions in amalgamating or amalgamated nanoparticles and particles inside
the solution is important for the scientific societies in the fields of
physical, chemical and mathematical sciences. Observing live dynamics of nanoparticles
and particles inside the solution is a challenging task. Again, it is not an appropriate
way to discuss amalgamating nanoparticles and particles based only on visualized
dynamics. However, suitably captured microscopic images can identify different
modes of forcing or forced exertions in amalgamated nanoparticles and particles.
Nanoparticles and particles when just at resting positions amalgamate under resultant
differences of exerting forces, which are not only related to poles of occupied
quadrants, but also related to their own drawn poles. So, colloidal nanoparticles
and particles amalgamate from sides experiencing a greater exertion of force. In
amalgamation of nanoparticles and particles, the exerted force successively remains
in mute, alert and functioning mode. Contrarily, the energy behavior successively
remains in functioning, alert and mute mode. Amalgamation of nanoparticles and
particles depends on their features and conceived focusing lengths. This is
through the resultant differences of exerting forces for two frame of
references. Particles of geometrical shapes largely experience the even
exertion of forces in their amalgamation, which is not the case for distorted particles.
Nanoparticles and particles inside the solution are the best candidates to
track nature of exerting forces, and so is the case with energy behaviors, too. | Mubarak Ali; I-Nan Lin | Microscopy; Nanocatalysis - Catalysts & Materials; Transport Phenomena (Chem. Eng.); Chemical Kinetics; Interfaces; Physical and Chemical Processes; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f380f50db8096397378/original/forcing-or-forced-exertions-in-amalgamation-of-nanoparticles-and-particles-inside-the-solution.pdf |
64bc3e39b605c6803b2eb72b | 10.26434/chemrxiv-2023-sz64b | Solvent Effects on the Rate of Ozonolysis: Development of a Homogeneous Flow Ozonolysis Protocol | Herein we describe the effect of organic solvents on ozone solubility and rate of ozonolysis reactions using rapid injection NMR spectroscopy. The tabulated solubility and kinetic data allowed for the design of a homogeneous ozonolysis flow reactor capable of delivering precise quantities of dissolved ozone to various olefin substrates. | Danniel Arriaga ; Seokmin Kang; Andy Thomas | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bc3e39b605c6803b2eb72b/original/solvent-effects-on-the-rate-of-ozonolysis-development-of-a-homogeneous-flow-ozonolysis-protocol.pdf |
60c751d7337d6c29bbe285f8 | 10.26434/chemrxiv.13215467.v1 | Photoactivatable Metabolic Warheads Enable Precise and Safe Ablation of Target Cells in Vivo | Photoactivatable molecules enable ablation of malignant cells under the control of light, yet current
agents can be ineffective at early stages of disease when target cells are similar to healthy surrounding
tissues. In this work, we describe a chemical platform based on amino-substituted benzoselenadiazoles
to build photosensitizers that mimic native metabolites as indicators of disease onset and progression.
Through a series of synthetic derivatives, we have identified the key chemical groups in the
benzoselenadiazole scaffold responsible for its photodynamic activity, and subsequently designed
photosensitive metabolic warheads to target cells associated with various diseases, including bacterial
infections and cancer. We demonstrate that versatile benzoselenadiazole metabolites can selectively
kill pathogenic cells -but not healthy cells- with high precision after exposure to non-toxic visible light,
reducing any potential side effects in vivo. This chemical platform provides powerful new tools to
exploit cellular metabolic signatures for safer therapeutic and surgical approaches. <br /> | Sam Benson; Fabio de Moliner; Antonio Fernandez; Erkin Kuru; Nicholas Asiimwe; Jun-Seok Lee; Lloyd Hamilton; Dirk Sieger; Isabel Ribeiro Bravo; Abigail Elliot; Yi Feng; Marc Vendrell | Bioorganic Chemistry; Photochemistry (Org.); Microscopy; Chemical Biology; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2020-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751d7337d6c29bbe285f8/original/photoactivatable-metabolic-warheads-enable-precise-and-safe-ablation-of-target-cells-in-vivo.pdf |
649d01a8ba3e99daef38f16f | 10.26434/chemrxiv-2023-311rv | Deflecting dendrites by introducing compressive stress in Li7La3Zr2O12 using ion implantation | Lithium dendrites belong to the key challenges of solid-state battery research. They are unavoidable due to the imperfect nature of surfaces containing defects of a critical size that can be filled by lithium until fracturing the solid electrolyte. The penetration of Li metal occurs along the propagating crack until a short circuit takes place. We hypothesise that ion implantation can be used to introduce stress states into Li6.4La3Zr1.4Ta0.6O12 which enable an effective deflection and arrest of dendrites. The compositional and microstructural changes are studied via atom probe tomography, FIB-SEM with correlative TOF-SIMS, STEM and nano XRD indicating that Ag-ions can be implanted up to 1 µm deep and amorphization takes place down to 650-700 nm, in good agreement with kinetic Monte Carlo simulations. Based on nano XRD results pronounced stress states up to -700 MPa are generated in the near-surface region. Such a stress zone and the associated microstructural alterations exhibit the ability to not only deflect mechanically introduced cracks but also dendrites, as demonstrated by nano-indentation and galvanostatic cycling experiments with subsequent FIB-SEM observations. These results demonstrate ion implantation as a viable technique to design “dendrite-free” solid-state electrolytes for high-power and energy-dense solid-state batteries. | Florian Flatscher; Juraj Todt; Manfred Burghammer; Hanne-Sofie Soreide; Lukas Porz; Yanjun Li; Sigurd Wenner; Viktor Bobal; Steffen Ganschow; Bernhard Sartory; Roland Brunner; Constantinos Hatzoglou; Jozef Keckes; Daniel Rettenwander | Physical Chemistry; Materials Science; Energy; Ceramics; Energy Storage; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2023-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649d01a8ba3e99daef38f16f/original/deflecting-dendrites-by-introducing-compressive-stress-in-li7la3zr2o12-using-ion-implantation.pdf |
66b235ebc9c6a5c07a2b7984 | 10.26434/chemrxiv-2024-vwvph | MolAnchor – Explaining Compound Predictions Based on Substructures | In medicinal chemistry, the impact of machine learning remains limited if predictions are not understood, which often precludes experimental follow-up. Therefore, chemically intuitive approaches that aid in model understanding and interpretation at the molecular level of detail are sought after. While feature attribution methods quantifying feature importance for model decisions are widely used in many areas, they must typically be combined with visualization techniques, if possible, to render the results accessible from a chemical viewpoint. On the other hand, there are approaches such as counterfactuals that yield closely related chemical structures with different prediction outcomes, providing direct access to structural features that critically influence model decisions. Herein, we introduce another approach designed to rationalize chemical predictions based on molecular structure. Therefore, we adapt principles underlying the anchor concept from explainable artificial intelligence (XAI) and alter them for molecular machine learning. The resulting method, termed MolAnchor, systematically identifies substructures in test compounds that determine property predictions, thus ensuring chemical interpretability. The MolAnchor methodology is made freely to the medicinal chemistry community available as a part of our study. | Alec Lamens; Jürgen Bajorath | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b235ebc9c6a5c07a2b7984/original/mol-anchor-explaining-compound-predictions-based-on-substructures.pdf |
62cc6314516311549f1c2027 | 10.26434/chemrxiv-2022-3177p | Temperature-dependent study of AcFc-FeIII(acac)3 redox couple for non-aqueous redox flow battery | This article describes the temperature dependence electrochemical analysis of acetyl ferrocene (AcFc) and iron(III) acetylacetonate ([Fe(acac)3]) for non-aqueous redox flow batteries. An electrochemical cell consisting of AcFc and ([Fe(acac)3]) as catholyte and anolyte species, respectively, were constructed with a cell voltage of 1.41 V and Coulombic efficiencies >99% for up to 50 total cycles at 25o C (RT) and 0o C. Rotating ring disk electrode (RRDE) experiments suggest that diffusion coefficient decreases as the temperature decreases but overall storing capacity far better than aqueous redox flow battery (ARFBs). The electrochemical kinetic rate constant (k0) of AcFc was found larger than Fe(acac)3 but remains similar at both temperatures. NMR study shows no structural change in changing temperature and after battery experiments. | MD MOTIUR RAHAMAN MAZUMDER; Rezoanul Islam | Inorganic Chemistry; Energy; Electrochemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cc6314516311549f1c2027/original/temperature-dependent-study-of-ac-fc-fe-iii-acac-3-redox-couple-for-non-aqueous-redox-flow-battery.pdf |
675b9e3bf9980725cfe8476a | 10.26434/chemrxiv-2024-shw8x | Employing the active learning strategy to construct full-dimensional intermolecular potential energy surfaces within spectroscopic accuracy | In this work, we employed an uncertainty-driven active learning strategy to achieve highly efficient point sampling for full-dimension potential energy surface constructions. The model uncertainty is defined as the weighted square energy difference between two neural network (NN) models trained with the same dataset, and the local maximums of uncertainty would be added into the training set by two criteria. A two-step sampling procedure was introduced to reduce the computational costs of expansive double-precision neural network training. The 6-D H$_2$O-He system was chosen as the test system. A reference PES was constructed firstly by the newly developed MLRNet model with a weighted RMSE of 0.028 cm$^{-1}$, where the full-dimension long-range function was fitted by a pruned basis expansion method. Our tests demonstrate that it is also reliable for the long-range switched fundamental invariant neural network (LS-FI-NN) to construct spectroscopically accurate PES, however, it is less inefficient for the newly developed MLRNet model. For the first single-precision sampling, the LS-FI-NN only requires 472 fitting points to achieve a weighted-RMSE of 0.3253 cm$^{-1}$ for 47945 test points. In comparison, the MLRNet requires 652 points to reach a similar accuracy. Notably, the MLRNet demonstrated lower training errors across all sampling cycles and lower test errors in the first few cycles with less trainable parameters, which indicates its potential with an appropriate sampling procedure. For the second double-precision sampling, the LS-FI-NN achieved a test RMSD of 0.0710 cm$^{-1}$ with only 613 points, while the MLRNet can't converge to a given threshold for tens of iterations. The spectroscopic calculations were performed to further validate the accuracy of these PESs. The energy levels of the double precision LS-FI-NN showed great agreement with the reference PES's results, with only 0.0161 cm$^{-1}$ and 0.0044 cm$^{-1}$ average errors for vibrational levels and the band origin shifts. | You Li; Xiao-Long Zhang; Hui Li | Theoretical and Computational Chemistry; Physical Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675b9e3bf9980725cfe8476a/original/employing-the-active-learning-strategy-to-construct-full-dimensional-intermolecular-potential-energy-surfaces-within-spectroscopic-accuracy.pdf |
62f4ec8c6948b9e115b46e0d | 10.26434/chemrxiv-2022-vjh5w | Common Trends of Chiral Induced Spin Selectivity and Optical Dichroism with Varying Helix Pitch: A First-Principles Study | Electrons transported through a chiral molecule become spin-polarized; this phenomenon is known as chiral induced spin selectivity (CISS). It has implications for spintronics, for electrochemical and enantioselective reactions, and for electron transfer in biological systems. The CISS-induced spin polarization in simulations and in experiment differs by orders of magnitude, and the detailed underlying mechanism is still an open question. Structure-property relationships can help elucidate this question. For this purpose, the effect of helix pitch is studied for a model helix of 20 carbon atoms for two quantities that have been found to correlate in some experiments: spin-polarization in transmitted electrons and electronic circular dichroism (ECD). We find that even though the chirality of these model helices goes down with increased pitch, ECD and CISS go up, along with UV-Vis and magnetic and electric transition dipole moments. Orbital contributions to the most intense UV-Vis transition do not show a consistent qualitative picture. Tentatively, we can assign the increase in these properties to an increase of the electric polarizability with the spatial extension of these helices by changing pitch. | Carmen Herrmann; Aida Saghatchi; Vladimiro Mujica; Sumit Naskar | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f4ec8c6948b9e115b46e0d/original/common-trends-of-chiral-induced-spin-selectivity-and-optical-dichroism-with-varying-helix-pitch-a-first-principles-study.pdf |
60c73ddd469df418e3f427aa | 10.26434/chemrxiv.6216383.v1 | Imidazolium-Based Ionic Liquids Affect Morphology and Rigidity of Living Cells: an Atomic Force Microscopy Study | The study of the toxicity, biocompatibility, and environmental sustainability of room-temperature Ionic Liquids (ILs) is still in its infancy. Understanding the impact of ILs on living organisms, especially from the aquatic ecosystem, is urgent, since on one side large amounts of these substances are widely employed as solvents in industrial chemical processes, and on the other side evidences of toxic effects of ILs on microorganisms and single cells have been observed. To date, the toxicity of ILs have been investigated by means of macroscopic assays aimed at characterizing the effective concentrations (like the EC50) that cause the dead of a significant fraction of the population of microorganisms and cells. These studies allowed to identify the cell membrane as the first target of the IL interaction, whose effectiveness was correlated to the lipophilicity of the cation, i.e. to the length of the lateral alkyl chain. Our study aimed at characterizing the molecular mechanisms of the toxicity of ILs. To this purpose, we carried out a combined topographic and mechanical analysis by Atomic Force Microscopy of living breast metastatic cancer cells (MDA-MB-231) upon interaction with imidazolium-based ILs. We showed that ILs are able to induce modifications of the overall rigidity (effective Young modulus) and morphology of the cells. Our results demonstrate that ILs act on the physical properties of the cell membrane, and possibly induce cytoskeletal reorganization, already at concentrations below the EC50. These potentially toxic effects are stronger at higher IL concentrations, as well as with longer lateral chains in the cation.<br /> | Massimiliano Galluzzi; Carsten Schulte; Paolo Milani; Alessandro Podestà | Cell and Molecular Biology; Interfaces; Physical and Chemical Processes; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ddd469df418e3f427aa/original/imidazolium-based-ionic-liquids-affect-morphology-and-rigidity-of-living-cells-an-atomic-force-microscopy-study.pdf |
60c73d934c8919ff0dad1c47 | 10.26434/chemrxiv.5952655.v1 | Networking Chemical Robots Using Twitter for #RealTimeChem | <p>Herein we present a chemistry capable robot built with a standard set of hardware and software protocols that can be networked to coordinate many chemical experiments in real time, such that the different chemical reactions can be distributed over many sites simultaneously. We demonstrate how multiple chemical processes can be done with two internet connected robots collaboratively, exploring a set of azo-coupling reactions in a fraction of time needed for a single robot, as well as encoding and decoding information into a network of oscillating BZ reactions transferring a message between two different locations using chemical reactions. The system can also be used to assess the reproducibility of chemical reactions and discover new reaction outcomes using game playing to explore a list of reaction conditions not accessible when the robots instead take it in turn to each a pre-define reaction from a list.<br /></p> | Dario Caramelli; Daniel Salley; Alon Henson; Gerardo Aragon Camarasa; Salah Sharabi; Graham Keenan; Leroy Cronin | Organic Synthesis and Reactions; Analytical Apparatus; Chemoinformatics; Imaging; Microscopy; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Machine Learning; Artificial Intelligence; Chemical Kinetics; Clusters; Self-Assembly; Robotics | CC BY NC 4.0 | CHEMRXIV | 2018-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d934c8919ff0dad1c47/original/networking-chemical-robots-using-twitter-for-real-time-chem.pdf |
61b758f302d90d526d612bca | 10.26434/chemrxiv-2021-vcmzz | Improving ΔΔG predictions with a multi-task convolutional Siamese Network | The lead optimization phase of drug discovery refines an initial hit molecule for desired properties, especially potency. Synthesis and experimental testing of the small perturbations during this refinement can be quite costly and time consuming. Relative binding free energy (RBFE, also referred to as ∆∆G) methods allow the estimation of binding free energy changes after small changes to a ligand scaffold. Here we propose and evaluate a Convolutional Neural Network (CNN) Siamese network for the prediction of RBFE between two bound ligands. We show that our multi-task loss is able to improve on a previous state-of-the-art Siamese network for RBFE prediction via increased regularization of the latent space. The Siamese network architecture is well suited to the prediction of RBFE in comparison to a standard CNN trained on the same data (Pearson’s R of 0.553 and 0.5, respectively). When evaluated on a left-out protein family, our CNN Siamese network shows variability in its RBFE predictive performance depending on the protein family being evaluated (Pearson’s R ranging from-0.44 to 0.97). RBFE prediction performance can be improved during generalization by injecting only a few examples (few-shot learning) from the evaluation dataset during model training. | Andrew McNutt; David Koes | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2021-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b758f302d90d526d612bca/original/improving-g-predictions-with-a-multi-task-convolutional-siamese-network.pdf |
60c7556ff96a00738f28886f | 10.26434/chemrxiv.13204064.v3 | Full Optical Rotation Tensor at CCSD Level in the Modified Velocity Gauge | <div>
<div>
<p>
</p><div>
<div>
<div>
<p>This work presents the first simulations of the full optical rotation (OR) tensor at coupled cluster with single
and double excitations (CCSD) level in the modified velocity gauge (MVG) formalism. The CCSD-MVG OR
tensor is origin independent, and each tensor element can in principle be related directly to experimental
measurements on oriented systems. We compare the CCSD results with those from two density functionals, B3LYP and CAM-B3LYP, on a test set of 22 chiral molecules. The results show that the functionals
consistently overestimate the CCSD results for the individual tensor components and for the trace (which is
related to the isotropic OR), by 10-20% with CAM-B3LYP and 20-30% with B3LYP. The data show that
the contribution of the electric dipole-magnetic dipole polarizability tensor to the OR tensor is on average
twice as large as that of the electric dipole-electric quadrupole polarizability tensor. The difficult case of
(1S,4S)-(–)-norbornenone also reveals that the evaluation of the former polarizability tensor is more sensitive
than the latter. We attribute the better agreement of CAM-B3LYP with CCSD to the ability of this functional to better reproduce electron delocalization compared with B3LYP, consistently with previous reports
on isotropic OR. The CCSD-MVG approach allows the computation of reference data of the full OR tensor,
which may be used to test more computationally efficient approximate methods that can be employed to
study realistic models of optically active materials. </p>
</div>
</div>
</div>
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</div> | Kaihua Zhang; Ty Balduf; Marco Caricato | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7556ff96a00738f28886f/original/full-optical-rotation-tensor-at-ccsd-level-in-the-modified-velocity-gauge.pdf |
60c749af4c8919c8bbad3103 | 10.26434/chemrxiv.12098142.v1 | A Pseudo Five-Fold Symmetrical Ligand Drives Geometric Frustration in Porous Metal-Organic and Hydrogen Bonded Frameworks | Reticular framework materials thrive on designability, but unexpected reaction outcomes are crucial in exploring new structures and functionalities. By combining “incompatible” building blocks, we employed geometric frustration in reticular materials leading to emergent structural features. The combination of a pseudo C<sub>5</sub> symmetrical organic building unit based on a pyrrole core, with a C<sub>4</sub> symmetrical copper paddlewheel synthon led to three distinct frameworks by tuning the synthetic conditions. The frameworks show structural features typical for geometric frustration: self-limiting assembly, internally stressed equilibrium structures and topological defects in the equilibrium structure, which manifested in the formation of a hydrogen bonded framework, distorted and broken secondary building units and dangling functional groups, respectively. The influence of geometric frustration on the CO<sub>2</sub> sorption behavior and the discovery of a new secondary building unit shows geometric frustration can serve as a strategy to obtain highly complex porous frameworks. | Frederik Haase; Gavin Craig; Mickaele Bonneau; kunihisa sugimoto; Shuhei Furukawa | Hybrid Organic-Inorganic Materials; Coordination polymers; Coordination Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2020-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749af4c8919c8bbad3103/original/a-pseudo-five-fold-symmetrical-ligand-drives-geometric-frustration-in-porous-metal-organic-and-hydrogen-bonded-frameworks.pdf |
60c73ed9f96a006bec285fc4 | 10.26434/chemrxiv.7123181.v1 | The Jones-Ray Effect Is Not Caused by Surface Active Impurities | <p>Pure aqueous
electrolyte solutions display a minimum in surface tension at concentrations of
~ 2 mM. This effect has been a source of
controversy since first reported by Jones and Ray in the 1930s. The Jones-Ray
effect and many other surface phenomena have frequently
been dismissed as an artifact and linked
to the presence of surface-active impurities. Herein we systematically consider
the effect of surface-active impurities by purposely adding nanomolar
concentrations of surfactants to dilute electrolyte solutions. Trace amounts of
surfactant are indeed found to decrease the surface tension and influence the
surface chemistry. However, surfactants can be removed by repeated aspiration
and stirring cycles, that eventually deplete the surfactant from solution
creating a “surface chemically pure” interface.
Upon following this cleaning procedure, a reduction in the surface tension of millimolar concentrations of salt is still observed. Consequently, we demonstrate
the Jones-Ray effect is not caused by surface
active impurities. </p> | Halil I. Okur; Chad Drexler; Eric Tyrode; Paul S. Cremer; Sylvie Roke | Solution Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed9f96a006bec285fc4/original/the-jones-ray-effect-is-not-caused-by-surface-active-impurities.pdf |
638a01b0b103af1b8d07b542 | 10.26434/chemrxiv-2022-dwk5l | Direct Force Constants for Spectroscopic Analysis from Quantum Mechanical Information: SmartField Force Field | The classical modelling of organic molecules is based on force fields of commercial standard libraries, which might be limited and can be potentially inaccurate
for compounds outside the data set. One common solution to this is the derivation of ad-hoc force field parameters for new molecules. However, this approach might be long and expensive even for experienced chemist. In this prospective, we propose an integrated and automated toolkit, called SmartField, to obtain intra- and intermolecular force field parameters with a good degree of accuracy and a margin of transferability. SmartField extracts all bonded parameters directly from the quantum mechanical Hessian, while CM5 charge, and Lennard-Jones parameter are retrived from standard outputs. We assessed the accuracy of SmartField by comparing vibrational frequencies and geometries of data set of rigid and flexible compounds with their quantum counterpart. Furthermore, SmartField parameters are employed for the computation of the absorption and emission spectra of the indole moiety, and tryptophan amino acid, in water. A direct comparison with the available experimental data is good and it gives a support of SmartField-derived force fields, which can be exploited for the modelling of novel and more complex compounds. | emanuele falbo | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638a01b0b103af1b8d07b542/original/direct-force-constants-for-spectroscopic-analysis-from-quantum-mechanical-information-smart-field-force-field.pdf |
60c74cab567dfe0695ec51a0 | 10.26434/chemrxiv.12449081.v2 | Drug Repurposing and New Therapeutic Strategies for SARS-CoV-2 Disease Using a Novel Molecular Modeling-AI Hybrid Workflow | <p>The recent<b> </b>outbreak of the novel coronavirus (SARS-CoV-2) poses a significant challenge to the scientific and medical communities to find immediate treatments. The usual process of identifying viable molecules and transforming them into a safe and effective drug takes 10-15 years, with around 5 years of that time spent in preclinical research and development alone. The fastest strategy is to identify existing drugs or late-stage clinical molecules (originally intended for other therapeutic targets) that already have some level of efficacy. To this end, we tasked our novel molecular modeling-AI hybrid computational platform with finding potential inhibitors of the SARS-CoV-2 main protease (M<sup>pro</sup>, 3CL<sup>pro</sup>). Over 13,000 FDA-approved drugs and clinical candidates (represented by just under 30,000 protomers) were examined. This effort resulted in the identification of several promising molecules. Moreover, it provided insight into key chemical motifs surely to be beneficial in the design of future inhibitors. Finally, it facilitated a unique perspective into other potentially therapeutic targets and pathways for SARS-CoV-2.</p> | Scott Bembenek | Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cab567dfe0695ec51a0/original/drug-repurposing-and-new-therapeutic-strategies-for-sars-co-v-2-disease-using-a-novel-molecular-modeling-ai-hybrid-workflow.pdf |
639392400a81277055dafc0a | 10.26434/chemrxiv-2022-57s56 | Intercomparison of six national empirical models for PM2.5 air pollution in the contiguous US | Empirical models, previously called land-use regression (LUR), are used to understand and predict spatial variability in levels of outdoor air pollution at unmeasured locations, for example, to conduct health risk assessment, environmental epidemiology, or environmental justice analysis. Many methods are used to generate empirical models, yet almost no research compares models generated by separate research groups. We intercompare six national-scale empirical models for year-2010 concentrations of PM2.5 in the US, each generated by a different research group. Despite substantial differences in the statistical methods and input data used to build the models, our main finding is a relatively high degree of agreement among model predictions. For example, in pairwise intercomparisons, the average Pearson correlation coefficient is 0.87 (range: 0.84 to 0.92); the RMSD (root-mean-square-difference; units: μg/m3) is 1.1 on average (range: 0.8 to 1.4), or ~12% of the average concentration; and many best-fit lines are near the 1:1 line. The underlying reason for this agreement is likely that, while the methods and the independent variables differ among the models, in all cases the models are built using, and are calibrated to, the same information: publicly available measurement at US EPA regulatory monitoring stations. Findings here suggest that future improvements to national empirical models will come not from further refinements to the methods (e.g., more-advanced models) but from employing a fundamentally different set of observations, in addition to regulatory monitoring data. | Matthew J. Bechle; Michelle L. Bell; Daniel L. Goldberg; Steve Hankey; Tianjun Lu; Albert A. Presto; Allen L. Robinson; Joel Schwartz; Liuhua Shi; Yang Zhang; Julian D. Marshall | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639392400a81277055dafc0a/original/intercomparison-of-six-national-empirical-models-for-pm2-5-air-pollution-in-the-contiguous-us.pdf |
60c7478e4c8919f2c9ad2d5a | 10.26434/chemrxiv.11590950.v2 | Pigmentation Chemistry and Radical-Based Collagen Degradation in Alkaptonuria and Osteoarthritic Cartilage | <p>Alkaptonuria (AKU) is a rare disease characterized by high levels of homogentisic acid (HGA). Although HGA is excreted substantially via urine, AKU patients often suffer from ochronosis, a dark brown pigmentation of joint cartilage, heart valves, and spinal discs, leading subsequently to severe, early osteoarthropathy. A molecular mechanism linking elevated HGA to ochronosis has not yet been found; the chemical identity of the pigment is still not known, nor the mechanism by which pigmentation induces degradation in the physico-mechanical properties of joint cartilage. Here we give key insight on HGA-derived pigment composition and collagen disruption in AKU cartilage. Synthetically derived pigment and pigmented human cartilage tissue both showed hydroquinone-resembling NMR signals, but the previously hypothesized benzoquinone functionality is not observed. EPR spectroscopy showed a radical species in the synthetically derived pigment. Moreover, we observed disruption of collagen triple helix, at the interstrand hydrogen bonds, in pigmented AKU human cartilage. Cartilage from patients with osteoarthritis showed similar disruption. Our results led us to propose a new mechanism for collagen degradation via glycyl radicals, the formation of which is enhanced in AKU due to the redox environment generated by pigmentation.</p> | Wing Ying Chow; Brendan P Norman; Norman Roberts; Lakshminarayan Ranganath; Christian Teutloff; Robert Bittl; Melinda J. Duer; James Gallagher; Hartmut Oschkinat | Biological Materials; Biopolymers; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2020-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7478e4c8919f2c9ad2d5a/original/pigmentation-chemistry-and-radical-based-collagen-degradation-in-alkaptonuria-and-osteoarthritic-cartilage.pdf |
65ff11349138d231611fe36d | 10.26434/chemrxiv-2024-n89hr-v2 | Development of Highly Potent and Selective Covalent FGFR4 Inhibitors Based on SNAr Electrophiles | Fibroblast Growth Factor Receptor 4 (FGFR4) is thought to be a driver in several cancer types, most notably in hepatocellular carcinoma. One way to achieve high potency and isoform-selectivity for FGFR4 is covalently targeting a rare cysteine (C552) in the hinge region of its kinase domain that is not present in other FGFR family members (FGFR1-3). Typically, this cysteine is addressed via classical acrylamide electrophiles. We demonstrate that non-canonical covalent “warheads” based on nucleophilic aromatic substitution (SNAr) chemistry can be employed in a rational manner to generate highly potent and (isoform )selective FGFR4 inhibitors with a low intrinsic reactivity. Key compounds showed low- to subnanomolar potency, efficient covalent inactivation, and excellent selectivity over other FGFRs, kinases with an equivalent cysteine and a representative subset of the kinome. Moreover, these compounds achieved nanomolar potencies in cellular assays and demonstrated good microsomal stability highlighting the potential of SNAr-based approaches in covalent inhibitor design. | Moritz Schwarz; Maksym Kurkunov; Florian Wittlinger; Ramona Rudalska; Guiqun Wang; Martin P. Schwalm; Alexander Rasch; Benedikt Wagner; Stefan A. Laufer; Stefan Knapp; Daniel Dauch; Matthias Gehringer | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ff11349138d231611fe36d/original/development-of-highly-potent-and-selective-covalent-fgfr4-inhibitors-based-on-sn-ar-electrophiles.pdf |
60c74d06702a9b3c7e18b7ad | 10.26434/chemrxiv.12571235.v1 | RetroBioCat: Computer-Aided Synthesis Planning for Biocatalytic Reactions and Cascades | As the enzyme toolbox for biocatalysis has expanded, so has the potential for the construction of powerful enzymatic cascades for efficient and selective synthesis of target molecules. Additionally, recent advances in computer-aided synthesis planning (CASP) are revolutionizing synthesis design in both synthetic biology and organic chemistry. However, the potential for biocatalysis is not well captured by tools currently available in either field. Here we present RetroBioCat, an intuitive and accessible tool for computer-aided design of biocatalytic cascades, freely available at retrobiocat.com. Our approach uses a set of expertly encoded reaction rules encompassing the enzyme toolbox for biocatalysis, and a system for identifying literature precedent for enzymes with the correct substrate specificity where this is available. Applying these rules for automated biocatalytic retrosynthesis, we show our tool to be capable of identifying promising biocatalytic pathways to target molecules, validated using a test-set of recent cascades described in the literature. | William Finnigan; Lorna J. Hepworth; Nicholas J. Turner; Sabine Flitsch | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d06702a9b3c7e18b7ad/original/retro-bio-cat-computer-aided-synthesis-planning-for-biocatalytic-reactions-and-cascades.pdf |
60c749d2702a9b722618b1cf | 10.26434/chemrxiv.12111483.v1 | Nanostructured Electrode Enabling Fast and Fully Reversible MnO2-to-Mn2+ Conversion in Mild Buffered Aqueous Electrolytes | On account of their low-cost, earth abundance,
eco-sustainability, and high theoretical charge storage capacity, MnO<sub>2</sub>
cathodes have attracted a renewed interest in the development of rechargeable
aqueous batteries. However, they currently suffer from limited gravimetric
capacities when operating under the preferred mild aqueous conditions, which
leads to lower performance as compared to similar devices operating in strongly
acidic or basic conditions. Here, we demonstrate how to overcome this limitation
by combining a well-defined 3D nanostructured conductive electrode, which
ensures an efficient reversible MnO<sub>2</sub>-to-Mn<sup>2+</sup> conversion
reaction, with a mild acid buffered electrolyte (pH 5). A reversible
gravimetric capacity of 560 mA·h·g<sup>-1</sup>
(close to the maximal theoretical capacity of 574 mA·h·g<sup>-1</sup>
estimated from the MnO<sub>2</sub> average oxidation state of 3.86)
was obtained over rates ranging from 1 to 10 A·g<sup>-1</sup>. The
rate capability was also remarkable, demonstrating a capacity retention of 435 mA·h·g<sup>-1</sup> at a
rate of 110 A·g<sup>-1</sup>. These
good performances have been attributed to optimal regulation of the mass
transport and electronic transfer between the three process actors, <i>i.e.</i> the 3D conductive scaffold, the MnO<sub>2</sub>
active material filling it, and the soluble species involved in the reversible
conversion reaction. Additionally, the high reversibility and cycling stability
of this conversion reaction is demonstrated over 900 cycles with a Coulombic
efficiency > 99.4 % at a rate of 44 A·g<sup>-1</sup>.
Besides these good performances, also demonstrated in a Zn/MnO<sub>2</sub> cell
configuration, we discuss the key parameters governing the efficiency of the
MnO<sub>2</sub>-to-Mn<sup>2+</sup> conversion. Overall, the present study
provides a comprehensive framework for the rational design and optimization of
MnO<sub>2</sub> cathodes involved in rechargeable mild aqueous batteries. | Mickaël Mateos; Kenneth D. Harris; Benoit Limoges; Véronique Balland | Nanostructured Materials - Nanoscience; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d2702a9b722618b1cf/original/nanostructured-electrode-enabling-fast-and-fully-reversible-mn-o2-to-mn2-conversion-in-mild-buffered-aqueous-electrolytes.pdf |
6135dbf290051e9768ea1cc6 | 10.26434/chemrxiv-2021-zr8nt-v2 | Alteration in H-bond strength affects the stability of codon-anticodon interaction at in-frame UAG stop codon during in vitro translation | We have studied the decoding ability of a non-standard nucleobase modified tRNA for non-natural amino acid mutagenesis. The insertion of 2, 6-diaminopurine (D) base at the 3rd position of a tRNA anticodon enabled us to evaluate the effect of an additional hydrogen bond during translation. The presence of D at the tRNA anticodon led to stabilization of the codon-anticodon interaction due to an additional H-bond between the N2-exocyclic amine of D and the C2 carbonyl group of uracil during protein translation. While decoding UAG codons using stop codon suppression methodology, the enhanced codon-anticodon interaction improved codon readthrough and synthesis of modified protein with a non-natural amino acid at multiple sites. Our findings imply that the number of hydrogen bonds at the tRNA-mRNA duplex interface is an important criterion during mRNA decoding and improves protein translation at multiple UAG stop sites. This work provides valuable inputs towards improved non-natural amino acid mutagenesis for creating functional proteins. | Purnima Mala; Ishu Saraogi | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6135dbf290051e9768ea1cc6/original/alteration-in-h-bond-strength-affects-the-stability-of-codon-anticodon-interaction-at-in-frame-uag-stop-codon-during-in-vitro-translation.pdf |
66567c0f418a5379b0845dce | 10.26434/chemrxiv-2024-v4z85 | BracketMaker: Visualization and Optimization of Chemical Protein Synthesis | Chemical protein synthesis (CPS), in which custom peptide segments of ~20-60 aa are produced by solid-phase peptide synthesis and then stitched together through sequential ligation reactions, is an increasingly popular technique. The workflow of CPS is often depicted with a “bracket” style diagram detailing the starting segments and the order of all ligation, desulfurization, and/or deprotection steps to obtain the product protein. Brackets are invaluable tools for comparing multiple possible synthetic approaches and serve as blueprints throughout a synthesis. Drawing CPS brackets by hand or in standard graphics software, however, is a painstaking and error-prone process. Furthermore, the CPS field lacks a standard bracket format, making side-by-side comparisons difficult. To address these problems, we developed BracketMaker, an open-source Python program with built-in graphic user interface for the rapid creation and analysis of CPS brackets. BracketMaker contains a custom graphics engine which converts a text string (a protein sequence annotated with reaction steps, introduced herein as a standardized format for brackets) into a high-quality vector or PNG image. To aid with new syntheses, BracketMaker’s “AutoBracket” tool automatically performs retrosynthetic analysis on a set of segments to draft and rank all possible ligation orders using standard native chemical ligation, protection, and desulfurization techniques. AutoBracket, in conjunction with an improved version of our previously reported Automated Ligator (Aligator) program, provides a pipeline to rapidly develop synthesis plans for a given protein sequence. We demonstrate the application of both programs to develop a blueprint for 65 proteins of the minimal E. coli ribosome. | Judah Evangelista; Michael S. Kay | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66567c0f418a5379b0845dce/original/bracket-maker-visualization-and-optimization-of-chemical-protein-synthesis.pdf |
649d6f669ea64cc1672b68a3 | 10.26434/chemrxiv-2023-k7zft | General role of amorphous aggregates in crystal nucleation | There is mounting evidence that crystal nucleation from supersaturated solution involves the formation and reor-ganisation of pre-nucleation clusters contradicting classical nucleation theory. Here, a wide range of amino acids and peptides is investigated using light scattering, mass spectrometry, and in-situ terahertz Raman spectroscopy to demonstrate that the presence of amorphous aggregates with a wide range of sizes is a general phenomenon in supersaturated solutions. Additionally, these amorphous aggregates act as intermediates for laser-induced crystal nucleation. These observations are inconsistent not only with classical nucleation theory, but also non-classical theories involving liquid-liquid phase separation, requiring a new approach. | Zhiyu Liao; Ankita Das; Christina Robb; Rebecca Beveridge; Klaas Wynne | Physical Chemistry; Physical and Chemical Processes; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649d6f669ea64cc1672b68a3/original/general-role-of-amorphous-aggregates-in-crystal-nucleation.pdf |
60c7546e4c891974e3ad450c | 10.26434/chemrxiv.13660988.v1 | A Natural Rubber Waste Derived Surfactant for High Internal Phase Emulsion Templating of Poly(dicyclopentadiene) | The use of a surfactant derived from the degradation of natural rubber gloves via cross-metathesis with methyl acrylate and subsequent saponification of the ester group for the stabilization of water in dicyclopentadiene high internal phase emulsions is described. The versatility of the resulting high internal phase emulsion was demonstrated by polymerizing the continuous dicyclopentadiene phase via Ring-opening Metathesis Polymerization yielding macroporous poly(dicyclopentadiene) foams with a porosity of 82 %. The use of the ionic surfactant allows for the preparation of foams, which are resistant to absorb water. This property was hitherto not accessible with protocols involving the use of non-ionic surfactants commonly employed in emulsion templating of polymers.<br /> | Viktor Schallert; Christian Slugovc | Polymer scaffolds | CC BY NC 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7546e4c891974e3ad450c/original/a-natural-rubber-waste-derived-surfactant-for-high-internal-phase-emulsion-templating-of-poly-dicyclopentadiene.pdf |
63e5530e9da0bc6b33a4aaf8 | 10.26434/chemrxiv-2023-g84n4-v2 | The production of Biodiesel from Algae using flocculation and Nanoparticles | Although fossil fuels propelled society to our current level of technology, the future of energy lies in renewable resources, beginning with vehicles. Despite accounting for only 5% of total vehicles in the US, medium to heavy-duty trucks that run on diesel fuel account for an astounding 23% of annual CO2 emissions in the transportation sector. The full implementation of greener biodiesel is frequently regarded as an impractical method of pollution reduction because the production of such biodiesel competes directly with the agricultural industry for available arable land. (“Optimizing Nannochloropsis Growing Conditions for ...”) Energy-dense algae are better biodiesel feedstocks because they avoid many of the issues that current biodiesel feedstocks do, and their potential can be used to propel the biodiesel industry into the future of sustainable energy. Because of its high productivity and lipid content, Nannochloropsis is a promising algae genus. The research shows how to quantify the constituent fatty acid type and composition in order to optimize the growing medium composition for increased biodiesel quality while maintaining high productivity (GC). The algae are grown in three 2.5 L glass jugs with three different nitrate and phosphate concentrations. Throughout the trials, a growing "1/2" medium is used. A flocculating solution of aluminum sulfate and vacuum filtration are used to harvest the algae. In situ transesterification is used to maximize fatty acid conversion into fatty acid methyl esters, which are then analyzed using GC. After 32 days of growth, the algae grown in low, medium, and high nutrient concentrations had average absorbance values (a measure of biomass concentration) at 750 nm of 0.91, 0.99, and 1.18, respectively. In a low nutrient concentration, the maximum monounsaturated fatty acid (MUFA) concentration of 62.68 percent of total fatty acids was achieved, corresponding to high-quality biodiesel. This study resulted in a scientific breakthrough by maximizing both the quality of biodiesel produced, which is superior to any currently available biodiesel, and the quantity, with a productivity that is more than one hundred times that of current biodiesel feedstocks. The research also discusses nano-technology application that concluded nanomaterials could stimulate microorganism metabolism, implying that including nanomaterials in cultivation could boost microalgae lipid production. Furthermore, the use of nanomaterials could improve the efficiency of lipid extraction while causing no harm to the microalgae., as well as the research needs and future directions for sustainable microalgal biofuel production. Since we did not have access to the materials needed, the information gathered in this study was culled from a variety of sources. | Gehad Ibrahim; Lemar Al Ghabra | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Fuels - Energy Science; Fuel Cells; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e5530e9da0bc6b33a4aaf8/original/the-production-of-biodiesel-from-algae-using-flocculation-and-nanoparticles.pdf |
64958655853d501c00628247 | 10.26434/chemrxiv-2023-k1j77 | Scope 1, 2, and 3 net zero pathways for the chemical industry in Japan | Scope 1, 2, and 3 net zero is a major technological challenge for the chemical industry in Japan, but a failure or even a delay in achieving this goal could result in exclusion from international financing and supply chains. This study presents, for the first time to the best of our knowledge, multiple quantitative pathways from today until 2050 for the chemical industry operating in Japan to reach scope 1, 2, and 3 net zero. These pathways indicate that the demand for basic chemicals in Japan could decrease by 43% by 2050 owing to a combination of population decline and advances in circularity. Furthermore, these pathways demonstrate that securing access to bio-based feedstock and carbon capture and storage (CCS) is essential to avoid a supply limit that could be imposed under scope 3 net zero. Given the uncertainty of Japan’s access to both, the chemical industry should pursue both concurrently, while maximizing recycling. Specifically, it should secure long-term and stable sources of sustainable bio-based feedstock and aid in implementing carbon dioxide capture from incinerators in the waste management. This approach could also apply to chemical industries in other countries and regions with similar constraints. | Daisuke Kanazawa; Andreas Wagner; Alexandre B. Kremer; Jane J. Leung; Shajeeshan Lingeswaran; Peter Goult; Sophie Herrmann; Naoko Ishii; Yasunori Kikuchi | Energy | CC BY 4.0 | CHEMRXIV | 2023-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64958655853d501c00628247/original/scope-1-2-and-3-net-zero-pathways-for-the-chemical-industry-in-japan.pdf |
63603be5ecdad55f0af4c152 | 10.26434/chemrxiv-2022-mw1cs-v3 | The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets | The steric stability of inorganic colloidal particles in an apolar solvent is usually described in terms of the balance between three contributions: the van der Waals attraction, the free energy of mixing, and the ligand compression.
However, in the case of nanoparticles, the discrete nature of the ligand shell and the solvent has to be taken into account. Cadmium selenide nanoplatelets are a special case. They combine a weak van der Waals attraction and a large facet to particle size ratio. We use coarse grained molecular dynamics simulations of nanoplatelets in octane to demonstrate that solvation forces are strong enough to induce the formation of nanoplatelet stacks, and by that have a crucial impact on the steric stability. In particular, we demonstrate that for sufficiently large nanoplatelets, solvation forces are proportional to the interacting facet area, and their strength is intrinsically tied to the softness of the ligand shell. | Nanning Petersen; Martin Girard; Andreas Riedinger; Omar Valsson | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63603be5ecdad55f0af4c152/original/the-crucial-role-of-solvation-forces-in-the-steric-stabilization-of-nanoplatelets.pdf |
65130f76ade1178b2429cd68 | 10.26434/chemrxiv-2023-s8t6s-v2 | Materials Funnel 2.0 - Data-driven hierarchical search for exploration of vast chemical spaces | Innovating ways to explore the materials phase space accelerates functional materials discovery. For breakthrough materials, faster exploration of larger phase spaces is a key goal. High-throughput computational screening (HTCS) is widely used to rapidly search for materials with the desired functional property. This article redefines the HTCS methods to combine multiple deep learning models and physics-based simulation to explore much larger chemical spaces than possible by pure physics-driven HTCS. Deep generative models are used to autonomously create materials libraries with a high likelihood of desired properties, inverting the standard design paradigm. Additionally, machine-learned surrogates enable the next layer of screening to prune the set further so that high-quality quantum-mechanical simulations can be performed. With organic photovoltaic (OPV) molecules as a test bench, the power of this redesigned HTCS approach is shown in the inverse design of OPV molecules with very limited computational expense using only 1% of the original physics-based screening dataset. | Raul Ortega Ochoa; Bardi Benediktsson; Renata Sechi; Peter Bjørn Jørgensen; Arghya Bhowmik | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65130f76ade1178b2429cd68/original/materials-funnel-2-0-data-driven-hierarchical-search-for-exploration-of-vast-chemical-spaces.pdf |
639702179e687ba77a48537d | 10.26434/chemrxiv-2022-lh6s3 | Exciton states of azobenzene aggregates: A first-principles study | Interaction between azobenzene-containing molecules in supramolecular structures or self-assembled monolayers (SAMs) results in the formation of molecular exciton states. These
states determine photophysical and photochemical processes in such assemblies. Here,
using first-principles quantum chemical calculations, we study optical spectra and exciton
delocalization of the exciton states in model clusters of azobenzene molecules. Specifically,
we consider one-dimensional linear chains and two-dimensional SAM-like arrangements,
and compute the exciton states by means of time-dependent long-range corrected density
functional theory (TD-lc-DFT) and ab initio configuration interaction singles (CIS), for
clusters including up to 18 azobenzene molecules. We analyze the nature of the exciton
states using transition density matrix analysis. In addition, we make a connection to
periodic systems applying the Bethe–Salpeter equation (BSE) / Green’s function many-body perturbation theory (GW) approach to a selected system. We find that the brightest
excitons are dominated by local excitations. The energetic location of charge transfer
states in the electronic spectra of aggregates depends to a large extent on a given method
and distance between nearest neighbours. Furthermore, we analyze how an excitonic
delocalization pattern changes with varying molecular orientation in the unit cell of SAMs. | Evgenii Titov; Alkit Beqiraj | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639702179e687ba77a48537d/original/exciton-states-of-azobenzene-aggregates-a-first-principles-study.pdf |
67357ab1f9980725cf208e6c | 10.26434/chemrxiv-2024-p2zwf-v2 | Fast Fourier Transform-Based Distribution of Relaxation Times Analysis for Efficient and Flexible Time-Domain Electrochemical Impedance Characterization | Electrochemical impedance spectroscopy (EIS) is a powerful analytical technique for studying electrochemical systems, offering broad frequency range coverage and straightforward implementation. However, EIS measurements at low frequencies are limited by both lengthy acquisition times and the risk of disrupting steady-state conditions, which is a particular challenge for battery systems. While the distribution of relaxation times (DRT) method has emerged as an effective tool for interpreting EIS data and accelerating impedance acquisition, existing acquisition approaches are limited to pulse-based input signals and their linear combinations. Here, we present a novel fast Fourier transform-based DRT formulation that enables rapid EIS acquisition using arbitrary current signals. Our approach demonstrates improved DRT and impedance recovery while ensuring computational efficiency. This advancement in DRT analysis and time-based measurements opens new possibilities for fast and efficient EIS characterization. | Baptiste Py; Francesco Ciucci | Energy; Energy Storage; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67357ab1f9980725cf208e6c/original/fast-fourier-transform-based-distribution-of-relaxation-times-analysis-for-efficient-and-flexible-time-domain-electrochemical-impedance-characterization.pdf |
651ff0ed45aaa5fdbb6b813e | 10.26434/chemrxiv-2023-tm21m-v2 | Piperazine-fused cyclic disulfides: high-performance bioreduction-activated cores for bifunctional probes and reagents | We report piperazine-fused six-membered-cyclic dichalcogenides as rapid-response redox substrates that interface with thiol/disulfide redox biology. Combining the stability of 1,2-dithianes with unprecedentedly rapid kinetics of self-immolation after reduction, these motifs are uniquely high-performance reduction-responsive motifs for live cell probes. We develop scalable, diastereomerically pure, six-step synthetic routes with just one chromatographic purification to access four key cis- and trans-piperazine-fused cyclic disulfide and diselenide cores. Fluorogenic redox probes using the disulfide-piperazines are activated >100-fold faster than the previously known monoamines, allowing us to deconvolute the kinetics of the reduction and the cyclisation steps during activation. The cis- and trans-fused diastereomers have remarkably different reductant specificities: the cis disulfides are activated only by strong vicinal dithiol reductants, but the trans-fused disulfides are activated even by moderate concentrations of monothiols such as GSH. Thus, although both disulfides are substrates for redoxins, in cellular applications the cis-disulfide probes were found to selectively report on reductive activity of thioredoxins, while the trans-disulfides are more rapidly but more promiscuously reactive. Finally, we showcase efficient late-stage synthetic diversification of the piperazine-disulfides, promising their broad applicability as robust cleavable cores for redox probes and prodrugs in biology, for solid phase synthesis and purifications, and as stimulus-responsive linkers for bifunctional reagents and antibody-drug conjugates. | Lukas Zeisel; Jan G. Felber; Karoline C. Scholzen; Carina Schmitt; Alexander J. Wiegand; Leonid Komissarov; Elias S. J. Arnér; Oliver Thorn-Seshold | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Biochemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651ff0ed45aaa5fdbb6b813e/original/piperazine-fused-cyclic-disulfides-high-performance-bioreduction-activated-cores-for-bifunctional-probes-and-reagents.pdf |
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