id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
66133f4b21291e5d1d564ce4 | 10.26434/chemrxiv-2024-42j6j | Synthesis of N-beta-brominated alkenyl isothiocyanates via dehydrogenation of alkyl isothiocyanates | This study presents a new dehydrogenative synthesis of alkenyl isothiocyanates, providing compounds with bromo and isothiocyanate groups. These reactive functionalities offer versatility for further transformations. Application in an amine sensor utilizing a coumarin-attached product demonstrates practical utility. This streamlined approach facilitates access to alkenyl isothiocyanates, valuable tools for biological studies. | Bumpei Maeda; Ryohei Akiyoshi; Daisuke Tanaka; Kohei Sato; Kei Murakami | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66133f4b21291e5d1d564ce4/original/synthesis-of-n-beta-brominated-alkenyl-isothiocyanates-via-dehydrogenation-of-alkyl-isothiocyanates.pdf |
61a97bab63557c06c994d4f2 | 10.26434/chemrxiv-2021-pgfm8 | Thermal Stability and Decomposition Pathways in Volatile
Molybdenum(VI) Bis-Imides | The vapor deposition of many molybdenum-containing films relies on the delivery of volatile compounds with the general bis(tert-butylimido)molybdenum(VI) framework, both in atomic layer deposition and chemical vapor deposition. We have prepared a series of (tBuN)2MoCl2 adducts using neutral N,N’-chelates and investigated their volatility, thermal stability, and decomposition pathways. Volatility has been determined by thermogravimetric analysis, with the 1,4-di-tert-butyl-1,3-diazabutadiene adduct (5) found to be the most volatile (1 Torr of vapor pressure at 135 ºC). Thermal stability was measured primarily using differential scanning calorimetry, and the 1,10-phenanthroline adduct (4) was found to be the most stable, with an onset of decomposition of 303 ºC. We have also investigated molybdenum compounds with other alkyl-substituted imido groups: these compounds all follow a similar decomposition pathway, γ-H activation, with varying reaction barriers. The tert-pentyl, 1-adamantyl, and a cyclic imido (from 2,5-dimethylhexane-2,5-diamine) were systematically studied to probe the kinetics of this pathway. All of these compounds have been fully characterized, including via single-crystal X-ray diffraction, and a total of 19 unique structures are reported. | Michael Land; Goran Bacic; Katherine Robertson; Sean Barry | Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a97bab63557c06c994d4f2/original/thermal-stability-and-decomposition-pathways-in-volatile-molybdenum-vi-bis-imides.pdf |
668812065101a2ffa87cc122 | 10.26434/chemrxiv-2024-6kdjr | Explicit solution of the reversible isomerization followed by
zeroth-order kinetics | An explicit solution to the kinetics problem consisting of a reversible isomerization followed by a zeroth-order
process is presented. Exact expressions for the area under the curve and the peak, termination and crossing
times were also derived and found to involve the Lambert W function. We discuss in detail the passage to the irreversible
limit and test it on the first stages of alcohol elimination in humans. The solution of the generalized
problem where both A and B species can undergo a zeroth-order irreversible transformation is presented. The
exact solution for the consecutive problem that starts with a zeroth-order kinetics and is followed by a reversible
isomerization is also obtained. We comment on the situations where the obtained solutions could be helpful. | Alejandro Perez Paz | Physical Chemistry; Biophysical Chemistry; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668812065101a2ffa87cc122/original/explicit-solution-of-the-reversible-isomerization-followed-by-zeroth-order-kinetics.pdf |
656d9819cf8b3c3cd7be7df6 | 10.26434/chemrxiv-2023-mrrgq | Deciphering the Role of Internal Donors in Shaping Heterogeneous Ziegler-Natta Catalysts Based on Non-Empirical Structural Determination | The addition of internal donors (IDs) to the heterogeneous Ziegler-Natta catalyst for propylene polymerization is fundamental to obtain highly isotactic polypropylene, but its role in shaping the stereospecific structure of the catalyst is still not comprehended. In this work, we apply non-empirical structure determination, based on a genetic algorithm and density functional theory calculations, to ternary systems composing MgCl2, TiCl4, and ID. We found that the co-presence of TiCl4 and ID led to the preferential formation of specific surface motifs, involving sharp edges and concavities. This was achieved by concerted adsorption of chelating ID and octahedral TiCl4, and significantly promoted TiCl4 situated in stereospecific environments. The multiplicity of adsorption modes of IDs was found to have a direct consequence in the structural diversity, where phthalate exhibited far greater diversity than 1,3-diether. In conclusion, this study revealed the essentiality of ID-driven reconstruction of MgCl2 in understanding the structure and function of this catalyst. | João Marcos da Silveira; Hiroki Chikuma; Gentoku Takasao; Toru Wada; Patchanee Chammingkwan; Toshiaki Taniike | Catalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656d9819cf8b3c3cd7be7df6/original/deciphering-the-role-of-internal-donors-in-shaping-heterogeneous-ziegler-natta-catalysts-based-on-non-empirical-structural-determination.pdf |
61418c8aac32192c457c32e6 | 10.26434/chemrxiv-2021-xwlt8 | Operando surface chemistry of micro- and nanocubic copper catalysts for electrochemical CO2 reduction | The electrochemical reduction of CO2 (CO2RR) into multicarbon compounds is a promising pathway towards renewable chemicals. Structure-product selectivity studies highlight that copper (100) facets favour C2+ product formation. However, the atomic processes leading to the formation of (100)-rich Cu cubes remains elusive. Herein, we use Cu and graphene-protected Cu surfaces to reveal the differences in structure and composition of common Cu-based electrocatalysts, from nano to micrometer scales. We show that stripping/electrodeposition cycles lead to thermodynamically controlled growth of Cu2O micro/nanocubes, while multi-layered Cu nanocuboids form universally during CO2RR upon polarization-driven re-organization of Cu0 atoms. A synergy of electrochemical
characterization by scanning tunnelling microscopy (EC-STM), operando EC-Raman and quasi-operando X-Ray Photoemission spectroscopy (XPS) allows us to shed light on the role of oxygen on the dynamic interfacial processes of Cu, and to demonstrate that chloride is not needed for the stabilization of cubic Cu nanostructures. | Karla Banjac; Thanh Hai Phan; Fernando P. Cometto; Patrick Alexa; Yunchang Liang; Rico Gutzler; Magalí Lingenfelder | Physical Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61418c8aac32192c457c32e6/original/operando-surface-chemistry-of-micro-and-nanocubic-copper-catalysts-for-electrochemical-co2-reduction.pdf |
679284cc81d2151a02a622dd | 10.26434/chemrxiv-2025-4mbsk-v2 | Wiggle150: Benchmarking Density Functionals And Neural Network Potentials On Highly Strained Conformers | Accurate benchmarks are key to assessing the accuracy and robustness of computational methods, yet most available benchmark sets focus on equilibrium geometries, limiting their utility for applications involving non-equilibrium structures such as ab initio molecular dynamics and automated reaction-path exploration. To address this gap, we introduce Wiggle150, a benchmark comprising 150 highly strained conformations of adenosine, benzylpenicillin, and efavirenz. These geometries—generated via metadynamics and scored using DLPNO-CCSD(T)/CBS reference energies—exhibit substantially larger deviations in bond lengths, angles, dihedrals, and relative energies than other conformer benchmarks. We evaluate a diverse array of computational methods, including density-functional theory, composite quantum chemical methods, semiempirical models, neural network potentials, and force fields, on predicting relative energies for this challenging benchmark set. The results highlight multiple methods along the speed–accuracy Pareto frontier and identify AIMNet2 as particularly robust among the NNPs surveyed. We anticipate that Wiggle150 will be used to validate computational protocols involving non-equilibrium systems and guide the development of new density functionals and neural network potentials. | Rebecca Brew; Ian Nelson; Meruyert Binayeva; Amlan Nayak; Wyatt Simmons; Joseph Gair; Corin Wagen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679284cc81d2151a02a622dd/original/wiggle150-benchmarking-density-functionals-and-neural-network-potentials-on-highly-strained-conformers.pdf |
66d20f24a4e53c48762afa65 | 10.26434/chemrxiv-2024-g95j5-v2 | Impact of Molecular Representations on Deep Learning Model Comparisons in Drug Response Predictions | Deep learning (DL) plays a crucial role in tackling the complexity and heterogeneity of cancer, particularly in predicting drug response. However, the effectiveness of these models is often hindered by inconsistent benchmarks and disparate data sources. To address the gaps in comparisons, we introduce CoMParison workflow for Cross Validation (CMP-CV), an automated cross-validation framework that trains multiple models with user-specified parameters and evaluation metrics. The effectiveness of DL models in predicting drug responses is closely tied to the methods used to represent drugs at the molecular level. In this contribution, we benchmarked commonly leveraged drug representations (graph, molecular descriptors, molecular fingerprints, and SMILES) to learn and understand the predictive capabilities of the models. We compare the ability of different drug representations to encode different structural properties of the drugs by using prediction errors made by models in different drug descriptor domains. We find that, in terms of the average prediction error over the entire test set, molecular descriptors and Morgan fingerprints perform slightly better than the others. However, we also observe that the rankings of the model performance vary in different regions over the descriptor space studied in this work, emphasizing the importance of domain-based model comparison when selecting a model for a specific application. Our efforts are part of CANcer Distributed Learning Environment (CANDLE), enhancing the model comparison capabilities in cancer research and driving the development of more effective strategies for drug response prediction and optimization. | Gihan Panapitiya; Rajeev Jain; Carter Knuston; Andrew McNaughton; Justin M. Wozniak; Thomas Brettin; Rick Stevens; Neeraj Kumar | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d20f24a4e53c48762afa65/original/impact-of-molecular-representations-on-deep-learning-model-comparisons-in-drug-response-predictions.pdf |
60c74f70bdbb89f30ea39d83 | 10.26434/chemrxiv.12084918.v2 | Protein Denaturation Zero Entropy Temperature, and the Structure of Water Around Hydrophobic and Amphiphilic Solutes | The hydrophobic effect plays a key role in many chemical and biological processes, including protein folding. Nonetheless, a comprehensive picture of the effect of temperature on hydrophobic hydration and protein denaturation remains elusive. Here, we study the effect of temperature on the hydration of model hydrophobic and amphiphilic solutes through molecular dynamics aiming at getting insight on the singular behavior of water concerning the zero entropy temperature Ts and entropic convergence also observed upon protein denaturation. We show that, similar to hydrocarbons and proteins, polar amphiphilic solutes exhibit a Ts, although strongly dependent upon solute-water interactions, opposite to hydrocarbons. Further, the temperature dependence of the hydration entropy normalized by the solvent accessible surface area is shown to be nearly solute size independent for hydrophobic but not for amphiphilic solutes, for similar reasons. These results are further discussed in the light of information theory (IT) and the structure of water around hydrophobic groups The latter shows that the tetrahedral enhancement of some water molecules around hydrophobic groups, associated with the reduction of water defects, leads to the strengthening of the weakest hydrogen bonds, relative to bulk water. However, a larger tetrahedrality is found in low density water populations, demonstrating that pure water has encoded structural information similar to that associated with hydrophobic hydration, consistent with IT assumptions. The source of the differences between Kauzmann's "hydrocarbon model" on protein denaturation and hydrophobic hydration is also discussed with relatively large amphiphilic hydrocarbons displaying a more similar behavior to globular proteins, than aliphatic hydrocarbons.<br /> | kazimieras Tamoliūnas; Nuno Galamba | Biophysical Chemistry; Physical and Chemical Processes; Solution Chemistry; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f70bdbb89f30ea39d83/original/protein-denaturation-zero-entropy-temperature-and-the-structure-of-water-around-hydrophobic-and-amphiphilic-solutes.pdf |
66f12f9712ff75c3a1313dc8 | 10.26434/chemrxiv-2024-jhsbk | EM-HyChem: Bridging molecular simulations and chemical reaction neural network-enabled approach to modelling energetic material chemistry | This study introduced a physics-inspired, top-down approach for modelling the reaction kinetics of energetic materials, based on observations of the time scale separation between pyrolysis and oxidation reactions. This modelling approach, named EM-HyChem, was developed with the inspiration of the original hybrid chemistry (HyChem) model, in which the reaction mechanism is divided into two submodels: pyrolysis and oxidation. In EM-HyChem, the key pyrolysis products and reaction mechanism are identified from the perspective of molecular fragments via geometry analysis, which is validated via neural network potential-enabled molecular dynamic simulations. A chemical reaction neural network (CRNN) model is applied to extract the rate parameters for the pyrolysis step from the reproduction of thermogravimetric experiments. An EM-HyChem model is later constructed by combining the pyrolysis step together with the oxidation models for the pyrolysis products. Two representative EMs, i.e., 1,3,5-trinitroperhydro-1,3,5-triazine (RDX) and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), are considered here to evaluate the performance of the EM-HyChem model. The predicted burning rates across a wide range of pressure conditions (1–100 atm) are in good agreement with the experimental measurements and the results of other models. Further agreement among the temperate profile, melt layer thickness and surface temperatures support the EM-HyChem model. | Xinzhe Chen; Yabei Xu; Mingjie Wen; Kehui Pang; Shengkai Wang; Qingzhao Chu; Dongping Chen | Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f12f9712ff75c3a1313dc8/original/em-hy-chem-bridging-molecular-simulations-and-chemical-reaction-neural-network-enabled-approach-to-modelling-energetic-material-chemistry.pdf |
60c742b0bb8c1aa4443da1a7 | 10.26434/chemrxiv.8477168.v1 | Theoretical Bounds on Electron Energy Filtering in Disordered Nanomaterials | This manuscript presents a theoretical model for determining the electron energy filtering properties of nanocomposite materials. Individual nanoparticles can serve as energy filters for tunneling electrons due their discretized energy levels. Nanomaterials comprised of many individual nanoparticles can in principle serve the same purpose, however, particle polydispersity can lead to an additional source of energetic broadening. We describe a simple theoretical model that includes the effects of discrete energy levels and inhomogeneous broadening. We use this model to identify the material parameters needed for effective energy filtering by quantum dot solids. | Amro Dodin; Brian F. Aull; Roderick R. Kunz; Adam Willard | Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b0bb8c1aa4443da1a7/original/theoretical-bounds-on-electron-energy-filtering-in-disordered-nanomaterials.pdf |
66b35c4101103d79c5060e46 | 10.26434/chemrxiv-2024-wrn9s | T1 T2* Relaxation Time Correlation NMR Monitoring of the Mechanochemical Formation of Quinoxaline Derivatives | Despite the increased use of mechanochemistry for chemical reactions few options for reaction monitoring or solid state analysis are available. This work explores using T1 T2* 1H NMR to monitor the reaction between benzil or 4,4’ dimethybenzil with o phenylenediamine. For both reactions, the T1 T2* correlation plots show differences in relaxation times throughout the reaction. This work demonstrates using two different strageties to monitor the reaction progression. In the first case the reaction is monitered by the appearance of signals corresponding to the product, and side product water. In the second case the reaction is monitored by the replacement of the signals corresponding to the starting material, by signals corresponding to the product. This magnetic resonance correlation measurement provides an excellent option for whole sample solid state analysis by virtue of its simplicity and versatility. | Madeleine Leger; Jiangfeng Guo; Mason Lawrence; Bryce MacMillan; Bruce Balcom; Barry Blight | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b35c4101103d79c5060e46/original/t1-t2-relaxation-time-correlation-nmr-monitoring-of-the-mechanochemical-formation-of-quinoxaline-derivatives.pdf |
67a2e88a6dde43c908a0ac11 | 10.26434/chemrxiv-2025-81k3n | Nuclear Coupled Electronic States Analyses Expose Nuclear Quantum Effects in Nucleobase Pairs | Tautomerization by double proton transfer of nucleobase pairs leads to point mutations of nucleic acids. A series of constrained nuclear-electronic orbital calculations, combined with natural bond orbital and kinetic analyses, has quantitatively revealed the importance of nuclear quantum effects in the reaction. Compared to the case where the nuclei are treated classically, the probability of the formation of the tautomeric isomers of Cytosine-Guanine, explicitly taking into account the NQEs, increased by a factor of 8.0 in the gas phase and by a factor of 20.5 in water. This could be explained by the increase in the number of electrons occupying the reaction site’s antibonding orbitals. The proportion of Cytosine-Guanine tautomeric isomers formed by double proton transfer was estimated to be 246 pairs per human genome. | Kohei Motoki; Hirotoshi Mori | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a2e88a6dde43c908a0ac11/original/nuclear-coupled-electronic-states-analyses-expose-nuclear-quantum-effects-in-nucleobase-pairs.pdf |
638986a97b7c914f1ddf6089 | 10.26434/chemrxiv-2022-k6dr2-v3 | DeepWEST: Deep learning of kinetic models with the Weighted Ensemble Simulation Toolkit for enhanced sampling | Recent advances in computational power and algorithms have made molecular dynamics (MD) simulations reach greater timescales. However, for observing conformational transitions associated with biomolecular processes, MD simulations still have limitations. Several enhanced sampling techniques seek to address this challenge, including the weighted ensemble (WE) method, which samples transition between metastable states using many weighted trajectories to estimate kinetic rate constants. However, initial sampling of the potential energy surface has a significant impact on the performance of WE, i.e., convergence and efficiency. We thereby introduce deep-learned kinetic modeling approaches that extract statistically relevant information from short MD trajectories to provide a well-sampled initial state distribution for WE simulation. This hybrid approach overcomes any statistical bias to the system as it runs short unbiased MD trajectories and identifies meaningful metastable states of the system. It is shown to provide a more refined free energy landscape closer to steady-state that could efficiently sample kinetic properties such as rate constants. | Anupam Ojha; Saumya Thakur; Surl-Hee Ahn; Rommie Amaro | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638986a97b7c914f1ddf6089/original/deep-west-deep-learning-of-kinetic-models-with-the-weighted-ensemble-simulation-toolkit-for-enhanced-sampling.pdf |
627e219244bdd59ebc61e985 | 10.26434/chemrxiv-2022-9cw47-v2 | Photocaged Activity-Based Probes for Spatiotemporal Detection of Protein S-sulfenylation in Living Cells | Protein cysteine residues have unique reactivity due to the low redox potential of its thiol side chain. Protein S-sulfenylation (protein sulfenic acid), as one of the most significant oxidative post-translational modifications (OxiPTMs), plays a vital role in regulating protein function. Due to the transient presence of sulfenic acid in living cell, many detecting methods have been limited. Activity-based probes provide powerful tools to elucidate this process, so their discovery has been at the forefront of redox biology. In this study, two caged cysteine sulfenic acid probes DYn-2-ONB, DYn-2-Cou with either an o-nitrobenzyl or coumarin protecting group were developed. Both probes can be efficiently uncaged via irradiation to produce the active C-nucleophile probe DYn-2. Labeling assay in living cells demonstrated DYn-2-ONB exhibited better labeling capacity compared with DYn-2, providing it as a powerful tool to detect protein S-sulfenylation in spatio-temporally controllable manner. | Jiahao Zhang; Haiyue Peng; Zi'an Chen; Guorui Li; Jing Huang | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627e219244bdd59ebc61e985/original/photocaged-activity-based-probes-for-spatiotemporal-detection-of-protein-s-sulfenylation-in-living-cells.pdf |
60c75741842e653789db465a | 10.26434/chemrxiv.14386814.v1 | Photocatalytic Deoxygenation of N–O Bonds with Rhenium Complexes: From the Reduction of Nitrous Oxide to Pyridine N-Oxides | The accumulation of nitrogen oxides in the environment calls for new pathways to interconvert the various oxidation states of nitrogen, and especially their reduction. The large spectrum of reduction potentials covered by nitrogen oxides makes it however difficult to find general systems capable of efficiently reducing various N-oxides. Here photocatalysis unlocks high energy species able to both circumvent the inherent low reactivity of the greenhouse gas and oxidant N<sub>2</sub>O (E°(N<sub>2</sub>O/N<sub>2</sub>) = +1.77 V vs. SHE), and reduce pyridine N-oxides (E<sub>1/2</sub>(pyridine N-oxide/pyridine) = –1.04 V vs. SHE). The rhenium complex [Re(4,4’-tBu-bpy)(CO)<sub>3</sub>Cl] proved to be efficient to perform both reactions under ambient conditions, enabling the deoxygenation of N<sub>2</sub>O as well as synthetically relevant and functionalized pyridine N-oxides.<br /> | Marianne Kjellberg; Alexia Ohleier; Pierre Thuéry; Emmanuel Nicolas; Lucile Anthore-Dalion; Thibault Cantat | Photochemistry (Org.); Photocatalysis; Catalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75741842e653789db465a/original/photocatalytic-deoxygenation-of-n-o-bonds-with-rhenium-complexes-from-the-reduction-of-nitrous-oxide-to-pyridine-n-oxides.pdf |
67af169e81d2151a02683521 | 10.26434/chemrxiv-2025-w3tzb | Red emissive 1D Copper(I) Thiolates vs. green emissive 2D Copper(I) Halide Thiolates displaying second harmonic generation and two-photon absorption processes | Copper(I), as a d10 metal, is a promising affordable non-critical raw material finding great interest for the development of photoluminescent materials. Halide and thiolate-based copper(I) compounds are known for their efficient emission and good stability. In order to rationalize the effect of these two anions in the structure and photoemission of Cu(I) compounds, two new families of coordination polymers have been synthesized: the copper(I)-thiolates: [Cu(p-SPhX)]n (X = F, Cl, Br), and the copper halide thiolates : [Cu3Cl(p-SPhX)2]n (X = F, Cl, Br). The two families display different structural dimensionalities: 1D [Cu(p-SPhX)]n vs. 2D [Cu3Cl(p-SPhX)2]n and they exhibit distinct photophysical properties: [Cu(p-SPhX)]n show usual solid-state red emission, while [Cu3Cl(p-SPhX)2]n have intense solid-state green anti-Stokes emission, associated, for the non-centrosymmetric compounds, X = F and Br, to non-linear optical response (NLO), pointing out the effect of the weak halogen interactions of the thiolate ligands on the symmetry and the properties. | Saly Hawila; Buqin Xu; Florian Massuyeau; Romain Gautier; Nathalie Guillou; Alexandra Fateeva; Sébastien Lebegue; Inhwan Oh; Won June Kim; Gilles Ledoux; Miguel Monge; Adel Mesbah; Aude Demessence | Physical Chemistry; Optics | CC BY NC 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af169e81d2151a02683521/original/red-emissive-1d-copper-i-thiolates-vs-green-emissive-2d-copper-i-halide-thiolates-displaying-second-harmonic-generation-and-two-photon-absorption-processes.pdf |
60c74294ee301c7796c78e8d | 10.26434/chemrxiv.8313086.v1 | Effect of Film Thickness on the Far- and Near-Field Optical Response of Nanoparticle-on-Film Systems | <p>We study the near-field and far-field optical response of
nanoparticle-on-film systems using single-nanoparticle spectroscopy and
numerical simulations. We find that the optical spectra contain three dominant
modes - a transverse dipole and quadrupole mode, and a dominant vertical
antenna mode. We vary the thickness of the metal film from 10 – 45 nm, and find
that the vertical antenna mode wavelength is nearly independent of the film
thickness. In contrast, we find that the associated near-field enhancement in
the gap between the particle and the film strongly depends on the film
thickness. This trend is also observed in the far-field where the vertical antenna
mode strongly increases in amplitude for increasing film-thicknesses up to the
skin depth of gold. These findings are in good agreement with a numerical model
and pave the way to study field-mediated processes such as fluorescence, SERS,
and localized chemistry at the same resonance wavelength but at varying degrees
of field enhancement.</p> | Rachel Armstrong; Willeke van Liempt; Peter Zijlstra | Thin Films; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74294ee301c7796c78e8d/original/effect-of-film-thickness-on-the-far-and-near-field-optical-response-of-nanoparticle-on-film-systems.pdf |
6661b51b21291e5d1d33a199 | 10.26434/chemrxiv-2023-d0dqp-v3 | Graph Neural Networks for Identifying Protein-Reactive Compounds | The identification of protein-reactive electrophilic compounds is critical to the design of new covalent modifier drugs, screening for toxic compounds, and the exclusion of reactive compounds from high throughput screening. In this work, we employ traditional and graph machine learning (ML) algorithms to classify molecules being reactive towards proteins or nonreactive. For training data, we built a new dataset, ProteinReactiveDB, composed primarily of covalent and noncovalent inhibitors from the DrugBank, BindingDB, and CovalentInDB databases. To assess the transferability of the trained models, we created a custom set of covalent and noncovalent inhibitors, which was constructed from the recent literature. Baseline models were developed using Morgan fingerprints as training inputs, but they performed poorly when applied to compounds outside the training set. We then trained various Graph Neural Networks (GNNs), with the best GNN model achieving an Area Under the Receiver Operator Characteristic (AUROC) curve of 0.80, precision of 0.89, and recall of 0.72. We also explore the interpretability of these GNNs using Gradient Activation Mapping (GradCAM), which shows regions of the molecules GNNs deem most relevant when making a prediction. These maps indicated that our trained models can identify electrophilic functional groups in a molecule and classify molecules as protein-reactive based on their presence. We demonstrate the use of these models by comparing their performance against common chemical filters, identifying covalent modifiers in the ChEMBL database and generating a putative covalent inhibitor based on an established noncovalent inhibitor. | Victor Hugo Cano Gil; Christopher Rowley | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661b51b21291e5d1d33a199/original/graph-neural-networks-for-identifying-protein-reactive-compounds.pdf |
6225c07c7c13f42dc16a0836 | 10.26434/chemrxiv-2022-n7gj3 | Enhanced susceptibility of SARS-CoV-2 spike RBD protein assay targeted by cellular receptors ACE2 and CD147: multivariate data analysis of multisine impedimetric response | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the cells through the binding of spike protein to the host cell surface-expressing angiotensin-converting enzyme 2 (ACE2) or by endocytosis mediated by extracellular matrix metalloproteinase inducer (CD147). We present extended statistical studies of the multisine dynamic electrochemical impedance spectroscopy (DEIS) revealing interactions between Spike RBD and cellular receptors ACE2 and CD147, and a reference anti-RBD antibody (IgG2B) based on a functionalised boron-doped diamond (BDD) electrode. The DEIS was supported by a multivariate data analysis of a SARS-CoV-2 Spike RBD assay and cross-correlated with the atomic-level information revealed by molecular dynamics simulations. Our approach allowed us to study and detect subtle changes in the electrical properties responsible for the susceptibility of
cellular receptors to SARS-CoV-2, revealing their interactions. Changes in electrical homogeneity in the function of the RBD concentration led to the conclusion that the ACE2 receptor delivers the most homogeneous surface, delivered by the high electrostatic potential of the relevant docking regions. For higher RBD concentrations, the differences in electrical homogeneity between electrodes with different receptors vanish. Collectively, this study reveals interdependent virus entry paths involving separately ACE2, CD147, and spike protein, provided by a developed biosensing platform for the rapid screening of cellular interactions (i.e. testing various mutations of SARS-CoV-2 or screening of therapeutic drugs). | Mateusz Brodowski; Mattia Pierpaoli; Monika Janik; Marcin Kowalski; Mateusz Ficek; Pawel Slepski; Bartosz Trzaskowski; Greg Swain; Jacek Ryl; Robert Bogdanowicz | Analytical Chemistry; Biochemical Analysis; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6225c07c7c13f42dc16a0836/original/enhanced-susceptibility-of-sars-co-v-2-spike-rbd-protein-assay-targeted-by-cellular-receptors-ace2-and-cd147-multivariate-data-analysis-of-multisine-impedimetric-response.pdf |
61326a27d5f080805bba0d77 | 10.26434/chemrxiv-2021-54w4m | Urazole as an unorthodox functional group for fabrication of anionic hydrogels and ion-exchange materials | In this study, highly ionazable protons (pKa 5-6) of urazole were exploited to obtain an anionic hydrogel in two simple and scalable steps. Commercially available multiisocyanate, poly(hexamethylene)diisocyanate, was used to prepare urazole containing gel. Urazole formation was confirmed by FT-IR and 1H-NMR spectroscopy. The hydrogel were characterized by microscopy imaging, spectroscopic and gravimetric analysis. Mechanical analysis and cell viability test were performed for its initial biocompatibility evaluation. The prepared hydrogel is a highly porous hydrogel with a Young’s modulus of 0.91MPa, has swelling ratio of 87% and capable of exchanging ions in a medium. In this report, we demonstrated a strategy to overcome synthetic challenge of incorporating urazole into a material via precursor path rather than attempting to embeding urazole groups directly. | Saltuk Hanay; Ali Fallah; Efsun Senturk; Ferdows Afghah; Hulya Yilmaz; Mustafa Culha; Bahattin Koc | Materials Science; Biocompatible Materials; Biological Materials; Carbon-based Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61326a27d5f080805bba0d77/original/urazole-as-an-unorthodox-functional-group-for-fabrication-of-anionic-hydrogels-and-ion-exchange-materials.pdf |
635aa74d31107245e6f253ac | 10.26434/chemrxiv-2022-1hv1c | Visible-light promoted N-aminoalkylation of quinazolinones | A visible-light promoted direct coupling of quinazolinones and simple alkylamides to approach highly functionalized N-aminoalkyl quinazolinones was reported. This protocol serves as a highly efficient and straightforward strategy for N-aminoalkylation transformation of quinazolinones employing tert-Butyl peroxybenzoate as an oxidant in combination with visible-light irradiation conditions. This process features mild reaction conditions and tolerance for a wide range of functional groups. Synthetically important and highly functionalized N-aminoalkyl quinazolinones were afforded high levels of yields (up to 86% yield). | Wenwen Cui; Yang Fan; Zhi-Bin Wang; Xiao- Wei Liang; Shou-Guo Wang | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635aa74d31107245e6f253ac/original/visible-light-promoted-n-aminoalkylation-of-quinazolinones.pdf |
60c73d0eee301c4491c784f3 | 10.26434/chemrxiv.5414065.v1 | A common mechanism links activities of butyrate in the colon | Two biological activities of butyrate in the
colon (suppression of proliferation of colonic epithelial stem cells and
inflammation) correlate with inhibition of histone deacetylases. Cellular and biochemical studies of molecules
similar in structure to butyrate, but different in molecular details (functional
groups, chain-length, deuteration, oxidation level, fluorination, or degree of unsaturation)
demonstrated that these activities were sensitive to molecular structure, and were
compatible with the hypothesis that butyrate acts by binding to the Zn<sup>2+</sup>
in the catalytic site of histone deacetylases. Structure-activity
relationships drawn from a set of 36 compounds offer a starting point for the design
of new compounds targeting the inhibition of histone deacetylases. The observation that butyrate was more potent
than other short-chain fatty acids is compatible with the hypothesis that
crypts evolved (at least in part), to separate stem cells at the base of crypts
from butyrate produced by commensal bacteria. | Mohit S. Verma; Michael J. Fink; Gabriel L Salmon; Nadine Fornelos; Takahiro E. Ohara; Stacy S. Ryu; Hera Vlamakis; Ramnik J. Xavier; Thaddeus S. Stappenbeck; George M. Whitesides | Biochemistry; Cell and Molecular Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0eee301c4491c784f3/original/a-common-mechanism-links-activities-of-butyrate-in-the-colon.pdf |
662c5098418a5379b0d502af | 10.26434/chemrxiv-2024-st6vk | Poly(aryl piperidium)-based AEMs utilizing spirobifluorene as a branching agent | We here developed high-performance anion exchange membranes (AEMs) by incorporating 9,9'-spirobifluorene as a three-dimensional branching agent, addressing the common trade-off between ion conductivity and dimensional/mechanical stability. By fine-tuning the ratio of terphenyl to biphenyl and the amount of the branching agent, we refined the AEM, achieving high conductivity (approximately 190 mS/cm at 80 °C in 1 M KOH) with decent dimensional/mechanical properties, comparable to the recently reported state-of-the-art membranes. Investigations using gas pycnometry and atomic force microscopy demonstrated that spirobifluorene enhances the fractional free volume around the membrane's backbone and more precisely modulates the separation between hydrophobic and hydrophilic domains, thus boosting both ion conductivity and mechanical stability. This membrane also displayed excellent chemical stability, with negligible degradation at 80 °C in 1 M KOH over 1000 h. With such a membrane, we achieved excellent cell performance, with a current density of 11.2 A/cm² at 80 °C, 2 V. | Geun Woong Ryu; Sang Hun Shin; In Wook Song; Ki Chang Kwon; Sun Hwa Park; Jang Yong Lee; Min Sang Kwon | Materials Science; Polymer Science; Polyelectrolytes - Materials; Organic Polymers; Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662c5098418a5379b0d502af/original/poly-aryl-piperidium-based-ae-ms-utilizing-spirobifluorene-as-a-branching-agent.pdf |
613e08ec27d9062aa3857fc1 | 10.26434/chemrxiv-2021-rm8vr | Lighting up Electrochemiluminescent Inactive Dyes by Intramolecular Resonance Energy Transfer | By virtue of near-zero optical background and photobleaching, electrochemiluminescence (ECL), an optical phenomenon excited by electrochemical reactions, has drawn extensive attention in both fundamental studies and wide applications especially of ultrasensitive bioassay. Developing diverse ECL emitters is crucial to unlock their multiformity and performances, but remains a formidable challenge, due to the rigorous requirements for ECL. Herein, we report a general intramolecular ECL resonance energy transfer (iECL-RET) strategy to light up ECL-inactive dyes in aqueous solutions using an existing high-performance ECL initiators. As a proof-of-concept, a series of luminol donor-dye acceptor based ECL emitters with near unity RET efficiency and coarse/fine tunable emission wavelengths were demonstrated. Different to previous exploitation of new molecule single-handedly to address all the prerequisites of ECL, each unit in the proposed ECL ensemble performed maximally its own functions. The iECL-RET strategy would greatly expand the family members of ECL emitters for more demanding future applications. | Yongjun Zheng; Hong Yang; Lufang Zhao; Yuhan Bai; Xinghua Chen; Kaiqing Wu; Songqin Liu; Yanfei Shen; Yuanjian Zhang | Analytical Chemistry; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613e08ec27d9062aa3857fc1/original/lighting-up-electrochemiluminescent-inactive-dyes-by-intramolecular-resonance-energy-transfer.pdf |
6797b23b81d2151a022bfd83 | 10.26434/chemrxiv-2025-n6x46 | Artificial Intelligence-Empowered Automated Double Emulsion Droplet Library Generation | Double emulsions, with core-shell structures, are versatile materials used in diverse applications such as cell culture, drug delivery, and materials synthesis. A library of double emulsions with precisely controlled dimensions and properties would streamline the process of screening and optimization for specific applications. Microfluidic droplet generation offers precise control over droplet dimensions and properties, making it ideal for the preparation of droplet libraries; however, their preparation is tedious because fluid flow control and emulsion collection are typically performed manually and microfluidic devices are vulnerable to minor disturbances, requiring continuous intervention by skilled operators. To address these challenges, we present an artificial intelligence (AI)-empowered automated double emulsion droplet library generator. Leveraging a convolutional neural network (CNN)-based object detection model fine-tuned on a custom dataset, the system integrates decision-making and feedback control for automated droplet generation and collection. The system monitors droplet generation every 171 ms —faster than the reaction time of Formula 1 drivers —ensuring rapid response to disruptions and consistent production of single-core double emulsions. The library generator autonomously generates libraries consisting of 25 distinct monodisperse droplets with user-specified properties. This system significantly improves droplet-based experiments by reducing labor and waste, improving precision, and supporting rapid, reliable droplet library generation. | Seonghun Shin; Owen Land; Warren Seider; Jinkee Lee; Daeyeon Lee | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Process Control; Quality Control; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797b23b81d2151a022bfd83/original/artificial-intelligence-empowered-automated-double-emulsion-droplet-library-generation.pdf |
60c7530fee301c7ed2c7ad0f | 10.26434/chemrxiv.13194110.v2 | Triplet Stabilization for the Enhanced Drug Photorelease from Sunscreen-Based Photocages | <p>Recently, sunscreen-based drug photocages have been introduced to provide UV protection to photoactive drugs, thus increasing their photosafety. Here, combined experimental and theoretical studies performed on a photocage based on the commercial UVA filter avobenzone (AB) and on the photosensitizing non-steroidal anti-inflammatory drug ketoprofen (KP) are presented unveiling the photophysical processes responsible for the light-triggered release. Particular attention is paid to solvent stabilization of the drug and UV filter excited states, respectively, which leads to a switching between the triplet excited state energies of the AB and KP units. Most notably, <a>we show that the stabilization of the AB triplet excited state in ethanol solution is the key requirement for an efficient photouncaging. By contrast, in apolar solvents, in particular hexane, KP has the lowest triplet excited state, hence acting as an energy acceptor quench</a>ing the AB triplet manifold, thus inhibiting the desired photoreaction.</p> | Mauricio Lineros-Rosa; Maria Consuelo Cuquerella; Antonio Francés-Monerris; Antonio Monari; Miguel Angél Miranda; Virginie Lhiaubet-Vallet | Biophysical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7530fee301c7ed2c7ad0f/original/triplet-stabilization-for-the-enhanced-drug-photorelease-from-sunscreen-based-photocages.pdf |
60c74fcaee301c20cec7a765 | 10.26434/chemrxiv.12941702.v1 | Structural Causes of Singlet/triplet Preferences of Norrish Type II Reactions in Carbonyls | Photolysis thresholds are calculated
for the Norrish Type II (NTII) intramolecular γ-hydrogen abstraction reaction in 22 structurally informative
carbonyl species. The B2GP-PLYP excited state <i>S</i><sub>1</sub> and <i>T</i><sub>1</sub> thresholds agree
well with triplet quenching experiments.
However, many linear-response methods deliver poor <i>S</i><sub>1</sub> energetics, which
is explained by a <i>S</i><sub>1</sub>/<i>S</i><sub>0</sub> conical intersection in close proximity to the <i>S</i><sub>1
</sub>transition state. Multiconfigurational
CASSCF calculations confirm a conical
intersection features across all carbonyl
classes. <div><br /></div><div>Structure–activity relationships are
determined that could be used in atmospheric carbonyl photochemsitry modelling. This is exemplified for butanal,
whose NTII quantum yields are too
low when used as a ‘surrogate’ for
larger carbonyls, since butanal lacks the
γ-substitution that stabilises the 1,4-
biradical. Reaction on <i>T</i><sub>1</sub> dominates
only in species where the <i>S</i><sub>1</sub> thresholds
are high — typically ketones. The α, β-unsaturated carbonyls cannot cleave
the α–β bond, causing them to photoisomerise. A concerted <i>S</i><sub>0</sub> NTII mechanism is calculated to be viable and
may explain the recent detection of
NTII photoproducts in the photolysis
of pentan-2-one below the <i>T</i><sub>1</sub> threshold.</div> | Keiran Rowell; Scott Kable; Meredith J. T. Jordan | Atmospheric Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fcaee301c20cec7a765/original/structural-causes-of-singlet-triplet-preferences-of-norrish-type-ii-reactions-in-carbonyls.pdf |
60c75942bb8c1a19c23dcba6 | 10.26434/chemrxiv.14679405.v1 | Origins of the Instability of Non-precious HER Catalysts at Open Circuit Potential | <p>Non-precious hydrogen evolution reaction (HER) catalysts commonly suffer from severe dissolution under open circuit potential (OCP). In this work, using calculated Pourbaix diagrams, we quantitatively analyze the stability of a set of well-known active HER catalysts (MoS<sub>2</sub>, MoP, CoP, Pt in acid, and Ni<sub>3</sub>Mo in base) under working conditions. We determine that the large thermodynamic driving force towards decomposition created by the electrode/electrolyte interface potential is responsible for the substantial dissolution of non-precious HER catalysts at OCP. Our analysis further shows the stability of HER catalysts in acidic solution is ordered as Pt ∼ MoS<sub>2 </sub><i>> </i>MoP <i>> </i>CoP, which is confirmed by the measured dissolution rates using an inductively coupled plasma mass spectrometer. Based on gained insights, we suggest strategies to circumvent the catalyst dissolution in aqueous solution.</p> | Zhenbin Wang; Ya-Rong Zheng; Joseph H. Montoya; Degenhart Hochfilzer; Ang Cao; Jakob Kibsgaard; Ib Chorkendorff; Jens Kehlet Nørskov | Catalysts; Electrochemistry; Theory - Computational; Electrocatalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75942bb8c1a19c23dcba6/original/origins-of-the-instability-of-non-precious-her-catalysts-at-open-circuit-potential.pdf |
60c73e139abda2866cf8b80c | 10.26434/chemrxiv.6303710.v1 | Is Lewis Acidity in Metal Dications Triggered by Solvent Shell Fluctuations? | Using experimental data collected on the stabilities of gas phase clusters consisting of metal dications in association with water molecules, a model is proposed to account for Lewis acidity. It is suggested that acidity is driven be fluctuations in the numbers of water molecules surrounding a metal ion, and that these fluctuations reduce numbers in the coordination shells to below those need to stabilise a +2 charge on the metal. The timescale on which these fluctuations are calculated to occur is approximately 6 orders of magnitude longer than any of the measure mean residence times of water molecules surrounding a central metal ion. This time difference reflects both the rarity of the event require to drive acidity and the extreme nature of some of the fluctuations. | Tony Stace | Theory - Computational; Physical and Chemical Processes; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e139abda2866cf8b80c/original/is-lewis-acidity-in-metal-dications-triggered-by-solvent-shell-fluctuations.pdf |
60c741660f50db4abb395ad7 | 10.26434/chemrxiv.8039006.v1 | Nucleophilic Substitution Reactions of Cyclic Thiosulfinates Are Accelerated by Hyperconjugative Interactions | Strain energy has been shown to promote the nucleophilic substitution reactions of cyclic disulfides, the reactivities of cyclic thiosulfinate nucleophilic substitution is unexplored. We used density functional theory calculations [M06-2X/6-311++G(d,p)] to determine the activation and reaction free energies for the reactions of 3—10-membered cyclic thiosulfinates and cyclic disulfides with methyl thiolate. | Daniel Donnelly; Jeffrey Agar; Steven Lopez | Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741660f50db4abb395ad7/original/nucleophilic-substitution-reactions-of-cyclic-thiosulfinates-are-accelerated-by-hyperconjugative-interactions.pdf |
60c74c47ee301c9d91c7a038 | 10.26434/chemrxiv.12459800.v1 | A New Native Mass Spectrometry Platform Identifies Inhibitors of the HSP90 – HOP Protein-Protein Interaction | This communication discusses for the first time, the use of mass spectrometry as a platform for screening for PPI inhibitors, without protein tethering or labeling. Furthermore, in the context of cancer drug discovery, this study demonstrates the ligandability and therefore the potential druggability of HOP, whose PPI with HSP90 has been routinely discussed as a difficult to drug target of substantial potential. | Clinton Veale; Mateos-Jimenez, Maria; Michaelone Vaaltyn; Ronel Müller; Matodzi Makhubu; Mahama Alhassan; Beatriz G. de la
Torre; Fernando Albericio; C. Logan Mackay; Adrienne L. Edkins; David Clarke | Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c47ee301c9d91c7a038/original/a-new-native-mass-spectrometry-platform-identifies-inhibitors-of-the-hsp90-hop-protein-protein-interaction.pdf |
67ceb0c2fa469535b9b41db9 | 10.26434/chemrxiv-2025-5cxdf | Mentoring doctoral students in the chemical sciences | The relevance of effective mentoring of doctoral students in the chemical sciences is now widely recognized. However, the scholarly literature on the topic is virtually non-existent, and most approaches to faculty education on mentoring are based on “tips” and “guidelines. Following the analysis of current mentorship practices, we suggest a new approach based on evidence resulting from surveys of doctoral students, and on theory derived from studies in social and human sciences. | Rosaria Ciriminna; Cristina Della Pina; Rafael Luque; Mario Pagliaro | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ceb0c2fa469535b9b41db9/original/mentoring-doctoral-students-in-the-chemical-sciences.pdf |
621d0251c3e9da5d5d7b7495 | 10.26434/chemrxiv-2022-x935v-v2 | Membrane Catalysed Formation of Nucleotide Clusters and Its Role in the Origins of Life | One of the mysteries in studying the molecular “Origin of Life” is the emergence of RNA and
RNA-based life forms, where non-enzymatic polymerization of nucleotides is a crucial hypothesis
in formation of large RNA chains. The non-enzymatic polymerization can be mediated by various
environmental settings such as cycles of hydration and dehydration, temperature variations and
proximity to a variety of organizing matrices such as clay, salt, fatty acids, lipid membrane and
mineral surface. In this work, we explore the influence of different phases of the lipid membrane
towards nucleotide organization and polymerization in a simulated prebiotic setting. We calculate
the free energy cost of localizing a mononucleotide, Uridine monophosphate (UMP), in distinct
membrane settings and we perform all-atom molecular dynamics (MD) simulations to estimate
the role of the monophasic and biphasic membrane in modifying the behavior of UMPs localization
and their clustering mechanism. Based on the free-energy and diffusion data from our MD
calculations, we develop a lattice based model to explore the thermodynamic limits of the observations
made from the MD simulations. The mathematical model substantiates our hypothesis that
the lipid layers can act as unique substrates for ‘catalyzing’ polymerization of mononucleotides
due to the inherent spatiotemporal heterogeneity and phase change behavior. | Rajlaxmi Saha; Prathyush Poduval; Krishnakanth Baratam; Jayashree Nagesh; Anand Srivastava | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621d0251c3e9da5d5d7b7495/original/membrane-catalysed-formation-of-nucleotide-clusters-and-its-role-in-the-origins-of-life.pdf |
6381d95a1234cb02cb23aafb | 10.26434/chemrxiv-2022-2fhkp | [4Fe-4S]-mediated proton-coupled electron transfer enables the efficient degradation of chloroalkenes by reductive dehalogenases | Reductive dehalogenases (RDases) are key enzymes involved in the degradation of organohalide compounds. Despite extensive experi-mental and computational studies, the catalytic mechanism of RDases remains unclear. We show here that the proximal [4Fe-4S]1+ cluster of the reductive dehalogenase PceA can mediates a proton-coupled electron transfer (PCET) process to quench the substrate radical. Such [4Fe-4S]1+-mediated PCET process is enhanced by both exchange and super-exchange interactions. The participation of [4Fe-4S]1+ in mediating a PCET process in RDases is unexpected, though well known in reducing Co(II). In addition, in RDases the Arg305 residue acts as an efficient proton donor for the PCET reactions. The deprotonated Tyr246 serves to maintain the favorable conformation of Arg305 during catalysis, and sustains its proton donation ability, which is requested during the PCET reaction. Such a novel mechanism enables the efficient detoxification of chloroalkene pollutants by the reductive dehalogenase PceA. These results highlight the critical role of the proximal [4Fe-4S] | Xuan Zhang; Zikuan Wang; Zhen Li; Sason Shaik; Binju Wang | Theoretical and Computational Chemistry; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6381d95a1234cb02cb23aafb/original/4fe-4s-mediated-proton-coupled-electron-transfer-enables-the-efficient-degradation-of-chloroalkenes-by-reductive-dehalogenases.pdf |
60c73dbcbb8c1a14763d97d9 | 10.26434/chemrxiv.5818122.v2 | Using electropolymerization based doping for electro-addressable functionalization of a multielectrode array probe for nucleic acid detection | <div>Here, we report a facile method for electro-addressable functionalization of a probe comprising of closely spaced three individually addressable carbon fiber electrodes for detection of nucleic acids. First, a multi electrode array probe comprising three adjacent carbon fiber electrodes was fabricated through pulling a three-barrel glass capillary with a single carbon fiber in each barrel using a micropuller. Second, electropolymerization based doping was used for electro-addressable functionalization of the multi-electrode array probe. To demonstrate that the current strategy works, anti-miR-34a was electrografted on only one of three electrodes by electropolymerization of pyrrole on the specific electrode. A second electrode was coated only with polypyrrole (PPy) and the third was left unmodified. Electrochemical impedance spectroscopy (EIS) was used for analysis and the results clearly showed charge transfer resistance of the PPy + anti-miR-34a modified electrode increased significantly after hybridization, while charge transfer resistance of the other two electrodes remained almost constant. The results demonstrate that the present strategy has great potential for constructing multiplex nucleic acid micro/nano biosensors for local and in situ detection of multiple nucleic acid molecules such as miRNAs at a time.</div> | Mustafa Sen | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dbcbb8c1a14763d97d9/original/using-electropolymerization-based-doping-for-electro-addressable-functionalization-of-a-multielectrode-array-probe-for-nucleic-acid-detection.pdf |
62b03bf3eb1f0cecbb8f8f73 | 10.26434/chemrxiv-2022-mr0lp | A graceful break-up: serendipitous self-assembly of a ferromagnetically coupled [NiII14] wheel | The complex [NiII14(HL2)12(HCOO)14Cl14] describes an aesthetically pleasing wheel displaying ferromagnetic nearest neighbour exchange. | Euan Brechin; Eleftheria Agapaki; Mukesh Singh; Angelos Canaj; Gary Nichol; Jürgen Schnack | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Transition Metal Complexes (Inorg.) | CC BY 4.0 | CHEMRXIV | 2022-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b03bf3eb1f0cecbb8f8f73/original/a-graceful-break-up-serendipitous-self-assembly-of-a-ferromagnetically-coupled-ni-ii14-wheel.pdf |
67abc3856dde43c90871524e | 10.26434/chemrxiv-2025-q8q77 | Gauss-Legendre-Spherical-t (GLST) Cubature-Based Factorization of Long-Range Electrostatics in Simulations | We develop a highly parallelizable algorithm to calculate long-range electrostatic interactions named the Gauss-Legendre-Spherical-t (GLST) cubature method. Motivated by our recent spherical grid and treecode method, we utilize the Gauss-Legendre quadrature for integration over a finite range and spherical t-design for integration over a unit sphere. The resulting GLST cubature breaks the long-range interaction term into a sum of terms that can be calculated in parallel with minimal inter-processor communication. The simulation box is divided into cells that are grouped with a separate GLST cubature applied to each group, based on their distance from the atom or cell for which the long-range interaction is calculated. Periodic boundary condition is handled at two levels, first by `wrapping-around' other cells about the cell under consideration, then by repeating the wrapped-around box over pre-computed number of times that make the relative error of the calculated force to meet the target accuracy. With its high granularity, tunable accuracy, and adaptability to different box geometries, the GLST method is suitable for simulation of large systems on computer hardware where many cores or threads are available. | Wonmuk Hwang; James Gonzales; Bernard Brooks | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67abc3856dde43c90871524e/original/gauss-legendre-spherical-t-glst-cubature-based-factorization-of-long-range-electrostatics-in-simulations.pdf |
67b31b6efa469535b9b4fd47 | 10.26434/chemrxiv-2024-k9w3s-v2 | Ring-opening Polymerization of Unprotected Hydroxyproline N-Carboxyanhydride for the Facile Synthesis of Linear and Branched Poly-L-hydroxyproline | Poly-L-hydroxyproline (PHyp) represents an important model for comprehending polyproline II helix and a key step toward mimicking collagen, the most abundant protein for animals, and holds immense potential for broad biomedical applications. The synthesis of PHyp, however, involves inefficient protection-deprotection steps and has been restricted to relatively low molecular weight (MW) and linear topology. Here, we report the first ring-opening polymerization (ROP) of unprotected hydroxyproline N-carboxyanhydrides (Hyp-NCA) for the facile one-step synthesis of PHyp with tunable linear or branching topologies. Employing an innovative water-assisted ultrafast polymerization technique, the research achieves the synthesis of linear PHyp with MW up to 11.0 kDa, featuring adjustable terminal groups and narrow dispersity. The study further introduces a tertiary amine-triggered one-pot polymerization method in DMSO, which leads to the facile preparation of branched PHyp (B-PHyp) within 2 h with MW up to 438 kDa, ~40 times higher than previous record of PHyp. Experimental and computational studies collectively uncovered novel details about the initiation, branching, and propagation steps of the reaction, providing fresh insights into the general mechanism regarding the ROP of NCA. Facile post-polymerization modification of B-PHyp affords injectable hydrogels with a critical gelization concentration as low as 1.0%. The polymers, characterized by their distinctive collagen-like polyproline type II (PPII) helices, offer significant prospects in drug delivery, wound healing, and other biomedical applications. | Letian Wang; Wencan Wang; Xinyi Zhu; Chenming Tang; Xiaodong Jing; Yahui He; Justin Amengual; Yao Lin; Zhixiang Yu; Hua Lu | Polymer Science; Biopolymers; Hydrogels; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b31b6efa469535b9b4fd47/original/ring-opening-polymerization-of-unprotected-hydroxyproline-n-carboxyanhydride-for-the-facile-synthesis-of-linear-and-branched-poly-l-hydroxyproline.pdf |
6331369c114b7e2a6a1db2e1 | 10.26434/chemrxiv-2022-wq3dm | Sequence-Specific Recognition of Double-Stranded DNA by Using Only PNAs in Parallel with Natural Nucleobases | The sequence-specific recognition of double-stranded DNA (dsDNA) is a key property for the control of DNA function. Peptide nucleic acid (PNA) can be utilised for the direct recognition of dsDNA via the formation of a unique invasion complex. Strand invasion by PNA induces local changes in the structure of dsDNA and is useful for the regulation of gene expression and genome editing. However, the fact that nucleobases modification is required for efficient invasion, has stymied the wide-spread application of PNA. Herein, we succeeded in the efficient recognition of target dsDNA sequences via formation of invasion complex by utilising only parallel-stranded and unmodified PNAs. This approach also streamlines synthesis by permitting the use of a peptide synthesiser rather than the manual synthesis we had been dependent upon for nucleobase-modified PNAs. Our new method also exhibited high sequence specificity and flexibility for target dsDNA sequences. | Masanari Shibata; Yuichiro Aiba; Masaki Hibino; Osami Shoji | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6331369c114b7e2a6a1db2e1/original/sequence-specific-recognition-of-double-stranded-dna-by-using-only-pn-as-in-parallel-with-natural-nucleobases.pdf |
64f3c8573fdae147fa58cafe | 10.26434/chemrxiv-2023-8lhws | Tailoring Performance of the LiNi0.8Mn0.1Co0.1O2 Cathode by Al2O3 and MoO3 artificial cathode electrolyte interphase (CEI) layers through plasma-enhanced atomic layer deposition (PEALD) Coating | The Ni-rich layered oxide cathode conceptus has shown high energy density, proper rate capability, and longevity of the rechargeable battery, while poor stability and capacity fading are assumed as its common cons. To address this obstacle, the prospective cathode materials are synthesized by integrating the lithium transition metal oxides with an artificial cathode electrolyte interphase (CEI) layer. Herein, plasma-enhanced atomic layer deposition (PEALD) was employed to coat the LiNi0.8Mn0.1Co0.1O2 (NMC811) configuration with Al2O3 and MoO3. The combined results from morphological examinations revealed the formation of uniform Al2O3 and MoO3 sheets after 200 cycles of PEALD coating. Consistent results from the XRD analysis demonstrate the Al2O3 and MoO3 artificial CEI can reduce the Li-Ni mixing. To shed light on the oxidation-reduction kinetic. The modified NMC811 structures with Al2O3 and MoO3 represented a remarkable improvement in terms of capacity retention. The coated cathode with Al2O3 clearly outperformed the modified configuration with MoO3 with reference to ionic conductivity, charge/discharge reversibility, and capacity retention. The promising results obtained in this study opened possibilities to synthesize the Ni-rich cathodes with boosted electrochemical performance. | Zilong Zhuang; Vijaykumar Jadhav; Seyedeh Banitaba; Sanaz Khademolqorani; Dayakar Gandlar; Fuming Zhang; Daniel Tan | Materials Science; Inorganic Chemistry; Energy; Coating Materials; Electrochemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f3c8573fdae147fa58cafe/original/tailoring-performance-of-the-li-ni0-8mn0-1co0-1o2-cathode-by-al2o3-and-mo-o3-artificial-cathode-electrolyte-interphase-cei-layers-through-plasma-enhanced-atomic-layer-deposition-peald-coating.pdf |
67522e12f9980725cf306f33 | 10.26434/chemrxiv-2024-547lt-v2 | Optical Properties of Phenylthiolate Capped CdS Nanoparticles | Using many-body perturbation theory we study the optical properties of phenylthiolate capped cadmium sulifde nanoparticles to understand the origin of the experimentally observed blueshift in those properties with decreasing particle size. We show that the absorption spectra predicted by many-body perturbation theory agree well with the experimentally measured spectra. The results of our calculations demonstrate that all low-energy excited-states correspond to a mixture of two fundamental types of excitations, intraligand and ligand to metal charge-transfer excitations. We find that for each excited-state the intraligand excitation contribution is dominant and that bright excited-states, corresponding to the clear peaks in the absorption spectra, have a larger ligand to metal charge-transfer contribution. There are no low-energy bulk-like excitons, excited-states for which both the hole and the excited-electron component are predominantly delocalised over the inorganic core of the particles. Phenylthiolate capped cadmium sulifde nanoparticles appear not to behave like the textbook cartoon picture of quantum dots. We speculate that the observed blueshift is the result of a combination of a Stark-like shift of the intraligand contribution modulated by a change in the charge of the inorganic core and the confinement of the excited electron component of the ligand to metal charge transfer contribution. | Eimear Madden; Martiijn Zwijnenburg | Theoretical and Computational Chemistry; Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Spectroscopy (Inorg.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67522e12f9980725cf306f33/original/optical-properties-of-phenylthiolate-capped-cd-s-nanoparticles.pdf |
60c75130702a9b22ae18bed7 | 10.26434/chemrxiv.13133465.v1 | Combined Graph/relational Database Management System for Calculated Chemical Reaction Pathway Data | Nowadays quantum chemical calculations are widely used to generate extensive datasets for machine learning applications, however, generally these sets only include information on equilibrium structures and some close conformers. Exploration of potential energy surface provides an important information on ground and transition states, but analysis of such data is complicated due to the number of possible reaction pathways. Here, we present RePathDB, a database system for managing 3D structural data for both ground and transition states resulted from quantum chemical calculations. Our tool allows to store, to assemble and to analyze reaction pathway data. It combines relational database CGR DB for handling compounds and reactions as molecular graphs with a graph database architecture for the pathway analysis by graph algorithms. Original Condensed Graph of Reaction Technology is used to store any chemical reaction as a single graph. | Timur Gimadiev; Ramil Nugmanov; Dinar Batyrshin; Timur Madzhidov; Satoshi Maeda; Pavel Sidorov; Alexandre Varnek | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75130702a9b22ae18bed7/original/combined-graph-relational-database-management-system-for-calculated-chemical-reaction-pathway-data.pdf |
60c7517f9abda23977f8dc0c | 10.26434/chemrxiv.13174415.v1 | Tumor Necrosis Factor Alpha Converting Enzyme (TACE) as Possible Therapeutic Target in SARS-CoV-2 Induced Acute Respiratory Distress Syndrome (ARDS) | <div>This study reveals, for the first time, that rosiglitazone and pioglitazone, two thiazolidinedione drugs already approved as therapeutic agents to treat type II diabetes, were found to bind favorably to tumor necrosis factor alpha converting enzyme catalytic site with highlighted binding features.</div><div><br /></div>This study suggests that rosiglitazone and pioglitazone, acting as TACE inhibitors agents might avoid or attenuate the hyperexcitability proteolytic activity state of TACE, represent a new potential therapeutic approach to treat SARS-CoV-2 infection-associated severe systemic inflammatory responses observed among severely or critically ill SARS-CoV-2 patients and, consequently, to diminish severe inflammatory‐induced lung injury, ARDS development and death rates.<br /><br /> | Joao Batista Junior | Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517f9abda23977f8dc0c/original/tumor-necrosis-factor-alpha-converting-enzyme-tace-as-possible-therapeutic-target-in-sars-co-v-2-induced-acute-respiratory-distress-syndrome-ards.pdf |
6412a1a82bfb3dc251d75d72 | 10.26434/chemrxiv-2023-z04vt | Stability and Metastability of Li3YCl6 and Li3HoCl6 | Metastable solid electrolytes exhibit superior conductivity compared to stable ones, making them a subject of considerable interest. However, solid-state synthesis of the metastable phase is affected by multiple thermodynamic and kinetic parameters, leading to ambiguity in the categorization of stability and metastability. This study categorizes remnant and intermediate metastability based on thermodynamic principles. The intermediate metastable phase, which is less stable than the temperature-independent stable phase, typically transforms into the stable phase(s) at high temperatures. In contrast, the remnant metastable phase, such as the high-temperature stable phase obtained by fast cooling, becomes the most stable phase, and annealing of the remnant metastable phase causes the phase transition to the low-temperature stable phase. Investigating Li+ conducting chlorides, Li3MCl6 (M = Y and Ho), this study shows that heating starting materials to approximately 600 K produced low-temperature Li3MCl6 phase with one formula unit; high-temperature Li3MCl6 with three formula units were observed by further heating. Annealing of quenched Li3MCl6 at 573 K resulted in a phase transition from high-temperature to low-temperature, indicating that the high-temperature phase was remnant metastable at low temperatures. XRD patterns of low-temperature phases suggest the presence of stacking faults that stabilize low-temperature structures with high symmetry. | Hiroaki Ito; Yuki Nakahira; Naoki Ishimatsu; Yosuke Goto; Aichi Yamashita; Yoshikazu Mizuguchi; Chikako Moriyoshi; Takashi Toyao; Ken-ichi Shimizu; Hiroshi Oike; Masanori Enoki; Nataly Carolina Rosero-Navarro; Akira Miura; Kiyoharu Tadanaga | Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6412a1a82bfb3dc251d75d72/original/stability-and-metastability-of-li3y-cl6-and-li3ho-cl6.pdf |
62a4ae38fe677d63174c1871 | 10.26434/chemrxiv-2022-chjjw | On-the-fly Non-adiabatic Dynamics Simulations of Single-Walled Carbon Nanotubes with Covalent Defects | Single-walled carbon nanotubes (SWCNTs) with covalent surface defects have been explored recently due to their promise for use in single-photon telecommunication emission and in spintronic applications. The dynamical evolution of excitons (the primary electronic excitations) in these systems has only been loosely explored due to the limitations of these large systems (> 300 atoms). We present computational modeling of non-radiative relaxation on a variety of SWCNT chiralities with single-defect functionalization schemes. Our modeling uses a trajectory surface hopping algorithm accounting for excitonic effects with a configuration interaction approach. We find a strong chirality and defect-composition dependence on the population relaxation (50 – 500 fs) between the nanotube band-gap excitation and the defect-associated, single-photon-emitting state, giving insight into the dynamic trapping nature of these localized excitonic states. Engineering fast population decay into the quasi-two-level sub-system with weak coupling to higher-energy states increases the effectiveness and controllability of these quantum light emitters. | Braden Weight; Andrew Sifain; Brendan Gifford; Han Htoon; Sergei Tretiak | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a4ae38fe677d63174c1871/original/on-the-fly-non-adiabatic-dynamics-simulations-of-single-walled-carbon-nanotubes-with-covalent-defects.pdf |
6396ab4992f084ccc531f764 | 10.26434/chemrxiv-2022-x3zhz | Low bandgap high entropy alloy for visible light-assisted photocatalytic degradation of pharmaceutically active compounds | The incessant accumulation of pharmaceutically active compounds (PhACs) in various environmental compartments represents a global menace. Herein, an equimolar and environmentally benign FeCoNiCuZn HEA is synthesized via a facile and scalable method, and its effectiveness in eliminating four different PhACs from aqueous matrices is rigorously examined. Attributing to its relatively low bandgap and multielement active sites, the as synthesized quinary HEA demonstrates more pronounced photocatalytic decomposition efficiency, towards tetracycline (86%), sulfamethoxazole (94%), ibuprofen (80%), and diclofenac (99%), than conventional semiconductor-based photocatalysts, under visible light irradiation. Additionally, radical trapping assays are conducted, and the dissociation intermediates are
identified, to probe the plausible photocatalytic degradation pathways. Further, the end-products of FeCoNiCuZn-mediated photocatalysis are eco-friendly, and the HEA can be successfully recycled repeatedly, with no obvious leaching of heavy metal ions. Overall, the findings of this study testify the applicability of FeCoNiCuZn HEA as a visible light-active photocatalyst, for treating wastewaters contaminated with PhACs. | Chandra Sekhar Tiwary; Shubhasikha Das; M Sanajy; Abhay Raj Singh Gautam; Rakesh Behera; Shamik Chowdhury | Materials Science; Earth, Space, and Environmental Chemistry; Catalysts; Materials Processing; Environmental Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6396ab4992f084ccc531f764/original/low-bandgap-high-entropy-alloy-for-visible-light-assisted-photocatalytic-degradation-of-pharmaceutically-active-compounds.pdf |
61139fdf424ea3baee878b4a | 10.26434/chemrxiv-2021-qt38v | Biodegradable Polyimidazole Particles as Contrast Agents produced by Direct Arylation Polymerization | Conjugated polymer particles provide an important platform for the development of theranostic nanoagents. However, the number of biocompatible and foremost biodegradable π-conjugated polymers is limited. Imidazole is a π-conjugated motif that is abundant in biological systems. Oxidative degradation of imidazole is present in nature via enzymatic or free radical processes. In this work, we introduce polymer particles consisting purely of polyimidazole. We employ direct arylation polymerization and adapt it to a dispersion polymerization protocol to yield uniform and narrowly dispersed nanoparticles. We employ this mechanism to produce linear and crosslinked polymer particles to tune the optical properties from fluorescent to photoacoustically active. We show that the particles can be degraded by H2O2 as well as by reactive oxygen species produced by cells and we detect the degradation products. Altogether our results suggest that polyimidazole particles represent ideal candidates for theranostic applications. | Felicitas Jansen; Philipp Schuster; Markus Lamla; Christian Trautwein; Alexander Kühne | Biological and Medicinal Chemistry; Materials Science; Polymer Science; Biodegradable Materials; Imaging Agents; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61139fdf424ea3baee878b4a/original/biodegradable-polyimidazole-particles-as-contrast-agents-produced-by-direct-arylation-polymerization.pdf |
62174ca891a2e63d99d9bd35 | 10.26434/chemrxiv-2021-8rtq4-v2 | Palladium Catalyzed Asymmetric Hydrophosphination of Internal Alkynes: Access to Phosphine-Functionalized Axially Chiral Olefins | Palladium-catalyzed unprecedented atroposelective hydrophosphination of sterically hindered internal alkynes with secondary phosphines has been realized, affording C-N axially chiral trisubstituted olefins (vinylphosphines) in excellent regioselectivity, (E)-selectivity, and enantioselectivity. The axial chirality was constructed via integration of hydrophosphination and dynamic kinetic transformation of the alkynes, with both symmetrical and nonsymmetrical secondary phosphines being applicable.
| Danqing Ji; Jierui Jing; Yi Wang; Zisong Qi; Fen Wang; Xingwei Li | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62174ca891a2e63d99d9bd35/original/palladium-catalyzed-asymmetric-hydrophosphination-of-internal-alkynes-access-to-phosphine-functionalized-axially-chiral-olefins.pdf |
60c73f1c337d6c6a66e264bd | 10.26434/chemrxiv.7243472.v1 | Modifying Methylalumoxane via Alkyl Exchange | Methylalumoxane (MAO) ionizes highly
selectively in the presence of octamethyltrisiloxane (OMTS) to generate [Me<sub>2</sub>Al∙OMTS]<sup>+</sup>
[(MeAlO)<sub>16</sub>(Me<sub>3</sub>Al)<sub>6</sub>Me]<sup>–</sup>. We can take
advantage of this transformation to examine the reactivity of a key component
of MAO using electrospray ionization mass spectrometry (ESI-MS), and here we
describe the reactivity of this pair of ions with other trialkyl aluminum (R<sub>3</sub>Al)
components. This alkyl exchange reaction bears relevance to the various
modified methylalumoxanes (MMAOs) available, which differ from regular MAO in
being adulterated with different alkyl groups. We found Et<sub>3</sub>Al to
exchange much faster and extensively (<i>t</i><sub>½</sub> ~ 2 sec, up
to 25 exchanges of Me for Et) than
<i>i</i>Bu<sub>3</sub>Al (<i>t</i><sub>½</sub> ~ 40 sec, up
to 11 exchanges) or Oct<sub>3</sub>Al (<i>t</i><sub>½</sub> ~ 200 sec, up
to 7 exchanges). The exchanges are reversible and the methyl groups on the
cation are also observed to exchange with the added R<sub>3</sub>Al species. These
studies are the first to offer concrete insights into the solution
transformations of MAO. | Harmen S. Zijlstra; Anuj Joshi; Mikko Linnolahti; Scott Collins; J Scott McIndoe | Mass Spectrometry; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Organometallic Compounds; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1c337d6c6a66e264bd/original/modifying-methylalumoxane-via-alkyl-exchange.pdf |
60c74a13469df404e0f43c9a | 10.26434/chemrxiv.12055389.v1 | Tri- and Tetrameric Proanthocyanidins with Dentin Bioactivities from Pinus massoniana | Guided by dentin biomechanical bioactivity, this phytochemical study led to the elucidation of an extended set of structurally demanding proanthocyanidins (PACs). Unambiguous structure determination involved detailed spectroscopic and chemical characterization of four A-type dimers (2, 4–6), seven trimers (10–16), and six tetramers (17–22). New outcomes confirm the feasibility of determining the absolute configuration of the catechol monomers in oligomeric PACs by 1D and 2D NMR. Electronic circular dichroism (ECD) as well as phloroglucinolysis followed by MS and chiral phase HPLC analysis generated the necessary chiral reference data. | Bin Zhou; Yvette Alania; Mariana Reis; Rasika Phansalkar; Joo-Won Nam; James McAlpine; Shao-Nong Chen; Ana K. Bedran-Russo; Guido Pauli | Natural Products; Organic Compounds and Functional Groups; Stereochemistry | CC BY 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a13469df404e0f43c9a/original/tri-and-tetrameric-proanthocyanidins-with-dentin-bioactivities-from-pinus-massoniana.pdf |
60c740a1bb8c1a56ae3d9e04 | 10.26434/chemrxiv.7269506.v3 | Atomic Layer Deposition of InN Using Trimethylindium and Ammonia Plasma | <div>InN is a low band gap, high electron mobility semiconductor material of interest to optoelectronics and telecommunication. Such applications require the deposition of uniform crystalline InN thin films on large area substrates, with deposition temperatures compatible with this temperature-sensitive material. As conventional chemical vapor deposition (CVD) struggles with the low temperature tolerated by the InN crystal, we hypothesize that a time-resolved, surface-controlled CVD route could offer a way</div><div>forward for InN thin film deposition. In this work, we report atomic layer deposition of crystalline, wurtzite InN thin films using trimethylindium and ammonia plasma on Si (100). We found a narrow ALD window of 240–260 °C with a deposition rate of 0.36 Å/cycle and that the flow of ammonia into the plasma is an important parameter for the crystalline quality of the film. X-ray photoelectron spectroscopy measurements shows nearly stoichiometric InN with low carbon level (< 1 atomic %) and oxygen level (< 5 atomic %) in the film bulk. The low carbon level is attributed to a favorable surface chemistry enabled by the NH<sub>3</sub> plasma. The film bulk oxygen content is attributed to oxidation upon exposure to air via grain boundary diffusion and possibly by formation of oxygen containing species in the plasma discharge.</div> | Petro Deminskyi; Polla Rouf; Ivan G. Ivanov; Henrik Pedersen | Materials Processing; Optical Materials; Thin Films; Organometallic Compounds; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a1bb8c1a56ae3d9e04/original/atomic-layer-deposition-of-in-n-using-trimethylindium-and-ammonia-plasma.pdf |
6100f7e47bf0c94886615fcb | 10.26434/chemrxiv-2021-278l6-v2 | Design, Synthesis and Biological Activity of 16,17-Dihydroheronamide C and ent-Heronamide C | 16,17-Dihydroheronamide C (8) and ent-heronamide C (ent-1) were designed as probes for the mode-of-action analysis of heronamide C (1). These molecules were synthesized by utilizing a highly modular strategy developed in the preceding paper. Evaluation of the antifungal activity of these compounds revealed the exceptional importance of the C16-C17 double bond for the biological activity of heronamide C, and the existence of chiral recognition between heronamide C (1) and cell membrane components. | Naoki Kanoh; Ryusei Terashima; Hiromichi Nishiyama; Yuta Terajima; Shota Nagasawa; Yusuke Sasano; Yoshiharu Iwabuchi; Hiroaki Saito; Syusuke Egoshi; Kosuke Dodo; Mikiko Sodeoka; Chengqian Pan; Yoshinobu Ikeuchi; Shinichi Nishimura; Hideaki Kakeya | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6100f7e47bf0c94886615fcb/original/design-synthesis-and-biological-activity-of-16-17-dihydroheronamide-c-and-ent-heronamide-c.pdf |
65325a5487198ede07e03211 | 10.26434/chemrxiv-2023-13w9r | Enhancing N-arylation Productivity:
The Amplified Potential of Electrophotocatalysis in Flow | The recent advances in the area of electrophotocatalysis (EPC) show that it is a highly suitable technique to yield greener and more sustainable organic synthesis. The overall productivity of EPC however is constrained by a multitude of practical limitations, which impose difficulties in effectively harmonizing the photochemical and electrochemical steps, let alone in accelerating both steps simultaneously. In this contribution, we have tackled these limitations by developing a parallel plate flow cell that permits the execution of EPC in continuous flow. By using a transparent electrode, such as fluorine-doped tin oxide (FTO) or indium tin oxide (ITO) coated glass, the interelectrode distance could be reduced while improving photon absorption. By enhancing both the photochemical and electrochemical steps simultaneously, a notable increase in productivity and space-time-yield (a ten-fold and 300-fold improvement, respectively) of the N-arylation of different azoles was observed. In addition, this was achieved in a single-pass process under electrolyte-free conditions. | Thomas Heugebaert; Jolien De Ketelaere | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Photochemistry (Org.); Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65325a5487198ede07e03211/original/enhancing-n-arylation-productivity-the-amplified-potential-of-electrophotocatalysis-in-flow.pdf |
612f7aeed5f0806b03b7fc44 | 10.26434/chemrxiv-2021-mbmq5 | Fluorescent Staining of Silicone Micro-and Nano-patterns for Their Optical Imaging | Performance of engineered surfaces can be enhanced by making them hydrophobic or superhydrophobic via coating them with low-surface-energy micro-and nano-patterns. However, the wetting phenomena of particularly irregular shape and spacing (super)hydrophobic patterns such as polysiloxane coatings are not yet fully understood from a microscopic perspective. Here, we show a new method to collect 3D confocal images from irregular polysiloxane micro-and nanorods from a single rod resolution to discuss their wetting response over long liquid/solid interaction times and quantify the length and diameter of these rods. To collect such 3D confocal images, fluorescent dye containing water droplets were left on our superhydrophobic and hydrophobic polysiloxane coated surfaces. Then their liquid/solid interfaces were imaged at different staining scenarios: (i) using different fluorescent dyes, (ii) when the droplets were in contact with surfaces, or (iii) after the droplets were taken away from the surface at the end of staining. Using such staining strategies, we could resolve the micro-and nanorods from root to top and determine their length and diameter, which were then found to be in good agreement with those obtained from their electron microscopy images. 3D confocal images in this paper, for the first time, present the long-time existence of more than one wetting state under the same droplet in contact with surfaces, as well as external and internal three-phase contact lines shifting and pinning. In the end, these findings were used to explain the time-dependent wetting kinetics of our surfaces. We believe that the proposed imaging strategy here will, in the future, be used to study many other irregular patterned (super)antiwetting surfaces to describe their wetting theory, which is today impossible due to the complicated surface geometry of these irregular patterns. | H. Samet Varol; Stefan Seeger | Physical Chemistry; Materials Science; Polymer Science; Dyes and Chromophores; Nanostructured Materials - Materials; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612f7aeed5f0806b03b7fc44/original/fluorescent-staining-of-silicone-micro-and-nano-patterns-for-their-optical-imaging.pdf |
639088a8836ceb7b7d76ff7b | 10.26434/chemrxiv-2022-6x97c | Click to learn, learn to click: Undergraduate Synthetic Organic Chemistry experiments | The optimization of an undergraduate experiment for Organic Chemistry students is described to explore the concept of click chemistry. The preparation of a terminal fluorescent alkyne and an organic azide is reported consisting of simple steps. These are employed in the Cu(I)-catalized azide-alkyne cycloaddition to obtain a novel molecule containing a triazole ring whose characterization allows the students to practice a variety of techniques: NMR (1H, 13C, COSY and HSQC), melting point, thin layer chromatography, IR, MS and fluorescence spectroscopy to confirm the structure of their obtained product. An alternative methodology in a one-pot reaction is also explored and a full laboratory manual provided. | Alejandro Lopez-Ruiz; Mariano Ortega-Muñoz; Francisco Santoyo-Gonzalez; Alicia Megia-Fernandez | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639088a8836ceb7b7d76ff7b/original/click-to-learn-learn-to-click-undergraduate-synthetic-organic-chemistry-experiments.pdf |
67d0cbf4fa469535b9eb9ae9 | 10.26434/chemrxiv-2025-hnwz1 | Comparative study on protocols to prepare slippery liquid-like PDMS coatings - pitfalls and time-savers | Slippery covalently attached liquid surfaces (SCALS, also called quasi-liquid surfaces, liquid-like surfaces, and slippery omniphobic covalently attached surfaces) have recently emerged as a new family of materials with many useful properties --- such as droplet-shedding, anti-icing, and anti-fouling --- and can serve as model systems in studies of wetting, evaporation, and self-assembly phenomena. They are made of nano-thin layers of polymers or oligomers that are liquid at ambient temperature and covalently attached to a smooth substrate. Herein we lay out protocols for preparation of the most common SCALS system: polydimethylsiloxane (PDMS) bound to silica surfaces via silane chemistry. The apparent simplicity of these layers and their methods of preparation is misleading, and obtaining reproducible results requires careful control of the reaction parameters. Exact details of the synthetic methods for SCALS determine the observed results, and reporting them is required for reproducibility and to advance understanding of the field. Here a range of synthetic methods used in the literature were reproduced in three different laboratories across the world, their comparative advantages and disadvantages discussed, and resulting SCALS characterised. For each synthetic method the key parameters that contribute to their performance and ease of reproducibility were identified and optimised. | Isaac J. Gresham; Hernan Barrio-Zhang; Jae Hyung Cho; Behrooz Khatir; Gary G. Wells; Kevin Golovin; Glen McHale; Chiara Neto | Physical Chemistry; Materials Science; Coating Materials; Thin Films; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d0cbf4fa469535b9eb9ae9/original/comparative-study-on-protocols-to-prepare-slippery-liquid-like-pdms-coatings-pitfalls-and-time-savers.pdf |
636a4ebcafea7fa1cf9b22c2 | 10.26434/chemrxiv-2022-dj8mv | Near-Infrared Photoredox Catalyzed Tryptophan Functionalization for Peptide Stapling and Protein Labeling in Complex Tissue Environments | The chemical transformation of aromatic amino acids has emerged as an attractive alternative to non-selective lysine or cysteine labeling for the modification of biomolecules. However, this strategy has largely been limited by the scope of functional groups and biocompatible reaction conditions available. Herein, we report the implementation of near-infrared-activatable photocatalysts, TTMAPP and n-Pr-DMQA+, capable of generating fluoroalkyl radicals for selective tryptophan functionalization within simple and complex biological systems. At the peptide level, a diverse set of iodo-perfluoroalkyl reagents were used to install bioorthogonal handles for downstream applications or link inter- or intramolecular tryptophan residues for peptide stapling. We also found this photoredox transformation amenable to biotinylation of intracellular proteins in live cells for downstream confocal imaging and mass spectrometry-based analysis. Given the inherent tissue penetrant nature of near-infrared light we further demonstrated the utility of this technology to achieve photocatalytic protein fluoroalkylation in physiologically relevant tissue and tumor environments. | Keun Ah Ryu; Tamara Reyes-Robles; Thomas P. Wyche; Tyler J. Bechtel; Jayde M. Bertoch; Jin Zhuang; Christopher May; Sharon Wilhelm; Ishtiaque Quasem; Annika Yau; Sampat Ingale; Andrew Szendrey; Margaret Duich; Rob C. Oslund; Olugbeminiyi O. Fadeyi | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636a4ebcafea7fa1cf9b22c2/original/near-infrared-photoredox-catalyzed-tryptophan-functionalization-for-peptide-stapling-and-protein-labeling-in-complex-tissue-environments.pdf |
677310fbfa469535b949f611 | 10.26434/chemrxiv-2025-x6t1z | Fundamental acoustic vibrations in nanoscale aluminum coatings. | The proper design of optical nanoscale devises, such as Fabry-Perot interferometers used for polariton construction, relies on scientists and engineers understanding the fundamental physical properties of metallic coatings. While properties such as the extinction coefficient, refractive index, and skin depth are well understood and have been modeled for many metals, acoustic phonon vibrations within metallic films at nanoscale thicknesses have only recently become a topic of discussion within the optical community. This is largely because the observance of acoustic phonon vibrations in thin films is relegated to having an impact on ultrafast transient spectroscopy, which has only become a major research tool over the past few decades. Through this manuscript the optical properties of aluminum thin films is discussed. It is determined that the period of the phonon vibration has a linear relationship to film thickness. A formalism relating phonon period to film thickness via the speed of sound is introduced, and it is shown to closely match with the well-stablished Debye equation used to model phonon vibrations. | Aleksandr Avramenko | Physical Chemistry; Materials Science; Thin Films; Optics; Quasiparticles and Excitations | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677310fbfa469535b949f611/original/fundamental-acoustic-vibrations-in-nanoscale-aluminum-coatings.pdf |
6406dd1ccc600523a3c8e4ca | 10.26434/chemrxiv-2023-qfsdc | Constructing Narrowband Heavy Metal Platinum (II) Complex by Integrating Multiple Resonance Molecular System | The narrowband emission required by wide color gamut display is an extremely important research topic for any luminescence mechanism, which has made significant progress in traditional fluorescence and thermally activated delayed fluorescence (TADF) based on purely organic compounds, but is far from mature in phosphorescence based on metal organic complexes. Herein, we propose a feasible molecular design paradigm for constructing the desirable narrowband-emission organic electroluminescence (EL) emitter by integrating an original multi-resonance thermally activated delayed fluorescent (MR-TADF) fragment into the classical heavy metal platinum (II) complex. The target model platinum (II) complex BNCPPt shows green emission with a single peak at 497 nm and the quite narrow full-width at half-maximum (FWHM) of 27 nm in toluene. | Yu Feng; Xuming Zhuang; Yincai Xu; Jianan Xue; Qingyang Wang; Yu Liu; Yue Wang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6406dd1ccc600523a3c8e4ca/original/constructing-narrowband-heavy-metal-platinum-ii-complex-by-integrating-multiple-resonance-molecular-system.pdf |
60c73dfd702a9bafd9189c98 | 10.26434/chemrxiv.5370778.v2 | Kinetic Solvent Effects in Organic Reactions | <div>
<div>
<div>
<p>This article reviews prior work studying reaction kinetics in solution, with the goal
of using this information to improve detailed kinetic modeling in the solvent phase.
Both experimental and computational methods for calculating reaction rates in liquids
are reviewed. Previous studies, which used such methods to determine solvent effects,
are then analyzed based on reaction family. Many of these studies correlate kinetic
solvent effect with one or more solvent parameters or properties of reacting species,
but it is not always possible, and investigations are usually done on too few reactions
and solvents to truly generalize. From these studies, we present suggestions on how
best to use data to generalize solvent effects for many different reaction types in a high
throughput manner. </p>
</div>
</div>
</div> | Belinda Slakman; Richard West | Chemical Kinetics; Solution Chemistry | CC BY 4.0 | CHEMRXIV | 2018-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dfd702a9bafd9189c98/original/kinetic-solvent-effects-in-organic-reactions.pdf |
60c749cbbdbb89be07a3925a | 10.26434/chemrxiv.12107010.v1 | (2-Fluoroallyl)palladium Complexes as Intermediates in Pd-Catalyzed Tsuji-Trost 2-Fluoroallylations: Synthesis and Reactivity | The first examples of (2-fluoroallyl)palladium complexes were synthesized, isolated and characterized including chloride dimers, neutral chloride and ionic triflate complexes bearing PPh<sub>3</sub> or SPhos as the ligands. Preliminary reactivity patterns indicating strong dependence of the chemoselectivity on "hardness" of the nucleophile and the ligand type were studied.<br /> | Angelina Yu. Bobrova; Maxim Novikov; Igor A. Mezentsev; Yury V. Tomilov | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749cbbdbb89be07a3925a/original/2-fluoroallyl-palladium-complexes-as-intermediates-in-pd-catalyzed-tsuji-trost-2-fluoroallylations-synthesis-and-reactivity.pdf |
642afbd5a029a26b4cdb19b3 | 10.26434/chemrxiv-2023-2gt6z | Mechanism of Stoichiometrically Governed Titanium Oxide Brownian Tree Formation on Stepped Au(111) | Previously observed formation of sub-stoichiometric titanium oxide dendritic
structures across terraces of Au(111) are computationally studied and shown to follow the
classical fractal formation mechanism of diffusion limited aggregation (DLA). Globally
optimized gas-phase oxide cluster structures were sampled in a variety of landing formations on
gold surfaces and shown to favor isomers driving polymerization to Brownian tree fractal
structures. Mobility of Ti3O5 monomers is shown to be extremely high, with diffusion barriers of
0.21 eV or less. Through bonding stabilization, polymerization of these monomers is
energetically favorable and irreversible on the 111 terrace, but geometrically impossible to
propagate along the step edge. Simulated STM images show strong similarity to experiment. By
contrast, observation of Ti3O6 aggregating as wires along step edges is explained by affinity of
oxygen to step edges and statistical arguments for aggregation entropy at the step, in addition to
low barriers for monomer diffusion and polymerization. | Robert H. Lavroff; Jason Wang; Michael G. White; Philippe Sautet; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642afbd5a029a26b4cdb19b3/original/mechanism-of-stoichiometrically-governed-titanium-oxide-brownian-tree-formation-on-stepped-au-111.pdf |
66525f2591aefa6ce1fe0c2d | 10.26434/chemrxiv-2024-pcdp4 | Zinc and manganese redox potentials in organic solvents and their influence on nickel-catalyzed cross-electrophile coupling | Zinc and manganese are widely used as reductants in synthetic methods, such as nickel-catalyzed cross-electrophile coupling (XEC) reactions, but their redox potentials are unknown in organic solvents. Here, we show how open-circuit potential measurements may be used to determine the thermodynamic potentials of Zn and Mn in different organic solvents and in the presence of common reaction additives. The impact of these Zn and Mn potentials is analyzed for a pair of Ni-catalyzed reactions, each showing a preference for one of the two reductants. Ni-catalyzed coupling of N-alkyl-2,4,6-triphenylpyridinium reagents (Katritzky salts) with aryl halides are then compared under chemical reaction conditions, using Zn or Mn reductants, and under electrochemical conditions, performed at applied potentials corresponding to the Zn and Mn reduction potentials and at potentials optimized to achieve the maximum yield. The collective results illuminate the important role of reductant redox potential in Ni-catalyzed XEC reactions. | Zhi-Ming Su; Ruohan Deng; Shannon Stahl | Organic Chemistry; Catalysis; Organometallic Chemistry; Electrocatalysis; Electrochemistry - Organometallic; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66525f2591aefa6ce1fe0c2d/original/zinc-and-manganese-redox-potentials-in-organic-solvents-and-their-influence-on-nickel-catalyzed-cross-electrophile-coupling.pdf |
60c756e2842e65857bdb459e | 10.26434/chemrxiv.14343743.v1 | SARS-CoV-2 VOCs Immune Evasion from Previously Elicited Neutralizing Antibodies Is Mainly Driven by Lower Cross-Reactivity Due to Spike RBD Electrostatic Surface Changes | <div>
<div>
<div>
<p>Leveraging structural data and computer modelling techniques, we
investigated the variation in the binding free-energy (𝛥𝛥𝐺) profile of VOCs and VOIs
SARS-CoV-2 lineages with hACE2 and with a dataset of known human nAbs. In
agreement with the available experimental data, our results show only a marginal
impact of VOC RBD amino acid changes to hACE2 affinity. On the other hand, we found
that VOCs RBDs have a significant unfavorable 𝛥𝛥𝐺 to nAbs that can be related to
changes in the electrostatic potential surface profiles, hence identifying the molecular
and thermodynamical components behind SARS-CoV-2 antibody evasion. In addition,
our data suggests that a close attention should be given to lineage P.3, as it likely holds
a high spreading potential in a human population with rising immunity. In summary,
the current observed higher transmission of SARS-CoV-2 VOCs is likely associated with
a partial or complete failure of the antibody recognition and neutralization in
individuals previously exposed to SARS-CoV-2 non-VOC variants. These results have
key implications on i. the basic understanding of VOCs emergence and maintenance;
ii. on the rational design of antibody-based therapeutics; iii. vaccine efficacy and
updates; and iv. may be exploited to rapidly screen immune scape worrisome lineages.
</p>
</div>
</div>
</div> | Matheus Ferraz; EMERSON MOREIRA; Danilo F. Coêlho; Gabriel Wallau; Roberto Lins | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e2842e65857bdb459e/original/sars-co-v-2-vo-cs-immune-evasion-from-previously-elicited-neutralizing-antibodies-is-mainly-driven-by-lower-cross-reactivity-due-to-spike-rbd-electrostatic-surface-changes.pdf |
60c74377ee301c7976c78ff6 | 10.26434/chemrxiv.9209213.v1 | BOKEI: Bayesian Optimization Using Knowledge of Correlated Torsions and Expected Improvement for Conformer Generation | <div>A key challenge in conformer sampling is to find low-energy conformations with a small number of energy evaluations. We have recently demonstrated Bayesian optimization as an effective method to search for energetically favorable conformations. This approach balances between <i>exploitation</i> and <i>exploration</i>, and lead to superior performance when compared to exhaustive or random search methods. In this work, we extend strategies on proteins and oligopeptides (e.g. Ramachandran plots of secondary structure) to study the correlated torsions in small molecules. We use a bivariate von Mises distribution to capture the correlations, and use it to constrain the search space. We validate the performance of our Bayesian optimization with prior knowledge (BOKEI) on a dataset consisting of 533 diverse small organic molecules, using a force field (MMFF94) and a semi empirical method (GFN2). We compare BOKEI with Bayesian optimization with expected improvement (BOA-EI), and a genetic algorithm (GA), using a fixed number of energy evaluations. In 70(± 2.1)% of the cases examined, BOKEI finds lower energy conformations than global optimization with BOA-EI or GA. More importantly, these patterns find correlated torsions in 10-15% of molecules in larger data sets, 3-8 times more frequently than previous work. We also find that the BOKEI patterns not only describe steric clashes, but also reflect favorable intramolecular interactions, including hydrogen bonds and π-π stacking. Further understanding of the conformational preferences of molecules will help find low energy conformers efficiently for a wide range of computational modeling applications.</div> | Lucian Chan; Geoffrey Hutchison; Garrett Morris | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74377ee301c7976c78ff6/original/bokei-bayesian-optimization-using-knowledge-of-correlated-torsions-and-expected-improvement-for-conformer-generation.pdf |
61f8ef1dc18d67d7758b9be9 | 10.26434/chemrxiv-2022-x2qxq | A Comparative Evaluation of Indirect Sequence-Specific Magnetoextraction-aided Fluorescence and Electrochemical LAMP with SARS-CoV-2 Nucleic Acid as the Analyte | Since the beginning of the SARS-CoV-2 pandemic, nucleic acid amplification test (NAAT) such as quantitative real-time reverse transcriptase PCR (qRT-PCR) has remained the primary intervention for diagnostics and containment of SARS-CoV-2. Despite its remarkable clinical as well as analytical specificity and sensitivity, qRT-PCR necessitates pure nucleic acid free of any polymerase inhibitors (from complex biological matrices) as its substrate. Similarly, isothermal NAATs (iNAATs), despite their advantage over qRT-PCR in terms of thermal cycler independence, still require pure nucleic acid as a template. The requirement of pure nucleic acid in turn warrants the use of spin-column mediated extraction with centralized high-speed centrifuges. Additionally, utilization of centralized real-time fluorescence readout and use of sequence-specific molecular probes like TaqMan further prevent their deployment in decentralized locations. To circumvent these disadvantages, we have envisioned a sample-to-answer workflow comprising of indirect sequence-specific magneto-extraction (also referred to as magnetocapture, magneto-preconcentration, or magneto-enrichment in this manuscript) followed by in situ fluorescence or electrochemical LAMP. This study, using SARS-CoV-2 nucleic acid as the analyte, compared the analytical effectiveness of indirect and direct sequence-specific magneto-extraction followed by LAMP. Since contamination carryover may affect the efficacy of sequence-specific indirect magnetocapture, its performance in presence of excess host nucleic acid or serum was probed. Through these experiments, we have established a comprehensive limited resource-adoptable and highly specific nucleic acid detection method with the limit of detection of 2.5 copies/L. Its advantage lies in the flexibility of using either centralized real-time SYBR-based fluorescence LAMP or portable electrochemical LAMP as the readout. Simultaneously, the performance with magneto-capture aided fluorescence and electrochemical LAMP readouts were weighed against each other in terms of analytical sensitivity, specificity, and turnaround time. Additionally, the analytical efficacy of the magnetocapture-LAMP workflow was also checked against that of LAMP using pure nucleic acid as a template. Besides being the first report utilizing electrochemical LAMP to detect SARS-CoV-2 nucleic acid, this would probably be the first study to make the analytical comparative assessment of magnetic preconcentration combined with in situ fluorescence and electrochemical LAMP. It is probably also the first study (to the best of our knowledge) to compare the analytical efficacy of a sequence-specific magnetic target enrichment-LAMP (fluorescence and electrochemical) to that of a LAMP assay using pure nucleic acid as a template. | Sayantan Tripathy; Tanvi Agarkar; Arunansu Talukdar; Mrittika Sengupta; Ashvani Kumar; Souradyuti Ghosh | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Electrochemical Analysis; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f8ef1dc18d67d7758b9be9/original/a-comparative-evaluation-of-indirect-sequence-specific-magnetoextraction-aided-fluorescence-and-electrochemical-lamp-with-sars-co-v-2-nucleic-acid-as-the-analyte.pdf |
627d278a6b12b6fe066fb1f2 | 10.26434/chemrxiv-2022-04jdf | The origin of delayed polymorphism in molecular crystals under mechanochemical conditions | Control over ball milling transformations is needed before the transformative potential of mechanochemical processing can be realized. Many parameters are known to affect the outcome of mechanochemical polymorphism, yet the energy of ball milling is itself often overlooked. We here demonstrate how milling energy can exert significant influence over the polymorphic outcome of ball mill grinding and be used to control the overall reaction profile. Milling energy exerts its effect on the reaction profile by changing the rate at which structural defects form in crystalline phases. These defects destabilize a crystal to drive the system step-by-step towards polymorphic transformation. Our results demonstrate decisively that careful design and interpretation of ball milling experiments are necessary to obtain control over mechanochemical polymorphism | Kevin Linberg; Paulina Szymoniak; Andreas Schonhals; Franziska Emmerling; Adam Michalchuk | Physical Chemistry; Physical and Chemical Processes; Structure; Materials Chemistry; Crystallography | CC BY NC 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d278a6b12b6fe066fb1f2/original/the-origin-of-delayed-polymorphism-in-molecular-crystals-under-mechanochemical-conditions.pdf |
62e2997a64068dd90aea8168 | 10.26434/chemrxiv-2022-0chcd | Preferred Experimental Practices for Photocatalytic Nitrogen Fixation | Ammonia is synthesized through the Haber-Bosch process, and has the highest carbon footprint of any synthetic chemical commodity. This prompts the need for green alternatives to meet net-zero goals in the chemical sector. Photocatalytic conversion of nitrogen to ammonia is one such alternative gaining attention. The current progress in photocatalytic nitrogen reduction suggests, however, that there exists a large gap in performance, before commercial use is viable. One of the major challenges is that highly active photocatalysts have not yet been developed. Furthermore, the development of photocatalysts is greatly hindered by false positive or non-reproducible data. This is because the current photocatalyst produce very low ammonia concentration, therefore the ammonia measurement can be easily affected by adventitious ammonia from the environment. Here, we will describe the current known causes of non-reproducible results in photocatalytic nitrogen fixation literature. We also will present the solution to mitigate these false positive results. Finally, we highlight the main challenges that remain to be overcome in this field. We aim to help researchers design more reliable experiments and inspire practical research in developing photocatalytic nitrogen fixation. | Po-Wei Huang; Marta Hatzell | Catalysis; Electrocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e2997a64068dd90aea8168/original/preferred-experimental-practices-for-photocatalytic-nitrogen-fixation.pdf |
60c74e42337d6ce58ee27f5b | 10.26434/chemrxiv.12730964.v1 | A Stable Cathode-Solid Electrolyte Composite for Long-Cycle-Life, High Voltage Solid-State Sodium-ion Batteries | <p>Rechargeable
solid-state sodium-ion batteries (SSSBs) hold great promise for safer and more energy-dense
energy storage. However, the poor electrochemical stability between current sulfide-based
solid electrolytes and high-voltage oxide cathodes has limited their long-term
cycling performance and practicality. Here, we report the discovery of Na<sub>3-<i>x</i></sub>Y<sub>1-<i>x</i></sub>Zr<i><sub>x</sub></i>Cl<sub>6</sub>
(NYZC) as an ion conductor that is both electrochemically stable (up to 3.8 V
vs. Na/Na<sup>+</sup>) and chemically compatible with oxide cathodes. Its high ionic
conductivity of 6.6 x 10<sup>-5</sup> S cm<sup>-1</sup><sub> </sub>at ambient temperature,
several orders of magnitude higher than oxide coatings, is attributed to
abundant Na vacancies and cooperative MCl<sub>6</sub> rotation, resulting in an
extremely low interfacial impedance. A SSSB comprising a NaCrO<sub>2</sub>+NYZC
composite cathode, Na<sub>3</sub>PS<sub>4</sub> electrolyte, and Na-Sn anode
exhibits an exceptional first-cycle Coulombic efficiency of 97.1% at room
temperature and can cycle over 1000 cycles with 89.3% capacity retention at 40°C. These findings
highlight the immense potential of halide ion conductors for SSSB applications.</p> | Erik Wu; Swastika Banerjee; HANMEI TANG; Peter M. Richardson; Jean-Marie Doux; Ji Qi; Zhuoying Zhu; Antonin Grenier; Yixuan Li; Enyue Zhao; Grayson Deysher; Han Nguyen; Ryan Stephens; Guy Verbist; Karena W. Chapman; Raphaële J. Clément; Abhik Banerjee; Ying Shirley Meng; Shyue Ping Ong | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e42337d6ce58ee27f5b/original/a-stable-cathode-solid-electrolyte-composite-for-long-cycle-life-high-voltage-solid-state-sodium-ion-batteries.pdf |
60c759a7702a9b379d18cf24 | 10.26434/chemrxiv.14717349.v1 | CSI-LSTM: A Web Server to Predict Protein Secondary Structure Using Bidirectional Long Short Term Memory and NMR Chemical Shifts | The description and understanding of protein
structure rely on secondary structure heavily. Secondary structure
determination and prediction are widely used in protein structure related
research. The secondary structure prediction methods based on NMR chemical
shifts are convenient to use, so they are popular in protein NMR research. In
recent years, there is significant improvement in deep neural network, which is
consequently applied in many search fields. Here we proposed a deep neural
network based on bidirectional long short term memory (biLSTM) to predict
protein 3-state secondary structure using NMR chemical shifts of backbone
nuclei. Compared with the existing methods of the same sort, the accuracy of
the proposed method was improved. And a web server was built to provide
secondary structure prediction service using this method. | Zhiwei Miao; Qianqian Wang; Xiongjie Xiao; Linhong Song; Xu Zhang; Conggang Li; Xin Zhou; Bin Jiang; Maili Liu; 滨 蒋 | Biochemical Analysis; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759a7702a9b379d18cf24/original/csi-lstm-a-web-server-to-predict-protein-secondary-structure-using-bidirectional-long-short-term-memory-and-nmr-chemical-shifts.pdf |
60c750d2ee301c7974c7a938 | 10.26434/chemrxiv.13055873.v2 | Specific and Rapid SARS-CoV-2 Identification Based on LC-MS/MS Analysis | This study describes the development of a novel assay for SARS-CoV-2
identification using LC-MS/MS analysis. A multi-step procedure for the rational
down-selection of a set of markers has leaded to the discovery of six
SARS-CoV-2 specific and sensitive markers, enabling the reliable identification
of the virus. A rapid and simple assay was developed, successfully applied to
clinical nasopharyngeal samples. The assay may potentially serve as a
complementary approach for SARS-CoV-2 identification. | Ofir Schuster; Anat Zvi; Osnat Rosen; Hagit Achdout; Amir Ben-Shmuel; Ohad Shifman; Shmuel Yitzhaki; Orly Laskar; Liron Feldberg | Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750d2ee301c7974c7a938/original/specific-and-rapid-sars-co-v-2-identification-based-on-lc-ms-ms-analysis.pdf |
65d9001de9ebbb4db913a260 | 10.26434/chemrxiv-2024-n10tr-v3 | Monte Carlo simulations of water pollutant adsorption at parts-per-billion concentration: A study on 1,4-dioxane | 1,4-dioxane is an emerging water pollutant with high production volumes and a probable human carcinogen. The inadequacy of conventional treatment processes demonstrates a need for an effective remediation strategy. Crystalline nanoporous materials are cost-effective adsorbents due to their high capacity and selective separation in mixtures. This study explores the potential of all-silica zeolites for separation of 1,4-dioxane from water. These zeolites are highly hydrophobic and can preferentially adsorb nonpolar molecules from mixtures. We investigated six zeolite frameworks (BEA, EUO, FER, IFR, MFI, MOR) using Monte Carlo simulations in the Gibbs ensemble. The simulations indicate high selectivity by FER and EUO, especially at low pressures, which we attribute to pore sizes and shapes with more affinity to 1,4-dioxane. We also demonstrate a Monte Carlo simulation workflow using gauge cells to model the adsorption of an aqueous solution of 1,4-dioxane at 0.35 ppb concentration. We quantify 1,4-dioxane and water coadsorption, and observe selectivities ranging from 1.1 x 10^5 in MOR to 8.7 x 10^6 in FER. We also demonstrate that 1,4-dioxane is in the infinite dilution regime in both the aqueous and adsorbed phases at this concentration. This simulation technique can be extended to model other emerging water contaminants such as per- and polyfluoroalkyl substances (PFAS), chlorofluorocarbons, and others, which are also found in extremely low concentrations. | Samiha Sharlin; Rodrigo Lozano; Tyler R. Josephson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d9001de9ebbb4db913a260/original/monte-carlo-simulations-of-water-pollutant-adsorption-at-parts-per-billion-concentration-a-study-on-1-4-dioxane.pdf |
6447b80383fa35f8f63921de | 10.26434/chemrxiv-2023-gb366 | EVOLVE: An Evolutionary Toolbox for the Design of Peptides and Proteins | We report the development and application of a versatile evolutionary algorithm toolbox (EVOLVE) targeted at the engineering and optimisation of peptides and proteins via atomistic simulation. As a benchmark study, we have applied the singleobjective genetic algorithm within EVOLVE to a prototypical 20 amino acid long alpha-helix, ALA6-X8-ALA6, where the sequence of the central eight amino acids (X) has been optimised in di erent chemical environments. The tness function driving the optimisation is based on a molecular mechanics evaluation of the energy of a given sequence with respect to a reference homo-ALA helix, coupled with implicit solvent corrections. The simulations performed show EVOLVE consistently converges to low-energy solutions in a vast search space of 177^8 = ca. 10^17 possible sequences and side chain conformations, and relatively few iterations are required to reach these near-optimal structures. In all environments, the identi ed optimal sequences of the alpha-helices are considerably more stable than all possible homo-helices, and thus go
beyond what is accessible via exfoliative enumeration. | Nicholas J. Browning; Marta A.S. Perez; Elizabeth Brunk; Ursula Rothlisberger | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6447b80383fa35f8f63921de/original/evolve-an-evolutionary-toolbox-for-the-design-of-peptides-and-proteins.pdf |
637a89cf20798134fe2e6586 | 10.26434/chemrxiv-2022-x7llq | Glass-Ceramic Sodium-Deficient Chlorides with High Sodium-ion Conductivity | Solid-state batteries are a promising energy storage technology that can potentially offer both improved safety and energy density. The solid electrolyte is the defining feature and plays a significant role in the electrochemical performance of a solid-state cell, especially at room temperature. Herein, we report a series of glass-ceramic, sodium-deficient chloride solid electrolytes, NaxY0.25Zr0.75Cl3.75+x (0.25 x 0.875), possessing significantly improved ionic conductivities when compared to their stoichiometric counterpart, Na2.25Y0.25Zr0.75Cl6 (x = 2.25). By tuning both the sodium molar content and the sample’s crystallinity, the composition Na0.625Y0.25Zr0.75Cl4.375 (x = 0.625) was found to exhibit the highest Na+ conductivity of 0.4 mS cm−1 at room temperature. Furthermore, the relationship between composition, structure, and conductivity for these compositions in the NaCl−YCl3−ZrCl4 system was evaluated using a combination of X-ray diffraction (XRD), solid-state nuclear magnetic resonance spectroscopy (ss-NMR), and electrochemical impedance spectroscopy (EIS) techniques. Materials characterization reveals that sodium-deficiency (i.e., lower molar % of NaCl) results in reduced crystallinity and preferred occupancy of prismatic Na local environments. These combined factors contribute to a lower activation energy for Na+ hopping, an increased ionic conductivity, and improved electrochemical performance at both higher cycling rates and at room temperature. | Phillip Ridley; Long Hoang Bao Nguyen; Elias Sebti; George Duong; Yu-Ting Chen; Baharak Sayahpour; Ashley Cronk; Grayson Deysher; So-Yeon Ham; Jin An Sam Oh; Erik A. Wu; Darren H. S. Tan; Jean-Marie Doux; Raphaële Clément; Jihyun Jang; Ying Shirley Meng | Materials Science; Inorganic Chemistry; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637a89cf20798134fe2e6586/original/glass-ceramic-sodium-deficient-chlorides-with-high-sodium-ion-conductivity.pdf |
66b4887d01103d79c52dd269 | 10.26434/chemrxiv-2024-n085z-v2 | A new view of missense mutations in
α-mannosidosis using molecular dynamics
conformational ensembles | The mutation of remote positions on enzyme scaffolds and how these residue changes
can affect enzyme catalysis is still far from being fully understood. One paradigmatic
example is the group of lysosomal storage disorders, where the enzyme activity of a
lysosomal enzyme is abolished or severity reduced. In this work, we analyze molec-
ular dynamics simulation conformational ensembles to unveil the molecular features
controlling the deleterious effects of the 43 reported missense mutations in the human
lysosomal α-mannosidase. Using residue descriptors for protein dynamics, their cou-
pling with the active site, and their impact on protein stability, we have assigned the
contribution of each of the missense mutations into these three categories. We demon-
strate here that the use of conformational ensembles is a powerful approach not only
to better understand missense mutations at the molecular level, but to revisit the mis-
sense mutations reported in lysosomal storage disorders in order to aid the treatment
of these diseases. | Spela Mandl; Bruno Di Geronimo; Santiago Alonso-Gil; Gibu George; Ulrika Ferstl; Sereina Annik Herzog; Bojan Zagrovic; Christoph Nusshold; Pedro Alejandro Sánchez-Murcia | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b4887d01103d79c52dd269/original/a-new-view-of-missense-mutations-in-mannosidosis-using-molecular-dynamics-conformational-ensembles.pdf |
65c1934066c13817290c1589 | 10.26434/chemrxiv-2024-0tnfr | N-Phenyl-2-Pyridone-Derived Endoperoxide Exhibiting Dual Activity by Suppressing both Lung Cancer and Idiopathic Pulmonary Fibrosis | Conventional light-driven photodynamic therapy (PDT) to generate toxic singlet oxygen are potential for cancer therapeutics but limited by the light penetrability and hypoxia tumor. PDT-involved combinational therapy could enhance overall therapeutic effects and reduce drug resistance, while disadvantages such as diverse pharmacokinetics among different ingredients, low active-ingredient loading, inevitably utilization of non-functional components need to be addressed. Here we report an endoperoxide E5 synthesized via ‘in vitro’ PDT could spontaneously deliver singlet oxygen, triplet oxygen and 3-methyl-N-phenyl-2-pyridone as an analogue of pirfenidone (Approved drug for treatment of idiopathic pulmonary fibrosis), showing great potential for treating non-small cell lung cancer and idiopathic pulmonary fibrosis. In aqueous solution, E5 could undergo a clear cycloreversion to afford three components with a half-life time of 8.3 hours and it efficiently suppress the migration and invasion of lung cancer cell as well as the TGF-b1 induced fibrosis in vitro. In vivo experiments suggest that E5 not only efficiently inhibits tumor growth, decreases the HIF-1α protein levels, relieves idiopathic pulmonary fibrosis, but shows good biocompatibility. Many evidence reveal that both singlet oxygen and 3-methyl-N-phenyl-2-pyridone are therapeutic ingredients, and triplet oxygen could relieve tumor hypoxia which is an inevitable issue in conventional PDT. Our study validates that endoperoxides as single active components containing multiple ingredients including singlet oxygen are of exceptionally therapeutic potential. | Lei Wang; Hao Wu; Ziang Liu; Yanping Li; Yu Si; Rensong Sun; Yun Nie; Yuan Qiao; Xiao Qian; Shengli Zhang; Wen Sun; Yue Pan; Engin U. Akkaya | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c1934066c13817290c1589/original/n-phenyl-2-pyridone-derived-endoperoxide-exhibiting-dual-activity-by-suppressing-both-lung-cancer-and-idiopathic-pulmonary-fibrosis.pdf |
6418cd112bfb3dc2511659d2 | 10.26434/chemrxiv-2023-mmkfg | Adhesive Release via Elasto-Osmotic Stress Driven Surface Instability | Recent studies demonstrated that an elastomer containing hygroscopic inclusions absorbs moisture and swell. Here we show that a thin film of such an elastomer bonded to a rigid substrate undergoes morphological instability upon absorption of water, the wavelength of which increases linearly with its thickness. As the driving force for such a morphological instability arises from the difference of the chemical potential of water between its source and that in the film, its development is slowed down as the salinity of the water increases. Nonetheless, the wavelength of the fully developed morphology, but not its amplitude, is independent of the salinity. We also demonstrate that if a domed disk-shaped adherent is attached to the hygro-elastomeric film before moisture absorption, the elastic force generated during the morphological transition is able to dislodge it completely without the need of any external force. These patterns, once developed in pure water, is subdued when the salinity of water increases or if it is exposed to dry air. They re-emerge when the film is immersed in water again. Such an active response could be important in fouling release when a ship coated with such a hygro-elastomer changes its location during its long travel through sea, where salinity varies from place to place. | Khulood Al-sakkaf; Monicka Kullappan; Manoj Chaudhury | Materials Science; Polymer Science; Controlled-Release Systems; Elastic Materials; Thin Films | CC BY 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6418cd112bfb3dc2511659d2/original/adhesive-release-via-elasto-osmotic-stress-driven-surface-instability.pdf |
60c74f47469df41cddf44666 | 10.26434/chemrxiv.12885407.v1 | Activatable Superparamagnetic Iron Oxide Nanoparticles Scavenge Reactive Oxygen Species in Macrophages and Endothelial Cells | <p>This study centers around diagnostic medicine, and severity staging of inflammatory diseases. Previously,
we showed that complexation of PEG and Poly(gallol) on superparamagnetic iron
oxide nanoparticles turn OFF the MRI contrasting ability of the nanoparticle.
However, in the presence of reactive oxygen species, the contrast agent will
turn ON. In this article, for the first time, we provide evidence that our MRI
contrast agent is sensitive to physiologically relevant ROS and induces
antioxidant activity on immune and endothelial cells. This study provides
initial evidence of IPC-SPIOs cellular ROS sensitivity and potential activatable
properties in biological conditions.</p> | Chukwuazam Nwasike; Eunsoo Yoo; Erin Purr; Amber L. Doiron | Biocompatible Materials; Imaging Agents; Magnetic Materials; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f47469df41cddf44666/original/activatable-superparamagnetic-iron-oxide-nanoparticles-scavenge-reactive-oxygen-species-in-macrophages-and-endothelial-cells.pdf |
60c7457e842e6528e2db2639 | 10.26434/chemrxiv.10038458.v1 | Simultaneous Monitoring of Crystalline Active Materials and Resistance Evolution in Lithium-Sulfur Batteries | Operando X-ray diffraction (XRD) is a valuable tool for studying secondary battery materials as it allows for the direct correlation of electrochemical behavior with structural changes of crystalline active materials. This is especially true for the lithium-sulfur chemistry, in which energy storage capability depends on the complex growth and dissolution kinetics of lithium sulfide (Li2S) and sulfur (S8) during discharge and charge, respectively. In this work, we present a novel development of this method through combining operando XRD with simultaneous and continuous resistance measurement using an Intermittent Current Interruption (ICI) method. We show that a coefficient of diffusion resistance, which reflects the transport properties in the sulfur/carbon composite electrode, can be determined from analysis of each current interruption. Its relationship to the established Warburg impedance model is validated theoretically and experimentally. We also demonstrate for an optimized electrode formulation and cell construction that the diffusion resistance increases sharply at the discharge end point, which is consistent with the blocking of pores in the carbon host matrix. The combination of XRD with ICI allows for a direct correlation of structural changes with not only electrochemical properties but also energy loss processes at a non-equilibrium state, and therefore is a valuable technique for the study of a wide range of energy storage chemistries.<br /> | Yu-Chuan Chien; Ashok Menon; William Brant; Daniel Brandell; Matthew Lacey | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457e842e6528e2db2639/original/simultaneous-monitoring-of-crystalline-active-materials-and-resistance-evolution-in-lithium-sulfur-batteries.pdf |
60c759424c89190cefad4d30 | 10.26434/chemrxiv.14676096.v1 | Combined Experimental and Theoretical Study on Photoionization Cross Sections of Benzonitrile and o/m/p-Cyanotoluene | Toluene is one of the most abundant aromatic compounds in the atmosphere of Titan, and CN group has been regarded as an indicator for observing aromatic compounds in interstellar medium due to the large dipole moments resulted from the CN substituents. In the present work, the photoionization cross-sections (PICS) of benzonitrile and o/m/p-cyanotoluene, which are the products of CN + toluene were obtained at the photon energy ranging from ionization threshold to 14 eV combining experimental and theoretical methods. The synchrotron vacuum ultraviolet photoionization mass spectrometry (SVUV-PIMS) was employed, and theoretical calculations based on the frozen-core Hartree-Fock approximation and Franck-Condon simulations were carried out to cross-verify the measurements. In addition, the generalized charge decomposition analysis was used to investigate the characteristics of ionized molecular orbitals. Our results are valuable for quantifying these key species (especially by the SVUV-PIMS technique) and estimating related parameters such as dissociation rates in interstellar space. | Jiabin Huang; Can Huang; Xiaoqing Wu; Qifeng Hou; Guangjun Tian; Jiuzhong Yang; Feng Zhang | Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759424c89190cefad4d30/original/combined-experimental-and-theoretical-study-on-photoionization-cross-sections-of-benzonitrile-and-o-m-p-cyanotoluene.pdf |
64e8ca7cdd1a73847f826a8a | 10.26434/chemrxiv-2022-hn1vh-v4 | Molecular Aromaticity at the Edge of the Periodic Table | The recent discovery of the cyclically delocalized three-center two-electron σ-bonding in the crystalline actinide cluster isolated by Liddle and co-workers has sparked a heated debate on the role of molecular aromaticity on the periphery of the periodic table. It has been suggested that the tri-thorium ring at the heart of the cluster features considerable aromatic stabilization comparable to the heterocyclic π-aromatic rings such as thiophene. In this Communication we challenge previous conclusions by showing from first principles that the tri-thorium bonding does not fulfill the very fundamental requirement by IUPAC of being distinctly stabilized by cyclic delocalization of electrons, and therefore it should be classified as non-aromatic once and for all. | Dariusz Szczepanik | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e8ca7cdd1a73847f826a8a/original/molecular-aromaticity-at-the-edge-of-the-periodic-table.pdf |
60e82ebf609d0d39f1d8f9b2 | 10.26434/chemrxiv-2021-rrg7q-v2 | 3D-printed hierarchical pillar array electrodes for high performance semi-artificial photosynthesis | The re-wiring of photosynthetic bio-machineries to electrodes is a forward-looking semi-artificial route for sustainable bio-electricity and fuel generation. Currently, it is unclear how the bio-material interface can be designed to meet the complex requirements for high bio-photoelectrochemical performance. Here, we developed an aerosol jet printing method for generating hierarchical electrode structures using indium tin oxide nanoparticles. We printed libraries of micropillar array electrodes varying in height and sub-micron surface features and studied the energy/electron transfer processes across the bio-electrode interfaces. When wired to the cyanobacterium Synechocysis sp. PCC 6803, micropillar array electrodes with micro-branches exhibited favourable biocatalyst loading, light utilisation and electron flux output, ultimately almost doubling the photocurrent of state-of-the-art porous structures of the same height. When the micropillars’ heights were increased from 50 to 600 µm, milestone mediated photocurrent densities of 245 µA cm–2 (the closest thus far to theoretical predictions) and external quantum efficiencies of up to 29% could be reached. This study demonstrates how bioenergy from photosynthesis could be more efficiently harnessed in the future and provide new tools for 3D electrode design. | Jenny Zhang; Xiaolong Chen; Joshua Lawrence; Laura Wey; Qingshen Jing ; Sohini Kar-Narayan; Lukas Schertel ; Silvia Vignolini ; Christopher Howe | Materials Science; Catalysis; Energy; Materials Processing; Biocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e82ebf609d0d39f1d8f9b2/original/3d-printed-hierarchical-pillar-array-electrodes-for-high-performance-semi-artificial-photosynthesis.pdf |
647e36f2e64f843f416117df | 10.26434/chemrxiv-2023-hpssl | Proton NMR Relaxometry as a Rapid and Non-Destructive Technique for Probing Degradation of Supported Poly(ethylenimine) for CO2 Direct Air Capture | Aminopolymer-based adsorbents are commonly investigated for CO2 direct air capture (DAC). In the presence of high temperature and O2, which could happen during process upset, oxidative degradation can significantly contribute to limiting the adsorbent lifetime. Here, we demonstrate the use of a portable, benchtop NMR sensor to collect proton relaxometry profiles to track the degradation of a PEI/Al2O3 sample exposed to controlled accelerated oxidation conditions and correlate the extent of oxidation as measured by loss in amine efficiency with T2 (spin-spin) relaxation times. We hypothesize that T2 relaxation accurately tracks oxidative degradation in aminopolymers because of reduced polymer mobility resulting from radical-induced crosslinking that can occur during the oxidation process. The advantage of using NMR relaxometry as a non-destructive technique to probe degradation is demonstrated on a 1-inch square-channel monolith adsorbent exposed to actual DAC service conditions, highlighting the potential for using this technique as a rapid and non-destructive method of probing adsorbent health. | Elwin Hunter-Sellars; Hannah V. Eshelman; Julia D. Kerr; Zoe A. Pollard; Miles A. Sakwa-Novak; Maxwell A. T. Marple; Simon H. Pang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647e36f2e64f843f416117df/original/proton-nmr-relaxometry-as-a-rapid-and-non-destructive-technique-for-probing-degradation-of-supported-poly-ethylenimine-for-co2-direct-air-capture.pdf |
60c741eff96a0048fb28652d | 10.26434/chemrxiv.8202242.v1 | Asymmetric Total Synthesis of Arcutinidine and Arcutinine | We have accomplished the asymmetric total
synthesis of arcutinidine and arcutinine, two arcutine-type C20-diterpenoid
alkaloids. A pentacyclic intermediate was rapidly assembled by using two
Diels−Alder reactions. A cascade sequence of Prins cyclization and
Wagner−Meerwein rearrangement was then developed to construct the core of arcutinidine,
which was further elaborated into an oxygenated pentacycle through a scalable
route. Chemoselective reductive amination followed by spontaneous imine
formation furnished the pyrroline motif at a final stage. | Shupeng Zhou; Kaifu Xia; Ang Li | Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741eff96a0048fb28652d/original/asymmetric-total-synthesis-of-arcutinidine-and-arcutinine.pdf |
64c2664a9ed5166e938ebaf4 | 10.26434/chemrxiv-2023-md389 | Gas evolution in sodium ion batteries – DEMS setup, data evaluation and application to a Mn-rich layered cathode material | Exceeding the electrochemical stability window of battery cells causes side reactions that are often accompanied by the release of gas molecules. A powerful operando method to analyze such side reactions and their onset potentials is differential electrochemical mass spectrometry (DEMS). While the method provides valuable information, the correct assignment of the DEMS signals and deriving quantitative information on the amounts and types of gases released can be challenging. A frequent limitation is that gas concentrations are often calculated from single m/z ratios only. This has the drawback of overlooking unexpected gases which can moreover cause misinterpretation of the signal intensities, or even the attribution to gases which are not actually formed. Here, we describe a multiple concentration determination (MCD) algorithm, that uses the full MS spectra as a basis. The approach allows a more reliable determination of the gas release and is, to our knowledge, for the first time applied to DEMS for batteries. As study case, Na-ion half cells with P2-Na0.67Mn3/4Ni1/4O2 (NaMNO) as cathode active material (CAM) are chosen. The gassing behavior for two electrolyte formulations (1M NaPF6 in propylene carbonate (PC) and 1M NaPF6 in diglyme (2G)) and for two different upper cut-off potentials (4.25 and 3.80 V) is determined. Against the general belief that glymes lead to more gassing at high potentials, we find that gas evolution for PC electrolytes is generally larger compared to 2G electrolytes. In case of 2G, dimethyl ether is found as decomposition product. Pressure change measurements in a closed cell are used as a second, independent method to validate the gas quantification of the MCD algorithm. The study also highlights the relevance for implementing a reference electrode into DEMS cell setups. | Jonas Geisler; Lukas Pfeiffer; Guillermo Alvarez Ferrero; Peter Axmann; Philipp Adelhelm | Analytical Chemistry; Energy; Electrochemical Analysis; Mass Spectrometry; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c2664a9ed5166e938ebaf4/original/gas-evolution-in-sodium-ion-batteries-dems-setup-data-evaluation-and-application-to-a-mn-rich-layered-cathode-material.pdf |
65e896e2e9ebbb4db90fe29a | 10.26434/chemrxiv-2024-808lg | “Quantum-Chemoinformatics” for Design and Discovery of New Molecules and Reactions | We give an overview of the role of “quantum-chemoinformatics” in drug development. Quantum- chemoinformatics is a data-driven chemistry using descriptors on the basis of theoretical chemistry, especially quantum chemistry (QC) and ab initio molecular dynamics (MD) simulations. We focus especially on quantum-chemoinformatics for chemical reaction design and prediction, which is one of the important processes in basic research of drug development. We start with a brief historical overview and then introduces two projects of quantum-cheminformatics. The RMap project uses QC-based chemical reaction route networks for discovery and design of new molecules and reactions. The other project is related to environmental pollution by drug molecules, a property which should be taken into account in drug design and evaluation. The last section describes our recent attempt to accelerate QC-data acquisition by utilizing a limited amount of experimental data and machine learning (ML) technology. | Hiroko Satoh; Vincenz-Maria Steiner; Jürg Hutter | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e896e2e9ebbb4db90fe29a/original/quantum-chemoinformatics-for-design-and-discovery-of-new-molecules-and-reactions.pdf |
665668e6418a5379b0837ca7 | 10.26434/chemrxiv-2024-52z7b | Palladium-Catalyzed Tsuji-Trost-Type Vinyl Epoxide Cross-Coupling with Umpolung Hydrazones | Recognized as versatile building blocks, vinyl epoxides have been used as electrophiles to generate compounds of high synthetic value. However, selective functionalization of vinyl epoxides via carbon-carbon (C–C) bond formation has been a major challenge for many years due to its unique chemical reactivity. Current methodologies involve transition metal-activated vinyl epoxides with both stabilized and non-stabilized carbon nucleophiles. Procedures involving stabilized carbanions have limited applicability due to the use of pre-functionalized cyano-, sulphonyl or carbonyl derivatives. Non-stabilized carbanions in the form of organometallic reagents have shown to be robust and versatile reagents in C–C bond formation; however, they are employed in superstoichiometric quantities, require the protection of active functional groups, and generate copious amounts of metallic waste. Therefore, the development of alternative mild carbanion sources is highly desired. In this work, we report a highly chemo- and regioselective palladium-catalyzed vinyl epoxide cross-coupling utilizing hydrazones as organometallic equivalents (HOME). Hydrazones, generated from carbonyl-containing renewable feedstocks, enable a more sustainable reaction, and provide an alternative to highly reactive and sensitive unstabilized organometallic reagents. A broad substrate scope, with high functional group tolerance, is demonstrated along with the late-stage functionalization of natural product derivatives. | Evan Chen; Chao-Jun Li | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665668e6418a5379b0837ca7/original/palladium-catalyzed-tsuji-trost-type-vinyl-epoxide-cross-coupling-with-umpolung-hydrazones.pdf |
652421cabda59ceb9a2f14cc | 10.26434/chemrxiv-2023-jdhxk | Metal Ions Turn on a Stereoselective Nonenzymatic Reduction of Keto Acids by the Coenzyme NADH | The relationship between genetic molecules and metabolism is one of the longest standing
problems for the origin of life. A central molecule within early metabolism is the coenzyme nicotinamide adenine dinucleotide (NAD(H)), a modified ribonucleotide and reducing agent. Yet, without enzymes, NADH does not reduce carbonyl compounds, its primary metabolic
substrates, leading to an apparent paradox regarding its role in the evolution of metabolism. We now report that abundant metal ions turn on a nonenzymatic, stereoselective, and potentially primordial reduction reaction of keto acids by NADH. Kinetic, mechanistic, and computational studies elucidate the reaction mechanism and the way stereochemistry is transferred. Complexes of metals with RNA-derived coenzymes could have mediated the transition from inorganic to organic reducing agents and the propagation of chirality in early metabolism. | Robert Mayer; Joseph Moran | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Stereochemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652421cabda59ceb9a2f14cc/original/metal-ions-turn-on-a-stereoselective-nonenzymatic-reduction-of-keto-acids-by-the-coenzyme-nadh.pdf |
67338292f9980725cff777cc | 10.26434/chemrxiv-2024-7cc6d | Identification and Characterisation of Pyrimidine Nucleoside 2'-Hydroxylase | Functionalisation of nucleosides at the 2'-position has become an important modification for therapeutic purposes to tailor pharmacological properties. Chemical synthesis of these molecules is challenging, and recent studies have explored bottom-up strategies with enzymes of the nucleoside salvage pathway and late-stage functionalisation capabilities. More than 55 years ago, a pyrimidine nucleoside 2'-hydroxylase (PDN2'H) activity was described in three fungal species. However, the corresponding protein sequences have never been reported. This study describes the identification and characterisation of PDN2'H from Neurospora crassa, which naturally hydroxylates thymidine at the 2'-position as now verified by NMR. Site-directed mutagenesis confirmed the protein to be an α-ketoglutarate-/Fe(II)-dependent dioxygenase. We performed investigation of its substrate scope, phylogeny, thermostability and elucidated the enzymatic mechanism with help of PDN2'H’s crystal structure co-crystallised with thymidine. This work adds a long sought-after and important nucleoside-modifying protein to the biocatalytic portfolio. | Ferdinand Genz; Florian Friedrich; Christoph Lönarz; Oliver Einsle; Manfred Jung; Michael Müller; Nico D. Fessner | Biological and Medicinal Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67338292f9980725cff777cc/original/identification-and-characterisation-of-pyrimidine-nucleoside-2-hydroxylase.pdf |
65f81fa7e9ebbb4db9ef5e72 | 10.26434/chemrxiv-2024-np1kh-v2 | A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations | The rate constants of enzyme-catalyzed reactions (k_cat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, without introducing the transition state theory assumptions, and takes into account the dynamical equilibrium between the reactive and non-reactive conformations of the enzyme:substrate complex. Our computed k_cat values are in order-of-magnitude agreement with the experimental data for two representative enzymatic reactions. | Dhiman Ray; Sudip Das; Umberto Raucci | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f81fa7e9ebbb4db9ef5e72/original/a-kinetic-view-of-enzyme-catalysis-from-enhanced-sampling-qm-mm-simulations.pdf |
60c75866bdbb893f8ca3ad63 | 10.26434/chemrxiv.14544666.v1 | Biocatalytic Synthesis of Non-Standard Amino Acids by a Decarboxylative Aldol Reaction | The formation of carbon-carbon bonds lies at the
heart of organic chemistry, but relatively few C-C bond forming enzymes have
found their way into the biocatalysis toolbox. We report that the enzyme UstD
performs a highly selective decarboxylative aldol addition with diverse
aldehyde substrates to make non-standard, γ-hydroxy amino acids. We increased
the activity of UstD through three rounds of classic directed evolution and an
additional round of computationally-guided engineering. The enzyme that emerged,
UstD<sup>2.0</sup>, is very efficient in a whole-cell biocatalysis format and
readily crystallizes. The X-ray crystal
structure of UstD<sup>2.0 </sup>at 2.25 Å reveals the active site and empowers
future studies. The utility of UstD<sup>2.0</sup> was demonstrated via the
stereoselective gram-scale syntheses of non-standard amino acids. | Jonathan Ellis; Meghan Campbell; Prasanth Kumar; Craig Bingman; Andrew Buller; Eric Geunes | Biochemistry; Bioengineering and Biotechnology; Biocatalysis; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75866bdbb893f8ca3ad63/original/biocatalytic-synthesis-of-non-standard-amino-acids-by-a-decarboxylative-aldol-reaction.pdf |
60c7449ff96a002951286a76 | 10.26434/chemrxiv.9866912.v1 | Improving the Accuracy of Protein-Ligand Binding Affinity Prediction by Deep Learning Models: Benchmark and Model | <b>Introduction:</b> The ability to discriminate among ligands binding to the same protein target in terms of their relative binding affinity lies at the heart of structure-based drug design. Any improvement in the accuracy and reliability of binding affinity prediction methods decreases the discrepancy between experimental and computational results.<br /><b>Objectives:</b> The primary objectives were to find the most relevant features affecting binding affinity prediction, least use of manual feature engineering, and improving the reliability of binding affinity prediction using efficient deep learning models by tuning the model hyperparameters.<br /><b>Methods:</b> The binding site of target proteins was represented as a grid box around their bound ligand. Both binary and distance-dependent occupancies were examined for how an atom affects its neighbor voxels in this grid. A combination of different features including ANOLEA, ligand elements, and Arpeggio atom types were used to represent the input. An efficient convolutional neural network (CNN) architecture, DeepAtom, was developed, trained and tested on the PDBbind v2016 dataset. Additionally an extended benchmark dataset was compiled to train and evaluate the models.<br /><b>Results: </b>The best DeepAtom model showed an improved accuracy in the binding affinity prediction on PDBbind core subset (Pearson’s R=0.83) and is better than the recent state-of-the-art models in this field. In addition when the DeepAtom model was trained on our proposed benchmark dataset, it yields higher correlation compared to the baseline which confirms the value of our model.<br /><b>Conclusions:</b> The promising results for the predicted binding affinities is expected to pave the way for embedding deep learning models in virtual screening and rational drug design fields. | Mohammad Rezaei; Yanjun Li; Xiaolin Li; Chenglong Li | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7449ff96a002951286a76/original/improving-the-accuracy-of-protein-ligand-binding-affinity-prediction-by-deep-learning-models-benchmark-and-model.pdf |
60c74586337d6cf19ee26fcd | 10.26434/chemrxiv.10044272.v1 | Optimizing Electrostatic Similarity for Virtual Screening: A New Methodology | <div>Ligand Based Virtual Screening (LBVS) methods are widely used in drug discovery as filters for subsequent in-vitro and in-vivo characterization. This means, increasing accuracy of LBVS approaches may have a huge impact on increasing chances of success. Since the databases processed in drug discovery campaigns are enormously large, this pre-selection process requires the use of fast and precise methodologies. The similarity between compounds can be measured using different descriptors such as shape, pharmacophore or electrostatic similarity. The latter is the goal of this work, i.e., we want to improve the process of obtaining the compounds most similar to a query in terms of electrostatic similarity. To do so, the current and widely proposed methodology in the literature is based on the use of ROCS to assess the similarity of compounds in terms of shape and then evaluate a small subset of them with ZAP for prioritization regarding electrostatic similarity. This paper proposes an alternative methodology that consists of directly optimizing electrostatic similarity and works with the entire database of compounds without using shape cut-offs. For this purpose, a new and improved version of the OptiPharm software has been developed. OptiPharm implements a parameterizable metaheuristic algorithm able to solve any optimization problems directly related to the involved molecular conformations. We show that our new method completely outperforms the classical proposal widely used in the literature. Accordingly, we are able to conclude that many of the compounds proposed with our novel approach could not be discovered with the classical one. As a result, this methodology opens up new horizons in Drug Discovery.</div> | Savíns Puertas Martín; Juana Lopez Redondo; Horacio Pérez-Sánchez; Pilar Martínez Ortigosa | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74586337d6cf19ee26fcd/original/optimizing-electrostatic-similarity-for-virtual-screening-a-new-methodology.pdf |
66ab359901103d79c56a11a9 | 10.26434/chemrxiv-2024-xfkbb | Photoredox-Catalyzed Allylic C-H Fluorosulfonylation of Alkenes: Accessing Allyl Sulfonyl Fluorides | Recently, the radical fluorosulfonylation of alkenes is emerging as an appealing strategy for the rapid construction of diverse sulfonyl fluorides, which are in high demand across various scientific disciplines, particularly in chemical biology and drug discovery. However, most existing methodologies have primarily focused on the vicinal difunctionalization of C=C bonds, while the selective allylic C-H fluorosulfonylation of alkenes remains an underexplored and challenging transformation. This study reported a novel and unprecedented photoredox-catalyzed protocol for direct allylic C-H fluorosulfonylation of alkenes with FABI (1-fluorosulfonyl 2-aryl benzoimidazolium triflate salts). This mild protocol exhibited excellent compatibility with various functional groups, broad substrate scope, and promising scalability, enabling convenient access to a wide range of allyl sulfonyl fluorides with exceptional regioselectivity. The synthetic robustness of this strategy was further demonstrated by the late-stage functionalization of natural products and their further ligation with other drugs via SuFEx chemistry. Experimental and theoretical analyses indicated that this transformation proceeds through a photoredox mechanism, where the selective formation of allylic sulfonyl fluorides was governed by both the dynamics and thermodynamic processes. | Zhi-Min Yan; Chun-Fang Zhang; Hua Li; Jia-Hua Yang; Lin Qi; Yu-Xue Ma; Yi-Chen Dong; Wei Li; Li-Jing Wang | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ab359901103d79c56a11a9/original/photoredox-catalyzed-allylic-c-h-fluorosulfonylation-of-alkenes-accessing-allyl-sulfonyl-fluorides.pdf |
60c74351bdbb89f035a3861b | 10.26434/chemrxiv.9037481.v1 | The Interplay among Molecular Structures, Crystal Symmetries and Lattice Energy Landscapes Revealed by Unsupervised Machine Learning: A Closer Look at Pyrrole Azaphenacenes | The ability to perform large-scale crystal structure predictions (CSP) have significantly advanced the synthesis of functional molecular solids by designs. In our recent work [Chem. Mater., 30, 4361 (2018)], we demonstrated our latest developments in organic CSPs by screening a set of 28 pyrrole azaphenacene isomers which led to one new molecule with higher thermodynamic stability and carrier mobilities in its crystalline form, compared to the one reported experimentally. Hereby, using the lattice energy landscapes for pyrrole azaphenacenes as examples, we applied machine-learning techniques to statistically reveal in more details, on how molecular symmetry and Z' values translate to the crystal packing landscapes, which in terms affect the coverage of landscape through quasi-random crystal structure samplings. A recurring theme in crystal engineering is to identify the probabilities of targeting isostructures to a specific reference crystal upon chemical functionalisations. For this, we propose here a global similarity index in conjunction with the Energy-Density Isostructurality (EDI) map to analyse the lattice energy landscapes for halogen substituted pyrrole azaphenacenes. A continue effort in the field is to accelerate CSPs for sampling a much wider chemical space for high-throughput material screenings, we propose a potential solution to this challenge drawn upon this study. Our work will hopefully stimulate the crystal engineering community in adapting a more statistically-oriented approach in understanding crystal packing of organic molecules in the age of digitisation. | Jack Yang; Nathan Li; Sean Li | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74351bdbb89f035a3861b/original/the-interplay-among-molecular-structures-crystal-symmetries-and-lattice-energy-landscapes-revealed-by-unsupervised-machine-learning-a-closer-look-at-pyrrole-azaphenacenes.pdf |
66a96ed5c9c6a5c07a8baaf5 | 10.26434/chemrxiv-2024-sqbf7 | Effects of solvation and temperature on the energetics of BiVO4 surfaces with varying composition for solar water splitting | Photoelectrodes used in solar water splitting must operate in aqueous media. However, many computational studies on oxide photoelectrodes assume vacuum conditions and investigate dry surfaces. To date, computational studies that explicitly compare the dry and solvated photoelectrode energetics at finite temperature and the impact of photoelectrode surface composition, including the presence of surface defects, are lacking. In this study, we used first-principles molecular dynamics simulations to investigate the solvation and thermal effects on the energetics of the BiVO4 (010) surface with different surface compositions and oxygen vacancies, a common defect responsible for the intrinsic n-type behavior of BiVO4. We find that the alignment of the photoelectrode electronic bands with the water redox potentials is modified in the presence of water, similar to other oxides, and that solvation effects and thermal fluctuations are more prominent for Bi-rich surfaces. We also predict that infrared sensitive spectroscopies should be useful to distinguish between the stoichiometric and Bi-rich surfaces. Our results provide a detailed understanding of the behavior of BiVO4photoanodes operating in aqueous media and are directly comparable with experiments conducted on the stoichiometric and Bi-rich surface. | Giacomo Melani; Wennie Wang; Francois Gygi; Kyoung-Shin Choi; Giulia Galli | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Interfaces; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a96ed5c9c6a5c07a8baaf5/original/effects-of-solvation-and-temperature-on-the-energetics-of-bi-vo4-surfaces-with-varying-composition-for-solar-water-splitting.pdf |
634e95993e8d999cc11e6a33 | 10.26434/chemrxiv-2022-d5hhf | Reactivity of Single-Atom Alloys as Easy as Counting to Ten | Single-Atom Alloys (SAAs) have recently emerged as highly active and selective alloy catalysts. Unlike pure metals, SAAs escape the well-established conceptual framework developed nearly three decades ago for predicting catalytic performance. Here, based on high throughput density functional theory calculations, we reveal a 10-electron count rule for the binding of adsorbates on the dopant of SAA surfaces. A simple molecular orbital approach rationalises this rule and the nature of the adsorbate/dopant interaction. In addition, our intuitive model can accelerate the rational design of SAA catalysts. Indeed, we illustrate how the unique insights provided by the electron count rule help identify the most promising dopant for an industrially relevant hydrogenation reaction, thereby reducing the number of potential materials by more than one order of magnitude. | Julia Schumann; Michail Stamatakis; Angelos Michaelides; Romain Réocreux | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634e95993e8d999cc11e6a33/original/reactivity-of-single-atom-alloys-as-easy-as-counting-to-ten.pdf |
61ec51594b950092c006d72e | 10.26434/chemrxiv-2022-x2qdz | Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids | Polymer-protein hybrids are intriguing materials that can bolster protein stability in non-native environments, thereby enhancing their utility in diverse medicinal, commercial, and industrial applications. One stabilization strategy involves designing synthetic random copolymers with compositions attuned to the protein surface, but rational design is complicated by a vast chemical and composition space.
Here, we report a strategy to design protein-stabilizing copolymers based on active machine learning, facilitated by automated material synthesis and characterization platforms. The versatility and robustness of the approach is demonstrated by the successful identification of copolymers that preserve, or even enhance, the activity of three chemically distinct enzymes following exposure to thermal denaturing conditions. Although systematic screening results in mixed success, active learning appropriately identifies unique chemistries for each enzyme. Overall, this work broadens our capabilities to design fit-for-purpose synthetic copolymers that promote or otherwise manipulate protein activity, with extensions towards the design of robust polymer-protein hybrid materials. | Matthew Tamasi; Roshan Patel; Carlos Borca; Shashank Kosuri; Heloise Mugnier; Rahul Upadhya; N. Sanjeeva Murthy; Michael Webb; Adam Gormley | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Polymer chains; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ec51594b950092c006d72e/original/machine-learning-on-a-robotic-platform-for-the-design-of-polymer-protein-hybrids.pdf |
673259f75a82cea2fad091fb | 10.26434/chemrxiv-2024-2nd8t | Stepwise kinetics of the Early-Stage Nucleation in Chiral Perovskites via Ab Initio Molecular Dynamics and Free- Energy Calculations | This study provides a comprehensive molecular-level understanding of the early-stage nucleation process in chiral hybrid organic-inorganic perovskites (HOIPs). A combination of ab-initio molecular dynamics (AIMD) based on density functional theory (DFT) and parallel bias metadynamics simulations was designed to explore a broad spectrum of the nucleation scenarios, disclosing how structural deviations affect the formation of chiral aggregates at the atomic scale. The workflow uses parallel replicas initialized from configurations characterised by different root-mean-square deviations (RMSD) relative to the crystallographic coordinates of the chiral ligands. The free-energy landscape and the kinetic pathways involved in chiral aggregate formation indicate a stepwise mechanism that governs the transition from disordered to chiral states. The computed free-energy barriers and corresponding transition timescales uncover several critical stages in this process, including rapid initial relaxations as well as slower, free-energy-intensive steps, with overall timescales on the order of microseconds as the system approaches its most chiral configuration. | Adriana Pietropaolo; Mariagrazia Fortino; Gioacchino Schifino; Matteo Salvalaglio | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673259f75a82cea2fad091fb/original/stepwise-kinetics-of-the-early-stage-nucleation-in-chiral-perovskites-via-ab-initio-molecular-dynamics-and-free-energy-calculations.pdf |
62c5ee2214201fe4ec285cb8 | 10.26434/chemrxiv-2022-1x9rq | A Synthetic Cycle for Heteroarene Synthesis by Nitride Insertion | [cis-terpyOsNCl2]PF6 inserts nitrogen into indenes to afford isoquinolines. The insertion proceeds through an azaallenium intermediate, with mechanistic and computational studies suggesting that azaallenium formation occurs via a stepwise aziridination followed by electrocyclic ring opening. Examination of a substrate diverted from aromatization resulted in inner-sphere ligand rearrangement to afford an azaallyl chloride complex; kinetic studies suggest this species forms via an analogous azaallenium intermediate. Studies on base-promoted release of the isoquinoline suggest that the azaallyl chloride is not an obligate intermediate for aromatization and the parent azaallenium can directly eliminate to give a neutral dichloroosmium(II)-isoquinoline intermediate. The heteroarene can subsequently be thermally liberated to afford an osmium(II) acetonitrile complex, which can be oxidized to regenerate the nitride over two steps. First, in the presence of ammonia, oxidation affords an osmium(III) amidine, with subsequent oxidation in the presence of toluene sulfonic acid ultimately regenerating the nitride. The mechanistic foundation set by this synthetic cycle opens the door to the further development of nitrogen insertion heteroarene syntheses promoted by late transition metal nitrides. | Patrick Kelly; Alexander Filatov; Mark Levin | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Organometallic Compounds; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c5ee2214201fe4ec285cb8/original/a-synthetic-cycle-for-heteroarene-synthesis-by-nitride-insertion.pdf |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.