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60cee928b912f8d9465aa3c0 | 10.26434/chemrxiv-2021-bb7b1-v2 | A study of boosting molecular descriptors with quantum-derived features in prediction of maximum emission wavelengths of chromophores. | The following research assesses the capability of machine learning in predicting maximum emission wavelengths of organic compounds. The predictions are based on molecular descriptors and fingerprints widely applied in cheminformatics. In an effort to further improve accuracy, developed machine learning models were enriched with quantum mechanics derived features. Multi linear, gradient boosting and random forest regressions were applied. Computers were trained and tested with database of experimental data of optical properties. | Bartłomiej Fliszkiewicz | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cee928b912f8d9465aa3c0/original/a-study-of-boosting-molecular-descriptors-with-quantum-derived-features-in-prediction-of-maximum-emission-wavelengths-of-chromophores.pdf |
65b9445f66c1381729995bc8 | 10.26434/chemrxiv-2024-pjnw1 | In Situ Techniques for Quinone-Mediated Electrochemical Carbon Capture and Release in Aqueous Environments | We present two novel experimental techniques designed to quantify the contributions of nucleophilicity-swing and pH-swing mechanisms to carbon capture in the electrochemical aqueous quinone-based CO2 capture process. Through thermodynamic analysis, we elucidate the intricate interplay between these two mechanisms, and emphasize the critical role of understanding this interplay in the material discovery cycle for carbon capture applications. This insight prompts the development of two innovative in situ techniques. The first technique capitalizes on discernible voltage signature differences between quinone, and quinone-CO2 adducts. By incorporating a reference electrode into the carbon capture cell setup, we apply this method to investigate bis[3-(trimethylammonio)propyl]-anthraquinones (BTMAPAQs). Our findings reveal the isolated contributions of nucleophilicity-swing and pH-swing mechanisms to overall carbon capture capacity under varying wait times and CO2 partial pressures. The second method is developed based on our finding that the adduct form of the quinone exhibits a fluorescence emission from an incident light at wavelengths distinct from the fluorescence of the reduced form, enabling differentiation through optical band-pass filtering at each unique fluorescent signature. Thus, we introduce a non-invasive, in situ approach using fluorescence microscopy, providing the unique capability to distinguish between oxidized, reduced, and adduct species with sub-second time resolution at single digit micrometer resolution. This powerful technique holds significant promise for studying such systems, representing an advancement in our ability to understand carbon capture processes. | Kiana Amini; Thomas Cochard; Yan Jing; Jordan Sosa; Dawei Xi; Maia Alberts; Michael Emanuel; Emily Kerr; Roy Gordon; Michael Aziz | Organic Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Organic Compounds and Functional Groups; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b9445f66c1381729995bc8/original/in-situ-techniques-for-quinone-mediated-electrochemical-carbon-capture-and-release-in-aqueous-environments.pdf |
64dc986ddfabaf06ff5c5e34 | 10.26434/chemrxiv-2023-jf6mq | Enabling Long-term Cycling Stability of Na3V2(PO4)3/C vs. Hard Carbon Full-cells | Sodium-ion batteries are becoming an increasingly important complement to lithium-ion batteries. However, while extensive knowledge on the preparation of Li-ion batteries with excellent cycling behavior exists, studies on applicable long-lasting sodium-ion batteries are still limited. Therefore, this study focuses on the cycling stability of batteries composed of Na3V2(PO4)3/C based cathodes and hard carbon anodes. It is shown that full cells with a decent stability are obtained for ethylene carbonate / propylene carbonate electrolyte and the conducting salt NaPF6. With cathode loadings of 1.2 mAh/cm², after cell formation discharge capacities up to 92.6 mAh/g are obtained, and capacity retentions > 90 % over 1000 charge / discharge cycles at 0.5 C / 0.5 C are observed. It is shown that both, the additive fluoroethylene carbonate and traces of water in the cell, negatively affect the overall discharge capacity and cycling stability and should therefore be avoided. Remarkably, the internal resistances of well-balanced and wellbuilt cells did not increase over 1500 cycles and 5 months of testing, which is a very promising result regarding the possible lifespan of the cells. The initial loss of active sodium in hard carbon remains a major problem, which can only be partially reduced by proper balancing. | Pirmin Stüble; Cedric Müller; Julian Klemens; Philip Scharfer; Wilhelm Schabel ; Marcel Häringer; Joachim R. Binder; Andreas Hofmann; Anna Smith | Materials Science; Inorganic Chemistry; Energy; Electrochemistry; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dc986ddfabaf06ff5c5e34/original/enabling-long-term-cycling-stability-of-na3v2-po4-3-c-vs-hard-carbon-full-cells.pdf |
630c1855d858fb3d4f6003db | 10.26434/chemrxiv-2022-stt9q | The Structure and Magnetic Properties of a New Family of 1D Chromium Thiolate Coordination Polymers | The synthesis, structure, and magnetic properties of two novel, pseudo-1D chromium thiolate coordination polymers (CPs), CrBTT and Cr2BDT3, are reported. The structures of these materials were determined using X-ray powder diffraction revealing highly symmetric 1D chains embedded within a CP framework. The magnetic coupling of this chain system was measured by SQUID magnetometry, revealing a switch from antiferromagnetic to ferromagnetic behavior dictated by the angular geometrical constraints within the CP scaffold consistent with the Goodenough-Kanamori-Anderson rules. Intrachain magnetic coupling constants JNN of −32 K and +5.7 K were found for CrBTT and Cr2BDT3 respectively using the 1D Bonner-Fisher model of magnetism. The band structure of these materials has also been examined by optical spectroscopy and Density Functional Theory (DFT) calculations revealing semiconducting behavior. Our findings here demonstrate how CP scaffolds can support idealized low-dimensional structural motifs and dictate magnetic interactions through tuning of geometry and inter-spin couplings. | Andrew Ritchhart; Alexander Filatov; Ie-Rang Jeon; John Anderson | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630c1855d858fb3d4f6003db/original/the-structure-and-magnetic-properties-of-a-new-family-of-1d-chromium-thiolate-coordination-polymers.pdf |
651d0fe1bda59ceb9ad7579c | 10.26434/chemrxiv-2023-1whvw | Process Condition Optimization for Li3PO4–Li3BO3–Li2SO4 Lithium-Ion Conductors Using Gaussian Process and Genetic Algorithm | This paper reports on a method of material development with multiple recommendations using a Gaussian process and a genetic algorithm(GA). Conventional Bayesian optimization(BO) was an inefficient method because it updates the predictive model sequentially with one recommendation and one experiment, furthermore there was a possibility of reaching local solutions in the huge search space. Therefore, we devised an evaluation index based on GA, which is different from the evaluation function used in BO, and developed a multiple recommendation method to efficiently visualize and grasp the enormous material search space. Multiple recommendations were able to efficiently explore a huge search space, and furthermore, deviant experimental prosses conditions were constrained by introducing a prior knowledge model. We found the optimum composition and sintering temperature of a Li3PO4–Li3BO3–Li2SO4 ternary mixture system to be 22:16:62 (mol%) and 723°C, respectively, and Lithium-ion conductivity is measured to be 1.3 × 10−3 S/cm at 300°C, which is more than twice the maximum conductivity (4.9 × 10−4 S/cm) observed in a previous report. | Kenji Homma; Akito Maruo; Masashi Yoshinaga; Kaito Fujiwara; Yuki Usui; Hideyuki Jippo | Materials Science; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d0fe1bda59ceb9ad7579c/original/process-condition-optimization-for-li3po4-li3bo3-li2so4-lithium-ion-conductors-using-gaussian-process-and-genetic-algorithm.pdf |
64a8074e6e1c4c986bf75c0b | 10.26434/chemrxiv-2023-h17m5 | Fast, Efficient, Narrowband Room-Temperature Phosphorescence from Metal-Free 1,2-Diketones: Rational Design and Mechanism | We report metal-free organic 1,2-diketones that exhibit fast and highly efficient room-temperature phosphorescence (RTP) with high color purity under various conditions, including solutions. RTP quantum yields reached 38.2% in solution under Ar, 54% in a polymer matrix in air, and 50% in a crystalline solids in air. Moreover, the narrowband RTP consistently dominated the steady-state emission, regardless of the molecular environment. A detailed investigation of the emission mechanism using ultrafast spectroscopy, single-crystal X-ray structure analysis, and theoretical calculations revealed picoseconds intersystem crossing followed by RTP from a planar conformation. Thus, we attribute the high efficiency RTP across diverse molecular environments to an inherent ~5000-s–1 phosphorescence rate constant comparable to that of platinum porphyrin complexes. The planar conformation reflected a design principle for fast and narrowband RTP. This strategy complements the streamlined persistent RTP approach and enables the development of organic phosphors with emissions independent of environmental conditions, thereby offering alternatives to precious-metal based phosphors. | Yosuke Tani; Kiyoshi Miyata; Erika Ou; Yuya Oshima; Mao Komura; Morihisa Terasaki; Shuji Kimura; Takumi Ehara; Koki Kubo; Ken Onda; Takuji Ogawa | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Photochemistry (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a8074e6e1c4c986bf75c0b/original/fast-efficient-narrowband-room-temperature-phosphorescence-from-metal-free-1-2-diketones-rational-design-and-mechanism.pdf |
67a0c2b581d2151a02091a91 | 10.26434/chemrxiv-2025-g5cqm | Fluoroacetyl Carbene Transfer from Sulfonium Salts | The synthesis of organofluorine compounds is vital in developing innovative pharmaceuticals, materials, and agrochemicals. Fluorinated carbene transfer offers a promising strategy for forming new carbon-carbon and carbon-heteroatom bonds, facilitating the incorporation of fluorine into target structures. In this study, we introduce a novel fluoroacetyl sulfonium reagent, (2-ethoxy-1-fluoro-2-oxoethyl)(phenyl)(2,3,4,5-tetramethylphenyl)sulfonium tetrafluoroborate (1), serving as an effective alternative to the currently unknown 2-diazo-2-fluoroacetate for ethyl fluoroacetyl carbene transfer. This reagent is applied in Doyle-Kirmse and cyclopropanation reactions, operating under mild conditions with the use of earth-abundant metal catalysts. This approach enables the efficient synthesis of valuable monofluorinated products. | Arturs Sperga; Artis Kinens; Janis Veliks | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a0c2b581d2151a02091a91/original/fluoroacetyl-carbene-transfer-from-sulfonium-salts.pdf |
65c2362066c138172913f0e0 | 10.26434/chemrxiv-2024-c5xw4 | Asparaginyl Endopeptidase-Mediated Peptide Ligation and Cyclization for Phage Display | Genetically encoded cyclic peptide libraries are invaluable for peptide drug discovery. Here we report an enzymatic strategy for asparaginyl endopeptidase-mediated peptide ligation and cyclization, and its application in the construction of phage-displayed cyclic peptide libraries. Introduction of a low-reactive chloroacetyl group into the tripeptide recognition sequence of OaAEP1 allows intramolecular cyclization with Cys residues to generate macrocyclic peptides. By optimzing OaAEP1 activation conditions and OaAEP1-catalyzed peptide ligation, we establish an efficient OaAEP1-based enzymatic peptide ligation under acidic conditions. The OaAEP1-based enzymatic ligation is fully compatible with phage display and enables the construction of genetically encoded monocyclic and bicyclic peptide libraries. By using OaAEP1-based phage display, we identify macrocyclic peptide ligands targeting TEAD4 at the nanomolar level. One of the bicyclic peptides binds to TEAD4 with a KD value of 139 nM,16-fold lower than its linear analogue, indicating the contribution of the bicyclic scaffold to its biological activity and demonstrating the utility of the technology platform in the discovery of high-affinity cyclic peptide ligands. | Xiao-Cui Wan; Yan-Ni Zhang; Ying Chen; Zhi-Hui Cui; Hua Zhang; Wen-Jing Zhu; Ge-Min Fang | 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/65c2362066c138172913f0e0/original/asparaginyl-endopeptidase-mediated-peptide-ligation-and-cyclization-for-phage-display.pdf |
60c741ad567dfe5624ec3e2c | 10.26434/chemrxiv.8115860.v1 | Radical Capture at Ni(II) Complexes: C-C, C-N, and C-O Bond Formation | <p>The dinuclear b-diketiminato Ni<sup>II</sup><i>tert</i>-butoxide {[Me<sub>3</sub>NN]Ni}<sub>2</sub>(<i>μ</i>-O<i><sup>t</sup></i>Bu)<sub>2 </sub>(<b>2</b>), synthesized from [Me<sub>3</sub>NN]Ni(2,4-lutidine) (<b>1</b>) and di-<i>tert</i>-butylperoxide, is a versatile precursor for the synthesis of a series of Ni<sup>II</sup>complexes [Me<sub>3</sub>NN]Ni-FG to illustrate C-C, C-N, and C-O bond formation at Ni<sup>II </sup>via radicals. {[Me<sub>3</sub>NN]Ni}<sub>2</sub>(<i>μ</i>-O<i><sup>t</sup></i>Bu)<sub>2 </sub>reacts with nitromethane, alkyl and aryl amines, acetophenone, benzamide, ammonia and phenols to deliver corresponding mono- or dinuclear [Me<sub>3</sub>NN]Ni-FG species (FG = O<sub>2</sub>NCH<sub>2</sub>, R-NH, ArNH, PhC(O)NH, PhC(O)CH<sub>2</sub>, NH<sub>2</sub>and OAr). Many of these Ni<sup>II </sup>complexes are capable of capturing the benzylic radical PhCH(•)CH<sub>3 </sub>to deliver corresponding PhCH(FG)CH<sub>3 </sub>products featuring C-C, C-N or C-O bonds. DFT studies shed light on the mechanism of these transformations and suggest two competing pathways that depend on the nature of the functional groups. These radical capture reactions at [Ni<sup>II</sup>]-FG complexes outline key C-C, C-N, and C-O bond forming steps and suggest new families of nickel radical relay catalysts.</p> | Abolghasem (Gus) Bakhoda; Stefan Wiese; Christine Greene; Bryan C. Figula; Jeffery A. Bertke; Timothy H. Warren | Kinetics and Mechanism - Inorganic Reactions; Organometallic Compounds; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ad567dfe5624ec3e2c/original/radical-capture-at-ni-ii-complexes-c-c-c-n-and-c-o-bond-formation.pdf |
628bdbcd6cae1c5f5c148516 | 10.26434/chemrxiv-2022-dfjvv | Reconciling methane emission measurements for offshore oil and gas platforms with detailed emission inventories: Accounting for emission intermittency | Comparisons of observation-based emission estimates with emission inventories for oil and gas production operations have demonstrated that intermittency in emissions is an important factor to be accounted for in reconciling inventories with observations. Most emission inventories do not directly report data on durations of active emissions, and the variability in emissions over time must be inferred from other measurements or engineering calculations. This work examines a unique emission inventory, assembled for offshore oil and gas production platforms in United States coastal waters, which reports production-related sources on individual platforms, along with estimates of emission duration for individual sources. Platform specific emission rates, derived from the inventory, were compared to shipboard measurements made at 72 platforms. The reconciliation demonstrates that emission duration reporting, by source, can lead to predicted ranges in emissions that are orders of magnitude broader than those based on annual average emission rates. Total emissions reported in the inventory for the matched platforms were 20-30% larger than total emissions estimated based on observations. The distributions of emissions were similar, with 75% of platform total emission rates falling between 0 and 49 kg/hr for the observations and between 0.59 and 54 kg/hr for the inventory. | Zhichao Chen; Tara I. Yacovitch; Conner Daube; Scott C. Herndon; Darcy Wilson; Stacie Enoch; David T. Allen | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628bdbcd6cae1c5f5c148516/original/reconciling-methane-emission-measurements-for-offshore-oil-and-gas-platforms-with-detailed-emission-inventories-accounting-for-emission-intermittency.pdf |
60c7403cf96a00631a286268 | 10.26434/chemrxiv.7666292.v1 | Single Oxygen Molecule Sensitivity of Organolead Halide Perovskite Photoluminescence | The photoluminescence (PL) of organolead halide
perovskites (OHPs) is sensitive to its surface conditions, especially surface
defect states, making the PL of small OHP crystals an effective way to report their
surface states. At the ensemble level, when averaging a lot of nanocrystals,
the photoexcitation of OHP nanorods under inert nitrogen (N<sub>2</sub>) atmosphere
leads to PL decline, while subsequent exposure to oxygen (O<sub>2</sub>)
results to reversible PL recovery. At the single-particle level, individual OHP
nanorods photoblinks, whose probability is dependent on both the excitation
intensity and the O<sub>2</sub> concentration. Combining the two sets of
information, we are able to quantitatively evaluating the interaction between a
single surface defect and a single O<sub>2</sub> molecule using a kinetic
model. This model provides fundamental insights that could help reconcile the
contradicting views on the interactions of molecular O<sub>2</sub> with OHP
materials and help design a suitable OHP interface for a variety of
applications in photovoltaics and optoelectronics. | Juvinch R. Vicente; Ali Rafiei Miandashti; Kurt Waldo E. Sy Piecco; Joseph R. Pyle; Martin E. Kordesch; Jixin Chen | Chemical Kinetics; Optics; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7403cf96a00631a286268/original/single-oxygen-molecule-sensitivity-of-organolead-halide-perovskite-photoluminescence.pdf |
67a56d386dde43c908de08df | 10.26434/chemrxiv-2025-g97zs | All-Solution-Processed Mid-Infrared Electrochromics (ASPIRE) for Thermoregulation with Arbitrary Curvatures | Mid-infrared (mid-IR) electrochromism is a promising technology that enables new ways to control radiative heat, which is particularly crucial for applications such as building thermoregulation efficiency, industrial process efficiency, spacecraft thermal engineering, and personal heat management. However, most mid-IR electrochromic devices are fabricated on planar substrates with fixed surface topography. When these planar devices are applied to three-dimensional and arbitrarily curved objects, they cannot fully conform to the objects’ surfaces, leaving an air gap and, thus, substantial thermal contact resistance that significantly compromises the efficacy of radiative thermoregulation. To address this long-standing issue, in this study, we developed a fabrication methodology that enables all-solution-processed electrochromic devices on the surface of arbitrarily curved 3D objects, effectively transforming the object surface into an electrically variable emittance layer. The key components are poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) as the active layer and charge storage layer, separated by the heterogeneous mixed ionic-electronic conductor consisting of HNO3-doped carbon nanotubes (CNTs) and crosslinked polyacrylamide (PAM)/lithium chloride (LiCl), all of which conform to the object surface layer-by-layer. The mid-IR electrochromic device exhibits an apparent temperature difference of 6.1 ℃ by adjusting emissivity on the planar substrate and 1.8 ℃ on the curved substrates. Our work demonstrates a promising approach and platform to achieve outward-facing flexible electrochromic cells with broad scientific and technological impacts on light and heat management. | Pei-Jan Hung; Qizhang Li; Ting-Hsuan Chen; Ching-Tai Fu; Yu Han; Ronghui Wu; Gangbin Yan; Qingsong Fan; Jiadong Liu; Pin-Ruei Huang; Yuanke Chen; Chenxi Sui; Genesis Higueros; Alex Flores; Fengyuan Shi; Po-Chun Hsu | Materials Science; Energy; Materials Processing; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a56d386dde43c908de08df/original/all-solution-processed-mid-infrared-electrochromics-aspire-for-thermoregulation-with-arbitrary-curvatures.pdf |
629e27c5d18cdf416051388d | 10.26434/chemrxiv-2022-0z4gm | Thermally Activated Tunneling in the Two-Water Bridge Catalyzed Tautomerization of Phosphinylidene Compounds | Phosphinylidenes are an important class of organophosphorus compounds that can exhibit tautomerization between tricoordinated P(III) hydroxide (R1R2POH) and a pentacoordinated P(V) oxide (R1R2P(O)H) form. Herein we show, using the canonical variational transition state theory combined with multidimensional small-curvature tunneling approximation, the dominance of proton tunneling in the two-water-bridged tautomerizations of phosphinous acid and model phosphinylidenes comprising phosphosphinates, H-phosphonates, H-phosphinates and secondary phosphine oxides. Based on the studied system, the contribution of thermally activated tunneling is predicted to speed up the semiclassical reaction rate by ca. threefold to as large as two orders of magnitude at 298.15 K in the gas phase. The large KIE and the concavity in the Arrhenius plots are further fingerprints of tunneling. The simulations also predicted that the rapid tunneling rate and short half-life span for the forward reaction, as opposed to the reverse reaction in fluorinated secondary phosphine oxides, would result in P(V) being fleetingly stable and only P(III) being isolable, which agrees with previous experiments where only P(III) was detected by IR and NMR spectroscopy. We also explored the role of solvent and predicted tunneling to be substantial. | Ashim Nandi; Gershom Martin | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629e27c5d18cdf416051388d/original/thermally-activated-tunneling-in-the-two-water-bridge-catalyzed-tautomerization-of-phosphinylidene-compounds.pdf |
60c74373842e6546f4db228e | 10.26434/chemrxiv.9177878.v1 | Heterobifunctional Molecules Induce Dephosphorylation of Kinases - a Proof of Concept Study | Previous work has shown that heterodimeric molecules, in some instances referred to as PROteolysis Targeting Chimeras, promote proximity of an E3-ligase to a target of interest to induce target ubiquitination. We hypothesize that many other PTMs, beyond ubiquitination, can be catalyzed in a similar matter. This work utilizes recruitment of PP1 (protein phosphatase 1) to induce de phosphorylation of target proteins (AKT and EGFR). To our knowledge, this work represents the first examples of small molecules recruiting non-native partners to induce removal of a PTM. <br /> | Sayumi Yamazoe; Steve Staben | Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74373842e6546f4db228e/original/heterobifunctional-molecules-induce-dephosphorylation-of-kinases-a-proof-of-concept-study.pdf |
60c752a94c8919d488ad4160 | 10.26434/chemrxiv.13332464.v1 | The Influence of the Artificial Nanostructure on the LiF Formation at the Solid-electrolyte Interphase of Carbon-based Anodes | The solid-electrolyte interphase (SEI) is of crucial importance for the performance of Li-ion batteries. Here, Density Functional Theory (DFT) calculations are used to study the formation of one of the simplest and early appearing components of the SEI layer, namely LiF, which is produced by splitting HF impurities. The process is investigated on different models representing the basal and edge planes of a graphitic anode, and on covalently connected carbon nanotubes and graphene sheets, known as pillared graphene. The results show that 2 Li atoms are required to bind F in the ?initial state in order to make the reaction energetically favorable, or alternatively a H atom must be pre-adsorbed. The Li adsorption energy, and thereby the Li coverage at a given potential, varies for the diff?erent carbon structures, demonstrating that the arti?ficial nanostructure of the carbon can in?fluence the formation of the SEI. | Katrine Louise Svane; Sebastian Zimmer Lefmann; Mads Schousboe Vilmann; Jan Rossmeisl; Ivano E. Castelli | Carbon-based Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752a94c8919d488ad4160/original/the-influence-of-the-artificial-nanostructure-on-the-li-f-formation-at-the-solid-electrolyte-interphase-of-carbon-based-anodes.pdf |
60c7447cee301c440bc79189 | 10.26434/chemrxiv.9841406.v1 | DFT Based Computational Methodology of IC50 | A new method derived from the relative toxicity equation termed as RICM, for the computation of IC<sub>50</sub>, is reported here. It is tested for both organic and organometallic compounds as HIV-1 capsid A inhibitors and cancer drugs. Computed results match very well with the experiment. This new method is very easily applicable for the organic molecules as well as organometallic compounds. Most importantly, this method does not require any computation facility provided we know the dipole moments of the unknown compound and reference compound. Applicability and accuracy of this method showed very good agreement with the experiment. Since RICM needs only the dipole moment of a compound for the computation of IC<sub>50</sub>, it may be used as a search criterion for the High Throughput Screening (HTS) used at the fi rst step of the in-silico drug designing. This would ease the algorithm for HTS and increase the success rate. | Arijit Bag | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7447cee301c440bc79189/original/dft-based-computational-methodology-of-ic50.pdf |
660a22a5e9ebbb4db917b00e | 10.26434/chemrxiv-2024-j89w5 | Trends in carbon nanotube research and development: A
landscape view of emerging applications and materials | Developing new materials for biomedical applications represents a dynamic and fast-growing interdisciplinary field of research. In this study, six emerging areas were identified in nanoscale materials in the context of biomedical applications by leveraging big data from the CAS Content Collection using quantitative analysis based on natural language processing (NLP). These emerging areas in biomaterials include self-healing, bioelectronic, programmable, lipid-based, protein-based, and antibacterial materials. In this perspective, we will examine the use of nanoscale materials in these areas. These uses range from enhancing the physical and electronic properties of materials used to interface with human tissue, to executing complex functions such as programmable drug delivery. | Kevin Hughes; Kavita Iyer; Robert Bird; Julian Ivanov; Saswata Banerjee; Gilles Georges; Qiongqiong Zhou | Materials Science; Carbon-based Materials; Composites; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660a22a5e9ebbb4db917b00e/original/trends-in-carbon-nanotube-research-and-development-a-landscape-view-of-emerging-applications-and-materials.pdf |
60c74c32337d6c3ae9e27be4 | 10.26434/chemrxiv.12445505.v1 | Amentoflavone: A Bifunctional Metal Chelator that Controls the Formation of Neurotoxic Soluble Aβ42 Oligomers | <p>Alzheimer's disease (AD) is
the most common neurodegenerative disorder, yet the cause and progression of
this disorder are not completely understood. While the main hallmark of AD is
the deposition of amyloid plaques
consisting of the β-amyloid (Aβ) peptide, transition metal ions are also
known to play a significant role in disease pathology by expediting the
formation of neurotoxic soluble β-amyloid (Aβ) oligomers, reactive oxygen
species (ROS), and oxidative stress. Thus, bifunctional metal chelators that
can control these deleterious properties are highly desirable. Herein, we show that amentoflavone (AMF) – a natural
biflavonoid compound, exhibits good metal-chelating properties, especially for chelating
Cu<sup>2+</sup> with very high affinity (pCu<sub>7.4</sub> = 10.44). In
addition, AMF binds to Aβ fibrils with a high affinity (<i>K<sub>i</sub></i> = 287 ± 20 nM) – as revealed by a competition thioflavin T (ThT) assay,
and specifically labels the amyloid plaques <i>ex vivo</i> in the brain
sections of transgenic AD mice – as confirmed via immunostaining with an Ab antibody. The effect of AMF on Aβ<sub>42</sub>
aggregation and disaggregation of Aβ<sub>42</sub> fibrils was also
investigated, to reveal that AMF can control the formation of neurotoxic
soluble Aβ<sub>42</sub> oligomers, both in absence and presence of metal ions,
and as confirmed via cell toxicity studies. Furthermore, an ascorbate
consumption assay shows that AMF exhibits potent antioxidant properties and can
chelate Cu<sup>2+</sup> and significantly diminish the Cu<sup>2+</sup>-ascorbate
redox cycling and reactive oxygen species (ROS) formation. Overall, these studies strongly suggest that AMF acts
as a bifunctional chelator that can interact with various Aβ aggregates and
reduce their neurotoxicity, can also bind Cu<sup>2+</sup> and mediate its
deleterious redox properties, and thus AMF has the potential to be a lead
compound for further therapeutic agent development for AD. </p> | Liang Sun; Anuj K. Sharma; Byung-Hee Han; Liviu M. Mirica | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c32337d6c3ae9e27be4/original/amentoflavone-a-bifunctional-metal-chelator-that-controls-the-formation-of-neurotoxic-soluble-a-42-oligomers.pdf |
657285f329a13c4d47f183c2 | 10.26434/chemrxiv-2023-4362s | Fluorosulfide La2.7Ba6.3F8.7S6 with Double-Layer Honeycomb Structure Enabling Fluoride-Ion Conduction | Mixed-anion compounds comprise anion-ordered layered structures with fluoride ionic conducting layers, which are not found in conventional metal fluorides. Hence, they represent a new frontier in the search for fluoride-ion conductors. Previous studies investigated only mixed-anion compounds with known crystal structures, but failed to exploit a flexible structural design. In this study, we performed a materials search based on the ternary phase diagram of BaS-LaF3-BaF2 for new fluorosulfide phases and found an unreported fluorosulfide, La2.7Ba6.3F8.7S6, showing the fluoride ion conductivity of 4.23×10−7 S cm−1 at 343 K. La2.7Ba6.3F8.7S6 forms an anion-ordered two-dimensional crystal lattice with double-honeycomb (La-Ba)F2 fluoride-ion-conducting layers, which cannot be realized in single-anion compounds. In the (La-Ba)F2 layers, the fluoride ion conduction is realized through normal F1 site and interstitial F2 site via a vacancy mechanism. The presence of sulfide ions in the crystal structure contributes to the spreading of (La-Ba)F2 layers along the ab plane, resulting in a longer La-F distance. Material development using a systematic phase diagram search on fluorosulfides allows to increase the variation of the crystal structure for fluoride ion conductors and to discover the novel fluoride ion conducting layers that are inaccessible to single anion compounds. | Shintaro Tachibana; Chengchao Zhong; Takeshi Tojigamori; Hidenori Miki; Toshiyuki Matsunaga; Yuki Orikasa | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657285f329a13c4d47f183c2/original/fluorosulfide-la2-7ba6-3f8-7s6-with-double-layer-honeycomb-structure-enabling-fluoride-ion-conduction.pdf |
60c74120469df45714f42d88 | 10.26434/chemrxiv.7539839.v2 | Electrocatalytic CO2 reduction at low overpotentials using iron(III) tetra(meso-thienyl)porphyrins | <p>The optical and electrochemical properties, as well as the CO<sub>2</sub> reduction capability of two different iron(III) thienyl-porphyrins, iron(III) tetra(<i>meso</i>-thien-2-yl)porphyrin (<b>FeTThP</b>) and iron(III) tetra(<i>meso</i>-5-methylthien-2-yl)porphyrin (<b>FeTThMeP</b>), are directly compared to those of iron(III) tetra(<i>meso</i>-phenyl)porphyrin (<b>FeTPP</b>). Through exploitation of mesomeric stabilization effects, <b>FeTThP</b> and <b>FeTThMeP</b> both reduced CO<sub>2</sub> to CO with comparable faradaic efficiencies and TON<sub>CO</sub> <sub> </sub>relative to <b>FeTPP</b>, with an overpotential 150 mV lower than the benchmark catalyst. </p> | Josh D. B. Koenig; Janina Willkomm; Roland Roesler; Warren Piers; Gregory C. Welch | Electrochemistry; Ligands (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74120469df45714f42d88/original/electrocatalytic-co2-reduction-at-low-overpotentials-using-iron-iii-tetra-meso-thienyl-porphyrins.pdf |
66333c31418a5379b039ea6a | 10.26434/chemrxiv-2024-8cxlz-v2 | From poison to promotor –unique Rh4 structural motifs in supported rhodium sulphides as hydroformylation catalysts | The hydroformylation of alkenes is a cornerstone transformation for the chemical industry, central for both functionalizing and extending the carbon backbone of an alkene. In our study, we explored silica-supported crystalline rhodium sulfide nanoparticles as heterogeneous catalysts in hydroformylation reactions, and found that RhxSy systems (x=17, y=15 or x=2, y=3 with 1 wt.% Rh on SiO2) greatly outperform metallic Rh nanoparticles. These systems proved to be exceptionally competitive when benchmarked against other cutting-edge catalysts in terms of activity, with Rh17S15/SiO2 being the superior catalyst candidate. By employing local environment descriptors, unsupervised machine learning and density functional theory, we have examined structure-performance relationships. Our results highlight that the presence of S in close proximity to the catalytic site unlocks the tunability of the surface catalytic properties. This allows for the substrate affinity to be modulated, in particular for Rh17S15, with adsorption energies rivaling those of pristine Rh and improved spatial resolution. | Arjun Neyyathala; Edvin Fako; Sandip De; Daria Gashnikova; Florian Maurer; Jan-Dierk Grunwaldt; Stephan A. Schunk; Schirin Hanf | Catalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66333c31418a5379b039ea6a/original/from-poison-to-promotor-unique-rh4-structural-motifs-in-supported-rhodium-sulphides-as-hydroformylation-catalysts.pdf |
676b8ccb6dde43c9083d70c6 | 10.26434/chemrxiv-2024-zn3fw | Regulating extracellular vesicle trafficking and intercellular communications with photo-reversible viscoelastic hydrogels | Extracellular vesicle (EV) mediated intercellular communication determines various physiological and pathological processes that show great potential as therapeutic reagents. While EV trafficking through extracellular matrix (ECM) is influenced by both vesicle deformation and medium re-organization or viscoelasticity, how matrix mechanics regulates EV intercellular transportation remains unclear. In this work, we introduced a photo-tunable hydrogel platform as ECM mimicry that allows well-defined viscoelasticity changes of the matrix to manipulate EV trafficking. The light-responsive dynamic bond formation/disruption in hydrogel triggers a sharp transformation of hydrogel between fast stress relaxation (ca. 50 s) and slow stress relaxation (> 1000 s) states. Such large viscoelasticity discrepancy leads to a varied transportation rate of EVs (ca. 2-fold) and consequential programmed cellular migration behaviors to the recipient fibroblast NIH-3T3 cells through photo-responsive hydrogel platform. Furthermore, using model membrane systems, we revealed how membrane rigidity and ECM viscoelasticity contribute together during EV intercellular trafficking. | Zi-Yuan Li; Yan-Wen Wang; Poh-Ching Tan; Meng Li; Yifan Ge; Shuang-Bai Zhou; Qing-Feng Li; Junji Zhang; He Tian | Organic Chemistry; Polymer Science; Photochemistry (Org.); Hydrogels; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676b8ccb6dde43c9083d70c6/original/regulating-extracellular-vesicle-trafficking-and-intercellular-communications-with-photo-reversible-viscoelastic-hydrogels.pdf |
6245790a9f61ca6b9ffcdd17 | 10.26434/chemrxiv-2022-k12lw | Ligand-free Nickel-catalyzed carboxylate O-arylation: Mechanistic in-sight into NiI/NiIII cycles | Nickel-catalyzed cross-coupling reactions have become a powerful methodology to construct C–heteroatom bonds. How-ever, many protocols suffer from competitive off-cycle reaction pathways and require non-equimolar amounts of cou-pling partners to suppress them. Here, we report on mechanistic examination of carboxylate O-arylation under thermal conditions, in both the presence and absence of an exogeneous bipyridine-ligand. Furthermore, spectroscopic studies of the novel ligand-free carboxylate O-arylation reaction unveiled the resting state of the nickel catalyst, the crucial role of the alkylamine base and the formation of a catalytically relevant NiI–NiII dimer upon reduction. This study provides in-sights into the competition between productive catalysis and deleterious pathways (comproportionation and pro-todehalogenation) that exist for all elementary steps in the commonly proposed self-sustained NiI/NiIII catalytic cycle. Thereby we show that for productive nickel-catalyzed carboxylate O-arylation a choice must be made between either mild conditions or equimolar ratios of substrates. | Lukas A. Wolzak; Felix J. de Zwart; Jean-Pierre H. Oudsen; Stuart A. Bartlett; Bas de Bruin; Joost N.H. Reek; Moniek Tromp; Ties J. Korstanje | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Spectroscopy (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6245790a9f61ca6b9ffcdd17/original/ligand-free-nickel-catalyzed-carboxylate-o-arylation-mechanistic-in-sight-into-ni-i-ni-iii-cycles.pdf |
60c73d0ebdbb89bb16a37bfc | 10.26434/chemrxiv.5393281.v1 | Bacterial detection and differentiation via direct volatile organic compound sensing with surface enhanced Raman spectroscopy | Through the direct detection of bacterial volatile organic compounds
(VOCs), via surface enhanced Raman spectroscopy (SERS), we report here a reconfigurable
assay for the identification and monitoring of bacteria. We demonstrate differentiation
between highly clinically relevant organisms: <i>Escherichia coli</i>, <i>Enterobacter
cloacae</i>, and <i>Serratia marcescens</i>.
This is the first differentiation of bacteria via SERS of bacterial VOC
signatures. The assay also detected as few as 10 CFU/ml of <i>E. coli</i> in under 12 hrs, and detected <i>E. coli</i> from whole human blood and human urine in 16 hrs at
clinically relevant concentrations of 10<sup>3</sup> CFU/ml and 10<sup>4</sup>
CFU/ml, respectively. In addition, the recent emergence of portable Raman
spectrometers uniquely allows SERS to bring VOC detection to point-of-care
settings for diagnosing bacterial infections. | Caitlin S. DeJong; David I. Wang; Aleksandr Polyakov; Anita Rogacs; Steven J. Simske; Viktor Shkolnikov | Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0ebdbb89bb16a37bfc/original/bacterial-detection-and-differentiation-via-direct-volatile-organic-compound-sensing-with-surface-enhanced-raman-spectroscopy.pdf |
6683af9401103d79c5c13fc9 | 10.26434/chemrxiv-2024-tdjrk | Modulating the Coordination Properties of 4-Coordinate Copper(I) Using Catenane Ligands Composed of Differently Sized Macrocycles | Upon coordination to catenane ligands derived from interlocked macrocycles of different size, gradual deviation of the coordination structure of the resulting 4-coordinate copper(I) complexes from the preferred tetrahedral geometry is resulted, and such structural distortion represents a new mechanism for modulating the thermodynamic, kinetic, photophysical and electrochemical properties of the transition metal complexes via ligand mechanical interlocking. Results from this study hence not only first demonstrate that the extend of catenand effect on metal coordination properties can be tuned by a physical attribute characteristic to mechanical interlocking, but also are implicated in the reactivity and potential applications of a distinct, rarely studied class of transition metal complexes supported by mechanically bonded ligands. | Yulin Deng; Zigang Lu; Samuel Kin-Man Lai; Xiaoyong Mo; Shan He; David Lee Phillips; Edmund Chun Ming Tse; Ho Yu Au-Yeung | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6683af9401103d79c5c13fc9/original/modulating-the-coordination-properties-of-4-coordinate-copper-i-using-catenane-ligands-composed-of-differently-sized-macrocycles.pdf |
60c741b5567dfe440cec3e39 | 10.26434/chemrxiv.7072646.v3 | Ni(0)-Catalyzed α-Allylic Alkylation of Regular Ketones with 1,3-Dienes under pH and Redox-neutral Conditions | <p>We report a
Ni(0)-catalyzed cross coupling reaction between simple ketones and 1,3-dienes. A
variety of a-allylic
alkylation products were formed in an 1,2-addition manner with excellent regioselectivity.
Water was found to significantly accelerate this transformation. A HO-Ni-H
species generated from oxidative addition of Ni(0) to H<sub>2</sub>O is
proposed to play a “dual role” in activating both the ketone and the diene
substrate.</p> | Tiantian Chen; Yang Yang; Liyu Xie; Haijian Yang; Guangbin Dong; Dong Xing | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741b5567dfe440cec3e39/original/ni-0-catalyzed-allylic-alkylation-of-regular-ketones-with-1-3-dienes-under-p-h-and-redox-neutral-conditions.pdf |
60c74dbe469df45313f44354 | 10.26434/chemrxiv.12659354.v1 | Microstructure and Pressure Driven Electrodeposition Stability in Solid-State Batteries | Interfacial deposition stability at the lithium metal-solid electrolyte interface in all solid-state batteries (ASSB) is governed by the stress-transport-electrochemistry coupling in conjunction with the polycrystalline/amorphous solid electrolyte architecture. In this work, we delineate the optimal solid electrolyte microstructure comprising of grains, grain boundary and voids possessing desirable ionic conductivity and elastic modulus for superior transport and strength. An analytical formalism is provided to discern the impact of external “stack” pressure induced mechanical stress on electrodeposition stability; stress magnitude obtained are in the megapascal range considerably diminishing the stress-kinetics effects. For experimental stack pressures ranging up to 10 MPa, the impact of stress on reaction kinetics is negligibly small and electrolyte transport overpotentials dictate electrodeposition stability. We detail the deposition stability phase map as a function of solid electrolyte to Li metal shear modulus and molar volume ratios under varying operating conditions including external pressure, surface roughness, applied current density and ambient temperature. High current density operation with stable deposition can be ensured with ample external pressure, high temperature and low surface roughness operation for low shear modulus ratio of the solid electrolyte to Li metal.
<br /> | Ankit Verma; Hiroki Kawkami; Hiroyuki Wada; Anna Hirowatari; Nobuhisa Ikeda; Yoshifumi Mizuno; Toshikazu Kotaka; Koichiro Aotani; Yuichiro Tabuchi; Partha P. Mukherjee | Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dbe469df45313f44354/original/microstructure-and-pressure-driven-electrodeposition-stability-in-solid-state-batteries.pdf |
678ff5736dde43c90897e505 | 10.26434/chemrxiv-2025-40cnn | The Type D Hyperporphyrin Effect | DFT and TDDFT calculations lend credence to the importance of a Type D resonance form for triply protonated 5,10,15-tris(4-aminophenyl)-20-(4-pyridyl)porphyrin (with all central nitrogens and the pyridine nitrogen protonated), in which all four meso-aryl groups engage in conjugative interactions with the porphyrin core. The LUMO of this species is strongly stabilized relative to the HOMO and LUMO+1 as a result of such an interaction with the pyridinium group, which leads to both a narrowing of the HOMO-LUMO gap and strongly split HOMO-to-LUMO and HOMO-to-LUMO+1 transitions in the Q region. This orbital energy pattern also explains key elements of the hyperporphyrin character of the species, strong redshifts of both the HOMO-to-LUMO transition in the Q region and the HOMO-1-to-LUMO transition in the Soret region. | Carl C. Wamser; Jeanet Conradie; Abhik Ghosh | Theoretical and Computational Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ff5736dde43c90897e505/original/the-type-d-hyperporphyrin-effect.pdf |
6465d217f2112b41e9bebcc8 | 10.26434/chemrxiv-2022-6gx8k-v2 | CHEMICAL SPACE ANALYSIS AND PROPERTY PREDICTION FOR CARBON CAPTURE AMINE MOLECULES | Carbon capture and storage is part of the roadmap towards net zero for many countries around the
world, since emissions from existing infrastructure are close to estimated carbon budgets. To address
this problem, currently 87 carbon capture projects are proposed worldwide in the next 10 years.
A major class of commercial carbon capture technology involves capture systems using solvents.
Commonly carbon capture solvents feature blends of amines and water. Whilst these blends have
proved valuable there is an increasing need to identify new candidate molecules which are more
efficient and improve performance. Systematic approaches to improve on the current technology
are now needed with increasing urgency to expedite the introduction of cutting edge carbon capture
methods. Here, we present a chemical space analysis of amines and carbon capture usage. We
proceed to show a framework for computational screening relevant to carbon capture solvents. We
demonstrate the use of cloud computing, novel molecular representations and machine learning to
screen potential candidates. We show the utility of machine learning in this field for high throughput
virtual screening with an exemplar application to absorption capacity classification. Additionally, we
highlight the need for improved data awareness and accessibility to enable this field to advance at a pace commensurate to its global importance. Our research brings together multiple methods and
domains of expertise to accelerate the discovery of carbon capture solvents. | James McDonagh; Stamatia Zavitsanou; Alexander Harrison; Dimitry Zubarev; Benjamin Wunsch; Theordore van Kessel; Flaviu Cipcigan | Theoretical and Computational Chemistry; Materials Science; Earth, Space, and Environmental Chemistry; Environmental Science; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6465d217f2112b41e9bebcc8/original/chemical-space-analysis-and-property-prediction-for-carbon-capture-amine-molecules.pdf |
67ce07c4fa469535b9a70512 | 10.26434/chemrxiv-2024-gstxb-v4 | Mechanism of DNA Chemical Denaturation | We developed a method to evaluate the degree of influence of attraction and electrostatic repulsion forces in DNA during its chemical denaturation. Our approach shows that when a target molecule can be split apart by a solution in which it is placed, the forces inside the molecule can be deduced by analyzing the properties of the surrounding solution. Our method can be suitable for selecting DNA (or other systems with controllable denaturation) targeted for specific applications and/or to optimize the denaturants for any given DNA. Our theory has been developed for DNA chemical denaturation for low and medium denaturation degrees, including but not limited to 50\% denaturation as a reversible first-order reaction. Specifically, we show the degrees of influence of hydrogen bonding, dispersion, polar forces, proton donor/acceptor ratio, dipole induction, orientation parameter, and electrostatic interaction on the denaturation process of DNA. The absolute enthalpy values for DNA chemical denaturation are significantly lower than those in the thermal denaturation process (positive). We show that the mechanism for reaching 50\% DNA denaturation differs thermally and chemically. The thermal denaturation process mainly involves breaking hydrogen bonds via heating, while the chemical denaturation process involves replacing the hydrogen bonding of DNA with denaturants. We show that hydrogen bonding is the most significant part of the enthalpy of chemical denaturation for the T4 bacteriophage DNA, and the proton-donor effect is the dominant mechanism in disrupting hydrogen bonds in DNA denaturation. The influence of this effect is two times greater than that of the proton-acceptor effect. We also show that another essential factor for DNA denaturation is the orientation component, which is part of the polar cohesion parameter. We show that the total cohesion parameter measured at 50\% of DNA chemical denaturation represents the electrostatic (repulsion) forces that maintain the DNA helix. The conclusions above were achieved using the cohesive energy density approach and corresponding equations based on the thermodynamics of the denaturation process. Independent experimental data, which we analyzed using our theory, supported these conclusions. | Daniel Ostrovsky; Mikhail Ostrovsky | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Biophysics; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ce07c4fa469535b9a70512/original/mechanism-of-dna-chemical-denaturation.pdf |
60c752bebb8c1abb9c3dbef9 | 10.26434/chemrxiv.13340579.v1 | Practically Achievable Process Performance Limits for Pressure-Vacuum Swing Adsorption Based Post-Combustion CO2 Capture | Practically achievable limits for pressure-vacuum swing adsorption (PVSA)-based post-combustion carbon capture are evaluated. The adsorption isotherms of CO2 and N2 are described by competitive Langmuir isotherms. Two low-energy process cycles are considered and a machine learning surrogate-model is trained with inputs from an experimentally-validated detailed PVSA model. Several case studies are considered to evaluate two critical performance indicators, namely, minimum energy and maximum productivity. For each case study, the genetic algorithm optimizer that is coupled to the machine learning surrogate model, searches tens of thousands of combinations of isotherms and process operating conditions. The framework pairs the optimum material properties with the optimum operating conditions, hence providing the limits of achievable performance. The results indicate that very low pressures ( <~0.2 bar) may be required to achieve process constraints for low feeds with low feed compositions ($<0.15$ mol fraction), indicating that PVSA may not be favourable. At higher CO2 feed compositions, PVSA can be attractive and can be operated at practically achievable vacuum levels. Further, the gap between the energy consumption of available adsorbents and the achievable limits with a hypothetical -best adsorbent varies between 20% to 2.5% as the CO2 feed composition changes between 0.05 to 0.4. This indicates a limited potential for development of new adsorbents of PVSA-based CO2 capture. Future work for PVSA should focus on flue gas streams with high CO2 compositions | Kasturi Nagesh Pai; Vinay Prasad; Arvind Rajendran | Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752bebb8c1abb9c3dbef9/original/practically-achievable-process-performance-limits-for-pressure-vacuum-swing-adsorption-based-post-combustion-co2-capture.pdf |
60c74df1bdbb89cf6da39aa5 | 10.26434/chemrxiv.12673436.v1 | Copper(II) Inhibition of the SARS-CoV-2 Main Protease | In an analysis of the structural stability of the coronavirus main protease (Mpro), we identified regions of the protein that could be disabled by cobalt(III)-cation binding to histidines and cysteines [1]. Here we have extended our work to include copper(II) chelates, which we have docked to HIS 41 and CYS 145 in the Mpro active-site region. We have found stable docked structures where Cu(II) could readily bond to the CYS 145 thiolate, which would be lethal to the enzyme. We also started studying the Spike Protein, PDB ID: 6VXX and the region around the D614G mutant. | Roberto A. Garza-Lopez; John J. Kozak; Harry B. Gray | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Biochemistry; Computational Chemistry and Modeling; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df1bdbb89cf6da39aa5/original/copper-ii-inhibition-of-the-sars-co-v-2-main-protease.pdf |
60c754669abda21f3cf8e18b | 10.26434/chemrxiv.13270184.v2 | Benchmarking binding energy calculations for organic structure-directing agents in pure-silica zeolites | Molecular modeling plays an important role in the discovery of organic structure-directing agents (OSDAs) for zeolites. By quantifying the intensity of host-guest interactions, it is possible to select cost-effective molecules that maximize binding towards a given zeolite framework. Over the last decades, a variety of methods and levels of theory have been used to calculate these binding energies. Nevertheless, there is no consensus on the best calculation strategy for high-throughput virtual screening undertakings. In this work, we compare binding affinities from density functional theory (DFT) and force field calculations for 272 zeolite-OSDA pairs obtained from static and time-averaged simulations. Enabled by automation software, we show that binding energies from the frozen pose method correlate best with DFT time-averaged energies. They are also less sensitive to the choice of initial lattice parameters and optimization algorithms, as well as less computationally expensive. Furthermore, we demonstrate that a broader exploration of the conformation space from molecular dynamics simulations does not provide significant improvements in binding energy trends over single-point calculations. The code and benchmark data are open-sourced and provide robust and computationally-efficient guidelines to calculating binding energies in zeolite-OSDA pairs. | Daniel Schwalbe-Koda; Rafael Gomez-Bombarelli | Catalysts; Hybrid Organic-Inorganic Materials; Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754669abda21f3cf8e18b/original/benchmarking-binding-energy-calculations-for-organic-structure-directing-agents-in-pure-silica-zeolites.pdf |
61a99cec03232f11e3241f6f | 10.26434/chemrxiv-2021-862d4 | Synthesis and styrene copolymerization of novel alkoxy ring-substituted tert-butyl phenylcyanoacrylates | Novel alkoxy ring-substituted tert-butyl phenylcyanoacrylates, RPhCH=C(CN)CO2C(CH3)3 (where R is 2-methoxy, 3-methoxy, 4-methoxy, 2-ethoxy, 3-ethoxy, 4-ethoxy, 4-propoxy, 4-butoxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and tert-butyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were radically copolymerized with styrene in solution at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Ana K Delgado Ayala; Ellie C. Mink; Surbhee J. Patil; Abdul Rafay; Aisha A. Shoneye; Jonathan Tran; Spencer J. Weis; Judy Zakieh; Sara M. Rocus; William Schjerven; Gregory Kharas | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a99cec03232f11e3241f6f/original/synthesis-and-styrene-copolymerization-of-novel-alkoxy-ring-substituted-tert-butyl-phenylcyanoacrylates.pdf |
60c744c30f50db78fb39616e | 10.26434/chemrxiv.9916622.v1 | Solvent-Free Powder Synthesis and Thin Film Chemical Vapour Deposition of a Zinc Bipyridyl-Triazolate Framework | MAF-252, a non-porous crystalline coordination polymer, is obtained from the solvent-free reaction of ZnO with 3-(2-pyridyl)-5-(4-pyridyl)-1,2,4-triazole. MAF-252 can be synthesized in powder form and deposited as thin films, starting from ZnO powder and layers, respectively. Chemical vapour deposition (CVD) of MAF-252 enables conformal and patterned thin films, even on high aspect ratio features. | Timothée Stassin; Ivo Stassen; Nathalie Wauteraerts; Alexander John Cruz; Marianne Kräuter; Anna Maria Coclite; Dirk De Vos; Rob Ameloot | Hybrid Organic-Inorganic Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744c30f50db78fb39616e/original/solvent-free-powder-synthesis-and-thin-film-chemical-vapour-deposition-of-a-zinc-bipyridyl-triazolate-framework.pdf |
65ba4b9c66c1381729a58f31 | 10.26434/chemrxiv-2024-08847-v2 | Late-stage reshaping of phage-displayed libraries to macrocyclic and bicyclic landscapes using multipurpose linchpin | Genetically-encoded libraries (GEL) are increasingly used for discovery of ligands for ‘undruggable’ targets that cannot be addressed with small molecules. Foundational GEL platforms like phage-, yeast-, ribosome- and mRNA-display enabled display of libraries composed of 20 natural amino acids (20AA). Today, numerous strategies expand GEL beyond 20AA space by incorporating unnatural amino acids (UAA) and chemical post-translational modification (cPTM) to build linear, cyclic, and bicyclic peptides. The standard operating procedure for UAA and cPTM libraries starts from a "naïve" chemically-upgraded library with 108-1012 compounds, uses target of interest and rounds of selection to narrow down to a set of receptor binding hits. However, such approach uses zero knowledge of natural peptide-receptor interactions which already exists in libraries with 20AA space. There is currently no consensus whether ‘zero knowledge’ naïve libraries or libraries with pre-existing knowledge can offer a more effective path to discovery of molecular interactions. In this manuscript, we evaluated the feasibility of discovery of macrocyclic and bicyclic peptide from "non-zero knowledge" libraries. We approach this problem by late-stage chemical reshaping of phage-displayed landscape of 20AA binders to NS3aH1 protease. The re-shaping is performed under a novel multifunctional C2-symmetric linchpin, 3,5-bis(bromomethyl)benzaldehyde (termed KYL), that combines two electrophiles that react with thiols and aldehyde group that reacts with N-terminal amine. KYL diversified phage-displayed peptides into bicyclic architectures and delineates 2 distinct sequence populations: (i) peptides that retained binding upon bicyclization (ii) peptides that lost binding once chemically modified. Our report provides a case study for discovering advanced, chemically-upgraded macrocycles and bicycles from libraries with pre-existing knowledge. The results imply that thousands of selection campaigns completed in 20AA space, in principle, can serve for late-stage reshaping and as a starting point for discovery of advanced peptide-derived ligands. | Kejia Yan; Mark Miskolzie; Fernando Bañales Mejia; Chuanhao Peng; Arunika I. Ekanayake; Dustin J. Maly; Ratmir Derda | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba4b9c66c1381729a58f31/original/late-stage-reshaping-of-phage-displayed-libraries-to-macrocyclic-and-bicyclic-landscapes-using-multipurpose-linchpin.pdf |
60c74850842e653e3ddb2b93 | 10.26434/chemrxiv.11888619.v1 | A Molecular Boron Cluster-Based Chromophore with Dual Emission | Bromination of the luminescent borane, anti-B18H22, via electrophilic substitution using AlCl3 and Br2 yields the monosubstituted derivative 4-Br-anti-B18H21 as an air-stable crystalline solid. In contrast to the unsubstituted parent compound, 4-Br-anti-B18H21 product possesses dual emission upon excitation with UV light and exhibits fluorescence at 410 nm and phosphorescence at 503 nm, with Фtotal = 0.07 in oxygen-free cyclohexane. Increased oxygen content in cyclohexane solution quenches the phosphorescence signal. The fluorescent signal intensity remains unaffected by oxygen, suggesting that this molecule could be used as a ratiometric oxygen probe. | Kierstyn P. Anderson; Mary A. Waddington; Gary J. Balaich; Julia M. Stauber; Justin
R. Caram; Peter
I. Djurovich; Alexander Spokoyny | Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74850842e653e3ddb2b93/original/a-molecular-boron-cluster-based-chromophore-with-dual-emission.pdf |
67442c717be152b1d0aecbe6 | 10.26434/chemrxiv-2024-wswdn | Development of first-in-class PROTAC degraders of TAK1 | Transforming growth factor (TGF)-β-activated kinase 1 (TAK1) is a serine/threonine kinase serving as a critical signaling node in cellular responses to various inflammatory stimuli. Dysregulation of TAK1-mediated pathways is commonly associated with inflammatory diseases and cancer, rendering TAK1 a promising pharmacological target for therapeutic intervention. In this study, we report the design and development of proteolysis-targeting chimeras (PROTACs) specifically tailored to degrade TAK1, offering a novel therapeutic approach for TAK1-related diseases. Takinib-based heterobifunctional compounds 11 and 16 induced potent, proteasome-dependent TAK1 depletion in tumor necrosis factor-alpha (TNF-α)-stimulated cancer cells. In cellular assays, these PROTACs demonstrated superior efficacy over takinib and its combination with corresponding E3 ligase ligands in reducing cancer cell viability and inducing apoptosis. The TAK1 degraders presented here provide valuable tools to further investigate the biological roles of TAK1 in diverse pathological and physiological contexts. | Nika Strašek Benedik; Aleša Bricelj; Maciej Suski; Dong Zhu; Matej Sova; Justyna Godyń; Anna Więckowska; Michael Gütschow; Christian Steinebach; Dongwen Lv; Martina Gobec; Izidor Sosič | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67442c717be152b1d0aecbe6/original/development-of-first-in-class-protac-degraders-of-tak1.pdf |
675e4d6d085116a13371a8d8 | 10.26434/chemrxiv-2024-0ps6q | Transforming carbon dioxide into high-value chemicals via sustainable solid oxide electrochemical reactor | Achieving a carbon-neutral society requires strategies that seamlessly integrate environmental sustainability with economic viability. Solid oxide electrochemical reactors (SOERs) hold the potential to concurrently recycle CO2 while synthesizing high-value propylene from low-cost gases using surplus renewable electricity. However, existing SOER designs face significant challenges in slow reaction kinetics and instability. We present evidence that Fe-Ni-Ru alloy@FeOx core-shell nanoparticles on the Sr2Fe1.5Mo0.4Ni0.05Ru0.05O6-δ electrode of SOER substantially enhance electrochemical CO2 reduction at the cathode, and propane conversion to propylene and ethylene at the anode through the promotion of active oxygen species at the surfaces. The formation of core-shell nanoparticles lowers the activation energy of polarization resistance from 2.1 eV to 0.82 eV, facilitating high current densities and 150 h of stable SOER operation with an 80% selectivity for propylene and ethylene production. Density functional theory calculations suggest that this enhancement is due to the reduced activation energy for dissociative CO2 reduction on the surface of Fe-Ni-Ru alloy@FeOx core-shell nanoparticles. These results show the potential of the self-organized core-shell nanoparticles in SOERs for economical CO2 recycling, offering a promising approach in the pursuit of a carbon-neutral future. | Nai Shi; Xueyu Hu; Yun Xie; Shaowei Zhang; Junji Hyodo; Kang Zhu; Zongping Shao; Yoshihiro Yamazaki | Materials Science; Catalysis; Energy | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675e4d6d085116a13371a8d8/original/transforming-carbon-dioxide-into-high-value-chemicals-via-sustainable-solid-oxide-electrochemical-reactor.pdf |
65ccd96e66c1381729a31148 | 10.26434/chemrxiv-2024-tz8vc | Redox-powered autonomous unidirectional rotation about a C–C bond under enzymatic control | Living biological systems rely on the continuous operation of chemical reaction networks. These networks sustain out-of-equilibrium regimes in which chemical energy is continually converted into controlled mechanical work and motion. Out-of-equilibrium reaction networks have also enabled the design and successful development of artificial autonomously operating molecular machines, in which networks comprising pairs of formally—but non-microscopically—reverse reaction pathways drive controlled motion at the molecular level. In biological systems, the concurrent operation of multiple reaction pathways is enabled by the chemoselectivity of enzymes and their co-factors, and nature’s dissipative reaction networks involve several classes of reactions. In contrast, the reactivity that has been harnessed to develop chemical reaction networks in pursuit of artificial molecular machines is limited to a single reaction type. Only a small number of synthetic systems exhibit chemically fuelled continuous controlled molecular-level motion, and all exploit the same class of acylation–hydrolysis reaction. Here we show that a redox reaction network, comprising concurrent oxidation and reduction pathways, can drive chemically fuelled continuous autonomous unidirectional motion about a C–C bond in the most structurally simple synthetic molecular motor yet reported, an achiral biphenyl. The combined use of an oxidant and reductant as fuels, and the directionality of the motor, are both enabled by exploiting the enantioselectivity and functional separation of reactivity inherent to enzyme catalysis. | Beatrice Collins; Jonathan Clayden; Jordan Berreur; Olivia Watts; Theo Bulless; Nicholas O'Donoghue; Ashley Winter | Organic Chemistry; Catalysis; Stereochemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ccd96e66c1381729a31148/original/redox-powered-autonomous-unidirectional-rotation-about-a-c-c-bond-under-enzymatic-control.pdf |
64c012a1b053dad33ae21932 | 10.26434/chemrxiv-2023-q11q4-v2 | Real-World Molecular Out-Of-Distribution: Specification and Investigation | This study presents a rigorous framework for investigating Molecular Out-Of-Distribution (MOOD) generalization in drug discovery. The concept of MOOD is first clarified through a problem specification that demonstrates how the covariate shifts encountered during real-world deployment can be characterized by the distribution of sample distances to the training set. We find that these shifts can cause performance to drop by up to 60% and uncertainty calibration by up to 40%. This leads us to propose a splitting protocol that aims to close the gap between deployment and testing. Then, using this protocol, a thorough investigation is conducted to assess the impact of model design, model selection and dataset characteristics on MOOD performance and uncertainty calibration. We find that appropriate representations and algorithms with built-in uncertainty estimation are crucial to improve performance and uncertainty calibration. This study sets itself apart by its exhaustiveness and opens an exciting avenue to benchmark meaningful, algorithmic progress in molecular scoring. All related code can be found on Github at https://github.com/valence-labs/mood-experiments. | Prudencio Tossou; Cas Wognum; Michael Craig; Hadrien Mary; Emmanuel Noutahi | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2023-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c012a1b053dad33ae21932/original/real-world-molecular-out-of-distribution-specification-and-investigation.pdf |
6615c24821291e5d1d7c2e48 | 10.26434/chemrxiv-2024-60ngs | Modeling intermolecular Coulombic decay with non-Hermitian real-time time-dependent density functional theory | In this work, we investigate the capability of using real-time time-dependent density functional theory (RT-TDDFT) in conjunction with a complex absorbing potential (CAP) to simulate the intermolecular Coulombic decay (ICD) processes following the ionization of an innervalence electron. We examine the ICD dynamics in a series of non-covalent bonded dimer systems, including H2O-H2O, HF-HF, Ar-H2O, Ne-H2O and Ne-Ar. We consider an initial state generated from an inner-valence excitation on either monomer within each dimer, as the monomers are symmetrically not equivalent. In comparison to previous RT-TDDFT studies, we show that RT-TDDFT simulations with a CAP correctly capture the ICD phenomenon in systems exhibiting a stronger binding energy. The calculated time-scales for ICD of the studied systems are in the range of 5-50 fs in agreement with previous studies. However, there is a break-down in the accuracy of the methodology for the more weakly bound, pure van der Waals bonded systems. The accuracy in the former is attributed to both the use of the CAP and the choice of a long-range corrected functional with diffuse basis functions. The benefit of the presented real-time methodology is that it provides direct time-dependent population information without necessitating any a-priori assumptions about the electronic relaxation mechanism. As such, the RT-TDFFT/CAP simulation protocol provides a powerful tool to differentiate between competing electronic relaxation pathways following inner-valence or core ionization. | Yi-Siang Wang; James Zhong Manis; Matthew Rohan; Thomas Orlando; Joshua Kretchmer | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615c24821291e5d1d7c2e48/original/modeling-intermolecular-coulombic-decay-with-non-hermitian-real-time-time-dependent-density-functional-theory.pdf |
661697e091aefa6ce142c9d8 | 10.26434/chemrxiv-2023-prk53-v2 | Guided docking as a data generation approach facilitates structure-based machine learning on kinases | Drug discovery pipelines nowadays rely on machine learning models to explore and evaluate large chemical spaces. While including 3D structural information is considered beneficial, structural models are hindered by the availability of protein-ligand complex structures. Exemplified for kinase drug discovery, we address this issue by generating kinase-ligand complex data using template docking for the kinase compound subset of available ChEMBL assay data. To evaluate the benefit of the created complex data, we use it to train a structure-based E(3)-invariant graph neural network (GNN). Our evaluation shows that binding affinities can be predicted with significantly higher precision by models that take synthetic binding poses into account compared to ligand or DTI models only. | Michael Backenköhler; Joschka Groß; Verena Wolf; Andrea Volkamer | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661697e091aefa6ce142c9d8/original/guided-docking-as-a-data-generation-approach-facilitates-structure-based-machine-learning-on-kinases.pdf |
6357c6b61db0bd295038c26c | 10.26434/chemrxiv-2022-4pg74-v2 | One-pot approach for multi-step, iterative synthesis of sequence-defined oligocarbamates | High-yielding and scalable methods for iterative synthesis of sequence-defined macromolecules is a great challenge in modern polymer chemistry. Sequence-defined macromolecules are fabricated by multi-step iterative processes that involve high reagents and solvents consumption. Moreover, every step causes yield losses that result in low overall yield. Despite the envisioned valuable functions and applications of sequence-defined polymers, the synthetic limitations constitute a barrier for the exploitation of their practical potential. Here, we investigated the one-pot synthesis of oligocarbamates without the purification of intermediates. To control monomer sequence without isolation, we introduced a monitoring feedback loop to fuel the exact amount of reagents to the reaction mixture, assuring full conversion of each reaction. Based on a one-pot strategy, we have developed a facile approach for the preparation of uniform, oligocarbamates with full control of monomer order and defined stereochemistry. The great advantage of the presented methodology is the scalability of the process (demonstrated for synthesis of 50 g) and high yield (up to 90%). Oligomers obtained on a large scale can be further used as precursors for the synthesis of polymers with high molar mass. One-pot methods combined with chemoselective reactions bear the potential to overcome existing synthesis limitations and unlock the practical use of sequence-defined macromolecules. The presented concept might be further extended to different multi-step processes. | Pawel Cwynar; Pawel Pasikowski; Roza Szweda | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6357c6b61db0bd295038c26c/original/one-pot-approach-for-multi-step-iterative-synthesis-of-sequence-defined-oligocarbamates.pdf |
6672107601103d79c587ccc0 | 10.26434/chemrxiv-2024-hf4cq | Heterogeneous Doping via Nanoscale Coating Impacts Mechanics of Li Intrusion in Brittle Solid Electrolytes | Lithium metal electroplating and short-circuiting limit fast charging in solid-state batteries, yet the mechanisms and methods to regulate lithium intrusions are not well-understood. In this work, we discover that nanoscale heterogeneous Ag+ doping dramatically affects lithium intrusion in Li6.6La3Zr1.6Ta0.4O12 (LLZO), a brittle solid electrolyte. We generate nanoscale Ag+ doping by thermally annealing a 3-nm-thick metallic film. The metallic Ag undergoes Ag-Li ion exchange, completely disappears, and diffuses into LLZO bulk and grain boundaries to a depth of 20-50 nm. Density functional theory calculations predict this Ag-Li ion exchange exhibits negligible impact on electronic properties. Mechanically, nanoindentation experiments (n = 69) show a fivefold increase in the force required to fracture Ag+ surface-doped LLZO (Ag+-LLZO), providing direct evidence that surface modification due to Ag+ incorporation prevents crack opening. Conducting 121 plating experiments via operando microprobe scanning electron microscopy, we further confirm that the Ag+-LLZO surface exhibits improved lithium plating even under a large local indentation stress of 3 GPa. Surprisingly, microprobe plating reveals that Ag+ increases the diameter of plated Li at failure by more than 4 times, demonstrating its role in enhancing the defect tolerance of LLZO. Our study reveals a chemo-mechanical mechanism via surface heterogeneous doping, complementing the present bulk design rules to prevent mechanical failures in solid-state batteries. | Xin Xu; Teng Cui; Geoff McConohy; Harsh Jagad; Yufei Yang; Sunny Wang; Samuel Lee; Celeste Melamed; Edward Barks; Emma Kaeli; Leah Narun; Yi Cui; Zewen Zhang; Hye-Ryoung Lee; Rong Xu; Melody Wang; Ajai Romana; Alexis Geslin; Robert Sinclair; Yi Cui; Yue Qi; Wendy Gu; William Chueh | Materials Science; Nanoscience; Energy; Ceramics; Nanostructured Materials - Nanoscience; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6672107601103d79c587ccc0/original/heterogeneous-doping-via-nanoscale-coating-impacts-mechanics-of-li-intrusion-in-brittle-solid-electrolytes.pdf |
64bc03ccae3d1a7b0d29f65b | 10.26434/chemrxiv-2023-w6c7p | Oxidative Cleavage of Ketoximes to Ketones using Photoexcited Nitroarenes | Methoximes are a versatile directing group for a variety of C–H functionalizations. Despite their importance as a powerful functional handle, their conversion to the parent ketone, which is often desired, usually requires harsh and functional group intolerant reaction conditions that make their application in a late-stage context problematic. Here, we present an alternative set of conditions to achieve mild and functional group tolerant conversion of methoximes to the parent ketones using photoexcited nitroarenes. The utility of this methodology is showcased in its application in the total synthesis of cephanolide D. Furthermore, mechanistic insight into this transformation obtained using isotope labeling studies as well as the analysis of reaction byproducts is provided. | Lucas Göttemann; Stefan Wiesler; Richmond Sarpong | Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bc03ccae3d1a7b0d29f65b/original/oxidative-cleavage-of-ketoximes-to-ketones-using-photoexcited-nitroarenes.pdf |
675ae355f9980725cfd783d6 | 10.26434/chemrxiv-2024-70tj6 | Applying the Maxwell-Stefan Diffusion Framework to Multicomponent Battery Electrolytes | The Doyle-Fuller-Newman model is widely applied for the simulation of Li-ion batteries (LIBs), and considers a binary electrolyte (one anion, one cation, one solvent) using Maxwell-Stefan diffusion. However, commercial electrolytes composed of LiPF6 dissolved in a mixture of cyclic and linear organic carbonates, are not accurately captured within this description. Here, using Raman spectroscopy of an optically-accessible electrochemical cell, we obtain concentration profiles for each electrolyte species, confirming they deviate significantly from those expected from a single-solvent assumption. Starting from parameters obtained from classical molecular dynamics, we thus develop an iterative fitting approach to parametrize multicomponent LIB electrolytes based on such concentration profiles. Importantly, each electrolyte component can be accurately simulated, to better understand their contributions to battery performance and degradation. The robust methodology developed for the parameterization of multicomponent LIB electrolytes is expected to aid the development and optimization of future LIBs. | Conor Phelan; Jack Swallow; Robert Weatherup | Theoretical and Computational Chemistry; Materials Science; Energy; Polyelectrolytes - Materials; Theory - Computational; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675ae355f9980725cfd783d6/original/applying-the-maxwell-stefan-diffusion-framework-to-multicomponent-battery-electrolytes.pdf |
65b22d189138d23161b23829 | 10.26434/chemrxiv-2024-0xclc | Isolation of Fidaxomicin and Shunt Metabolites from Actinoplanes deccanensis | A protocol for the isolation of the antibiotic fidaxomicin (Fdx) from Actinoplanes deccanensis and the isolation of shunt metabolites from A. deccanensis fdxG2- is reported. We constructed the mutant strain A. deccanensis fdxG2- by genetic manipulation which enabled the isolation of shunt metabolites as useful starting points for semisynthetic analogues of Fdx. Furthermore, a synthetic protocol for the conversion of complex A. deccanensis fdxG2- extracts into the single compound FdxG2-OH via methanolysis is presented. This synthetic procedure is complemented by images and practical notes. Full structure assignment is given in the SI and the characterization data files are published to aid experimentalists. The protocol is also suitable as an undergraduate laboratory project. We hope to facilitate research into new Fdx derivatives through the availability of this procedure. | Erik Jung; Maja Hunter; Andrea Dorst; Alexander Major; Tatjana Teofilovic; Rolf Müller; Karl Gademann | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b22d189138d23161b23829/original/isolation-of-fidaxomicin-and-shunt-metabolites-from-actinoplanes-deccanensis.pdf |
60c741a7842e65f61cdb1f1d | 10.26434/chemrxiv.7687358.v2 | Fused Hybrid Linkers for Metal–Organic Frameworks-Derived Bifunctional Oxygen Electrocatalysts | <div>
<div>
<div>
<p>Preparation of electrocatalysts often relies on the use of multiple starting materials – inorganic
salts or organometallic precursors, nanostructured carbon supports, organic additives, dopants
and carbonization under modifying atmospheres (e.g. NH<sub>3 </sub>or H<sub>2</sub>) – with the examples of
electrocatalysts arising from a single precursor being much less common. Herein, we have
surveyed a series of heterobivalent scaffolds to identify an iron/benzimidazole-based metal–
organic framework as a uniform starting material. By merging the catechol and imidazole units
together, we get direct entry into a highly efficient bifunctional oxygen electrocatalyst, which
alleviates the need for additional dopants and modifying conditions (ORR: <i>E</i><sub>on</sub> = 1.01 V, <i>E</i><sub>1/2</sub> =
0.87 V vs. RHE in 0.1 M KOH; OER: 1.60 V @10 mA cm<sup>–2</sup> in 0.1 M KOH; ∆<i>E</i> = 0.73 V). We
demonstrate that by fine-tuning the chemical nature of an organic linker, one is able modulate the
electrochemical properties of a single precursor-derived electrocatalyst material.
</p>
</div>
</div>
</div> | Kefeng Ping; Alan Braschinsky; Mahboob Alam; Rohit Bhadoria; Valdek Mikli; Arvo Mere; Jaan Aruväli; Päärn Paiste; Sergei Vlassov; Mati Kook; Mihkel Rähn; Väino Sammelselg; Kaido Tammeveski; Nadezda Kongi; Pavel Starkov | Carbon-based Materials; Catalysts; Fuels - Materials; Hybrid Organic-Inorganic Materials; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a7842e65f61cdb1f1d/original/fused-hybrid-linkers-for-metal-organic-frameworks-derived-bifunctional-oxygen-electrocatalysts.pdf |
653ff85f48dad23120b7f7e5 | 10.26434/chemrxiv-2023-r6vz1 | Laryngeal Cancer Diagnosis via miRNA-based Decision Tree Model | Purpose Laryngeal cancer (LC) is the most common head and neck cancer, which often goes undiagnosed due to the expensiveness and inaccessible nature of current diagnosis methods. Many recent studies have shown that microRNAs (miRNAs) are crucial biomarkers for a variety of cancers. Methods In this study, we create a decision tree model for the diagnosis of laryngeal cancer using a calculated miRNAs’ attributes, such as sequence-based characteristics, predicted miRNA target genes, and gene pathways. This series of attributes is extracted from both differentially expressed blood-based miRNAs in laryngeal cancer and random, non-associated with cancer miRNAs. Results Several machine-learning (ML) algorithms were tested in the ML model, and the Hoeffding Tree (HT) classifier yields the highest accuracy (86.8%) in miRNAs-based recognition of laryngeal cancer. Furthermore, HT-based model is validated with the independent laryngeal cancer datasets and can accurately diagnose laryngeal cancer with 86% accuracy. We also explored the biological relationships of the attributes used in HT-based model to understand their relationship with cancer proliferation or suppression pathways. Conclusion Our study demonstrates that the proposed model and an inexpensive miRNA testing strategy have the potential to serve as a cost-effective and accessible method for diagnosing laryngeal cancer. | Aarav Arora; Igor Tsigelny; Valentina Kouznetsova | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653ff85f48dad23120b7f7e5/original/laryngeal-cancer-diagnosis-via-mi-rna-based-decision-tree-model.pdf |
64a39606ba3e99daef795285 | 10.26434/chemrxiv-2023-7s65b | Ultrasensitive Ionophore-Based Liquid Sensors for Colorimetric Ion Measurements in Whole Blood | Self-monitoring of electrolytes using a small volume of capillary blood is needed for the management of many chronic dis-eases. Herein we report an ionophore-based colorimetric sensor for electrolyte measurements in a small drop of blood. The sensor is a pipette microtip preloaded with a segment of oil (plasticizer) containing a pH-sensitive chromoionophore, a cation exchanger, and an ionophore. The analyte is extracted from the sample into the oil via a mixing protocol controlled by a stepper motor. The oil with an optimized ratio of sensing chemicals shows an unprecedentedly large color response for elec-trolytes in the very narrow concentration range of clinical relevance. This ultrahigh sensitivity is based on an exhaustive re-sponse mode with a novel mechanism of defining lower and higher limits of detection. Compared to previous optodes and molecular probes for ions, the proposed platform is especially suitable for at-home blood electrolyte measurements because 1) the oil sensor is interrogated independently from the sample and, therefore, works for whole blood without requiring plasma separation; 2) the liquid sensor does not need individual calibration as the consistency between sensors from the same solution or different batches of solution is high compared to solid sensors such as ion-selective electrodes and optodes; 3) the sensing system consisting of a disposable oil sensor, a programmed stepper motor, and a smartphone is portable, cost-effective, and user-friendly. The accuracy and precision of Ca2+ sensors are validated in 51 blood samples with varying con-centrations of total plasma Ca2+. Oil sensors with an ultrasensitive response can also be obtained for other ions such as K+. | Nasrin Ghanbari Ghalehjoughi; Renjie Wang; Savannah Kelley; Xuewei Wang | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a39606ba3e99daef795285/original/ultrasensitive-ionophore-based-liquid-sensors-for-colorimetric-ion-measurements-in-whole-blood.pdf |
60c74efe4c891954b4ad3b1b | 10.26434/chemrxiv.11914377.v2 | DFT Calculations Investigate Competing Pathways to Form Dimeric Neopentylpalladium(II) Amido Complexes | Computational methods were utilized to study the formation of a dimeric neopentylpalladium(II) amido complex (D). The dimeric core of D contains asymmetric bridging of the anilide groups. Electron density analyses indicate that each palladium center of D forms a dative bond to the nitrogen trans to the coordinated phosphine, while the bond to the nitrogen cis to the phosphine lies closer to the covalent regime. Analysis of the structure of D was corroborated by study of the frontier orbitals and the energetics of dimerization. D was likely generated by the monomers with cis P,N configuration rather than those with trans P,N configuration, which is an important side reaction that inhibits the desired C–N bond coupling. Calculations further revealed the critical importance of dispersion interactions upon dimerization and suggested one possible dimeric isomer Q.<br /> | Quan Jiang; Thomas Cundari | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74efe4c891954b4ad3b1b/original/dft-calculations-investigate-competing-pathways-to-form-dimeric-neopentylpalladium-ii-amido-complexes.pdf |
65dad40066c138172979c8df | 10.26434/chemrxiv-2023-0d815-v3 | Room Temperature Phosphorescent Nanofiber Membranes by Bio-fermentation | Stimuli-responsive materials exhibiting exceptional room temperature phosphorescence (RTP) hold promise for emerging technologies. However, constructing such systems in a sustainable, scalable, and processable manner remains challenging. This work reports a bio-inspired strategy to develop RTP nanofiber materials using bacterial cellulose (BC) via bio-fermentation. The green fabrication process, high biocompatibility, non-toxicity, and abundant hydroxyl groups make BC an ideal biopolymer for constructing durable and stimuli-responsive RTP materials. Remarkable RTP performance is observed with long lifetimes of up to 1636.79 ms at room temperature. Moreover, moisture can repeatedly quench and activate phosphorescence in a dynamic and tunable fashion by disrupting cellulose rigidity and permeability. With capabilities for repeatable moisture-sensitive phosphorescence, these materials are highly suitable for applications such as anti-counterfeiting and information encryption. This pioneering bio-derived approach provides a reliable and sustainable blueprint for constructing dynamic, scalable, and processable RTP materials beyond synthetic polymers. | Xiaolin Nie; Junyi Gong; Zeyang Ding; Bo Wu; Feng Gao; Guoqing Zhang; Parvej Alam; Yu Xiong; Zheng Zhao; Zijie Qiu; Ben Zhong Tang | Materials Science; Aggregates and Assemblies; Biocompatible Materials; Fibers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dad40066c138172979c8df/original/room-temperature-phosphorescent-nanofiber-membranes-by-bio-fermentation.pdf |
6272930bf053df0c260ef2a9 | 10.26434/chemrxiv-2022-25r49 | Elucidation of Complex Triplet Excited State Dynamics in Pd(II) Biladiene Tetrapyrroles | Pd(II) biladienes have been developed over the last five years as non-aromatic oligotetrapyrrole complexes that support a rich triplet photochemistry. In this work, we have undertaken the first detailed photophysical interrogation of three homologous Pd(II) biladienes bearing different combinations of methyl- and phenyl-substituents on the frameworks’ sp3-hybridized meso-carbon (i.e., the 10-position of the biladiene framework). These experiments have revealed unexpected excited-state dynamics that are dependent on the wavelength of light used to excite the biladiene. More specifically, transient absorption spectrosco-py revealed that higher-energy excitations (exc ~ 350-500 nm) led to an additional lifetime (i.e., an extra photophysical pro-cess) compared to experiments carried out following excitation into the lowest-energy excited states (exc = 550 nm). Each Pd(II) biladiene complex displayed an intersystem crossing lifetime on the order of tens of ps and a triplet lifetime of ~20 s, regardless of the excitation wavelength. However, when higher-energy light is used to excite the complexes, a new life-time on the order of hundreds of ps is observed. The origin of the ‘extra’ lifetime observed upon higher energy excitation of the Pd(II) biladiene complexes was revealed by detailed computational modeling using density functional theory (DFT) and time-dependent DFT (TDDFT). These efforts demonstrated that excitation into higher-energy metal-mixed-charge-transfer excited states with high spin-orbit coupling to higher energy metal-mixed-charge-transfer triplet states leads to the additional excitation deactivation pathway. Importantly, time-resolved spectroscopy and electronic structure calculations carried out for the analogous aromatic Pd(II) meso-tetrakis(pentafluorophenyl)porphyrin (Pd[TPFPP]) demonstrated this traditional tetrapyrrole does not display the excitation-wavelength dependent photophysics observed for the Pd(II) biladienes. These experiments confirm that the unusual photophysics we observe are unique to low-symmetry biladienes and do not apply to more well-studied porphyrinoids. The results of this work demonstrate that Pd(II) biladienes support a unique triplet photo-chemistry that may be exploited for development of new photochemical schemes and applications. | Shea Martin; Gil Repa; Robert Hamburger; Craig Pointer; Kaytlin Ward; Trong-Nhan Pham; Maxwell Martin; Joel Rosenthal; Lisa Fredin; Elizabeth Young | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6272930bf053df0c260ef2a9/original/elucidation-of-complex-triplet-excited-state-dynamics-in-pd-ii-biladiene-tetrapyrroles.pdf |
634538b40e3c6acf223d2619 | 10.26434/chemrxiv-2022-ql13w | Crystallographic and Computational Analysis of Solid Form Landscape of Three Structurally Related Imidazolidine-2,4-dione Active Pharmaceutical Ingredients: Nitrofurantoin, Furazidin and Dantrolene | We present a crystallographic and computational study of three hydantoin-based active pharmaceutical ingredients nitrofurantoin, furazidin, and dantrolene aimed at identifying factors resulting in different propensities of these compounds to form polymorphs, hydrates, solvates, and solvate hydrates. This study is a continuation of our research towards understanding how small structural differences in closely related compounds affect their propensity to form different crystal phases, as all three compounds contain an imidazolidine-2,4-dione scaffold and a N-acyl hydrazone moiety and all form multiple crystalline phases. Crystallographic and computational analysis of the already known and newly obtained nitrofurantoin, furazidin and dantrolene crystal structures was performed by dissecting the properties of individual molecules and searching for the differences in tendency to form hydrogen bonding patterns and characteristic packing features. The propensity to form solvates was found to correlate with the relative packing efficiency of neat polymorphs and solvates and the ability of molecules to pack efficiently in several different ways. Additionally, the differences in propensity to form solvate-hydrates were attributed to the different stability of the hydrate phases. | Aija Trimdale-Deksne; Artis Kons; Liāna Orola; Anatoly Mishnev; Dmitrijs Stepanovs; Liliana Mazur; Magdalena Skiba; Marta K. Dudek; Nicolas Fantozzi; David Virieux; Evelina Colacino; Agris Bērziņš | Physical Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634538b40e3c6acf223d2619/original/crystallographic-and-computational-analysis-of-solid-form-landscape-of-three-structurally-related-imidazolidine-2-4-dione-active-pharmaceutical-ingredients-nitrofurantoin-furazidin-and-dantrolene.pdf |
62ca93f6e1aaae64dc231551 | 10.26434/chemrxiv-2022-j8fzb | Reprogramming of the biosynthetic network of Daphniphyllum alkaloids into a chemically synthetic network through generalized biomimetic strategies | Biomimetic synthesis is a fundamental approach to the chemical synthesis of natural products, which, due to the intrinsic correlation between the biogenesis and the structure of natural products, offers many advantages. Conventional biomimetic strategies have evolved on a principle featuring “(essentially) the same substrates, similar reactions, and similar pathways”, which defines the pattern of biomimetic synthesis from the structural, mechanistic, and sequential perspectives. In practice, such highly imitative approaches have proved considerably feasible and efficient. However, applicability of this type of approach is also limited by the principle. To enhance the power of biomimetic synthesis, we envision generalized biomimetic strategies focusing on the key bond formation/cleavage sites implied by the biogenesis of natural products, which allow us to take full advantage of altered substrates, reactions, and pathways while retaining the inherent advantages of biomimetic synthesis. In this study, we showcased the utility of generalized biomimetic strategies in the synthesis of fourteen Daphniphyllum alkaloids from the macrodaphniphyllamine, calyciphylline A, daphnilongeranin A, and daphnicyclidin D subfamilies. The biosynthetic network of these alkaloids was reprogrammed into a powerful chemically synthetic network through substrate-, reaction-, and pathway-altering biomimetic strategies. | Wenhao Zhang; Ming Lu; Lu Ren; Xiang Zhang; Peng Yang; Ang Li | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ca93f6e1aaae64dc231551/original/reprogramming-of-the-biosynthetic-network-of-daphniphyllum-alkaloids-into-a-chemically-synthetic-network-through-generalized-biomimetic-strategies.pdf |
6626f55491aefa6ce1225c05 | 10.26434/chemrxiv-2024-996qd | Design of Experiments-Based Optimization of an Electrochemical
Decarboxylative Alkylation using a Spinning Cylinder Electrode
Reactor | A design of experiments model has been developed to optimize an electrochemical protocol for
the decarboxylative N-alkylation of pyrazole in a spinning cylinder electrode reactor. The
electrochemical reaction requires the incorporation of molecular sieves as an additive to ensure
the absence of moisture and prevent potential electrode corrosion issues. The spinning cylinder
electrode reactor proved to be an idea platform to scale up this transformation, involving a
suspension of solid particles, to multigram scales. The reaction model, which showed an
excellent fitting with the experimental data, provided insights on the effect of important
electrolysis parameters unique to this reactor design, such as the electrode spinning speed, on
the reaction conversion and selectivity. Furthermore, the design of experiments also supplied
optimal electrolysis parameters for this complex multivariable reaction system, resulting in full
conversion of the substrate and excellent selectivity for a 600 mL volume reaction in
recirculation flow mode, with 94% isolated yield for the target N-alkylated product. | Nikola Petrović; Graham R. Cumming; Christopher A. Hone; María José Nieves- Remacha; Pablo García-Losada; Óscar de Frutos; C. Oliver Kappe; David Cantillo | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6626f55491aefa6ce1225c05/original/design-of-experiments-based-optimization-of-an-electrochemical-decarboxylative-alkylation-using-a-spinning-cylinder-electrode-reactor.pdf |
63e413c15c37ece322bce2d9 | 10.26434/chemrxiv-2022-khqgj-v2 | TiO2/WO3/graphene for photocatalytic H2 generation and benzene removal: widely employed still an ambiguous system | Clean energy, as well as air and water pollution, have become key challenges in today's society. Photocatalysis could be one of the ways to address them. It is considered as an advanced oxidation method that involves light to activate a semiconductor. Semiconductors based on titanium dioxide (TiO2) are widely regarded as photocatalytically active materials. However, the performance of TiO2 has limitations due to its wide band gap (~3.2 eV), and a high recombination rate of the photo-generated electron-hole (e−−h+) pair. To overcome these drawbacks, TiO2 in heterojunction with tungsten trioxide (WO3) is well recognized as one of the most explored systems for photocatalytic applications. Depending on the synthesis technique, and the photocatalytic application, various yet contrasting behaviour can be found in the literature.
In this work, the photocatalytic properties of the TiO2/WO3 system were thoroughly examined in the removal of gaseous benzene, and generation of H2. Graphene nanoplatelets were included into the TiO2/WO3 system to increase transport and life-time of the photo-generated exciton. The investigation of various parameters that affected the photocatalytic activity of synthesised materials were carried out, including the ratio of WO3 to TiO2, the presence of graphene, and the nature of the photocatalytic application. It has been observed that the position of the conduction bands played indeed a key-role in case of hydrogen generation. A type II heterojunction was found in the TiO2/WO3 system. Modification of TiO2/WO3 with graphene nanoplatelets improved the photocatalytic hydrogen generation, which was particularly evident in samples with higher WO3 content. The most significant increase in hydrogen production was observed with the photocatalyst with 15 mol% WO3 and 1 wt% graphene − a five-fold increase in yield, compared to its counter-part with no graphene.
| Alaoui Chakib; Karmaoui Mohamed ; Ahmed Bekka; Miroslava Filip Edelmannová ; Juan Jesus; javier navas; Touati Wassila; Imene Kadi allah; Bruno Figueiredoe ; Joao Antonio Labrincha; Kamila Koci ; David Maria Tobaldi | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e413c15c37ece322bce2d9/original/ti-o2-wo3-graphene-for-photocatalytic-h2-generation-and-benzene-removal-widely-employed-still-an-ambiguous-system.pdf |
62406db6a4ed9570a22fa516 | 10.26434/chemrxiv-2022-62w47 | Time Evolution of Entanglement of Electrons and Nuclei and Partial Traces in Ultrafast Photochemistry | Broad in energy optical pulses induce ultrafast molecular dynamics where nuclear degrees of freedom are entangled with electronic ones. We discuss a matrix representation of wave functions of such entangled systems. Singular Value Decomposition, (SVD) of this matrix provides a representation as a sum of separable terms. Their weights can be arranged in decreasing order. The representation provided by the SVD is equivalent to a Schmidt decomposition. If there is only one term or if one term is already a good approximation, the system is not entangled. The SVD also provides either an exact or a few term approximation for the partial traces. A simple example, the dynamics of LiH upon ultrafast excitation to several non-adiabatically coupled electronic states is provided. The major contribution to the entanglement is created during the exit from the Franck Condon region. An additional contribution is the entanglement due to the nuclear motion induced non-adiabatic transitions. | Martin Blavier; Raphael D. Levine; Francoise Remacle | Theoretical and Computational Chemistry; Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62406db6a4ed9570a22fa516/original/time-evolution-of-entanglement-of-electrons-and-nuclei-and-partial-traces-in-ultrafast-photochemistry.pdf |
60c75110337d6c9253e2849a | 10.26434/chemrxiv.13007945.v2 | Chelating Agent: The Health Protector of Researchers in Lead Halide Perovskite Laboratory | <p>Lead halide
perovskites have achieved substantial success in various optoelectronic devices
owing to their remarkable physical properties. However, lead (Pb) as a heavy
metal, long-lasting toxic to the body has become a health hazard for
researchers. How to completely remove the residual lead in the laboratory and
prevent lead from entering the human body have always been an important topic
in laboratory safety. Here we develop an operable method to treat
lead sources with low-cost and eco-friendly chelating agent (EDTA-2Na), which
can reduce the concentration of free lead ions to 10<sup>-11 </sup>ppm theoretically.
Moreover, experiments have demonstrated that the chelating agent possess a
strong ability on the removal of lead ions from the lab surface, gloves and lab
coats. This approach paves the way to protect the health of researchers in lead
halide perovskite laboratory. </p> | Yu-Hao Deng | Environmental biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75110337d6c9253e2849a/original/chelating-agent-the-health-protector-of-researchers-in-lead-halide-perovskite-laboratory.pdf |
61a621c1ceb7d316bd010728 | 10.26434/chemrxiv-2021-zr4xn | Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease | We present several workflows for protein-ligand docking and free energy calculation for use in the workflow management system Galaxy. The workflows are composed of several widely used open-source tools, including rDock and GROMACS, and can be executed on public infrastructure using either Galaxy's graphical interface or the command line. We demonstrate the utility of the workflows by running a high-throughput virtual screening of around 40000 compounds against the SARS-CoV-2 main protease, a system which has been the subject of intense study in the last year. | Simon Bray; Tim Dudgeon; Rachael Skyner; Rolf Backofen; Björn Grüning; Frank von Delft | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a621c1ceb7d316bd010728/original/galaxy-workflows-for-fragment-based-virtual-screening-a-case-study-on-the-sars-co-v-2-main-protease.pdf |
656df8cb5bc9fcb5c906aa0d | 10.26434/chemrxiv-2023-5jd6t | Lightening Copper: Unleashing Radical Reactivity of Diazo Arylidene Succinimides to Enable One Step Synthesis of PMDI Core | Visible light promoted direct and convenient synthesis of pyromellitic diimides (PMDI) starting from vinyl diazo arylidene succinimides via copper catalysis has been achieved in one step. This novel and convenient transformation involves an unusual formation of carbon radicals directly from diazo arylidene succinimides instead of the traditional reactive carbene intermediate. This unprecedented and efficient copper-catalyzed chemoselective radical cyclization proceeds through the proton transfer (PT) followed by the electron transfer (ET) process. Notably, the choice of NaSCN along with the copper catalyst plays a pivotal role in this overall photoinduced transformation. Additionally, we have synthesized a known PMDI molecule in a single step, which displayed prominent aggregation-induced emission (AIE) properties. The protocol has been further extended for direct access to unsymmetrically substituted PMDI from two different diazo arylidene succinimides. A detailed controlled experiment, UV-visible spectroscopic as well as EPR studies have been performed to gain mechanistic insights into the reaction pathway. | Kajal B. Meher; Debasish Laha; Pankaj D. Dharpure; Dr. Ramakrishna G. Bhat | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656df8cb5bc9fcb5c906aa0d/original/lightening-copper-unleashing-radical-reactivity-of-diazo-arylidene-succinimides-to-enable-one-step-synthesis-of-pmdi-core.pdf |
652e50b98bab5d2055852dde | 10.26434/chemrxiv-2023-fw8n4-v3 | Leveraging Large Language Models for Predictive Chemistry | Machine learning has revolutionized many fields and has recently found applications in chemistry and materials science. The small datasets commonly found in chemistry sparked the development of sophisticated machine-learning approaches that incorporate chemical knowledge for each application and, therefore, require much expertise to develop. Here, we show that large language models trained on vast amounts of text extracted from the internet can easily be adapted to solve various tasks in chemistry and materials science by fine-tuning them to answer chemical questions in natural language with the correct answer. We compared this approach with dedicated machine-learning models for many applications spanning properties of molecules and materials to the yield of chemical reactions. Surprisingly, this approach performs comparable to or even outperforms the conventional techniques---particularly in the low data limit. In addition, we can perform inverse design successfully by simply inverting the questions. The high performance, especially for small data sets, combined with the ease of use, can fundamentally impact how we leverage machine learning in the chemical and material sciences. Next to a literature search, querying a foundation model might become a routine way to bootstrap a project by leveraging the collective knowledge encoded in these foundation models or to provide a baseline for predictive tasks. | Kevin Maik Jablonka; Philippe Schwaller; Andres Ortega-Guerrero; Berend Smit | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e50b98bab5d2055852dde/original/leveraging-large-language-models-for-predictive-chemistry.pdf |
60c747c79abda2fde8f8c99b | 10.26434/chemrxiv.11782266.v1 | Electrochemical Reduction of [Ni(Mebpy)3]2+. Elucidation of the Redox Mechanism by Cyclic Voltammetry and Steady-State Voltammetry in Low Ionic Strength Solutions. | <p>Bipyridine
complexes of Ni are used as catalysts in a variety of reductive transformations. Here, the electroreduction of [Ni(Mebpy)<sub>3</sub>]<sup>2+</sup>
(Mebpy = 4,4’-dimethyl-2,2’-bipyridine) in dimethylformamide is reported, with
the aim of determining the redox mechanism and oxidation states of products
formed under well-controlled electrochemical conditions. Results from cyclic
voltammetry, steady-state voltammetry (SSV) and chronoamperometry demonstrate
that [Ni(Mebpy)<sub>3</sub>]<sup>2+</sup> undergoes two sequential 1<i>e</i> reductions at closely separated
potentials (<i>E</i><sup>0’</sup><sub>1 </sub>=
-1.06 ± 0.01 V and <i>E</i><sup>0<i>’</i></sup><sub>2 </sub>=<sub> </sub>-1.15 ±
0.01 V vs Ag/AgCl (3.4 M KCl)).
Homogeneous comproportionation to generate [Ni(Mebpy)<sub>3</sub>]<sup>+
</sup>is demonstrated in SSV experiments in low ionic strength solutions. The comproportionation rate constant is
determined to be > 10<sup>6</sup> M<sup>-1</sup>s<sup>-1</sup>, consistent
with rapid outer-sphere electron transfer.
Consequentially, on voltammetric time scales, the 2<i>e</i> reduction of [Ni(Mebpy)<sub>3</sub>]<sup>2+</sup> results in
formation of [Ni(Mebpy)<sub>3</sub>]<sup>1+</sup> as the predominant species
released into bulk solution. We also demonstrate that [Ni(Mebpy)<sub>3</sub>]<sup>0</sup><sub>
</sub>slowly loses a Mebpy ligand (~10 s<sup>-1</sup>).</p> | Koushik Barman; Martin
A. Edwards; David
P. Hickey; Christopher Sandford; Yinghua Qiu; rui gao; Shelley D. Minteer; Henry White | Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c79abda2fde8f8c99b/original/electrochemical-reduction-of-ni-mebpy-3-2-elucidation-of-the-redox-mechanism-by-cyclic-voltammetry-and-steady-state-voltammetry-in-low-ionic-strength-solutions.pdf |
61b18d1b689c87abbfdb6cd7 | 10.26434/chemrxiv-2021-qk59n | Synthesis and styrene copolymerization of novel phenoxy and benzyloxy ring-substituted tert-butyl phenylcyanoacrylates | Novel phenoxy and benzyloxy ring-substituted tert-butyl phenylcyanoacrylates, RPhCH=C(CN)CO2C(CH3)3 (where R is 3-phenoxy, 3-(4-chlorophenoxy), 3-(4-methoxyphenoxy), 3-(4-methylphenoxy), 2-benzyloxy, 3-benzyloxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and tret-butyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the ethylenes were copolymerized with styrene in solution with radical initiation at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Divya Reddy; Sierra S. Schmitt; Paige E. Sevald; Teodora Simic; Catalina S. Torres Reyes; Daya K. Yadav; Sara Rocus; William S. Schjerven; Gregory Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2021-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b18d1b689c87abbfdb6cd7/original/synthesis-and-styrene-copolymerization-of-novel-phenoxy-and-benzyloxy-ring-substituted-tert-butyl-phenylcyanoacrylates.pdf |
62cbd44dc79aca1ea85bb6ca | 10.26434/chemrxiv-2022-s9df5 | C-H activation of indole-derivatives catalysed by Pd-nanobiohybrids under mild conditions | A mild C-H activation of protected L-tryptophan catalyzed by palladium bionanohybrids was developed. Several Pd-biohybrids were synthesized and the influence of temperature or different enzymes as scaffolds were investigated. The reaction efficiency of Pd hybrids was also tested in combination with CuNPs-biohybrids. | Noelia Losada-Garcia; A. Sofia Santos; M. Manuel B. Marques; Jose M. Palomo | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cbd44dc79aca1ea85bb6ca/original/c-h-activation-of-indole-derivatives-catalysed-by-pd-nanobiohybrids-under-mild-conditions.pdf |
63d98e2a2d1431fca8cd07f3 | 10.26434/chemrxiv-2023-v0rj6 | Prediction of enzyme catalysis by computing reaction energy barriers via steered QM/MM Molecular Dynamics Simulations and Machine Learning | The prediction of enzyme activity in a general extend is maybe one of the main challenges nowadays in catalysis. Computer-assisted methods have been proven to be able to simulate the reaction mechanism at the atomic level of detail. However, these methods tend to be expensive to be used in a large scale as it is needed in protein engineering campaigns. To alleviate this situation, machine learning methods can help in the generation of predictive-decision models. Herein we train different regression algorithms for the prediction of the reaction energy barrier of the rate-limiting step of the hydrolysis of mono-(2-hydroxyethyl)terephthalic acid by the MHETase of Ideonella sakaiensis. As training data set we use steered QM/MM MD simulation snapshots and their corresponding pulling work values. We have explored three algorithms together with three chemical representations. As outcome, our trained models are able to predict pulling works along the steered QM/MM MD simulations with a mean absolute error below 3 kcal mol-1 and a score value above 0.90. More challenging is the prediction of the energy maximum with a single geometry. Whereas the use of the initial snapshot of the QM/MM MD trajectory as input geometry yields a very poor prediction of the reaction energy barrier, the use of an intermediate snapshot of the former trajectory brings the score value above 0.40 with a low mean absolute error (ca. 3 kcal mol-1). Altogether, in this work we have faced some initial challenges of the final goal of getting an efficient workflow for the semi-automatic prediction of enzyme-catalyzed energy barriers and catalytic efficiencies. | Daniel Platero-Rochart; Tatyana Krivobokova; Michael Gastegger; Gilbert Reibnegger; Pedro Alejandro Sánchez-Murcia | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d98e2a2d1431fca8cd07f3/original/prediction-of-enzyme-catalysis-by-computing-reaction-energy-barriers-via-steered-qm-mm-molecular-dynamics-simulations-and-machine-learning.pdf |
60c74d93469df463dff44301 | 10.26434/chemrxiv.12638906.v1 | Docking Studies of Usnic Acid and Sodium Usnate on SARS CoV-2 Main Protease and Spike Protein RBD | <p><b>SARS
CoV-2 a pandemic influenza like infectious disease emerged in December 2019 has
spread throughout the world within few months. Scientists are trying their best
to find medicine and vaccine. Usnic acid and its derivatives as herbal
supplements are widely used as mouth wash, cosmetics, antiviral agents. In this
study, usnic acid and its derivative-sodium usnate in comparison with
favipiravir are docked with main protease and spike protein RBD </b><b>6M0J of SARS Cov-2. Usnic acid and sodium usnate exhibit better
binding affinities for main protease and spike RBD. The data has been compared
with favipiravir. Favipiravir, usnic acid, sodium usnate shows binding affinity
of -4.25, -8.05 and -8.55 kcal/mol respectively with main protease. While favipiravir,
usnic acid and sodium usnate exhibit binding affinities of -4.25, -6.02 and
-6.53 kcal/mol with spike RBD respectively. One of the interesting features is that
the inhibition constant values of usnic acid is 1.27 µM and sodium usnate is
539.86 nM in comparison to favipiravir (764.13 µM) with main protease. </b></p> | Roopa Guthappa | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d93469df463dff44301/original/docking-studies-of-usnic-acid-and-sodium-usnate-on-sars-co-v-2-main-protease-and-spike-protein-rbd.pdf |
6722800b7be152b1d07f5777 | 10.26434/chemrxiv-2024-1jcnw | Redox-Active Bisphosphonate-Based Viologens as Negolytes for Aqueous Organic Flow Batteries | Viologen derivatives feature two reversible one-electron redox processes and have been extensively utilized in aqueous organic flow batteries (AOFBs). However, the early variant, methyl viologen (MVi), exhibits low stability in aqueous electrolytes, restricting its practical implementation in AOFB technology. In this context, leveraging the tunability of organic molecules, various substituents have been incorporated into the viologen core to achieve better stability, lower redox potential, and improved solubility. In this work, we introduce bisphosphonate-substituted viologens as candidates for AOFBs. The bulkiness and negative charges of the bisphosphonate groups enhance the solubility and the electrostatic repulsion among viologen molecules, minimizing the bimolecular side reactions that lead to degradation. Additionally, the electron-donating effect of this new substituent significantly lowers the redox potential. As a result, the proposed viologen derivatives exhibit high solubility (1.66 - 1.81 M in water) and stability (capacity decay of 0.009 %/cycle or 0.229%/day when tested at 0.5 M). These parameters are coupled with the lowest redox potentials exceeding all previously reported viologens utilized in AOFBs (–0.503 V and –0.550 V against SHE for mono- and bis-phosphonate viologen, respectively). | Gabriel Gonzalez; Anton Nechaev; Vsevolod Peshkov; Eduardo Martínez-González; Andrey Belyaev; Mahsa Shahsavan; Petri Pihko; Pekka Peljo | Organic Chemistry; Materials Science; Energy; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6722800b7be152b1d07f5777/original/redox-active-bisphosphonate-based-viologens-as-negolytes-for-aqueous-organic-flow-batteries.pdf |
65477d7b48dad231201d2181 | 10.26434/chemrxiv-2023-b9zdf | Fe/Thiol Cooperative HAT Olefin Hydrogenation: Mechanistic Insights that Inform Enantioselective Catalysis | Asymmetric hydrogenation of activated olefins using transition metal catalysis is a powerful tool for synthesis of complex molecules, but traditional metal catalysts have difficulty with enantioselective reduction of electron-neutral, electron-rich, and minimally functionalized olefins. Hydrogenation based on radical, metal-catalyzed hydrogen atom transfer (mHAT) mechanisms offers an outstanding opportunity to overcome these difficulties, enabling mild reduction of these challenging olefins with selectivity that is complementary to traditional hydrogenations with H2. Further, mHAT presents an opportunity for asymmetric induction through cooperative hydrogen atom transfer (cHAT) using chiral thiols. Here, we report insights from an in-depth mechanistic study of an iron-catalyzed achiral cHAT reaction and leverage these insights to deliver stereocontrol from chiral thiols. Mechanistic studies, including kinetic analysis and variation of silane structure, point to the transfer of hydride from silane to iron as the likely rate-limiting step. The data indicate that the selectivity-determining step is quenching of the alkyl radical by thiol, which becomes a more potent H-atom donor when coordinated to iron(II). The resulting iron(III)-thiolate complex is in equilibrium with other iron species, including FeII(acac)2, which is shown to be the predominant off-cycle species. The enantiodetermining nature of the thiol trapping step enables enantioselective net hydrogenation of olefins through cHAT using a commercially available glucose-derived thiol catalyst, with up to 80:20 enantiomeric ratio. To the best of our knowledge, this is the first demonstration of asymmetric hydrogenation via iron-catalyzed mHAT. These findings advance our understanding of cooperative radical catalysis and enable development of enantioselective catalysis predicated upon asymmetric iron-catalyzed mHAT reactions. | Sarah Buzsaki; Savannah Mason; Padmanabha Kattamuri; Juan Serviano; Dinora Rodriguez; Conner Wilson; Drew Hood; Jonathan Ellefsen; Yen-Chu Lu; Jolie Kan; Julian West; Scott Miller; Patrick Holland | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65477d7b48dad231201d2181/original/fe-thiol-cooperative-hat-olefin-hydrogenation-mechanistic-insights-that-inform-enantioselective-catalysis.pdf |
67c8393a81d2151a0229f7d4 | 10.26434/chemrxiv-2025-1b0mv | Diamondiyne: A 3D carbon allotrope with mixed valence hybridization | Carbon is arguably the most versatile element in the periodic table. It can form bonds to other elements in one-, two- and three-dimensions, allowing the formation of structurally and electronically diverse materials. Carbon allotropes, materials made only of carbon, were for long limited to diamond, graphite, fullerene, carbon nanotubes, and graphene. However, recently a series of zero- one- and two-dimensional carbon allotropes have been made. Until now, diamond is the only known three-dimensional carbon allotrope. Here we report the successful synthesis of a new 3D carbon allotrope, which we refer to as diamondiyne. The synthesis of diamondiyne is performed using inexpensive laboratory glassware. It is formed as a film at a liquid-liquid interface, and we show that the method is scalable in both the thickness and lateral area of the film. The received films are polycrystalline, and the crystal structure has been confirmed using transmission electron microscopy. Our results enrich the carbon allotrope family, enabling non-naturally occurring ones extending in full 3D space. New carbon allotropes have historically found widespread use in materials science, and we look forward to what applications might emerge for diamondiyne. | Yizhou Yang; Jie Xu; Yanyan Chen; Yu Xia; Clara Schäfer; Martin Ratsch; Martin Rahm; Tom Willhammar; Karl Börjesson | Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Carbon-based Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8393a81d2151a0229f7d4/original/diamondiyne-a-3d-carbon-allotrope-with-mixed-valence-hybridization.pdf |
60c746874c8919388cad2b77 | 10.26434/chemrxiv.11345042.v1 | Hydrolysis of Scandium Alkyl Derivatives Supported by a Pentadentate Diborate Ligand: Interconversion of Hydroxo and Oxo Complexes | Uncontrolled
reaction of water with scandium alkyls (compounds <b>1-R</b>) supported by a dianionic, pentadentate ligand leads to rapid
formation of an oxo-bridged dimer (<b>2</b>).
Solid state samples can be exposed to ambient atmosphere to generate samples
enriched in the bridging dihydroxo dimer <b>3</b>,
which slowly converts to the m-oxo species with elimination of water. DFT computations show that <b>3</b> is actually more thermodynamically
stable than <b>2</b>, but the reactivity of
<b>3</b> with the water eliminated leads to
its decomposition to <b>2</b> and several
hydrolysis products. Some of these products were characterized by X-ray crystallography,
specifically a hexameric scandium dihydroxo cluster (<b>4</b>) in which the pentadentate ligand has partially demetallated.
Attempts to synthesize hydroxo complex <b>3</b>
by protonation of <b>2</b> also lead to
hydrolysis products. | Daniel W. Beh; Warren Piers; Laurent Maron; Yan Yang; Benjamin
S. Gelfand; Jian-Bin Li | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746874c8919388cad2b77/original/hydrolysis-of-scandium-alkyl-derivatives-supported-by-a-pentadentate-diborate-ligand-interconversion-of-hydroxo-and-oxo-complexes.pdf |
626d7c50ebac3ad048e8ecce | 10.26434/chemrxiv-2022-ql9f8 | Hidden dynamics of noble-metal-bound thiol monolayers revealed by SERS-monitored entropy-driven exchange of cysteine isotopologues | Vibrational spectroscopy coupled with isotopic labeling provides many insights into dynamic processes within various molecular systems. Here, a newfound utility of surface-enhanced Raman scattering (SERS) spectroscopy as a tool to study noble metal-anchored thiol monolayers is demonstrated for a pair of L-cysteine isotopologues competing to bind the surface of silver nanoparticles (AgNPs). According to our DFT calculations, SERS spectra of L-Cys could be sensitive to 12C/13C and 14N/15N isotopic substitutions, which has been experimentally confirmed for the pair of L-Cys isotopologues: Cys-cabn (all 12C/14N) and Cys-CABN (all 13C/15N). In the AgNP-anchored state, the two isotopologues reveal distinct Raman shift values (1577 cm-1 / 1633 cm-1) of the band assigned to C=O stretching. This characteristic SERS feature has been subsequently employed to probe various exchange scenarios between AgNP-bound and free L-Cys molecules. As the exchange involves two spectrally distinct but chemically identical molecules, the process is exclusively entropy-driven ultimately leading to the equilibrium state in which Cys-cabn/Cys-CABN concentration ratios in the Ag surface-bound layers and the bulk solution are identical. In a system containing AgNP-L-Cys and an excess of free L-Cys molecules, the exchange energy barrier limits the overall kinetics. Although the SERS-monitored rate of progression toward the equilibrium state under ambient conditions (25 °C) is negligible, a very steep acceleration of the exchange is observed at 50 °C. While the temperature-induced transition is very abrupt, it is still reversible with cooling. We argue that the dramatic acceleration of the dynamics of the L-Cys exchange between free and AgNP-bound molecules may be rationalized as a collective phase transition to an excited and reaction-prone state. Our work highlights unexplored potential of SERS spectroscopy coupled to isotopic exchange as a tool to study obscured dynamic phenomena within metal-anchored adsorbate layers. | Marcin Witkowski; Agata Królikowska; Janusz Cukras; Wojciech Dzwolak | Physical Chemistry; Nanoscience; Interfaces; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626d7c50ebac3ad048e8ecce/original/hidden-dynamics-of-noble-metal-bound-thiol-monolayers-revealed-by-sers-monitored-entropy-driven-exchange-of-cysteine-isotopologues.pdf |
60c741e6567dfeede1ec3e67 | 10.26434/chemrxiv.8150657.v1 | Optimality Conditions of Minimum Energy Crossing Point | We focus on the geometric nature of minimum energy crossing point (MECP) and give a reduced vibrational analysis (RVA) method for testing sufficiency of MECP candidate solution. Furthermore, an example is used to illustrate the risk if the test is ignored. In the support information, a detailed algorithm is given. The Gaussian and GaussView software are used in the example.<br /> | kun liu; yuxue li; jingbo zhang; yue lu; bin wang | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e6567dfeede1ec3e67/original/optimality-conditions-of-minimum-energy-crossing-point.pdf |
60c75429bb8c1a79c03dc1b5 | 10.26434/chemrxiv.13619378.v1 | Organomagnesium Crown Ethers and Their Binding Affinities with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ Ions - a Theoretical Study | Novel organomagnesium crown ether molecules have been computationally
characterized for the first time using density functional theory (DFT).
Monomer units of MgC6 have been used as building blocks. The potential
energy surface of the parent elemental composition, MgC6H2, has been
extensively explored using both DFT and coupled-cluster methods. It is
concluded that the seven-membered ring isomer,
1-magnesacyclohept-4-en-2,6-diyne, is the thermodynamically most stable
molecule at all levels. Thus, the latter has been used as the building
block for organomagnesium crown ethers. Both alkali (Li+, Na+, and K+)
and alkaline-earth (Be2+, Mg2+, and Ca2+) metal ions selective complexes
have been theoretically identified. Binding energies (Delta E at 0 K) and
thermally corrected Gibbs free energies (Delta G at 298.15 K) have<br />been computed for these metal ions with MgC6-9-crown-3 and MgC6-12-crown-4 to gauge their binding affinities.Novel organomagnesium crown ether molecules have been computationally
characterized for the first time using density functional theory (DFT).
Monomer units of MgC6 have been used as building blocks. The potential
energy surface of the parent elemental composition, MgC6H2, has been
extensively explored using both DFT and coupled-cluster methods. It is
concluded that the seven-membered ring isomer,
1-magnesacyclohept-4-en-2,6-diyne, is the thermodynamically most stable
molecule at all levels. Thus, the latter has been used as the building
block for organomagnesium crown ethers. Both alkali (Li+, Na+, and K+)
and alkaline-earth (Be2+, Mg2+, and Ca2+) metal ions selective complexes
have been theoretically identified. Binding energies (Delta E at 0 K) and
thermally corrected Gibbs free energies (Delta G at 298.15 K) have been computed for these metal ions with MgC6-9-crown-3 and MgC6-12-crown-4 to gauge their binding affinities. | Krishnan Thirumoorthy; Uday Kumar Padidela; Pothiappan Vairaprakash; Venkatesan S. Thimmakondu | Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75429bb8c1a79c03dc1b5/original/organomagnesium-crown-ethers-and-their-binding-affinities-with-li-na-k-be2-mg2-and-ca2-ions-a-theoretical-study.pdf |
60c759b9469df4fc60f458ee | 10.26434/chemrxiv.14727327.v1 | Spectroscopic Investigation of Polyaniline Co Poly Meta Amino Benzene Sulfonic Acid | Similar to metals, conducting polymers possess an extraordinary ability to conduct electricity due to their intrinsic properties. There has been considerable focus on the synthesis and development of such materials for a wide variety of applications. In this regard, polyaniline and its derivatives have versatile applications including use as active electronic material, fabrication of modified electrode, sensors, in secondary batteries and in microelectronic and electrochromic device. Introduction of potential polymers like PAN and PPY or PTF as conductive co-polymer, interpenetrating network or blends would be a challenging step towards the preparation of novel and cheap material with modified antistatic properties. In this work we used poly (m-amino benzene sulfonic acid) and poly aniline for the preparation of composite. Aniline and m-amino benzene sulfonic acid can be fast polymerized in water to yield conducting nano composites. The composites were easily water dispersable and showed prolonged stability. <br /><br /><br /> | Jayanta Ray; Leena Bhowmik | Organic Synthesis and Reactions; Composites; Nanostructured Materials - Materials; Organic Polymers; Polymer blends; Polymerization (Polymers); Polymer scaffolds; Nanofabrication; Nanostructured Materials - Nanoscience; Polymers; Electrocatalysis; Heterogeneous Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Organocatalysis; Polymerization (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759b9469df4fc60f458ee/original/spectroscopic-investigation-of-polyaniline-co-poly-meta-amino-benzene-sulfonic-acid.pdf |
67578c71085116a133e2f0ce | 10.26434/chemrxiv-2024-3mcc5-v3 | Merging Photoexcited Nitroarenes with Lewis Acid Catalysis for the Anti-Markovnikov Oxidation of Alkenes | Herein we describe the oxidation of alkenes to carbonyls and acetonides via the interplay of photoexcited nitroarenes and Lewis acid catalysis. A wide range of alkenes were oxidized to aldehyde and ketone products with anti-Markovnikov selectivity, and to acetonides when acetone was employed as a co-solvent. Mechanistic studies support that Lewis acid coordination to the 1,3,2-dioxazolidine intermediate results in a 1,2-shift to generate carbonyl derivatives and a nucleophilic substitution pathway for the formation of acetonides. | Joshua Paolillo; Mahmoud Saleh ; Ethan Junk; Marvin Parasram | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67578c71085116a133e2f0ce/original/merging-photoexcited-nitroarenes-with-lewis-acid-catalysis-for-the-anti-markovnikov-oxidation-of-alkenes.pdf |
60c742a9469df407cdf43003 | 10.26434/chemrxiv.8325356.v1 | Simulating Surfactant-Iron Oxide Interfaces: From Density Functional Theory to Molecular Dynamics | <div>Understanding the behaviour of surfactant molecules on iron oxide surfaces is important for many industrial applications. Molecular dynamics (MD) simulations of such systems have been limited by the absence of a force-feild (FF) which accurately describes the molecule-surface interactions. In this study, interaction energies from density functional theory (DFT) + U calculations with a van der Waals functional are used to parameterize a classical FF for MD simulations of amide surfactants on iron oxide surfaces. The Original FF, which was derived using mixing rules and surface Lennard-Jones (LJ) parameters developed for nonpolar molecules, were shown to signi cantly underestimate the adsorption energy and overestimate the equilibrium adsorption distance compared to DFT. Conversely, the Optimized FF showed excellent agreement with the interaction energies obtained from DFT calculations for a wide range of surface coverages and molecular conformations near to and adsorbed on a-Fe2O3(0001). This was facilitated through the use of a Morse potential for strong chemisorption interactions, modi fied LJ parameters for weaker physisorption interactions, and adjusted partial charges for the electrostatic interactions. The Original FF and Optimized FF were compared in classical nonequilibrium molecular dynamics (NEMD) simulations of amide molecules con fined between iron oxide surfaces. When the Optimized FF was employed, the amide molecules were pulled closer to the surface and the orientation of the headgroups was more similar to that observed in the DFT calculations compared to the Original FF. The Optimized FF proposed here facilitates classical MD simulations of amide-iron oxide interfaces in which the interactions are representative of accurate DFT calculations.</div> | Carlos Ayestaran Latorre; James Ewen; Chiara Gattinoni; Daniele Dini | Computational Chemistry and Modeling; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742a9469df407cdf43003/original/simulating-surfactant-iron-oxide-interfaces-from-density-functional-theory-to-molecular-dynamics.pdf |
60c73dfd0f50db38fa395591 | 10.26434/chemrxiv.6264644.v1 | Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in Aqueous Environment | <p>We develop and test specific coarse-grained models for charged amphiphilic systems such as palmitoyloleoyl phosphatidylglycerol (POPG) lipid bilayer, and sodium dodecyl sulphate (SDS) surfactant in aqueous environment, to verify the ability of the hybrid particle-field method to provide a realistic description of polyelectrolyte soft-matter systems. The intramolecular interactions are treated by a standard molecular Hamiltonian and the non-electrostatic intermolecular forces are described by density fields. Electrostatics is introduced as an additional external field obtained by a modified particle-mesh Ewald procedure. Molecular dynamics simulations indicate that the methodology is robust with respect to the choice of the relative dielectric constant, yielding the same correct qualitative behavior for a broad range of dielectric values. In particular, our methodology reproduces well the organization of the POPG bilayer, as well as the SDS concentration-dependent change in the morphology of the micelles from spherical to microtubular aggregates. </p> | Hima Bindu Kolli; Antonio de Nicola; Sigbjørn Løland Bore; Ken Schäfer; Gregor Diezemann; Jürgen Gauss; Toshihiro Kawakatsu; Zhong-Yuan Lu; You-Liang Zhu; Giuseppe Milano; Michele Cascella | Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dfd0f50db38fa395591/original/hybrid-particle-field-molecular-dynamics-simulations-of-charged-amphiphiles-in-aqueous-environment.pdf |
661fec7f418a5379b00ae036 | 10.26434/chemrxiv-2024-kd11b | MolPipeline : A python package for processing molecules with RDKit in scikit-learn | The open-source package scikit-learn provides various machine learning algorithms and data processing tools, including the Pipeline class, which allows users to prepend custom data transformation steps to the machine learning model. We introduce the MolPipeline package, which extends this concept to chemoinformatics by wrapping default functionalities of RDKit, such as reading and writing SMILES strings or calculating molecular descriptors from a molecule object. We aimed to build an easy-to-use Python package to create completely automated end-to-end pipelines that scale to large data sets. Particular emphasis was put on handling erroneous instances, where resolution would require manual intervention in default pipelines. In addition, we included common cheminformatics tasks, like scaffold splits and molecular standardization, natively in the pipeline framework and adaptable for the needs of various projects. | Jochen Sieg; Christian Wolfgang Feldmann; Jennifer Hemmerich; Conrad Stork; Frederik Sandfort; Philipp Eiden; Miriam Mathea | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661fec7f418a5379b00ae036/original/mol-pipeline-a-python-package-for-processing-molecules-with-rd-kit-in-scikit-learn.pdf |
60c74847469df47808f43993 | 10.26434/chemrxiv.10062365.v4 | Fullerenes and PAHs: A Novel Model Explains their Formation via Sequential Cycloaddition Reactions Involving C2 Dimers | Based on a new understanding of the nature of the bonding in the C<sub>2</sub> dimer, a novel bottom-up model is offered that can explain the growth processes of fullerenes and polycyclic aromatic hydrocarbons (PAHs). It is shown how growth sequences involving C<sub>2</sub> dimers, that take place in carbon vapor, combustion systems, and the ISM, could give rise to a variety of bare carbon clusters. Among the bare carbon clusters thus formed, some could lead to fullerenes, while others, after hydrogenation, could lead to PAHs. We propose that the formation of hexagonal rings present in these bare carbon clusters are the result of [2+2+2] and [4+2] cycloaddition reactions that involve C<sub>2</sub> dimers. In the C<sub>60</sub> and C<sub>70</sub> fullerenes, each of the twelve pentagons is surrounded by five hexagons and thereby “isolated” from each other. To explain why, we suggest that in bowl-shaped clusters the pentagons can form as the consequence of closures of “cove regions” that exist between hexagonal rings, and that they can also form during cage-closure, which results in the creation of six “isolated” pentagonal rings, and five hexagonal rings. The proposed growth mechanisms can account for the formation of fullerene isomers without the need to invoke the widely used Stone-Wales rearrangement. Considering processes that take place in combustion systems, it is proposed that soot particle inception can result from oligomerization of the bare carbon clusters that originated from cycloadditions involving C<sub>2</sub> dimers. In future work, the insights offered in this article could provide a better understanding of nanotube growth, with or without defects. | Sylvain Smadja | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74847469df47808f43993/original/fullerenes-and-pa-hs-a-novel-model-explains-their-formation-via-sequential-cycloaddition-reactions-involving-c2-dimers.pdf |
60c74a98bdbb89753ba393da | 10.26434/chemrxiv.12226859.v1 | Local Structuring of Diketopyrrolopyrrole (DPP)-Based Semiconducting Polymers Using Molecular Dynamics Simulations | High performing organic semiconducting polymers show great potentials for use in electronic devices which is greatly dependent on the material crystallinity and packing. A series of short oligomers of the diketopyrrolopyrrole (DPP)-based materials that have shown to have high charge mobility are studied to understand the local structuring at atomic level for these materials. The simulations show that the tendency for this material class to form aggregates is driven by the interaction between DPP fragments, but this is modulated by the other conjugated fragments of the materials which afect the rigidity of the polymer and the ability to form aggregates of larger size.<br /> | Maryam Reisjalali; Jose Javier Burgos Marmol; Alessandro Troisi | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a98bdbb89753ba393da/original/local-structuring-of-diketopyrrolopyrrole-dpp-based-semiconducting-polymers-using-molecular-dynamics-simulations.pdf |
673c9af07be152b1d09eedbb | 10.26434/chemrxiv-2024-fcwnc-v2 | Rethinking the 'Best Method' Paradigm: The Effectiveness of Hybrid and Multidisciplinary Approaches in Chemoinformatics | In Chemoinformatics, as in many other computational-related disciplines, it is a common practice to identify the “single best” approach or methodology, for instance, identify the best fingerprint representation, the best single virtual screening approach or protocol, the optimal representation of the chemical space, the best predictive model, to name a few. In molecular modeling, a typical example is finding the best docking program. However, it is also known that each approach has its advantages and limitations. There are examples of benchmark studies comparing different approaches to find the most appropriate solution, and it is common to find that there are no single best programs in such studies. Yet, searching for the “best” methods is still common. The main goal of this work is to survey hybrid methodologies recently developed in Chemoinformatics. The list of approaches is not exhaustive, but it aims to cover several representative applications. One of the major outcomes of the survey is that, for various purposes, individual methods do not perform as well as the combination of approaches because single methods have inherent limitations with advantages and disadvantages. | Jose L. Medina-Franco; Johny R. Rodríguez-Pérez; Héctor F. Cortés-Hernández; Edgar López-López | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673c9af07be152b1d09eedbb/original/rethinking-the-best-method-paradigm-the-effectiveness-of-hybrid-and-multidisciplinary-approaches-in-chemoinformatics.pdf |
60c758ecee301cdcafc7b7e1 | 10.26434/chemrxiv.14601327.v1 | Relay Dual Catalysis: Photoredox and NHC-Catalyzed Cross-Double C-H Functionalizations of Aldehydes and Alkenes | Direct functionalizations of two distinct inert C-H bonds represent the
most ideal ways to construct C-C bonds. Herein, we report an intermolecular vinylation
of aldehydes using alkenes as the vinylating reagents through sequential two-fold C-H
functionalizations. The merging of visible light and NHC-catalysis allows for the direct
coupling of alkenes with aldehydes through an unprecedented relay dual catalysis
enabled cross-dehydrogenative coupling mechanism. The use of diphenoquinone is
essential for the success of this reaction, which plays an intriguing two-fold role in the
reaction, as both an electron acceptor as well as a radical reservoir for the radical
coupling enabling C-C forming-process. | MIng-Shang Liu; Lin Min; Bi-Hong Chen; Wei Shu | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ecee301cdcafc7b7e1/original/relay-dual-catalysis-photoredox-and-nhc-catalyzed-cross-double-c-h-functionalizations-of-aldehydes-and-alkenes.pdf |
61f12679c18d67b1168504ef | 10.26434/chemrxiv-2021-mkkfv-v2 | From operando Raman mechanochemistry to "NMR crystallography": understanding the structures and interconversion of Zn-terephthalate networks using selective 17O-labelling. | The description of the formation, structure and reactivity of coordination networks and MOFs remains a real challenge in a number of cases. This is notably true for compounds composed of Zn2+ ions and terephthalate ligands (benzene 1,4-dicarboxylate, BDC), because of the difficulties in isolating them as pure phases and/or because of the presence of structural defects. Here, using mechanochemistry in combination with operando Raman spectroscopy, the observation of the formation of various zinc-terephthalate compounds was rendered possible, allowing the distinction and isolation of three intermediates during the ball-milling synthesis of Zn3(OH)4(BDC). An “NMR crystallography” approach was then used, combining solid-state NMR (1H, 13C and 17O) and DFT calculations, in order to refine the poorly described crystallographic structures of these phases. Particularly noteworthy are the high-resolution 17O NMR analyses, which were made possible in a highly efficient and cost-effective way, thanks to the selective 17O-enrichment of either hydroxyl or terephthalate groups by ball-milling. This allowed the presence of defect sites to be identified for the first time in one of the phases, and the nature of the H-bonding network of the hydroxyls to be established in another. Lastly, the possibility of using deuterated precursors (e.g. D2O and d4-BDC) during ball-milling is also introduced, as a means for observing specific transformations during operando Raman spectroscopy studies, that would not have been possible with hydrogenated equivalents. Overall, the synthetic and spectroscopic approaches developed herein are expected to push forward the understanding of the structure and reactivity of other complex coordination networks and MOFs. | César Leroy; Thomas-Xavier Métro; Ivan Hung; Zhehong Gan; Christel Gervais; Danielle Laurencin | Theoretical and Computational Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f12679c18d67b1168504ef/original/from-operando-raman-mechanochemistry-to-nmr-crystallography-understanding-the-structures-and-interconversion-of-zn-terephthalate-networks-using-selective-17o-labelling.pdf |
60c746d8702a9bb30618acb3 | 10.26434/chemrxiv.11418585.v1 | Mechanosynthesis of Noels-type NHC-Ruthenium Complexes and Applications in ROMP | The use of ball-mills enabled the efficient mechanosynthesis of a variety of N-aryl,N-alkyl imidazolium salts and of corresponding NHC-silver(I) complexes. Transmetalation with ruthenium via mechanochemistry allowed the rapid access (1.5 min to 1 h) to complexes having a similar structure to Noels-type precatalysts. Evaluation of the complexes in the Ring-Opening Metathesis Polymerization of norbornene in different solvent, including non-toxic ones, showed a high catalytic activity for one of them, comparable to the one of Noels catalyst.<br /> | François Quintin; Julien Pinaud; Frédéric Lamaty; Xavier Bantreil | Catalysis; Coordination Chemistry (Organomet.); Polymerization (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746d8702a9bb30618acb3/original/mechanosynthesis-of-noels-type-nhc-ruthenium-complexes-and-applications-in-romp.pdf |
60c74cee702a9b630318b780 | 10.26434/chemrxiv.12277868.v3 | On the Importance of Catalysis in Photocatalysis: Triggering of Photocatalysis at Well-Defined Anatase TiO2 Crystals Through Facet-Specific Deposition of Oxygen Reduction Cocatalyst | Well-defined
anatase TiO<sub>2</sub> crystals with co-exposed {101} and {001} facets represent
a promising platform for fundamental studies in photocatalysis and for the
development of novel photocatalytic systems exhibiting higher than usual
quantum efficiencies. Herein, we present protocols enabling the photoreductive
deposition of Pt nanoparticles onto anatase TiO<sub>2</sub> micro-sized (1-3 mm) crystals prepared by hydrothermal growth in
fluoride-containing solutions to be carried out either facet-selectively (on
{101} facets only) or facet non-selectively (on both {101} and {001} facets). The
photocatalytic behavior of resulting photocatalysts is studied using
investigations of oxidative photodegradation of a test pollutant (4-chlorophenol,
4-CP), photocurrent measurements, and kinetic analysis of the open-circuit photopotential
decay. We demonstrate that the deposition of Pt nanoparticles effectively
triggers the photocatalytic degradation of 4-CP at anatase crystals which are
otherwise completely inactive. The role of Pt in triggering the photocatalysis is
demonstrated to consist chiefly in the catalytic enhancement of the reaction
rate of oxygen reduction by photogenerated electrons. Only platinized {101}
facets contribute to photocatalysis, whereas the {001} facets, in the
literature often referred to as “highly reactive”, are even after platinization
completely inactive, most likely due to (1 × 4) surface reconstruction upon the
heat treatment necessary to decrease the amount of surface fluorides. Based on
our results, we highlight the eminent role of efficient surface catalysis for
effective charge separation, and provide specific design rules for further
development of photocatalysts with high quantum efficiencies. | Christiane Adler; Dariusz Mitoraj; Igor Krivtsov; Radim Beranek | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cee702a9b630318b780/original/on-the-importance-of-catalysis-in-photocatalysis-triggering-of-photocatalysis-at-well-defined-anatase-ti-o2-crystals-through-facet-specific-deposition-of-oxygen-reduction-cocatalyst.pdf |
66d9b35951558a15ef203c71 | 10.26434/chemrxiv-2024-xvmbg | The Effect of Silver Particle Distribution in a Carbon Nanocomposite Interlayer on Lithium Plating in Anode-Free All-Solid-State Batteries | Solid-state batteries can outperform lithium-ion batteries in energy per unit mass and per unit volume when operating with a Li metal anode. However, metallic Li anodes pose significant manufacturing challenges. Anode-free cells avoid these challenges by plating metallic Li at the anode on the first charge, but subsequent non-uniform cyclic Li stripping and plating encourages unwanted Li dendrite growth, decreased coulombic efficiency, and early cell failure. We report a new spray-printed nanocomposite bilayer of silver/carbon black (Ag/CB) between the anodic current collector and Li6PS5Cl solid electrolyte with Ag concentrated at the current collector. Compared with previous Ag/CB mixtures, the bilayer ensured more uniform Li anode formation and improved cycling performance. Cells with a high-Ni oxide cathode had initial discharge capacity > 190 mAh/g and coulombic efficiency > 98% over 100 cycles. The Li plating uniformity with the structured Ag/CB interlayer was confirmed using secondary-ion mass spectrometry (SIMS) imaging. | Michael Metzler; Christopher Doerrer; Yige Sun; Guillaume Matthews; Enzo Liotti; Patrick S. Grant | Materials Science; Energy | CC BY NC 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d9b35951558a15ef203c71/original/the-effect-of-silver-particle-distribution-in-a-carbon-nanocomposite-interlayer-on-lithium-plating-in-anode-free-all-solid-state-batteries.pdf |
60c740824c89199a87ad2143 | 10.26434/chemrxiv.7756097.v1 | CRISPR-Clear: A Fieldable Detection Procedure for Potential CRISPR-Cas9 Gene Drive Based Bioweapons | <p>Rapid progression in genetic modification
research has made gene editing increasingly cheaper and easier to use.
CRISPR-Cas9 for example, allows for the specific alteration of the genome of an
organism with relative simplicity and low costs. This raised a worrying
question; can genetic modification techniques be used to create novel
bioweapons? A specific scenario is the initiation of a synthetic gene drive for
malicious purposes. A synthetic gene drive can be used to quickly spread a
mutation through an entire population. This mutation could alter vectors in
such a way that they will spread human diseases or eradicate essential
organisms. Since a gene drive spreads efficiently through a population, timely
detection is essential. Thus, a quick and field deployable screening method is
needed to counteract the malicious use of gene drives. </p>
<p>Here, we show a battery-operated, sensitive
screening method, named CRISPR-Clear, for the detection of gene drive modified
organisms. CRISPR-Clear is based on the combination of three components: 1) A DNA
amplification technique known as loop-mediated isothermal amplification (LAMP)
for detecting the presence of a gene drive; b) a portable battery-operated
Arduino device which heats up the sample to allow DNA amplification, and c) a naked-eye visualization of the results. </p>
<p>We designed and tested six LAMP primers
targeting a Cas9 endonuclease-based gene drive, assembled a battery-operated
Arduino device and tested the naked-eye visualization method. In addition, we were
able to detect the presence of the Cas9 gene, extracted from a transformed
bacteria, providing a proof-of-concept of the CRISPR-Clear device.</p> | Anna C. Nieuwenweg; Martijn M. van Galen; Angelina Horsting; Jorrit W. Hegge; Aldrik Velders; Vittorio Saggiomo | Biochemistry; Bioengineering and Biotechnology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740824c89199a87ad2143/original/crispr-clear-a-fieldable-detection-procedure-for-potential-crispr-cas9-gene-drive-based-bioweapons.pdf |
612e26eb90051e4763e587cb | 10.26434/chemrxiv-2021-kjbtk | Synthesis and Use of Versatile [1.1.1]Bicyclopentylaldehyde Building Blocks | The [1.1.1] bicyclopentane (BCP) motif is an emerging scaffold in medicinal chemistry due to its bioisosterism to 1,4-phenylene and 1,2-alkynyl functions. Current drawback of their use is the lack of stable versatile synthetic building blocks. Aldehydes are amongst the most useful functionalities in organic chemistry. In this paper a simple one-pot procedure from aryl-halides and [1.1.1]propellane is described. Preparation of various BCP molecules is conducted to showcase the versatility of these stable in-termediates. | Dániel Lasányi; Dániel Máth; Gergely L. Tolnai | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e26eb90051e4763e587cb/original/synthesis-and-use-of-versatile-1-1-1-bicyclopentylaldehyde-building-blocks.pdf |
670452b151558a15ef6967f2 | 10.26434/chemrxiv-2024-h481j | Mechanistic Insights into the Base-Mediated Deuteration of Pyridyl Phosphonium and Ammonium Salts | Pyridines can be deuterated at remote sites by treatment with KOtBu in DMSO-d6, although without discrimination between the meta- and para-position. Herein, base-catalyzed deuterations have been studied, computationally and experimentally, on a series of pyridyl phosphonium and ammonium salts having a temporary electron-withdrawing group to block the para-position while increasing the acidity in the other positions. | Arianna Montoli; Alessandro Dimasi; Miriana Guarnaccia; Andrea Citarella; Paolo Ronchi; Delia Blasi; Sergio Rossi; Daniele Passarella; Valerio Fasano | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670452b151558a15ef6967f2/original/mechanistic-insights-into-the-base-mediated-deuteration-of-pyridyl-phosphonium-and-ammonium-salts.pdf |
65f800dc9138d23161b0ae71 | 10.26434/chemrxiv-2024-ptc70 | Study of Solid-state Diffusion Impedance in Li-ion Batteries using Parallel-diffusion Warburg Model | Anomalous diffusion impedance due to the solid-state Li+ diffusion in Li-ion batteries is often troublesome for the analysis. In this work, we propose a novel analytical Parallel-diffusion Warburg (PDW) model and couple it with the conventional equivalent electrical circuit model (EECM) analysis to tackle this long-standing challenge. The analytical expression of the PDW is derived from the classical Fickian diffusion framework, introducing non-unified diffusion coefficients that originate from the diverse crystalline conditions of Li+ diffusion paths, as theoretically demonstrated in the atomistic modelling results. The proposed approach (EECM + PDW) is successfully employed to study the diffusion impedance of thin-film LiNi0.5Mn1.5O2 (LNMO) electrodes and porous LiNi0.80Co0.15Al0.05O2 (NCA) electrodes, demonstrating the applicability and robustness of this method. | Xinhua Zhu; Marta Cazorla Soult; Benny Wouters; Mesfin Haile Mamme | Physical Chemistry; Materials Science; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f800dc9138d23161b0ae71/original/study-of-solid-state-diffusion-impedance-in-li-ion-batteries-using-parallel-diffusion-warburg-model.pdf |
60c74bce702a9b15ac18b51c | 10.26434/chemrxiv.12262010.v2 | Polymer-Assisted Modification of Metal-Organic Framework MIL-96 (Al): Influence on Particle Size, Crystal Morphology and Perfluorooctanoic Acid (PFOA) Removal | <div><b>Abstract</b></div><div>A new synthesis method was developed to prepare an aluminum-based metal organic framework (MIL-96) with a larger particle size and different crystal habits. A low cost and water-soluble polymer, hydrolyzed polyacrylamide (HPAM), was added in varying quantities into the synthesis reaction to achieve >200% particle size enlargement with controlled crystal morphology. The modified adsorbent, MIL-96-RHPAM2, was systematically characterized by SEM, XRD, FTIR, BET and TGA-MS. Using activated carbon (AC) as a reference adsorbent, the effectiveness of MIL-96-RHPAM2 for perfluorooctanoic acid (PFOA) removal from water was examined. The study confirms stable morphology of hydrated MIL-96-RHPAM2 particles as well as a superior PFOA adsorption capacity (340 mg/g) despite its lower surface area, relative to standard MIL-96. MIL-96-RHPAM2 suffers from slow adsorption kinetics as the modification significantly blocks pore access. The strong adsorption of PFOA by MIL-96-RHPAM2 was associated with the formation of electrostatic bonds between the anionic carboxylate of PFOA and the amine functionality present in the HPAM backbone. Thus, the strongly held PFOA molecules in the pores of MIL-96-RHPAM2 were not easily desorbed even after eluted with a high ionic strength solvent (500 mM NaCl). Nevertheless, this simple HPAM addition strategy can still chart promising pathways to impart judicious control over adsorbent particle size and crystal shapes while the introduction of amine functionality onto the surface chemistry is simultaneously useful for enhanced PFOA removal from contaminated aqueous systems.<br /></div> | Luqman Hakim Mohd Azmi; Daryl R. Williams; Bradley P. Ladewig | Hybrid Organic-Inorganic Materials; Environmental Science; Coordination Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2020-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bce702a9b15ac18b51c/original/polymer-assisted-modification-of-metal-organic-framework-mil-96-al-influence-on-particle-size-crystal-morphology-and-perfluorooctanoic-acid-pfoa-removal.pdf |
60c74914bdbb893250a390dd | 10.26434/chemrxiv.12022908.v1 | Catalyst Free, Nitromethane Assisted Facile Ring Opening of Epoxide with Less Reactive Aromatic Amines | <p>Nucleophilic ring opening reactions of epoxides with aromatic amines are in the forefront of the synthetic organic chemistry research to build new bioactive scaffolds. Here, a convenient, green and highly efficient regioselective ring opening of sterically hindered (2R,3S)-3-(<i>N</i>-Boc-amino)-1-oxirane-4-phenylbutane with various poorly reactive aromatic amines are accomplished under microwave irradiation in nitromethane. All the reactions effectively implemented for various aromatic amines involves reuse of nitromethane that supports its dual role as a solvent and catalyst. The corresponding new β-alcohol analogs of hydroxyethylamine (HEA) are isolated in 41-98% yields. The reactions proceed under mild conditions for a broad range of less reactive and sterically hindered aromatic amines. Proton NMR and UV-visible spectroscopic studies suggest that the nucleophilicity of amines is influenced by nitromethane, which is substantiated by the extensive computational studies. Overall, this methodology elucidates the first time use of nitromethane as a solvent for the ring opening reactions under microwave conditions involving equimolar ratio of epoxide and aromatic amine without any catalyst, facile ring opening of complex epoxide by less reactive aromatic amines, low reaction time, less energy consumption, recycling of the solvent and simple workup procedures.</p> | Sumit Kumar; Meenakshi Bansal; Charu Upadhyay; Maria Grishina; Vladimir Potemkin; Brijesh Rathi; Poonam . | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74914bdbb893250a390dd/original/catalyst-free-nitromethane-assisted-facile-ring-opening-of-epoxide-with-less-reactive-aromatic-amines.pdf |
6730680d5a82cea2faa8025d | 10.26434/chemrxiv-2024-8xjfw | Dye-loaded polymeric nanorods as bright fluorescent nano-platforms for efficient cellular uptake and bioimaging | Fluorescent dye-loaded polymeric nanoparticles have been extensively developed for cellular imaging as they are bright and versatile tools with large choice of polymers, dyes and surface chemistry. Here, we report preparation of fluorescent polymeric nanomaterials with high aspect ratio – nanorods, and study their cellular uptake for bioimaging applications. Fluorescent polymeric nanorods are prepared by scission of electrospun nanofibers using ultrasonication. To achieve high brightness, they are loaded with cationic fluorescent dyes (rhodamine or cyanines) with bulky hydrophobic counterions that prevent aggregation-caused quenching. The obtained nanorods of 400 nm diameter and 2-4 µm length show good fluorescence quantum yields (40% at 5% dye loading) and 800-fold higher brightness compared to 60-nm polymeric nanoparticles. Cellular studies reveal several remarkable features of nanorods vs NPs. First, nanorods internalization depends on the cell type, which was not the case of NPs. Second, we found that internalization of nanorods is nearly 100-fold more efficient than that of polymeric NPs, reaching ~3 wt% of the cell mass. The internalization of nanorods is an active process (endocytosis), which is inhibited by low temperature, absence of growth medium or nanorods treatment by a non-ionic surfactant. Despite this efficient internalization, nanorods exhibit negligible cytotoxicity according to three different types of assays. Due to high accumulation inside the cells, the labelled cells present ~100-fold higher fluorescence signal vs NPs, which remains for at least 6 days. This exceptional cell brightness enables single-cell tracking in two near-infrared spectral regions under the chicken skin. This work reveals exceptional capacity of polymeric nanorods to accumulate inside the cells, which allows efficient fluorescence labelling of cells for robust imaging and long-term tracking. | Remi Pelletier; Anila Hoskere Ashoka; Deep S. Biswas; Elisabete Cruz Da Silva; Andrey S. Klymchenko | Materials Science; Nanoscience; Biocompatible Materials; Nanostructured Materials - Materials; Optical Materials | CC BY 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6730680d5a82cea2faa8025d/original/dye-loaded-polymeric-nanorods-as-bright-fluorescent-nano-platforms-for-efficient-cellular-uptake-and-bioimaging.pdf |
60c7470e0f50db72f039654a | 10.26434/chemrxiv.11494584.v1 | Efficient Photoluminescence of Isotropic Rare-Earth Oxychloride Nanocrystals from a Solvothermal Route | Eu3+-doped sub-10 nm LaOCl nanocrystals with 43 % photoluminescence quantum yield were prepared by solvothermal synthesis from hydrated rare-earth chlorides. As-obtained nanocrystals are nearly spherical, monodisperse and stable as colloidal dispersions. These combined features should intensify the interest for nanocrystalline rare-earth oxyhalides and their optical properties. | Guillaume Gouget; Morgane Pellerin; Lauriane Pautrot-d’Alençon; Thierry Le Mercier; Christopher B. Murray | Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7470e0f50db72f039654a/original/efficient-photoluminescence-of-isotropic-rare-earth-oxychloride-nanocrystals-from-a-solvothermal-route.pdf |
61e73d2677a416fb2ed5e45f | 10.26434/chemrxiv-2022-svlqz | Mapping the Proteoform Landscape of Five Human Tissues | A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term “proteoform” encapsulates this complexity at the level of chemical composition. Comprehensive mapping of the proteoform landscape in human tissues necessitates analytical techniques with increased sensitivity and depth of coverage. Here, we took a top-down proteomics approach, combining data generated using capillary zone electrophoresis (CZE) and nanoflow reversed-phase liquid chromatography (RPLC) hyphenated to mass spectrometry to identify and characterize proteoforms from human lung, heart, spleen, small intestine, and kidney. CZE and RPLC provided complementary post-translational modification (PTM) and proteoform selectivity, thereby enhancing overall proteome coverage when used in combination. Of the 11,466 proteoforms identified in this study, 7,373 (64%) were not reported previously. Large differences in protein- and proteoform-level were readily quantified, with initial inferences about proteoform biology operative in the analyzed organs. Differential proteoform regulation of defensins, glutathione transferases, and sarcomeric proteins across tissues generate hypotheses about how they function and are regulated in human health and disease. | Bryon Drown; Kevin Jooß; Rafael Melani; Cameron Lloyd-Jones; Jeannie Camarillo; Neil Kelleher | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e73d2677a416fb2ed5e45f/original/mapping-the-proteoform-landscape-of-five-human-tissues.pdf |
67146094cec5d6c142a6639f | 10.26434/chemrxiv-2024-hg770 | Formulation and evaluation of nanoemulsion-based nanocream using green ingredients exhibiting enhanced performance characteristics | The present study focuses on the formulation and evaluation of a nanoemulsion-based nanocream using green ingredients, aimed at enhancing performance, stability, and sustainability. The nanoemulsion was developed through the low-energy phase inversion temperature (PIT) method, which successfully protected green bioactive compounds like vitamin E, cinnamon oil, jojoba oil, and peppermint oil from degradation. A series of nanoemulsions were prepared using varying ratios of oils and surfactants and evaluated for thermodynamic stability, transparency, and droplet size. The optimized nanoemulsion, with a mean droplet size of 121.3±1.19 nm and a low polydispersity index (PDI) of 0.094±0.001, demonstrated high uniformity and stability. This optimized nanoemulsion was further used as the cream’s aqueous phase, forming a nanocream that exhibits enhanced permeation of nanoscale bioactives through a membrane and improved overall performance characteristics. In vitro membrane permeation studies revealed that the optimized nanocream achieved a permeation rate of 97.15%, substantially outperforming the control cream. In vitro antimicrobial studies showed comparable efficacy to standard market preparations containing synthetic agents. The nanocream also demonstrated long-term stability over six months, maintaining structural integrity without phase separation or significant changes in pH and spreadability. The nanoemulsion-based nanocream formulated with eco-friendly ingredients hence offers enhanced skin permeation, superior bioactive delivery, and stable performance, making it a promising candidate for topical skincare and antimicrobial applications. | Daphne Nguyen; Manish Kumar | Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67146094cec5d6c142a6639f/original/formulation-and-evaluation-of-nanoemulsion-based-nanocream-using-green-ingredients-exhibiting-enhanced-performance-characteristics.pdf |
677aea666dde43c90867c0aa | 10.26434/chemrxiv-2025-7f2c4 | Order to disorder transition due to entropy in layered and 2D carbides | There is controversy surrounding the moniker “high-entropy” materials due to the unclear effect of entropy and enthalpy. The unique nanolayered structure of MAX phases, with its structural covalent-metallic-covalent carbide interfaces, allowed us to address this controversy systematically. Here, we synthesized nearly 40 known and novel MAX phases containing 2 to 9 metals and found that their enthalpic preference for short-range order remains until entropy increases enough to achieve all configurations of the transition metals in their atomic planes. In addition, we transformed all these MAX phases into two-dimensional (2D) MXenes and showed the effects of the order vs. disorder on their surface properties and electronic behavior. This study indicates that short-range ordering in high-entropy materials determines the impact of entropy vs. enthalpy on their structures and properties. | Brian Wyatt; Yinan Yang; Paweł Michałowski ; Tetiana Parker; Yamilée Morency ; Francesca Urban ; Givi Kadagishvili ; Manushree Tanwar ; Sixbert Muhoza ; S. Kartik Nemani; Annabelle Bedford; Hui Fang; Zachary Hood; Junwoo Jang; Krutarth Kamath; Bethany Wright; Rebecca Disko; Anupma Thakur; Sanguk Kan; Neil Ghosh; Xianfan Xu; Zahra Fakhraai; Yury Gogotsi; Aleksandra Vojvodic ; De-en Jiang; Babak Anasori | Materials Science; Nanoscience; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677aea666dde43c90867c0aa/original/order-to-disorder-transition-due-to-entropy-in-layered-and-2d-carbides.pdf |
60c746529abda2c4b7f8c72a | 10.26434/chemrxiv.11307710.v1 | S(IV)–Mediated Unsymmetrical Heterocycle Cross-Couplings | <p>Herein we
report a sulfur (IV) mediated cross-coupling for facile synthesis of heteroaromatic
substrates. Addition of heteroaryl nucleophiles onto a simple,
readily-accessible alkyl sulfinyl (IV) chloride allows formation of a trigonal
bipyramidal sulfurane intermediate. Reductive elimination therefrom provides bis-heteroaryl
products in a practical and efficient fashion. <br /></p> | Min Zhou; Jet Tsien; Tian Qin | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746529abda2c4b7f8c72a/original/s-iv-mediated-unsymmetrical-heterocycle-cross-couplings.pdf |
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