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67da8ddf81d2151a02fad652 | 10.26434/chemrxiv-2025-g4pqn | Equivalence Between Synthetic Decoupling and 2-Field Autocorrelation NMR Spectroscopy | It is shown that the recently introduced synthetic decoupling method, which correlates two lists of single-transition NMR frequencies acquired at two different fields to construct in silico a pure-shift spectrum, is equivalent to an experiment where free evolution periods at these two fields are autocorrelated in a 2D fashion. Numerical simulations are utilized to investigate these hypothetical 2-field 2D experiments that yield isotropic chemical-shift information by refocusing either scalar or quadrupolar couplings, in solution and solid state, respectively. In this latter case, both static and magic-angle spinning conditions are considered. It is shown that projections of the 2D data set taken at angles amounting to arctan(1) and arctan(1/), where = B0high/B0low, for scalar and quadrupolar couplings, respectively, are isotropic and can be scaled to directly yield the pure chemical shifts. For such purpose, a scaling factor is introduced. In the case of quadrupolar spins, the obtained pure-shift projections are also free from the isotropic part of the second-order quadrupolar broadening. The spectral resolution achieved by different relative strengths of the two external fields is considered. | Diego Carnevale | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67da8ddf81d2151a02fad652/original/equivalence-between-synthetic-decoupling-and-2-field-autocorrelation-nmr-spectroscopy.pdf |
60c75500702a9b4e0618c602 | 10.26434/chemrxiv.11894547.v3 | Halogen bonding: an underestimated player in membrane-ligand interactions | <div>Halogen bonds (XBs) are noncovalent interactions where halogen atoms act as electrophilic species interacting with Lewis bases. These interactions are relevant in biochemical systems being increasingly explored in drug discovery, mainly to modulate protein–ligand interactions, but are also found in engineered protein or nucleic acid systems. In this work, we report direct evidence for the existence of XBs in the context of biological membrane systems thus expanding the scope of application of these interactions. Indeed, our molecular dynamics simulations show the presence of favorable interactions between halobenzene derivatives and both phosphate or ester oxygen acceptors from model phospholipid bilayers, thus supporting the existence of XB mediated phospholipid–halogen recognition phenomena influencing the membrane insertion profile of the ligands and their orientational preferences. This represents a relevant interaction, previously overlooked, eventually determining the pharmacological or toxicological activity of halogenated compounds and hence with potential implications in drug discovery and development, a place where such species account for a significant part of the chemical space. We also provide insights into a potential role for XBs in water-to membrane insertion of halogenated ligands as XBs are systematically observed during this process. Therefore, our data strongly suggests that, as the ubiquitous hydrogen bond, XBs should be accounted for in the development of membrane partition models.</div> | Rafael Nunes; Diogo Vila Viçosa; Paulo J. Costa | Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75500702a9b4e0618c602/original/halogen-bonding-an-underestimated-player-in-membrane-ligand-interactions.pdf |
66d7397c12ff75c3a148cae4 | 10.26434/chemrxiv-2024-cvlt2-v2 | A Versatile Silica Functionalization Strategy for Organic Phase Nanomaterials | Chemical interactions between nanoparticles and their surroundings are governed by their surface chemistry. Therefore, a versatile strategy for surface functionalization that is compatible with a variety of particle compositions would empower nanotechnology research. Silica coating offers a promising approach, but the ease with which silica shells can be synthesized is determined by the initial solution state of the nanoparticle, since the silica sol-gel chemistry typically occurs in an aqueous phase. While protocols for coating water-soluble particles are well-established, protocols for nanomaterials suspended in organic solvents require phase-transfer during the coating process, often leading to inconsistent reproducibility, non-uniform thicknesses, difficulty in producing thin coatings, and particle aggregation during functionalization. Here, we demonstrate that these challenges stem from insufficient stabilization of the organic-phase particles during the phase transfer, and can be overcome by adding excess surface ligands during the silica growth process. The inclusion of these excess ligands sufficiently alters the nanoparticles’ surface chemistry to suppress particle aggregation, allowing deposition of shells as thin as 0.7 nm on a wide range of nanoparticle compositions, sizes, and shapes. The versatility and reproducibility of this approach is illustrated through its application to isotropic magnetite nanoparticles with diameters between 20-28 nm, anisotropic magnetite nanodiscs >200 nm in diameter, and CdSe/ZnS quantum dots. These silica-coated nanomaterials retain their functional properties, and the silica shell can be further modified with application-specific organic moieties. This approach therefore provides a versatile means of stabilizing nanomaterials for applications that demand precise control over their surface chemistry independent of their functional properties. | Keisuke Nagao; Katherine Lei; Peyton Worthington; Noah Kent; Michika Onoda; Elian Malkin; Emmanuel Vargas Paniagua; Rebecca Leomi; Robert J. Macfarlane; Polina Anikeeva | Materials Science; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d7397c12ff75c3a148cae4/original/a-versatile-silica-functionalization-strategy-for-organic-phase-nanomaterials.pdf |
628508156cae1c62220e6019 | 10.26434/chemrxiv-2022-zbcsb | Synthesis and styrene copolymerization of novel fluoro, methoxy and methyl ring-disubstituted octyl phenylcyanoacrylates | Novel fluoro, methoxy, and methyl ring-disubstituted octyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 2-fluoro-3-methoxy, 2-fluoro-4-methoxy, 2-fluoro-5-methoxy, 2-fluoro-6-methoxy, 3-fluoro-4-methoxy, 4-fluoro-3-methoxy, 2-fluoro-5-methyl, 2-fluoro-6-methyl, 3-fluoro-4-methyl, 4-fluoro-2-methyl, 4-fluoro-3-methyl) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Mahmoud D. Awadallah; Izza A. Awan; Grace M. Carlino; Zachary K. Cherian; Sophia J. Dimonte; Madeline A. Purkey; Juvy L. Rabelas; Yash Y. Singapori; Bajeel Syeda; Victoria J. Wisniewski; Sara M. Rocus; William S. Schjerven; Gregory B Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628508156cae1c62220e6019/original/synthesis-and-styrene-copolymerization-of-novel-fluoro-methoxy-and-methyl-ring-disubstituted-octyl-phenylcyanoacrylates.pdf |
6439620f73c6563f14d8d2e1 | 10.26434/chemrxiv-2023-fzj5t | Design Rules for Two-Dimensional Organic Semiconductor-Incorporated Perovskites (OSiP) Gleaned from Thousands of Simulated Structures | Organic-inorganic hybrid perovskite semiconductors are under investigation for many applications owing to their excellent optoelectronic properties and relatively simple processing. Two-dimensional (2D) halide perovskites are an attractive class of hybrid perovskites that have additional optoelectronic tunability due to their accommodation of relatively large organic ligands. Nevertheless, contemporary ligand design depends on either expensive trial-and-error testing of whether a ligand can be integrated within the lattice or conservative heuristics that unduly limit the scope of ligand chemistries. Here, the structural determinants of ligand incorporation and perovskite stability are established by molecular dynamics (MD) simulations of over ten thousand perovskites, including an algorithmically generated set of prospective ligand chemistries and all previously reported experimental primary ammonium ligands based on C, H, O, S, and N. The simulation results show near-perfect predictions of positive and negative literature examples, predict trade-offs between several ligand features and perovskite stability, and ultimately predict an inexhaustibly large 2D-compatible ligand design space. This dataset is used to train machine learning classifiers capable of predicting the geometric stability of perovskite structures based solely on generalizable ligand features, thus providing an inexpensive tool for screening putative ligands. As a demonstration, the model was used to down-select five new ligands that were successfully synthesized and incorporated into 2D perovskites. This work provides a new paradigm for future low-dimensional perovskite design. | Zih-Yu Lin; Jiaonan Sun; Stephen Shiring; Letian Dou; Brett Savoie | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6439620f73c6563f14d8d2e1/original/design-rules-for-two-dimensional-organic-semiconductor-incorporated-perovskites-o-si-p-gleaned-from-thousands-of-simulated-structures.pdf |
60c75832702a9bbb0118cc8b | 10.26434/chemrxiv.14394773.v2 | Rapid and Mild Synthesis of Au-NHC Complexes in a Simple Two-Phase Flow Reactor | <p>We describe a simple two-phase flow reactor which allows for the
efficient and rapid synthesis of several Au(I)-NHC complexes under mild
conditions, with minimal workup, and avoiding common problems with
decomposition to Au(0). An optional second stage allows for direct synthesis of
Au(III)-NHC complexes, without isolation of the Au(I)-NHC intermediate.</p> | Helgi Freyr Jónsson; Anne Fiksdahl; Andrew Harvie | Process Chemistry; Organometallic Compounds; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75832702a9bbb0118cc8b/original/rapid-and-mild-synthesis-of-au-nhc-complexes-in-a-simple-two-phase-flow-reactor.pdf |
60c7576d4c891991afad49f1 | 10.26434/chemrxiv.13143167.v3 | Masked Graph Modeling for Molecule Generation | De novo, in-silico design of molecules is a challenging problem with applications in drug discovery and material design. We introduce a masked graph model, which learns a distribution over graphs by capturing conditional distributions over unobserved nodes (atoms) and edges (bonds) given observed ones. We train and then sample from our model by iteratively masking and replacing different parts of initialized graphs.<br />We evaluate our approach on the QM9 and ChEMBL datasets using the GuacaMol distribution-learning benchmark. We find that validity, KL-divergence and Fréchet ChemNet Distance scores are anti-correlated with novelty, and that we can trade off between these metrics more effectively than existing models. On distributional metrics, our model outperforms previously proposed graph-based approaches and is competitive with SMILES-based approaches. Finally, we show our model generates molecules with desired values of specified properties while maintaining physiochemical similarity to the<br />training distribution. | Omar Mahmood; Elman Mansimov; Richard Bonneau; Kyunghyun Cho | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7576d4c891991afad49f1/original/masked-graph-modeling-for-molecule-generation.pdf |
657d72b466c13817295149c9 | 10.26434/chemrxiv-2023-51js9 | A red-shifted donor-acceptor hemicyanine-based probe for mitochondrial pH in live cells | pH dynamically regulates diverse cellular functions and processes. At the Inner Mitochondrial Membrane (IMM), nanoscale pH gradients generated by the Electron Transport Chain (ETC) play a critical role in contributing to mitochondrial membrane potential that drives ATP synthesis and thermogenesis. However, tools to decouple pH gradients from the overall IMM potential in living cells are limited. This study integrates a fluorescent “benzo-indole” chromophore with a pH-sensitive “phenol” moiety into a single covalent skeleton to build a sensitive, red-shifted, cell-permeable pH probe (Mito-pH2). Mito-pH2 localizes inside mitochondria with high specificity presumably to the mitochondrial inner membrane by virtue of being an amphiphilic cation and can report dynamic changes in mitochondrial pH in living cells. Our design ensures that Mito-pH2 exhibits pH-sensitive dual-excitation and dual-emission peaks enabling ratiometric pH-sensing. Further, Mito-pH2 reports an increase in pH in the pH range of 3-9 through a striking colour change from yellow to purple making it a sensitive all-purpose colorimetric pH probe. A combination of DFT calculations and spectroscopy shed light on likely sensing mechanisms including photophysics. Quantitative live-cell fluorescence imaging reveals that Mito-pH2 can detect dynamic changes in mitochondrial pH upon extracellular pH modulation with little or no measurable cytotoxicity during live imaging. Red-emitting Mito-pH2 opens new avenues of quantitative mapping of physiological mitochondrial membrane pH and significantly enhances the repertoire of environment-sensitive and low-toxicity mitochondrial probes that link mitochondrial state and micro-environment. | Fouzia Kalim; Sivaraman Gandhi; Arati Ramesh; Sufi O. Raja; Akash Gulyani | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657d72b466c13817295149c9/original/a-red-shifted-donor-acceptor-hemicyanine-based-probe-for-mitochondrial-p-h-in-live-cells.pdf |
676b923081d2151a02d4ddc0 | 10.26434/chemrxiv-2024-5x2pv-v2 | Reflexive Chirality Transfer (RCT): Asymmetric 1,3-Dipolar Cycloaddition of α-Amino Acid Schiff Base with Non-Chiral Copper Catalyst | Although optically pure α-amino acids are ubiquitous, their chirality is usually lost during the α-C–H deprotonation. Consequently, precious chiral catalysis has been necessary to synthesize optically active α-tetrasubstituted unnatural α-amino acid derivatives, even when starting with optically pure α-amino acids. However, here we report a catalytic asymmetric 1,3-dipolar cycloaddition that preserves the α-carbon chirality of α-amino acid derivatives. This process directly converts readily available optically active α-amino acid Schiff bases into optically active α-tetrasubstituted pyrrolidine derivatives without external chiral additives, despite the temporary loss of α-carbon chirality through the formation of planar 1,3-dipole intermediates. Mechanistic studies revealed that the α-carbon chirality of the α-amino acid Schiff base is transiently transferred to metal-centered chirality in 1,3-dipoles and subsequently restored as carbon-centered chirality of the products. This conceptually novel "Reflexive Chirality Transfer (RCT)" strategy offers a simple and cost-effective approach to optically active unnatural α-amino acid derivatives, addressing the current limitations of chiral pool synthesis. | Kazuhiro Morisaki; Yuto Furuki; Rento Kousaka; Serika Nagai; Yoshihiro Oonishi; Yoshihiro Sato | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676b923081d2151a02d4ddc0/original/reflexive-chirality-transfer-rct-asymmetric-1-3-dipolar-cycloaddition-of-amino-acid-schiff-base-with-non-chiral-copper-catalyst.pdf |
65e822589138d23161c69590 | 10.26434/chemrxiv-2024-606hv | Photoassisted amplification of chain-growth in CO2 hydrogenation: Switching selectivities of heterogeneously catalyzed reactions with light | Selective carbon-carbon bond formation is a major challenge for chemical transformations to meet the global sustainability targets, which requires game-changing concepts instead of further improvement of conventional catalyst materials. In this work, a new paradigm to tune the selectivity of thermal catalytic systems is presented by using light as an external trigger to switch the selectivity from pure reduction to carbon-carbon bond formation. In a ruthenium-catalyzed CO2 hydrogenation reaction, chain-growth is initiated through irradiation with light, eventually leading to the formation of higher hydrocarbons instead of solely methane. Photoassisted reaction control was differentiated from photokinetic and photothermal effects by sophisticated thermal imaging and kinetic modelling. A light-induced change of the sorption properties of the solid catalyst surface was identified as reason for the changes in selectivity. The results render the exploitation of photoassisted effects as highly potent general strategy for comprehensive reaction control of reactions catalyzed by solids. | Henning Becker; Dirk Ziegenbalg; Robert Güttel | Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e822589138d23161c69590/original/photoassisted-amplification-of-chain-growth-in-co2-hydrogenation-switching-selectivities-of-heterogeneously-catalyzed-reactions-with-light.pdf |
672102dcf9980725cf45d9c3 | 10.26434/chemrxiv-2024-pf3ph | Conformal Selection for Efficient and Accurate Compound Screening in Drug Discovery | In drug discovery, the reliability of compound screening based on manual assessments is compromised by potential bias, while existing methods lack robust risk control measures. To address these challenges, we introduced conformal selection as an enhanced approach to optimize the compound screening process with balanced risks and benefits. Leveraging conformal inference, our approach constructs p-values for each candidate molecule to quantify statistical evidence for selection. The final selection of molecules is determined by comparing these p-values against thresholds derived from multiple testing principles. Our approach offers rigorous control over the false discovery rate, ensuring validity independent of dataset size and requiring minimal assumptions. By avoiding the estimation of prediction errors required in previous approaches, our method achieves higher accuracy (power), thereby improving the ability to identify promising candidates. Furthermore, our method demonstrates superior computational efficiency. We validate these advantages through numerical simulations on real-world datasets. | Tian Bai; Peng Tang; Yuting Xu; Vladimir Svetnik; Abbas Khalili; Xiang Yu; Archer Yang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672102dcf9980725cf45d9c3/original/conformal-selection-for-efficient-and-accurate-compound-screening-in-drug-discovery.pdf |
66100d15418a5379b0280213 | 10.26434/chemrxiv-2024-np2ww | Orthogonal Nano-Engineering (ONE): Modulating Nanotopography and Surface Chemistry of Aluminum Oxide for Superior Antifouling and Enhanced Chemical Stability | Decoupling certain material surface properties can be key to attaining critical property-activity relationships that underpin their antifouling performance. Here, we employed Orthogonal Nano-Engineering (ONE) to decouple the influences of nanotopography and surface chemistry on surface antifouling. Nanotopography and surface chemistry were systematically varied with a two-step process. Controlled nanotopography was obtained by electrochemical anodization of aluminum, which generated anodic aluminum oxide (AAO) surfaces with cylindrical nanopores (diameters: 15 nm, 25 nm, 100 nm). To modify surface chemistry while preserving nanotopography, an ultrathin (~5 nm) yet stable zwitterionic coating of poly(divinylbenzene-4-vinylpyridyl sulfobetaine) was deposited on these surfaces using initiated chemical vapor deposition (iCVD). Antifouling performance was assessed by quantifying 48-h biomass formed by Gram positive and negative bacteria. The ONE surfaces demonstrated enhanced antifouling performance, with small-pore nanotopography and zwitterionic chemistry each lowered biomass accumulation by tested species, with potential additive effects. The most effective chemistry-topography combination (ZW-AAO15) enabled an overall reduction of 91% for Escherichia coli, 76% for Staphylococcus epidermidis, 69% for Listeria monocytogenes, and 67% for Staphylococcus aureus, relative to the uncoated nanosmooth control. Additionally, the composite ZW coating exhibited encouraging anticorrosion properties under both static and turbulent cleaning conditions, vital to antifouling applications in healthcare and food industries. | Hanyu Chen; Felicia Fianu; Carmen Moraru; Rong Yang; Yifan Cheng | Nanoscience; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66100d15418a5379b0280213/original/orthogonal-nano-engineering-one-modulating-nanotopography-and-surface-chemistry-of-aluminum-oxide-for-superior-antifouling-and-enhanced-chemical-stability.pdf |
659533e4e9ebbb4db95303d2 | 10.26434/chemrxiv-2024-7mq3w | Understanding Selective Hydrogenation of Phenylacetylene on PdAg Single Atom Alloy: DFT Insights on Molecule Size and Surface Ensemble Effects | Single atom alloys (SAA) have proven to be effective catalysts, offering customizable properties for diverse chemical processes. Various metal combinations are used in SAAs and Pd dispersed materials are frequently employed in catalyzing hydrogenation reactions. Herein, we explore the hydrogenation of phenylacetylene to styrene and ethylbenzene on PdAg SAA using density functional theory calculations. Our results show that while PdAg SAA does improve the activity of the host Ag towards hydrogenation, a dilute PdAg SAA surface with isolated Pd-atoms is not selective towards partial hydrogenation of phenylacetylene. Additionally, we investigate how the size of the reactant molecule, the size of the metal alloy ensemble, and a ligand effect impact the hydrogenation process. The SAA enhances the binding strengths of various organic adsorbates, although this effect diminishes as the adsorbate size increases. Our findings indicate the dilute PdAg exhibits selectivity towards hydrogenation of smaller molecules such acetylene due to its distinct adsorption geometry. The selective hydrogenation of phenylacetylene necessitates a surface Pd dimer ensemble. Our research highlights the importance of both reactant molecule size and surface configurations in SAA catalysts. This is particularly crucial when dealing with the adsorption of sizable organic molecules where the functional group can adopt different adsorption modes. | Hanan Ibrahim; Timo Weckman; Dmitry Murzin; Karoliina Honkala | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659533e4e9ebbb4db95303d2/original/understanding-selective-hydrogenation-of-phenylacetylene-on-pd-ag-single-atom-alloy-dft-insights-on-molecule-size-and-surface-ensemble-effects.pdf |
60c74f41702a9bddb418bb44 | 10.26434/chemrxiv.12510011.v2 | Human Neuraminidases Have Reduced Activity Towards Modified Sialic Acids on Glycoproteins | This work investigated the substrate specificity of hNEU enzymes for a
glycoprotein substrate (bovine submaxillary mucin) containing 9-<i>O</i>-acetylated
and Neu5Gc residues. Using this model substrate, we observe a general trend for
hNEU tolerance of Neu5Ac>Neu5Gc>>>Neu5,9Ac<sub>2</sub>, consistent
with our previous results with glycolipid substrates. These results expand our
understanding of hNEU enzyme specificity and suggest that naturally occurring
modifications of sialic acids can play a role in regulating hNEU activity. | Carmanah
D. Hunter; Elizabeth Porter; Christopher Cairo | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f41702a9bddb418bb44/original/human-neuraminidases-have-reduced-activity-towards-modified-sialic-acids-on-glycoproteins.pdf |
62161f41c3e9dad2d7743106 | 10.26434/chemrxiv-2022-jzsx2 | How do the Mutations in PfK13 Protein
Promote Anti-malarial Drug Resistance? | Plasmodium falciparum develops resistance to artemisinin upon exposure to the anti-malarial drug. Various mutations in the Plasmodium falciparum Kelch13 (PfK13) protein such as Y493H, R539T, I543T, and C580Y have been associated with antimalarial drug resistance. (Ariey et al., Nature, 2014, 505, 50-55) These mutations impede the regular ubiquitination process that eventually invokes drug resistance. However, the relationship between the mutation and the mechanism of drug resistance has not yet been fully elucidated. The comparative protein dynamics are studied by performing the classical molecular dynamics (MD) simulations and subsequent analysis of the trajectories adopting root-means-square fluctuations, the secondary-structure predictions and the dynamical cross-correlation matrix analysis tools. Here we observed
that the mutations in the Kelch-domain does not have any structural impact on the mutated site, however, it significantly alters the overall dynamics of the protein.
The loop-region of the BTB-domain especially for Y493H and C580Y mutants are found to have the enhanced dynamical fluctuations. The enhanced fluctuations in the
BTB-domain could affect the protein-protein (PfK13-Cullin) binding interactions in the ubiquitination process and eventually leads to anti-malarial drug resistance. | Shikha Sharma; Md. Ehesan Ali | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62161f41c3e9dad2d7743106/original/how-do-the-mutations-in-pf-k13-protein-promote-anti-malarial-drug-resistance.pdf |
60c745b7469df4ad2ef43536 | 10.26434/chemrxiv.10115936.v1 | Is There a Gender Gap in Chemical Sciences Scholarly Communication? | <p></p><p>The Royal Society of Chemistry is committed to investigating and addressing the barriers and biases which face women in the chemical sciences. The cornerstone of this is a thorough analysis of data regarding submissions, review and citations for Royal Society of Chemistry journals from January 2014 until July 2018, since the number and impact of publications and citations are an important factor when seeking research funding and for the progression of academic career. We have applied standard statistical techniques to multiple data sources to perform this analysis, and have investigated whether interactions between variables are significant in affecting various outcomes (author gender; reviewer gender; reviewer recommendations and submission outcome) in addition to considering variables individually. By considering several different data sources, we found that a baseline of approximately a third of chemistry researchers are female overall, although this differs considerably with Chemistry sub-discipline. Rather than one dominant bias effect, we observe complex interactions and a gradual trickle-down decrease in this female percentage through the publishing process and each of these female percentages is less than the last: authors of submissions; authors of RSC submissions which are not rejected without peer review; authors of accepted RSC publications; authors of cited articles. The success rate for female authors to progress through each of these publishing stages is lower than that for male authors. There is a decreasing female percentage when progressing through from first authors to corresponding authors to reviewers, reflecting the decreasing female percentage with seniority in Chemistry research observed in the “Diversity landscape of the chemical sciences” report1. Highlights and actions from this analysis form the basis of an accompanying report to be released from the Royal Society of Chemistry.</p><p></p> | Aileen Day; Peter Corbett; John Boyle | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745b7469df4ad2ef43536/original/is-there-a-gender-gap-in-chemical-sciences-scholarly-communication.pdf |
6554ede92c3c11ed71743357 | 10.26434/chemrxiv-2023-9r018 | Assessment of embedding schemes in a hybrid machine learning/classical potentials (ML/MM) scheme | Machine Learning (ML) methods have reached high accuracy levels for the prediction of in vacuo molecular properties. However, the simulation of large systems through solely ML methods (like those based on neural network potentials) is still a challenge. In this context, one of the most promising frameworks for integrating ML schemes in the simulation of complex molecular systems are the so-called ML/MM methods. These multiscale approaches combine ML methods with classical forcefields (MM), in the same spirit as the succesful hybrid quantum mechanics-molecular mechanics methods (QM/MM). The key issue for such ML/MM methods is the adequate description of the coupling between the region of the system described by ML and the region described at the MM level. In the context of QM/MM schemes, the main ingredient of the interaction is electrostatic, and the state of the art is the so called electrostatic-embedding. In this study, we analyze the quality of simpler mechanical embedding-based approaches, specifically focusing on their application within a ML/MM framework utilizing atomic partial charges derived in vacuo. Taking as reference electrostatic embedding calculations performed at a QM(DFT)/MM level, we explore different atomic charges schemes, as well as a polarization correction computed using atomic polarizabilites. Our benchmark data set comprises a set of about 80k small organic structures from the ANI-1x database, solvated in water. The results suggest that the MBIS atomic charges yield the best agreement with the reference coupling energy. Remarkable enhancements are achieved by including a simple polarization correction. | Juan Santiago Grassano; Jonathan Alexis Semelak; Ignacio Javier Pickering; Roitberg Adrian; Mariano Camilo Gonzalez Lebrero; Estrin Dario Ariel | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6554ede92c3c11ed71743357/original/assessment-of-embedding-schemes-in-a-hybrid-machine-learning-classical-potentials-ml-mm-scheme.pdf |
6151c51dd9c956ad84e22362 | 10.26434/chemrxiv-2021-m2wqr | Correlations between Precipitation Reactions and Electrochemical Performance of Lithium–Sulfur Batteries
| A comprehensive description of the electrochemical processes in the positive electrode of lithium–sulfur batteries is crucial for the enhancement of sulfur utilization. However, the discharge mechanisms are complicated due to the various reactions in multiple phases and the tortuosity of the highly porous carbon matrix. While previous studies have focused on the precipitation of lithium sulfide, the effect of the limited mass transport inside the micropores and mesopores of an electrode with optimized surface area have largely been neglected. In this work, in-operando small-angle scattering with three different contrasts, and wide-angle scattering measurements are made while the internal and diffusion resistances are measured simultaneously. The results indicate that the precipitates grow mostly in number, not in size, and that the structure of the carbon matrix is not affected. The comparison of the small-angle and wide-angle scattering reveals the amorphous discharge products found at a low discharge rate. Further analyses demonstrate the correlation between the diffusion resistance and the composition of material in the mesopores at the end of discharge, which suggests that Li-ion deficiency is the limiting factor of sulfur utilization at a medium discharge rate. | Yu-Chuan Chien; Matthew J. Lacey; Nina-Juliane Steinke; Daniel Brandell; Adrian R. Rennie | Inorganic Chemistry; Energy; Electrochemistry; Kinetics and Mechanism - Inorganic Reactions; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6151c51dd9c956ad84e22362/original/correlations-between-precipitation-reactions-and-electrochemical-performance-of-lithium-sulfur-batteries.pdf |
60c753d1567dfe32f1ec5fbf | 10.26434/chemrxiv.13543154.v1 | Cyclobenzoin Esters as Hosts for Thin Guests | Nitriles and terminal alkynes are important compounds in industrial and academic settings. Their supramolecular binding has been challenging without the intervention of metals, because of the small dimensions of their linear –C≡N and –C≡CH groups. Using a combination of crystallography and computation, we have shown that cyclotetrabenzoin esters can host terminal triple bonds of alkynes and nitriles in their electron-poor cavities. Within these cavities, π-clouds of triple bonds can establish favorable and virtually equidistant interactions with the four aromatic walls of the cyclotetrabenzoin skeleton. Binding is selective for aliphatic nitriles and terminal alkynes, with their aromatic counterparts residing outside of the cyclotetrabenzoin cavity. These findings are of relevance in the binding, separations, and activation of these and other linear molecular guests. | Corie M. McHale; Lucas J. Karas; Xiqu Wang; Judy, I. Wu; Ognjen Miljanic | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d1567dfe32f1ec5fbf/original/cyclobenzoin-esters-as-hosts-for-thin-guests.pdf |
625ef58b6c989c8e6fbe1ec3 | 10.26434/chemrxiv-2022-lgslx | The crux of time: A meta-analysis of ex vivo whole blood degradation | Estimating the time since deposition (TSD) of a bloodstain can provide important medico-legal information for crime scene investigation. Research in this area primarily investigates the degradation of either hemoglobin or genetic material over time. In this work, we present a comprehensive meta-analysis on bloodstain TSD research. Our results are interpreted from 25 quantitative studies used to probe the effect of biomolecule studied, analytical technique used, substrate porosity, environmental conditions, and blood source on TSD estimates. There was an overall strong effect of time across studies (Fisher’s Zr = 1.66, r = 0.93), and generally, we found that the type of biomolecule studied (e.g., hemoglobin, DNA) had equal effect sizes for TSD estimation. Differences in the mean TSD effect size were also observed between substrate porosity. Interestingly, the blood source does not significantly influence the magnitude of the effect sizes in TSD estimation. Despite the clear effect of time, forensically relevant prediction of bloodstain TSD remains complicated by inter-donor variability, type of substrate and environmental conditions. We recommend that future bloodstain TSD research increase sample size, include summary statistics and standardize experimental methodologies so that we can develop a quantitative understanding of the physicochemical processes involved in whole blood degradation in ex vivo conditions. | Colin Elliott; Aaron Shafer; Theresa Stotesbury | Analytical Chemistry; Analytical Chemistry - General | CC BY 4.0 | CHEMRXIV | 2022-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625ef58b6c989c8e6fbe1ec3/original/the-crux-of-time-a-meta-analysis-of-ex-vivo-whole-blood-degradation.pdf |
651e6ea28bab5d2055ae84e9 | 10.26434/chemrxiv-2023-3mq11 | Designing Sustainable Polymers: Lactate Esters for 3D Printing and Upcycling | The search for sustainable polymer systems is key to tackling the current climate crisis. However, the use of bio-based polymers does not suffice to achieve this goal. Additionally, new chemical approaches enabling the re- or upcycling of polymer materials need to be explored. Herein, we exploit lactate esters with different substituents as readily available bio-based molecules for the synthesis of printable monomers. The synthesis of these lactate ester-based monomers follows green chemistry principles by establishing a solvent-free, one-pot approach, relying on a reusable catalyst, and achieving high conversions (84 – 100%) at mild conditions. Further, these monomers are utilized in 3D printable ink formulations for digital light processing (DLP) for the first time in combination with a recycled crosslinker. The resulting 3D printed structures display complex geometries with high resolution. A key attribute of the presented system is that the 3D printed polymer material can be upcycled via aminolysis affording a pre-cursor of the crosslinker, which is in turn incorporated into the further ink formulations, introducing a material circularity into the system. These results demonstrate a powerful approach by combining bio-based monomers and chemical upcycling with sustainable 3D printing techniques. | Pia S. Klee; Clara Vazquez-Martel; Lilliana Florido Martins; Eva Blasco | Polymer Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e6ea28bab5d2055ae84e9/original/designing-sustainable-polymers-lactate-esters-for-3d-printing-and-upcycling.pdf |
66e08532cec5d6c142b27ff8 | 10.26434/chemrxiv-2024-3l5n4 | Turning Trash to Treasure: The Influence of Carbon Waste Source on the Photothermal Behaviour of Plasmonic Titanium Carbide Interfaces | Pyrolysis of carbonaceous waste materials has emerged as an effective recycling method to generate value-added products. In addition to producing pyrolytic oil and gas, the thermal degradation process yields solid pyrolytic char, which can be further processed. In this study, local waste materials, birch wood residue, Japanese knotweed stems, spent coffee grounds, tire rubber, and lobster shells were assessed for their potential to form pyrolytic char. After a simple acid treatment, many of these chars were successfully incorporated into solid-state synthesis of plasmonic titanium carbide (TiC) nanoparticles (NPs). Each char exhibited unique physical and chemical properties, which were leveraged to synthesize TiC NPs with distinct characteristics. To evaluate the plasmonic behavior of these TiC samples, solar-driven desalination experiments were performed. Notably, TiC derived from tire rubber demonstrated a high broadband absorbance and achieved a solar-to-vapor generation efficiency of 95%, corresponding to an evaporation rate of 1.40 ± 0.01 kg m⁻² h⁻¹ under one-sun illumination. This performance is the highest among all chars tested and ranks among the top reported values in the literature. Additionally, the evaporation interface maintained its performance over multiple cycles and under highly hypersaline conditions. | Matthew Margeson; Mark Atwood; Mita Dasog | Materials Science; Nanoscience; Carbon-based Materials; Materials Processing; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e08532cec5d6c142b27ff8/original/turning-trash-to-treasure-the-influence-of-carbon-waste-source-on-the-photothermal-behaviour-of-plasmonic-titanium-carbide-interfaces.pdf |
60c757db702a9b1e2118cba0 | 10.26434/chemrxiv.14472681.v1 | A Zirconium Metal-Organic Framework with SOC Topological Net for Catalytic Peptide Bond Hydrolysis | <div>The discovery of nanozymes for selective cleavage of proteins would boost the emerging areas of modern proteomics, however, the development of efficient and reusable artificial catalysts for peptide bond hydrolysis is challenging. Here we report the detailed catalytic properties of a microporous zirconium carboxylate metal-organic framework, MIP-201, in promoting peptide bond hydrolysis in a simple dipeptide, as well as in horse-heart myoglobin (Mb) protein that consists of 153 amino acids. We demonstrate that MIP-201 features an excellent catalytic activity and selectivity, a good tolerance toward reaction conditions covering a wide range of different pH values, and importantly, an exceptional recycling ability associated with easy regeneration process. Taking into account the excellent catalytic performance of MIP-201 and its other advantages such as 6-connected Zr6 cluster active sites, the green, scalable and cost-effective synthesis, and an outstanding chemical and architectural stability, our finding suggests that MIP-201 may be a promising and practical alternative to the current commercially available catalysts for peptide bond hydrolysis.</div> | Sujing Wang; Antoine Tissot; Guillaume Maurin; Tatjana Parac-Vogt; Christian Serre; Hong Giang
T. Ly; Mohammad Wahiduzzaman; Iurii Dovgaliuk | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757db702a9b1e2118cba0/original/a-zirconium-metal-organic-framework-with-soc-topological-net-for-catalytic-peptide-bond-hydrolysis.pdf |
6682d5c25101a2ffa80721b6 | 10.26434/chemrxiv-2024-2qfxx | Exploring the Theoretical Landscape of the Hexalacunary Wells-Dawson Anion: A Comprehensive Study | The hexalacunary polyoxometalate (POM) [P2W12O48]14− can be used as a building block for larger POMs, such as [P8W48O184]40−, but we still know relatively little about their chemistry and only a handful of different species have been discovered. With this in mind, we modelled and ran DFT-level calculations on the known hexalacunary POM species, namely [As2W12O48]14−, [P2W12O48]14−, and [Se2W12O46]14−, with the aim of understanding key properties and improving our capacity to apply inverse design to these POMs. By creating several subfamilies of our POMs, each with different combinations of countercations and/ or protons, we discerned that there was no ‘best model’ for hexalacunaries, with some subfamilies replicating certain empirical data better than others. The dimensions of structures with countercations, such as K3[P2W12O48]11−, were the most akin to their empirical counterparts, whilst the presence of protons in the model provided a relatively accurate picture of charge-neutral electron distribution whilst keeping computational costs to a minimum. There is no benefit to including both countercations and protons in the model, and a structure with a reduced anionic charge is no more accurate a model than one with only a handful of charge balancing cations. | Daniel Malcolm ; Laia Vilà-Nadal | Theoretical and Computational Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6682d5c25101a2ffa80721b6/original/exploring-the-theoretical-landscape-of-the-hexalacunary-wells-dawson-anion-a-comprehensive-study.pdf |
66b530ffc9c6a5c07a886fe5 | 10.26434/chemrxiv-2024-pmjn8 | Path Toward High-Throughput Synthesis Planning via Performance Benchmarking | Rapid generation and evaluation of diverse synthesis pathways play a critical role in exploring a
broader chemical space and identifying potent drug candidates. Drug discovery often relies on laborintensive
manual processes for retro synthetic route finding, resulting in challenges related to scalability
and reproducibility. Autonomous chemical synthesis platforms, like ASPIRE aim to address this bottleneck
by the development of high-throughput synthesis capabilities. While AI/ML-based predictive methods
exist that can generate synthesis routes rapidly, evidence based synthesis route search, often relying
on knowledge graphs, poses its own challenges for scalability. In this study, we present a comprehensive
benchmarking framework and analysis employed on the ASPIRE Integrated Computational Platform
(AICP), that led to a breakthrough in the light of high-throughput synthesis planning. Our strategy encompasses
query optimization and domain-driven data engineering techniques, which worked in accord
to reduce the synthesis route finding time by orders of magnitude. As a result, AICP is equipped with
a high-throughput, evidence-based computer assisted synthesis planning method that has the ability to
automatically identify viable synthesis routes to 2000 target molecules within approximately 40 minutes.
Complementing existing retrosynthetic approaches, with the use of knowledge graph of 1.2M chemical
reactions, AICP represents a significant advancement towards automating high-throughput synthesis in
drug discovery, thus paving the way for more efficient drug candidate identification and development. | Brandon Walker; Nathan Miller; Brett Yang; Dhatri V. L. Penna; Sridhar Vuyyuru; Jeyaraman Soundararajan; Ilia Vorontcov; Andrew Girvin; Amin Mannaa; Maya Choudhury; Hailey Fox; Mihir Bafna; Eduardo Luiggi Lopez; Hugo Hernandez; Jennifer King; Thierry Masquelin; Samuel G. Michael; Alexander G. Godfrey; Gergely Zahoránszky-Kőhalmi | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Theory - Computational; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b530ffc9c6a5c07a886fe5/original/path-toward-high-throughput-synthesis-planning-via-performance-benchmarking.pdf |
60c73e16bb8c1a834e3d986b | 10.26434/chemrxiv.6432155.v1 | Rapid, Non-Toxic Synthesis of Beta Zeolites | Molecular sieves with beta zeolite topology are promising catalysts for various reactions as they exhibits extraordinary Lewis acidity. However, their industrial application and related research in academica is hindered because their synthesis is time consuming and typically involves toxic chemicals as hydrofluoric acid. Therefore, tetraethylammonium fluorid was tested as a non-toxic fluotide source for the synthesis of beta zeolites. In combination with the previously reported nano-seeded growth method, a fast synthesis of beta zeolites only involving non-toxic chemicals was possible. Synthesized zeolites show comparable selectivity in the Bayer-Villinger oxidation as conventional zeolites synthesized with hydrofluoric acid.<br /> | Felix Hemmann; Jonathan Hackebeil; Andreas Lißner; Florian Mertens | Nanocatalysis - Catalysts & Materials; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e16bb8c1a834e3d986b/original/rapid-non-toxic-synthesis-of-beta-zeolites.pdf |
66431c8b418a5379b036430e | 10.26434/chemrxiv-2024-vrqzf-v2 | Refining EI-MS library search results through atomic-level insights | The inherent complexity of mass spectra and the lack of direct correlation between spectral and structural similarities retards structure elucidation and accurate peak annotation. For more accurate mass-to-fragment mapping, we propose a new approach combining CFM-EI, a fragmentation likelihood modeling tool in electron-ionization mass spectrometry (EI-MS) data, with an artificial-intelligence (AI) assisted multi-step complexity reduction strategy. Our methodology used modified atomic environments to represent fragments of super small organic molecules, and trained the Transformer model to predict the structural content of compounds based on their mass and intensity data with a peak precision of 86.1% and a recall rate of 78.4%. This holistic solution not only aids in interpreting EI-MS data by providing insights into atom types but also refines cosine similarity rankings by suggesting the inclusion or exclusion of certain atom types. Benchmark results using the NIST database demonstrated that our approach complements conventional methods by improving spectra matching through an in-depth atomic-level analysis. | Umit Volkan Ucak; Islambek Ashyrmamatov; Juyong Lee | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66431c8b418a5379b036430e/original/refining-ei-ms-library-search-results-through-atomic-level-insights.pdf |
66cf399cf3f4b0529062a80a | 10.26434/chemrxiv-2024-xdx2c | Near-Infrared Room-Temperature Phosphorescence from Mono-cyclic Luminophores | Compact luminophores with long emission wavelengths have aroused considerable theoretical and practical interest. Organ-ics with room-temperature phosphorescence (RTP) are also desirable for their longer lifetimes and larger Stokes shifts com-pared to fluorescence. Utilizing the low electronic transition energy intrinsic to thiocarbonyl compounds, electron-withdrawing groups were attached to the 4H-pyran-4-thione core to further lower the excited states energies. The resulting mini-phosphors were doped into appropriate polymer matrices. Both pure organic, amorphous materials emitted near-infrared (NIR) RTP. Having a molar mass of only 162 g·mol-1, one of the phosphors emitted RTP that peaked at 750 nm, with a very large Stokes shift of 15485 cm-1 (403 nm). Thanks to the good processability of the polymer film, light-emitting didoes (LEDs) with NIR emission was easily fabricated by coating doped polymer on ultraviolet LEDs. This work provides an interesting strategy to achieve NIR RTP using compact luminophores. | Zi-Ang Yan; Chenjia Yin; He Tian; Xiang Ma | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf399cf3f4b0529062a80a/original/near-infrared-room-temperature-phosphorescence-from-mono-cyclic-luminophores.pdf |
66013a16e9ebbb4db979bd5b | 10.26434/chemrxiv-2024-mk3qh | Reversible control of gene expression by guest-modified adenosines in a cell-free system via host–guest interaction | Gene expression technology has become an indispensable tool for elucidating biological processes and developing bio-technology. Cell-free gene expression (CFE) systems offer a fundamental platform for gene expression-based technology, in which the reversible and programmable control of transcription can expand its use in synthetic biology and medicine. This study shows that CFE can be controlled via the host–guest interaction of cucurbit[7]uril (CB[7]) with N6-guest-modified adenosines. These adenosine derivatives were conveniently incorporated into the DNA strand by a post-synthetic approach and formed a selective and stable base pair with complementary thymidine in DNA. Meanwhile, alternate addition of CB[7] and the exchanging guest molecule induced the reversible formation of a duplex structure through the formation and dissociation of a bulky complex on DNA. The kinetics of the reversibility were fine-tuned by changing the size of the modified guest moieties. When incorporated into a specific region of the T7 promoter sequence, the guest-modified adenosines enabled the tight and reversible control of in vitro transcription and protein expression in the CFE system. The present study marks the first utility of the host-guest interaction for the gene expression control in the CFE system, opening new avenues for developing DNA-based technology, particularly for precise gene therapy and DNA nano-technology. | Hidenori Okamura; Takeyuki Yao; Fumi Nagatsugi | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66013a16e9ebbb4db979bd5b/original/reversible-control-of-gene-expression-by-guest-modified-adenosines-in-a-cell-free-system-via-host-guest-interaction.pdf |
60c7409f842e65a451db1cea | 10.26434/chemrxiv.7770338.v1 | Tenacious Mass Transfer Limitations Drive Catalytic Selectivity during Electrochemical Carbon Dioxide Reduction | <p>This study evaluated the performance of the
commonly used strong buffer electrolytes, i.e. phosphate buffers, during CO<sub>2</sub> electroreduction in neutral pH conditions by using in-situ surface enhanced
infrared absorption spectroscopy (SEIRAS). Unfortunately, the buffers break
down a lot faster than anticipated which has serious implications on many
studies in the literature such as selectivity and kinetic analysis of the
electrocatalysts. Increasing electrolyte concentration, surprisingly, did not
extend the potential window of the phosphate buffers due to dramatic increase
in hydrogen evolution reaction. Even high concentration phosphate buffers (1
M) break down within the potentials (-1 V vs RHE) where hydrocarbons are formed
on copper electrodes. We have extended the discussion to high surface area
electrodes by evaluating electrodes composed of copper nanowires. We would like
highlight that it is not possible to cope with high local current densities on
these high surface area electrodes by using high buffer capacity solutions and
the CO<sub>2</sub> electrocatalysts are needed to be evaluated by casting thin
nanoparticle films onto inert substrates as commonly employed in fuel cell
reactions and up to now scarcely employed in CO<sub>2</sub> electroreduction.
In addition, we underscore that normalization of the electrocatalytic
activity to the electrochemical active
surface area is not the ultimate solution due to concentration gradient along
the catalyst layer.This will “underestimate” the activity of
high surface electrocatalyst and the degree of underestimation will depend on
the thickness, porosity and morphology of the catalyst layer. </p>
<p> </p> | Kailun Yang; Recep Kas; Wilson A. Smith | Transport Phenomena (Chem. Eng.); Electrocatalysis; Energy Storage; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7409f842e65a451db1cea/original/tenacious-mass-transfer-limitations-drive-catalytic-selectivity-during-electrochemical-carbon-dioxide-reduction.pdf |
60c73f9c337d6c3a9de2653f | 10.26434/chemrxiv.7415603.v1 | Surface-Induced Dissociation of Noncovalent Protein Complexes in an Extended Mass Range Orbitrap Mass Spectrometer | Herein we demonstrate the first adaptation of surface-induced dissociation in a modified high-mass range, high-resolution Orbitrap mass spectrometer. The SID device was designed to be installed in the Q-Exactive series of Orbitrap mass spectrometers with minimal disruption of standard functions. The performance of the SID-Orbitrap instrument has been demonstrated with several protein complex and ligand-bound protein complex systems ranging from 53 to 336 kDa. We also address the effect of ion source temperature on native protein-ligand complex ions as assessed by SID. Results are consistent with previous findings on quadrupole time-of-flight instruments and suggest that SID coupled to high-resolution MS is well-suited to provide information on the interface interactions within protein complexes and ligand-bound protein complexes. <br /> | Zachary VanAernum; Joshua D. Gilbert; Mikhail E. Belov; Alexander
A. Makarov; Stevan R. Horning; Vicki H. Wysocki | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9c337d6c3a9de2653f/original/surface-induced-dissociation-of-noncovalent-protein-complexes-in-an-extended-mass-range-orbitrap-mass-spectrometer.pdf |
60c754a8842e6590bedb41bd | 10.26434/chemrxiv.13708201.v1 | Diastereoselective Synthesis of b-Branched a-Amino Acids via Bio-catalytic Dynamic Kinetic Resolution | We report a biocatalytic transamination method to prepare a broad range of b-branched a-amino acids that proceeds with high diastereo- and enantioselectivity. Mechanistic studies show that the transformation proceeds through a dynamic kinetic resolution process that is unique to the optimal enzyme. To highlight its utility and practicality, the biocatalytic reaction is applied to the synthesis of several cyclic fragments and in the first total synthesis of jomthonic acid A. | Fuzhuo Li; Li-Cheng Yang; Jingyang Zhang; Jason Chen; Hans Renata | Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754a8842e6590bedb41bd/original/diastereoselective-synthesis-of-b-branched-a-amino-acids-via-bio-catalytic-dynamic-kinetic-resolution.pdf |
651ff50d8bab5d2055c39dcc | 10.26434/chemrxiv-2023-8bmd5-v2 | Deflection-Penetration Criterion in defect ridden slanted interfaces: A continuum scale study in 2D Fracture Mechanics and 3D printable models | This paper presents a deeper understanding of the effect of interface orientation and varying defect density within the interface on toughness in 2D media. Our study focuses on a pre-deflected crack that has a majority of its length parallel to the line of symmetry in the horizontal direction, with a small deflected region present in the interface, perpendicular to the line of symmetry. We vary the interface orientation at varying angles with 0 2.5, 5, 7.5, 10, 12.5, 15, 20, 25, 30, 37.5, 45, and 50. For all of the theta , we initially create 10 increments of interface properties, and within each of these combinations, we vary the defect densities ranging from 5 defects to 15 defects. Previous results have shown that higher defect densities in the interface region lead to an overall higher material toughness, while in turn making the interface weaker, allowing for cracks to propagate and deflect with the help of the defects. In this paper, we hope to understand 4 main ideas, (i) How do higher interface angle orientations vs lower angle orientations affect the deflection-penetration criterion? (ii) What is the effect of higher variations vs lower variations of defect densities on the deflection-penetration when faced with differing angles? (iii) How do the Elastic Energy and Stress fields react to changes within the angle of the interface? (iv) Can we recreate the computational results with 3D printable models through tensile testing? Overall, it is quiet clear that in terms of material toughness and stress concentration at the crack tip, the higher angle cases are a clear benefit to the toughness of the material; however, when considering the elastic energy and time needed for failure, the lower angled cases showcase a more preferable case. | Suraj Reddy | Materials Science; Nanoscience; Composites; Granular Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651ff50d8bab5d2055c39dcc/original/deflection-penetration-criterion-in-defect-ridden-slanted-interfaces-a-continuum-scale-study-in-2d-fracture-mechanics-and-3d-printable-models.pdf |
6201ec7aa6fb4d090b4e6a30 | 10.26434/chemrxiv-2022-qttvk | Time-Resolved Dynamics of Stable Open- and Closed-Shell Neutral Radical and Oxidized Tripyrrindione Complexes | Stable open- and closed-shell Pd(II) and Cu(II) complexes of hexaethyl tripyrrin-1,14-dione (TD1) produce triplet, doublet or singlet states depending on the metal center and the redox state of the ligand. Pd(II) and Cu(II) form neutral TD1 complexes featuring ligand-based radicals, thus resulting in doublet and triplet states, respectively. The reversible one-electron oxidation of the complexes removes an unpaired electron from the ligand, generating singlet and doublet states. The optical properties and time-resolved dynamics of these systems are studied here using steady-state and ultrafast transient absorption (pump-probe) measurements. Fast relaxation with recovery of the ground state in 10s of picoseconds is observed for the copper neutral radical and oxidized complexes as well as for the palladium neutral radical complex. Significantly longer timescales are observed for the oxidized palladium complex. The ability to tune the overall spin state of the complexes through their stable open shell configurations as well as the reversible redox activity of the tripyrrolic systems makes them particularly interesting for catalytic applications as well as exploring magnetism and conductivity properties. | Byungmoon Cho; Alicia Swain; Ritika Gautam; Elisa Tomat; Vanessa Huxter | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6201ec7aa6fb4d090b4e6a30/original/time-resolved-dynamics-of-stable-open-and-closed-shell-neutral-radical-and-oxidized-tripyrrindione-complexes.pdf |
63fc3232937392db3d1b9d18 | 10.26434/chemrxiv-2023-w54wn | SMiPoly: Generation of Synthesizable Polymer Virtual Library using Rule-based Polymerization Reactions | Recent advances in machine learning have led to the rapid adoption of various computational methods for de novo molecular design in polymer research, including high-throughput virtual screening and inverse molecular design. In such workflows, molecular generators play an essential role in the creation or sequential modification of candidate polymer structures. Machine learning-assisted molecular design has made great technical progress over the past few years. However, its practical deployment has not progressed as much as expected. One reason for this is the difficulty in determining the synthetic routes to such designed polymers. To address this technical limitation, we present SMiPoly, a Python library for virtual polymer generation that implements 22 chemical rules for commonly applied polymerization reactions. For given small organic molecules to form a candidate monomer set, the SMiPoly generator conducts possible polymerization reactions to generate an exhaustive list of potentially synthesizable polymers. In this study, using 1,083 readily available monomers, we generated 169,347 unique polymers forming seven different molecular types: polyolefin, polyester, polyether, polyamide, polyimide, polyurethane, and polyoxazolidone. By comparing the distribution of the virtually created polymers with approximately 16,000 real polymers synthesized so far, it was found that the coverage and novelty of the SMiPoly-generated polymers can reach 48% and 53%, respectively. | Mitsuru Ohno; Yoshihiro Hayashi; Qi Zhang; Yu Kaneko; Ryo Yoshida | Theoretical and Computational Chemistry; Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fc3232937392db3d1b9d18/original/s-mi-poly-generation-of-synthesizable-polymer-virtual-library-using-rule-based-polymerization-reactions.pdf |
661ebdaa418a5379b0fb52de | 10.26434/chemrxiv-2024-3rb2t | Artificial manganese metalloenzymes with laccase-like activity: Design, Synthesis and Characterization | Laccase is an oxidase of great industrial interest due to its ability to catalyse oxidation processes of phenols and persistent organic pollutants. However, it is susceptible to denaturation at high temperatures, sensitive to pH and in the presence of high concentrations of solvents, which is a problem for industrial use. To solve this problem, this work develops the synthesis in aqueous medium of a new Mn metalloenzyme with laccase oxidase mimetic catalytic activity. To do this, Geobacillus thermocatenulatus lipase (GTL) is used as a "scaffold" enzyme, which is mixed with a manganese salt at 50ºC in an aqueous medium. This produces in situ formation of manganese (IV) oxide nanowires that interact with the enzyme, obtaining the GTL-Mn bionanohybrid. On the other hand, its oxidative activity was evaluated using the ABTS assay, obtaining a catalytic efficiency 300 times greater than the laccase from Trametes versicolor. These new Mn-metalloenzyme turned out to be 2 times more stable at 40 ºC, 3 times more stable in the presence of 10% acetonitrile and 10 times more stable at 20% acetonitrile than laccase Novozym 51003®. Furthermore, the site-selective immobilized GTL-Mn showed much higher stability then the soluble form. Oxidase-like activity of these Mn-metalloenzyme was successfully performed against other substrates such as L-DOPA or phloridzin in oligomerization reactions. | Carla Garcia-Sanz; Alicia Andreu; Mirosława Pawlyta; Ana Vukoicic; Ana Milivojevic; Blanca de las Rivas; Dejan Bezbradica; Jose Miguel Palomo | Biological and Medicinal Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Chemical Biology; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661ebdaa418a5379b0fb52de/original/artificial-manganese-metalloenzymes-with-laccase-like-activity-design-synthesis-and-characterization.pdf |
675b759a7be152b1d0c96ada | 10.26434/chemrxiv-2024-810kh | In-vitro Delivery of Hydrophilic Drugs from Alginate–Montmorillonite Nanocomposite Hydrogels Cross-linked with Multivalent Cations | Alginate hydrogels cross-linked with various cations have numerous applications in targeted drug delivery. To enhance drug encapsulation efficiency, montmorillonite (MMT) clay nanoplatelets are incorporated into the alginate network. This study focuses on the effects of cations (Fe3+, Cu2+, Sr2+, and Ca2+) and concentration of MMT on the kinetics of the in-vitro release of diclofenac sodium from alginate–MMT nanocomposite hydrogels. Drug release is assessed in pH 7 solutions at 37 °C using a UV/Vis spectrophotometer. MMT affects the total drug release differently based on the formation constants of the cations. Drug release data are fitted to a model to identify the release mechanism. The release kinetics for alginate–MMT gels cross-linked with Fe3+ ions differ from those for gels bridged by Cu2+, Sr2+, and Ca2+ ions. Scanning Electron Microscopy analyzes the structural morphology of CO2-supercritical dried gels. Mesh size and diffusion coefficient are calculated from swelling tests. It is found that gel morphology, mesh size, egg-box junction reorganization, and drug release kinetics are strongly affected by the formation constant of cations. This study establishes a correlation between the formation constant and diffusivity, providing a predictive framework for diffusivity across different cations. | Haniyeh Malektaj; Aleksey D. Drozdov; Pavel Gurikov; Baldur Schroeter; Elham Fini; Jesper deClaville Christiansen | Polymer Science; Biopolymers; Drug delivery systems; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675b759a7be152b1d0c96ada/original/in-vitro-delivery-of-hydrophilic-drugs-from-alginate-montmorillonite-nanocomposite-hydrogels-cross-linked-with-multivalent-cations.pdf |
60c73e9af96a0034c3285f6c | 10.26434/chemrxiv.7057874.v1 | Phase-Transferable Force Field for Alkali Halides | A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to handle or compounds that have not yet been created. Progress towards this goal has been limited as most work has concentrated on just one phase, often determined by particular applications. In the framework of the development of the Alexandria force field we present here new polarizable force fields for alkali halides with Gaussian charge distributions for molecular dynamics simulations. We explore different descriptions of the Van der Waals interaction, like the commonly applied 12-6 Lennard-Jones (LJ), and compare it to \softer" ones, such as 8-6 LJ, Buckingham and a modified Buckingham potential. Our results for physico-chemical properties of the gas, liquid and solid phase of alkali halides, are compared to experimental data and calculations with reference polarizable and non-polarizable force fields. The new polarizable force field that employs a modified Buckingham potential predicts the tested properties for gas, liquid and solid phases with a very good accuracy. In contrast to reference force fields, this model reproduces the correct crystal structures for all alkali halides at low and high temperature. Seeing that experiments with molten salts may be tedious due to high temperatures and their corrosive nature, the models presented here can contribute significantly to our understanding of alkali halides in general and melts in particular.<br /> | Marie-Madeleine Walz; Mohammad Ghahremanpour; Paul J. van Maaren; David van der Spoel | Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e9af96a0034c3285f6c/original/phase-transferable-force-field-for-alkali-halides.pdf |
60c74f590f50db94793973b5 | 10.26434/chemrxiv.12894800.v1 | Using Domain-specific Fingerprints Generated Through Neural Networks to Enhance Ligand-based Virtual Screening. | Molecular fingerprints are essential for different cheminformatics approaches like similarity-based virtual screening. In this work, the concept of neural (network) fingerprints in the context of similarity search is introduced in which the activation of the last hidden layer of a trained neural network represents the molecular fingerprint. The neural fingerprint performance of five different neural network architectures was analyzed and compared to the well-established Extended Connectivity Fingerprint (ECFP) and an autoencoder-based fingerprint. This is done using a published compound dataset with known bioactivity on 160 different kinase targets. We expect neural networks to combine information about the molecular space of<br />already known bioactive compounds together with the information on the molecular structure of the query and by doing so enrich the fingerprint. The results show that indeed neural fingerprints can greatly improve the performance of similarity searches. Most importantly, it could be shown that the neural fingerprint performs well even for kinase targets that were not included in the training. Surprisingly, while Graph Neural Networks (GNNs) are thought to offer an advantageous alternative, the best performing neural fingerprints were based on traditional fully connected layers using the ECFP4 as input. The best performing kinase-specific neural fingerprint will be provided for public use. | Janosch Menke; Oliver Koch | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f590f50db94793973b5/original/using-domain-specific-fingerprints-generated-through-neural-networks-to-enhance-ligand-based-virtual-screening.pdf |
60c73e13842e65297adb184d | 10.26434/chemrxiv.6300959.v1 | Non-Equilibrium Crystallization Pathways of Manganese Oxides in Aqueous Solution | <p>Aqueous precipitation of transition
metal oxides often proceeds through non-equilibrium phases, whose appearance
cannot be anticipated from traditional phase diagrams. Without a precise
understanding of which metastable phases form, or their lifetimes, targeted
synthesis of specific metal oxides can become a trial-and-error process. Here, we derive a new thermodynamic potential for the
free-energy of a metal oxide in water, which reveals a hidden metastable energy
landscape above the equilibrium Pourbaix diagram. By combining this ‘Pourbaix
potential’ with classical nucleation theory, we interrogate how solution
conditions can influence the multistage oxidation pathways of manganese oxides.
We calculate that even within the same phase stability region of a Pourbaix
diagram, subtle variations in <i>p</i>H and
redox potential can redirect a crystallization pathway through different
metastable phases. Our theoretical framework offers a predictive platform to navigate
through the thermodynamic and kinetic energy landscape towards the rational
synthesis of target metal oxide phases.</p> | Wenhao Sun; Daniil A. Kitchaev; Denis Kramer; Gerbrand Ceder | Materials Processing; Theory - Inorganic; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e13842e65297adb184d/original/non-equilibrium-crystallization-pathways-of-manganese-oxides-in-aqueous-solution.pdf |
62336c0c74104f5c8ba82841 | 10.26434/chemrxiv-2022-50c3j-v2 | Mechanochemical approach towards multi-functionalized 1,2,3-triazoles and anti-seizure drug Rufinamide analogs using copper beads | Highly regiospecific, copper salts-free and neat conditions have been demonstrated for the 1,3-dipolar Azide-Alkyne Cycloaddition (AAC) reactions under mechanochemical conditions. A group of structurally challenging alkynes and heterocyclic derivatives was efficiently implemented to achieve highly functionalized 1,4-disubstituted-1,2,3-triazoles in good to excellent yield by using the Cu beads without generation of unwanted byproducts. Furthermore, high-speed ball milling (HSBM) strategy has also been extended to the synthesis of commercially available pharmaceutical agent, Rufinamide, an antiepileptic drug (AED) and its analogues. The same strategy was also applied for the synthesis of Cl-derivative of Rufinamide. Analysis of the single crystal XRD data of the triazole was also performed for the final structural confirmation. The Cu beads can be easily recoverable from the reaction mixture and used for the further reactions without any special treatment. | Dhananjay Bhattacherjee; Igor S. Kovalev; Dmitry S. Kopchuk; Matiur Rahman; Sougata Santra; Grigory V. Zyryanov; Pralay Das; Rituraj Purohit; Vladimir L. Rusinov; Oleg N. Chupakhin | Organic Chemistry; Bioorganic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62336c0c74104f5c8ba82841/original/mechanochemical-approach-towards-multi-functionalized-1-2-3-triazoles-and-anti-seizure-drug-rufinamide-analogs-using-copper-beads.pdf |
60c7578ebb8c1af5b73dc876 | 10.26434/chemrxiv.14417552.v1 | Run-and-Halt Behavior of Motile Droplets in Response to Light | <p>We
report the run-and-halt behavior of motile droplets immersed in an aqueous
solution of amphiphilic molecular switch. These oil droplets move autonomously as
the switch solubilizes the oil into the water. Droplet movement stops in
response to UV light, and picks up again in response to visible light. This
motile behavior is a consequence of the reversible <i>trans-</i>to-<i>cis</i> photo-conversion
of the switch in water, because the <i>trans</i>
photo-isomer stabilizes the oil droplets better than the <i>cis</i> photo-isomer, and therefore it also solubilizes the droplet
more effectively. Notably, the droplets also evolve positive photokinesis under
illumination with visible light, and, in patchy light environments, their complex
motility pattern directs the droplets at the periphery of the illuminated areas.
</p> | Alexander Ryabchun; Dhanya Babu; Jacopo Movilli; Rémi Plamont; Nathalie Katsonis | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7578ebb8c1af5b73dc876/original/run-and-halt-behavior-of-motile-droplets-in-response-to-light.pdf |
60c74cdbf96a00b698287857 | 10.26434/chemrxiv.12058959.v4 | Conformations and Three-Dimensional Structures of Selected SARS-CoV-2 Drug Candidates | <div>Quantum mechanical theories are used to search and optimize the conformations of proposed small molecule candidates for treatment of SARS-CoV-2. These candidate compounds are taken from what is reported in the news and in other pre-peer-reviewed literature (e.g. ChemRxiv, bioRxiv). The goal herein is to provide predicted structures and relative conformational stabilities for selected drugs and ligands, in the hopes that other research groups can make use of them for developing a treatment. The following six compounds are investigated: <b>chloroquine</b>, <b>hydroxychloroquine</b>, <b>eriodictyol</b>, <b>silmitasertib</b> and <b>valproic acid</b>.<br /></div><div><br />Initial exploration for conformations are performed at the HF/6-31G(d)//HF/6-31G(d) theory level, which are then further optimized at more rigorous theory levels (e.g. B97-D3BJ/cc-pVTZ//B97-D3BJ/cc-pVTZ). The resulting structures are made available via GitHub.</div> | Karl Kirschner; Javed Razzaq; Rudolf Berrendorf; Wolfgang Heiden | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cdbf96a00b698287857/original/conformations-and-three-dimensional-structures-of-selected-sars-co-v-2-drug-candidates.pdf |
62ab57296124c23d6d1c5424 | 10.26434/chemrxiv-2022-s2dcb | Polar organic chemical integrative sampler (POCIS) allows compound specific isotope analysis of substituted chlorobenzenes at trace levels | Compound specific isotope analysis (CSIA) is an established tool to demonstrate in situ degradation of traditional groundwater contaminants at heavily contaminated sites, usually at mg/L range aqueous concentrations. Currently, an efficient preconcentration method is lacking to expand CSIA to low aqueous concentration environmental samples. This work demonstrated the compatibility of polar organic chemical integrative sampler (POCIS) with CSIA of C, H, and N isotopes for four NH2- and NO¬2-substituted chlorobenzenes at low μg/L. Diffusion and sorption showed insignificant carbon isotope fractionation (<0.7‰) in laboratory experiment, except for a reproducible shift of 1.6‰ for 3,4-dichloronitrobenzene. A similar constant reproducible shift of 0.8-2‰ was evident for N-CSIA. Whereas, the compatibility of POCIS for H-CSIA seems to be analyte specific possibly reflecting the adsorption mechanism to POCIS by H-bonding. Performance of the POCIS-CSIA method was evaluated in a pilot constructed wetland where comparable C- and N-CSIA results were obtained from grab sampling and POCIS. This work opens the potential of CSIA application to the low concentration polar emerging contaminants in the environment, such as pesticides, pharmaceuticals, and flame-retardants. | Shamsunnahar Suchana; Sávia Gavazza; Natanna Melo; Elizabeth Edwards; Line Lomheim; E. Erin Mack; Elodie Passeport | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ab57296124c23d6d1c5424/original/polar-organic-chemical-integrative-sampler-pocis-allows-compound-specific-isotope-analysis-of-substituted-chlorobenzenes-at-trace-levels.pdf |
60c7422f469df46a76f42f6b | 10.26434/chemrxiv.8242604.v1 | The Effect of Structural Dimensionality on Carrier Mobility in Lead-Halide Perovskites | <p>Methylammonium
lead iodide (MAPI) is a prototypical photo absorber in perovskite solar cells
(PSCs), reaching efficiencies above 20%. However, its hygroscopic nature has prompted
the quest to find water-resistant alternatives. Recent studies have suggested
that mixing MAPI with lower dimensional, bulky-<i>A</i>-site-cation perovskites helps mitigate this environmental
instability. On the other hand, low dimensional perovskites suffer from poor
device performance, which has been suggested to be due to limited out-of-plane
charge carrier mobility resulting from structural dimensionality and large
binding energy of the charge carriers. To understand the effects of
dimensionality on performance, we systematically mixed MA-based 3D perovskites with
larger <i>A</i>-site cation,
dimethylammonium, iso-propylammonium, and t-butylammonium lead iodide
perovskites. During the shift from MAPI to lower dimensional (LD) PSCs, the
efficiency is significantly reduced by 2 orders of magnitude, with
short-circuit currents decreasing from above 20 mA/cm<sup>2</sup> to less than
1 mA/cm<sup>2</sup>. In order to explain these decrease in performance, we
studied the charge carrier mobilities of these materials using optical-pump/
terahertz-probe, time-resolved microwave photoconductivity, and
photoluminescence measurements. The results show that as we add more of the low
dimensional perovskites, the mobility decreases by a factor of 20 when it reaches
pure LD perovskites. In addition, the photoluminescence decay fitting is
slightly slower for the mixed perovskites, suggesting some improvement in the
recombination dynamics. These findings indicate that changes in structural
dimensionality by mixing<i> A</i>-site
cations play an important role in measured charge carrier mobility, and in the performance
of perovskite solar cells.</p> | Noor Titan Putri Hartono; Shijing Sun; María Gélvez-Rueda; Polly Pierone; Matthew Erodici; Jason Yoo; Fengxia Wei; Moungi Bawendi; Ferdinand Grozema; Meng-ju Sher; Tonio Buonassisi; Juan-Pablo Correa-Baena | Hybrid Organic-Inorganic Materials; Thin Films; Photovoltaics; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422f469df46a76f42f6b/original/the-effect-of-structural-dimensionality-on-carrier-mobility-in-lead-halide-perovskites.pdf |
64fba8a499918fe5379c22dc | 10.26434/chemrxiv-2023-hbk8d | Engineering Pt-Pt coordination environment to enhance the four-electron oxygen reduction reaction | The oxygen reduction reaction (ORR) in proton exchange membrane fuel cells plays an important role in the H2 economy. Pt-based alloy catalysts with tuned d-band centres are widely regarded as the most efficient catalysts. Here we report that the average size of Pt domains in a Pt-Pd alloy, described as the Pt-Pt coordination number (C.N.), may measure the coordination environment of Pt and its effect on the d-states, to serve as a key geometric descriptor for the ORR activity. The decrease of Pt-Pt C.N. from 10.8 in commercial Pt nanoparticles to 1.33 in Pt1Pd493 alloy leads to an exponential increase in the Pt mass activity from 0.18 to 4.86 A/mgPt. Density functional theory calculations show that low C.N. sites of Pt within the Pd host have low O-O dissociation barriers, favouring the four-electron dissociative pathway. The precise engineering of Pt-Pt C.N. in an alloy is critical for optimising metal use in the activation of chemically stable compounds, particularly in the context of catalysis for renewable energy. | Sushila Marlow; Matthew T. Darby; Ruoyu Xu; Liqun Kang; Hao Gu; Bolun Wang; Christopher S. Allen; Hiroyuki Asakura; Michail Stamatakis; Feng Ryan Wang | Materials Science; Catalysis; Nanoscience; Alloys; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fba8a499918fe5379c22dc/original/engineering-pt-pt-coordination-environment-to-enhance-the-four-electron-oxygen-reduction-reaction.pdf |
63534daa31107214caea86fd | 10.26434/chemrxiv-2022-dhq8q | Synthesis of Uronic Acid 1-Azasugars as Putative Inhibitors of a-Iduronidase, b-Glucuronidase and Heparanase | 1-Azasugar analogues of L-iduronic acid (L-IdoA) and D-glucuronic acid (D-GlcA) and their corresponding enantiomers were synthesized as potential pharmacological chaperones for mucopolysaccharidosis I (MPS I), a lysosomal storage disease caused by mutations in the gene encoding a-iduronidase (IDUA). The compounds were efficiently synthesized in nine or ten steps from D- or L-arabinose and the structures were confirmed by X-ray crystallographic analysis of key intermediates. All compounds were inactive against IDUA, although L-IdoA-configured 8 moderately inhibited b-glucuronidase (b-GLU). The D-GlcA-configured 9 was a potent inhibitor of b-GLU and a moderate inhibitor of the endo-b-glucuronidase heparanase. Co-crystallization of 9 with heparanase revealed that the endocyclic nitrogen of 9 forms close interactions with both the catalytic acid and catalytic nucleophile. | Gareth Doherty; Geraldine Ler; Norbert Wimmer; Paul Bernhardt; Roger Ashmus; David Vocadlo; Zach Armstrong; Gideon Davies; Marco Maccarana; Jin-ping Li; Yasmin Kayal; Vito Ferro | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63534daa31107214caea86fd/original/synthesis-of-uronic-acid-1-azasugars-as-putative-inhibitors-of-a-iduronidase-b-glucuronidase-and-heparanase.pdf |
60c757af567dfe3e20ec66dd | 10.26434/chemrxiv.14449875.v1 | Machine Learning of Atomic Forces from Quantum Mechanics: a Model Based on Pairwise Interatomic Forces | <p>We present a new chemically intuitive
approach, pairF-Net, to directly predict the atomic forces
in a molecule to quantum chemistry accuracy using machine learning
techniques. A residual artificial neural network has been designed and trained with
features and targets based on pairwise interatomic forces,
to determine the Cartesian atomic forces suitable for use in
molecular mechanics and dynamics calculations. The scheme
implicitly maintains rotational and translational invariance
and predicts Cartesian forces as a linear combination of a set of force
components in an <a>interatomic basis.</a> We
show that the method can predict the reconstructed Cartesian atomic forces for a
set of small organic molecules to less than 2 kcal mol<sup>-1</sup> Å<sup>-1</sup>
from the reference force values obtained via density functional theory. The
pairF-Net scheme utilises a simple and chemically intuitive route to furnish atomic
forces at a quantum mechanical level but at a fraction of the cost, providing a
step towards the efficient calculation of accurate thermodynamic
properties. </p> | Ismaeel Ramzan; Linghan Kong; Richard Bryce; Neil Burton | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757af567dfe3e20ec66dd/original/machine-learning-of-atomic-forces-from-quantum-mechanics-a-model-based-on-pairwise-interatomic-forces.pdf |
660447bce9ebbb4db9b1f5b1 | 10.26434/chemrxiv-2024-4vg2s | Direct catalytic photodecarboxylative amination of carboxylic acids with diazirines: Divergent access to amines, hydrazines, and nitrogen-containing heterocycles | Amines, hydrazines, and nitrogen-containing heterocycles are pivotal species in medicine, agriculture, fine chemicals, and materials. Diazirines have been recently reported to serve as versatile electrophilic amination reagents for the synthesis of building blocks or late-stage C–N bond formation. Here we report the catalytic photodecarboxylative amination of carboxylic acids with diazirines under mild conditions. The substrate scope includes broad functional group tolerance, such as ketones, esters, olefins, and alcohols, along with the late-stage amination of naproxen, ibuprofen, gemfibrozil, and gibberellic acid. Synthetic applications leverage the versatility of the intermediate diaziridines and include the regioselective preparation of a suite of 1H-indazoles, 2H-indazoles, and fluoroquinolones. | Vishala Maharaj; Paresh Athawale; Preeti Chandrachud; Justin Lopchuk | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660447bce9ebbb4db9b1f5b1/original/direct-catalytic-photodecarboxylative-amination-of-carboxylic-acids-with-diazirines-divergent-access-to-amines-hydrazines-and-nitrogen-containing-heterocycles.pdf |
649d81a49ea64cc1672c0c58 | 10.26434/chemrxiv-2023-9w3w7 | Diffusion across particle-laden interfaces in Pickering droplets | Emulsions stabilized by nanoparticles, known as Pickering emulsions, exhibit remarkable stability which enables many applications, from encapsulation, to advanced materials, to chemical conversion. The layer of nanoparticles at the interface of Pickering droplets forms a semi-permeable barrier between the two liquid phases, which can affect the rate of release of encapsulates, and the interfacial transfer of reactants and products in biphasic chemical conversion. The current lack of understanding of diffusion in multi-phase systems with particle-laden interfaces limits the optimal development of these applications. To address this gap, we developed an experimental approach for in-situ, real-time quantification of concentration fields in Pickering droplets in a Hele-Shaw geometry and investigated the effect of the layer of nanoparticles on diffusion of solute across a liquid-liquid interface. The experiments did not reveal a significant hindrance on the diffusion of solute across an interface densely covered by nanoparticles. We interpret this result using an unsteady diffusion model to predict the spatio-temporal effect of particles on diffusion across a particle- laden interface. We find that the concentration field of solute is only affected in the immediate vicinity of the layer of particles, where the area available for diffusion is affected by the particles. This defines a characteristic time scale for the problem, which is the time for diffusion across the layer of particles. The far-field concentration profile evolves towards that of a bare interface. This localized effect of the particle hindrance is not measurable in our experiments, which take place over a much longer time scale. Our model also predicts that the hindrance by particles can be more pronounced depending on the particle size and physicochemical properties of the liquids and can ultimately affect performance in applications. | Yanyan Liu; Mingjun Xu; Luis M. Portela; Valeria Garbin | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Transport Phenomena (Chem. Eng.); Interfaces | CC BY NC 4.0 | CHEMRXIV | 2023-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649d81a49ea64cc1672c0c58/original/diffusion-across-particle-laden-interfaces-in-pickering-droplets.pdf |
622c184c9e8766e954e55877 | 10.26434/chemrxiv-2022-jv5n7 | Biosynthesis of the unusual carbon skeleton of nocuolin A | Nocuolin A is a cytotoxic cyanobacterial metabolite that is proposed to be produced by enzymes of the noc biosynthetic gene cluster. Nocuolin A features a 1,2,3-oxadiazine moiety, a structural feature unique among natural products and, so far, inaccessible through organic synthesis, suggesting that novel enzymatic chemistry might be involved in its biosynthesis. This heterocycle is substituted with two alkyl chains and a 3-hydroxypropanoyl moiety. We report here our efforts to elucidate the origin of the carbon skeleton of nocuolin A. Supplementation of cyanobacterial cultures with stable isotope-labeled fatty acids revealed that the central C13 chain is assembled from two medium-chain fatty acids, hexanoic and octanoic acids. Using biochemical assays, we show that a fatty acyl-AMP ligase, NocH, activates both fatty-acids as acyl adenylates, which are loaded onto acyl carrier protein domains and undergo a non-decarboxylative Claisen condensation catalyzed by the ketosynthase NocG. This enzyme is part of a phylogenetically well-defined clade within similar genomic contexts. NocG presents a unique combination of characteristics found in other ketosynthases, namely in terms of substrate specificity and reactivity. Further supplementation experiments indicate that the 3-hydroxypropanoyl moiety of 1 originates from methionine, through an as-yet-uncharacterized mechanism. This work provides ample biochemical evidence connecting the putative noc biosynthetic gene cluster to nocuolin A and identifies the origin of all its carbon atoms, setting the stage for elucidation of its unusual biosynthetic chemistry. | Teresa Martins; Nathaniel Glasser; Duncan Kountz; Paulo Oliveira; Emily Balskus; Pedro Leão | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622c184c9e8766e954e55877/original/biosynthesis-of-the-unusual-carbon-skeleton-of-nocuolin-a.pdf |
67c1505f81d2151a02679a0d | 10.26434/chemrxiv-2025-s7cm0 | Tuning f band for Enhanced Surface Redox in Strained Rare Earth Oxides | Reducible rare earth oxides (REO2-x) are essential in catalysis due to their 4f band–governed surface redox properties, which influence crucial reactions such as hydrogen dissociation and water formation. However, correlating 4f band structure with catalytic activity has been a long-standing challenge due to the complexities of manipulating and characterizing 4f electrons. Here, we demonstrate that tensile strain effectively modulates the 4f electronic structure, narrowing the band gap and activating surface oxygen, leading to enhanced redox activity. Using atomically flat ceria ultrathin films under up to 7% biaxial strain range, we observed a 5-fold increase in surface reaction kinetics via time-resolved ambient pressure X-ray photoelectron spectroscopy. Complementary density functional theory calculations reveal that tensile strain reduces energy barriers for key catalytic steps by narrowing the 4f–2p band gap. These findings highlight RE 4f electronic structure as a critical descriptor for catalysis and demonstrate the utility of atomically flat model systems. | Hongyang Su; Jing Chai; Zixian Guan; Hendrik Bluhm; Ziyuan Zhang; Yidan Cao; Zhi Liu; Yuan-hua Lin; William C. Chueh; Liang Zhang; Di Chen | Theoretical and Computational Chemistry; Materials Science; Catalysis; Ceramics; Thin Films; Nanocatalysis - Reactions & Mechanisms | CC BY NC 4.0 | CHEMRXIV | 2025-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1505f81d2151a02679a0d/original/tuning-f-band-for-enhanced-surface-redox-in-strained-rare-earth-oxides.pdf |
67bf39ab81d2151a022c38b0 | 10.26434/chemrxiv-2025-xm4jc | Complex-variable equation-of-motion coupled-cluster singles and doubles theory with the resolution-of-the-identity approximation | We present an implementation of complex-variable equation-of-motion coupled- cluster singles and doubles (EOM-CCSD) theory with the resolution-of-the-identity (RI) approximation. Complex-variable methods are used in the framework of non- Hermitian quantum chemistry to treat electronic resonances. As test cases, we study differenttypesofresonancesofN2 andCO, namelytemporaryanions, Starkresonances, autoionizing Rydberg states and core-ionized states that decay by the Auger-Meitner effect. Temporary anions are treated with the complex basis function (CBF) method and different variants of the complex absorbing potential (CAP) method. The other resonances are only treated with CBFs. The memory requirements of our implementa- tion are significantly lower than those of canonical EOM-CCSD. We demonstrate that the RI error is smaller than the basis set error for all types of resonances. However, when the size of the decay width approaches the magnitude of the RI error, the width is predicted qualitatively wrong with the RI approximation. In addition, when an ad- equate auxiliary basis set is not available, i.e., for autoionizing Rydberg states and for core-ionized states, the RI error in the total decay width increases by a factor 10. | Simen Camps; Cansu Utku; Joel Creutzberg; Thomas-C. Jagau | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf39ab81d2151a022c38b0/original/complex-variable-equation-of-motion-coupled-cluster-singles-and-doubles-theory-with-the-resolution-of-the-identity-approximation.pdf |
60c74e299abda203a2f8d5a5 | 10.26434/chemrxiv.12011673.v2 | An Alternate Energy-Conserved Pathway for the Morita-Baylis-Hillman (MBH) Reaction | An new overall lower energy pathway for the amine-catalysed
Morita-Baylis-Hillman reaction is proposed from computations at the M06-2X/6-311++G(d,p)
level. The pathway involves proton-transfer from the
ammonium ion to the alkoxide formed from the aldol reaction through a seven-membered
ring transition state (TS) structure followed by highly exothermic Hofmann<i> </i>elimination through a five-membered ring
TS structure to form the product and also release the catalyst to carry on with
the process all over again. | Veejendra Yadav | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e299abda203a2f8d5a5/original/an-alternate-energy-conserved-pathway-for-the-morita-baylis-hillman-mbh-reaction.pdf |
6670b65c01103d79c56d3038 | 10.26434/chemrxiv-2024-lw7r2-v2 | A Single-Shot Technique for Measuring Broadband Two-Photon Absorption Spectra in Solution | Applications involving two-photon activation, including two-photon fluorescence imaging, photodynamic therapy, and 3D data storage, require precise knowledge of the two-photon absorption (2PA) spectra of target chromophores. Broadband pump-probe spectroscopy using femtosecond laser pulses provides wavelength-dependent 2PA spectra with absolute cross sections, but the measurements are sometimes complicated by cross-phase modulation effects and dispersion of the broadband probe. Here, we introduce a single-shot approach that eliminates artifacts from cross-phase modulation and enables more rapid measurements by avoiding the need to scan the time delay between the pump and probe pulses. The approach uses counter-propagating beams to automatically integrate over the full interaction between the two pulses as they cross. We demonstrate this single-shot approach for a common 2PA reference, coumarin 153 (C153), in three different solvents using the output from a Yb:KGW laser. This approach provides accurate 2PA cross sections that are more reliable and easier to obtain compared with scanning pump-probe methods using co-propagating laser beams. The single-shot method for broadband two-photon absorption (BB-2PA) spectroscopy also has significant advantages compared with single-wavelength measurements, such as z-scan and two-photon fluorescence. | Prasenjit Srivastava; Christopher G. Elles | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6670b65c01103d79c56d3038/original/a-single-shot-technique-for-measuring-broadband-two-photon-absorption-spectra-in-solution.pdf |
65edbbba66c1381729ae3ed3 | 10.26434/chemrxiv-2024-97r5j | Reusability report: Annotating metabolite mass spectra with domain-inspired chemical formula transformers | We present an in-depth exploration of the Metabolite Inference with Spectrum Transformers (MIST) tool for annotating small molecule mass spectrometry (MS) data, focusing on its reproducibility and generalizability. MIST innovates by integrating a “chemical formula transformer” to process MS/MS spectra, aiming to bridge the substantial knowledge gap in untargeted MS studies, where only a fraction of spectra are confidently annotated. Here, we critically assess MIST’s reproducibility by following the tool’s original training and testing protocols, encountering minor challenges but largely succeeding in replicating results. We also evaluate MIST’s generalizability by applying it to an external dataset from the CASMI 2022 challenge, revealing insights into the model’s performance on previously unseen data. An ablation study further investigates the impact of various model features on database retrieval performance, suggesting that some algorithmic complexities may not significantly enhance performance. Through rigorous evaluation, this work underscores the challenges and considerations in developing robust computational tools for MS data analysis. We advocate for community-wide efforts in benchmarking, transparency, and data sharing to foster advancements in metabolomics and computational biology. | Janne Heirman; Wout Bittremieux | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65edbbba66c1381729ae3ed3/original/reusability-report-annotating-metabolite-mass-spectra-with-domain-inspired-chemical-formula-transformers.pdf |
60cc9a14461f567e4347902f | 10.26434/chemrxiv-2021-rsrqb | Homogeneous hydrogenation of saturated bicarbonate slurry to formates using multiphase catalysis | Formic acid and formate salts are key intermediates along the pathways for CO2 utilization and hydrogen storage. Herein we report a highly efficient multiphase catalytic system utilizing ruthenium PNP pincer catalyst for converting supersaturated bicarbonate solutions and slurries to aqueous formate solutions up to 12M in molarity. The biphasic catalytic system delivers turnover frequencies up to 73 000 h-1 and remains stable for up to 474’000 turnovers once reaction conditions are optimized. | Christophe Rebreyend; Evgeny Pidko; Georgy Filonenko | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cc9a14461f567e4347902f/original/homogeneous-hydrogenation-of-saturated-bicarbonate-slurry-to-formates-using-multiphase-catalysis.pdf |
60c74fe24c891907ebad3c97 | 10.26434/chemrxiv.12956456.v1 | Organic Photostimulated Luminescence | Photostimulated luminescence, which allows energy or data to be stored and released using electromagnetic waves as both the input and output, has attracted considerable interest in the fields of biomedical and informatics technologies, but this phenomenon is mostly limited to solid inorganic materials. Here, we report photostimulated luminescence from purely organic blend films composed of electron donor, acceptor, and trap/emitter molecules. In the films, charges are accumulated as radical ions by ultraviolet light irradiation and then extracted by near infrared light irradiation to produce visible light. Films are capable of multiple cycles (>10 times) of organic photostimulated luminescence, which was still observable from films left in the dark at room temperature for one week after excitation, and emission color could be varied by changing the trap/emitter molecules. These findings will broadly impact existing applications and provide new prospects for innovative flexible devices. | Manabu Sakurai; Ryota Kabe; Masaaki Fuki; Zesen Lin; Kazuya Jinnai; Yasuhiro Kobori; Chihaya Adachi; Takashi Tachikawa | Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fe24c891907ebad3c97/original/organic-photostimulated-luminescence.pdf |
63e662e41d2d184063404dbf | 10.26434/chemrxiv-2023-pb9pp | Characterizing the Organohalogen Iceberg: Extractable, multi-halogen mass balance determination in municipal wastewater treatment plant sludge | The large number and diversity of organohalogen compounds (OHCs) occurring in the environment poses a grand challenge to analytical chemists. Since no single targeted method can identify and quantify all OHCs, the size of the OHC iceberg may be underestimated. We sought to address this problem in municipal wastewater treatment plant (WWTP) sludge by quantifying the unidentified fraction of the OHC iceberg using targeted analyses of major OHCs together with measurements of total- and extractable (organo)halogen (TX and EOX, respectively; where X=F, Cl, or Br). In addition to extensive method validation via spike/recovery and combustion efficiency experiments, TX and/or EOX were determined in reference materials (BCR-461 and NIST SRMs 2585 and 2781) for the first time. Application of the method to WWTP sludge revealed that chlorinated paraffins (CPs) accounted for most (~92%) of the EOCl, while brominated flame retardants and per- and polyfluoroalkyl substances (PFAS) accounted for only 54% of the EOBr and 2% of the EOF, respectively. Moreover, unidentified EOF in non-polar CP extracts points to the existence of organofluorine(s) with physical-chemical properties unlike those of target PFAS. This study represents the first multi-halogen mass balance in WWTP sludge, and offers a novel approach to prioritization of sample extracts for follow-up investigation. | Kyra M. Spaan; Bo Yuan; Merle M. Plassmann; Jonathan P. Benskin; Cynthia A. de Wit | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e662e41d2d184063404dbf/original/characterizing-the-organohalogen-iceberg-extractable-multi-halogen-mass-balance-determination-in-municipal-wastewater-treatment-plant-sludge.pdf |
60c74c5f337d6c4893e27c11 | 10.26434/chemrxiv.12465680.v1 | The SARS-COV-2 Spike Protein Binds Sialic Acids, and Enables Rapid Detection in a Lateral Flow Point of Care Diagnostic Device | <div>
<div>
<div>
<p>There is an urgent need to understand the behavior of novel coronavirus (SARS-COV-2), which is the causative
agent of COVID-19, and to develop point-of-care diagnostics. Here, a glyconanoparticle platform is used to discover that N-acetyl neuraminic acid has high affinity towards the SARS-COV-2 spike glycoprotein, demonstrating its glycan-binding function. Optimization of the particle size and coating enabled detection of the spike glycoprotein in lateral flow and showed
selectivity over the SARS-COV-1 spike protein. Using a viral particle mimic, paper-based lateral flow detection was demonstrated in under 30 minutes showing the potential of this system as a low-cost detection platform.
</p>
</div>
</div>
</div> | Alexander N. Baker; Sarah-Jane Richards; Collette S. Guy; Thomas
R. Congdon; Muhammad Hasan; Alexander J. Zwetsloot; anne straube; Marc Walker; Simona Chessa; Giulia Pergolizzi; Simone Dedola; Robert Field; Matthew Gibson | Organic Polymers; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2020-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c5f337d6c4893e27c11/original/the-sars-cov-2-spike-protein-binds-sialic-acids-and-enables-rapid-detection-in-a-lateral-flow-point-of-care-diagnostic-device.pdf |
60c73ec1bdbb89407fa37eaa | 10.26434/chemrxiv.7092821.v1 | New Modular Calamitic Ligands for Self-Assembly of Thermostable Quantum Dot Microcapsules via Nematic Templating | The
design, synthesis, properties, and performance of a new class of promesogenic calamitic
side-tethering organic ligands used to direct quantum dot nanoparticle
self-assembly via nematic templating are described. This work was motivated by inadequate
modularity, step count, and yield associated with syntheses of existing
ligands. Attaching the new ligands to quantum dots and dispersing them in a
liquid crystal host affords hollow micron-sized capsules via nematic templating.
The capsules resist thermal decomposition up to 350 °C — significantly higher than any previously
reported microcapsules assembled from side-tethering calamitic
ligand-functionalized nanoparticle. Evaluation of the capsules by small-angle X-ray scattering shows that interparticle
spacing varies from 10–13 nm depending on the ligand used, and is correlated to
aminoalkyl chain length. | Amir Keshavarz; Sheida Riahinasab; Linda Hirst; Ben Stokes | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Aggregates and Assemblies; Core-Shell Materials; Liquid Crystals; Metamaterials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ec1bdbb89407fa37eaa/original/new-modular-calamitic-ligands-for-self-assembly-of-thermostable-quantum-dot-microcapsules-via-nematic-templating.pdf |
60c748194c8919126ead2e7a | 10.26434/chemrxiv.11857905.v1 | The Cyclopropane Ring as a Reporter of Radical Leaving-Group Reactivity for Ni-Catalyzed C(sp3)–O Arylation | <div><p>The ability to understand and predict reactivity is highly important for the development of new reactions. In the context of Ni-catalyzed C(sp<sup>3</sup>)–O functionalization, we have developed a unique strategy employing activated cyclopropanols to aid the design and optimization of a redox-active leaving group for C(sp<sup>3</sup>)–O arylation. In this chemistry, the cyclopropane ring acts as a reporter of leaving-group reactivity, since the ring-opened product is obtained under polar (2e) conditions, and the ring-closed product is obtained under radical (1e) conditions. Mechanistic studies demonstrate that the optimal leaving group is redox-active, and are consistent with a Ni(I)/Ni(III) catalytic cycle. The optimized reaction conditions are also used to synthesize a number of arylcyclopropanes, which are valuable pharmaceutical motifs.</p></div> | Reginald Mills; John. J. Monteith; Sophie Rousseaux | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748194c8919126ead2e7a/original/the-cyclopropane-ring-as-a-reporter-of-radical-leaving-group-reactivity-for-ni-catalyzed-c-sp3-o-arylation.pdf |
60c755c5567dfe4396ec634a | 10.26434/chemrxiv.14156732.v1 | Mechanically Stable Monolithic Porous Boron Nitride with High Volumetric Adsorption Capacity | <p>The development of adsorbents into structured and robust forms remains a challenge for emerging porous materials. In the context of porous boron nitride (BN), studies point to a tradeoff between mechanical stability, porosity, density, and adsorption kinetics. Approaches towards shaping and densification of porous BN have been mostly empirical since a detailed understanding of its formation mechanism, and how it impacts mechanical strength and porosity, is lacking. Here, we demonstrate a synthesis method that can directly produce a mechanically robust monolithic porous BN (mpBN) from an easily scalable polymeric precursor, which results in the highest volumetric surface area among porous BN samples to date. mpBN exhibits a high bulk density, 50% higher than BN powders and over ten times higher than the structured BN aerogels, while maintaining fast sorption kinetics. mpBN presents good mechanical strength, with hardness of 66.4 ± 4.5 MPa, <i>i.e. </i>one to two orders of magnitude higher than structured aerogels. We propose a mpBN formation mechanism which reveals that the crosslinked intermediates are responsible for the high mechanical strength of the final material. Our approach produces a form of BN that addresses the limitations of other adsorbents, and facilitate their application in gas separation and storage technologies. <br /></p> | Tian Tian; Jingwei Hou; Humera Ansari; Ying Xiong; Anouk L'Hermitte; David Danaci; Ronny Pini; Camille Petit | Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c5567dfe4396ec634a/original/mechanically-stable-monolithic-porous-boron-nitride-with-high-volumetric-adsorption-capacity.pdf |
66d93ab151558a15ef1727f7 | 10.26434/chemrxiv-2024-br178 | Star-like docking to F mutations of respiratory syncytial virus | The respiratory syncytial virus (RSV) causes abundant annual fatalities on young children and elder adults by infecting human cells mediated by RSV fusion (F) surface homotrimeric proteins. Despite their RSV fusion in vitro inhibitors, anti-F therapeutic molecules are not yet clinically available because of emergent resistant mutations. Here, alternative therapeutic strategies are explored to dock mutated F protein models. For that thousands of trimeric drug-like candidates were computationally generated/selected by parent-children co-evolution. New top-children candidates may help experimental tests since they display 3-fold star-like molecules fitting similar trimeric F cavities than previous in vitro inhibitors but improved higher sub-nanoMolar affinities. Additionally, some top-children also successfully targeted F mutations previously implicated in RSV fusion drug-resistances | julio coll | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d93ab151558a15ef1727f7/original/star-like-docking-to-f-mutations-of-respiratory-syncytial-virus.pdf |
62bca50ce60d98659df1b92c | 10.26434/chemrxiv-2022-b8tsf | Joining and Arrangement of Multilayers (JAM): A string representation for honeycomb layered materials.
| Herein we introduce a new and straightforward notation for identifying stacking sequences in high-symmetric honeycomb lattice layered materials. The Joining and Arrangement of Multilayers (JAM) notation assigns a string of characters to the structure of a polytype using only its chemical symbols. A pair of basic rules based on the symmetry is enough to identify those JAM strings that provide unique polytypes (canonical JAMs). This notation is the first step in transcribing layered materials into a series of characters for more accurate identification of stacking sequences.
| Jessica Arcudia; Filiberto Ortiz-Chi; Alán Aspuru-Guzik; Gabriel Merino | Theoretical and Computational Chemistry; Materials Science; Multilayers; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bca50ce60d98659df1b92c/original/joining-and-arrangement-of-multilayers-jam-a-string-representation-for-honeycomb-layered-materials.pdf |
64f98ac6b338ec988a0867d7 | 10.26434/chemrxiv-2023-06wsj | Investigating the photodynamics of trans-azobenzene with coupled trajectories | In this work, we present the first implementation of the coupled-trajectory Tully surface hopping (CT-TSH) suitable for applications to molecular systems. We combine CT-TSH with the semiempirical Floating Occupation Molecular Orbitals-Configuration Interaction (FOMO-CI) electronic structure method to investigate the photoisomerization dynamics of trans-azobenzene. Our study shows that CT-TSH can capture correctly decoherence effects in this system, yielding consistent electronic and nuclear dynamics in agreement with (standard) decoherence-corrected TSH. Specifically, CT-TSH is derived from the exact factorization and the electronic coefficients’ evolution is directly influenced by the coupling of trajectories, resulting in the improvement of internal consistency if compared to standard TSH. | Carlotta Pieroni; Eduarda Sangiogo Gil; Lea-Maria Ibele; Maurizio Persico; Giovanni Granucci; Federica Agostini | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f98ac6b338ec988a0867d7/original/investigating-the-photodynamics-of-trans-azobenzene-with-coupled-trajectories.pdf |
65b93f6ae9ebbb4db94dbc05 | 10.26434/chemrxiv-2024-lhpg8 | 2D Mixed Halide Perovskites for Ultraviolet
Light-emitting Diodes | Advances in perovskite light-emitting diodes (PeLEDs) have established them as viable candidates for next-generation displays and lighting across the entire visible spectrum, with recent investigations extending their emissive properties into the deep blue and violet regions. These materials have the potential to overcome the fabrication complexities inherent in conventional III-V semiconductors by circumventing the necessity for lattice-matching, instead allowing for straightforward deposition of polycrystalline films without relying on metal-organic chemical vapor deposition. However, achieving shorter emission wavelengths presents a significant challenge due to the larger bandgaps required of both the perovskite and charge transport materials, compounding the difficulty in managing electron-hole pair recombination dynamics necessary for efficient electroluminescence. In this work, we address these challenges by precisely tuning the halide composition in two-dimensional perovskites, successfully extending the bandgap to 3.1 eV and achieving photoluminescent emission at 393 nm. By introducing an optimized dual electron transport layer architecture, we improve electron injection and hole confinement within the perovskite matrix, culminating in a high-purity electroluminescent emission at 399 nm. This strategy yields a maximum external quantum efficiency of 0.16%, a new benchmark for PeLEDs operating in this spectral domain. These findings highlight the potential of large bandgap perovskite materials for next-generation light-emitting applications. | Manchen Hu; Junrui Lyu; Natalia Murrietta; Sebastian Fernández; William Michaels; Qi Zhou; Pournima Narayanan; Daniel Congreve | Materials Science; Nanoscience; Energy; Optical Materials; Thin Films; Nanodevices | CC BY 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b93f6ae9ebbb4db94dbc05/original/2d-mixed-halide-perovskites-for-ultraviolet-light-emitting-diodes.pdf |
662e8f62418a5379b0f62251 | 10.26434/chemrxiv-2024-vm4n3 | A general method for near-infrared photoswitching in biology, demonstrated by the >700 nm photocontrol of GPCR activity in brain slices
| Azobenzene molecular switches are widely used to photocontrol material properties, and biological activity in cell culture, via photoisomerisation between E and Z isomers. However, because population photoswitching is incomplete, their dynamic range of property control is often small; and because they cannot be operated with red/NIR light, they are usually not applicable in deep tissue. Here, we demonstrate a general method for efficient single-photon photocontrol of azobenzenes, and of glutamate receptor activity, at >700 nm in live tissue. We use red/NIR chromophore auxiliaries to perform intramolecular energy transfer to bioactive azobenzenes, which drives fast bulk Z→E isomerisation up to even >97% completeness. The auxiliary/azobenzene dyads allow >700 nm photoswitching with photon-efficiency that can be even higher than for direct azobenzene E→Z isomerisation in the UV region; and they are biocompatible and photostable. Crucially, their performance properties are intrinsic, i.e. auxiliary-based intramolecular switching will perform identically at any dilution and will not be affected by biodistribution. We show that these dyads can be created straightforwardly from most azobenzene systems, with most auxiliary chromophores, without tricky molecular redesign or re-optimisation. After outlining some rules of auxiliary-based photoswitching, which can guide its broader adoption, we conclude by using dyads to make the first demonstration of single-photon NIR chemical photoswitching control over biological activity, in cell culture and intact brain tissue. | Benedikt Baumgartner; Viktorija Glembockyte; Alberto J. Gonzalez-Hernandez; Abha Valavalkar; Robert J. Mayer; Lucy L. Fillbrook; Adrian Müller-Deku; Jinhua Zhang; Florian Steiner; Christoph Gross; Martin Reynders; Hermany Munguba; Anisul Arefin; Armin Ofial; Jonathon E. Beves; Theobald Lohmueller; Benjamin Dietzek-Ivanšic; Johannes Broichhagen; Philip Tinnefeld; Joshua Levitz; Oliver Thorn-Seshold | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662e8f62418a5379b0f62251/original/a-general-method-for-near-infrared-photoswitching-in-biology-demonstrated-by-the-700-nm-photocontrol-of-gpcr-activity-in-brain-slices.pdf |
66b90380c9c6a5c07aece3bc | 10.26434/chemrxiv-2024-xtczv | State-of-the-art local correlation methods enable affordable gold standard quantum chemistry for up to hundreds of atoms | We review the current capabilities of local electron correlation methods up to the coupled cluster model with single, double, and perturbative triple excitations [CCSD(T)], which is a gold standard in quantum chemistry. The main computational aspects of the local method types are assessed from the perspective of applications, but the focus is kept on how to achieve chemical accuracy (i.e., <1 kcal/mol uncertainty), as well as on the broad scope of chemical problems made accessible.
The performance of state-of-the-art methods are also compared, including the most employed DLPNO and, in particular, our local natural orbital (LNO) CCSD(T) approach. The high accuracy and efficiency of the LNO method makes chemically accurate CCSD(T) computations accessible for molecules of hundreds of atoms with resources affordable to a broad computational community (days on a single CPU and 10–100 GB of memory). Recent developments in LNO-CCSD(T) enable systematic convergence and robust error estimates even for systems of complicated electronic structure or larger size (up to 1000 atoms). The predictive power of current local CCSD(T) methods, usually at about 1–2 order of magnitude higher cost than hybrid density functional theory (DFT), has become outstanding on the palette of computational chemistry applicable for molecules of practical interest.
We also review more than 50 LNO-based and other advanced local-CCSD(T) applications for realistic, large systems across molecular interactions as well as main group, transition metal, bio-, and surface chemistry. The examples show that properly executed local-CCSD(T) can contribute to binding, reaction equilibrium, rate constants, etc. which are able to match measurements within the error estimates. These applications demonstrate that modern, open-access, and broadly affordable local methods, such as LNO-CCSD(T), already enable predictive computations and atomistic insight for complicated, real-life molecular processes in realistic environments. | Peter Nagy | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b90380c9c6a5c07aece3bc/original/state-of-the-art-local-correlation-methods-enable-affordable-gold-standard-quantum-chemistry-for-up-to-hundreds-of-atoms.pdf |
60c755110f50dbc8f2397e2a | 10.26434/chemrxiv.14038871.v1 | Unravelling Defect Passivation Mechanisms in Sulfur-treated Sb2Se3 | <p>Sb<sub>2</sub>Se<sub>3 </sub>has emerged as an important photoelectrochemical (PEC) and photovoltaic (PV) material due to its rapid rise in photoconversion efficiencies. However, despite its binary nature, Sb<sub>2</sub>Se<sub>3 </sub>has a complex defect chemistry, which reduces the maximum photovoltage that can be obtained. Thus, it is important to understand these defects and to develop passivation strategies in order to further improve this material. In this work, a comprehensive investigation of the charge carrier dynamics of Sb<sub>2</sub>Se<sub>3</sub> and the influence of sulfur treatment on its optoelectronic properties was performed using time resolved microwave conductivity (TRMC), photoluminescence (PL) spectroscopy and low frequency Raman spectroscopy (LFRS). The key finding in this work is that upon sulfur treatment of Sb<sub>2</sub>Se<sub>3</sub>, the carrier lifetime is increased by the passivation of deep defects in Sb<sub>2</sub>Se<sub>3</sub> in both the surface region and the bulk, which is evidenced by increased charge carrier lifetime of TRMC decay dynamics, increased radiative recombination efficiency and decreased deep defect level emission (PL), and improved long-range order in the material (LFRS). These findings provide crucial insights into the defect passivation mechanisms in Sb<sub>2</sub>Se<sub>3</sub> paving the way for developing highly efficient PEC and PV devices.</p> | Rajiv
Ramanujam Prabhakar; Thomas Moehl; Dennis Friedrich; Marinus Kunst; Sudhanshu Shukla; Damilola Adeleye; Vinayaka H. Damle; Sebastian Siol; Wei Cui; Laxman Gouda; Jihye Suh; Yaakov R. Tischler; Roel van de Krol; David Tilley | Thin Films; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755110f50dbc8f2397e2a/original/unravelling-defect-passivation-mechanisms-in-sulfur-treated-sb2se3.pdf |
67a242f8fa469535b90beb86 | 10.26434/chemrxiv-2025-k5mzk | Refinement and Truncation of DNA Aptamers based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation | Aptamers have proven useful for a wide variety of applications, such as drug delivery systems and analytical reagents for diagnosis or food safety control. Conventional aptamer selection methods typically produce sequences longer than necessary, which are optimized through a post-selection trial and error process to obtain the shortest-length sequence that preserves binding affinity. Herein, we describe a general strategy to obtain the tridimensional structure of DNA aptamers using a semiautomated molecular dynamics protocol, which serves as a guide to rationally improve experimentally selected candidates. Based on this approach, we designed truncated aptamers from previously described ligands recognizing different peptides and proteins, which are 20-35% shorter than the original candidates and present similar or even improved binding affinities. Moreover, we also discriminate between energetically similar secondary structures in terms of the energetic scoring of the molecular dynamics trajectories, and rationally explain the role of poly-thymine spacers in the (de)stabilization of the structure. This work demonstrates how a protocol for generating the aptamers tridimensional structure can accelerate their optimization for obtaining better analytical reagents and therapeutic agents. | Ana Díaz-Fernández; Camen S. Ciudad; Natalia Díaz; Dimas Suárez; Noemí de-los-Santos-Álvarez; M. Jesús Lobo-Castañón | Theoretical and Computational Chemistry; Analytical Chemistry; Electrochemical Analysis; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a242f8fa469535b90beb86/original/refinement-and-truncation-of-dna-aptamers-based-on-molecular-dynamics-simulations-computational-protocol-and-experimental-validation.pdf |
654fca3edbd7c8b54b159e82 | 10.26434/chemrxiv-2023-wrq52 | Electrode Surface Heating with Organic Films Improves CO2 Reduction Kinetics on Copper | Management of the electrode surface temperature is an understudied aspect of (photo)electrode reactor design in both fundamental studies and optimized systems for complex reactions such as CO2 reduction. In this work, we study the impact of local electrode heating on electrochemical CO2 reduction. Using the ferri/ferrocyanide open circuit voltage as a reporter of the effective reaction temperature, we reveal how the interplay of surface heating and convective cooling poses a challenge for co-optimizing mass transport and thermal assistance of electrochemical reactions, where we focus on reduction of CO2 to carbon-coupled (C2+) products. The introduction of an organic coating on the electrode surface facilitates well-behaved electrokinetics with near-ambient bulk electrolyte temperature, enabling the discovery that surface heating to 60 °C decreases the voltage required for peak C2+ performance by ca. 100 mV compared to ambient conditions. This approach to thermal management offers a new dimension to electrochemical systems design. It moreover offers the opportunity to further probe thermal effects in electrochemical reactions, as demonstrated through Bayesian inference of Butler-Volmer kinetic parameters from a suite of high throughput experiments. | Nicholas Watkins; Yungchieh Lai; Zachary Schiffer; Virginia Canestraight; Harry Atwater; Theodor Agapie; Jonas Peters; John Gregoire | Catalysis; Energy; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654fca3edbd7c8b54b159e82/original/electrode-surface-heating-with-organic-films-improves-co2-reduction-kinetics-on-copper.pdf |
660fe33f418a5379b0257475 | 10.26434/chemrxiv-2024-p49p5-v2 | Low-Temperature Catalytic Methane Deep Oxidation over Sol-gel derived Mesoporous Hausmannite (Mn3O4) Spherical Particles | Herein, Mn3O4 spherical particles (SPs) were synthesized by the sol-gel process, followed by thermal annealing at 400 °C. The sample was analyzed by XRD, FTIR, SEM, SBET, XPS, H2-TPR and UV-vis spectroscopy. XRD and FTIR analysis show that Mn3O4 exhibits a tetragonal spinel structure. SEM and SBET analysis display a porous homogeneous surface made of strongly agglomerated spherical-like grains size with an estimated average particle size of ~35 nm, corresponding to a large specific surface area (SBET) of ~81.5 m2/g. XPS analysis indicated that, Mn3O4 were composed of metallic cations (Mn4+, Mn3+, Mn2+) and oxygen species (O2-, OH- and CO32-). The optical energy band gap energy was ~2.55eV. Moreover, Mn3O4 SPs were successfully tested as catalyst with almost 100% conversion of CH4 to CO2 and H2O at a gas hourly space velocity (GHSV) of 72 000 mL3.g-1h-1. The observed performance can be assigned to the cooperated effects of the smallest spherical-like grain size with mesoporous structure as responsible for the larger SBET, and the available surface-active oxygenated species. The cooperative effect of the good reducibility, the higher ratio of active species (OLat/OAds), as well as Density Functional Theory (DFT) calculations suggested that, CH4 total oxidation over the mesoporous Mn3O4 SPs might follow a two-term process in which both Langmuir-Hinshelwood and Mars-van Krevelen mechanisms are cooperatively involved. | Patrick Ndouka ndouka; Stephane Kenmoe; Jacques Richard Mache; Elie Acayanka; Dick Hartmann Douma; Ralph Gebauer; Patrick Kouotou Mountapmbeme | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660fe33f418a5379b0257475/original/low-temperature-catalytic-methane-deep-oxidation-over-sol-gel-derived-mesoporous-hausmannite-mn3o4-spherical-particles.pdf |
62125a014e899ec61a549a09 | 10.26434/chemrxiv-2022-5g2bz | Cryolithionite as a novel pseudocapacitive electrode material for lithium-ion capacitors | Lithium-ion insertion/deinsertion in anode at slow rates limits the power performance of energy storage devices. Here, a new pseudocapacitive electrode with high reversible capacity during cycling has been proposed for a lithium-ion capacitor. The lithium-fluoride garnet, namely Na3Fe2Li3F12, is obtained via precipitation from an aqueous solution at room temperature using abundant materials and exhibits a high discharge capacity of 746 mAh/g. After the first charging cycle, energy is stored via fast pseudocapacitive faradaic reactions which are facilitated by the nanocrystalline transport pathways with no structural modification to the electrode. The high stability window of F-garnet allows extracting cell voltages of 2.2—3.2 V in a lithium-ion capacitor where it is coupled with a porous carbon-based positive electrode, with a high energy efficiency of 93% maintained for 10000 charge/discharge cycles. This study opens new research direction concerning pseudocapacitive anode materials for the enhanced power performance and even replacing the traditional battery-like anode materials. | Lukas Ladenstein; Xuexue Pan; Daniel Knez; Martin Philipp; Gerald Kothleitner; Günther J. Redhammer; Qamar Abbas; Daniel Rettenwander | Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62125a014e899ec61a549a09/original/cryolithionite-as-a-novel-pseudocapacitive-electrode-material-for-lithium-ion-capacitors.pdf |
60c74ae9bdbb89cf61a3947a | 10.26434/chemrxiv.12253052.v1 | Functionalized Polyesters via Stereoselective Electrochemical Ring-Opening Polymerization of O-Carboxyanhydrides | Ring-opening polymerization is used to prepare
polyesters with precisely controlled molecular weights, molecular weight distributions,
and tacticities. Herein, we report a newly developed Co/Zn catalytic system
that can be activated by an electrical current to mediate efficient
ring-opening polymerization of enantiopure <i>O</i>-carboxyanhydrides,
allowing for the synthesis of isotactic functionalized polyesters with high
molecular weights (>140 kDa) and narrow molecular weight distributions (<i>M</i><sub>w</sub>/<i>M</i><sub>n</sub> < 1.1). We also demonstrate that these catalysts
can be used for stereoselective ring-opening polymerization of racemic <i>O</i>-carboxyanhydrides to synthesize
syndiotactic or stereoblock copolymers with different glass transition
temperatures compared with their atactic counterparts. | Yongliang Zhong; quanyou feng; xiaoqian wang; jia chen; wenjun cai; Rong Tong | Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae9bdbb89cf61a3947a/original/functionalized-polyesters-via-stereoselective-electrochemical-ring-opening-polymerization-of-o-carboxyanhydrides.pdf |
60c74713469df4361af43786 | 10.26434/chemrxiv.11535663.v1 | Total Synthesis of Putative Xestocyclamine A | The first total synthesis of putative xestocyclamine A (-)-<b>1</b>
is reported, a compound taking center stage on the the pathway
explaining the biosynthesis of a prominent family of polycyclic
alkaloids (Baldwin-Whitehead pathway). The identity of the synthetic
sample is unambiguous but the recorded spectral data deviate from those
of xestocyclamine A reported in the literature. | Zhanchao Meng; Alois Fürstner | Natural Products; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74713469df4361af43786/original/total-synthesis-of-putative-xestocyclamine-a.pdf |
6194ca1d2e10ad438249f79e | 10.26434/chemrxiv-2021-2d0h6 | Polymerase-mediated synthesis of artificial RNA-DNA metal base pairs | Metal-mediated base pairs are formed by the connection of two nucleobases via coordination to a metal cation. The resulting metal-containing duplexes have been used in a large variety of applications ranging from allosteric control of functional nucleic acids to the construction of nanowires. Recently, enzymatic approaches are being developed for the construction of metal-mediated base pairs. Here, we have studied the possibility of constructing HgII- and AgI-mediated DNA/RNA hetero base pairs using primer extension reactions. The high kinetic and thermodynamic stabilities of metal base pairs can be harnessed to trigger the formation of multiple rU-HgII-dT base pairs. | Fabienne Levi-Acobas; Luke McKenzie; Marcel Hollenstein | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6194ca1d2e10ad438249f79e/original/polymerase-mediated-synthesis-of-artificial-rna-dna-metal-base-pairs.pdf |
60c747850f50db4eb73965fc | 10.26434/chemrxiv.11701854.v1 | Assessing the Performance of Density Functional Theory Methods on the Prediction of Low-Frequency Vibrational Spectra | The low-frequency (terahertz) dynamics of condensed phase materials provide valuable insight into numerous bulk phenomena. However, the assignment and interpretation of experimental results requires computational methods due to the complex mode-types that depend on weak intermolecular forces. Solid-state density functional theory has been used in this regard with great success, yet the selection of specific computational parameters, namely the chosen basis set and density functional, has a profound influence on the accuracy of predicted spectra. In this work, the role of these two parameters is investigated in a series of organic molecular crystals, in order to assess the ability of various methods to reproduce intermolecular forces, and subsequently experimental terahertz spectra. Specifically, naphthalene, oxalic acid, and thymine were chosen based on the varied intermolecular interactions present in each material. The results highlight that unconstrained geometry optimizations can be used as an initial proxy for the accuracy of interatomic forces, with errors in the calculated geometries indicative of subsequent errors in the calculated low-frequency vibrational spectra, providing a powerful metric for the validation of theoretical results. Finally, the origins of the observed shortcomings are analyzed, providing a basic framework for further studies on related materials. | Peter Banks; Zihui Song; Michael Ruggiero | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747850f50db4eb73965fc/original/assessing-the-performance-of-density-functional-theory-methods-on-the-prediction-of-low-frequency-vibrational-spectra.pdf |
66ebc4e312ff75c3a1ccd6a1 | 10.26434/chemrxiv-2024-vmk13 | Molecular photothermal activation assisted synthesis, and orthogonal assembly of metal-organic-framework | Temperature is a fundamental parameter in any chemical process, affecting reaction rates, selectivity, and more. Typically, chemists think of temperature as a homogeneous property, remaining unchanged throughout the reaction in space and time. Recently, photothermal materials have been emerging as an exciting tool opening new paths for innovative research, challenging the viewpoint described above. Herein, we develop a synthesis and in-situ assembly technique for metal-organic frameworks (MOFs) based on the distinct heterogeneous heating of photothermal materials under visible light. Notably, a simple cobalt chloride molecular complex was utilized as an efficient and stable light-to-heat converter for initial MOF formation. A thorough investigation of the assembly mechanism revealed the key role photothermal activation had in the formation of the superstructures. Finally, palladium nanoparticles (NP) were utilized as competing photothermal agents shedding light on the dynamics between different heat sources within a reaction and resulting in MOF-NP composites. This work highlights the versatility of the photothermal approach in the synthesis of advanced materials introducing a promising route to the micro/nano assembly of different materials. | Yossi Weizmann; Aritra Biswas; Nir Lemcoff; Ofir Shelonchik | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ebc4e312ff75c3a1ccd6a1/original/molecular-photothermal-activation-assisted-synthesis-and-orthogonal-assembly-of-metal-organic-framework.pdf |
67bb106a6dde43c90817a531 | 10.26434/chemrxiv-2025-3fvd0 | Co-Solvent-aided Opto-Thermophoretic Printing of Gold Nanorod Assemblies | The controlled deposition of plasmonic nanoparticles on solid surfaces is critical for the fabrication of medical diagnostics, devices and sensors. Despite recent advances in harnessing thermal gradients to achieve controlled deposition of nanoparticles at a laser spot, the deposition of anisotropic gold nanoparticles via opto-thermophoresis could not be achieved in aqueous solution. Herein, the use of ethanol as a co-solvent was shown to enable rapid (<10 s) and effective deposition of gold nanorods in the presence of polyvinylpyrrolidone on unmodified glass substrates. The influence of key parameters, including polymer concentration and molecular weight, co-solvent content, nanoparticle concentration, and laser power, were studied. While ethanol content and polymer size had the largest impact on the assembly structure, all had an impact on the assembly growth rate. Polymer size was found to significantly impact the degree of nanorod assembly found in the pattern, which led to a surface-enhanced Raman scattering enhancement factor up to 10^8. In summary, this approach utilizes thermal gradients to direct the formation of highly localized plasmonic assemblies without the need of functionalization of the substrate. This simple, fast, and adaptable approach is a promising platform for the scalable patterning of plasmonic nanostructures. | Ana Jimenez Amaya; Claire Goldmann; Maike Haidasch; Cyrille Hamon; Eric Hill | Physical Chemistry; Nanoscience; Nanofabrication; Plasmonic and Photonic Structures and Devices; Self-Assembly; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bb106a6dde43c90817a531/original/co-solvent-aided-opto-thermophoretic-printing-of-gold-nanorod-assemblies.pdf |
67c6c61581d2151a0201041f | 10.26434/chemrxiv-2025-2z3pd | Copper transport across cell membranes by calix[4]arene-based cationophores leading to potent biological activity | Lipid bilayers are impermeable to ions, including copper cations. Copper is an essential trace element for life, present in the active site of various enzymes, whereas free copper is detrimental inside cells. Copper homeostasis is thus finely controlled, involving Cu(I) transporting membrane proteins Ctr1 and ATP7A/B. Disruption of copper homeostasis has been reported as a potential anti-cancer strategy. With this objective, we have developed a series of lipophilic compounds with two copper coordinating (benz)imidazole groups that are able to function as ionophores, transporting copper cations across membranes. This was firstly demonstrated in liposomes with a Cu(I) sensitive fluorescent probe encapsulated. Secondly, five of these compounds were shown to restore the growth of yeast cells that had Ctr1 deleted, suggesting that these ionophores were able to transport copper into yeast cells. Thirdly, cytotoxicity studies in hepatocarcinoma cells highlighted the crucial role of the lipophilicity of Cu ionophores for their activity in cells. The impact of one of the most active compounds, named Cuphoralix, was further studied, showing no increase of intracellular Cu levels of the hepatocytes, but clear indications of metallic stress. Synchrotron X-ray fluorescence studies were then employed to study the effect of Cuphoralix on the subcellular copper distribution, revealing a redistribution of copper from vesicles to the cytosol. This explains the potent cytotoxicity of this novel class of copper ionophores, warranting further studies of their anti-cancer effects. | Nathan Renier; Gianluca Weyckmans Mele; Pierre Lelièvre; Mélanie Boeckstaens; Roy Lavendomme; Akin Aydogan; Yannick Dussein; Peggy Charbonnier; Laurens Puillet Anselme; Benoit Chovelon; Hiram Castillo-Michel ; Nikolay Tumanov; Johan Wouters; Lucie Sancey; Benoit Busser; Anna Maria Marini; Giulia Veronesi; Ivan Jabin; Aurélien Deniaud; Hennie Valkenier | Biological and Medicinal Chemistry; Organic Chemistry; Organometallic Chemistry; Supramolecular Chemistry (Org.); Biochemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6c61581d2151a0201041f/original/copper-transport-across-cell-membranes-by-calix-4-arene-based-cationophores-leading-to-potent-biological-activity.pdf |
627d193a3f1e7c9523bb9661 | 10.26434/chemrxiv-2022-6lr3q | Synthesis and styrene copolymerization of novel dimethyl and dimethoxy ring-substituted octyl phenylcyanoacrylates | Novel dimethyl and dimethoxy ring-substituted octyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2(CH2)6CH3 (where R is 2,3-dimethyl, 2,4-dimethyl, 2,5-dimethyl, 2,6-dimethyl, 3,4-dimethyl, 3,5-dimethyl, 2,3-dimethoxy, 2,4-dimethoxy, 2,5-dimethoxy, 2,6-dimethoxy, 3,4-dimethoxy, 3,5-dimethoxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and octyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis. | Martin S. Wasilewski; Grant W. Boyson; Georgina N. Canavesio; Sarah N. Keaton; Matthew R. Lee; Luke Meyer; Zoe A. Ryan; Diane S. Samon; Eric Seeger; Mahmood I. Shah; Rebeca M. Tojo Suárez; Anahi F. Toolabian; Bernadette C. Tudor; Sara M. Rocus; William S. Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d193a3f1e7c9523bb9661/original/synthesis-and-styrene-copolymerization-of-novel-dimethyl-and-dimethoxy-ring-substituted-octyl-phenylcyanoacrylates.pdf |
660256e99138d231614c13f2 | 10.26434/chemrxiv-2024-qrln0 | Towards Quantifying the Chemical Sensitivity of Nuclear Spin Surface Relaxivity in Mesoporous Media | Low-field nuclear magnetic resonance (NMR) relaxation is a promising non-invasive technique for characterizing solid-liquid interactions within functional porous materials. However, the ability of the solid-liquid interface to enhance adsorbate relaxation rates, known as the surface relaxivity, in the case of different solvents and reagents involved in various chemical processes has yet to be evaluated in a quantitative manner. In this study, we systematically explore the surface relaxation characteristics of ten liquid adsorbates (cyclohexane, acetone, water, and seven alcohols, including ethylene glycol) confined within mesoporous silicas with pore sizes between 6 nm and 50 nm using low-field (12.7 MHz) two-dimensional 1H T1 – T2 relaxation measurements. Functional group specific relaxation phenomena associated with the alkyl and hydroxyl groups of the confined alcohols are clearly distinguished; we report the dependence of both longitudinal (T1) and transverse (T2) relaxation rates of these 1H-bearing moieties on pore surface-to-volume ratio, facilitating the quantification and assignment of surface relaxivity values to specific functional groups within the same adsorbate molecule for the first time. We further demonstrate that alkyl group transverse surface relaxivities correlate strongly with the alkyl/hydroxyl ratio of the adsorbates assessed, providing evidence for a simple, quantitative relationship between surface relaxivity and interfacial chemistry. Overall, our observations highlight potential pitfalls in the application of NMR relaxation for the evaluation of pore size distributions using hydroxylated probe molecules, and provide motivation for the exploration of nuclear spin relaxation measurements as a route to adsorbate identity within functional porous materials. | Shuang Dong; Libin Liu; Nicholas Ling; Eric May; Michael Johns; Neil Robinson | Analytical Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660256e99138d231614c13f2/original/towards-quantifying-the-chemical-sensitivity-of-nuclear-spin-surface-relaxivity-in-mesoporous-media.pdf |
60c753a2567dfe1d0aec5f40 | 10.26434/chemrxiv.13519091.v1 | Robust and General Procedure for Carbon Isotope Labeling of Linear Urea Derivatives with Carbon Dioxide | Carbon isotope labeling
is a traceless technology, which allows tracking the fate of organic compounds
either in the environment or in living organisms. Despite recent advances in
the field, the development of robust and general technologies remains a
significant task. This full article reports on a general approach to label urea
derivatives with all carbon isotopes, including <sup>14</sup>C and <sup>11</sup>C.
Based on a Staudinger aza-Wittig sequence, it provides access to all
aliphatic/aromatic urea combinations as well as to semicarbazides,
sulfonylureas, hydroxyl ureas, and simple terminal ureas. A de-risking approach
was developed to evaluate the robustness of the reaction. This technology is
based on [<sup>14</sup>C]CO<sub>2</sub> screening that allowed to investigate
the tolerance of the procedure with most representative heterocycles and
functional groups found in FDA approved drugs. | Victor Babin; Antoine Sallustrau; Olivier Loreau; Fabien Caillé; Amélie Goudet; Héloïse Cahuzac; Antonio Del Vecchio; Frédéric Taran; Davide Audisio | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a2567dfe1d0aec5f40/original/robust-and-general-procedure-for-carbon-isotope-labeling-of-linear-urea-derivatives-with-carbon-dioxide.pdf |
6308a2070187d92d2da1eaa9 | 10.26434/chemrxiv-2022-sgq04-v3 | Integrated exposomics/metabolomics for rapid exposure and effect analyses | The totality of environmental exposures and lifestyle factors, commonly referred to as the exposome, are poorly understood. Measuring the myriad of chemicals that humans are exposed to is immensely challenging and identifying disrupted metabolic pathways is even more complex. Here, we present a novel technological approach for the comprehensive, rapid and integrated analysis of the endogenous human metabolome and the chemical exposome. By combining reverse-phase and hydrophilic interaction liquid chromatography and fast polarity switching, molecules with highly diverse chemical structures can be analyzed in 15 minutes with a single analytical run as both column’s effluents are combined before analysis. Standard reference materials and authentic standards were evaluated to critically benchmark performance. Highly sensitive median limits of detection (LOD) with 0.04 µM for >140 quantitatively assessed endogenous metabolites and 0.08 ng/mL for the >100 model xenobiotics and human estrogens in solvent were obtained. In matrix, the median LOD values were higher with 0.7 ng/mL (urine) and 0.5 ng/mL (plasma) for exogenous chemicals. To prove the dual-column approach’s applicability, real-life urine samples from sub-Saharan Africa (high exposure scenario) and Europe (low exposure scenario) were assessed in a targeted and non-targeted manner. Our LC-HRMS approach demonstrates the feasibility of quantitatively and simultaneously assessing the endogenous metabolome and the chemical exposome for the high-throughput measurement of environmental drivers of disease. | Mira Flasch; Veronika Fitz; Evelyn Rampler; Chibundu N. Ezekiel; Gunda Koellensperger; Benedikt Warth | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6308a2070187d92d2da1eaa9/original/integrated-exposomics-metabolomics-for-rapid-exposure-and-effect-analyses.pdf |
67ae034ffa469535b92e0c5a | 10.26434/chemrxiv-2025-8bj2t-v2 | Solvation free energies of anions: from new reference data to predictive models | Predicting the physicochemical properties of ionizable solutes, including solubility and lipophilicity, is of broad significance. Such predictions rely on the accurate determination of solvation free energies for ions. However, the limited availability of high-quality reference data poses a challenge in developing accurate, inexpensive computational prediction methods. In this study, we address both issues of data quality and availability. We present three databases and models related to ionic phenomena: 1 (1) 8,241 pK a datapoints across 8 solvents, (2) 5,536 gas-phase acidities from DLPNO- CCSD(T) QM calculations, and (3) 6,090 solvation free energies of anions across 8 solvents obtained from a thermodynamic cycle. We also report 6,088 solvation free energies of neutral conjugate solutes computed using the COSMO-RS method. The pKa data were obtained from the iBonD database, cleaned, and combined with a separate compilation of trustworthy reference pKa data. Gas-phase acidities were computed for most of the acids present in the pKa corpus. Leveraging these data, we compiled values for solvation free energies of anions. We then trained several graph neural network models, which can be used as an alternative to QM approaches to quickly estimate these properties. The pKa and gas-phase acidity models accept reaction SMILES strings of the acid dissociation as inputs, whereas the solvation energy model accepts the SMILES string of the anion. Our microscopic pKa model achieves good accuracy, with an overall test mean average error of 0.58 units on unseen solutes and 0.59 on the SAMPL7 challenge (the lowest error so far among multi-solvent models). Our gas-phase acidity model had mean absolute errors slightly above 3 kcal/mol when evaluated against experimental data. The anionic solvation free energy model had mean absolute errors of less than 3 kcal/mol in several test evaluations, comparable to (though less reliable than) several widely-used QM-based solvation models. The models and data are free and publicly available. | Thomas Nevolianis; Jonathan Zheng; Simon Müller; Matthias Baumann; Sofja Tshepelevitsh; Ivari Kaljurand; Ivo Leito; Irina Smirnova; William Green; Kai Leonhard | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae034ffa469535b92e0c5a/original/solvation-free-energies-of-anions-from-new-reference-data-to-predictive-models.pdf |
6563dea229a13c4d470f9eea | 10.26434/chemrxiv-2023-ncx12-v2 | Binding of Per- and Polyfluoroalkyl Substances to β-Lactoglobulin from Bovine Milk | Per- and polyfluoroalkyl substances (PFAS) are known for their high environmental persistence and potential toxicity. The presence of PFAS has been reported in many dairy products. However, the mechanisms underlying PFAS accumulation in these products and the impact of these contaminants on milk protein function remain unclear. Here, we used native mass spectrometry and molecular dynamics simulations to probe the interactions between 19 PFAS of environmental concern and two isoforms of the major bovine whey protein β-lactoglobulin (β-LG). We observed that six of these PFAS bound to both protein isoforms with low to mid-micromolar dissociation constants. Based on competitive binding experiments with endogenous ligands, PFAS can bind orthosterically and preferentially to β-LG’s hydrophobic ligand-binding calyx. Interestingly, we also observed that β-cyclodextrin can suppress PFAS binding to β-LG, owing to the ability of β-cyclodextrin to directly sequester PFAS from solution. Together, this research sheds light on PFAS—β-LG binding, suggesting that such interactions could impact lipid/fatty acid transport in bovine mammary glands. Furthermore, our results highlight the potential use of β-cyclodextrin in mitigating PFAS binding, providing insights towards the development of strategies to reduce PFAS accumulation in dairy products and other biological systems. | P. Chi Pham; Mackenzie Taylor; Giang Nguyen; Jeunesse Beltran; Jack Bennett; Junming Ho; William Donald | Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Mass Spectrometry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6563dea229a13c4d470f9eea/original/binding-of-per-and-polyfluoroalkyl-substances-to-lactoglobulin-from-bovine-milk.pdf |
663f359491aefa6ce1b7e829 | 10.26434/chemrxiv-2024-rr1m3-v2 | Materials Challenges for Electric Vehicles | Electric vehicles provide the ability to substantially reduce or eliminate greenhouse gas emissions from transportation. Such vehicles utilize a fundamentally different powertrain technology compared to conventional vehicles based on the internal combustion of liquid fuels. In this series of articles, we discuss material challenges related to three key subsystems related to the powertrain of electric vehicles: batteries, power electronics, and permanent magnets. Given that electric vehicles currently occupy ~20% of the market share and are projected to rapidly rise, a cross-cutting challenge among these systems is the sustainability and resilience of the global supply chain of critical minerals to enable this adoption of electric vehicles. | Yiyang Li; Maria R. Lukatskaya | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663f359491aefa6ce1b7e829/original/materials-challenges-for-electric-vehicles.pdf |
6489e7c1e64f843f41c885a7 | 10.26434/chemrxiv-2023-lwkdd | A Review on Photocatalytic CO2 Reduction using Nanomaterial | Photocatalytic CO2 reduction using nanomaterials has emerged as a promising approach for addressing the global challenge of carbon dioxide (CO2) emissions. This abstract provides an overview of recent advancements and key findings in the field of photocatalytic CO2 reduction using nanomaterials. Various nanomaterials, such as quantum dots, metal oxides, graphitic carbon nitride (g-C3N4), and semiconductors, have been investigated for their photocatalytic activity towards CO2 reduction. These nanomaterials possess unique properties such as high surface area, short charge transfer pathways, and tunable band gaps, enabling efficient absorption of solar energy and generation of electron-hole pairs. However, challenges such as charge carrier recombination, low surface area, and low electrical conductivity hinder the photocatalytic activity of some nanomaterials. To overcome these limitations, modifications and doping strategies have been employed to enhance their photocatalytic performance. These modifications include surface functionalization, co-catalyst deposition, and incorporation of carbon-based materials. Size-dependent effects have been observed, where nanoparticles of optimal sizes exhibit enhanced photocatalytic activity. Furthermore, the choice of solvent and reaction conditions plays a crucial role in achieving high selectivity and efficiency in CO2 reduction. Selective reduction products, including methane (CH4), methanol (CH3OH), formaldehyde (HCHO), and formic acid (HCOOH), can be obtained depending on the catalyst and reaction conditions. | Rezoanul Islam ; Md Akteruzzaman; MD MOTIUR R. Mazumder | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6489e7c1e64f843f41c885a7/original/a-review-on-photocatalytic-co2-reduction-using-nanomaterial.pdf |
6463efaaa32ceeff2dc1fefb | 10.26434/chemrxiv-2023-gfh8l | Modular Chemoenzymatic Synthesis of Ten Fusicoccane Diterpenoids | Fusicoccane diterpenoids display intriguing biological activities, including the ability to act as molecular glue modulators of 14-3-3 protein–protein interaction. However, their innate structural complexity and diverse oxygenation patterns present enormous synthetic challenges. Here, a modular chemoenzymatic approach to this natural product family that combines de novo skeletal construction and late-stage hybrid C–H oxidations is presented. A convergent fragment coupling strategy allowed rapid access to a key tricyclic intermediate, which was subjected to chemical and enzymatic C–H oxidations to modularly prepare five oxidized family members. Complementarily, a biomimetic skeletal remodeling was conceived to render five rearranged fusicoccanes with unusual bridgehead double bonds synthetically accessible for the first time. | Yanlong Jiang; Hans Renata | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6463efaaa32ceeff2dc1fefb/original/modular-chemoenzymatic-synthesis-of-ten-fusicoccane-diterpenoids.pdf |
652f1ae58bab5d2055910d52 | 10.26434/chemrxiv-2023-2dnhh | Evaluating mass spectrometry based hydroxyl radical protein foot-printing of a benchtop Flash oxidation system against a synchrotron X-ray beamline. | Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation and mass spectrometry is a well-validated structural biology method that is providing critical insights into macromolecular dynamics. Numerous alternative sources for HRPF such as laser photolysis and plasma irradiation complement synchrotron-based HRPF. A recently developed commercially available instrument based on flash lamp photolysis, the Fox® system, enables access to laboratory benchtop HRPF. Here, we evaluate the feasibility of standardizing HRPF experiments in-house with a benchtop Fox® instrument as a precursor to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase enzyme (LOx) as a model system, we carried out hydroxyl radical (•OH) labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed with high glucose concentrations to mimic highly scavenging conditions in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the Fox® and XFP HRPF methods was compared, and we found that tuning •OH dosage enabled an optimum labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of Fox® and XFP labeling approaches, showing that benchtop instruments such as Fox® photolysis system can increase throughput and accessibility of HRPF technology. | Rohit Jain; Nanak S. Dhillon; Kanchustambham Vijayalakshmi; David T. Lodowski; Erik R. Farquhar; Janna Kiselar; Mark R. Chance | Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652f1ae58bab5d2055910d52/original/evaluating-mass-spectrometry-based-hydroxyl-radical-protein-foot-printing-of-a-benchtop-flash-oxidation-system-against-a-synchrotron-x-ray-beamline.pdf |
66ae5c01c9c6a5c07aeed492 | 10.26434/chemrxiv-2024-zgffb | Enantioselective Dearomatizing Formal (3+3) Cycloadditions of Bicyclobutanes with Aromatic Azomethine Imines: Access to Fused 2,3-Diazabicyclo[3.1.1]heptanes | Although cycloadditions of bicyclobutanes (BCBs) have emerged as a reliable approach for producing bicyclo[n.1.1]alkanes such as azabicyclo[3.1.1]heptanes (aza-BCHeps), serving as saturated bioisosteres of arenes, the catalytic asymmetric variant remains underdeveloped and presents challenges. Herein, we developed several Lewis acid-catalyzed systems for the challenging dearomatizing (3+3) cycloaddition of BCBs and aromatic azomethine imines. This resulted in fused 2,3-diazabicyclo[3.1.1]heptanes, introducing a novel chemical space for the caged hydrocarbons. Moreover, an asymmetric Lewis acid catalysis strategy was devised for the (3+3) cycloadditions of BCBs and N-iminoisoquinolinium ylides, forming chiral diaza-BCHeps with up to 99% yield and 97% ee. This work represents the first successful demonstration of asymmetric (3+3) cycloaddition by introducing a chiral environment through the activation of BCBs. | Xue-Chun Yang; Feng Wu; Wen-Biao Wu; Xu Zhang; Jian-Jun Feng | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ae5c01c9c6a5c07aeed492/original/enantioselective-dearomatizing-formal-3-3-cycloadditions-of-bicyclobutanes-with-aromatic-azomethine-imines-access-to-fused-2-3-diazabicyclo-3-1-1-heptanes.pdf |
60c741e8f96a00773f2864f2 | 10.26434/chemrxiv.8156741.v1 | Unusual Rearrangement of Modified PNP Ligand based Ru Complexes Relevant to Alcohol Dehydrogenation Catalysis | We report the synthesis of
‘hangman-type’ PNP pincer ligands and their associated Ru complexes. Upon
deprotonation, the complexes undergo sp<sup>2</sup>-sp<sup>3</sup> C-C bond
cleavage and subsequent C-C formation processes to form a new, one carbon unit longer
backbone motif. Unlike the starting geometry, the products are completely
inactive in alcohol dehydrogenation catalysis. DFT and mechanistic studies
suggest an intramolecular isomerization process via a spyrocycle cyclopropane
intermediate, dependent upon arm pyridine coordination and ligand sterics. | Shubham Deolka; Naziha Tarannam; Robert R. Fayzullin; sebastian kozuch; Eugene Khaskin | Bond Activation; Catalysis; Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e8f96a00773f2864f2/original/unusual-rearrangement-of-modified-pnp-ligand-based-ru-complexes-relevant-to-alcohol-dehydrogenation-catalysis.pdf |
60c7584d0f50db52633983f9 | 10.26434/chemrxiv.14534388.v1 | Proofreading Experimentally Assigned Stereochemistry Through Q2MM Predictions in Pd-Catalyzed Allylic Aminations | We present a modelling method which can predict the enantioselectivity of Pd-catalyzed allylic amination with P,N-ligands. The Q2MM method employed here is accurate enough to identify errors in enantiomer assignment from literature data. | Jessica Wahlers; Jèssica Margalef; Eric Hansen; Armita Bayesteh; Paul Helquist; Montserrat Diéguez; Oscar Pàmies; Olaf Wiest; Per-Ola Norrby | Organic Synthesis and Reactions; Computational Chemistry and Modeling; Homogeneous Catalysis; Catalysis; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7584d0f50db52633983f9/original/proofreading-experimentally-assigned-stereochemistry-through-q2mm-predictions-in-pd-catalyzed-allylic-aminations.pdf |
6345c0f91f323d61d7567624 | 10.26434/chemrxiv-2022-ntd3r | MELLODDY: cross pharma federated learning at unprecedented scale unlocks benefits in QSAR without compromising proprietary information | Federated multi-partner machine learning can be an appealing and efficient method to increase the effective training data volume and thereby the predictivity of models, particularly when the generation of training data is resource intensive. In the landmark MELLODDY project, each of ten pharmaceutical companies realized aggregated improvements on its own classification and/or regression models through federated learning. To this end, they leveraged a novel implementation extending multi-task learning across partners, on a platform audited for privacy and security. The experiments involved an unprecedented cross-pharma dataset of 2.6+ billion confidential experimental activity data points, documenting 21+ million physical small molecules and 40+ thousand assays in on-target and secondary pharmacodynamics and pharmacokinetics. Appropriate complementary metrics were developed to evaluate predictive performance in the federated setting. In addition to predictive performance increases in labeled space, the results point towards an extended applicability domain in federated learning. Increases in collective training data volume, including by means of auxiliary data resulting from single concentration high-throughput and imaging assays, continued to boost predictive performances, albeit with saturating return. Markedly higher improvements were observed for pharmacokinetics and safety panel assay-based task subsets. | Wouter Heyndrickx; Lewis Mervin; Tobias Morawietz; Noé Sturm; Lukas Friedrich; Adam Zalewski; Anastasia Pentina; Lina Humbeck; Martijn Oldenhof; Ritsuya Niwayama; Peter Schmidtke; Nikolas Fechner; Jaak Simm; Adam Arany; Nicolas Drizard; Rama Jabal; Arina Afanasyeva; Regis Loeb; Shlok Verma; Simon Harnqvist; Matthew Holmes; Balasz Pejo; Maria Telenczuk; Nicholas Holway; Arne Dieckmann; Nicola Rieke; Friederike Zumsande; Djork-Arné Clevert; Michael Krug; Christopher Luscombe; Darren Green; Peter Ertl; Peter Antal; David Marcus; Nicolas Do Huu; Hideyoshi Fuji; Stephen Pickett; Gergely Acs; Eric Boniface; Bernd Beck; Yax Sun; Arnaud Gohier; Friedrich Rippmann; Ola Engkvist; Andreas H. Göller; Yves Moreau; Mathieu N. Galtier; Ansgar Schuffenhauer; Hugo Ceulemans | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6345c0f91f323d61d7567624/original/melloddy-cross-pharma-federated-learning-at-unprecedented-scale-unlocks-benefits-in-qsar-without-compromising-proprietary-information.pdf |
666ddcf201103d79c54c4750 | 10.26434/chemrxiv-2024-c9qmw | Demystifying hydridic hydrogen bonds using energy decomposition analysis | We investigate hydridic hydrogen bonds formed by trimethylsilane (Me3SiH), where the Si atom is more electropositive than the donor hydrogen, using energy decomposition analysis methods. The primary contributions to binding, orbital interactions involved, and origins of the redshift in Si−H stretching frequency are identified and contrasted with the scenario of conventional protonic hydrogen bonds. | David W. Roberts; Yuezhi Mao | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666ddcf201103d79c54c4750/original/demystifying-hydridic-hydrogen-bonds-using-energy-decomposition-analysis.pdf |
67d01d9281d2151a02fcbb41 | 10.26434/chemrxiv-2025-0qvxs | Structural Insights into the Catalytic Mechanism of cis-Eunicellane Cyclase AriE | Eunicellane diterpenoids, with over 360 known examples characterized by a cis- or trans-6/10-bicyclic carbon skeleton, exhibit diverse biological activities. To date, four eunicellane cyclases (ECs) have been reported: cis-ECs (Bnd4 and EcTPS1) and trans-ECs (AlbS and MicA), yet the structural basis and molecular mechanisms governing their distinct cis- or trans-cyclization modes remain unsolved. Here, we present the crystal structure of a cis-EC AriE from Amycolatopsis arida, which catalyzes geranylgeranyl diphosphate into cis-6/10-fused bicyclic benditerpe-2,6,15-triene (1) in aridacin biosynthesis. Through surface entropy reduction, we obtained the 1.87 Å resolution structure of AriED128A. Structure-guided mutagenesis identified W73 as a key regulatory hotspot controlling product diversity, with its variants generating diverse diterpene products. L96V specifically produced 1, while Y203A converted AriE into a highly specific (–)-(R)-cembrene A synthase. Our findings provide the first structural insights into this type of terpene synthase and demonstrate the feasibility of engineering EC variants for selective product formation. | Fang-Ru Li; Qian Yang; Jingyi He; Xinru Sun; Xingming Pan; Hui-Min Xu; Jeffrey D. Rudolf; Liao-Bin Dong | Biological and Medicinal Chemistry; Biochemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d01d9281d2151a02fcbb41/original/structural-insights-into-the-catalytic-mechanism-of-cis-eunicellane-cyclase-ari-e.pdf |
66f93f00cec5d6c142948809 | 10.26434/chemrxiv-2024-3k21g-v2 | Formation of H2O2 in Near-Neutral Zn-air Batteries Enables Efficient Oxygen Evolution Reaction | Rechargeable Zn-air batteries with near-neutral electrolytes hold promise as cheap, safe and sustainable devices, but they suffer from slow charge kinetics and remain poorly studied. Here we reveal a charge storage mechanism of near-neutral Zn-air batteries that is mediated by H2O2 formation upon cell discharge and its oxidation upon charge. The manifestation of this mechanism strongly depends on the electrolyte composition and positive electrode material, being pronounced when ZnSO4 solutions and carbon nanotubes are employed. Oxidation of dissolved H2O2 is facile, enabling oxygen evolution reaction (OER) at low potentials (~1.5 V vs. Zn2+/Zn) which, in contrast to conventional four-electron OER, does not induce corrosion of carbon electrodes. Facilitation of the H2O2-mediated pathway might therefore be helpful for developing high-performance near-neutral Zn-air batteries. | Roman Kapaev; Nicole Leifer; Alagar Raja Kottaichamy; Amit Ohayon; Langyuan Wu; Menny Shalom; Malachi Noked | Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f93f00cec5d6c142948809/original/formation-of-h2o2-in-near-neutral-zn-air-batteries-enables-efficient-oxygen-evolution-reaction.pdf |
660e74ec418a5379b00adef0 | 10.26434/chemrxiv-2024-prlhb-v2 | Ratiometric Near Infrared Fluorescence Imaging of Dopamine with 1D and 2D nanomaterials | Neurotransmitters are released by neuronal cells to exchange information. Resolving their spatiotemporal patterns is crucial to understand chemical neurotransmission. Here, we present a ratiometric sensor for the neurotransmitter dopamine that combines Egyptian Blue (CaCuSi4O10) nanosheets (EB-NS) and single-walled carbon nanotubes (SWCNTs). They both fluoresce in near infrared (NIR), which is beneficial due to ultra-low background and phototoxicity. (GT)10-DNA functionalized monochiral (6,5)-SWCNTs increase their fluorescence (1000 nm) in response to dopamine, while EB-NS serves as stable reference (936 nm). A robust ratiometric imaging scheme is implemented by directing these signals on two different NIR sensitive cameras. Additionally, we demonstrate stability against mechanical perturbations and image dopamine release from differentiated dopaminergic Neuro 2a cells. Therefore, this technique enables robust ratiometric and non-invasive imaging of cellular responses. | Bjoern F. Hill; Jennifer M. Mohr; Isabelle K. Sandvoss; Juliana Gretz; Phillip Galonska; Lena Schnitzler; Luise Erpenbeck; Sebastian Kruss | Physical Chemistry; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e74ec418a5379b00adef0/original/ratiometric-near-infrared-fluorescence-imaging-of-dopamine-with-1d-and-2d-nanomaterials.pdf |
65bccca1e9ebbb4db9825591 | 10.26434/chemrxiv-2024-b9dk0 | Organocatalytic silicon-free SuFEx click reactions of SO2F2 | An organocatalytic method for silicon-free SuEEx click reaction of SO2F2 is described. Different organic bases such as DBU, TBD, triethylamine and Hünig’s base can efficiently catalyze the SuFEx of SO2F2 with various phenols to produce aryl fluorosulfates in 61-97% yields. Under the same conditions, pyridone, pyrazolone and secondary amines can also react with SO2F2 to afford the corresponding heteroaryl fluorosulfates or sulfamoyl fluorides in good yields. In this process, molecular sieves absorb the acidic HF efficiently, which avoid the using of stoichiometric amount of silicon reagents and excess of bases. | Yu Xie; Muze Lin; Zhihang Wei; Zhihua Cai; Lin He; Guangfen Du | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bccca1e9ebbb4db9825591/original/organocatalytic-silicon-free-su-f-ex-click-reactions-of-so2f2.pdf |
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