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65ec5d199138d23161161b2c | 10.26434/chemrxiv-2024-chjqg | Design and synthesis of dinuclear bismuth(III) complexes with potent ribonuclease-like activity | Several metal complexes with ribonuclease-like activity have been developed as chemical biology tools for RNA regulation. However, their RNA-cleavage activity is insufficient under physiological conditions. Here, we have identified novel dinuclear bismuth(III) complexes that contain dipyridine/dipicolinate-based ligands as artificial ribonucleases to induce efficient RNA cleavage. Our optimization studies of the ligand structure indicated that the dipyridine/dipicolinate scaffold of the ligands plays a key role in maintaining the dinuclear arrangement of the bismuth(III) centers and tuning the Lewis acidity of the bismuth(III) ions to achieve potent RNA-cleavage activity. The mechanistic analysis of the RNA-cleavage reaction suggested that cooperative activation of a phosphate group in RNAs and water molecules coordinated by two bismuth(III) centers results in a rapid nucleophilic attack of the 2′-hydroxy group of a ribose to the phosphate and facilitates the removal of a 5′-alkoxide by protonation to generate a 2′,3′-cyclic phosphate and a 5′-hydroxy product. Thus, the developed dinuclear bismuth(III) complexes represent promising tools for chemical biology studies. | Yutaro Hanatani; Takashi Kurohara; Yasunobu Yamashita; Sacha Marynberg; Yuri Takada; Yukihiro Itoh; Takayoshi Suzuki | Biological and Medicinal Chemistry; Catalysis; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ec5d199138d23161161b2c/original/design-and-synthesis-of-dinuclear-bismuth-iii-complexes-with-potent-ribonuclease-like-activity.pdf |
667f154c5101a2ffa8d09a20 | 10.26434/chemrxiv-2024-srxfv | NQO1-responsive Prodrug for in Cellulo Release of Cytochalasin B as Cancer Cell-targeted Migrastatic | Migrastatic drugs targeting cell motility and thereby suppress invasiveness of solid cancer cells, including their ability to metastasize and establish secondary tumors, are of high interest and have the potential to bring about a paradigm shift in the treatment of solid cancer. Cytochalasans, such as cytochalasin B, are known to disrupt cytoskeletal dynamics by inhibiting actin polymerization and have attracted considerable attention as potential migrastatics over the last decades, but are limited by selectivity issues so far. We herein report on the design, synthesis and evaluation of a bioresponsive prodrug BQTML-CB cleavable by the quinone-oxidoreductase NQO1, discussed as therapeutic target for the treatment of cancer. | Mervic D. Kagho; Katharina Schmidt; Christopher Lambert; Lili Jia; Klemens Rottner; Marc Stadler; Theresia Stradal; Philipp Klahn | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667f154c5101a2ffa8d09a20/original/nqo1-responsive-prodrug-for-in-cellulo-release-of-cytochalasin-b-as-cancer-cell-targeted-migrastatic.pdf |
66870100c9c6a5c07a4df229 | 10.26434/chemrxiv-2024-r21dm | Boosting Synergistic Effects Between PtGe Nanoalloys and 2D Materials for PEMFC Applications | In the present work we have investigated the stability, CO poisoning tendency and HOR and ORR activities of small-sized monometallic Pt and bimetallic PtGe nanoclusters deposited on a series of 2D supports. By means of global minima search and mechanistic studies at the density functional theory (DFT) level, a screening of size, composition and support material has been carried out to obtain the optimal catalyst compositions that will boost the catalytic performance. Alloying and support effects work in two directions. On the one hand, the support increases the stability and modifies the electronic structure of the cluster via metal-support interaction. On the other hand, the cluster can change the electronic properties and catalytic activity of the support, which can be modulated with its size and composition. In addition, the 2D support assists pure Pt clusters in reducing the propensity to undergo CO poisoning, which can be further reduced by Ge alloying. This effect can be exploited to the point that the interaction with CO is not even favorable, as in Pt5Ge5/germanene, thus completely inhibiting the CO poisoning on the catalyst. Regarding the catalytic activities, all the catalysts studied in this work yield too high overpotentials for the ORR in acidic conditions, due to the presence of too oxophilic active sites which results in the overbinding of oxygenated species. However, the combination of Ge alloying and 2D support yield remarkable results in the HOR performance. The simultaneous tailoring of catalyst composition and support is demonstrated to be an effective strategy to successfully adjust the catalytic properties. | Andoni Ugartemendia; Ramón M. Bergua; Jose M. Mercero; Elisa Jimenez-Izal | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66870100c9c6a5c07a4df229/original/boosting-synergistic-effects-between-pt-ge-nanoalloys-and-2d-materials-for-pemfc-applications.pdf |
60c7442b842e657dcbdb23c4 | 10.26434/chemrxiv.8085143.v3 | Macrocycles of Higher ortho-Phenylenes: Assembly and Folding | <p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p> | Zacharias Kinney; Viraj Kirinda; Scott Hartley | Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7442b842e657dcbdb23c4/original/macrocycles-of-higher-ortho-phenylenes-assembly-and-folding.pdf |
60c747ce337d6cb87fe27406 | 10.26434/chemrxiv.11799096.v1 | H–Abstraction from Dimethyl Sulfide in the Presence of an Excess of Hydroxyl Radicals. A Quantum Chemical Evaluation of Thermochemical and Kinetic Parameters Unveil an Alternative Pathway to Dimethyl Sulfoxide. | <div> Elucidation of the oxidation mechanism of naturally emitted reduced sulfur compounds, especially dimethyl sulfide, plays a central role in understanding background acid precipitation in the natural environment. Most frequently, theoretical studies of the addition and H-elimination reactions of dimethyl sulfide with hydroxyl radicals are studied considering the presence of oxygen that further reacts with the radicals formed in the initial steps. Although the reaction of intermediate species with additional hydroxyl radicals has been considered as part of the global mechanism of oxidation, few if any attention has been dedicated to the possibility of reactions of the initial radicals with a second •OH molecule. In this work we performed a computational study using quantum-chemical methods, of the mechanism of H-abstraction from dimethyl sulfide under normal atmospheric conditions and in reaction chambers at different O2 partial pressure, including complete absence of oxygen. Additionally, important rate coefficients were computed using canonical and variational transition state theory. The rate coefficient for abstraction affords a 4.72 x 10-12 cm3 molecule1 s-1 value, very close to the most recent experimental one (4.13 x 10-12 cm3 molecule-1 s-1). According to our best results, the initial methyl thiomethyl radical was obtained at -25.2 kcal/mol (experimentally -22.4 kcal/mol), and four important paths were identified on the potential energy surface. From the interplay of thermochemical and kinetic arguments, it was possible to demonstrate that the preferred product of the reaction of dimethyl sulfide with two hydroxyl radicals, is actually dimethyl sulfoxide. </div><div> </div> | Zoi Salta; Jacopo Lupi; Vincenzo Barone; Oscar Ventura | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747ce337d6cb87fe27406/original/h-abstraction-from-dimethyl-sulfide-in-the-presence-of-an-excess-of-hydroxyl-radicals-a-quantum-chemical-evaluation-of-thermochemical-and-kinetic-parameters-unveil-an-alternative-pathway-to-dimethyl-sulfoxide.pdf |
60c744ba702a9b2d8618a8be | 10.26434/chemrxiv.9899675.v1 | Visualizing Solid-State Molecular Motion by a Common Structural Determination Technique | Solid-state molecular
motion plays a vital role in many advanced technologies. However, visualization
of these processes is still challenging due to the limitation of characterization
method. In this work, a common structural determination technique, single-crystal
X-ray diffraction, is applied to “see” the static and dynamic molecular motions
in tetraphenylethylene (TPE) which exhibits aggregation-induce emission (AIE)
effect. Five kinds of motions, stretching, torsion, twisting, rocking, and wagging
are observed and analyzed. As the static molecular motions, the middle double
bond in TPE becomes short and twisted and the peripheral phenyl rings as a
whole tend to be more twisted with the raising of testing temperature (150 to
298 K). Meanwhile, dynamic motions of phenyl-rings rocking and wagging are
found to be more and more vigorous along with the increase of temperature. This
work provides a platform for visualizing solid-state molecular motion based on
a common technique. It also affords direct evidence for the AIE mechanism of
restriction of intramolecular motions. | Jun Zhang; Haoke Zhang; Junkai Liu; Jacky W. Y. Lam; Ben Zhong Tang | Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744ba702a9b2d8618a8be/original/visualizing-solid-state-molecular-motion-by-a-common-structural-determination-technique.pdf |
645c406ea32ceeff2d6f4d9a | 10.26434/chemrxiv-2023-5m85h | A general photocatalytic strategy for nucleophilic amination of primary and secondary benzylic C–H bonds | We report a visible-light photoredox-catalyzed method that enables nucleophilic amination of primary and secondary
benzylic C(sp3)–H bonds. A novel amidyl radical precursor and organic photocatalyst operate in tandem to transform primary and secondary benzylic C(sp3)–H bonds into carbocations via sequential hydrogen atom transfer (HAT) and oxidative radical-polar crossover (ORPC). The resulting carbocation can be intercepted by a variety of N centered nucleophiles, including nitriles (Ritter reaction), amides, carbamates, sulfonamides, and azoles for the construction of pharmaceutically-relevant C(sp3)–N bonds under unified reaction conditions. Mechanistic studies indicate that HAT is amidyl radical-mediated and that the photocatalyst operates via a reductive quenching pathway. These findings establish a mild, metal-free, and modular protocol for the rapid diversification of C(sp3)–H bonds to a library of aminated products. | Madeline Ruos; R. Garrison Kinney; Oliver Ring; Abigail Doyle | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645c406ea32ceeff2d6f4d9a/original/a-general-photocatalytic-strategy-for-nucleophilic-amination-of-primary-and-secondary-benzylic-c-h-bonds.pdf |
60e90d48af9cdb8c3eda5a73 | 10.26434/chemrxiv-2021-tk6rt-v2 | An Integrative Resource for Network-Based Investigation of COVID-19 Combinatorial Drug Repositioning and Mechanism of Action | An effective monotherapy to target the complex and multifactorial pathology of SARS-CoV-2 infection poses a challenge to drug repositioning, which can be improved by combination therapy. We developed an online network pharmacology-based drug repositioning platform, COVID-CDR (http://vafaeelab.com/COVID19repositioning.html), that enables a visual and quantitative investigation of the interplay between the drug primary targets and the SARS-CoV-2–host interactome in the human protein-protein interaction network. COVID-CDR prioritizes drug combinations with the potential to act synergistically through different, yet potentially complementary pathways. It provides the options for understanding multi-evidence drug-pair similarity scores along with several other relevant information on individual drugs or drug pairs. Overall, COVID-CDR is the first-of-its-kind online platform that provides a systematic approach for pre-clinical in silico investigation of combination therapies for treating COVID-19 at the fingertips of the clinicians and researchers. | A K M Azad; Shadma Fatima; Alexander Capraro; Shafagh A. Waters; Fatemeh Vafaee | Biological and Medicinal Chemistry; Analytical Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e90d48af9cdb8c3eda5a73/original/an-integrative-resource-for-network-based-investigation-of-covid-19-combinatorial-drug-repositioning-and-mechanism-of-action.pdf |
60c73e3bee301c57d2c786ca | 10.26434/chemrxiv.6233393.v2 | Antimicrobial Chitosan-G-poly(AMPS-Co-AA-Co-AM)/Ground Basalt Composite Hydrogel: Synthesis and Characterization | This paper presents for the first time the introduction of ground basalt into the network of a chitosan based hydrogel and the enhancement of the bactericidal activity of<br /> the hydrogel.<br /> | Majd said; yomen atassi; Mohammad Tally; Maissa Kattan; Lamia Kouba | Biopolymers; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e3bee301c57d2c786ca/original/antimicrobial-chitosan-g-poly-amps-co-aa-co-am-ground-basalt-composite-hydrogel-synthesis-and-characterization.pdf |
60f0b8a21053174f5340c8fc | 10.26434/chemrxiv-2021-pjr3l-v2 | MB-Fit: Software Infrastructure for Data-Driven Many-Body Potential Energy Functions | Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions, from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the auto- mated development of MB-PEFs for generic molecules within the TTM-nrg (“Thole-type model energy”) and MB-nrg (“many-body energy”) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy/force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, we believe that MB-Fit will enable routine, predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.
| Ethan Bull-Vulpe; Marc Riera; Andreas Goetz; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f0b8a21053174f5340c8fc/original/mb-fit-software-infrastructure-for-data-driven-many-body-potential-energy-functions.pdf |
62d572c74e76bf7ac794808a | 10.26434/chemrxiv-2022-97gp2 | Structure elucidation, biosynthesis, total synthesis and antibacterial in-vivo efficacy of myxobacterial Corramycin | Herein, we describe the myxobacterial natural product Corramycin (1) isolated from Corallococcus coralloides (C. coralloides). Corramycin is a linear peptide containing an unprecedented (2R,3S) N-methyl-β-hydroxy histidine moiety and exhibiting anti-Gram-negative activity against Escherichia coli. Moreover, we describe the Corramycin biosynthetic gene cluster (BGC) and propose a biosynthesis model involving a 12-modular non-ribosomal peptide synthetase (NRPS)/polyketide synthase (PKS). Bioinformatic analysis of the BGC combined with the development of a total synthesis route allowed for the elucidation of the molecule’s absolute configuration. Furthermore, we show that the uptake of Corramycin in E. coli depends on two transporter systems, SbmA and YejABEF. Importantly, intravenous administration of 30 mg kg 1 of Corramycin in an E. coli mouse infection model resulted in significantly reduced colony forming units (CFU) and in 60 % survival of animals, with no toxic effects observed in vitro or in vivo. Corramycin is thus an intriguing innovative starting point to develop a potent antibacterial drug against hospital acquired infections. | Cédric Couturier; Sebastian Groß; Alexander von Tesmar; Judith Hoffmann; Selina Deckarm; Anouchka Fievet; Nelly Dubarry; Thomas Taillier; Christoph Pöverlein; Heike Stump; Michael Kurz; Luigi Toti; Sabine Haag Richter; Dietmar Schummer; Philippe Sizun; Michael Hoffmann; Ram Prasad Awal; Nestor Zaburannyi; Kirsten Harmrolfs; Joachim Wink; Emilie Lessoud; Thierry Vermat; Veronique Cazals; Sandra Silve; Armin Bauer; Michael Mourez; Laurent Fraisse; Corinne Leroi-Geissler; Astrid Rey; Stéphanie Versluys; Eric Bacqué; Rolf Müller; Stephane Renard | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d572c74e76bf7ac794808a/original/structure-elucidation-biosynthesis-total-synthesis-and-antibacterial-in-vivo-efficacy-of-myxobacterial-corramycin.pdf |
64a516a89ea64cc167760139 | 10.26434/chemrxiv-2023-625fl | Ortho O-Annulated AzaBenzannulated PeryleneDiimide and BisAzaCoroneneDiimide | The development of new n-type organic semiconductors is crucial to the development of organic electronics. The introduction of heteroatoms into electron-acceptor units enables their properties to be fine-tuned and new applications to emerge. In this study, we present the preparation of BisAzaCoroneneDiimide derivatives annulated by the insertion of oxygen in their ortho position. These compounds exhibit high planarity and their properties are sensitive to the extension of their π-system. Their performance in preliminary organic electronics studies is also reported. | Arthur H. G. David; Daryna Shymon; Hayley Melville; Lou-Ann Accou; Adèle Gapin; Magali Allain; Olivier Alévêque; Maximilien Force; Alexis Grosjean; Pietrick Hudhomme; Laura Le Bras; Antoine Goujon | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a516a89ea64cc167760139/original/ortho-o-annulated-aza-benzannulated-perylene-diimide-and-bis-aza-coronene-diimide.pdf |
670c523351558a15eff8ead0 | 10.26434/chemrxiv-2024-3rp1x | Thermochemical Heterolytic Hydrogenation Catalysis Proceeds Through Polarization-Driven Hydride Transfer | Heterolytic hydrogenations, which split H2 across a hydride acceptor and proton acceptor, are a key class of reactions that span the chemical value chain, including CO2 hydrogenation to formate and NADH regeneration from NAD+. The dominant mechanistic models for heterogeneous catalysis of these reactions invoke classical surface mechanisms that ignore the role of interfacial charge separation. Herein, we quantify the electrochemical potential of the catalyst during turnover and uncover evidence supporting an interfacial electrochemical hydride transfer mechanism for this overall thermochemical reaction class. We find that the proton acceptor induces spontaneous electrochemical polarization of the metal catalyst surface, thereby controlling the thermodynamic hydricity of the surface M–H intermediates and driving rate-determining electrochemical hydride transfer to the hydride acceptor substrate. Overall, this model invokes that heterolytic hydrogenations proceed via the coupling of two electrochemical half-reactions, the hydrogen reduction reaction (HRR) and hydrogen oxidation reaction (HOR), which convert H2 to hydride and proton, respectively. This mechanistic framework, which applies across diverse reaction media and for the hydrogenation of CO2 to formate and NAD+ to NADH, enables the determination of intrinsic reaction kinetics and exposes design principles for the future development of sustainable hydrogenation reactivity. | Hai-Xu Wang; Yogesh Surendranath | Inorganic Chemistry; Catalysis; Electrochemistry; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c523351558a15eff8ead0/original/thermochemical-heterolytic-hydrogenation-catalysis-proceeds-through-polarization-driven-hydride-transfer.pdf |
60c751a9f96a00e81a28806d | 10.26434/chemrxiv.13138751.v1 | Collaborative Profile-QSAR: A Natural Platform for Building Collaborative Models Among Competing Companies | Article describing collaborative modeling between competitor companies by sharing single-task models and incorporating them into stacked multi-task Profile-QSAR models, without sharing chemical structures, activity data or biological targets. Data are ~20 million pIC50s from ~12,000 Novartis internal dose-response assays tested on a total of ~1.9 million compounds. They were divided into pseudo-companies based on the several companies that historically merged to form Novartis. | Eric Martin; Xiangwei Zhu | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751a9f96a00e81a28806d/original/collaborative-profile-qsar-a-natural-platform-for-building-collaborative-models-among-competing-companies.pdf |
60c7420b842e65af08db1fc2 | 10.26434/chemrxiv.8206247.v1 | A Strategy for Thioamide Incorporation During Fmoc Solid-Phase Peptide Synthesis with Robust Stereochemical Integrity | We describe a method to protect the sensitive stereochemistry of the thioamide—in analogy to the protection of the functional groups of amino acid side chains—in order to preserve the thioamide moiety during peptide elongation.<br /> | luis camacho III; Bryan J. Lampkin; Brett VanVeller | Stereochemistry; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7420b842e65af08db1fc2/original/a-strategy-for-thioamide-incorporation-during-fmoc-solid-phase-peptide-synthesis-with-robust-stereochemical-integrity.pdf |
6660325921291e5d1d1e2005 | 10.26434/chemrxiv-2024-mm5qz | Water-templated growth of interfacial superglue polymers for tunable thin films and in-situ fluid encapsulation | Thin polymer films are indispensable elements in numerous technologies ranging from liquid encapsulation to biotechnology to electronics. However, their production typically relies on wet chemistry involving organic solvents or chemical vapor deposition, necessitating elaborate equipment and often harsh conditions. Here, we demonstrate the eco-friendly, fast, and facile synthesis of water-templated interfacial polymers based on cyanoacrylates (superglues) that yield thin films with tailored properties. Specifically, by exposing a cationic surfactant-laden water surface to cyanoacrylate vapors, surfactant-modulated anionic polymerization produces a manipulable thin polymer film with a thickness growth rate of 8 nm/min. Furthermore, the shape and color of the film are precisely controlled by the polymerization kinetics, wetting conditions, and/or exposure to patterned light. Using various interfaces as templates for film growth, including the free surface of drops and soap bubbles, the developed method advantageously enables in-situ packaging of chemical and biological cargos in liquid phase as well as the encapsulation of gases within solidified bubbles. Simple, versatile, and biocompatible, this technology constitutes a potent platform for programmable coating and soft/smart encapsulation of fluids. | Jampani VSR; Miha Skarabot; Urban Mur; Damien Baigl; Ulrich Jonas; Jan Lagerwall; Miha Ravnik; Manos Anyfantakis | Materials Science; Polymer Science; Nanoscience; Surfactants; Thin Films; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6660325921291e5d1d1e2005/original/water-templated-growth-of-interfacial-superglue-polymers-for-tunable-thin-films-and-in-situ-fluid-encapsulation.pdf |
60c756e1842e65d1d2db459d | 10.26434/chemrxiv.14338907.v1 | Record High Magnetic Anisotropy in Three Coordinate MnIII and CrII Complexes: A Theoretical Perspective | <p><i>Ab
initio</i> calculations performed in two
three-coordinate complexes [Mn{N(SiMe<sub>3</sub>)<sub>2</sub>}<sub>3</sub>]
(1) and [K(18-crown-6)(Et<sub>2</sub>O)<sub>2</sub>][Cr{N(SiMe<sub>3</sub>)<sub>2</sub>}<sub>3</sub>]
(2) reveal record-high magnetic anisotropy with the <i>D</i> values -64 cm<sup>-1</sup> and -15 cm<sup>-1</sup> respectively,
enlisting d<sup>4 </sup>ion back in the race for single-ion magnets. For the
first time, a detailed spin-vibrational analysis was performed in <b>1</b> and <b>2</b>
that suggest a dominant under barrier relaxation due to flexible coordination
sphere around the metal ion offering design clues for low coordinate transition
metal SIMs.<b> </b></p> | Arup Sarkar; Reshma Jose; Harshit Ghosh; Rajaraman Gopalan; Gopalan Rajaraman | Coordination Chemistry (Inorg.); Magnetism; Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e1842e65d1d2db459d/original/record-high-magnetic-anisotropy-in-three-coordinate-mn-iii-and-cr-ii-complexes-a-theoretical-perspective.pdf |
62558d745b90099a9a0bc0c1 | 10.26434/chemrxiv-2022-9fr99 | Expanding the PROTAC Toolbox: Targeted Degradation of the Deubiquitinase USP7 in Cancer | Targeting deubiquitinating enzymes (DUBs) has emerged as a promising therapeutic approach in several human cancers and other diseases. DUB inhibitors are exciting pharmacological tools but often exhibit limited cellular potency. Here we report PROTACs based on an ubiquitin-specific protease 7 (USP7) inhibitor scaffold to degrade USP7. The hit compound CST967 caused highly selective degradation of USP7 and inhibited proliferation of USP7-dependent cancer cells. We present the first DUB degrader, which will be a useful tool to deepen our understanding of USP7. | Arunima Murgai; Izidor Sosič; Martina Gobec; Patricia Lemnitzer; Matic Proj; Sophie Wittenburg; Michael Gütschow; Jan Krönke; Christian Steinebach | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62558d745b90099a9a0bc0c1/original/expanding-the-protac-toolbox-targeted-degradation-of-the-deubiquitinase-usp7-in-cancer.pdf |
60c74545842e652e97db25e3 | 10.26434/chemrxiv.9942680.v2 | Photophysical Investigation of 8-amino 2-Naphthol in Different Micellar Environment | *8-amino 2-naphthol (8A2NP) is an interesting molecule containing both proton acceptor (-NH<sub>2</sub>) and proton
donating (-OH) groups. Our earlier investigation on the
photophysics / photochemistry of 8A2NP reveals that its prototropic behavior is sensitive to the solvent polarity and pH. Interesting
photophysical properties of 8A2NP in homogeneous environment prompting towards the study of the said probe in in different surfactants<b>.</b> In the present work, 8A2NP has been studied in cationic (CTAB), anionic
(SDS) and non-ionic (TX-100) surfactants and changes in the excited state
deactivation are explored in the mentioned surfactants | Neetu Pandey; Richa Gahlaut; Pramod Pandey; Priyanka Arora; Kalpana Tiwari; Neeraj K. Joshi; Hem C. Joshi; Sanjay Pant | Dyes and Chromophores; Surfactants | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74545842e652e97db25e3/original/photophysical-investigation-of-8-amino-2-naphthol-in-different-micellar-environment.pdf |
60c75667469df4f59bf452e1 | 10.26434/chemrxiv.14237336.v1 | Prediction of Co and Ru Nanocluster Morphology on 2D MoS2 from Interaction Energies | Layered materials, such as \ce{MoS2}, have a wide range of potential applications due to the properties of a single layer which often differ from the bulk material. They are of particular interest as ultra-thin diffusion barriers in semi-conductor device interconnects and as supports for low dimensional metal catalysts. Understanding the interaction between metals and the \ce{MoS2} monolayer is of great importance when selecting systems for specific applications. In previous studies the focus has been largely on the strength of the interaction between a single atom or a nanoparticle of a range of metals, which has created a significant knowledge gap in understanding thin film nucleation on 2D materials. In this paper, we present a density functional theory (DFT) study of the adsorption of small Co and Ru structures, with up to four atoms, on a monolayer of \ce{MoS2}. We explore how the metal-substrate and metal-metal interactions contribute to the stability of metal clusters on \ce{MoS2}, and how these interactions change in the presence of a sulphur vacancy, to develop insight to allow prediction of thin film morphology. The strength of interaction between the metals and \ce{MoS2} is in the order Co > Ru. The competition between metal-substrate and metal-metal interaction allows us to conclude that 2D structures should be preferred for Co on \ce{MoS2}, while Ru prefers 3D structures on \ce{MoS2}. However, the presence of a sulphur vacancy decreases the metal-metal interaction, indicating that with controlled surface modification 2D Ru structures could be achieved. Based on this understanding, we propose Co on \ce{MoS2} as a suitable candidate for advanced interconnects, while Ru on \ce{MoS2} is more suited to catalysis applications. | Cara-Lena Nies; Michael Nolan | Catalysts; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75667469df4f59bf452e1/original/prediction-of-co-and-ru-nanocluster-morphology-on-2d-mo-s2-from-interaction-energies.pdf |
60c747459abda24993f8c8a2 | 10.26434/chemrxiv.11591973.v1 | Controlling the Morphology of Copper-Silica Nanocomposites from Laser Ablation in Liquid | <div>
<div>
<div>
<p>Synthesis of copper-silica nanocomposites with controllable morphology and
composition were produced with a one-step femtosecond reactive laser ablation
in liquid (fs-RLAL) technique. The composite nanomaterials were generated
by focusing femtosecond near-IR laser pulses onto a silicon wafer immersed in
an aqueous copper(II) nitrate solution, with the solution pH adjusted using nitric acid or potassium hydroxide. Under acidic conditions (pH 3.0 and 5.4),
little copper was incorporated in the predominantly silica product (1.4 and 1.5
wt.%). These acidic conditions yielded large ~30-80 nm silica particles, with
some particles consisting of copper core/silica shell. In contrast, increasing the
solution pH to 10.4 resulted in extremely high Cu loading of 31.5 wt.% and a
composite product consisting of 1.5 nm copper clusters distributed throughout a
matrix of amorphous silica and copper phyllosilicate. The relationship between
the precursor solution pH and the product morphology and copper loading is
attributed to the point of zero charge (PZC) of silica, in which the high solution
pH allows for electrostatic adsorption to occur between the deprotonated silica
clusters from the ablated silicon wafer and the copper hydroxide dimer formed
in solution.
</p>
</div>
</div>
</div> | Mallory John; Katharine Tibbetts | Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747459abda24993f8c8a2/original/controlling-the-morphology-of-copper-silica-nanocomposites-from-laser-ablation-in-liquid.pdf |
60c755ad9abda20ceef8e3f3 | 10.26434/chemrxiv.13660982.v3 | Large Scale Profiling of SARS-CoV-2-Infected Patients Identified Potential Therapeutic Host Targets and Drug Candidates for COVID-19 | Given the rapid spread of SARS-CoV-2 and rising death toll of COVID-19 in the current
absence of effective treatments, it is imperative that therapeutics are developed and made
available to patients as quickly as possible. Publicly available COVID-19 patient data can be used
to identify host therapeutic targets, tailoring treatments to the disease signatures observed in
patients. In this study, we identify potential host therapeutic targets based on gene expression
alterations observed in COVID-19 patients. We analyzed RNAseq data from airway samples of
COVID-19 patients and healthy controls to detect significantly differentially expressed genes and
pathways that present potential therapeutic targets. Our analysis revealed expression changes in
key genes involved in activation of immune pathways, as well as genes targeted by SARS-CoV2 to interfere with normal host cell functioning. Critical changes were observed in a number of
genes, including EIF2AK2, which was shown to play important roles in activating the interferon
response and interfering with host cell translational machinery in SARS-CoV-2 infection,
presenting a prospective therapeutic target. We also identified drugs with potential to modulate
multiple therapeutic targets within the most significant pathways. Our results both validate key
genes, pathways, and drug candidates that have been reported by other studies and suggest
others that have not been well-characterized and warrant further investigation by future studies.
Further investigation of these therapeutic targets and their drug interactions may lead to effective
therapeutic strategies to combat the current COVID-19 pandemic and protect against future
outbreaks.<br /> | Sidharth Jain; Samantha Rego; Sivanesan Dakshanamurthy | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755ad9abda20ceef8e3f3/original/large-scale-profiling-of-sars-co-v-2-infected-patients-identified-potential-therapeutic-host-targets-and-drug-candidates-for-covid-19.pdf |
6725f0315a82cea2facb81e8 | 10.26434/chemrxiv-2024-5j3fm | A Cooperative Model for Metallocene Catalyst Activation by Methylaluminoxane | Activation of rac-Me2Si(η5-Ind)2ZrMe2 (SBIZrMe2) and sheet models for MAO, (MeAlO)6(Me3Al)4 (6,4), (MeAlO)7(Me3Al)5 (7,5), and (MeAlO)26(Me3Al)9 (26,9) has been studied by DFT. These activators can reversibly form an outer-sphere ion-pair (OSIP) [SBIZrMe2AlMe2] [(MeAlO)n(Me3Al)mMe] 3 ([n,m]− = [7,4]−and [26,8]−) or a contact ion-pair (CIP) SBIZrMe-μ-Me-6,4 (2b)from SBIZrMe2. Dissociation of Me3Al from 3 to form CIP SBIZrMe-μ-Me-n,m (2) is generally unfavourable but reversible in toluene continuum. Propene insertion involving CIP 2 features uniformly high barriers of 90-100 kJ mol-1 which is much higher than experiment for MAO-activated catalysts, though the calculated barriers do track with the coordinating ability of the MAO-based anion, as also suggested from the position of the Me3Al-binding equilibria. Binding of neutral sheet 6,4 to anion [7,4]− leads to a hybrid anion [13,8]−. The barrier to propene insertion involving CIP SBIZrMe-μ-Me-13,8 (2e) is lower than 60 kJ mol-1. Formation of [SBIZrMe2AlMe2][13,8] (3e) from SBIZrMe2, 7,5 and 6,4 is favorable though dissociation into 2e and ½ Al2Me6 is not. Simulations of catalyst speciation vs. [Al] at constant [Zr] indicate that formation of species like 2e or 3e from two components of MAO may explain the high activity seen for MAO-activated metallocene complexes at sufficiently high Al:Zr ratios. | Scott Collins; Mikko Linnolahti | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis; Polymerization (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6725f0315a82cea2facb81e8/original/a-cooperative-model-for-metallocene-catalyst-activation-by-methylaluminoxane.pdf |
668db4e001103d79c58887d3 | 10.26434/chemrxiv-2024-st71n | Theoretical calculation of structural, electronic, magnetic, and thermoelectric properties of KMO2 (M = Sm3+, Tb3+, and Dy3+) oxides by ab initio method. | Structural, electronic, optical, thermoelectric and magnetic characteristics of potassium-based rare earth oxides are discussed in this paper. Density-functional theory (DFT) based on a full-potential linear augmented plane wave plus local orbital (FP-LAPW + lo) system within Wien2k software; for the exchange-correlation energy (PBE + GGA) approximation was carried out. Crystal structures of these materials have a hexagonal form with a space group (166_R-3m). Therefore, volume-optimized graph results depicted that studied compounds are more energetically stable in ferromagnetic states than in anti-ferromagnetic and non-magnetic states. Moreover, spin polarize band structure and Density of States (DOS) of studied materials shows metallic and semiconductor nature for corresponding spin channels. However, studied materials have half metallic nature with 100% spin polarization at EF. Total and partial magnetic moments of KMO2 and individual atoms existed due to lanthanide ions due to unpaired 4f electronic states that are present at Fermi level EF. Finally, the energy difference between anti-ferromagnetism and ferromagnetism energy versus volume optimization curve gives the value of Curie temperature TC and noticed that room temperature ferromagnetism is possible. | Khawar Ismail; Ayesha Parveen; Hassan Ali; Asim Ali; Ghulam Murtaza; Sayada Ayesha Zia Bukhari; Muhammad Sohail Abbas | Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Theory - Inorganic; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668db4e001103d79c58887d3/original/theoretical-calculation-of-structural-electronic-magnetic-and-thermoelectric-properties-of-kmo2-m-sm3-tb3-and-dy3-oxides-by-ab-initio-method.pdf |
663268d621291e5d1d2b0681 | 10.26434/chemrxiv-2024-3rr2d | Investigating the Properties of Fatty Acid-based Ionic Liquids: Advancement in AMOEBA Force Field | Developing the multipolar-polarizable AMOEBA force field for large molecules presents its own set of complexities. However, by segmenting the molecules into smaller fragments and ensuring that each fragment is transferable to other systems, the process of parameterizing large molecules such as fatty acids can be simplified without compromising accuracy. In this study, we present a fragment- based AMOEBA FF development for long-chain fatty acid ionic liquids (LCFA-ILs). AMOEBA enables us to incorporate polarization to measurably enhance the precision in modeling these large highly charged systems. This is of significant importance since the computational investigation of ILs needs accurate modeling. Additionally, to leverage the tunability of ILs, it is essential to test numerous anion and cation combinations to identify the most suitable formulation for each application. However, conducting such experiments can be resource-intensive and time-consuming, but accurate molecular modeling can expedite the exploration process. Here, the newly developed parameters were evaluated by comparing the decomposed intermolecular interaction energies for ion pairs with energies determined by quantum mechanics calculations as a reference. By employing this FF in molecular dynamics simulations, we predicted bulk and structural properties including density, enthalpy of vaporization, diffusion coefficient, and radial distribution function of diverse LCFA-ILs. Notably, the good agreement between the experimental data and those calculated using our parameters validates the accuracy of our methodology. Therefore, this new procedure provides an accurate approach to parameterizing large systems, paving the way for studying more complicated systems such as lipids, polymers, micelles and membrane proteins. | Sahar Heidari; Hedieh Torabifard | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663268d621291e5d1d2b0681/original/investigating-the-properties-of-fatty-acid-based-ionic-liquids-advancement-in-amoeba-force-field.pdf |
64c6068c9ed5166e93b7bc24 | 10.26434/chemrxiv-2023-qt5jf-v2 | Examining the Influence of Desalinated Water on Iodine Concentration in Tap Water in Israel | Abstract
Introduction: In Israel, desalinated water is a major source of drinking water. Previous studies have suggested that the levels of iodine in water provided by authorities may not accurately reflect the levels reaching end-users.
Materials and Methods. We analyzed 21 tap water samples collected from different localities across Israel, 13 post-treated desalinated water samples from three of the largest Israeli desalination plants, and several natural water samples. An improved method of ICP-MS developed in our laboratory was used to analyze the content of iodine and other macro-elements, and determination of iodine was performed in alkaline media.
Results: Our results showed that it is possible to distinguish between sample groups based on iodine concentration, water hardness, and Ca/Mg ratio. The median iodine concentrations for four groups of tap water samples ranged from 0.3 to 12.3 µg/L, which is lower than the concentrations previously reported by other researchers in Israel. Based on typical consumption, the water samples can provide no more than 3.39% of the recommended dietary allowance level for iodine. The analysis of post-treated desalinated water samples indicated that these waters comply with industrial specifications but contain only trace concentrations of iodine and much less magnesium than recommended by different public health authorities for public consumption of drinking water.
Conclusion: The total iodine concentrations found were lower than several observations reported in previous years in the literature. There are currently no strict regulations regarding iodine and magnesium levels in drinking and/or softened (desalinated) water, but the intensive desalination plant application is already exhibiting a negative impact on public health. Further investigations are needed, but the present study provides useful insights for developing an effective policy to ensure adequate iodine supply for the population of Israel through drinking water.
| Vasiliy V. Rosen; Orit Gal; Yulianna Andrushchenko; Yona Chen | Analytical Chemistry; Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2023-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c6068c9ed5166e93b7bc24/original/examining-the-influence-of-desalinated-water-on-iodine-concentration-in-tap-water-in-israel.pdf |
62439b4a80488216c9fea1ec | 10.26434/chemrxiv-2022-jgxc7 | Enhancing Li-ion Transport in Solid Electrolytes by Confined Water | Developing new oxide solid electrolytes with fast Li-ion transport and high stability is an important step to realize high-performance solid-state Li-ion batteries. Hydrates materials containing confined water widely exist in nature or can be easily synthesized. However, they have seldom been explored as Li solid electrolytes due to the stereotype that the presence of water limits the electrochemical stability window of a solid electrolyte. In this work, we demonstrate that confined water can enhance Li-ion transport while not compromising the stability window of solid electrolytes using Li-H-Ti-O quaternary compounds as an example system. Three Li-H-Ti-O quaternary compounds containing different amounts of confined water were synthesized, and their ionic conductivity and electrochemical stability are compared. The compound contains nano-confined pseudo-water is demonstrated to have an ionic conductivity that is 2~3 order of magnitude higher than the water-free Li4Ti5O12 and similar stability window. A solid-state battery is made with this new compound as the solid electrolyte, and good rate and cycling performance are achieved, which demonstrates the promise of using such confined-water-containing compounds as Li-ion solid electrolytes. The knowledge and insights gained in this work open a new direction for designing solid electrolytes for future solid-state Li-ion batteries. Broadly, by confining water into solid crystal structures, new design freedoms for tailing the properties of ceramic materials are introduced, which creates new opportunities in designing novel materials to address critical problems in various engineering fields. | Yutong Li; Shitong Wang; Jin Leng; Zunqiu Xiao; Zhongtai Zhang; Tao Gao; Zilong Tang | Materials Science; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62439b4a80488216c9fea1ec/original/enhancing-li-ion-transport-in-solid-electrolytes-by-confined-water.pdf |
60c7407f469df4102cf42c41 | 10.26434/chemrxiv.7756214.v1 | The Geometry of the Catalytic Active Site in [FeFe]-Hydrogenases is Determined by Hydrogen Bonding and Proton Transfer | The H2 conversion and CO inhibition reactivity of nine [FeFe]-hydrogenase constructs with semi-artificial cofactors was studied by in situ and time-resolved infrared spectroscopy, X-ray crystallography, and theoretical methods. Impaired hydrogen turnover and proton transfer as well as characteristic CO inhibition/ reactivation kinetics are assigned to varying degrees of hydrogen-bonding interactions at the active site. We show that the probability to adopt catalytic intermediates is modulated by intramolecular and protein-cofactor interactions that govern structural dynamics at the active site of [FeFe]-hydrogenases.<br /> | Jifu Duan; Stefan Mebs; Moritz Senger; Konstantin Laun; Florian Wittkamp; Joachim Heberle; Thomas Happe; Eckhard Hofmann; Ulf-Peter Apfel; Martin Winkler; Michael Haumann; Sven T. Stripp | Bioinformatics and Computational Biology; Biophysics; Theory - Computational; Biocatalysis; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7407f469df4102cf42c41/original/the-geometry-of-the-catalytic-active-site-in-fe-fe-hydrogenases-is-determined-by-hydrogen-bonding-and-proton-transfer.pdf |
60c73dce702a9b172e189c1a | 10.26434/chemrxiv.6081203.v1 | Divergent Total Syntheses of Enmein-Type Natural Products: (–)-Enmein, (–)-Isodocarpin and (–)-Sculponin R | Divergent
total syntheses of enmein-type natural
products, (–)-enmein, (–)-isodocarpin and (–)-sculponin R, have been achieved in a concise fashion. Key features of the strategy include (a) an efficient
early-stage cage formation to control succeeding diastereoselectivity, (b) an
one-pot acylation/akylation/lactonization to construct the C-ring and C8
quarternary center, (c) a reductive alkenylation approach to construct enmain
D/E rings and (d) a flexible route to allow divergent syntheses of three
natural products. | Guangbin Dong; Saiyong Pan; Sicong Chen | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dce702a9b172e189c1a/original/divergent-total-syntheses-of-enmein-type-natural-products-enmein-isodocarpin-and-sculponin-r.pdf |
61af9ea07ada9545db6c9b04 | 10.26434/chemrxiv-2021-2lg87 | Oxygen Stable Electrochemical CO2 Capture and Concentration through Alcohol Additives | Current methods for CO2 capture and concentration (CCC) are energy intensive due to their reliance on thermal cycles, which are intrinsically Carnot limited in efficiency. In contrast, electrochemically driven CCC (eCCC) can operate at much higher theoretical efficiencies. However, most reported systems are sensitive to O2, precluding their practical use. In order to achieve O2 stable eCCC, we pursued the development of molecular redox carriers with reduction potentials positive of the O2/O2- redox couple. Prior efforts to chemically modify redox carriers to operate at milder potentials resulted in a loss in CO2 binding. To overcome these limitations, we used common alcohols additives to anodically shift the reduction potential of a quinone redox carrier, 2,3,5,6-tetrachloro-p-benzoquinone (TCQ), by up to 350 mV, conferring O2 stability. Intermolecular hydrogen-bonding interactions to the dianion and CO2-bound forms of TCQ were correlated to alcohol pKa to identify ethanol as the optimal additive, as it imparts beneficial changes to both the reduction potential and CO2 binding constant, the two key properties for eCCC redox carriers. We demonstrate a full cycle of eCCC in aerobic simulated flue gas using TCQ and ethanol, two commercially available compounds. Based on the system properties, an estimated minimum of 21 kJ/mol is required to concentrate CO2 from 10% to 100%, or twice as efficient as state-of-the-art thermal amine capture systems and other reported redox carrier-based systems. Furthermore, this approach of using hydrogen-bond donor additives is general and can be used to tailor the redox properties of other quinones/alcohol combinations for specific CO2 capture applications. | Jenny Yang; Jeffrey Barlow | Organic Chemistry; Energy; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61af9ea07ada9545db6c9b04/original/oxygen-stable-electrochemical-co2-capture-and-concentration-through-alcohol-additives.pdf |
6640035921291e5d1d09b71f | 10.26434/chemrxiv-2024-dkvgt | Continuous collective analysis of chemical reactions | Modularized synthesis of small organic molecules is transforming our capacity to create medicines and materials. Disruptive acceleration of this molecule building strategy will broadly unlock its functional potential and requires integration of many new assembly chemistries. Recent advances in high-throughput chemistry stand to enable selection of appropriate chemical reaction conditions from the vast range of potential options. However, a disconnect between the rates of exploration and evaluation has limited progress. Here we report how intrinsic fragmentation features of chemical building blocks generalizes their analysis to yield sub-second readouts of reaction outcomes. Central to this advance was identifying that groups typically attached to boron, nitrogen, and oxygen atoms fragment in a specific and selective manner by mass spectrometry, enabling target agnostic analysis. Combining these features with acoustic droplet ejection mass spectrometry we could eliminate slow chromatographic steps and continuously evaluate chemical reaction outcomes in multiplexed formats. This allowed rapid assignment of reaction conditions to molecules derived from ultra-high throughput chemical synthesis experiments. | Maowei Hu; Lei Yang; Nathaniel Twarog; Jason Ochoada; Yong Li; Brandon Young; Jeanine Price; Kevin McGowan; Theresa Nguyen; Zhe Shi; Mary Ashley Rimmer; Shea Mercer; Zoran Rankovic; Anang Shelat; Daniel Blair | Organic Chemistry; Catalysis; Analytical Chemistry; Combinatorial Chemistry; Organic Synthesis and Reactions; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6640035921291e5d1d09b71f/original/continuous-collective-analysis-of-chemical-reactions.pdf |
667d4fcc01103d79c5447e12 | 10.26434/chemrxiv-2024-3dx2g | ATP-triggered Fe(CN)2CO synthon transfer from the maturase HypCD to the active site of apo-[NiFe]-hydrogenase | [NiFe]-hydrogenases catalyze the reversible activation of H2 using a unique NiFe(CN)2CO metal site, which is assembled by a sophisticated multi-protein machinery. The [4Fe–4S]-cluster-containing HypCD complex, which possesses an ATPase activity with an hitherto unknown function, serves as the hub for the assembly of the Fe(CN)2CO sub-fragment. HypCD is also thought to be responsible for the subsequent transfer of the iron fragment to the apo-form of the catalytic hydrogenase subunit, but the underlying mechanism remained unexplored. Here, we performed a thorough spectroscopic characterization of different HypCD preparations using infrared, Mössbauer and NRVS spectroscopy, revealing molecular details of the coordination of the Fe(CN)2CO fragment. Moreover, biochemical assays in combination with spectroscopy, AlphaFold structure predictions, protein-ligand docking calculations and crosslinking MS deciphered unexpected mechanistic aspects of the ATP requirement of HypCD, which we found to actually trigger the transfer of the Fe(CN)2CO fragment to the apo-hydrogenase. | Anna Kwiatkowksi; Giorgio Caserta; Anne-Christine Schulz; Stefan Frielingsdorf; Vladimir Pelmenschikov; Kilian Weisser; Adam Belsom; Juri Rappsilber; Ilya Sergueev; Christian Limberg; Maria-Andrea Mroginski; Ingo Zebger; Oliver Lenz | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Microbiology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d4fcc01103d79c5447e12/original/atp-triggered-fe-cn-2co-synthon-transfer-from-the-maturase-hyp-cd-to-the-active-site-of-apo-ni-fe-hydrogenase.pdf |
6527fea08bab5d205534456b | 10.26434/chemrxiv-2023-zdk7d | 200 GHz single chip dynamic nuclear polarization microsystems | The single chip integration of the sensitivity relevant part of nuclear magnetic resonance (NMR) [1-17], electron spin resonance (ESR) [18-26], and dynamic nuclear polarization (DNP) enhanced NMR detectors [27] is a promising approach to improve the limit of detection, especially for nanoliter and subnanoliter samples. Recently, the single chip integration of a DNP microsystem operating at 11 GHz (ESR)/16 MHz (NMR) has been demonstrated [27]. Here, we report on single chip DNP microsystems operating at 200 GHz (ESR)/300 MHz (NMR). The single chip integrated microsystems consist of a single or an array of microwave oscillators operating at about 200 GHz for ESR excitation/detection and of a radio frequency receiver operating at about 300 MHz with frequency downconversion for NMR detection. The proposed microsystems, integrated into a single chip of about 1 mm^2, eliminate the need of a high power microwave generator (e.g., a gyrotron) and high quality microwave waveguides. The NMR excitation is performed with a non-integrated coil. To exemplify its possible applications, 1H DNP enhanced NMR experiments on solid samples of volumes from 100 pL to 4 nL are performed at temperatures from 15 to 300 K. DNP enhancements as large as 50 are achieved with 2% α,γ-bisdiphenylene-β-phenylallyl in polystyrene (2% BDPA:PS) at 15 K. This work demonstrates the possibility of extending the single chip approach to the realization of probes for DNP studies of nanoliter and subnanoliter samples at high frequency, high field, and low temperature. | Nergiz Sahin Solmaz; Reza Farsi; Giovanni Boero | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6527fea08bab5d205534456b/original/200-g-hz-single-chip-dynamic-nuclear-polarization-microsystems.pdf |
60c75629f96a0021a9288a03 | 10.26434/chemrxiv.14199695.v1 | An Engineered Nonribosomal Peptide Synthetase Shows Opposite Amino Acid Loading and Condensation Specificity | <div>
<p>Engineering of nonribosomal peptide
synthetases (NRPS) has faced numerous obstacles despite being an attractive
path towards novel bioactive molecules. Specificity filters in the nonribosomal
peptide assembly line determine engineering success, but the relative contribution
of adenylation (A-) and condensation (C-)domains is under debate. In the engineered,
bimodular NRPS sdV-GrsA/GrsB1, the first module is a subdomain-swapped chimera
showing substrate promiscuity. On sdV-GrsA and evolved mutants, we have employed
kinetic modelling to investigate product specificity under substrate
competition. Our model contains one step, in which the A-domain acylates the
thiolation (T-)domain, and one condensation step deacylating the T-domain. The
simplified model agrees well with experimentally determined acylation
preferences and shows that the condensation specificity is mismatched with the
engineered acylation specificity. Our model predicts changing product
specificity in the course of the reaction due to dynamic T-domain loading, and that
A-domain overrules C-domain specificity when T-domain loading reaches a
steady-state. Thus, we have established a tool for investigating poorly
accessible C-domain specificity through nonlinear kinetic modeling and gained critical
insights how the interplay of A- and C-domains determines the product
specificity of NRPSs.</p>
</div> | Aleksa Stanišić; Annika Hüsken; Philipp Stephan; David L. Niquille; Jochen Reinstein; Hajo Kries | Biochemistry; Bioengineering and Biotechnology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75629f96a0021a9288a03/original/an-engineered-nonribosomal-peptide-synthetase-shows-opposite-amino-acid-loading-and-condensation-specificity.pdf |
635b46dcca86b87e4cc6b696 | 10.26434/chemrxiv-2022-f8mh3 | Mechanical Force Enables an Anomalous Dual Ring-Opening Re-action of Naphthodipyran | Multimodal mechanophores that exhibit complex mechanochromic behavior beyond the typical binary response are capable of distinguishing between multiple stress states through discrete changes in color. Naphthodipyran photoswitches contain two pyran rings fused to a central naphthalene core and represent a potentially promising framework for multimodal reactivity. However, the concurrent ring opening of both pyran moieties has previously proven inaccessible via photochemical activation. Here, we demonstrate that mechanical force supplied to naphthodipyran through covalently bound polymer chains generates the elusive dual ring-opened dimerocyanine product with unique near-infrared absorption properties. Trapping with boron trifluoride renders the merocyanine dyes thermally persistent and reveals unusual sequential ring-opening behavior that departs from the reactivity of previously studied mechanophores under the high strain rates imposed by ultrasound-induced solvodynamic chain extension. | Molly E. McFadden; Skylar K. Osler; Yan Sun; Maxwell J. Robb | Physical Chemistry; Organic Chemistry; Polymer Science; Photochemistry (Org.); Physical Organic Chemistry; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b46dcca86b87e4cc6b696/original/mechanical-force-enables-an-anomalous-dual-ring-opening-re-action-of-naphthodipyran.pdf |
60c749d1702a9b389818b1c9 | 10.26434/chemrxiv.12104040.v1 | Sonocrystallization as an Efficient Way to Control Size, Morphology and Purity of Coordination Compounds Microcrystallites: Application to Single-Chain Magnets | <p>
Size, morphology and purity control of
coordination compounds powders is a key stage for their conversion
into materials and devices. In particular, surface science techniques
require highly pure bulk materials with a narrow crystallite‑size
distribution together with straightforward, scalable and reproducible
crystallization procedures. In this work we demonstrate how
sonocrystallization, <i>i.e.</i> application of ultrasounds during
the crystallization process, can afford, very quickly, powders made
of crystallites with controlled size, morphology and purity. We show
that this process drastically diminishes the crystallite‑size
distribution (low Polydispersity Indexes, PDI) and crystallite aspect
ratio. By comparing sonicated samples with various silent
crystallization conditions, we unambiguously show that the
improvement of the crystallite morphologies and size‑distribution
is not due to any thermal effect but to the sonication of the
crystallizing media. The application of sonocrystallization on
crystallization batches of Single‑Chain Magnets (SCM) maintains
SCMs chemical integrity together with their original magnetic
behavior. Moreover, luminescent measurements show that
sonocrystallization induces an efficient micromixing that drastically
enhances the purity of the SCMs powders. We thus propose that
sonocrystallization, which is already used on organic or MOF
compounds, can be applied to (magnetic) coordination compounds to
readily afford bulk powders for characterization or shaping
techniques that require pure, morphology‑ and
crystallite‑size‑controlled powder samples.</p>
<p><br />
</p> | Quentin Evrard; Felix Houard; Carole Daiguebonne; guillaume calvez; yan suffren; olivier guillou; Matteo Mannini; Kevin Bernot | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d1702a9b389818b1c9/original/sonocrystallization-as-an-efficient-way-to-control-size-morphology-and-purity-of-coordination-compounds-microcrystallites-application-to-single-chain-magnets.pdf |
64a4931a6e1c4c986bceca7a | 10.26434/chemrxiv-2023-r1n4m | Discovering Molecular Coordination Environments for Selective Ion Binding Using Machine Learning | The design of ion-selective materials with improved separations efficacy and efficiency is paramount, as current technologies fail to meet real-world deployment challenges. In this study, we utilize a data-driven approach to investigate design features to enhance ion selectivity. We curate a dataset of 563 alkali metal coordinating molecular complexes from the Cambridge Structural Database and obtain ion binding energies from density functional theory calculations. Our analysis reveals that energetic preferences are related to ion size and are largely due to chemical interactions rather than structural reorganization. We identify unique trends in the selectivity for Li+ over other alkali ions including the presence of N coordination atoms, planar coordination geometry, and small coordinating ring sizes. We use machine learning models to identify the key contributions of both geometric and electronic features in predicting selective ion binding strength. These physical insights offer guidance toward the design of optimal membranes for ion selectivity. | Shuwen Yue; Aditya Nandy; Heather Kulik | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Solution Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a4931a6e1c4c986bceca7a/original/discovering-molecular-coordination-environments-for-selective-ion-binding-using-machine-learning.pdf |
61a91617704d05f2fa3dcce6 | 10.26434/chemrxiv-2021-fk45p-v4 | A Generalized Kinetic Model for Compartmentalization of Organometallic Catalysis | Compartmentalization is an attractive approach to enhance catalytic activity by retaining reactive intermediates and mitigating deactivating pathways. Such a concept has been well explored in biochemical and more recently, organometallic catalysis to ensure high reaction turnovers with minimal side reactions. However, a scarcity of theoretical framework towards confined organometallic chemistry impedes a broader utility for the implementation of compartmentalization. Herein, we report a general kinetic model and offer design guidance for a compartmentalized organometallic catalytic cycle. In comparison to a non-compartmentalized catalysis, compartmentalization is quantitatively shown to prevent the unwanted intermediate deactivation, boost the corresponding reaction efficiency (γ), and subsequently increase catalytic turnover frequency (TOF). The key parameter in the model is the volumetric diffusive conductance (F_V) that describes catalysts’ diffusion propensity across a compartment’s boundary. Optimal values of F_V for a specific organometallic chemistry are needed to achieve maximal values of γ and TOF. As illustrated in specific reaction examples, our model suggests that a tailored compartment design, including the use of nanomaterials, is needed to suit a specific organometallic catalytic cycle. This work provides justification and design principles for further exploration into compartmentalizing organometallics to enhance catalytic performance. The conclusions from this work are generally applicable to other catalytic systems that need proper design guidance in confinement and compartmentalization. | Brandon Jolly; Nathalie Co; Ashton Davis; Paula Diaconescu; Chong Liu | Materials Science; Catalysis; Organometallic Chemistry; Nanostructured Materials - Materials; Homogeneous Catalysis; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a91617704d05f2fa3dcce6/original/a-generalized-kinetic-model-for-compartmentalization-of-organometallic-catalysis.pdf |
64cd86644a3f7d0c0d9ea620 | 10.26434/chemrxiv-2023-k1t7j | Region of Interest Selection for GC×GC-MS Data using a Pseudo Fisher Ratio Moving Window with Connected Components Segmentation | Comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data present several challenges for analysis largely because chemical factors drift along the chromatographic modes across different chromatographic runs, and there is frequently a lack of reliable molecular ion measurements with which to align data across multiple samples. Tensor decomposition techniques such as Parallel Factor Analysis (PARAFAC2/PARAFAC2×N) allow analysts to deconvolve closely eluting signals for quantitative and qualitative purposes. These techniques make relatively few assumptions about chromatographic peak shapes or the relative abundance of noise and allow for highly accurate representations of the underlying chemical phenomena using well-characterized and scrutinized principles of chemometrics. However, expert intervention and supervision is required to select appropriate Regions of Interest (ROI) and numbers of chemical components present in each ROI. We previously reported an automated ROI selection algorithm for GC-MS data in Giebelhaus et al. where we observed the ratio of the first and second eigenvalues within a moving window across the entire chromatogram. Here, we present an extension of this work to automatically detect ROIs in GC×GC-MS chromatograms, while making no assumptions about peak shape. First we calculate the probabilities of each acquisition being in a ROI, then apply connected components segmentation to discretize the regions of interest. For sparse chromatograms we found the algorithm detected spurious peaks. To address this, we implemented an iterative ROI selection process where we autoscaled the moving window to the standard deviation of the noise from the previous iteration. Using three user-defined parameters, we generated informative ROIs on a wide range of GC×GC-TOFMS chromatograms. | Ryland Giebelhaus; A. Paulina de la Mata; James Harynuk | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cd86644a3f7d0c0d9ea620/original/region-of-interest-selection-for-gc-gc-ms-data-using-a-pseudo-fisher-ratio-moving-window-with-connected-components-segmentation.pdf |
60c748f0bb8c1a06143dad5e | 10.26434/chemrxiv.12000171.v1 | The Use of Copper and Vanadium Mineral Ores in Catalyzed Mechanochemical Carbon–carbon Bond Formations | Under mechanochemical conditions in ball mills, copper- and vanadium-containing minerals initiate atom transfer radical cyclizations and oxidative couplings, respectively. Only catalytic quantities of the minerals are required, and the reactions proceed either under neat conditions or in the presence of a minimal amount of solvent. | Francesco Puccetti; Christian Schumacher; Hermann Wotruba; José G. Hernández; Carsten Bolm | Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2020-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748f0bb8c1a06143dad5e/original/the-use-of-copper-and-vanadium-mineral-ores-in-catalyzed-mechanochemical-carbon-carbon-bond-formations.pdf |
66b687e8c9c6a5c07aabd1a2 | 10.26434/chemrxiv-2024-1cl1f-v2 | molli: A General-Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction. | The construction, management and analysis of large in silico molecular libraries is critical in many areas of modern chemistry. Herein, we introduce the MOLecular LIibrary toolkit, “molli”, which is a Python 3 cheminformatics module that provides a streamlined interface for manipulating large in silico libraries. Three-dimensional, combinatorial molecule libraries can be expanded directly from two-dimensional chemical structure fragments stored in CDXML files with high stereochemical fidelity. Geometry optimization, property calculation, and conformer generation are executed by interfacing with widely used computational chemistry programs such as OpenBabel, RDKit, ORCA, NWChem, and xTB/CREST. Conformer-dependent grid-based feature calculators provide numerical representation, and interface to robust three-dimensional visualization tools that provide comprehensive images to enhance human understanding of libraries with thousands of members. The package includes a command-line interface in addition to Python classes to streamline frequently used workflows. Parallel performance is benchmarked on various hardware platforms, and common workflows are demonstrated for different tasks ranging from optimized grid-based descriptor calculation on catalyst libraries to an NMR chemical shift prediction workflow from CDXML files. | Alexander S. Shved; Blake E. Ocampo; Elena S. Burlova; Casey L. Olen; N. Ian Rinehart; Scott E. Denmark | Theoretical and Computational Chemistry; Organic Chemistry; Stereochemistry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b687e8c9c6a5c07aabd1a2/original/molli-a-general-purpose-python-toolkit-for-combinatorial-small-molecule-library-generation-manipulation-and-feature-extraction.pdf |
60c743109abda20c1df8c10d | 10.26434/chemrxiv.8874455.v1 | Modular Synthesis of Functionalized Butenolides by Oxidative Furan Fragmentation | The development of new chemical transformations
to simplify the synthesis of valuable building blocks is a challenging task in
organic chemistry and has been the focus of considerable research effort. From
a synthetic perspective, it would be ideal if the natural reactivities of
feedstock chemicals could be diverted to the production of high value-added
compounds which are otherwise tedious to prepare. Here we report a chemical
transformation that enables facile and modular synthesis of synthetically
challenging yet biologically important functionalized butenolides from easily
accessible furans. Specifically, Diels–Alder reactions between furans and
singlet oxygen generate versatile hydroperoxide intermediates, which undergo
iron(II)-mediated radical fragmentation in the presence of Cu(OAc)<sub>2</sub>
or various radical trapping reagents to afford butenolides bearing a wide
variety of appended remote functional groups, including olefins, halides,
azides and aldehydes. The practical utility of this transformation is
demonstrated by easy diversification of the products by means of cross-coupling
reactions and, most importantly, by its ability to simplify the syntheses of
known building blocks of eight biologically active natural products. | Jiajing Bao; Hailong Tian; Peicheng Yang; Jiachen Deng; Jinghan Gui | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743109abda20c1df8c10d/original/modular-synthesis-of-functionalized-butenolides-by-oxidative-furan-fragmentation.pdf |
60c753af337d6c9bf3e288d4 | 10.26434/chemrxiv.13525505.v1 | Effects of External Field Wavelength and Solvation on the Photophysical Property and Optical Nonlinearity of 1,3-Thiazolium-5-Thiolates Mesoionic Compound | <p>The photophysical property and optical nonlinearity of an electronic
push-pull mesoionic compond, 2-(4-trifluoromethophenyl)-3-methyl-4-(4-methoxyphenyl)-1,3-thiazole-5-thiolate were theoretically investigated with a reliable
computing strategy. The essence of the
optical properties were then explored through a variety of wave function
analysis methods, such as the natural transition
orbital analysis, hole-electron analysis, (hyper)polarizability density
analysis, decomposition of the (hyper)polarizability contribution by numerical
integration, and (hyper)polarizability tensor analysis, at the level of
electronic structures. The influence of the electric field and solvation on the
electron absorption spectra and (hyper)polarizabilities
of the molecule are highlighted and clarified. This work will help people to
understand the influence of external field wavelength and solvent on the
optical properties of mesoionic-based molecules, and provide a theoretical reference
for the rational design of chromophores with adjustable properties in the
future.<br /></p><br /> | Shugui Hua; Zeyu Liu; Tian Lu | Optics | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753af337d6c9bf3e288d4/original/effects-of-external-field-wavelength-and-solvation-on-the-photophysical-property-and-optical-nonlinearity-of-1-3-thiazolium-5-thiolates-mesoionic-compound.pdf |
6245c5128048824540002730 | 10.26434/chemrxiv-2022-vts5z | Dual-Band Electrochromism: Plasmonic and Polaronic Mechanisms | Electrochromic windows that dynamically absorb incident solar irradiation are
envisioned as smart technology devices that can reduce power consumption in buildings and
accelerate progress toward sustainable development. While regulating the visible light in interior
spaces to suite the comfort of occupants, electrochromic windows also offer thermal control by
controlling the flux of solar energy, including infrared radiation. The ability to selectively
modulate visible and the infrared solar transmittance is denoted as dual-band electrochromism.
Dual-band control can be achieved by employing materials that absorb light in different spectral
regions when electrochemically charged, with light absorption due to either a polaronic or a
plasmonic mechanism, depending on the charging conditions. In this perspective, we discuss how
adopting a plasmonic or a polaronic approach can affect the performance of an electrochromic
device in terms of different quantitative figures-of-merit, and the challenges and opportunities for
designing better dual-band electrochromic devices in the future. | Bharat Tandon; Hsin-Che Lu; Delia J. Milliron | Nanoscience; Energy; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6245c5128048824540002730/original/dual-band-electrochromism-plasmonic-and-polaronic-mechanisms.pdf |
60c7468fee301cf292c7956a | 10.26434/chemrxiv.11356703.v1 | Dithiasuccinoyl-Caged Amines Enables COS/H2S Release Lacking Electrophilic Byproducts | <p>The
enzymatic conversion of carbonyl sulfide (COS) to hydrogen sulfide (H<sub>2</sub>S)
by carbonic anhydrase has been used to develop self-immolating thiocarbamates
as COS-based H<sub>2</sub>S donors to further elucidate the impact of reactive
sulfur species in biology. The high modularity of this approach has provided a
library of COS-based H<sub>2</sub>S donors that can be activated by specific
stimuli. A common limitation, however, is that many such donors result in the
intermediate formation of an electrophilic quinone methide byproduct during
donor activation. As a mild alternative, we demonstrate here that
dithiasuccinoyl groups can function as COS/H<sub>2</sub>S donor motifs and that
these groups release two equivalents of COS/H<sub>2</sub>S and uncage an amine
payload under physiologically relevant conditions. Additionally, we demonstrate
that COS/H<sub>2</sub>S release from this donor motif can be altered by
electronic modulation and alkyl substitution. These insights are further
supported by DFT investigations, which reveal that aryl and alkyl
thiocarbamates release COS with significantly different activation energies.</p> | Matthew M. Cerda; Jenna L. Mancuso; Emma J. Mullen; Christopher
H. Hendon; Michael Pluth | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7468fee301cf292c7956a/original/dithiasuccinoyl-caged-amines-enables-cos-h2s-release-lacking-electrophilic-byproducts.pdf |
61d464df02c2148ded3c2a96 | 10.26434/chemrxiv-2022-z24vr | Electrification of a Milstein-type Catalyst for Alcohol Reformation | Novel energy and atom efficiency processes will be keys to develop the sustainable chemical industry of the future. Electrification could play an important role, by allowing to fine-tune energy input and using the ideal redox agent: the electron. Here we demonstrate that a commercially available Milstein ruthenium cata-lyst (1) can be used to promote the electrochemical oxidation of ethanol to ethyl acetate and acetate, thus demonstrating the four electron oxidation under preparative conditions. Cyclic voltammetry and DFT-calculations are used to devise a possible catalytic cycle based on a thermal chemical step generating the key hydride intermediate. Successful electrification of Milstein-type catalysts opens pathway to use alcohols as renewable feedstock for the generation of esters and other key building blocks in organic chemistry, thus contributing to increase energy efficiency in organic redox chemistry. | Niklas von Wolff; Damien Tocqueville; Esther Nubret; Marc Robert; David Milstein | Catalysis; Organometallic Chemistry; Electrocatalysis; Homogeneous Catalysis; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d464df02c2148ded3c2a96/original/electrification-of-a-milstein-type-catalyst-for-alcohol-reformation.pdf |
6762cbc181d2151a021cc162 | 10.26434/chemrxiv-2024-0jqdw | Regioselective 1,2-Alkylboration of Non-conjugated Alkenes Utilizing Diazo Compounds as Alkylating agents Enabled by Pd-catalysis | A modular and straightforward three-component coupling strategy towards structurally complex alkylboranes via a Pd(II)-catalyzed 1,2-alkylboration of non-conjugated alkenes is disclosed herein by employing a diverse range of organoboron nucleophiles and diazo-electrophiles. The reaction proceeds under mild conditions and afforded good to moderate yields and good syn-selectivity in a highly regio- and diastereoselective fashion. The pathway of the transformation involves a carbene migratory insertion using a diazo electrophile as the key mechanistic step. Deborylation and DG-removal further adds an additional importance to the methodology. | Princi Gupta; Neel Satishbhai Maradiya; Manmohan Kapur | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6762cbc181d2151a021cc162/original/regioselective-1-2-alkylboration-of-non-conjugated-alkenes-utilizing-diazo-compounds-as-alkylating-agents-enabled-by-pd-catalysis.pdf |
60c73d4e0f50db445339543b | 10.26434/chemrxiv.5545096.v1 | First-Principles Analysis of the Stability of Water on the Oxidised and Reduced CuO(111) Surface | <div>We use fi rst-principles Density Functional Theory calculations with inclusion of the Hubbard +U correction (DFT+U) on the Cu 3d states, to investigate the interaction of water with the CuO(111) surface. We compute adsorption energies and the stability of different water coverages, with a particular focus on the interaction of water with oxygen vacancy sites, and how vacancy stabilization occurs. We study energetics, geometry and electronic structure of relevant confi gurations finding that there are only small changes to the local geometry around the water adsorption site(s) and the electronic properties. The inclusion of van der Waals interactions has no signi ficant impact on the stability of water on CuO(111). We extend the analysis to include realistic environmental conditions within the ab-initio atomistic thermodynamics framework, which allows us to assess the stability of the water/copper-oxide system as a function of ambient conditions, and focus on three important surface processes: water adsorption/desorption on the stoichiometric surface, conditions for dissociation, and oxygen vacancy stabilization. </div> | Marco Fronzi; Michael Nolan | Catalysts; Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2017-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4e0f50db445339543b/original/first-principles-analysis-of-the-stability-of-water-on-the-oxidised-and-reduced-cu-o-111-surface.pdf |
636dc891dcecb44a0426cb4a | 10.26434/chemrxiv-2022-n5sm7 | Chiral Counteranion-Controlled Chemoselectivity in Gold-Catalysed Hydroamination/Enantioselective Formal 1,3-Allylic Alcohol Isomerisation of -Amino-1,4-enynols | A synthetic method for the preparation of 1,8-dihydroindeno[2,1-b]pyrroles and pyrrol-2-yl methanols in an enantioselective manner that relies on the chiral gold(I)-catalysed reactions of -amino-1,4-enynols is described. A divergence in product selectivity was achieved by exploiting the electrostatic interactions between the chiral counteranion of the metal catalyst and the substrate. With a gold(I) complex containing a chiral triflylamide-based counteranion, tandem dehydrative Nazarov-type electrocyclization/hydroamination of the substrate was found to selectively occur to afford the indeno-fused pyrrole adduct. In contrast, changing to a chiral phosphate-based counteranion was observed to result in a hydroamination/1,3-allylic alcohol isomerisation cascade pathway to give the 1H-pyrrole derivative. | Lorenzo Carli; Anyawan Tapdara; Jianwen Jin; Yichao Zhao; Philip Wai Hong Chan | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636dc891dcecb44a0426cb4a/original/chiral-counteranion-controlled-chemoselectivity-in-gold-catalysed-hydroamination-enantioselective-formal-1-3-allylic-alcohol-isomerisation-of-amino-1-4-enynols.pdf |
63505e4086473a0d5b1a35f4 | 10.26434/chemrxiv-2022-n118r | Accurate and Efficient Polymorph Energy Ranking with XDM-corrected hybrid DFT | Accurate and efficient computation of relative energies of molecular-crystal polymorphs is of central importance for solid-state pharmaceuticals and in the field of crystal engineering. In recent years, dispersion corrected density-functional theory (DFT) has emerged as the pre-eminent energy-ranking method for crystal structure prediction (CSP). However, planewave implementations of these methods are hindered by poor scaling for large unit cells and are limited to semi-local functionals that suffer from delocalisation error. In this work, we demonstrate that a recent implementation of the exchange-hole dipole moment (XDM) dispersion correction in the Fritz Haber Institute ab initio molecular simulation (FHI-aims) package provides excellent performance for the energy ranking step of CSP. Thanks to its use of highly optimized numerical atom-centred orbitals, FHI-aims provides effectively linear scaling with system size and allows efficient use of hybrid density functionals with minimal basis-set incompleteness errors. We assess the performance of this methodology for the 26 compounds that formed the first 6 CSP blind tests. The hybrid results show significant improvements for 4/26 compounds, where delocalisation error affects the quality of predicted crystal-energy landscapes | Alastair Price; R. Alex Mayo; Alberto Otero de la Roza; Erin Johnson | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63505e4086473a0d5b1a35f4/original/accurate-and-efficient-polymorph-energy-ranking-with-xdm-corrected-hybrid-dft.pdf |
60c74e770f50db63c3397227 | 10.26434/chemrxiv.12760352.v1 | Monomeric and Dimeric Bromophenols from the Red Alga Ceramium Sp. with Antioxidant and Anti-Inflammatory Activities | <p>LC-MS<sup>2</sup>-based
molecular networking using the Global Natural Products Social (GNPS) tool
revealed a rich assortment of brominated compounds present in the antioxidant
fraction of a red algal extract (<i>Ceramium</i>
sp.) Further chemical investigation led to discovery of one monomeric
bromophenol (lanosol isopropyl ether, <b>1</b>)
and seven dimeric ones (bromourceolatols A-G, <b>2</b>-<b>8</b>),
all of which are previously undescribed. Their structures were elucidated by extensive
analysis of their spectroscopic data. Compounds <b>2</b>-<b>8 </b>were
determined to be racemic trans-type isomers by NOESY, specific optical
rotation, and ECD. Compounds <b>1</b> and <b>3</b>
displayed antioxidant activity with their EC<sub>50</sub> of 44.4 and 47.0 μM, respectively, for
scavenging DPPH free radicals while compounds <b>2</b> and <b>4</b> had approximate EC<sub>50</sub>
values of ~ 64 μM.
Furthermore, compounds <b>2</b>, <b>3</b>, and <b>7</b> exhibited relatively potent anti-inflammatory activity at 32 μM by quenching 97%, 47%,
and 73% of nitric oxide induced by bacterial lipopolysaccharide in macrophage
RAW264.7 cells, respectively.</p> | Yi Zhang; Evgenia Glukhov; Haobin Yu; Lena Gerwick; Pieter Dorrestein; William Gerwick | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e770f50db63c3397227/original/monomeric-and-dimeric-bromophenols-from-the-red-alga-ceramium-sp-with-antioxidant-and-anti-inflammatory-activities.pdf |
6764777281d2151a0240e706 | 10.26434/chemrxiv-2024-xbnmh | Linear-Scaling Local Natural Orbital-based Full Triples Treatment in Coupled-Cluster Theory | We present an efficient, asymptotically linear-scaling implementation of the canonically O(N^8) coupled-cluster method with singles, doubles, and full triples excitations (CCSDT) method. We apply the domain-based local pair natural orbital (DLPNO) approach for computing CCSDT amplitudes. Our method, called DLPNO-CCSDT, uses the converged coupled-cluster amplitudes from a preceding DLPNO-CCSD(T) computation as a starting point for the solution of the CCSDT equations in the local natural orbital basis. To simplify the working equations, we t1-dress our two-electron integrals and Fock matrices, allowing our equations to take on the form of CCDT. With appropriate parameters, our method can recover more than 99.99% of the total canonical CCSDT correlation energy. In addition, we demonstrate that our method consistently yields sub-kJ mol^-1 errors in relative energies when compared to canonical CCSDT, and, likewise, when computing the difference between CCSDT and CCSD(T). Finally, to highlight the low scaling of our algorithm, we present timings on linear alkanes (up to 30 carbons and 730 basis functions) and water clusters (up to 131 water molecules and 3144 basis functions). | Andy Jiang; Henry Schaefer III; Justin Turney | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6764777281d2151a0240e706/original/linear-scaling-local-natural-orbital-based-full-triples-treatment-in-coupled-cluster-theory.pdf |
6348f8f83e8d994bda193f3d | 10.26434/chemrxiv-2022-2pl58 | Discovery of Oxygen Induced Chemoselectivity in Pd-catalyzed C-H Functionalization: Cross Dehydrogenative Coupling vs C-H Amination | The functionalization of unactivated C-H bonds at will for the strategic introduction of bonds or functionalities have been a matter of extensive investigation for the last couple of decades. We have come across a substrate namely, 5-benzoyl-pyrrolo[2,1-a]isoquinoline in which three different functionalizable C-H bonds were identified that could be judiciously transformed site selectively for the generation of complex polyring fused N-heterocycles. At first, we attempted a Pd-catalyzed cross-dehydrogenative coupling in 5-benzoyl-pyrrolo[2,1-a]isoquinoline towards the synthesis of 8H-indeno-pyrrolo[2,1-a]isoquinolinones. Later, we identified a hitherto unknown oxygen induced palladium catalyzed selective C-H amination in 5-benzoyl-pyrrolo[2,1-a]isoquinoline towards a pentacene viz., 9H-indolo-pyrrolo[2,1-a]isoquinoline. Finally, we came across an unexpected site selective C-H amination towards the formation of multiring fused benzazepine which is believed to form due to its stability and to the higher electron density at the reaction centre on isoquinoline ring. | Sheba Ann Babu; Sunil Varughese; Jomon Mathew; Jubi John | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6348f8f83e8d994bda193f3d/original/discovery-of-oxygen-induced-chemoselectivity-in-pd-catalyzed-c-h-functionalization-cross-dehydrogenative-coupling-vs-c-h-amination.pdf |
60c74d24ee301ceebdc7a1e0 | 10.26434/chemrxiv.12588965.v1 | Catalyst Halogenation Enables Rapid and Efficient Polymerizations with Visible to Near-Infrared Light | Driving rapid polymerizations with visible to
near-infrared (NIR) light will enable nascent technologies in the emerging
fields of bio- and composite-printing. However, current photopolymerization
strategies are limited by long reaction times, high light intensities, and/or
large catalyst loadings. Improving efficiency remains elusive without a
comprehensive, mechanistic evaluation of photocatalysis to better understand
how composition relates to polymerization metrics. With this objective in mind,
a series of methine- and aza-bridged boron dipyrromethene (BODIPY) derivatives
were synthesized and systematically characterized to elucidate key
structure-property relationships that facilitate efficient photopolymerization
driven by visible to NIR light. For both BODIPY scaffolds, halogenation was
shown as a general method to increase polymerization rate, quantitatively
characterized using a custom real-time infrared spectroscopy setup.
Furthermore, a combination of steady-state emission quenching experiments,
electronic structure calculations, and ultrafast transient absorption revealed
that efficient intersystem crossing to the lowest excited triplet state upon
halogenation was a key mechanistic step to achieving rapid photopolymerization
reactions. Unprecedented polymerization rates were achieved with extremely low
light intensities (< 1 mW/cm<sup>2</sup>) and catalyst loadings (< 50 μM),
exemplified by reaction completion within 60 seconds of irradiation using
green, red, and NIR light-emitting diodes. | Alex Stafford; Dowon Ahn; Emily Raulerson; Kun-You Chung; Kaihong Sun; Danielle Cadena; Elena Forrister; Shane Yost; Sean Roberts; Zachariah Page | Polymerization (Polymers); Polymerization catalysts; Polymerization kinetics; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d24ee301ceebdc7a1e0/original/catalyst-halogenation-enables-rapid-and-efficient-polymerizations-with-visible-to-near-infrared-light.pdf |
6152faf9aef99c32dd04d151 | 10.26434/chemrxiv-2021-gw53x-v2 | Navigate flying molecular elephants safely to the ground: mass-selective soft landing up to the Mega-Dalton range by Electrospray Controlled Ion-Beam Deposition | The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultra-high vacuum (UHV) is presented, along with encouraging performance data obtained on four model species which are thermolabile or not sublimable. The test panel comprises two small organic compounds, a protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMS) and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated Electrospray Controlled Ion Beam Deposition (ES-CIBD). Full control is achieved by i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMS allowing for investigation, purification and deposition of a virtually unlimited m/z range, ii) the adjustable landing energy of ions down to ~2 eV/z enabling integrity-preserving soft-landing, iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and iv) direct coverage control via the deposited charge. The maximum resolution of R=650 and overall efficiency up to T_total=4.4% calculated from solution to UHV deposition are remarkable as well, while the latter is mainly limited by the not yet optimized ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigation of the deponents demonstrating a selective, structure-preserving process and atomically clean layers. | Andreas Walz; Karolina Stoiber; Annette Huettig; Hartmut Schlichting; Johannes V Barth | Materials Science; Analytical Chemistry; Nanoscience; Analytical Apparatus; Mass Spectrometry; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6152faf9aef99c32dd04d151/original/navigate-flying-molecular-elephants-safely-to-the-ground-mass-selective-soft-landing-up-to-the-mega-dalton-range-by-electrospray-controlled-ion-beam-deposition.pdf |
66bd7badf3f4b05290ebbdd7 | 10.26434/chemrxiv-2024-4gnff-v2 | Microfluidic generation of cell-sized liposomes using a budding strategy | Cell-sized liposomes have emerged as valuable tools in biological applications, such as artificial cells and synthetic biology. The microfluidic production of liposomes using polydimethylsiloxane (PDMS) microfluidic devices offers superior reproducibility and precise control over liposome properties. However, the hydrophobicity of PDMS hinders the formation of liposome precursors, water-in-oil-in-water (W/O/W) double-emulsion droplets, which requires hydrophilic surface treatment of the channels. In this study, we present a microfluidics-based strategy called ”Budding” to prepare cell-sized, monodisperse, unilamellar liposomes rapidly, bypassing the W/O/W double-emulsion droplet formation step and eliminating the impact of hydrophobic channels on liposome preparation. The resulting liposomes were monodispersed (coefficient of variation = 2.9-7.5%) with precise size control (14.4-55.5 μm) achieved by adjusting the flow rate. The unilamellar and water permeability of the liposomes were confirmed through α-hemolysin insertion assays and osmotic swelling assays, respectively. Additionally, the ability to create multi-compartment liposomes was demonstrated, highlighting their potential as versatile tools in various biological applications. | Jiajue Ji; Ryuji Kawano | Materials Science; Chemical Engineering and Industrial Chemistry; Biocompatible Materials; Biological Materials; Fluid Mechanics; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bd7badf3f4b05290ebbdd7/original/microfluidic-generation-of-cell-sized-liposomes-using-a-budding-strategy.pdf |
62d59dfd4e76bf986c94e81c | 10.26434/chemrxiv-2022-9grb8-v2 | Repurposing amine and carboxylic acid building blocks with an automatable esterification reaction | New methodologies to unite amines and carboxylic acids that complement the popular amide coupling can significantly expand accessible chemical space because they yield products distinct from the classic R–NHC(O)–R’ amide arrangement. Here we have developed an amine–acid esterification reaction based on pyridinium salt activation of amine C–N bonds to create products of type R–OC(O)–R’ upon reaction with alkyl and aryl carboxylic acids. The protocol is robust and facile, as demonstrated by automation on open-source robotics. | Andrew McGrath; Rui Zhang; Khadija Shafiq; Tim Cernak | Organic Chemistry; Combinatorial Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d59dfd4e76bf986c94e81c/original/repurposing-amine-and-carboxylic-acid-building-blocks-with-an-automatable-esterification-reaction.pdf |
6304c0620187d93ebb9e35fe | 10.26434/chemrxiv-2022-sqj97 | Photochemical Ring Editing: Access to Privileged 1,2,5-Thiadiazole Scaffolds via Efficient Carbon Excision from Thiadiazines Under Ambient, Aerobic Conditions | Thiadiazoles are a privileged motif in medicinal chemistry, however selective mono-oxidation of the endocyclic sulfur, without over oxidation, is challenging. Herein, we report the quantitative conversion of 1,2,6-thiadiazines to 1,2,5-thiadiazole 1-oxides in the presence of visible light and molecular oxygen under ambient conditions. Experimental and computational studies reveal a probable mechanistic pathway for the cycloaddition-ring contraction cascade: under visible light irradiation in the presence of molecular oxygen, 1,2,6-thiadiazines act as triplet photosensitisers that produce singlet oxygen and subsequently undergo an unprecedented, chemoselective [3 + 2] cycloaddition reaction. The resulting endoperoxide undergoes a ring contraction, with selective carbon atom excision and complete atom economy. The reaction was optimised under both batch and continuous-flow conditions and proven to be efficient in wide range of solvents, including green solvents. Flow conditions enabled precise control over irradiance exposure, enabling exclusive access to photosensitive thiadiazole products. A comprehensive scope of 1,2,6-thiadiazines provided 35 examples of novel, difficult-to-access 1,2,5-thiadiazole 1-oxide structures. | Emmanouil Broumidis; Christopher G. Thomson; Brendan Gallagher; Lia Sotorríos; Kenneth G. McKendrick; Stuart A. Macgregor; Martin J. Paterson; Janet E. Lovett; Gareth O. Lloyd; Georgina M. Rosair; Andreas S. Kalogirou; Panayiotis A. Koutentis; Filipe Vilela | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304c0620187d93ebb9e35fe/original/photochemical-ring-editing-access-to-privileged-1-2-5-thiadiazole-scaffolds-via-efficient-carbon-excision-from-thiadiazines-under-ambient-aerobic-conditions.pdf |
60c740aabb8c1aa4723d9e4a | 10.26434/chemrxiv.7813460.v1 | Synthesis of a Hominal Bis(difluoromethyl) Fragments | <div>
<div>
<p>This paper describes the synthesis of discrete units of hominal bis(gem-CF2). The
controlled introduction of fluorine atoms is a powerful synthetic tool to introduce dipole moments with minimal impact to sterics. Polyvinylidene fluoride (PVDF) is a
striking example of the influence of fluorine atoms, which impart ferroelectric
behavior from the alignment of the dipole moments of CF2 units, however, it is
prepared via direct polymerization of vinylidene difluoride. Thus, a different
synthetic pathway is required to produce synthons containing discrete numbers of
CF2 groups in a hominal relation to each other. We found out that, in the case of
short chains, the consecutive deoxofluorination of sequentially-introduced keto groups
is very inefficient, as it requires harsh conditions and sharply decreasing yields at
each step. To solve this problem, we combined the selective desulfurative fluorination
of dithiolanes with pyridinium fluoride and the deoxofluorination of keto groups with
morpholinosulfur trifluoride. This strategy is highly reproducible and scalable,
allowing the synthesis of the hominal bis(gem-CF2) fragment as a shelf-stable tosylate, which can be used to install discrete chains of hominal bis(gem-CF2) on a
variety of synthons and monomers.</p>
</div>
</div> | Viktor Viktor Ivasyshyn; Hans Smit; Ryan Chiechi | Organic Synthesis and Reactions; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740aabb8c1aa4723d9e4a/original/synthesis-of-a-hominal-bis-difluoromethyl-fragments.pdf |
6712802812ff75c3a1cd714b | 10.26434/chemrxiv-2024-jbzr7-v2 | Automatic Process Exploration Driven by Diversity in Local Atomic Environments: Beyond Look-Up Table Kinetic Monte Carlo | We present an efficient automatic process explorer (APE) framework to overcome the reliance on human intuition to empirically establish relevant elementary processes of a given system, e.g. in prevalent kinetic Monte Carlo (kMC) simulations based on fixed process lists. Use of a fuzzy machine-learning classification algorithm minimizes redundancy in the transition-state searches by driving them toward hitherto unexplored local atomic environments. APE application to island diffusion at a Pd(100) surface immediately reveals a large number of up to now disregarded low-barrier collective processes that lead to a significant increase in the kMC-determined island diffusivity as compared to classic surface hopping and exchange diffusion mechanisms. | King Chun Lai; Patricia Poths; Sebastian Matera; Christoph Scheurer; Karsten Reuter | Theoretical and Computational Chemistry; Catalysis; Nanoscience; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6712802812ff75c3a1cd714b/original/automatic-process-exploration-driven-by-diversity-in-local-atomic-environments-beyond-look-up-table-kinetic-monte-carlo.pdf |
62f57f101803730901a24337 | 10.26434/chemrxiv-2022-cj953 | Room Temperature design of Ce(IV)-MOFs: from photocatalytic HER and OER to overall water splitting under simulated sunlight irradiation | Room temperature synthesis (RTS) of tetravalent MOFs is a promising strategy to design MOFs and their related (nano)composites. By employing these mild conditions, herein, we report for the first time an efficient sustainable way to form highly redox active Ce(IV)-MOFs that are inaccessible at elevated temperatures. Consequently, not only highly crystalline Ce-UiO-66-NH2 is synthesized, but also many other derivatives and topologies (8 and 6-connected phases) without compromise in space-time yield. Their photocatalytic HER and OER activity under simulated sunlight irradiation are in good agreement with their energy level diagrams: Ce-UiO-66-NH2 and Ce-UiO-66-NO2 are the most active photocatalysts for the HER and OER, respectively, with a higher activity than other metals-based UiO-type MOFs. Combining Ce-UiO-66-NH2 with supported Pt NPs results finally in one of the most active and reusable photocatalysts for the overall water splitting into H2 and O2 under simulated sunlight irradiation, due to its efficient photoinduced charge separation evidenced by laser flash photolysis and photoluminescence spectroscopies. | Shan Dai; Eva Montero-Lanzuela; Antoine Tissot; Hermenegildo Garcia Baldovi; Hermenegildo García; Sergio Navalón; Christian Serre | Materials Science; Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Photocatalysis; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f57f101803730901a24337/original/room-temperature-design-of-ce-iv-mo-fs-from-photocatalytic-her-and-oer-to-overall-water-splitting-under-simulated-sunlight-irradiation.pdf |
66542bf8418a5379b060753e | 10.26434/chemrxiv-2024-1h1z0 | Time-Resolved Mechanism of the Cycloaddition Reaction between Difluorocarbene and Norbornadiene | Cycloaddition between difluorocarbene and norbornadiene is a stepwise process where a non-linear cheletropic transition state (TS1) leads to a diradical intermediate, followed by 1,2- and 1,4-addition. Quasi-classical molecular dynamic simulation correctly predicts the selectivity of 1,4-addition product over the 1,2-addition one, however, transition state theory failed. Dynamic effect is observed during simulation, in which the velocity of vibrational mode 2 of TS1 influences the destination of trajectories, the velocity of vibrational mode 4/6 influences the time spent by trajectories to reach 1,4- and 1,2-addition product. The fast trajectories constitute ballistic mechanism. | Yueqian Sang; Yuchen Zhang; Xiao-Song Xue | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66542bf8418a5379b060753e/original/time-resolved-mechanism-of-the-cycloaddition-reaction-between-difluorocarbene-and-norbornadiene.pdf |
617151bdac379f75c5b65c21 | 10.26434/chemrxiv-2021-x41bm-v2 | On the Utility of Coated POSS-Polyimides for Vehicles in Very Low Earth Orbit (VLEO) | The environment encountered by space vehicles in very low Earth orbit (VLEO, 180 – 350 km altitude) contains predominantly atomic oxygen (AO) and molecular nitrogen (N2), which collide with ram surfaces at relative velocities of ~7.5 km s-1. Structural, thermal-control, and coating materials containing organic polymers are particularly susceptible to AO attack at these high velocities, resulting in erosion, roughening, and degradation of function. Copolymerization or blending of a polymer with polyhedral oligomeric silsesquioxane (POSS) yields a material that can resist AO attack through the formation of a passivating silicon-oxide layer. Still, these hybrid organic/inorganic polymers become rough through AO reactions as the passivating layer is forming. Surface roughness may enhance satellite drag because it promotes energy transfer and scattering angle randomization during gas-surface collisions. As potential low-drag and AO-resistant materials, we have investigated POSS-containing films of clear and Kapton-like polyimides that have an atomically smooth AO-resistant coating of Al2O3 that is grown by atomic layer deposition (ALD). Coated and uncoated films were exposed to hyperthermal molecular beams containing atomic and molecular oxygen to investigate their AO resistance, and molecular beam-surface scattering studies were conducted to characterize the gas-surface scattering dynamics on pristine and AO-exposed surfaces to inform drag predictions. The AO erosion yield of Al2O3 ALD-coated films is essentially zero. Simulations of drag on a representative satellite structure that are based on the observed scattering dynamics suggest that the use of the Al2O3 ALD-coated POSS-polyimides on external satellite surfaces have the potential to reduce drag to less than half that predicted for diffuse scattering surfaces. These smooth and AO-resistant polymer films thus show promise for use in the extreme oxidizing and high-drag environment in VLEO. | Timothy Minton; Thomas Schwartzentruber; Chenbiao Xu | Physical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Interfaces; Surface; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617151bdac379f75c5b65c21/original/on-the-utility-of-coated-poss-polyimides-for-vehicles-in-very-low-earth-orbit-vleo.pdf |
619e16ae78480574ab990fd9 | 10.26434/chemrxiv-2021-qn823 | Reorganization energies of flexible organic molecules as a challenging target for machine learning enhanced virtual screening | The molecular reorganization energy $\lambda$ strongly influences the charge carrier mobility of organic semiconductors and is therefore an important target for molecular design. Machine learning (ML) models generally have the potential to strongly accelerate this design process (e.g. in virtual screening studies) by providing fast and accurate estimates of molecular properties. While such models are well established for simple properties (e.g. the atomization energy), $\lambda$ poses a significant challenge in this context. In this paper, we address the questions of how ML models for $\lambda$ can be improved and what their benefit is in high-throughput virtual screening (HTVS) studies. We find that, while improved predictive accuracy can be obtained relative to a semiempirical baseline model, the improvement in molecular discovery is somewhat marginal. In particular, the ML enhanced screenings are more effective in identifying promising candidates but lead to a less diverse sample. We further use substructure analysis to derive a general design rule for organic molecules with low $\lambda$ from the HTVS results. | Ke Chen; Christian Kunkel; Karsten Reuter; Johannes T. Margraf | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2021-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619e16ae78480574ab990fd9/original/reorganization-energies-of-flexible-organic-molecules-as-a-challenging-target-for-machine-learning-enhanced-virtual-screening.pdf |
60c756cd567dfe5333ec656a | 10.26434/chemrxiv.13591283.v2 | Martini Coarse-Grained Nitrogen Gas Model for Lipid Nanobubble Simulations | <p>By integrating the advantages of lipids’ biocompatibility and nanobubbles’
potent physicochemical properties, lipid nanobubbles show a great potential in ultrasound
molecular imaging and biocompatible drug/gene delivery. However, under the
interactions of the ultrasound, lipid nanobubbles may fuse with the cell
membrane, changing the local membrane component and re-distributing encapsulated
gas molecules into the hydrophobic region of the cell membrane, which may greatly
affect the dynamics of certain membrane proteins and thus functions of cells. Although
molecular dynamics simulation provides a useful computational tool to reveal
the related molecular mechanisms, the lack of coarse-grained gas model greatly
restricts this purpose. In the current work, we developed a Martini-compatible
coarse-grained gas model based on the results of previous
experiments and atomistic simulations, which could be used for lipid nanobubble
simulations with complicated lipid components. By comparing the results of
well-designed lipid nanobubble, lipid bi-monolayer and lipid bilayer
simulations, we further revealed the role of membrane curvature and
interleaflet coupling in the liquid-liquid phase separation of lipid membranes.
It is worth mention that our developed coarse-grained nitrogen gas model can also be used for other gas-water
interface systems such as pulmonary surfactant, which may overcome the possible
artefacts arising from the usage of vacuum for gas phase. </p> | Xubo Lin; Fujia Tian; Siewert-Jan Marrink | Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756cd567dfe5333ec656a/original/martini-coarse-grained-nitrogen-gas-model-for-lipid-nanobubble-simulations.pdf |
6125edbfb136d6a3040eae60 | 10.26434/chemrxiv-2021-vj7k2-v2 | Sequence-sorted redox-switchable hetero[3]rotaxanes | From a library of five crown ether macrocycles with different ring sizes and redox-active moieties, such as tetrathiafulvalene (TTF) and naphthalene dimiide (NDI), directional heterocircuit[3]rotaxanes were constructed. Using an axle with two binding sites with different steric accessibility, the concept of integrative self-sorting was applied to program the sequence of functional units in heteropseudo[3]rotaxanes. Depending on binding strength and ring size of the smaller macrocycles, different heteropseudo[3]rotaxane selectivities and stabilities were determined by 2D NMR spectroscopy and tandem mass spectrometry. A heteropseudo[3]rotaxane with rotaxane-like behaviour was isolated chromatographically, displaying electrochemically "frustrated" properties. A robust synthetic procedure was developed allowing the synthesis of four new hetero[3]rotaxanes incorporating specific sequences of functional units. Sequence pseudoisomeric rotaxanes which have the naphthalene diimide subunit at two different positions show distinct electrochemical properties. DFT calculations suggest that this differences could arise from a folding of the structure, in which the redox-active moieties stack with a stopper unit. This study presents a blueprint for the construction of hetero[3]rotaxanes with sequential control of the functional units along the track of the axle and paves the way to extend the functionality of mechanically interlocked molecules. | Marius Gaedke; Henrik Hupatz; Felix Witte; Susanne Margot Rupf; Clara Douglas; Hendrik V. Schröder; Lukas Fischer; Moritz Malischewski; Beate Paulus; Christoph A. Schalley | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6125edbfb136d6a3040eae60/original/sequence-sorted-redox-switchable-hetero-3-rotaxanes.pdf |
65fc236de9ebbb4db92d1346 | 10.26434/chemrxiv-2024-0fpw3 | Implementation of a LC-MS based multi-attribute method (MAM) and intact multi-attribute method (iMAM) workflow for the characterisation of a GLP-Fc fusion protein. | Over the past few years, the implementation of mass spectrometry (MS) in QC laboratories has become a more common occurrence. The multi-attribute method (MAM), and emerging intact multi-attribute method (iMAM), are powerful analytical tools utilising liquid chromatography−mass spectrometry (LC-MS) methods that enable the monitoring of critical quality attributes (CQAs) in biotherapeutic proteins in compliant settings. Both MAM and iMAM are intended to replace or supplement several conventional assays with a single LC-MS method utilising MS data in combination with robust, semi-automated data processing workflows. MAM and iMAM workflows can also be implemented into current Good Manufacturing Practices environments due to the availability of CFR 11 compliant chromatography data system software. In this study, MAM and iMAM are employed for the analysis of 4 batches of a glucagon-like peptide-Fc fusion protein. MAM approach involved a first the discovery phase for the identification of CQAs and second, the target monitoring phase of the selected CQAs in other samples. New peak detection was performed on the data set to determine the appearance, absence or change of any peak. For native iMAM workflow both size exclusion and strong cation exchange chromatography were optimized for the identification and monitoring of CQAs at the intact level. | Ciarán Buckley; Silvia Millán-Martín; Sara Carillo; Florian Füssl; Ciara MacHale; Jonathan Bones | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc236de9ebbb4db92d1346/original/implementation-of-a-lc-ms-based-multi-attribute-method-mam-and-intact-multi-attribute-method-i-mam-workflow-for-the-characterisation-of-a-glp-fc-fusion-protein.pdf |
60c7576c469df48909f45480 | 10.26434/chemrxiv.13295888.v3 | FID-Net: A Versatile Deep Neural Network Architecture for NMR Spectral Reconstruction and Virtual Decoupling | <p>In
recent years, the transformative potential of deep neural networks (DNNs) for analysing
and interpreting NMR data has clearly been recognised. However, most
applications of DNNs in NMR to date either struggle to outperform existing
methodologies or are limited in scope to a narrow range of data that closely
resemble the data that the network was trained on. These limitations have prevented
a widescale uptake of DNNs in NMR. Addressing this, we introduce FID-Net, a
deep neural network architecture inspired by WaveNet, for performing analyses
on time domain NMR data. We first demonstrate the effectiveness of this
architecture in reconstructing non-uniformly sampled (NUS) biomolecular NMR spectra.
It is shown that a single network is able to reconstruct a diverse range of 2D NUS
spectra that have been obtained with arbitrary sampling schedules, with a range
of sweep widths, and a variety of other acquisition parameters. The performance
of the trained FID-Net in this case exceeds or matches existing methods
currently used for the reconstruction of NUS NMR spectra. Secondly, we present
a network based on the FID-Net architecture that can efficiently virtually
decouple <sup>13</sup>C<sub>α</sub>-<sup>13</sup>C<sub>β</sub> couplings in
HNCA protein NMR spectra in a single shot analysis, while at the same time leaving
glycine residues unmodulated. The ability for these DNNs to work effectively in
a wide range of scenarios, without retraining, paves the way for their
widespread usage in analysing NMR data. </p> | Gogulan Karunanithy; Flemming Hansen | Biophysics; Machine Learning; Artificial Intelligence; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7576c469df48909f45480/original/fid-net-a-versatile-deep-neural-network-architecture-for-nmr-spectral-reconstruction-and-virtual-decoupling.pdf |
62eb5ed6adfd35472c266209 | 10.26434/chemrxiv-2022-zw1lg | Photoredox C-H Functionalization Leads the Site-selective Phenylalanine Bioconjugation | Site-selectively chemical bioconjugation of peptides and proteins can improve the therapeutic exploration of modified protein drugs. Only 3.8% natural abundance of phenylalanine in protein and nearly 90% of proteins contain at least one phenylalanine residue in their sequenced, showing the potential in biopharmaceutical utility of the phenylalanine bioconjugation. However, the covalent bioconjugation of native phenylalanine is one of the most challenging problems in protein modification. Herein, an approach to protein modification is described that relies on a photoredox method for the site-selective bioconjugation of phenylalanine. This methodology has been validated on peptides as well as protein insulin using a straightforward and mild condition. In addition, based on characterization by near-UV CD spectroscopy and small angle X-ray scattering (SAXS), this pyrazole labeling approach permitted the insulin hexamer to completely dissociate into the monomeric form, thus making it a potential candidate for use as rapid-acting insulin for the treatment of diabetes. | Chien-Wei Chiang; Yue Weng; Chun-Jen Su; Haoyang Jiang | Biological and Medicinal Chemistry; Catalysis; Chemical Biology; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eb5ed6adfd35472c266209/original/photoredox-c-h-functionalization-leads-the-site-selective-phenylalanine-bioconjugation.pdf |
62de4c2db464fa0088721452 | 10.26434/chemrxiv-2022-v60mb | Reversible Discrete-to-Extended Metal–Organic Polyhedra Trans-formation by Sulfonic Acid Surface Functionalization | Metal-organic polyhedra (MOPs) are molecular porous units in which desired functionalities can be installed with precise geometrical and compositional control. By combing two complementary chemical moieties, such as sulfonic acid group and Rh(II)-carboxylate paddlewheel, we synthesized a robust water-soluble cuboctahedral MOP with excellent features in both solution and solid state. Herein, we demonstrate that the superior chemical stability of the Rh2 unit and the elevated number of functional groups on the surface (24 per cage) result in a porous cage with high solubility and stability in water, including acidic, neutral and basic pH conditions. We also prove that the sulfonic acid-rich form of the cage can be isolated through post-synthetic acid treatment. This transformation involves an improved gas uptake capacity, and the capability to reversibly assemble the cages into a 3D metal-organic framework (MOF) structure. Likewise, this sulfonic acid functionalization provides both MOP and MOF solids with high proton conductivities (> 10-3 S cm-1), comparable to previously reported high conducting metal-organic materials. The influence of the MOP-to-MOF processing in the gas adsorption capacity indicates this structural transformation can provide materials with higher and more controllable porous properties. These results illustrate the high potential of acidic MOPs as more flexible porous building units in terms of processability, structural complexity and tunability of the properties. | Javier Troyano; Satoshi Horike; Shuhei Furukawa | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62de4c2db464fa0088721452/original/reversible-discrete-to-extended-metal-organic-polyhedra-trans-formation-by-sulfonic-acid-surface-functionalization.pdf |
60c75594bdbb898109a3a856 | 10.26434/chemrxiv.14132213.v1 | Photoredox Catalysis Using Heterogenized Iridium Complexes | Heterogenized photoredox catalysts provide a path to generating chemicals in an environmentally friendly way, with facile reuse of catalysts in batch or continuous processes. In this study, heterogenized iridium complexes as photoredox catalysts were assembled via covalent attachment to three metal oxide surfaces (ITO, ZrO<sub>2</sub>, Al<sub>2</sub>O<sub>3</sub>) either in the form of thin films or nanopowders and tested as photoredox catalysts for reductive dehalogenation of bromoacetophenone to acetophenone. All catalysts produced acetophenone with high conversions and yields. The fastest reactions were complete in fifteen minutes under mild conditions using Al<sub>2</sub>O<sub>3</sub> surfaces, which provided the most robust and reusable supports. The catalytic performance was compared on both nanopowder and thin film supports, showing that both constructs could be used for photoredox catalysis. The nanopowder-based catalysts resulted in faster and more efficient catalysis, while the thin film-immobilized catalysts were more robust and easily reused. Importantly, the thin film constructs show promise for future photoelectrochemical and electrochemical photoredox setups. Finally, all catalysts could be reused 2-3 times, performing at least 1000 turnovers with Al<sub>2</sub>O<sub>3 </sub>supports, highlighting that heterogenized catalysts can perform photoredox catalysis in an environmentally friendly fashion. <br /> | Kelly L. Materna; Leif Hammarström | Thin Films; Photocatalysis; Redox Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75594bdbb898109a3a856/original/photoredox-catalysis-using-heterogenized-iridium-complexes.pdf |
66ccba7820ac769e5fe8537c | 10.26434/chemrxiv-2024-wbdbn-v2 | Conformer-based Multiple-Instance Learning for Predicting Biodegradability Classification | In-silico methods are increasingly becoming reliable tools to replicate and extend from experimental findings of chemical biodegradability. Information derived from quantitative activity-structure relationships (QSARs) have the potential to have rules extracted that can aid the understanding of biodegradation. Using semi-empirical quantum chemical calculations, the use of a conformer-based augmentation approach, along with dimensionality reduction methods, was studied in the context of achieving improved model accuracy and applicability. This work highlights molecular features, from graph-based features, 3-dimensional structural descriptors, to direct graph-based learning methods, that can be used to distinguish readily biodegradable compounds, and the role of unsupervised pre-processing in refining the training set and choice of features. | Qi Yao Yim | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ccba7820ac769e5fe8537c/original/conformer-based-multiple-instance-learning-for-predicting-biodegradability-classification.pdf |
60c73fe5567dfe1864ec3aef | 10.26434/chemrxiv.7364813.v1 | Transport Anomalies Emerging from Strong Correlation in Ionic Liquid Electrolytes | <div>Recent works on ionic liquid electrolyte systems motivate the present study of transport regimes where strong species interactions result in significant correlations and deviations from ideal solution behaviour. In order to obtain a complete description of transport in these systems we use rigorous concentrated solution theory coupled with molecular dynamics simulations, beyond the commonly used uncorrelated Nernst-Einstein equation. As a case study, we investigate the NaFSI - Pyr<sub>13</sub>\FSI room temperature ionic liquid electrolyte. When fully accounting for intra- and inter-species correlation, an anomalously low and even negative transference number emerges for NaFSI molar fractions lower than 0.2, emphasising that strong ion-ion coupling in the electrolyte can significantly impact the rate performance of the cell. With increasing concentration the transference number monotonically increases, approaching unity, while the total conductivity decreases as the system transitions to a state resembling a single-ion solid-state electrolyte. The degree of spatial ionic association is explored further by employing a variant of unsupervised single-linkage clustering algorithm. Using this combination of numerical techniques we examine the microscopic mechanisms responsible for the trade-off between key electrolyte transport properties, previously overlooked in both computational and experimental studies.</div> | Nicola Molinari; Jonathan P. Mailoa; Nathan Craig; Jake Christensen; Boris Kozinsky | Electrochemistry; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe5567dfe1864ec3aef/original/transport-anomalies-emerging-from-strong-correlation-in-ionic-liquid-electrolytes.pdf |
60c74d719abda2f290f8d456 | 10.26434/chemrxiv.11853405.v3 | Molecular Characterization of the Surface Excess Charge Layer in Droplets | <div>Charged droplets play a central role in native mass spectrometry, atmospheric aerosols and in serving as micro-reactors for accelerating chemical reactions. The surface excess charge layer (SECL) in droplets has often been associated with distinct chemistry. Using molecular simulations for droplets with Na+ and Cl- ions we have found that this layer is ≈ 1.5−1.7 nm thick and depending on the droplet size it includes 33%-55% of the total number of ions. Here, we examine the effect of droplet size and nature of ions in the structure of SECL by using molecular dynamics. We find that in the presence of simple ions the thickness of the surface excess charge layer is invariant not only with respect to droplet size but also with respect to the nature of the simple ions and it is not sensitive to fine details of different force fields used in our simulations.</div><div> In the presence of macroions the SECL may extend to 2.0. nm. For the same droplet size, iodide and model H3O+ ions show considerably higher concentration than the sodium and chloride ions. In nano-drops, the SECL does not have the highest concentration of ions. We identify the maximum ion concentration region that may overlap with SECL in nano-drops. We also find that the differences in the average water dipole orientation in the presence of cations and anions in this layer are reflected in the charge distributions. Within the surface charge layer, the number of hydrogen bonds reduces gradually relative to the droplet interior where the number of hydrogen bonds is on the average 2.9 for droplets of diameter < 4 nm and 3.5 for larger droplets. The decrease in the number of hydrogen bonds from the interior to the surface is less pronounced in larger droplets. In droplets with diameter < 4 nm and high concentration of ions the charge of the ions is not compensated only by the solvent polarization charge but by the total charge that also includes the other free charge. This finding shows exceptions to the commonly made assumption that the solvent compensates the charge of the ions in solvents with very high dielectric constant. The study provides molecular insight into the bi-layer droplet structure assumed in the equilibrium partitioning model (EPM) of C. Enke and assesses critical assumptions of the Iribarne-Thomson model for the ion-evaporation mechanism. We suggest the extension of the bi-layer droplet structure in EPM to include the maximum ion concentration region that may not coincide with SECL in nanodrops. We compute the ion concentrations in SECL, which are those that should enter the kinetic equation in the ion-evaporation mechanism, instead of the overall drop ion concentration that has been used thus far.<br /></div> | Victor Kwan; Styliani Consta | Clusters; Interfaces; Physical and Chemical Properties; Solution Chemistry; Statistical Mechanics; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d719abda2f290f8d456/original/molecular-characterization-of-the-surface-excess-charge-layer-in-droplets.pdf |
60c756c3bb8c1a15fd3dc699 | 10.26434/chemrxiv.14318741.v1 | Extracting Interface Correlations from the Pair Distribution Function of Composite Materials | <div>
<div>
<div>
<p>Using a non-negative matrix factorisation (NMF) approach,
we show how the pair distribution function (PDF) of complex
mixtures can be deconvolved into the contributions from
the individual phase components and also the interface between phases. Our focus is on the model system Fe||Fe3O4.
We establish proof-of-concept using idealised PDF data
generated from established theory-driven models of the
Fe||Fe3O4 interface. Using X-ray PDF measurements for
corroded Fe samples, and employing our newly-developed
NMF analysis, we extract the experimental interface PDF
(‘iPDF’) for this same system. We find excellent agreement
between theory and experiment. The implications of our
results in the broader context of interface characterisation
for complex functional materials are discussed.
</p>
</div>
</div>
</div> | Harry Geddes; Henry D. Hutchinson; Alex R Ha; Nicholas P. Funnell; Andrew Goodwin | Solid State Chemistry; Interfaces; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756c3bb8c1a15fd3dc699/original/extracting-interface-correlations-from-the-pair-distribution-function-of-composite-materials.pdf |
60c743ff0f50db4ac3396027 | 10.26434/chemrxiv.9733973.v1 | Machine Learning for Acute Oral System Toxicity Regression and Classification | <p><i>In vivo</i>toxicity testing remains a costly and time-consuming component of any pre-clinical drug development campaign. In particular, LD50 measurements require the loss of animal life but remain a critical component in preventing lethal compounds from entering the clinic. With advances in machine learning, <i>in silico</i>LD50 prediction now has the potential to greatly reduce this burden. We study various types of machine learning models to predict acute oral LD50 measurements in rats as regression and classification problems. We demonstrate that transfer learning a ResNet34 model pretrained on ImageNet with test time augmentation generates the best performing regression model and that random forest augmented with conformal prediction provides a robust methodology to perform classification.</p> | conor parks; Zied Gaieb; Rommie Amaro | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ff0f50db4ac3396027/original/machine-learning-for-acute-oral-system-toxicity-regression-and-classification.pdf |
67a6255681d2151a02849440 | 10.26434/chemrxiv-2025-l4g7c | Modelling of formic acid production using solventless trialkylamine reduction strategies | Solventless fed-batch experiments at elevated pressures were performed to gain insights into the performance of using triethylamine as an extraction base during the direct hydrogenation of CO2 to formic acid. No formic acid was observed in the bulk liquid after several hours of reaction. Analysis on the spent catalyst revealed significant formic acid build-up within the catalyst pores. A fundamental, continuum model based on Cahn-Hilliard spinodal decomposition was developed and validated to study the influence of the biphasic nature of formic acid – trialkylamine structures during reaction at pore level. The biphasic nature of the tertiary alkylamine – formic acid system was found to have significant implications for the reaction performance of the proposed system. | Anouk de Leeuw den Bouter; Adeline Miquelot; Larissa Brito; Pierre Olivier; John van der Schaaf | Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a6255681d2151a02849440/original/modelling-of-formic-acid-production-using-solventless-trialkylamine-reduction-strategies.pdf |
66683eb3409abc034526ab2a | 10.26434/chemrxiv-2024-kg4cp | Catalytic Enantioselective Synthesis of Planar Chiral
Pillar[5]arenes via Asymmetric Sonogashira Coupling | As a novel type of macrocycles with attractive planar chirality, pillar[5]arenes have gained increasing
research interest over the past decades, enabling their widespread applications in diverse fields such
as porous materials, molecular machines, and chiral luminescence materials. However, the catalytic
methodology towards the enantioselective synthesis of planar chiral pillar[5]arenes remains elusive.
Here we report a novel method for the enantioselective synthesis of planar chiral pillar[5]arenes via
asymmetric Sonogashira coupling, giving access to a wide range of highly functionalized planar chiral
pillar[5]arenes, including both homo- and hetero-rimmed ones, with excellent enantioselectivities.
Attractively, the resultant planar chiral pillar[5]arenes show great potential for widespread use in many
areas such as chiral luminescent materials. This work not only enables the successful synthesis of
planar chiral pillar[5]arenes with abundant structural and functional diversity as key building blocks
for practical applications but also enriches the asymmetric cross-coupling methodologies in organic
synthetic chemistry. | Xiao-Hua Zhou; Xin Zhang; Yi-Ru Song; Xue Li; Lin-Tao Bao; Wei-Tao Xu; Xu-Qing Wang; Hai-Bo Yang; Wei Wang | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66683eb3409abc034526ab2a/original/catalytic-enantioselective-synthesis-of-planar-chiral-pillar-5-arenes-via-asymmetric-sonogashira-coupling.pdf |
64f248dddd1a73847ffb6e0d | 10.26434/chemrxiv-2023-srlm6-v2 | Ni-Electrocatalytic Decarboxylative Arylation to Access Quaternary Centers | There is a pressing need, particularly in the field of drug discovery, for general methods that will enable direct coupling of tertiary alkyl frag-ments to (hetero)aryl halides. Herein a uniquely powerful and simple set of conditions for achieving this transformation with unparalleled generality and chemoselectivity is disclosed. This new protocol is placed in context with other recently reported methods, applied to simplify the routes of known bioactive building blocks molecules, and scaled up in both batch and flow. The role of pyridine additive as well as the mechanism of this reaction are interrogated through Cyclic Voltammetry studies, titration experiments, control reactions with Ni(0) and Ni(II)-complexes, and ligand optimization data. Those studies indicate that the formation of a BINAPNi(0) is minimized and the formation of an active pyridine-stabilized Ni(I) species are sustained during the reaction. Our preliminary mechanistic studies ruled out the involvement of Ni(0) species in this electrochemical cross-coupling, which is mediated by Ni(I) species via a Ni(I)-Ni(II)-Ni(III)-Ni(I) catalytic cycle. | Gabriele Laudadio; Philipp Neigenfind; Áron Péter; Camille Z. Rubel; Megan A. Emmanuel; Martins S. Oderinde; Tamara El-Hayek Ewing; Maximilian D. Palkowitz; Jack L. Sloane; Kevin W. Gillman; Daniel Ridge; Michael D. Mandler; Philippe Bolduc; Michael C. Nicastri; Benxiang Zhang; Sebastian Clementson; Nadia Nasser Petersen; Pablo Martín- Gago; Pavel Mykhailiuk; Keary M. Engle; Phil S. Baran | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f248dddd1a73847ffb6e0d/original/ni-electrocatalytic-decarboxylative-arylation-to-access-quaternary-centers.pdf |
67c01e7d6dde43c908ae9b3a | 10.26434/chemrxiv-2025-15v1c | Expanding metal catalyzed arene C–H borylation beyond boronate esters | The metal-catalyzed intermolecular C–H borylation of arenes is an extremely powerful C–H functionalization methodology. However, to date it is effectively restricted to forming organo-boronate esters (Aryl–B(OR)2) with its application to form other organoboranes rarely explored. Herein, we report a catalytic intermolecular arene C–H borylation method using the commercial and inexpensive hydroborane 9-borabicyclo-[3.3.1]-nonane, (H–BBN)2. This process is effective for mono- and di-borylation to form a range of Aryl–BBN compounds using either NacNacAl or NacNacZn ((NacNac={(2,6-iPr2C6H3)N(CH3)C}2CH) based catalysts. The crude Aryl–BBN products can be used in-situ for subsequent transformations, including an example that does not proceed using the analogous pinacol-boronate ester. Mechanistic studies indicated an unusual -bond metathesis process between NacNacZn–Aryl and the hydroborane, with first order kinetics in the hydroborane dimer ((H–BBN)2). Our proposed calculated metathesis pathway involves ligand non-innocence and addition of both H–BBN units in (H–BBN)2 to the NacNacZn–Aryl complex. This is in contrast to the conventional -bond metathesis mechanism using hydroboranes which invariably proceeds by reaction of one equivalent of a monomeric hydroborane with a M–C unit. Overall, this work demonstrates the utility of extending catalytic arene C–H borylation beyond the boronate esters that currently dominate this field, while highlighting that the -bond metathesis reaction can be mechanistically more complex when utilizing dimeric hydroboranes. | Milan Bisai; Justyna Losiewicz; Gary Nichol; Andrew Dominey; Stephen Thomas; Michael Ingleson; Stuart Macgregor | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Main Group Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c01e7d6dde43c908ae9b3a/original/expanding-metal-catalyzed-arene-c-h-borylation-beyond-boronate-esters.pdf |
667dcd7601103d79c55d622a | 10.26434/chemrxiv-2024-w6qcj | A multi-dimensional systems biology approach to elucidate the mechanism of action of Mycobacterium tuberculosis γ-carbonic anhydrase inhibitors | Background: Mycobacterium tuberculosis (Mtb) carbonic anhydrases (CAs) are critical enzymes that regulate pH by converting CO2 to HCO3-, essential for Mtb's survival in acidic environments. Inhibiting γ-CAs presents a potential target for novel antituberculosis drugs with unique mechanisms of action. Objective: This study aimed to explore the biological connections underlying Mtb pathogenesis and investigate the mechanistic actions of antituberculosis compounds targeting the Cas9 protein. Methods: We employed homology modeling and virtual screening to identify compounds with high binding affinities for Cas9 protein. This study used the homology modeling approach employing high-quality AlphaFold DB models for γ-CA. Furthermore, the systems biology approach was used for analyzing the mechanistic modeling of compounds, integrating data on genes, pathways, phenotypes, and molecular descriptors. Single-cell RNA sequencing was also conducted to profile gene expression. Results: Three compounds, F10921405, F08060425, and F14437079, potentially binding to Cas9 protein, have been identified. F10921405 and F08060425 showed significant overlap in their effects on pathways related to the immune response, while F14437079 displayed distinct mechanistic pathways. Expression profiling revealed high levels of genes such as PDE4D, ROCK2, ITK, MAPK10, and SYK in response to F1092-1405 and F0806-0425, and MMP2 and CALCRL in response to F1443-7079. These genes, which play a role in immune modulation and lung tissue integrity, are essential to fight against Mtb. Conclusion: The molecular relationship and pathways linked to the mentioned compounds give the study a holistic perspective of targeting Mtb, which is essential in designing specific therapeutic approaches. Subsequent research will involve experimental validation to demonstrate the efficacy of the promising candidates in Mtb infections. | Ashok Aspatwar; Ajay Manaithiya; Ratul Bhowmik; Kunal Bhattacharya; Rajarshi Ray; Sagar Singh Shyamal; Fabrizio Carta; Claudiu Supuran; Seppo Parkkila | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667dcd7601103d79c55d622a/original/a-multi-dimensional-systems-biology-approach-to-elucidate-the-mechanism-of-action-of-mycobacterium-tuberculosis-carbonic-anhydrase-inhibitors.pdf |
60c7422bbdbb8923d4a38462 | 10.26434/chemrxiv.8233385.v1 | Multiple Bonds in Novel Uranium-Transition Metal Complexes | We used density functional theory and multireference wave-function based methods to predict new heterobimetallic
complexes featuring a uranium and a first-row transition metal. The quantum mechanical calculations predict a five-fold bonding between uranium and manganese metals. | Prachi Sharma; Dale Pahls; Bianca Ramirez; Connie C. Lu; Laura Gagliardi | Lanthanides and Actinides; Theory - Inorganic; Transition Metal Complexes (Inorg.); Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422bbdbb8923d4a38462/original/multiple-bonds-in-novel-uranium-transition-metal-complexes.pdf |
6501f89ab338ec988a6c51bb | 10.26434/chemrxiv-2023-7sw0t-v3 | A Transfer Hydrogenation Approach to Activity-Based Sensing of Formate in Living Cells | Formate is a major reactive carbon species in one-carbon metabolism, where it serves as an endogenous precursor for amino acid and nucleic acid biosynthesis and a cellular source of NAD(P)H. On the other hand, aberrant elevations in cellular formate are connected to progression of serious diseases, including cancer and Alzheimer’s disease. Traditional methods for formate detection in biological environments often rely on sample destruction and/or extensive processing, resulting in a loss of spatiotemporal information. To help address these limitations, here we present the design, synthesis, and biological evaluation of a first-generation activity-based sensing system for live-cell formate imaging that relies on iridium transfer hydrogenation catalysis. Formate facilitates an aldehyde-to alcohol conversion on various fluorophore scaffolds to enable fluorescence detection of this one-carbon unit, including through a two-color ratiometric response with internal calibration. The resulting two-component probe system can detect changes in formate levels in living cells with high selectivity over potentially competing biological analytes. Moreover, this activity-based sensing system can visualize changes in endogenous formate fluxes through alterations of one-carbon pathways in cell-based models of human colon cancer, presaging the potential utility of this chemical approach to probe the continuum between one-carbon metabolism and signaling in cancer and other diseases. | Steven Crossley; Logan Tenney; Vanha Pham; Xiao Xie; Michelle Zhao; Christopher Chang | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6501f89ab338ec988a6c51bb/original/a-transfer-hydrogenation-approach-to-activity-based-sensing-of-formate-in-living-cells.pdf |
6759a5ecf9980725cfbb5f86 | 10.26434/chemrxiv-2024-d1pwp | Using a heavy inert diffusion additive for superconformal atomic layer deposition | The shrinking of device nodes increases the demand for deposition processes to seamlessly fill nanometer-scale features. Despite the precision of atomic layer deposition (ALD), it cannot deposit in a V-shaped fashion, characteristic of superconformal thin film deposition. We propose a strategy for superconformal ALD by adding a heavy inert gas as a diffusion additive. We show that the step coverage in an 18:1 aspect ratio feature increased from 1 to 1.6 with the addition of Kr in an ALD process for AlN from Al(CH3)3 and NH3. We speculate that the heavier Kr (84 amu) promotes the diffusion of the lighter NH3 (17 amu) down the trenches. Consequently, NH3 molecules are pushed to the trench bottom, resulting in a lower GPC at the trench openings. Further studies are needed to understand the effect of Kr, but we foresee that this approach to superconformal ALD is applicable to many ALD processes. | Arun Haridas Choolakkal; Pamburayi Mpofu; Pentti Niiranen; Jens Birch; Henrik Pedersen | Physical Chemistry; Materials Science; Nanoscience; Materials Processing; Thin Films; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759a5ecf9980725cfbb5f86/original/using-a-heavy-inert-diffusion-additive-for-superconformal-atomic-layer-deposition.pdf |
60c7437bbdbb89afa8a38668 | 10.26434/chemrxiv.9248918.v1 | Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist using Molecular Dynamics Simulations, Binding Free Energy Calculations and Mutagenesis | <p>Adenosine A<sub>3 </sub>receptor
(A<sub>3</sub>R), is a promising
drug target against cancer cell proliferation. Currently
there is no experimentally determined structure of A<sub>3</sub>R. Here, we have investigate a computational model,
previously applied successfully
for agonists binding to A<sub>3</sub>R, using
molecular dynamic (MD) simulations, Molecular Mechanics-Poisson Boltzmann
Surface Area (MM-PBSA) and Molecular Mechanics-Generalized Born Surface Area
(MM-GBSA) binding free energy calculations. Extensive
computations were performed to explore the binding profile of
O4-{[3-(2,6-dichlorophenyl)-5-methylisoxazol-4-yl]carbonyl}-2-methyl-1,3-thiazole-4-carbohydroximamide
(K18) to A<sub>3</sub>R. K18 is a new specific and competitive antagonist at
the orthosteric binding site of A<sub>3</sub>R, discovered using virtual
screening and characterized pharmacologically in our previous studies. The most plausible binding conformation for the dichlorophenyl
group of K18 inside the A<sub>3</sub>R is oriented
towards trans-membrane helices (TM) 5 and 6, according to the MM-PBSA
and MM-GBSA binding free energy calculations, and by the
previous results obtained by mutating residues of TM5, TM6 to alanine
which reduce antagonist potency. The results from 14 site-directed
mutagenesis experiments were interpreted using MD simulations and
MM-GBSA calculations which show that the relative binding free energies of the
mutant A<sub>3</sub>R - K18 complexes compare to the
WT A<sub>3</sub>R are in agreement with the effect of the mutations,
i.e. the reduction, maintenance or increase of antagonist potency. We show that
when the residues V169<sup>5.30</sup>, M177<sup>5.38</sup>, I249<sup>6.54</sup>
involved in direct interactions with K18 are mutated to alanine, the mutant A<sub>3</sub>R
- K18 complexes reduce potency, increase the RMSD value of K18 inside the
binding area and the MM-GBSA binding free energy compared to the WT A<sub>3</sub>R
complex. Our computational model shows that other mutant A<sub>3</sub>R
complexes with K18, including directly interacting residues, i.e. F168<sup>5.29</sup>A,
L246<sup>6.51</sup>A, N250<sup>6.55</sup>A complexes with K18 are not stable.
In these complexes of A<sub>3</sub>R mutated in directly interacting residues
one or more of the interactions between K18 and these residues are lost. In
agreement with the experiments, the computations show that, M174<sup>5.35</sup> a residue which does not make direct
interactions with K18 is critical for K18 binding. A
striking results is that the mutation of residue V169<sup>5.30</sup> to
glutamic acid maintained antagonistic potency. This effect is in agreement with
the binding free energy calculations and it is suggested that is due to K18
re-orientation but also to the plasticity of A<sub>3</sub>R binding area. The
mutation of direct interacting L90<sup>3.32</sup> in the low region and the
non-directly interacting L264<sup>7.35</sup> to alanine in the middle region
increases the antagonistic potency, suggesting that chemical modifications of
K18 can be applied to augment antagonistic potency. The
calculated binding energies Δ<i>G</i><sub>eff</sub>
values of K18 against mutant A<sub>3</sub>Rs displayed
very good correlation with experimental potencies (pA<sub>2</sub>
values). These results further approve the computational model for the
description of K18 binding with critical residues of the orthosteric binding
area which can have implications for the design of more effective antagonists
based on the structure of K18.</p> | Panagiotis Lagarias; Kerry Barkan; Eva Tzortzini; Eleni Vrontaki; Margarita Stampelou; Graham Ladds; Antonios Kolocouris | Biochemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7437bbdbb89afa8a38668/original/insights-to-the-binding-of-a-selective-adenosine-a3-receptor-antagonist-using-molecular-dynamics-simulations-binding-free-energy-calculations-and-mutagenesis.pdf |
6154f85b9e384070e7450e26 | 10.26434/chemrxiv-2021-rtpvw | Combining Metal-Metal Cooperativity, Metal-Ligand Cooperativity and Chemical Non-Innocence in Diiron Carbonyl Complexes | Several metalloenzymes, including [FeFe]-hydrogenase, employ cofactors wherein multiple metal atoms work together with surrounding ligands that mediate heterolytic and concerted proton-electron transfer (CPET) bond activation steps. Herein, we report a new dinucleating PNNP expanded pincer ligand, which can bind two low-valent iron atoms in close proximity to enable metal-metal cooperativity (MMC). In addition, reversible partial dearomatization of the ligand’s naphthyridine core enables both heterolytic metal-ligand cooperativity (MLC) and chemical non-innocence through CPET steps. Thermochemical and computational studies show how a change in ligand binding mode can lower the bond dissociation free energy of ligand C(sp3)–H bonds by ~25 kcal mol-1. H-atom abstraction enabled trapping of an unstable intermediate, which undergoes facile loss of two carbonyl ligands to form an unusual paramagnetic (S = 1/2) complex containing a mixed-valent iron(0)-iron(I) core bound within a partially dearomatized PNNP ligand. Finally, cyclic voltammetry experiments showed that these diiron complexes show catalytic activity for the electrochemical hydrogen evolution reaction. This work presents the first example of a ligand system that enables MMC, heterolytic MLC and chemical non-innocence, thereby providing important insights and opportunities for the development of bimetallic systems that exploit these features to enable new (catalytic) reactivity. | Cody Bernard Beek; Nicolaas P. van Leest; Martin Lutz; Robertus J. M. Klein Gebbink; Bas de Bruin; Daniël Laurens Johannes Broere | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Organometallic Compounds; Coordination Chemistry (Organomet.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6154f85b9e384070e7450e26/original/combining-metal-metal-cooperativity-metal-ligand-cooperativity-and-chemical-non-innocence-in-diiron-carbonyl-complexes.pdf |
628bf1a644bdd52c026deca6 | 10.26434/chemrxiv-2022-qsqj9 | Affinity Bioorthogonal Chemistry (ABC) Tags for Site-selective Conjugation, On-resin Protein-Protein Coupling, and Purification of Protein Conjugates | The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the Ni-IDA resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry tags (ABC-tags) serve a dual role by enabling affinity-based protein purification through metal chelation and still maintain their rapid kinetics in bioorthogonal reactions. ABC-tagging can be applied in conjunction with a range of site-selective bioconjugation methods, and is demonstrated for a range of proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. Importantly, the combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions for cleanly preparing protein-protein conjugates in minutes. | Joseph Fox; Samuel Scinto; Tyler Reagle | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628bf1a644bdd52c026deca6/original/affinity-bioorthogonal-chemistry-abc-tags-for-site-selective-conjugation-on-resin-protein-protein-coupling-and-purification-of-protein-conjugates.pdf |
64d4ebad4a3f7d0c0df0eaa2 | 10.26434/chemrxiv-2023-hmml5 | Predicting solvents with the help of Artificial Intelligence | The right solvent is a crucial factor in achieving environmentally friendly, selective, and highly converted chemical reactions. Artificial intelligence-based tools, often lack the ability to reliably predict reaction conditions such as the appropriate solvent. Here, we present a comprehensive investigation into the efficacy of data-driven machine-learning models for solvent prediction for a broad spectrum of single-solvent organic reactions. Remarkably, our models achieve a Top-3 accuracy of 86.88%, showcasing outstanding performance in predicting solvents from underrepresented classes. An uncertainty analysis revealed that the models' misclassifications could be explained by the fact that the reaction can be run in multiple solvents. In the experimental validation, 8 out of 11 reactions succeeded with the predicted solvent. Our work addresses a key challenge in organic synthesis and demonstrates the practical application of machine learning models in predicting reaction solvents for more efficient and sustainable chemical synthesis. | Oliver Tobias Schilter; Carlo Baldassari; Teodoro Laino; Philippe Schwaller | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d4ebad4a3f7d0c0df0eaa2/original/predicting-solvents-with-the-help-of-artificial-intelligence.pdf |
60c75748bb8c1a3e8e3dc7c9 | 10.26434/chemrxiv.13788865.v4 | The Relation Between Ejection Mechanism and Ion Abundance in the Electric Double Layer of Drops | <div> Charged droplets have been associated with distinct chemical reactivity. It is assumed that the composition of the surface layer plays a critical role in enhancing the reaction rates in the droplets relative to their bulk counterparts. We use atomistic modeling to relate the localization of the ions in the surface layer to their ejection propensity. We find that<br />the ion ejection takes place via a two-stage process. Firstly, a conical protrusion emerges as a result of a global droplet deformation that is insensitive to the locations of single ions. The ions are subsequently ejected as they enter the conical regions. The study provides mechanistic insight into the<br /> ion-evaporation mechanism, which can be used to revise the commonly used ion-evaporation models. We argue that atomistic molecular dynamics simulations of minute nano-drops, do not sufficiently distinguish the ion-evaporation mechanism from a Rayleigh fission. We explain mass spectrometry data on the charge state of small globular proteins and the existence of super-charged droplet states (above the Rayleigh limit) that have been detected in experiments. <br /></div><div><br /></div><div><br /></div><div><br /></div> | Victor Kwan; Ryan O'Dwyer; David Laur; Jiahua Tan; Styliani Consta | Mass Spectrometry; Clusters; Interfaces; Solution Chemistry; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75748bb8c1a3e8e3dc7c9/original/the-relation-between-ejection-mechanism-and-ion-abundance-in-the-electric-double-layer-of-drops.pdf |
6790158981d2151a02347774 | 10.26434/chemrxiv-2024-ztp85-v2 | DiffractGPT: Atomic Structure Determination from X-ray Diffraction Patterns using Generative Pre-trained Transformer | Crystal structure determination from powder diffraction patterns is a complex challenge in materials science, often requiring extensive expertise and computational resources. This study introduces DiffractGPT, a generative pre-trained transformer model designed to predict atomic structures directly from X-ray diffraction (XRD) patterns. By capturing the intricate relationships between diffraction patterns and crystal structures, DiffractGPT enables fast and accurate inverse design. Trained on thousands of atomic structures and their simulated XRD patterns from the JARVIS-DFT dataset, we evaluate the model across three scenarios: (1) without chemical information, (2) with a list of elements, and (3) with an explicit chemical formula. The results demonstrate that incorporating chemical information significantly enhances prediction accuracy. Additionally, the training process is straightforward and fast, bridging gaps between computational, data science, and experimental communities. This work represents a significant advancement in automating crystal structure determination, offering a robust tool for data-driven materials discovery and design. | Kamal Choudhary | Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Theory - Computational; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6790158981d2151a02347774/original/diffract-gpt-atomic-structure-determination-from-x-ray-diffraction-patterns-using-generative-pre-trained-transformer.pdf |
62b5dbc70bbbc11d8a74729d | 10.26434/chemrxiv-2022-bm062-v2 | Discovery of Amino Acid fingerprints transducing their amphoteric signatures by field-effect transistors | Protein sequencing is key to many biological fields to advance science and prospect medical applications based on proteomics. However, even with advanced techniques such as mass spectrometry it is hard to detect the fluctuations in AA sequences and optical/geometrical isomers, and cannot provide wide access to ex-novo sequencing of low quantities of proteins. We are presenting a new and disruptive method based on FET sensors for AA/polypeptide detection. We show unique signals (fingerprints) of every single AA and polypeptide mutations by solving the site-binding model self-consistently with the Gouy-Chapman-Stern model. The surface potential (Ψo), 2nd gradient of the surface potential (δΨo2/δpH2) and total surface capacitance (CT) are used as fingerprint signals to differentiate between the amino acids including the drain current variation as the signal transduction. These fingerprints are based on orthogonal properties of the AAs, which are the different proton affinities of each of the radicals, their dielectric constant and effective length, which is sensitive to the relative positions of the radicals to distinguish between isomers. We studied the generation of signals and proposed a novel noise-filtering technique based on the Fast-Fourier Transform (FFT) and the significantly improved analytical model which is solved iteratively to reduce data loss. The minimum combined fingerprint resolution is 0.1 units of pH for the separation of singularities found in δΨo2/δpH2, linked to the minimum capacitance of the AAs with a needed resolution of 0.01mF/m2 for surface densities of 1014cm-2, and which can be normalized to lower densities. The effect of noise (>SNR=10dB) and silanol sites can be negated by correlating the AAs signatures from δΨo2/δpH2 and capacitance. Thus, the designed methodology and approach can help immensely in designing a new and efficient tool for protein sequencing while solving the problems related to the signal transduction of sensors. | Naveen Kumar; Rakshita Pritam Singh Dhar; César Pascual García; Vihar Georgiev | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Nanodevices; Bioinformatics and Computational Biology; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b5dbc70bbbc11d8a74729d/original/discovery-of-amino-acid-fingerprints-transducing-their-amphoteric-signatures-by-field-effect-transistors.pdf |
614de98639ef6af8a828954b | 10.26434/chemrxiv-2021-2wvwp-v2 | Electrocatalytic H2 Evolution Promoted by a Bioinspired (N2S2)Ni(II) Complex at Low Acid Concentration | We have investigated a bioinspired (N2S2)Ni(II) electrocatalyst that produces H2 from CF3CO2H with a turnover frequency (TOF) of ~200,000 s–1 at low acid concentration (<0.043 M) in MeCN. We also propose an electrochemical mechanism for such an electrocatalyst toward H2 production and benchmarked its activity by comparing its TOF and overpotential with those of other reported molecular Ni H2 evolution electrocatalysts. | Soumalya Sinha; Giang N. Tran; Hanah Na; Liviu M. Mirica | Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614de98639ef6af8a828954b/original/electrocatalytic-h2-evolution-promoted-by-a-bioinspired-n2s2-ni-ii-complex-at-low-acid-concentration.pdf |
60c73dd6337d6c2125e26250 | 10.26434/chemrxiv.6205322.v1 | Directing the Reactivity of Metal Hydrides for Selective CO2 Reduction | A critical challenge in electrocatalytic CO<sub>2</sub> reduction to renewable fuels is product selectivity. Desirable CO<sub>2</sub> reduction products require proton equivalents, but key catalytic intermediates in CO<sub>2</sub> reduction can also be competent for direct proton reduction to H<sub>2</sub>. Understanding how to manage divergent reaction pathways at these shared intermediates is essential to achieving high selectivity. Both proton reduction to hydrogen and CO<sub>2</sub> reduction to formate generally proceed through a metal hydride intermediate. We apply thermodynamic relationships that describe the reactivity of metal hydrides with H+ and CO<sub>2</sub> to generate a modified Pourbaix diagram which outlines product favorability as a function of pro-ton activity and hydricity (ΔG<sub>H-</sub>), or hydride donor strength. The diagram outlines a region of metal hydricity and proton activity in which CO2 reduction is favorable and H+ reduction is suppressed. We apply our diagram to inform our selection of [Pt(dmpe)<sub>2</sub>](PF<sub>6</sub>)<sub>2</sub> as a potential catalyst because the corresponding hydride [HPt(dmpe)<sub>2</sub>]+ has the correct hydricity to access the region where selective CO2 reduction is possible. We validate our choice experimentally; [Pt(dmpe)<sub>2</sub>](PF6)<sub>2</sub> is a highly selective electrocatalyst for CO<sub>2</sub> reduction to formate (>90 % Faradaic efficiency) at an overpotential of less than 100 mV with no evidence of catalyst degradation after electrolysis. Our report of a new selective catalyst for CO<sub>2</sub> reduction illustrates how our modified Pourbaix diagrams can guide selective and efficient catalyst discovery. | Bianca M. Ceballos; Jenny Yang | Electrochemistry; Inorganic Acid/Base Chemistry; Kinetics and Mechanism - Inorganic Reactions; Organometallic Compounds; Reaction (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.); Electrocatalysis; Homogeneous Catalysis; Catalysis; Electrochemistry - Organometallic; Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.); Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd6337d6c2125e26250/original/directing-the-reactivity-of-metal-hydrides-for-selective-co2-reduction.pdf |
6769dc3a81d2151a02b75ef6 | 10.26434/chemrxiv-2024-1dw4q | Inverse Design of Complex Nanoparticle Heterostructures via Deep Learning on Heterogeneous Graphs | Applications of deep learning (DL) to design nanomaterials are hampered by a lack of suitable data representations and training data. We report efforts to overcome these limitations and leverage DL to optimize the nonlinear optical properties of core-shell upconverting nanoparticles (UCNPs). UCNPs, which have applications in e.g., biosensing, super-resolution microscopy, and 3D printing, can emit visible and ultraviolet light from near-infrared excitations. We report the first large-scale dataset of UCNP emission spectra based on accurate but expensive kinetic Monte Carlo simulations (N > 6,000) and use this data to train a heterogeneous graph neural network (GNN) using a novel representation of UCNP nanostructure. Applying gradient-based optimization on the trained GNN, we identify structures with 6.5 times higher predicted emission under 800nm illumination than any UCNP in our training set. Our work reveals new design principles for UCNPs and presents a roadmap for DL-based inverse design of nanomaterials. | Eric Sivonxay; Lucas Attia; Evan Walter Clark Spotte-Smith; Benjamin Lengeling; Xiaojing Xia; Daniel Barter; Emory Chan; Samuel Blau | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Machine Learning; Optics | CC BY 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6769dc3a81d2151a02b75ef6/original/inverse-design-of-complex-nanoparticle-heterostructures-via-deep-learning-on-heterogeneous-graphs.pdf |
60c751eb469df49128f44ab8 | 10.26434/chemrxiv.13203986.v1 | Rapid Screening of Diverse Biotransformations for Enzyme Evolution | <p>The lack of label-free
high-throughput screening technologies presents a major bottleneck in the
identification of active and selective biocatalysts, with the number of variants
often exceeding the capacity of traditional analytical platforms to assess
their activity in a practical timescale. Here we show the application of direct
infusion mass spectrometry (DiBT-MS) screening to a variety of enzymes, in
different formats, achieving sample throughputs equivalent to ~40 seconds per sample.
The heat-map output allows rapid selection of active enzymes within 96-well plates
facilitating identification of industrially relevant biocatalysts. This DiBT-MS
screening workflow has been applied to the directed evolution of a
phenylalanine ammonia lyase (PAL), enhancing its activity towards electron-rich cinnamic acid derivatives which
are relevant to lignocellulosic biomass degradation. Additional benefits of the
screening platform include the discovery of biocatalysts (kinases, imine
reductases) with novel activities and the incorporation of ion mobility
technology for the identification of product hits with increased confidence. </p> | Emily Kempa; James L. Galman; Fabio Parmeggiani; James Marshall; Julien Malassis; Clement Fontenelle; Jean-Baptiste Vendeville; Bruno Linclau; Simon J. Charnock; Sabine Flitsch; Nicholas Turner; Perdita Barran | High-throughput Screening; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751eb469df49128f44ab8/original/rapid-screening-of-diverse-biotransformations-for-enzyme-evolution.pdf |
63e5c76e1d2d18406337135d | 10.26434/chemrxiv-2023-h8905 | Improving Molecular Machine Learning Through Adaptive Subsampling with Active Learning | Data subsampling is an established machine learning pre-processing technique to reduce bias in datasets. However, subsampling can lead to the removal of crucial information from the data and thereby decrease performance. Multiple different subsampling strategies have been proposed, and benchmarking is necessary to identify the best strategy for a specific machine learning task. Instead, we propose to use active machine learning as an autonomous and adaptive data subsampling strategy. We show that active learning-based subsampling can lead to better molecular machine learning performance when compared to both training models on the complete training data and 19 state-of-the-art subsampling strategies. We find that active learning is robust to errors in the data, highlighting the utility of this approach for low quality datasets. Taken together, we here describe a new, adaptive machine learning pre-processing approach and provide novel insights into the behavior and robustness of active machine learning for molecular sciences. | Yujing Wen; Zhixiong Li; Yan Xiang; Daniel Reker | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e5c76e1d2d18406337135d/original/improving-molecular-machine-learning-through-adaptive-subsampling-with-active-learning.pdf |
679a1ff8fa469535b94c48e5 | 10.26434/chemrxiv-2025-g0rcx | Rotated Fourier transform (RFT) enables the quantification of anisotropic structure in high-moisture plant-protein extrudates | When producing plant-protein-based meat analogues via high moisture extrusion (HME), the structure of extrudates is determined by complex interactions between ingredient composition and processing conditions. To facilitate consumers in their transition towards a diet higher in plant-based proteins, the food industry aims to closely mimic the structure of meat of animal origin. Currently, insights into the structuring process are gained, for example, by imaging samples using MRI or confocal microscopy. Existing software for analysing these images, however, often lacks the ability to quantitively analyse structure and anisotropy. Here, we present a new image processing method, named Rotated Fourier Transform (RFT), that enables the quantification of anisotropic structures of extrudates from multimodal images acquired at different length scales. RFT can provide a single measure of structural anisotropy, namely the weighted order parameter (WOP), for either the entire image or subregions thereof. RFT utilises Fourier transforms to obtain the dominant angles representing the structural orientation detected within the image. For each dominant angle, we further calculate an amplitude relative to the background within each sub-image. These amplitudes depend on the signal-to-noise levels of the corresponding angular features, which enables reducing the influence of insignificant features on the WOP. Here, we used RFT to quantify anisotropy in images of soy protein concentrate HME samples. We identified both anisotropic and isotropic regions and further showed that the relative spatial extent of the anisotropic region, perpendicular to the flow direction, increases along the cooling die. While applied in this paper to the specific case of soy HME samples, RFT is a generic method applicable to any image displaying anisotropic features. Thus, RFT is a powerful and robust tool for comprehensive quantification of food structures and beyond. | Martijn I. Gobes; Sam A. Kuijpers; Camilla Terenzi; Ruud van der Sman; John P.M. Duynhoven; Johannes Hohlbein | Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a1ff8fa469535b94c48e5/original/rotated-fourier-transform-rft-enables-the-quantification-of-anisotropic-structure-in-high-moisture-plant-protein-extrudates.pdf |
60c74c689abda23c31f8d282 | 10.26434/chemrxiv.12469046.v1 | Terrestrial Trapping of the Interstellar Gas, Phosphorus Nitride | The N2 analogue phosphorus nitride (PN) was the first phosphorus containing compound to be detected in the interstellar medium, however this thermodynamically unstable compound has a fleeting existence on Earth. Here, we show that reductive coupling of iron(IV) nitride and molybdenum(VI) phosphide complexes assembles PN as a bridging ligand in a structurally-characterized bimetallic complex. Reaction with C≡N<sup>t</sup>Bu releases the mononuclear complex [(N<sub>3</sub>N)Mo-PN]<sup>−</sup>, N<sub>3</sub>N = [(Me<sub>3</sub>SiNCH<sub>2</sub>CH<sub>2</sub>)<sub>3</sub>N]<sup>3−</sup>), which undergoes light-induced linkage isomerization to provide [(N<sub>3</sub>N)Mo-NP]<sup>−</sup>, as revealed by photocrystallography. While structural and spectroscopic characterization, supported by electronic structure calculations reveal PN multiple bond character, coordination to molybdenum creates nucleophilic character at the terminal atom of the PN/NP ligands. Indeed, the linkage isomers can be trapped in solution by reaction with a Rh(I) electrophile. | Jorge L. Martinez; Sean A. Lutz; daniel beagan; Xinfeng Gao; Maren Pink; Chun-Hsing Chen; veronica carta; Pierre Moënne-Loccoz; Jeremy Smith | Bonding; Coordination Chemistry (Inorg.); Ligands (Inorg.); Organometallic Compounds; Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c689abda23c31f8d282/original/terrestrial-trapping-of-the-interstellar-gas-phosphorus-nitride.pdf |
660568d39138d231618b4e50 | 10.26434/chemrxiv-2024-46rxl | Docking-informed machine learning for kinome wide affinity prediction | Kinase inhibitors are an important class of anti-cancer drugs, with 80 inhibitors clinically approved, and >100 in active clinical testing. Most bind competitively in the ATP-binding site, leading to challenges with selectivity for a specific kinase, resulting in risks for toxicity and general off-target effects. Assessing the binding of an inhibitor for the entire kinome is experimentally possible but expensive. A reliable and interpretable computational prediction of kinase selectivity would greatly benefit the inhibitor discovery and optimisation process. Here, we use machine learning on docked poses to address this need. To this end, we aggregated all known inhibitor-kinase affinities and generated the complete accompanying 3D interactome by docking all inhibitors to the respective high quality X-ray structures. We then used this resource to train a neural network as a kinase-specific scoring function, which achieved an overall performance (R²) of 0.63-0.74 on unseen inhibitors across the kinome. The entire pipeline from molecule to 3D-based affinity prediction has been fully automated and wrapped in a freely available package. This has a graphical user interface which is tightly integrated with PyMOL to allow immediate adoption in the medicinal chemistry practice. | Jordy Schifferstein; Andrius Bernatavicius; Antonius P.A. Janssen | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660568d39138d231618b4e50/original/docking-informed-machine-learning-for-kinome-wide-affinity-prediction.pdf |
632e4727e665bd456410711b | 10.26434/chemrxiv-2022-fr63d-v2 | Polymer Relaxation Time Enhancement at Temperatures above Glass Transition Temperatures Predicted by Idealized Mode-Coupling Theory | The mode-coupling theory of glass transition predicts the relaxation time divergence of glass-forming materials at the crossover temperature, which is approximately 1.2 times the calorimetric glass transition temperature. However, this divergence has not been experimentally observed. This is known as the most serious drawback of the mode-coupling theory. The use of viscosity-sensitive single molecule fluorescence probes enables the detection of the poly(vinyl acetate) and poly(ethyl methacrylate) relaxation time enhancement around the crossover temperature, thereby supporting the prediction by the mode-coupling theory. | Mitsuru Ishikawa; Keita Matsumoto; Tomoya Yamazaki; Risa Fukase; Yutaka Ichikawa; Takayuki Uwada | Physical Chemistry; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632e4727e665bd456410711b/original/polymer-relaxation-time-enhancement-at-temperatures-above-glass-transition-temperatures-predicted-by-idealized-mode-coupling-theory.pdf |
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