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60c7432c0f50dbbe47395e58 | 10.26434/chemrxiv.8948831.v1 | Photoluminescence Emission Induced by Localized States in Halide Passivated Colloidal Two-Dimensional WS2 Nanoflakes | <p>Engineering physicochemical properties of
two-dimensional transition metal dichalcogenide (2D-TMD) materials by surface
manipulation is essential for their practical and large-scale application
especially for colloidal 2D-TMDs that are plagued by the unintentional
formation of structural defects during the synthetic procedure. However, the
available methods to manage surface states of 2D-TMDs in solution-phase are still
limited hampering the production of high quality colloidal 2D-TMD inks to be
straightforwardly assembled into actual devices. Here, we demonstrate an
efficient solution-phase strategy to passivate surface defect states of colloidally
synthetized WS<sub>2 </sub>nanoflakes with halide ligands, resulting in the activation
of the photoluminescence emission. Photophysical investigation and density
functional theory calculations suggest that halide atoms enable the suppression
of non-radiative recombination through the elimination deep gap trap states,
and introduce localized states in the energy band structure from which excitons
efficiently recombine. Halide passivated WS<sub>2</sub> nanoflakes importantly
preserve colloidal stability and photoluminescence emission after several weeks
of storing in ambient atmosphere, corroborating the potential of our developed
2D-TMD inks.</p> | Rosanna Mastria; Anna Loiudice; Jan Vávra; Concetta Nobile; Riccardo Scarfiello; P. Davide Cozzoli; Nicola Sestu; Daniela Marongiu; Francesco Quochi; Raffaella Buonsanti; Michele Saba; Arrigo Calzolari; Aurora Rizzo | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7432c0f50dbbe47395e58/original/photoluminescence-emission-induced-by-localized-states-in-halide-passivated-colloidal-two-dimensional-ws2-nanoflakes.pdf |
676c96ef81d2151a02eb42b2 | 10.26434/chemrxiv-2024-7591m-v2 | Binding mechanism of adenylate kinase-specific monobodies | Monobody, an antibody-mimetic protein, regulates enzyme functions through protein-protein interactions. In this study, we investigated the binding mechanisms of monobodies to adenylate kinase (Adk). Calorimetric and X-ray crystallographic analyses revealed that CL-1, a monobody specific for the CLOSED form of Adk, binds to the CORE domain of Adk in an enthalpy-driven manner, forming several hydrogen bonds and a cation-π interaction at the protein interface, without perturbating the Adk backbone. In contrast, OP-4, an OPEN-form-specific monobody, exhibited the entropy-driven binding. 1H–15N 2D nuclear magnetic resonance (NMR) and 31P-NMR studies revealed conformational perturbations to Adk by OP-4, while substrate access remained intact. The different thermodynamic and structural effects between the monobodies highlight the diverse binding mechanisms among monobodies. | Ibuki Nakamura; Hiroshi Amesaka; Satoshi Nagao; Shigeru Negi; Shun-ichi Tanaka; Takashi Matsuo | Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676c96ef81d2151a02eb42b2/original/binding-mechanism-of-adenylate-kinase-specific-monobodies.pdf |
6522e6c545aaa5fdbb8e7767 | 10.26434/chemrxiv-2023-79qj3 | Long Oligodeoxynucleotides: Chemical Synthesis, Isolation via Catching by Polymerization, Verification via Sequencing, and Gene Synthesis and Expression Demonstration | Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here we report direct de novo chemical synthesis of 400 nt ODNs, and their isolation from complex reaction mixture using the catching-by-polymerization (CBP) method. To determine the authenticity of the ODNs, 399 and 401 nt ODNs were synthesized and purified with CBP. The two were joined together using Gibson assembly to give the 800 nt green fluorescent protein (GFP) gene construct. The sequence of the construct was verified via Sanger sequencing. To demonstrate the potential use of the long ODN synthesis method, the GFP gene was expressed in E. coli. The long ODN synthesis and isolation method presented here provides a pathway to the production of genes and genomes containing long repeats or stable secondary structures that cannot be produced or are highly challenging to produce using existing technologies. | Yipeng Yin; Reed Arneson; Alexander Apostle; Adikari Eriyagama; Komal Chillar; Emma Burke; Martina Jahfetson; Yinan Yuan; Shiyue Fang | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6522e6c545aaa5fdbb8e7767/original/long-oligodeoxynucleotides-chemical-synthesis-isolation-via-catching-by-polymerization-verification-via-sequencing-and-gene-synthesis-and-expression-demonstration.pdf |
66eb7869cec5d6c1427ecdc0 | 10.26434/chemrxiv-2024-q6b3g | A Motif for Generating Coherently Degenerate States in A-D-D-A Type Organic Small Molecules | Encouraged by the superior performance of the D-A-A-D dimer in generating Wannier excitons, we developed a new motif to construct A-D-D-A type organic small molecules. The donor moieties consist of 4,4’-dimethyl-4”-((4-amino)styryl)-triphenylamine, while the acceptor is an s-triazine derivative. DFT studies, using two detection techniques, confirmed that a pair of Wannier exictons is generated in one of the newly designed compounds studied here. Based on the analysis of molecular orbitals and the UV-Vis spectrum, A-D-D-A-2 has been identified as the Wannier molecule. Although A-D-D-A-1 is not confirmed as a Wannier molecule based on the molecular orbital inspection, it may still generate Wannier excitons; however further studies with new techniques are needed to confirm this. A brief discussion of the double excitation in A-D-D-A-2 is also provided. The motif used in the formation of Wannier molecules of A-D-D-A type dimers, i.e. A-D-D-A-2, is the same motif as in the other high performing organic small molecules. This suggests that these high-performance organic molecules may already generate Wannier excitons, which could be the primary reason for their exceptional performance as photosensitizers in solar cells. | Junpeng Zhuang; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66eb7869cec5d6c1427ecdc0/original/a-motif-for-generating-coherently-degenerate-states-in-a-d-d-a-type-organic-small-molecules.pdf |
660a973566c13817296743e2 | 10.26434/chemrxiv-2024-dxz34 | A Dual Cobalt-Photoredox Catalytic Approach for Asymmetric Dearomatization of Indoles with Aryl Amides via C-H Activation | In this study, we unveil a novel method for the asymmetric dearomatization of indoles under cobalt/photoredox catalysis. By strategically activating C-H bonds of amides and subsequent migratory insertion of -bonds present in indole as reactive partner, we achieve syn-selective tetrahydro-5H-indolo[2,3-c]isoquinolin-5-one derivatives with excellent yields and enantiomeric excesses of up to >99%. The developed method operates without a metal oxidant, relying solely on oxygen as the oxidant and employing an organic dye as a photocatalyst under irradiation. Control experiments and stoichiometric studies elucidate the reversible nature of the enantiodetermining C-H activation step, albeit not being rate-determining. This study not only expands the horizon of cobalt-catalyzed asymmetric C-H bond functionalization, but also showcases the potential synergy between cobalt and photoredox catalysis in enabling asymmetric synthesis of complex molecules. | Abir Das; Subramani Kumaran; Harihara Subramanian Ravi Sankar; J. Richard Premkumar; basker sundararaju | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660a973566c13817296743e2/original/a-dual-cobalt-photoredox-catalytic-approach-for-asymmetric-dearomatization-of-indoles-with-aryl-amides-via-c-h-activation.pdf |
60c74854337d6c0235e2752f | 10.26434/chemrxiv.11891580.v1 | Dual Cobalt and Photoredox Catalysis Enabled Intermolecular Oxidative Hydrofunctionalization | A general protocol has been developed for the Markovnikov-selective intermolecular hydrofunctionalization based on visible-light-mediated Co/Ru dual catalysis. The key feature involves the photochemical oxidation of an organocobalt(III) intermediate derived from hydrogen atom transfer, which is supported by electrochemical analysis, quenching studies and stoichiometric experiments. This unique redox process enables the efficient branch-selective alkylation of pharmaceutically important nucleophiles (phenols, sulfonamides and various N-heterocycles) using a wide range of alkenes including moderately electron-deficient ones. Moreover, light-gated polar functionalization via organocobalt species was demonstrated. | Han-Li Sun; Fan Yang; Wei-Ting Ye; Jun-Jie Wang; Rong Zhu | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74854337d6c0235e2752f/original/dual-cobalt-and-photoredox-catalysis-enabled-intermolecular-oxidative-hydrofunctionalization.pdf |
63bf89201f125802679abd6e | 10.26434/chemrxiv-2023-ds7dp | Insights into the Mechanism of CO2 Electroreduction by Molecular Palladium-Pyridinophane Complexes | Herein we report the synthesis, characterization, and electrocatalytic CO2 reduction activity of a series of PdII complexes supported by tetradentate pyridinophane ligands. In particular, we focus on the electrocatalytic CO2 reduction activity of a PdII complex supported by the mixed hard/soft 2,11-dithia[3.3](2,6)pyridinophane (N2S2) ligand . This is one of the few examples of a Pd complexes supported by a mixed hard-soft ligand which selectively produces CO from the electrocatalytic reduction of CO2. Notably, unlike previously reported molecular Pd complexes, selective CO2RR occurs in presence of weak proton sources such as 2, 2, 2 trifluoroethanol (TFE) and phenol, at mild overpotentials (~160 mV) and with high rates (kobs = 4.5 x 103 s-1, with phenol as proton source) and at Faradaic efficiencies of up to 70% for CO, without any H2 being detected. As the catalyst was not stable to long term electrolysis, we analyzed possible decomposition routes for this catalyst and, based on the characterization of its reaction with CO by UV-vis, NMR, and IR spectroscopy, we propose the intermediacy of a binuclear [(N2S2)PdI(η2-CO)]2 species toward the ultimate decomposition of the catalyst into free ligand and Pd0. Overall, these studies offer important insights into Pd catalyst decomposition and may explain the historically poor performance of related Pd molecular catalysts for CO2 reduction. In addition, the structurally-related hard N-donor diazapyridinophane (RN4)Pd complexes are shown to be unstable towards bulk electrolysis at cathodic potentials, suggesting that such compounds are ill-suited for CO2 electroreduction. | Sagnik Chakrabarti; Toby J. Woods; Liviu Mirica | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Organometallic Compounds; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bf89201f125802679abd6e/original/insights-into-the-mechanism-of-co2-electroreduction-by-molecular-palladium-pyridinophane-complexes.pdf |
60c752dfee301c68d3c7aca9 | 10.26434/chemrxiv.13277321.v2 | Therapeutic Drug Monitoring: Performance of a FRET-Based Point-Of-Care Immunoassay for the Quantitation of Infliximab and Adalimumab in Blood | <p>Two
fast (<5 min), time-resolved fluorescence resonance energy transfer
(FRET)-based immunoassays (Procise IFX™ and Procise ADL™) were developed for
the quantitative detection of infliximab (IFX), adalimumab (ADL), and their respective
biosimilars for use in therapeutic drug monitoring (TDM) using 20 µL of finger
prick whole blood at the point-of-care or whole blood/serum in a central lab. Studies were performed to characterize
analytical performance of the Procise IFX and the Procise ADL assays on the
ProciseDx™ analyzer.</p>
<p><br /></p><p>The
Procise IFX and Procise ADL assays both showed good analytical performance with
respect to sensitivity, specificity, linearity, and precision suitable for
routine clinical use as well as excellent correlation to current commercial
ELISA IFX and ADL measurement methods.</p>
<p><br /></p><p>Results
indicated that the Procise IFX and Procise ADL assays are sensitive, specific,
and precise yielding results in less than 5 minutes from either whole blood or
serum. This indicates the Procise IFX and Procise ADL assays are useful for
obtaining fast and accurate IFX or ADL quantitation, thus avoiding delays
inherent to current methods and enabling immediate drug level dosing decisions
to be made during a single patient visit.</p> | Edgar Ong; Ruo Huang; Richard Kirkland; Stefan Westin; Jared Salbato; Kurt Bray; Larry Mimms; Michael Hale; Valerie Day | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752dfee301c68d3c7aca9/original/therapeutic-drug-monitoring-performance-of-a-fret-based-point-of-care-immunoassay-for-the-quantitation-of-infliximab-and-adalimumab-in-blood.pdf |
613f58ce42198e0152752890 | 10.26434/chemrxiv-2021-0cb4d | Long-lifetime, potentially low-cost anthraquinone flow battery chemistry developed from study of effects of water-solubilizing group and connection to core
| Water-soluble anthraquinones (AQs) hold great promise serving as redox-active species in aqueous organic redox flow batteries. Systematic investigations into how the properties of redox molecules depend on the water-solubilizing groups and the way in which they are bound to the redox core are, however, still lacking. We introduce water-solubilizing groups linked to anthraquinone by C=C bonds via Heck cross-coupling reactions and convert C=C bonds to CC bonds through hydrogenation. The anthraquinone and the ending groups are connected via branched or straight chains with either unsaturated or saturated bonds. We investigate the influence of water-solubilizing chains and ionic ending groups on redox potentials of molecules and identify three important trends. (1): The electron-withdrawing ending groups can affect redox potentials of AQs with two unsaturated hydrocarbons on the chains through π-conjugation. (2): For chains with two saturated or unsaturated straight hydrocarbons, water-solubilizing ending groups increase redox potentials of the AQs in the order of PO32 <CO2<SO3. (3): AQs with saturated and unbranched chains at high pH possess desirably low redox potentials, high solubilities, and high stability. Disproportionation leads to the formation of anthrone, which can be regenerated to anthraquinone. Tautomerization results in the saturation of alkene chains, stabilizing the structure. We utilize these observations to identify a potentially low-cost and long-lifetime negolyte that demonstrates a temporal fade rate as low as 0.0128%/day when paired with a potassium ferrocyanide posolyte. | Yan Jing; Eric Fell; Min Wu; Shijian Jin; Yunlong Ji; Daniel Pollack; Zhijiang Tang; Dian Ding; Meisam Bahari; Marc-Antoni Goulet; Tatsuhiro Tsukamoto; Roy Gordon; Michael Aziz | Materials Science; Energy; Carbon-based Materials; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f58ce42198e0152752890/original/long-lifetime-potentially-low-cost-anthraquinone-flow-battery-chemistry-developed-from-study-of-effects-of-water-solubilizing-group-and-connection-to-core.pdf |
60c750c6567dfe0e36ec5918 | 10.26434/chemrxiv.13079663.v1 | DEET Degradation by Titanium Dioxide–Zeolite Nanocomposites: Effects of Aggregation State, Water Chemistry, and Natural Organic Matter | Immobilization
of titanium dioxide nanoparticles (TiO<sub>2</sub> NPs) facilitates their removal
and reuse in water treatment applications. Composite materials of
electrostatically-bound TiO<sub>2</sub> NPs and zeolite particles have been
proposed, but limited mechanistic studies are available on their performance in
complex media. This study delineates the relative importance of homo- and
heteroaggregation, water chemistry, and surface fouling by natural organic
matter (NOM) on the photocatalytic degradation of diethyltoluamide (DEET) by
TiO<sub>2</sub>-zeolite composites. Zeolite adsorbs a portion of the DEET,
rendering it unavailable for degradation; corrections for this adsorption
depletion allowed appropriate comparison of the reactivity of the composites to
the NPs alone. The TiO<sub>2</sub>-zeolite composites showed enhanced DEET degradation
in moderately hard water (MHW) compared to deionized water (DIW), likely
attributable to the influence of HCO<sub>3</sub><sup>−</sup>, whereas a net decline in reactivity was observed
for the TiO<sub>2</sub> NPs alone upon homoaggregation in MHW. The composites also
better maintained reactivity in the presence of NOM in MHW, as removal of Ca<sup>2+</sup>
onto the zeolite mitigated fouling of the TiO<sub>2</sub> surface by NOM. However,
NOM induced partial dissociation of the composites. DEET byproduct formation, identified
by quadrupole–time of flight (QTOF) mass spectrometry, was generally unaffected
by the zeolite, while NOM fouling favored de-ethylation over hydroxylation
products. Overall, the most significant factor influencing TiO<sub>2</sub>
reactivity toward DEET was NOM adsorption, followed by homoaggregation, electrolytes
(here, MHW versus DIW), and heteroaggregation. These findings can inform a
better understanding of NP reactivity in engineered water treatment applications. | Tchemongo B. Berté; Anthony S. Chen; Riya A. Mathew; Sheyda Shakiba; Stacey M. Louie | Nanocatalysis - Catalysts & Materials; Water Purification; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c6567dfe0e36ec5918/original/deet-degradation-by-titanium-dioxide-zeolite-nanocomposites-effects-of-aggregation-state-water-chemistry-and-natural-organic-matter.pdf |
60c73f34ee301c982cc7886a | 10.26434/chemrxiv.7271288.v1 | A Synthetic Mimic of Inhibitor Binding in Phosphodiesterase Type 5 based on Corona Phase Molecular Recognition of Single Walled Carbon Nanotubes | <pre>Molecular recognition binding sites that specifically identify a target molecule are essential for research in the life sciences, clinical diagnoses and therapeutic development. Corona Phase Molecular Recognition is a technique introduced to generate synthetic recognition at the surface of a nanoparticle corona, but it remains an important question whether such entities can achieve the specificity of natural enzymes and receptors. In this work, we generate and screen a library of 24 amphiphilic polymers based on functional monomers including methacrylic acid, acrylic acid, styrene and so on, iterating upon a poly(methacrylic acid-co-styrene) motif that demonstrates a binding specificity remarkably similar to an enzyme - Phosphodiesterase Type 5 - in its molecular recognition. The corona phase binds selectively to an inhibitor - Vardenafil, as well as its derivatives, but not to another inhibitor and substrate that interact differently with the enzyme. Our study examines the specificity and sensitivity by mutation of the polymer structure and configuration, as well as the competition with native binding sites. We demonstrate that the recognition originates from the unique three-dimensional configuration of the corona phase. This work conclusively shows that corona phase molecular recognition can mimic key aspects of biological recognition sites and drug targets, opening up possibilities for new pharmaceutical and biological applications.</pre> | Juyao Dong; Michael Lee; Imon Rahaman; Jessica Sun; Ananth Rajan; Daniel Salem; Michael Strano | Carbon-based Materials; Analytical Chemistry - General; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f34ee301c982cc7886a/original/a-synthetic-mimic-of-inhibitor-binding-in-phosphodiesterase-type-5-based-on-corona-phase-molecular-recognition-of-single-walled-carbon-nanotubes.pdf |
60c74ad94c89191487ad3307 | 10.26434/chemrxiv.12237182.v1 | Impacts of Modifiable Factors on Ambient Air Pollution: A Case Study of COVID-19 Shutdowns | Modifiable sources of air pollution such as traffic, cooking, and electricity generation emissions can be modulated either by changing activity levels or source intensity. Although air pollution regulations typically target reducing emission factors rather than altering activity, the COVID-19 related closures offered a novel opportunity to observe and quantify the impact of activity levels of modifiable factors on ambient air pollution in real-time. We use data from a network of twenty-seven low-cost Real-time Affordable Multi-Pollutant (RAMP) sensor packages deployed throughout urban and suburban Pittsburgh along with data from EPA regulatory monitors. The RAMP locations were divided into four site groups based on land use (High Traffic, Urban Residential, Suburban Residential, and Industrial). Concentrations of PM2.5, CO, and NO2 following the COVID-related closures at each site group were compared to measurements from “business as usual” periods in March 2019 and 2020. Overall, PM2.5 concentrations decreased across the domain by 3 μg/m3. Intra-day variabilities of the pollutants were computed to attribute pollutant enhancements to specific emission sources (i.e. traffic and industrial emissions). There was no significant change in the industrial related intra-day variability of PM2.5 at the Industrial sites following the COVID-related closures. The morning rush hour induced CO and NO2 concentrations at the High Traffic sites were reduced by 57% and 43%, respectively, which is consistent with the observed reduction in commuter traffic (~50%). The morning rush hour PM2.5 enhancement from traffic emissions fell from ~1.5 μg/m3 to ~0 μg/m3 across all site groups. This translates to a reduction of 0.125 μg/m3 in the daily average PM2.5 concentration. If PM2.5 National Ambient Air Quality Standards (NAAQS) are tightened these calculations shed light on to what extent reductions in traffic related emissions are able to aid in meeting more stringent regulations. | Rebecca Tanzer-Gruener; Jiayu Li; s. rose eilenberg; Allen Robinson; Albert Presto | Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ad94c89191487ad3307/original/impacts-of-modifiable-factors-on-ambient-air-pollution-a-case-study-of-covid-19-shutdowns.pdf |
65884cc566c1381729f14761 | 10.26434/chemrxiv-2023-dc2qq | Supramolecular hydrogel biomaterials and water-channels of differing diameters from dipeptide isomers | Dipeptides stereoisomers and regioisomers composed of norleucine (Nle) and phenylalanine (Phe) self-assemble into hydrogels in physiological conditions that are suitable for cell culture. The supramolecular behavior, however, differs as the packing modes comprise amphipathic layers, or water channels, whose diameter is defined by either four or six dipeptide molecules. A variety of spectroscopy, microscopy, and synchrotron-radiation based techniques unveil fine details of intermolecular interactions that pinpoint the relationship between chemical structure and ability to form supramolecular architectures that define soft biomaterials. | Ottavia Bellotto; Erica Scarel; Giovanni Pierri; Petr Rozhin; Slavko Kralj; Maurizio Polentarutti; Antonella Bandiera; Barbara Rossi; Consiglia Tedesco; Silvia Marchesan | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Biocompatible Materials; Biodegradable Materials | CC BY 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65884cc566c1381729f14761/original/supramolecular-hydrogel-biomaterials-and-water-channels-of-differing-diameters-from-dipeptide-isomers.pdf |
60c75834469df47f67f455b9 | 10.26434/chemrxiv.14474127.v2 | DrugEx v2: De Novo Design of Drug Molecule by Pareto-based Multi-Objective Reinforcement Learning in Polypharmacology | <p>In polypharmacology, ideal drugs are required to bind to multiple specific targets to enhance efficacy or to reduce resistance formation. Although deep learning has achieved breakthrough in drug discovery, most of its applications only focus on a single drug target to generate drug-like active molecules in spite of the reality that drug molecules often interact with more than one target which can have desired (polypharmacology) or undesired (toxicity) effects. In a previous study we proposed a new method named <i>DrugEx</i> that integrates an exploration strategy into RNN-based reinforcement learning to improve the diversity of the generated molecules. Here, we extended our <i>DrugEx</i> algorithm with multi-objective optimization to generate drug molecules towards more than one specific target (two adenosine receptors, A<sub>1</sub>AR and A<sub>2A</sub>AR, and the potassium ion channel hERG in this study). In our model, we applied an RNN as the <i>agent</i> and machine learning predictors as the <i>environment</i>, both of which were pre-trained in advance and then interplayed under the reinforcement learning framework. The concept of evolutionary algorithms was merged into our method such that <i>crossover</i> and <i>mutation</i> operations were implemented by the same deep learning model as the <i>agent</i>. During the training loop, the agent generates a batch of SMILES-based molecules. Subsequently scores for all objectives provided by the <i>environment</i> are used for constructing Pareto ranks of the generated molecules with non-dominated sorting and Tanimoto-based crowding distance algorithms. Here, we adopted GPU acceleration to speed up the process of Pareto optimization. The final reward of each molecule is calculated based on the Pareto ranking with the ranking selection algorithm. The agent is trained under the guidance of the reward to make sure it can generate more desired molecules after convergence of the training process. All in all we demonstrate generation of compounds with a diverse predicted selectivity profile toward multiple targets, offering the potential of high efficacy and lower toxicity.</p> | Xuhan Liu; Kai Ye; Herman Van Vlijmen; Michael T. M. Emmerich; Adriaan P. IJzerman; Gerard van Westen | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75834469df47f67f455b9/original/drug-ex-v2-de-novo-design-of-drug-molecule-by-pareto-based-multi-objective-reinforcement-learning-in-polypharmacology.pdf |
63df6a4e45d4b84aae9e688c | 10.26434/chemrxiv-2022-p8jq4-v2 | Dense and Acidic Organelle-Targeted Visualization in Living Cells: Application of Viscosity-Responsive Fluorescence Utilizing Restricted Access to Minimum Energy Conical Intersection | Cell-imaging methods with functional fluorescent probes are an indispensable technique to evaluate physical parameters in cellular mi-croenvironments. In particular, molecular rotors, which take advantage of the twisted intramolecular charge transfer (TICT) process, have helped evaluate microviscosity. However, the involvement of charge-separated species in the fluorescence process potentially limits the quantitative evaluation of viscosity. Herein we developed viscosity-responsive fluorescent probes for cell imaging that are not depend-ent on the TICT process. We synthesized AnP2-H and AnP2-OEG, both of which contain 9,10-di(piperazinyl)anthracene, based on 9,10-bis(N,N-dialkylamino)anthracene that adopt a non-flat geometry at minimum energy conical intersection. AnP2-H and AnP2-OEG exhibited enhanced fluorescence as the viscosity increased, with sensitivities comparable to those of conventional molecular rotors. In living cell systems, AnP2-OEG showed low cytotoxicity and, reflecting its viscosity-responsive property, allowed specific visualization of dense and acidic organelles such as lysosomes, secretory granules and melanosomes under washout-free conditions. These results provide a new direction for developing functional fluorescent probes targeting dense organelles. | Junya Adachi; Haruka Oda; Toshiaki Fukushima; Beni Lestari; Hiroshi Kimura; Hiroka Sugai; Kentaro Shiraki; Kohei Sato; Kazushi Kinbara | Analytical Chemistry; Imaging | CC BY NC 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63df6a4e45d4b84aae9e688c/original/dense-and-acidic-organelle-targeted-visualization-in-living-cells-application-of-viscosity-responsive-fluorescence-utilizing-restricted-access-to-minimum-energy-conical-intersection.pdf |
629244ee6209e01d7954e9ba | 10.26434/chemrxiv-2022-3vkb5 | Evaluating Solvothermal and Mechanochemical Routes towards the Metal–Organic Framework Mg2(m-dobdc) | Metal–organic frameworks bearing coordinatively unsaturated Mg(II) sites are promising materials for gas storage, chemical separations, and drug delivery due to their low molecular weights and lack of toxicity. However, there remains a limited number of such MOFs reported in the literature. Herein, we investigate the gas sorption properties of the understudied framework Mg2(m-dobdc) (dobdc4− = 4,6-dioxido-1,3-benzenedicarboxylate) synthesized under both solvothermal and mechanochemical conditions. Both materials are found to be permanently porous, as confirmed by 77 K N2 adsorption measurements. In particular, Mg2(m-dobdc) synthesized under mechanochemical conditions using exogenous organic base displays one of the highest capacities reported to date (6.14 mmol/g) for CO2 capture in a porous solid under simulated coal flue gas conditions (150 mbar, 40 °C). As such, mechanochemically synthesized Mg2(m-dobdc) represents a promising new framework for applications requiring high gas adsorption capacities in a porous solid. | Elena Chen; Ruth Mandel; Phillip Milner | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629244ee6209e01d7954e9ba/original/evaluating-solvothermal-and-mechanochemical-routes-towards-the-metal-organic-framework-mg2-m-dobdc.pdf |
60c74742f96a0028ca286ecc | 10.26434/chemrxiv.11559102.v1 | Dewar Benzenoids Discovered In Carbon Nanobelts | Here we report the discovery that isomers containing two Dewar benzenoid rings are the preferred form for several sizes of cyclacene. The predicted lower polyradical character and higher singlet-triplet stability that these isomers possess compared with their pure benzenoid counterparts suggests that they may be more stable synthetic targets than the structures which have previously been identified. | Magnus Hanson-Heine; David Rogers; Simon Woodward; Jonathan D Hirst | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74742f96a0028ca286ecc/original/dewar-benzenoids-discovered-in-carbon-nanobelts.pdf |
629779d4a6101b033bd75215 | 10.26434/chemrxiv-2022-15cwv-v2 | Mechanochemical synthesis of structurally well-defined graphitic phosphorus-linked carbon nitride (g-PCN) with water splitting activity | Heteroatom-doped carbon nitride (CN) materials have shown much potential as metal-free photocatalysts for water splitting. Graphitic phosphorus-linked triazine network (g-PCN) materials are a unique class within this family of materials, but remain difficult to access due to long reaction times annealing at temperatures above 500 °C and often afford ill-understood structures. Here, we reveal a milder, lower temperature approach for the synthesis of catalytically active g-PCN materials through combining a room-temperature mechanochemical reaction of sodium phosphide and cyanuric chloride with brief (1 hour) annealing of the milled material at 300 °C. This rapid, low temperature procedure yields ordered g-PCN catalysts whose layered structure was determined through a combination of magic-angle spinning nuclear magnetic resonance (MAS NMR), X-ray photoelectron spectroscopy (XPS), powder X-ray diffraction (PXRD) and transmission electron microscopy (TEM). An excellent level of accuracy to simulated 31P MAS NMR signals and PXRD patterns were obtained for the structure of the synthesized layered phosphorus-linked triazine networks following dispersion-corrected density functional theory (DFT). The mechanochemically-generated g-PCN is a highly effective photocatalyst for the hydrogen evolution reaction, producing 122 µmol H2 h-1 g-1 under broad spectrum irradiation. | Blaine Fiss; Georgia Douglas; Michael Ferguson; Jorge Becerra; Jesus Valdez; Trong-On Do; Tomislav Friscic; Audrey Moores | Inorganic Chemistry; Catalysis; Main Group Chemistry (Inorg.); Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629779d4a6101b033bd75215/original/mechanochemical-synthesis-of-structurally-well-defined-graphitic-phosphorus-linked-carbon-nitride-g-pcn-with-water-splitting-activity.pdf |
63bce1d3a68d7b6544324660 | 10.26434/chemrxiv-2023-c66c5 | Enantioselective Catalysts Based on Metal-Organic Framework-Supported Nucleotides | Adenosine triphosphate (ATP) and other nucleotides can be irreversibly bound to the metal-organic framework (MOF) MIL-101(Cr). Analysis of X-ray diffraction data suggests that the location of the adsorbed ATP molecule is in proximity of the Cr3 clusters. Solid-state NMR and DFT calculations indicate that ATP is bound to MIL-101(Cr) through linkages of the terminal phosphate group with Cr(III) of the framework. In the presence of Cu(II) ions, the MOF-supported nucleotides can function as stable and reusable enantioselective heterogeneous catalysts for reactions like Diels-Alder and Michael addition. Compared to the corresponding homogeneous nucleotide-based artificial metalloenzymes (ArMs), the MOF-supported nucleotide-based ArMs exhibit significantly enhanced activity and selectivity in certain cases, demonstrating their potential as a new class of enantioselective heterogeneous catalysts. | Danyu Wang; Zhe Li; Tian-Yi Luo; Michael Schmithorst; Sunghwan Park; Wenqian Xu; Brandon Bukowski; Bradley Chmelka; Efrosini Kokkoli; Michael Tsapatsis | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bce1d3a68d7b6544324660/original/enantioselective-catalysts-based-on-metal-organic-framework-supported-nucleotides.pdf |
64faf015b338ec988a1b8ffe | 10.26434/chemrxiv-2023-cqfl6 | Synthesis of N-acyl carbazoles, phenoxazines and acridines from cyclic diaryliodonium salts | N-Acyl carbazoles can be efficiently produced through a single-step process using amides and cyclic diaryliodonium triflates. This convenient reaction is facilitated by copper iodide in p-xylene, using the commonly found activating ligand diglyme. We've tested this method with a wide range of amides and iodonium triflates, proving its versatility with numerous substrates. Beyond carbazoles, we also produced a variety of other N-heterocycles, such as acridines, phenoxazines, or phenazines, showcasing the robustness of our technique. In a broader sense, this new method creates two C-N bonds simultaneously based on a mono-halogenated starting material, thus allowing heterocycle formation with diminished halogen waste. | Nils Clamor; Mattis Damrath; Thomas Kuczmera; Daniel Duvinage; Boris Johannes Nachtsheim | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64faf015b338ec988a1b8ffe/original/synthesis-of-n-acyl-carbazoles-phenoxazines-and-acridines-from-cyclic-diaryliodonium-salts.pdf |
618410aee04a8e0e3027029b | 10.26434/chemrxiv-2021-f0k4f | CASPT2 molecular geometries of Fe(II) spin-crossover
complexes | Using fully internally contracted (FIC)-CASPT2 analytical gradients, geometry optimizations of spin-crossover complexes are reported. This approach is tested on a series of Fe(II) complexes with different sizes, ranging from 13 to 61 atoms. A combination of active space and basis set
choices are employed to investigate their role in determining reliable molecular geometries. The
reported strategy demonstrates that a wave function-based level of theory can be used to optimize the geometries of metal complexes in reasonable times and enables one to treat the molecular geometry and electronic structure of the complexes using the same level of theory. For a series of
smaller Fe(II) SCO complexes, strong field ligands in the LS state result in geometries with the largest differences between DFT and CASPT2; however, good agreement overall is observed between DFT and CASPT2. For the larger complexes, moderate sized basis sets yield geometries that compare well with DFT and available experimental data. We recommend using the (10e,12o) active space since convergence to a minimum structure was more efficient than with truncated active spaces (e.g., (6e,5o)) despite having similar Fe–ligand bond distances. | Brian A. Finney; Sabyasachi Roy Chowdhury; Clara Kirkvold; Bess Vlaisavljevich | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618410aee04a8e0e3027029b/original/caspt2-molecular-geometries-of-fe-ii-spin-crossover-complexes.pdf |
659f4e8b66c13817292beec6 | 10.26434/chemrxiv-2023-mq8s2-v3 | In situ polymer gelation in confined flow controls intermittent dynamics | Polymer flows through pores, nozzles and other small channels govern engineered and naturally occurring
dynamics in many processes, from 3D printing to oil recovery in the earth’s subsurface to a wide variety of biological flows. The crosslinking of polymers can change their material properties dramatically, and it is advantageous to know a priori whether or not crosslinking polymers will lead to clogged channels or cessation of flow. In this study, we investigate the flow of a common biopolymer, alginate, while it undergoes crosslinking by the addition of a crosslinker, calcium, driven through a microfluidic channel at constant flow rate. We map the boundaries defining complete clogging and flow as a function of flow rate, polymer concentration, and crosslinker concentration. Interestingly, the boundaries of the dynamic behavior qualitatively match the thermodynamic jamming phase diagram of attractive colloidal particles. That is, polymer clogging occurs in a region analogous to colloids in a jammed state, while the polymer flows in regions corresponding to colloids in a liquid phase. However, between the dynamic regimes of complete clogging and unrestricted flow, we observe a remarkable phenomenon in which the crosslinked polymer intermittently clogs the channel. This pattern of deposition and removal of a crosslinked gel is simultaneously highly reproducible, long-lasting, and controllable by system parameters. Higher concentrations of polymer and cross-linker result in more frequent ablation, while gels formed at lower component concentrations ablate less frequently. Upon ablation, the eluted gel maintains its shape, resulting in micro-rods several hundred microns long. Our results suggest both rich dynamics of intermittent flows in crosslinking polymers and the ability to control them.
| Barrett Smith; Sara Hashmi | Materials Science; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659f4e8b66c13817292beec6/original/in-situ-polymer-gelation-in-confined-flow-controls-intermittent-dynamics.pdf |
60c74db2337d6cd903e27e21 | 10.26434/chemrxiv.12579599.v2 | The Potential role of Procyanidin as a Therapeutic Agent against SARS-CoV-2: A Text Mining, Molecular Docking and Molecular Dynamics Simulation Approach | <p></p><p></p><p>A novel coronavirus
(SARS-CoV-2) has caused a major outbreak in human all over the world. There are
several proteins interplay during the entry and replication of this virus in
human. Here, we have used text mining and named entity recognition method to identify
co-occurrence of the important COVID 19 genes/proteins in the interaction
network based on the frequency of the interaction. Network analysis revealed a
set of genes/proteins, highly dense genes/protein clusters and sub-networks of
Angiotensin-converting enzyme 2 (ACE2), Helicase, spike (S) protein (trimeric),
membrane (M) protein, envelop (E) protein, and the nucleocapsid (N) protein.
The isolated proteins are screened against procyanidin-a flavonoid from plants
using molecular docking. Further, molecular dynamics simulation of critical
proteins such as ACE2, Mpro and spike proteins are performed to elucidate the
inhibition mechanism. The strong network of hydrogen bonds and hydrophobic
interactions along with van der Waals interactions inhibit receptors, which are
essential to the entry and replication of the SARS-CoV-2. The binding energy
which largely arises from van der Waals interactions is calculated (ACE2=-50.21
± 6.3, Mpro=-89.50 ± 6.32 and spike=-23.06 ± 4.39) through molecular mechanics
Poisson-Boltzmann surface area also confirm the affinity of procyanidin towards
the critical receptors.</p><p></p><p></p> | Nikhil Maroli; Balu Bhasuran; Jeyakumar Natarajan; Ponmalai Kolandaivel | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db2337d6cd903e27e21/original/the-potential-role-of-procyanidin-as-a-therapeutic-agent-against-sars-co-v-2-a-text-mining-molecular-docking-and-molecular-dynamics-simulation-approach.pdf |
66a138ac5101a2ffa8e0f3ec | 10.26434/chemrxiv-2024-w5wtb | Expanding Chemical Space in the Synthesis of Gold Bipyramids | Gold bipyramids (AuBPs), despite having superior properties compared to their spectroscopically similar counterparts, gold nanorods, have found comparatively limited applications. This discrepancy is primarily due to the lack of protocols to tailor their dimensions. Typically, concentration of Au seeds is virtually the sole factor that determines aspect ratio and thus, optical properties of AuBPs. As a result, varying the volumes of AuBPs while incurring minimal changes to their optical spectra remains a synthetically non-trivial task. Here, we expand the chemical space in the seeded growth of AuBPs, by exploiting the interplay between bromide, silver ions, and seed concentration for tuning the final dimensions and optical properties of AuBPs. Specifically, we achieved a 6-fold change in volumes of AuBPs while maintaining the fixed plasmon band position. Further overgrowth of as-prepared bipyramids broadens the realizable dimensions without compromising quality and initial morphology. Overall, our results expand the chemical toolbox in the wet-chemistry synthesis of anisotropic gold nanoparticles, which is relevant for health, colorimetric sensors, and energy applications. | Ana Sánchez-Iglesias; Marek Grzelczak | Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a138ac5101a2ffa8e0f3ec/original/expanding-chemical-space-in-the-synthesis-of-gold-bipyramids.pdf |
60c75942469df462c6f45821 | 10.26434/chemrxiv.14679084.v1 | Insights into Hydrogen Evolution Reaction on 2D Transition Metal Dichalcogenides | <p>Understanding the hydrogen evolution reaction (HER) behaviors over 2D transition metal dichalcogenides (2D-TMDs) is critical for the development of non-precious HER electrocatalysts with better activity. In this work, by combining density functional theory calculations with microkinetic modelling, we thoroughly investigated the HER mechanism on 2D-TMDs. We find there is an important dependence of simulated cell size on the calculated hydrogen adsorption energy and the activation barrier for MoS<sub>2</sub>. Distinct from previous “H migration” mechanisms proposed for the Heyrovsky reaction − the rate-determining step for MoS<sub>2</sub>, we propose the Mo site only serves as the stabilized transition state rather than H adsorption. In comparison to transition metal electrocatalysts, we find that the activation barrier of the Heyrovsky reaction on 2D-TMDs scales with the hydrogen adsorption energy exactly as for transition metals except that all activation energies are displaced upwards by <i>ca.</i> 0.4 eV. This higher Heyrovsky activation barrier is responsible for the substantially lower activity of 2D-TMDs. We further show that this higher activation barrier stems from the more positively charged adsorbed hydrogen on the chalcogenides interacting repulsively with the incoming proton. Based on these insights, we discuss potential strategies for the design of non-precious HER catalysts with activity comparable to Pt.</p> | Zhenbin Wang; Michael Tang; Ang Cao; Karen Chan; Jens Kehlet Nørskov | Catalysts; Electrocatalysis; Fuels - Energy Science; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75942469df462c6f45821/original/insights-into-hydrogen-evolution-reaction-on-2d-transition-metal-dichalcogenides.pdf |
60c74c99ee301c8575c7a0f6 | 10.26434/chemrxiv.12443654.v2 | A Self-Trapping, Bipolar Viologen Bromide Electrolyte for Aqueous Redox Flow Batteries | Aqueous organic redox flow batteries (AORFBs) have become increasing attractive for scalable energy storage. However, it remains challenging to develop high voltage, powerful AORFBs because of the lack of catholytes with high redox potential. Herein, we report methyl viologen dibromide (<b>[MV]Br<sub>2</sub></b>) as a facile self-trapping, bipolar redox electrolyte material for pH neutral redox flow battery applications. The formation of the <b>[MV](Br<sub>3</sub>)<sub>2</sub></b> complex was computationally predicted and experimentally confirmed. The low solubility <b>[MV](Br<sub>3</sub>)<sub>2</sub></b> complex in the catholyte during the battery charge process not only mitigates the crossover of charged tribromide species (Br<sub>3</sub><sup>-</sup>) and addresses the toxicity concern of volatile bromine simultaneously. A 1.53 V bipolar MV/Br AORFB delivered outstanding battery performance at pH neutral conditions, specifically, 100% total capacity retention, 133 mW/cm<sup>2</sup> power density, and 60% energy efficiency at 40 mA/cm<sup>2</sup>. | wenda wu; Jian Luo; Fang Wang; Bing Yuan; Tianbiao Liu | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c99ee301c8575c7a0f6/original/a-self-trapping-bipolar-viologen-bromide-electrolyte-for-aqueous-redox-flow-batteries.pdf |
60c74228842e651810db1feb | 10.26434/chemrxiv.8214422.v1 | Path-Augmented Graph Transformer Network | <div>Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we propose Path-Augmented Graph Transformer Networks (PAGTN) that are explicitly built on longer-range dependencies in graphstructured data. Specifically, we use path features in molecular graphs to create global attention layers. We compare our PAGTN model against the GCN model and show that our model consistently</div><div>outperforms GCNs on molecular property prediction datasets including quantum chemistry (QM7, QM8, QM9), physical chemistry (ESOL, Lipophilictiy) and biochemistry (BACE, BBBP)2.</div> | Benson Chen; Regina Barzilay; Tommi S Jaakkola | Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74228842e651810db1feb/original/path-augmented-graph-transformer-network.pdf |
6349b5133399721f848b1a63 | 10.26434/chemrxiv-2022-nb1sf | A Deep Blue Heteroatom Doped Nonacene That Exhibits Multi-Resonant Thermally Activated Delayed Fluorescence and its Use as an Emitter in High-Performance Deep Blue Organic Light-Emitting Diodes | We present a p- and n-doped nonacene compound, NOBNacene, that represents a rare example of a linearly extended ladder-type multiresonant thermally activated delayed fluorescence (MR-TADF) emitter. This compound shows efficient narrow deep blue emission (PL = 410 nm, FWHM = 38 nm, ФPL = 71%, d = 1.18 ms) in 1.5 wt% TSPO1 thin film. The organic light-emitting diode (OLED) using this compound as the emitter shows a comparable electrolumines-cence spectrum (EL = 409 nm, FWHM = 37 nm) and a maximum external quantum efficiency (EQEmax) of 8.5% at CIE coordinates of (0.173, 0.055). The EQEmax values were increased to 11.2% at 3 wt% doping of the emitter within the emissive layer of the device. At this concentra-tion, the electroluminescence spectrum broadened slightly, leading to CIE coordinates of (0.176, 0.068). | Subeesh Madayanad Suresh; Le Zhang; David Hall; Changfeng Si; Gaetano Ricci; Tomas Matulaitis; Alexandra Slawin; Stuart Warriner; Yoann Olivier; Ifor Samuel; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Materials Science; Organic Compounds and Functional Groups; Optical Materials; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6349b5133399721f848b1a63/original/a-deep-blue-heteroatom-doped-nonacene-that-exhibits-multi-resonant-thermally-activated-delayed-fluorescence-and-its-use-as-an-emitter-in-high-performance-deep-blue-organic-light-emitting-diodes.pdf |
638cc3f0cfb5ffe6cb5c9c61 | 10.26434/chemrxiv-2022-458tf | Carboxymethyl Cellulose-Zinc Alginate Hydrogels as Antibacterial Wound Dressings | Wound dressings need to have strong physical capabilities, good antibacterial qualities, and, more importantly, natural material components. In this study, zinc alginate and carboxymethyl cellulose were combined to obtain a novel wound dressing film based on natural materials. Film samples were characterized by Fourier transform infrared spectroscopy (FTIR), light transmittance, scanning electron microscopy (SEM), swelling experiments, and water vapor transmittance tests. Wound dressing based on zinc crosslinked alginate and carboxymethyl cellulose films gained antibacterial activity against Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria and had a good swelling capability in pure water and isotonic solution (0.9% NaCl), had UV-protective character and had a high value of water vapor transmission rate (WVTR) thanks to their porous structure. Results indicate that the presented formulation is a novel and promising wound dressing material. | Zahed Kochai; Burcu Orhan; Cansu Vatansever; Hakan Kaygusuz | Materials Science; Polymer Science; Biopolymers; Cellulosic materials; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638cc3f0cfb5ffe6cb5c9c61/original/carboxymethyl-cellulose-zinc-alginate-hydrogels-as-antibacterial-wound-dressings.pdf |
610e29824cb47963592a19c2 | 10.26434/chemrxiv-2021-c2ftp | Ritter-Type Iodo(III)amidation of Unactivated Alkynes for the Stereoselective Synthesis of Multisubstituted Enamides | The Ritter reaction, Brønsted- or Lewis acid-mediated amidation of alkene or alcohol with nitrile via a carbocation, represents a classical method for the synthesis of tertiary amides. Although analogous reaction through a vinyl cation or a species alike may offer a route to enamide, an important synthetic building block as well as a common functionality in bioactive compounds, such transformations remain largely elusive. Herein, we report on a Ritter-type trans- difunctionalization of alkynes with trivalent iodine electrophile and nitrile, which affords β-iodanyl enamides in moderate to good yields. Mediated by benziodoxole triflate (BXT), the reaction proves applicable to a variety of internal alkynes as well as to various alkyl- and arylnitriles. The benziodoxole group in the product serves as a versatile handle for further transformations, thus allowing for the preparation of various tri- and tetrasubstituted enamides that are not readily accessible by other means. | Naohiko Yoshikai; Jinkui Chai; Wei Ding; Shingo Ito; Junliang Wu | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610e29824cb47963592a19c2/original/ritter-type-iodo-iii-amidation-of-unactivated-alkynes-for-the-stereoselective-synthesis-of-multisubstituted-enamides.pdf |
66312b4191aefa6ce1d400d0 | 10.26434/chemrxiv-2024-ltvf9 | Correlating the Structure of Quinone-Functionalized Carbons with Electrochemical CO2 Capture Performance | Electrochemical carbon dioxide capture is emerging as an energy-efficient alternative to traditional carbon capture technology. In particular, redox-active molecules that can capture carbon dioxide when electrochemically reduced and release carbon dioxide when electrochemically re-oxidized are under active development. To prepare a carbon capture device these molecules can be incorporated in a solid electrode in a battery-like cell. In this work we explore the scope of a recently developed method where anthraquinones are covalently attached to porous carbon supports to obtain electrodes for electrochemical carbon dioxide capture. We functionalize four different porous carbon materials with varying porosities and surface chemistries, and use gas sorption analysis and solid-state NMR spectroscopy to probe the location of the grafted anthraquinones. All four functionalized materials show electrochemically mediated capture and release of carbon dioxide and we explore the factors that determine their performance. While the anthraquinone-functionalized mesoporous carbon, f-CMK-3, showed the highest quinone loading, it showed poor quinone utilization for CO2 capture, and poor long-term cycling stability. In contrast, the predominantly microporous functionalized carbon, f-YP-80F, showed a higher quinone utilization and improved cycling stability. Finally, thermal annealing experiments were conducted to remove pre-existing functional groups on a third carbon, but this did not improve the cycling stability of the resulting anthraquinone-functionalized material. Overall our measurements suggest that the pore environments in which anthraquinones are grafted play a crucial role in determining the electrochemical CO2 capture performance. This work can guide the design of functionalized carbon electrodes for electrochemical carbon dioxide capture. | Niamh Hartley; Zhen Xu; Thomas Kress; Alexander Forse | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66312b4191aefa6ce1d400d0/original/correlating-the-structure-of-quinone-functionalized-carbons-with-electrochemical-co2-capture-performance.pdf |
60c749359abda21c96f8cba3 | 10.26434/chemrxiv.12044061.v1 | C-H Functionalization Reactions of Unprotected N-Heterocycles by Gold Catalyzed Carbene Transfer | <p>The C-H functionalization reaction of N-heterocycles with unprotected N-H group is one of the most step-economic strategies to introduce functional groups without the need of installation and removal of protecting groups. Despite recent significant advances in C-H functionalization chemistry, this strategy remains unsatisfactorily developed. In this report, we disclose a simple and straightforward protocol to allow for the selective C-H functionalization of unprotected double benzannellated N-heterocycles via gold catalyzed carbene transfer reactions (29 examples, up to 86% yield). The scope of the reaction can also be expanded to the corresponding protected heterocycles (37 examples, up to 98% yield), further demonstrating the generality of this method. Mechanistic studies by DFT calculations underpin the importance of the gold catalyst and reveal that the selectivity of this reaction is driven by trace amounts of water present in the reaction mixture.</p> | Sripati Jana; Claire Empel; Chao Pei; Polina Aseeva; Thanh Vinh Nguyen; Rene Koenigs | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Carbon-based Materials; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749359abda21c96f8cba3/original/c-h-functionalization-reactions-of-unprotected-n-heterocycles-by-gold-catalyzed-carbene-transfer.pdf |
60c73fe79abda2f2def8bba1 | 10.26434/chemrxiv.7558823.v1 | Gold Nanorods as a High-Pressure Sensor of Phase Transitions and Refractive-Index Gauge | <div>The absorption peaks of surface plasmon
resonance (SPR) in Au NRs are highly sensitive to their surrounding medium and
to its refractive index (<i>RI</i>) changes. However, no applications of NRs
for detecting phase transitions have been reported. Here we show that Au NRs effectively
detect phase transitions of compressed compounds, liquid and solid, by measuring
their <i>RI</i>. Owing to the direct interaction of the NRs with their surrounding
medium, its subtle <i>RI</i> changes can be
observed by the use of high-pressure absorption Vis-NIR spectroscopy.</div><b></b> | Marcin Runowski; Szymon Sobczak; Jedrzej Marciniak; Ida Bukalska; Stefan Lis; Andrzej Katrusiak | Nanostructured Materials - Materials; Nanodevices; Plasmonic and Photonic Structures and Devices; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe79abda2f2def8bba1/original/gold-nanorods-as-a-high-pressure-sensor-of-phase-transitions-and-refractive-index-gauge.pdf |
634c753ca2c790708b499919 | 10.26434/chemrxiv-2022-0xnn3 | TeraChem Protocol Buffers (TCPB): Accelerating QM and QM/MM Simulations with a Client-Server Model | The routine use of electronic structure in many chemical simulation applications calls for efficient and easy ways to access electronic structure programs. We describe how the graphics processing unit (GPU) accelerated electronic structure program TeraChem can be set up as an electronic structure server, to be easily accessed by third-party client programs. We exploit Google’s protocol buffer framework for data serialization and communication. The client interface, called TeraChem protocol buffers (TCPB), has been designed for ease of use and compatibility with multiple programming languages, such as C++, Fortran, and Python. To demonstrate the ease of coupling third-party programs with electronic structure using TCPB, we have incorporated the TCPB client into Amber for quantum mechanics/molecular mechanics (QM/MM) simulations. The TCPB interface saves time with GPU initialization and I/O operations, achieving a speedup of more than 2x compared to a prior file-based implementation for a QM region with ~250 basis functions. We demonstrate the practical application of TCPB by computing the free energy profile of p-HBDI- – a model chromophore in green fluorescent proteins – on the first excited singlet state using Hamiltonian replica exchange (H-REMD) for enhanced sampling. All calculations in this work have been performed with the freely-available version of TeraChem, which is sufficient for many QM region sizes in common use. | Vinícius Wilian Cruzeiro; Yuanheng Wang; Elisa Pieri; Edward Hohenstein; Todd Martínez | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634c753ca2c790708b499919/original/tera-chem-protocol-buffers-tcpb-accelerating-qm-and-qm-mm-simulations-with-a-client-server-model.pdf |
674536d25a82cea2fadfbf1f | 10.26434/chemrxiv-2024-xmjml-v4 | Adapting a trapped ion mobility spectrometry-Q-TOF for high m/z native mass spectrometry and
surface-induced dissociation
| Native mass spectrometry (nMS) is increasingly popular for studying intact protein quaternary structure. When coupled with ion mobility, which separates ions based on their size, charge, and shape, it provides additional structural information on the protein complex of interest. In this study, we present a novel prototype TIMS (trapped ion mobility spectrometry)-Quadrupole-SID (surface-induced dissociation)-Time of Flight, TIMS-Q-SID-TOF, instrument for nMS. The modifications include changing the TIMS cartridge from concave to convex geometry electrodes and operating TIMS at 425 kHz to improve the trapping efficiency for high mass-to-charge (m/z) ion mobility analysis, such as 3 and 4 MDa hepatitis B virus capsids. The quadrupole radiofrequency driver was lowered to 385 kHz, which extends the isolation range from 3,000 to 17,000 m/z and allows isolation of a single charge state of GroEL at 16,200 m/z with an isolation window of 25 m/z. Finally, a 6-mm thick, 2-lens SID device replaced the collision cell entrance lens. SID dissociated 801 kDa GroEL into all combinations of subcomplexes, and the peaks were well-resolved allowing for confident assignment of product ions. This is the first time a novel prototype timsTOF Pro for nMS has been introduced with high resolving power ion mobility separation coupled to high m/z quadrupole selection and SID for protein complex fragmentation with product ion collection and detection across a broad m/z range of 1,500 to 40,000. | Yu-Fu Lin; Benjamin Jones; Mark Ridgeway; Erin Panczyk; Arpad Somogyi; Desmond Kaplan; Karen Kirby; Stefan Sarafianos; Ila Marathe; Sangho Yun; Arthur Laganowsky; Melvin Park; Vicki Wysocki | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674536d25a82cea2fadfbf1f/original/adapting-a-trapped-ion-mobility-spectrometry-q-tof-for-high-m-z-native-mass-spectrometry-and-surface-induced-dissociation.pdf |
63fa0ace32cd591f12760f16 | 10.26434/chemrxiv-2023-zc260 | Design of Cell-Penetrating Monobodies via Genetic Supercharging and Orthogonal Crosslinking | Domain antibodies such as monobodies provide an attractive immunoglobin fold for evolving high-affinity binders targeting the intracellular proteins implicated in cell signaling. However, it remains challenging to endow cell permeability to these small and versatile protein binders. Here, we report a streamlined strategy combining orthogonal crosslinking mediated by a genetically encoded beta-lactam-lysine (BeLaK) and genetic supercharging to generate cell-penetrating monobodies. When BeLaK was introduced site-specifically to the N-terminal beta-strand of a panel of supercharged monobodies, it enabled efficient interstrand crosslinking with a nearby lysine, generating the rigidified analogs. Compared to the non-crosslinked counterparts, the BeLaK-crosslinked supercharged monobodies exhibited higher thermostability and enhanced cellular uptake at concentrations as low as 40 nM. Most significantly, a +11 charged, orthogonally crosslinked monobody showed significant endosomal escape after endocytosis. The discovery of this stabilized immunoglobin fold should facilitate the design of cell-permeable domain antibodies for targeting intracellular proteins. | Johnathan Rabb; Lucas Kruse; Qing Lin | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fa0ace32cd591f12760f16/original/design-of-cell-penetrating-monobodies-via-genetic-supercharging-and-orthogonal-crosslinking.pdf |
60c75723567dfe53bdec6612 | 10.26434/chemrxiv.14371073.v1 | Constructing Narrowband Thermally Activated Delayed Fluorescence Materials with Emission Maxima Beyond 560 nm Based on Frontier Molecular Orbital Engineering | <p>The development of purely organic materials
with narrowband emission in long wavelength region beyond 560 nm still remains
a great challenge. Herein, we present a modification approach of multiple
resonance (MR) skeleton with electron donor based on frontier molecular orbital
engineering (FMOE), resulting in significant
red-shift emission of target molecules. Subsequently, the parent MR
skeleton is functionalized by boron esterification
reaction and changed into a universal building block,
namely, the key intermediate BN-Bpin, for molecular structure optimizations. BN-Bpin
has been employed to construct a series of highly efficient thermally activated
delayed fluorescence (TADF) materials with high color purity through one-step
Suzuki coupling reaction. The target molecule perfectly integrates the inherent advantages of MR
skeleton and spatial separation typical donor–acceptor (D–A) structure. The results demonstrate that the ingenious modulation of the acceptor is an effective approach to
achieve bathochromic emission and narrowband emission simultaneously.</p> | Xinliang Cai; Yincai Xu; Qingyang Wang; Chenglong Li; Yue Wang | Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75723567dfe53bdec6612/original/constructing-narrowband-thermally-activated-delayed-fluorescence-materials-with-emission-maxima-beyond-560-nm-based-on-frontier-molecular-orbital-engineering.pdf |
62ecb2aba05ea13a4a9399fb | 10.26434/chemrxiv-2022-vfwv0 | Photoinduced Dehydrogenative Borylation via Dihydrogen Bond Bridged Electron Donor and Acceptor Complexes | Air-stable amine- and phosphine-boranes are discovered as donors to integrate with pyridinium acceptor for generating pho-toactive electron-donor-acceptor (EDA) complexes. Experimental results and DFT calculations suggest a dihydrogen bond bridging the donor and acceptor. Illuminating the EDA complex enables an intramolecular single electron transfer to give boron-centered radical for dehydrogenative borylation with no need of external photosensitizer and oxidant. The deproto-nation of Wheland-like radical intermediate rather than its generation is believed to determine the very good ortho-selectivity based on DFT calculations. A variety of α-borylated pyridine derivatives have been readily synthesized with good functional group tolerance. | Zhiyong Wang; Jiaxin Chen; Zhenyang Lin; Yangjian QUAN | Organic Chemistry; Inorganic Chemistry; Photochemistry (Org.); Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ecb2aba05ea13a4a9399fb/original/photoinduced-dehydrogenative-borylation-via-dihydrogen-bond-bridged-electron-donor-and-acceptor-complexes.pdf |
67372f6b7be152b1d0291d9b | 10.26434/chemrxiv-2024-6pgl4 | Cation-π Interactions Involving Graphynes: An Intermolecular Force Field Formulation Featuring Ion-Induced Dipole Effects | Over the past few years, graphynes (GYs), one of the latest families of carbon allotropes, have been investigated as promising materials for various applications, including lithium-ion batteries. Developing analytic potentials for describing potential energy surfaces underlying cation-π interactions is a challenging task for large-scale simulations involving carbon-based materials. This study aimed to develop effective analytic models to overcome computational challenges in accurately capturing cation-π interactions between alkali metal ions (Li+, Na+, K+) and GYs, which are crucial for ion storage and transport within nanoporous GY frameworks. The high computational demands of ab initio methods for such large systems make analytic modeling increasingly essential. The absence of reliable analytic potentials and parameters needs to be urgently addressed. Here, we report that the commonly used 12-6 Lennard-Jones (LJ) potential combined with electrostatics (EL) is insufficient for representing cation-π interactions, as it fails to capture the ion-induced dipole effects that are crucial for the problem in hand. To address this, we propose modified 12-4 LJ + EL and improved Lennard-Jones (ILJ) potentials, which better capture the necessary short-range repulsions and long-range attractions. We developed and validated parameter sets based on interaction energy curves from density functional theory (DFT), enabling a reasonably accurate modeling of cation permeation and surface dynamics on GY sheets. This work not only advances the understanding of cation-π interactions in GYs but also introduces computationally efficient models that support the design of GYs for next-generation energy storage applications. | Akhil Kottayil; Medha Sangeetha Prakash; Rotti Srinivasamurthy Swathi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67372f6b7be152b1d0291d9b/original/cation-interactions-involving-graphynes-an-intermolecular-force-field-formulation-featuring-ion-induced-dipole-effects.pdf |
60c74024ee301c69f3c78a1e | 10.26434/chemrxiv.7547222.v2 | Terahertz Spectroscopy: An investigation of the Structural Dynamics of Freeze-Dried PLGA Microspheres | Biodegradable poly lactic-co-glycolic acid (PLGA) microspheres can be used to encapsulate peptide and offer a promising drug delivery vehicle. In this work we investigate the dynamics of PLGA microspheres prepared by freeze-drying and the molecular mobility at lower temperatures leading to the glass transition temperature, using temperature-variable terahertz time-domain spectroscopy (THz-TDS) experiments. The microspheres were prepared using a water-in-oil-in-water (w/o/w) double emulsion technique and subsequent freeze-drying of the samples. Physical characterisation was performed by morphology measurements, scanning electron microscopy (SEM), and helium pycnometry. The THz-TDS data show two distinct transition processes, T<sub>g,β</sub> in the range of 167-219 K, associated with local motions, and T<sub>g,α</sub> in the range of 313-330 K associated with large-scale motions, for the microspheres examined. Using FTIR measurements in the mid-infrared we were able to characterise the interactions between a model polypeptide, exendin-4, and the PLGA copolymer. We observe a relationship between the experimentally determined T<sub>g,β</sub> and T<sub>g,α</sub> and free volume and microsphere dynamics. <br /> | Talia Shmool; Philippa J. Hooper; Gabi Kaminski; Christopher F. van der Walle; J. Axel Zeitler | Controlled-Release Systems; Biopolymers; Drug delivery systems; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems; Spectroscopy (Physical Chem.); Structure | CC BY 4.0 | CHEMRXIV | 2019-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74024ee301c69f3c78a1e/original/terahertz-spectroscopy-an-investigation-of-the-structural-dynamics-of-freeze-dried-plga-microspheres.pdf |
60c753ae702a9b3b6c18c3d4 | 10.26434/chemrxiv.13515845.v1 | A Comparison of Separators vs. Membranes in Nonaqueous Redox Flow Battery Electrolytes Containing Small Molecule Active Materials | <p>The lack of suitable membranes for nonaqueous electrolytes limits cell capacity and cycle lifetime in organic redox flow cells. Using soluble, stable materials, we sought to compare the best performance that could be achieved with commercially available microporous separators and ion-selective membranes. We use organic species with proven stability to avoid deconvoluting capacity fade due to crossover and/or cell imbalance from materials degradation. We found a trade-off between lifetime and coulombic efficiency: non-selective separators achieve more stable performance but suffer from low coulombic efficiencies, while ion-selective membranes achieve high coulombic efficiencies but experience capacity loss over time. When electrolytes are pre-mixed prior to cycling, coulombic efficiency remains high, but capacity is lost due to cell imbalance, which can be recovered by electrolyte rebalancing. The results of this study highlight the potential for gains in nonaqueous cell performance that may be enabled by suitable membranes.</p> | Zhiming Liang; N. Harsha Attanayake; Katharine Greco; Bertrand Neyhouse; John L. Barton; Aman Preet Kaur; William Eubanks; Fikile Brushett; James Landon; Susan Odom | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753ae702a9b3b6c18c3d4/original/a-comparison-of-separators-vs-membranes-in-nonaqueous-redox-flow-battery-electrolytes-containing-small-molecule-active-materials.pdf |
60c73dd4567dfe8967ec3709 | 10.26434/chemrxiv.6157613.v1 | Ruthenium(II)-Catalyzed Intermolecular Cyclo(co)trimerization of 3-Halopropiolamides with Internal Alkynes | <div>A highly chemo- and regioselective cyclo(co)trimerization between 3-halopropiolamides and symmetrical internal alkynes is reported. The reaction is catalyzed by Ru(II)-complexes and proceeds at ambient temperature in ethanol to deliver fully substituted dihalogenated isophthalamides. 1,4-Butynediol was found to undergo spontaneous lactonization with halopropiolamides after trimerization to provide 5,7-dihalo-phthalide products.</div> | Anthony P. Silvestri; James S. Oakdale | Organic Synthesis and Reactions; Catalysis; Reaction (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4567dfe8967ec3709/original/ruthenium-ii-catalyzed-intermolecular-cyclo-co-trimerization-of-3-halopropiolamides-with-internal-alkynes.pdf |
62a971a2448398817776887b | 10.26434/chemrxiv-2022-wx8jg | CiD agonists: Circular DNA-based agonists for the fine-tuning of receptor signaling | Receptor dimerization geometry plays a significant role in signal transduction induced by growth factors and cytokines. A chemical strategy capable of controlling dimerization geometry provides a means for studying receptor activation mechanisms and designing novel agonists transducing fine-tuned receptor signaling. However, a generalized approach that can be applied to given receptors is still limited. In the present study, we propose a strategy using CiD agonists (circular DNA aptamer-based agonists), where circularized DNA is used as a rigid scaffold to present two receptor-binding aptamers from the duplex linker domain in a fixed distance and orientation. We targeted Met, a receptor for hepatocyte growth factor (HGF), and designed Met-binding CiD agonists with variable linker length. The designed CiD agonists demonstrated a distinctive periodic change in the receptor activation potential dependent on their linker length. This strategy represents a useful approach for the rational design of partial agonists that transduce fine-tuned receptor signaling and exert moderate biological activity. | Ryosuke Ueki; Yuma Watanabe; Momoko Akiyama; Esther Darley; Shinsuke Sando | Biological and Medicinal Chemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a971a2448398817776887b/original/ci-d-agonists-circular-dna-based-agonists-for-the-fine-tuning-of-receptor-signaling.pdf |
60c74f7b4c89192244ad3bd5 | 10.26434/chemrxiv.12907604.v1 | Effects of Wet Chemical Oxidation on Surface Functionalization and Morphology of Highly Oriented Pyrolytic Graphite | The knowledge of chemical functionalization for area selective deposition (ASD) is crucial for designing the next generation heterogeneous catalysis. Surface functionalization by oxidation was studied on the surface of highly oriented pyrolytic graphite (HOPG). The HOPG surface was exposed to with various concentrations of two different acids (HCl and HNO3). We show that exposure of the HOPG surface to the acid solutions produce primarily the same -OH functional group and also significant differences the surface topography. Mechanisms are suggested to explain these strikingly different surface morphologies after surface oxidation. This knowledge can be used to for ASD synthesis methods for future graphene-based technologies. | Mikhail Trought; Isobel Wentworth; Timothy Leftwich; Kathryn Perrine | Interfaces; Physical and Chemical Processes; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f7b4c89192244ad3bd5/original/effects-of-wet-chemical-oxidation-on-surface-functionalization-and-morphology-of-highly-oriented-pyrolytic-graphite.pdf |
630e27170187d9155da6ea5a | 10.26434/chemrxiv-2022-f40z9 | Physics-integrated Neural Differentiable (PiNDiff) Model for Composites Manufacturing | Various manufacturing technologies are being developed to improve the manufacturing of composites owing to their low weight and high performance. The mechanical properties of the composites depend on various variables and parameters of the manufacturing process, which are challenging, if not impossible, to determine and optimize experimentally. Traditional first-principle modeling approaches are not accessible due to the complex physics involved. A hybrid model that combines incomplete physics knowledge with available measurement data within a differentiable programming framework opens up new avenues to tackle the challenges. In this work, a physics-integrated neural differentiable (PiNDiff) model is developed, where the partially known physics is integrated into the recurrent network architecture to enable effective learning and generalization. The merit and potential of the proposed method have been demonstrated in modeling the curing process of thick thermoset composite laminates, whose governing physics is partially given. The proposed PiNDiff model shows the capability to learn unknown physics from the limited, indirect data and, meanwhile, can be used to infer unobserved variables and parameters. The performance of the PiNDiff model has been compared with two state-of-the-art (SOTA) black-box deep learning models, and its advantages over the purely data-driven models and first-principles physics-based models have been discussed in detail. The demonstrated PiNDiff strategy may provide a general strategy to model phenomena where physics is only partially known and sparse, indirect data are available. | Deepak Akhare; Tengfei Luo; Jian-Xun Wang | Theoretical and Computational Chemistry; Polymer Science; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630e27170187d9155da6ea5a/original/physics-integrated-neural-differentiable-pi-n-diff-model-for-composites-manufacturing.pdf |
60c74b4f0f50db2bc7396be2 | 10.26434/chemrxiv.12278801.v1 | Shermo: A General Code for Calculating Molecular Thermochemistry Properties | Calculation of molecular thermodynamic quantities is one of the most frequently involved task in daily quantum chemistry studies. In this article, we present a general, stand-alone, powerful and flexible code named Shermo for calculating various common thermochemistry data. This code is compatible with Gaussian, ORCA, GAMESS-US and NWChem and has many unique advantages: the output information is very easy to comprehend; thermodynamic quantities can be fully decomposed to contributions of various sources; temperature and pressure can be conveniently scanned; two quasi-rigid-rotor harmonic oscillator (quasi-RRHO) models are supported to properly deal with low frequencies; different frequency scale factors can be simultaneously specified for calculating different thermodynamic quantities; conformation weighted thermodynamic data can be directly evaluated; the code can be easily run and embedded into shell script. We hope the Shermo program will bring great convenience to quantum chemists. This code can be freely obtained at http://sobereva.com/soft/shermo. | Tian Lu; qinxue chen | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b4f0f50db2bc7396be2/original/shermo-a-general-code-for-calculating-molecular-thermochemistry-properties.pdf |
64e29b2000bbebf0e6849371 | 10.26434/chemrxiv-2023-tf81r | Convergent Total Synthesis of (–)-Cyclopamine | A concise and enantioselective total synthesis of the Veratrum alkaloid cyclopamine is disclosed. This highly convergent synthesis with a 15-step longest linear sequence (LLS) was enabled by a de novo synthesis of the trans-6,5 hetero-bicycle via a strain-inducing halocyclization process, a key Tsuji-Trost cyclization to construct the fully substituted, spirocyclic THF motif with exquisite diastereocontrol, and a late-stage ring-closing metathesis (RCM) reaction to forge the central tetrasubstituted olefin. | Manolis Sofiadis; Dongmin Xu; Anthony Rodriguez; Benedikt Nissl; Sebastian Clementson; Nadia Nasser Peterson; phil baran | Organic Chemistry; Natural Products | CC BY 4.0 | CHEMRXIV | 2023-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e29b2000bbebf0e6849371/original/convergent-total-synthesis-of-cyclopamine.pdf |
65b250119138d23161b3ffb3 | 10.26434/chemrxiv-2024-s3nxt | A novel twisted Donor-Acceptor structures with cyano substituents for advancements in Near-Infrared Red TADF Emitters | The designing and development of near-infrared (NIR) red emitters have attracted significant attention owing to the challenges of achieving the necessary energy levels for harvesting both singlet and triplet excitons and their unique requirements for this spectral range. Herein, we have reported the designing and synthesis of two novel red TADF emitters 4,4'-(3,6-bis(9,9-dimethylacridin-10(9H)-yl)dibenzo[a,c]phenazine-11,12-diyl)dibenzonitrile (Ac-PhCNDBPZ) and 4,4'-(3,6-di(10H-phenoxazin-10-yl)dibenzo[a,c]phenazine-11,12-diyl)dibenzonitrile (PXZ-PhCNDBPZ) having twisted donor-acceptor structures. A cyano substituent helps to increase the wavelength towards the redshift. These emitters show near-IR emissions at 602 and 698 nm. This work proves that the cyano substituent and rigid acceptor with a strong donor could be an effective approach to exploring high-efficiency red near-infrared TADF materials. | Atul Chaskar; Sunil Madagyal; Arindam Paul; Prabhakar Chetti | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b250119138d23161b3ffb3/original/a-novel-twisted-donor-acceptor-structures-with-cyano-substituents-for-advancements-in-near-infrared-red-tadf-emitters.pdf |
656cccec29a13c4d47925a18 | 10.26434/chemrxiv-2023-zvtfb | The retaining Pse5Ac7Ac pseudaminyltransferase KpsS1 defines a new glycosyltransferase family (GTXXX) | Cell surface sugar 5,7-diacetyl pseudaminic acid (Pse5Ac7Ac) is a bacterial analogue of the ubiquitous sialic acid, Neu5Ac, and contributes to the virulence of a number of multidrug resistant bacteria, including ESKAPE pathogens Pseudomonas aeruginosa, and Acinetobacter baumannii. Despite its discovery in the surface glycans of bacteria over thirty years ago, to date no glycosyltransferase enzymes (GTs) dedicated to the synthesis of a pseudaminic acid glycosidic linkage have been unequivocally characterised in vitro. Herein we demonstrate that A. baumannii KpsS1 is a dedicated pseudaminyltransferase enzyme (PseT) which constructs a Pse5Ac7Ac-(2,6)-Glcp linkage, and proceeds with retention of anomeric configuration. We utilise this PseT activity in tandem with the biosynthetic enzymes required for CMP-Pse5Ac7Ac assembly, in a two-pot, seven enzyme synthesis of an -linked Pse5Ac7Ac glycoside. Due to its unique activity and protein sequence, we also assign KpsS1 as the prototypical member of a new GT family (GTXXX). | Abigail Walklett; Emily Flack; Harriet Chidwick; Natasha Hatton; Tessa Keenan; Darshita Budhadev; Julia Walton; Gavin Thomas; Martin Fascione | Biological and Medicinal Chemistry; Catalysis; Chemical Biology; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2023-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656cccec29a13c4d47925a18/original/the-retaining-pse5ac7ac-pseudaminyltransferase-kps-s1-defines-a-new-glycosyltransferase-family-gtxxx.pdf |
60c73fdd842e651479db1b89 | 10.26434/chemrxiv.7498229.v1 | Building Markov State Models Using Optimal Transport Theory | Markov State Models (MSMs) describe the rates and routes in conformational dynamics of biomolecules. Computational estimation of MSMs can be expensive because<br />molecular simulations are slow to nd and sample the rare transient events. We describe here an ecient approximate way to determine MSM rate matrices by combining Maximum Caliber (maximizing path entropies) with Optimal Transport Theory (minimizing some path cost function, as when routing trucks on transportation<br />networks) to patch together transient dynamical information from multiple nonequilibrium<br />simulations. We give toy examples. | Purushottam Dixit; Ken Dill | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdd842e651479db1b89/original/building-markov-state-models-using-optimal-transport-theory.pdf |
66013d419138d231613cdaba | 10.26434/chemrxiv-2024-0tvmv | X-band single chip integrated pulsed electron spin resonance microsystem | We report on the design and characterization of a single chip integrated pulsed ESR detector operating at 9.1 GHz. The microsystem consists of an excitation microcoil, a detection microcoil, a low noise microwave preamplifier, a mixer, and an intermediate frequency amplifier. The chip area is about 0.7 mm^2. To exemplify its possible applications, we report the results of single pulse, Raby nutation, Hahn echo, two echoes, Carr-Purcell, and inversion recovery echo experiments performed on 0.02 and 0.05 nL samples of α,γ-bisdiphenylene-β-phenylallyl (BDPA) and 1% BDPA in polystyrene (BDPA:PS) at room temperature. The measured spin sensitivity is about 7x10^7 spins/Hz^(1/2) on a sensitive volume of about 0.1 nL. The microsystem power consumption is less than 100 mW, the RF input bandwidth is 8.8 to 9.8 GHz, the IF output bandwidth is DC to 350 MHz, and the deadtime is less than 30 ns. | Reza Farsi; Nergiz Sahin Solmaz; Giovanni Boero | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66013d419138d231613cdaba/original/x-band-single-chip-integrated-pulsed-electron-spin-resonance-microsystem.pdf |
61af8cd56927e32eebfb61e4 | 10.26434/chemrxiv-2021-pv54s-v2 | Evaluating Fast Methods for Static Polarizabilities on Extended Conjugated Oligomers | Given the importance of accurate polarizability calculations to many chemical applications, coupled with the need for efficiency when calculating the properties of sets of molecules or large oligomers, we present a benchmark study examining possible calculation methods for polarizable materials. We first investigate the accuracy of highly-efficient semi-empirical tight-binding method GFN2-xTB, and the popular D4 dispersion model, comparing its predicted additive polarizabilities to ωB97X-D results for a subset of PubChemQC and a compiled benchmark set of molecules spanning polarizabilities from approximately 3-600 Å^3, with a few compounds in the range of approximately 1200-1400 Å^3. Although we find GFN2 to have large errors with polarizability calculations, on large oligomers it would appear a quadratic correction factor can remedy this. We also compare the accuracy of DFT polarizability calculations run using basis sets of varying size and level of augmentation, determining that a non-augmented basis set may be used for highly polarizable species in conjunction with a linear correction factor to achieve accuracy extremely close to that of aug-cc-pVTZ. | Danielle Heiner; Dakota Folmsbee; Luke Langkamp; Geoffrey Hutchison | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61af8cd56927e32eebfb61e4/original/evaluating-fast-methods-for-static-polarizabilities-on-extended-conjugated-oligomers.pdf |
60c740a20f50db50d0395993 | 10.26434/chemrxiv.7781033.v1 | Modular 3D Printed Compressed Air Driven Continuous-Flow Systems for Chemical Synthesis | In this present study, we describe the development of a low-cost, small-footprint and modular 3D printed continuous-flow system that readily attaches to existing stirrer hotplates. Flow-rates are controlled by compressed air that is typically present in all fume hoods, making it suitable for use by synthetic chemists. The length of the flow-path and reaction residence time is regulated by control of the air-flow and pressure and by addition of one or more 3D printed polypropylene (PP) circular disk reactors that were designed to fit a DrySyn Multi-E base which is found in most synthetic laboratories. The ease of use of the system, the facile control of flow-rates and the solvent resistance of the PP reactors was demonstrated in a range of SNAr reactions to produce substituted ether derivatives highlighting the utility and modularity of the system.<br /> | Matthew Penny,; Zenobia Rao; Bruno Peniche; Stephen Hilton | Organic Polymers; Fluid Mechanics; Industrial Manufacturing; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a20f50db50d0395993/original/modular-3d-printed-compressed-air-driven-continuous-flow-systems-for-chemical-synthesis.pdf |
651333dda69febde9ebbc6ae | 10.26434/chemrxiv-2023-kfr9g | Distilling Coarse-Grained Representations of Molecular Electronic Structure with Continuously Gated Message Passing | Bottom-up methods for coarse-grained (CG) molecular modeling are critically needed to establish rigorous links between atomistic reference data and reduced molecular representations. For a target molecule, the ideal reduced CG representation is a function of both the conformational ensemble of the system and the target physical observable(s) to be reproduced at the CG resolution. However, there is an absence of algorithms for selecting CG representations of molecules from which complex properties, including molecular electronic structure, can be accurately modeled. We introduce continuously gated message passing (CGMP), a graph neural network (GNN) method for atomically decomposing molecular electronic structure sampled over conformational ensembles. CGMP integrates 3D-invariant GNNs and a novel gated message passing system to continuously reduce the atomic degrees of freedom accessible for electronic predictions, resulting in a one-shot importance ranking of atoms contributing to a target molecular property. Moreover, CGMP provides the first approach by which to quantify the degeneracy of ``good" CG representations conditioned on specific prediction targets, facilitating the development of more transferable CG representations. We further show how CGMP can be used to highlight multiatom correlations, illuminating a path to developing CG electronic Hamiltonians in terms of interpretable collective variables for arbitrarily complex molecules. | Charlie Maier; Chun-I Wang; Nicholas Jackson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651333dda69febde9ebbc6ae/original/distilling-coarse-grained-representations-of-molecular-electronic-structure-with-continuously-gated-message-passing.pdf |
643fb92f7be842788de61335 | 10.26434/chemrxiv-2023-nz4bt-v2 | Viscosity-sensitive membrane dyes as tools to estimate the crystalline structure of lipid bilayers | Lipid membranes are crucial for cellular integrity and regulation, and tight control of their structural and mechanical properties is vital to ensure that they function properly. Fluorescent probes sensitive to the mem-brane’s microenvironment are useful for investigating lipid membrane properties, however, there is currently a lack of quantitative correlation between the exact parameters of lipid organization and a readout from these dyes. Here, we investigate this relationship for ‘molecular rotors’, or microviscosity sensors, by simultaneously measuring their fluorescence lifetime to determine the membrane viscosity, while using the X-Ray diffraction the determine the membrane’s structural properties. Our results reveal a phase-dependent correlation be-tween the membrane’s structural parameters and mechanical properties measured by a BODIPY-based mo-lecular rotor, giving excellent predictive power for the structural descriptors of the lipid bilayer. We also demonstrate that differences in membrane thickness between different lipid phases is not a prerequisite for formation of lipid microdomains and that this requirement can be disrupted by the presence of line-active molecules. Our results underpin the use of membrane-sensitive dyes as reporters of the structure of lipid membranes. | Miguel Paez-Perez; Michael R. Dent; Nicholas J. Brooks; Marina K. Kuimova | Physical Chemistry; Analytical Chemistry; Imaging; Microscopy; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643fb92f7be842788de61335/original/viscosity-sensitive-membrane-dyes-as-tools-to-estimate-the-crystalline-structure-of-lipid-bilayers.pdf |
67b84ad3fa469535b9469efb | 10.26434/chemrxiv-2025-hj8ks | Polytypes and Planar Defects Revealed in the Purine
Base Xanthine using Multi-Dimensional Electron
Diffraction | Layered crystal structures are commonly found across organic and inorganic material systems. When in-plane atomic arrangement remains (nearly) identical, a stacking variation of these layers may result in twinning, planar disorder, or polytypes, a form of polymorphism derived
from altering stacking sequences. In this work, we use multi-dimensional electron diffraction (ED) modalities to explore the microstructure of xanthine, an archetypal purine base with a layered crystal structure. Firstly, we identify and characterise the twin operator relating domains of Form I xanthine. We then solve the structure of a new xanthine polymorph, revealing that it is a polytype of Form I. Finally, interfaces between twin and polytype domains are visualised, whilst streaking in the diffraction patterns reveals the presence of planar disorder. Given these observations in the xanthine system, this work suggests that disorder on the nanoscale may be a commonly occurring phenomenon in layered organic molecular
crystals. | Helen Leung; Royston Copley; Giulio Lampronti; Sarah Day; Lucy Saunders; Duncan Johnstone; Paul Midgley | Organic Chemistry; Materials Science; Analytical Chemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b84ad3fa469535b9469efb/original/polytypes-and-planar-defects-revealed-in-the-purine-base-xanthine-using-multi-dimensional-electron-diffraction.pdf |
63c85a0231c8b82dc91addd8 | 10.26434/chemrxiv-2022-lzmrc-v3 | Feature selection in molecular graph neural networks based on quantum chemical approaches | Feature selection is an important topic that has been widely studied in data science. Recently, graph neural networks (GNNs) and graph convolutional networks (GCNs) have also been employed in chemistry. To enhance the performance characteristics of the GNN and GCN in the field of chemistry, the feature selection should also be discussed in detail from the chemistry viewpoint. Thus, this study proposes a new feature in molecular GNNs based on the quantum chemical approaches and discusses the accuracy, overcorrelation between features, and interpretability. From the overcorrelation and accuracy, the important graph convolution (IGC) with molecular-atomic properties (MAP) proposed herein showed good performance. Moreover, the integrated gradients analysis showed that the machine learning model with the IGC(MAP) explained the prediction outputs reasonably. | Daisuke Yokogawa; Kayo Suda | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c85a0231c8b82dc91addd8/original/feature-selection-in-molecular-graph-neural-networks-based-on-quantum-chemical-approaches.pdf |
60c74833702a9b27f918af25 | 10.26434/chemrxiv.11726196.v2 | Chromatographic and Computational Studies on the Chiral Recognition of Sulfated β-Cyclodextrin on Enantiomeric Separation of Milnacipran | <p></p><p>A new,
cost-effective and fast chromatographic method using sulfated β-cyclodextrin
(SβCD) as a chiral mobile phase additive (CMPA) was developed and validated for
the enantiomeric separation of milnacipran. Milnacipran is an anti-depressant
drug. Levo-milnacipran is the active enantiomer with less adverse effects than
dextro-milnacipran. Hence, it is imperative to separate the enantiomers of
milnacipran. Various parameters affecting enantiomeric resolution, for
instance, the effect of type and concentration of cyclodextrins, the effect of
pH of the mobile phase, effect of type and concentration of the organic solvent
in the mobile phase and effect of type of achiral column, were investigated. We
demonstrated successful resolution of enantiomers of milnacipran on
reverse-phase HPLC with Kinetex C8 column (150x4.6mm, 5µ), using a mobile phase
consisting of 18:82 v/v acetonitrile: 10mM sodium dihydrogen orthophosphate
dihydrate buffer pH 3.0 (adjusted with orthophosphoric acid) containing 10mM
SβCD with a flow rate 1.0 ml/minute. The column temperature was ambient and UV
detection was carried out at 227 nm with an injection volume of 20µl. This
method for enantiomeric separation of milnacipran was validated in accordance
with ICH guidelines and successfully applied to the marketed formulation of
Levomilnacipran. Furthermore, molecular docking was used to identify the chiral
recognition mechanism. The results of molecular docking corroborated with our
experimental findings.</p><br /><p></p> | Pranav Pathak; Evans C. Coutinho; Krishnapriya Mohanraj; Elvis Martis; Vikalp Jain | Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74833702a9b27f918af25/original/chromatographic-and-computational-studies-on-the-chiral-recognition-of-sulfated-cyclodextrin-on-enantiomeric-separation-of-milnacipran.pdf |
60c747c50f50db4228396665 | 10.26434/chemrxiv.11782188.v1 | Exploring Coupled Redox and pH Processes with a Force Field-Based Approach: Applications to Five Different Systems | Coupled redox and pH-driven processes are at the core of many important biological mechanisms. As the distribution of protonation and redox states in a system is associated with the pH and redox potential of the solution, having efficient computational tools that can simulate under these conditions become very important. Such tools have the potential to provide information that complement and drive experiments. In previous publications we have presented the implementation of the constant pH and redox potential molecular dynamics (C(pH,E)MD) method in AMBER and we have shown how multidimensional replica exchange can be used to significantly enhance the convergence efficiency of our simulations. In the current work, after an improvement in our C(pH,E)MD approach that allows a given residue to be simultaneously pH- and redox-active, we have employed our methodologies to study five different systems of interest in the literature. We present results for: capped tyrosine dipeptide, two maquette systems containing one pH- and redox-active tyrosine (α3Y and peptide A), and two proteins that contain multiple heme groups (diheme cytochrome c from Rhodobacter sphaeroides and Desulfovibrio vulgaris Hildenborough cytochrome c3). We show that our results can provide new insights into previous theoretical and experimental findings by using a fully force field-based and GPUaccelerated approach, which allows the simulations to be executed with high computational performance. | Vinicius Cruzeiro; Gustavo Troiano Feliciano; Adrian Roitberg | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c50f50db4228396665/original/exploring-coupled-redox-and-p-h-processes-with-a-force-field-based-approach-applications-to-five-different-systems.pdf |
6385b6529b5b801888d9ca97 | 10.26434/chemrxiv-2022-m407m | Subverting covalency gives rise to ionic bonding in high spin states of heterodiatomics | Understanding chemical bonding in second row diatomics has been central to elucidating the basics of bonding itself.1 Bond strength and number of bonds are two factors
that decide the reactivity of molecules. While bond strengths have been theoretically computed accurately and experimentally determined, the number of bonds has been a
more contentious issue especially for complicated multi-reference systems such as C2.2,3 We have developed an experimentally verifiable approach to determine the number
of bonds from excited spin state potential energy surfaces. On applying this to a series of hetero-diatomics of the second row, we obtain the surprising phenomena of an inverted charge transfer ionic state after the covalent bonds in the species are broken via higher spin states. These ionic states are ubiquitous in all heterodiatomics and quite contrary to our expectations in non-metallic systems. | Ishita Bhattacharjee; Debashree Ghosh; Ankan Paul | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Chemical Education - General; Theory - Computational; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6385b6529b5b801888d9ca97/original/subverting-covalency-gives-rise-to-ionic-bonding-in-high-spin-states-of-heterodiatomics.pdf |
60c74638ee301c2914c7947e | 10.26434/chemrxiv.11108792.v1 | Zeolite Structure Direction: Identification, Strength and Involvement of Weak CH…O Hydrogen Bonds | Abstract: We demonstrate herein that weak CH…O hydrogen bonds (HB) play a significant role in zeolite structure direction using organocations. This type of HB were identified between alkyl groups of the organic structure directing agent (OSDA) and the silica framework in as synthesized silicalite-1 of complex topology (MFI) using a combination of experimental and theoretical data obtained at low and room temperatures. The 28 weak CH…O HB, evidenced along dynamics simulation at room temperature, represent 30% of the energy of the Coulomb electrostatic interaction between OSDA and the zeolite framework. The strongest and most stable HB found here connects the OSDA to the [415262] cage containing F atoms and should contribute to preserve zeolite topology during crystal growth. An inspection of other as-synthesized zeolites of very different framework topology indicates that the directional CH...O HBs have to be considered when discussing zeolite structure directing phenomena. | Tzonka Mineva; Eddy Dib; Arnold Gaje; Hugo Petitjean; Jean-Louis Bantignies; Bruno Alonso | Nanostructured Materials - Materials; Bonding; Spectroscopy (Inorg.); Computational Chemistry and Modeling; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74638ee301c2914c7947e/original/zeolite-structure-direction-identification-strength-and-involvement-of-weak-ch-o-hydrogen-bonds.pdf |
612e6798b817b40d020f8703 | 10.26434/chemrxiv-2021-5wg9q | Identifying the true origins of selectivity in chiral phosphoric acid catalyzed N-acyl-azetidine desymmetrizations | The first catalytic intermolecular desymmetrization of azetidines was reported by Sun and coworkers in 2015 using a BINOL-derived phosphoric acid catalyst (J. Am. Chem. Soc. 2015, 137, 5895-5898). To uncover the mechanism of the reaction and the origins of the high enantioselectivity, Density Functional Theory (DFT) calculations were performed at the B97D3 / 6-311+G(2d,2p) / SMD(toluene) // B97D3 / 6-31G(d,p) / CPCM(toluene) level of theory. Comparison of four possible activation modes confirms that this reaction proceeds through the bifunctional activation of the azetidine nitrogen and the thione tautomer of the 2-mercaptobenzothiazole nucleophile. Upon thorough conformational sampling of the enantiodetermining transition structures (TSs), a free energy difference of 2.0 kcal mol-1 is obtained, accurately reproducing the experimentally measured 88% e.e. at 80 °C. This energy difference is due to both decreased distortion and increased non-covalent interactions in the pro-(S) TS. To uncover the true origins of selectivity, the TSs optimized with the full catalyst were compared to those optimized with a model catalyst through steric maps. It is found that the arrangements displayed by the substrates are controlled by strict primary orbital interaction requirements at the transition complex, and their ability to fit into the catalyst pocket drives the selectivity. A general model of selectivity for phosphoric acid-catalyzed azetidine desymmetrizations is proposed, which is based on the preference of the nucleophile and benzoyl group to occupy empty quadrants of the chiral catalyst pocket. | Pier Alexandre Champagne | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Stereochemistry; Computational Chemistry and Modeling; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e6798b817b40d020f8703/original/identifying-the-true-origins-of-selectivity-in-chiral-phosphoric-acid-catalyzed-n-acyl-azetidine-desymmetrizations.pdf |
6419c4aadab08ad68f78a2c1 | 10.26434/chemrxiv-2023-fq1mv | Amino acid-based polyphosphorodiamidates with hydrolytically labile bonds for degradation-tuned photopolymers | Photochemical additive manufacturing technologies can produce complex geometries in short production times and thus have considerable potential as a tool to fabricate medical devices such as individualised patient-specific implants, prosthetics and tissue engineering scaffolds. However, most photopolymer resins degrade only slowly under the mild conditions required for many biomedical applications. Herein we report novel amino acid-based polyphosphorodiamidate (APdA) monomers with hydrolytically cleavable bonds. The substituent on the α-amino acid can be used as a handle for facile control of hydrolysis rates of the monomers into their endogenous components, namely phosphate and the corresponding amino acid. Furthermore, monomer hydrolysis is considerably accelerated at lower pH values. The monomers underwent thiol-yne photopolymerization and could be 3D structured via multi-photon lithography. Copolymerization with commonly used hydrophobic thiols demonstrates not only their ability to regulate the ambient degradation rate of thiol-yne polyester photopolymer resins but also rare but highly desirable surface erosion behaviour. Such degradation profiles, in the appropriate timeframes in suitably mild conditions, combined with their good cytocompatibility and 3D printability, render these novel photomonomers of significant interest for a wide range of biomaterial applications. | Stephan Haudum; Stefan Lenhart; Stefanie Müller; Disha Tupe; Christoph Naderer; Tilo Dehne; Michael Sittinger; Zoltan Major; Thomas Griesser; Oliver Brüggemann; Jaroslaw Jacak; Ian Teasdale | Polymer Science; Inorganic Polymers; Organic Polymers; Polymer scaffolds; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6419c4aadab08ad68f78a2c1/original/amino-acid-based-polyphosphorodiamidates-with-hydrolytically-labile-bonds-for-degradation-tuned-photopolymers.pdf |
60c741e6469df4314ef42ecc | 10.26434/chemrxiv.8025221.v2 | Applied Process Simulation-Driven Oil and Gas Separation Plant Optimization using Surrogate Modeling and Evolutionary Algorithms | In this article the optimization of a realistic oil and gas separation plant has
been studied. Two different fluids are investigated and compared in terms of
the optimization potential. Using Design of Computer Experiment (DACE) via
Latin Hypercube Sampling (LHS) and rigorous process simulations, surrogate
models using Kriging have been established for selected model responses. The
surrogate models are used in combination with a variety of different evolutionary algorithms for optimizing the operating profit, mainly by maximizing the
recoverable oil production. A total of 10 variables representing pressure and
temperature various key places in the separation plant are optimized to maximize the operational profit. The optimization is bounded in the variables and a
constraint function is included to ensure that the optimal solution allows export
of oil with an RVP < 12 psia. The main finding is that, while a high pressure is
preferred in the first separation stage, apparently a single optimal setting for the
pressure in downstream separators does not appear to exist. In the second stage
separator apparently two different, yet equally optimal, settings are revealed.
In the third and final separation stage a correlation between the separator pressure and the applied inlet temperature exists, where different combinations of
pressure and temperature yields equally optimal results.<br /> | Anders Andreasen | Natural Resource Recovery; Petrochemicals; Process Control; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e6469df4314ef42ecc/original/applied-process-simulation-driven-oil-and-gas-separation-plant-optimization-using-surrogate-modeling-and-evolutionary-algorithms.pdf |
60c7476a567dfe6875ec4813 | 10.26434/chemrxiv.11656494.v1 | On the Electronic and Optical Properties of Metal-Organic Frameworks: Case Study of MIL-125 and MIL-125-NH2 | <div>The photoactive MIL-125 and MIL-125-NH$_{2}$ Metal-Organic Frameworks (MOFs), despite a very similar crystalline structure, exhibit different optically behaviour. Luminescence in MIL-125 decays in about 1 ns while for its amino counterpart the lifetime of the charge-carriers is at least one order of magnitude larger. The origin of this difference is the key element for understanding the photocatalytic behaviour of MIL-125-NH<sub>2</sub> when associated with active nanoparticles, behaviour that is completely absent in MIL-125. By performing advanced</div><div>ab-initio electronic structure calculations, we find that charge-carriers interact differently in the two MOFs with subsequent effects on the luminescence lifetimes and their catalytic performances. To confirm the predictions of our model we synthesized a novel material in the MIL-125 family, MIL-125-NH<sub>2</sub>-[10%](OH)<sub>2</sub>, and confirm that our theory correctly predicts a faster decay compared to MIL-125-NH<sub>2</sub>.</div> | Gloria Capano; Francesco Ambrosio; Stavroula Kampouri; Kyriakos Stylianou; Alfredo Pasquarello; Berend Smit | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7476a567dfe6875ec4813/original/on-the-electronic-and-optical-properties-of-metal-organic-frameworks-case-study-of-mil-125-and-mil-125-nh2.pdf |
60c74228ee301ce5b7c78dca | 10.26434/chemrxiv.7789940.v2 | autoDIAS: A Python Tool for an Automated Distortion/Interaction Activation Strain Analysis | The Distortion/Interaction Activation Strain (DIAS) analysis
is a powerful tool for the investigation of energy barriers. However, setup and
data analysis of such a calculation can be cumbersome and requires lengthy intervention
of the user. We present autoDIAS, a python tool for the automated setup,
performance, and data extraction of the DIAS analysis, including automated
detection of fragments and relevant geometric parameters. | Dennis Svatunek; Kendall N. Houk | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74228ee301ce5b7c78dca/original/auto-dias-a-python-tool-for-an-automated-distortion-interaction-activation-strain-analysis.pdf |
60c74c2f337d6c9777e27bd6 | 10.26434/chemrxiv.12380330.v2 | Efficient Reduction of Electron-Deficient Alkenes Enabled by a Photoinduced Hydrogen Atom Transfer | Direct hydrogen atom transfer from a photoredox-generated Hantzsch ester radical cation to electron-deficient alkenes has enabled the<br />development of an efficient formal hydrogenation under mild, operationally simple conditions. The HAT-driven mechanism, key to circumvent<br />the problems associated with the low electron affinity of alkenes, is supported by experimental and computational studies. The reaction is applied<br />to a variety of cinnamate derivatives and related structures, irrespective of the presence of electron-donating or electron-withdrawing<br />substituents in the aromatic ring and with good functional group compatibility. | Xacobe Cambeiro; Natalia A. Larionova; Jun Miyatake Ondozabal | Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c2f337d6c9777e27bd6/original/efficient-reduction-of-electron-deficient-alkenes-enabled-by-a-photoinduced-hydrogen-atom-transfer.pdf |
6788052c6dde43c908b819f8 | 10.26434/chemrxiv-2025-ll8zq | Improved C5-amide bioisosteres for human neuraminidase 1 inhibitors based on 2-deoxy-2,3-didehydro-N-acetyl neuraminic acid (DANA) | Neuraminidase enzymes (NEU) play a crucial role in many physiological and pathological conditions. Humans have four isoenzymes of NEU and their specific roles continue to be investigated. Isoenzyme-selective inhibitors are needed as research tools and may lead to future therapeutics. We tested a series of new candidate inhibitors by replacing the C5-amide of 2-deoxy-2,3-dididehydro-N-acetyl neuraminic acid (DANA) with amide bioisosteres. Design of candidate inhibitors was accomplished using substituents that were components of previously identified NEU inhibitors combined with alternative amide bioisosteres. Compounds were tested for inhibition of the four human NEU, and inhibitory activities were compared to reference amide compounds. We observed that 1,4-disubstituted-1,2,3-triazole was the best bioisostere for inhibitors of NEU1. Inhibitor 542 showed high potency for NEU1 (K¬i = 0.4 ± 0.1 μM) and gave significant improvement in selectivity compared to the reference amide compound 502. Additionally, compound 542 had improved lipophilic characteristics which could provide improved pharmacokinetic properties. Screening of these inhibitors also identified a selective NEU2 inhibitor 543 (Ki = 2.6 ± 0.6 μM), illustrating that amide bioisostere replacement can identify improved inhibitors for multiple NEU isoenzymes. | Mostafa Radwan; Elisa Garcia Carvajal; Christopher Cairo | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6788052c6dde43c908b819f8/original/improved-c5-amide-bioisosteres-for-human-neuraminidase-1-inhibitors-based-on-2-deoxy-2-3-didehydro-n-acetyl-neuraminic-acid-dana.pdf |
65e5f14e9138d23161a5c012 | 10.26434/chemrxiv-2024-7bfmj | Probing ultrafast photochemical mechanisms of molecular and heterogenized rhodium bipyridine photocatalyst | Molecular and heterogenized rhodium bipyridine (Bpy) complexes are highly active and selective for the carbon dioxide photoreduction into formic acid using visible light as sole energy source. The excited state of the molecular 5,5’-di(pyren-1-yl)-2,2’-bipyridine Pyr2Bpy and of the corresponding conjugated microporous polymer PyrBpy-CMP, envisioned as macroligand, as well as of their organometallic complexes with pentamethylcyclopentadienyl (Cp*) rhodium [Pyr2Bpy]Cp*RhCl2 and Cp*Rh@PyrBpy-CMP have been investigated by femtosecond UV-vis transient absorption spectroscopy. In both polymers PyrBpy-CMP and Cp*Rh@PyrBpy-CMP the fs measurements reveal the formation of a broad excited state absorptions bands decaying in the sub-ns time scale. For Cp*Rh@PyrBpy-CMP , the ultrafast energy transfer from the framework to the catalytic centres is demonstrated. Pyr2Bpy and [Pyr2Bpy]Cp*RhCl2 have been studied as model molecular building blocks of the CMP. The results show the participation of a mesomeric intramolecular charge transfer (MICT) state and of a twisted intramolecular charge transfer state (TICT) stabilized by the torsion of the pyrene and bipyridine moiety, that are then converted into ligand to metal charge transfer states (LMCT) in [Pyr2Bpy]Cp*RhCl2. The photophysical parameters determined for the molecular compounds were applied to calculate the Förster Resonance Energy Transfer rate from the light-harvesting organic units to the heterogenized Rh metal centres. Finally, the role of the triethanolamine, a common sacrificial electron donor (SED) employed for the CO2 reduction, as an efficient quencher of the excited states of the Pyr2Bpy is demonstrated. This quenching reaction is expected to occur for a wide range of organic and organo-metallic photocatalysts, and its consequences on the reduction of the photoconversion yield are certainly underestimated for most of the applications. | Quentin Périnnet; Ashta C. Ghosh; Florian Wisser; Jérome Canivet; vincent de waele | Physical Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e5f14e9138d23161a5c012/original/probing-ultrafast-photochemical-mechanisms-of-molecular-and-heterogenized-rhodium-bipyridine-photocatalyst.pdf |
65e71af69138d23161b5f55c | 10.26434/chemrxiv-2024-8n32t | Heuristics? What about them? –Review on the operation of heuristics in chemical education in the past two decades | Heuristics are evident in students’ reasoning processes in chemical education. This review of heuristics is a novel attempt to understand the use of heuristics in chemical education in the last two decades. Searches across four databases resulted in 21374 raw hits and an ultimate sample of 27 screened articles. We performed a content analysis on three goals--How has the definition of heuristics operationalized in these studies, what different chemical topics and tasks have been linked to the types of heuristics, and the different interventions explored in such heuristic studies. Our review reveals a lack of consistent defining features of heuristics in the chemical education field, an inclination towards ranking and comparison tasks and organic-inorganic chemistry topics, and a lack of sufficient research dedicated towards heuristic refinement in students. Our review restates the need to bridge the gap between research and practice of heuristics in chemical education. | Rajashri Priyadarshini; Chandan Dasgupta | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e71af69138d23161b5f55c/original/heuristics-what-about-them-review-on-the-operation-of-heuristics-in-chemical-education-in-the-past-two-decades.pdf |
67cf041bfa469535b9bc28d4 | 10.26434/chemrxiv-2025-f9vdp | ECTS: An ultra-fast diffusion model for exploring chemical reactions with equivariant consistency | Unveiling reaction mechanisms through the exploration of reaction paths, including identification of transition states (TS), prediction of reaction energy barriers (), and mapping of reaction pathways, is crucial for the study of chemical reactions. However, this process usually requires extensive and computationally demanding quantum chemistry calculations. Here, we propose an equivariant consistency generative model ECTS, an ultra-fast diffusion method that unifies TS generation, energy prediction, and pathway search within one framework. Our results highlight that the efficiency of ECTS is at least two orders of magnitude higher than conventional diffusion models. TS structures generated by ECTS exhibit an error margin of just 0.12 Å root mean square deviation compared to the ground truth. Additionally, by continuously refining the energy barrier predictions in the denoising process, ECTS achieves a median error of merely 2.4 kcal/mol without any post-DFT calculations. Moreover, as a novel feature, ECTS can also generate reaction paths which are in general agreement with the true reaction paths, indicating ECTS could potentially be useful for exploring reaction mechanisms. | Mingyuan Xu; Bowen Li; Zhaojia Dong; Pavlo Dral; Tong Zhu; Hongming Chen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf041bfa469535b9bc28d4/original/ects-an-ultra-fast-diffusion-model-for-exploring-chemical-reactions-with-equivariant-consistency.pdf |
60c74cf24c89190b0aad371f | 10.26434/chemrxiv.12570950.v1 | Expanding the Scope of Pyclen-Picolinate Lanthanide Chelates to Po-Tential Theranostic Applications | A family of three picolinate pyclen based ligands,
previously investigated for the complexation of Y<sup>3+</sup> and some
lanthanide ions (Gd<sup>3+</sup>, Eu<sup>3+</sup>), was studied with <sup>161</sup>Tb
and <sup>177</sup>Lu in view of potential radiotherapeutic applications. The
set of six Tb<sup>3+ </sup>and Lu<sup>3+ </sup>complexes was synthesized and
fully characterized. The coordination properties in the solid state and in
solution were thoroughly studied. Potentiometric titrations, corroborated by
DFT calculations, showed the very high stability constants of the Tb<sup>3+</sup>
and Lu<sup>3+</sup> complexes, which are associated to remarkable kinetic inertness.
A complete radiolabeling study performed with both<sup> 161</sup>Tb and <sup>177</sup>Lu
radionuclides, including experiments with regard to the stability with and
without scavengers and kinetic inertness using challenging agents, proved that
the ligands could reasonably compete with the DOTA analogue. To conclude, the
potential of using the same ligand for both radiotherapy and optical imaging
was highlighted for the first time. | Gwladys Nizou; Chiara Favaretto; Francesca Borgna; Pascal V. Grundler; Nathalie Saffon-Merceron; Carlos Platas-Iglesias; Olivier Fougère; Olivier Rousseaux; Nicholas van der Meulen; Cristina Müller; Maryline Beyler; Raphael Tripier | Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.); Nuclear Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cf24c89190b0aad371f/original/expanding-the-scope-of-pyclen-picolinate-lanthanide-chelates-to-po-tential-theranostic-applications.pdf |
66c5ba0020ac769e5f50bbfa | 10.26434/chemrxiv-2024-xq3pl | PepFuNN: Novo Nordisk open-source toolkit to enable peptide in silico analysis | We present PepFuNN, a new open-source version of the PepFun package with functions to study the chemical space of peptide libraries and perform structure-activity relationship analyses. PepFuNN is a Python package comprising five modules to study peptides with natural amino acids and, in some cases, sequences with non-natural amino acids based on the availability of a public monomer dictionary. The modules allow calculating physicochemical properties, performing similarity analysis using different peptide representations, clustering peptides using molecular fingerprints or calculated descriptors, designing peptide libraries based on specific requirements, and a module dedicated to extracting matched pairs from experimental campaigns to guide the selection of the most relevant mutations in design new rounds. The code and tutorials are available at: https://github.com/novonordisk-research/pepfunn | Rodrigo Ochoa; Kristine Deibler | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c5ba0020ac769e5f50bbfa/original/pep-fu-nn-novo-nordisk-open-source-toolkit-to-enable-peptide-in-silico-analysis.pdf |
67bd8094fa469535b9d4fd73 | 10.26434/chemrxiv-2025-2n40d-v2 | Ternary Complex Modeling, Induced Fit Docking and Molecular Dynamics Simulations as a Successful Approach for the Design of VHL-mediated PROTACs Targeting the Kinase FLT3 | Proteolysis targeting chimeras (PROTACs) have proven to be a novel approach for the degradation of disease-causing proteins in drug discovery. One of the E3 ligases for which efficient PROTACs have been described is the Von-Hippel-Lindau factor (VHL). However, the development of PROTACs has so far often relied on a minimum of computational tools, so that it is mostly based on a trial-and-error process. Therefore, there is a great need for resource- and time-efficient structure-based or computational approaches to streamline PROTAC design. In this study, we present a combined computational approach that integrates static ternary complex formation, induced fit docking, and molecular dynamics (MD) simulations. Our methodology was tested using four experimentally derived ternary complex structures of VHL PROTACs, reported for BRD4, SMARCA2, FAK and WEE1. In addition, we applied the validated approach to model a recently in-house developed FLT3-targeted PROTAC (MA49). The results show that static ternary models generated with a protein-protein docking method implemented in the software MOE have a high predictive power for reproducing the experimental 3D structures. The induced fit-docking of different active PROTACs to their respective models showed the reliability of this model for the development of new VHL-mediated degraders. In particular, the induced-fit docking was sensitive to structural changes in the PROTACs, as evidenced by the failed binding modes of the PROTAC negative controls. Furthermore, MD simulations confirmed the stability of the generated complexes and emphasized the importance of dynamic studies for understanding the relationship between PROTAC structure and function. | Husam Nassar; Anne-Christin Sarnow; Ismail Celik; Mohamed Abdelsalam; Dina Robaa; Wolfgang Sippl | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd8094fa469535b9d4fd73/original/ternary-complex-modeling-induced-fit-docking-and-molecular-dynamics-simulations-as-a-successful-approach-for-the-design-of-vhl-mediated-prota-cs-targeting-the-kinase-flt3.pdf |
60c752729abda22a4df8de0d | 10.26434/chemrxiv.13296878.v1 | A Low-Cost Mechatronic System for Sol-Gel Spraypyrolysis Technique | This work presents a design of a low-cost spray pyrolysis automatized system which allows to manufacture high quality thin films. In particular, the thermal component of this instrument is modelled in different operation conditions, analyzed, and controlled. Also, different configurations for the whole instrument are analyzed. | Martin E. Oviedo; Fernando Alvira; Agustin Apaolaza; Juan F. Martiarena; Matías R. Tejerina | Materials Processing; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752729abda22a4df8de0d/original/a-low-cost-mechatronic-system-for-sol-gel-spraypyrolysis-technique.pdf |
62f57198e78f7056f43809b6 | 10.26434/chemrxiv-2022-j37tb | New Antitumor Organotitanium Complexes with a Pendant Biologically Active Diazo Group | The ligand of antitumor organotitanium or other metallodug complexes plays a pivotal role in
determining the mechanism of their cytotoxic action. Although the specific contribution of several
ligands is generally well established, our understanding of the overall mechanism of the cytotoxic
action of the complexes themselves is limited and incomplete in most cases, except perhaps in the case
of cis-platin. A strategy to monitor the mode of cytotoxic action of candidate antitumor complexes
requires tagging with bioactive side chains like a diazo group, for in-cell site-specific labelling. In this
review we expand on a previous publication [1] to discuss several new methods for the preparation of
potential antitumor organotitanium complexes with a pendant diazo group, aiming at better
understanding their mode of cytotoxic action. By introducing this new class of titanium-based
potential antitumor agents, we hope to contribute to the world-wide effort in this important area of
medicinal chemistry research, for an ultimate usable titanium-based antitumor drug. | Gregory Arzoumanidis | Biological and Medicinal Chemistry; Organometallic Chemistry; Drug Discovery and Drug Delivery Systems; Bioorganometallic Chemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f57198e78f7056f43809b6/original/new-antitumor-organotitanium-complexes-with-a-pendant-biologically-active-diazo-group.pdf |
6156552ecea2e9c41e03e6a7 | 10.26434/chemrxiv-2021-jpk9v | Efficient Dynamic Computational Strategy for Heterogeneous Catalysis Based on Neural Network Potential Energy Surface: A Case Study of Temperature-Dependent Thermodynamics and Kinetics for the Chemisorbed on-surface CO | As a favorable alternative and complement of experimental techniques, computational tools on top of ab initio calculations have played an indispensable role in revealing the molecular details, thermodynamics and kinetics in catalytic reactions. The static computational strategy, which recovers the reaction thermodynamics and kinetics based on the calculations of a few stationary geometries at zero temperature and some ideal statistic mechanics models, is the most popular approach in theoretical catalysis due to its simplicity. In comparison, the ab initio molecular dynamics (AIMD) is a well-tested approach to provide more precise descriptions of catalytic processes, however, experiencing a significantly expensive computational cost in the direct ab initio calculation of potential energy and gradients. Here we proposed a highly efficient dynamic computational strategy for the calculation of thermodynamic and kinetic properties in heterogeneous catalysis on the basis of neural network potential energy surface (NN PES) and MD simulations. Taking CO adsorbate on Ru(0001) surface as the illustrative model catalytic system, we demonstrated that our NN-PES-based MD simulations can efficiently generate the reliable smooth two-dimensional potential-of-mean-force (2-D PMF) surfaces in a wide range of temperatures (from 300 to 900 K), and thus temperature-dependent thermodynamic properties can be obtained in a comprehensive investigation on the whole PMF surface rather than a rough estimation using ideal models based on a few optimized geometries. Moreover, MD simulations offer an effective way to describe the surface kinetics such as the CO adsorbate on-surface movement, which goes beyond the most popular static estimation based on calculated free energy barrier and transition state theory (TST). By comparing the results obtained in the dynamic and static approaches, we further revealed that the dynamic strategy significantly improves the predictions of both thermodynamic and kinetic properties as compared to the popular ideal statistic mechanics approaches such as harmonic analysis and TST. It is expected that this accurate yet efficient dynamic strategy can be a powerful tool in understanding reaction mechanisms and reactivity of a catalytic surface system, and further guides the rational design of heterogeneous catalysts.
| Jun Chen; Tan Jin; Tonghao Shen; Mingjun Yang; Zhe-Ning Chen | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Chemical Kinetics; Statistical Mechanics | CC BY NC 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6156552ecea2e9c41e03e6a7/original/efficient-dynamic-computational-strategy-for-heterogeneous-catalysis-based-on-neural-network-potential-energy-surface-a-case-study-of-temperature-dependent-thermodynamics-and-kinetics-for-the-chemisorbed-on-surface-co.pdf |
61cff84fd1f662cd654c2f8a | 10.26434/chemrxiv-2021-pm752-v2 | Ultrafast Proton Transfer Reaction in Phenol–(Ammonia)n Clusters: An Ab-Initio Molecular Dynamics Investigation. | The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer process, the phenol molecule must be embedded in a cluster consisting of at least eight ammonia molecules, even though several local minima with proton transferred can be observed for clusters consisting of 5-7 ammonia molecules. Further, phenol solvated in large clusters of ammonia, the proton transfer is spontaneous with the proton transfer event being instantaneous (about 20-120 fs). These simulations indicate that the rate-determining step for the proton transfer process is the reorganization of the solvent around the OH group and the proton transfer process in phenol-(ammonia)n clusters. The fluctuations in the solvent occur until a particular set of configurations projects the field in excess of critical electric field along the O–H bond which drives the proton transfer process with a respone time of about 70 fs. Further, the proton transfer process follows a curvilinear path which includes the O–H bond elongation and out-of-plane movement of the proton and can be referred to as a “Bend-to-Break” process. | Reman Kumar Singh; Rakesh Pant; G Naresh Patwari | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cff84fd1f662cd654c2f8a/original/ultrafast-proton-transfer-reaction-in-phenol-ammonia-n-clusters-an-ab-initio-molecular-dynamics-investigation.pdf |
65bbf6e2e9ebbb4db976396d | 10.26434/chemrxiv-2023-3drsr-v2 | Polarized local excitons assist charge dissociation in Y6-based nonfullerene organic solar cells: a nonadiabatic molecular dynamics study | Y6-based nonfullerene organic solar cells (OSCs) have achieved an outstanding power conversion efficiency (PCE) of over 19% due to the low energy loss and high exciton dissociation efficiency with a small energy offset. However, the exciton dissociation mechanism is still under debate. It is unclear why a small energy offset can lead to efficient exciton dissociation in nonfullerene systems, but causes significant charge recombination in fullerene ones. Most of the previous theoretical studies have focused on the static properties of donor–acceptor heterojunctions, while neglecting excited electron dynamics and nonadiabatic effects. Here, we applied nonadiabatic molecular dynamics simulations to study the charge transfer dynamics in both donor:Y6 and donor:C60 crystalline systems. We found that thermal effects do not significantly influence the exciton dissociation in the NT-4T-FF:Y6 system, which aligns with experimental observations. Based on our simulations, we identified a five-step charge transfer process in nonfullerene systems. While previous studies suggested electrostatic interfacial fields from non-fullerene small molecule acceptors, our research reveals that strong donor-acceptor interactions primarily affect the local exciton states rather than the ground state. Consequently, the polarized local excitons play a key role in reducing the Coulomb attraction between electrons and holes, thus facilitating exciton dissociation with a small energy offset. In contrast, this mechanism is not observed in fullerene OSC systems. Our findings provide a fundamental basis for the further development of novel OSC materials with the potential for achieving even higher PCE. | Bin Liu; Philip Chow; Junzhi Liu; Ding Pan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bbf6e2e9ebbb4db976396d/original/polarized-local-excitons-assist-charge-dissociation-in-y6-based-nonfullerene-organic-solar-cells-a-nonadiabatic-molecular-dynamics-study.pdf |
60c741ed702a9b461218a369 | 10.26434/chemrxiv.7900277.v2 | A Quantitative Uncertainty Metric Controls Error in Neural Network-Driven Chemical Discovery | <p>Machine learning (ML) models, such as artificial neural networks, have emerged as a complement to high-throughput screening, enabling characterization of new compounds in seconds instead of hours. The promise of ML models to enable large-scale, chemical space exploration can only be realized if it is straightforward to identify when molecules and materials are outside the model’s domain of applicability. Established uncertainty metrics for neural network models are either costly to obtain (e.g., ensemble models) or rely on feature engineering (e.g., feature space distances), and each has limitations in estimating prediction errors for chemical space exploration. We introduce the distance to available data in the latent space of a neural network ML model as a low-cost, quantitative uncertainty metric that works for both inorganic and organic chemistry. The calibrated performance of this approach exceeds widely used uncertainty metrics and is readily applied to models of increasing complexity at no additional cost. Tightening latent distance cutoffs systematically drives down predicted model errors below training errors, thus enabling predictive error control in chemical discovery or identification of useful data points for active learning.</p> | Jon Paul Janet; Chenru Duan; Tzuhsiung Yang; Aditya Nandy; Heather Kulik | Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ed702a9b461218a369/original/a-quantitative-uncertainty-metric-controls-error-in-neural-network-driven-chemical-discovery.pdf |
64b55faeb053dad33a692084 | 10.26434/chemrxiv-2023-zbj6j | Neighbor List Artifacts in Molecular Dynamics Simulations | Molecular dynamics (MD) simulations are widely used in biophysical research. To aid non-expert users, most simulation packages provide default values for key input parameters. In MD simulations using the GROMACS package with default parameters, we found large membranes to deform under the action of a semi-isotropically coupled barostat. As the primary cause, we identified overly short outer cutoffs and infrequent neighbor list updates that result in missed long-range attractive Lennard-Jones interactions. Small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. We also observed rapid oscillations in averages of the instantaneous pressure tensor components and traced these to the use of a dual pair list with dynamic pruning. We confirmed that similar effects are present in MD simulations of neat water in atomistic and coarse-grained representations. Whereas the slight pressure imbalances likely have minimal impact in most current MD simulations, we expect their impact to grow in studies of ever-larger systems, in particular in combination with anisotropic pressure coupling. We present measures to diagnose problems with missed interactions and guidelines for practitioners to avoid them, including estimates for appropriate values for the outer cutoff r_l and the number of time steps nstlist between neighbor list updates. | HYUNTAE KIM; Balázs Fábián; Gerhard Hummer | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b55faeb053dad33a692084/original/neighbor-list-artifacts-in-molecular-dynamics-simulations.pdf |
615cf5127d3da5dd7bee4a22 | 10.26434/chemrxiv-2021-vx5r3 | PoreMatMod.jl: Julia package for in silico post-synthetic modification of crystal structure models | PoreMatMod.jl is a free, open-source, user-friendly, and documented Julia package for modifying crystal structure models of porous materials such as metal-organic frameworks (MOFs). PoreMatMod.jl functions as a find-and-replace algorithm on crystal structures by leveraging (i) Ullmann's algorithm to search for subgraphs of the crystal structure graph that are isomorphic to the graph of a query fragment and (ii) the orthogonal Procrustes algorithm to align a replacement fragment with a targeted substructure of the crystal structure for installation. The prominent application of PoreMatMod.jl is to generate libraries of hypothetical structures for virtual screenings via molecular simulations. For example, one can install functional groups on the linkers of a parent MOF, mimicking post-synthetic modification. Other applications of PoreMatMod.jl to modify crystal structure models include introducing defects and correcting artifacts of X-ray structure determination (adding missing hydrogen atoms, resolving disorder, and removing guest molecules). | E. Adrian Henle; Nickolas Gantzler; Praveen K. Thallapally; Xiaoli Z. Fern; Cory M. Simon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615cf5127d3da5dd7bee4a22/original/pore-mat-mod-jl-julia-package-for-in-silico-post-synthetic-modification-of-crystal-structure-models.pdf |
67ca97f481d2151a0272a751 | 10.26434/chemrxiv-2025-gn7lm-v2 | When Theory Came First: A Review of Theoretical Chemical Predictions Ahead of Experiments | For decades, computational theoretical chemistry has provided critical insights into molecular behavior, often anticipating experimental discoveries. This review surveys twenty notable examples from the past fifteen years in which computational chemistry successfully predicted molecular structures, reaction mechanisms, and material properties before experimental confirmation. Spanning fields such as bioinorganic chemistry, materials science, catalysis, and quantum transport, these case studies illustrate how quantum chemical methods have become essential for multidisciplinary molecular sciences. The impact of theoretical predictions across disciplines shows the indispensable role of computational chemistry in guiding experiments and driving scientific discovery. | Mario Barbatti | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca97f481d2151a0272a751/original/when-theory-came-first-a-review-of-theoretical-chemical-predictions-ahead-of-experiments.pdf |
64fbcf98b338ec988a249509 | 10.26434/chemrxiv-2023-wk00w-v3 | Modeling lithium plating onset on porous graphite elec- trodes under fast charging with hierarchical multiphase porous electrode theory | Lithium plating during fast charging of porous graphite electrodes in lithium-ion batteries accelerates degradation and raises safety concerns. Predicting lithium plating is challenging due to the close redox potentials of lithium reduction and intercalation, obscured by the nonlinear dynamics of electrochemically driven phase separation in hierarchical pore structures. To resolve dynamical resistance of realistic porous graphite electrodes, we introduce a model of porous secondary graphite particles to the multiphase porous electrode theory (MPET), based on electrochemical nonequilibrium thermodynamics and volume averaging. The resulting computational framework of "hierarchical MPET" is validated and tested against experimental data over a wide range of fast charging conditions and capacities. With all parameters estimated from independent sources, the model is able to quantitatively predict the measured cell voltages, and, more importantly, the experimentally determined capacity for lithium plating onset at fast 2C to 6C rates. Spatial and temporal heterogeneities in the lithiation of porous graphite electrodes are revealed and explained theoretically, including key features, such as idle graphite particles and non-uniform plating, which have been observed experimentally. | Huada Lian; Martin Bazant | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fbcf98b338ec988a249509/original/modeling-lithium-plating-onset-on-porous-graphite-elec-trodes-under-fast-charging-with-hierarchical-multiphase-porous-electrode-theory.pdf |
60c74aea337d6cc3ffe279be | 10.26434/chemrxiv.12252041.v1 | Synthesis of Pyridylsulfonium Salts and their Application in Transition Metal-Free Formation of Functionalized Bipyridines | An S-selective
arylation of pyridylsulfides with good functional group tolerance has been
developed. The resulting pyridylsulfonium salts have been used in a scalable
transition metal-free coupling protocol yielding functionalized bipyridine
scaffolds with extensive functional group tolerance and modularity.
Pyridylsulfonium salts were coupled to lithiated pyridines in a sulfur-mediated
synthesis of bipyridines. This modular methodology, permits selective
introduction of functional groups from commercially available pyridyl halides,
furnishing symmetrical and unsymmetrical 2,2’- and 2,3’-bipyridines. Iterative
application of the methodology enabled the synthesis of a functionalized
terpyridine with three different pyridine components. | Vincent K. Duong; Alexandra M. Horan; Eoghan McGarrigle | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aea337d6cc3ffe279be/original/synthesis-of-pyridylsulfonium-salts-and-their-application-in-transition-metal-free-formation-of-functionalized-bipyridines.pdf |
60c741e2567dfedeb7ec3e52 | 10.26434/chemrxiv.7289471.v3 | DNA Barcoding a Complete Matrix of Stereoisomeric Small Molecules | <p></p><p>It
is challenging to incorporate stereochemical diversity and topographic
complexity into DNA-encoded libraries (DELs) because DEL syntheses cannot fully
exploit the capabilities of modern synthetic organic chemistry. Here, we
describe the design, construction, and validation of DOS-DEL-1, a library of
107,616 DNA-barcoded chiral 2,3-disubsituted azetidines and pyrrolidines. We
used stereospecific C–H arylation chemistry to furnish complex scaffolds primed
for DEL synthesis, and we developed an improved on-DNA Suzuki reaction to
maximize library quality. We then studied both the structural diversity of the
library and the physicochemical properties of individual compounds using Tanimoto
multi-fusion similarity analysis, among other techniques. These analyses revealed
not only that most DOS-DEL-1 members have “drug-like” properties, but also that
the library more closely resembles compound collections derived from diversity
synthesis than those from other sources (<i>e.g.</i>,
commercial vendors). Finally, we performed validation screens against horseradish
peroxidase and carbonic anhydrase IX, and we developed a novel, Poisson-based
statistical framework to analyze the results. A set of assay positives were
successfully translated into potent carbonic anhydrase inhibitors (IC<sub>50</sub>
= 20.1–68.7 nM), which confirmed the success of the synthesis and screening
procedures. These results establish a strategy to synthesize DELs with
scaffold-based stereochemical diversity and complexity that does not require the
development of novel DNA-compatible chemistry.</p><p></p> | Christopher Gerry; Mathias Wawer; Paul Clemons; Stuart Schreiber | Combinatorial Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e2567dfedeb7ec3e52/original/dna-barcoding-a-complete-matrix-of-stereoisomeric-small-molecules.pdf |
60c9e3b13fc2cb674c000d4e | 10.26434/chemrxiv.14781498.v1 | Molecular Gatekeeper Discovery: Workflow for Linking Multiple Environmental Biomarkers to Metabolomics | The exposome reflects the many exposures to various factors across the life-course that can affect health. Sensitive techniques like metabolomics can reveal the underlying molecular basis linking exposures to disease and generate hypotheses for future quantitative toxicological studies. Current applications of metabolomics are primarily to identify metabolic changes linking a single exposure and a health outcome(s); there is no general framework for multiple exposures. Here, we explore the concept of ‘molecular gatekeepers’—key metabolites that link single or multiple exposure biomarkers with correlated clusters of endogenous metabolites—to inform health-relevant biological targets. We performed untargeted metabolomics on plasma from 152 adolescent girls participating in the Growing Up Healthy Study in New York City, using liquid chromatography-high resolution mass spectrometry (LC-HRMS). We then performed network analysis to link metabolites to environmental biomarkers including five trace elements (Cd, Mn, Pb, Se, and Hg) and five perfluorinated chemicals (PFCs; n-PFOS, Sm-PFOS, n-PFOA, PFHxS, PFNA) previously measured in the same samples. We defined any metabolite associated with at least one environmental biomarker and correlated with at least one other metabolite (Spearman rho > 0.9) as a ‘molecular gatekeeper’. Associations of gatekeepers with health outcomes (e.g., body mass index, age at menarche) were tested with linear models. After removing redundant peaks, 964 (positive mode) and 1784 (negative mode) metabolite features were used for network analysis. Of 95 and 138 metabolites, respectively, associated with at least one exposure, 28 and 43 were molecular gatekeepers. Further, lysophosphatidylcholine(16:0) and taurodeoxycholate were correlated with both n-PFOA and n-PFOS, suggesting a shared dysregulation from multiple xenobiotic exposures. One annotated gatekeeper, sphingomyelin(d18:2/14:0), was significantly associated with age at menarche; yet, no direct association was detected between any exposure biomarkers and age at menarche. Thus, molecular gatekeepers may provide a general data analysis framework to discover molecular linkages between exposure biomarkers and health outcomes that may otherwise be obscured by complex interactions in direct measurements. This framework may aid in identifying vulnerable biological pathways for future exposome research. | Miao Yu; Susan Teitelbaum; Georgia Dolios; Lam-Ha Dang; Peijun Tu; Mary Wolff; Lauren Petrick | Environmental Science; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b13fc2cb674c000d4e/original/molecular-gatekeeper-discovery-workflow-for-linking-multiple-environmental-biomarkers-to-metabolomics.pdf |
60c73d0ebb8c1ad6163d96a0 | 10.26434/chemrxiv.14685891.v2 | GenUI: Interactive and Extensible Open Source Software Platform for De Novo Molecular Generation | <div>This manuscript describes the development and architecture of the GenUI software platform for integration of molecular generators. The source code for the components of the platform is available in the following repositories:</div><div><br /></div><div>https://github.com/martin-sicho/genui</div><div>https://github.com/martin-sicho/genui-gui</div><div>https://github.com/martin-sicho/genui-docker<br /></div> | Martin Šícho; Xuhan Liu; Daniel Svozil; Gerard van Westen | Chemoinformatics; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0ebb8c1ad6163d96a0/original/gen-ui-interactive-and-extensible-open-source-software-platform-for-de-novo-molecular-generation.pdf |
646cb69fb3dd6a653099afdb | 10.26434/chemrxiv-2023-dgbdz | An efficient protocol for computing MCD spectra in a broad frequency range combining resonant and damped CC2 quadratic response theory | Coupled-cluster response theory offers a path to high-accuracy calculations of spectroscopic properties, such as magnetic circular dichroism (MCD). However, divergence or slow convergence issues or are often encountered for electronic transitions in high-energy regions with a high density of states. This is here addressed for MCD by an implementation of damped quadratic response theory for resolution-of-identity coupled cluster singles-and-approximate-doubles (RI-CC2), along with an implementation of the MCD A term from resonant response theory. Combined, damped and resonant response theory provide an efficient strategy to calculate MCD spectra over a broad frequency range and for systems that include highly symmetric molecules with degenerate excited states. The protocol is illustrated by application to Zink Tetrabenzoporphyrin in the energy region 2–8 eV and comparison to experimental data. Timings are reported for the resonant and damped approaches, showing that the greater part of the calculation time is consumed by the construction of the building 1blocks for the final MCD ellipticity. A recommendation on how to utilize the procedure is outlined. | Josefine H. Andersen; Sonia Coriani; Christof Hättig | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646cb69fb3dd6a653099afdb/original/an-efficient-protocol-for-computing-mcd-spectra-in-a-broad-frequency-range-combining-resonant-and-damped-cc2-quadratic-response-theory.pdf |
637b2b4a53ab80dfd22d7692 | 10.26434/chemrxiv-2022-001zq | ‘Exploration and Expansion’ in Peptide Sequence: Discovery of Structurally-Optimized Polymyxin Derivatives Facilitated by Peptide Scanning and in situ Screening Chemistry | Peptides can be converted to highly active compounds by introducing appropriate substituents on the suitable amino acid residue. Although modifiable residues in peptides can be systematically identified by peptide scanning methodologies, there is no practical method for optimization at the “scanned” position. With the purpose of using derivatives not only for scanning, but also as a starting point for further chemical functionalization, we herein report the ‘exploration and expansion’ strategy through chemoselective acylation of embedded threonine residues by a serine/threonine ligation (STL) with the help of in situ screening chemistry. We have applied this strategy to the optimization of the polymyxin antibiotics, which were selected as a model system to highlight the power of the rapid expansion of active scanning derivatives. Using this approach, we explored the structure-activity relationships of the polymyxins and successfully prepared derivatives with activity against polymyxin-resistant bacteria and those with P. aeruginosa selective antibacterial activity. This strategy opens up efficient structural exploration and further optimization of peptide sequences. | Rintaro Kaguchi; Akira Katsuyama; Toyotaka Sato; Satoshi Takahashi; Motohiro Horiuchi; Shin-ichi Yokota; Satoshi Ichikawa | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Combinatorial Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637b2b4a53ab80dfd22d7692/original/exploration-and-expansion-in-peptide-sequence-discovery-of-structurally-optimized-polymyxin-derivatives-facilitated-by-peptide-scanning-and-in-situ-screening-chemistry.pdf |
679367a281d2151a02c0c676 | 10.26434/chemrxiv-2025-q70cw-v2 | Methane enrichment from dilute sources: Performance limits and implications for methane removal and abatement | Methane (CH4), the second most potent greenhouse gas after carbon dioxide (CO2), profoundly impacts global warming, and its mitigation is crucial to meeting climate neutrality. However, most CH4 emissions originate from "non-point" distributed sources with dilute CH4 concentrations. This study investigates the feasibility of preconcentrating CH4 from these dilute sources using a three-step vacuum temperature swing adsorption (VTSA) cycle before converting CH4 to CO2 for permanent storage. The cycle performance limits are identified through integrated adsorbent-process optimizations at CH4 feed compositions of 2 ppm, 20 ppm, and 200 ppm. The optimizations focus on minimizing exergy consumption and maximizing productivity by varying adsorbent and process variables. The results demonstrated that CH4 enrichment to at least 1% is feasible using this cycle, especially from 20 ppm air feeds, when CO2 co-removal is also considered. More advanced VTSA cycles may be needed to effectively enrich CH4 from 2 ppm. The minimum exergy of the VTSA cycle ranges from 5.1 to 1.5 MJ/kg eq. CO2 for CH4 feed compositions of 2 ppm to 200 ppm, while maximum productivity varies from 0.5 to 8.3 kg eq. CO2/m3 h. Ideal adsorbent properties for CH4 exhibit moderate loadings of 0.1-0.3 mmol/g and high heats of adsorption of 31-32 kJ/mol, indicating a potential direction for future adsorbent development. | Sai Gokul Subraveti; Rahul Anantharaman | Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679367a281d2151a02c0c676/original/methane-enrichment-from-dilute-sources-performance-limits-and-implications-for-methane-removal-and-abatement.pdf |
60c755c7469df452f6f451c1 | 10.26434/chemrxiv.14112515.v2 | Nature Potential for COVID-19: Targeting SARS-CoV-2 Mpro Inhibitor with Bioactive Compound | <p>Corona viruses were first
identified in 1931 and SARS-CoV-2 is the most recent. COVID-19 is a pandemic
that put most of the world on lockdown and the search for therapeutic drugs is
still on-going. Therefore, this study uses <i>in silico</i> screening to
identify natural bioactive compounds from fruits, herbaceous plants and marine
invertebrates that are able to inhibit protease activity in SARS-CoV-2(PDB:
6LU7). We have used various screening strategies such as drug likeliness,
antiviral activity value prediction, molecular docking, ADME (absorption,
distribution, metabolism, and excretion), molecular dynamics (MD) simulation
and MM/GBSA (molecular mechanics/generalized born and surface area continuum
solvation). 17 compounds were shortlisted using Lipinski’s rule. 5 compounds
revealed significantly good predicted antiviral activity values and out of them
only 2 compounds, Macrolactin A and Stachyflin, showed good binding energy values of -9.22 and -8.00
kcal/mol within the binding pocket,
catalytic residues (HIS 41 and CYS 145) of M<sup>pro</sup>.
These two compounds were further analyzed for their ADME properties. The ADME evaluation of these 2 compounds
suggested that they could be effective as therapeutic agents for developing drugs for clinical trials. MD simulations showed that
protein-ligand complexes of Macrolactin A and Stachyflin were stable for 100
nano seconds. The MM/GBSA calculations of M<sup>pro</sup> – Macrolactin A
complex indicated higher binding free energy (-42.58 ± 6.35 kcal/mol) with M<sup>pro </sup>protein
target receptor (6LU7). DCCM and PCA analysis on the residual movement in the
MD trajectories confirmed the good stability on Macrolactin A bound state of
6LU7. This signify the stable conformation of 6LU7 with high binding energy
with Macrolactin A. Thus, this study showed that Macrolactin A could be an
effective therapeutical agent for SARS-CoV-2protease (6LU7) inhibition.
Additional <i>in vitro </i>and<i> in vivo </i>validations are needed to
determine efficacy and dose of Macrolactin A in biological systems.</p> | Kaushik Kumar Bharadwaj; Tanmay Sarkar; Arabinda Ghosh; Debabrat Baishya; Bijuli Rabha; Manasa Kumar Panda; Bryan R. Nelson; Akbar John; Hassan I. Sheikh; Bisnu Prasad Dash; Hisham A. Edinur; Siddhartha Pati | Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c7469df452f6f451c1/original/nature-potential-for-covid-19-targeting-sars-co-v-2-mpro-inhibitor-with-bioactive-compound.pdf |
60e4715c338e92c1a3086ebd | 10.26434/chemrxiv-2021-snjpz | Direct measurement of oxygen mass transport at the nanoscale | Tuning oxygen mass transport properties at the nanoscale offers a promising approach for developing high performing energy materials. A number of strategies for engineering interfaces with enhanced oxygen diffusivity and surface exchange has recently been proposed. However, the origin and the local magnitude of such local effects remain largely undisclosed to date. This is ascribed to the lack of direct measurement tools with sufficient resolution. In this work, we use atom probe tomography with sub-nanometric resolution to study oxygen mass transport on oxygen-isotope exchanged thin films of lanthanum chromite. We present a direct visualization of nanoscaled highly conducting oxygen incorporation pathways along grain boundaries, with reliable quantification of fast oxygen diffusion at grain boundaries and correlative link to local chemistries. Combined with finite element simulations of the precise 3D nanostructure, we quantify an enhancement in the grain boundary oxygen diffusivity and in the surface exchange coefficient of lanthanum chromite of about 4 and 3 orders of magnitude, respectively, compared to the bulk. This remarkable increase of the oxygen diffusivity in an interface-dominated material is unambiguously attributed to grain boundary conduction highways thanks to the use of a powerful technique that can be straightforwardly extended to the study of currently inaccessible multiple nanoscale mass transport phenomena. | Federico Baiutti; Francesco Chiabrera; David Diercks; Andrea Cavallaro; Lluis Yedra; Lluis Lopez-Conesa; Alex Morata; Sonia Estradé; Francesca Peiró; Ainara Aguadero; Albert Tarancon | Physical Chemistry; Materials Science; Energy; Thin Films; Electrochemistry - Mechanisms, Theory & Study; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e4715c338e92c1a3086ebd/original/direct-measurement-of-oxygen-mass-transport-at-the-nanoscale.pdf |
6315a998be03b231f3eab555 | 10.26434/chemrxiv-2022-9g62z-v2 | Strain-Release Controlled [4+2+1] Reaction of Cyclopropyl-Capped Diene-Ynes/Diene-enes and CO Catalyzed by Rhodium | ABSTRACT: Achieving transition metal-catalyzed reactions of diene-enes/diene-ynes and carbon monoxide (CO) to deliver [4+2+1] cycloadducts, rather than the kinetically favored [2+2+1] products, is challenging. Here, we report that this can be solved by adding a cyclopropyl (CP) cap to the diene moiety of the original substrates. The resulting cyclopropyl-capped diene-ynes/diene-enes can react with CO under Rh catalysis to give [4+2+1] cycloadducts exclusively without forming [2+2+1] products. This reaction has a broad scope and can be used to synthesize useful 5/7 bicycles with CP moiety. Of the same importance, the CP moiety in the [4+2+1] cycloadducts can act as the intermediate group for further transformations so that other challenging bicyclic 5/7 and tricyclic 5/7/5 and 5/7/6, 5/7/7 skeletons, which are widely found in natural products, can be obtained. The mechanism of this [4+2+1] reaction has been investigated by quantum chemistry calculations, and the role of the CP group in avoiding the possible side reaction of [2+2+1] reaction have been identified, showing that the [4+2+1] is controlled by releasing the ring strain in the methlenecyclopropyl (MCP) group (about 7 kcal/mol) in the CP-capped dienes. | Zhi-Xiang Yu; Chen-Long Li; Yusheng Yang; Zhao-Chen Duan; Yi Zhou | Theoretical and Computational Chemistry; Organic Chemistry; Organometallic Chemistry; Theory - Computational; Reaction (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6315a998be03b231f3eab555/original/strain-release-controlled-4-2-1-reaction-of-cyclopropyl-capped-diene-ynes-diene-enes-and-co-catalyzed-by-rhodium.pdf |
6720efbf5a82cea2fa35394f | 10.26434/chemrxiv-2024-xccl0 | NIR emissive probe for fluorescence turn-on based dead cell sorting and in-vivo viscosity mapping in C. elegans | Dead cell sorting is pivotal and plays a very significant role in homeostasis. Apoptosis and ferroptosis are the two major regulatory cell death processes. Apoptosis is a programmed cell death, while ferroptosis is a regulatory cell death process. Monitoring the dead cells coming out from these processes is extremely important to stop various cellular dysfunctions. Here, we present a single NIR emissive probe that can observe both apoptotic and ferroptosis regulatory cell deaths. We were able to directly visualize the dead cells both in animal and plant cells upon a significant increase in the fluorescence intensity of the probe. During cell death, the increased cytoplasm viscosity restricted the rotor motion and helped in the fluorescence turn-on of the probe. Lysosomal viscosity was found to play a crucial role in the ferroptosis pathway. On the other hand, the probe was not only efficient in mapping the viscosity in various parts of live Caenorhabditis elegans (C. elegans) bodies but also able to differentiate between live and dead animals. | Goraksha T. Sapkal; Farhan Anjum; Abdul Salam; Bodhidipra Mukherjee; Shilpa Chandra; Purabi Bala; Richa Garg; Shagun Sharma; Kush Kaushik; Chayan Kanti Nandi | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Microscopy; Cell and Molecular Biology | CC BY NC 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720efbf5a82cea2fa35394f/original/nir-emissive-probe-for-fluorescence-turn-on-based-dead-cell-sorting-and-in-vivo-viscosity-mapping-in-c-elegans.pdf |
6507f6cbb6ab98a41ca60e26 | 10.26434/chemrxiv-2023-mhp2x | A Benchmark for Accurate GPCR Ligand Binding Affinity Prediction with Free Energy Perturbation | G protein-coupled receptors (GPCRs) are among the most important drug targets in the pharmaceutical industry. Free energy perturbation (FEP), which can accurately predict the relative binding free energies of drug molecules, is now widely used in drug discovery. With the development of structural biology tools such as cryoelectron-microscopy (cryo-EM), the structures of a large number of GPCRs have been resolved, which provides the basis for FEP calculations. In this study, we developed an FEP protocol for GPCR FEP calculation. We performed calculations on 226 perturbation pairs of 139 ligands against 8 GPCRs, spanning 12 datasets (A2A , mGlu5 , D3, OX2 , CXCR4, β1, δ and TA1 receptors) and obtained promising results, particularly for agonist ligands in the TA1 datasets (R2, 0.58, RMSE, 1.07 kcal · mol−1 ). The average R2 is 0.61 and the average RMSE is 0.94 kcal · mol−1 , which is comparable to experimental accuracy(<1 kcal · mol−1 ). We also investigated factors that impact the accuracy of FEP results, including ligand binding pose, water placement, and protein structure. Our input structures for FEP calculation are publicly available as a benchmark dataset for future GPCR-FEP studies (https://doi.org/10.5281/zenodo.7988248). This represents the largest collection of GPCR FEP calculations known to us thus far. This work is expected to significantly contribute to the advancement of GPCR-targeted drug discovery. | Yu Guo; Yu Zhou; Qinru Bai; Zonghua Bo; Ke Song; Junhan Chang; Yuzhi Zhang; Maohua Yang; Yuqin Deng; Dongdong Wang | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6507f6cbb6ab98a41ca60e26/original/a-benchmark-for-accurate-gpcr-ligand-binding-affinity-prediction-with-free-energy-perturbation.pdf |
610975b8393cc9d4bb50d355 | 10.26434/chemrxiv-2021-h3381-v2 | Connecting lab experiments with computer experiments: Making "routine" simulations routine | Nowadays, computer simulations and experiments are closely interlocked. However, the data and analysis workflows are often barred into "silos" of knowledge — even for routine simulations.
Here, we show how a typical electronic laboratory notebook (ELN) environment can be seamlessly integrated with a computational modelling infrastructure. We developed a protocol to initiate advanced molecular or atomic simulations directly from an ELN. Such integration ensures that all the relevant sample and experimental data are transferred from the ELN to the modelling infrastructure, and — once the calculations have completed — back to the ELN. The presented protocol works similar to sending out a sample for external characterisation and enables experimentalists to routinely perform "routine" simulations to compare with their experiments while keeping track of the full experiment and simulation provenance.
We illustrate our protocol with some examples of geometry optimisation followed by the calculation of adsorption isotherms, but the implementation can be readily generalised to other techniques such as optical absorption or X-ray photoelectron spectroscopy. | Kevin Maik Jablonka; Michaël Zasso; Luc Patiny; Nicola Marzari; Giovanni Pizzi; Berend Smit; Aliaksandr V. Yakutovich | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610975b8393cc9d4bb50d355/original/connecting-lab-experiments-with-computer-experiments-making-routine-simulations-routine.pdf |
667093d25101a2ffa8cc09e3 | 10.26434/chemrxiv-2024-q17mn | Machine Learning Enables a Top-Down Approach to Mechanistic Elucidation | General reaction behavior is rarely reported in asymmetric catalysis, not simply because it is difficult to achieve, but also due to the methods used for its identification and study. Traditional approaches involve compartmentalization, where the impact of individual components is first analyzed, followed by assimilation using simple response and structure matching techniques. However, extending this method to accommodate complex conditions and diverse reactions proves challenging. Here, we present a data-driven method that relies on clusterwise linear regression to derive and predictively apply general mechanistic models of enantioinduction, with minimal human intervention. When applied to the palladium-catalyzed decarboxylative asymmetric allylic alkylation (DAAA) reaction, unexpected interactions governing enantioselectivity are revealed, supported by high-level computations and additional experiments. Our results demonstrate this workflow as a powerful new tool for automating mechanistic elucidation and effectively identifying general reaction performance. | Isaiah Betinol; Yutao Kuang; Junshan Lai; Christopher Yousofi; Jolene Reid | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667093d25101a2ffa8cc09e3/original/machine-learning-enables-a-top-down-approach-to-mechanistic-elucidation.pdf |
60c750c70f50db1a6a397624 | 10.26434/chemrxiv.13079750.v1 | Coupled Nuclear-Electronic Decay Dynamics of O2 Inner Valence Excited States Revealed by Attosecond XUV Wave-Mixing Spectroscopy | Multiple Rydberg series converging to the O<sub>2</sub><sup>+</sup> 𝑐 <sup>4</sup>Σ<sub>𝑢</sub><sup>−</sup> state, accessed by 20-25 eV extreme ultraviolet (XUV) light, serve as important model systems for the competition between nuclear dissociation and electronic autoionization. The dynamics of the lowest member of these series, the <i>3sσg</i> state around 21 eV, has been challenging to study owing to its ultra-short lifetime (< 10 fs). Here, we apply transient wave-mixing spectroscopy with an attosecond XUV pulse to investigate the decay dynamics of this electronic state. Lifetimes of 5.8±0.5 fs and 4.5±0.7 fs at 95% confidence intervals are obtained for v=0 and v=1 vibrational levels of the 3s Rydberg state, respectively. A theoretical treatment of predissociation and electronic autoionization finds that these lifetimes are dominated by electronic autoionization. The strong dependence of the electronic autoionization rate on the internuclear distance because of two ionic decay channels that cross the <i>3s</i> Rydberg state results in the different lifetimes of the two vibrational levels. The calculated lifetimes are highly sensitive to the location of the <i>3s</i> potential with respect to the decay channels; by slight adjustment of the location, values of 6.2 and 5.0 fs are obtained computationally for the v=0 and v=1 levels, respectively, in good agreement with experiment. Overall, an intriguing picture of the coupled nuclear-electronic dynamics is revealed by attosecond XUV wave-mixing spectroscopy, indicating that the decay dynamics are not a simple competition between isolated autoionization and predissociation processes. | Yen-Cheng Lin; Ashley Fidler; Arvinder Sandhu; Robert R. Lucchese; C. William McCurdy; Stephen Leone; Daniel Neumark | Chemical Kinetics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750c70f50db1a6a397624/original/coupled-nuclear-electronic-decay-dynamics-of-o2-inner-valence-excited-states-revealed-by-attosecond-xuv-wave-mixing-spectroscopy.pdf |
678166adfa469535b97e766a | 10.26434/chemrxiv-2025-3p3kn | An extensive scaling-up oriented investigation on carbon felt flow- through and interdigitated Vanadium Flow Batteries cells | In this work, 3D multiphysics model for Vanadium flow batteries (VFBs) was formulated and validated to computationally predict battery performance. The model showed an accuracy >2 % on the cell polarization curve. The electrode permeability, conductivity and internal cell resistance were experimentally measured while electrolyte density and viscosity were identified through novel empirical formulations. An extensive comparative analysis was performed between the flow-through (FTFF) and flow-by interdigitated (IDFF) flow field configurations for a 50 cm2 cell, varying the number and width of channels for the latter. A total of 90 3D simulations were conducted, first imposing constant flow rates of 20, 50 and 80 mL min−1 and subsequently using the resulting pressure drops for the flow-trough cell as input condition. At imposed flow rates, the FTFF configuration demonstrates superior perfor- mance, achieving a peak net power up to 6 % higher than the interdigitated configuration at 50 mL min−1. Conversely, under imposed pressure drop con- ditions, the behavior is more nuanced, showing that IDFF cells can deliver higher net peak power (up to 10 %) for intermediate imposed pressure. This operating condition, rarely investigated in the literature for medium-sized cells, matches closely the working conditions of industrial-scale VFB stacks. Our work aims to provide a detailed explanation of the interplay between fluid dynamics and electrochemical phenomena for the FTFF and the IDFF flow-by configuration cells, focusing on operational aspects and providing valuable scaling-up guidelines. | Davide Bordignon; Nicolò Zatta; Andrea Trovò | Theoretical and Computational Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Fluid Mechanics; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678166adfa469535b97e766a/original/an-extensive-scaling-up-oriented-investigation-on-carbon-felt-flow-through-and-interdigitated-vanadium-flow-batteries-cells.pdf |
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