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673abeb25a82cea2fa7c1b3b | 10.26434/chemrxiv-2024-bxr73-v2 | Discovery of Clonixeril as a Sub-Femtomolar Modulator of the Human STING Receptor | Stimulator of interferon genes (STING) is a transmembrane endoplasmic reticulum (ER) resident protein involved in innate immunity. STING activation occurs by binding of cyclic guanosine-(2'→5')-monophosphate-adenosine-(3'→5')-monophosphate (2’,3’-cGAMP) to STING, which leads to downstream production of type 1 interferons (IFN-1). We generated molecular dynamics (MD) equilibrated agonist and antagonist models of human STING (hSTING) for computer based screening and now report the discovery of clonixeril (CXL) as the most potent non-nucleotide hSTING modulator discovered to date. We demonstrate in vitro and in cellulo that CXL has two modes of interaction with hSTING, one with an EC50 above 1 nM and the other with an EC50 in the 1 fM - 100 aM range (10-15 – 10-16 M). In cell based experiments, when CXL is titrated below 1 nM, it displays inverse dose dependent antagonistic behavior toward hSTING. We have substantiated that CXL displays this exceptionally strong inhibitory effect on hSTING mediated IFN 1 production using a THP 1 cell luciferase reporter for interferon regulatory factor 3 (IRF3). Further characterization of CXL was performed in HEK293 cells and by using biophysical and biochemical techniques. | Robert Sparks; William Lawless; Anna Kharitonova; Rainer Metcalf; Jamie Nunziata; Grace Binder; Sauradip Chaudhury; Christine Gambino; Michelle Wilde; Linette Harding; Jaret Crews; Mansi Gopu; Emilia Dalamangus; Sarah Lawless; Mark Eschenfelder; Robert Green; Elizabeth Nompleggi; Timothy Tran; Kathy Yang; Donna Trask; Paul Thompson; Niketa Patel; Rekha Patel; Wesley Brooks; Guy Bradley; Mildred Acevedo-Duncan; Alan Mullen; James Leahy; Kenyon Daniel; Wayne Guida | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673abeb25a82cea2fa7c1b3b/original/discovery-of-clonixeril-as-a-sub-femtomolar-modulator-of-the-human-sting-receptor.pdf |
60c73fa49abda2945df8bb49 | 10.26434/chemrxiv.7469726.v1 | Online Measurement of Glucose Consumption from HepG2 Cells Using an Integrated Bioreactor and Enzymatic Assay | In this work, we developed a microfluidic bioreactor for optimizing growth and maintaining structure and function of HepG2, and when desired, the device could be removed and the extracellular output from the bioreactor combined with enzymatic glucose reagents into a droplet-based microfluidic system. The intensity of the resulting fluorescent assay product in the droplets was measured, and was directly correlated to glucose concentration, allowing the effect of insulin on glucose consumption in the HepG2 cells to be observed and quantified online and in near real-time. | Anna Adams; Radha Krishna Murthy Bulusu; Nikita Mukhitov; Jose Mendoza-Cortes; Michael Roper | Analytical Chemistry - General; Biochemistry; Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa49abda2945df8bb49/original/online-measurement-of-glucose-consumption-from-hep-g2-cells-using-an-integrated-bioreactor-and-enzymatic-assay.pdf |
61f9aafd537af8e7daad48f4 | 10.26434/chemrxiv-2021-gs0wj-v3 | Data-driven matching of experimental crystal structures and gas adsorption isotherms of metal-organic frameworks | Porous metal-organic frameworks are a class of materials with great promise in gas separation and gas storage applications.
Due to the large material space, computational screening techniques have long been an important part of the scientific toolbox.
However, a broad validation of molecular simulations in these materials is hampered by the lack of a connection between databases of gas adsorption experiments and databases of the atomic crystal structure of corresponding materials.
This work aims to connect the gas adsorption isotherms of metal-organic frameworks collected in the NIST/ARPA-E Database of Novel and Emerging Adsorbent Materials to a corresponding crystal structure in the Cambridge Structural Database.
With tens of thousands of isotherms and crystal structures reported to date, an automatic approach is needed to establish this link, which we describe in this paper.
As a first application and consistency check, we compare the pore volume deduced from low-temperature argon or nitrogen isotherms to the geometrical pore volume computed from the crystal structure.
Overall, 545 argon or nitrogen isotherms could be matched to a corresponding crystal structure.
We find that the pore volume computed via the two complementary methods shows acceptable agreement only in about 35% of these cases.
We provide the subset of isotherms measured on these materials as a seed for a future, more complete reference data set for computational studies. | Daniele Ongari; Leopold Talirz; Kevin M. Jablonka; Daniel W. Siderius; Berend Smit | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Hydrogen Storage Materials; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f9aafd537af8e7daad48f4/original/data-driven-matching-of-experimental-crystal-structures-and-gas-adsorption-isotherms-of-metal-organic-frameworks.pdf |
6756346b085116a133ca9e28 | 10.26434/chemrxiv-2024-rqbzn | Development and Validation of a Process Model and Open-Source Process Simulator for Microalgae-Based Tertiary Phosphorus Recovery | Microalgae-based tertiary wastewater treatment has the potential to meet stringent effluent phosphorus limits, with the added benefit of producing a marketable feedstock. However, the lack of validated mechanistic models and their implementation in process simulators have limited the adoption of this technology. In this study, an updated lumped pathway metabolic model (Phototrophic-Mixotrophic Process Model, PM2), including both photoautotrophic and heterotrophic metabolisms of microalgae, was developed to predict effluent phosphorus concentration and biomass yield in response to dynamic influent and varying environmental conditions. The model was implemented in QSDsan – an open-source, Python-based design and simulation platform – for robust simulation under uncertainty. A global sensitivity analysis was performed to prioritize model parameters for calibration. The model was then calibrated and validated using batch experimental data and 45 days of continuous online monitoring data from a full-scale (568 m3·d-1) microalgae-based tertiary wastewater treatment plant (EcoRecover process). In particular, along with dynamic influent composition, temperature and light intensity data with diel variation were provided as model inputs to reflect the microalgal behavior under day-night cycling. Overall, the QSDsan-based microalgae process simulator was able to predict effluent phosphorus within 0.02–0.04 mg-P·L-1, while also capturing the general trends of state variables according to nutrient availability. | Ga-Yeong Kim; Hannah Molitor; Xinyi Zhang; Yalin Li; Brian Shoener; Stephanie Schramm; Eberhard Morgenroth; Spencer Snowling; Elaine Hartnett; Ian Bradley; Ameet Pinto; Jeremy Guest | Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Process Control; Water Purification | CC BY 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756346b085116a133ca9e28/original/development-and-validation-of-a-process-model-and-open-source-process-simulator-for-microalgae-based-tertiary-phosphorus-recovery.pdf |
661455e2418a5379b06b84ef | 10.26434/chemrxiv-2024-xnq0h | Calculation of quasi-diabatic states within the DFT/MRCI(2) framework: the QD-DFT/MRCI(2) method | We describe a procedure for the calculation of quasi-diabatic states within the recently introduced DFT/MRCI(2) framework [J. Chem. Phys., 157, 164103 (2022)]. Based on an effective Hamiltonian formalism, the proposed procedure, which we term QD-DFT/MRCI(2), has the advantageous characteristics of being simultaneously highly efficient and effectively black box in nature, while directly yielding both quasi-diabatic potentials and wave functions of high quality. The accuracy and efficiency of the QD-DFT/MRCI(2) formalism are demonstrated via the simulation of the vibronic absorption spectra of furan and chlorophyll a. | Simon Neville; Michael Schuurman | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661455e2418a5379b06b84ef/original/calculation-of-quasi-diabatic-states-within-the-dft-mrci-2-framework-the-qd-dft-mrci-2-method.pdf |
645f67a2f2112b41e97bcb3a | 10.26434/chemrxiv-2023-n578f-v2 | N-terminal cysteine as minimalistic handle for dual, site-selective bioconjugation: application to an anti-HER2 affibody reveals synergy of two conjugated drugs | Site-selective, dual-conjugation approaches for the incorporation of distinct payloads are key for the development of molecularly targeted biomolecules, such as antibody conjugates, endowed with better properties. Combinations of cytotoxic drugs, imaging probes, or pharmacokinetics modulators enabled for improved outcomes in both molecular imaging, and therapeutic settings. We have developed an efficacious dual-bioconjugation strategy to target the N-terminal cysteine of a chemically-synthesized, third-generation anti-HER2 affibody. Such two-step, one-purification approach can be carried out under mild conditions (without chaotropic agents, neutral pH) by means of a slight excess of commercially available N-hydroxysuccinimidyl esters and maleimido-functionalized payloads, to generate dual conjugates displaying drugs (DM1/MMAE) or probes (sulfo-Cy5/biotin) in high yield and purity. Remarkably, the double drug conjugate exhibited an exacerbated cytoxicity against HER2-expressing cell lines as compared to a combination of two monoconjugates, demonstrating a potent synergistic effect. Consistently, affibody-drug conjugates did not decrease the viability of HER2-negative cells, confirming their specificity for the target. | Ana Novak; Florian Kersaudy; Sylvie Berger; Séverine Morisset-Lopez; François Lefoulon; Carlo Pifferi; Vincent Aucagne | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645f67a2f2112b41e97bcb3a/original/n-terminal-cysteine-as-minimalistic-handle-for-dual-site-selective-bioconjugation-application-to-an-anti-her2-affibody-reveals-synergy-of-two-conjugated-drugs.pdf |
664d1c7321291e5d1de54fcd | 10.26434/chemrxiv-2024-0h9zw-v2 | Sulfonate group improves the solubility and electrocatalytic performance of Ru-based bda- and pda-type water oxidation catalysts under neutral conditions | Four ruthenium water oxidation catalysts that bear carboxylate and sulfonate groups in the active site have been synthesized and analyzed for their catalytic activity. The developed catalysts are modified from highly active species that traditionally have two carboxylate groups in the active site and are used to probe the effects of sulfonate substitution as well as the effects of other structural changes of the catalyst. The sulfonate-containing catalysts show higher electrochemical activity in pH 7 phosphate buffer with 3-5 times larger catalytic current, improved durability with sacrificial oxidant, and increased solubility compared to their dicarboxylate counterparts. Density functional theory calculations suggest that the sulfonate group provides more favorable geometry for water nucleophilic attack, of which is both the most energetically favorable mechanism calculated and experimentally predicted mechanism under electrochemical conditions. Further experimental studies have been performed to show that under certain conditions catalysts can perform well electrochemically under pH conditions as low as 1.6 and that various structural components can greatly change solubility and catalytic operation. | Jake T. Kerkhof; Colton J. Breyer; Diane K. Smith; Yuezhi Mao; Douglas B. Grotjahn | Inorganic Chemistry; Catalysis; Electrochemistry; Transition Metal Complexes (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664d1c7321291e5d1de54fcd/original/sulfonate-group-improves-the-solubility-and-electrocatalytic-performance-of-ru-based-bda-and-pda-type-water-oxidation-catalysts-under-neutral-conditions.pdf |
6629348c418a5379b09c8fa7 | 10.26434/chemrxiv-2024-9vqjf | A versatile fabrication route for screening block copolymer membranes for bioprocessing | Traditional polyethersulfone (PES) filters, widely used for sterile, viral and ultrafil- tration often exhibit limited selectivity-permeability due to the heterogenous pore size distribution. Such limitations have sparked interest in developing novel isoporous mem- brane materials and fabrication techniques to overcome the selectivity-permeability upper bound. Among several promising candidates, block copolymer membranes pro- duced via the self-assembly and non-solvent induced phase separation (SNIPS) method offer distinct advantages, such as customisable pore size, narrow dispersity, high poros- ity and mechanical flexibility. However, achieving the desired structure formation in SNIPS remains a complex optimisation procedure, rendering this approach unsuitable for the rapid screening of new block copolymer candidates. This study explores a direct spin coating method to fabricate a poly(styrene)-block- poly(methyl methacrylate) (PS-b-PMMA) thin film composite membrane, integrating a block copolymer layer with rigid anodic aluminium oxide (AAO) support. The pro- cess involves depositing the polymer solution onto a water-filled AAO substrate via spin coating. Compared with the SNIPS method, this fabrication process greatly re- duces the complexity of optimisation to yield an isoporous membrane structure for filtration purposes. We present this approach as a straightforward and reliable plat- form method for the rapid screening and evaluation of block copolymer membranes in their initial development stages. When compared to commercial PES membranes with similar molecular weight cut-offs, these novel PS-b-PMMA thin film composite membranes showed similar transmission rates for Bovine Serum Albumin and a Mon- oclonal Antibody while providing a 9 fold enhancement in Thyroglobulin rejection. This indicates a superior performance in terms of cut-off precision. The membranes demonstrate potential for the removal of viruses and antibody aggregates in the down- stream processing of monoclonal antibody production, which could reduce the burden of chromatographic polishing steps. An advance which offers promise for improving efficiency and reducing costs in biopharmaceutical manufacturing. | Ke Meng; Alberto Alvarez-Fernandez; Stefan Guldin; Daniel G. Bracewell | Materials Science; Polymer Science; Nanoscience; Biocompatible Materials; Nanostructured Materials - Materials; Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629348c418a5379b09c8fa7/original/a-versatile-fabrication-route-for-screening-block-copolymer-membranes-for-bioprocessing.pdf |
60c7490e469df43b05f43b3e | 10.26434/chemrxiv.12021294.v1 | Metabolomics Reveals the Markers of Frying Vegetable Oil | <p>Fried foods have
potential adverse effects on health. However, the compounds produced during the
process of frying in different vegetable oils are unknown. A
metabolomics study was first conducted to analyze
the changes of compounds in 8 different vegetable oils before and after heating
without any foods and reveal the potential markers of frying oil. And then
these markers were validated in used frying oil. Our results of metabolomics
indicated that both heating or frying significantly changed the compounds of
vegetable oils. The 36 markers associated with
heating from the 8 different oils were identified in used frying oils and were
common markers of frying oil. Additionally,
22 markers detected in only
one vegetable oil were the unique markers of frying oils. These
markers can be used to distinguish used frying oil and have potential to reveal the
associated physiological harm.<b></b></p> | Zixiang Li; Yongzhi Sun; Feng Dong; Qingli Yu; Lina Fan; Jiali Zhao; maoqing wang | Mass Spectrometry; High-throughput Screening; Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490e469df43b05f43b3e/original/metabolomics-reveals-the-markers-of-frying-vegetable-oil.pdf |
66345d4f91aefa6ce105501a | 10.26434/chemrxiv-2024-37kvr | Cine-Substitution of Enolates: Enolate Dance/Coupling of Cycloalkenyl Pivalates by Nickel Catalysis | This manuscript describes the development of Ni/dcype-catalyzed enolate dance/coupling reaction of alkenyl pivalates with nucleophiles, resulting in cine-substitution. Pivalates derived 1-tetralone undergo this reaction, to produce C2-functionalized dihydronaphthalenes. The direct utilization of 1-tetralone is also feasible, employing Piv2O to generate the corresponding enol pivalate in situ. Mechanistic investigations including stoichiometric experi-ments, suggest that the reaction proceeds via C–O oxidative addition, nickel 1,2-translocation, and subsequent cou-pling with a nucleophile. | Eito Moriya; Kei Muto; Junichiro Yamaguchi | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66345d4f91aefa6ce105501a/original/cine-substitution-of-enolates-enolate-dance-coupling-of-cycloalkenyl-pivalates-by-nickel-catalysis.pdf |
60c73edb4c891968a4ad1e90 | 10.26434/chemrxiv.7157507.v1 | Self-Assembling Micelles Based on an Intrinsically Disordered Protein Domain | Herein, we describe a new series of fusion proteins that have been developed to self-assemble spontaneously into stable micelles that are 27 nm in diameter after enzymatic cleavage of a solubilizing protein tag. The sequences of the proteins are based on a human intrinsically disordered protein, which has been appended with a hydrophobic segment. The micelles were found to form across a broad range of pH, ionic strength, and temperature conditions, with critical micelle concentration (CMC) values below 1 µM being observed in some cases. The reported micelles were found to solubilize hydrophobic metal complexes and organic molecules, suggesting their potential suitability for catalysis and drug delivery applications. | Sarah Klass; Matthew
J. Smith; Tahoe Fiala; Jessica Lee; Anthony Omole; Kenneth Downing; Matthew Francis | Biocompatible Materials; Biological Materials; Biodegradable Materials; Surfactants; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edb4c891968a4ad1e90/original/self-assembling-micelles-based-on-an-intrinsically-disordered-protein-domain.pdf |
639867200a812753a4dfedc5 | 10.26434/chemrxiv-2022-md67l | Carbodiimide Ring-opening Metathesis Polymerization | Controlled incorporation of nitrogen into macromolecular skeletons is a long-standing challenge whose resolution would enable the preparation of soft materials with the scalability of man-made plastics and functionality of Nature’s proteins. Nylons and polyurethanes notwithstanding, nitrogen-rich polymer backbones remain scarce, and their synthesis typically lacks precision. Here we report a strategy that begins to address this limitation founded on a mechanistic discovery: ring-opening metathesis polymerization (ROMP) of carbodiimides followed by carbodiimide derivatization. An iridium guanidinate complex was found to initiate and catalyze ROMP of N-aryl and N-alkyl cyclic carbodiimides. Nucleophilic addition to the resulting polycarbodiimides enabled the preparation of polyureas, polythioureas, and polyguanidinates with varied architectures. This work advances the foundations of metathesis chemistry and opens the door to systematic investigations of structure-folding-property relationships in nitrogen-rich macromolecules. | J. Drake Johnson; Samuel Kaplan; Jozsef Toth; Zian Wang; Mitchell Maw; Sergei Sheiko; Aleksandr Zhukhovitskiy | Materials Science; Organometallic Chemistry; Polymer Science; Polymerization (Polymers); Polymer scaffolds; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639867200a812753a4dfedc5/original/carbodiimide-ring-opening-metathesis-polymerization.pdf |
653e860cc573f893f162cfec | 10.26434/chemrxiv-2023-ml9pj | Gold nanoclusters/MIL-100(Fe) bimodal nanovector for the therapy of inflammatory disease through attenuation of Toll-like receptor signaling. | A better understanding of the molecular and cellular events involved in the inflammation process has opened novel perspectives in the treatment of inflammatory diseases, particularly through the development of well-designed nanomedicines. Here we describe the design of a novel class of anti-inflammatory nanomedicine (denoted as Au@MIL) synthesized through a one-pot, cost-effective and green approach by coupling a benchmark mesoporous iron(III) carboxylate Metal Organic Frameworks (MOF) (i.e. MIL-100(Fe)) and glutathionate protected gold nanoclusters (i.e. Au25SG18 NCs). This nano-carrier exhibits a low toxicity and excellent colloidal stability combined with high loading capacity of the glucocorticoid dexamethasone phosphate (DexP) whose pH-dependent delivery was observed. The drug loaded Au@MIL nanocarrier has shown high anti-inflammatory activity due to its capacity to specifically hinder the inflammatory cells growth, scavenge intracellular reactive oxygen species (ROS) and downregulate pro-inflammatory cytokines secretion. In addition, this formulation has the capacity to inhibit the Toll-like receptor (TLR) signaling cascade namely the nuclear factor kappa B (NF-κB) and the interferon regulatory factor (IRF) pathways. This not only provides new avenue for nanotherapy of inflammatory diseases but enhances our fundamental knowledge of the role of nanoMOF based nanomedicine in the regulation of innate immune signaling. | Heng Zhao; Sonia Becharef; Eddy Dumas; Florent Carn; Gilles Patriarche; Simona Mura; Florence Gazeau; Christian Serre; NATHALIE STEUNOU | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653e860cc573f893f162cfec/original/gold-nanoclusters-mil-100-fe-bimodal-nanovector-for-the-therapy-of-inflammatory-disease-through-attenuation-of-toll-like-receptor-signaling.pdf |
6405a43d37e01856dc3cece4 | 10.26434/chemrxiv-2023-rqpzt | Generation and Transfer of Triplet Electron Spin Polarization at Solid-Liquid Interface | The photoexcited triplet state of dyes can generate highly polarized electron spins for sensing and dynamic nuclear polarization. However, while triplets exhibit long spin-lattice relaxation times (T1) on the microsecond scale in solids, the polarization quickly relaxes on the nanosecond scale in solution due to the rotational motion of chromophores. Here, we report that the immobilization of dye molecules on a solid surface allows molecular contact with a liquid while maintaining high polarization and long T1 as in a solid. By adsorbing anionic porphyrins on cationic mesoporous silica gel, porphyrin triplets exhibit high polarization and long T1 at the solid-liquid interface of silica and toluene. Furthermore, porphyrin triplets on the solid surface can exchange spin polarization with TEMPO radicals in solution. This simple and versatile method using the solid-liquid interface will open the way for utilizing the photo-induced triplet spin polarization in solution, which has been mainly limited to the solid-state. | Reiya Yabuki; Koki Nishimura; Tomoyuki Hamachi; Naoto Matsumoto; Nobuhiro Yanai | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6405a43d37e01856dc3cece4/original/generation-and-transfer-of-triplet-electron-spin-polarization-at-solid-liquid-interface.pdf |
620da11d4e899e01b450bd0e | 10.26434/chemrxiv-2022-lvgln | Sources of ambient PM2.5 exposure in 96 global cities | To improve air quality, knowledge of the sources and locations of air pollutant emissions is critical. However, for many global cities, no previous estimates exist of how much exposure to fine particulate matter (PM2.5), the largest environmental cause of mortality, is caused by emissions within the city vs. outside its boundaries. We use the Intervention Model for Air Pollution (InMAP) global-through-urban reduced complexity air quality model with a high-resolution, global inventory of pollutant emissions to quantify the contribution of emissions by source type and location for 96 global cities. Among these cities, we find that the fraction of PM2.5 exposure caused by within-city emissions varies widely (µ=51%; σ=23%) and is not well-explained by surrounding population density. The list of most-important sources also varies by city. Compared to a more mechanistically detailed model, InMAP predicts urban measured concentrations with less bias but more error. Predictive accuracy in urban areas is not particularly high with either model, suggesting an opportunity for improving global urban air emission inventories. We expect the results herein can be useful as a screening tool for policy options and in many cases may be robust enough to inform policy action to improve public health. | Mei Tessum; Susan Anenberg; Zoe Chafe; Daven Henze; Gary Kleiman; Iyad Kheirbek; Julian Marshall; Christopher Tessum | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620da11d4e899e01b450bd0e/original/sources-of-ambient-pm2-5-exposure-in-96-global-cities.pdf |
662174a121291e5d1d1e975c | 10.26434/chemrxiv-2024-8wd6z | Extremely long-lived charge donor states formed by visible irradiation of quantum dots | Using cyclic voltammetry under illumination, we recently demonstrated that CdS quantum dots (QDs) form charge donor states that live for at least several minutes after illumination ends, ~12 orders of magnitude longer than expected for free carriers. This timescale suggests that the conventionally accepted mechanism of charge transfer, wherein charges directly transfer to an acceptor following exciton dissociation, cannot be complete. Because of these long timescales, this unconventional pathway is not readily observed using time-resolved spectroscopy to probe charge transfer dynamics. Here, we investigated the chemical nature of these charge donor states using cyclic voltammetry under illumination coupled with NMR spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and optical spectroscopy. Our data reveal that charges are stored locally rather than as free carriers, and the number of charges stored is dependent on the QD surface ligation and stoichiometry. Altogether, our results confirm that electrons are stored at ligated surface Cd, these sites are competent charge donors, and this storage is charge balanced by X-type ligand desorption. We found that charge storage occurs in every QD system studied, including CdS, CdSe, and InP capped with carboxylate and phosphonate ligands. | Micaela Homer; Helen Larson; Grant Dixon; Emily Miura-Stempel; Neal Armstrong; Brandi Cossairt | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662174a121291e5d1d1e975c/original/extremely-long-lived-charge-donor-states-formed-by-visible-irradiation-of-quantum-dots.pdf |
61f441398d70c3742c111e36 | 10.26434/chemrxiv-2022-4rt78 | Solvent-Mediated Charge Transfer Dynamics of a Model Brown Carbon Aerosol Chromophore: Photophysics of 1-Phenylpyrrole Induced by Water Solvation | Nitrogen heterocycles are known to be important light-absorbing chromophores in a relatively new class of aerosols, commonly referred to as ‘brown carbon’ (BrC) aerosols. Due to their significant absorption and spectral overlap with the solar actinic flux, these BrC chromophores steer the physical and optical properties of aerosols. To model the local aqueous solvation environment surrounding BrC chromophores, we generated cold molecular complexes with water and a prototypical BrC chromophore, 1-phenylpyrrole (1PhPy), using supersonic jet-cooling and explored their intermolecular interactions using single-conformation spectroscopy. Herein, we utilized resonant two-photon ionization (R2PI) and UV holeburning (UV HB) double-resonance spectroscopies to obtain a molecular-level understanding of water microsolvation’s role in charge transfer upon photoexcitation of 1PhPy. Quantum chemical calculations and one-dimensional discrete variable representation simulations revealed insights into the charge transfer efficacy of 1PhPy with and without single water molecule addition. Taken together, our results indicate that the intermolecular interactions with water guide the geometry of 1PhPy to adopt a more twisted intramolecular charge transfer (TICT) configuration, thus facilitating charge transfer from the pyrrole donor to the phenyl ring acceptor. Fluorescence measurements with increasing H2O %volume corroborated our gas-phase studies by indicating that a polar water solvation environment stabilizes the TICT configuration of 1PhPy in the excited electronic state, from which emission is observed at lower energy compared to the locally-excited configuration. | Brianna Peterson; Megan Alfieri; David Hood; Christian Hettwer; Daniel Costantino; Daniel Tabor; Nathanael Kidwell | Physical Chemistry; Clusters; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f441398d70c3742c111e36/original/solvent-mediated-charge-transfer-dynamics-of-a-model-brown-carbon-aerosol-chromophore-photophysics-of-1-phenylpyrrole-induced-by-water-solvation.pdf |
6712537d51558a15ef6fe49a | 10.26434/chemrxiv-2024-75n7q-v2 | Photoluminescent Properties of Tb-UiO-66 Metal–Organic Framework Analogues | Three new analogues of Tb-UiO-66 with various functional groups (–F, –Br, –NH2) on the terephthalic acid linker of the metal–organic framework (MOF) are synthesized and characterized. The photoluminescent properties of these analogues, as well as Tb-UiO-66 and Tb-UiO-66-(OH)2, are studied and correlated to the calculated energies for the triplet (T1) states of each linker. The results show that the addition of electron withdrawing groups, such as –F and –Br, lead to higher T1 energies, resulting in quantum yields in the range of 6-31 %. The addition of electron donating groups, on the other hand, lowers the T1 energy of the organic linker and inhibits energy transfer such that emission is not observed. | Ximena A. Canales Galvez; Micaela Richezzi; Hudson A. Bicalho; Natalia Labadie; Silvina C. Pellegrinet; Hatem M. Titi; Ashlee J. Howarth | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6712537d51558a15ef6fe49a/original/photoluminescent-properties-of-tb-ui-o-66-metal-organic-framework-analogues.pdf |
663764f0418a5379b07d388c | 10.26434/chemrxiv-2024-dbgx3-v2 | Electron Tunneling Barriers in Marcus Theory of Electron Transfer: Incorporating Bridge State Thermal Fluctuations | The semi-classical and quantum theories of electron transfer (ET) are extensively used to understand and predict tunnelling ET reaction rates in condensed phase and build on the two-state Donor-Acceptor thermodynamic framework of Marcus theory. Previously, Marcus two-state model has been extended to a three-state model which assumes a harmonic dependence of donor (D), bridge (B), and acceptor (A) free energies on the reaction (e.g. solvent polarization) coordinate. Here, we examine the previously proposed three-state extended Marcus model (EMM) and generalize it to an (N+2)-state model for N bridge sites separating the D from the A. Using the EMM, an analytic expression for the electron tunnelling barrier is derived. The EMM model predicts that relative thermodynamics of the D-A states and B state reorganization energies can both influence the D-A electronic coupling. We discuss signatures of bridge state thermal fluctuations using the EMM on the driving force and distance dependence of ET rates which can be tested experimentally. | Ravinder Kumar; Ravindra Venkatramani | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663764f0418a5379b07d388c/original/electron-tunneling-barriers-in-marcus-theory-of-electron-transfer-incorporating-bridge-state-thermal-fluctuations.pdf |
67bb9b36fa469535b9994516 | 10.26434/chemrxiv-2025-g5fz9 | Synthesis of sensitive oligodeoxynucleotides containing acylated cytosine, adenine, and guanine nucleobases | The synthesis of oligodeoxynucleotides (ODNs) containing the sensitive N6-acetyladenosine (6acA), N2-acetylguanosine (2acG), and N4-methyoxycarbonyldeoxycytidine (4mcC), as well as up to four N4-acetyldeoxycytidine (4acC) modifications is described. The meDmoc group was used for the protection of the exo-amino groups of nucleobases, and the Dmoc group was used as the linker for solid phase synthesis. Deprotection and cleavage were achieved under non-nucleophilic conditions, under which the highly sensitive 4acC, 6acA, 2acG, and 4mcC were found completely stable. Among the modified nucleotides, 4acC has been found in nature, and proven beneficial to DNA duplex stability. Although 6acA, 2acG and 4mcC have not been found in nature, a synthetic route to ODNs containing them is expected to facilitate projects aimed at studying their biophysical properties as well as potential for antisense, RNAi, CRISPR, and mRNA therapeutic applications. | Komal Chillar; Rohith Awasthy; Marina Tanasova; Shiyue Fang | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bb9b36fa469535b9994516/original/synthesis-of-sensitive-oligodeoxynucleotides-containing-acylated-cytosine-adenine-and-guanine-nucleobases.pdf |
65e0a47e9138d2316154665b | 10.26434/chemrxiv-2024-rjq4j | Self-Formation of Compositionally Complex Surface Oxides on High Entropy Alloys: A Route to Sustainable Catalysts | Sustainable catalysts rely on abundant elements which are prone to oxidation. A new route to non-noble electro-catalysts is opened by directing the formation of unavoidable surface oxides towards creating a few atomic layers of an active and stable electrocatalyst, which is in direct contact with its metallic, conducting support. This is enabled by combining the possibilities of compositionally complex solid solutions with accelerated atomic-scale surface characterization. Surface composition changes from the as-synthesized state to states after exposure to the oxygen evolution reaction (OER) are investigated using a Cantor-alloy-catalyst-coated tip array for atom probe tomography. Whereas the as-deposited film has a 3 nm thick native oxide, initial and prolonged OER exposures result in an oxygen-influenced surface layer equilibrium, which shows a lower oxidation depth and altered metal composition. This demonstrates that as-synthesized complex compositions can be used to obtain active and stable surface oxides under electrochemical load. | Valerie Strotkoetter; Yujiao Li; Tobias Loeffler; Wolfgang Schuhmann; Alfred Ludwig | Materials Science; Catalysis; Nanoscience; Alloys; Thin Films; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0a47e9138d2316154665b/original/self-formation-of-compositionally-complex-surface-oxides-on-high-entropy-alloys-a-route-to-sustainable-catalysts.pdf |
61a13b4da129237c224fac09 | 10.26434/chemrxiv-2021-6ddp9 | Giving preparative thin layer chromatography some tender loving care | Preparative thin layer chromatography (prepTLC) is a commonly used method of purification suitable for small scale reactions. However, descriptions of the preferred methodology to load, run, and recover samples from prepTLC are non-standard and varied, making it part of the “hidden curriculum” of laboratory technique. In this article we report on the simple, cost-effective methods we use to load and collect samples from a plate, which enhance the convenience, speed, and precision of this technique. | John Hayward; Lavleen Mader; John Trant | Organic Chemistry; Analytical Chemistry; Chemical Education; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a13b4da129237c224fac09/original/giving-preparative-thin-layer-chromatography-some-tender-loving-care.pdf |
64c849469ed5166e93d2f55e | 10.26434/chemrxiv-2023-qth2q | Branched-Selective Cross-Electrophile Coupling of 2-Alkyl Aziridines and (Hetero)aryl Iodides Using Ti/Ni Catalysis | The arylation of 2-alkyl aziridines by nucleophilic ring-opening or transition metal-catalyzed cross-coupling enables facile access to biologically relevant beta-phenethylamine derivatives. However, both approaches largely favor C–C bond formation at the less substituted carbon of the aziridine, thus enabling access to only linear products. Consequently, despite the attractive bond disconnection it poses, the synthesis of branched arylated products from 2-alkyl aziridines has remained inaccessible. Herein, we address this long-standing challenge and report the first branched-selective cross-coupling of 2-alkyl aziridines with aryl iodides. This unique selectivity is enabled by a Ti/Ni dual-catalytic system. We demonstrate the robustness of the method by a two-fold approach: an additive screening campaign to probe functional group tolerance and a feature-driven substrate scope to study the effect of the local steric and electronic profile of each coupling partner on reactivity. Furthermore, the diversity of this feature-driven substrate scope enabled the generation of predictive reactivity models that guided mechanistic understanding. Mechanistic studies demonstrated that the branched selectivity arises from a Ti(III)-induced radical ring-opening of the aziridine. | Wendy L. Williams; Neyci E. Gutiérrez-Valencia; Abigail Doyle | Organic Chemistry; Catalysis; Organometallic Chemistry; Physical Organic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c849469ed5166e93d2f55e/original/branched-selective-cross-electrophile-coupling-of-2-alkyl-aziridines-and-hetero-aryl-iodides-using-ti-ni-catalysis.pdf |
65671d8a5bc9fcb5c9a51a28 | 10.26434/chemrxiv-2023-7nwcd | A Conjugated Porous Organic Polymer as the Bifunctional Electrocatalyst for Enhanced Water Splitting | A conjugated porous organic polymer (SMCOP-4) with imine linkage was rationally designed and synthesized by an imine condensation reaction. The π-conjugated network structure of SMCOP-4 facilitates electron mobility, enhancing electrochemical activity. The bifunctional electrocatalyst SMCOP-4 shows superior performance for HER and OER with a low overpotential of 127 mV and 295 mV, respectively, at 10 mA cm-2 current density and with small Tafel slopes in alkaline electrolytes. Along with the low overpotential values, the electrocatalyst is highly stable at electrochemical conditions. | Argha Chakraborty; Saraswati Roy; * Pragti; Sayantan Sarkar; Sounak Roy; Suman Mukhopadhyay | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65671d8a5bc9fcb5c9a51a28/original/a-conjugated-porous-organic-polymer-as-the-bifunctional-electrocatalyst-for-enhanced-water-splitting.pdf |
6287a9e36b12b6a3d878b13c | 10.26434/chemrxiv-2022-47ksr | Reply to the Correspondence on "How Globally Aromatic Are Six-Porphyrin Nanorings?" | A recent article by Anderson and co-workers challenges our conclusions on the aromaticity of the four oxidation states of a butadiyne-linked six-porphyrin nanoring, ased on the experimental 1H-NMR data and some recent calculations they have performed using the BLYP35
unctional. Here, we show that BLYP35 should be taken with caution and demonstrate that the indirect evidence of a ring current from experimental 1 H-NMR data is not a definite proof of aromaticity. | Irene Casademont-Reig; Luis Soriano-Agueda; Eloy Ramos-Cordoba; Miquel Torrent-Sucarrat; Eduard matito | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287a9e36b12b6a3d878b13c/original/reply-to-the-correspondence-on-how-globally-aromatic-are-six-porphyrin-nanorings.pdf |
610d615f42d165d1993abf58 | 10.26434/chemrxiv-2021-w32rs | Efficient discovery of visible light-activated azoarene photoswitches with long half-lives
using active search | Photoswitches are molecules that undergo a reversible, structural isomerization after exposure to different wavelengths of light. The dynamic control offered by molecular photoswitches is favorable for applications in materials chemistry, photopharmacology, and catalysis. Ideal photoswitches absorb visible light and have long-lived metastable isomers. We used high throughput virtual screening to predict the absorption maxima (λmax) of the E-isomer and half-lives (t1/2) of the Z-isomer. However, computing the photophysical and kinetic properties of each entry of a virtual molecular library containing 103–106 entries with density functional theory is prohibitively time-consuming. We applied active search, a machine learning technique to intelligently search a chemical search space of 255991 photoswitches based on 29 known azoarenes and their derivatives. We iteratively trained the active search algorithm based on whether a candidate absorbed visible light (λmax > 450 nm). Active search was found to triple the discovery rate compared to random search. Further, we projected 1962 photoswitches to 2D using the Uniform Manifold Approximation and Projection (umap) algorithm and found that λmax depends on the core, which is tunable with substituents. We then incorporated a second stage of screening with to predict the stabilities of the Z-isomers for the top 1% of candidates. We identified four ideal photoswitches that concurrently satisfy λmax > 450 nm and t1/2 > 2 hours; the range of λmax and t1/2 range from 465 to 531 nm and hours to years, respectively.
| Fatemah Mukadum; Quan Nguyen; Daniel Adrion; Gabriel Appleby; Rui Chen; Haley Dang; Remco Chang; Roman Garnett; Steven Lopez | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610d615f42d165d1993abf58/original/efficient-discovery-of-visible-light-activated-azoarene-photoswitches-with-long-half-lives-using-active-search.pdf |
65e61d6f9138d23161a8b14a | 10.26434/chemrxiv-2024-m8vwx | Axial H-bonding Solvent Controls Inhomogeneous Spectral Broadening, Peripheral H-bonding Solvent Controls Vibronic Broadening: Cresyl Violet in Methanol | The dynamics of the nuclei of both chromophore and its condensed phase environment control many spectral features, including the vibronic and inhomogeneous broadening present in spectral lineshapes. For the cresyl violet chromophore in methanol, we here analyze and isolate the effect of specific chromophore-solvent interactions on simulated spectral densities, reorganization energies, and linear absorption spectra. Employing both force field and ab initio molecular dynamics trajectories along with the inclusion of only certain solvent molecules in the excited state calculations, we determine that the methanol molecules axial to the chromophore are responsible for the majority of the inhomogeneous broadening, with a single methanol molecule that forms an axial hydrogen bond dominating the response. The strong peripheral hydrogen bonds do not contribute to spectral broadening, as they are very stable throughout the dynamics and do not lead to increased energy gap fluctuations. We also find that treating the strong peripheral hydrogen bonds as molecular mechanical point charges during the molecular dynamics simulation underestimates the vibronic coupling. Including these peripheral hydrogen bonding methanol molecules in the quantum mechanical region in a geometry optimization increases the vibronic coupling, suggesting that a more advanced treatment of these strongly interacting solvent molecules during the molecular dynamics trajectory may be necessary to capture the full vibronic spectral broadening. | Christopher A. Myers; Shao-Yu Lu; Sapana Shedge; Arthur Pyuskulyan; Katherine Donahoe; Liang Shi; Christine M. Isborn | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e61d6f9138d23161a8b14a/original/axial-h-bonding-solvent-controls-inhomogeneous-spectral-broadening-peripheral-h-bonding-solvent-controls-vibronic-broadening-cresyl-violet-in-methanol.pdf |
6793b49e81d2151a02ca7a21 | 10.26434/chemrxiv-2025-t9m19 | Gold(I)-Mediated Reactivity of Allenes with Mesoionic Nucleophiles: A Computational Study | We explore the factors leading to regioselective nucleophilic additions in gold(I)-mediated reactions with allenes through DFT analysis of model systems. The reactivity and selectivity are determined by both steric and electronic effects. The feasibility of intermolecular nucleophilic attack by sydnones and münchnones was evaluated by comparison to several known nucleophiles, with the transition state barriers of the latter being particularly accessible. The resulting intermediates are more likely to undergo formal (3+3) cyclisations instead of the more usual (3+2) pathways. While initial decarboxylation is not readily accessed, a computational mechanistic exploration suggests that the ultimate products are likely to be substituted dihydropyridines. We propose that the use of mesoionic reagents in gold(I)-mediated processes is feasible, should regioselectively access different heterocycles, and may lead to the development of new methodology in gold(I)-mediated synthesis. | Eduardo Garcia-Padilla; Feliu Maseras | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793b49e81d2151a02ca7a21/original/gold-i-mediated-reactivity-of-allenes-with-mesoionic-nucleophiles-a-computational-study.pdf |
6508380db6ab98a41ca93964 | 10.26434/chemrxiv-2023-fv4m7 | Revealing the Formation Dynamics of Janus Polymer Particles: Insights from Experiments and Molecular Dynamics. | Seeded emulsion polymerization is one of the best-known methods for preparing polymer particles with controlled size, composition, and shape. It first requires the preparation of seed particles, which are then swollen with additional monomer (the same as the one used for the seed or a different one), to either increase the seed's size or change its morphology. The use of surfactants plays a central role in guaranteeing the required colloidal stability and contributing to the final shape and structure of the particles by lowering the interfacial energy between the polymer of the seed and the added monomer. We here study the polymerization of methyl methacrylate in the presence of polystyrene seed particles at various surfactant concentrations, in the presence and absence of a surfactant (sodium dodecyl sulfate). We first show experimentally that the morphology of the colloidal particles can be tuned from Janus to core-shell, depending on the presence or absence of surfactant on the seeds particles’ surface. Furthermore, using classical molecular dynamics simulations, we investigate the mechanism and behavior of surfactants during the first stages of the polymerization process. We use a newly developed approach based on contact statistical analysis to confirm the critical role played by the organization of surfactant molecules on the seed particles’ surface in dictating the final particle morphology. | Miroslava Nedyalkova; Philip Loche ; Giovanni Russo; Marco Lattuada | Theoretical and Computational Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6508380db6ab98a41ca93964/original/revealing-the-formation-dynamics-of-janus-polymer-particles-insights-from-experiments-and-molecular-dynamics.pdf |
6666e12112188379d8c44aa5 | 10.26434/chemrxiv-2024-0ks0p | DASH Properties: Estimating Atomic and Molecular Properties from a Dynamic Attention-Based Substructure Hierarchy | Recently, we presented a method to assign atomic partial charges based on the DASH tree (dynamic attention-based substructure hierarchy) with high efficiency and quantum mechanical (QM) like accuracy. Additionally, the approach can be considered “rule based” – where the rules are derived from the attention values of a graph neural network – and thus, each assignment is fully explainable by visualizing the underlying molecular substructures. In this work, we demonstrate that these hierarchically sorted substructures capture the key features of the local environment of an atom and allow us to predict different atomic properties with high accuracy without building a new DASH tree for each property. The fast prediction of atomic properties in molecules with the DASH tree can for example be used as an efficient way to generate feature vectors for machine learning without the need for expensive QM calculations. | Marc T. Lehner; Paul Katzberger; Niels Maeder; Gregory A. Landrum; Sereina Riniker | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666e12112188379d8c44aa5/original/dash-properties-estimating-atomic-and-molecular-properties-from-a-dynamic-attention-based-substructure-hierarchy.pdf |
647c9ec4e64f843f4151c5d2 | 10.26434/chemrxiv-2023-1wg9b-v2 | A Very Deep Graph Convolutional Network for 13C NMR Chemical Shift Calculation with Density Functional Theory Level Performance for Structure Assignment | Nuclear magnetic resonance (NMR) chemical shift calculation is a powerful tool for structural elucidation, and has been extensively employed in both synthetic and natural product chemistry. However, density functional theory (DFT) NMR chemical shift calculations are usually time-consuming, while fast data-driven methods often lack reliability, making it challenging to apply them to computationally intensive tasks. Herein, we have constructed a 54-layer deep graph convolutional network for 13C NMR chemical shift calculation, which achieved high accuracy with low time-cost, and performed competitively with DFT NMR chemical shift calculations on structure assignment benchmarks. Our model utilizes a semi-empirical method, GFN2-xTB, and is compatible with a broad variety of organic systems, including those composed of hundreds of atoms or elements ranging from H to Rn. We used this model to resolve the controversial J/K rings junction problem of maitotoxin, which is the largest whole molecule assigned by NMR calculation to date. This model has been developed into a user-friendly software, providing a useful tool for routinary rapid structure validation and assignation, as well as a new approach to elucidate the large structures that were previously unsuitable for NMR calculation. | Wen-Jing Ai; Jing Li; Dongsheng Cao; Shao Liu; Yi-Yun Yuan; Yan Li; Gui-Shan Tan; Kang-Ping Xu; Xia Yu; Fenghua Kang; Zhen-Xing Zou; Wen-Xuan Wang | Theoretical and Computational Chemistry; Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647c9ec4e64f843f4151c5d2/original/a-very-deep-graph-convolutional-network-for-13c-nmr-chemical-shift-calculation-with-density-functional-theory-level-performance-for-structure-assignment.pdf |
60c7518c567dfe1fa9ec5aac | 10.26434/chemrxiv.13176773.v1 | Modification of TiO2 with Metal Chalcogenide Nanoclusters for Hydrogen Evolution | Using density functional theory, corrected for on-site Coulomb
interactions (DFT+U), we have investigated surface modification of TiO<sub>2</sub>
with metal chalcogenide nanoclusters for hydrogen evolution. The nanoclusters
have composition M<sub>4</sub>X<sub>4</sub> (M = Sn, Zn; X = S, Se) and are
adsorbed at the rutile (110) surface. The nanoclusters adsorb exothermically,
with adsorption energies in the range -3.00 eV to -2.70 eV. Computed density of
states (DOS) plots show that cluster-derived states extend into the band-gap of
the rutile support, which indicates that modification produces a redshift in
light absorption. After modification, photoexcited electrons and holes are
separated onto surface and cluster sites, respectively. The free energy of H
adsorption is used to assess the performance of metal chalcogenide modified TiO<sub>2</sub>
as a catalyst for HER. Adsorption of H at nanocluster (S, Se) and surface (O)
sites is considered, together with the effect of H coverage. Adsorption free
energies at cluster sites in the range (-0.15 eV, 0.15 eV) are considered to be
favourable for HER. The results of this analysis indicate that the sulphide
modifiers are more active towards HER than the selenide modifiers and exhibit
hydrogen adsorption free energies in the active range, for most coverages.
Conversely, the adsorption free energies at the selenide nanoclusters are only
in the active range at low H coverages. Our results indicate that surface
modification with small, dispersed nanoclusters of appropriately selected
materials can enhance the photocatalytic activity of TiO<sub>2</sub> for HER
applications. | Stephen Rhatigan; Lorenzo Niemitz; Michael Nolan | Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7518c567dfe1fa9ec5aac/original/modification-of-ti-o2-with-metal-chalcogenide-nanoclusters-for-hydrogen-evolution.pdf |
65a5d7439138d231610202b5 | 10.26434/chemrxiv-2024-sd6mz | Molecular-Strain Driven Phosphinidene Reactivity of a Phosphanorcaradiene | Herein we report straightforward synthesis, characterization and reactivity studies of a phosphanorcaradiene, in which one of the benzene rings in the flanking fluorenyl substituents is intramolecularly dearomatized through attachment to the phosphorus atom. It was facilely obtained by the reduction of phosphorus(III) dichloride MsFluidtBu-PCl2 supported by a hydrindacene substituent with potassium graphite. Despite being thermally robust, it serves as an elegant precursor for transient phosphinidene. It reacted with trimethylphosphine and isonitrile to yield phosphanylidene-phosphorane and 1-phospha-3-azaallene, respectively. Moreover, it was capable of activating ethylene and 4-tertbutylphenylacetylene to afford [1+2] cycloaddition products, as well as oxidative cleavage of Si–H and N–H bonds to yield secondary phosphines. All the reactions proceeded smoothly at room temperature without the presence of transition metals. The driving force for these reactions is most likely the high ring-constraint of the three-membered PC2 ring and recovery of the aromaticity of the benzene ring. | Gengwen Tan; Yizhen Chen; Dongmin Wang; Li Zhang | Inorganic Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a5d7439138d231610202b5/original/molecular-strain-driven-phosphinidene-reactivity-of-a-phosphanorcaradiene.pdf |
66b91b0b01103d79c5aa4fbf | 10.26434/chemrxiv-2024-k9r7j | STUDIES ON ACTIVATED CLAY ENCAPSULATED WITH NANOPARTICLES FOR THE DECOLARISATION OF VEGETABLE OIL | Kaolinite clay, a crucial component of kaolin, is widely utilized in various applications, including pottery and adsorbent production. Despite effective beneficiation methods, concerns persist regarding their cost and environmental impact. The process of palm oil bleaching, crucial in refining, commonly employs activated carbon. Modifying clay minerals enhances adsorption, with acid activation and impregnation being prevalent methods. The properties of Nigerian kaolinite clay are pivotal in applications like paints, rubber, and adsorbents. This research aims to develop and characterize adsorbents encapsulated with nanoparticles from active kaolin clays for oil refineries and specific processes. The study explores reaction mechanisms, beneficiation processes, and synthesis techniques. Beneficiated Kaolin undergoes acid treatment to remove impurities, followed by zinc oxide (ZnO) synthesis using Moringa leaf extract. The resulting ZnO/Kaolin composite nanoparticles are analyzed using a Central Composite Design (CCD) to optimize process variables like calcination, set at high (5) and low (1) levels, with temperatures of 600°C and 300°C, and times of 60 mins and 30 mins. Characterization techniques include scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) and UV-Vis spectrophotometry of Beneficiated Kaolin and ZnO-K NP in Dosages, also calculating bleaching efficiency. Results indicate successful synthesis and activation of ZnO/Kaolin nanocomposites with enhanced adsorption properties. ANOVA analysis shows p-values categorized as follows: p < 0.05 (significant), 0.05 ≤ p < 0.1 (marginally significant), and p ≥ 0.1 (not significant). The quadratic model for iodine value yields an actual value of 198.54, with DOE highlighting significant process parameter optimization for adsorption efficiency. Recommendations include further parameter optimization, investigation of adsorption kinetics/mechanisms, exploring environmental applications, scale-up for industrial use, and comparative studies with other adsorbents. The study reveals the physiosorbed water at 1.9% total weight loss and the dihydroxylation of Kaolin resulting in a 13% weight loss during beneficiation. Elemental composition analysis via SEM-EDS shows elements such as silicon (Si), calcium (Ca), oxygen (O), and aluminum (Al) in both Beneficiated Kaolin and ZnO-K NP, with only ZnO-K NP exhibiting zinc (Zn) presence among detected elements. This research enhances understanding and application of ZnO/Kaolin nanocomposites in adsorption processes, providing sustainable solutions for various industries. | Aisha Awwal; Zakari Ladan; Bako Myek | Nanoscience; Chemical Engineering and Industrial Chemistry; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Reaction Engineering; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b91b0b01103d79c5aa4fbf/original/studies-on-activated-clay-encapsulated-with-nanoparticles-for-the-decolarisation-of-vegetable-oil.pdf |
66de4cc012ff75c3a1cf5cff | 10.26434/chemrxiv-2024-p305k | 2D Interfacial Crystallization Stabilized by Short-Chain Aliphatic Interfaces | We report the formation of interface sealing crystalline sheets based on amino acid and peptoid-monomer amphiphiles. This process, interfacial crystallization (IFC), is demonstrated using a range of halide salts of amidated peptoid monomers and amino acid amide bases with varied aliphatic sidechains. In our investigation, we identified that sufficient dynamic freedom of attached sidechains is a crucial design principle underpinning the viability of IFC for a given molecule. In addition, our results indicated that a combination of ionic coordination, hydrogen bonding and dispersion interactions all contribute significantly to the formation of these structures, and they are consistent with a hypothesis of interfacial ion migration playing a critical role in structure formation. A comprehensive range of techniques, including AFM, FT-IR, TOF-SIMs, X-ray crystallography, salt exchange experiments, quantum mechanical (QM) calculations and molecular dy-namics (MD) simulation studies were used to characterize this phenomenon. The formation of these hierarchical nanostructures, and the simplicity of the chemistry involved, suggests that IFC may have applications in formation of 2D supramolecular materials and barriers. | Hamish W. A. Swanson; Kenny Barriales; Emmet A. Sherman; Tai-De Li; Alan R. Kennedy; Tell Tuttle; Rein V. Ulijn; King Hang Aaron Lau | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66de4cc012ff75c3a1cf5cff/original/2d-interfacial-crystallization-stabilized-by-short-chain-aliphatic-interfaces.pdf |
60c75553702a9b601b18c6a0 | 10.26434/chemrxiv.13295879.v2 | CH4-to-CH3OH on Mononuclear Cu(II) Sites Supported on Al2O3: Structure of Active Sites from Electron Paramagnetic Resonance | The selective conversion of methane to methanol remains one of the holy grails of chemistry, where Cu-exchanged zeolites have been shown to selectively convert methane to methanol under stepwise conditions. Over the years, several active sites have been proposed, ranging from mono-, di- to trimeric Cu(II). Herein, we report the formation of well-dispersed monomeric Cu(II) species supported on alumina using surface organometallic chemistry and their reactivity towards the selective and stepwise conversion of methane to methanol. Extensive studies using various transition alumina supports combined with spectroscopic characterization, in particular electron paramagnetic resonance (EPR), show that the active sites are associated with specific facets, which are typically found in gamma- and eta-alumina phase, and that their EPR signature can be attributed to species having a tri-coordinated [(Al<sub>2</sub>O)Cu<sup>II</sup>O(OH)]<sup>-</sup>,T-shape geometry. Overall, the selective conversion of methane to methanol, a two-electron process, involve two of these isolated monomeric Cu(II) sites that play in concert. | Jordan Meyet; Anton Ashuiev; Gina Noh; Mark Newton; Daniel Klose; Keith Searles; Alexander van Bavel; Andrew Horton; Gunnar Jeschke; Jeroen A. van Bokhoven; Christophe Copéret | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75553702a9b601b18c6a0/original/ch4-to-ch3oh-on-mononuclear-cu-ii-sites-supported-on-al2o3-structure-of-active-sites-from-electron-paramagnetic-resonance.pdf |
671f9db798c8527d9ea0f3f9 | 10.26434/chemrxiv-2024-smlz3 | Decoupling Degradation at the Electrode Interfaces in Prussian White Full Cells | Prussian blue analogues (PBAs) for sodium ion battery (SIB) cathodes are growing in popularity as next generation energy storage devices. Prussian White (PW) with formula NaxFe[Fe(CN)6]y•nH2O is leading the trend, having already been commercialized. However, capacity fade (PW/electrolyte degradation) and safety concerns (cyanide/cyanogen release) still raise concerns. Online electrochemical mass spectrometry (OEMS), supported by both operando Fourier transform infrared spectroscopy (FTIR) and Mössbauer spectroscopy (MöS), is herein used to analyse degradation processes in PW based Na-ion full cells. Apart from the typical cell formation reactions, hydrogen is observed to evolve during cell discharge and evidenced to stem from oxidation of NaH, accumulated upon charge. Over-oxidation of PW after full desodiation releases CN, which not only forms (CN)2 but also degrades the electrolyte. Loss of CN likely results in a nanometric (~4 nm) surface-reconstructed passivation layer on PW thus inhibiting further degradation. Fundamental understanding of degradation reactions in PW full-cells, as gathered herein, shows that the aforementioned capacity fade and safety concerns are wholly addressable and hence guides the further development of Na-ion batteries for wider ranges of applications. | Casimir Misiewicz; Alexandra E. Ulander; Tim Melin; Aram Hall; Erik J. Berg | Analytical Chemistry; Energy; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f9db798c8527d9ea0f3f9/original/decoupling-degradation-at-the-electrode-interfaces-in-prussian-white-full-cells.pdf |
60c753574c8919c683ad42e1 | 10.26434/chemrxiv.13480263.v1 | Electrochemical Synthesis of Isoxazolines: Method and Mechanism | An electrochemical method for the green and practical
synthesis of a broad range of substituted isoxazoline cores is presented. Both
aryl and more challenging alkyl aldoximes are converted to the desired
isoxazoline <i>via</i> an electrochemically
enabled regio- and diastereoselective reaction with electron-deficient alkenes.
Additionally, <i>in-situ</i> reaction
monitoring methods compatible with electrochemistry equipment have also been
developed in order to probe the reaction pathway. Supporting analyses from
kinetic (time-course) modeling and density functional theory support a
stepwise, radical-mediated mechanism, and discounts hypothesized involvement of
closed shell [3+2] cycloaddition pathways. | Samuel David Lee Holman; Neal Fazakerley; Darren poole; Diane M. Coe; Leonard Berlouis; Marc Reid | Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry; Computational Chemistry and Modeling; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753574c8919c683ad42e1/original/electrochemical-synthesis-of-isoxazolines-method-and-mechanism.pdf |
627feaf859f0d657f6908b4f | 10.26434/chemrxiv-2022-kzzn4 | The Economically Sustainable Hydrothermal Synthesis of Dextrosil-Viologen as a Robust Anolyte in Aqueous Redox Flow Batteries | Aqueous organic redox flow batteries (RFBs) are promising for grid-scale energy storage, but identifying stable and inexpensive organic redox couples suitable for practical applications has been challenging. Here we report a new, inexpensive, and robust anolyte, Dextrosil-Viologen (Dex-Vi), that demonstrates a record overall RFB performance for anolyte redox species in neutral aqueous media, including ultralow anion-exchange membrane permeability, high volumetric capacity capability, and outstanding chemical stability. Remarkably, at a high concentration of 1.5 M (40.2 Ah·L-1 theoretical anolyte volumetric capacity), Dex-Vi shows extremely stable cycling performance without observable capacity decay over one-month cycling. Furthermore, by rationalizing a high-yield hydrothermal synthetic approach that has never been applied to viologen RFB molecules along with a low-cost precursor, the predicted mass production cost of Dex-Vi is below $10/kAh. These results not only establish a new benchmark organic anolyte promising for practical RFB applications but also shows that the properties of organic redox species can be enhanced with minute performance tradeoffs through rationalized structural and synthetic design. | Xiu-Liang Lv; Patrick Sullivan; Hui-Chun Fu; XuanXin Hu; Honghao Liu; Song Jin; Wenjie Li; Dawei Feng | Organic Chemistry; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627feaf859f0d657f6908b4f/original/the-economically-sustainable-hydrothermal-synthesis-of-dextrosil-viologen-as-a-robust-anolyte-in-aqueous-redox-flow-batteries.pdf |
60c74e3e567dfe3dedec54b8 | 10.26434/chemrxiv.12728459.v1 | Ultra-Rapid Uptake and Highly Stable Storage of Methane as Combustible Ice | <p>Ever-increasing natural gas (NG) consumption trends due
to its cleanest tag and abundant availability point towards an inevitable transition
into an NG dominated economy. Solidified Natural Gas (SNG) storage via combustible
ice or clathrate hydrates presents an economically sound prospect, promising
high volume density, and long-term storage. Here we establish 1,3-dioxolane
(DIOX), as a highly efficient dual-action (thermodynamic and kinetic promoter) additive
for clathrate (methane sII) hydrate formation. By synergistically combining a small
concentration (300 ppm) of kinetic promoter L-tryptophan with DIOX, we further
demonstrate ultra-rapid hydrate formation with a methane uptake of 83.81 (±0.77) volume of gas/volume of hydrate (v/v) within 15
minutes. To the best of our knowledge, this is the fastest reaction time ever
reported for sII hydrates related to SNG technology and represents a 147% increase
in the hydrate formation rate compared to the standard water-DIOX system. Mixed
methane-DIOX hydrates in pelletized form also exhibit incredible stability when
stored at atmospheric pressure and moderate temperature of 268.15 K, thereby
showcasing potential to be industrially adoptable for the development of a
large-scale NG storage system.</p> | Marcus N. Goh; Gaurav Bhattacharjee; Sonia E.K. Arumuganainar; Praveen Linga | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3e567dfe3dedec54b8/original/ultra-rapid-uptake-and-highly-stable-storage-of-methane-as-combustible-ice.pdf |
65fc658366c13817297c0783 | 10.26434/chemrxiv-2024-5hf2x | Deciphering competitive interactions: Phosphate and organic matter binding on goethite through experimental and theoretical insights | The adsorption of phosphorus (P) onto active soil surfaces plays a pivotal role in immobilizing P, thereby influencing soil fertility and the filter function of soil to protect freshwater systems from eutrophication. Competitive anions, such as organic matter (OM), significantly affect the strength of this P-binding, eventually controlling P mobility and release, but surprisingly, these processes are insufficiently understood at the molecular level. In this study, we provide a molecular-level perspective on the influence of OM on P binding at the goethite-water interface using a combined experimental-theoretical approach. By examining the impact of citric acid (CIT) and histidine (HIS) on the adsorption of orthophosphate (OP), glycerolphosphate (GP), and inositol hexaphosphate (IHP) through adsorption experiments and molecular dynamics simulations, we address fundamental questions regarding P binding trends, OM interaction with the goethite surface, and the effect of OM on P adsorption. Our findings reveal the complex nature of P adsorption on goethite surfaces, where the specific OM, treatment conditions (including covering the surface with OM or simultaneous co-adsorption), and initial concentrations collectively shape these interactions. P adsorbs on goethite with an order of GP < OP < IHP. Crucially, this trend remains consistent across all adsorption experiments, regardless of the presence or absence of OM, CIT, or HIS, and irrespective of the specific treatment method. Notably, OP is particularly susceptible to inhibition by OM, while adsorption of GP depends on specific OM treatments. Despite being less sensitive to OM, IHP shows reduced adsorption, especially at higher initial P concentrations. Of significance is the strong inhibitory effect of CIT, particularly evident when the surface is pre-covered, resulting in a substantial 70% reduction in OP adsorption compared to bare goethite. The sequence of goethite binding affinity to P and OM underscores a higher affinity of CIT and HIS compared to OP and GP, suggesting that OM can effectively compete with both OP and GP and replace them at the surface. In contrast, the impact of OM on IHP adsorption appears insignificant, as IHP exhibits a higher affinity than both CIT and HIS toward the goethite surface. The coverage of goethite surfaces with OM results in the blocking of active sites and the generation of an unfavorable electric potential and field, inhibiting anion adsorption and consequently reducing P binding. It is noteworthy that electrostatic interactions predominantly contribute more to the binding of P and OM to the surface compared to dispersion interactions. | Ashour A. Ahmed; Mohsen Morshedizad; Oliver Kühn; Peter Leinweber | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Interfaces | CC BY NC 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc658366c13817297c0783/original/deciphering-competitive-interactions-phosphate-and-organic-matter-binding-on-goethite-through-experimental-and-theoretical-insights.pdf |
6285c04f59f0d67921958bd1 | 10.26434/chemrxiv-2022-qll2k | DNA-based immobilization for improved electrochemical carbon dioxide reduction | Electrochemical reduction of carbon dioxide (CO2) is a promising route for the up-conversion of this industrial by-product. However, to perform this reaction with a small-molecule catalyst, the catalyst must be proximal to an electrode surface. Efforts to immobilize these catalysts on electrodes have been stymied by the need to optimize immobilization chemistries on a case-by-case basis. As with many reactions, Nature has evolved catalysts with high specificity, selectivi-ty, and activity. By taking inspiration from biological porphyrins and combining it with the specificity of DNA hybridiza-tion, we have developed an improved electrocatalyst platform for CO2 reduction. The addition of single-stranded DNA to the porphyrin-based catalysts improved their stability, and DNA-catalyst conjugates were immobilized on screen-printed carbon electrodes using DNA hybridization with nearly 100% efficiency. Increased turnover frequency (TOF) and catalyst stability were observed with the DNA-immobilized catalysts as compared to the unmodified small molecules. This work demonstrates the importance of taking inspiration from Nature and demonstrates the potential of DNA hybridization as a general strategy for molecular catalyst immobilization. | Gang Fan; Nathan Corbin; Thomas Gill; Amruta Karbelkar; Ariel Furst | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6285c04f59f0d67921958bd1/original/dna-based-immobilization-for-improved-electrochemical-carbon-dioxide-reduction.pdf |
618a7c7298309b03df575f5e | 10.26434/chemrxiv-2021-0wzfl | One-Pot Preparation of (NH)-Phenanthridinones and Amide-Functionalized [7]Helicene-like Molecules from Biaryl Dicar-boxylic Acids | A one-pot transformation of biaryl dicarboxylic acids to (NH)-phenanthridinone derivatives based on a Curtius rearrangement and subsequent basic hydrolysis was developed. This method is also applicable for the preparation of optically active amide-functionalized [7]helicene-like molecules. Furthermore, aza[5]helicene derivatives with a phosphate moiety were isolated as a product of the Curtius rearrangement step in the case of substrates that bear chalcogen atoms. The stereostructures of these products, revealed by X-ray diffraction analysis, suggested that chalcogen-bonding and pnictogen-bonding interactions might contribute to their stabilization. The configurational stability of the helicene-like molecules and their chiroptical properties were further investigated. | Takumi Furuta; Takuya Murai; Yongning Xing; Mayu Kurokawa; Toshifumi Kuribayashi; Masanori Nikaido; Elghareeb E. Elboray; Shohei Hamada; Yusuke Kobayashi; Takahiro Sasamori; Takeo Kawabata | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618a7c7298309b03df575f5e/original/one-pot-preparation-of-nh-phenanthridinones-and-amide-functionalized-7-helicene-like-molecules-from-biaryl-dicar-boxylic-acids.pdf |
61e817574a603dd715357506 | 10.26434/chemrxiv-2022-n8lbf | Ion mobility studies of Pyrroloquinoline Quinone Aza-Crown Ether-Lanthanide Complexes | Lanthanide-dependent enzymes and their biomimetic complexes have arisen as an interesting target of research in the last decade. These enzymes, specifically, pyrroloquinoline quinone (PQQ)-bearing methanol dehydrogenases, efficiently turn over alcohols to the respective aldehydes. To rationally design bioinspired alcohol dehydrogenation catalysts, it is imperative to understand the species involved in catalysis. However, given the extremely flexible coordination sphere of lanthanides, it is often difficult to assess the number and nature of the active species. Here we show how such questions can be addressed by using a combination of ion mobility spectrometry, mass spectrometry and quantum chemical calculations to study the test systems PQQ and lanthanide-PQQ-crown ether ligand complexes. Specifically, we determine the gas phase structures of [PQQH2]-, [PQQH2+H2O]-, [PQQH2+MeOH]-, [PQQ-15c5+H]+ and [PQQ-15c5+Ln+NO3]+ (Ln=La to Lu, except Pm). In the latter case a trend to smaller collision cross sections across the lanthanide series is clearly observable, in line with the well-known lanthanide contraction. We hope that in future such investigations will help to guide the design and understanding of lanthanide based biomimetic complexes optimized for catalytic function. | Alexander Schäfer; Violeta Vetsova; Erik Schneider; Manfred Kappes; Michael Seitz; Lena Daumann; Patrick Weis | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e817574a603dd715357506/original/ion-mobility-studies-of-pyrroloquinoline-quinone-aza-crown-ether-lanthanide-complexes.pdf |
66ff89f4cec5d6c1421ada0e | 10.26434/chemrxiv-2024-vm2gx-v2 | Oligolysine Promotes and Inhibits DNA Condensate Formation | The formation of biomolecular condensates via phase separation relates to various cellular functions. Reconstituting these condensates with designed molecules allows for exploring their mechanisms and potential applications. Sequence-designed DNA nanostructures enable the investigation of the effects of structural design on condensate formation and construction of functional artificial condensates. Despite the high designability of DNA-based condensates, the presence of free nanostructures that do not assemble into condensates remains a challenge. Herein, we report the effects of cationic oligolysines on DNA condensate formation assembled from Y-shaped DNA nanostructures. Experimental results showed that DNA condensate formation was enhanced by adding oligolysines at an appropriate N/P ratio, the ratio of positively-charged amine groups (N) to negatively-charged nucleic acid phosphate groups (P), maintaining the sequence specificity of DNA. On the other hand, surprisingly, oligolysines significantly inhibited condensate formation depending on the N/P ratio and residue number, which was likely attributed to the deformation of the nanostructures induced by oligolysines. These results suggested that the amount and length of cationic peptides significantly affected the self-assembly of branched DNA nanostructures. We believe that this study will deepen our understanding of biomolecular condensates and provide insights for further development of DNA/peptide hybrid condensates to enhance the functions of artificial condensates for use in artificial cells and molecular robots. | Hiroaki Ohno; Takuya Mabuchi; Yosuke Ochi; Junichi Taira; Yusuke Sato | Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ff89f4cec5d6c1421ada0e/original/oligolysine-promotes-and-inhibits-dna-condensate-formation.pdf |
6555def4dbd7c8b54b5efb88 | 10.26434/chemrxiv-2023-4pl7l-v2 | Flavin-N5OOH: A powerful nucleophile and base in nature | Flavoenzymes can mediate a large variety of oxidation reactions via the activation of oxygen. As such, the chemistry of flavoenzymes is an important field that has not yet attained its full scope/recognition. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that flavin-N5OOH acts as a powerful nucleophile that promotes C–N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplishes the generally selective general base catalysis, and the C–X (X= N, S, Cl, O) cleavage reactions that are otherwise challenging by solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes. | Qiaoyu Zhang; Qianqian Chen; Sason Shaik; Binju Wang | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555def4dbd7c8b54b5efb88/original/flavin-n5ooh-a-powerful-nucleophile-and-base-in-nature.pdf |
6651b51921291e5d1d3ceae9 | 10.26434/chemrxiv-2024-d1l1b | Logics for Developing Regioselective Histone Acetylating Catalysts | The combination of post-translational modifications (PTMs) of histones, a major component of chromatin, defines “histone code” having distinct impact on chromatin structures and gene expression. Therefore, methods to introduce histone PTMs at desired positions are useful tools for investigating the functions of epigenetic marks, especially to understand consequences of specific modifications in histones. Chemical catalysts, such as lysine (Lys)-acetylating catalysts, have been emerged to regioselectively promote histone PTMs without relying on histone-modifying enzymes. However, it has been poorly under-stood what factors determine Lys-residue selectivity of the histone acetylating catalysts. Here we show that the intrinsic reac-tivity, distance from the catalytically active site, and conformational flexibility of Lys residues, are the critical factors for determining acetylation yield and regioselectivity. Combining molecular dynamics simulations of catalyst-nucleosome com-plexes and experimental optimization of the catalyst structure, we developed three catalysts that selectively acetylated K43, K108, and K120 of H2B, respectively. Biochemical analyses of the regioselectively acetylated nucleosomes revealed that each Lys acetylation showed distinct impacts on inter-nucleosomal interactions and the affinity to a nucleosome-binding molecule. Our data provide a guideline for developing regioselective histone acetylation catalysts and may further accelerate studies of epigenetics regulated by histone PTMs. | Tamiko Nozaki; Mayu Onoda; Misuzu Habazaki; Yuma Takeuchi; Hisashi Ishida; Yuko Sato; Tomoya Kujirai; Kayo Hanada; Kenzo Yamatsugu; Hitoshi Kurumizaka; Hiroshi Kimura; Hidetoshi Kono; Shigehiro Kawashima; Motomu Kanai | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6651b51921291e5d1d3ceae9/original/logics-for-developing-regioselective-histone-acetylating-catalysts.pdf |
665f41f2418a5379b013d4e1 | 10.26434/chemrxiv-2024-l0v7x | An Activity-Based Sensing Approach to Multiplex Mapping of Labile Copper Pools by Stimulated Raman Scattering | Molecular imaging with analyte-responsive probes offers a powerful chemical approach to study biological processes. The most common types of reagents for bioimaging employ a fluorescence readout, but the relatively broad emission bands of this modality and need to alter the chemical structure of the fluorophore to achieve different signal colors can potentially limit multiplex imaging. Here we report a generalizable approach to multiplex analyte imaging by leveraging the comparably narrow spectral signatures of stimulated Raman scattering (SRS) in an activity-based sensing (ABS) mode. We illustrate this concept by developing two Copper Raman Probes (CRPs), CRP2181 and CRP2153.2, that react selectively with loosely-bound Cu(I/II) and Cu(II) ions, respectively, termed the labile copper pool, through copper-directed acyl imidazole (CDAI) chemistry. These reagents label proximal proteins in a copper-dependent manner using a dye scaffold bearing a 13C≡N or 13C≡15N isotopic SRS tag but otherwise having nearly identical physiochemical properties in terms of shape and size. SRS imaging with CRP2181 and CRP2153.2 enables duplex monitoring of changes in intracellular labile Cu(I) and Cu(II) pools upon exogenous copper supplementation or copper depletion, or through genetic perturbations to essential copper transport proteins. Moreover, CRP imaging reveals reciprocal increases in labile Cu(II) pools upon decreases in activity of the antioxidant response transcription factor nuclear factor-erythroid 2-related factor 2 (NRF2) in cellular models of lung adenocarcinoma. By showcasing the use of narrow-bandwidth, ABS probes for multiplex imaging of copper pools in different oxidation states and identifying alterations in labile metal nutrient pools in cancer, this work provides a starting point for the broader development of SRS for analyte-responsive, multiplex imaging in biological systems. | Yishu Jiang; Elsy El Khoury; Aidan T. Pezacki; Naixin Qian; Miku Oi; Laura Torrente; Sophia Miller; Martina Ralle; Gina DeNicola; Wei Min; Christopher Chang | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665f41f2418a5379b013d4e1/original/an-activity-based-sensing-approach-to-multiplex-mapping-of-labile-copper-pools-by-stimulated-raman-scattering.pdf |
60c7595fee301c4808c7b8c2 | 10.26434/chemrxiv.14686740.v1 | Reaction Pathway for Coke-Free Methane Steam Reforming on a Ni/CeO2 Catalyst: Active Sites and Role of Metal-Support Interactions | <p>Methane steam reforming (MSR) plays a key role in the production of
syngas and hydrogen from natural gas. The increasing interest in the use of
hydrogen for fuel cell applications demands the development of catalysts with
high activity at reduced operating temperatures. Ni-based catalysts are
promising systems because of their high activity and low cost, but coke
formation generally poses a severe problem. Studies of ambient-pressure X-ray
photoelectron spectroscopy (AP-XPS) indicate that CH<sub>4</sub>/H<sub>2</sub>O
gas mixtures react with Ni/CeO<sub>2</sub>(111) surfaces to form OH, CH<i><sub>x</sub></i>
and CH<i><sub>x</sub></i>O at 300 K. All these species are easy to form and
desorb at temperatures below 700 K when the rate of the MSR process
accelerates. Density functional theory (DFT) modeling of the reaction over
ceria-supported small Ni nanoparticles predicts relatively low activation
barriers between 0.3–0.7 eV for the complete dehydrogenation of methane to
carbon and the barrierless activation of water at interfacial Ni sites. Hydroxyls
resulting from water activation allow CO formation via a COH intermediate with
a barrier of about 0.9 eV, which is much lower than that through a pathway
involving lattice oxygen from ceria. Neither methane nor water activation are
rate-determining steps, and the OH-assisted CO formation through the COH
intermediate constitutes a low-barrier pathway that prevents carbon accumulation.
The interaction between Ni and the ceria support and the low metal loading are
crucial for the reaction to proceed in a coke-free and efficient way. These
results could pave the way for further advances in the design of stable and highly
active Ni-based catalysts for hydrogen production.</p> | Agustin Salcedo; Pablo Lustemberg; Ning Rui; Robert M. Palomino; Zongyuan Liu; Slavomir Nemsak; Sanjaya D. Senanayake; José A. Rodriguez; M. V. Ganduglia-Pirovano; Beatriz Irigoyen | Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7595fee301c4808c7b8c2/original/reaction-pathway-for-coke-free-methane-steam-reforming-on-a-ni-ce-o2-catalyst-active-sites-and-role-of-metal-support-interactions.pdf |
616245e72aca53835b5eaaad | 10.26434/chemrxiv-2021-3bzl6 | Tetraphenylporphyrin Enters the Ring: First Example of a Complex Between Highly Bulky Porphyrins and a Protein | Tetraphenylporphyrin (TPP) is a synthetic porphyrin whose properties can be readily modified, endowing it with significant benefits over naturally occurring porphyrins. Yet, their insolubility in water and/or steric bulk have rendered them incompatible with biological systems. Herein, we report the first example of a native biomolecule capturing TPP as well as its derivatives. The haemoprotein HasA, secreted by certain pathogens to scavenge haem from their hosts, can capture various metal- and meso-substituted TPPs. The rapid crystallisation of TPP derivatives captured by HasA revealed the binding mode of TPP at excellent resolutions. A single-site mutation (L85A) of HasA enlarged the binding pocket, allowing the incorporation of a bulkier derivative of TPP. HasA binding TPP derivatives was also demonstrated to inhibit proliferation of the opportunistic pathogen Pseudomonas aeruginosa. This study not only represents a simple method for the complexation of TPP derivatives with a native protein, but also opens the door for the future use of TPP derivatives as biological tools. | Yuma Shisaka; Erika Sakakibara; Kazuto Suzuki; Joshua Kyle Stanfield; Hiroki Onoda; Garyo Ueda; Miu Hatano; Hiroshi Sugimoto; Osami Shoji | Inorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616245e72aca53835b5eaaad/original/tetraphenylporphyrin-enters-the-ring-first-example-of-a-complex-between-highly-bulky-porphyrins-and-a-protein.pdf |
65204709bda59ceb9a02b1bb | 10.26434/chemrxiv-2023-3b9p3 | Pocket Crafter: A 3D Generative Modeling Based Workflow for the Rapid Generation of Hit Molecules in Drug Discovery | We present a user-friendly molecular generative pipeline called Pocket Crafter, specifically designed to facilitate hit finding activity in the drug discovery process. This workflow utilized a 3D (three-dimensional) generative modeling method, e.g. Pocket2Mol, for the de novo design of molecules in spatial perspective for the targeted protein structures, followed by filters for chemical-physical properties and drug-likeness, SAR (structure-activity relationship) analysis, and clustering to generate top virtual hit scaffolds. In our WDR5 case study, we acquired a focused set of 2029 compounds after a targeted searching within Novartis archived library based on the virtual scaffolds. Subsequently, we experimentally profiled these compounds, resulting in a novel chemical scaffold series that demonstrated activity in biochemical and biophysical assays. Pocket Crafter successfully prototyped an effective end-to-end 3D generative chemistry-based workflow for the exploration of new chemical scaffolds, which represents a promising approach in early drug discovery for the identification of novel active compounds. | Lingling Shen; Jian Fang; Lulu Liu; Fei Yang; Jeremy L. Jenkins; Peter S. Kutchukian; He Wang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65204709bda59ceb9a02b1bb/original/pocket-crafter-a-3d-generative-modeling-based-workflow-for-the-rapid-generation-of-hit-molecules-in-drug-discovery.pdf |
67627fccfa469535b9f63cfa | 10.26434/chemrxiv-2024-dvp75 | Electron-deficient Alkyne Lipids Enable Efficient Synthesis of Comparable Polymer Lipids via Copper-free Azide-Alkyne Cycloaddition | Polymer lipids (PLs) are essential components of liposomes and lipid nanoparticles (LNPs) for drug and gene delivery, providing colloidal stabilization and defining the biological interface. While poly(ethylene glycol) (PEG)-based PLs are the current standard, they are suspected to be responsible for rare adverse reactions, e. g. to LNP-based Covid-19 vaccines. Therefore, PLs based on alternative stealth polymers are being intensively investigated for their use in LNPs. However, alternative PLs often lack comparability due to different synthesis protocols and are often not easily accessible. Herein we present a catalyst-free, efficient and versatile coupling procedure for PL synthesis based on azide-functionalized polymers and electron-deficient acetylene dicarboxylate lipids. To highlight the versatility of this approach, we prepared PLs based on PEG and 4 alternative stealth polymers with quantitative coupling efficiencies. The linker structure showed appropriate pH stability and all PLs enabled the preparation of well-defined liposomes with excellent stability. Our facile and versatile approach yields comparable PLs with minimized linker size, making them promising candidates for future comparative studies and biomedical applications. | Florian T. Kaps; Anna-Lena Ziegler; Paul Fritsche; Ekaterina Takmakova; Andrew Kerr; Susanne Boye; Albena Lederer; Robert Luxenhofer | Organic Chemistry; Analytical Chemistry; Polymer Science; Drug delivery systems; Organic Polymers; Analytical Chemistry - General | CC BY NC 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67627fccfa469535b9f63cfa/original/electron-deficient-alkyne-lipids-enable-efficient-synthesis-of-comparable-polymer-lipids-via-copper-free-azide-alkyne-cycloaddition.pdf |
60c73f1d567dfe3385ec3981 | 10.26434/chemrxiv.7252160.v1 | Numerical Evaluation of Coulomb Integrals For 1, 2 and 3-electron Distance Operators, RC1 -nRD1 -m , RC1 -n r12 -m and r12 -n r13 -m with Real (N, M) and The Descartes Product of 3 Dimension Common Density Functional Numerical Integration Scheme | Analytical solutions to integrals are far more
useful than numeric, however, the former is not available in many cases. We
evaluate integrals indicated in the title numerically that are necessary in
some approaches in quantum chemistry. In the title, where R stands for
nucleus-electron and r for electron-electron distances, the n, m= 0 case is trivial,
the (n, m)= (1,0) or (0,1) cases are well known, a fundamental milestone in the
integration and widely used in computational quantum chemistry, as well as
analytical integration is possible if Gaussian functions are used. For the rest
of the cases the analytical solutions are restricted, but worked out for some,
e.g. for n, m= 0,1,2 with Gaussians. In this work we generalize the
Becke-Lebedev-Voronoi 3 dimensions numerical integration scheme (commonly used
in density functional theory) to 6 and 9 dimensions via Descartes product to
evaluate integrals indicated in the title, and test it. This numerical recipe
(up to Gaussian integrands with seed exp(-|<b>r</b><sub>1</sub>|<sup>2</sup>), as well as positive and negative real n and m values) is useful for
manipulation with higher moments of inter-electronic distances, for example, in
correlation calculations; more, our numerical scheme works for Slaterian type functions
with seed exp(-|<b>r</b><sub>1</sub>|) as well. | Sandor Kristyan | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1d567dfe3385ec3981/original/numerical-evaluation-of-coulomb-integrals-for-1-2-and-3-electron-distance-operators-rc1-n-rd1-m-rc1-n-r12-m-and-r12-n-r13-m-with-real-n-m-and-the-descartes-product-of-3-dimension-common-density-functional-numerical-integration-scheme.pdf |
628c4ded44bdd554696e3ad1 | 10.26434/chemrxiv-2022-z39sz | A stable luminescent covalent organic framework nanosheet for sensitive molecular recognition | Despite the rapid development of fluorescence detectors over the past decade, it still remains a considerable challenge to exploit a highly stable, sensitive, and selective fluorescence platform for molecular recognition. In this study, we report a stable carbazole-based sp2 carbon fluorescence covalent organic framework (COF) nanosheet, termed JUC-557-nanosheet. Owing to the synergistic effect of AIE- and ACQ-based chromophores in JUC-557-nanosheet, this architecture shows high absolute quantum yields (up to 23.0%) in solid state and the dispersed in various solvents and excellent sensing performance toward specific analytes, such as iodine (Ka: 2.10 105 M-1 and LOD: 302 ppb), 2,4,6-trinitrotoluene (Ka: 4.38 105 M-1 and LOD: 129 ppb), and especially nitrobenzene (Ka: 6.18 106 M-1 and LOD: 5 ppb), which is superior to those of fluorescence detection materials reported so far, including porous materials, small molecule probes and inorganics. Furthermore, its fluorescence quenching mechanism has been demonstrated to be a synergistic effect of static quenching and energy transfer quenching by a combined theoretical and experimental study, including time-resolved photoluminescence measurements, UV-vis absorption spectroscopy, and density functional theory calculations. As a chemically stable material, JUC-557-nanosheet preserves strong luminescence and sensitive recognition even under harsh conditions (such as strong acid with pH = 1 or strong base with pH = 14), and allows trace detection of various analytes via a handheld UV lamp. Therefore, these findings pave the way for developing stable ultrathin COF nanomaterials for highly sensitive and selective molecular detection. | Qianrong Fang; Yaozu Liu; Junxia Ren; Yujie Wang; Xin Zhu; Xinyu Guan; Zisheng Wang; Yida Zhou; Liangkui Zhu; Shilun Qiu; Shengxiong Xiao | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628c4ded44bdd554696e3ad1/original/a-stable-luminescent-covalent-organic-framework-nanosheet-for-sensitive-molecular-recognition.pdf |
6402eeb437e01856dc20fd25 | 10.26434/chemrxiv-2023-jbjh2 | Efficient C(sp3)-H carbonylation of light and heavy hydrocarbons with carbon monoxide via HAT photocatalysis in flow | Despite their abundance in organic molecules, considerable limitations still exist in synthetic methods that target the direct C-H functionalization at sp3-hybridized carbon atoms. This is even more the case for light alkanes, which bear some of the strongest C-H bonds known in Nature, requiring extreme activation conditions that are not tolerant to most organic molecules. To bypass these issues, synthetic chemists rely on prefunctionalized alkyl halides or organometallic coupling partners. However, new synthetic methods that target regioselectively C-H bonds in a variety of different organic scaffolds would be of great added value, not only for the late-stage functionalization of biologically active molecules but also for the catalytic upgrading of cheap and abundant hydrocarbon feedstocks. Here, we describe a general, mild and scalable protocol which enables the direct C(sp3)-H carbonylation of saturated hydrocarbons, including natural products and light alkanes, using photocatalytic hydrogen atom transfer (HAT) and gaseous carbon monoxide (CO). Flow technology was deemed crucial to enable high gas-liquid mass transfer rates and fast reaction kinetics, needed to outpace deleterious reaction pathways, but also to leverage a scalable and safe process. | Fabian Raymenants ; Tom Masson; Jesus San Jose Orduna; Timothy Noel | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6402eeb437e01856dc20fd25/original/efficient-c-sp3-h-carbonylation-of-light-and-heavy-hydrocarbons-with-carbon-monoxide-via-hat-photocatalysis-in-flow.pdf |
66e01156cec5d6c142aae3f5 | 10.26434/chemrxiv-2024-cjnmw | A nanoparticle contrast agent enables dynamic microscale X-ray computed tomography imaging of the soil aqueous phase | The current need to develop alternative agricultures that preserve soil health with a reduced contribution to climate change, has led to a growth of interest in understanding natural processes within soil. This creates a demand for 3D imaging techniques that dynamically image soil processes such as fluid and nutrient transport with high resolution. Microscale X-ray computed tomography (X-CT) delivers high-contrast and high-resolution (down to ~1 m) imaging of soil mineral phases. However it does not readily distinguish low-density aqueous and organic phases, nor image water transport. Here we have developed polymer-templated gold nanoparticles as a contrast agent to label the aqueous phase in soil, with gold selected for low toxicity. Nanoparticles are generated by templated synthesis within pre-assembled block copolymer micelles, poly(2-(dimethylamino)ethyl methacrylate)-block-poly[poly(ethylene glycol) methyl ether methacrylate)], poly(DEAEMA-b-PEGMA), to intrinsically exhibit a stabilizing PEG-bottlebrush corona. Block copolymers are generated by group transfer polymerization (GTP). Overall, this process generates gold nanoparticles at high concentrations and in large volumes for soil imaging. The nanoparticles show exceptional colloidal stability (to at least 4M ionic strength), and are stable in the challenging soil environment, showing no adsorption to the soil mineral phase. X-CT imaging within soil distinguished aqueous phase labelled with the nanoparticle contrast agent from unlabelled aqueous phase, at ~ 5 mg/ml Au. In a transport experiment, we determined the effective bulk diffusion constant of the nanoparticle system in water to be 1.1 0.3 10-10 m2s-1. Intriguingly, this is greater than the single particle diffusion constant in dilute solution, suggesting a role for crowding effects. Taken together, these results demonstrate this nanoparticle system as an effective and practical contrast agent for imaging flow and transport processes in living soil. | Shuchen Wang; Anna Constantinou; Guanglei Zhang; Yihuai Zhang; Mohammad Javad Shojaei; Bo Zhou; Davey Jones; Tiina Roose; Martin Blunt; Theoni Georgiou; Iain Dunlop | Polymer Science; Nanoscience; Agriculture and Food Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e01156cec5d6c142aae3f5/original/a-nanoparticle-contrast-agent-enables-dynamic-microscale-x-ray-computed-tomography-imaging-of-the-soil-aqueous-phase.pdf |
6627ed4c91aefa6ce13969ca | 10.26434/chemrxiv-2024-m8q63 | De novo design of inhibitors of DNA methyltransferase 1: A critical comparison of ligand- and structure-based approaches | Designing and developing inhibitors against the epigenetic target DNA methyltransferase (DNMT) is an attractive strategy in epigenetic drug discovery. DNMT1 is one of the epigenetic enzymes with significant clinical relevance. Structure-based de novo design is a drug discovery strategy used in combination with similarity searching to identify a novel DNMT inhibitor with a novel chemical scaffold and warrants further exploration. This study aimed to continue exploring the potential of de novo design to build epigenetic-focused libraries targeted toward DNMT1. Herein, we report the results of an in-depth and critical comparison of ligand- and structure-based de novo design of screening libraries focused on DNMT1. The newly designed chemical libraries focused on DNMT1 are freely available on GitHub at https://github.com/DIFACQUIM/De-Novo_DNMT1. | Diana L. Prado-Romero; Fernanda I. Saldívar-González; Iván López-Mata; Pedro A. Laurel-García; Norberto Sánchez-Cruz; José L. Medina-Franco | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627ed4c91aefa6ce13969ca/original/de-novo-design-of-inhibitors-of-dna-methyltransferase-1-a-critical-comparison-of-ligand-and-structure-based-approaches.pdf |
65aa8e4266c1381729d16503 | 10.26434/chemrxiv-2024-c5mzp | HCN Dimers to HCN Tetramers: Computational Exploration of Binary Reactions | This study explores the self and cross-dimerization of HCN and HNC dimers, key elements in prebiotic chemistry, to explore potential phenomena crucial to the early stages of life on Earth, Titan, and other extraterrestrial environments. We utilise computational analysis to reveal various reaction products, predominantly featuring imine, nitrile, amine, and iminoamine functional groups, along with N-heterocycles like aziridines, azetenes, and triazole. Transition state search methods illuminate the mechanistic details of these reactions. Notably, we identify biomarkers such as a func- tional isomer of DAMN (D95) and imidazole derivatives (D45, D76, D79), which are potential precursors to nucleobases such as adenine, and polyimines that may serve as precursors to DNA and RNA helical structures. This study enhances our under- standing of the complex chemical pathways that may have contributed to the genesis of life’s foundational molecules in various cosmic settings. | Sunanda Panda; Saikat Roy; Maya Khatun; Anakuthil Anoop | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Space Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aa8e4266c1381729d16503/original/hcn-dimers-to-hcn-tetramers-computational-exploration-of-binary-reactions.pdf |
672b75e4f9980725cf4fbb48 | 10.26434/chemrxiv-2024-c0shc-v2 | Protein-driven electron transfer process in a fatty acid photodecarboxylase | Naturally occurring photoenzymes are rare in nature, but among them, fatty acid photodecarboxylases derived from Chlorella variabilis (CvFAPs) have emerged as promising photobiocatalysts capable of performing redox-neutral, light-induced decarboxylation of free fatty acids (FAs) into C1-shortened n-alka(e)nes. Using a hybrid QM/MM approach combined with a polarizable embedding scheme, we identify the structural changes of the active site and determine the energetic landscape of the forward electron transfer (fET) from the FA substrate to the excited flavin adenine dinucleotide. We obtain a charge-transfer diradical structure where a water molecule rearranges spontaneously to form an H-bond interaction with the excited flavin, while the FA’s carboxylate group twists and migrates away from it. Together, these structural modifications provide the driving force necessary for the fET to proceed in a downhill direction. Moreover, by examining the R451K mutant where the FA substrate is farther from the flavin core, we show that the marked reduction of the electronic coupling is counterbalanced by an increased driving force, resulting in a fET lifetime similar to the WT, thereby suggesting a resilience of the process to this mutation. Finally, through QM/MM molecular dynamic simulations we reveal that, following fET, the decarboxylation of the FA radical occurs within tens of ps, overcoming an energy barrier of ~0.1 eV. Overall, by providing an atomistic characterization of the photoactivation of CvFAP, this work can be used for future protein engineering. | Giacomo Londi; Giacomo Salvadori; Patrizia Mazzeo; Lorenzo Cupellini; Benedetta Mennucci | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672b75e4f9980725cf4fbb48/original/protein-driven-electron-transfer-process-in-a-fatty-acid-photodecarboxylase.pdf |
64066d9dcc600523a3c3c5a3 | 10.26434/chemrxiv-2023-m7wql | From corrosion casting to virtual dissection: contrast-enhanced vascular imaging using hafnium oxide nanocrystals | Vascular corrosion casting is a method used to visualize the three dimensional anatomy and branching pattern of blood vessels, guiding insight into health and cardiovascular disease pathogenesis and progression. A polymer resin is injected in the vascular system and, after curing, the surrounding tissue is removed. This corrosion
process often deforms or even fractures the fragile cast, resulting in an overall loss of information. Here, we propose a method that does not require corrosion of the tissue,
based on in-situ high-resolution computed tomography (micro-CT) scans. Since there is a lack of CT contrast between the polymer cast and the animals’ surrounding soft
tissue, we introduce hafnium oxide nanocrystals (HfO2 NCs) as CT contrast agents into the resin. The NCs dramatically improve the overall CT contrast of the cast and
allow for straightforward segmentation in the CT scans. We designed the NC surface chemistry to ensure colloidal stability of the NCs in the casting resin, resulting
in a homogeneous dispersion that remains stable during casting and curing. Using only 5 m% of HfO2 NCs, high-quality casts of both zebrafish and mouse models could
be segmented using CT imaging software, allowing us to differentiate even μm scale details, without having to alter the resin injection method or affecting the resin’s mechanical properties. Our new method of virtual dissection by visualizing casts in-situ using contrast enhanced CT imaging greatly expands the application potential of the technique. | Eline Goossens; Loren Deblock; Lisa Caboor; Dietger Van den Eynden; Ivan Josipovic; Pablo Reyes Isaacura; Elizaveta Maksimova; Matthias Van Impe; Anne Bonnin; Pieter Cornillie; Matthieu Boone; Isabel Van Driessche ; Ward De Spiegelaere; Jonathan De Roo; Patrick Sips; Klaartje De Buysser | Materials Science; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64066d9dcc600523a3c3c5a3/original/from-corrosion-casting-to-virtual-dissection-contrast-enhanced-vascular-imaging-using-hafnium-oxide-nanocrystals.pdf |
6669c03b12188379d8f2d9c9 | 10.26434/chemrxiv-2024-krf7h-v2 | Beyond L-proline: Investigation of the properties of other natural amino acids in an organocatalytic warfarin synthesis | Proline is indisputably the model organocatalytic amino acid. However, other naturally occurring amino acids remain a potent and perhaps overlooked source of organocatalytic potential. In this work, we investigate the capacity of various natural amino acids to promote enantioselectivity in a synthesis of warfarin. We have identified L- and D-arginine as enantioselective catalysts for this reaction and have developed a recrystallization method to isolate the enantiomers of warfarin with high enantiopurity. In addition, we use methylated derivatives of arginine provide insight into the reaction mechanism. | Anna Wurz; Naomi Benson; Sierra Carr; Ketan Chamakura; Lizbeth Chirinos; Sydney Coll; Arhemy Franco-Gonzalez; Kayla Ivory; Hope Jankowski; Trinity Lamb; Shaya LeBauer; Grace McPherson; Thanh Nguyen; Jeimy Nolasco Guevara; Lily Parsad; Phuong Pham; Emma Piner; Kaci Richardson; Abdelhadi Bendjellal; Chelsea McRae; Robert Hughes | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6669c03b12188379d8f2d9c9/original/beyond-l-proline-investigation-of-the-properties-of-other-natural-amino-acids-in-an-organocatalytic-warfarin-synthesis.pdf |
67ade54b6dde43c908b48936 | 10.26434/chemrxiv-2025-vc37r | Synthesis of vinyl- azetidines and beta-lactams from allenamides via energy-transfer relay | Azetidines and beta-lactams are useful and versatile building blocks, with ample synthetic applications and pharmaceutical uses. However, few general methods provide densely functionalized monocyclic derivatives, and none could easily afford both azetidines and beta-lactams. Herein, we solved this issue with allenamides. The challenging substrates were activated by energy-transfer combining a tailor-made Ir(III) complex and a binaphthyl co-catalyst, which acts as a triplet-state relay and stabilizes intermediates via dispersion interactions. A triplet intermediate with a vinyl-radical character gives the strained heterocycles upon 1,5 hydrogen-atom-transfer. Products have a congested all-carbon quaternary center and a useful allylamino unit, and are prepared at room temperature with complete atom-economy. The utility of the method is showed by further downstream derivatization. | Sara Sparascio; Gabriele Scarica; Alessandro Cerveri; Giulia Russo; Davide Spataro; Luciano Marchiò; Matteo Lanzi; Giovanni Maestri | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ade54b6dde43c908b48936/original/synthesis-of-vinyl-azetidines-and-beta-lactams-from-allenamides-via-energy-transfer-relay.pdf |
616fccbaa3d2c9f67edce1cb | 10.26434/chemrxiv-2021-7kd63 | Perfluorocycloparaphenylenes: Fully fluorinated carbon nanorings by Ni-mediated one-pot synthesis | Perfluorinated aromatic compounds, the so-called perfluoroarenes, are widely used in materials science owing to their high electron affinity and characteristic intermolecular interactions. However, methods to synthesize highly strained perfluoroarenes have remained elusive so far, which greatly limits their structural diversity. Herein, we report the synthesis and isolation of perfluorocycloparaphenylenes (PFCPPs) as a class of ring-shaped perfluoroarenes. Using macrocyclic nickel complexes, we succeeded in synthesizing PF[n]CPPs (n = 10, 12, 14, 16) in one-pot without noble metals. The molecular structures of PF[n]CPPs (n = 10, 12) were determined by X-ray crystallography to confirm their tubular alignment. Photophysical and electrochemical measurements revealed that PF[n]CPPs (n = 10, 12) exhibit wide HOMO–LUMO gaps, high electron affinity, and strong phosphorescence at low temperature. PFCPPs are not only useful as electron-accepting organic semiconductors but can also be used for accelerating the creation of topologically unique molecular nanocarbon materials. | Kenichiro Itami; Hiroki Shudo; Motonobu Kuwayama; Masafumi Shimasaki; Taishi Nishihara; Youhei Takeda; Takuya Kuwabara; Akiko Yagi; Yasutomo Segawa | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616fccbaa3d2c9f67edce1cb/original/perfluorocycloparaphenylenes-fully-fluorinated-carbon-nanorings-by-ni-mediated-one-pot-synthesis.pdf |
65dbec369138d23161052792 | 10.26434/chemrxiv-2024-wxfhv | Study on the Transient Absorption Spectroscopy of a D-π-A Structure Aggregation-Induced Emission Luminogen and Its Photodynamic Therapy Application | Photodynamic therapy (PDT) represents an emerging and noninvasive modality that has gained clinical approval for the treatment of cancers, leveraging photosensitizers for optimal therapeutic efficacy. In this study, we synthesized a photosensitizer (denoted as DTCSPP) exhibiting a donor-π-acceptor (D-π-A) structural motif. The DTCSPP manifests aggregation-induced emission (AIE) characteristics, along with good biocompatibility and mitochondrial targeting capabilities attributed to its intrinsic charge and D-π-A architecture. The excited-state intramolecular charge transfer of DTCSPP was systematically investigated in both solution and aggregate states using femtosecond transient absorption spectroscopy (fs-TA). The fs-TA results revealed that DTCSPP exhibited a more rapid and facile excited-state molecular motion in the solution state compared to the aggregate state, implying the predominance of nonradiative decay in its photophysical processes within the solution. Given its ability to simultaneously generate type I and type II reactive oxygen species and induce ferroptosis and autophagy in cancer cells, DTCSPP demonstrates effectiveness in PDT at both cellular and in vivo levels. This study contributes a comprehensive understanding of the excited-state intramolecular charge transfer dynamics of charged D-π-A type AIE photosensitizers, shedding light on their potential application in PDT. The multifaceted capabilities of DTCSPP underscore its promise in advancing the field of anticancer therapeutics, providing valuable insights for the identification of anticancer targets and the development of novel drugs. | Siwei Zhang; junqiao Wang; Zaiyu Wang; Ming Shao; Chen Zhang; Jianwei Sun; Jacky Lam; Ben Zhong Tang | Biological and Medicinal Chemistry; Organic Chemistry; Physical Organic Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dbec369138d23161052792/original/study-on-the-transient-absorption-spectroscopy-of-a-d-a-structure-aggregation-induced-emission-luminogen-and-its-photodynamic-therapy-application.pdf |
61a9699a704d0593903e2568 | 10.26434/chemrxiv-2021-108w2 | Synergistic Brønsted/Lewis Acid Catalyzed Aromatic Alkylation with Unactivated Tertiary Alcohols or Di-tert-Butylperoxide to Synthesize Quaternary Carbon Centers | Dual Brønsted/Lewis acid catalysis involving environmentally benign, readily accessible protic acid and iron promotes site-selective tert-butylation of electron-rich arenes using di-tert-butylperoxide. This transformation inspired the development of a synergistic Brønsted/Lewis acid catalyzed aromatic alkylation that fills a gap in the Friedel–Crafts reaction literature by employing unactivated tertiary alcohols as alkylating agents, leading to new quaternary carbon centers. Corroborated by DFT calculations, the Lewis acid serves a role in enhancing the acidity of the Brønsted acid. The use of non-allylic, non-benzylic, and non-propargylic tertiary alcohols represents an underexplored area in Friedel–Crafts reactivity. | Aaron Pan; Maja Chojnacka; Robert Crowley; Lucas Gottemann; Brandon Haines; Kevin Kou | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Theory - Computational; Acid Catalysis | CC BY 4.0 | CHEMRXIV | 2021-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a9699a704d0593903e2568/original/synergistic-br-nsted-lewis-acid-catalyzed-aromatic-alkylation-with-unactivated-tertiary-alcohols-or-di-tert-butylperoxide-to-synthesize-quaternary-carbon-centers.pdf |
60c7559ebdbb89215ba3a85f | 10.26434/chemrxiv.14138147.v1 | Comparison of Structure- and Ligand-Based Scoring Functions for Deep Generative Models: A GPCR Case Study | <p></p><p>Deep generative models have shown the
ability to devise both valid and novel chemistry, which could significantly
accelerate the identification of bioactive compounds. Many current models, however,
use molecular descriptors or ligand-based predictive methods to guide molecule
generation towards a desirable property space. This restricts their application
to relatively data-rich targets, neglecting those where little data is
available to sufficiently train a predictor. Moreover, ligand-based models often
bias molecule generation towards previously established chemical space, thereby
limiting their ability to identify truly novel chemotypes. In this work, we assess
the ability of using molecular docking <i>via </i>Glide – a structure-based
approach – as a scoring function to guide the deep generative model REINVENT
and compare model performance and behaviour to a ligand-based scoring function.
Additionally, we modify the previously published MOSES benchmarking dataset to
remove any induced bias towards non-protonatable groups. We also propose a new
metric to measure dataset diversity, which is less confounded by the
distribution of heavy atom count than the commonly used <i>internal diversity </i>metric.
With respect to the main findings, we found that when optimizing the docking
score against DRD2, the model improves predicted ligand affinity beyond that of
known DRD2 active molecules. In addition, generated molecules occupy
complementary chemical and physicochemical space compared to the ligand-based approach,
and novel physicochemical space compared to known DRD2 active molecules. Furthermore,
the structure-based approach learns to generate molecules that satisfy crucial residue
interactions, which is information only available when taking protein structure
into account. Overall, this work demonstrates the advantage of using molecular
docking to guide <i>de novo</i> molecule generation over ligand-based
predictors with respect to predicted affinity, novelty, and the ability to
identify key interactions between ligand and protein target. Practically, this
approach has applications in early hit generation campaigns to enrich a virtual
library towards a particular target, and also in novelty-focused projects,
where <i>de novo</i> molecule generation either has no prior ligand knowledge available
or should not be biased by it.</p><p></p> | Morgan Thomas; Rob Smith; Noel M. O’Boyle; Chris de Graaf; Andreas Bender | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7559ebdbb89215ba3a85f/original/comparison-of-structure-and-ligand-based-scoring-functions-for-deep-generative-models-a-gpcr-case-study.pdf |
677feed46dde43c908dfa14e | 10.26434/chemrxiv-2024-hdk1p-v2 | Solvation Thermodynamic Costs of Cognate Binding Site Formation | Conformational flexibility complicates the identification of lead molecules that are shape and charge complementary to target proteins. Solvation thermodynamics has typically not been integrated into the exploration of alternate protein conformations. Here, we study the variation of solvation thermodynamic potentials as proteins adopt different conformations. Specifically, we analyze solvation thermodynamics of protein binding cavities with conformations obtained from molecular dynamics simulations with mobile side chains and side chains restrained about their cognate bound structure. We find that the reorganization of protein side chains has a significant effect on the structure and thermodynamics of binding site solvation and, in the vast majority of cases, that there is a significant solvation free energetic cost to forming cognate ligand bound structures when the ligand is absent. We discuss how understanding the interplay between solvation thermodynamics and protein structural fluctuations is crucial for discovering alternative binding pockets, estimating the contribution to binding affinity of displacing water upon ligand binding, and assessing revealed cryptic pocket bindability. | Yeonji Ji; Vjay Molino; Steven Ramsey; Tom Kurtzman | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677feed46dde43c908dfa14e/original/solvation-thermodynamic-costs-of-cognate-binding-site-formation.pdf |
60c743ab567dfed2f4ec4141 | 10.26434/chemrxiv.9396623.v1 | Can Machine Learning Find Extraordinary Materials? | <p>One of the most common criticisms of machine learning is an
assumed inability for models to extrapolate, i.e. to identify extraordinary
materials with properties beyond those present in the training data set. To
investigate whether this is indeed the case, this work takes advantage of
density functional theory calculated properties (bulk modulus, shear modulus,
thermal conductivity, thermal expansion, band gap and Debye temperature) to
investigate whether machine learning is truly capable of predicting materials
with properties that extend beyond previously seen values. We refer to these
materials as extraordinary, meaning they represent the top 1% of values in the
available data set. Interestingly, we show that even when machine learning is
trained on a fraction of the bottom 99% we can consistently identify 3/4 of the
highest performing compositions for all considered properties with a precision
that is typically above 0.5. Moreover, we investigate a few different modeling
choices and demonstrate how a classification approach can identify an
equivalent amount of extraordinary compounds but with significantly fewer false
positives than a regression approach. Finally, we discuss cautions and
potential limitations in implementing such an approach to discover new
record-breaking materials.</p> | Steven Kauwe; Jake Graser; Ryan Murdock; Taylor Sparks | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ab567dfed2f4ec4141/original/can-machine-learning-find-extraordinary-materials.pdf |
60c74ec3ee301cae75c7a593 | 10.26434/chemrxiv.12707957.v2 | Reversible Switching Between Positive and Negative Thermal Expansion in a Metal-Organic Framework DUT-49 | Three-dimensional architectures constructed via coordination of metal ions to organic linkers (broadly termed as metal-organic frameworks, MOFs), are highly interesting for many demanding applications such as gas adsorption, molecular separation, heterogeneous catalysis, molecular sensing etc. Being constructed from heterogeneous components, such framework solids show characteristic features from both of the individual components as well as framework-specific features. One such interesting physicochemical property is thermal expansion, which arises from thermal vibration from the organic linker and metal ions. Herein, we show a very unique example of thermal responsiveness for DUT-49 framework, a MOF well-known for its distinctive negative gas adsorption (NGA) property. In the guest-free form, the framework shows another counter-intuitive phenomenon of negative thermal expansion (NTE), i.e. lattice size increase with decrease of temperature. However, in the solvated state, it shows both NTE and positive thermal expansion (i.e. lattice size decreases with lowering of temperature, PTE) based on a specific temperature range. When the solvent exists in liquid form inside the MOF pore, it retains the pristine NTE nature of the bare framework. But freezing of the solvent inside the pores induces a strain, which causes a structural transformation through in-plane bending of the linker and this squeezes the framework by ~10 % of the unit cell volume. This effect has been verified using 3 different solvents where the structural contraction occurs immediately at the freezing point of individual solvent. Furthermore, studies on a series of DUT-49(M) frameworks with varying metal confirm the general applicability of this mechanism.<br /> | Bikash Garai; Volodymyr Bon; Anastasia A. Efimova; Martin Gerlach; Irena Senkovska; Stefan Kaskel | Nanostructured Materials - Nanoscience; Physical and Chemical Properties; Structure; Surface; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ec3ee301cae75c7a593/original/reversible-switching-between-positive-and-negative-thermal-expansion-in-a-metal-organic-framework-dut-49.pdf |
674048fa5a82cea2fa5b789d | 10.26434/chemrxiv-2024-723mb | Discovery of Fluorotelomer Sulfones in the Blubber of Greenland Killer Whales (Orcinus Orca) | Most known per- and polyfluoroalkyl substances (PFAS) bioaccumulate by binding to proteins or partitioning to phospholipids, leading to their prevalence in liver and blood. As a result, efforts to improve PFAS exposure estimates by identifying novel bioaccumulative substances, have focused on these tissues. However, the recent discovery of high concentrations of unidentified extractable organofluorine (EOF) in the blubber of a killer whale (Orcinus orca) from Greenland suggests that some fluorinated substances bioaccumulate preferentially in storage lipids. The present work builds on this initial finding by characterizing EOF in an additional 3 killer whales (2 from Greenland, 1 from Sweden), and then subjecting extracts from all 4 whales to analysis via gas chromatography-atmospheric pressure chemical ionization-ion mobility mass spectrometry. Using collision cross sections, we prioritized features suspected to be highly fluorinated, and then selected 5 for manual annotation. Custom synthesised standards confirmed 10:2 and 12:2 fluorotelomer methylsulfone, 10:2 and 12:2 fluorotelomer chloromethylsulfone, and 6:2 bisfluorotelomer sulfone in all blubber samples from Greenland at concentrations ranging from <0.4-72.5 ng/g, explaining 34-75% of blubber EOF. None of these substances were observable in liver, suggesting preferential accumulation in storage lipids. To the best of our knowledge, this is the first report of fluorotelomer sulfones in wildlife and the first observation of lipophilic, highly fluorinated PFAS. | Mélanie Z. Lauria; Xiaodi Shi; Faiz Haque; Merle Plassmann; Anna Roos; Malene Simon; Jonathan P. Benskin; Karl J. Jobst | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Environmental Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674048fa5a82cea2fa5b789d/original/discovery-of-fluorotelomer-sulfones-in-the-blubber-of-greenland-killer-whales-orcinus-orca.pdf |
64ac46086e1c4c986b28616a | 10.26434/chemrxiv-2023-53bfx | Water-soluble ionic carbon nitride as unconventional stabilizer for highly catalytically active ultrafine gold nanoparticles | Ultrafine metal nanoparticles (NPs) hold promise for applications in many fields, including catalysis. However, ultrasmall NPs are typically prone to aggregation, which often leads to performance losses, such as severe deactivation in catalysis. Conventional stabilization strategies (e.g., immobilization, embedding, or surface modification by capping agents) are typically only partly effective and often lead to loss of catalytic activity. Herein, a novel type of stabilizers based on water-soluble ionic (K+ and Na+ containing) polymeric carbon nitride (i.e., K, Na-poly(heptazine imide) = K,Na-PHI) is reported that enables effective stabilization of highly catalytically active ultrafine (size of ~2-3 nm) gold NPs. Experimental and theoretical comparative studies using different structural units of K,Na-PHI (i.e., cyanurate, melonate, cyamelurate) indicate that the presence of functionalized heptazine moieties is crucial for the synthesis and stabilization of small Au NPs. The K,Na-PHI-stabilized Au NPs exhibit remarkable dispersibility and outstanding stability even in solutions of high ionic strength, which is ascribed to more effective charge delocalization in the large heptazine units, resulting in more effective electrostatic stabilization of Au NPs. The outstanding catalytic performance of Au NPs stabilized by K,Na-PHI is demonstrated using the selective reduction of 4-nitrophenol to 4-aminophenol by NaBH4 as a model reaction, in which they outperform even the benchmark “naked” Au NPs electrostatically stabilized by excess NaBH4. This work thus establishes ionic carbon nitrides (PHI) as alternative capping agents enabling effective stabilization without compromising surface catalysis, and opens up a route for further developments in utilizing PHI-based stabilizers for the synthesis of high-performance nanocatalysts. | Mohamed M. Elnagar; Johannes Liessem; Changbin Im; Dariusz Mitoraj; Ludwig A. Kibler; Christof Neumann; Andrey Turchanin; Robert Leiter; Ute Kaiser; Timo Jacob; Igor Krivtsov; Radim Beranek | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ac46086e1c4c986b28616a/original/water-soluble-ionic-carbon-nitride-as-unconventional-stabilizer-for-highly-catalytically-active-ultrafine-gold-nanoparticles.pdf |
62c6a9facd7a997eeabc1b35 | 10.26434/chemrxiv-2022-jl3gd | G-type Halohydrin Dehalogenases Catalyze Ring Opening Reactions of Cyclic Epoxides with Diverse Anionic Nucleophiles | Halohydrin dehalogenases are promiscuous biocatalysts, which enable asymmetric ring opening reactions of epoxides with various anionic nucleophiles. However, despite the increasing interest in such asymmetric transformations, the substrate scope of G-type halohydrin dehalogenases toward cyclic epoxides has remained largely unexplored, even though this family is the only one known to display activity with these sterically demanding substrates. Herein, we report on the exploration of the substrate scope of the two G-type halohydrin dehalogenases HheG and HheG2 and a newly identified, more thermostable member of the family, HheG3, with a variety of sterically demanding cyclic epoxides and anionic nucleophiles. This work shows that, in addition to azide and cyanide, these enzymes facilitate ring-opening reactions with cyanate, thiocyanate, formate, and nitrite, significantly expanding the known repertoire of accessible transformations. | Jennifer Solarczek; Felix Kaspar; Pia Bauer; Anett Schallmey | Catalysis; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c6a9facd7a997eeabc1b35/original/g-type-halohydrin-dehalogenases-catalyze-ring-opening-reactions-of-cyclic-epoxides-with-diverse-anionic-nucleophiles.pdf |
62fb972b1d6a9924f90615d7 | 10.26434/chemrxiv-2022-dbd8s | Dioxygen Splitting by a Tantalum(V) Complex Ligated by a Rigid, Redox Non-innocent Pincer Ligand | Reaction of TaMe3Cl2 with the rigid acridane-derived trisamine H3NNN (1) yields the tantalum(V) complex [TaCl2(NNNcat)] (2). Subsequent reaction with dioxygen results in the full four-electron reduction of O2 yielding the oxo-bridged bimetallic complex [{TaCl2(NNNsq)}2O] (5). This dinuclear complex exhibits an open-shell ground state due to partial ligand oxidation and was comprehensively characterized by single crystal X-ray diffraction, LIFDI mass spectrometry, NMR, EPR, IR and UV/VIS/NIR spectroscopy. The mechanism of O2 activation was investigated by DFT calculations revealing initial binding of O2 to the tantalum(V) center followed by complete O2 scission to produce a terminal oxo-complex. | Jack Underhill; Eric S. Yang; Till Schmidt-Räntsch; William K. Myers; Jose M. Goicoechea; Josh Abbenseth | Inorganic Chemistry; Organometallic Chemistry; Ligands (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fb972b1d6a9924f90615d7/original/dioxygen-splitting-by-a-tantalum-v-complex-ligated-by-a-rigid-redox-non-innocent-pincer-ligand.pdf |
651db983bda59ceb9ae01111 | 10.26434/chemrxiv-2023-0rfzj | Dynamic Worm-Gel Materials as Tunable, Regenerable Adsorbents for Water Treatment | Introducing facile regenerability into adsorbent materials can potentially increase sustainability in water treatment systems enabled by extended use. Herein, we detail our recent syntheses of dynamic, nanostructured worm-gel materials and their implementation as regenerable adsorbents for water treatment. Photo-controlled atom transfer radical polymerization-induced self-assembly (PhotoATR-PISA) was employed to synthesize various polymer nanstructures, including dispersed spheres, worms, and vesicles, and nanostructured worm-gels, via the synthesis and simultaneous, in situ assembly of BAB triblock copolymers. Two dynamic, disulfide-functionalized macroinitiators (SS-MI-1 and 2) with different degree of polymerization and one non-dynamic macroinitiator (CC-MI) were synthesized via polymerization of oligo(ethylene glycol methyl ether methacrylate) (OEGMA). PhotoATR-PISA was then implemented via the chain extension from SS-MI-1, 2 and CC-MI with glycidyl methacrylate (GMA) or benzyl methacrylate (BMA) forming BAB-type triblock copolymer nanoparticles in situ. The final morphology in PhotoATR-PISA was influenced not only by conventional factors such as solids content and block DP but also by unimer exchange rates yielding arrested, nanostructured worm-gels in many instances and arrested vesicle-gels in one instance. These PISA-gel materials were implemented as adsorbents for phenanthrene, a model compound registered as a priority pollutant by US EPA, from aqueous solutions. The chemical tunability of these materials enabled enhanced, targeted removal of phenanthrene facilitated by π-π interactions as evidenced by the increased adsorption capacities of PBMA-based PISA-gels when compared to PGMA. Furthermore, the dynamicity of disulfide worm-gels (SS-WG) enabled disulfide exchange-induced regeneration stimulated by UV light. This UV-responsive exchange was investigated for POEGMA macroinitiators as well as dissolved triblock copolymers, dispersed nanoparticles and SS-WG materials. Finally, the regenerability of the PNT-saturated SS-WG adsorbents induced by UV irradiation (λ = 365 nm) was examined and compared to control worm-gels without disulfides demonstrating enhanced recovery of adsorption capacity under mild irradiation conditions. | Ali Shahrokhinia; Shayesteh Tafazoli; Sahaj Rijal; Dylan Shuster; Randall Scanga; David Morefield; Jaelese Garay; Raylene Rocheleau; Mohammad Bagheri Kashani; Ramaswamy Nagarajan; Onur Apul; James Reuther | Polymer Science; Earth, Space, and Environmental Chemistry; Organic Polymers; Polymer morphology; Environmental Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651db983bda59ceb9ae01111/original/dynamic-worm-gel-materials-as-tunable-regenerable-adsorbents-for-water-treatment.pdf |
6493424724989702c2baf2e5 | 10.26434/chemrxiv-2023-j823z | Per- and polyfluoroalkyl substances (PFAS) in PubChem: 7 million and growing | Per- and polyfluoroalkyl substances (PFAS) are of high concern, with calls to regulate these as a class. In 2021, the Organisation for Economic Co-operation and Development (OECD) revised the definition of PFAS to include any chemical containing at least one saturated CF2 or CF3 moiety. The consequence is that one of the largest open chemical collections, PubChem, with 115 million compounds, now contains over 7 million PFAS under this revised definition. These numbers are several orders of magnitude higher than previously established PFAS lists (typically thousands of entries) and pose an incredible challenge to researchers and computational workflows alike. This article describes a dynamic, openly accessible effort to navigate and explore the >7 million PFAS and >21 million fluorinated compounds (17 June 2023) in PubChem by establishing the “PFAS and Fluorinated Compounds in PubChem” Classification Browser (or “PubChem PFAS Tree”). A total of 36,500 nodes support browsing of the content according to several categories, including classification, structural properties, regulatory status, or presence in existing PFAS suspect lists. Additional annotation and associated data can be used to create subsets (and thus manageable suspect lists or databases) of interest for a wide range of environmental, regulatory, exposomics and other applications. | Emma Schymanski; Jian Zhang; Paul Thiessen; Parviel Chirsir; Todor Kondic; Evan Bolton | Theoretical and Computational Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Chemoinformatics; Environmental Analysis | CC BY 4.0 | CHEMRXIV | 2023-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6493424724989702c2baf2e5/original/per-and-polyfluoroalkyl-substances-pfas-in-pub-chem-7-million-and-growing.pdf |
63404696114b7e44d12cb3c2 | 10.26434/chemrxiv-2022-6tzsb | Sulfonamide as Photoinduced Hydrogen Atom Transfer Catalyst for Organophotoredox Hydrosilylation and Hydrogermylation of Activated Alkenes | Readily available, sterically, and electronically tunable sulfonamides have been developed as effective photoinduced hydrogen atom-transfer (HAT) catalysts for selective Si−H functionalizations of a broad range of silanes. N-centered radicals, catalytically generated from sulfonamides by photoredox catalyzed single-electron oxidation, are the key intermediates that enable an effective HAT process for silyl radical generation to achieve hydrosilylation of activated alkenes. Additionally, this catalytic system can also be applied for the activation of Ge-H bond for hydrogermylation of activated alkenes through hydrogen atom transfer by sulfonamide derived nitrogen centered radical. The ability to generate silyl and germyl radical using this photochemical HAT process offers new avenue towards the sustainable synthesis of organosilicon and organogermanium compounds. | Kalu Ram Bajya; Manjeet Kumar; Azaj Ansari; Sermadurai Selvakumar* | Organic Chemistry; Catalysis; Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63404696114b7e44d12cb3c2/original/sulfonamide-as-photoinduced-hydrogen-atom-transfer-catalyst-for-organophotoredox-hydrosilylation-and-hydrogermylation-of-activated-alkenes.pdf |
61c4ce36a53f1b4c1ea608be | 10.26434/chemrxiv-2021-tjb1v | Balancing high energy density and chemical stability in redox flow batteries with symmetric tetrazines | Nonaqueous redox flow batteries are a promising technology for grid-scale energy storage, however, their commercial success relies on identifying redox active materials that exhibit extreme potentials, high solubilities in all states of charge, and long cycling stabilities. Meeting these requirements has been particularly challenging for molecules capable of storing negative charge. Within this context, the symmetric tetrazines remain unexplored despite their unique structural properties that enable them to meet these challenges. Herein, we prepared s-tetrazines substituted with methyl, methoxy, and thiomethyl substituents and evaluated their electrochemical properties, solubility, and cycling stability. These studies revealed that 3,6-dimethoxy-s-tetrazine undergoes a reversible one-electron reduction to generate a soluble (>0.5 M in electrolyte/solvent) and stable (t1/2 > 1240 h) radical anion. When implemented in a lab-scale flow battery, it exhibited a relatively slow capacity fade of 13% over 100 cycles (38 h). Given their uncommonly high solubility and cycling stability, we believe that s-tetrazine derivatives should be further explored for non-aqueous redox flow batteries. | Gloria De La Garza; Aman Kaur; Ilya Shkrob; Lily Robertson; Susan Odom; Anne McNeil | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c4ce36a53f1b4c1ea608be/original/balancing-high-energy-density-and-chemical-stability-in-redox-flow-batteries-with-symmetric-tetrazines.pdf |
6555a9fb2c3c11ed717dc6fa | 10.26434/chemrxiv-2023-ltgjf | Reversible 1,2-Methyl Migration to an N-Heterocyclic Carbene in a PCNHCP Cobalt(I) Complex Enables Stereoselective (E and Z) Allyl Ether Isomerization | With growing efforts pushing towards sustainable catalysis, using earth-abundant metals has become increasingly important. Here we present the first examples of cobalt PCNHCP pincer complexes that demonstrate dual stereoselectivity for allyl ether isomerization. While the cationic cobalt complex [((PCNHCP)Co)2-μ-N2][BAr4F]2 (3) affords the Z-isomer of the enol ether predominantly, the corresponding methyl complex [(PCNHCP)CoMe)] (4) mostly gives the E-isomer. The dichotomy in selectivity is investigated computationally, revealing important contributions from the steric profile of the substituents on the metal (Me or N2), including an unprecedented migration of the methyl substituent from cobalt to the N-heterocyclic carbene carbon, which is further explored in this report. | Subhash Garhwal; Sakthi Raje; Katarzyna Młodzikowska-Pieńko; Tofayel Sheikh Mohammed; Ron Raphaeli; Natalia Fridman; Linda Shimon; Renana Poranne; Graham de Ruiter | Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555a9fb2c3c11ed717dc6fa/original/reversible-1-2-methyl-migration-to-an-n-heterocyclic-carbene-in-a-pcnhcp-cobalt-i-complex-enables-stereoselective-e-and-z-allyl-ether-isomerization.pdf |
6753257e7be152b1d0284431 | 10.26434/chemrxiv-2024-v9565 | Rhodium/Indium Heterobimetallic Alloy as an Effective Catalyst for Reductive C(sp3)–O Silylation of Ethers with Chlorosilanes | C(sp3)–O bonds are ubiquitous in natural and synthetic small molecules as well as polymers. The methodology for functionalizing C(sp3)–O bonds is of great importance for reforming these molecular structures into high-value-added chemical feedstocks. Here, we describe the reductive C(sp3)–O bond silylation of ethers with chlorosilanes and magnesium reductants by cooperative rhodium and indium catalysis. This methodology allows the incorporation of silyl moieties into the C(sp3)–O bond of various unactivated cyclic and acyclic alkyl ethers using chlorotriorganosilanes. Not only the mixture of rhodium complex with indium reagent but also rhodium nanoparticles supported on indium oxide showed high catalytic activity, indicating a remarkable cooperative effect by the two metals. Notably, in both cases, the generation of rhodium/indium heterobimetallic alloy nanoparticles were revealed by mechanistic studies including XRD, XAS, and TEM imaging. This research advances the development of heterogeneous nanoparticle catalysts as an option to enable organic transformations that have not yet been achieved using homogeneous catalysts. | Rin Seki; Haruka Kido; Kana Ko; Kaoru Imoto; Hiroki Miura; Tetsuya Shishido; Yoshiaki Nakao | Organic Chemistry; Catalysis; Organometallic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6753257e7be152b1d0284431/original/rhodium-indium-heterobimetallic-alloy-as-an-effective-catalyst-for-reductive-c-sp3-o-silylation-of-ethers-with-chlorosilanes.pdf |
64758d1abe16ad5c572640fb | 10.26434/chemrxiv-2023-7w3gk | Dissipation Lifetime of Catalysis as a Dynamical System | Catalysis is a critical mechanism to direct chemical reactions in biology and chemistry. However,
quantitatively predicting their properties such as activity or stability is difficult, due to the lack
of an equation which can be applied to various reaction mechanisms. Here, we report an equation
which estimates the lifetime of a catalyst by analyzing their mechanism from a dynamical systems
perspective. Furthermore, as proof of concept, we show its consistency with experiments by performing
the oxygen evolution reaction on manganese oxide. The equation successfully rationalizes
the time until the activity decreases to 10 % of the initial value with an expected error of 20 %,
providing the first quantitative model to predict the lifetime of a chemical system. | Hideshi Ooka; Marie E. Wintzer; Hirokazu Komatsu; Kiyohiro Adachi; Ailong Li; Shuang Kong; Daisuke Hashizume; Atsushi Mochizuki; Ryuhei Nakamura | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64758d1abe16ad5c572640fb/original/dissipation-lifetime-of-catalysis-as-a-dynamical-system.pdf |
61e86e37deeafa86a722dd67 | 10.26434/chemrxiv-2022-t86ws | Robust dicopper(I) µ-boryl complexes supported by a dinucleating naphthyridine-based ligand | Copper boryl species have been widely invoked as reactive intermediates in Cu-catalysed C−H borylation reactions, but their isolation and study have been challenging. Use of the robust dinucleating ligand DPFN (2,7-bis(fluoro-di(2-pyridyl)methyl)-1,8-naphthyridine) allowed for the isolation of two very thermally stable dicopper(I) boryl complexes, [(DPFN)Cu2(µ-Bpin)][NTf2] (2) and [(DPFN)Cu2(µ-Bcat)][NTf2] (4) (pin = 2,3-dimethylbutane-2,3-diol; cat = benzene-1,2-diol). These complexes were prepared by cleavage of the corresponding diborane via reaction with the alkoxide [(DPFN)Cu2(µ-OtBu)][NTf2] (3). Reactivity studies illustrated the exceptional stability of these boryl complexes (thermal stability in solution up to 100 °C) and their role in the activation of C(sp)−H bonds. X-ray diffraction and computational studies provide a detailed description of the bonding and electronic structures in these species, and suggest that the dinucleating character of the naphthyridine-based ligand is largely responsible for their remarkable stability. | Pablo Ríos; Matthew S. See; Rex C. Handford; T. Don Tilley | Inorganic Chemistry; Organometallic Chemistry; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e86e37deeafa86a722dd67/original/robust-dicopper-i-boryl-complexes-supported-by-a-dinucleating-naphthyridine-based-ligand.pdf |
60f5ddd0032114b62fb668ca | 10.26434/chemrxiv-2021-2s2lw | Rapid fabrication by digital light processing 3D printing of a SlipChip
with movable ports for local delivery to ex vivo organ cultures
| SlipChips are two-part microfluidic devices that can be reconfigured to change fluidic pathways for a wide range of functions, including tissue stimulation. Currently, fabrication of these devices at the prototype stage requires a skilled microfluidic technician, e.g. for wet etching or alignment steps. In most cases, SlipChip functionality requires an optically clear, smooth, and flat patterned surface that is fluorophilic and hydrophobic. Here, we tested digital light processing (DLP) 3D printing, which is rapid, reproducible and easily shared, as a solution for fabrication of SlipChips at the prototype stage. As a case study, we sought to fabricate a SlipChip intended for local de-livery to live tissue slices through a movable microfluidic port. The device was comprised of two multi-layer components: an enclosed channel with a delivery port and a culture chamber for tissue slices with a permeable support. Once the design was optimized, we demonstrated its function by locally delivering a chemical probe to slices of hydrogel and to living tissue with up to 120-µm spatial resolution. By establishing the design principles for 3D printing of SlipChip devices, this work will enhance the ability to rapidly prototype such devices at mid-scale levels of production. | Megan Catterton; Alexander Ball; Rebecca Pompano | Analytical Chemistry; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f5ddd0032114b62fb668ca/original/rapid-fabrication-by-digital-light-processing-3d-printing-of-a-slip-chip-with-movable-ports-for-local-delivery-to-ex-vivo-organ-cultures.pdf |
61b7daa2689c874261e36222 | 10.26434/chemrxiv-2021-674rl | Biocatalytic asymmetric construction of secondary and tertiary fluorides from β-fluoro-α-ketoacids | Fluorine is a critical element for the design of bioactive compounds, but its incorporation with
high regio- and stereoselectivity using environmentally friendly reagents and catalysts remains an area of
development. Stereogenic tertiary fluorides pose a particular synthetic challenge and are thus present in
only a few approved pharmaceuticals such as fluticasone, solithromycin, and sofosbuvir. The aldol reaction
of fluorinated donors provides an atom-economical approach to asymmetric C-F motifs via C-C bond
formation. Here we report that the type II pyruvate aldolase HpcH and engineered mutants thereof are
biocatalysts for carboligation of ß-fluoro-α-ketoacids (including fluoropyruvate, ß-fluoro-α-ketobutyrate, and
ß-fluoro-α-ketovalerate) with many diverse aldehydes. The reaction proceeds with kinetic resolution in the
case of racemic donors. The reactivity of HpcH towards these new donors, which are non-native in both
steric and electronic properties, grants access to enantiopure fragments with secondary or tertiary fluoride
stereocenters. In addition to representing the first asymmetric synthesis of tertiary fluorides via biocatalytic
carboligation, the afforded products could improve the diversity of fluorinated building blocks and enable
the synthesis of fluorinated drug analogs. | Jason Fang; Laura Turner; Michelle Chang | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biochemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2021-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b7daa2689c874261e36222/original/biocatalytic-asymmetric-construction-of-secondary-and-tertiary-fluorides-from-fluoro-ketoacids.pdf |
636b896680c9bf79e18f8f90 | 10.26434/chemrxiv-2022-0d7h2 | Multi-enzyme co-immobilization on tri-heterofunctional supports | Multi-enzyme cascade biotransformations in one pot are gaining momentum since they have demonstrated enhanced catalytic performance than traditional step-by-step transformations requiring sequential pots. Although their evident advantages, the co-immobilization of several enzymes requiring different anchoring chemistries and stability conditions is still challenging. In this work, we exploited an heterofunctional support activated with three different chemical functionalities in order to immobilize a wide variety of different enzymes under mild conditions. This support is based on agarose microbeads activated with aldehyde, amino and cobalt-chelates moieties that allow a fast and irreversible immobilization of enzymes (5 to 30 min), making most of the heterogeneous biocatalysts highly thermostable (up to 21-fold higher than the soluble one). We also demonstrated the potential of this tri-functional support to efficiently co-immobilize a multi-enzyme system composed by an alcohol dehydrogenase, a NADH oxidase and a catalase. The confined multi-enzymatic system demonstrates higher performance than the soluble enzyme counterparts reaching and accumulated TTN of 1x104 during five batch consecutive cycles under operational conditions. Finally, we expanded the versatility of the described exploited heterogeneous chemistry to other frequently used immobilization supports such as cellulose microbeads and commercial methacrylate porous beads. We envision this solid material to be a reference platform for co-immobilizing multi-enzyme systems with enhanced properties to catalyze stepwise biotransformations. | Javier Santiago-Arcos; Susana Velasco-Lozano; Fernando López Gallego | Catalysis; Biocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636b896680c9bf79e18f8f90/original/multi-enzyme-co-immobilization-on-tri-heterofunctional-supports.pdf |
67c566ddfa469535b9b9766b | 10.26434/chemrxiv-2025-3tlbz | Utilization of Synthetic Oxygen-Functionalized, Carboxylate-Rich Alicyclic Molecule Analogues in Liquid Chromatography and Tandem Mass Spectrometric Analysis of Dissolved Organic Matter | Dissolved organic matter (DOM) is one of the most complex chemical mixtures known, with its chemical composition long puzzling biogeochemists. Identifying the chemical structures within DOM is essential for unraveling its origins and environmental fate. However, DOM’s complexity has impeded structural elucidation, with accurate functional group compositions from recalcitrant DOM poorly represented in the synthetic and isolative literature. Consequently, hypothesized DOM compounds are derived from models that inadequately represent true structures. To address this, carboxylic acid-only CRAM analogues were previously synthesized but failed to replicate the extensive fragmentation observed in marine DOM during tandem mass spectrometry (MS2).
Here, we prepared CRAM analogues with numerous oxygen-functionalities to enable more diverse fragmentation pathways. Liquid chromatography studies showed functional group composition better predicted LC polarity than O/C ratio, and that alcohols represented early-eluting DOM profiles, while ethers ketones and lactones better represented central isomers. MS2 studies revealed α-hydroxy ketones and 1,2-diols led to the greatest backbone fragmentation, but remained less extensive than that of DOM. Ether and ester functionalities were labile even at low fragmentation energy, suggesting that such groups are likely contributors to core marine DOM carbon backbones, and contribute to the extensive fragmentation observed in all MS2 experiments.
| Jeffrey Hawkes; Agnes Flygare; Lindon W. K. Moodie; Alexander Craig | Earth, Space, and Environmental Chemistry; Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c566ddfa469535b9b9766b/original/utilization-of-synthetic-oxygen-functionalized-carboxylate-rich-alicyclic-molecule-analogues-in-liquid-chromatography-and-tandem-mass-spectrometric-analysis-of-dissolved-organic-matter.pdf |
679ce02c81d2151a02aecb91 | 10.26434/chemrxiv-2025-63fgd | Decoding Lusichelins A-E: An In-Depth Look at the Metallophores of Lusitaniella coriacea LEGE 07167 – Structure, Production, and Functionality | Essential trace metals are vital for cellular processes such as respiration, DNA replication, and photosynthesis. Cyanobacteria must tightly regulate metal homeostasis to prevent deficiency or toxicity, yet their metallophores remain overlooked. Here, we report lusichelins A-E (1-5), new metallophores isolated from the marine cyanobacterium Lusitaniella coriacea LEGE 07167. Their structures and configurational assignments were determined using NMR, mass spectrometry, TD-DFT calculations, and retrobiosynthetic insights. Lusichelins feature a unique structural arrangement with thiazoline/thiazole rings connected by a vinyl group, an aliphatic carbon chain, or directly, enabling potential for hexadentate metal coordination. Genomic analysis identified a hybrid PKS/NRPS biosynthetic gene cluster consistent with the structure of lusichelins and bearing traits characterisitic of metallophore biosynthesis. Notably, lusichelin production was influenced by salt composition in the culture medium rather than iron availability, suggesting an atypical regulatory mechanism. Functionally, lusichelins acted as copper detoxifiers, and lusichelin B (2) exhibited cytotoxicity against colon carcinoma cells while reversing multidrug resistance via ABCB1 efflux pump modulation. These findings expand the understanding of cyanobacterial metallophores in microbial metal homeostatis and highlight their potential in biological applications | Maria Lígia Sousa; Leonor Ferreira; Dora Ferreira; Abel M Forero; Raquel Castelo-Branco; Nikoletta Szemerédi; Gabriella Spengler; Jaime Rodríguez; Carlos Jiménez; Pedro N Leão; Vitor Vasconcelos; Mariana Reis | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679ce02c81d2151a02aecb91/original/decoding-lusichelins-a-e-an-in-depth-look-at-the-metallophores-of-lusitaniella-coriacea-lege-07167-structure-production-and-functionality.pdf |
624d6682855ee51c8de388a9 | 10.26434/chemrxiv-2022-j625s | Application of quantum chemical topology force field FFLUX
to condensed matter simulations: liquid water | We present here the first application of the quantum chemical topology force field FFLUX to condensed
matter simulations. FFLUX offers many‐body potential energy surfaces learnt exclusively from ab initio
data using Gaussian process regression. FFLUX also includes high‐rank, polarisable multipole moments
(up to quadrupole moments in this work) that are learnt from the same ab initio calculations as the
potential energy surfaces. Many‐body effects (where a body is an atom) and polarisation are captured by
the machine learning models. The choice to use machine learning in this way allows the force field’s
representation of reality to be improved (e.g. by including higher order many‐body effects) with no
detriment to the computational scaling of the code. In this manner, FFLUX is inherently future‐proof. The
“plug and play" nature of the machine learning models also ensures that FFLUX can be applied to any
system of interest, not just liquid water. In this work we study liquid water across a range of temperatures
and compare the predicted bulk properties to experiment as well as other state‐of‐the‐art force fields
AMOEBA(+CF), HIPPO, MB‐Pol and SIBFA21. We find that FFLUX finds a place amongst these. | Paul Popelier; Ben Symons | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624d6682855ee51c8de388a9/original/application-of-quantum-chemical-topology-force-field-fflux-to-condensed-matter-simulations-liquid-water.pdf |
66955fb65101a2ffa877edb4 | 10.26434/chemrxiv-2024-v338f | Biomimetic Total Synthesis of Lappaceolides A and B | A two-step total synthesis of lappaceolides A and B is achieved using a biomimetic vinylogous-Michael–oxa-Michael domino reaction. The domino reaction proceeds with Cs2CO3 in 1,2-DCE at elevated temperatures and requires careful kinetic control. The total synthesis provides further proof to the biosynthetic hypothesis of lappaceolides as being dimers of the natural product siphonodin. | Rajanish Pallerla; Jenna Hakola; Leevi Härkönen; Juha Siitonen | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66955fb65101a2ffa877edb4/original/biomimetic-total-synthesis-of-lappaceolides-a-and-b.pdf |
60c7426d469df47318f42fb4 | 10.26434/chemrxiv.8273654.v1 | Hypergolic Triggers as Cocrystal Formers: Cocrystallization for Creating New Hypergolic Materials with Tunable Energy Content | We demonstrate a cocrystal-based strategy to create new solid hypergols, i.e. materials exhibiting spontaneous ignition in contact with an oxidant, in which the energy content and density of the material can be changed without affecting the ignition delay. Using an imidazole-substituted decaborane as a hypergolic "trigger" component, in combination with energy-rich but non-hypergolic nitrobenzene, provides a hypergolic cocrystal with an ultrashort ignition delay, composed of hypergolic and fuel-containing domains.<br /> | Hatem M. Titi; Mihails Arhangelskis; Giovanni Rachiero; Tomislav Friscic; Robin Rogers | Supramolecular Chemistry (Org.); Fuels - Materials; Solid State Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426d469df47318f42fb4/original/hypergolic-triggers-as-cocrystal-formers-cocrystallization-for-creating-new-hypergolic-materials-with-tunable-energy-content.pdf |
64d26de769bfb8925a975e60 | 10.26434/chemrxiv-2023-11vqb | Fitting q-Gaussians onto Anatase TiO2 Raman Bands | In previous studies, we used the Tsallis q-Gaussian functions for the analysis of Raman spectra, providing several successful examples. Here we apply q-Gaussians to anatase TiO2 Raman spectra from literature, and from RRUFF and ROD databases. We will discuss, in particular, the Raman band about 515 cm−1, and its decomposition in A1g and B1g modes. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d26de769bfb8925a975e60/original/fitting-q-gaussians-onto-anatase-ti-o2-raman-bands.pdf |
62c10e5852acb774027c6129 | 10.26434/chemrxiv-2022-q97g5 | Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: II. Regression and Dielectric Constant | End-point free energy calculations as a powerful tool have been widely applied in protein-ligand and protein-protein interactions. It is often recognized that these end-point techniques serve as an option of intermediate accuracy and computational cost compared with more rigorous statistical mechanic models (e.g., alchemical transformation) and coarser molecular docking. However, it is observed that this intermediate level of accuracy does not hold in relatively simple and prototypical host-guest systems. Specifically, in our previous work investigating a set of carboxylated-pillar[6]arene host-guest complexes, end-point methods provide free energy estimates deviating significantly from the experimental reference, and the rank of binding affinities is also incorrectly computed. These observations suggest the unsuitability and inapplicability of standard end-point free energy techniques in host-guest systems, and alteration and development are required to make them practically usable. In this work, we consider two ways to improve the performance of end-point techniques. The first one is the PBSA_E regression that varies the weights of different free energy terms in the end-point calculation procedure, while the second one is considering the interior dielectric constant as an additional variable in the end-point equation. By detailed investigation of the calculation procedure and the simulation outcome, we prove that these two treatments (i.e., regression and dielectric constant) are manipulating the end-point equation in a somehow similar way, i.e., weakening the electrostatic contribution and strengthening the non-polar terms, although there are still many detailed differences between these two methods. With the trained end-point scheme, the RMSE of the computed affinities is improved from the standard ~12 kcal/mol to ~2.4 kcal/mol, which is comparable to another altered end-point method (ELIE) trained with system-specific data. This phenomenon along with the extremely efficient optimized-structure computation procedure suggests the regression (i.e., PBSA_E as well as its GBSA_E extension) as a practically applicable solution that brings end-point methods back into the library of usable tools for host-guest binding. However, the dielectric-constant-variable scheme cannot effectively minimize the experiment-calculation discrepancy for absolute binding affinities, but is able to improve the calculation of affinity ranks. This phenomenon is somehow different from the protein-ligand case and suggests the difference between host-guest and biomacromolecular (protein-ligand and protein-protein) cases. Therefore, the spectrum of tools usable in protein-ligand cases could be unsuitable for host-guest binding, and numerical validations are necessary to screen out really workable solutions in these ‘prototypical’ situations. | Xiao Liu; Lei Zheng; Yalong Cong; Zhihao Gong; Zhixiang Yin; John Zhang; Zhirong Liu; Zhaoxi Sun | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c10e5852acb774027c6129/original/comprehensive-evaluation-of-end-point-free-energy-techniques-in-carboxylated-pillar-6-arene-host-guest-binding-ii-regression-and-dielectric-constant.pdf |
60c750e5567dfef907ec5932 | 10.26434/chemrxiv.13095764.v1 | Synthesis and Preclinical Evaluation of [18F]PF04217903, a Selective MET PET Tracer | <p>The
tyrosine kinase MET (hepatocyte growth factor receptor)
is abnormally activated in a wide range of cancers and is often correlated with
a poor prognosis. Precision medicine with positron emission tomography (PET)
can potentially aid in the assessment of tumor biochemistry and heterogeneity,
which can prompt the selection of the most effective therapeutic regimes. The selective
MET inhibitor PF04217903 (<b>1</b>) formed
the basis for a bioisosteric replacement to the deoxyfluorinated analogue [<sup>18</sup>F]<b>2</b>, intended as a PET tracer for MET. [<sup>18</sup>F]<b>2 </b>could be synthesized with a “hydrous
fluoroethylation” protocol in 6.3 ± 2.6% radiochemical yield and a molar
activity of >50 GBq/µmol. <i>In vitro</i>
autoradiography indicated that [<sup>18</sup>F]<b>2 </b>specifically binds to MET in PC3 tumor tissue, and <i>in vivo</i> biodistribution in mice showed
predominantly a hepatobiliary excretion along with a low retention of
radiotracer in other organs. </p> | Vegard Torp Lien; Emily Hauge; Syed Nuruddin; Jo Klaveness; Dag Erlend Olberg | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e5567dfef907ec5932/original/synthesis-and-preclinical-evaluation-of-18f-pf04217903-a-selective-met-pet-tracer.pdf |
64fb3a88b6ab98a41c15d44c | 10.26434/chemrxiv-2023-q6tf3 | Spontaneous formation of magnetic-plasmonic liposomes with tunable optical and magnetic properties | Magnetoplasmonic NPs have shown remarkable potential in hyperthermia, Magnetic Resonance Imaging (MRI), and Surface Enhanced Raman Scattering (SERS) imaging and diagnostics. However, despite their potential, effective clinical translation remains extremely limited due to a lack of fundamental knowledge about the biological response to these materials, and ongoing efforts seek to bridge the gap between nanomaterial production and effective application. To overcome these hurdles, the combination of inorganic NPs with lipid membranes has emerged as a promising strategy for the biocompatibilization of nanomaterials, preserving the inherent properties of each component and exhibiting novel synergistic functionalities. In this study, we synthesize magnetic-plasmonic-liposome adducts via spontaneous self-assembly. The interaction between magnetic-plasmonic NPs and liposomes was addressed from a physicochemical point of view as a function of liposome composition and concentration. By combining Cryogenic Microscopy, UV-visible spectroscopy and Dynamic Light Scattering we demonstrated that the rigidity of the lipid membrane affects the aggregation of the NPs and the colloidal stability of the NPs-vesicle hybrids. The magnetic responsivity of the hybrids is enhanced as a consequence of the colocalization and crowding of NPs on the lipid membranes and can be finely modulated by varying the number of particles per vesicle. Overall, these results pave the way for the development of multifunctional materials with controlled magnetic-plasmonic properties for a variety of technological applications. | Jacopo Cardellini; Alessandro Surpi; Beatrice Muzzi; Valentina Pacciani; Claudia Innocenti; Claudio Sangregorio; Valentin Alek Dediu; Costanza Montis; Debora Berti | Physical Chemistry; Clusters; Self-Assembly | CC BY NC 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fb3a88b6ab98a41c15d44c/original/spontaneous-formation-of-magnetic-plasmonic-liposomes-with-tunable-optical-and-magnetic-properties.pdf |
60da00abfca4909a12c980ef | 10.26434/chemrxiv-2021-brv78 | A Simplified State Interaction for Matrix Product State Wave Functions | We present an approximation to the state-interaction approach for matrix product state (MPS) wave functions (MPSSI) in a non-orthogonal molecular orbital basis, first presented by Knecht et al. [J. Chem. Theory Comput., 2016, 28, 5881], that allows for a significant reduction of the computational cost without significantly compromising its accuracy. The approximation is well-suited if the molecular orbital basis is close to orthogonality, and its reliability may be estimated a-priori with a single numerical parameter. For an example of a platinum azide complex, our approximation offers up to 63-fold reduction in computational time compared to the original method for wavefunction overlaps and spin-orbit couplings, while still maintaining numerical accuracy. | Leon Freitag; Alberto Baiardi; Stefan Knecht; Leticia González | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60da00abfca4909a12c980ef/original/a-simplified-state-interaction-for-matrix-product-state-wave-functions.pdf |
61537c76ef08e6605e1c13a9 | 10.26434/chemrxiv-2021-h9ms2-v2 | Precise control of the degree and regioselectivity of functionalization in nitro- and amino-functionalized di(trispyrazolylborato)iron(II) spin crossover complexes | Di(trispyrazolylborato)iron(II) ([Tp2Fe]) complexes represent one of the most robust class of spin crossover complexes. Their stability renders them particularly suitable for integration in nanoscale devices, e.g. as sensors or information storage units. While prior studies of the functionalization of those derivatives have been focused on the electronic and steric effect of alkyl and -CF3 groups in position 3, a pyrazole exchange reaction between nitropyrazole and either trispyrazolylborate or its iron complex allows the regioselective installation of nitro substituents in positions 3, 4 and 5 of [Tp2Fe] complexes. The degree of substitution can be varied from 1 to 4 functionalized pyrazoles per complex. The amine functionalized analogues are accessed by reduction of the nitro analogues under hydrogen transfer conditions. With the exception of di- and tetra-3-NO2 substituted complexes, all derivatives display spin crossover properties in the solid state, with transition temperatures ranging from 180 to 380 K and showing different degree of abruptness, but no hysteresis. The Slichter-Drickamer model was used to extract empirical thermodynamic transition parameters, allowing a systematic investigation of the influence of stoichiometry, position, and electronic nature of the substitution on the magnetic properties of the complexes. Steric effects dominate for substitution in position 3, but electronic effects are significant for the other positions. | Chenyang Ma; Claire Besson | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Magnetism | CC BY NC 4.0 | CHEMRXIV | 2021-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61537c76ef08e6605e1c13a9/original/precise-control-of-the-degree-and-regioselectivity-of-functionalization-in-nitro-and-amino-functionalized-di-trispyrazolylborato-iron-ii-spin-crossover-complexes.pdf |
60c74416469df4057bf432a1 | 10.26434/chemrxiv.9741701.v1 | Crystal Engineering of Bi2WO6 to Polar Aurivillius-Phase Oxyhalides | The Aurivillius phases of complex bismuth oxides have attracted considerable attention due to their lattice polarization (ferroelectricity) and photocatalytic activity. We report a first-principles exploration of Bi<sub>2</sub>WO<sub>6</sub> and the replacement of W<sup>6+</sup> by pentavalent (Nb<sup>5+</sup>, Ta<sup>5+</sup>) and tetravalent (Ti<sup>4+</sup>, Sn<sup>4+</sup>) ions, with charge neutrality maintained by the formation of a mixed-anion oxyhalide sublattice. We find that Bi<sub>2</sub>SnO<sub>4</sub>F<sub>2</sub> is thermodynamically unstable, in contrast to Bi<sub>2</sub>TaO<sub>5</sub>F, Bi<sub>2</sub>NbO<sub>5</sub>F and Bi<sub>2</sub>TiO<sub>4</sub>F<sub>2</sub>. The electric dipoles introduced by chemical substitutions in the parent compound are found to suppress the spontaneous polarization from 61.55 μC/cm<sup>2</sup> to below 15.50 μC/cm<sup>2</sup>. Analysis of the trends in electronic structure, surface structure, and ionization potentials are reported. This family of materials can be further extended with control of layer thicknesses and choice of compensating halide species.<br /> | Kazuki Morita; Ji-Sang Park; Sunghyun Kim; Kenji Yasuoka; Aron Walsh | Theory - Inorganic; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74416469df4057bf432a1/original/crystal-engineering-of-bi2wo6-to-polar-aurivillius-phase-oxyhalides.pdf |
65a1e5bf66c1381729526179 | 10.26434/chemrxiv-2023-1qfw8-v2 | Advancing Material Property Prediction: Using Physics-Informed Machine Learning Models for Viscosity | In materials science, accurately computing properties like viscosity, melting point, and glass transition temperatures solely through physics-based models is challenging. Data-driven machine learning (ML) also poses challenges in constructing ML models, especially in the material science domain where data is limited. To address this, we integrate physics-informed descriptors from molecular dynamics (MD) simulations to enhance the accuracy and interpretability of ML models. Our current study focuses on accurately predicting viscosity in liquid systems using MD descriptors. In this work, we curated a comprehensive dataset of over 4,000 small organic molecules’ viscosities from scientific literature, publications, and online databases. This dataset enabled us to develop quantitative structure–property relationships (QSPR) consisting of descriptor-based and graph neural network models to predict temperature-dependent viscosities for a wide range of viscosities with considerable accuracy. The QSPR models reveal that including MD descriptors improves prediction accuracies of experimental viscosities, particularly at the small data set scale of fewer than a thousand data points. Furthermore, feature importance tools reveal that intermolecular interactions captured by MD descriptors are most important for accurate viscosity predictions. Finally, the QSPR models can accurately capture the inverse relationship between viscosity and temperature for six battery-relevant solvents, some of which were not included in the original data set. Our research highlights the effectiveness of incorporating MD descriptors into QSPR models, which leads to improved accuracy for properties that are difficult to predict when using physics-based models alone or when limited data is available. | Alex K. Chew; Matthew Sender; Zachary Kaplan; Anand Chandrasekaran; Jackson Chief Elk; Andrea R. Browning; H. Shaun Kwak; Mathew D. Halls; Mohammad Atif Faiz Afzal | Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Analytical Chemistry - General; Chemoinformatics; Fluid Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a1e5bf66c1381729526179/original/advancing-material-property-prediction-using-physics-informed-machine-learning-models-for-viscosity.pdf |
66d5cd0412ff75c3a12b0fa4 | 10.26434/chemrxiv-2024-zk6gr | Dynamic Proton Coupled Electron Transfer Quenching as Sensing Modality in Fluorescent Probes | Fluorescent off-on probes based on a modular design where an analyte sensitive PET moiety is attached to a fluorophore are extremely successful. Here we report a new modular fluorescence probe design switched by dynamic quenching due to proton coupled electron transfer (PCET) mediated by collision with weak bases in solution. The fluorescence lifetime of this probe directly report on the rate of deprotonation by the weak bases in the solution. We investigate the probe design, mechanism of response, and sensitivity to various abundant weak bases/metabolites including; acetate, gluta-mate, phosphate, valine, and amines. We find that this modular PCET based probe design, contrary to traditional PET probes, can work efficiently with a fluorescence lifetime readout providing a calibration free probe for weak bases. Upon further development we envision such dynamic PCET probes as sensitive tools for studies of cellular buffer systems and metabolite pools. | Rasmus K. Jakobsen; Stine G. Stenspil; Junsheng Chen; Bo Laursen | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d5cd0412ff75c3a12b0fa4/original/dynamic-proton-coupled-electron-transfer-quenching-as-sensing-modality-in-fluorescent-probes.pdf |
60c758c2bb8c1a54573dcabb | 10.26434/chemrxiv.14207252.v3 | Surfactant-free Aqueous Fabrication of Macroporous Silicone Monoliths for Flexible Thermal Insulation | Hydrophobic silicone macroporous materials prepared in an aqueous solution by the sol–gel method have been considered for various applications such as separation media, heat insulators, and liquid nitrogen adsorbents. In the conventional preparation process, surfactants are used to suppress phase separation to obtain a uniform bulk material. However, a large amount of solvent and time is required to remove them before drying, which hinders industrial-scale synthesis. By copolymerizing tetra-, tri-, and bifunctional organosilicon alkoxides in an aqueous acetic acid–urea solution, flexible macroporous silicone monoliths were successfully obtained. The marshmallow-like monoliths recovered their original shape even after 80 % uniaxial compression and significant bending and water repellency. The thermal conductivity of those materials was ~0.035 W m<sup>−1</sup> K<sup>−1</sup> and did not increase even under 60 % uniaxial compression. This characteristic property can be used for thermal insulation on surfaces with various shapes and in confined spaces under harsh conditions. | Gen Hayase | Elastic Materials; Hybrid Organic-Inorganic Materials; Thermal Conductors and Insulators | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c2bb8c1a54573dcabb/original/surfactant-free-aqueous-fabrication-of-macroporous-silicone-monoliths-for-flexible-thermal-insulation.pdf |
662117a2418a5379b01b05cc | 10.26434/chemrxiv-2024-0m62p-v2 | Aspirin-NHS Ester Mediated Acetylation of Lysine Residues in β-Conglycinin: Implications for Cancer Research in NF-κB | Post-translational modifications (PTMs) represent a dynamic and intricate layer of cellular regulation that significantly contributes to the diversification of protein functions (1). Among these modifications, lysine acetylation stands out as a crucial regulatory mechanism that modulates protein activities, subcellular localization, and interactions (2). This study focuses on expanding the role of lysine acetylation, a significant post-translational modification, within the nuclear factor-kappa B (NF-κB) transcription factor complex. NF-κB plays a crucial role in inflammation, immune responses, and cell survival, making it a pertinent target for cancer research (3). Dysregulation of NF-κB is implicated in various pathological conditions, emphasizing the need to explore lysine acetylation within this context. To perform the acetylation, we would a empt to use a common medication, Aspirin. Aspirin, or acetylsalicylic acid, is a widely studied non-steroidal anti-inflammatory drug (NSAID) that has been extensively used for its anti-inflammatory, analgesic, and antipyretic effects. In addition, the presence of an acetyl group on Aspirin results in a versatile molecule that can acetylate various proteins. (4). We synthesized Aspirin NHS ester (Aspirin-NHS) to capitalize on this versatility in acetylating biomolecules. This tailored approach allows for the selective targeting of lysine residues within proteins, offering a specific tool to examine the functional consequences of lysine acetylation within the NF-κB complex. For this study, a model protein system was used. We selected β-Conglycinin, a soy protein, that offers a pragmatic platform for investigating lysine acetylation within the NF-κB complex. β-Conglycinin is rich in lysine residues, similar to NF-κB, making it homologous to this line of inquiry (5). We can examine the theoretical considerations of lysine acetylation with practical experimental observations, providing a comprehensive understanding of the regulatory dynamics within the NF-κB complex. This research contributes not only to the expanding toolkit for precise protein acetylation modulation but also enhances our understanding of NF-κB's regulatory dynamics in the context of cancer, establishing a bridge between chemical synthesis and biological investigation. | Syon Schlecht; Emily Gunderson; Takara Aguilar | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662117a2418a5379b01b05cc/original/aspirin-nhs-ester-mediated-acetylation-of-lysine-residues-in-conglycinin-implications-for-cancer-research-in-nf-b.pdf |
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