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66a7ddc7c9c6a5c07a6c8ccb | 10.26434/chemrxiv-2024-2t7jc | Nylon Analogue Substrates Allow for Continuous Quantification of Polyamidase Activity in Nylon-Degrading Enzymes | Nylon-hydrolyzing enzymes have been of increased interest recently in the context of bioremediation. The aminohexanoate oligomer hydrolases (NylCs) are thus far the most promising biocatalysts identified to this end. Protein engineering has been used to increase the thermal stability of these enzymes, but relatively little work has been done to improve their catalytic activity, due in part to a lack of high-throughput assays. Herein we report the design, synthesis, and enzymatic hydrolysis of polyamide analogue substrates mimicking various nylon architectures. We observed hydrolysis of diamide analogues 2, 4, and 5 in a continuous and quantitative manner via a light-scattering assay, which is amenable to a high-throughput screen in 96-well plates. The reaction products were characterized by liquid chromatography-coupled mass spectrometry, revealing insight into the structural elements required for recognition of substrates by NylC enzymes. The assay may be performed in minutes at elevated temperatures, allowing for efficient screening of thermostable nylonase enzymes. The activity of the NylC enzymes towards substrate 2 correlated to their corresponding enzymatic hydrolysis of Nylon-6 film, indicating that these substrates are surrogates for bulk nylon hydrolysis. Finally, we demonstrate the applicability of this assay to cell lysate, further enabling protein engineering efforts. | Alana Rangaswamy; Francis Roy; Jeffrey Keillor | Biological and Medicinal Chemistry; Organic Chemistry; Polymer Science; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a7ddc7c9c6a5c07a6c8ccb/original/nylon-analogue-substrates-allow-for-continuous-quantification-of-polyamidase-activity-in-nylon-degrading-enzymes.pdf |
60c742f0f96a00817c2866e6 | 10.26434/chemrxiv.8856419.v1 | Acid Dissociation in (HX)n(H2O)n Clusters (X = F, Cl, Br, I; N = 2, 3) | The interactions between two or three hydrogen halide molecules and the same number of water moieties are investigated through a systematic exploration of the corresponding potential energy surfaces using a stochastic methodology in conjunction with density functional theory computations. Our results indicate that HF, the weakest acid in the series, is partially dissociated. Similarly, HCl, HBr, and HI undergo dissociation in the presence of three, two, and two water molecules, respectively. The decrease in the number of water molecules required for dissociation, when compared with clusters with one single HX molecule, suggests cooperative effects. Interestingly, the hydrogen-bridged bihalide anions (XHX<sup>-</sup>) are present in the global minimum of (HX)n(H2O)n<sub> </sub> clusters with X = Br, I and n = 2, 3.<br /> | Alba Vargas-Caamal; Eugenia Dzib; Filiberto Ortiz-Chi; Albeiro Restrepo; Gabriel Merino | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f0f96a00817c2866e6/original/acid-dissociation-in-hx-n-h2o-n-clusters-x-f-cl-br-i-n-2-3.pdf |
60c741eabb8c1af4e23da036 | 10.26434/chemrxiv.8181230.v1 | A New Tool for Validating Theoretically Derived Anisotropic Displacement Parameters with Experiment: Directionality of Prolate Displacement Ellipsoids | X-ray diffraction on crystalline solids provides the electron density in the unit cell, typically interpreted as atom types, fractional coordinates, and anisotropic displacement parameters (ADPs). Given the chemical composition, not only coordinates but also ADPs can be obtained from first-principles calculations. In order to validate the latter, we suggest comparing the direction of the maximum main axes for sufficiently anisotropic theoretical and experimental ellipsoids, in addition to their scalar properties. This new criterion provides additional insight: while the amplitude of motion is generally underestimated by the computationally inexpensive harmonic approximation, the relative orientation may still be in good agreement with the experimental findings. This approach can complement the already established scatter plot of main-axes components and the similarity index, and it is also chemically intuitive by giving a direct picture of the relative orientation of the ellipsoids.<br /> | Damian Mroz; Janine George; Marius Kremer; Ruimin Wang; Ullrich Englert; Richard Dronskowski | Computational Chemistry and Modeling; Theory - Computational; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741eabb8c1af4e23da036/original/a-new-tool-for-validating-theoretically-derived-anisotropic-displacement-parameters-with-experiment-directionality-of-prolate-displacement-ellipsoids.pdf |
6407337ccc600523a3cd2921 | 10.26434/chemrxiv-2023-bjmd1 | Incorporation of Tungsten or Cobalt into TaN Barrier
Layers Controls Morphology of Deposited Copper | Progress in semiconductor devices, which has enabled the information and communications technology explosion of
the 21st century, has been driven by Moore’s Law and the accompanying aggressive scaling of transistors. However,
it is now acknowledged that the currently used copper interconnects are becoming a bottleneck in sub-nm scaling.
Semiconductor devices require a diffusion barrier and a seed layer in the volume available to the interconnect metal.
This then limits the minimum size of the interconnect and copper suffers from a preference to form 3D islands which
are non-conducting rather than conducting films. Therefore there is a pressing need to either replace copper, which
has its own difficulties, or to reduce the volume taken up by the diffusion barrier and liner; ideally finding a single
material displaying both properties is needed. We have previously shown that incorporation of Ru into the surface
layer of TaN is a strong alternative to the usual TaN/Ta or TaN/Ru stacks. In this work we study other possible
metals that can be incorporated into TaN, namely Co and W, which are less expensive and critical than Ru and can
potentially outperform it. Our first principles density functional theory (DFT) results from static relaxations and ab initio Molecular Dynamics (aiMD) show that there are several compositions of both Co- and W-doped TaN which
should promote growth of 2D copper interconnects without compromising the barrier properties of TaN. With this
selection of materials it should be possible to design new experimental processes that promote downscaled copper
interconnects for the next generation of electronic devices. Additionally, our work presents an improved method
towards prediction of thin film morphology on a given substrate, which can be of use for a variety of materials
science applications. | Cara-Lena Nies; Michael Nolan | Theoretical and Computational Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6407337ccc600523a3cd2921/original/incorporation-of-tungsten-or-cobalt-into-ta-n-barrier-layers-controls-morphology-of-deposited-copper.pdf |
66e0244ccec5d6c142ac09ea | 10.26434/chemrxiv-2024-fvvlt | Structural analysis of four cyclic antimicrobial hexapeptides in aqueous solution and in micelles, towards membrane-mimicking nanodiscs | Cationic, antimicrobial peptides (AMPs) are abundantly present in nature as host-defensive peptides, forming the backbone of the natural defence of many organisms. Their primary interaction with bacterial membranes is thought to be a binding to the outer layer, followed by a disruption of the lipid membrane. Investigating the mode-of-action of AMPs is an ever-growing field, where a plethora of different biophysical experiments are used to investigate this. Here, we explore the experimental limitation in NMR spectroscopy as we migrate towards increasingly realistic but larger membrane model systems with the aim to scout which data we could realistically extract from AMPs interacting with self-aligning nanodiscs.
A set of cyclic hexapeptides were used as model compounds, in water, DMSO, and SDS micelles. The quality of isotropic and anisotropic NMR parameters decreased as the result of faster relaxation due to size and dynamics, as well as the need for water suppression and buffer salts. Chemical shifts, scalar couplings, NOE derived distances, and simulated annealing suggested that the backbone conformation of both peptides remained mostly rigid, forming two β-turns, while the sidechains remain flexible in all environments. The difference between Lys or Arg did not change the backbone conformation, even though the two peptides have different MIC concentrations, indicating that amino acid composition is more important than conformation for antimicrobial activity. Theoretical structures in an explicit lipid bilayer were simulated showing similar structures.
Pilot experiments on SMA-QA nanodiscs indicated that they are viable as membrane model for investigating the interaction between AMPs and lipid membranes. It was shown that signal can be obtained from bound peptide, but further investigations with isotopically labelled peptides are needed to extract relevant structural data under conditions where the nanodisc is not over-saturated by peptides.
| Fredrik G. Rylandsholm; Philip Rainsford; Monika Krupova; Tone Kristoffersen; Tonje Haugen; Bjørn Olav Brandsdal; John Sigurd Svendsen; Johan Isaksson | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e0244ccec5d6c142ac09ea/original/structural-analysis-of-four-cyclic-antimicrobial-hexapeptides-in-aqueous-solution-and-in-micelles-towards-membrane-mimicking-nanodiscs.pdf |
6421405c647e3dca9992f1da | 10.26434/chemrxiv-2023-sxqct | Impact of residence time distributions in reacting magnesium packed-beds on Grignard reagent formation – Pump-induced flow behaviour in non-reacting magnesium beds (part 1) | Grignard reagent formation in continuously operated magnesium packed-bed reactors can be influenced by finetuning the residence time distribution within the magnesium packing. By decreasing the magnesium turning size and increasing the packing density, more narrow residence time distributions and therefore improved Bodenstein numbers can be obtained. The utilized pump system and its induced flow behaviour also havean impact on the residence time distributions in packed-bed reactors. By using oscillatory flow rates instead of pulsation-free pumps, Bodenstein numbers within a magnesium filled reactor cartridge can be increased by 25 % for fine magnesium turnings and by 70 % for coarse magnesium turnings, resulting in minimized backmixing and approaching plug flow behaviour. | Eva Deitmann; Michael Maskos; Gabriele Menges-Flanagan; Dirk Ziegenbalg | Organic Chemistry; Organometallic Chemistry; Chemical Engineering and Industrial Chemistry; Process Chemistry; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421405c647e3dca9992f1da/original/impact-of-residence-time-distributions-in-reacting-magnesium-packed-beds-on-grignard-reagent-formation-pump-induced-flow-behaviour-in-non-reacting-magnesium-beds-part-1.pdf |
671985afd433919392fe1938 | 10.26434/chemrxiv-2024-nx480 | Ligand Substitution, Catalyst Activation, and Oxidative Addition Studies of a Stable Dialkyl Palladium Precatalyst | Palladium-catalyzed cross-coupling reactions are indispensable in chemical synthesis, but efficient in situ catalyst activation remains a persistent challenge. Current Pd(II) precatalysts often lead to inefficient catalyst activation, necessitating higher catalyst loadings and limiting selectivity. We investigated the ligand substitution and activation mechanism of the stable Pd(II) dialkyl complex (DMPDAB)Pd(CH2SiMe3)2 in real-time using mass spectrometric monitoring. The introduction of charged phosphine ligands enabled the detection of key catalytic intermediates and identification of off-cycle species. Our findings demonstrate a low activation energy for the ligand dissociation of the DMPDAB ligand and the reductive elimination of (Me3SiCH2)2 resulting in rapid formation of monoligated LPd(0) species, the active catalytic species for oxidative addition. These mechanistic insights offer a path towards developing more efficient and selective Pd-catalyzed processes, offering valuable guidance for the future design of precatalysts with improved performance. | Ian C. Chagunda; Antonia Kropp; David C. Leitch; J. Scott McIndoe | Catalysis; Analytical Chemistry; Organometallic Chemistry; Mass Spectrometry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671985afd433919392fe1938/original/ligand-substitution-catalyst-activation-and-oxidative-addition-studies-of-a-stable-dialkyl-palladium-precatalyst.pdf |
6720ee0b7be152b1d0281b68 | 10.26434/chemrxiv-2024-7n62r | Digital flow platform for the synthesis of high-quality multi-material perovskites | Perovskite materials have demonstrated great potential for a wide range of optoelectronic applications due to their exceptional electronic and optical properties. However, synthesising high-quality perovskite films remains a significant challenge, often hindered by batch-wise processes that suffer from limited control over reaction conditions, scalability and reproducibility. In this study, we present a novel approach for synthesising single-crystal perovskites with an optimised continuous-flow reactor. Our methodology utilises a 3D printed system that enables precise control over reactant concentrations, reaction times, and temperature profiles. The reaction chamber was designed and optimised by combining residence time distribution (RTD) studies and computational fluid dynamics (CFD) simulations. High-quality single-crystal perovskites with different formulations were obtained employing seeding and seedless conditions. The possibility of synthesising mixed halide single crystal perovskites with different compositions along its structure was demonstrated by simply shifting the feedstock solution during the crystallisation, demonstrating the versatility of this technology | Diego Iglesias; Cristopher Tinajero; Simone Marchetti; Jaume Luis Gomez; Raul Martinez Cuenca; Jose Fuentes Ballesteros; Clara Aranda; Alejandro Martínez Serra; Maria Asensio; Rafael Abargues; Pablo Boix; Marcileia Zanatta; Victor Sans | Materials Science; Chemical Engineering and Industrial Chemistry; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720ee0b7be152b1d0281b68/original/digital-flow-platform-for-the-synthesis-of-high-quality-multi-material-perovskites.pdf |
629642856057b1eb2b8bea25 | 10.26434/chemrxiv-2022-3dp7v | Automated Device for Multi-Stage Paper-Based Assays Enabled by an Electroosmotic Pumping Valve | This work presents the use of electroosmotic flow generation in porous media in combination with a hydrophobic air gap to create a controllable valve capable of operating in either finite dosing or continuous flow mode, enabling the implementation of multi-step biochemical assays on paper-based devices. A hierarchical superhydrophobic surface placed between two paper pads creates an air gap, keeping the valve nominally closed. To open the valve, a pair of electrodes are activated to generate electroosmotic pressure that overcomes the barrier. The study provides an experimentally validated model describing the governing parameters, and a detailed investigation of the closed valve stability. From these, a straightforward design for a compact and fully automated device is derived. The design is based on paper pads placed on printed circuit boards (PCB), equipped with heating and actuation electrodes and additional power and logic capabilities. The device is applied to the detection of SARS-CoV-2 sequences directly from raw saliva samples, using loop-mediated isothermal amplification (LAMP) requiring sample lysis followed by enzymatic deactivation and sample distribution to multiple amplification pads. Since PCB costs scale favorably with mass production, we believe that this approach could lead to low-cost diagnostic devices with the sensitivity of amplification methods. | Baruch Rofman; Rawi Naddaf; Maya Bar-Dolev; Tal Avi-Gefen; Nadav Ben-Assa; Naama Geva-Zatorsky; Moran Bercovici | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Apparatus; Biochemical Analysis; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629642856057b1eb2b8bea25/original/automated-device-for-multi-stage-paper-based-assays-enabled-by-an-electroosmotic-pumping-valve.pdf |
60c749fd702a9b828b18b20c | 10.26434/chemrxiv.12136002.v1 | Comparative Docking Analysis of Rational Drugs Against COVID-19 Main Protease | COVID-19, a new strain of coronavirus (CoV), was identified in Wuhan, China, in 2019. No specific therapies are available, and investigations regarding COVID-19 treatment are lacking. Crystallised COVID-19 main protease (Mpro), which is a potential drug target. The present study aimed to assess drugs found in literature as potential COVID-19 Mpro inhibitors, using a molecular docking study. Molecular docking was performed using Autodock 4.2, with the Lamarckian Genetic Algorithm, to analyse the probability of docking. The docking was cross-validated using Swiss Dock. COVID-19 Mpro was docked with several compounds, and docking was analysed by Biovia Discovery Studio 2020. Quinine and hydroxychloroquine were used as standards for comparison. The binding energies obtained from the docking of 6LU7, 2GTB with screened drugs viz., Quinine, Artesunate, Clotrimazol, Artemether, Quercetin, Mefloquine, ciprofloxacin, clindamycin, cipargamin, SJ-733 were in between -7.0 to -9.6 kcal/mol. On consideration of similar binding energy obtained from Autodock vina and SWISSDock and interaction residue pattern specifically (GLU 166,CYS 145, CYS44 and MET 49 residue) for SJ-733 & JPC-3210 may represent potential treatment options, and appeared to have the best potential to act as COVID-19 Mpro inhibitors. However, further research is necessary to investigate their potential medicinal use against CoV. | LALIT SAMANT; Vyomesh Javle | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749fd702a9b828b18b20c/original/comparative-docking-analysis-of-rational-drugs-against-covid-19-main-protease.pdf |
670d937312ff75c3a16e3d32 | 10.26434/chemrxiv-2024-1pwm3 | An Umpolung Mechanism for Oxidative Addition | In the presence of an appropriate base, electrophilic transition metal complexes can heterolytically activate nonpolar bonds H–H/H–X/X–X (X = SiR3, or CR3 as examples). In MeCN, the extreme electrophile {PtII(EtXantphos)2}2+ ({PtII}2+) appears to spontaneously heterolyze H2, yielding {H–PtII(EtXantphos)2}+ ({H–PtII}+) and a solvated proton. As the solution acidifies, a solvated proton can return to the hydride associated {H–PtII}+ to generate the oxidative addition product {(H)2PtIV(EtXantphos)2}2+ ({H–PtIV–H}2+). The net reaction – a heterolytic rebound – corresponds to an umpolung mecha-nism for oxidative addition, with the substrate acting as nucleophile. The rate constants for association of H2 and D2 to {PtII}2+ were measured as 8.4 and 8.5 ( 10-3 psi-1 hr-1), respectively. This minimal kinetic isotope effect (kH/kD = 0.99) is consistent with an intermediate σ-complex featuring negligible backbonding. Our observations comprise a framework for under-standing small molecule activation at the electrophilic extreme. | Nisha Rao; Jonathan Kuo | Organometallic Chemistry; Bond Activation; Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d937312ff75c3a16e3d32/original/an-umpolung-mechanism-for-oxidative-addition.pdf |
6284ea4287d01f6557e953c6 | 10.26434/chemrxiv-2022-83xg5 | Capturing sialyl-glycan via a site-selective installation of boronic acid repertoire in peptides | The broad spectrum of covalent binding modes and interactions has ‘magically’ popularized the submission of boronic acid-mediated chemistry into chemical biology and medicinal chemistry. Since borono peptide-based applications are emerging, simplistic methods for direct late-stage and site-selective installation of a versatile boronic acid (BA) repertoire onto peptides are desirable, given the limited chemical strategies. Here, we investigate the efficacy of thiol-ene click chemistry for installing functionally versatile BA derivatives on numerous bioactive, native peptides in a site-selective manner. The work emphasizes adaptable applications with BA-modified peptides, such as cyclization, conjugation, and biomolecule recognition. To this end, the click method enables us to nurture the sialyl-glycans binding aptitude of various BA-modified WGA peptides concurrently. The consequence reveals that the WGA peptide (in silico derived from wheat germ agglutinin), which shows a considerably low affinity to sialic acid, turns into a potent and selective binder in the attendance of a suitable BA probe to it. The synergistic recognition intensified the binding and profiling of sialyl-glycan on cancer cell lines compared with widely used lectin, Sambucus nigra. | Saurav Chatterjee; Arnab Chowdhury; Sheetanshu Saproo; Nitesh Mani; Srivatsava Naidu; Anupam Bandyopadhyay | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6284ea4287d01f6557e953c6/original/capturing-sialyl-glycan-via-a-site-selective-installation-of-boronic-acid-repertoire-in-peptides.pdf |
61211275dff0bacd54fd1b1d | 10.26434/chemrxiv-2021-1km1q | Long-lived Excited State in a Solubilized Graphene Nanoribbon | Graphene nanoribbons exhibit excellent light-absorbing properties, but often exhibit short excited-state lifetimes that prevent their applications in photocatalysis. Here, we report a long-lived charge-transfer triplet excited state in a well solubilized, chlorinated graphene nanoribbon (Cl-GNR) with edges modified by bipyrimidine (bpm) moieties. The photophysical behavior of Cl-GNR was observed and characterized by steady-state UV-vis absorption and emission spectroscopy, transient absorption spectroscopy on the ps-ms timescale, and density functional theory (DFT) calculations. Both the Cl-GNR and its monomeric subunit, chlorinated graphene quantum dot (Cl-GQD), were synthesized using bottom-up techniques to produce the H- analogs of the compounds followed by edge-chlorination to achieve soluble products. The absorption spectra of Cl-GQD and Cl-GNR appear in the UV-vis range with lowest-energy peaks at 375 and 600 nm, respectively. The excitons in Cl-GNR were found to exhibit charge-transfer character with the bpm edges serving as electron acceptors. DFT calculations indicate that the excitons are relatively localized, spreading over at most two monomeric units of the GNR. Transient absorption spectroscopy shows that singlet excited states of Cl-GQD and Cl-GNR undergo intersystem crossing with ~300 ps lifetime to form triplet state that lasts for 15.7 μs (Cl-GQD) and 106 μs (Cl-GNR). These properties, combined with the ability of bpm sites to coordinate transition metals, make Cl-GNRs promising light-harvesting motifs for photocatalytic applications. | Matthew Drummer; Ksenija Glusac; Lin Chen; Xiaosong Li; Amy Cordones; Andrew Valentine; Brian Phelan; Nikita Gupta; Ravindra Weerasooriya | Physical Chemistry; Energy; Photochemistry (Physical Chem.); Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61211275dff0bacd54fd1b1d/original/long-lived-excited-state-in-a-solubilized-graphene-nanoribbon.pdf |
60c749e4bb8c1a55f03daeee | 10.26434/chemrxiv.12123834.v1 | Synthesis of A Pentaarylcarbazole: Installation of Different Aryl Groups on Benzenoid Moiety | We report here a novel strategy for the synthesis of pentaarylcarbazole. In this method, an N-alkynylation of sulfonamide facilitated by an iodonium salt, and spontaneous cycloaddition of the resulting ynamide were crucial for the rapid construction of the central carbazole core. | Junichiro Yamaguchi; Takashi Asako; Shuhei Tanaka; Eisuke Ota | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749e4bb8c1a55f03daeee/original/synthesis-of-a-pentaarylcarbazole-installation-of-different-aryl-groups-on-benzenoid-moiety.pdf |
64c383b2658ec5f7e54fa64a | 10.26434/chemrxiv-2023-77wp7 | A self-healing crystal that repairs multiple cracks | We report self-healing in crystals during topochemical polymerization. Pursuing our interest in chiral crystalline polymers, we synthesized a squaramide-based monomer for topochemical azide-alkyne cycloaddition polymerization. The squaramide unit biased the molecular packing in the crystal and aligned the molecules in head-to-tail fashion as designed, positioning the azide and alkyne units of adjacent molecules at proximity in an arrangement suitable for their topochemical click reaction. This monomer undergoes single-crystal-to-single-crystal (SCSC) polymerization, spontaneously at room temperature, via regiospecific 1,3-dipolar cycloaddition, yielding the corresponding triazole-linked polymer, in a few days. When heated at 60 oC, the polymerization completes in 24 h, in a SCSC manner. Interestingly, upon continuous heating from rt to 110 oC, the monomer crystals develop multiple cracks and they self-heal immediately. Increase in heating rate leads to the formation of longer and wider cracks, which also heal instantaneously. The self-healed crystals retained their integrity and for the first time, crystal structure of a self-healed crystal could be analyzed by single-crystal X-ray diffraction. The quality of the self-healed crystal and its diffraction data are as good as the fully reacted crystals, at rt or 60 oC, without developing cracks. Rational analyses for cracking and self-healing are presented. | Kana Sureshan; Javed Pathan | Materials Science; Polymer Science; Granular Materials; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c383b2658ec5f7e54fa64a/original/a-self-healing-crystal-that-repairs-multiple-cracks.pdf |
676f690881d2151a0227db16 | 10.26434/chemrxiv-2025-nkbgv | Transmetalation for DNA-based Molecular Electronics | The rational design of molecular electronics remains a grand challenge of materials science. DNA nanotechnology has offered unmatched control over molecular geometry, but direct electronic functionalization has been a challenge. We present here a generalized method for tuning the local band structure of DNA using transmetalation in metal- mediated base pairs (mmDNA). We develop a method for time-resolved X-ray diffraction using self-assembling DNA crystals to establish the exchange of Ag+ and Hg2+ in T:T base pairs driven by pH exchange. Transmetalation is tracked over six reaction phases as crystal pH is changed from pH 8.0 to 11.0, and vice versa. We then perform a detailed computational analysis of the electronic configuration and transmission in the ensuing crystal structures. Our findings reveal a high conductance contrast in the lowest unoccupied molecular orbitals (LUMO) as a result of metalation. The ability to exchange single transition metal ions as a result of environmental stimuli heralds a means of modulating the conductance of DNA-based molecular electronics. In this way, we establish both a theoretical and experimental basis by which mmDNA can be leveraged to build rewritable memory devices and nanoelectronics. | Arpan De; Brandon Lu; Yoel P. Ohayon; Karol Woloszyn; William Livernois; Chu-fan Yang; Lara Perren; Chengde Mao; Antia S. Botana; Joshua Hihath; James W. Canary; Ruojie Sha; M.P. Anantram; Simon Vecchioni | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676f690881d2151a0227db16/original/transmetalation-for-dna-based-molecular-electronics.pdf |
60c74ae2337d6c7d27e2799f | 10.26434/chemrxiv.11946234.v3 | Anion Charge and Lattice Volume Maps for Searching Lithium Superionic Conductors | <p><a>The effects of anion charge and lattice volume (lithium-anion bond length) on lithium ion migration have been investigated by utilizing the density functional theory calculations combined with the anion sublattice models, e.g. <i>fcc</i>, <i>hcp</i> and <i>bcc</i>. It is found that the anion charge and lattice volume have great impacts on the activation energy barrier (E<sub>a</sub>) of lithium ion migration, which is validated by some reported sulfides. For the tetrahedrally occupied lithium, the less negative anion charge is, the lower the lithium ion migration barrier is likely to be. While for the octahedrally occupied lithium, the more negative anion charge is, the lower the lithium ion migration barrier is. There are opposite effects of anion charge on E<sub>a</sub> and optimum lattice volumes for minimum E<sub>a</sub> of lithium ion migration along the <i>Tet-Oct-Tet</i> and <i>Oct-Tet-Oct </i>pathways in the <i>hcp</i>-type sublattices. Based on the full understandings of anion sublattice model, general design strategies for developing lithium superionic conductors were proposed. Adjusting the electronegativity difference between the anion element and non-mobile cation element by selecting the most suitable non-mobile cation element without changing the crystal structure sublattice can achieve low E<sub>a</sub> for lithium ion migration. For the desired lithium superionic conductors with tetrahedrally occupied lithium ions, the fine non-mobile cation element should give preferences to those elements located at the right top of the periodic table of elements with large electronegativities. For the lithium superionic conductors with octahedrally occupied lithium ions, the fine non-mobile cation element should give preferences to the elements located at the left bottom of the periodic table with small electronegativities.</a><br /></p> | Zhenming Xu; Hong Zhu | Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae2337d6c7d27e2799f/original/anion-charge-and-lattice-volume-maps-for-searching-lithium-superionic-conductors.pdf |
65258008bda59ceb9a46fbe3 | 10.26434/chemrxiv-2023-rvnn0 | Size-resolved identification and quantification of micro/nano-plastics in indoor air using pyrolysis gas chromatography-ion mobility mass spectrometry | Humans are exposed to differing levels of micro-/nanoplastics (MNPs) through inhalation, but few studies have attempted to measure <1 µm MNPs in air, in part due to a paucity of analytical methods. We developed an approach to identify and quantify MNPs in indoor air using a novel pyrolysis gas chromatographic cyclic ion mobility mass spectrometer (pyr-GCxcIMS). Four common plastic types were targeted for identification, namely (polystyrene (PS), polyethylene (PE), polypropylene (PP), and polymethyl methacrylate (PMMA). The method was applied to size-resolved particulate (56 nm-18µm) collected from two different indoor environments using a Micro-Orifice Uniform Deposit Impactors (MOUDI) model 110 cascade impactor. Comprehensive two-dimensional separation by GCxcIMS also enabled the retrospective analysis of other polymers and plastic additives. The mean concentrations of MNP particles with diameters <10 µm and <2.5 µm in the laboratory were 47 ± 5 and 27 ± 4 µg/m3 respectively. In the private residence, the concentrations were 24 ± 3 and 16 ± 2 µg/m3. PS was the most abundant MNP type in both locations. Approximately 57-67% of MNPs were characterized by particle diameters <2.5 µm, and 50-60% of the total particulate matter in the private residence was plastic. Non-targeted screening revealed the presence of plastic additives, such as TDCPP (Tris(1,3-dichloro-2-propyl)phosphate) whose abundance correlated with that of polyurethane (PU). This is consistent with their use as flame retardants in PU-based upholstered furniture and building insulation. This study provides evidence of exposure to MNPs which constitute over half of PM2.5 indoors and underlines the need for further study of this route of exposure to MNPs and the plastics additives carried with them. | Mahin Hashemihedeshi; Ethan Haywood; Daniel Gatch; Liisa Jantunen; Paul Helm; Miriam Diamond; Frank Dorman; Lindsay Cahill; Karl Jobst | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65258008bda59ceb9a46fbe3/original/size-resolved-identification-and-quantification-of-micro-nano-plastics-in-indoor-air-using-pyrolysis-gas-chromatography-ion-mobility-mass-spectrometry.pdf |
60c74a7b702a9b48ad18b292 | 10.26434/chemrxiv.12210845.v1 | In-Silico Drug Repurposing for Targeting SARS-CoV-2 Mpro | <p>COVID-19, caused by novel coronavirus or
SARS-CoV-2, is a viral disease which has infected millions worldwide.
Considering the urgent need of the drug for fighting against this infectious
disease, we performed in-silico drug repurposing. The main protease (M<sup>pro</sup>)
is one of the best characterized drug targets among coronaviruses, therefore,
this was screened for already known drugs, including chemical constituents of
Ayurvedic drugs, using docking and MD simulation. The results suggest EGCG,
withaferin A and artesunate may act as potential inhibitors of the main protease
(M<sup>pro</sup>).</p> | Shilpa Sharma; Shashank Deep | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a7b702a9b48ad18b292/original/in-silico-drug-repurposing-for-targeting-sars-co-v-2-mpro.pdf |
60c74997469df49c1ef43c06 | 10.26434/chemrxiv.12081999.v1 | Controlling Intramolecular Interactions in the Design of Selective, High-Affinity, Ligands for the CREBBP Bromodomain | <p>CREBBP (CBP or KAT3A) and its paralogue P300 (also KAT3B) are lysine acetyltransferases (KATs) that are essential for human development. They each comprise ten domains through which they interact with over 400 proteins, making them important transcriptional co-activators, and key nodes in the human protein-protein interactome. The bromodomain of CREBBP and P300 enables binding of acetylated lysine residues from histones, and a number of other important proteins, including p53, p73, E2F and GATA1. Here we report work to develop a high affinity, small molecule, ligand for the CREBBP and P300 bromodomains [(−)-OXFBD05] that shows >100-fold selectivity over the BET bromodomains. Key to the development of (−)-OXFBD05 were fundamental studies on molecular conformation in solution and when bound to the CREBBP bromodomain. In particular, the effect of an intramolecular hydrogen bond on solution state conformation, and use of an amide bioisostere, enabled the development of (−)-OXFBD05. Initial cellular studies using this ligand demonstrate that inhibition of the CREBBP/P300 bromodomain in HCT116 colon cancer cells results in lowered levels of c-Myc, and a modest but repeatable reduction in H3K18 acetylation. In hypoxia (<0.1% O<sub>2</sub>), inhibition of the CREBBP/P300 bromodomain results in enhanced stabilization of HIF-1α. This presents an opportunity for modulating proteins that are affected by HIF-1α levels, including ACE2, which mediates SARS-CoV-2 infection of human cells.</p> | Michael Brand; James Clayton; Mustafa Moroglu; Matthias Schiedel; Sarah Picaud; Joseph Bluck; Anna Skwarska; Anthony Chan; Corentine Laurin; Amy Scorah; Larissa See; Timothy Rooney; Oleg Fedorov; Gabriella Perell; Prakriti Kalra; Wilian Cortopassi; Kirsten Christensen; Richard Cooper; Robert Paton; William Pomerantz; Philip Biggin; Ester M. Hammond; Panagis Filippakopoulos; Stuart Conway | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74997469df49c1ef43c06/original/controlling-intramolecular-interactions-in-the-design-of-selective-high-affinity-ligands-for-the-crebbp-bromodomain.pdf |
627ce9ea70876755c6500621 | 10.26434/chemrxiv-2022-5d45c | Advanced materials engineering in historical gypsum plaster formulations | We show how historical gypsum plaster preparation methods affect the microstructure and the nanoscale hydrophilic properties of the final stucco materials. We reproduced a traditional Persian recipe (Gach-e Koshteh, ~14th c. AD), which involves a continuous mechanical treatment during plaster hydration. The Koshteh samples were compared with a lab-replicated historical recipe from Renaissance Italy (Gesso Sottile, ~15th c. AD), and contemporary plaster. The Iranian recipe induces the formation of gypsum platelets displaying preferential orientation in the plaster bulk. In contrast, the Italian and regular plasters comprise a typical needle-like morphology of gypsum crystals. The platelets in Koshteh expose the hydrophilic {010} face of gypsum in a much more pronounced manner than needles. Consequently, the Iranian plaster exhibits enhanced wettability, enabling their direct use for water-based decoration purposes without mixing it with any binder material, as is the case for Sottile. Contrary, the preparation of Sottile promotes the exposure of the more hydrophobic gypsum faces conferring a more water repelling character to this type of plaster. These observations highlight the development of advanced functional plaster materials already during the pre-modern era.
| Moslem Mishmastnehi; Alexander Van Driessche; Glen Smales; Alicia Moya; Tomasz Stawski | Materials Science; Chemical Engineering and Industrial Chemistry; Geological Materials; Materials Processing; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627ce9ea70876755c6500621/original/advanced-materials-engineering-in-historical-gypsum-plaster-formulations.pdf |
60c73f5b337d6c0b4ce26506 | 10.26434/chemrxiv.7314779.v1 | Luminescent Water Dispersible Microporous Polymeric Nanospheres | <p>Water-dispersible porous polymeric dispersions (PPDs) have been
synthesised by reversible addition-fragmentation chain transfer mediated
polymerisation-induced self-assembly (RAFT-mediated PISA). The core-shell
particles posses a microporous core formed from divinylbenzene and
fumaronitrile while the outer polyethylene glycol shell enables the particles
to be dispersible in a wide range of solvents. The PPD was shown to have a
heirarchical structure of small primary nanoparticles within larger, well-defined
aggregates of 220 nm as measured by electron microscopy and small angle x-ray
scattering (SAXS) and exhibited a surface area of 274 m<sup>2</sup>/g.
Furthermore these samples were found to be fluoresent and demonstrate selective
detection of harmful nitroaramatics in solution with extremly low limits of
detection, 169 ppb for picric acid, as well as possessing a CO<sub>2</sub>
uptake of 1.1 mmol/g at 273 K.</p> | Alex James; Matthew Derry; Jennifer Train; Robert Dawson | Core-Shell Materials; Organic Polymers; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5b337d6c0b4ce26506/original/luminescent-water-dispersible-microporous-polymeric-nanospheres.pdf |
679d7dddfa469535b99dcb65 | 10.26434/chemrxiv-2024-dmm7x-v2 | X-ray Spectroscopy Characterization of Electronic Structure and Metal-Metal Bonding in Dicobalt Complexes | Developing multimetallic complexes with tunable metal-metal interactions has long been a target of synthetic inorganic chemistry efforts, due to the unique and desirable properties that such compounds can exhibit. However, understanding the relationship between metal-metal bonding and chemical properties in multimetallic compounds is challenging due to system-dependent factors that can influence metal-metal and metal-ligand interactions including ligand identity, coordination geometry, and metal-metal distance. In this work we apply a combination of X-ray absorption and emission spectroscopy and quantum chemical calculations to describe the electronic structure and bonding properties in a series of dicobalt complexes supported by expanded pincer PNNP ligands. The compounds with silane ligands and a pseudo-octahedral coordination geometry exhibit Co-Co σ and multicentered bonding character, which we characterize from both the occupied and vacant perspectives via their strong contributions to the Co K-edge X-ray emission and absorption spectra, respectively. In contrast, the dicobalt complexes with a pseudo-tetrahedral coordination environment do not exhibit Co-Co bonding, due to symmetry constraints on orbital overlap and the 3d orbital occupancies of Co2+ ions in a tetrahedral ligand field. We extend the spectroscopically driven insights to theoretical evaluation of related dicobalt complexes with silane and hydride ligands to explain the presence or absence of a Co-Co bond in these species based on ligand coordination and symmetry arguments. This work highlights how fundamental insights into electronic structure and bonding through X-ray spectroscopy uncover important factors governing metal-metal interactions and guide the rational design of multimetallic complexes with tunable metal-metal bonds. | Arun Asundi; Roel Bienenmann; Daniel Broere; Ritimukta Sarangi | Theoretical and Computational Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Spectroscopy (Organomet.); Theory - Organometallic | CC BY 4.0 | CHEMRXIV | 2025-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679d7dddfa469535b99dcb65/original/x-ray-spectroscopy-characterization-of-electronic-structure-and-metal-metal-bonding-in-dicobalt-complexes.pdf |
60c75781f96a008f3a288c9c | 10.26434/chemrxiv.14381087.v2 | Selective Electrosynthetic Hydrocarboxylation of alpha,beta-Unsaturated Olefins with Carbon Dioxide | <p>Electrosynthetic hydrocarboxylation of <i>alpha</i><i>,beta</i>-unsaturated olefins with excellent regioselectivity is reported. No sacrificial electrode is required and is thus amenable to a flow configuration. The products are purified by simple crystallisation. Synthesis of a precursor to ethosuximide, which contains an all-carbon quaternary centre, illustrates the potential of the process. Finally a robustness study has benchmarked the process for future users.</p> | Ahmed Sheta; Anas Alkayal; Andrei Malkov; Benjamin Buckley | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75781f96a008f3a288c9c/original/selective-electrosynthetic-hydrocarboxylation-of-alpha-beta-unsaturated-olefins-with-carbon-dioxide.pdf |
6709b42551558a15efd0269a | 10.26434/chemrxiv-2024-g5s95 | Screening of newly synthesized Ionic Liquids and Deep eutectic solvent for enhancing the activity and stability of fungal laccase: empowering kinetic parameters and long-term conservation | Ionic Liquids (ILs) and Deep Eutectic Solvents (DES) are currently with great interest due to their highly interesting physicochemical properties, it was studied throughout many chemical and biological approaches and it was used intensively in biocatalysis and biomedicine. In the present study, 10 newly synthesized ILs and 04 newly synthesized DES has been used to study their effect on laccase enzyme. Hence ILs and DES have been screened in conventional reaction buffered medium (25°C and pH 7.0) and using ABTS and DMP as substrates to study the catalytic ability and the stability of the enzyme. From 14 newly synthetized items, only three water-miscible ILs ([BMIM][Ac], [Chol][Ac], and [Chol][Prop]) and one DES ([Chol][Ac.Ox]) have shown interest for improving the enzyme activity and stability. Among them, the [BMIM][Ac] has shown impressive empowering power for the laccase activity (almost 20 folds enhancement versus control) however it was not efficient to protect the enzyme against high temperature or long conservation. The two Choline based ILs, [Chol][Ac] and [Chol][Prop], have allowed the increase of laccase activity with a rate of 1.7 folds and 7.8 folds, respectively and it was shown interesting properties to protect the enzyme against temperature and storage. Regarding the DES [Chol][Ac.Ox], it was improved the laccase at about 8.9 folds but this rate has not been stable along the experiment due to the high hydrophobic nature of the solution, it could be more useful when applied in high temperature. The four screened items in general improved the activity of the enzyme especially at pH7.0 and shown a great sensitivity against temperature. By kinetic studies versus [BMIM][Ac], it was demonstrated that the IL can improve the laccase activity by increasing the catalytic markers (Vm and Kcat), however a decrease of the affinity has been notified by Km decreasing, which testify that the interaction of the enzyme with ILs can affect the proteinic structure in aqueous medium. | Sihem Haj Kacem; Rafaela Silva; Andreia Rosatella; Carlos Afonso; Souheil Omar; Said Galai | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6709b42551558a15efd0269a/original/screening-of-newly-synthesized-ionic-liquids-and-deep-eutectic-solvent-for-enhancing-the-activity-and-stability-of-fungal-laccase-empowering-kinetic-parameters-and-long-term-conservation.pdf |
660581be9138d231618d603a | 10.26434/chemrxiv-2022-m8l33-v3 | Construction of balanced, chemically dissimilar training, validation and test sets for machine learning on molecular datasets | When preparing training, validation and test sets for machine learning on molecular datasets, it is desirable to combine two requirements: 1) robustness, i.e. making a test set that is chemically dissimilar from the training set; 2) data balance, i.e. ensuring that the proportion of data points and the distribution of data labels (categorical) / data values (continuous) are as homogeneous as possible among the sets, for each individual property to model, while partitioning the overall set of compounds as required. Recent literature shows that meeting both these requirements simultaneously is sometimes very difficult. This is especially true for multi-task learning, but also for single-task learning if one aims to balance the distribution of data labels or values, too. In this work we present a method that resolves this issue by first carrying out a chemistry-guided clustering of the initial dataset to ensure the separation of chemical matter, and subsequently applying linear programming to select the lists of clusters that – once assembled into the final sets – result in the best possible data balance. | Giovanni A. Tricarico; Johan Hofmans; Eelke B. Lenselink; Miriam López-Ramos; Marie-Pierre Dréanic; Pieter F. W. Stouten | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660581be9138d231618d603a/original/construction-of-balanced-chemically-dissimilar-training-validation-and-test-sets-for-machine-learning-on-molecular-datasets.pdf |
633bc74b0e3c6a382432cc48 | 10.26434/chemrxiv-2022-s8hz2-v4 | Stacked Antiaromaticity in the π-Congested Space Between the Aromatic Rings in the Anthracene Dimer | Substance containing two π-congested aromatic systems are attractive targets in synthetic studies as well as efforts designed to explore the unique properties that originate from π-congestion. Since the time of the computational studies by Schleyer and Warner, the concept of stacked aromaticity created by the encounter of two antiaromatic rings has received much attention. In contrast, questions about what happens when two aromatic rings are closely stacked have remained unanswered. To the best of our knowledge, only one computational study has been performed by Herges, the results of which suggest that [2.2]paracyclophane, possessing short distance (<3.00 Å) between two aromatic ring planes, has a paratropic ring current between two the benzene rings. This observation is consistent with the conclusion that stacked antiaromaticity exists within the π-congested space between aromatic rings. Herein, we investigated the antiaromaticity of highly π-congested anthracene dimers using anthracenophane, which possesses a short inter-plane carbon-carbon distance of ca. 2.80 Å. The absorption spectrum of this substance contains a weak broad band from 450 to 550 nm that is attributed from HOMO-LUMO transition. These properties exist in planar cyclooctatetraene derivatives that having 8π-electron antiaromaticity. The results of nucleus-independent chemical shift and anisotropy of the induced current density calculations indicate that relatively weak antiaromatic character exists between the central six-membered rings of the two anthracene moieties in anthracenophane. In addition, an attempt to enhance the stacked antiaromaticity of anthracenophane using pressure to enhance π-congestion using was unsuccessful. | Tomohiko Nishiuchi; Yuta Makihara; Ryohei Kishi; Hiroyasu Sato; Takashi Kubo | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633bc74b0e3c6a382432cc48/original/stacked-antiaromaticity-in-the-congested-space-between-the-aromatic-rings-in-the-anthracene-dimer.pdf |
657e8f2c9138d23161d80fb9 | 10.26434/chemrxiv-2022-c98gc-v2 | A Machine Learning Based Approach to Reaction Rate Estimation | Chemical kinetic models are vital to accurately predicting phenomena in a wide variety of fields from combustion to atmospheric chemistry to electrochemistry. However, building an accurate chemical kinetic model requires the efficient and accurate estimation of many reaction rate coefficients for many reaction classes with highly variable amounts of available training data. Current techniques for fast automatic rate estimation tend to be poorly optimized and tedious to maintain and extend. We have developed a machine learning algorithm for automatically training subgraph isomorphic decision trees (SIDT) to predict rate coefficients for arbitrary reaction types. This method is fully automatic, scalable to virtually any dataset size, human readable, can incorporate qualitative chemical knowledge from experts and provides detailed uncertainty information for estimates. The accuracy of the algorithm is tested against the state of the art rate rules scheme in the RMG-database for five selected reaction families. The SIDT method is shown to significantly improve estimation accuracy across all reaction families and considered statistics. The estimator uncertainty estimates are validated against actual errors. | Matthew S. Johnson; William H. Green | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657e8f2c9138d23161d80fb9/original/a-machine-learning-based-approach-to-reaction-rate-estimation.pdf |
60c742f5ee301c0b5fc78f34 | 10.26434/chemrxiv.8868476.v1 | The Effects of Benzene Substituents and Intermediate Linkage on Local Anesthetic Effectiveness | <p> There are many experimental studies on the effectiveness of clinically effective local anesthetics (LA). Although an atomic analysis of LAs would contribute to understanding the factors that influence their effectiveness, there have been no theoretical studies performed thus far. Previous prominent papers in the field have examined the aromatic ring and amine terminal of LAs in great detail. In this paper, I establish which type of intermediate linkage – ester or amide – lends to a relatively greater effectiveness. I also elucidate the extent to which substitutions on the LA’s benzene ring differentially influence amino esters’ and amino amides’ relative effectiveness. Using novel structure-based drug design (SBDD) techniques, I observed that LA effectiveness is influenced more by benzene ring substitutions and, to a lesser degree, by the type of intermediate linkage.</p><div><br /></div> | Vikas Bommineni | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742f5ee301c0b5fc78f34/original/the-effects-of-benzene-substituents-and-intermediate-linkage-on-local-anesthetic-effectiveness.pdf |
6711901e12ff75c3a1bbf3fe | 10.26434/chemrxiv-2024-wltzg | Intervalence charge transfer in osmium(IV) tetra(ferrocenylaryl) complexes | Tetra(ferrocenylaryl) complexes comprising Os(IV) or sp3-hybridized C and Si central atoms are prepared through Negishi cross-coupling from brominated precursors and structurally characterized using single-crystal X-ray diffraction. Solution voltammetric studies reveal access to mixed-valence states is uniquely provided by the Os(IV) species, which we show through spectroelectrochemical studies exhibit near-IR features characteristic of intervalence charge transfer processes. Together, this work highlights the potential utility of such metal tetraaryl complexes as building blocks for extended, three-dimensional molecular materials with improved electronic properties. | Luana Zagami; Thomas Saal; Cynthia Avedian; Michael Inkpen | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Spectroscopy (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6711901e12ff75c3a1bbf3fe/original/intervalence-charge-transfer-in-osmium-iv-tetra-ferrocenylaryl-complexes.pdf |
60c73f14bdbb89ca20a37ef1 | 10.26434/chemrxiv.7187540.v1 | CANDOCK: Chemical Atomic Network Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials | Small molecule docking has proven to be invaluable for drug design and discovery. However, existing docking methods have several limitations, such as, ignoring interactions with essential components in the chemical environment of the binding pocket (e.g. cofactors, metal-ions, etc.), incomplete sampling of chemically relevant ligand conformational space, and they are unable to consistently correlate docking scores of the best binding pose with experimental binding affinities. We present CANDOCK, a novel docking algorithm that utilizes a hierarchical approach to reconstruct ligands from an atomic grid using graph theory and generalized statistical potential functions to sample chemical relevant ligand conformations. Our algorithm accounts for protein flexibility, solvent, metal ions and cofactors interactions in the binding pocket that are traditionally ignored by current methods. We evaluate the algorithm on the PDBbind and Astex proteins to show its ability to reproduce the binding mode of the ligands that is independent of the initial ligand conformation in these benchmarks. Finally, we identify the best selector and ranker potential functions, such that, the statistical score of best selected docked pose correlates with the experimental binding affinities of the ligands for any given protein target. Our results indicate that CANDOCK is a generalized flexible docking method that addresses several limitations of current docking methods by considering all interactions in the chemical environment of a binding pocket for correlating the best docked pose with biological activity. | Jonathan Fine; Janez Konc; Ram Samudralal; Gaurav Chopra | Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f14bdbb89ca20a37ef1/original/candock-chemical-atomic-network-based-hierarchical-flexible-docking-algorithm-using-generalized-statistical-potentials.pdf |
60c7472bbdbb897e24a38d2d | 10.26434/chemrxiv.9985334.v2 | Re-Programming Hydrogel Properties using a Fuel-driven Reaction Cycle | Nature uses catalysis as an indispensable tool to control assembly and reaction cycles in vital non-equilibrium supramolecular processes. For instance, enzymatic methionine oxidation regulates actin (dis)assembly, and catalytic guanosine triphosphate hydrolysis is found in tubulin (dis)assembly. Here we present a completely artificial reaction cycle which is driven by a chemical fuel that is catalytically obtained from a ‘pre-fuel’. The reaction cycle controls the disassembly and re-assembly of a hydrogel, where the rate of pre-fuel turnover dictates the morphology as well as the mechanical properties. By adding additional fresh aliquots of fuel and removing waste, the hydrogels can be re-programmed time after time. Overall, we show how catalysis can control fuel generation to control reaction / assembly kinetics and materials properties in life-like non-equilibrium systems. | Nishant Singh; Bruno Lainer; Georges Formon; Serena De Piccoli; Thomas Hermans | Aggregates and Assemblies; Fibers; Fuels - Materials; Acid Catalysis; Chemical Kinetics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7472bbdbb897e24a38d2d/original/re-programming-hydrogel-properties-using-a-fuel-driven-reaction-cycle.pdf |
60c7494c842e65d66edb2cfc | 10.26434/chemrxiv.12047532.v1 | Pyclen Based Ln(III) Complexes as Highly Luminescent Bioprobes for in Vitro and in Vivo 1P and 2P Bioimaging Applications | Two pyclen based lanthanide chelators, <b>L<sup>4b</sup> </b>and <b>L<sup>4c</sup>, </b>bearing two specific picolinate 2P antennas
(tailor-made for each targeted metal) and one acetate arm arranged in a
dissymmetrical manner, have been synthesized to form, with the already
described ligand <b>L<sup>4a</sup>,</b> a
complete family of lanthanide luminescent bioprobes: [Eu<b>L<sup>4a</sup></b>], [Sm<b>L<sup>4a</sup></b>],
[Yb<b>L<sup>4b</sup></b>], [Tb<b>L<sup>4c</sup></b>] and [Dy<b>L<sup>4c</sup></b>]. Additionally,
symmetrically arranged regioisomer <b>L<sup>4a’</sup>
</b>was also synthesized as well as its [Eu<b>L<sup>4a’</sup></b>]
complex to highlight the astonishing positive impact of the dissymmetrical <i>N</i>-distribution of the functional
chelating arm. The investigation clearly shows the high performance of each
bioprobe, which, depending on the complexed lanthanide, could be used in
various applications. Each presents high brightness, quantum yields and lifetimes.
Staining of the complexes into living human breast cancer cells was observed.
In addition, <i>in vivo</i> 2P-microscopy
was performed for the first time on a living Zebrafish model with [Eu<b>L<sup>4a</sup></b>]. No apparent toxicity
was detected on the growth of the zebrafish and images of high quality were
obtained. | Nadège Hamon; Amandine Roux; Maryline Beyler; Jean-Christophe Mulatier; Chantal Andraud; Christophe Nguyen; Marie Maynadier; Nadir Bettache; Alain Duperray; Alexei Grichine; Sophie Brasselet; Magali Gary-Bobo; Olivier MAURY; Raphael Tripier | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.); Sensors; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494c842e65d66edb2cfc/original/pyclen-based-ln-iii-complexes-as-highly-luminescent-bioprobes-for-in-vitro-and-in-vivo-1p-and-2p-bioimaging-applications.pdf |
60c73f5ebb8c1ab28c3d9ac7 | 10.26434/chemrxiv.7172369.v2 | Canvass: A Crowd-Sourced, Natural Product Screening Library for Exploring Biological Space | Natural products and
their derivatives continue to be wellsprings of nascent therapeutic potential.
However, many laboratories have limited resources for biological evaluation, leaving
their previously isolated or synthesized compounds largely or completely untested.
To address this issue, the Canvass library of natural products was assembled,
in collaboration with academic and industry researchers, for quantitative high-throughput
screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization
of the library in terms of physicochemical properties, structural diversity,
and similarity to compounds in publicly available libraries indicates that the
Canvass library contains many structural elements in common with approved drugs.
The assay data generated were analyzed using a variety of quality control
metrics, and the resultant assay profiles were explored using statistical
methods, such as clustering and compound promiscuity analyses. Individual
compounds were then sorted by structural class and activity profiles. Differential
behavior based on these classifications, as well as noteworthy activities, are
outlined herein. One such highlight is the activity of (–)-2(<i>S</i>)-cathafoline,
which was found to stabilize calcium levels in the endoplasmic reticulum. The
workflow described here illustrates a pilot effort to broadly survey the
biological potential of natural products by utilizing the power of automation
and high-throughput screening. | Sara E. Kearney; Gergely Zahoránszky-Kőhalmi; Kyle R. Brimacombe; Mark J. Henderson; Caitlin Lynch; Tongan Zhao; Kanny K. Wan; Zina Itkin; Christopher Dillon; Min Shen; Dorian M. Cheff; Tobie D. Lee; Danielle Bougie; Ken Cheng; Nathan Coussens; Dorjbal Dorjsuren; Richard T. Eastman; Ruili Huang; Mike Iannotti; Surendra Karavadhi; Carleen Klumpp-Thomas; Jacob Roth; Srilatha Sakamuru; Wei Sun; Steven A. Titus; Adam Yasgar; Ya-Qin Zhang; Jinghua Zhao; Rodrigo B. Andrade; M. Kevin Brown; Noah Z. Burns; Jin K. Cha; Emily E. Mevers; Jon Clardy; Jason A. Clement; Peter A. Crooks; Gregory D. Cuny; Jake Ganor; Jesus Moreno; Lucas
A. Morrill; Elias Picazo; Robert B. Susick; Neil K. Garg; Brian C. Goess; Robert B. Grossman; Chambers
C. Hughes; Jeffrey N. Johnston; Madeleine M. Joullié; A. Douglas Kinghorn; David G.I. Kingston; Michael J. Krische; Ohyun Kwon; Thomas J. Maimone; Susruta Majumdar; Katherine N. Maloney; Enas Mohamed; Brian T. Murphy; Pavel Nagorny; David E. Olson; Larry E. Overman; Lauren E. Brown; John K. Snyder; John A. Porco, Jr.; Fatima Rivas; Samir A. Ross; Richmond Sarpong; Indrajeet Sharma; Jared T. Shaw; Zhengren Xu; Ben Shen; Wei Shi; Corey Stephenson; Alyssa L. Verano; Derek S. Tan; Yi Tang; Richard E. Taylor; Regan J. Thomson; David A. Vosburg; Jimmy Wu; William M. Wuest; Armen Zakarian; Yufeng Zhang; Tianjing Ren; Zhong Zuo; James Inglese; Sam Michael; Anton Simeonov; Wei Zheng; Paul Shinn; Ajit Jadhav; Matthew B. Boxer; Matthew D. Hall; Menghang Xia; Rajarshi Guha; Jason M. Rohde | Natural Products; Biochemistry; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5ebb8c1ab28c3d9ac7/original/canvass-a-crowd-sourced-natural-product-screening-library-for-exploring-biological-space.pdf |
60c74c06bdbb892d8ca396de | 10.26434/chemrxiv.12416303.v1 | Proteolysis-Targeting Chimeras (PROTACs) Based on Macrocyclic Tetrapeptides Selectively Degrade Class I Histone Deacetylases 1–3 | Histone deacetylases (HDACs) remove acetyl groups from histone proteins and are implicated in gene regulation. They have been recognized as drug targets for treatment of cancer and other human diseases and several inhibitors are already clinically used. Here, we report the design, synthesis, and cellular characterization of a proteolysis-targeting chimera (PROTAC) capable of selectively degrading class I HDACs 1–3 in cells. These novel chemotypes are based on potent and class I-selective macrocyclic tetrapeptide inhibitors, which were linked to thalidomide by modular synthesis, employing copper-catalyzed azide–alkyne “click” chemistry. In HEK293T cells, these conjugates lead to degradation of HDAC1–3 in a time- and concentration-dependent manner. Concomitant histone hyperacetylation without leading to cytotoxic effects was observed by western blot. These chemotypes enable the study of the biological roles of class I HDAC enzymes by short-term temporal deletion. Our compounds represent the first examples of degraders with demonstrated selectivity for class I HDACs 1–3. Importantly, this study highlights the utility of cyclic peptides as target-binding elements for PROTAC design in general. | Martin Roatsch; Anja Vogelmann; Daniel Herp; Manfred Jung; Christian Adam Olsen | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c06bdbb892d8ca396de/original/proteolysis-targeting-chimeras-prota-cs-based-on-macrocyclic-tetrapeptides-selectively-degrade-class-i-histone-deacetylases-1-3.pdf |
66827a0401103d79c59dd5b4 | 10.26434/chemrxiv-2024-21b1k-v3 | Application of the Adiabatic Connection Random Phase Approximation to Electron-Nucleus Hyperfine Coupling Constants | The electron-nucleus hyperfine coupling constant is a challenging property for density functional methods. For accurate results, hybrid functionals with a large amount of exact exchange are often needed and there is no clear "one-for-all" functional, which describes the hyperfine coupling interaction for a large set of nuclei. To alleviate this unfavorable situation, we apply the adiabatic connection random phase approximation (RPA) in its post-Kohn-Sham fashion to this property as a first test. For simplicity, only the Fermi-contact and spin--dipole terms are calculated within the non-relativistic and the scalar-relativistic exact two-component framework. This requires to solve a single coupled-perturbed Kohn-Sham equation to evaluate the relaxed density matrix, which comes with a modest increase in computational demands. RPA performs remarkably well and substantially improves upon its Kohn-Sham (KS) starting point while also reducing the dependence on the KS reference. For main-group systems, RPA outperforms global, range-separated, and local hybrid functionals—at similar computational costs. For transition-metal compounds and lanthanide complexes, a similar performance as for hybrid functionals is observed. In contrast, related post-Hartree-Fock methods such as Mølller-Plesset perturbation theory or CC2 perform worse than semilocal density functionals. | Florian Bruder; Florian Weigend; Yannick J. Franzke | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66827a0401103d79c59dd5b4/original/application-of-the-adiabatic-connection-random-phase-approximation-to-electron-nucleus-hyperfine-coupling-constants.pdf |
6763db526dde43c90899b8e2 | 10.26434/chemrxiv-2024-5dwkv | Unusual high fluorescence of a 7,7'-diazaisoindigo derivative: a photophysical study | 7,7'-Diazaisoindigos are π-conjugated compounds but with poor luminescence properties. Their poor luminescence is generally attributed to the twisting around the central C7−C7' bond in the excited state which favors non-radiative decay. We have found an unusual high fluorescence quantum yield (ΦF ≈ 15%) in a N,N‑Octyl-7,7′-diazaisoindigo derivative incorporating two triphenylamine (TPA) subunits at 5,5′-positions (called compound 12). There are very few examples of fluorescent 7,7'-diazaisoindigos have been reported and the emission mechanism is generally associated by the hindering of the rotation around the central C7−C7' bond. Unexpectedly, 12 also experiences a twisting around the central C7−C7' bond in the excited state but is highly emissive. The intense fluorescence emission of 12 was attributed to the coexistence of two TPA-7-azaoxindole subunits acting as two fluorophores into a single molecule. The fluorescence emission of 12 is also sensitive to the polarity of the solvent. The intramolecular charge transfer character of the excited state was studied combining spectroscopic and theoretical methods. | Mónica Moral; Rocío García; Andrés Garzón-Ruiz; Eva M. García Frutos | Physical Chemistry; Materials Science; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6763db526dde43c90899b8e2/original/unusual-high-fluorescence-of-a-7-7-diazaisoindigo-derivative-a-photophysical-study.pdf |
629f1b272e6269c3f07a518f | 10.26434/chemrxiv-2021-4z45w-v3 | Design of metal-organic assemblies via shape complementarity and conformational constraints in dual curvature ligands | While common in biological systems, building blocks with low symmetry and flexibility pose numerous problems for synthetic self-assembly such as the formation of isomers of assemblies that are usually difficult to distinguish and purify. We herein report a design and synthesis strategy relying on shape complementarity and conformational constraints in dual curvature ligands that effectively promotes high selectivity during self-assembly and self-sorting of metal-organic assemblies. Three aromatic amide-based ligands (L1-L3) with a central 1,8-diazatriptycene core were designed and used for self-assembly with Pd2+. While hundreds of stereoisomers based on the conformational flexibility around the amides and the unsymmetrical non-planar structure of the core are possible upon coordination with the metal, the constraints designed into the ligands direct the self-assembly towards only a single Pd2L4 cage (L1) or Pd4L8 double-walled metallomacrocycle (L2) structure, even in mixtures of the ligands. We further demonstrate that this structural approach and the modularity of the ligand synthesis affords ready access to the first deep endohedral functionalized double-walled Pd4L8 cavitands (L3). These results highlight the potential of this new design strategy and open the door to selectively functionalized cavity-based architectures for numerous applications. | Cui-Lian Liu; Eduard Bobylev; Brice Kauffmann; Koen Robeyns; Yann Garcia; Joost Reek; Michael Singleton | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629f1b272e6269c3f07a518f/original/design-of-metal-organic-assemblies-via-shape-complementarity-and-conformational-constraints-in-dual-curvature-ligands.pdf |
64c9331c658ec5f7e59164b5 | 10.26434/chemrxiv-2023-nn7jz-v2 | NMR and smFRET insights into fast protein motions and their relation to function | Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, while the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review we focus on the contribution of single-molecule FRET and NMR spectroscopies to the study of conformational dynamics. We describe briefly the state-of-the- art in each of each of these techniques and then point to their similarities and differences, as well as to the relative strengths and weaknesses of each. Several case studies in which the connection between fast conformational dynamics and slower function has been demonstrated are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies. | Paul Schanda; Gilad Haran | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c9331c658ec5f7e59164b5/original/nmr-and-sm-fret-insights-into-fast-protein-motions-and-their-relation-to-function.pdf |
60c73f1a4c891923c0ad1ee7 | 10.26434/chemrxiv.7234658.v1 | Oxidation States of Binary Oxides from Data Analytics of the Electronic Structure | <p>A connection between the oxidation state (OS) and Bader charge has been
missing so far. To our knowledge, all previous work tried to connect OS with
Bader charges only with few compounds. The aim of this work was to find a
dependency between OS and Bader charge, using <a>a large
number of compounds from an open database</a>. We show that a <a>correlation indeed exists between OSs and Bader charges</a>
using the simplest machine learning algorithm, linear regression. The
applicability of determining OS by Bader charges in mixed-valence compounds and
surfaces is considered.</p> | Sergei Posysaev; Olga Miroshnichenko; Matti Alatalo; Duy Le; Talat
S. Rahman | Materials Processing; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1a4c891923c0ad1ee7/original/oxidation-states-of-binary-oxides-from-data-analytics-of-the-electronic-structure.pdf |
66760a495101a2ffa82d71f9 | 10.26434/chemrxiv-2024-7km9r | A combined first-principles and data-driven computational framework to analyze the surface structure, composition, and stability of binary alloy catalysts | Pt-based bimetallic alloys are considerably more active than Pt for the oxygen reduction reaction (ORR). This increased activity has been attributed to weakening of the adsorption of ORR intermediates due to the presence of Pt “skins.” Density functional theory (DFT) calculations have, in turn, pointed to the importance of surface segregation energies and Pt leaching on the formation and stability of the skins on close-packed surfaces of Pt alloys. The generalizability of these insights across different chemical environments, surface compositions, and facets, however, remains a subject of active research and is the focus of this work. We present a generalized computational framework combining DFT calculations and data-driven methods to predict the stability of different Pt3X (X = Ni, Co, Fe, and Cu) alloy facets under vacuum conditions and in the presence of an electrochemical environment, wherein we analyze the combined effect of segregation, intrasurface phase separation, leaching, and surface oxidation as a function of electrode potential. The analysis reveals that a subtle interplay of these factors influences Pt skin formation and stability, with Pt segregation being a strong function of the surface structure, and continuous base metal dissolution being thermodynamically, although not always kinetically, favored at ORR-relevant voltages. | Gaurav Deshmukh; Pushkar Ghanekar; Jeffrey Greeley | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Electrocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66760a495101a2ffa82d71f9/original/a-combined-first-principles-and-data-driven-computational-framework-to-analyze-the-surface-structure-composition-and-stability-of-binary-alloy-catalysts.pdf |
60c748c69abda25b7ef8caed | 10.26434/chemrxiv.11965521.v1 | Enantioselective Intramolecular Allylic Substitution via Synergistic Palladium/Chiral Phosphoric Acid Catalysis: Insight into Stereoinduction through Statistical Modeling | The mode of asymmetric
induction in an enantioselective intramolecular allylic substitution reaction
catalyzed by a combination of palladium and a chiral phosphoric acid was
investigated by a combined experimental and statistical modeling approach. Experiments
to probe nonlinear effects, the reactivity of deuterium-labeled substrates, and
control experiments revealed that the chiral phosphate anion is involved in stereoinduction.
Using multivariable linear regression analysis, we identified that the presence
of multiple noncovalent interactions with the chiral environment of the phosphate
anion are integral to enantiocontrol in the transition state. The synthetic
protocol to form chiral pyrrolidines was further applied to the asymmetric
construction of C−O bonds
at fully-substituted carbon centers in the synthesis of chiral
2,2-disubstituted benzomorpholines. | Cheng-Che Tsai; Christopher Sandford; Tao Wu; Buyun Chen; Matthew S. Sigman; F. Dean Toste | Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748c69abda25b7ef8caed/original/enantioselective-intramolecular-allylic-substitution-via-synergistic-palladium-chiral-phosphoric-acid-catalysis-insight-into-stereoinduction-through-statistical-modeling.pdf |
6661b53f21291e5d1d33a38f | 10.26434/chemrxiv-2024-q81sk | Measuring Kinetics under Vibrational Strong Coupling: Testing for a Change in the Nucleophilicity of Water and Alcohols | Vibrational Strong Coupling (VSC) has been reported to change the rate of organic reactions. However, a lack of convenient and reliable methods to measure reaction kinetics under VSC makes it challenging to obtain mechanistic insight into its influence, hindering progress in the field. Here, we use recently developed fixed-width optical cavities to obtain large kinetic datasets under VSC with small errors (± 1-5%) in an operationally simple manner using UV-vis spectroscopy. The setup is used to test whether VSC changes a fundamental kinetic property of polar reactions, nucleophilicity, for water and alcohols, species commonly used in VSC-modified chemistry. We determined the rate constants for nucleophilic capture with a library of benzhydrilium ions as reference electrophiles with and without strong coupling of the nucleophile’s key vibrations. For all investigated combinations of electrophiles and nucleophiles, only minor changes in the observed rate constants of the reactions were observed, independently of the coupled bands. These results indicate that VSC does not substantially alter the nucleophilicity of water and alcohols, suggesting that polar reactions are modified through other, presently unknown mechanisms. Fixed-width cavities allow for convenient and reproducible UV-vis kinetics, facilitating mechanistic studies of VSC-modified chemistry. | Cyprien Muller; Robert J. Mayer; Maciej Piejko; Bianca Patrahau; Valentin Bauer; Joseph Moran | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Chemical Kinetics; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6661b53f21291e5d1d33a38f/original/measuring-kinetics-under-vibrational-strong-coupling-testing-for-a-change-in-the-nucleophilicity-of-water-and-alcohols.pdf |
65bbed08e9ebbb4db975d2a1 | 10.26434/chemrxiv-2024-933kk | Diversification of 2,2’-Bipyridines and Azaheterocycles via Nucleophilic Displacement of Trimethylaminiums | Bipyridines and azaarenes are an important class of ligands that impart unique and tunable properties to transition metal complexes and catalysts. While some derivatives are commercially available, noncommercial analogues are often challenging to prepare and purify. Herein we report a general nucleophilic aromatic substitution reaction that converts cationic trimethylaminated bipyridines into a series of functionalized bipyridines. Our method showcases a series of C–O, C–S, and C–F bond forming reactions as well as a selective monodemethylation that converts the electron-deficient trimethylaminium to an electron-rich dimethylamine. The approach was further applied to diversification of pharmaceuticals and natural products, and was applied to the total synthesis of Graveolinine and the preparation of Graveolinine derivatives. | Jenny Yang; Ryan King | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Ligands (Inorg.); Ligand Design; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bbed08e9ebbb4db975d2a1/original/diversification-of-2-2-bipyridines-and-azaheterocycles-via-nucleophilic-displacement-of-trimethylaminiums.pdf |
65a02573e9ebbb4db9f237b7 | 10.26434/chemrxiv-2024-dvr55 | The Effects of Irradiation on Structure and Leaching of Pure and Doped Thin-Film Ceria SIMFUEL Models Prepared via Polymer-Templated Deposition | When studying hazardous materials such as spent nuclear fuel (SNF), minimisation of sample volumes is essential, together with the use of chemically-similar surrogates where possible. For example, the bulk behaviour of urania (UO2) can be mimicked by appropriately-engineered thin films of sufficient thickness and inactive materials such as ceria (CeO2) can be used to study effects within radioactive systems used to fuel nuclear fission. However, thin film properties are sensitive to the preparative method, many of which require the use of highly toxic precursors and specialised apparatus e.g. chemical vapour deposition. To address this, we present the development of a flexible, tuneable, scalable method for the preparation of thin-film CeO2 SIMFUEL models with a thickness of ≈ 5 μm. The effects of γ irradiation (up to 100 kGy) and dopants including trivalent lanthanides (Ln3+) and simulant ε-particles on the structure and long-term leaching of these systems under SNF storage conditions are explored, alongside the context of this within further work. It was found that the sensitivity of CeO2 films to reduction upon irradiation, particularly in the presence of simulant ε-particles results in increased leaching of Ce (as CeIII), while trivalent lanthanides (Nd3+ and Eu3+) have minimal effect on Ce leaching. | Alistair F. Holdsworth; Zizhen Feng; Ruth Edge; John P. Waters; Alice M. Halman; David Collison; Kathryn George; Louise S. Natrajan; Melissa A. Denecke | Inorganic Chemistry; Energy; Nuclear Chemistry; Power; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a02573e9ebbb4db9f237b7/original/the-effects-of-irradiation-on-structure-and-leaching-of-pure-and-doped-thin-film-ceria-simfuel-models-prepared-via-polymer-templated-deposition.pdf |
65734646cf8b3c3cd721a882 | 10.26434/chemrxiv-2023-n2016 | Processive Catalytic Polymerization via Molecularly Confined Catalyst | Controlling the reactivity of the propagating chain end in polymerization reactions is crucial for achieving well-defined polymers in both synthetic polymer chemistry1,2 and biology3. Processive enzymes in nature have evolved substrate-enclosing structures to protect the catalytic center from reaccess by the nascent polymer4. However, substrate enclosure has not been adopted in polymer chemistry for improving catalytic processivity. Here, we present a strategy for processive catalytic polymerization by encapsulating catalysts for ring-opening metathesis polymerization (ROMP) into the sub-surface cages of a metal-organic framework. The sub-surface encapsulation of the catalysts within the framework protects the propagating polymer chain end from the secondary metathesis reaction with the alkenes in the backbone of the nascent polymer, while allowing the nascent polymer to grow out of the framework with little impedance and achieve continuous chain growth. As a result, ultra-high-molecular-weight polymers with low dispersity were generated from the ROMP of low-strain cyclic olefins such as cis-cyclooctene and cyclopentene. We demonstrate that ultra-high-molecular-weight polymers with degradable backbones and enhanced mechanical and adhesive properties could be readily generated from this approach. | Zefeng Zhou; Wei-Shang Lo; Gavin J. Giardino; Kanika Lalit; Wenqi Wang; Chloe Fields; Alfred Barney; Chia-Kuang Tsung; Wenyu Huang; Jia Niu | Organic Chemistry; Catalysis; Polymer Science; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65734646cf8b3c3cd721a882/original/processive-catalytic-polymerization-via-molecularly-confined-catalyst.pdf |
6119cc15e540bbd8b578f947 | 10.26434/chemrxiv-2021-rw953 | Room temperature hydrolysis of benzamidines and benzamidiniums in weakly basic water | Benzamidinium compounds have found widespread use in both medicinal and supramolecular chemistry. In this work, we show that benzamidiniums hydrolyse at room temperature in aqueous base to give the corresponding primary amide. This reaction has a half-life of 300 days for unsubstituted benzamidinium at pH 9, but is relatively rapid at higher pHs (e.g. t1/2 = 6 days at pH 11 and 15 hours at pH 13). Quantum chemistry combined with first principles kinetic modelling can reproduce these trends and explain them in terms of the dominant pathway being initiated by attack of HO– on benzamidine. Incorporation of the amidinium motif into a hydrogen bonded framework offers a substantial protective effect against hydrolysis. | Lijuan Yu; Duncan Cullen; Mahbod Morshedi; Michelle Coote; Nicholas White | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6119cc15e540bbd8b578f947/original/room-temperature-hydrolysis-of-benzamidines-and-benzamidiniums-in-weakly-basic-water.pdf |
67a9b01381d2151a02d48b41 | 10.26434/chemrxiv-2024-zm9fw-v2 | MECHANOCHEMICAL ACTIVATION OF NAHCO3: A CO2 SOLID SURROGATE IN CARBOXYLATION REACTIONS | Carbon dioxide, a primary driver of global warming, offers a promising feedstock for valuable chemical synthesis. Nonetheless, the reliance on highly pressurized canisters and specialized equipment limits its practical application in fine chemical synthesis. This study explores the innovative use of sodium bicarbonate (NaHCO3) as a safe, solid on-demand source of CO2 under mechanochemical conditions to perform carboxylation reactions. In one example, we report the mechanochemical synthesis of cyclic carbamate, enabling more practical and sustainable conditions for the synthesis of these compounds respect to solution-based precedents. In a second application, we disclose the synthesis of organic carbonates from bicarbonate, which has no precedents in solution. We further showcase the potential of our approach in the pharmaceutical industry by demonstrating the solvent-minimized synthesis of pharmaceutically relevant molecules and introducing a novel 13C-labeling strategy utilizing NaH13CO3. | Francesco Mele; Andrea Aquilini; Ana Maria Constantin; Francesco Pancrazzi; Lara Righi; Andrea Porcheddu; Raimondo Maggi; Daniele Alessandro Cauzzi; Giovanni Maestri; Elena Motti; Luca Capaldo; Nicola Della Ca' | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a9b01381d2151a02d48b41/original/mechanochemical-activation-of-nahco3-a-co2-solid-surrogate-in-carboxylation-reactions.pdf |
660d65fd91aefa6ce1b38c52 | 10.26434/chemrxiv-2024-g58v2 | Hybrid mass spectrometry applied across the production of antibody biotherapeutics. | Post expression from the host cell, a bio-therapeutic will be subjected to several downstream processing steps prior to final formulation. Analysis of the product under various buffer conditions at each stage is desirable to show that the integrity of the sample is maintained and to monitor any potential product loss. In this study we examine how varying buffer conditions during downstream processing impact the structural integrity of a biopharmaceutical product, with a specific focus on the model IgG1 antibody, mAb4, provided by FUJIFILM Diosynth Biotechnologies. Flexibility, stability, aggregation propensity, and bulk properties were evaluated across the buffers of four sample points, including perfusion media, purification stages, and formulation buffer. Comparisons with Herceptin, an extensively studied IgG1 antibody, were conducted in a mass spectrometry-compatible buffer. Although mAb4 and Herceptin present with similar charge state distributions (CSD) in native mass spectrometry (MS) experiments, they exhibit distinct unfolding patterns during the activated ion mobility-mass spectrometry (aIM-MS) and differential scanning fluorimetry (DSF). The greater structural stability and aggregation onset temperature (Tagg) observed in Herceptin, are primarily attributed to the heavier glycosylation and kappa-class light chains present in Herceptin compared to the lambda-class light chains in mAb4. Hydrogen deuterium exchange mass spectrometry (HDX-MS) revealed that while mAb4 experiences substantial structural changes during purification, characterized by high flexibility, a low melting temperature (Tm), and prevalent repulsive protein-protein interactions, it eventually transitions to a highly compact and stable structure in buffers with higher salt concentrations and during formulation. Notably, in the formulated environment, the third constant domain (CH3) of the heavy chain retains flexibility and is identified as a region of interest for aggregation formation. Here we showcase the integration of MS and orthogonal techniques to attain comprehensive information which can be utilized early in the development stage to aid in decision-making regarding targeted mutations or to guide the design space of bioprocesses and formulation choices. | Emilia Christofi; Mark O'Hanlon; Robin Curtis; Arghya Barman; Jeff Keen; Tibor Nagy; Perdita Barran | Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Mass Spectrometry; Bioengineering and Biotechnology; Industrial Manufacturing | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660d65fd91aefa6ce1b38c52/original/hybrid-mass-spectrometry-applied-across-the-production-of-antibody-biotherapeutics.pdf |
60c74aa5702a9b4c1c18b2d4 | 10.26434/chemrxiv.12032712.v2 | Screening of Clinically Approved and Investigation Drugs as Potential Inhibitors of SARS-CoV-2 Main Protease and Spike Receptor-Binding Domain Bound with ACE2 COVID19 Target Proteins: A Virtual Drug Repurposing Study | In this virtual drug repurposing study, we used 7922 FDA approved drugs and compounds in clinical investigation from NPC database. Both apo and holo forms of SARS-CoV-2 Main Protease as well as Spike Protein/ACE2 were used for virtual screening. Initially, docking was performed for these compounds at target binding sites. The compounds were then sorted according to their docking scores which represent binding energies. The first 100 compounds from each docking simulations were initially subjected to short (10 ns) MD simulations (in total 300 ligand-bound complexes), and average binding energies during MD simulations were calculated using the MM/GBSA method. Then, the selected promising hit compounds based on average MM/GBSA scores were used in long (100-ns and 500-ns) MD simulations. In total around 15 µs MD simulations were performed in this study. Both docking and MD simulations binding free energy calculations showed that holo form of the target protein is more appropriate choice for virtual drug screening studies. These numerical calculations have shown that the following 8 compounds can be considered as SARS-CoV-2 Main Protease inhibitors: Pimelautide, Rotigaptide, Telinavir, Ritonavir, Pinokalant, Terlakiren, Cefotiam and Cefpiramide. In addition, following 5 compounds were identified as potential SARS-CoV-2 ACE-2/Spike protein domain inhibitors: Denopamine, Bometolol, Naminterol, Rotigaptide and Benzquercin. These compounds can be clinically tested and if the simulation results validated, they may be considered to be used as treatment for COVID-19. | Serdar Durdagi; Busecan Aksoydan; Berna Dogan; Kader Sahin; Aida Shahraki; Necla Birgül-İyison | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa5702a9b4c1c18b2d4/original/screening-of-clinically-approved-and-investigation-drugs-as-potential-inhibitors-of-sars-co-v-2-main-protease-and-spike-receptor-binding-domain-bound-with-ace2-covid19-target-proteins-a-virtual-drug-repurposing-study.pdf |
6718d14283f22e4214e6054f | 10.26434/chemrxiv-2024-7v7pv | Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry | Fragment-based quantum chemistry methods offer a means to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation to compute protein–ligand interaction energies in systems with several thousand atoms, using a new software platform for managing fragment-based calculations that implements a screened many-body expansion. Convergence tests using a minimal-basis semi-empirical method (HF-3c) indicate that two-body calculations, with single-residue fragments and simple hydrogen caps, are sufficient to reproduce interaction energies obtained using conventional supramolecular electronic structure calculations, to within 1 kcal/mol at about 1% of the computational cost. We also demonstrate that the HF-3c results are illustrative of trends obtained with density functional theory in basis sets up to augmented quadruple-zeta quality. Strategic deployment of fragmentation facilitates the use of converged biomolecular model systems alongside high-quality electronic structure methods and basis sets, bringing ab initio quantum chemistry to systems of hitherto unimaginable size. This will be useful for generation of high-quality training data for machine learning applications. | Paige Bowling; Dustin Broderick; John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718d14283f22e4214e6054f/original/convergent-protocols-for-computing-protein-ligand-interaction-energies-using-fragment-based-quantum-chemistry.pdf |
63312eadba8a6d2f525d30b7 | 10.26434/chemrxiv-2022-x9fkg-v2 | Free-Atom-Like d States Beyond the Dilute Limit of Single-Atom Alloys | Through a data-mining and high-throughput density functional theory approach, we identify a diverse range of metallic compounds that are predicted to have transition metals with “free-atom-like” d states that are highly localized in energy space. Design principles that can favor the formation of localized d states are uncovered, among which we note that site isolation is often necessary but that the dilute limit, as in most single-atom alloys, is not a pre-requisite. Additionally, the majority of localized d state transition metals identified from the computational screening study exhibit partial anionic character due to charge transfer from neighboring metal species. Using CO as a representative probe molecule, we show that localized d states for Rh, Ir, Pd, and Pt tend to reduce the binding strength of CO compared to their pure elemental analogues, whereas this does not occur as consistently for the Cu binding sites. These trends are rationalized through the d-band model, which suggests that the significantly reduced d-band width results in an increased orthogonalization energy penalty upon CO chemisorption. With the multitude of inorganic solids that are predicted to have highly localized d states, the results of the screening study may lead to new avenues for heterogeneous catalyst design from an electronic structure perspective. | Andrew Rosen; Sudarshan Vijay; Kristin Persson | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63312eadba8a6d2f525d30b7/original/free-atom-like-d-states-beyond-the-dilute-limit-of-single-atom-alloys.pdf |
60c7457cee301c28afc79318 | 10.26434/chemrxiv.10032131.v1 | Heterolytic Hydrogen Activation: Understanding Support Effects in Water-Gas Shift, Hydrodeoxygenation, and CO Oxidation Catalysis | Identifying the role of oxide supports in transition metal catalysis is critical toward our understanding of heterogeneous catalysis. The water-gas shift (WGS) reaction is a prototypical example where oxide support dictates catalytic activity, yet the cause for this remains uncertain. Herein, we show that a single descriptor—the equilibrium constant for hydroxyl formation—relates the WGS turnover frequency across disparate oxide supports. The dissimilar equilibrium constant, or oxophilicity, between early and late transition metals exemplify the utility of metal-support interfacial sites to circumvent adsorption-energy scaling restrictions, thereby providing bifunctional gains for the WGS reaction class. In relation, the equilibrium constant for hydroxyl formation is equivalent to the equilibrium constant for the formal heterolytic dissociation of hydrogen, and therefore, reflects the ability of the metal-support interface to participate in hydrogen heterolysis. The ubiquitous coexistence, yet divergent chemical behavior of homo- and heterolytically activated hydrogen renders oxide support identity central toward our understanding of hydrogenation catalysis. | Nicholas Nelson; János Szanyi | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457cee301c28afc79318/original/heterolytic-hydrogen-activation-understanding-support-effects-in-water-gas-shift-hydrodeoxygenation-and-co-oxidation-catalysis.pdf |
61dd9f42a16050682f9d4812 | 10.26434/chemrxiv-2022-8vr18 | Photocatalytic overall water splitting under visible light enabled by a particulate conjugated polymer loaded with iridium | The production of hydrogen from water via solar water splitting is a potential method to overcome the intermittency of the Sun’s energy by storing it as a chemical fuel. Inorganic semiconductors
have been studied extensively as photocatalysts for overall water splitting, but polymer photocatalysts
are also receiving growing attention. So far, most studies involving organic polymers report hydrogen
production with sacrificial electron donors, which is unsuitable for large-scale hydrogen energy production. Here we show that a linear conjugated polymer photocatalyst can be used for overall water splitting
to produce stoichiometric amounts of H2 and O2. We studied a range of different metal co-catalysts in
conjunction with the linear polymer photocatalyst, the homopolymer of dibenzo[b,d]thiophene sulfone
(P10). Photocatalytic activity was observed for palladium/iridium oxide-loaded P10, while other co-catalysts resulted in materials that showed no activity for overall water splitting. The reaction conditions were
further optimized and the overall water splitting using the IrO2-loaded P10 was found to proceed steadily
for an extended period (>60 hours) after the system stabilized. These results demonstrate that conjugated polymers can act as single component photocatalytic systems for overall water splitting when
loaded with suitable co-catalysts, albeit currently with low activities. Significantly, though, organic polymers can be designed to absorb a large fraction of the visible spectrum, which can be challenging with
inorganic catalysts. Transient spectroscopy shows that the IrO2 co-catalyst plays an important role in the
generation of the charge separated state required for water splitting, with evidence for fast hole transfer
to the co-catalyst. This solid-state approach should be transferable to other polymer photocatalysts, allowing this field to move away from sacrificial hydrogen production towards overall water splitting. | Yang Bai; Chao Li; Lunjie Liu; Yuichi Yamaguchi; Bahri Mounib; Haofan Yang; Adrian Gardner; Martijn Zwijnenburg; Nigel Browning; Alexander Cowan; Akihiko Kudo; Andrew Cooper; Reiner Sebastian Sprick | Physical Chemistry; Energy; Energy Storage; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dd9f42a16050682f9d4812/original/photocatalytic-overall-water-splitting-under-visible-light-enabled-by-a-particulate-conjugated-polymer-loaded-with-iridium.pdf |
61aae175f35d4c5e0950df2a | 10.26434/chemrxiv-2021-g0mq2 | The Probabilistic Deconvolution of the Distribution of Relaxation Times with Finite Gaussian Processes | Electrochemical impedance spectroscopy (EIS) is a tool widely used to study the properties of electrochemical systems. The distribution of relaxation times (DRT) has emerged as one of the main methods for the analysis of EIS spectra. Gaussian processes can be used to regress EIS data, quantify uncertainty, and deconvolve the DRT, but current implementations do not constrain the DRT to be positive and can only use the imaginary part of EIS spectra. Herein, we overcome both issues by using a finite Gaussian process approximation to develop a new framework called the finite Gaussian process distribution of relaxation times (fGP-DRT). The analysis on artificial EIS data shows that the fGP-DRT method consistently recovers exact DRT from noise-corrupted EIS spectra while accurately regressing experimental data. Furthermore, the fGP-DRT framework is used as a machine learning tool to provide probabilistic estimates of the impedance at unmeasured frequencies. The method is further validated against experimental data from fuel cells and batteries. In short, this work develops a novel probabilistic approach for the analysis of EIS data based on Gaussian process, opening a new stream of research for the deconvolution of DRT. | Adeleke Maradesa; Baptiste Py; Emanuele Quattrocchi; Francesco Ciucci | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aae175f35d4c5e0950df2a/original/the-probabilistic-deconvolution-of-the-distribution-of-relaxation-times-with-finite-gaussian-processes.pdf |
652dd26e45aaa5fdbb276546 | 10.26434/chemrxiv-2023-jvqhr-v2 | Novel Computational Chemistry Infrastructure for Simulating Astatide in Water: From Basis Sets to Force Fields Using Particle Swarm Optimization | Using the example of astatine, the heaviest naturally occurring halogen whose isotope At-211 has promising medical applications, we propose a new infrastructure for large-scale computational models of heavy elements with strong relativistic effects. In particular, we focus on developing an accurate force field for At– in water based on reliable relativistic DFT calculations. To ensure such calculations' reliability, we design novel basis sets for relativistic DFT, via the particle swarm optimization algorithm to optimize the coefficients of the new basis sets and the polarization-consistent basis set idea's extension to heavy elements, to eliminate the basis-set error from DFT calculations. The resulting basis sets enable the well-grounded evaluation of relativistic DFT against "gold-standard" CCSD(T) results. Accounting for strong relativistic effects, including spin-orbit interaction, via our redesigned infrastructure, we elucidate a noticeable dissimilarity between At– and I– in halide-water force field parameters, radial distribution functions, diffusion coefficients, and hydration energies. This work establishes the framework for the systematic development of polarization-consistent basis sets for relativistic DFT and accurate force fields for molecular dynamics simulations to be used in large-scale models of complex molecular systems with the elements from the bottom of the periodic table, including actinides and even superheavy elements. | Kennet Espinosa; Alexei Kananenka; Alexander Rusakov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Quantum Mechanics; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652dd26e45aaa5fdbb276546/original/novel-computational-chemistry-infrastructure-for-simulating-astatide-in-water-from-basis-sets-to-force-fields-using-particle-swarm-optimization.pdf |
644801f2e4bbbe4bbf3d6796 | 10.26434/chemrxiv-2021-gkff1-v2 | Lipophilic modification of Salirasib modulate the antiproliferative and antimigratory activity. | Salirasib, or farnesylthiosalicylic acid (FTS), is a salicylic acid derivative with demonstrated antineoplastic activity. While designed as a competitor of the substrate S-farnesyl cysteine on Ras, it is a potent competitive inhibitor of isoprenylcysteine carboxymethyl transferase. Although different salirasib derivatives have been reported, the isoprenyl tail has not been modified. In this study, we used a series of synthetic salirasib analogues with lipophilic thioether modifications, including those with or without a 1,2,3-triazole linker, and tested their antiproliferative activity against six different solid tumor cell lines. We carried out a combination of bioassay, cheminformatics, and in silico ADME-Tox to identify new potent analogues. SAR analysis revealed structural and physicochemical features that enhance antiproliferative activity. Analogues with three or more isoprene units or a long aliphatic chain exhibited the most potent activity. Furthermore, we identified three compounds with superior antiproliferative activity than salirasib and similar potency compared to control anticancer drugs across all tested solid tumor cell lines. In addition, the behaviour of the collection on migration and invasion, the key processes in tumor metastasis, were also studied. Three analogs with specific antimigratory activity were identified with differential structural features.
The combination of the antiproliferative and antimigratory results prompts to propose that the modification on the thiol aliphatic/prenyl substituents can modulate the activity. Our findings provide valuable insight on the lipophilic salirasib analogues with enhanced antiproliferative activity against solid tumor cell lines. Also, we have been able to identify analogues with specific antimigratory activity that could be the starting points on the development of new antimetastatic agents.
| María Sol Ballari; Exequiel O. J. Porta; Evelyn Arel Zalazar; Carla M. Borini Etichetti; José M. Padrón; Javier Girardini; Guillermo R. Labadie | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644801f2e4bbbe4bbf3d6796/original/lipophilic-modification-of-salirasib-modulate-the-antiproliferative-and-antimigratory-activity.pdf |
6246f943804882fa9000e9fe | 10.26434/chemrxiv-2022-9w88q | Screening for Generality in Asymmetric Catalysis | Research in the field of asymmetric catalysis over the past half century has resulted in landmark advances,
enabling the efficient synthesis of chiral building blocks, pharmaceuticals, and natural products. A small number
of asymmetric catalytic reactions have been identified that display high selectivity across a broad scope of
substrates; not coincidentally, these are the reactions that have the greatest impact on how enantioenriched
compounds are synthesized. We postulate that substrate generality in asymmetric catalysis is rare not simply
because it is intrinsically difficult to achieve, but also because of the way chiral catalysts are identified and
optimized. Typical discovery campaigns rely on a single model substrate, and thus select for high performance
in a narrow region of chemical space. Here, we put forth a practical approach for using multiple model substrates
to select simultaneously for both enantioselectivity and generality in asymmetric catalysis from the outset. Multisubstrate screening is achieved by conducting high-throughput chiral analyses via supercritical fluid
chromatography-mass spectrometry (SFC-MS) with pooled samples. When applied to Pictet–Spengler
reactions, the multi-substrate screening approach revealed a promising and unexpected lead for the general
enantioselective catalysis of this important transformation. | Corin C. Wagen; Spencer E. McMinn; Eugene E. Kwan; Eric N. Jacobsen | Organic Chemistry; Catalysis; Agriculture and Food Chemistry; Organic Synthesis and Reactions; Acid Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6246f943804882fa9000e9fe/original/screening-for-generality-in-asymmetric-catalysis.pdf |
66c9d14420ac769e5fb4ddd1 | 10.26434/chemrxiv-2024-wdv4b | Water in zeolites of natrolite group and its OH-stretching region in Raman spectroscopy | Natrolite, Na2(Si3Al2)O10·2H2O, is a member of a group of zeolite minerals, made of hydrated aluminosilicate minerals. Due to their structure, zeolites have channels, through which water and ions can move. In the RRUFF database, we find the following members of the group: natrolite, mesolite, scolecite, and gonnardite. In the database, Raman spectra are provided where we can easily observe the OH-stretching region of water. We propose the deconvolutions in q-Gaussian functions of these spectra, comparing the obtained results with those available from literature. A review of literature about natrolite is also proposed. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c9d14420ac769e5fb4ddd1/original/water-in-zeolites-of-natrolite-group-and-its-oh-stretching-region-in-raman-spectroscopy.pdf |
66e2f595cec5d6c142df44e3 | 10.26434/chemrxiv-2024-xd6t3 | Electronic and magnetic properties of Co3 O4 and Co3−xNixO4 from theoretical XANES spectroscopy at the Co K-edge | We present theoretical XANES spectroscopy at the Co K-edge, combined with DFT+U calcula-tions, to investigate the electronic and magnetic properties of Co3 O4 normal spinel and the nickel doped system Co3−x Nix O4 . Two configurations have been considered for the nickel doped system : the configurations in which one nickel atom substitutes a tetrahedral and an octahedral cobalt, respectively. The Co K-edge XANES spectrum shows two pre-peaks in Co3O4 normal spinel, while only one pre-peak is observed in the cases of doped systems. We attribute the disapearance of one pre-peak in the doped systems to the shift toward high energies of tetrahedral cobalt 3d empty states. We demonstrated that, nickel doping causes the oxidation state of tetrahedral cobalt to increase slightly, while that of octahedral cobalt remains almost unchanged. Moreover, nickel possesses a magnetization when substituting octahedral cobalt, and contributes to render Co3O4 a half metal system, while this magnetization decreases when nickel substitutes a tetrahedral cobalt. | Dick Hartmann Douma; Stephane Kenmoe | Theoretical and Computational Chemistry; Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e2f595cec5d6c142df44e3/original/electronic-and-magnetic-properties-of-co3-o4-and-co3-x-nix-o4-from-theoretical-xanes-spectroscopy-at-the-co-k-edge.pdf |
60c75307842e65d3c7db3e87 | 10.26434/chemrxiv.13380089.v1 | A Mass Spectrometry-Cleavable N-Terminal Tagging Strategy for System-Level Protease Activity Profiling | Proteolysis is one of the most important protein post-translational modifications (PTMs) that influences the functions, activities, and structures of nearly all proteins during their lifetime. This irreversible PTM is regulated and catalyzed by proteases through hydrolysis reaction in the process of protein maturation or degradation. The identification of proteolytic substrates is pivotal in understanding the specificity of proteases and the physiological role of proteolytic process. However, tracking these biological phenomena in native cells is very difficult due to their low abundances. Currently, no efficient methods are available to identify proteolytic products from large-scale samples. To facilitate the targeted identification of low-abundant proteolytic products, we devise a strategy incorporating a novel biotinylated reagent PFP (pentafluorophenyl)-Rink-biotin to specifically target, enrich and identify proteolytic N-terminus. Within the PFP-Rink-biotin reagent, an MS-cleavable feature is designed to assist in the unambiguous confirmation of the enriched proteolytic N-termini. This is the first reported study of identifying proteolytic N-terminus by MS-cleavable feature widely adopted in studying low-abundant protein PTMs and cross-linking/MS. The proof-of-concept study was performed with multiple standard proteins whose N-terminus were successfully modified, enriched and identified by a signature ion (SI) in the MS/MS fragmentation, along with the determination of N-terminal peptide sequences by multistage tandem MS of the complementary fragment generated after the cleavage of MS-cleavable bond. For large-scale application, the enrichment and identification of protein N-termini from Escherichia.coli cells were demonstrated along with a bioinformatics workflow. We believe this method can be very useful to locate proteolytic products in native cellular environment with high confidence.<br /> | Zixiang Fang; Maheshika SK Wanigasekara; Akop Yepremyan; Brandon Lam; Pawan Thapa; Frank Foss; Saiful Chowdhury | Analytical Chemistry - General; Mass Spectrometry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75307842e65d3c7db3e87/original/a-mass-spectrometry-cleavable-n-terminal-tagging-strategy-for-system-level-protease-activity-profiling.pdf |
60c749d20f50db4b6c39696c | 10.26434/chemrxiv.12111480.v1 | Statistical Study of Carbon Intensities in the GOM and PB | In addressing carbon emissions as the primary contributor to climate change, a study was conducted to examine the total carbon dioxide equivalent (CO2e) emitted into the atmosphere from the production of crude oil and gas in the two largest producing regions of the U.S: the Permian Basin (PB) and the Gulf of Mexico (GOM). The objective of this report is not to compare the carbon intensities between PB and GOM, but rather to understand the causes of deviations observed between the two Basins, particularly in the years 2016 to 2018. This report details the initiative, including the research of emissions and production data from three federal agencies: the U.S. Environmental Protection Agency (EPA), U.S. Energy Information Administration (EIA), and the Bureau of Ocean Energy Management (BOEM). High-level analysis was conducted on six greenhouse gases: carbon dioxide, nitrous oxide, methane, sulfur hexafluoride, perfluorocarbons, and hydrofluorocarbons. Some major findings of this study include the establishment of a clear trend in which GHG emission rates increase as production increases. The mean carbon intensity, derived from the log normal distribution, for PB production and GOM production was determined to be 14.83 ± 3.374 kg CO2e/BOE and 7.86 ± 2.32 kg CO2e/BOE, respectively, for the year 2018 with 95% confidence interval. While three years of data is not sufficient to conclude a trend, both GOM and PB experienced lower carbon intensity rates in 2017 compared to 2016 and a higher carbon intensity rate in year 2018 compared to 2017. The primary causes for the PB’s higher carbon intensity are flaring practices, transportation, hydraulic fracturing and weather-related impacts, which will be further discussed in this report. | Ama Motiwala; Dr. Huzeifa Ismail | Environmental Science; Machine Learning; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d20f50db4b6c39696c/original/statistical-study-of-carbon-intensities-in-the-gom-and-pb.pdf |
63d8408cd1632f652be8d5e4 | 10.26434/chemrxiv-2023-hxxkz | Nondestructively Visualizing and Understanding "Soft Short" and Li Creeping in All-solid-state Lithium-Metal Batteries | All-solid-state Li-metal batteries (ASLMBs) have the potential to outperform conventional Li-ion batteries in terms of high energy density and safety; however, their applications are challenged by the dendrite-related short circuit. Therefore, it is imperative to understand the mechano-electro-chemo behavior of Li. For the first time, we nondestructively visualize the Li behavior in ASLMBs through operando neutron imaging and X-ray computed tomography (XCT). The 2D neutron radiography tracks the real-time Li evolutions before and after the "soft short". The 3D neutron tomography evidences the Li-metal deformation, and XCT provides 3D views of the battery after the "soft short". Despite "soft short", our observation indicates that Faradaic processes persist. Meanwhile, the coupling of stacking pressure and plating-induced stress triggers the Li-metal deformation toward the current collector and the SE, which results in the "soft short". This work inspires future research on stabilizing the Li metal in ASLMBs from the mechano-electro-chemo aspect. | Daxian Cao; Wei Li; Yuxuan Zhang; Tongtai Ji; Xianhui Zhao; Ercan Cakmak; Juner Zhu; Arturas Adomkevicius; Hongli Zhu | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d8408cd1632f652be8d5e4/original/nondestructively-visualizing-and-understanding-soft-short-and-li-creeping-in-all-solid-state-lithium-metal-batteries.pdf |
669ab39ac9c6a5c07ae03b77 | 10.26434/chemrxiv-2024-lkl5t-v4 | pKa predictions for arsonic acid derivatives. | Food, water, air, and soil are regularly contaminated with natural and artificially occurring forms of arsenic, of which arsonic acid derivatives RAsO(OH)2 are the major pentavalent compounds present in aqueous media. At a given pH, the resulting ionization state for these derivatives affects their lipophilicity, solubility, protein binding, and their ability to cross plasma membranes, potentially increasing their toxicity. Knowing their pKa values not only characterizes them but also helps design a strategy for bioremediation. Numerous challenges are associated with predicting pKa, and existing models are limited to specific chemical spaces. To leverage a pKa model for arsonic acids, we contrast machine learning (ML) methods based in Support Vector Machine and three DFT-based models: correlation to the maximum surface electrostatic potential (VS,max) at the ωB97XD/cc-pVTZ level of theory; correlation to carboxylate atomic charges in conjunction with a density-based solvation model (SMD) at the level of M06L/6-311G(d,p); and the scaled solvent-accessible surface approach, which yielded high mean unsigned errors for predicted pKa, and therefore it is not an efficient method for calculating the pKas of arsenic acids, in contrast with reported data for carboxylic acids, aliphatic amines, and thiols. The highest agreement was obtained with the atomic charges calculation on the conjugated arsonate base. ML-based and Vs.,max models rank second and third, respectively, in terms of prediction performance. | Miroslava Nedyalkova; Diana Heredia; Marco Lattuada; Joaquín Barroso-Flores | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669ab39ac9c6a5c07ae03b77/original/p-ka-predictions-for-arsonic-acid-derivatives.pdf |
66e6cd4a51558a15ef0b6322 | 10.26434/chemrxiv-2024-9q65r | Tandem Diels-Alder reaction overrules entropy: the gate to a thermally stable, yet thermally recyclable furan-based polymers | The study investigates the kinetics and thermodynamics of the reversible tandem Diels-Alder (tDA) reaction between difuranic compounds and maleimides, leading to the quantitative formation of tDA adducts at rates comparable to their counterparts from the “classical” Diels-Alder (DA) reaction. The tDA adducts exhibited unprecedented thermal stability up to 250 °C, which is 100 °C higher than that of the DA adducts, owing to the higher activation energy (Ea) required for the initial intramolecular step of the reverse process. The stability of the tDA adducts was exploited in the AA + BB type polymerization of tetrafuranic monomers with bis(maleimides), yielding thermally stable (up to 200 °C) yet depolymerasable linear polymers with molecular weights of 10-20 kDa. Only furanic groups were identified as the end-groups of the resulting polymers, suggesting the possibility for post-polymerization and end-group modifications. NMR and GPC kinetic data offered insights into the intermediate formation of classical adducts during polymerization, as well as the stereochemistry of tDA adducts in the polymer chains. Combined thermal analysis (DSC, TGA, and TMA) provided a comprehensive understanding of the reverse DA reaction in the resulting materials. This relatively clean, catalyst- and byproduct-free, well-controlled process, which uses derivatives of biorenewables as monomers, heralds the formation of a new class of thermally recyclable polymers. | Daria Zakharova; Rinat Aysin; Dmitry Khanin; Alexander Pavlov; Elena Platonova; Yulia Nelyubina; Alexander Polezhaev | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Stereochemistry; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e6cd4a51558a15ef0b6322/original/tandem-diels-alder-reaction-overrules-entropy-the-gate-to-a-thermally-stable-yet-thermally-recyclable-furan-based-polymers.pdf |
666de2a0c9c6a5c07a8e5f18 | 10.26434/chemrxiv-2024-k8ld5 | Accessing the Low-polar Molecular Composition of Boreal and Arctic Peat Burning Organic Aerosol via Thermal Analysis and Ultrahigh-Resolution Mass Spectrometry: Structural Motifs and Their Formation | Peatland fires emit organic carbon rich particulate matter into the atmosphere. Boreal and Arctic peatlands are becoming more vulnerable to wildfires, resulting in a need for better understanding of the emissions of these special fires. Extractable, non-, and low-polar organic aerosol species emitted from laboratory-based boreal and Arctic peat burning experiments are analyzed by direct-infusion atmospheric pressure photoionization (APPI) ultrahigh-resolution mass spectrometry (UHRMS) and compared to time-resolved APPI UHRMS evolved gas analysis from the thermal analysis of peat under inert nitrogen (pyrolysis) and oxidative atmosphere. The chemical composition is characterized on a molecular level, revealing abundant aromatic compounds that partially contain oxygen, nitrogen or sulfur and are formed at characteristic temperatures. Two main structural motifs are identified: single-core and multicore, and their temperature dependent formation is assigned to the thermal degradation of the lignocellulose building blocks and other parts of peat. | Eric Schneider; Anika Neumann; Martha Chacón-Patiño; Markus Somero; Meri Ruppel; Mika Ihalainen; Kajar Köster; Olli Sippula; Hendryk Czech; Christopher Paul Rüger; Ralf Zimmermann | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666de2a0c9c6a5c07a8e5f18/original/accessing-the-low-polar-molecular-composition-of-boreal-and-arctic-peat-burning-organic-aerosol-via-thermal-analysis-and-ultrahigh-resolution-mass-spectrometry-structural-motifs-and-their-formation.pdf |
64f8c9433fdae147faa38934 | 10.26434/chemrxiv-2023-b005t | Photosensitizer-Free Photoinduced Ground-State Triplet Carbene-Assisted Aryloxy Radical Generation via HAT | Carbene is the pivotal reactive intermediate and its reactivity potential has been extensively explored in a variety of synthetic transformations ranging from cycloaddition to site-selective C–H functionalizations. However, controlling the reactivity of carbene is a key parameter for achieving the selective carbene transfer reactions. Usually, strategies rely on the combined effect of metal catalysts and ligands to accomplish the selective transformations via the generation of singlet carbene intermediate. Contrarily, the triplet carbene has gained a very little attention from the researchers as its generatation and reactivity relies on the use of specific metal complexes thus limiting its wider utility. Neverthless, the organic transformations involving a triplet spin state carbene have been explored with diazo compounds under visible light utilizing photosensitizer. However, the development of the visible light induced sensitizer-free strategy for the generation of triplet carbene is highly challenging and is seldom reported. Herein, we have demonstrated vinyl diazosuccinimide as a new class of diazo compound which upon exposure to blue LEDs (456 nm) generates ground-state triplet carbene (without ISC) in the absence of any photosensitizer. We have successfully explored this strategy and utilzed to construct the biologically relavant scaffold such as 2H-chromenes. A series of control experiments, EPR studies as well as DFT calculations have supported the existence of ground-state triplet carbene followed by the aryloxy radical during the course of the reaction. | Debasish Laha; Onkar S. Bankar; Balu S. Navale; Supriyo Santra; Dr. Debashree Ghosh; Dr. Ramakrishna G. Bhat | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f8c9433fdae147faa38934/original/photosensitizer-free-photoinduced-ground-state-triplet-carbene-assisted-aryloxy-radical-generation-via-hat.pdf |
60c756fc702a9b934c18c9d2 | 10.26434/chemrxiv.14350610.v1 | Transmol: Repurposing Language Model for Molecular Generation | Recent advances in convolutional neural networks have inspired the application of deep learning to other disciplines. Even though image processing and natural language processing have turned out to be the most successful, there are many other areas that have benefited, like computational chemistry in general and drug design in particular. From 2018 the scientific community has seen a surge of methodologies related to the generation of diverse molecular libraries using machine learning. However, no algorithm used an attention mechanisms for <i>de novo</i> molecular generation. Here we employ a variant of transformers, a recent NLP architecture, for this purpose. We have achieved a statistically significant increase in some of the core metrics of the MOSES benchmark. Furthermore, a novel way of generating libraries fusing two molecules as seeds has been described. | Rustam Zhumagambetov; Vsevolod A. Peshkov; Siamac Fazli | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756fc702a9b934c18c9d2/original/transmol-repurposing-language-model-for-molecular-generation.pdf |
67dde97281d2151a025fd6f4 | 10.26434/chemrxiv-2025-wvfn2 | Examining the silicon-fluorine gauche effect in 3-fluoro silacyclohexanes | Two 3-fluorosilinanes featuring different substitution at silicon were synthesized and their conformations analyzed by NMR and DFT. Based on the results, both compounds prefer a conformation wherein the fluorine atom is oriented equatorial rather than axial, which would have placed the partially negative fluorine (Fδ-) closer in space to partially positive silicon (Siδ+). Therefore, the conformational preference of these systems is thought to be controlled primarily by sterics as well as hyperconjugative stabilization (σC-Si → σ*C-F). | Kerry Wier; Samantha Connor; Robert Berger; Gregory O'Neil | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dde97281d2151a025fd6f4/original/examining-the-silicon-fluorine-gauche-effect-in-3-fluoro-silacyclohexanes.pdf |
60c75242842e6582bfdb3cd4 | 10.26434/chemrxiv.13272443.v1 | Theoretical Study of Stability, Structure, and Optical Spectra of Ultra-Small Silver Clusters Using Density Functional Theory | Our article is a systematic study toward understanding the mechanism of silver cluster formation. We calculated optical spectra of ultra-small silver clusters using time-dependent density functional theory (TDDFT) and compared our results with time-resolved UV-Vis spectra obtained from pulse radiolysis experiments during early stages of cluster formation. This comparative study indicates that the formation mechanism of silver clusters occurs through both monomer and ion addition growth pathways. Also, we calculated free energy of formation of small cationic and neutral clusters using density functional theory (DFT) which shows the thermodynamic stability of cationic clusters. In a conventional experimental system with the common reducing agents, the formation of cationic clusters is kinetically favored owing to the dominance of charged ions relative to neutral atoms in the system. While we show the stability of small cationic clusters relative to neutral clusters, collectively, we deduce that the monomer addition along with ion addition growth pathway is involved in silver cluster formation mechanism. We further show the effect of solvent and water ligands on structure, stability, and optical properties of small clusters. | Mohsen Farshad; Duwage Perera; jayendran Rasaiah | Aggregates and Assemblies; Computational Chemistry and Modeling; Clusters; Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.); Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75242842e6582bfdb3cd4/original/theoretical-study-of-stability-structure-and-optical-spectra-of-ultra-small-silver-clusters-using-density-functional-theory.pdf |
60c7437cbb8c1a04f33da33c | 10.26434/chemrxiv.8792243.v3 | Non-Directed, Copper Catalyzed Benzylic C-H Amination Avoiding Substrate Excess | <div>
<p>We report the development of a benzylic C-H amination protocol
that addresses two common drawbacks in non-directed, intermolecular benzylic
C-H aminations: (i) the need to use an excess of substrate and (ii) the
limitation to only introduce one type of nitrogen source. Key to this discovery
is the use of the strong oxidant <i>N</i>-fluorobenzenesulfonimide
(NFSI) in combination with a Cu/diimine ligand catalyst system and an added nitrogen nucleophile. The established
conditions allow to lower the C-H substrate loading to 1.0 equivalent and
provide up to 95% yield of C-H amination product. Furthermore, sulfonamides and
benzamides can be employed as nitrogen sources/nucleophiles, resulting in access to a
diverse product scope. </p>
</div> | Anqi Wang; Cristina C. DeOliveira; Marion Emmert | Organic Synthesis and Reactions; Physical Organic Chemistry; Homogeneous Catalysis; Redox Catalysis; Bond Activation; Catalysis; Ligands (Organomet.); Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7437cbb8c1a04f33da33c/original/non-directed-copper-catalyzed-benzylic-c-h-amination-avoiding-substrate-excess.pdf |
60c75574567dfe266dec62a9 | 10.26434/chemrxiv.14109950.v1 | Selective Ring Opening Allene Metathesis: Polymerization or Ruthenium Vinylidene Formation | Selective ring-opening allene metathesis polymerization (ROAlMP) and ruthenium vinylidene formation from 1,2-cyclononadiene (<b>1</b>) by simple catalyst selection are discussed. Grubbs second generation catalyst (G2) favors the formation of an alkylidene leading to the ROAlMP of (<b>1</b>). Grubbs first generation catalyst (G1) favors vinylidene formation and prevents the homopolymerization of (<b>1</b>) even at elevated temperatures. Isolation and characterization of poly(<b>1</b>) by NMR analysis and MALDI-TOF confirms the generation of a well-defined polyallene that exhibits good thermal stability (<i>T</i><sub>D</sub> ca. 400 ºC) and fluorescent properties. Ring-opening metathesis polymerization (ROMP) of a high strained norbornene derivative (NBE-<sup>i</sup>Pr) at 80 ºC using the ruthenium vinylidene generated from (<b>1</b>) is also investigated. The discovery of ROAlMP allows for the simple accesses of well-defined polyallenes from commercially available catalysts and will ultimately guide structure-property determinations of polyallenes. | William Neary; Yunyan Sun; Jeffrey S. Moore | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75574567dfe266dec62a9/original/selective-ring-opening-allene-metathesis-polymerization-or-ruthenium-vinylidene-formation.pdf |
63c2c2cb1f125840d19dba28 | 10.26434/chemrxiv-2023-dmfqh | Spectroscopic and Computational Study of Organocatalytic Umpolung of Bromocations: An Accelerated Stereoselective Dibromination Protocol | Herein, the reversal of polarity of cationic bromine, organocatalytically, is presented. NBS, a proven bromocation source was converted to a superior bromoanion reagent by H/Br exchange with a secondary amine, substantiated with spectroscopic and computational evidences. The concept has further been used in a successful accelerated organocatalyzed dibromination of olefins, in a non-hazardous, commercially viable process with a wide substrate scope. The reactivity of key entities has been observed through NMR kinetics and reaction acceleration using 10 mol% of catalyst loading accounts for its major success. The nucleophilicity of the bromoanion was found to be superior in comparison to other nucleophiles such as MeOH, H2O etc. and the protocol dominates over competing allylic bromination reaction. | Jeetendra Panda; Jigyansa Sahoo; Juhi Dutta; Himansu Sekhar Biswal; Gokarneswar Sahoo | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c2c2cb1f125840d19dba28/original/spectroscopic-and-computational-study-of-organocatalytic-umpolung-of-bromocations-an-accelerated-stereoselective-dibromination-protocol.pdf |
60c749910f50db2712396914 | 10.26434/chemrxiv.11424783.v5 | Geometric and energetic data from quantum chemical calculations of halobenzenes and xylenes | <p>This article presents theoretical data on
geometric and energetic features of halobenzenes and xylenes. Data were obtained from <i>ab initio</i> geometry optimization and frequency calculations at HF,
B3LYP, MP2 and CCSD levels of theory on 6-311++G(d,p) basis set. In total, 1504 structures of halobenzenes,
three structures of xylenes and one structure of benzene were generated and
processed by custom-made codes in Mathematica.
The quantum chemical calculation was completed in Q-Chem software
package. Geometric and energetic data of
the compounds are presented in this paper as supplementary tables. Raw output files as well as codes and scripts
associated with production and extraction of data are also provided.</p> | Sopanant Datta; Taweetham Limpanuparb | Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749910f50db2712396914/original/geometric-and-energetic-data-from-quantum-chemical-calculations-of-halobenzenes-and-xylenes.pdf |
63298bc4cf382978b9ab216f | 10.26434/chemrxiv-2022-t04v9 | On the Instability of Iodides of Heavy Main Group Atoms in their Higher Oxidation State | Inert pair effect—the tendency of s orbital of heavy atoms to stay unreactive, is a consequence of relativistic contraction of the s orbitals. While the manifestations of this, on the reactivity depends on the nature of the substituents, this aspect is often overlooked. Divalent Pb prefers inorganic substituents, whereas tetravalent Pb prefers organic substituents. Among the inorganic substituents, again there are specific preferences—tetravalent Pb prefers F and Cl more than Br and I. It is as though the relativistic contraction of s orbital of Pb is more significant with Br and I substituents, than with Cl, F and alkyl substituents. Herein, we address the problem using molecular orbital approach. We explain why typical hypervalent systems, like 12-X-6, 10-X-5 (X is a heavy atom, the number preceding X is the number of valence electrons surrounding X, and the number after X is the coordination number) with less electronegative substituents carrying lone pair (such as Iodine), and Lewis octet molecules like PbI4 are unstable, but their dianions (14-X-6, 12-X-5, PbI42-) are not. For heavy atoms, the relativistic contraction of s orbital renders the antibonding combination of s with ligand orbitals (σ1*) very low-lying, making it a good acceptor of electrons. Thus compounds where σ1* is empty are kinetically unstable, when an electron donor with appropriate energy (such as lone pair on Iodine or bromine) is present in the vicinity. Donor-acceptor interaction between σ1* and the lone pair on I or Br (F and Cl lone pairs are energetically far away from σ1*) is responsible for the instability of such compounds. The kinetic stability of tetraalkyl lead compounds is due to the absence of lone pairs on the alkyl substituents. This work illustrates the key factor responsible for the instability of heavy element iodides and provides a molecular-level insight on extended solid-state structures via quasi-relativistic density functional computations. | Priyakumari Chakkingal Parambil; Sathya S R R Perumal | Inorganic Chemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63298bc4cf382978b9ab216f/original/on-the-instability-of-iodides-of-heavy-main-group-atoms-in-their-higher-oxidation-state.pdf |
60c740e39abda25c35f8bd8e | 10.26434/chemrxiv.7853552.v1 | Continuous Flow Mode Biocatalytic Transamination Using Macrocellular Silica Monoliths: Optimizing Support Functionalisation and Enzyme Grafting | <div>Transaminases are immobilized onto macrocellular silica monoliths and used for carrying a continuous flow mode transamination reaction. Monoliths were prepared via an emulsion-templated sol-gel method and functionalized by amino-moieties (APTES) in order to covalently immobilize the enzymes, using glutaraldehyde as a cross-linking agent. In order to obtain higher performance and improved reproducibility, we investigate the key parameters of APTES functionalization and of enzyme grafting. Four functionalization protocols were studied. It is shown that controlling the moisture levels in monolith and in the functionalisation solution led to a 3-fold increase in activity as compared to the previously reported data, and greatly improved the reproducibility. Additionally, we report a strong beneficial effect of running the enzyme immobilization at room temperature instead of 4°C, further enhancing the obtained activity. Finally, the popular method which consists in stabilizing the covalent attachment of the enzyme by reducing the imine bonds formed between the enzyme and the functionalized surface was investigated. We highlight a strong enzyme deactivation caused by cyanoborohydride, making this strategy irrelevant in this case. All in all, the improvements presented here for enzyme immobilization in macrocellular silica monoliths, lead to the preparation of more active materials for continuous flow mode biocatalysis.<br /></div> | Ludivine van den Biggelaar; Patrice Soumillion; Damien Debecker | Catalysts; Hybrid Organic-Inorganic Materials; Biocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e39abda25c35f8bd8e/original/continuous-flow-mode-biocatalytic-transamination-using-macrocellular-silica-monoliths-optimizing-support-functionalisation-and-enzyme-grafting.pdf |
61eebe37e4d9b8de99f658ea | 10.26434/chemrxiv-2022-pn3x0 | Photochemistry of Common Xanthene Fluorescent Dyes as Efficient Visible-light Activatable CO-Releasing Molecules | Xanthene derivatives are organic dyes, some of which are routinely used in different chemical and biological applications, including human medicine. In this work, we investigated the photochemistry of some of the most common ones, fluorescein, eosin Y, and rose bengal, and major products of their photodegradation using optical spectroscopy, NMR, chromatography and mass spectroscopy techniques. These substances, usually considered (photo)chemically stable, were found to liberate carbon monoxide (CO) in 40–80% chemical yields upon extensive irradiation with visible light in aqueous solutions during their multistep concomitant degradation processes. In addition, a number of low-mass secondary photoproducts, such as phthalic and formic acids, were identified in the irradiated mixtures. We demonstrate that these common fluorescent dyes can also be considered as visible-light activatable carbon monoxide (CO)-releasing molecules (photoCORMs) under specific conditions with potential biological implications. | Marek Martínek; Lucie Ludvíková; Mária Šranková; Rafael Navrátil; Lucie Muchová; Jiří Huzlík; Libor Vítek; Petr Klán; Peter Šebej | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61eebe37e4d9b8de99f658ea/original/photochemistry-of-common-xanthene-fluorescent-dyes-as-efficient-visible-light-activatable-co-releasing-molecules.pdf |
60c748dbbdbb892351a3905d | 10.26434/chemrxiv.10050071.v2 | Structure Evolution of Organic Compounds in Shale Plays by Spectroscopy (1H & 13C−NMR, XPS, and FTIR) Analysis | Amorphous organic matter in geomaterials also known
as kerogen undergoes significant alteration in chemical structure during
thermal maturation which is characterized using a combination of solid−state <sup>1</sup>H
& <sup>13</sup>C−NMR, X−ray photoelectron spectroscopy (XPS), and Fourier
transform infrared (FTIR) techniques. | Hyeonseok Lee; Nuri Oncel; Mohammadreza Shokouhimehr; Mehdi Ostadhassan; Bo Liu; Rajender S. Varma | Environmental Analysis; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748dbbdbb892351a3905d/original/structure-evolution-of-organic-compounds-in-shale-plays-by-spectroscopy-1h-13c-nmr-xps-and-ftir-analysis.pdf |
673501ee7be152b1d0fbeab1 | 10.26434/chemrxiv-2024-lrnvj | High-resolution photoelectron spectroscopy of NO3− vibrationally excited along its 𝜈3 mode | The nitrate (NO3) radical has long been the subject of both experimental and theoretical studies due to its complex electronic structure resulting from vibronic interactions between the 𝑋 ̃ 2𝐴′2 and 𝐵 ̃ 2𝐸′ states. In particular, the definite assignment of the fundamental of its degenerate stretching vibration (𝜈3) is still under debate. Here, we extend the available spectroscopic information by reporting high-resolution photoelectron spectra of vibrationally pre-excited NO3− using the recently developed IR-cryo-SEVI technique. The anions are excited through infrared (IR) excitation near 1350 cm−1, accessing the 𝜈3 and 2𝜈3(𝑒′) vibrational levels with band centers at 1350.5 cm−1 and ~2700 cm−1, respectively. The IR-cryo-SEVI spectrum for 2𝜈3 pre-excitation shows clear evidence for an intense 3_2^1 transition. From the position of this feature (30031 cm−1), the electron affinity of NO3 also determined in this work (31680 cm−1), and the IR excitation energy, we obtain a fundamental frequency of 1051 cm−1 for the 𝜈3 fundamental of the NO3 radical. This assignment and other features in the IR-cryo-SEVI spectra are supported by spectral simulations based on a vibronic Köppel-Domcke-Cederbaum Hamiltonian. The simulations also show that nearly all features in the IR-cryo-SEVI spectra arise because of pseudo-Jahn-Teller coupling between the 𝑋 ̃ and 𝐵 ̃ state of NO3. The results and analysis presented here settle a long-standing controversy regarding the 𝜈3 frequency of NO3. | Jascha A. Lau; Martin DeWitt; Peter R. Franke; John F. Stanton; Daniel M. Neumark | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673501ee7be152b1d0fbeab1/original/high-resolution-photoelectron-spectroscopy-of-no3-vibrationally-excited-along-its-3-mode.pdf |
60c75321bb8c1ab2973dbfb1 | 10.26434/chemrxiv.13399307.v1 | Cu(OTf)2-Mediated Ionizing Cross-Coupling of N(sp) and N(sp2) with Arylboronic Acids | Metal-catalyzed C–N cross-coupling generally forms C–N bonds by reductive elimination from metal complexes bearing covalent C- and N-ligands. We have identified a Cu-mediated C–N cross-coupling that uses a dative N-ligand in the bond forming event, which, in contrast to conventional methods, generates reactive cationic products. Mechanistic studies suggest the process operates via transmetalation of an aryl organoboron to a Cu(II) complex bearing neutral N-ligands, such as nitriles or N-heterocycles. Subsequent generation of a putative Cu(III) complex enables the oxidative C–N coupling to take place, delivering nitrilium intermediates and pyridinium products. The reaction is general for a range of N(sp) and N(sp<sup>2</sup>) precursors and can be applied to drug synthesis and late-stage N-arylation, and the limitations in the methodology are mechanistically evidenced. | Allan Watson; Nicola Bell; Chao Xu; James Fyfe; Julien Vantourout; Jeremy Brals; sonia chabbra; Bela Bode; David Cordes; Alexandra Slawin; Thomas McGuire | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75321bb8c1ab2973dbfb1/original/cu-o-tf-2-mediated-ionizing-cross-coupling-of-n-sp-and-n-sp2-with-arylboronic-acids.pdf |
65d1ea9ee9ebbb4db99f4cbd | 10.26434/chemrxiv-2024-fq8fv-v2 | Target-selective cytosolic delivery of cargo proteins using the VHH-presented OLE-ZIP capsules | In the pursuit of a new generation of protein pharmaceuticals, the efficient delivery of these therapeutics into cells stands out as a crucial challenge. In this study, we have developed a novel approach utilizing protein capsules modified with VHH antibodies as cytosolic carriers for protein pharmaceuticals. For the protein capsule component, we opted for the OLE-ZIP protein capsules, which can be prepared from the amphiphilic two-helix bundled protein OLE-ZIP using the water-in-oil (w/o) emulsion method. The spacious interior of the OLE-ZIP capsules allows for the stable encapsulation of over 200 molecules of protein pharmaceuticals, such as RNase A and Cre recombinase, in one capsule. By presenting the VHH antibody with an affinity for cell-type-specific receptors such as the epidermal growth factor receptor (EGFR) on the capsule surface, we achieved cell-type selective endocytic uptake in A431 cell lines (high expression level of EGFR) over NHDF and MCF-7 cells (normal expression level of EGFR). This selective uptake was followed by the subsequent release of the encapsulated protein pharmaceuticals into the cytosol of the target cells. Unlike our previous version of the OLE-ZIP protein capsules modified with IgG antibodies, cytosolic delivery of pharmaceutical proteins was little impacted by the presence of other IgGs, which are abundant in the bloodstream. This improved characteristic suggests potential advantages for practical applications, including intravenous administration. | Kousuke Takahashi; Yasumichi Inoue; Shigeaki Hida; Naoki Umezawa; Isamu Akiba; Mitsuo Umetsu; Toshihisa Mizuno | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d1ea9ee9ebbb4db99f4cbd/original/target-selective-cytosolic-delivery-of-cargo-proteins-using-the-vhh-presented-ole-zip-capsules.pdf |
622f202e299f7dc6c276d162 | 10.26434/chemrxiv-2021-6r888-v3 | Machine Learning Optimization of Lignin Properties in Green Biorefineries | Novel biorefineries could transform lignin, an abundant biopolymer, from byproduct waste to high-value products for a sustainable society. Here we report the optimization of the AquaSolv omni biorefinery for lignin via Bayesian optimization, a machine learning framework for sample-efficient and guided data collection. This tool allows us to relate the biorefinery conditions like hydrothermal pretreatment reaction severity and temperature with multiple experimental outputs such as lignin structural features characterized using 2D nuclear magnetic resonance spectroscopy. By applying a Pareto front analysis to our models, we can find the processing conditions that simultaneously optimize the lignin yield and the amount of β-O-4 linkages for the depolymerization of lignin into platform chemicals. Our study demonstrates the potential of machine learning to accelerate the development of sustainable chemical processing techniques for targeted applications and products. | Joakim Löfgren; Dmitry Tarasov; Taru Koitto; Patrick Rinke; Mikhail Balakshin; Milica Todorović | Materials Science; Chemical Engineering and Industrial Chemistry; Biological Materials; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622f202e299f7dc6c276d162/original/machine-learning-optimization-of-lignin-properties-in-green-biorefineries.pdf |
60c747ed0f50db2b523966b7 | 10.26434/chemrxiv.11821347.v1 | The Superior Hydrothermal Stability of Pd/SSZ-39 in Low Temperature Passive NOx Adsorption (PNA) and Methane Combustion | We successfully synthesized uniform SSZ-39 with an average crystal size of about a micron. Pd (0.7 - 3 wt%) was supported on SSZ-39 with Si/Al ratio ~12. The as-synthesized materials were characterized by FTIR, XRD, Helium Ion Microscopy, HAADF-STEM imaging, 27Al, 29Si and H solid state NMR spectroscopic techniques. <br />FTIR studies with CO and NO probe molecules reveal that the 0.7 wt% Pd/SSZ-39 material with Si/Al ~12 has the majority of Pd dispersed atomically as isolated Pd(II) and Pd(II)-OH centers, and thus can be used as a low-temperature passive NOx adsorber. Pd(II)-NO, Pd(II)(OH)(NO) and Pd(II)(CO)(NO) complexes form during PNA in this material. We compare this PNA material directly with the Pd/SSZ-13 system (with Si/Al ratio ~12) and show its superior hydrothermal stability. Remarkably, Pd/SSZ-39 with Si/Al ratio ~12 survives hydrothermal aging up to 815 ºC in 10% H2O/Air vapor for 16 hours without significant loss in activity. The SSZ-39 crystal structure remains intact during hydrothermal aging up to 1,000 ºC as we elucidate it with XRD and HAADF-STEM imaging/EDS mapping. However, changes to the framework during such harsh hydrothermal treatment significantly change the NOx release profiles during PNA as evidenced by high-field 27Al NMR on fresh and aged Pd/SSZ-39 samples as well as PNA performance measurements. <br />Besides PNA application, these hydrothermally very stable materials (3 wt% Pd on SSZ-39 with Si/Al ratio ~12) can be used as a robust methane combustion catalyst under industrially relevant conditions (GHSV~600,000hr-1). This catalyst shows minimal deactivation after both harsh hydrothermal aging at 750 and 800 ºC, and prolonged time on stream (105 hrs) at 425 ⁰C. In contrast, both 3wt% Pd/alumina and 3wt% SSZ-13 supported samples lose a significant portion of their activity.<br /> | Konstantin Khivantsev; Nicholas
R. Jaegers; Libor Kovarik; Meng Wang; Jian Zhi Hu; Yong Wang; Miroslaw A. Derewinski; János Szanyi | Catalysts; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747ed0f50db2b523966b7/original/the-superior-hydrothermal-stability-of-pd-ssz-39-in-low-temperature-passive-n-ox-adsorption-pna-and-methane-combustion.pdf |
65cccabb66c1381729a22c58 | 10.26434/chemrxiv-2024-0g7wk | Dual-Band Electrochromic Devices Utilizing Niobium Oxide Nanocrystals | In this study we realize functioning electrochromic devices based on colloidal niobium oxide nanocrystals which show dual-band electrochromic behavior, with spectral
selectivity between near-infrared and visible wavelengths. Minimally coloring vanadium
oxide counter electrodes allow for full electrochromic devices that embody the dual-band
electrochromic behavior of the niobium oxide component. The devices are fabricated
using solution processing on both glass and flexible substrates, demonstrating that our
platform has potential for the development of low-cost dual-band electrochromic devices
for dynamic solar control in a variety of form factors and applications. | Benjamin Zydlewski; Delia Milliron | Nanoscience; Energy; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cccabb66c1381729a22c58/original/dual-band-electrochromic-devices-utilizing-niobium-oxide-nanocrystals.pdf |
67735b62fa469535b94e4abe | 10.26434/chemrxiv-2024-dhtsr | Esculin as a Novel Inhibitor of CCR1: Insights into Its Potential Role in Modulating Immune Responses | Background: Chemokine receptor CCR1 plays a pivotal role in regulating immune responses, including leukocyte migration and inflammatory signaling pathways. Dysregulation of CCR1 has been implicated in chronic inflammatory diseases, autoimmune disorders, and acute pulmonary inflammation, including hyperinflammatory responses in COVID-19 patients. Natural compounds, with their structural diversity and multifunctional biological activities, present an untapped resource for therapeutic discovery. Among them, Esculin, a coumarin derivative exhibits promising anti-inflammatory and antioxidant properties. However, the precise molecular mechanisms underlying Esculin's interaction with CCR1 remain unclear.
Methods: We investigated Esculin, a coumarin derivative with known anti-inflammatory properties, using molecular docking, 200 ns molecular dynamics (MD) simulations, and binding free energy (MMGBSA) analysis. Structural stability, residue-specific interactions, and pharmacokinetic properties (ADMET analysis) were comprehensively evaluated.
Results: Molecular docking revealed that Esculin effectively occupied the CCR1 ligand-binding pocket, with a favorable binding energy of -7.4 kcal/mol. MD simulation trajectories demonstrated structural stability of the Esculin-CCR1 complex. Key residues, including Trp90, Tyr93, Lys94, and Tyr113, were identified as critical contributors to binding stability. MMGBSA analysis confirmed energetically favorable interactions (Av. ΔG = -28.32 kcal/mol), with specific residues contributing significantly to the overall binding energy. ADMET analysis highlighted Esculin's optimal pharmacokinetic profile, high bioavailability, non-toxic nature, and absence of mutagenic or cardiotoxic risks.
Conclusion: Esculin demonstrates stable and energetically favorable binding with CCR1, suggesting its potential as a therapeutic modulator of CCR1-mediated immune responses. These findings highlight Esculin as a promising candidate for treating CCR1-associated diseases, including COVID-19-induced inflammation and chronic inflammatory conditions. Further in vitro and in vivo validation will be essential to confirm its therapeutic efficacy.
| Shivangi Agrawal; Ekta Pathak; Rajeev Mishra | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67735b62fa469535b94e4abe/original/esculin-as-a-novel-inhibitor-of-ccr1-insights-into-its-potential-role-in-modulating-immune-responses.pdf |
6678032701103d79c5eca4c5 | 10.26434/chemrxiv-2024-51zzb | 2D-IR spectroscopy of azide-labeled carbohydrates in H2O | Carbohydrates constitute one of the key classes of biomacromolecules, yet vibrational spectroscopic studies involving carbohydrates remain scarce as spectra are highly congested and lack significant marker vibrations. Recently, we introduced and characterized a thiocyanate-labeled glucose1 demonstrating the use of vibrational reporter groups for 2D-IR spectroscopy of carbohydrates. Here, we expand upon those results and elucidate the performance of azide groups as vibrational reporter for carbohydrates. Originating from applications in click-chemistry, different azide-labeled carbohydrates are readily available. We have characterized azide-labeled glucose, galactose, acetylglucosamine and lactose in water using IR and 2D-IR spectroscopy. Our findings indicate that their absorption profiles are primarily determined by the labeling position on the ring. However, we also observe additional variations between samples with the same labeling position. Furthermore, we demonstrate that their usage remains feasible at biologically relevant concentrations. | Philip Gasse; Till Stensitzki; Henrike M. Müller-Werkmeister | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6678032701103d79c5eca4c5/original/2d-ir-spectroscopy-of-azide-labeled-carbohydrates-in-h2o.pdf |
61a5ee49f93ad3e995b92211 | 10.26434/chemrxiv-2021-3gfh6 | Buckling versus crystal expulsion controlled by deformation rate of particle-coated air bubbles in oil | Oil foams stabilized by crystallizing agents exhibit outstanding stability and show promise for applications in consumer products. The stability and mechanics imparted by the interfacial layer of crystals underpin product shelf-life, as well as optimal processing conditions and performance in applications. Shelf-life is affected by the stability against bubble dissolution over a long time scale, which leads to slow compression of the interfacial layer. In processing flow conditions, the imposed deformation is characterized by much shorter time scales. In practical situations, the crystal layer is therefore subjected to deformation on extremely different time scales. Despite its importance, our understanding of the behavior of such interfacial layers at different time scales remains limited. To address this gap, here we investigate the dynamics of single, crystal-coated bubbles isolated from an oleofoam, at two extreme timescales: the diffusion-limited timescale characteristic of bubble dissolution 10,000 s, and a fast time scale characteristic of processing flow conditions, 0.001 s. In our experiments, slow deformation is obtained by bubble dissolution, and fast deformation in controlled conditions with real-time imaging is obtained using ultrasound-induced bubble oscillations. The experiments reveal that the fate of the interfacial layer is dramatically affected by the dynamics of deformation: after complete bubble dissolution, a continuous solid layer remains; while after fast, oscillatory deformation of the layer, small crystals are expelled from the layer. This observation shows promise towards developing stimuli-responsive systems, with sensitivity to deformation rate, in addition to the already known thermo- and photo-responsiveness of oleofoams. | Saikat Saha; Francis Pagaud; Bernard P. Binks; Valeria Garbin | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.); Interfaces; Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a5ee49f93ad3e995b92211/original/buckling-versus-crystal-expulsion-controlled-by-deformation-rate-of-particle-coated-air-bubbles-in-oil.pdf |
63c06eaecac318d5519ea53e | 10.26434/chemrxiv-2023-2ndds | High Rates of Quinone-Alkyne Cycloaddition Reactions are Dictated by Entropic Factors | Reaction rates of strained cycloalkynes and cycloalkenes with 1,2-quinones were quantified by stopped flow UV-Vis spectroscopy. Surprisingly, it was determined that 8-membered BCN-OH reacts substantially (16 times) faster than the more strained 7-membered THS. Thermodynamic activation parameters, obtained from the linearized Eyring equation and stopped-flow measurements, revealed that the reaction of both BCN-OH and THS with ortho-quinones is entropycontrolled, ruling out a relevant contribution of secondary orbital interactions (SOIs) as earlier proposed. | Johannes Damen; Jorge Escorihuela; Han Zuilhof; Floris van Delft; Bauke Albada | Organic Chemistry; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c06eaecac318d5519ea53e/original/high-rates-of-quinone-alkyne-cycloaddition-reactions-are-dictated-by-entropic-factors.pdf |
67cab47c6dde43c908e10a9e | 10.26434/chemrxiv-2025-nfc38 | TUB41: A Robust MOF for Industrial Gas Separation | Herein, we report on the thermal and chemical stability and CO2 and water vapor adsorption of a mixed linker phosphonate-MOF [Cu(4,4’‐bpy)0.5(1,4‐NDPAH2)], namely TUB41 (bpy = bipyridine and NDPAH4 = naphthalenediphosphonic acid). TUB41 exhibits reversible phase transitions upon heating until 330 °C. TUB41 is a very stable MOF across a pH range of 1 to 11 and after two years of repeated adsorption experiments and activation at 80 °C and ambient humidity. While gases with larger kinetic diameter do not access the narrow pores of TUB41, it can efficiently adsorb CO2 and water vapor, which have smaller kinetic diameter compared to other atmospheric gases. TUB41 exhibits a moderate enthalpy of adsorption for CO2, which is favorable compared to water vapor at low pressure, indicating its potential for selective CO2 separation in the presence of water vapor. TUB41 has an estimated optical band gap between 2.7 and 3.0 eV, which is within the bluish-violet range. | Robert Oestreich; Marcus Fetzer; Andreas Schreiber; Alexander Knebel; Markus Suta; Christoph Janiak; Gündoğ Yücesan | Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cab47c6dde43c908e10a9e/original/tub41-a-robust-mof-for-industrial-gas-separation.pdf |
60c748e4842e658d68db2c80 | 10.26434/chemrxiv.11994696.v1 | The Role of the Active Site Tyrosine in the Mechanism of Lytic Polysaccharide Monooxygenase | Natural polysaccharides (such as cellulose) comprise a large bio-renewable resource. However, exploitation of this resource requires energy-efficient polysaccharide degradation, which is currently limited by the inherent recalcitrance of many naturally occurring polysaccharides. Catalytic breakdown of polysaccharides can be achieved more efficiently by means of the enzymes lytic polysaccharide monooxygenases (LPMOs). However, the LPMO mechanism has remained controversial, preventing full exploitation of their potential. One of the controversies has centered around an active site tyrosine, present in most LPMOs. Different roles for this tyrosine have been proposed without direct evidence, but two recent investigations have for the first time obtained direct (spectroscopic) evidence for that chemical modification of this tyrosine is possible. Surprisingly, the spectroscopic features obtained in the two investigations are remarkably different. In this paper we use density functional theory (DFT) in a QM/MM formulation to reconcile these (apparently) conflicting results. By modeling the spectroscopy as well as the underlying reaction mechanism we can show how formation of two isomers (both involving deprotonation of tyrosine) explain the difference in the experimental observed spectroscopic features. The link between our structures and the observed spectroscopy provides a firm ground to investigate the role of tyrosine. | Aina McEvoy; Joel Creutzberg; Raushan Kumar Singh; Morten J. Bjerrum; Erik Hedegård | Computational Chemistry and Modeling; Theory - Computational; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748e4842e658d68db2c80/original/the-role-of-the-active-site-tyrosine-in-the-mechanism-of-lytic-polysaccharide-monooxygenase.pdf |
675d0a0c7be152b1d0ee3197 | 10.26434/chemrxiv-2024-mtcdv | NIR emissive fluorescence turn-on probe for selective detection of serum albumin proteins in biofluids and living cells | The quantitative detection of serum albumin in body fluids and living cells is crucial for the diagnosis of various diseases. Here, we report a near-infrared (NIR) emissive fluorescent probe with an emission at around 800 nm for the selective and sensitive detection of both bovine serum albumin (BSA) and human serum albumin (HSA) in biofluids and in living cells. The probe showed turn-on fluorescence upon interaction with both proteins. The docking simulation studies confirmed the strong binding of the probes to the proteins. Electrostatic, hydrophobic, and hydrogen bonding interactions with the neighboring amino acid residues played a major role in the binding of the probe. The fluorescence intensity of the probe was found to be stable within the physiological pH of the mammalian cells. The probe was highly efficient in detecting BSA in fetal bovine serum (FBS) with a limit of detection (LOD) of 12 nM, while it detected the HSA from urine with LOD of 18.2 nM. The probe showed its efficient potential for in-vitro sensing of both the proteins in HeLa and HEK 293T cells. | Chayan Kanti Nandi; Goraksha T. Sapkal; Abdul Salam; Purabi Bala; Shagun Sharma; Kush Kaushik; Richa Garg | Organic Chemistry; Analytical Chemistry; Organic Synthesis and Reactions; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675d0a0c7be152b1d0ee3197/original/nir-emissive-fluorescence-turn-on-probe-for-selective-detection-of-serum-albumin-proteins-in-biofluids-and-living-cells.pdf |
60c744fc469df45191f43428 | 10.26434/chemrxiv.9943640.v1 | Molecular Origin of Positive and Negative Electromechanical Response in Hydrogen-Bonded Systems | Hydrogen bonds, ubiquitous in organic and biological materials, involve weak electrostatic interactions, which can geometrically distort in response to an applied electric field. This electromechanical response is a key component in a range of piezoelectric materials in applications including energy harvesting and sensing. In this work, we apply electronic structure methods across a combinatorial pool of over 218 hydrogen-bonded dimers to examine the connection between the electrostatics, potential energy surface, and the resulting electromechanical response. Strikingly, while inorganic piezomaterials typically exhibit positive piezo response, expanding in response to an applied field, we find that hydrogen bonding interactions instead typically exhibit negative response, contracting due to the local electrostatics between the hydrogen bond donor and acceptor functional groups. | Keith Werling; Daniel Lambrecht; Geoffrey Hutchison | Biological Materials; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fc469df45191f43428/original/molecular-origin-of-positive-and-negative-electromechanical-response-in-hydrogen-bonded-systems.pdf |
653b31a1a8b423585a526e2e | 10.26434/chemrxiv-2023-nv011 | The SAMPL9 Host-Guest Blind Challenge: An Overview of Binding Free Energy Predictive Accuracy | We report the results of the SAMPL9 host-guest blind challenge for predicting binding free energies. The challenge focused on macrocycles from pillar[n]-arene and cyclodextrin host families, including WP6, and bCD and HbCD. A variety of methods were used by participants to submit binding free energy predictions. A machine learning approach based on molecular descriptors achieved the highest accuracy (RMSE of 2.04 kcal/mol) among ranked methods in the WP6 dataset. Interestingly, predictions for WP6 obtained via docking tended to outperform all methods (RMSE of 1.70 kcal/mol), most of which are MD based and computationally more expensive. In general, methods applying force fields achieved better correlation with experiments for WP6 opposed to the machine learning and docking models. In the cyclodextrin-phenothiazine challenge, the ATM approach emerged as the top performing method with RMSE less than 1.86 kcal/mol. Correlation metrics of ranked methods in this dataset was relatively poor compared to WP6. We also highlight several lessons learned to guide future work and help improve studies on the systems discussed. For example, WP6 may be present in other microstates other than its -12 state in the presence of certain guests. Machine learning approaches can be used to fine tune or help train force fields for certain chemistry (i.e WP6-G4). Certain phenothiazines occupy distinct primary and secondary orientations, some of which were considered individually for accurate binding free energies. The accuracy of predictions from certain methods while starting from a single binding pose/orientation demonstrate the sensitivity of calculated binding free energies to the orientation, and in some cases the likely dominant orientation for the system. Computational and experimental results suggest that guests phenothiazine core traverses both secondary and primary faces of the cyclodextrin hosts, bulky catioinic side chain will primarily occupy the primary face, and the phenothiazine core substituent resides at the larger secondary face. | Martin Amezcua; Jeffry Setiadi; David L. Mobley | Physical Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653b31a1a8b423585a526e2e/original/the-sampl9-host-guest-blind-challenge-an-overview-of-binding-free-energy-predictive-accuracy.pdf |
66b813fd01103d79c5925e3f | 10.26434/chemrxiv-2024-qx8tz-v2 | Exploration of the Global Minimum and Conical Intersection with Bayesian Optimization | Conventional molecular geometry searches on a potential energy surface (PES) utilize energy gradients from quantum chemical calculations. However, replacing energy calculations with noisy quantum computer measurements generates errors in the energies, which makes geometry optimization using the energy gradient difficult. One gradient-free optimization method that can potentially solve this problem is Bayesian optimization (BO). To use BO in geometry search, an acquisition function (AF), which involves an objective variable, must be defined suitably. In this study, we propose a strategy for geometry searches using BO and examine the appropriate AFs to explore two critical structures: the global minimum (GM) on the singlet ground state (S0) and the most stable conical intersection (CI) point between S0 and the singlet excited state. We applied our strategy to two molecules and located the GM and the most stable CI geometries with high accuracy for both molecules. We also succeeded in the geometry searches even when artificial random noises were added to the energies to simulate geometry optimization using noisy quantum computer measurements. | Riho Somaki; Taichi Inagaki; Miho Hatanaka | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b813fd01103d79c5925e3f/original/exploration-of-the-global-minimum-and-conical-intersection-with-bayesian-optimization.pdf |
60c74a529abda252e9f8ce10 | 10.26434/chemrxiv.12155361.v1 | Repurposing of SARS Inhibitors Against COVID 19 | Till this date there is no vaccine or drug for coronavirus responsible
for COVID-19 which has created a major challenge to stop the spread of disease.
Repurposing of a drug could be a solution for this challenge, as many
previously available drugs hold great potential to act as a drug molecule. The
coronavirus mainly affects the host by binding to its specific receptor with
the help of its surface glycoprotein or spike glycoprotein. Thus, interfering
this interaction could be a potent mechanism to stop the viral infection and
propagation. In this paper, we have discussed about the surface glycoprotein
and how previously available drug could be repurposed to act as a potent
inhibitor. Homology modelling and docking studies has been mainly done to
identify the interaction and binding affinity of previous drugs and how they
could act as a potential solution to stop the overall spread of the disease in
case of pandemic like COVID-19 where unavailability of specific drug or vaccine
is responsible for taking to the lives of many. | Priyanka Rajbhar; Dikshant Singh; Ruchi Yadav | Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a529abda252e9f8ce10/original/repurposing-of-sars-inhibitors-against-covid-19.pdf |
67b7d732fa469535b9391b65 | 10.26434/chemrxiv-2025-fltgh | Confirmation of pentavalent carbon in Protonated Methane (CH5+ ): Insights from Molecular Handycam Technique | The existence of pentavalent carbon has intrigued scientists since the discovery of CH5+ in 1952 but remains elusive due to the lack of definitive evidence. The present study unveils the mystery through a comprehensive investigation of the structural and bonding nature of CH5+ employing the newly developed Molecular Handycam technique (MHT) by Bag and co-workers, focusing on its formation pathways and energetic favorability. Computational analysis at the level of coupled-cluster theory (CCSD), we examine the formation of CH5+ through the association of CH3+ and H2 compared to the protonation of methane. Our findings reveal a preference for the former pathway, highlighting distinct structural configurations, including a global minimum and two alternative geometries. We demonstrate the participation of higher orbitals of carbon (3dz^2 ) and its interaction with the bond pair of the approaching H_2 molecule in forming and stabilizing the fifth C-H bond. This analytical approach provides critical insights into the expanded valency of carbon, which could lead to a new class of carbon compounds. | Moumita Dinda; Sudipta Nayak; Arijit Bag | Physical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b7d732fa469535b9391b65/original/confirmation-of-pentavalent-carbon-in-protonated-methane-ch5-insights-from-molecular-handycam-technique.pdf |
67adc762fa469535b928038f | 10.26434/chemrxiv-2025-102pn | Cryogenic milling of consumer plastics for high-throughput characterization of polydisperse, amorphous microplastics | Microplastics - defined as tiny polymer fragments less than 5 mm in size - pose a clear threat to a wide range of small organisms through ingestion, leading to starvation. In addition, there are many reports of their occurrence both in remote geographical areas and in the human body. Small and made of mostly inert materials, they pose a significant analytical challenge. While primary microplastics i.e., those manufactured intentionally, have defined characteristics, secondary microplastics resulting from the degradation of larger plastic debris are much less understood. Cryogenic milling has emerged as one of the best ways to generate realistic samples with potential for use as references in studies. Here, we use this technique to generate and study the shapes and properties of a wide range of consumer plastics, providing an overview of optical and analytical properties. | Charlie Maslen; Purnesh Chattopadhyay; Marie Theres Kühne; Gail McConnell; Juliane Simmchen | Materials Science; Polymer Science; Earth, Space, and Environmental Chemistry; Granular Materials; Environmental Science; Wastes | CC BY 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67adc762fa469535b928038f/original/cryogenic-milling-of-consumer-plastics-for-high-throughput-characterization-of-polydisperse-amorphous-microplastics.pdf |
63e3d97b3067856f18bb18d0 | 10.26434/chemrxiv-2023-c8h70 | Assessing the Accuracy of Density Functional Approximations for Predicting Hydrolysis Reaction Kinetics | Hydrolysis reactions are ubiquitous in biological, environmental, and industrial chemistry. Density functional theory (DFT) is commonly employed to study the kinetics and reaction mechanisms of hydrolysis processes. Here, we present a new dataset, Barrier Heights for HydrOlysis - 36 (BH2O-36), to enable the design of density functional approximations (DFA) and the rational selection of DFAs for applications in aqueous chemistry. BH2O-36 consists of 36 diverse organic and inorganic forward and reverse hydrolysis reactions with reference energy barriers calculated at the CCSD(T)/CBS level. Using BH2O-36, we evaluate 63 DFAs. In terms of mean absolute error (MAE) and mean relative absolute error (MRAE), wB97M-V is the best-performing DFA tested, while MN12-L-D3(BJ) is the best-performing pure (non-hybrid) DFA. Broadly, we find that range-separated hybrid DFAs are necessary to approach chemical accuracy (0.043 eV). Although the best-performing DFAs include a dispersion correction to account for long-range interactions, we find that dispersion corrections do not generally improve MAE or MRAE for this dataset. | Alexander R. Epstein; Evan Walter Clark Spotte-Smith; Maxwell C. Venetos; Oxana Andriuc; Kristin A. Persson | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e3d97b3067856f18bb18d0/original/assessing-the-accuracy-of-density-functional-approximations-for-predicting-hydrolysis-reaction-kinetics.pdf |
60c746ca4c891922abad2bce | 10.26434/chemrxiv.11409396.v1 | Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor | Pregnane X receptor (PXR) is a master
xenobiotic-sensing transcription factor with a key role in drug metabolism and
disposition. Its activity regulates a number of physiological processes in the
liver and intestine, and it is now a validated target for human diseases
associated with inflammation and dysregulation of the immune system. The
identification of chemical probes to investigate the therapeutic relevance of
the receptor is still highly desired. In fact, currently available PXR ligands
are not highly selective and can exhibit toxicity and/or potential off-target
effects. In this study, we have identified the naturally-occurring garcinoic
acid as a selective and efficient PXR agonist. The properties of garcinoic acid
as a specific PXR agonist was demonstrated using different approaches -
screening on a panel of nuclear receptors, physical and thermodynamic
evaluation of binding affinity, and co-crystallization study. Cytotoxicity
assays, transcriptional and functional experiments were carried out in human liver
cells, in mouse liver and gut tissue to prove compound activity and target
engagement. Taken together, these data support the conclusion that garcinoic
acid efficiently activates PXR and may prove to be an amenable lead toward the
development of differentially acting PXR regulating compounds. | Desirée Bartolini; Francesca De Franco; Pierangelo Torquato; Rita Marinelli; Bruno Cerra; Riccardo Ronchetti; Arne Schön; Francesca Fallarino; Antonella De Luca; Guido Bellezza; Ivana Ferri; Angelo Sidoni; William G. Walton; Samuel J. Pellock; Matthew R. Redinbo; Sridhar Mani; Roberto Pellicciari; Antimo Gioiello; Francesco Galli | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ca4c891922abad2bce/original/garcinoic-acid-is-a-natural-and-selective-agonist-of-pregnane-x-receptor.pdf |
6337288dea6a22625103f828 | 10.26434/chemrxiv-2022-2c8c2 | Polyethylene glycol-b-polylactic acid polymersome elongation through osmotic pressure mediated membrane tension and fusion | Polyethylene glycol-b-polylactic acid (PEGPLA) polymersomes elongate under osmotic pressure. Hypertonic NaCl solutions statistically increased the zeta potential from negative to neutral. Change in charge and PLA hydrophilicity allow for binding of polymersomes depots to increase membrane surface area. PEGPLA polymersomes exhibit biomimicry in their homeostatic responses to increased osmotic pressure. | Owen Tabah; Christopher Pierce; Jessica Larsen | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biodegradable Materials; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6337288dea6a22625103f828/original/polyethylene-glycol-b-polylactic-acid-polymersome-elongation-through-osmotic-pressure-mediated-membrane-tension-and-fusion.pdf |
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