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65dfa1369138d23161429fb7 | 10.26434/chemrxiv-2024-38z8l | Optical Chopper for LOngitudinal-Detected (LOD) EPR | Dynamic nuclear polarization (DNP) is a nuclear magnetic resonance (NMR) hyperpolarization technique that mediates polarization transfer from unpaired electrons to nuclear spins. DNP performance can vary significantly depending on the types of polarizing agents employed, and the criteria for optimum DNP efficiency are not fully understood. Thus, a better understanding of the structure, electron paramagnetic resonance (EPR) linewidths, and relaxation properties would aid in designing more efficient DNP polarizing agents. However, EPR characterizations of the polarizing agents are typically performed in different environments (e.g., strength of magnetic field and microwave power) than typical DNP experiments. Here, we demonstrate a low-cost and home-built setup that enables in-situ EPR detection in a dual resonance DNP-NMR/EPR probe using an optical chopper. The chopper modulates the microwave irradiation, thereby modulating the longitudinal magnetization (Mz) of the electron spins. Our results of DNP and EPR spectra on TEMPOL using a solid-state microwave source at 6.7 T / 188 GHz and 4.2 K showed a good agreement. In principle, an optical chopper should be compatible with a wide range of microwave sources, including gyrotrons that output high-power microwaves. To verify this, we placed an optical chopper in between the waveguides of a 527 GHz gyrotron and successfully reproduced a DNP field profile similar to the case without a chopper. Hence, our work provides a proof-of-principle setup that could enable a gyrotron-based EPR spectrometer in the future. | Utsab Banerjee; Zhenfeng Pang; Thanh Phong Lê; Andrea Cappozi; Kong Ooi Tan | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dfa1369138d23161429fb7/original/optical-chopper-for-l-ongitudinal-detected-lod-epr.pdf |
60c74c77842e65d945db3314 | 10.26434/chemrxiv.12485786.v1 | Redox-neutral Photocatalytic C-H Carboxylation of Arenes and Styrenes with CO2 | Carbon
dioxide (CO<sub>2</sub>) is an attractive one-carbon (C1) building block in
terms of sustainability and abundance. However, its low reactivity limits applications
in organic synthesis as typically high-energy reagents are required to drive
transformations. Here, we present a redox-neutral C−H carboxylation of arenes
and styrenes using a photocatalytic approach. Upon blue-light excitation, the anthrolate
anion photocatalyst is able to reduce many aromatic compounds to their
corresponding radical anions, which react with CO<sub>2</sub> to afford
carboxylic acids. High-throughput screening and computational analysis suggest
that a correct balance between electron affinity and nucleophilicity of substrates
is essential. This novel methodology enables the carboxylation of numerous
aromatic compounds, including many that are not tolerated in classical
carboxylation chemistry. Over 50 examples of C−H functionalizations using CO<sub>2</sub>
or ketones illustrate a broad applicability. The method opens new opportunities
for late-stage C−H carboxylation and valorization of common arenes. | Matthias Schmalzbauer; Thomas D. Svejstrup; Florian Fricke; Peter Brandt; Magnus J. Johansson; Giulia Bergonzini; Burkhard Koenig | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c77842e65d945db3314/original/redox-neutral-photocatalytic-c-h-carboxylation-of-arenes-and-styrenes-with-co2.pdf |
65196d80a69febde9e090911 | 10.26434/chemrxiv-2023-hs8t9 | Unraveling the Intricacies of Surface Salt Formation on Mg(0001): Implications for Chloride-Ion Batteries | We present a density functional theory study of the initial steps of chlorine deposition on the Mg(0001) surface. Such processes occur in chloride-ion batteries in which lithium and magnesium are used as anode materials. In addition, it is also of fundamental interest, as halide adsorption on metal electrodes is an important process in interfacial electrochemistry. We discuss the adsorption properties and determine the stable adsorption structures, both with respect to the free chlorine molecule but also as a function of the electrode potential. We find indications of the immediate formation of the MgCl2 surface salt structure upon exposure of Cl to a Mg surface. These findings are discussed with respect to the conversion of the Mg anode to a MgCl2 configuration which provides the thermodynamical driving force for the discharge of a Cl-ion battery. | Kanchan Sarkar; Darius Hübner; Daniel Stottmeister; Axel Gross | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Surface | CC BY NC 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65196d80a69febde9e090911/original/unraveling-the-intricacies-of-surface-salt-formation-on-mg-0001-implications-for-chloride-ion-batteries.pdf |
64f899b679853bbd783ade06 | 10.26434/chemrxiv-2023-4d99t | Exploring the Use of ChatGPT as a Learning and Teaching Tool in Material Science and Nanotechnology Engineering Education | There is an increasing interest in using AI-based tools in university education, particularly in software education. However, it is essential to investigate its integration into learning hard sciences such as chemistry and physics. As the multidisciplinary field of Nanotechnology continues its trajectory of growth and significance, the incorporation of cutting-edge technological tools like ChatGPT will play a crucial role. In this work, we explore the innovative use of ChatGPT as a learning and teaching tool, specifically within the realm of nanotechnology education. To this end, we use a qualitative research approach; we ask nanotechnology-related questions to ChatGPT to generate data, and we evaluate the responses we receive based on their quality and usability (i.e., correctness, relevance, and educational value). Thus, we discuss the profound effects and capabilities of ChatGPT in assisting students’ learning of complex nanotechnological concepts and educators’ enhancement of their teaching methodologies. We also highlight the opportunities, challenges, and ethical concerns. | Burcu Ünlütabak; Zeliha Cansu Canbek Ozdil; Elif Sümeyye Cirit | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f899b679853bbd783ade06/original/exploring-the-use-of-chat-gpt-as-a-learning-and-teaching-tool-in-material-science-and-nanotechnology-engineering-education.pdf |
67bda1fffa469535b9dad3c4 | 10.26434/chemrxiv-2025-56x1p | Meta effect enables redder and larger Stokes shift
chromophores by enhanced aromaticity reversal | Compact fluorescent molecules with meta-positioned donor (D) and acceptor (A) groups have recently demonstrated extraordinary photophysical properties such as red emission and large Stokes shifts for advanced bioimaging and optoelectronic applications. However, it remains elusive how such simple D–A configuration can give rise to these unique properties which para isomers lack. Herein, we unlock the fundamental photophysics and its origin of “meta effect” by systematically investigating series of para and meta chromophores with varying donor and acceptor structures. Compared to the para isomers, meta chromophores possess redder emission, larger Stokes shifts, stronger solvatochromism, solvent-dependent fluorescence quantum yields (FQYs), and lower extinction coefficients. We reveal that the redder emission and larger Stokes shift in meta chromophores stem from the enhanced aromaticity reversal and ensuing relief of
excited-state antiaromaticity, amplified by solvation. Since large Stokes shifts hurt FQYs mainly via conical intersections, we propose feasible mitigation strategies to improve meta chromophores toward “all-in-one” fluorophores. | Cheng Chen; Jiawei Liu; Ivan N. Myasnyanko; Daniil I. Rudik; Anita H. Adams; Alice R. Walker; Mikhail S. Baranov; Chong Fang | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bda1fffa469535b9dad3c4/original/meta-effect-enables-redder-and-larger-stokes-shift-chromophores-by-enhanced-aromaticity-reversal.pdf |
67b14dd2fa469535b98acb94 | 10.26434/chemrxiv-2025-t2dr4 | Capillary Zone Electrophoresis-Mass Spectrometry of Intact G Protein-Coupled Receptors Enables Proteoform Profiling | G protein-coupled receptors (GPCRs) are the largest class of integral membrane receptors and responsible for transmitting diverse signals in response to extracellular stimuli. Post-translational modifications serve to dictate the subcellular trafficking and function of a GPCR across space and time. Despite significant interest in mapping the diversity of GPCR modification states (proteoforms), technical challenges have hindered this characterization. While advancements in membrane mimetics and mass spectrometry instrumentation have improved analysis, current workflows require large amounts of homogenous protein, limiting the study of many GPCRs from mammalian sources. Here, we present capillary zone electrophoresis (CZE) as an inline separatory tool for characterizing proteoforms of both intact and partially digested GPCRs. This method allowed for the characterization of multiple proteoforms of both the beta-2-adrenergic receptor and metabotropic glutamate receptor 2 using low sample volumes and without buffer optimization. Notably, in the case of smaller phosphorylated analytes, CZE was able to readily separate positional phosphorylation isomers, and provide superior fragmentation coverage to conventional reverse phase-liquid chromatography (RP-LC). | Ashley Ives; Kevin Jooss; Rafael Melani; Ryan Fellers; John Janetzko; Neil Kelleher | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b14dd2fa469535b98acb94/original/capillary-zone-electrophoresis-mass-spectrometry-of-intact-g-protein-coupled-receptors-enables-proteoform-profiling.pdf |
64a455789ea64cc1676e7c78 | 10.26434/chemrxiv-2023-rwvcx | Multivariate Metal-Organic Frameworks based pH-responsive dual-drug delivery system for chemotherapy and chemodynamic therapy | Combination therapy has emerged as a promising strategy due to its synergistic therapeutic pathways that enhance anticancer efficacy and limits the emergence of drug resistance. In this work, MIL-88B type multivariate (MTV-1) nanocarriers based on mixed linker (1, 4-benzenedicarboxylic acid and biphenyl-4,4'-dicarboxylic acid ) and metals (iron and cobalt) were synthesized. Presence of the distinct linkers modified the pore makeup of MTV-1 and facilitated the co-encapsulation of two anticancer drugs of varying molecular sizes; 5-Fluorouracil (5-FU) and Curcumin (CUR). The drug loading measurements on MTV-1@5-FU+CUR represented a loading capacity of 15.9wt% for 5-FU and 9.3wt% for CUR, respectively. They further exhibited a pH-responsive drug release pattern with higher concentrations of 5-FU and CUR released at pH 5.5 (simulating cancer microenvironment) compared to pH 7.4 (physiological environment). Moreover, we also demonstrated that MTV-1 MOFs, due to the presence of mixed valence metal ions, could perform peroxidase-like activity and catalyzes H2O2 decomposition to produce •OH radicals for chemodynamic therapy. Cell cytotoxicity assays exhibited significant inhibitory effects of MTV-1@5-Fu+CUR against HepG2 cells with an IC50 of 78.7 g/mL. Together with dual-drug loading, pH-responsive release, and chemodynamic therapy, MTV-1 show excellent potential for multifunctional anticancer treatment. | Muhammad Usman Akbar; Arslan Akbar; Umair Ali Khan Saddozai; Malik Ihsan Ullah Khan; Muhammad Zaheer; Muhammad Badar | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a455789ea64cc1676e7c78/original/multivariate-metal-organic-frameworks-based-p-h-responsive-dual-drug-delivery-system-for-chemotherapy-and-chemodynamic-therapy.pdf |
65fc5ce4e9ebbb4db9310ac2 | 10.26434/chemrxiv-2024-pwdpj | A Biomimetic Multi-Component Subunit Vaccine via Ratiometric Loading of Hierarchical Hydrogels | The development of subunit vaccines that mimic the molecular complexity of attenuated vaccines has been limited by the difficulty in reliably delivering multiple chemically diverse payloads at controllable concentrations. We report on hydrogels that use a single homopolymer structure of poly(propylene sulfone) to enable the ratiometric loading of a protein antigen and four physicochemically distinct adjuvants in a hierarchical manner. The optimized vaccine consisted of immunostimiulants that were either adsorbed to or encapsulated within nanogels, which were capable of noncovalent anchoring to subcutaneous tissues via protein-affinity coronas. These 5-component nanogel vaccines demonstrated enhanced humoral and cell-mediated immune responses compared to formulations with standard single adjuvant and antigen pairing. The use of a single simple homopolymer capable of rapid and stable loading and deliver of diverse molecular cargoes holds promise for facile development and optimization of scalable subunit vaccines and complex therapeutic formulations for a wide range of biomedical applications. | Fanfan Du; Simseok Yuk; Yuan Qian; Michael Vincent; Sharan Bobbala; Tirzah Abbott; Hyeohn Kim; Yang Li; Haoyu Li; Sijia Baofu; Baofu Qiao; Evan Scott | Materials Science; Aggregates and Assemblies; Biological Materials; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc5ce4e9ebbb4db9310ac2/original/a-biomimetic-multi-component-subunit-vaccine-via-ratiometric-loading-of-hierarchical-hydrogels.pdf |
66ce5ba7f3f4b052905063ce | 10.26434/chemrxiv-2024-xzx5t | Reversible Dinitrogen Binding by an Intermediate Spin Monovalent Chromium Complex | A unique low valent 15 e- Cr(I) species, Cp*Cr(CNArDipp2)2 (2) (Cp* = Me5C5, CNArDipp2 = 2,6-(2,6-(iPr)2C6H3)2C6H3) was isolated under Ar atmosphere. It’s intermediate spin ground state (S = 3/2) was determined via Evans’s method with 1H NMR spectroscopy, and electron paramagnetic resonance (EPR) spectroscopy. N2 reversibly binds 2 to afford a 17 e- low spin (S = 1/2) complex, Cp*CrN2(CNArDipp2)2 (2-N2), This dynamic N2 coordination was characterized based upon their distinct magnetic properties via collaborative analysis of Evans’s method and SQUID magnetometry. One electron reduction of 2 or 2-N2 under N2 atmosphere effectively suppress the N2 elimination to give a saturated monoanionic species, KCp*CrN2(CNArDipp2)2 (4). Compound 2 can also be further reduced with 2 equiv. of KC8 to generate a dianionic unsaturated metalloradical, K2Cp*Cr(CNArDipp2)2 (5), The exceedingly red shifted vCN stretching bands suggest highly activated C-N triple bond of the bulky terphenyl isocyanide ligands. | Shuai Wang; Jeremy Hilgar; Arnold Rheingold; Jeffrey Rinehart ; Joshua Figueroa | Organometallic Chemistry; Coordination Chemistry (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ce5ba7f3f4b052905063ce/original/reversible-dinitrogen-binding-by-an-intermediate-spin-monovalent-chromium-complex.pdf |
60c74a620f50dbe983396a71 | 10.26434/chemrxiv.9853856.v4 | Discovering new lipidomic features using cell type specific fluorophore expression to provide spatial and biological specificity in a multimodal workflow with MALDI IMS | <p></p><div>
<p>Identifying the spatial distributions
of biomolecules in tissue is crucial for understanding integrated function.
Imaging Mass Spectrometry (IMS) allows simultaneous mapping of thousands of
biosynthetic products such as lipids but has needed a means of identifying
specific cell-types or functional states to correlate with molecular
localization. We report here advances starting from identity marking with a
genetically encoded fluorophore. The fluorescence emission data were integrated
with IMS data through multimodal image processing with advanced registration
techniques and data-driven image fusion. In an unbiased analysis of spleens,
this integrated technology enabled identification of ether lipid species
preferentially enriched in germinal centers. We propose that this use of genetic
marking for microanatomical regions of interest can be paired with molecular
information from IMS for any tissue, cell-type, or activity state for which
fluorescence is driven by a gene-tracking allele and ultimately with outputs of
other means of spatial mapping.</p>
</div><br /><p></p> | Marissa A. Jones; Sung Hoon Cho; Nathan Heath Patterson; Raf Van de Plas; Jeffrey Spraggins; Mark R. Boothby; Richard M. Caprioli | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a620f50dbe983396a71/original/discovering-new-lipidomic-features-using-cell-type-specific-fluorophore-expression-to-provide-spatial-and-biological-specificity-in-a-multimodal-workflow-with-maldi-ims.pdf |
62503c615b90093a95083d4e | 10.26434/chemrxiv-2022-lfbdn | Reactivities of 1,2-, 1,3-, and 1,4- Dihydroxynaphthalenes toward Electrogenerated Superoxide in N,N-Dimethylformamide through Proton-coupled Electron Transfer | We have carried out an electrochemical and theoretical study on the reactivity of 1,2-, 1,3-, and 1,4-dihydroxynaphthalenes (1<i>n</i>H<sub>2</sub>NQ, <i>n</i> = 2, 3, 4) toward electrogenerated superoxide radical anion (O<sub>2</sub><sup>•−</sup>) in <i>N</i>,<i>N</i>-dimethylformamide. Cyclicvoltammetry and in situ electrolytic electron spin resonance measurements revealed that the quinone–hydroquinone π-conjugation plays an important role in a successful O<sub>2</sub><sup>•−</sup> scavenging by 12H<sub>2</sub>NQ and 14H<sub>2</sub>NQ through proton-coupled electron transfer (PCET) reaction. The reactivities of 12H<sub>2</sub>NQ and 14H<sub>2</sub>NQ toward O<sub>2</sub><sup>•−</sup> were mediated by the ortho- (catechol) or para-diphenol (hydroquinone) moieties, as experimentally confirmed in comparative analyses with catechol, hydroquinone, and 13H<sub>2</sub>NQ, aided by density functional theory (DFT) calculations. The electrochemical and DFT results suggested that a concerted PCET mechanism involving two-proton transfers and one-electron transfer proceeds with a superior kinetic, demonstrating a successful O<sub>2</sub><sup>•−</sup> scavenging by 12H<sub>2</sub>NQ and 14H<sub>2</sub>NQ. Furthermore, a subsequent electron transfer between molecular dioxygen and product-naphthoquinone-radicals was observed, where O<sub>2</sub><sup>•−</sup> was generated. The DFT analysis suggested that the spin distribution on the planar naphthalene ring embodies the superior kinetics of the PCET and the subsequent generation of O<sub>2</sub><sup>•−</sup> from dioxygen demonstrated in the electrochemical results. | Tatsushi Nakayama; Uno Bunji | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Electrochemical Analysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62503c615b90093a95083d4e/original/reactivities-of-1-2-1-3-and-1-4-dihydroxynaphthalenes-toward-electrogenerated-superoxide-in-n-n-dimethylformamide-through-proton-coupled-electron-transfer.pdf |
60c750859abda2e498f8da59 | 10.26434/chemrxiv.13028192.v1 | A Single Point Mutation Converts a Proton-pumping Rhodopsin into a Turn-on Fluorescent Sensor for Chloride | <p>The visualization of chloride in living cells with fluorescent sensors is linked to our ability to design hosts that can overcome the energetic penalty of desolvation to bind chloride in water. Fluorescent proteins can be used as biological supramolecular hosts to address this fundamental challenge. Here, we showcase the power of protein engineering to convert the fluorescent proton-pumping rhodopsin GR from <i>Gloeobacter violaceus</i> into GR1, a turn-on fluorescent sensor for chloride in detergent micelles and in live <i>Escherichia coli</i>. This non-natural function was unlocked by mutating D121, which serves as the counterion to the protonated retinylidene Schiff base chromophore. Substitution from aspartate to valine at this position (D121V) creates a binding site for chloride. The addition of chloride tunes the p<i>K</i><sub>a </sub>of the chromophore towards the protonated, fluorescent state to generate a pH-dependent response. Moreover, ion pumping assays combined with bulk fluorescence and single cell fluorescence microscopy experiments with <i>E. coli</i>, expressing a GR1 fusion with cyan fluorescent protein, show that GR1 does not pump ions nor sense membrane potential but instead provides a reversible, ratiometric readout of chloride. This discovery sets the stage to use natural and laboratory-guided evolution to build a family of rhodopsin fluorescent chloride sensors for cellular applications and learn how proteins can evolve and adapt to bind anions in water.</p> | Jasmine Tutol; Jessica Lee; Hsichuan Chi; Farah Faizuddin; Sameera Abeyrathna; Qin Zhou; Faruck Morcos; Gabriele Meloni; Sheel Dodani | Supramolecular Chemistry (Org.); Imaging; Spectroscopy (Anal. Chem.); Bioinorganic Chemistry; Sensors; Biochemistry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750859abda2e498f8da59/original/a-single-point-mutation-converts-a-proton-pumping-rhodopsin-into-a-turn-on-fluorescent-sensor-for-chloride.pdf |
63651df4ee31864b167f691c | 10.26434/chemrxiv-2022-dv25j | 4D Printed Biocompatible Magnetic Composite for Minimally Invasive Deployable Structures | 4D printing of shape memory polymers (SMPs) and composites has been realized for a multitude of applications spanning healthcare, soft robotics, environment, space, etc. However, demonstrating such materials for in vivo applications has not been possible to a large extent due to the unavailability of suitable materials with recovery temperatures around physiological levels. Also, direct heating to trigger shape recovery in SMPs is not a practical and elegant approach in many cases. In this study, polylactide-co-trimethylene carbonate (PLMC), an SMP, has been endowed with magnetic iron oxide (Fe3O4) nanoparticles to realize remote heating under alternating magnetic field and at temperatures around 40°C. The PLMC-5% Fe3O4 composite was 3D printed into a variety of shapes, including scaffolds, fixed into pre-programmed temporary shapes to be deployed minimally invasively, and then recovered into original shapes under magnetic actuation. The shape recovery was excellent (>99%) and fast (under 20-30 s). Additionally, these magnetic composites could potentially be guided to the site of deployment through permanent magnets. Both PLMC and its composites were printed in distinct regions of a single structure, deformed, and then recovered by selective and sequential stimulation of magnetic field and heat, respectively. The materials (both PLMC and its nanocomposite) exhibited favorable in vitro and in vivo biocompatibility, thus highlighting their usefulness for being used as deployable tissue scaffolds and medical devices, among other implantable applications. | Saswat Choudhury; Akshat Joshi; Debayan Dasgupta; Ambarish Ghosh; Sonal Asthana; Kaushik Chatterjee | Materials Science; Polymer Science; Nanoscience; Composites; Magnetic Materials; Materials Processing | CC BY NC 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63651df4ee31864b167f691c/original/4d-printed-biocompatible-magnetic-composite-for-minimally-invasive-deployable-structures.pdf |
65f80db166c138172938cd83 | 10.26434/chemrxiv-2023-gmpmg-v2 | Predicting Redox Potentials by Graph-Based Machine Learning Methods | The evaluation of oxidation and reduction potentials is a pivotal task in various chemical fields. However, their accurate prediction by theoretical computations, which is a complementary task and sometimes the only alternative to experimental measurement, may be often resource-intensive and time-consuming. This paper addresses this challenge through the application of machine learning techniques, with a particular focus on graph-based methods (such as graph edit distances, graph kernels, and graph neural networks) that are reviewed to enlighten their deep links with theoreti- cal chemistry. To this aim, we establish the ORedOx159 database, a comprehensive, homogeneous (with reference values stemming from density functional theory calculations), and reliable resource containing 318 one-electron reduction and oxidation reactions and featuring 159 large organic com- pounds. Subsequently, we provide an instructive overview of the good practice in machine learning and of commonly utilized machine learning models. We then assess their predictive performances on the ORedOx159 dataset through extensive analyses. Our simulations using descriptors that are computed in an almost instantaneous way result in a notable improvement in prediction accuracy, with mean absolute error (MAE) values equal to 5.6 kcal mol−1 for reduction and 7.2 kcal mol−1 for oxidation potentials, which paves a way toward efficient in silico design of new electrochemical systems. | Linlin Jia; Éric Brémond; Larissa Zaida; Benoit Gaüzere; Vincent Tognetti; Laurent Joubert | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f80db166c138172938cd83/original/predicting-redox-potentials-by-graph-based-machine-learning-methods.pdf |
62b99d855983a9ad63713190 | 10.26434/chemrxiv-2022-6xln5 | Experimentally-validated ab initio crystal structure prediction of novel metal-organic framework materials | First-principles crystal structure prediction (CSP) is the most powerful approach for materials discovery, enabling the prediction and evaluation of properties of new solid phases based only on a diagram of their underlying components. Here, we present the first CSP-based discovery of metal-organic frameworks (MOFs), offering a broader alternative to conventional techniques which rely on geometry, intuition and experimental screening. Phase landscapes were calculated for three systems involving flexible Cu(II) nodes, which could adopt a potentially limitless number of network topologies and are not amenable to conventional MOF design. The CSP procedure was validated experimentally, through synthesis of materials whose structures perfectly matched those found among the lowest energy calculated structures, and whose relevant properties, such as combustion energies, could immediately be evaluated from CSP-derived structures. | Yizhi Xu; Joseph M. Marrett; Hatem M. Titi; James P. Darby; Andrew J. Morris; Tomislav Friščić; Mihails Arhangelskis | Theoretical and Computational Chemistry; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b99d855983a9ad63713190/original/experimentally-validated-ab-initio-crystal-structure-prediction-of-novel-metal-organic-framework-materials.pdf |
60c74cab4c89191a26ad3695 | 10.26434/chemrxiv.11881542.v2 | Enlighten2: Molecular Dynamics Simulations of Protein-Ligand Systems Made Accessible | <div>Motivation: Experimental structural data can allow detailed insight into protein structure and protein-ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein-ligand interactions is obtained, whereas dynamical information is often required for deeper understanding and to assess the effect of mutations. Molecular dynamics (MD) simulations can provide such information, but setting up and running these simulations is not straightforward and requires expert knowledge. There is thus a need for a tool that makes protein-ligand simulation easily accessible to non-expert users.</div><div>Results: We present Enlighten2: efficient simulation protocols for protein-ligand systems alongside a user-friendly plugin to the popular visualization program PyMOL. With Enlighten2, non-expert users can straightforwardly run and visualize MD simulations on protein-ligand models of interest. There is no need to learn new programs and all underlying tools are free and open source.</div><div>Availability: The Enlighten2 Python package and PyMOL plugin are free to use under the GPL3.0 licence and can be found at https://enlighten2.github.io. We also provide a lightweight Docker image via DockerHub that includes Enlighten2 with all the required utilities.</div> | Kirill Zinovjev; Marc W. van der Kamp | Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2020-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cab4c89191a26ad3695/original/enlighten2-molecular-dynamics-simulations-of-protein-ligand-systems-made-accessible.pdf |
643e817583fa35f8f6d8ac7c | 10.26434/chemrxiv-2023-52t9s-v2 | Charge transport in perovskite solar cells – a material interface study of transition metal chalcogenides with MAPbX3 | Hetero junctions are expected to show an induced electric field generation at their material interface/s that influences the exci-ton separation and transport in solar cell devices. Since Perov-skite Solar cells (PSCs) having multi material junction interfac-es in their configurations, their performance is inevitably influ-enced by this feature. The differences in the crystallization process at the confluences of the materials regarding manufac-turing might lead to differences in the electronic charge rear-rangement between the materials and form an induced electric field generation. In this study, an Ab initio Density Functional Theory (DFT) study is employed to scrutinize the charge re-distribution among the MAPbI3 and two-dimensional (2D) lay-ered, transition metal chalcogenides (TMCs, i.e., TcS2, TcSe2) material interfaces. These 2D materials have been assessed for their potential feasibility for either electron or hole transporting layers (ETL and HTL) application in PSCs. The electronic band edges of these materials were compared between three MAPbX3 (X=Cl, Br, or I) materials to investigate this possibility for PSCs. Quantitative inter layer charge redistribution and internal electric field analysis between perovskite and these TMCs is conducted and compared using Bader charge analysis. The effects of induced strain in 2D materials, because of lattice mismatch on band edge positions, is also delineated. The re-vised band edges have considerably altered the initially predict-ed charge transport effectiveness. | Sri K M; Aijun Du; Salvy P. Russo | Theoretical and Computational Chemistry; Materials Science; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643e817583fa35f8f6d8ac7c/original/charge-transport-in-perovskite-solar-cells-a-material-interface-study-of-transition-metal-chalcogenides-with-ma-pb-x3.pdf |
6527eddfbda59ceb9a6df970 | 10.26434/chemrxiv-2023-8f8n8 | Moisture-Assisted Hydroboration of Nitriles and Conversion Thereof to N-Heterocyles and N-Containing Derivatives | The recent revelation of hidden-borane catalysis has revolutionized the field of catalytic hydroboration in organic synthesis. Many nucleophilic reaction promoters, previously believed to be the catalysts, in fact primarily facilitated the formation of borane (BH3), which subsequently acted as the true catalyst. This revelation prompted us to explore the untapped potential of these unexpected transformations, with a view to simplify hydroboration using more cost-effective and environmentally friendly nucleophilic pre-catalysts. Via computational studies, we were able to identify that water can actually undertake that role. Herein, we report a study on simple hydroboration of nitriles, a notorious-ly challenging yet synthetically valuable class of substrates, using nothing more than moisture as an activating agent. This moisture-assisted nitrile hydroboration process can seamlessly integrate with a range of downstream transfor-mations in a one-pot fashion to produce valuable N-containing products such as symmetrical imines, thioureas and bis(alcohol)amines as well as N-heterocyclic derivatives such as pyrroles, pyridines, pyridinium salts, 2-iminothiazolines and carbazoles. | Hoai Son Doan; Khanh Binh Mai; Thanh Vinh Nguyen | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6527eddfbda59ceb9a6df970/original/moisture-assisted-hydroboration-of-nitriles-and-conversion-thereof-to-n-heterocyles-and-n-containing-derivatives.pdf |
60c74169bb8c1ab6be3d9f47 | 10.26434/chemrxiv.8049938.v1 | Biodegradable Hybrid Block Copolymer – Lipid Vesicles as Potential Drug Delivery Systems | <p>The anticipated benefits of nano-formulations
for drug delivery are well known: for nanomedicines to achieve this potential,
new materials are required with predictive and tuneable properties. Excretion
of excipients following delivery is advantageous to minimise the possibility of
adverse effects; biodegradability to non-toxic products is therefore desirable.
With this in mind, we aim to develop tuneable hybrid lipid-block copolymer
vesicle formulations where the hydrophilic polymer block is polyethylene glycol
(PEG), which has accepted biocompatibility, and the hydrophobic block of the
polymer is biodegradable: polycaprolactone (PCL) or polylactide (PLA). We
investigate five different block copolymers for the formation of 1:1 phospholipid:polymer
hybrid vesicles, compare their properties to the appropriate unitary liposome
(POPC) and polymersome systems and assess their potential for future development
as nanomedicine formulations. The PEG-PCL polymers under investigation do not
form polymersomes and exhibit poor colloidal and/or encapsulation stability in
hybrid formulations with lipids. The properties of PEG-PLA hybrid vesicles are
found to be more encouraging: they have much enhanced passive loading of a
hydrophilic small molecule (carboxyfluorescein) compared to their respective polymersomes
and exhibit more favourable release kinetics in the presence of serum compared
to the liposome. Significantly, burst release from hybrid vesicles can be
substantially reduced by making the polymer components of the hybrid vesicle a
mixture containing 10 mol% of PEG<sub>16</sub>-PLA<sub>25</sub> that is
intermediate in size between the phospholipid and larger PEG<sub>45</sub>-PLA<sub>54</sub>
components. We conclude that hybrid lipid/PEG-PLA vesicles warrant further
assessment and development as candidate drug delivery systems.</p> | Sanobar Khan; James McCabe; Kathryn Hill; Paul Beales | Biopolymers; Drug delivery systems; Polymer blends; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74169bb8c1ab6be3d9f47/original/biodegradable-hybrid-block-copolymer-lipid-vesicles-as-potential-drug-delivery-systems.pdf |
62f507b9a014474ea5b3da32 | 10.26434/chemrxiv-2022-xgdnx | Organic Near Infrared Photothermal Materials with Temperatures up to 450 oC Constructed by Cycloaddition-Retroelectrocyclization Click Reaction | Organic photothermal materials, especially those with near-infrared (NIR) absorbance and excellent photothermal properties, have attracted considerable attention for applications in energy conversion and biomedical therapy. In generally, synthesis of above organic photothermal materials require the use of high temperature, expensive noble metal catalysts, or UV lamp radiation. Herein, a facile [2+2] cycloaddition-cycloreversion ([2+2] CA-CR) reaction is employed for the efficient synthesis of nonplanar molecule (2ATPE-2F4) containing triphenylamine (TPA) and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4-TCNQ) under ambient conditions by taking advantage of its click feature, atom-economic, unity yield, and simple purified procedure, etc. The resultant product exhibits exceptional properties including broad absorption edge over 1000 nm, and substantial radical characters with paramagnetic behavior, etc. Excitingly, it exhibits excellent photothermal properties and the temperature could be swiftly increased to as high as 450 °C in solid powder upon photo-irradiation. Thanks to the excellent photothermal properties, 2ATPE-2F4 was used for the construction of high temperature (> 200 oC) shape memory actuators triggered with NIR light. In addition, upon assembling the 2ATPE-2F4 into nanoparticle (2ATPE-2F4 NPs), it displayed good biocompatibility, excellent photothermal stability, and high photothermal conversion efficiency (PCE), enable it to be used to realize high-efficiency photothermal therapy. This work demonstrates the excellent potential of [2+2] CA-CR reactions for the synthesis of high-performance organic NIR photothermal materials. | Pengbo Han; Guiquan Zhang; He Xu; Rong Hu; Anjun Qin; Ben Zhong Tang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f507b9a014474ea5b3da32/original/organic-near-infrared-photothermal-materials-with-temperatures-up-to-450-o-c-constructed-by-cycloaddition-retroelectrocyclization-click-reaction.pdf |
60c73cc94c891981e9ad1af3 | 10.26434/chemrxiv.14727573.v1 | Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost | Recent concurrent advances in methodology development, computer hardware and simulation software has transformed our ability to make practical, quantitative predictions of relative ligand binding affinities to guide rational drug design. In the past, these calculations have been hampered by the lack of affordable software with highly efficient implementations of state-of-the-art methods on specialized hardware such as graphical processing units, combined with the paucity of available workflows to streamline throughput for real-world industry applications. Herein we discuss recent methodology development, GPU-accelerated implementation, and workflow creation for alchemical free energy simulation methods in the AMBER Drug Discovery Boost (AMBER-DD Boost) package available as a patch to AMBER20. Among the methodological advances are 1) new methods for the treatment of softcore potentials that overcome long standing end-point catastrophe and softcore imbalance problems and enable single-step alchemical transformations between ligands, and 2) new adaptive enhanced sampling methods in the "alchemical" (or "λ") dimension to accelerate convergence and obtain high precision ligand binding affinity predictions, 3) robust network-wide analysis methods that include cycle closure and reference constraints and restraints, and 4) practical workflows that enable streamlined calculations on large datasets to be performed. Benchmark calculations on various systems demonstrate that these tools deliver an outstanding combination of accuracy and performance, resulting in reliable high-throughput binding affinity predictions at affordable cost.<br /> | Tai-Sung Lee; Hsu-Chun Tsai; Abir Ganguly; Timothy J Giese; Darrin M. York | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc94c891981e9ad1af3/original/robust-efficient-and-automated-methods-for-accurate-prediction-of-protein-ligand-binding-affinities-in-amber-drug-discovery-boost.pdf |
64c2b96b658ec5f7e5489081 | 10.26434/chemrxiv-2023-j9h92 | The Challenge of Balancing Model Sensitivity and Robustness in Predicting Yields: A Benchmarking Study of Amide Coupling Reactions | Accurate prediction of reaction yield is the holy grail for computer-assisted synthesis, but current models have failed to generalize to large literature datasets. To understand the causes and inspire future design, we systematically benchmarked the yield prediction task. We carefully curated and augmented a literature dataset of 41,239 amide coupling reactions, each with information on reactants, products, intermediates, yields, and reaction contexts, and provided 3D structures for the molecules. We calculated molecular features related to 2D and 3D structure information, as well as physical and electronic properties. These descriptors were paired with 4 categories of machine learning methods (linear, kernel, ensemble, and neural network), yielding valuable benchmarks about feature and model performance. Despite the excellent performance on a high-throughput experiment (HTE) dataset (R2 around 0.9), no method gave satisfying results on the literature data. The best performance was an R2 of 0.395 ± 0.020 using stack technique. Error analysis revealed that reactivity cliff and yield uncertainty are the main reasons for incorrect predictions. Removing reactivity cliffs and uncertain reactions boosted the R2 to 0.457 ± 0.006. These results highlight that yield prediction models must be sensitive to the reactivity change due to the subtle structure variance, as well as be robust to the uncertainty associated with yield measurements. | Zhen Liu; Yurii S. Moroz; Olexandr Isayev | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c2b96b658ec5f7e5489081/original/the-challenge-of-balancing-model-sensitivity-and-robustness-in-predicting-yields-a-benchmarking-study-of-amide-coupling-reactions.pdf |
65bbe2dee9ebbb4db9757a3a | 10.26434/chemrxiv-2024-1td17 | Leveraging Temperature-Dependent (Electro)Chemical Kinetics for High-Throughput Flow Battery Characterization | The library of redox-active organics that are potential candidates for electrochemical energy storage in flow batteries is exceedingly vast, necessitating high-throughput characterization of molecular lifetimes. Demonstrated extremely stable chemistries require accurate yet rapid cell cycling tests, a demand often frustrated by time-denominated capacity fade mechanisms. We have developed a high-throughput setup for elevated temperature cycling of redox flow batteries, providing a new dimension in characterization parameter space to explore. We utilize it to evaluate capacity fade rates of aqueous redox-active organic molecules, as functions of temperature. We demonstrate Arrhenius-like behaviour in the temporal capacity fade rates of multiple flow battery electrolytes, permitting extrapolation to lower operating temperatures. Collectively, these results highlight the importance of accelerated decomposition protocols to expedite the screening process of candidate molecules for long lifetime flow batteries. | Eric Fell; Thomas George; Yan Jing; Roy Gordon; Michael Aziz | Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bbe2dee9ebbb4db9757a3a/original/leveraging-temperature-dependent-electro-chemical-kinetics-for-high-throughput-flow-battery-characterization.pdf |
62d13b137aab588480bfc092 | 10.26434/chemrxiv-2022-wl2h1 | The Effect of Cation Exchange on the Pore Geometry of Zeolite L | Zeolites with the LTL framework topology are attractive materials for use in optoelectronics, gas adsorption and as chemical reactors. This is due to their unique, one-dimensional (1D) channel systems which are large enough to act as hosts for organic dye molecules and other guest materials. Here, we use high-resolution X-ray diffraction to show the effect of cation exchange on the pore geometry of LTL-type zeolites. The nature of the exchanging cation is shown to influence the free access diameter, volume and water content of the 12-ring (12R) channel systems. As such, cation exchange can be used to tune the molecular sieving and adsorption properties of LTL-type zeolites. This offers new possibilities for these materials in technologically relevant applications. | Lisa Price; Zoe Jones; Antony Nearchou ; Gavin Stenning ; Daniel Nye ; Asel Sartbaeva | Materials Science; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d13b137aab588480bfc092/original/the-effect-of-cation-exchange-on-the-pore-geometry-of-zeolite-l.pdf |
6710cc6c51558a15ef537212 | 10.26434/chemrxiv-2024-g248c | Hydrogenation of Organic Molecules via Direct Mechanocatalysis | Mechanochemical hydrogenation of unsaturated C-C and C-O, as well as N-O and C-X bonds is successfully achieved without the use of solvents, ligands, or catalyst powders via ball milling. A variety of catalysts are electroplated onto the walls of the milling vessel, allowing for simple recycling and reuse of the catalytic material. Hydrogen gas is directly introduced into the milling vessel, eliminating the need for hydrogen donor compounds which contribute to waste production and suboptimal atom economy. This approach enables quantitative hydrogenation of unsaturated carbon-carbon bonds at ambient temperature and pressures as low as 1.5 bar in as little as 20 minutes. Mechanistic investigations suggest the reaction to be following established mechanisms for hydrogenation. Finally, chemoselective hydrogenation of various reducible functional groups was explored, demonstrating the versatility and efficiency of this solvent-free mechanochemical approach with simple catalyst recycling for hydrogenation reactions. | Maike Mayer; Maximilian Wohlgemuth; Sven Graetz; Lars Borchardt | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710cc6c51558a15ef537212/original/hydrogenation-of-organic-molecules-via-direct-mechanocatalysis.pdf |
66825eb3c9c6a5c07adedf7e | 10.26434/chemrxiv-2024-4nscw | Facile access to heterobimetallic MII/CuI complexes with a multichelate platform and their response towards CO2RR. | We describe the selective formation of heterobimetallic complexes, exploiting the coordination trends of the developed bis-terpyridyl trans-1,2-cyclohexadiamine platform (L) towards tetrakisacetonitrile transition metal precursors, [M(MeCN)4][BF4]2, M = Fe or Ni, and [Cu(MeCN)4][BF4]. The four species obtained are structurally characterised, and their cyclic voltammetry analysis reveals the impact of the CuI-atom presence on the heterobimetallic complexes under argon and carbon dioxide. Furthermore, carbon dioxide photoreduction studies are presented. | Samantha L. Peralta-Arriaga; Carlos García Bellido; Miguel Angel Martín-Neri; Francisco José Fernández-de-Córdova; Marc Robert; Orestes Rivada Wheelaghan | Inorganic Chemistry; Coordination Chemistry (Inorg.); Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66825eb3c9c6a5c07adedf7e/original/facile-access-to-heterobimetallic-mii-cu-i-complexes-with-a-multichelate-platform-and-their-response-towards-co2rr.pdf |
63ebcf0a9da0bc6b33ee99a4 | 10.26434/chemrxiv-2022-pbt49-v3 | Large Decrease in Melting Point of Benzoquinones via High-n Eutectic Mixing Predicted by a Regular Solution Model | Decreasing the melting point (Tm) of a mixture is of interest in cryopreservatives, molten salts, and battery electrolytes. One general strategy to decrease Tm, exemplified by deep eutectic solvents, is to mix components with favorable (negative) enthalpic interactions. We demonstrate a complementary strategy to decrease Tm by mixing many components with neutral or slightly positive enthalpic interactions, using the number of components (n) to increase the entropy of mixing and decrease Tm. In theory, under certain conditions this approach could achieve an arbitrarily low Tm. Furthermore, if the components are small redox-active molecules, such as the benzoquinones studied here, this approach could lead to high energy density flow battery electrolytes. Finding the eutectic composition of a high-n mixture can be challenging due to the large compositional space, yet is essential for ensuring the existence of a purely liquid phase. We reformulate and apply fundamental thermodynamic equations to describe high-n eutectic mixtures of small redox-active molecules (benzoquinones and hydroquinones). We illustrate a novel application of this theory by tuning the entropy of melting, rather than the enthalpy, in systems highly relevant to energy storage. We demonstrate with differential scanning calorimetry measurements that 1,4-benzoquinone derivatives exhibit eutectic mixing that decreases their Tm, despite slightly positive enthalpies of mixing (0-5 kJ/mol). By rigorously investigating all 21 binary mixtures of a set of seven 1,4-benzoquinone derivatives with alkyl substituents (Tm's between 44-120 °C), we find that the eutectic melting point of a mixture of all seven achieves a large decrease in Tm to -6 °C. We further determine that the regular solution model shows improvement over an ideal solution model in predicting the eutectic properties for this newly investigated type of mixture composed of many small redox-active organic molecules. | Antonio Baclig; Devi Ganapathi; Victoria Ng; Emily Penn; Jonathan Saathoff; William Chueh | Physical Chemistry; Materials Science; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ebcf0a9da0bc6b33ee99a4/original/large-decrease-in-melting-point-of-benzoquinones-via-high-n-eutectic-mixing-predicted-by-a-regular-solution-model.pdf |
62f58797180373f509a248e3 | 10.26434/chemrxiv-2022-rvxzx | Convenient Confinement: Interplay of Solution Conditions and Graphene Oxide Film Structure on Rare Earth Separations | Graphene oxide (GO) membranes are excellent candidates for a range of applications, including rare earth separations and radionuclide decontamination. Membrane performance varies widely under different conditions, as water and ion interactions with the membrane are strongly affected by small system changes. Feed solution pH is one critical factor, as pH, GO surface functionality, and ion speciation are interconnected parameters that cannot be controlled individually. Understanding nanoscale water and ion behavior near interfacial GO is critical for groundbreaking membrane advances, including improved selectivity and permeability.
We experimentally examine the impact of solution conditions on water and lanthanide interactions with self-assembled GO films and connect these results to GO membrane performance. The investigation of the confined films at the air-water interface with a combination of surface-specific spectroscopy and X-ray scattering techniques allows us to understand water and ion behaviors separately. Sum frequency generation spectroscopy reveals a dramatic change in interfacial water organization because of graphene oxide film deprotonation. Interfacial X-ray fluorescence measurements show a 17x increase in adsorbed lanthanide to the GO film from subphase pH 3 to pH 9. Liquid surface X-ray reflectivity data show an additional 2.7 e- per Å2 for GO films at pH 9 versus pH 3 as well. These data are connected to GO membrane performance, which show increased selectivity and decreased flux for membranes filtering pH 9 solutions. We posit insoluble lanthanide hydroxides form at higher pHs. Take together, these results highlight the importance of interfacial experiments on model GO systems.
| Amanda J. Carr; Seung Eun Lee; Raju R. Kumal; Wei Bu; Ahmet Uysal | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f58797180373f509a248e3/original/convenient-confinement-interplay-of-solution-conditions-and-graphene-oxide-film-structure-on-rare-earth-separations.pdf |
662f451f418a5379b0012795 | 10.26434/chemrxiv-2024-t8882 | Solvmate - A hybrid physical/ML approach to solvent recommendation leveraging a rank-based problem framework | The solubility in a given organic solvent is a key parameter in the synthesis, analysis and chemical processing of an active pharmaceutical ingredient. In this work, we introduce a new tool for organic solvent recommendation that ranks possible solvent choices requiring only the SMILES representation of the solvents and solute involved. We report on three additional innovations: First, a differential/relative approach to solubility prediction is employed, in which solubility is modeled using pairs of measurements with the same solute but different solvents. We show that a relative framing of solubility as ranking solvents improves over a corresponding absolute solubility model across a diverse set of selected features. Second, a novel semiempirical featurization based on extended tight-binding (xtb) is applied to both the solvent and the solute, thereby providing physically meaningful representations of the problem at hand. Third, we provide an open-source implementation of this practical and convenient tool for organic solvent recommendation. Taken together, this work could be of benefit to those working in diverse areas, such as chemical engineering, material science, or synthesis planning. | Jan Wollschläger; Floriane Montanari | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662f451f418a5379b0012795/original/solvmate-a-hybrid-physical-ml-approach-to-solvent-recommendation-leveraging-a-rank-based-problem-framework.pdf |
67b0b89881d2151a029c72c7 | 10.26434/chemrxiv-2025-x0q3g | An In-Silico Study on Transient Enzyme Diffusion and Adsorption within Lignocellulosic Biomass using a Multi-Scale Model | Diffusion of hydrolytic enzymes into biomass particles is a potential limiting step, which has yet to be studied in detail separate from intrinsic hydrolysis kinetics. We developed and applied a pore-enzyme diffusion model for both adsorbing and non-adsorbing enzymes and coupled them to reactor-level mass balance equations. With this multi-scale model, the effects of biomass particle porosity, size, and adsorption capacity on the characteristic time of enzyme diffusion and adsorption were predicted over an expected range of these parameters. Using a hydrolysis limiting threshold characteristic time for enzyme diffusion of 6 hours, this model mapped the transport parameter space between two distinct zones: diffusion limiting and non-diffusion limiting. The model also predicted a decrease in characteristic time with an increase in the biomass-to-enzyme loading ratio. At the particle level, characteristic time was most strongly affected by firstly adsorption capacity, then particle radius, adsorption affinity, and porosity. | Saketh Merugu; David Shonnard | Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Bioengineering and Biotechnology; Reaction Engineering; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b0b89881d2151a029c72c7/original/an-in-silico-study-on-transient-enzyme-diffusion-and-adsorption-within-lignocellulosic-biomass-using-a-multi-scale-model.pdf |
638f961b14d92d1b1da34965 | 10.26434/chemrxiv-2022-zm0kr | Understanding How Metal-Ligand Coordination Enables Solvent Free Ionic Conductivity in PDMS | Ionically conductive polymers are commonly made of monomers containing high polarity moieties to promote high ion dissociation, like poly(ethylene oxide) (PEO), polyvinylidene difluoride (PVDF), poly(vinyl alcohol) (PVA). However, the glass transition temperature ($T_g$) of these polymers are relatively high, and therefore yields a glassy state at room temperature and limits the mechanical flexibility of the material. Although polydimethylsiloxane (PDMS) has many attractive physical and chemical properties, including low glass transition temperature, mechanical flexibility, and good biocompatibility, its low dielectric constant suppresses ion dissociation. In this paper, we overcome this shortage by functionalizing the PDMS with ligands that can form labile coordination with metal ions, which greatly promotes the ion dissociation and improves the ionic conductivity by orders of magnitude. By combining an experimental study with a fully atomistic molecular dynamics simulation, we systematically investigated the ion transport mechanisms in this low $T_g$, low intrinsic conductivity material. | Xinyue Zhang; Jinyue Dai; Max Tepermeister; Jingjie Yeo; Meredith Silberstein | Theoretical and Computational Chemistry; Materials Science; Organometallic Chemistry; Aggregates and Assemblies; Electrochemistry - Organometallic; Ligands (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638f961b14d92d1b1da34965/original/understanding-how-metal-ligand-coordination-enables-solvent-free-ionic-conductivity-in-pdms.pdf |
66fc255351558a15efb79776 | 10.26434/chemrxiv-2024-gwrzq | Technoeconomic Insights into Metal Hydrides for Stationary Hydrogen Storage | Metal hydrides (MHs) are promising candidates for hydrogen storage due to their high volumetric energy densities and safety features. Recent developments suggest hydride systems can cycle and operate at pressures and temperatures favorable coupling with fuel cells for stationary long-duration energy storage applications. In this study, we present a conceptual design of a metal hydride-based storage system for backup power (0 to 20 MW supplied over 0 to 100 hours), and benchmark system cost and performance. Leveraging experimental hydrogen absorption and desorption data, we determine the uptake/release of hydrogen across likely pressure and temperature conditions, and estimate the equipment power, upfront capital cost, levelized cost of storage, land footprint, and energy density for a select number of metal hydrides and hypothetical operation scenarios. Our findings indicate that hydride-based storage systems hold significant size advantage in physical footprint, requiring up to 65% less land than the 170-bar compressed gas storage options. Metal hydride systems can be cost competitive with 350-bar compressed gas systems, with TiFe0.85Mn0.05 achieving $0.453/kWh and complex MH 2Mg(NH2)2-2.1LiH-0.1KH achieving $0.383/kWh, compared to $0.397/kWh for 350 bar compressed gas in the base case scenario. However, these advantages are sensitive to charging and discharging rate requirements, operational cycles and material manufacturing prices. Extending charging times and increasing operating cycles significantly reduce LCOS, especially for complex MHs, making them more competitive for applications with slow charging and long duration energy storage needs. Key strategies to further enhance the competitiveness of MHs include leveraging waste heat from fuel cells, increasing hydrogen uptake, and achieving metal hydride production costs of US$10/kg. | Xinyi Wang; Peng Peng; Matthew Witman; Vitalie Stavila; Mark Allendorf; Hanna Breunig | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc255351558a15efb79776/original/technoeconomic-insights-into-metal-hydrides-for-stationary-hydrogen-storage.pdf |
60c7436a0f50db0db4395ecf | 10.26434/chemrxiv.9121739.v1 | Visualized Spontaneous Molecular Directed Motion in Solid State | The real-time <a>monitoring of</a> spontaneous molecular directed motion is a highly important but very challenging task. In this work, a rod-like
<a>aggregation-induced emission</a> (AIE) molecule of
salicylaldehyde 4-butoxyaniline Schiff base (<b>SBA</b>) was deliberately
designed and facilely synthesized, which exhibits unique self-recovery property
from semi-ordered structure to ordered structure alongwith significant fluorescence change after grinding. The monitoring of the
fluorescence change provides rich kinetic information including kinetic order,
rate constants, half-life and apparent activation energy of
the spontaneous molecular directed motion process. Unlike instrumental
analytical methods such as PXRD and AFM, which only give the information of a
stable state of samples, the
fluorescence method provided a new perspective to real-time visualize
spontaneous molecular directed motion <i>in situ</i> in solid state. | Jianxun Liu; Chang Xing; Donghui Wei; Cuiping Yang; Qiuchen Peng; Hongwei Hou; Yuanyuan Li; Kai Li | Aggregates and Assemblies | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436a0f50db0db4395ecf/original/visualized-spontaneous-molecular-directed-motion-in-solid-state.pdf |
670d0de851558a15ef07c30d | 10.26434/chemrxiv-2024-4jzln | On the dependence of the catalytic activity of nickel ferrite nanoparticles in the oxidative dehydrogenation of 2-propanol on the crystallite size | Nickel ferrite spinel nanoparticles of different crystallite sizes were prepared in a glycine assisted sol-gel autocombustion reaction and characterised by powder x-ray diffraction, attenuated total reflection infrared spectroscopy, near ambient pressure x-ray photoelectron spectroscopy, nitrogen physisorption, hydrogen and carbon monoxide temperature programmed reduction and oxygen and carbon dioxide temperature programmed desorption. A different distribution of Ni2+ cations in the tetrahedrally and octahedrally coordinated sites of the spinel lattice and an increased reducibility of the smaller crystallite size sample were identified as the main impacts of different crystallite size. Their catalytic activity in the oxidative dehydrogenation of 2-propanol was investigated by temperature programmed reaction studies using different ratios of 2-propanol:O2 as well as of possible parallel and consecutive reactions at atmospheric pressure and maximum 400 °C. Operando-DRIFTS-MS studies at different 2-propanol:O2 ratios were carried out under continuous-flow conditions at atmospheric pressure as well. Thereby, the increased reducibility of the small crystallite size sample could be linked to an unselective activity for dehydrogenation yielding acetone and hydrogen, partial oxidation of 2-propanol and acetone, and total combustion leading to a complex network of reactions going on, being further pushed by an excess of oxygen. Ex-situ x-ray diffraction measurements were performed following the temperature programmed reaction experiments. The large crystallite size sample was found to be generally less active, but more selective towards non-oxidative dehydrogenation. Ex-situ x-ray diffraction measurements performed following the temperature programmed reaction experiments confirmed the increased reducibility of the smaller crystallite size sample. In the operando IR studies, 2-propoxide, adsorbed acetone, carbonates and acetates were identified as species occurring in the reaction. | Michael Pittenauer; Raffael Rameshan; Florian Schrenk; Chunlei Wang; Moritz Maximilian Joachim Eder; Gareth Parkinson; Christoph Rameshan; Karin Föttinger | Catalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d0de851558a15ef07c30d/original/on-the-dependence-of-the-catalytic-activity-of-nickel-ferrite-nanoparticles-in-the-oxidative-dehydrogenation-of-2-propanol-on-the-crystallite-size.pdf |
616dfb19fb86192308fd2c7f | 10.26434/chemrxiv-2021-rn4p1 | Stability of oxidized states of ceria-supported PtOx particles under a wide range of gas-phase conditions | Nanostructured materials based on non-inert oxides CeO2 and PtyOx play a fundamental role in catalyst design. However, their characterization is often challenging due to their structural complexity and the tendency of the materials to change under reaction conditions. In this work, we combine calculations based on the density functional theory, a machine-learning assisted global optimization method (GOFEE) and ab initio thermodynamics to characterize stable oxidation states of ceria-supported PtyOx clusters in different environments. The collection of global minima for different stoichiometries resulting from the global optimisation effort is used to assess the effect of temperature, oxygen pressure, and support interactions on the phase diagrams, oxidation states, and structural properties of the PtyOx particles. We thus identify favoured structural motifs and O/Pt ratios, revealing that oxidized states of ceria-supported particles are more stable than reduced ones under a wide range of conditions. These results indicate that studies rationalizing activity of ceria-supported Pt clusters must consider such oxidized states, and that previous understanding of such materials obtained only with fully reduced Pt clusters may be incomplete. | Jon Eunan Quinlivan Domínguez; Konstantin Neyman; Albert Bruix | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2021-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616dfb19fb86192308fd2c7f/original/stability-of-oxidized-states-of-ceria-supported-pt-ox-particles-under-a-wide-range-of-gas-phase-conditions.pdf |
675c0fbb085116a13346df8a | 10.26434/chemrxiv-2024-qb4mt | Cage Alkyl Carbenes Provide Experimental Evidence for Isotope-Controlled Selectivity | We report the gas-phase synthesis and reactivity of adamantylidene and pentacyclo[5.4.0.02.6.03.10.05.9]undecanylidene. The latter, a previously unreported carbene, represents only the second alkyl carbene spectroscopically characterized to date. The singlet carbenes were generated through irradiation of their corresponding diazirine precursors followed by trapping the products in argon or nitrogen matrices at 3.5 K. Analyses using IR and UV/Vis spectroscopy, together with density functional theory computations provide strong evidence for the successful preparation of these reactive species. Adamantylidene (∆EST = –3.0 kcal mol–1) undergoes a slow hitherto unreported but theoretically predicted quantum mechanical tunneling (QMT) C–H-bond insertion and ring-closure to 2,4-dehydroadamantane. In contrast, pentacyclo[5.4.0.02.6.03.10.05.9]undecanylidene (∆EST = –5.2 kcal mol–1) remains unchanged under cryogenic conditions but rearranges to homohypostrophene upon = 627 nm irradiation. Attempts to prepare protoadamantylidene (∆EST = –5.1 kcal mol–1) in a similar fashion did not allow the direct observation of the free carbene, but enabled follow-up QMT reactions, whose selectivities are determined by the 1H and 2H isotopologs, thereby demonstrating isotope-controlled selectivity (ICS). | Akkad Danho; Bastian Bernhardt; Dennis Gerbig; Marija Alešković; Peter Richard Schreiner | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c0fbb085116a13346df8a/original/cage-alkyl-carbenes-provide-experimental-evidence-for-isotope-controlled-selectivity.pdf |
612c4a7fabeb630143c3aa1a | 10.26434/chemrxiv-2021-wq61q | Multistimuli Responsive Dynamic Effects in a One-Dimensional Coordination Polymer | The development of multistimuli receptive actuators demands rational combination of suitable functionalities. Achieving such actuating properties in a single crystalline material is a challenge. In spite of several investigation on photo-, thermo- and mechano- responsive crystals, single crystalline material displaying all these effects is unknown. By a judicious combination of photoreactive 2-fluoro-4’-styrylpyridine units and flexible Pb(SCN)2 units, multistimuli responsive 1D CP showing all these dynamic effects has been fabricated. Single crystals of the CP display rapid ballistic events upon UV irradiation triggered by [2+2] cycloaddition of the photoreactive ligands. In addition, macroscopic jumping, bending, splitting of the crystals were observed during both heating and cooling cycles, because of the reversible phase transition. In addition, slander crystals of the CP exhibt elastic deformation upon the application of mechanical force. With handful examples CPs showing macroscopic dynamic effects, this CP paves the way for designing multistimuli responsive multi-salient actuating materials. | Bibhuti Bhusan Rath; Mayank Gupta; Jagadese J. Vittal | Materials Science; Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612c4a7fabeb630143c3aa1a/original/multistimuli-responsive-dynamic-effects-in-a-one-dimensional-coordination-polymer.pdf |
64878f974f8b1884b733b447 | 10.26434/chemrxiv-2023-pj66w | Oxidation of Alcohols and Oxidative Cyclization of Diols
using NaBr and Selectfluor | We present protocols for the oxidation of alcohols and aldehydes and for the oxidative cyclization of diols
which use a combination of Selectfluor and NaBr. For most substrates, the optimal solvent system is a 1:1
mixture of CH3CN/H2O, but, in select cases, biphasic 1:1 mixtures of EtOAc/H2O or CH2Cl2/H2O are
superior. This procedure is operationally simple, uses inexpensive and readily available reagents, and
tolerates a variety of functional groups. Mechanistic studies suggest that the active oxidant is hypobromous
acid, generated by the almost instantaneous oxidation of Br– by Selectfluor in an aqueous milieu. | Shyam Sathyamoorthi; Harshit Joshi; Debobrata Paul | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64878f974f8b1884b733b447/original/oxidation-of-alcohols-and-oxidative-cyclization-of-diols-using-na-br-and-selectfluor.pdf |
64d9253469bfb8925ae0185e | 10.26434/chemrxiv-2023-l672b | Computational investigation of MAX as intercalation host for rechargeable aluminum-ion battery | Layered carbides and their analogs with MAX phase (general formula AMn+1Xn) have emerged as promising candidates for energy storage and conversion applications. One frontier for energy storage is using MAX as an Al-ion intercalation electrode. Given that many MAXs have their A sites being Al, the structure can potentially serve as a stable host for Al intercalation. Here in this work, we computationally enumerated 425 ternary MAX Al-ion battery electrodes. Specifically, we perform first principal phase diagram calculations on the combinatorial space of 17 types of typical transition metals, 5 types of anions (C, N, B, Si, P), three types of stoichiometries (n=1, 2, 3) and two types of layered stackings (α and β). Among all the ternary MAX materials, 44 candidates show reasonable synthetic accessibility and 5 shows extraordinary performance than most reported Al-ion battery electrodes. With the phase stability, electrochemical performance (average voltage, theoretical capacity, energy density and Al diffusion barrier), our work provide comprehensive computational assessment of the great opportunities behind MAX based Al-ion battery. | Lin Wang; Jingyang Wang; Bin Ouyang | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d9253469bfb8925ae0185e/original/computational-investigation-of-max-as-intercalation-host-for-rechargeable-aluminum-ion-battery.pdf |
64496a1cdf78ec50156ec7fc | 10.26434/chemrxiv-2023-hsg0j | Rationalizing the Formation of Porosity in Mechanochemically-Synthesized Polymers | In this study, we present a matrix of 144 mechanochemically synthesized polymers. All polymers were constructed by the solvent free Friedel Crafts polymerization approach, employing 16 aryl containing monomers and 9 halide containing linkers, which were processed in a high speed ball mill. This Polymer Matrix was utilized to investigate the origin of porosity in Friedel Crafts polymerizations in detail. By examining the physical state, molecular size, geometry, flexibility, and electronic structure of the utilized monomers and linkers, we identified the most important factors influencing the formation of porous polymers. We analyzed the significance of these factors for both monomers and linkers based on the yield and specific surface area of the generated polymers. Our in-depth evaluation serves as a benchmark study for future targeted design of porous polymers by the facile and sustainable concept of mechanochemistry. | Annika Krusenbaum; Steffi Krause Hinojosa; Sven Fabig; Valentin Becker; Sven Graetz; Lars Borchardt | Polymer Science; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64496a1cdf78ec50156ec7fc/original/rationalizing-the-formation-of-porosity-in-mechanochemically-synthesized-polymers.pdf |
65a315279138d23161da7677 | 10.26434/chemrxiv-2024-f594p | Multigram Synthesis of 4,4-disubstituted-3-oxopyrrolidones – efficient starting material for diverse 3 functionalized pyrrolidones | The practical rapid development of chemical leads for drug discovery is strongly dependent on scalable procedures for building block synthesis. N-heterocyclic moieties, especially unsaturated ones, remain essential tools in the hands of screening and medicinal chemists. Here, we report four novel chemical block families and the interconversions between them. 4,4-disubstituted-3-oxopyrrolidones synthesis was an essential milestone in the diversity-oriented production of 3-aminopyrrolidones, 3-hydroxypyrrolidones and 3,3’-difluoropyrrolidines. Those can be functionalized with conformationally flexible spirocyclic substituents. We developed the multigram procedure for 4,4-disubstituted-3-oxopyrrolidones from commercially accessible and cost-saving reagents via the short three-step procedure. Also, here we are reporting the robust conversion procedure of 3-oxopyrrolidones to 3-aminopyrrolidones, 3,3’-difluoropyrrolidones and 3-hydroxypyrrolidones, involving a minimal amount of steps. We demonstrate the scope and limitations and further perspectives for such synthetic approaches. | Semen Bondarenko; Anatolii Fedorchenko; Pavlo Novosolov; Oleksandr Marchenko; Anton Hanopolskyi; Yulian Volovenko; Dmytro Volochnyuk; Serhiy Ryabukhin | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a315279138d23161da7677/original/multigram-synthesis-of-4-4-disubstituted-3-oxopyrrolidones-efficient-starting-material-for-diverse-3-functionalized-pyrrolidones.pdf |
634d063686473a0c6c15c73a | 10.26434/chemrxiv-2022-x468n-v2 | ReNeGate: Reaction Network Graph Theoretical tool for automated mechanistic studies in computational homogeneous catalysis | Exploration of the chemical reaction space of chemical transformations in multicomponent mixtures is a challenge for modern computational protocols. In order to remove expert bias from mechanistic studies and to discover new chemistries, an automated graph-theoretical methodology is proposed to provide mechanistic analysis in catalytic systems. The primary advantage of the presented three-step approach over the existing automated pathways generation methods is the integrated ability to handle multicomponent catalytic systems of arbitrary complexity (mixtures of reactants, catalyst precursors, ligands, additives, and solvent). It is not limited to pre-defined chemical rules, does not require pre-alignment of reaction mixture components consistent with a reaction coordinate and is not agnostic to the chemical nature of transformations. Conformer exploration, Reactive event identification and Reaction network analysis are the main steps taken for understanding the underlying mechanistic pathways in catalytic mixtures given the reaction mixture as the input. Such a methodology allows to comprehensively explore the catalytic systems in realistic conditions for either previously observed or completely unknown reactive events. The expert bias is sought to be removed in either of the steps and chemical intuition is limited to the choice of the thermodynamic constraint imposed by the applicable experimental conditions in terms of threshold energy values for allowed transformations. The capabilities of the proposed methodology have been tested by exploring reactivity of Mn complexes relevant for catalytic hydrogenation chemistry to verify previously postulated activation mechanisms and unravel unexpected reaction channels relevant to rare deactivation events. | Ali Hashemi; Sana Bougueroua; Marie-Pierre Gaigeot; Evgeny Pidko | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634d063686473a0c6c15c73a/original/re-ne-gate-reaction-network-graph-theoretical-tool-for-automated-mechanistic-studies-in-computational-homogeneous-catalysis.pdf |
642b01aedb1a20696e76d6ca | 10.26434/chemrxiv-2023-2gkr3 | Improved label-free quantification of intact proteoforms using field asymmetric ion mobility spectrometry | The high-throughput quantification of intact proteoforms using a label-free approach is typically performed on proteins in the 0-30 kDa mass range extracted from whole cell or tissue lysates. Unfortunately, even when high-resolution separation of proteoforms is achieved by either high performance liquid chromatography or capillary electrophoresis, the number of proteoforms that can be identified and quantified is inevitably limited by the inherent sample complexity. Here we benchmark label-free quantification of proteoforms of Escherichia coli by applying gas-phase fractionation (GPF) via field asymmetric ion mobility spectrometry (FAIMS). Recent advances in Orbitrap instrumentation have enabled the acquisition of high-quality intact and fragmentation mass spectra without the need for averaging time-domain transients prior to Fourier transform. The resulting speed improvements allowed for the application of multiple FAIMS compensation voltages in the same liquid chromatography-tandem mass spectrometry experiment without increasing the overall data acquisition cycle. As a result, the application of FAIMS to label-free quantification based on intact mass spectra substantially increases the number of both identified and quantified proteoforms without penalizing quantification accuracy in comparison to traditional label-free experiments that do not adopt GPF. | Jake T. Kline; Michael W. Belford; Jingjing Huang; Joseph B. Greer; David Bergen; Ryan T. Fellers; Sylvester M. Greer; David M. Horn; Vlad Zabrouskov; Romain Huguet; Cornelia L. Boeser; Kenneth R. Durbin; Luca Fornelli | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b01aedb1a20696e76d6ca/original/improved-label-free-quantification-of-intact-proteoforms-using-field-asymmetric-ion-mobility-spectrometry.pdf |
66589f1821291e5d1daae723 | 10.26434/chemrxiv-2023-3fldg-v4 | Streamlined Synthesis of Eudesmane Sesquiterpenoids through Site-switchable Olefin Functionalization Strategy | Herein, we demonstrate a concise synthesis of oxidized eudesmanes using a late-stage site-selective olefin functionalization strategy. To implement this strategy, we synthesized a common intermediate comprising two identical olefins within a hydroxy-carrying eudesmane core via an asymmetric tandem Michael addition and Aldol reaction, along with an Au(I)-catalyzed Alder-ene reaction. Subsequent late-stage site-selective olefin hydrogenation and epoxidation techniques were employed to synthesize nine eudesmane congeners without using protecting groups. This study highlights the applicability and effectiveness site-selective functionalization of identical olefins in facilitating the access to intricate terpenes and their derivatives. | Ashutosh Panigrahi ; KIRAN KUMAR PULUKURI | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66589f1821291e5d1daae723/original/streamlined-synthesis-of-eudesmane-sesquiterpenoids-through-site-switchable-olefin-functionalization-strategy.pdf |
6435e0490784a63aeef3d67f | 10.26434/chemrxiv-2022-gthrk-v2 | Light-mediated synthesis of aliphatic anhydrides by Cu-catalyzed carbonylation of alkyl halides | Acid anhydrides are valuable in the chemical industry for their role in synthesizing polymers, pharmaceuticals, and other commodities, but their syntheses often involve multiple steps with precious metal catalysts. The simplest anhydride, acetic anhydride, is currently produced by two Rh-catalyzed carbonylation reactions on bulk scale for its use in synthesizing products ranging from aspirin to cellulose acetate. Here, we report a light-mediated, Cu-catalyzed process for producing aliphatic, symmetric acid anhydrides directly by carbonylation of alkyl (pseudo-)halides in a single step without any precious metal additives. The transformation requires only simple Cu salts and abundant bases to generate a heterogeneous Cu0 photocatalyst in situ, maintains high efficiency and selectivity upon scale up, and operates by a radical mechanism with several beneficial features. This discovery will enable engineering of bulk processes for producing commodity anhydrides efficiently and sustainably. | Pinku Tung; Neal Mankad | Organic Chemistry; Catalysis; Organometallic Chemistry; Photocatalysis; Catalysis; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6435e0490784a63aeef3d67f/original/light-mediated-synthesis-of-aliphatic-anhydrides-by-cu-catalyzed-carbonylation-of-alkyl-halides.pdf |
66f42ed651558a15ef15c33f | 10.26434/chemrxiv-2024-nbcsr | Wavelength-Selective Reactivity of Iron(III) Halide Salts in Photocatalytic C–H Functionalization | The utility of halogen radicals in hydrocarbon functionalization extends from early examples of photochemical halogenation to recent reports using photoredox catalysis with iridium complexes and simple transition metals salts such as FeCl3. The majority of these methods (uncatalyzed and iron-catalyzed) require UV light (lambda≤ 390 nm) and systematic efforts to enable the use of visible light remain valuable. We report the use of a simple Fe(III) salt that enables a C–H to C–C and C–N func-tionalization under visible light. The reactivity and selectivity profile using different light sources demonstrate wavelength-selective behavior, which was further investigated with deuterium kinetic isotope effect experiments and DFT calculations. These results show that control over the reactive intermediates in this iron-catalyzed reaction can be achieved through proper choice of the wavelength of irradiation. | Cory Ludwig; Isiaka Owolabi; Logan Evans; Gabriel Smith; Alexander Ramos; James Shepherd; David Martin | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f42ed651558a15ef15c33f/original/wavelength-selective-reactivity-of-iron-iii-halide-salts-in-photocatalytic-c-h-functionalization.pdf |
64c129e2ce23211b209636b7 | 10.26434/chemrxiv-2023-qxf1q | Amorphization of different furosemide polymorphic forms during ball milling: tracking solid-to-solid phase transformations | Ball milling is used, not only to reduce the particle size of pharmaceutical powders, but also to induce changes in the physical properties of drugs. In this work we prepared three crystal forms of furosemide (forms Ⅰ, Ⅱ, and Ⅲ) and studied their solid phase transformations during ball milling. Powder X-ray diffraction and modulated differential scanning calorimetry were used to characterize the samples after each milling time on their path to amorphization. Our results show that forms Ⅰ and III directly converted into an amorphous phase, while form Ⅱ first undergoes a polymorphic transition to form Ⅰ, and then gradually loses its crystallinity, finally reaching full amorphousness. During ball milling of forms Ⅰ and Ⅱ, the glass transition temperature (Tg) of the amorphous fraction of the milled material remains almost unchanged at 75℃ and 74℃, respectively (whilst the amorphous content increases). In contrast, the Tg values of the amorphous fraction of milled form III increase with increasing milling times, from 63℃ to 71℃, indicating an unexpected phenomenon of amorphous-to-amorphous transformation. The amorphous fraction of milled forms I and II samples presented a longer structural relaxation (i.e., lower molecular mobility) than the amorphous fraction of milled form III samples. Moreover, the structural relaxation time remained the same for the increasing amorphous fraction during milling of forms I and II. In contrast, the structural relaxation times were always shorter for the amorphous fraction of form III, but increased with increasing amorphous content during milling, confirming amorphous-to-amorphous transformation. | Mengwei Wang; Junbo Gong; Thomas Rades; Inês C. B. Martins | Physical Chemistry; Materials Science; Materials Processing; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c129e2ce23211b209636b7/original/amorphization-of-different-furosemide-polymorphic-forms-during-ball-milling-tracking-solid-to-solid-phase-transformations.pdf |
669e075c01103d79c5187252 | 10.26434/chemrxiv-2024-zz2r0 | Photocatalytic Silylation of Aryl Alkynoates: Synthesis of Silylated Coumarins | We report a highly efficient protocol for the synthesis of 3-silyl coumarins using hydrosilanes as the silyl radical source with aryl alkynoates. Readily prepared N-aminopyridinium salts act as hydrogen atom transfer reagents for generating silyl radicals under mild conditions via photoredox catalysis. The reaction proceeds through silyl radical addition to alkyne followed by radical cascade cyclization/migration with subsequent oxidation and aromatization to give desired 3-silyl coumarins in good to excellent yields. | SERMADURAI SELVAKUMAR; Ravikumar Ladumor; Sourav Samanta | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e075c01103d79c5187252/original/photocatalytic-silylation-of-aryl-alkynoates-synthesis-of-silylated-coumarins.pdf |
676e0446fa469535b9ec2a08 | 10.26434/chemrxiv-2024-gcmnn-v2 | Effective Volume Correction for Lennard-Jones Static Potential Matching on Coarse-Graining Small Molecules | Coarse-grained (CG) models have been widely employed in simulating the functionality of complex systems due to their lower computational demand, and the accuracy of their simulation outcomes critically depends on their parameters. In the previous study, we developed a general CG potential matching method called the Lennard-Jones Static Potential Matching (LJSPM) method for Lennard-Jones (LJ) interactions, which enables users to derive inter-system transferable LJ parameters efficiently by using only one arbitrary molecular structure. The LJSPM offers a significant means for developing physical-based non-bonded interaction parameters in CG models. However, previous results show that LJSPM generally underestimates LJ repulsive contributions, which leads to mismatching of the CG and AA LJ potential energy surfaces for short-ranged non-bonded pairs. In this work, a physical-based, general, and efficient method named the effective volume correction (EVC) is proposed to fulfill the underestimated short-ranged LJ exclusion effects for CG-LJ parameters matched by the LJSPM method. This new EVC-based LJSPM method can accurately reproduce density, the rational distribution function, and the solvation free energy of small organic molecules including alkanes, alcohols, and amines. This indicates that the EVC-based LJSPM method exhibits good transferability for the development of CG models in small molecules. | Qingdong Zhu; Yuwei Zhang; Fei Xia | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e0446fa469535b9ec2a08/original/effective-volume-correction-for-lennard-jones-static-potential-matching-on-coarse-graining-small-molecules.pdf |
63dac570d8f55fd0aa9be409 | 10.26434/chemrxiv-2023-51dxc | A Simple Topology-based Model for Predicting Activation Barriers of Chemical Reactions at 0 K | This works exploits two topological concepts for developing a model capable of predicting activation energies at 0 K. Experimental barriers of 17 exergonic reactions were fit via simple linear regression analysis, leading to the model which accurately predicted activation energy of both organic and organometallic reaction systems under different conditions, for instance, gas-phase/solvent media and temperature. This linear function was further recalibrated to enhance its predicting capabilities, generating such a refining process the equation characterized by a squared Pearson correlation coefficient (r2 = 0.9774) 1.1 times higher. Surprisingly, the performance of the corrected fit equation was only slightly better. Moreover, both linear fits failed to provide reasonable energy values for the epoxidation of isobutene and -methylstyrene by dimethyldioxirane. This issue might be explained considering our results suggest that it is paramount to use a level of theory that guarantee an adequate description of the physical and chemical properties of the reacting system in order for the model to predict reasonable activation barriers. Since the fitted data involves reactions experimentally studied within the range [293, 748] K, a high degree of inaccuracy should be expected when applying the model to reactions investigated under laboratory conditions involving temperatures outside the indicated interval. | Leandro Henríquez | Theoretical and Computational Chemistry; Physical Chemistry; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dac570d8f55fd0aa9be409/original/a-simple-topology-based-model-for-predicting-activation-barriers-of-chemical-reactions-at-0-k.pdf |
630b693358843b6bbaa09a41 | 10.26434/chemrxiv-2022-1rgh4 | Fatty acid capped, metal oxo clusters as smallest conceivable nanocrystal prototypes | Metal oxo clusters of the type \ce{M6O4(OH)4(RCOO)12} (M = Zr of Hf) are valuable building blocks for material science. Here, we develop them as smallest conceivable nanocrystal prototypes. We synthesize a series of zirconium and hafnium oxo clusters with ligands that are typically used to stabilize oxide nanocrystals (fatty acids with long and/or branched chains). In contrast to previously reported discrete oxo clusters with short/rigid carboxylates (e.g., acetate, benzoate), the fatty acid capped oxo clusters have a high solubility but do not crystallize, precluding traditional purification and single-crystal XRD analysis of clusters. We thus develop alternative purification strategies and structural analysis tools. We use X-ray total scattering and Pair Distribution Function (PDF) analysis as our main tool to elucidate the structure of the cluster core. In contrast to traditional PDF analysis of larger clusters and nanocrystals, we show that the structure models need to include the carboxylate binding groups to obtain excellent refinements. Our methodology is able to pick up the correct structure from a series of possible structure models (\textbf{Zr4}, \textbf{Zr6}, \textbf{Zr12}). Further supporting evidence for the cluster composition (including their ligand shell) is provided by nuclear magnetic resonance (NMR), infrared spectroscopy (FTIR), thermogravimetry analysis (TGA) and mass spectrometry (MS). We find that the ligands have multiple binding modes and that hydrogen bonded carboxylic acid is an intrinsic part of the oxo cluster. Using our analytical tools, we elucidate the conversion from \textbf{Zr6} monomer to \textbf{Zr12} dimer (and vice versa), induced by carboxylate ligand exchange. Finally, we compared the catalytic performance of \textbf{Zr12}-oleate clusters with oleate capped, 3-5 nm zirconium oxide nanocrystals in the esterification of oleic acid with ethanol. The oxo clusters are much more catalytically active, due to their higher surface area. Since the oxo clusters are the limit of downscaling oxide nanocrystals, we thus propose them here as appealing catalytic materials, or at least as atomically precise model systems. In addition, our analytical (PDF) methodology is generally applicable and expected to find use in other areas of clusters as well, and will be especially valuable for clusters with weakly scattering core atoms.
| Dietger Van den Enyden; Rohan Pokratath; Jikson Pulparayil Mathew; Eline Goossens; Klaartje De Buysser; Jonathan De Roo | Inorganic Chemistry; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630b693358843b6bbaa09a41/original/fatty-acid-capped-metal-oxo-clusters-as-smallest-conceivable-nanocrystal-prototypes.pdf |
60c75462337d6c3783e28a31 | 10.26434/chemrxiv.13633301.v1 | Ligand Rearrangement Leads to Tetrahydrothiophene-Functionalized N,S-Heterocyclic Carbene Palladium(II) Complexes | Tetrahydrothiophene-functionalized <i>N</i>,<i>S</i>-heterocyclic carbene palladium(II) complexes are synthesized through an unexpected rearrangement that proceeds with palladium(II) trifluoroacetate and not with palladium(II) acetate, palladium(II) bromide, or palladium(II) chloride. A series of these complexes were isolated and characterized by X-ray crystallography. The mechanism of formation of these [3.2.1]-palladabicycles was explored, and the catalytic capabilities of these complexes were demonstrated in representative C–C coupling reactions. | Andrew Romine; Matthew Demer; Milan Gembicky; Arnold L. Rheingold; Keary Engle | Organic Compounds and Functional Groups; Coordination Chemistry (Organomet.); Ligand Design; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75462337d6c3783e28a31/original/ligand-rearrangement-leads-to-tetrahydrothiophene-functionalized-n-s-heterocyclic-carbene-palladium-ii-complexes.pdf |
66f9edbb51558a15ef8985eb | 10.26434/chemrxiv-2024-53l7j | Chiral Phosphoric Acid-Catalyzed Asymmetric Synthesis of Axially Chiral Arylpyrazole | A chiral phosphoric acid-catalyzed efficient, operationally simple, general method for straightforward syntheses of axially chiral arylpyrazole employing 3-aryl-5-aminopyrazoles reacting with azonaphthalenes was firstly reported. A wide variety of axially chiral heterobiaryl diamines in generally good yields with excellent enantioselectivities were obtained under mild conditions. In addition, a scale-up experiment and postmodification of the chiral product further highlighted the synthetic utility. | Shi-Wu Li; Yu Qi; Shujun Tong; Jiaqi Pu | Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f9edbb51558a15ef8985eb/original/chiral-phosphoric-acid-catalyzed-asymmetric-synthesis-of-axially-chiral-arylpyrazole.pdf |
679724d7fa469535b9027ba6 | 10.26434/chemrxiv-2025-qw32n | Theoretical Calculation of Paternó-Büchi reaction between methanal and (2,2-dimethyl-1,3-dioxan-5-ylidene)methanamine in twisted-boat conformation | This paper is investigated the Paternó-Büchi reaction between methanal and (2,2-dimethyl-1,3-dioxan-5-ylidene)methanamine. The conformer is twisted boat dominant and hence affect the stereochemistry of the product. | Ka Wa Fan | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679724d7fa469535b9027ba6/original/theoretical-calculation-of-paterno-buchi-reaction-between-methanal-and-2-2-dimethyl-1-3-dioxan-5-ylidene-methanamine-in-twisted-boat-conformation.pdf |
638d884744ccbcb23f0e63fe | 10.26434/chemrxiv-2022-p3w88 | Central role of entropy in thermodynamics | Providing a simple description of entropy as the foundation of thermodynamics is necessary for researchers in explaining physical phenomena in the universe. Here we dive deep into the meaning of entropy starting from the basics and ending with the Newton's second law of motion which may be rooted in a hidden dimension as the foundation of entropy. Toward this end, after coming up with a general relation for the net entropic energy of a process regardless of its irreversibility, we recover the entropy production relation. Using this relation, we show how the inequality in macroscopic states between work and Helmholtz free energy during the non-equilibrium process converts to equality between reversible microscopic works of microscopic degrees of freedom and Helmholtz free energy change of maximum useful work. In the end, we provide a mathematical solution to this equality that may tell us about the foundation of entropy from underlying degrees of freedom that currently remain unknown to us.
| Mohsen Farshad | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638d884744ccbcb23f0e63fe/original/central-role-of-entropy-in-thermodynamics.pdf |
6422d09a62fecd2a83937199 | 10.26434/chemrxiv-2022-8khth-v2 | Multistep retrosynthesis combining a disconnection aware triple transformer loop with a route penalty score guided tree search | Computer-aided synthesis planning (CASP) aims to automatically learn organic reactivity from literature and perform retrosynthesis of unseen molecules. CASP systems must learn reactions sufficiently precisely to propose realistic disconnections while avoiding overfitting to leave room for diverse options, and explore possible routes such as to allow short synthetic sequences to emerge. Herein we report an open-source CASP tool proposing original solutions to both challenges. First, we use a triple transformer loop (TTL) predicting starting materials (T1), reagents (T2), and products (T3) to explore various disconnections sites defined by combining exhaustive, template-based and transformer-based tagging procedures. Second, we integrate TTL into a multistep tree search algorithm (TTLA) prioritizing sequences using a route penalty score (RPScore) considering the number of steps, their confidence score, and the simplicity of all intermediates along the route. Our approach favours short synthetic routes to commercial starting materials, as exemplified by retrosynthetic analyses of recently approved drugs. | David Kreutter; Jean-Louis Reymond | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422d09a62fecd2a83937199/original/multistep-retrosynthesis-combining-a-disconnection-aware-triple-transformer-loop-with-a-route-penalty-score-guided-tree-search.pdf |
65c3a2b6e9ebbb4db9dbf46c | 10.26434/chemrxiv-2024-d01vd | Development of a sampling protocol for collecting leaf surface material for multiphase chemistry studies | Plant leaves and water drops residing on them interact with atmospheric oxidants, impacting the deposition and emission of trace gases and mediating leaf damage from air pollution. Characterizing the chemical composition and reactivity of the water-soluble material on leaf surfaces is thus essential for improving our understanding of atmosphere-biosphere interactions. However, the limited knowledge of sources and nature of these chemicals challenges sampling decisions. This work investigates how sampling variables and environmental factors impact the quantity and composition of water-soluble material sampled from wet leaves and proposes a flexible protocol for its collection. The ratio of solvent volume-to-leaf area, the solvent-to-leaf contact time, and environmental parameters – including the occurrence of rain, plant location and its metabolism – drive solute concentration in leaf soaks. Despite minor variations, UV-Vis absorption spectra of leaf soaks are comparable to authentic raindrops collected from the same tree and share features with microbial dissolved organic matter – including overall low aromaticity, low chromophore content, and low average molecular weight. In addition to guiding the development of a sampling protocol, our data corroborate recent hypotheses on the amount, origin, nature, and reactivity of water-soluble organics on wet leaves, providing new directions of research into this highly interdisciplinary topic. | Rachele Ossola; Rose K. Rossell; Mj Riches; Cameron Osburn; Delphine Farmer | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c3a2b6e9ebbb4db9dbf46c/original/development-of-a-sampling-protocol-for-collecting-leaf-surface-material-for-multiphase-chemistry-studies.pdf |
60c740c9ee301cd872c78b01 | 10.26434/chemrxiv.7834907.v1 | Computational Study of Absorption Spectra of Eumelanin Constituents: Key Role of Oxidized Species in the Red Edge Absorption | We have computed the vertical absorption of the
basic components of eumelanin, oligomers of 5,6-dihydroxyindole (DHI) and
5,6-dihydroxyindole-2-carboxylic acid (DHICA), at the TD-DFT level. Here we
present a preliminary report on the results for 73 DHI and 58 DHICA oligomers
that cover the structural and redox diversity found in eumelanin. We have
identified several structures that absorb at wave lengths above 800 nm, all of
which contain oxidized DHI units, <i>ie</i>
quinones or quinone methides. The transitions also have a pronounced charge
transfer character, which suggests that they may give rise to proton-coupled
electron transfer radiationless decay mechanisms that are important for the
photoprotecting function. | Gerard Riesco; Aleix Casademont; Lluís Blancafort | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740c9ee301cd872c78b01/original/computational-study-of-absorption-spectra-of-eumelanin-constituents-key-role-of-oxidized-species-in-the-red-edge-absorption.pdf |
62a11cd4bb7519172f47c971 | 10.26434/chemrxiv-2022-99gl2 | Synthesis of 3-Borylated Cyclobutanols from Epihalohydrins or Epoxy Alcohol Derivatives | There is an increasing interest in cyclobutanes within the medicinal chemistry community. Therefore, methods to prepare cyclobutanes that contain synthetic handles for further elaboration are of interest. Herein, we report a new approach for the synthesis of 3-borylated cyclobutanols via a formal [3+1]-cycloaddition using readily accessible 1,1-diborylalkanes and epihalohydrins or epoxy alcohol derivatives. 1-Substituted epibromohydrin starting materials provide access to borylated cyclobutanols containing substituents at three of the four positions on the cyclobutane core, and enantioenriched epibromohydrins lead to enantioenriched cyclobutanols with high levels of enantiospecificity (>98% es). Finally, derivatization studies demonstrate the synthetic utility of both the OH and Bpin handles. | Tyler McDonald; Sophie Rousseaux | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a11cd4bb7519172f47c971/original/synthesis-of-3-borylated-cyclobutanols-from-epihalohydrins-or-epoxy-alcohol-derivatives.pdf |
65325cf8c3693ca993b808f3 | 10.26434/chemrxiv-2023-79hb8 | Charge transfer in superbase n-type doping of PCBM induced by deprotonation | N-type electronic doping of organic semiconductors (OSCs) by using superbase compounds shows
high doping efficiency (Adv. Mater. 2023, 35, 2300084). While a deprotonation reaction is believed
to trigger the doping process, the detailed mechanism therein is not yet fully understood. In the
present work we theoretically study the electronic structure of the deprotonated Phenyl-C61-butyric
acid methyl ester (PCBM) molecule, as well as the charge transfer (CT) between PCBM and its
deprotonated species. We find that deprotonated PCBM without formation of a new bond between
the deprotonated side chain and fullerene induces electronic structure with broken spin symmetry,
where an in-gap state is singly occupied by an unpaired electron. A second scenario that we find to
be possible is the formation of a new bond between the deprotonated side chain and a fullerene. This
leads to a spin symmetric electronic structure with partially localized in-gap state, which is expected
to contribute less to the effective doping. These results show that the deprotonated PCBM species
without new bond formation predominantly accounts for the effective n-type doping of PCBM, an
insight that will be useful for optimization of this recently discovered doping method. | Chuanding Dong; Fabian Bauch; Yuanyuan Hu; Stefan Schumacher | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65325cf8c3693ca993b808f3/original/charge-transfer-in-superbase-n-type-doping-of-pcbm-induced-by-deprotonation.pdf |
60c73f61ee301c4d8ec788d7 | 10.26434/chemrxiv.7366973.v1 | Dataset Bias in the Natural Sciences: A Case Study in Chemical Reaction Prediction and Synthesis Design | <div><div><div><div><div><div><p>Datasets in the Natural Sciences are often curated with the goal of aiding scientific understanding and hence may not always be in a form that facilitates the application of machine learning. In this paper, we identify three trends within the fields of chemical reaction prediction and synthesis design that require a change in direction. First, the manner in which reaction datasets are split into reactants and reagents encourages testing models in an unrealistically generous manner. Second, we highlight the prevalence of mislabelled data, and suggest that the focus should be on outlier removal rather than data fitting only. Lastly, we discuss the problem of reagent prediction, in addition to reactant prediction, in order to solve the full synthesis design problem, highlighting the mismatch between what machine learning solves and what a lab chemist would need. Our critiques are also relevant to the burgeoning field of using machine learning to accelerate progress in experimental Natural Sciences, where datasets are often split in a biased way, are highly noisy, and contextual variables that are not evident from the data strongly influence the outcome of experiments.</p></div></div></div></div></div></div> | Ryan-Rhys Griffiths; Philippe Schwaller; Alpha Lee | Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f61ee301c4d8ec788d7/original/dataset-bias-in-the-natural-sciences-a-case-study-in-chemical-reaction-prediction-and-synthesis-design.pdf |
67b76a8d6dde43c908bd127a | 10.26434/chemrxiv-2025-cjq5h | Base-Promoted Dynamic Amide Exchange: Efficient Access to Isotopically Enriched Tertiary Amides | Amide isotope labeling is a crucial tool in drug discovery and development. However, current methods label the desired peptide bond in a multi-step fashion. This study presents novel strategies for amide isotope exchange through transamidation and amide metathesis. By optimizing reaction conditions and exploring substrate scope, we achieved direct labeling of both amine and carbonyl moieties without need for precursors preparation. These findings pave the way for sustainable isotope labeling technologies. Furthermore, preliminary examples of isotope-containing waste recycling demonstrate a crucial step towards a greener future for isotope chemistry. | Quentin Lemesre; Rémy Blieck; Antoine Sallustrau; Timothée D'Anfray; Frédéric Taran; Davide Audisio | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b76a8d6dde43c908bd127a/original/base-promoted-dynamic-amide-exchange-efficient-access-to-isotopically-enriched-tertiary-amides.pdf |
63e5de8ffcfb27a31f837e38 | 10.26434/chemrxiv-2023-1jsp4 | Adamantane-annulation to arenes: A simple strategy for property modulation of aromatic pi-systems | Peripheral structural modifications of arenes are widely used to control or improve the optoelectronic properties, molecular assembly, and stability of aromatic pi-materials as well as to explore new functions. However, known modifications are often tedious and complex; therefore, a simple yet powerful modification strategy is needed. We discovered that annulation with a simple adamantane scaffold exerts a significant impact on the properties, alignment, and stability of aromatic pi-systems. This unprecedented adamantane annulation was achieved by a two-step transformation of metalated arenes and 4-protoadamantanone, generating a range of adamantane-annulated arenes. Analysis on structural and electronic property uncovered unique effects of the process, such as high solubility and enhanced conjugation. The oxidation of adamantane-annulated perylenes produced strikingly stable cationic species with emission extended to near-infrared region. This simple property modulation of aromatic pi-systems would not only create potentially ground-breaking oi-materials but also novel nanocarbon materials, such as diamond-graphene hybrids. | Takaku Yoshihara; Hiroki Shudo; Akiko Yagi; Kenichiro Itami | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e5de8ffcfb27a31f837e38/original/adamantane-annulation-to-arenes-a-simple-strategy-for-property-modulation-of-aromatic-pi-systems.pdf |
63594b2dac45c7ce2b99186c | 10.26434/chemrxiv-2022-qmvcg | X- and Q-band EPR with cryogenic amplifiers independent of sample temperature | Inspired by the success of NMR cryoprobes, we recently reported a leap in X-band EPR sensitivity by equipping an ordinary EPR probehead with a cryogenic low-noise microwave amplifier placed closed to the sample in the same cryostat [Šimėnas et al. J. Magn. Reson. 322, 106876 (2021)]. Here, we explore, theoretically and experimentally, a more general approach, where the amplifier temperature is independent of the sample temperature. This approach brings a number of important advantages, enabling sensitivity improvement irrespective of sample temperature, as well as making it more practical to combine with ENDOR and Q-band resonators, where space in the sample cryostat is often limited. Our experimental realisation places the cryogenic preamplifier within an external closed-cycle cryostat, and we show CW and pulsed EPR and ENDOR sensitivity improvements at both X- and Q-bands with negligible dependence on sample temperature. The cryoprobe delivers signal-to-noise ratio enhancements that reduce the equivalent measurement time by 16x at X-band and close to 5x at Q-band. Using the theoretical framework we discuss further improvements of this approach which could be used to achieve even greater sensitivity. | Vidmantas Kalendra; Justinas Turcak; Juras Banys; John J.L. Morton; Mantas Simenas | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63594b2dac45c7ce2b99186c/original/x-and-q-band-epr-with-cryogenic-amplifiers-independent-of-sample-temperature.pdf |
622b6f762d8374ee0b7e0c15 | 10.26434/chemrxiv-2022-k6l4p | H-atom Abstraction Reactivity through the Lens of Asynchronicity and Frustration with their Counter-Acting Effects on Barriers | Hydrogen atom abstraction (HAA) is central to life and its importance in synthetic chemistry continues to grow. Enzymes rely on HAA to trigger life-sustaining reaction cascades, and greener synthetic routes are attainable by in situ capture of the carbon-centered radicals generated by HAA. Despite the potential of HAA for the diversification of molecular complexity and the late-stage functionalization of bioactive compounds, readily applicable and reliable models translating experimentally or computationally accessible thermodynamic quantities into relative free energy barriers are missing. In this work, we discovered a complete thermodynamic basis for the description of HAA reactivity, which consists of three components. Besides, the traditional linear free energy relationship and the recently introduced factor of asynchronicity (Srnec et al, PNAS 2018, 115, E10287-E10294), we present the third thermodynamic component of H-atom abstraction reactions – factor of frustration that arises from the dissimilarity of the species competing over a hydrogen atom in their overall ability to acquire electron and proton. Incorporating these non-classical descriptors into a Marcus-type model, the approach herein presented allows nearly quantitative prediction of relative barriers in six sets of metal-oxo-mediated HAA reactions, outperforming existing methods even in a stringent test with >200 computational HAA reactions. | Mauricio Maldonado-Domínguez; Martin Srnec | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b6f762d8374ee0b7e0c15/original/h-atom-abstraction-reactivity-through-the-lens-of-asynchronicity-and-frustration-with-their-counter-acting-effects-on-barriers.pdf |
630f1b79eadd9a9acd8865bb | 10.26434/chemrxiv-2022-8lx76 | Reversible Dihydrogen Activation and Catalytic H/D Exchange with Group 10 Heterometallic Complexes | Reaction of a hexagonal planar palladium complex with a [PdMg3H3] core with H2 is reversible and leads to the formation of a new [PdMg2H4] tetrahydride species alongside an equivalent of a magnesium hydride co-product [MgH]. While the reversibility of this process prevented isolation and structural characterisation of [PdMg2H4], analogous [PtMg2H4] and [PdZn2H4] complexes could be isolated and characterised through independent syntheses. Computational analysis (DFT, AIM, NCIPlot) of the bonding in a series of heterometallic tetrahydride compounds (Ni-Pt; Mg and Zn) suggests that these complexes are best described as square planar with marginal metal–metal interactions; the strength of which increases as group 10 is descended and increases from Mg to Zn. DFT calculations support a mechanism for H2 activation involving a ligand-assisted oxidative addition to Pd. These findings were exploited to develop a catalytic protocol for H/D exchange into magnesium hydride and zinc hydride bonds. | Martí Garçon; Andreas Phanopoulos; Andrew White; Mark Crimmin | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630f1b79eadd9a9acd8865bb/original/reversible-dihydrogen-activation-and-catalytic-h-d-exchange-with-group-10-heterometallic-complexes.pdf |
60c7457c0f50db9b8e396294 | 10.26434/chemrxiv.10032170.v1 | Identifying the Molecular Edge Termination of Exfoliated Hexagonal Boron Nitride Nanosheets with Solid-State NMR Spectroscopy and Plane-Wave DFT Calculations | Hexagonal boron nitride nanosheets (h-BNNS), the isoelectric analog to graphene, have received much attention over the past decade due to their high thermal oxidative resistance, high bandgap, catalytic activity and low cost. The molecular functional groups that terminate boron and nitrogen zigzag and/or armchair edges directly affect their chemical, physical and electronic properties. However, an understanding of the exact molecular edge termination present in h-BNNS is lacking. Here, high-resolution magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy and plane-wave density-functional theory (DFT) calculations are used to determine the exact molecular edge termination in exfoliated h-BNNS. 1H→11B cross-polarization MAS (CPMAS) SSNMR spectra of h-BNNS revealed multiple hydroxyl/oxygen coordinate boron edge sites that were not detectable in direct excitation experiments. A dynamic nuclear polarization (DNP)-enhanced 1H→15N CPMAS spectrum of h-BNNS displayed four distinct 15N resonances while a 2D 1H{14N} dipolar-HMQC spectrum revealed three distinct 14N environments. Plane-wave DFT calculations were used to construct model edge structures and predict the corresponding 11B, 14N and 15N SSNMR spectra. Comparison of the experimental and predicted SSNMR spectra confirms that zigzag and armchair edges with both amine and boron hydroxide/oxide termination are present. The detailed characterization of h-BNNS molecular edge termination will provide usefulness for many material science applications and the techniques outlined here should be applicable to comprehensively understand the molecular edge terminations in other 2D materials. | Rick W. Dorn; Matthew J. Ryan; Tae-Hoon Kim; Tian Wei Goh; Patrick M. Heintz; Lin Zhou; Wenyu Huang; Aaron Rossini | Nanostructured Materials - Materials; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457c0f50db9b8e396294/original/identifying-the-molecular-edge-termination-of-exfoliated-hexagonal-boron-nitride-nanosheets-with-solid-state-nmr-spectroscopy-and-plane-wave-dft-calculations.pdf |
649253ff24989702c2b0ad2a | 10.26434/chemrxiv-2023-pd83k | Photochemical CO2 Capture and Release in Water Enabled By Photoacid Under Visible Light | The urgency to address climate change and its environmental consequences demands the development of effective carbon capture technologies. The relationship between rising global temperatures and increased atmospheric CO2 levels necessitates innovative approaches for mitigating this critical issue. Here, we present a novel photochemical strategy utilizing photoacids in an aqueous bicarbonate buffer system for reversible carbon capture and release. We investigated the photochemical modulation of hydrophilic pyranine as a model photoacid, showcasing its ability to facilitate the capture and release CO2. Control experiments provided evidence of the photoacid effect and its contribution to CO2 release, complemented by the photothermal effect. Cyclic experiments demonstrate the efficiency and reliability of the photochemical carbon capture strategy across multiple cycles. In addition, we explored the potential use of meta-stable state photoacids for this purpose. This research introduces possibilities for the advancement of photochemical carbon capture systems, offering promising avenues for addressing the challenges associated with climate change. | Hyowon Seo; T. Alan Hatton | Energy; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649253ff24989702c2b0ad2a/original/photochemical-co2-capture-and-release-in-water-enabled-by-photoacid-under-visible-light.pdf |
67c17aaf81d2151a026b6f4a | 10.26434/chemrxiv-2025-0f2zg | Evaluating the performance and suitability of MIL-91(Ti) MOF for post-combustion carbon capture by vacuum pressure swing adsorption (VPSA) | A multiscale study was carried out to evaluate MIL-91 (Ti) sorbent for post-combustion CO2 capture in industrially relevant conditions. Initially, the process performance of the MOF was assessed using molecular simulated adsorption isotherms, which predicted an energy consumption of 1.65 MJ/kg and a productivity value of 0.42 mol/m³ ads s. Subsequently, MIL-91 (Ti) was characterized using several complementary experimental techniques, and the characterization data were supplied to a process simulator to assess energy consumption and productivity values for 95% purity and 90% recovery targets. The experimental adsorption isotherms resulted even better process performance, with a minimum energy consumption of 1.03 MJ/kg, and a maximum productivity of 0.61 mol/m3 ads s, compared to the GCMC simulated adsorption isotherms. This discrepancy can be attributed to the use generic force filed in the molecular simulation, which cannot accurately capture host-guest intermolecular interactions with the MOF pore surface in a highly confined environment of MOFs like MIL-91. However, the lower energy consumption and higher productivity of actual MIL-91 (Ti), which are both desirable outcomes for CO2 capture processes, suggests the viability of MIL-91 (Ti) for the implications in real CCS applications. | Shreenath Krishnamurthy; Nicolas Heymans; Mohammad Wahidduzzaman; Guillaume maurin; Shyamapada Nandi; Richard Blom; Marco Daturi; Debanjan Chakraborthy; Christian Serre; Georges Mouchaham; Guy De Weireld | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c17aaf81d2151a026b6f4a/original/evaluating-the-performance-and-suitability-of-mil-91-ti-mof-for-post-combustion-carbon-capture-by-vacuum-pressure-swing-adsorption-vpsa.pdf |
60c74eaebdbb8929c2a39bf4 | 10.26434/chemrxiv.12787463.v1 | An Insight into the Interaction Between α-Ketoamide-Based Inhibitor and Coronavirus Main Protease: A Detailed in Silico Study | <div>
<p>The search for therapeutic drugs
that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the
main focus of current research. The coronavirus main protease (M<sub>pro</sub>)
is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very
effective as a reversible covalent-inhibitor against cysteine proteases.
Herein, we report on the non-covalent to the covalent adduct formation mechanism
of α‑ketoamide-based inhibitor with the enzyme active site amino acids by
QM/SQM model (QM= quantum mechanical, SQM= semi-empirical QM). To uncover the
mechanism, we focused on two
approaches: a concerted and
a stepwise fashion.
The concerted pathway proceeds <i>via</i> deprotonation
of the thiol of cysteine (here, Cys<sub>145</sub> SgH)
and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide
warhead. In this work, we propose three plausible
concerted pathways. On the contrary, in a traditional two-stage pathway, the
first step is proton transfer from Cys<sub>145</sub> SgH to
His<sub>41</sub> Nd
forming an ion pair, and consecutively, in the second step, the thiolate ion attacks
the a-keto
group to form a thiohemiketal. In this reaction, we find that the stability of
the tetrahedral intermediate oxyanion/hydroxyl hole plays an important role. Moreover,
as the α-keto group has two faces <i>Si</i> or <i>Re</i> for the nucleophilic
attack, we considered both possibilities of attack leading to S- and
R-thiohemiketal.
We computed the structural, electronic, and energetic parameters of all
stationary points including transition states <i>via</i> ONIOM methodology at B3LYP/6-31G(d):PM6 level. Furthermore,
to get more accurate results, we also calculated the single-point dispersion-corrected energy profile by
using ωB97X-D/6-31G(d,p):PM6 level. Additionally, to characterize covalent,
weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced
density gradient (NCI-RDG) methods along with Bader’s Quantum Theory of
Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.</p>
</div>
<br /> | Snehasis Banerjee | Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eaebdbb8929c2a39bf4/original/an-insight-into-the-interaction-between-ketoamide-based-inhibitor-and-coronavirus-main-protease-a-detailed-in-silico-study.pdf |
65d2f9a866c1381729f6f0dd | 10.26434/chemrxiv-2024-m0cww-v3 | Point Sensor Networks Struggle to Detect and Quantify Short Controlled Releases at Oil and Gas Sites | This study evaluated multiple commercially available continuous monitoring (CM) point sensor network (PSN) solutions under single-blind controlled release testing conducted at operational upstream and midstream oil and natural gas (O&G) sites. During releases, PSNs reported site-level emission rate estimates of 0 kg/h between 38-86% of the time. When non-zero site-level emission rate estimates were provided, no linear correlation between release rate and reported emission rate estimate was observed. The average, aggregated across all PSN solutions during releases, shows 5% of mixing ratio readings at downwind sensors were greater than the site's baseline plus two standard deviations. Four of six total PSN solutions tested during this field campaign provided site-level emission rate estimates with the site average relative error ranging from -100% to 24% for solution D, -100% to -43% for solution E, -25% for solution F (solution F was only at one site), and -99% to 430% for solution G, with an overall average of -29% across all sites and solutions. Of all the individual site-level emission rate estimates, only 11% were within +/- 2.5 kg/h of the study team's best estimate of site-level emissions at the time of the releases. | Rachel Elizabeth Day; Ethan Emerson; Clay Bell; Daniel Zimmerle | Energy | CC BY NC 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d2f9a866c1381729f6f0dd/original/point-sensor-networks-struggle-to-detect-and-quantify-short-controlled-releases-at-oil-and-gas-sites.pdf |
67b6d480fa469535b91edba7 | 10.26434/chemrxiv-2025-sz07p | Metastable Sodium closo-Hydroborates for Low Temperature All-Solid-State Battery with Thick Cathode | All-solid-state batteries featuring a thick cathode layer paired with a high-capacity alloy anode offer enhanced energy density1,2 and reliable performance, even at subzero temperatures, can outperform their liquid-based counterparts. Enabling such technology requires a solid electrolyte with high ionic conductivity, mechanical formability, and excellent electrochemical stability3. While non-close-packed frameworks offer lower symmetry and irregular coordination between mobile ions and anions due to distortion, resulting in higher ionic conductivity4,5, fast ionic diffusion in hydroborate chemistry is often associated with close-packed or cubic anion frameworks6-9. Here, we demonstrate that a metastable, non-close-packed orthorhombic Na3(B12H12)(BH4) phase possesses superionic conductivity of 4.6 mS cm−1 at 30 °C, three orders of magnitude improvement over its precursors, alongside excellent reduction stability. High-throughput molecular dynamic simulations reveal that the propensity for anion motion significantly enhances the population of highly mobile Na+ without affecting the activation energy. By leveraging its high conductivity across a wide temperature range, this material enables the development of all-solid-state sodium-ion batteries with ultra-thick cathodes, delivering reliable functionality at room temperature and in subzero environments. This study expands our understanding of hydroborate-based solid electrolytes, highlighting their potential for high ionic conductivity and broad electrochemical stability windows in next-generation energy storage systems. | Jin An Sam Oh; Zihan Yu; Chen-Jui Huang; Phillip Ridley; Alex Liu; Tianren Zhang; Bingjoe Hwang; Kent Griffith; Shyue Ping Ong; Ying Shirley Meng | Materials Science; Inorganic Chemistry; Energy; Electrochemistry; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b6d480fa469535b91edba7/original/metastable-sodium-closo-hydroborates-for-low-temperature-all-solid-state-battery-with-thick-cathode.pdf |
62468db98048827ce3009c3f | 10.26434/chemrxiv-2022-9gmxz | Engineering Highly Stable, Fluorescent and Non-toxic Cu Nanoclusters via Reaction Parameter Optimization | Metal Nanoclusters (NCs) composed of the least number of atoms (few to tens) became very attractive for their emerging properties owing to their ultrasmall size. Preparing copper nanoclusters (Cu NCs) in an aqueous medium with high emission properties, strong colloidal stability, and low toxicity has been a long-standing challenge. Although they are earth-abundant and inexpensive, they are comparatively less explored due to their limitations such as ease of surface oxidation, poor colloidal stability, and high toxicity. To overcome these constraints, we established a facile synthetic route by optimizing the reaction parameters, especially altering the effective concentration of the reducing agent to influence their optical characteristics. The improvement of photoluminescence intensity and superior colloidal stability was modeled from a theoretical standpoint. Moreover, the as-synthesized Cu NCs showed a significant reduction of toxicity in both in vitro and in vivo models. The possibilities of using such Cu NCs as a diagnostic probe towards C. elegans were explored. Also, the extension of our approach towards improving the photoluminescence intensity of the Cu NCs on other ligand systems was demonstrated. | Kumar Babu Busi; Kotha Jyothi; Shamili Bandaru; Jyothi Priyanka Gantashala; Haseena Sheik; Keerti Bhamidipati; Nagaprasad Puvvada; Mahesh Kumar Ravva; Manjunatha Thondamal; Sabyasachi Chakrabortty | Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62468db98048827ce3009c3f/original/engineering-highly-stable-fluorescent-and-non-toxic-cu-nanoclusters-via-reaction-parameter-optimization.pdf |
60c74b9f702a9b40d618b49e | 10.26434/chemrxiv.12364121.v1 | A Kinetic View on Proximity-dependent Selectivity of Carbon Dioxide Reduction on Bifunctional Catalysts | Multifunctional catalysts with distinct functional
components are known to have much improved selectivity. However, the well-known
proximity-dependent selectivity observed in several high profile experiments is
yet to be understood. Here, we reveal that such dependence is closely
associated with the kinetics involved.
Based on reaction-diffusion dynamics together with kinetic Monte Carlo simulation on a coarse-grained model, one famous example of bifunctional catalysis, namely the proximity-dependent selectivity from carbon dioxide to liquid fuels on a bifunctional catalyst composed of HZSM-5 and In<sub>2</sub>O<sub>3</sub>, has been systematically examined. It is found that the diffusion kinetics of
the intermediate methanol generated on In<sub>2</sub>O<sub>3</sub> plays a decisive
role for the selectively. For different In<sub>2</sub>O<sub>3</sub>/HZSM-5
proximities, the local methanol concentration induce a shift of the dominant
process for subsequent methanol-to-hydrocarbon reactions inside HZSM-5,
resulting in a preferred reaction window to generate favorable liquid fuels
with profound high selectivity. Our findings emphasize the importance of the
largely overlooked kinetic in the design of multifunctional catalysts. | Huijun Jiang; Zhonghuai Hou; Yi Luo | Computational Chemistry and Modeling; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b9f702a9b40d618b49e/original/a-kinetic-view-on-proximity-dependent-selectivity-of-carbon-dioxide-reduction-on-bifunctional-catalysts.pdf |
60e1e725e0330e4c5313ea4e | 10.26434/chemrxiv-2021-qh8zd | Development of Diazaborines as ROS Sensitive Linkers for the Construction of Stimuli-Responsive Antibody Drug Conjugates | Antibody-drug conjugates (ADCs) are a new class of therapeutics that combine the lethality of potent cytotoxic drugs with the targeting ability of antibodies to selectively deliver drugs to cancer cells. The synthesis of ADCs is challenging, and studies in this area show that their therapeutic effect is highly dependent on the chemistries used to connect both functions. Therefore, the linker evolved in recent years from being a simple chemical spacer to a functional structure that controls the potency and selectivity of ADCs. The linker provides a platform to integrate mechanisms to access synthetic homogeneity, stability in circulation and more importantly the installation of chemical units that release the drug as a response to the disease chemical environment. In this study we show for the first time the synthesis of a reactive-oxygen-species (ROS) responsive ADC (VL-DAB31-SN-38) that is highly selective and cytotoxic to B-cell lymphoma (CLBL-1 cell line, IC50 value of 54.1 nM). The synthesis of this ADC was possible due to the discovery that diazaborines (DABs) are a very effective ROS responsive unit (0.422 and 0.103M-1S-1 with 100 and 10 equiv. of H2O2 respectively), that is also very stable in buffer (over 14 days at different pHs) and in plasma (over 5 days). DFT calculation performed on this system revealed a favourable energetic profile (ΔGR = –74.3 kcal/mol) similar to the oxidation mechanism of aromatic boronic acids. DABs very fast formation rate and modularity enabled the construction of different ROS responsive linkers featuring self-immolative modules, bioorthogonal functions and bioconjugation handles. These structures were used in the site-selective functionalization of a VL antibody and in the construction of the homogeneous ADC. The enclosed ROS-responsive linker technology based on DABs, is expected to become a valuable tool to prepare stimuli responsive therapeutic materials, as ROS is a very important hallmark in several important diseases | Pedro Gois; João António; Joana Carvalho; Ana André; Joana Dias; Hélio Faustino; Ricardo Lopes; Luis Veiros; Gonçalo Bernardes; Frederico Silva | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e1e725e0330e4c5313ea4e/original/development-of-diazaborines-as-ros-sensitive-linkers-for-the-construction-of-stimuli-responsive-antibody-drug-conjugates.pdf |
626288e6368ab6ed95891e8b | 10.26434/chemrxiv-2022-0dkm2 | Enzyme-like reactivity for increasing selectivity in CO2 electrochemical reduction | The development of selective catalysts for the reduction of CO2 mostly focuses on electrocatalytic approaches and aims at increasing the selectivity of the reaction while keeping a high activity, which is difficult to achieve. Metalloporphyrins are good catalysts for CO2 reduction because they have favorable electronic properties and offer the possibility to make use of secondary coordination sphere effects. Here, we present a new approach to CO2 reduction, which is based on host-guest chemistry enabled by an iron porphyrin cage catalyst. When this iron porphyrin cage catalyst is immobilized on a conducting carbon support the selectivity for CO2 reduction to CO stays above 90 % in a wide range of overpotentials. The hosting of potassium ions in the cage of the catalyst decreases the overpotential of the reduction and increases the catalytical activity while retaining the high selectivity. DFT calculations show that the potassium ions assist the reduction of CO2 by making the 2-electron transfer from iron(0) to CO2 exothermic. Upon protonation, the Fe-COOH intermediates have been trapped by combining an electrochemical cell with an electrospray ionization mass spectrometer and their structure has been characterized by cryogenic ion spectroscopy. | Adarsh Koovakattil Surendran; Guilherme L. Tripodi; Eva Pluharova; Aleksandr Y. Pereverzev; Jeroen P. J. Bruekers; Johannes A. A. W. Elemans; Evert Jan Meijer; Jana Roithova | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Electrocatalysis; Spectroscopy (Physical Chem.); Structure | CC BY NC 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626288e6368ab6ed95891e8b/original/enzyme-like-reactivity-for-increasing-selectivity-in-co2-electrochemical-reduction.pdf |
62822e8b44bdd51f26650d67 | 10.26434/chemrxiv-2022-67s7p | Electrochemical Impedance Spectroscopy (EIS) Based Label-Free Immunosensors | Electrochemical Impedance Spectroscopy (EIS) is a surface sensitive technique which examines the impedance of an electrochemical cell over a range of frequencies. By immobilising an antigen or antibody to the electrode surface, EIS shows potential for highly specific and sensitive immunosensor performance. Following an introduction into antibodies and EIS, this review presents immobilisation techniques for an immunosensor’s bioreceptor. It highlights electrode modifications such as self-assembled monolayers (SAMs), polymers and nanostructures for anchoring the bioreceptor to the surface. Stable immobilisation directly to these modifications is not always possible. Immobilisation techniques to these modified surfaces are explored including cross-linking and controlled orientation. EIS allows for label-free detection by monitoring the change in charge-transfer resistance or capacitance caused by changes in the electrode surface. Label-free immunosensors are the focus of this paper as they show potential for point-of-care (POC) devices. | Caoimhe Robinson; VUSLAT B. JUSKA; Alan O'Riordan | Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62822e8b44bdd51f26650d67/original/electrochemical-impedance-spectroscopy-eis-based-label-free-immunosensors.pdf |
67a111fe6dde43c9087d4563 | 10.26434/chemrxiv-2025-l0ptc | Dearomative C2–Borylation of Indoles | The dearomative borylation of indoles is challenging and typically requires transition metal catalysts, strong bases, or harsh conditions. We report the metal- and base-free C2-borylation of indoles using bis(1-methyl-ortho-carboranyl)borane as an electrophilic borylating reagent to generate borylated indolines under mild conditions. | Ayesha Begum; Manjur Oyasim Akram; Caleb Martin | Organic Chemistry; Organometallic Chemistry; Bond Activation; Main Group Chemistry (Organomet.); Reaction (Organomet.) | CC BY 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a111fe6dde43c9087d4563/original/dearomative-c2-borylation-of-indoles.pdf |
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