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658d680166c1381729349118 | 10.26434/chemrxiv-2023-5mqmp | Strategic Approach to Pyrazinoquinoxaline Molecular Design for Enhanced Performance | The availability of affordable organic compounds with thermally activated delayed fluorescence (TADF) properties represents a unique class of materials for addressing key challenges in organic electronics. In this context, we have successfully designed and synthesised three novel hybrid molecules 2-(4-(3,6-di-tert-butyl-9H-carbazol-9-yl)phenyl)-3,7,8-triphenylpyrazino[2,3-g]quinoxaline (tCz-PyrQx), 4-(tert-butyl)-N-(4-(tert-butyl)phenyl)-N-(4-(3,7,8-triphenylpyrazino[2,3-g]quinoxalin-2-yl)phenyl)aniline (tDPA-PyrQx), and 2-(4-(9,9-dimethylacridin-10(9H)-yl)phenyl)-3,7,8-triphenylpyrazino[2,3-g]quinoxaline (Ac-PyrQx) comprising electron-donating 3,6-di-tert-butyl-9H-carbazole, bis(4-(tert-butyl)phenyl)amine, and (9,9-dimethyl-9,10-dihydroacridine) with electron-accepting pyrazinoquinoxaline groups. The incorporation of highly planar and rigid pyrazinoquinoxaline electron-accepting moieties holds significant importance due to their unique properties like efficient charge transfer, and reduced steric hindrance. Their planar structure facilitates strong π-π stacking interactions and efficient charge transfer within the molecular framework, leading to improved exciton formation and enhanced reverse intersystem crossing (RISC) rates, which are critical for TADF processes. The three different electron-donating groups with pyrazinoquinoxaline were synthesised with the view of tuning the photophysical and electrochemical properties of the hybrids. | Sunil Madagyal; Pratima Yadav; Prabhakar Chetti; Atul Chaskar | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658d680166c1381729349118/original/strategic-approach-to-pyrazinoquinoxaline-molecular-design-for-enhanced-performance.pdf |
6178a207ff3ba94be5a4a168 | 10.26434/chemrxiv-2021-r5dn6 | Genetic Encoding of Cyanopyridylalanine for In-Cell Protein Macrocyclization by the Nitrile-Aminothiol Click Reaction | Cyanopyridylalanines are non-canonical amino acids that react with aminothiol compounds under physiological conditions in a biocompatible manner without requiring added catalyst. Here we present newly developed aminoacyl-tRNA synthetases for genetic encoding of meta- and para-cyanopyridylalanine to enable the site-specific attachment of a wide range of different functionalities. The outstanding utility of the cyanopyridine moiety is demonstrated by examples of (i) post-translational functionalization of proteins, (ii) in-cell macrocyclization of peptides and proteins, and (iii) protein stapling. The biocompatible nature of the protein ligation chemistry enabled by the cyanopyridylalanine amino acid opens a new path to specific in vivo protein modifications in complex biological environments. | Elwy Abdelkader; Haocheng Qianzhu; Josemon George; Rebecca Frkic; Colin Jackson; Christoph Nitsche; Gottfried Otting; Thomas Huber | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6178a207ff3ba94be5a4a168/original/genetic-encoding-of-cyanopyridylalanine-for-in-cell-protein-macrocyclization-by-the-nitrile-aminothiol-click-reaction.pdf |
60c74398337d6c4640e26c27 | 10.26434/chemrxiv.9273395.v1 | Characterization of a Reactive Rh2 Nitrenoid by Crystalline Matrix Isolation | Here we report the first X-ray
crystal structure of a reactive Rh<sub>2</sub> nitrenoid, enabled by N<sub>2</sub>
elimination from an organic azide ligand within a single-crystal matrix. The
resulting high-resolution data set demonstrates a long Rh–N bond, consistent
with a triplet electronic structure. The demonstration of facile access to
reactive metal nitrenoids within a crystalline matrix provides a platform for
structural characterization of the elusive transient species at the heart of
C–H functionalization. | Anuvab Das; Yu-Sheng Chen; Joseph Reibenspies; David Powers | Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74398337d6c4640e26c27/original/characterization-of-a-reactive-rh2-nitrenoid-by-crystalline-matrix-isolation.pdf |
67cb2be6fa469535b9653979 | 10.26434/chemrxiv-2024-t88r2-v6 | Alternating Current Voltammetry: Predicting and Visualizing Harmonics | Alternating current voltammetry (ACV) is gaining popularity for its ability to improve the yield of electrochemical syntheses, and for its ability to improve the sensitivity of electroanalytical measurements. Chief among the analytical advantages of ACV is its ability to generate an alternating current at integer multiples (harmonics) of the applied frequency, effectively gathering several datasets at once. However, interpretation of ACV data is hindered by the lack of a unified theory to predict higher harmonics for arbitrary reaction schemes, and by the experimental artefacts of uncompensated cell resistance and background current. The present paper outlines a method for predicting an arbitrary number of harmonics for systems with up to two charge transfer events and any number of coupled first-order chemical reactions, accounting also for cell resistance and background current described by a constant phase element. Results for an ``ideal" experiment (no cell resistance and no background current) are presented up to the third harmonic for schemes with first-order reactions, and up to the first harmonic for schemes with second-order reactions. After these ``ideal" cases, the effects of cell resistance and background current are explored. In general, irreversible charge transfer causes smaller phase angles, and coupled chemical reactions cause the aspect ratios of complex-plane ACV plots to become more circular. Uncompensated cell resistance can also lower the phase angle, imitating the effects of slow charge transfer or fast chemical reactions. At high frequencies, a combination of cell resistance and capacitance can cause the error in the potential to be so great that the current magnitude actually decreases with the onset of charge transfer. An ability to interpret the electrochemical fingerprints of each system in ACV experiments, as a function of the underlying physical parameters, can aid in the design of electrochemical devices that rely on the controlled utilization of electrochemical reactivity. | Chase Bruggeman | Theoretical and Computational Chemistry; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Electrochemical Analysis; Theory - Computational; Transport Phenomena (Chem. Eng.) | CC BY 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cb2be6fa469535b9653979/original/alternating-current-voltammetry-predicting-and-visualizing-harmonics.pdf |
66325e5d418a5379b02d3b0a | 10.26434/chemrxiv-2024-7325z | Fast-Charging Lithium Iron Phosphate Cathodes by Flash Carbon Coating | Carbon coating has been used to address the poor rate performance of lithium iron phosphate (LiFePO4, LFP) due to its low intrinsic electronic and ionic conductivities. Various processes have been developed to synthesize carbon coated LFP. However, most in situ strategies introduce carbon sources during synthesis, which can interact with the LFP growth process. In this work, we developed an ex situ carbon coating method by rapidly decomposing the precursors through flash Joule heating (FJH). A uniform, amorphous carbon layer was achieved on LFP by depositing carbon-heteroatom species in a confined space within 10 seconds. Simultaneously, different heteroatoms can be introduced into the surface carbon layer to facilitate a uniform cathode-electrolyte interphase (CEI). LFP cathodes with fluorinated carbon coatings exhibited the highest capacity of 151 mAh g-1 at 0.2 C and 96 mAh g-1 at 10 C, indicating its excellent rate capability over commercial LFP (58 mAh g-1 at 10 C). A dense CEI layer with a thickness of 10 nm was observed during cycling, which effectively promotes electron and ion transport and restricts side reactions. This solvent-free, versatile cathode surface modification is shown for other cathode types, providing an efficient platform for electrode-electrolyte interphase engineering through a surface post-treatment. | Jinhang Chen; Obinna Onah; Yi Cheng; Karla Silva; Chi Choi; Weiyin Chen; Shichen Xu; Lucas Eddy; Yimo Han; Boris Yakobson; Yufeng Zhao; James Tour | Materials Science; Energy; Coating Materials; Materials Processing; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66325e5d418a5379b02d3b0a/original/fast-charging-lithium-iron-phosphate-cathodes-by-flash-carbon-coating.pdf |
60c7525b4c89191f44ad40fb | 10.26434/chemrxiv.13289336.v1 | Characterization of a Library of Vitamin A-Functionalized Polymethacrylate-Based Nanoparticles for siRNA Delivery | <p>A 60-membered library of vitamin A-functionalized P(MMA-<i>stat</i>-DMAEMA)-<i>b</i>-PPEGMA block copolymers was synthesized by RAFT polymerization. Subsequently, retinoic acid was coupled to hydroxyl groups present in the hydrophilic PPEGMA block. The polymers were investigated for their ability to encapsulate ribonucleic acids through nanoparticle (NP) formulation using the emulsion/solvent evaporation method. The localization of vitamin A in surface-near regions of the NPs was indicated by surface enhanced Raman spectroscopy, and the interaction of the NPs with a retinol binding protein was investigated by analytical ultracentrifugation. The systematic analysis of the NP library in terms of the encapsulation efficiency of the ribonucleic acids, the toxicity of the NPs, and the cellular uptake helped identifying suitable candidates for cellular internalization studies. The cell uptake was investigated by flow cytometry and fluorescence microscopy and reveals structure dependent uptake behavior of the examined particles. </p> | Paul Klemm; Sophie Huschke; Marko Rodewald; Nadia Ehteshamzad; Mira Behnke; Xinyue Wang; Gizem Cinar; Ivo Nischang; Stephanie Hoeppener; Christine Weber; Adrian Press; Christiane Höppener; Tobias Meyer; Volker Deckert; Michael Schmitt; Jürgen Popp; Michael Bauer; Stephanie Schubert | Drug delivery systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7525b4c89191f44ad40fb/original/characterization-of-a-library-of-vitamin-a-functionalized-polymethacrylate-based-nanoparticles-for-si-rna-delivery.pdf |
66e5604312ff75c3a14ca465 | 10.26434/chemrxiv-2024-xtmjk | Multiexciton absorption cross-sections of CdSe@CdS nanorods studied using Pump-rePump-Probe Spectroscopy | Understanding the multiexciton properties of nanocrystals is the basis for harnessing their full potential for various device applications. The multiexciton dynamics in semiconductor nanocrystals are widely explored. However, the absorption cross-sections for multiexcitons of varying order are not so well understood. To gain insights into the absorption cross sections for multiexcitons, we performed pump-repump-probe transient absorption (ppp-TA) spectroscopic measurement on CdSe@CdS nanorods. By tuning the pump-repump delay time and repump intensity, we were able to generate and reexcite various transiently living multiexcitonic species. We modelled the ppp-TA data using a Markov Chain Monte Carlo target analysis method, with this we determined the spectral shape and lifetime of higher order excitons (up to tri-excitons). This method also enabled us to extract absorption cross-section parameters for different multiexcitonic states. Our results indicate that for 400 nm excitation, the absorption cross-sections of excited state species are largely independent of exciton order. | Krishan Kumar; Jens Uhlig; Raktim Baruah; Shivani Yadav; Maria Wächtler | Physical Chemistry; Nanoscience; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e5604312ff75c3a14ca465/original/multiexciton-absorption-cross-sections-of-cd-se-cd-s-nanorods-studied-using-pump-re-pump-probe-spectroscopy.pdf |
6516778ea69febde9ee728ef | 10.26434/chemrxiv-2023-z95xl | Palladium Catalyzed C3-(sp2)-H Alkenylation of Pyrroles: A Direct Access to Novel Organic Thermally Activated Delayed Fluorescence (TADF) Materials | A Pd (II)-catalyzed direct C3-(sp2)-H alkenylation of heteroarenes using benzothiazole as a directing group has been successfully achieved. A wide range of 2-N-alkylpyrroles undergo an oxidative coupling with a variety of acrylates to furnish highly regio- and chemo-selective E-alkenylation products at C3 position. An important intermediate complex has been isolated and characterized so as to have an insight into the mechanism. This convenient protocol proved to practical to access novel thermally activated delayed fluorescence materials (TADF). These molecules proved to be blue emitting TADF materials (~ms life time). A detailed and systematic investigation has been carried out to study the photophysical properties and this has been further validated by the time dependent (TD) density functional theory (DFT) calculations. | Javed Y. Shaikh; Anindita Bhowmick; Abhijit Chatterjee; Debasish Laha; Dr. Ramakrishna G. Bhat | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516778ea69febde9ee728ef/original/palladium-catalyzed-c3-sp2-h-alkenylation-of-pyrroles-a-direct-access-to-novel-organic-thermally-activated-delayed-fluorescence-tadf-materials.pdf |
672925b7f9980725cf178826 | 10.26434/chemrxiv-2024-jnxq4 | Models and Measurements Quantify Photon Recycling, Charge-Carrier Diffusion, and Photon Scattering Contributions to Photoluminescence in InP Nanowire Arrays | Nanowire arrays present many unique advantages for solar-to-chemical energy conversion and are good model systems to investigate how the performance of one nanowire can influence others in an array. Spatially resolved photoluminescence is a powerful experimental characterization tool to quantify optical and electronic coupling between nanowires in an array. However, three underlying mechanisms of incident photon scattering, photon recycling, and charge-carrier diffusion dictate this coupling. In this study, we present a comprehensive analysis of light absorption and emission of a single nanowire at open circuit, and subsequent re-absorption and re-emission by a neighboring nanowire. We developed a novel correlated single nanowire micro-spectroscopy and widefield imaging methodology to spatially resolve photon communication pathways between neighboring nanowires and selectively image re-emitted and reflected photons. Unique multiphysics models have been developed to couple wave optics and semiconductor photophysics to especially isolate contributions from photon recycling and electronic transport to photon emission from neighboring nanowires. By systematically varying the morphologies of the nanowires modeled, we identify pathways to maximize photon recycling between neighboring nanowires. We conclude that the measured photoluminescence is more strongly influenced by the diffusion of charge-carriers as compared to photon recycling in materials with moderate-to-large charge-carrier mobilities (> 10 cm2 V-1 s-1), and that photon recycling dictates photoluminescence intensity only when the charge-carrier mobility is low (< 1 cm2 V-1 s-1). The experimental and simulation platforms developed herein for photon management strategies can be leveraged by the semiconductor photocatalysis community to enhance solar-to-chemical conversion efficiencies in semiconductor nanowire arrays. | Danielle Lustig; Fangqi Chen; Wentao Zhang; Olivia Bird; Javier Fajardo Jr.; Shane Ardo; Shu Hu; A. Alec Talin; Rohini Bala Chandran; Justin Sambur | Nanoscience; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672925b7f9980725cf178826/original/models-and-measurements-quantify-photon-recycling-charge-carrier-diffusion-and-photon-scattering-contributions-to-photoluminescence-in-in-p-nanowire-arrays.pdf |
60c74db10f50db505439709a | 10.26434/chemrxiv.12649826.v1 | Polymer-Based Chemical Nose Systems for Optical Pattern Recognition of Gut Microbiota | Understanding the status of gut microbiota has been
recognized as crucial in health management and disease treatment. To meet the
demands of medical and biological applications where rapid evaluation of gut
microbiota in limited research environment is essential, we developed new sensing
systems able to readout the overall characteristics of complex microbiota. Response
patterns generated by a synthetic library of 12 charged block-copolymers with aggregation-induced
emission units were analyzed with pattern recognition algorithms, allowing to
identify the species/phyla of 16 axenic cultures of intestinal bacterial
strains. More importantly, our method clearly classified artificial models of
obesity-associated gut microbiota, and further succeeded in detecting sleep
disorders in mice through comparative analysis of the normal/abnormal mouse gut
microbiota. Our techniques can analyze complex bacterial samples far more
quickly, simply and inexpensively than common metagenome-based methods, offering
a powerful and complementary tool for gut microbiome analysis for practical
use, e.g., in clinical settings. | Shunsuke Tomita; Hiroyuki Kusada; Naoshi Kojima; Sayaka Ishihara; Koyomi Miyazaki; Hideyuki Tamaki; Ryoji Kurita | Polyelectrolytes - Polymers; Biochemical Analysis; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db10f50db505439709a/original/polymer-based-chemical-nose-systems-for-optical-pattern-recognition-of-gut-microbiota.pdf |
6520286fbda59ceb9a00bf91 | 10.26434/chemrxiv-2023-r0qn7 | Quantification of inhomogeneous local proton density distributions in soft matter, unstructured macromolecules and non-Anfinsen biomacromolecules | A new method to quantitatively analyse inhomogeneous distributions of local proton densities around paramagnetic centers in unstructured bio-polymers, disordered biomolecules and soft matter is introduced, and its feasibility is demonstrated on aqueous solutions of stochastically spin-labeled polysaccharides. The technique is based on a dipolar EPR pulse sequence ih-RIDME (intermolecular hyperfine relaxation-induced dipolar modulation enhancement). The global analysis of a series of RIDME traces offers a mathematically stable transformation of the time-domain data to the proton density distribution. Novel pulse EPR sequences are proposed and primarily tested, which combine the ih-RIDME block and the double-electron-electron resonance (DEER) experiment. These new pulse sequences can be potentially used to correlate the local proton distributions with the overall macromolecule chain conformational distribution. | Sergei Kuzin; Dario Stolba; Xiaowen Wu; Victoria Syryamina; Samy Boulos; Gunnar Jeschke; Laura Nyström; Maxim Yulikov | Physical Chemistry; Biological and Medicinal Chemistry; Polymer Science; Organic Polymers; Biophysical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6520286fbda59ceb9a00bf91/original/quantification-of-inhomogeneous-local-proton-density-distributions-in-soft-matter-unstructured-macromolecules-and-non-anfinsen-biomacromolecules.pdf |
60c74684469df41169f4366a | 10.26434/chemrxiv.8950718.v2 | Mapping the Optoelectronic Property Space of Small Aromatic Molecules | <p><i>We perform a high-throughput
virtual screening using the xTB family of density functional tight-binding
methods to map the optoelectronic property space of ~250,000 aromatic molecules and quinone derivatives
that find application in organic transistors, solar-cells, thermoelectrics,
batteries and photocatalysts. The large volume of data generated allows for a
broad understanding of how the presence of a wide range of heteroatoms and
functional groups affect the ionisation potential, electron affinity and
optical gap values of these molecular semiconductors and how the structural
features – on their own or in combination with one another – allow access to
particular regions of the optoelectronic property space. Finally, we identify the
apparent boundaries of the optoelectronic property space for these molecules:
regions of property space that appear off limits for any small conjugated
cyclic organic molecule.</i></p> | Liam Wilbraham; Denisa Smajli; isabelle Heath-Apostolopoulos; Martijn Zwijnenburg | Physical Organic Chemistry; Carbon-based Materials; Catalysts; Dyes and Chromophores; Optical Materials; Photosensitizers; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Energy Storage; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74684469df41169f4366a/original/mapping-the-optoelectronic-property-space-of-small-aromatic-molecules.pdf |
63b55c62e9d0fd72a7352e8b | 10.26434/chemrxiv-2023-fd9kr | Experimental and computational studies of the production of 1,3-butadiene from 2,3-butanediol using SiO2-supported H3PO4 derivatives | Silica-supported phosphoric acid and metal phosphate catalyzed 1,3-butadiene (BDE) production from 2,3-butanediol (2,3-BDO) was studied using experimental and computational techniques. The catalyst was initially tested in a continuous flow reactor using commercially available 2,3-BDO, leading to maximum BDE yields of 63 C%. Quantum chemical mechanistic studies revealed 1,2-epoxybutane is a kinetically viable and thermodynamically stable intermediate, supported by experimental demonstration that this epoxide can be converted to BDE under standard reaction conditions. Newly proposed E2 and SN2’ elementary steps were studied to rationalize the formation of BDE and all detected side-products. Additionally, using QM/MM (ONIOM) calculations, we modeled silica-supported phosphate catalysts to study the effect of the alkali metal center. Natural population analysis showed that phosphate oxygen atoms are more negatively charged in CsH2PO4/SiO2 than in H3PO4/SiO2. In combination with temperature-programmed desorption experiments using CO2, the results of this study suggest that the improved selectivity achieved when adding the metal center is related to an increase in the basicity of the catalyst. | Juan Vicente Alegre Requena; Glenn R. Hafenstine; Xiangchen Huo; Yanfei Guan; Jim Stunkel; Frederick G. Baddour; Kinga A. Unocic; Bruno C. Klein; Ryan E. Davis; Robert S. Paton; Derek R. Vardon; Seonah Kim | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b55c62e9d0fd72a7352e8b/original/experimental-and-computational-studies-of-the-production-of-1-3-butadiene-from-2-3-butanediol-using-si-o2-supported-h3po4-derivatives.pdf |
63491428e3f3ee88e759bbc3 | 10.26434/chemrxiv-2022-m7750 | Highly Porous and Drug Loaded Amorphous Solid Dispersions Microfiber Scaffolds of Indomethacin prepared by Melt Electrowriting | Melt electrowriting (MEW) is an additive manufacturing technology enabling the production of highly porous microfiber scaffolds, suggested in particular for use in biomedical applications, including drug delivery. indomethacin (IND) is a non-selective anti-inflammatory drug, for which sublingual delivery could offer advantages such as rapid absorption by the veins in the mouth
floor while overcoming the side-effects of peroral delivery such as damage to gastrointestinal mucosa barrier. This study introduces MEW as a processing method to obtain rapid-dissolving drug releasing scaffolds, containing IND as a model drug, for sublingual drug delivery applications. For this, an amorphous solid dispersion of IND in combination of a novel poly(2-oxazoline) based amphiphilic triblock copolymer excipient is introduced, enabling ultra-high drug loading. We prepared highly porous, melt electrowritten drug-loaded scaffolds with different polymer:IND w/w ratios up to 1:2 and assessed their morphology, amorphicity, and IND release rate. The results show completely amorphous dispersion of the polymer and drug after MEW processing resulting in smooth and uniform fibers, and rapid dissolution of the polymer. These first water soluble melt electrowritten IND-loaded microfiber scaffolds break ground as a model for rapid sublingual delivery of ultra-high drug loaded amorphous solid dispersions. | Larissa Keßler; Zeynab Mirzaei; Juliane C. Kade; Robert Luxenhofer | Biological and Medicinal Chemistry; Materials Science; Polymer Science | CC BY 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63491428e3f3ee88e759bbc3/original/highly-porous-and-drug-loaded-amorphous-solid-dispersions-microfiber-scaffolds-of-indomethacin-prepared-by-melt-electrowriting.pdf |
648452a44f8b1884b719b50f | 10.26434/chemrxiv-2023-kfqdc | P-Band Intermediate States Mediate Electron Transfer at Confined Nanoscale | In this perspective article, mainly based on the model of structural water molecules (SWs) as bright color emitters, we briefly summarize the development and theoretical elaboration of P-band intermediate state (PBIS) theory and its application in catalysis, especially in several representative redox reactions. In particular, with a simple equation (2∫ψ2σ1’ + ∫ψ2σ2 + ∫ψ2π =1), we define how the interface sate correlate with the three basic parameters of heterogenous catalysis (conversion, selectivity and stability), and what is the dynamic nature of catalytic active sites. Overall, the proposal of SWs dominated PBIS theory provides new insights into the physical origin of photoluminescence emission of low-dimensional quantum nanodots and the physical nature of nanoconfinement and nanoconfined catalysis. | Kun Zhang; Ming-Yuan He | Physical Chemistry; Catalysis; Nanoscience; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648452a44f8b1884b719b50f/original/p-band-intermediate-states-mediate-electron-transfer-at-confined-nanoscale.pdf |
65603a9a5bc9fcb5c94139aa | 10.26434/chemrxiv-2023-42f5t | Liquid-Liquid Phase Separation for Analyte Enrichment in Coacervates for Ultra-Sensitive Biosensing | Efficient isolation and concentration of biomolecules are foundational for rapid diagnostics. Traditional methods, often reliant on solid surfaces, necessitate complex and labor-intensive procedures. Liquid-liquid phase separation (LLPS) systems emerged as promising due to their ability to extract biomolecules via the partition effect. Inspired by the biomolecular compartmentalization observed in cellular organelles, we form coacervates via associative LLPS for concentrating a diverse range of biomolecules, significantly enhancing sensitivity and lowering detection limits of biomolecules by condensing biomolecules in compartments. We demonstrate that under optimal conditions these coacervates can achieve an enrichment factor of up to 22.8 for DNA, surpassing the efficiency of segregative LLPS. This results in significantly enhanced sensitivity for DNA detection. Through fluorescence microscopy, microplate readers, and flow cytometry, we establish that coacervate droplets are approximately 21 times more effective in reducing the limit of detection (LOD) for DNA compared to segregative LLPS droplets. The superior performance of coacervates is attributed to non-covalent interactions between DNA and molecules within coacervates, enabling ultra-sensitive quantification without the need for complex instrumentation or signal amplification. By creating distinct compartments for biomolecule condensation, our approach not only simplifies the detection process but also significantly lowers detection thresholds, paving the way for more accessible and rapid diagnostic methods. | Chaofeng Cen; Xudong Ma; Xi Lu; Hui Zhou; Yinliang Lin; Si Meng; Wenwen Chen; Zhou Liu; cheng qi; Tiantian Kong | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65603a9a5bc9fcb5c94139aa/original/liquid-liquid-phase-separation-for-analyte-enrichment-in-coacervates-for-ultra-sensitive-biosensing.pdf |
60c75676702a9bf6bc18c8f0 | 10.26434/chemrxiv.13521377.v2 | The CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions? | <div>
<div>
<p>
</p><div>
<div>
<div>
<p>We present the CHAL336 benchmark set—the most comprehensive database for
the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises
336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen,
and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic
overestimation of interaction energies for some dispersion-corrected DFT methods does
not hint at problems with the chosen dispersion correction, but is a consequence of large
density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and -uncorrected DFT methods, and carry out a detailed analysis of 80 of
them. Double-hybrid functionals are the most reliable approaches for CB interactions,
and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ).
The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ).
We do not recommend using the popular B3LYP functional nor the MP2 approach,
which have both been frequently used to describe CB interactions in the past. We hope
to inspire a change in computational protocols surrounding CB interactions that leads
away from the commonly used, popular methods to the more robust and accurate ones
recommended herein. We would also like to encourage method developers to use our set
for the investigation and reduction of density-driven errors in new density functional
approximations. </p>
</div>
</div>
</div>
</div>
</div> | Nisha Mehta; Thomas Fellowes; JONATHAN WHITE; Lars Goerigk | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75676702a9bf6bc18c8f0/original/the-chal336-benchmark-set-how-well-do-quantum-chemical-methods-describe-chalcogen-bonding-interactions.pdf |
622cf182702f04e9dfba0e23 | 10.26434/chemrxiv-2022-44rx6 | Anaerobic defluorination of chlorine-substituted per- and polyfluorinated carboxylic acids triggered by microbial dechlorination | Chlorinated per- and polyfluoroalkyl substances (Cl-PFAS) have been manufactured and widely used in industrial and commercial products. Here, we report on significant anaerobic biodefluorinaiton structures and novel defluorination pathways of specific Cl-PFAS triggered by anaerobic microbial dechlorination. Compared to the H-substituted counterparts, the Cl-substituted per- and polyfluoroalkyl carboxylic acids PFCAs exhibited faster and deeper defluorination, which was attributed to the highly bioreactive Cl-substitutions. The Cl-PFCAs underwent reductive, hydrolytic, and eliminative dehalogenation reactions. It was the hydrolytic dechlorination that led to the following significant spontaneous defluorination forming di-carboxylic acids. The more Cl-substitutions, the more likely the hydrolytic dechlorination would occur at the multiple Cl-substitutions, leading to much higher defluorination and chain-shortening products. About 80% total defluorination was achieved for the chlorotrifluoroethylene tetramer carboxylic acid with four Cl-substitutions. The reductive dechlorination was a non-defluorinating pathway, and the H-substituted products were more recalcitrant to biodefluorination. This study advances the knowledge of the structure-biodegradability and the biodefluorination pathways of Cl-PFCAs in anaerobic conditions. It provides important guidance to assess the environmental fate and transport of Cl-PFAS, including fluoropolymers, and the potential environmental risks. It also sheds light on PFAS source-tracking by suggesting Cl-PFAS as an important source of some emergent PFAS structures detected in impacted fields. | Bosen Jin; Shun Che; Jinyu Gao; Yaochun Yu; Jinyong Liu; Yujie Men | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622cf182702f04e9dfba0e23/original/anaerobic-defluorination-of-chlorine-substituted-per-and-polyfluorinated-carboxylic-acids-triggered-by-microbial-dechlorination.pdf |
646b465ff2112b41e9f49997 | 10.26434/chemrxiv-2023-kz1pb | TeachOpenCADD goes Deep Learning: Open-source Teaching Platform Exploring Molecular DL Applications | TeachOpenCADD is a free online platform that offers solutions to common computer-aided drug design (CADD) tasks using Python programming and open-source data and packages. The material is presented through interactive Jupyter notebooks, accommodating users from various backgrounds and programming levels. Due to the tremendous impact of deep learning (DL) methods in drug design, the TeachOpenCADD platform has been expanded to include an introduction to molecular DL tasks. This edition provides an overview of DL and its application in drug design, highlighting the usage of diverse molecular representations in this field. The platform introduces various neural network architectures, including graph neural networks (GNNs), equivariant graph neural networks (EGNNs), and recurrent neural networks (RNNs). It demonstrates how to use these architectures for developing predictive models for molecular property and activity prediction, exemplified by the Quantum Machine 9 (QM9), ChEMBL, and Kinase Inhibitor BioActivity (KiBA) data sets. The DL edition covers methods for evaluating the performance of neural networks using uncertainty estimation. Furthermore, it introduces an application of GNNs for protein-ligand interaction predictions, incorporating protein structure and ligand information. The TeachOpenCADD platform is continuously updated with new content and is open to contributions, bug reports, and questions from the community through its GitHub repository (https://github.com/volkamerlab/teachopencadd). It can be used for self-study, classroom instruction, and research applications, accommodating users from beginners to advanced levels. | Michael Backenköhler; Paula Linh Kramer; Joschka Groß; Gerrit Großmann; Roman Joeres; Azat Tagirdzhanov; Dominique Sydow; Hamza Ibrahim; Floriane Odje; Verena Wolf; Andrea Volkamer | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Education; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b465ff2112b41e9f49997/original/teach-open-cadd-goes-deep-learning-open-source-teaching-platform-exploring-molecular-dl-applications.pdf |
670810b712ff75c3a1126a0f | 10.26434/chemrxiv-2024-z06wg | Beyond Core-Shell Micellar Structures: complex structures in simple surfactants | Small-angle X-ray/neutron scattering (SAXS/SANS) techniques provide valuable nanostructural information of self-assembling molecules. However, extracting the information from these experiments can be a challenging task, usually relying on predetermined assumptions. Conventional models for surfactant micelles consider a core-shell structure with a hydrophobic tail encapsulated by the hydrophilic part. This approach is successful in many cases, but can fail even for common surfactants such as Triton X-100 (TX-100). We employ SAXS and SANS combined with Metainference molecular simulations to investigate TX-100 assemblies, showing how more complex models, with diffuse core-shell boundaries, multilayering, and polydispersity, are needed to explain the aggregation. Compared to regular micelles formed by chemically similar C12EO10 molecules, we discuss the role of the hydrophobic core in micellization, finding that the relatively shorter and less hydrophobic tail of TX-100 favours polymorphism. | Henrique Musseli Cezar; Victoria Ariel Bjørnestad; Sylvain Prévost; Reidar Lund; Michele Cascella | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670810b712ff75c3a1126a0f/original/beyond-core-shell-micellar-structures-complex-structures-in-simple-surfactants.pdf |
6361f41d18a8ccb4dc5ac701 | 10.26434/chemrxiv-2022-4hw9h-v2 | Unique Spin Crossover Pathways Differentiated by Scan Rate in a New Dinuclear Fe(II) Triple Helicate: Mechanistic Deductions Enabled by Synchrotron Radiation Studies | The achievement of targeted properties in spin crossover (SCO) materials is complicated by often unpredictable cooperative interactions in the solid state. Herein, we report a dinuclear Fe(II) triple helicate 1, which is a rare example of a SCO material possessing two distinct magnetic behaviors that depend upon the thermal scan rate. Desolvated 1 was seen to undergo spin transition (ST) which was complete following slow cooling (1 K min-1), but incomplete ST (corresponding to 50% conversion) on fast cooling (10 K min-1). The incomplete ST observed in the latter case was accompanied by a higher temperature onset of ST, differing from TIESST (Temperature-Induced Excited Spin-State Trapping) materials. The two SCO pathways have been shown to arise from the interconversion between two structural phases (a and b), with both phases having associated high spin (HS) and low spin (LS) states. SCXRD (Single Crystal X-ray Diffraction) experiments using controlled cooling rates and a synchrotron light source enabled short collection times (2-3 minutes per dataset) which has enabled the identification of a mechanism by which the slow-cooled material may fully relax. In contrast, fast-cooled materials exhibit disordered arrangements of multiple structural phases, which has in turn revealed that the [HS-LS] ↔ [LS-HS] equilibria are controllable in the solid by varying the scan rate. Such behavior has been previously observed in solution studies, but its control in solids has not been reported up to now. This study demonstrates how intermolecular cooperativity can allow multiple distinct magnetic behaviors, and provides some insight into how [HS-LS] ↔ [LS-HS] equilibria can be controlled in the solid state, which may assist in the design of next-generation logic and signaling devices. | Matthew J. Wallis; Alexander R. Craze; Hikaru Zenno; Ryuya Tokunaga; Takahiro Taira; Hyunsung Min; Mohan M. Bhadbhade; Saroj Kumar Bhattacharyya; Ruoming Tian; Anne M. Rich; Shinya Hayami; Jack K. Clegg; Christopher E. Marjo; Leonard F. Lindoy; Feng Li | Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism | CC BY NC 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6361f41d18a8ccb4dc5ac701/original/unique-spin-crossover-pathways-differentiated-by-scan-rate-in-a-new-dinuclear-fe-ii-triple-helicate-mechanistic-deductions-enabled-by-synchrotron-radiation-studies.pdf |
67104e8612ff75c3a1a5b67c | 10.26434/chemrxiv-2024-sw9kw | Electrochemically-Induced Partial Cation Disorder Eliminates Lattice Collapse in Compositionally-Simple LiNi0.9Mn0.1O2
| Virtually all layered oxide positive electrodes (cathodes) for lithium-ion batteries exhibit abrupt shrinkage along the c lattice (c-collapse) at high states-of-charge, limiting cycle life. In this work, we suppress c-collapse by electrochemically inducing partial disorder permanently throughout the bulk of compositionally-simple LiNi0.9Mn0.1O2. Our approach leverages irreversible oxygen oxidation in the as-synthesized Li-excess Ni-rich oxides to activate partial disordering of the cation sublattice, while preserving the long-range layered structure. Using this method, Li-stoichiometric transition metal oxides with variable extents of cation disorder are readily fabricated by adjusting the starting Li-excess in the as-synthesized materials. Surprisingly, at a TMLi concentration of ≥12%, the c lattice parameter remains nearly invariant during (de)lithiation, leading to decreased chemical strain, enhanced microstructural integrity, and improved battery cycle life. We demonstrate a combination of high specific capacity and long cycle life, along with negligible voltage hysteresis and decay. This concept opens the opportunity for designing materials by inducing persistent intrinsic disorder electrochemically. | Junghwa Lee; Zhelong Jiang; Nicolas Liang; Howie Nguyen; Grace Busse; Jin Hwan Kwak; Yiseul Yoo; Hari Ramachandran; Kipil Lim; Peter Csernica; Tianyi Li; Xin Xu; Kyung Yoon Chung; Kathrin Michel; Joop Frerichs; William Gent; Raphaële Clément; Jungjin Park; William Chueh | Materials Science; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67104e8612ff75c3a1a5b67c/original/electrochemically-induced-partial-cation-disorder-eliminates-lattice-collapse-in-compositionally-simple-li-ni0-9mn0-1o2.pdf |
674755f77be152b1d019291d | 10.26434/chemrxiv-2024-ftq9n | Aluminum Photosensitizers with Long-lived Triplet States on Trial: Synthesis, Crystal Structures, Photophysical and Photobiological Properties of Tris(dipyrrinato)aluminum(III) Complexes | Metal coordination compounds are currently a focus of research in developing new photosensitizers for materials and medicinal applications. As an abundant element in the earth’s crust aluminum is a suitable target element. However, only limited studies are available on its use in photoactive systems. We now report the facile preparation of a library of homoleptic tris(dipyrrinato)aluminum(III) [AL(DIPY)3] complexes. The majority of complexes was characterized by single crystal X-ray analysis and their photophysical properties upon photoexcitation and their tendency to react with the molecular oxygen of the microenvironment and generate singlet oxygen - in polar and non-polar environment was investigated. These studies are complemented by density functional theory (DFT) calculations to assess the possible electronic distribution on the frontier molecular orbitals within the complexes. As a result of charge transfer states, long-lived triplet excited states were formed and allowed for singlet oxygen generation. An initial screening of the AL(DIPY)3 complexes via in vitro phototoxicity studies against a mouse colon carcinoma cell line (CT26) was promising as these complexes were able to trigger cell death upon irradiation at safe nanomolar and micromolar concentrations. The results highlight the potential of aluminum dipyrrin complexes as a broadly applicable class of photosensitizers. | Zoi Melissari; Brendan Twamley; Lígia C. Gomes-da-Silva; John E. O'Brien; Fábio A. Schaberle; Christopher J. Kingsbury; René M. Williams; Mathias O. Senge | Physical Chemistry; Organic Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674755f77be152b1d019291d/original/aluminum-photosensitizers-with-long-lived-triplet-states-on-trial-synthesis-crystal-structures-photophysical-and-photobiological-properties-of-tris-dipyrrinato-aluminum-iii-complexes.pdf |
65c23dcfe9ebbb4db9c8cf98 | 10.26434/chemrxiv-2024-8wcfp | Predicting the price of molecules using their predicted synthetic pathways | Currently, numerous metrics allow chemists and computational chemists to refine and filter libraries of virtual molecules in order to prioritize their synthesis. Some of the most commonly used metrics and models are QSAR models, docking scores, diverse druggability metrics, and synthetic feasibility scores to name only a few. Among the known metrics, a function which estimates the price of a novel virtual molecule and which takes into account the availability and price of starting materials has never been considered before. Being able to make such a prediction could improve and accelerate the decision-making process related to the cost-of-goods. Taking advantage of recent advances in the field of Computer Aided Synthetic Planning (CASP), we decided to investigate if the predicted retrosynthetic pathways of a given molecule and the prices of its associated starting materials could be good features to predict the price of that compound. In this work, we present a deep learning model, RetroPriceNet, that predicts the price of molecules using their predicted synthetic pathways. On a holdout test set, the model achieves better performance than the state-of-the-art model. The developed approach takes into account the synthetic feasibility of molecules and the availability and prices of the starting materials. | Massina Abderrahmane; Hamza Tajmouati; Vinicius Barros Ribeiro da Silva; Quentin Perron | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c23dcfe9ebbb4db9c8cf98/original/predicting-the-price-of-molecules-using-their-predicted-synthetic-pathways.pdf |
60c745cf0f50db1d3a396329 | 10.26434/chemrxiv.10269713.v1 | Electrochemical Isoperibolic Calorimetry for D2O Electrolysis | Equations developed for isoperibolic electrochemical calorimetry were tested for the electrolysis of D2O in an open calorimetric cell. The derivatives of these equations gave correct values within the experimental error range for the important rate of change of the cell temperature with time (dT/dt). In addition, these calorimetric equations were also tested directly in determining the enthalpy change (ΔH) for the D2O electrolysis reaction. The mean experimental value at 298.15 K was ΔH = 294.4 ± 0.3 kJ/mole. This compares favorably (within 0.10%) with the literature value of ΔH = 294.600 kJ/mole. The accuracy of these ΔH measurements could be even further improved by more accurate cell voltage and cell temperature measurement.
<br /> | Melvin Miles | Electrochemistry - Mechanisms, Theory & Study; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745cf0f50db1d3a396329/original/electrochemical-isoperibolic-calorimetry-for-d2o-electrolysis.pdf |
67d1b68b6dde43c9088d88b7 | 10.26434/chemrxiv-2025-x3p76 | A convergent approach to resorcinolic macrolides to expand structural diversity | The resorcinolic macrolide (RM) class of natural products is characterized by a resorcinolic ester core linked to a 10-14-membered macrocyclic lactone, encompassing over 50 members with diverse biological activities. Among the most notable is radicicol, a potent natural inhibitor of the 90-kDa heat-shock protein (Hsp90). Here we present an enantioselective, modular synthetic strategy to access diverse RMs, focusing on the modification of the C15 position, covalent warheads, and rigidity of the macrocycle to explore their effects on Hsp90 inhibitory activity and isoform selectivity. We synthesized 27 RM derivatives and evaluated their inhibitory activity against Hsp90𝛼 and Hsp90β isoforms and KRas. Compound 12A exhibited the highest potency with IC50 values of 14 µM and 37 µM against Hsp90𝛼 and Hsp90β, respectively. Additionally, compound 1C displayed high selectivity for Hsp90𝛼. These findings indicate that targeted modifications at C15 can yield novel RMs with potential as biological probes and therapeutic leads, offering a new avenue for the development of Hsp90 or KRas inhibitors with reduced resistance and improved specificity. | Jesus Madrigal Lombera; Xi Feng; Xiaokun Shu; Ian Seiple | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1b68b6dde43c9088d88b7/original/a-convergent-approach-to-resorcinolic-macrolides-to-expand-structural-diversity.pdf |
60c7582a0f50db614d3983de | 10.26434/chemrxiv.14515539.v1 | Thiol-Ene Click Inspired Late-Stage Modification of Long-Chain Polyurethane Dendrimers | Compared to the synthesis of polyurethane polymers, construction of well-defined polyurethane dendrimers is
challenging due to the high reactivity of externally added or in-situ formed isocyanates leading to the formation of side products. For
this reason, the synthesis of dendritic polyurethanes is limited to very few reports. With primary focus of dendrimer research on the
interaction of the periphery and the core, we report the synthesis of a common polyurethane dendron, which allows for late-stage
variation of both the periphery and the core. The periphery can be varied simply by installing a clickable unit in the dendron and then
attaching to the core and vice-versa. Thus, a common dendron allows for varying periphery and core in just two steps. To accomplish
this, protecting group free one-pot multicomponent Curtius reaction was utilized to afford a robust and versatile AB2 type
polyurethane dendron employing commercially available simple molecules 5-hydroxyisophthalic acid, 11-bromoundecanol, and 4-
penten-1-ol. Subsequent late-stage modification of either dendrons or dendrimers via thiol-ene click reaction gave surface?functionalized alternating aromatic-aliphatic polyurethane homodendrimers to generation-three (G3). The dendrons and the
dendrimers were characterized by NMR, mass spectrometry, and FT-IR analysis. A bifunctional AB2 type dendritic monomer
demonstrated this approach's versatility that can either undergo a thiol-one click or attachment to the core. This approach enables the
incorporation of functionalities at the periphery and the core that may not withstand the dendrimer growth for the synthesis of
polyurethane dendrimers and other dendritic macromolecules | Dhruba Poudel; Richard Taylor | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7582a0f50db614d3983de/original/thiol-ene-click-inspired-late-stage-modification-of-long-chain-polyurethane-dendrimers.pdf |
60c7548d4c8919e878ad4558 | 10.26434/chemrxiv.13308875.v3 | On the Common Ground of Thermodynamics and Kinetics: How to Pin Down Overpotential to Reversible Metal Hydride Formation and the Complete Ideal Gas Theory of Reversible Chemical Hydrogen Storage | Ti-doped NaAlH<sub>4</sub> requires at 125 °C for [AlH<sub>4</sub>] formation more than twice the equilibrium pressure; while it is straightforward to relate this conditional surplus in hydrogenation pressure respective chemical potential to kinetic hindrance, it appears strange that this matter has not been duly theoretically addressed in literature to this day. The interest in identifying such overpotentials is not of purely academic interest but touches a problem of very practical significance as the maximum applied pressure is an important threshold to metal hydride tank design. A theory-based tool would be a resource-efficient complement or even alternative to PCI measurements. This paper tracks the formation overpotential issue down to its root and outlines a simple yet accurate general method based on Arrhenius and van’t Hoff data. Rather unexpectedly, the result is also the final missing piece towards a comprehensive understanding of reversible chemical hydrogen storage with regard to attainable hydrogen storage capacity. | Roland Hermann Pawelke | Catalysts; Fuels - Materials; Hydrogen Storage Materials; Chemical Education - General; Nanocatalysis - Catalysts & Materials; Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Small Molecule Activation (Inorg.); Solid State Chemistry; Theory - Inorganic; Reaction Engineering; Thermodynamics (Chem. Eng.); Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis; Catalysis; Small Molecule Activation (Organomet.); Theory - Organometallic; Energy Storage; Fuels - Energy Science; Fuel Cells; Chemical Kinetics; Physical and Chemical Processes; Physical and Chemical Properties; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7548d4c8919e878ad4558/original/on-the-common-ground-of-thermodynamics-and-kinetics-how-to-pin-down-overpotential-to-reversible-metal-hydride-formation-and-the-complete-ideal-gas-theory-of-reversible-chemical-hydrogen-storage.pdf |
6163a6b47d3da54a78f3c502 | 10.26434/chemrxiv-2021-z9nvp-v2 | A Validation Study on the Simultaneous Quantification of Multiple Wine Aroma Compounds with Static Headspace-Gas Chromatography-Ion Mobility Spectrometry (SHS-GC-IMS) | A new quantitative method based on static headspace−gas chromatography−ion mobility spectrometry (SHS−GC−IMS) is proposed, which enables the simultaneous quantification of multiple aroma compounds in wine. The method was first evaluated for its stability and the necessity of using internal standards as a quality control measure. The two major hurdles in applying GC-IMS in quantification studies, namely, non-linearity and multiple ion species, were also investigated using the Boltzmann function and generalized additive model (GAM) as potential solutions. Metrics characterizing the model performance, including root mean squared error, bias, limit of detection, limit of quantification, repeatability, reproducibility, and recovery were investigated. Both non-linear fitting methods, Boltzmann function and GAM, were able to return desirable analytical outcomes with an acceptable range of error. Potential pitfalls that would cause inaccurate quantification i.e., effects of ethanol content and competitive ionization, were also discussed. The performance of the SHS-GC-IMS method was subsequently compared against a currently established method, namely, GC-MS, using actual wine samples. These findings provide an initial validation of a GC-IMS-based quantification method, as well as a starting point for further enhancing the analytical scope of GC-IMS. | Wenyao Zhu; Frank Benkwitz; Bahareh Sarmadi; Paul Kilmartin | Analytical Chemistry; Agriculture and Food Chemistry; Analytical Apparatus; Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6163a6b47d3da54a78f3c502/original/a-validation-study-on-the-simultaneous-quantification-of-multiple-wine-aroma-compounds-with-static-headspace-gas-chromatography-ion-mobility-spectrometry-shs-gc-ims.pdf |
65b1f5389138d23161afa38f | 10.26434/chemrxiv-2024-qql65 | Liquid structure in mixtures of imidazolium based ionic liquid/carbonate solvents for application in next generation lithium ion battery electrolytes: molecular dynamics simulation | We used molecular dynamics (MD) simulations based on classical force field to provide the liquid structure in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid in the presence of ethylene, dimethyl carbonate co-solvents and 1M LiTFSI mixtures which are currently being targeted for applications in next-generation Li-ion battery electrolytes. To show the dependence of the properties on the concentration, we simulated both pure IL and ternary mixtures of IL, EC and DMC with different mixing ratios. The solvation of lithium cations in pure and mixed IL/organic carbonate solvents has been investigated. The MD simulations have predicted a preference of Li+ ions to interact with DMC molecules within its first solvation shell rather than with the highly polar EC ones in the IL/carbonate mixtures, a phenomon which is attributed to the local tetrahedral packing of the solvent molecules in the first solvation shell of Li+ ions.The coordination of the O/N atoms of the bis(trifluoromethylsulfonyl)imide anion to Li+ ions as well as to the most acidic H atom of 1-ethyl-3-methylimidazolium cation has also been analysed, which showed a marked increase in the amplitude of RDF peaks with increase in carbonate concentration, indicating that the interaction between the ions was enhanced by the presence of high carbonate content. Furthermore, in the pure ionic liquid, adjacent cations are almost exclusively located on top and below the ring cation, whereas the anions mainly coordinate to the cation within the ring plane. The addition of large amount of carbonate co-solvents disturb the original near ordering which is found in the pure ionic liquid. | Abraham Molla Wagaye Wagaye; Teketel Yohannes; Getachew Adam Workneh | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b1f5389138d23161afa38f/original/liquid-structure-in-mixtures-of-imidazolium-based-ionic-liquid-carbonate-solvents-for-application-in-next-generation-lithium-ion-battery-electrolytes-molecular-dynamics-simulation.pdf |
60c7509d0f50db68a03975d2 | 10.26434/chemrxiv.13034381.v1 | Co-doped ZnO Nanowires for Low Temperature Methane Sensing Operational in Humid Environments | <p>Sensitive and selective detection of methane is essential due to its role in the greenhouse effect, relevance to industrial safety and recently discovered importance as a biomarker for gastrointestinal health. However, obtaining a reliable response to low concentrations (<100 ppm) of methane at low temperatures, especially in presence of humidity still remains a great challenge. In this work, a metal-oxide based sensor capable of low methane concentration detection and humidity resistance is reported. Chemiresistive sensors based on ZnO nanowire films were grown by a hydrothermal process and doped with Co. In terms of methane detection, Co-doping of the ZnO nanowires enabled the sensor to operate optimally at the low operating temperature of 50<sup>o</sup>C and an improved sensitivity of response (lowest measured concentration: 1 ppm) was observed when compared to that of pure ZnO nanowire films. This increased sensitivity was attributed to an increase in donor-type vacancies and enhanced oxygen adsorption on the surface. A mesoporous silica molecular sieve was further integrated as a moisture filter layer to mitigate the effect of humidity. It is envisaged that based on the sensors’ performance characteristics reported here, that the sensor could be applicable for emerging diagnostic applications tracking methane emissions from the breath. </p> | Aoife Morrin; Niyanta Datta | Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7509d0f50db68a03975d2/original/co-doped-zn-o-nanowires-for-low-temperature-methane-sensing-operational-in-humid-environments.pdf |
641239b12bfb3dc251d43527 | 10.26434/chemrxiv-2022-73k4f-v2 | Colloidal, Room Temperature Growth of Metal Oxide Shells on InP Quantum Dots | We demonstrate colloidal, layer-by-layer growth of metal oxide shells on InP quantum dots (QDs) at room temperature. We show with computational modeling that native InP QD surface oxides give rise to nonradiative pathways due to the presence of surface-localized dark states near the band edges. Replacing surface indium with zinc to form a ZnO shell results in reduced nonradiative decay and a density of states at the valence band edge that resembles defect-free, stoichiometric InP. We then developed a synthetic strategy using stoichiometric amounts of common atomic layer deposition precursors in alternating cycles to achieve layer-by-layer growth. Metal oxide-shelled InP QDs show bulk and local structural perturbations as determined by X-ray diffraction and extended X-ray absorption fine structure spectroscopy. Upon growing ZnSe shells of varying thickness on the oxide-shelled QDs, we observe increased photoluminescence quantum yields and narrowing of the emission linewidths that we attribute to decreased ion diffusion to the shell, as supported by P X-ray emission spectroscopy. These results present a versatile strategy to control QD interfaces for novel heterostructure design by leveraging surface oxides. This work also contributes to our understanding of the connections between structural complexity and PL properties in technologically relevant colloidal optoelectronic materials. | Nayon Park; Ryan Beck; Kevin Hoang; Dylan Ladd; Jared Abramson; Ricardo Rivera; Hao Nguyen; Madison Monahan; Gerald Seidler; Michael Toney; Xiaosong Li; Brandi Cossairt | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641239b12bfb3dc251d43527/original/colloidal-room-temperature-growth-of-metal-oxide-shells-on-in-p-quantum-dots.pdf |
60c7426dbb8c1a07d93da129 | 10.26434/chemrxiv.7448021.v2 | Analysis and reporting recommendations for theoretical and experimental ionization potentials based on the study of 53 medium sized molecules using the IP-EOMCCSD method. | <div>
<div>
<div>The precision and
accuracy of theoretical vertical
ionization
potential calculations has improved to the point where more
care is needed to make valid comparisons with experimental
measurements then
is currently the norm.
Vertical
ionization potentials (IPs) computed using the IP-EOMCCSD
method
are reported for 53 medium sized molecules (6
– 32 atoms)
and
compared with statistically
evaluated
experimental vertical IPs.
Based
on this comparison, theoretical IPs should be extrapolated to the
complete basis set limit and corrected for vibrational zero-point
energy, while for experimental data the intensity weighted mean band
position should be reported as the vertical IP. Experimental
data available for ethylene,
E-2-butene, 2,5-dihydrofuran and pyrrole were
re-analyzed and compared with zero-point energy corrected
complete
basis set theoretical estimates, yielding
an average discrepancy of 0.05 eV between theory and experiment. In
contrast the average of
reported experimental
vertical IPs
(the comparison usually made) yielded an average discrepancy of 0.25
eV between theory and experiment for
these molecules.
Further
analysis of the remaining molecules in
the data set
suggests
that the majority of reported experimental vertical
IPs are low because band asymmetries
were not accounted for when assigning IP values. This
leads to fortuitous good agreement between experiment
and computations
using the smaller aug-cc-pVDZ
basis set without
zero-point correction. In
the case of 1,4-cyclohexadiene
there
is strong evidence for experimental
uncertainty
accounting
for the discrepency between theory and experiment.
The
presented results provide a benchmark for evaluating both
experimental and theoretical estimates of vertical ionization
potentials for the 53 molecules studied.
</div>
</div>
</div> | Marissa Buzzanca; Brandon Brummeyer; Jonathan Gutow | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426dbb8c1a07d93da129/original/analysis-and-reporting-recommendations-for-theoretical-and-experimental-ionization-potentials-based-on-the-study-of-53-medium-sized-molecules-using-the-ip-eomccsd-method.pdf |
60c75932702a9baa0818ce61 | 10.26434/chemrxiv.14671908.v1 | Air Inequality: Global Divergence in Urban Fine Particulate Matter Trends | <p>Fine particle air pollution (PM<sub>2.5</sub>) is the largest global environmental risk factor for ill-health and is implicated in >7% of all human deaths. Improved air quality is a key policy goal for cities, yet in-situ PM<sub>2.5</sub> measurements are missing for >50% of the world’s urban population. Here, we apply satellite remote sensing to develop a 21-year time series of ground-level PM<sub>2.5</sub> concentrations for the 4231 urban areas with populations >100,000 (2.9 billion people) from 1998 -2018. Globally, we find the most polluted cities are generally small (<1 million population) and lack PM<sub>2.5 </sub>monitors. Since 1998, we observe a growing divide in urban air quality between cities in lower and higher-income regions, with the PM<sub>2.5</sub> disparity increasing by >50% (from 25 to 39 µg m<sup>-3</sup>) between the highest- and lowest income quartiles of world cities. Within Asia, a sharp divergence is underway, with sustained PM<sub>2.5</sub> increases in South Asian cities (+48%) contrasted against dramatic improvements in Chinese cities (-40% since 2011). While 85% of the world’s urban population experiences PM<sub>2.5</sub> higher than World Health Organization guidelines, urban PM<sub>2.5</sub><sup> </sup>concentrations are tightly linked to regional conditions, suggesting that city-level efforts alone may be insufficient to address this major health threat.<b></b></p> | Joshua Apte; Sarah Seraj; Sarah Chambliss; Melanie Hammer; Veronica Southerland; Susan Anenberg; Aaron van Donkelaar; Michael Brauer; Randall Martin | Environmental Science | CC BY 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75932702a9baa0818ce61/original/air-inequality-global-divergence-in-urban-fine-particulate-matter-trends.pdf |
67d98b4781d2151a02dee92a | 10.26434/chemrxiv-2025-8rpvf | Quantum-Embedded Equation-of-Motion Coupled-Cluster Approach to Single-Atom Magnets on Surfaces | We investigate electronic states and magnetic properties of transition-metal atoms on surfaces using projection-based density embedding that combines equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) theory with density functional theory (DFT). As a case study, we explore Co adsorbed on MgO(001), an ideal model for single-atom magnet design, known for its record magnetic anisotropy among transition-metal adatoms. Periodic DFT-based calculations of the magnetic anisotropy energy, i.e., the energy required to rotate the magnetization from parallel to perpendicular relative to the surface normal, predict in-plane magnetic anisotropy, contradicting the experimentally observed easy-axis anisotropy. This failure stems from the inability of the approximate density functionals to describe the multiconfigurational, non-aufbau spin states of Co/MgO(001). In contrast, embedded EOM- CCSD calculations on Co/Mg9O9 finite models of the adsorption complex capture the system’s unquenched orbital angular momentum (L ≈ 3) and strong spin-orbit coupling, leading to easy-axis anisotropy and a spin-inversion energy barrier that agrees with experiment within spectroscopic accuracy. When treating both the oxygen adsorption site and the Co magnetic center at the EOM-CCSD level of theory, embedded calculations accurately reproduce the state ordering, spin-orbit coupling, and susceptibility curve of all-atom EOM-CCSD calculations. These results demonstrate that embedded EOM-CCSD provides a reliable description of the electronic states and magnetic properties of magnetic adsorbates on surfaces, offering a robust framework for future investigations of surface-bound magnetic systems. | Maristella Alessio; Tobias Schaefer; Thomas-C. Jagau; Andreas Grueneis | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d98b4781d2151a02dee92a/original/quantum-embedded-equation-of-motion-coupled-cluster-approach-to-single-atom-magnets-on-surfaces.pdf |
670d32ef51558a15ef0b02f3 | 10.26434/chemrxiv-2024-vz4nq | Amination of Alkylboronic Esters | Alkylboronic esters are high value chemical building blocks which can be used to make complex, C-sp3 rich molecules. The ability to convert the C-B bond in a range of C-C and C-heteroatom bond-forming reactions, in addition to their broad functional group compatibility, gives alkylboronic esters significant synthetic utility. Methods to convert boronic esters into amines have particular interest, due to the wide prevalence of nitrogen-based functional groups in biologically active compounds, functional materials, and catalysts. In this review, we explore different methods for the amination of alkylboronic esters. These can be split into three distinct classes based on the mechanism of reaction: amination through 1,2-metallate rearrangement, amination using nucleophilic ‘ate’ complexes, and alkyl variants of the Chan-Lam reaction. | Norah Almutairi; Nada Elsharif; Telma Kamranifard; Junning Wang; Benjamin Partridge | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d32ef51558a15ef0b02f3/original/amination-of-alkylboronic-esters.pdf |
6401c0a163e8d44e594addea | 10.26434/chemrxiv-2023-28r9s | A transferable double exponential potential for condensed phase simulations of small molecules | The Lennard-Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major consideration and this potential was particularly convenient numerically. At present, it persists because the effort that would be required to re-write molecular modelling software and train new force fields has, until now, been prohibitive. Here, we present smirnoff-plugins as a flexible framework to extend the Open Force Field software stack to allow custom force field functional forms. We deploy smirnoff-plugins with the automated Open Force Field infrastructure to train a transferable, small molecule force field based on the recently-proposed double exponential functional form, on over 1000 experimental condensed phase properties. Extensive testing of the resulting force field shows improvements in transfer free energies, with acceptable conformational energetics, run times and convergence properties compared to state-of-the-art Lennard-Jones based force fields. | Joshua Horton; Simon Boothroyd; Pavan Behara; David Mobley; Daniel Cole | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6401c0a163e8d44e594addea/original/a-transferable-double-exponential-potential-for-condensed-phase-simulations-of-small-molecules.pdf |
672d2a905a82cea2fa6c694d | 10.26434/chemrxiv-2024-g1x43 | In Situ Synthesis of Degradable Polymer Prodrug Nanoparticles | The in-situ synthesis of degradable polymer prodrug nanoparticles is still a challenge to be met, which would make it possible to remedy both the shortcomings of traditional formulation of preformed polymers (e.g., low nanoparticle concentrations) and those of the physical encapsulation of drugs (e.g., burst release, poor drug loadings). Herein, by the combination of radical ring-opening polymerization (rROP) and polymerization-induced self-assembly (PISA) under appropriate experimental conditions, we report the successful preparation of high solid contents, degradable polymer prodrug nanoparticles, exhibiting multiple drug moieties covalently linked to a degradable vinyl copolymer backbone. Such rROPISA process relied on a chain extension of a biocompatible poly(ethylene glycol)-based solvophilic block with a mixture of lauryl methacrylate (LMA), cyclic ketene acetal (CKA) and drug-bearing methacrylic esters by reversible addition fragmentation chain transfer (RAFT) copolymerization at 20 wt % solids content. This novel approach was exemplified with two different CKA monomers and two different anticancer drugs, namely paclitaxel and gemcitabine, to demonstrate its versatility. After transferring to water, remarkably stable aqueous suspensions of core-degradable polymer prodrug nanoparticles of 56-225 nm in diameter with tunable amounts of CKA units (7-26 mol.%) and drug loadings up to 33 wt % were obtained. Incorporation of ester groups in the copolymers was demonstrated by hydrolytic degradation of both the copolymers and the nanoparticles under accelerated conditions. The nanoparticles showed significant cytotoxicity on A549 cells, used as a lung cancer model. Fluorescence labeling of the solvophilic block also enabled effective monitoring of their cell internalization by confocal microscopy, with the potential for theranostic applications. | Chen Zhu; Hannah Beauseroy; Julie Mougin; Maëlle Lages; Julien Nicolas | Polymer Science; Drug delivery systems; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672d2a905a82cea2fa6c694d/original/in-situ-synthesis-of-degradable-polymer-prodrug-nanoparticles.pdf |
60c74a53469df45440f43d21 | 10.26434/chemrxiv.12181404.v1 | In-Silico Identification of Potent Inhibitors of COVID-19 Main Protease (Mpro) and Angiotensin Converting Enzyme 2 (ACE2) from Natural Products: Quercetin, Hispidulin, and Cirsimaritin Exhibited Better Potential Inhibition than Hydroxy-Chloroquine Against COVID-19 Main Protease Active Site and ACE2 | COVID-19 is rapidly spreading and there are currently no specific clinical treatments available. The absence of an immediate available vaccine against SARS-CoV-2 made it hard for health professionals to tackle the problem. Thus, the need of ready to use prescription drugs or herbal remedies is urgent. SARS-CoV-2 main protease (Mpro) and Angiotensin Converting Enzyme2 (ACE2) protein structure are made available to facilitate finding solutions to the present problem. In this brief research, we compare the efficacy of some natural compounds against COVID-19 Mpro and ACE2 to that of Hydroxy-Chloroquine in silico.<br />Molecular docking investigations were carried out using AutoDock. Virtual screening was performed using AutoDock Vina and the best ligand / protein mode was identified based on the binding energy. Amino Acids residues of ligands interactions were identified using PyMOL. According to present research results, Quercetin, Hispidulin, Cirsimaritin, Sulfasalazine, Artemisin and Curcumin exhibited better potential inhibition than Hydroxy-Chloroquine against COVID-19 main protease active site and ACE2. Our provided docking data of these compounds may help pave a way for further advanced research to the synthesis of novel drug candidate for COVID-19.<br /> | Sekiou Omar; Ismail Bouziane; Zihad Bouslama; Abdelhak Djemel | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a53469df45440f43d21/original/in-silico-identification-of-potent-inhibitors-of-covid-19-main-protease-mpro-and-angiotensin-converting-enzyme-2-ace2-from-natural-products-quercetin-hispidulin-and-cirsimaritin-exhibited-better-potential-inhibition-than-hydroxy-chloroquine-against-covid-.pdf |
65018c9999918fe537e024d8 | 10.26434/chemrxiv-2023-rb8r3-v2 | Isolation and structure determination of new neolignans and cabagranin D, an unusual meroterpenoid from Piper cabagranum | A novel meroterpenoid cabagranin D was isolated along with related neolignans cabagranins A-C from the leaves of Piper cabagranum (Costa Rica). Cabagranins A-C represent the first examples of 3,3’-neolignans isolated from the Piper genus of plant and the meroterpenoid cabagranin D, representing an unprecedented Diels-Alder conjugate of an unsubstituted phenylpropenone and alpha-phellandrene. Details of the full structural elucidation of these compounds and a discussion of the potential biosynthetic relationships are presented. | Celso de Oliveira Jr.; Zachary D. Ledvina; Michael D. Leonard; Samuel Odoh; Craig D. Dodson; Christopher S. Jeffrey | Organic Chemistry; Natural Products; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65018c9999918fe537e024d8/original/isolation-and-structure-determination-of-new-neolignans-and-cabagranin-d-an-unusual-meroterpenoid-from-piper-cabagranum.pdf |
60c756a2bb8c1a8d7b3dc667 | 10.26434/chemrxiv.14291434.v1 | Substitution Effect on 2-(Oxazolinyl)-phenols: Emission Color-Tunable, Minimalistic Excited-State Intramolecular Proton Transfer (ESIPT)-based Luminophores | The synthesis and optical characterization of novel single-benzene ESIPT-based fluorophores is described in solid state and in solution. Special attention is given towards the influence of their unique substitution pattern on their optical properties. Depending on this pattern, aggregation induced emission or aggregation caused quenching (ACQ) is observed in the solid state.<br /> | Dominik Göbel; Pascal Rusch; Daniel Duvinage; Tim Stauch; Nadja C. Bigall; Boris Nachtsheim | Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry; Optics; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756a2bb8c1a8d7b3dc667/original/substitution-effect-on-2-oxazolinyl-phenols-emission-color-tunable-minimalistic-excited-state-intramolecular-proton-transfer-esipt-based-luminophores.pdf |
60c73eda0f50db756e3956fa | 10.26434/chemrxiv.7150013.v1 | Volatilization, dissolution and equilibrium isotope effects (2H, 13C, 37Cl) of trichloromethane, trichloroethene and methanol dissolved in water | This draft of a paper presents isotopic enrichment factors obtained from volatilization, dissolution and equilibration experiments of three organics dissolved in water. <br /> | Axel Horst; Georges Lacrampe-Couloume | Environmental Science; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eda0f50db756e3956fa/original/volatilization-dissolution-and-equilibrium-isotope-effects-2h-13c-37cl-of-trichloromethane-trichloroethene-and-methanol-dissolved-in-water.pdf |
64f74524dd1a73847f3e76e8 | 10.26434/chemrxiv-2022-hjnmr-v2 | Probing the Chemical "Reactome" with High Throughput Experimentation Data | High-throughput experimentation (HTE) has the potential to improve our understanding of organic chemistry by systematically interrogating reactivity across diverse chemical spaces. Notable bottlenecks include few publicly available large-scale datasets and the need for facile interpretation of these data's hidden chemical insights. Herein we report the development of a High Throughput Experimentation Analyzer (HiTEA), a robust and statistically rigorous framework which is applicable to any HTE dataset regardless of size, scope, or target reaction outcome. We improve the HTE data landscape with the disclosure of 39,000+ previously proprietary HTE reactions. HiTEA is validated on this dataset, showcasing the elucidation of hidden relationships between reaction components and outcomes as well as highlighting reaction space that necessitates further investigation. | Emma King-Smith; Simon Berritt; Louise Bernier; Xinjun Hou; Jacquelyn Klug-McLeod; Jason Mustakis; Neal Sach; Joseph Tucker; Qingyi Yang; Roger Howard; Alpha Lee | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f74524dd1a73847f3e76e8/original/probing-the-chemical-reactome-with-high-throughput-experimentation-data.pdf |
671a80a71fb27ce124726f25 | 10.26434/chemrxiv-2024-p9sw8 | Anti-Electrophoretic Response Driven Bending-Tilting Deformation of Cationic Polyelectrolyte Brushes Drives Massively Non-Linear Electroosmotic Transport in Brush-Grafted Nanochannels | The interplay of the electric field-driven response of charged polyelectrolyte (PE) brushes and the supported counterions and water molecules dictate the intriguing fluid dynamics in a PE-brush-grafted nanochannel. Such combined brush-ion-fluid dynamics can be captured in unprecedented atomistic details using all-atom molecular dynamics (MD) simulations unraveling a plethora of new and fascinating nanoscale science. In this paper, we use such simulations to describe a most remarkable non-linearly enhanced large electroosmotic (EOS) flow, where, in a nanochannel grafted with cationic PMETAC ([Poly(2-(Methacryloyloxy)Ethyl) Trimethylammonium Chloride]) brushes, a two-fold increase in the electric field strength leads to a several-fold (much more than two-fold) increase in the EOS flow strength and volume flow rate. The electric field enforces the PMETAC brushes to undergo a bending-tilting driven deformation with a significant portion of the brush layer becoming parallel to the grafting surface. In response, a substantial fraction of the counterions come out of the brush layer (hence become more mobile), but instead of going into the bulk, accumulate at the brush-bulk interface, i.e., stay in close proximity of the brush segments aligned parallel to the grafting surface. This creates a fascinating situation, where the counterions are not completely within the brush layer, yet they fully screen the brush charges. Such “freer” conditions enable the counterions to achieve very high velocity, which eventually ensures that the water solvating the counterions themselves move very fast triggering the significantly augmented EOS transport. Probing deeper we can identify that the bending-tilting driven brush deformation, enforcing the brushes to align parallel to the substrate, results from the anti-electrophoretic behavior of the brushes, where despite being positively charged, the brushes move against the electric field direction: such a highly unprecedented behavior can be associated with the very fast velocities of the negatively charged counterions and the electrostatic coupling of the counterions with the positive functional groups of the brushes. We anticipate that the findings of this paper will not only open up novel strategies for flow enhancement in functionalized nanochannels and shed light on a myriad of applications associated with the anti-electrophoretic response of charged polymer chains, it will kindle interests in the need for understanding the detailed chemical architecture of polyelectrolyte systems (beyond coarse-graining based simplifications) in nanoscale science and engineering. | Raashiq Ishraaq; Siddhartha Das | Materials Science; Polyelectrolytes - Materials | CC BY 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a80a71fb27ce124726f25/original/anti-electrophoretic-response-driven-bending-tilting-deformation-of-cationic-polyelectrolyte-brushes-drives-massively-non-linear-electroosmotic-transport-in-brush-grafted-nanochannels.pdf |
60fac1588f6bf618007073b6 | 10.26434/chemrxiv-2021-qpmws | On the nature of extra-framework aluminum species and improved catalytic properties in steamed zeolites | Steamed zeolites have improved catalytic properties for hydrocarbon activation (alkane cracking reaction as well as alkane dehydrogenation). The nature of this practically important phenomenon has remained a mystery for the last six decades and was speculated to be related to increased Bronsted acidity during dealumination. We now prove that during steaming aluminum oxide clusters evolve (due to hydrolysis of Al out of framework positions with the following clustering) in the zeolitic micropores with properties very similar to (nano)facets of hydroxylated transition-alumina surfaces. Bronsted acidity of zeolite does not increase and the total number of Bronsted acid sites decreases during steaming. O5Al(VI)-OH surface sites of alumina clusters dehydroxylate at elevated temperatures to form penta-coordinate Al1O5 sites that are capable of initiating alkane cracking by breaking the first C-H bond very effectively, with the following reaction steps catalyzed by nearby zeolitic Bronsted acid sites. This explains the underlying reason behind the improved alkane cracking and alkane dehydrogenation activity of steamed zeolites: heterolytic C-H bond breaking occurs on penta Al(V)1O5 sites of aluminum oxide clusters confined in zeolitic pores. Furthermore, slightly decreased number of adjacent Al framework sites (due to Al dislodgement from the framework) decreases the coking activity, prolonging catalyst lifetime. Our findings explain the origin of enhanced activity of steamed zeolites at the molecular level and provide the missing understanding of the nature of extra-framework Al species formed in steamed/dealuminated zeolites. Furthermore, our findings suggest that similar La2O3 clusters exist for La-containing zeolites and the origin of their cracking activity promotion should be similar. | Konstantin Khivantsev; Nicholas Jaegers; Libor Kovarik; Ja-Hun Kwak; Miroslaw Derewinski; Janos Szanyi | Physical Chemistry; Materials Science; Catalysis; Acid Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fac1588f6bf618007073b6/original/on-the-nature-of-extra-framework-aluminum-species-and-improved-catalytic-properties-in-steamed-zeolites.pdf |
65e9f54566c13817297bfb6b | 10.26434/chemrxiv-2024-7tf0j | Python and MATLAB implementations of a fast numerical method for the solution of multiple chemical equilibria | Determining the distribution of multiple chemical species at equilibrium for a given system is a common problem that must be routinely addressed by scholars. While simple systems consisting of a few species and reactions can be solved manually, most of these problems require the definition and solution of higher-order equations and are intractable without reliable numerical methods, that can be slow and inefficient. In this work, we introduce straightforward Python and MATLAB implementations of the geometric-programming algorithm developed by Thomas Wayne Wall (1984) and we provide clear and easy-to-use scripts and examples for researchers approaching the problem. The code is readily available online in a package called equpy. The performance and stability of the algorithm are tested versus out-of-the-box MATLAB numerical solver (vpasolve) and the solver employed in chempy - one of the most complete opensource chemistry packages available to this date - showing an execution time reduced by as much as two orders of magnitudes. | MARCO TODISCO | Physical Chemistry; Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e9f54566c13817297bfb6b/original/python-and-matlab-implementations-of-a-fast-numerical-method-for-the-solution-of-multiple-chemical-equilibria.pdf |
60c7426e337d6c3f1be26a73 | 10.26434/chemrxiv.8285804.v1 | Ground State Destabilization in Uracil DNA Deglycosylase (UDG): Let’s Not Forget “Tautomeric Strain” in Substrates | QM and QM/MM computations reveal that some enzymes, like the uracil DNA deglycosylase, may achieve ground state destabilization through substrate "tautomeric strain." | Ranjita Das; Erik A. Vázquez-Montelongo; G. Andres Cisneros; Judy Wu | Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426e337d6c3f1be26a73/original/ground-state-destabilization-in-uracil-dna-deglycosylase-udg-let-s-not-forget-tautomeric-strain-in-substrates.pdf |
65e6d3bc9138d23161b20f2c | 10.26434/chemrxiv-2024-r3j9s | Exploring Metal Electroplating for Energy Storage by Quartz Crystal Microbalance: a review | Herein the development and application of Electrochemical Quartz Crystal Microbalance (EQCM) sensing to study metal electroplating, especially for energy storage purposes, are reviewed. The roles of EQCM in describing electrode/electrolyte interface dynamics, such as the electric double-layer build-up, ionic/molecular adsorption, metal nucleation, and growth, are addressed. Modeling of the QCM sensor is introduced and its importance is emphasized. Challenges of metal electrode use, including side reactions and dendrite formation, along with their mitigation strategies are reviewed. Numerous factors affecting the electroplating processes, such as electrolyte composition, additives, temperature, and current density, and their influence on the electroplated metals’ mass, structural, and mechanical characteristics are discussed. Looking forward, the need for deeper fundamental understanding and advancing simulations of the QCM signal response as a result of electroplating metal nanostructures is stressed. Further development and integration of innovative EQCM-strategies will provide unique future means to fundamentally understand and optimize metal electroplating for energy storage and application alike. | Viktor Vanoppen; Diethelm Johannsmann; Xu Hou; Jens Sjölund; Peter Broqvist; Erik J. Berg | Theoretical and Computational Chemistry; Energy; Machine Learning; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e6d3bc9138d23161b20f2c/original/exploring-metal-electroplating-for-energy-storage-by-quartz-crystal-microbalance-a-review.pdf |
60c73cc0567dfe8ea5ec3568 | 10.26434/chemrxiv.14763075.v1 | Effective Removal of Water-Soluble Methylated Arsenic Contaminants with Phosphorene Oxide Nanoflakes: A DFT Study | This work explores by DFT calculations the ability of oxidized phosphorene to simultaneously remove methylarsenicals from contaminated water sources via adsorption in solid phases.<br /> | Kerry Wrighton-Araneda; Daniela E. Ortega; Diego Cortes-Arriagada | Alloys; Nanostructured Materials - Materials; Thin Films; Environmental Science; Wastes; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Interfaces; Physical and Chemical Properties; Quantum Mechanics; Surface | CC BY 4.0 | CHEMRXIV | 2021-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc0567dfe8ea5ec3568/original/effective-removal-of-water-soluble-methylated-arsenic-contaminants-with-phosphorene-oxide-nanoflakes-a-dft-study.pdf |
63bea75cee6f183b129c77b5 | 10.26434/chemrxiv-2023-m6cxg | Cleavage of the Au−P Bond in Au-Substituted Phosphines | Three protocols that involve the cleavage of the Au−P bond in Au-substituted phosphines (AuPhos) have been demonstrated, namely i) direct demetallation with a strong anionic base; ii) protonation followed by demetallation with a neutral base; iii) oxidation-triggered metal migration. Specifically, direct demetallation of (CAAC)AuPPh2 (1a) (CAAC = cyclic (alkyl)(amino)carbene) with KP(TMS)2 or LiC(N2)TMS yields (CAAC)AuPTMS2 (2) or (CAAC)AuC(N2)TMS (3), respectively. Treatment of (NHC)AuPPh2 (1b) (NHC = N-heterocyclic carbene) with HOTf followed by the corresponding neutral phosphine gives scarce examples of aurophosphonium salts [(NHC)AuPHAd2][OTf] (5) and [((NHC)Au)2PPh2][OTf] (6). Oxidation of 1a or 1b with Se affords LAuSeP(Se)Ph2 (L = CAAC, 7a; NHC, 7b). | Rui Wei; Xin-Feng Wang; Liu Leo Liu | Inorganic Chemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bea75cee6f183b129c77b5/original/cleavage-of-the-au-p-bond-in-au-substituted-phosphines.pdf |
61d81d92f51b22552b0c3414 | 10.26434/chemrxiv-2021-f6l32-v2 | Remarkable Enhancement of Catalytic Activity of Cu-Complexes in the Electrochemical Hydrogen Evolution Reaction (HER) by Using Triply-Fused Porphyrin | Developing efficient molecular catalysts for the electrocatalytic hydrogen evolution reaction (HER) is a highly important goal in contemporary science. We report here on a bimetallic triply fused copper porphyrin complex (1) comprising two monomeric porphyrin units linked through β–β, meso–meso, β′–β′ triple covalent linkages, that exhibits remarkable enhancement of catalytic activity for the electrochemical HER in comparison to the analogous monomeric copper porphyrin complex (2). Spectroscopic characterization, in association with magnetic measurements, clearly establish the ground state structures of both the bimetallic and monometallic complexes as containing two and one copper (II) centers, respectively. The fused metalloporphyrin complex is found to undergo electrochemical reduction at a lower negative applied potential compared to the metalloporphyrin monomer, as evident from the significant anodic shift (~800mV) in the potential of the first reduction process. Electrochemical investigations in the presence of a proton source (trifluoroacetic acid) confirm that the catalytic activity of the fused metalloporphyrin occurs at a significantly lower onset potential, (overpotential decreased by ~320 mV), compared to the non-fused monomer. Controlled potential electrolysis combined with the kinetic analysis of catalysts 1 and 2 confirm the production of hydrogen, with 96% and 71% faradaic efficiencies and turnover numbers of 102 and 18, respectively. Kinetic investigations further reveal an observed rate constant of around 107 (s-1), implying high efficiency of the bimetallic catalyst towards hydrogen evolution reaction. Mechanistic insights are presented by using a combination of UV-vis-NIR and EPR spectroscopy and electrochemistry. Our results thus firmly establish the triply fused porphyrin ligands as candidates for generating highly efficient molecular electrocatalysts in combination with transition metal centers. | Biprajit Sarkar; Shubhadeep Chandra; Arijit Singha Hazari; Qian Song; David Hunger; Nicolas I. Neuman; Joris van Slageren; Elias Klemm | Inorganic Chemistry; Catalysis; Energy; Coordination Chemistry (Inorg.); Electrochemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d81d92f51b22552b0c3414/original/remarkable-enhancement-of-catalytic-activity-of-cu-complexes-in-the-electrochemical-hydrogen-evolution-reaction-her-by-using-triply-fused-porphyrin.pdf |
67d973066dde43c90845cba7 | 10.26434/chemrxiv-2024-6kdjr-v2 | Explicit solutions for some two-step kinetics problems involving reversible isomerization | We present explicit solutions to various two-step kinetics model systems involving reversible isomerization.
The first problem consists of the isomerization followed by a zeroth-order process. Exact expressions for the
area under the curve and the peak, termination and crossing times were also derived and found to involve the
Lambert W function. We discuss in detail the passage to the irreversible limit and test it on the first stages of
alcohol elimination in humans. The solution of the generalized problem where both isomerizing species can
simultaneously undergo a zeroth-order irreversible transformation is also presented. The exact solution for the
consecutive problem that starts with a zeroth-order kinetics and is followed by a reversible isomerization is also
obtained. In the second part of this work, we present the explicit solution for the two-step kinetics problem
consisting of an irreversible dimerization followed by a reversible isomerization of the dimer complex. Both the
homo- and cross-dimerization cases are presented and the solutions were found to involve the exponential integral
and the hypergeometric functions, respectively. We comment on the situations where the obtained solutions could
be helpful. | Alejandro Perez Paz | Physical Chemistry; Biophysical Chemistry; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d973066dde43c90845cba7/original/explicit-solutions-for-some-two-step-kinetics-problems-involving-reversible-isomerization.pdf |
60c755df469df4e533f451fa | 10.26434/chemrxiv.14175389.v1 | Beyond Thin Films: Clarifying the Impact of c-Li15Si4 Formation in Thin Film, Nanoparticle, and Porous Si Electrodes | Analysis of the role of c-Li15Si4 in performance of silicon-based anodes in lithium ion batteries. This work indicates that concerns about the <i>c</i>-Li<sub>15</sub>Si<sub>4</sub> phase in silicon nanoparticles and porous silicon electrodes should mainly focus on the stability of the SEI and a reduction of irreversible electrolyte reactions. | Jasper Woodard; W. Peter Kalisvaart; Sayed Youssef Sayed; Brian Olsen; Jillian Buriak | Nanostructured Materials - Materials; Energy Storage | CC BY 4.0 | CHEMRXIV | 2021-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755df469df4e533f451fa/original/beyond-thin-films-clarifying-the-impact-of-c-li15si4-formation-in-thin-film-nanoparticle-and-porous-si-electrodes.pdf |
60c75486bdbb89fbbda3a67a | 10.26434/chemrxiv.13670737.v1 | Correlation Between Yield and Reduced Mass of Raw Materials in Enzymatic Reactions | Correlation
between the yield in the enzymatic reaction and the molecular weight of the
substrate as an approximation of the reduced mass of the raw materials was clarified.
The correlation was expressed by the same regression equation as in general
organic chemical reactions. The coefficient of the regression equation to
distinguish between intramolecular and intermolecular reactions were better when
the values for intramolecular reactions were used in the plot of literature
yields versus predicted yields. It was also found that the adjustment of the
reduced mass by the number of rotatable bonds was not necessary and was found
to be a good representation of the characteristics of the enzymatic reaction. | Masatoshi Kawashima | Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75486bdbb89fbbda3a67a/original/correlation-between-yield-and-reduced-mass-of-raw-materials-in-enzymatic-reactions.pdf |
60c744a2842e65d2a7db24c2 | 10.26434/chemrxiv.9873143.v1 | Intraresidual Correlated Motions in Peptide Chain | Conformational flexibility of polypeptide chains is mainly
driven by changes in the (phi, psi) dihedrals of each residue. Such motions, however,
are not completely independent, as certain (anti)correlated motions are
favored. In this work, we investigate the correlations between the dihedral
displacements of adjacent residues, (Δphi i, Δpsi i+1) and (Δphi i-1, Δpsi i), i.e. interresidual, and within the same residue, (Δphi i, Δpsi i), i.e. intraresidual, by analyzing extensive
Molecular Dynamics trajectories of initially extended polyalanine chains in
detail. Correlations are evaluated individually at different residue
conformations covering the whole (phi, psi)-space. From these we draw maps which clearly show
how the coupled motions strongly depend on the conformation, thus unveiling an
unprecedented strong intramolecular correlation displaying opposite
(correlated/anticorrelated) behaviors at different conformations. By developing
a tailored model, it is also demonstrated that both inter and intraresidual
correlations arise from the propensity of the peptide to minimize the overall
atomic displacements along the whole polypeptide chain. | Adolfo Bastida; Javier Carmona-García; José Zúñiga; Alberto Requena; Javier Cerezo | Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744a2842e65d2a7db24c2/original/intraresidual-correlated-motions-in-peptide-chain.pdf |
67565b8e7be152b1d05ee375 | 10.26434/chemrxiv-2024-ltncz-v2 | Explainable Synthesizability Prediction of Inorganic Crystal Polymorphs using Large Language Models | We evaluate the ability of machine learning to predict whether a hypothetical crystal structure can be synthesized and explain those predictions to scientists. Fine-tuned large language models (LLMs) trained on a human-readable text description of the target crystal structure perform comparably to previous bespoke convolutional graph neural network methods, but better prediction quality can be achieved by training a positive-unlabeled learning model on a text-embedding representation of the structure. An LLM-based workflow can then be used to generate human-readable explanations for the types of factors governing synthesizability, extract the underlying physical rules, and assess the veracity of those rules. These explanations can guide chemists in modifying or optimizing non-synthesizable hypothetical structures to make them more feasible for materials design. | Seongmin Kim; Joshua Schrier; Yousung Jung | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67565b8e7be152b1d05ee375/original/explainable-synthesizability-prediction-of-inorganic-crystal-polymorphs-using-large-language-models.pdf |
6254d4fdef2ade388c2c4194 | 10.26434/chemrxiv-2022-xztxl-v2 | Assessing recent time-dependent double-hybrid density functionals on doublet-doublet excitations | This work is the first thorough investigation of time-dependent double-hybrid density functionals (DHDFs) for the calculation of doublet- doublet excitation energies. It sheds light on the current state-of-the-art techniques in the field and clarifies if there is still room for future improvements. Overall, 29 hybrid functionals and DHDFs are investigated. We separately analyze the individual impacts of the Tamm-Dancoff approximation (TDA), range separation, and spin-component/opposite scaling (SCS/SOS) on 45 doublet-doublet excitations in 23 radicals before concluding with an overarching analysis that includes and excludes challenging excitations with double-excitation or multi-reference character. Our results show again that so-called ’non-empirical’ DHDFs are outperformed by semi-empirical ones. While the best assessed functionals are DHDFs, some of the worst are also DHDFs and outperformed by all assessed hybrids. SCS/SOS is particularly beneficial for range-separated DHDFs. Spin-scaled, range-separated DHDFs paired with the TDA belong to the best tested methods here and we particularly highlight SCS-ωB2GP-PLYP, SOS-ωB2PLYP, SOS- ωB2GP-PLYP, SOS-ωB88PP86, SOS-RSX- QIDH, and SOS-ωPBEPP86. When comparing our functional rankings with previous studies on singlet-singlet and singlet-triplet excitations, we recommend TDA-SOS-ωB88PP86 and TDA-SOS-ωPBEPP86 as robust methods for excitation energies in general until further improvements have been achieved that surpass the chemical accuracy threshold for challenging ex- citations without increasing the computational effort. | Joshua Van Dijk; Marcos Casanova-Paez; Lars Goerigk | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6254d4fdef2ade388c2c4194/original/assessing-recent-time-dependent-double-hybrid-density-functionals-on-doublet-doublet-excitations.pdf |
6713d585b91c6e99717fe391 | 10.26434/chemrxiv-2024-vxlph | Effect of Cation-π Interactions on the Phase Behavior and Viscoelastic Properties of Polyelectrolyte Complexes | Aromatic rings are a common feature of biological and synthetic polymers that form polyelectrolyte complexes and coacervates. These functional groups can engage in cation-π interactions, but the impact of such interactions on the physical properties of polyelectrolyte complex materials is not well-understood. Here, we investigate the effect of cation-π interactions on the phase behavior and viscoelasticity of polyelectrolyte complexes of poly(styrene sulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA), which contain aromatic functional groups on every repeat unit of the PSS polyanion. We prepare samples with matched polymer and/or salt concentrations using salts with different cation-π interaction strengths. Characterization by turbidity, thermogravimetric analysis, and rheology reveals that salts that engage in stronger cationπ interactions destabilize coacervation and speed up the viscoelastic relaxation of the materials. By contrast, polyelectrolyte complexes composed of polymers that do not contain aromatic rings (poly(2-acrylamido-2-methyl propane sulfonate) (PAMPS) and PDADMA) are found to be insensitive to the cation-π interaction strength of the salt. These results reveal that cation-π interactions play a significant role in determining the phase behavior and viscoelasticity of polyelectrolyte complexes and coacervates made from polymers with aromatic functional groups, and suggest that cation-π interactions may be a useful molecular handle for tuning coacervate properties. | Conner Chee; Aijie Han; Gileanna Ortiz; Lexi Knight; Jennifer Laaser | Polymer Science; Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6713d585b91c6e99717fe391/original/effect-of-cation-interactions-on-the-phase-behavior-and-viscoelastic-properties-of-polyelectrolyte-complexes.pdf |
60c754e6f96a00c6de288743 | 10.26434/chemrxiv.13817243.v1 | Structure-Guided Design, Synthesis, and Evaluation of 1-Indanone and 1,3-Indandione Derivatives as Ligands for Misfolded α-Synuclein Aggregates | <p>The development of imaging
agents for in vivo detection of alpha-synuclein (α-syn) pathologies faces
several challenges. A major gap in the field is the lack of diverse molecular
scaffolds with high affinity and selectivity to α-syn fibrils for in vitro
screening assays. Better in vitro
scaffolds can instruct the discovery of better in vivo agents. We report the
rational design, synthesis, and in vitro evaluation of a series of novel
1-indanone and 1,3-indandione derivatives from a Structure-Activity
Relationship (SAR) study centered on some existing α-syn fibril binding
ligands. Our results from fibril saturation binding experiments show that two
of the lead candidates bind α-syn fibrils with binding constants (K<sub>d</sub>)
of 9.0 and 18.8 nM, respectively, and selectivity of greater than 10x for α-syn
fibrils compared with amyloid-β (Aβ) fibrils. Our results demonstrate that the
lead ligands avidly label all forms of α-syn on PD brain tissue sections, but
only the dense core of senile plaques in AD brain tissue, respectively. These
results are corroborated by ligand-antibody colocalization data from Syn211,
which shows immunoreactivity towards all forms of α-syn aggregates, and Syn303,
which displays preferential reactivity towards mature Lewy pathology. Our results reveal that 1-indanone derivatives
have desirable properties for the biological evaluation of α-synucleinopathies.</p> | Xianwei Sun; Prasad Admane; Zbigniew A. Starosolski; Jason L Eriksen; Ananth V. Annapragada; Eric Tanifum | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754e6f96a00c6de288743/original/structure-guided-design-synthesis-and-evaluation-of-1-indanone-and-1-3-indandione-derivatives-as-ligands-for-misfolded-synuclein-aggregates.pdf |
60c74b35ee301c558cc79dc8 | 10.26434/chemrxiv.12309755.v1 | Poly(alkylene 2,5-Furanoate)s Thin Films: Morphology, Crystallinity and Nanomechanical Properties | Poly(alkylene 2,5-furanoate)s are considered as the most attractive and interesting alternatives to replace oil-based terephthalic polymers. These furan-based polyesters can be synthesized using fully bio-based synthetic strategies, allowing to reduce the environmental impact of plastics. At the same time, these polymers have shown outstanding thermal, mechanical and gas-barrier properties. All these results envisage their industrial use in the near future. Now, considering the downscaling of the products’ size towards the nanometer scale, we present a study of the morphology and nanomechanical properties of poly(alkylene 2,5-furanoate) thin films. Using Atomic Force Microscopy, we report the development of nanostructures upon crystallization, following different thermal treatments, for thin films with thicknesses below 200 nm. Moreover, we studied the impact of crystal growth in the nanomechanical properties of these materials. We found that the polymer thin films preserve their excellent mechanical response even in the confined geometry, as proved by the Young’s moduli values close to the GPa, accompanied by high surface stiffness, and low indentation depths. The poly(alkylene 2,5-furanoate) thin films were found to have nanomechanical properties comparable to those of the oil-based poly(ethylene terephthalate), a further evidence that in the future they could replace traditional polymers in several applications. | Beatriz Robles-Hernández; Michelina Soccio; Iker Castrillo; Giulia Guidotti; Nadia Lotti; Angel Alegria; Daniel E Martínez-Tong | Biocompatible Materials; Biodegradable Materials; Thin Films; Organic Polymers; Polymer morphology; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b35ee301c558cc79dc8/original/poly-alkylene-2-5-furanoate-s-thin-films-morphology-crystallinity-and-nanomechanical-properties.pdf |
60c745feee301c60aac7942a | 10.26434/chemrxiv.10308071.v1 | Ultrasound Responsive Carbon Monoxide Releasing Micelle | Carbon monoxide releasing molecules (CORMs) have
been intensively studied in the past decade due to the therapeutic effects of
CO. The potential to control the release of CO to a specific target is one of the
major advantages of CORM. In this work an ultrasound responsive micelle with
pluronic as the shell and CORM-2 as the core were developed. The micelle
released CO in the presence of cysteine. After the CO release stopped, applying
ultrasound to the micelle suspension produced additional CO. About 1/3 of total
CO can be controllably released by ultrasound. The mechanism of the ultrasound
induced CO release is interpreted by the reaction between cysteine and CORM-2
inside the micelle. | Osamah Alghazwat; Somayeh Talebzadeh; Yi Liao | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745feee301c60aac7942a/original/ultrasound-responsive-carbon-monoxide-releasing-micelle.pdf |
60c74024f96a0025df286242 | 10.26434/chemrxiv.7660547.v1 | Fast and Selective Post-Polymerization Modification of Conjugated Polymers Using Dimethyldioxirane | Modification of functional groups attached to conjugated polymer backbones can drastically alter the material properties. Oxidation of electron-donating thioalkyl substituents to electron-withdrawing sulfoxides or sulfones is a particularly effective modification. However, so far, this reaction has not been studied for the modification of conjugated polymers used in organic electronics. Crucial questions regarding selectivity and reaction time waited to be addressed. Here, we show that the reaction is highly selective and complete within just a few minutes when using dimethyldioxirane (DMDO) for the oxidation of thioalkyl substituents attached to the well investigated conjugated polymers poly(9-(1-octylnonyl)carbazole-alt-4,7-dithienylbenzothiadiazole) (PCDTBT) and poly(9,9-dioctylfluorene-alt-benzothiadiazole) (F8BT). The selectivity was confirmed by comparison with polymers obtained from pre-oxidized monomers and by control experiments using related polymers without thioalkyl substituents. Using DMDO, the oxidation yields acetone as the only side-product, which reduces the work-up to mere evaporation of solvents and excessive reagent. Our results show that this oxidation is an exciting method for the preparation of electron-deficient conjugated polymers. It may even allow the preparation of electron acceptors for solar cells directly from the electron donors. | Emmanuel Reichsöllner; Adam Creamer; Shengyu Cong; Abby Casey; Simon Eder; Martin Heeney; Florian Glöcklhofer | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Thin Films; Conducting polymers; Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74024f96a0025df286242/original/fast-and-selective-post-polymerization-modification-of-conjugated-polymers-using-dimethyldioxirane.pdf |
60c743d40f50db74e7395fcd | 10.26434/chemrxiv.9642044.v1 | Controllable, Sequential, and Stereoselective C–H Allylic Alkylation of Alkenes | The direct conversion of C–H bonds into new C–C bonds represents a powerful approach to generate complex molecules from simple starting materials. However, a general and controllable method for the sequential conversion of a methyl group into a fully substituted carbon center remains a challenge. We report a new method for the selective and sequential replacement of three C-H bonds at the allylic position of propylene and other simple terminal alkenes with different carbon groups derived from Grignard reagents. A copper catalyst and electron-rich biaryl phosphine ligand facilitate the formation of allylic alkylation products in high branch-selectivity. We also present conditions for the generation of enantioenriched allylic alkylation products in the presence of catalytic copper and a chiral phosphine ligand. With this approach, diverse and complex products with substituted carbon centers can be generated from simple and abundant feedstock chemicals.<br /> | Ling Qin; Mohammed Sharique; Uttam Tambar | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743d40f50db74e7395fcd/original/controllable-sequential-and-stereoselective-c-h-allylic-alkylation-of-alkenes.pdf |
62bc851852acb7729877eccd | 10.26434/chemrxiv-2022-7187n-v2 | Molecular Modelling of Ionic Liquids: General Guidelines on Fixed-Charge Force Fields for Balanced Descriptions | It has been increasingly common to investigate dynamic and thermodynamic properties of green solvents at atomistic scales with molecular simulation. These designed solvents such as ionic liquids are often highly charged species, which pose a problem for molecular modelling with classical fixed-charge force fields. Simulation outcomes with atomic charges derived from ab initio calculations often show significant deviations from the experimental reference, and charge scaling is widely applied as a simple yet efficient solution to achieve satisfactory experiment-simulation accordance. Although the massive emphasis on the reproduction of bulk properties such as density of the liquids as charge scaling criteria, a more crucial thermodynamic observable is the solvation behavior of external agents in these green solvents. Astonishingly, our recent large-scale benchmark calculation on solvation thermodynamics suggests that the solvation-free-energy-derived scaling factor is generally slightly larger (~0.1) than the bulk-property-derived estimate. This phenomenon is rather not unexpected, as the density-matching estimate only considers the solvent-solvent interaction (overfitting), while accurate calculations of solvation free energies require balanced descriptions of solute-solvent and solvent-solvent interactions. A more interesting observation is that different solute-solvent pairs exhibit different responses to the variation of the scaling parameter, which arises from the competing electrostatic and vdW contributions. Another perspective provided in our previous extensive benchmark is about the suitability of general-purpose force fields for bonded and vdW interactions in the modelling of ionic liquids. The bond stretching and angle bending terms in pre-fitted GAFF derivatives are often problematic, while the torsional potential shows satisfactory reproduction of ab initio results. In the current work, we expect to accumulate more experiences from large-scale fast-growth solvation free energy simulations in ionic liquids with compositions different from our previous benchmark. The obtained new results are combined with our previous dataset to form a large solvation set (and also partition or water-ionic-liquids transfer set), from which a universally applicable charge scaling factor with at least half-optimal performance is derived. Aside from the force-field issue, another extremely important modelling detail considered in the current work is the finite-size effect. It is observed that the finite-size artifacts in solvation thermodynamics are much more severe than mass density, which emphasizes the use of a sufficiently large ionic solvent box in molecular simulations of ionic liquids derivatives. Finally, combining the extensive computational perspectives accumulated in our series works, general guidelines for molecular modelling of ionic liquids with fixed-charge force fields are summarized. | Zhaoxi Sun; Zhihao Gong; Lei Zheng; Payam Kalhor; Zhe Huai; Zhirong Liu | Physical Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Hydrology and Water Chemistry; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bc851852acb7729877eccd/original/molecular-modelling-of-ionic-liquids-general-guidelines-on-fixed-charge-force-fields-for-balanced-descriptions.pdf |
60c74ee8469df4721cf4458e | 10.26434/chemrxiv.12816497.v1 | Defluorosilylation of Trifluoromethane: Upgrading an Environmentally Damaging Fluorocarbon | <p>The rapid, room-temperature defluorosilylation of trifluoromethane, a highly potent greenhouse gas, has been achieved using a simple silyl lithium reagent. An extensive computational mechanistic analysis provides a viable reaction pathway and demonstrates the unexpected electrophilic nature of LiCF<sub>3</sub>. The reaction generates a bench stable fluorinated building block that shows promise as an easy-to-use difluoromethylating agent. The difluoromethyl group is an increasingly important bioisostere in active pharmaceutical ingredients, and therefore our methodology creates value from waste. The potential scalability of the process has been demonstrated by achieving the reaction on a gram-scale.</p> | Daniel Sheldon; Greg Coates; Mark Crimmin | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Environmental Science; Wastes; Bond Activation; Main Group Chemistry (Organomet.); Reaction (Organomet.); Small Molecule Activation (Organomet.); Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ee8469df4721cf4458e/original/defluorosilylation-of-trifluoromethane-upgrading-an-environmentally-damaging-fluorocarbon.pdf |
62cfd280fe12e37d08a10c0c | 10.26434/chemrxiv-2022-1w9zr | On the statistical mechanical interpretation of entropy: a revision | The statistical interpretation of entropy has simultaneously been one of the most influential and one of the most controversial findings in the history of science. The complications and challenges stemming from considering the particles of the same type either as distinguishable or indistinguishable, how each scenario shall impact the counted number of microstates and theoretical justifications for that, and above all, considering entropy either as an extensive or a non-extensive quantity, have been the subject of numerous debates for over a century. The main aim of the present study is to shed a new light on the statistical mechanical evaluation of entropy which allows resolving majority of the mentioned ambiguities. | Amin Alibakhshi | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Physical and Chemical Properties; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cfd280fe12e37d08a10c0c/original/on-the-statistical-mechanical-interpretation-of-entropy-a-revision.pdf |
6397dc96836ceb3d2f7f4b36 | 10.26434/chemrxiv-2022-4k6tg | Dinitrogen Binding and Functionalization in Low-Coordinate Alkynyliron Complexes | Alkynyl complexes of low-coordinate transition metals offer a sterically open environment and unusual bonding for reactivity. Here, we explore the capacity of iron(I) alkynyl complexes to bind N2, and isolate an N2 complex including its X-ray crystal structure. Silylation of this complex gives a formally iron(IV) complex with a disilylhydrazido(2–) ligand, but NBO analysis indicates that an iron(II) formulation is more accurate. The structure of this compound is similar to an earlier reported phenyl complex in which phenyl migration forms a new N–C bond, but the alkynyl group does not migrate. DFT calculations are used to test the possible reasons, and the most likely is the stronger Fe–C bond energy in the alkynyl complex. | Samuel Bhutto; Brandon Mercado; Patrick Holland | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Small Molecule Activation (Organomet.); Spectroscopy (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6397dc96836ceb3d2f7f4b36/original/dinitrogen-binding-and-functionalization-in-low-coordinate-alkynyliron-complexes.pdf |
65cad1b2e9ebbb4db937c2bc | 10.26434/chemrxiv-2024-pdtfq | Rapid synthesis of cationic cellulose with high degree of substitution values over 1.0 in aqueous pyrrolidinium hydroxide solutions | Cellulose is attracting attention for the development of environmentally friendly, carbon-neutral, sustainable materials. Cellulose derivatives with cationic groups have the potential for applications in various fields, e.g., electrolytes. However, the current situation is marked by a low degree of cationic group incorporation and a need for more efficient synthesis methods. In this study, cationic cellulose was synthesized using an epoxy derivative, 2,3-epoxypropyltrimethylammonium chloride (EPTMAC), in an aqueous pyrrolidinium hydroxide solution. Since an aqueous pyrrolidinium hydroxide solution is a strong alkaline solution, the solution not only exhibits a high cellulose solubility at room temperature but also facilitates the reaction between cellulose and the epoxy derivative. We investigated the influence of reaction time, temperature, cellulose concentration, cationic reagent concentration, and the selection of a precipitation solvent for purification on the degree of substitution (DS) value of cationic cellulose. The structure of the obtained cationic cellulose was examined using 1H NMR, 1H-1H TOCSY, 1H-13C HSQC measurements, and Fourier-transform infrared spectroscopy (FT-IR). As a result of increasing cellulose and EPTMAC concentrations, the DS value increased, reaching a maximum value of 1.9. Solubility tests indicated that the cationic cellulose with chloride counter-anions exhibited notable solubility even in ethanol when the DS values were over 1.2. Cationic cellulose with bis(trifluoromethylsulfonyl)amide (TFSA) anion synthesized with a view to battery applications was insoluble in water and exhibited a film-forming property. Thus, the solubility of cationic cellulose could be controlled by varying the anionic species. | Yutaro Hayashi; Mariya Usami; Elisabeth R. D. Ito; Yuko Takeoka; Masahiro Rikukawa; Masahiro Yoshizawa-Fujita | Organic Chemistry; Polymer Science; Cellulosic materials; Polyelectrolytes - Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cad1b2e9ebbb4db937c2bc/original/rapid-synthesis-of-cationic-cellulose-with-high-degree-of-substitution-values-over-1-0-in-aqueous-pyrrolidinium-hydroxide-solutions.pdf |
60c747fb0f50db40233966b8 | 10.26434/chemrxiv.11826843.v1 | Molecular Engineering for Boosting AIE-active Free Radical Photogenerator and Its High-performance in Hypoxia via Photodynamic Therapy | <div>
<p>Serious hypoxia in solid tumor as well as
vicious aggregation-caused fluorescence quenching (ACQ) of conventional photosensitizers
(PSs) limit the
progress of the fluorescence imaging-guided photodynamic (PDT) although it has obvious
advantages in precise spatial-temporal control and
noninvasive treatment. The photosensitizers featuring Type I reactive
oxygen species (ROS) based on free radical and novel aggregation-induced emission (AIE) characteristic (AIE-PSs)
could offer precious opportunity
to resolve above problems, but there was rare feasible molecular engineering in
previous reports. Herein, we proposed that the strategy of fabricating stronger
intermolecular charge transfer (ICT) effect in electron-rich anion-π<sup>+ </sup>AIE-active
luminogens (AIEgens) aimed to help suppressing
nonradiative internal conversion (IC) as well as promote radiative and
intersystem crossing (ISC) processes for boosting more free radical generation. Systematic and detailed
experimental and theoretical calculations proved our ideas when the
electron-donating abilities enhanced in collaborative
donors, and the AIE-PSs exhibited higher performance in near-infrared
red (NIR) fluorescence image-guided cancer PDT <i>in vitro/vivo</i>. This work would become an
important reference to the design of AIE-active free radical generators for overcoming ACQ
effect and tumor hypoxia
in future PDT.</p>
</div> | Qing Wan; Rongyuan Zhang; Zeyan Zhuang; Yuxuan Li; Zhiming Wang; Weijie Zhang; Jianquan Hou; Ben Zhong Tang | Biocompatible Materials; Biological Materials; Dyes and Chromophores; Photosensitizers | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747fb0f50db40233966b8/original/molecular-engineering-for-boosting-aie-active-free-radical-photogenerator-and-its-high-performance-in-hypoxia-via-photodynamic-therapy.pdf |
65777a49bec7913d2762f853 | 10.26434/chemrxiv-2023-b1krn | Structure-guided design of a highly potent RXR agonist with superior physicochemical properties | Retinoid X receptors (RXR, NR2B1-3) hold therapeutic potential in oncology, neurodegeneration and metabolic diseases but traditional RXR agonists mimicking the natural ligand 9-cis retinoic acid exhibit poor physicochemical properties, pharmacokinetics and safety profiles. Improved RXR ligands are needed to exploit RXR modulation as a promising therapeutic concept in various indications beyond its current role in second-line cancer treatment. Here we report the co-crystal structure of RXR in complex with a novel pyrimidine-based ligand and the structure-informed optimization of this scaffold to highly potent and highly soluble RXR agonists. Rigidization resulted in significantly improved potency and focused structure-activity relationship elucidation indicated potential avenues to RXRα preference. We obtained an optimized RXR agonist with low nanomolar potency, no cytotoxic activity and very favorable physicochemical properties highlighting this promising scaffold for the development of next-generation RXR agonist drugs. | Max Lewandowski; Melania Carmina; Loris Knümann; Minh Sai; Sabine Willems; Till Kasch; Julius Pollinger; Stefan Knapp; Julian A. Marschner; Apirat Chaikuad; Daniel Merk | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65777a49bec7913d2762f853/original/structure-guided-design-of-a-highly-potent-rxr-agonist-with-superior-physicochemical-properties.pdf |
62fceddff3b9665a35b11a92 | 10.26434/chemrxiv-2022-d8gfc | Cut-and-Pasting Ligands: The Structure/Function Relationships of a Thermally Robust Mo(VI) Precursor | The bis(tert-butylimido)-molybdenum(VI) framework has previously been used for the successful atomic layer deposition and chemical vapor deposition of many molybdenum-containing thin films. We have now prepared and fully characterized a new thermally robust bis(tert-butylimido)molybdenum(VI) complex, bis(tert-butylimido)-bis(N-2-(tertbutyliminomethyl)pyrrolato)-molybdenum(VI), (tBuN)2Mo(PyrIm)2 (1), that incorporates two N,N’-κ2-monoanionic ligands. The volatility and thermal stability of 1 was measured using thermogravimetric analysis and differential scanning calorimetry, where it was found to achieve a 1 Torr of vapor pressure at 212 ºC and had an onset of thermal decomposition at 273 ºC. Comparison of its thermal properties to the known ALD precursor (tBuN)2Mo(dpamd)2 (dpamd = N,N’-diisopropyl-acetamidinato) showed that 1 exhibits a similar volatility, but with a 78 ºC improvement in thermal stability. Since 1
exhibits an excellent thermal range (61 ºC), it should be further explored for use as a vapor deposition precursor. | Michael Land; Dexter Dimova; Katherine Robertson; Seán Barry | Inorganic Chemistry; Ligands (Inorg.); Transition Metal Complexes (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fceddff3b9665a35b11a92/original/cut-and-pasting-ligands-the-structure-function-relationships-of-a-thermally-robust-mo-vi-precursor.pdf |
60c74917bdbb894737a390de | 10.26434/chemrxiv.11868261.v2 | Endogenous Binding of Steroid Molecules to DNA Nucleotides by a Ca2+/PO4- Process to Enable Gene Transcription | Steroid hormones, such as cortisol, testosterone and estrogen, have powerful control over human physiology, growth, and reproduction, but efforts to deploy its potential, such as with glucocorticoids, a first-line defense of inflammation, are often met with severe side effects. Unfortunately, much is unknown about the basic interaction of steroid molecules with DNA, including its receptors, activators, factors, and the gene transcription procedure. In this research article, a remarkable finding is shown for the first time, in which it is illustrated through structural analysis that the base pairings of the four DNA nucleotides, adenine with thymine (A-T) and cytosine with guanine (C-G), form perfectly the classic four ring structure of the steroid molecule, which indicates the profound result put forth in this article that steroid molecules bind directly to DNA for the purpose of gene transcription. Further, critical to a basic understanding of DNA, it is resolved here of the location of the unusual ``missing" hydrogen bond of the A-T and T-A pairings, which has only two internal hydrogen bonds whereas C-G and G-C have three hydrogen bonds. It is shown that the third hydrogen bond for A-T and T-A is formed when the A-T and T-A nucleotides are coupled with corticosteroids, such as cortisol, which has an oxygen functional group that is perfectly positioned to form a hydrogen bond with the accessible oxygen-based functional group of thymine. In addition, to facilitate the binding process, it is shown that Ca$^{2+}$ ions, which are associated with the ligand binding domain of the steroid receptor prior to its association with DNA, couple the oxygen-based functional groups at each end of the steroid molecule with the PO$_4^-$ ions of adjacent nucleotides and thus bind the steroid molecule directly to the nucleic acid. Additionally, the basis of initiating the transcription process is described in which the energy stabilization due to the binding of the ion-steroid complex to DNA is dissipated through the DNA molecule to initiate strand separation locally by increasing the length of hydrogen bonds, thus allowing RNA polymerase action. The results are further amplified by analysis of the cortisol hormone and the ligand binding domain of the glucocorticoid receptor in its interaction with the A-T nucleotide pairing. | Charles Schaper | Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74917bdbb894737a390de/original/endogenous-binding-of-steroid-molecules-to-dna-nucleotides-by-a-ca2-po4-process-to-enable-gene-transcription.pdf |
60c753a5f96a001b412884da | 10.26434/chemrxiv.13522313.v1 | Epigenetic Target Prediction with Accurate Machine Learning Models | <p>Epigenetic
targets are a significant focus for drug discovery research, as demonstrated by
the eight approved epigenetic drugs for treatment of cancer and the increasing
availability of chemogenomic data related to epigenetics. This data represents
a large amount of structure-activity relationships that has not been exploited
thus far for the development of predictive models to support medicinal
chemistry efforts. Herein, we report the first large-scale study of 26318 compounds
with a quantitative measure of biological activity for 55 protein targets with
epigenetic activity. Through a systematic comparison of machine learning models
trained on molecular fingerprints of different design, we built predictive
models with high accuracy for the epigenetic target profiling of small
molecules. The models were thoroughly
validated showing mean precisions up to 0.952 for the epigenetic target
prediction task. Our results indicate that the herein reported models
have considerable potential to identify small molecules with epigenetic
activity. Therefore, our results were implemented as freely accessible and easy-to-use
web application.</p> | Norberto Sánchez-Cruz; Jose L. Medina-Franco | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a5f96a001b412884da/original/epigenetic-target-prediction-with-accurate-machine-learning-models.pdf |
6414a9b8aad2a62ca1ed1a04 | 10.26434/chemrxiv-2023-pcln6 | Studying Kinetics of a Surface Reaction using Elastocapillary Effect | Hypothesis : When a liquid is inserted inside a microfluidic channel, embedded within a soft elastomeric layer, e.g. poly(dimethylsiloxane) (PDMS), the thin wall of the channel deforms, due to change in solid-liquid interfacial energy. This phenomenon is known as Elastocapillary effect. The evolution of a new species at this interface too alters the interfacial energy and consequently the extent of deformation. Hence, it should be possible to monitor dynamics of physical and chemical events occurring near to the solid-liquid interface by measuring this deformation by a suitable method, e.g., optical profilometer.
Experiments: Aqueous solution of a metal salt inserted into these channels reacts with Silicon-hydride present in PDMS, yielding metallic nanoparticles at the channel surface. The kinetics of this reaction was captured in real time, by measuring the wall deformation. Similarly, physical adsorption of a protein: Bovine Serum Albumin, on PDMS surface too was monitored.
Finding : The rate of change in deformation can be related to rate of these processes to extract the respective reaction rate constant. These results show that Elastocapillary effect can be a viable analytical tool for in-situ monitoring of many physical and chemical processes for which, the reaction site is inaccessible to conventional analytical methods. | Nitish Singh; Ajeet Kumar; Animangsu Ghatak | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6414a9b8aad2a62ca1ed1a04/original/studying-kinetics-of-a-surface-reaction-using-elastocapillary-effect.pdf |
60c74c3a842e65524fdb328c | 10.26434/chemrxiv.12443411.v1 | Bio- and medicinally compatible α-amino acid modification via merging photo-redox and N-heterocyclic carbene catalysis | An NHC and photo-redox co-catalyzed α-amino acid
decarboxylative carbonylation reaction was presented here. This method displayed
good scope generality, providing an easy and direct pathway to access various
downstream α-amino ketones from readily accessible starting materials under bio- and medicinally compatible conditions. Moreover, this
strategy is appealing to chemical biology since it
has great potential for chemical modification of peptides or late-stage
synthesis of keto-peptides. | Jie Feng; Ding Du; Kuili Zhang; Jian Gao; Tao Lu; Rui Ma; Zhihao Shi | Organocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c3a842e65524fdb328c/original/bio-and-medicinally-compatible-amino-acid-modification-via-merging-photo-redox-and-n-heterocyclic-carbene-catalysis.pdf |
66bb42aea4e53c48763e3085 | 10.26434/chemrxiv-2024-c9p3f | 3,3-Difluorooxetane – a Versatile Functional Group for Bioisosteric Replacements in Drug Discovery | Functional group (FG) is one of the cornerstone concepts in organic chemistry and related areas. Wide spread of bioisosterism ideas in medicinal chemistry and beyond caused a striking rise in demand for novel FGs with defined impact on the developed compound properties. In this work, evaluation of 3,3-difluorooxetane unit (3,3-diFox) as a functional group for bioisosteric replacements is disclosed. Comprehensive experimental study (including multigram building block synthesis, quantification of steric and electronic properties, measurements of pKa, LogP, chemical stability, and biological evaluation of the 3,3-diFox-derived bioisostere of a drug candidate) revealed a prominent behavior of the 3,3-diFox fragment as a versatile substituent for early drug discovery programs. | Oleksandr Liashuk; Anastasiya Fedinchyk; Kostiantyn Melnykov; Maksym Herasymchuk; Diana Alieksieieva; Dmytro Lesyk; Yulia Bas; Tatiana Keda; Andriy Yatsymyrskiy; Yuliia Holota; Petro Borysko; Volodymyr Yarmolchuk; Oleksandr Grygorenko | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bb42aea4e53c48763e3085/original/3-3-difluorooxetane-a-versatile-functional-group-for-bioisosteric-replacements-in-drug-discovery.pdf |
6629443591aefa6ce153a63b | 10.26434/chemrxiv-2024-hn590 | Electron Transfer Dynamics at Dye-Sensitized SnO2/TiO2 Core-Shell Electrodes in Aqueous/Nonaqueous Electrolyte Mixtures | The dynamics and efficiency of photoinduced electron transfer were measured at dye-sensitized photoanodes in aqueous (acetate buffer), nonaqueous (acetonitrile), and mixed solvent electrolytes by nanosecond transient spectroscopy (TAS) and ultrafast optical-pump terahertz-probe spectroscopy (OPTP). Higher injection efficiencies were found in mixed solvent electrolytes for dye-sensitized SnO2/TiO2 core/shell electrodes, whereas the injection efficiency of dye-sensitized TiO2 electrodes decreased with the increasing acetonitrile concentration. The trend in injection efficiency for the TiO2 electrodes was consistent with the solvent-dependent trend in the semiconductor flat-band potential. Photoinduced electron injection in core-shell electrodes has been understood as a two-step process involving ultrafast electron trapping in the TiO2 shell followed by slower electron transfer to the SnO2 core. The driving force for shell-to-core electron transfer increases as the flat band potential of TiO2 shifts negatively with increasing concentration of acetonitrile. In acetonitrile-rich electrolytes, despite the larger driving force, electron injection is suppressed. Interestingly, a net negative photoconductivity in the SnO2 core is observed in mixed solvent electrolytes by OPTP. We hypothesize that an electric field is formed across the TiO2 shell from the oxidized dye molecules after injection. The intrinsic conduction band electrons in SnO2 are trapped at the core-shell interface by the electric field, resulting in a negative photoconductivity transient. The overall electron injection efficiency of the dye- sensitized SnO2/TiO2 core/shell photoanodes, measured on longer timescales, is optimized in mixed solvents. The ultrafast transient conductivity data illustrate the crucial role of the electrolyte in regulating the driving forces for electron injection and charge separation at dye-sensitized semiconductor interfaces. | Langqiu Xiao; Jacob Spies; Colton Sheehan; Zichen Zeng; Yunhan Gao; Tianyue Gao; Annika Ehrlacher; Michael Zuerch; Gary Brudvig; Thomas Mallouk | Physical Chemistry; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6629443591aefa6ce153a63b/original/electron-transfer-dynamics-at-dye-sensitized-sn-o2-ti-o2-core-shell-electrodes-in-aqueous-nonaqueous-electrolyte-mixtures.pdf |
63445fd4fee74e5dc35dc55b | 10.26434/chemrxiv-2022-pxr96 | Si–containing Carbon Composite Pillars Developed via Light–Induced Self–Writing | We report here the fabrication of Si-containing carbon pillars for Li-ion battery anodes using a processing technique known as Light-Induced Self-Writing (LISW). An array of optical beams generated using a photomask elicits the growth of vertically-aligned polymer pillars in nanoparticle-containing monomer mixtures. Simultaneously, we direct the Si nanoparticles to the outer walls of the polymer pillars based on established principles of nanoparticle phase-behavior during the LISW process. This concurrent structure growth and controlled nanoparticle distribution yields Si-decorated polymer pillars, which, upon pyrolysis, demonstrate promise as Li-ion battery anodes. Specifically, the composite pillar anodes demonstrate improved cycling stability over a standard planar electrode. This materials fabrication technique can be extended to other nanoparticle-monomer mixtures for other important applications such as chemical and gas sensing, cell-growth, and droplet manipulation. | Shreyas Pathreeker; Ian D. Hosein | Materials Science; Polymer Science; Energy; Composites; Materials Processing; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63445fd4fee74e5dc35dc55b/original/si-containing-carbon-composite-pillars-developed-via-light-induced-self-writing.pdf |
60c740e4842e656f24db1d82 | 10.26434/chemrxiv.7862480.v1 | Ab-Initio Study of Circular Dichroism and Circularly Polarized Luminescence of Spin-allowed and Spin-forbidden Transitions: From Organic Ketones to Lanthanide Complexes | <div><div><div><p>Complete and restricted active space self-consistent field (CAS-/RAS-SCF) wavefunction methods are applied for the calculation of circular dichroism (CD) and circularly polarized luminescence (CPL) of a series of molecules comprising four organic ketones, the chiral Cobalt(III) complex Λ-[Co(en)3]3+ and the Europium(III) complex [Eu(DPA)3]3–. The ab-initio results are in good agreement with the experimental data and previous results obtained with Kohn-Sham density functional theory in the case of the spin-allowed transitions. CD and CPL properties are calculated ab-initio for the first time for the spin-forbidden transitions of both a transition metal and a lanthanide complex.</p></div></div></div> | Frédéric Gendron; Barry Moore II; Olivier Cador; Fabrice Pointillart; Jochen Autschbach; Boris Le Guennic | Lanthanides and Actinides; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e4842e656f24db1d82/original/ab-initio-study-of-circular-dichroism-and-circularly-polarized-luminescence-of-spin-allowed-and-spin-forbidden-transitions-from-organic-ketones-to-lanthanide-complexes.pdf |
659516769138d2316113c719 | 10.26434/chemrxiv-2024-n6766 | Open-shell Oligo(3,4-dioxythiophene) Radical: Synthesis and Photothermal Conversion Performance | Open-shell radical meterials have received worldwide attention due to its potential application in highly efficient photothermal conversion field. However, it is still a challenge to enhance the chemical and photothermal stability of the open-shell small molecules and polymers. Herein, a stable open-shell oligo(3,4-dioxythiophene) radical PTTO2 was readily synthesized via simple BBr3-demethylation of the copolymer PTTOMe2 precursor prepared using cheap raw materials. The open-shell character of PTTO2 was carefully studied and confirmed via the signal-silent 1H-NMR spectrum, highly enhanced electron spin resonance signal comparing with PTTOMe2, as well as the ultral-wide UV-vis-NIR absorption and FTIR spectra and other technologies. Surprisingly, the powder of PTTO2 exhibit extremely wide absorption range from 300 to 2500 nm. The powder of PTTO2 can reach 274 ℃ under the same irradiation of 1.2 W cm-2, which is much higher 108 ℃ of the PTTOMe2. To date, PTTO2 stands as one of the low cost pure organic photothermal materials with super-high photothermal conversion performances. | Qi Wei; Chenghui Liao; Jiaxing Huang; Zesheng Zhang; Yuan Li | Organic Chemistry; Polymer Science; Energy; Organic Synthesis and Reactions; Conducting polymers; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659516769138d2316113c719/original/open-shell-oligo-3-4-dioxythiophene-radical-synthesis-and-photothermal-conversion-performance.pdf |
64f1f2b4dd1a73847ff65ed7 | 10.26434/chemrxiv-2023-x9pjf-v2 | SIMPD: an Algorithm for Generating Simulated Time Splits for Validating Machine Learning Approaches | Time-split cross-validation is broadly recognized as the gold standard for validating predictive models intended for use in medicinal chemistry projects. Unfortunately this type of data is not broadly available outside of large pharmaceutical research organizations. Here we introduce the SIMPD (simulated medicinal chemistry project data) algorithm to split public data sets into training and test sets that mimic the differences observed in real-world medicinal chemistry project data sets. SIMPD uses a multi-objective genetic algorithm with objectives derived from an extensive analysis of the differences between early and late compounds in more than 130 lead-optimization projects run within the Novartis Institutes for BioMedical Research. Applying SIMPD to the real-world data sets produced training/test splits which more accurately reflect the differences in properties and machine-learning performance observed for temporal splits than other standard approaches like random or neighbor splits. We applied the SIMPD algorithm to bioactivity data extracted from ChEMBL and created 56 public data sets which can be used for validating machine-learning models intended for use in the setting of a medicinal chemistry project. The SIMPD code and simulated data sets are available under open-source/open-data licenses at github.com/rinikerlab/molecular_time_series. | Gregory A. Landrum; Maximilian Beckers; Jessica Lanini; Nadine Schneider; Nikolaus Stiefl; Sereina Riniker | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1f2b4dd1a73847ff65ed7/original/simpd-an-algorithm-for-generating-simulated-time-splits-for-validating-machine-learning-approaches.pdf |
65aefa189138d2316182d18e | 10.26434/chemrxiv-2024-bmvkz | Optical control of TRPV1 channels in vitro with tethered photopharmacology | Transient receptor potential vanilloid 1 (TRPV1) is a nonselective cation channel that is important for nociception and inflammatory pain, and is activated by a variety of nociceptive stimuli—including lipids such as capsaicin (CAP) and endocannabinoids. TRPV1’s role in physiological systems is often studied by activating it with externally perfused ligands; however, this approach is plagued by poor spatiotemporal resolution. Lipid agonists are insoluble in physiological buffers and can permeate membranes to accumulate non-selectively inside cells, where they have off-target effects. To increase the spatiotemporal precision with which we can activate lipids on cells and tissues, we previously developed Optically-Cleavable Targeted (OCT)-ligands, which use protein tags (SNAP-tags) to localize a photocaged ligand on a target cellular membrane. After enrichment, the active ligand is released on a flash of light to activate nearby receptors. In this work, we expand the scope of OCT-ligand technology to target TRPV1. We synthesize a probe, OCT-CAP, that tethers to membrane-bound SNAP-tags and releases a TRPV1 agonist when triggered by UV-A irradiation. Using Ca2+ imaging and electrophysiology in HEK293T cells expressing TRPV1, we demonstrate that OCT-CAP uncaging activates TRPV1 with superior spatiotemporal precision when compared to standard diffusible ligands or photocages. This study demonstrates the versatility of OCT-ligands to manipulate ion-channel targets, and we anticipate that these tools will find many applications in controlling lipid signaling pathways in various cells and tissues. | Carmel Howe; David Icka-Araki; James Frank | Organic Chemistry; Bioorganic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aefa189138d2316182d18e/original/optical-control-of-trpv1-channels-in-vitro-with-tethered-photopharmacology.pdf |
60c73d51bdbb8932eca37c5c | 10.26434/chemrxiv.5702659.v1 | Improving the engine power of a catalytic Janus-sphere micromotor by roughening its surface | <div>
<div>
<div>
<p>Microspheres with catalytic caps have become a popular model system for studying self-
propelled colloids. Existing experimental studies involve predominantly “smooth” particle
surfaces. In this study we determine the effect of irregular surface deformations on the
propulsive mechanism with a particular focus on speed. The particle surfaces were
deformed prior to depositing a catalytic layer which resulted in the formation of nanoscopic
pillars of catalyst. These features were shown to boost speed (~2×) when the underlying
surface deformations are small (nanoscale), whilst large deformations afforded little
difference despite a substantial apparent catalytic surface area. Colloids with deformed
surfaces were more likely to display a mixture of rotational and translational propulsion than
their “smooth” counterparts. </p>
</div>
</div>
</div> | Brooke W. Longbottom; Stefan Bon | Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51bdbb8932eca37c5c/original/improving-the-engine-power-of-a-catalytic-janus-sphere-micromotor-by-roughening-its-surface.pdf |
670eda9312ff75c3a1894265 | 10.26434/chemrxiv-2024-znppb-v2 | LiProS: FAIR simulation workflow to Predict Accurate
Lipophilicity Profiles for Small Molecules | The consideration of the ionic partition coefficient in estimating pH-dependent lipophilicity profiles for small molecules has been previously emphasized through classification Machine Learning protocols. In alignment with the principles of Findable, Accessible, Interoperable, and Reusable (FAIR) data to enhance data management and sharing, we introduce LiProS: a FAIR workflow accessible via Google Colab. LiProS assists researchers in efficiently determining the appropriate pH-dependent lipophilicity profile based on the SMILES code of their molecules of interest. LiProS demonstrated its applicability in discerning the most suitable lipophilicity formalism based on small structural variations in potential cases of structure-based drug design. | Esteban Bertsch-Aguilar; Antonio Piedra; Daniel Acuña; Sebastian Suñer; Sylvana Pinheiro; William J. Zamora Ramírez | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670eda9312ff75c3a1894265/original/li-pro-s-fair-simulation-workflow-to-predict-accurate-lipophilicity-profiles-for-small-molecules.pdf |
6391775d9e687bf9da41b2ef | 10.26434/chemrxiv-2022-1n6r9 | 1,3-Difunctionalization of Vinyl Diazo Esters Enabled by a Cobalt Catalyzed C-H Activation/Carbene Migratory Insertion: A One Pot Domino Approach in a Three Component Coupling | We report herein, a modular, regioselective 1,3-oxyarylation of vinyl diazo esters via a Co-catalyzed C-H activation/carbene migratory insertion cascade. The transformation involves the formation of C-C and C-O bonds in a one-pot fashion and displays a broad substrate scope with respect to both, vinyl diazo esters as well as benzamides. The coupled products were subjected to hydrogenation to access elusive allyl alcohol scaffolds. Mechanistic investigations reveal interesting insights on the mode of transformation, involving C-H activation, carbene migratory insertion of the diazo compound followed by a radical addition as the key steps of the transformation. | Nandkishor Prakash Khot; Nitish Kumar Deo; Manmohan Kapur | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6391775d9e687bf9da41b2ef/original/1-3-difunctionalization-of-vinyl-diazo-esters-enabled-by-a-cobalt-catalyzed-c-h-activation-carbene-migratory-insertion-a-one-pot-domino-approach-in-a-three-component-coupling.pdf |
65cf2135e9ebbb4db97d52ad | 10.26434/chemrxiv-2023-1f09b-v2 | Unlocking twofold oxidation in phenothiazine polymers for application in symmetric all-organic anionic batteries | Organic redox-active polymers stand out as electrode materials for alternative energy storage devices due to their potentially higher sustainability and the variability of their structures and charge storage mechanisms. Structural design of redox-active moieties can tune the electrochemical properties of a resulting material significantly. We showcase this strategy by synthesizing a phenothiazine (PT)-based polymer, in which the commonly inaccessible second oxidation (towards the dication) is unlocked for use in conventional carbonate electrolytes by donor-substitution of the PT-core. The resulting crosslinked polymer poly(N-styryl-3,7-dimethoxy phenothiazine) (X-PSDMPT) showed excellent performance over both oxidation processes in Li half-cells, which enabled the fabrication of a first-of-its-kind symmetric all-organic anion-rocking chair battery using the first oxidation as the reaction at the negative electrode and the second oxidation at the positive electrode. The resulting full-cell delivered a specific capacity of Cspec = 60.3 mAh/g at charging rates of 1 C and a capacity retention of 40% at ultra-high rates (100 C) as well as excellent cycling stability. | Robin Wessling; Hendrik Koger; Fabian Otteny; Maximilian Schmidt; Arthur Semmelmaier; Birgit Esser | Organic Chemistry; Polymer Science; Energy; Organic Polymers; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf2135e9ebbb4db97d52ad/original/unlocking-twofold-oxidation-in-phenothiazine-polymers-for-application-in-symmetric-all-organic-anionic-batteries.pdf |
6494d7d324989702c2ce554e | 10.26434/chemrxiv-2023-3rq4x | Noncovalent modification of cycloparaphenylene by catenane formation using an active metal template strategy | Active metal template (AMT) strategy is a powerful tool for the formation of mechanically interlocked molecules (MIMs) such as rotaxane and catenane. This strategy allows the synthesis of a variety of MIMs, including π-conjugated and/or multicomponent macrocycles. Cycloparaphenylene (CPP) is an emerging molecule with unique cyclic π-conjugated structures and properties, whose diverse modifications are expected for its wide application. However, most CPP modifications require early-stage functionalization and multi-step protocols causing low yielding and less diversity. Although the direct modification of CPPs offers numerous advantages over the early-stage prefunctionalization method, the methodology is limited. Herein, we report the synthesis of a catenane consisting of [9]CPP and a 2,2´-bipyridine macrocycle as a new CPP analog that contains a reliable synthetic scaffold enabling diverse and concise post-functionalization. In accordance with the AMT strategy, [9]CPP–bipyridine catenane was successfully synthesized from cyclohexadiene-based V-shaped units and 2,2´-bipyridine macrocycle ligand through Ni-mediated aryl–aryl coupling followed by desilylation and reductive aromatization. Catalytic C–H borylation/cross-coupling and metal complexation at bipyridine macrocycle moiety, which are effective post-functionalization methods, were also demonstrated with [9]CPP–bipyridine catenane. The structural and photophysical properties of CPP–bipyridine catenane derivatives were investigated by nuclear magnetic resonance analysis, absorption/fluorescence/phosphorescence measurements, and computational studies, compared with properties of pristine [9]CPP. Single crystal X-ray structural analysis revealed that the [9]CPP–bipyridine catenane forms a tridentated complex with a Ag ion inside the CPP ring, which is attributed to the π–π interaction between the bipyridine unit in macrocycle moiety and benzene rings in [9]CPP moiety. The phosphorescence of the Ag complex of [9]CPP–bipyridine catenane was clearly enhanced by the heavy atom effect, demonstrating a new design of phosphorescence material with CPP. | Hisayasu Ishibashi; Manuel Rondelli; Hiroki Shudo; Takehisa Maekawa; Hideto Ito; Kiichi Mizukami; Nobuo Kimizuka; Akiko Yagi; Kenichiro Itami | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6494d7d324989702c2ce554e/original/noncovalent-modification-of-cycloparaphenylene-by-catenane-formation-using-an-active-metal-template-strategy.pdf |
6343fbecf764e6a4f9160dc1 | 10.26434/chemrxiv-2022-c32m5 | N-Carboxyanhydrides Directly from Amino Acids and Carbon Dioxide and their Tandem Reactions to Therapeutic Alkaloids | We report on the preparation of synthetically versatile N-carboxyanhydrides (NCAs) directly from amino acids and CO2 using n-propylphosphonic anhydride. Most of the NCAs were isolated with >95% purity after simple workup, avoiding the need for tedious purification procedures typically required using conventional methods. Because the reagents and conditions employed are mild, tandem reactions with moisture-sensitive NCAs were carried out to transform them into the medicinally active alkaloids tryptanthrin and phaitanthrin A in one pot. A qualitative analysis revealed that our NCA synthesis approach is more green than conventional methods, which all directly or indirectly use the highly poisonous gas phosgene. | Thi Tran; Yi Shen; Hieu Nguyen; Shijie Deng; Hootan Roshandel; Mason Cooper; Jose Watson; Jeffery Byers; Paula Diaconescu; Loi Do | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6343fbecf764e6a4f9160dc1/original/n-carboxyanhydrides-directly-from-amino-acids-and-carbon-dioxide-and-their-tandem-reactions-to-therapeutic-alkaloids.pdf |
60f3ebc47e679772844f812a | 10.26434/chemrxiv-2021-w7mvx | The missing piece: The Ti3C2Tx MXene structure and its role in the outstanding reversibility as negative electrode in sodium ion batteries | This study proposes the full structural characterization of the most common MXene composition, Ti3C2Tx, which presents outstanding stability as anode for sodium ion batteries (100% of capacity retention after 530 cycles with charge efficiency > 99.7%). The structural investigation is carried out with a multi-technique approach that allows to explore both the short- and long- range structure, combining the analysis of X ray absorption spectroscopy, X-ray and neutron diffraction data, and TEM images. The diffraction data have been analyzed with the approach embodied in the Faults software, that accounts for the evaluation of extended defects, thus allowing to fit, for the first time, the MXene diffraction patterns. The analysis shows that the presence of static disorder on the termination sites induces a variability in the interlayer distance which affects the electrochemical properties. | Chiara Ferrara; Antonio Gentile; Stefano Marchionna; Irene Quinzeni; Martina Fracchia; Paolo Ghigna; Simone Pollastri; Clemens Ritter; Giovanni Maria Vanacore; Riccardo Ruffo | Physical Chemistry; Materials Science; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Structure | CC BY NC 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f3ebc47e679772844f812a/original/the-missing-piece-the-ti3c2tx-m-xene-structure-and-its-role-in-the-outstanding-reversibility-as-negative-electrode-in-sodium-ion-batteries.pdf |
64926acaa2c387fa9aac4d9b | 10.26434/chemrxiv-2023-n2qsg | Geometry and Chemistry: Influence of Pore Functionalization on Molecular Transport and Diffusion in Solvent-Filled Zirconium Metal–Organic Frameworks | Post-synthetic modification (PSM) of metal–organic frameworks (MOFs) enables incorporation of diverse func-tionalities in pores for chemical separations, drug delivery, and heterogeneous catalysis. However, the effect of PSM on molecular transport, which is essential for most applications of MOFs, is rarely studied. In this paper, we used the perfluoroalkane-functionalized Zr-MOF NU-1008 as a platform to systematically interrogate transport processes and mechanisms in solvated pores. We anchored perfluoroalkanes onto NU-1008 nodes by solvent-assisted ligand incorporation (SALI-n, with n = 3, 5, 7, 9 denoting the number of fluorinated carbons). Transport of a luminescent molecule, BODIPY, through individual crystallites of four versions of methanol-filled SALI-n was monitored by confocal fluorescence microscopy as a function of time and location. In com-parison with the parent NU-1008, the diffusivity of the probe molecules within SALI-n declined by 2 to 7-fold depending on chain length and loading, presumably due to steric effects or adsorptive interactions with per-fluoroalkyl chains. Atomistic simulations were performed to uncover the microscopic behavior of BODIPY dif-fusion in SALI-n. BODIPY molecules, which preferably interact with linkers, were pushed to the interior of the channels as chain length increased, resulting in solvated diffusion and minor differences in the short-time mobility of BODIPY in SALI-n. This suggested that the observed decline of transport diffusivity in SALI-n mainly stemmed from the steric effect from these flexible chains. We anticipate that this proof-of-concept will assist in understanding how pore functionalization can physically and chemically affect mass transport in MOFs and will be useful in further guiding the design of PSM to realize the optimal performance of MOFs for various applications. | Rui Wang; Brandon Bukowski; Jiaxin Duan; Kun Zhang; Randall Snurr; Joseph Hupp | Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64926acaa2c387fa9aac4d9b/original/geometry-and-chemistry-influence-of-pore-functionalization-on-molecular-transport-and-diffusion-in-solvent-filled-zirconium-metal-organic-frameworks.pdf |
648ad469e64f843f41d06083 | 10.26434/chemrxiv-2023-t3zs0-v2 | Computational Insights into Ligand Influences on Hydrogen Generation with [Cp*Rh] Hydrides | This work reports a computational investigation of the effect of ancillary ligands on the activity of a Rh catalyst for hydrogen evolution based on the [Cp*Rh] motif (Cp* = η5-pentamethylcyclopentadienyl). Specifically, we investigate why a bipyridyl (bpy) ligand leads to H2 generation but diphenylphosphino-based (dpp) ligands do not. We compare the full ligands to simplified models and systematically vary structural features to ascertain their effect on the reaction energy of each catalytic step. The calculations, based on density functional theory, show that the main effect on reactivity is the choice of linker atom, followed by its coordination. In particular, P stabilizes the intermediate Rh-hydride species by donating electron density to the Rh, thus inhibiting the reaction towards H2 generation. Conversely N, a more electron withdrawing center, favors H2 generation at the price of destabilizing the hydride intermediate, which cannot be isolated experimentally and makes determining the mechanism for this reaction more difficult. We also find that steric effects of bulky substituents on the main ligand scaffold can lead to large effects on the reactivity, which may be challenging to fine-tune. On the other hand, structural features like the bite angle of the bidentate ligand have a much smaller impact on reactivity. Therefore, we propose that the choice of linker atom is key for the catalytic activity of this species, which can be further fine-tuned by a proper choice of electron-directing groups on the ligand scaffold. | Ty Balduf; James Blakemore; Marco Caricato | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Acid Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648ad469e64f843f41d06083/original/computational-insights-into-ligand-influences-on-hydrogen-generation-with-cp-rh-hydrides.pdf |
6498cd942e632767b0c6627d | 10.26434/chemrxiv-2023-tx97v | Potential Replacement of Toxic PVC Plasticizers with Urea, Its Derivatives, and Related Compounds
| The primary plasticizers for the world’s most plasticized polymer, poly(vinyl chloride) (PVC), are organic phthalates, this despite being categorized as probable human carcinogens by the EPA. Di-2-ethylhexyl phthalate (DEHP or DOP) is such a typical PVC plasticizer. We sought to find an alternative plasticizer that lowered the glass transition temperature (Tg) and softened PVC, but was not as harmful to the environment and for our health as the currently employed phthalate plasticizers. We recently discovered that urea (U) could complex with amorphous polymers, such as atactic poly(methyl methacrylate) (PMMA) and poly(vinyl acetate) (PVAc). Compared to neat samples, the Tgs of the PMMA-U and PVAc-U complexes were increased and decreased, respectively. However, when complexed with dimethylurea (DMU), the Tg of the PMMA-DMU complex was lowered. Since Tgs of PMMA and PVAc were lowered by either U or one of its derivatives, this prompted us to investigate whether they could interact and complex with another largely amorphous polymer PVC, that is often plasticized, to soften and lower its Tg. Shifts in the vibrational frequencies observed by Fourier-Transform Infrared spectroscopy and Differential Scanning Calorimetry thermograms indicated that U, its derivative tetramethylurea (TMU)], and the related compound Acetamide (AC) were complexing with PVC. All three complexes (PVC-U, -TMU, and –AC) showed significantly lowered Tgs. Preliminary mechanical property measurements of PVC-U and PVC-AC films showed they were softer and more pliable than PVC films. Consequently, we believe our preliminary results warrant further examination of U, AC, and TMU as potential effective and less harmful PVC plasticizers.
| Cristina Guillen Diaz; Jehlan White; Giovanni Sarnelli; Jiao Shen; Jialong Shen; Allison Folger; Jessica Pham; Sharaf Sharafim; Shanshan Li; Alan Tonelli | Polymer Science | CC BY 4.0 | CHEMRXIV | 2023-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6498cd942e632767b0c6627d/original/potential-replacement-of-toxic-pvc-plasticizers-with-urea-its-derivatives-and-related-compounds.pdf |
67dd42fa81d2151a024e71fa | 10.26434/chemrxiv-2024-twmlz-v2 | Active learning meets metadynamics: Automated workflow for reactive machine learning potentials | Atomistic simulations driven by machine learning-based potentials (MLPs) are a cost-effective alternative to ab initio molecular dynamics (AIMD). Yet, their broad applicability in reaction modelling remains hindered, in part, by the need for large training datasets that adequately sample the relevant potential energy surface, including high-energy transition state (TS) regions. To optimise dataset generation and extend the use of MLPs for reaction modelling, we present a workflow that combines automated active learning with well-tempered metadynamics, requiring no prior knowledge of TSs. Using data-efficient architectures, such as the linear Atomic Cluster Expansion, we illustrate the performance of this strategy in various organic reactions where the environment is described at different levels, including the SN2 reaction between fluoride and chloromethane in implicit water, the methyl shift of 2,2-dimethylisoindene in the gas phase, and a glycosylation reaction in explicit dichloromethane solution, where competitive pathways exist. The proposed training strategy yields accurate and stable MLPs for all three cases, highlighting its versatility for modelling reactive processes. | Valdas Vitartas; Hanwen Zhang; Veronika Juraskova; Tristan Johnston-Wood; Fernanda Duarte | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd42fa81d2151a024e71fa/original/active-learning-meets-metadynamics-automated-workflow-for-reactive-machine-learning-potentials.pdf |
60c74cf2842e65c953db33a2 | 10.26434/chemrxiv.12568595.v1 | Sea Urchin Pigments as Potential Therapeutic Agents Against the Spike Protein of SARS-CoV-2 Based on in Silico Analysis | Several studies have been published regarding the interaction between the spike protein of the novel coronavirus SARS-CoV-2 and ACE2 receptor in the host cells. In the presente work, we evaluated the in silico properties of two sea urchin pigments, Echinochrome A (EchA) and Spinochromes (SpinA) against the Spike protein (S) towards finding a potential therapeutic drug against the disease caused by the novel coronavirus (COVID-19). The best ensemble docking pose of EchaA and SpinA showed a binding affinity of -5.9 and -6.7 kcal mol-1, respectively. The linked aminoacids (T505, G496 and Y449 for EchA and Y449, Q493 and G496 for SpinA) are in positions involved in ACE2 binding in both RBDs frim SARS-CoV and SARS-CoV-2 suggesting that EchA and SpinA may interact with Spike proteins drom both viruses. The results suggest that these pigments could act as inhibitors of S protein, pointing them as antiviral drugs for SARS-CoV-2.<br /> | Elena Susana Barbieri; Tamara Rubilar; Ayelén Gázquez; Marisa Avaro; Erina Noé Seiler; Mercedes Vera-Piombo; Agustín Gittardi; Florencia Chaar; Jimena Pía Fernandez; Lucas Sepulveda | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cf2842e65c953db33a2/original/sea-urchin-pigments-as-potential-therapeutic-agents-against-the-spike-protein-of-sars-co-v-2-based-on-in-silico-analysis.pdf |
60c74e9b469df4af4ff444e2 | 10.26434/chemrxiv.12762452.v1 | Linkage Memory in Underivatized Protonated Carbohydrates | <p>Carbohydrates are
among the most complex class of biomolecules and even subtle variations in
their structures are attributed to diverse biological function. Mass
spectrometry has been essential for large scale glycomics and glycoproteomics
studies, but the gas-phase structures and sometimes anomalous fragmentation
properties of carbohydrates present longstanding challenges. Here we
investigate the gas-phase properties of a panel of isomeric protonated disaccharides
differing in their linkage configurations. Multiple conformations were evident
for most of the structures based on their fragment ion abundances by tandem
mass spectrometry, their ion mobilities in several gases, and their deuterium
uptake kinetics by gas-phase hydrogen deuterium exchange. Most notably, we find
that the properties of the Y-ion fragments are characteristically influenced by
the precursor carbohydrate’s linkage configuration. This study reveals how protonated
carbohydrate fragment ions can retain ‘linkage memory’ that provides structural
insight into their intact precursor.</p> | Abhigya Mookherjee; Sanjit S. Uppal; Taylor A. Murphree; Miklos Guttman | Mass Spectrometry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e9b469df4af4ff444e2/original/linkage-memory-in-underivatized-protonated-carbohydrates.pdf |
67116ac812ff75c3a1b9d5ef | 10.26434/chemrxiv-2024-2hxnb | Print-and-plate architected electrodes for electrochemical transformations under flow | Flow cell electrodes are typically composed of porous carbon materials, such as papers, felts, and cloths. However, their random architecture hinders fundamental characterization of electrode structure-performance relationships during in situ operation of porous electrochemical flow systems. Here, we report a “print-and-plate” method that uses high-resolution direct ink writing to produce periodic lattices followed by a two-step metal plating process to convert these lattices into highly conductive (sheet resistance 40 milli-Ohm per square) electrodes. We assessed their in operando performance in an anthraquinone disulfonic acid half-cell using electrochemical fluorescence microscopy, where output current and fluorescence intensity are in excellent agreement. We then compared the pressure drop of three electrode designs simulated with a high-fidelity numerical solution to the governing PDEs. The most efficient design was then fabricated via the print-and-plate method and confocal fluorescence microscopy was used to generate a 3D map of the state of charge (SOC) inside the working electrode. The experimental state of charge map is in good agreement with our simulations. By unlocking programmable architectures, print-and-plate electrodes offer new opportunities for fundamental investigations relating porous electrode microstructure to performance and direct replication of simulated structures. | Dylan M. Barber; Sofía Edgar; Michael S. Emanuel; Michael D. Nelwood; Bok Yeop Ahn; Benito Román-Manso; Thomas Cochard; Justin Platero; Kiana Amini; Chris H. Rycroft; Shmuel Rubinstein; Michael J. Aziz; Jennifer A. Lewis | Materials Science; Analytical Chemistry; Hybrid Organic-Inorganic Materials; Materials Processing; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67116ac812ff75c3a1b9d5ef/original/print-and-plate-architected-electrodes-for-electrochemical-transformations-under-flow.pdf |
678bf01d81d2151a02aa56f7 | 10.26434/chemrxiv-2025-mtbzl | Illuminating Lead Coordination in Perovskite Precursors via Fluorescence Spectroscopy | The properties of perovskite precursors critically determine the ultimate performance of perovskite devices, yet simple and accessible real-time precursor characterization methods remain scarce. Here, we systematically investigate the Pb coordination environment in perovskite precursors using fluorescence spectroscopy. By examining lead halide [PbX6]⁴⁻ octahedra (X = Cl, Br, I) and monitoring their luminescence under different solvents and A-site cation compositions, we unveil how [PbX6]4- distinct aggregation states give rise to characteristic fluorescence “fingerprints.” We find that halide choice, solvent coordination, and A-site cations collectively exert pronounced effects on the photoluminescence (PL) peak positions, full width at half maximum (FWHM), and photoluminescence quantum yield (PLQY). Moreover, we demonstrate that fluorescence spectroscopy can capture subtle changes in intermediate perovskite structures—including low-dimensional nanoscale clusters and the formation of higher-dimensional networks. This robust optical method offers a powerful and straightforward approach for tracing the nucleation stage, evaluating solvent-solute and solute–solute interactions, and differentiating Pb coordination states in real time. | Siwei Zhang; Jinjin Wang; Jinhui Jiang; Fulong Ma; Yifan Wang; Xinmeng Chen; Ryan KWOK ; zheng Zhao; Jacky Lam; Ben Zhong Tang | Materials Science; Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678bf01d81d2151a02aa56f7/original/illuminating-lead-coordination-in-perovskite-precursors-via-fluorescence-spectroscopy.pdf |
672cdfac5a82cea2fa64ab42 | 10.26434/chemrxiv-2024-qrnt9 | Chiral N-Alkylfluorenyl-Substituted N-Heterocyclic Carbenes in Gold(I)-Catalyzed Enantioselective Cycloisomerization of 1,6-Enynes | A series of chiral A*Flu-NHC-gold(I) complexes, where A*Flu-NHC is an N-heterocyclic carbene (imidazolin-2-ylidene or benzimidazolin-2-ylidene) bearing a chiral 9-alkyl-9-fluorenyl N-substituent and a 2,6-diisopropylphenyl or benzyl N’-substituent, were straightforward prepared in few steps from readily available 2,6-diisopropylamine, imidazole or benzimidazole. The chirality of the N-substituent lies in the presence of a chiral alcoholic alkyl chain on the fluorenyl, which results from the opening of commercially available chiral styrene oxide, yielding to a 2-hydroxy-2-phenylethyl or a 2-hydroxy-1-phenylethyl group. Four [AuCl(A*Flu-NHC)] complexes were tested as precatalysts in an enantioselective cycloisomerization of a 1,6-enyne. Notably, the best inductions were observed with the benzimidazolin-2-ylidene derivative bearing a 2-hydroxy-1-phenylethyl group on the fluorenyl ring, showing that a constrained rotation around the N-Cfluorenyl bond and a chiral center in a position of the fluorenyl ring are determining factors. Interestingly, a strong improvement of the induction with up to 72% ee was observed using AgOTf as activator. The presence of a hydrogen bond between the hydroxyl group and OTf- in the in situ generated active cationic gold(I) species probably stiffens its structure. This type of ligand-counteranion interaction represents a novel strategy for optimizing chirality transfer in asymmetric gold(I) catalysis. | Robin Heinrich; Giovany Marie-Rose; Christophe Gourlaouen; Patrick Pale; Eric Brenner; Aurélien Blanc | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672cdfac5a82cea2fa64ab42/original/chiral-n-alkylfluorenyl-substituted-n-heterocyclic-carbenes-in-gold-i-catalyzed-enantioselective-cycloisomerization-of-1-6-enynes.pdf |
6265833a11b146aa352e9cd4 | 10.26434/chemrxiv-2022-fjrqr | N-Aryl-2-iso-butylmercaptoacetamides: the discovery of highly potent and selective inhibitors of Pseudomonas aeruginosa virulence factor LasB and Clostridium histolyticum virulence factor ColH | Antimicrobial resistance is currently one of the serious global public health threats. Unlike the conventional antimicrobial drugs, antivirulence agents disarm rather than kill bacterial pathogens and therefore represent an alternative option to skirt the problem of resistance. Pseudomonas aeruginosa elastase (LasB) and Clostridium histolyticum collagenase (ColH) are extracellular bacterial proteases which play a critical role in the establishment and progression of the respective bacterial infection. In this study, we report the modulation of the α-position of the previously reported N aryl mercaptoacetamide class leading to a new type of highly potent LasB and ColH inhibitors (N aryl 2-iso-butylmercaptoacetamides). In addition to their non-toxicity and high selectivity over several human off-targets, selected derivatives may be considered unprecedented dual inhibitors of both LasB and ColH. Among the prepared derivatives, compound 37 showed the most promising properties: it had a favorable safety profile, maintained the viability and integrity of both skin- and lung-cells treated with P. aeruginosa supernatant, demonstrated in vivo efficacy in Galleria mellonella larvae, and revealed a good volume of distribution and moderate in vivo clearance in mice. Taking together, these results demonstrate that compound 37 is a promising candidate for antivirulence drug development. | Katrin Voos; Samir Yahiaoui; Jelena Konstantinović; Esther Schönauer; Alaa Alhayek; Asfandyar Sikandar; Khadidja Si Chaib; Tizian Ramspoth; Katharina Rox; Jörg Haupenthal; Jesko Köhnke; Hans Brandstetter; Christian Ducho; Anna Hirsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6265833a11b146aa352e9cd4/original/n-aryl-2-iso-butylmercaptoacetamides-the-discovery-of-highly-potent-and-selective-inhibitors-of-pseudomonas-aeruginosa-virulence-factor-las-b-and-clostridium-histolyticum-virulence-factor-col-h.pdf |
672c15fd7be152b1d045dcba | 10.26434/chemrxiv-2024-8j44h-v2 | Triethoxysilane-Catalyzed Single and Sequential Regioselective Hydroboration of Terminal Alkynes: Sustainable Access to E-Alkenylboronate and Alkyl Gem-Diboronate Esters by Non-Covalent Interactions | Triethoxysilane was found an efficient catalyst for the synthesis of E-alkenyl- and alkyldi-boronate esters by the single and sequential hydroboration of terminal alkynes respectively with pinacolborane. Mechanistic studies support that the formation of diboronate esters proceeds by a double hydroboration pathway with the steric and electronic profile at Si being key to enable the second hydroboration step. Weak non-covalent interactions involving the Si and the C≡C or C=C bonds in the alkynes or alkenylboronate esters have been identified as responsible for substrate activation toward the addition of HBPin, and the reaction of HSi(OEt)3 with HBPin as a catalyst deactivation pathway. | Harleen Kaur; Himani Ahuja; Rebeca Arevalo | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Compounds and Functional Groups; Main Group Chemistry (Inorg.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c15fd7be152b1d045dcba/original/triethoxysilane-catalyzed-single-and-sequential-regioselective-hydroboration-of-terminal-alkynes-sustainable-access-to-e-alkenylboronate-and-alkyl-gem-diboronate-esters-by-non-covalent-interactions.pdf |
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