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67d29954fa469535b90fbc4c | 10.26434/chemrxiv-2025-38lf5 | Comparative Analysis of Quantum-Mechanical and standard Single-Structure Protein-Ligand Scoring Functions with MD-Based Free Energy Calculations | Single-structure scoring functions have been considered inferior to expensive ensemble free energy methods in predicting protein-ligand affinities. We are revisiting this dogma with the recently developed semiempirical quantum-mechanical (SQM)-based scoring function, SQM2.20, comparing its performance to the standard scoring functions on one hand and state-of-the-art molecular dynamics (MD)-based free-energy methods on the other hand. The comparison is conducted on a well-established Wang dataset comprising eight protein targets with 200 ligands. The initial low correlation of SQM2.20 scores with the experimental binding affinities of R² = 0.21 was improved to R² = 0.47 by a systematic refinement of the input structures. Consequently, SQM2.20 representing accurate single-structure scoring functions, exhibited an average performance comparable to that of MD-based methods (R² = 0.52) and surpassed the performance of standard scoring functions (R² = 0.26). The per-target analysis highlighted the pivotal role of high-quality input structures on the outcomes of single-structure methods. In the instances where such structures are available, SQM2.20 scoring has been shown to rival or even exceed MD-based methods in predicting protein-ligand binding affinities, while exhibiting significantly reduced computation time. | Mehran Jalaie; Jindřich Fanfrlík; Adam Pecina; Martin Lepšík; Jan Řezáč | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d29954fa469535b90fbc4c/original/comparative-analysis-of-quantum-mechanical-and-standard-single-structure-protein-ligand-scoring-functions-with-md-based-free-energy-calculations.pdf |
645bdb95a32ceeff2d6c5429 | 10.26434/chemrxiv-2023-95cv3 | Thiourea catalysts for synthesis of Active Pharmaceutical Ingredients | Thiourea is an important building block found in several drug molecules such as thioacetazone, enzalutamide, thiocarlide etc. Thiourea derivatives have been used for activation of carbonyl and imine compounds to facilitate Michael addition reactions, and as an oxyanion stabilizer for [Ir] catalyzed amination of alcohols without using any base or acid. Chiral bifunctional thiourea catalysts have been successfully applied for asymmetric synthesis of several drug molecules. | Sharada Prasanna Swain; Kankanala Naveen Kumar; V. Ravichandiran | Biological and Medicinal Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645bdb95a32ceeff2d6c5429/original/thiourea-catalysts-for-synthesis-of-active-pharmaceutical-ingredients.pdf |
6276f20987d01f0f03dcbe10 | 10.26434/chemrxiv-2022-jt4sm | Equipping data-driven experiment planning for Self-driving Laboratories with semantic memory: case studies of transfer learning in chemical reaction optimization | Optimization strategies based on machine learning (ML), such as Bayesian optimization, show promise across the experimental sciences as a superior alternative to traditional design of experiment. Deploying ML optimization tools in R\&D operations increases productivity and efficiency, while reducing the time and cost necessary to identify new molecules, materials, and process parameters with desired target properties. Additional benefits can be captured when combining these ML algorithms with automated laboratory equipment with Atinary’s orchestration software platform SDLabs. The synergy of these technologies are referred to as Self-driving Laboratories, which hold the potential to revolutionize scientific experimentation, data collection, and materials discovery. Thus far, however, autonomous experimentation projects have not fully leveraged pre-existing knowledge and databases, often beginning from scratch and sequentially collecting measurements from new experiments. This is in stark contrast to experimentation by humans, where trained experts rely on intuition acquired from experience to select initial parameter settings for a novel experiment. In this work, we introduce Atinary’s transfer learning algorithm SeMOptt, a general-purpose Bayesian optimization framework which uses meta-/few-shot learning to efficiently transfer knowledge from related historical experiments and databases to a novel experimental campaign via a compound acquisition function. We apply SeMOpt to chemical reaction optimization, an important and challenging task in chemistry. Specifically, we perform two case studies: i) the optimization of five simulated cross-coupling reactions, which demonstrates the ability of our approach to adapt to data with unknown effects, such as the presence of a side reaction, catalyst deactivation, and measurement noise; ii) the optimization of palladium-catalyzed Buchwald-Hartwig cross-coupling of aryl halides with 4-methylaniline in the presence of potentially inhibitory additives. We find that SeMOpt accelerates the optimization rate by a factor of 10 or more compared to standard single-task ML optimizers (those without transfer learning capabilities to leverage historical experiments or databases). Moreover, these case studies show that \semopt outperforms several existing ML Bayesian optimization strategies that leverage historical data. Thus, we believe this work presents a valuable technical contribution for general-purpose optimization and makes the case to replace the traditional trial-and-error experimentation process with Self-driving Labs augmented with semantic memory. | Riley Hickman; Jurgis Ruža; Loïc Roch; Hermann Tribukait; Alberto García-Durán | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Machine Learning; Artificial Intelligence; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6276f20987d01f0f03dcbe10/original/equipping-data-driven-experiment-planning-for-self-driving-laboratories-with-semantic-memory-case-studies-of-transfer-learning-in-chemical-reaction-optimization.pdf |
66a6b90d5101a2ffa86ea278 | 10.26434/chemrxiv-2024-mx3zh | A global view of reactive coordinate manifolds from nonlinear dimensionality reduction | This work explores methods for generating low-dimensional representations of the internal molecular motion using nonlinear dimensionality reduction. The internal degrees of freedom are described as a Riemannian manifold by imposing a set of holonomic constraints. Manifold points are generated by Markov chain Monte Carlo with average-distance and Jacobian-norm weighted sampling. We investigate intrinsic dimension estimates and the reconstruction errors of low-dimensional nonlinear embeddings using Isomap and locally linear embedding methods. Using the Nyström method, the embedding of the coordinate manifold can be applied to project arbitrary molecular structures into the reduced-dimensional representation. We illustrate this approach by generating a two-dimension visualization of the critical points of the CH 2 O potential energy surface. | Dmitrij Rappoport | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a6b90d5101a2ffa86ea278/original/a-global-view-of-reactive-coordinate-manifolds-from-nonlinear-dimensionality-reduction.pdf |
6231d0da13d478fe9790a3a6 | 10.26434/chemrxiv-2022-dnl9p | Understanding the Structural Collapse During Activation of Metal–Organic Frameworks with Copper Paddlewheels | Many metal-organic frameworks (MOFs) suffer from stability issues as they can be easily amorphized from various external stimuli. In particular, it is common to observe structural collapse during the activation process of removing the synthesis solvent. In this study, we conduct high-throughput computational analysis that focuses on activation status of MOFs that possess copper paddlewheel metal nodes. From the analysis, various mechanical properties (e.g. bulk, young, and shear moduli) were found to be good predictors for collapse. Furthermore, we have identified anomalies MOFs with good mechanical stability that were previously reported to collapse. Accordingly, the activation process was re-attempted with improved techniques, and these MOFs were successfully activated. | Saad Aldin Mohamed; Yeongjin Kim; Junkee Lee; Wonyoung Choe; Jihan Kim | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231d0da13d478fe9790a3a6/original/understanding-the-structural-collapse-during-activation-of-metal-organic-frameworks-with-copper-paddlewheels.pdf |
67dc594f6dde43c9089b052e | 10.26434/chemrxiv-2025-tx3gk | An Iridium-Lewis Acid Bifunctional Catalyst Enabled Regio- and Enantioselective C(sp2)–H meta-Borylation of α,α-Diarylcarboxamides | Enantioselective C(sp²)–H activation typically relies on forming rigid five- or six-membered metallacyclic intermediates. Examples involving direct metalation at remote C(sp²)–H bonds, which require larger metallacycles, remain scarce. Herein, we report a series of 1,1′-bi-2-naphthol (BINOL)-derived chiral bipyridine ligands that enable iridium-catalyzed regio- and enantioselective meta-borylation of α,α-diarylcarboxamides generating an all-carbon quaternary stereocenter in high yields and excellent regio- and enantioselectivities. The chiral sidearm, BINOL, holds a Lewis acid aluminum center and interacts with the Lewis basic substrate to control the reaction outcome. The strategy enables the effective transfer of the chiral information, overcoming the challenges of long-range asymmetric induction, presumably due to the closer proximity of the chiral scaffold of the ligand and the (pro)stereogenic center of the substrate. The prochiral substrates were desymmetrized with up to an excellent 99% ee. An unprecedented kinetic resolution for such transformation has also been disclosed with moderate to good selectivity (s-factor up to 19.5). The synthetic utility was demonstrated through a successful scale-up experiment and subsequent transformation of the boronate ester to various functional groups. Further, mechanistic studies indicate that the catalyst primarily governs the enantioselectivity of the desymmetrization reaction, while the kinetic resolution of the mono-borylated product plays a secondary role in further enhancing the product’s enantioselectivity. Finally, density functional theory (DFT) calculations have been performed to understand the reaction mechanism and the crucial non-covalent interactions involved in the transition states that dictate observed enantioselectivity. | Netai Aditya; Shovan Das; Ayan Datta; Biplab Maji | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc594f6dde43c9089b052e/original/an-iridium-lewis-acid-bifunctional-catalyst-enabled-regio-and-enantioselective-c-sp2-h-meta-borylation-of-diarylcarboxamides.pdf |
67377a797be152b1d02ff7ef | 10.26434/chemrxiv-2024-3bh17 | Molecular diffusion enhanced performance evaluation of metal-organic frameworks for CO2 capture | Molecular diffusion is a fundamental property that limits the performance of solid sorbents in carbon dioxide capture and separation applications. Unique to each sorbent, gas diffusion is determined by the physical and chemical interactions that occur between the gas molecules and a sorbent’s surface atoms. At the process level where carbon dioxide capture performance is validated, however, simulations are typically carried out using generalized parameters that omit the structure-specific, molecular kinetics occurring in each sorbent. Here, we report process-scale simulations of carbon dioxide capture performance in metal-organic frameworks (MOF) informed by molecular adsorption predictions that represent the unique structural properties of each MOF. By evaluating a total of 10,143 MOFs for post-combustion carbon dioxide capture, we demonstrate that the inclusion of the material-specific, molecular diffusion dynamics significantly alters their simulated, process-level performance. Specifically, the inclusion of molecular diffusion relegates up to 20% of the MOF candidates of the initial rank-order while the top 27 MOFs exhibit productivity and energy consumption metrics that surpass those of all known materials used in today’s industrial applications. The method could be applied to evaluate a broader class of solid sorbents, including covalent organic frameworks and zeolites. For validation and reuse, we provide access to data and simulation code. | Rodrigo Neumann Barros Ferreira; Yogesh V. Joshi; Felipe Lopes Oliveira; Anantha Sundaram ; Ashish B. Mhadeshwar ; Jayashree Kalyanaraman; Binquan Luan; Mathias Steiner | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67377a797be152b1d02ff7ef/original/molecular-diffusion-enhanced-performance-evaluation-of-metal-organic-frameworks-for-co2-capture.pdf |
60c756d8ee301c01ebc7b435 | 10.26434/chemrxiv.14333936.v1 | Nanospheres to Nanosheets: Unfolding the Morphological Influence of Microporous Organic Polymers on Micropollutants Removal | <p>Nanoporous organic polymers with distinct
morphologies are of immense interest for a broad spectrum of applications
ranging from catalysis to molecular separation, energy storage, and energy conversion.
However, developing facile and versatile methodologies to obtain
well-orchestrated morphologies along with high specific surface area pertinent
to a specific application is still a formidable challenge. The design of the task-specific
networks can be benefitted through further
analysis of subtle variations in the polymerization
conditions. Herein, we have critically examined the fabrication of
triptycene-based hypercrosslinked polymers (HCPs), exhibiting contrasting
morphologies developed through three distinct polymerization routes.
Astonishingly, a remarkable variation of nanostructured morphology of irregular
aggregates, nanospheres, and nanosheets was noticeable in the resultant network
polymers through Friedel-Crafts crosslinking using dimethoxymethane as an
external crosslinker, Scholl coupling, and solvent knitting using
dichloromethane as an external crosslinker and solvent, respectively. The
dramatic role of reaction temperature, catalysts, and solvents driving the
formation of specific nanostructured HCPs was elucidated. Mechanistic
investigations coupled with spectroscopic and microscopic studies revealed that
the 2D-nanosheets of highly porous solvent-knitted HCP (SKTP, S<sub>BET</sub>: 2385
m<sup>2</sup> g<sup>-1</sup>) evolved through the hierarchical self-assembly of
rigid nanospheres into nanoribbons followed by the formation of nanosheets. We
further demonstrated a structure-activity correlation of the pristine as well
as post-synthetically sulfonated HCPs for the removal of a gamut of organic
micropollutants from water. Solvent
knitted triptycene polymer (SKTP) and its sulfonated derivative (SKTPS, S<sub>BET</sub>:
1444 m<sup>2</sup> g<sup>-1</sup>) owing to high specific surface areas,
excellent dispersity in water, and better accessibility of analytes through
2D-sheet like morphology exhibited ultrafast sequestration (30 s to 5 min) of an
extensive array of persistent organic micropollutants, including ionic dyes,
plastic components, steroids, antibiotic drugs, and herbicides with excellent
recyclability. The current study holds the promise that a delicate control over
the morphologies of nanoporous polymers by tuning the fabrication conditions
paves the way for the development of advanced porous materials for environmental
remediation.</p> | ARKAPRABHA GIRI; Subha Biswas; Tapas Dutta; MD. WASEEM HUSSAIN; Abhijit Patra | Fibers; Materials Processing; Organic Polymers; Polymer morphology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756d8ee301c01ebc7b435/original/nanospheres-to-nanosheets-unfolding-the-morphological-influence-of-microporous-organic-polymers-on-micropollutants-removal.pdf |
674a29525a82cea2fa71f45e | 10.26434/chemrxiv-2024-lp5c0 | Computational design of synthetic fluorescent nucleotides: tuning electron transfer and fluorescence competition with functionalization location of perylene tag | Synthetic fluorescent nucleotides (SFNs) have a wide variety of applications in biochemical tracking, imaging, and diagnostic assays. There are many SFNs in active development to enhance their fluorescence wavelengths, environmental sensitivity, photostability, and photochemical/photoswitchable properties. However, there are few systematic theoretical studies of their fluorescence properties. In this work, we apply excited state QM/MM dynamics with TDDFT to nucleic acids tagged with perylene, which is particularly photostable, fluorescent and bright (fluorescence quantum yield = 0.94) in isolation. We probe the importance of geometry, dynamics, and functionalization location of the perylene tag on the nucleobase. We confirm charge transfer pathways consistent with previous experiments within our 2 ps timescale, and note that the directionality of the electron transfer stems primarily from the nucleic acid type. Additionally, we find that the functionalization point on specific nucleobases, along with key dihedral angles and orbital overlap, directly influences the probability of charge transfer and thus the final SFN fluorescence properties. | Solomon Yamoah Effah; Mark A. Hix; Alice Walker | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674a29525a82cea2fa71f45e/original/computational-design-of-synthetic-fluorescent-nucleotides-tuning-electron-transfer-and-fluorescence-competition-with-functionalization-location-of-perylene-tag.pdf |
6544be6bc573f893f1b886e5 | 10.26434/chemrxiv-2023-k79f8-v2 | Computer Aided Recipe Design: Optimization of Polydisperse Chemical Mixtures using Molecular Descriptors | A workflow has been developed allowing for the computer aided design and optimization of reactive systems using the concept of molecular descriptor-based similarity. Unlike single-molecule models most often used in polymer informatics, an important feature of this approach is to allow for a more realistic description of reaction mixtures by accounting for polydispersity and individual chain topology.
Starting from a specific set of ingredients, i.e., a chemical recipe or formulation, simulations based on Gillespie’s kinetic Monte Carlo scheme are used to generate oligo- and polymeric reaction mixtures. By using the distance / similarity in molecular and topological descriptor space as a metric, the initial recipe is then modified iteratively using a Bayesian optimizer. Target of the optimization procedure is either another chemical recipe with different ingredients or alternatively, a set of desirable descriptors and properties. A key step of the process is the transformation of the graph representing individual polymer species as obtained by the kinetic simulation into atomistic species described as SMILES strings, which enables the computation of a rich set of additional descriptors. This rather general mapping is achieved exploiting similarities between the BNGL and the SMILES notation. The workflow is demonstrated on common polyether and polyester oligomeric systems as typically used in polymer industry, but is generally applicable to other polymer chemistries.
| Anja Massolle; Jakob Schneider; Jan Meyer; Christoph Loschen | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Reaction Engineering; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6544be6bc573f893f1b886e5/original/computer-aided-recipe-design-optimization-of-polydisperse-chemical-mixtures-using-molecular-descriptors.pdf |
66ba23c25101a2ffa818340a | 10.26434/chemrxiv-2024-kq6nx | Rhenium tricarbonyl complexes of thiazolohydrazinylidene-chroman-2,4-diones derivatives: antibacterial activity and in vivo efficacy. | Antimicrobial resistance (AMR) is a major threat to public health, causing serious issues in the successful prevention and treatment of persistent diseases. Transition metal complexes are currently evaluated for the possible development of alternative antimicrobial agents. In our ongoing efforts to identify safe and effective rhenium-based antibiotics, we have prepared a family of compounds bearing derivatives of thiazolohydrazinylidene-chroman-2,4-diones. Two compounds were identified as being active and nontoxic in vivo (zebrafish-S. aureus ATCC43300 model of infection), efficiently eradicating Methicillin-resistant Staphylococcus aureus (MRSA) infection at doses of 500 and 520 ng/mL respectively. In vitro studies indicate that, contrary to other known active rhenium complexes, the compounds do not affect peptidoglycan synthesis or compromise the integrity of the cytoplasmic membrane, but rather that bacterial membrane depolarization may play a role in their antibiotic activity. | Fatlinda Rahmani; Gozde Demirci; Nikola Plackic; Bettina Tran; Aurelien Crochet; Youri Cortat; Stefan Salentinig; Aleksandar Pavic; Fabio Zobi | Biological and Medicinal Chemistry; Inorganic Chemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ba23c25101a2ffa818340a/original/rhenium-tricarbonyl-complexes-of-thiazolohydrazinylidene-chroman-2-4-diones-derivatives-antibacterial-activity-and-in-vivo-efficacy.pdf |
60c74b5c567dfec95bec4f30 | 10.26434/chemrxiv.12318806.v1 | HYSCORE and DFT Studies of Proton-Coupled Electron Transfer in a Bioinspired Artificial Photosynthetic Reaction Center | <p>Light-driven water oxidation in algae, cyanobacteria, and higher plants generates dioxygen that supports life on Earth. The water-oxidation reaction is catalyzed by the oxygen-evolving complex (OEC) in photosystem II (PSII) that is comprised of the tetranuclear manganese calcium-oxo (Mn<sub>4</sub>CaO<sub>5</sub>) cluster, with participation of the redox-active tyrosine residue (Y<sub>Z</sub>) and a hydrogen-bonded network of amino acids and water molecules. Y<sub>Z</sub> mediates successive proton-coupled electron transfer (PCET) reactions that are essential for the oxidation of water to dioxygen at the Mn<sub>4</sub>CaO<sub>5</sub> cluster. It has been proposed that the strong hydrogen bond between Y<sub>Z</sub> and and its conjugate base, D1-His190, likely renders Y<sub>Z</sub> kinetically and thermodynamically competent leading to highly efficient water oxidation.<sup>1</sup> However, a detailed understanding of PCET at Y<sub>Z</sub> remains elusive due to the transient nature of its intermediate states. In this study, we utilize a combination of high-resolution two-dimensional (2D) <sup>14</sup>N hyperfine sublevel correlation (HYSCORE) spectroscopy and density functional theory (DFT) methods to investigate the electronic structure of a bioinspired artificial photosynthetic reaction center, benzimidazole-phenol porphyrin (BiP–PF<sub>10</sub>), that mimics the PCET process at the Y<sub>Z</sub> residue of PSII. The results of these studies underscore the importance of proximal water molecules and charge delocalization on the electronic structure of the artificial reaction center.</p> | Dalvin D Méndez-Hernández; Amgalanbaatar Baldansuren; Vidmantas Kalendra; Philip Charles; Brian Mark; William Marshall; Brian Molnar; Thomas
A. Moore; K. V. Lakshmi; Ana L. Moore | Computational Chemistry and Modeling; Energy Storage; Fuels - Energy Science; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b5c567dfec95bec4f30/original/hyscore-and-dft-studies-of-proton-coupled-electron-transfer-in-a-bioinspired-artificial-photosynthetic-reaction-center.pdf |
668528cf5101a2ffa8445941 | 10.26434/chemrxiv-2024-rt5jl | Evaluation of Hydrogen Evolution Activity by Bubbles Growth Rates as Descriptor | Evaluation of the electrocatalytic behavior in the high current density region is critical toward the applications in the industrial water electrolysis system. Here, we utilized the bubble growth rate as descriptor for evaluation of hydrogen evolution reaction. Ag electrode was selected as a model electrode. Pressure-controlled cell was used for the evaluation of the bubble behavior under the wider range in the overpotential. Hydrogen bubble evolution behavior was evaluated by video observation under electrochemical potential control. Even in the presence of the complex processes such as nucleation, growth and detachment of the bubbles, the hydrogen evolution behavior is evaluated with respect to the classical Tafel analyses even in high overpotential region. These analyses provide the methods for the rapid screening toward the material discovery of the green hydrogen production in high current density region. | Daiki Sato; Nobuaki Oyamada; Tomohiro Fukushima; Kei Murakoshi | Catalysis; Energy; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668528cf5101a2ffa8445941/original/evaluation-of-hydrogen-evolution-activity-by-bubbles-growth-rates-as-descriptor.pdf |
60c757e6bdbb898c33a3acb3 | 10.26434/chemrxiv.14413457.v2 | Electric Field Induced Biomimetic Transmembrane Electron Transport using Carbon Nanotube Porins as Bipolar Electrodes | <p>Cells modulate their homeostasis through the control of redox reactions via transmembrane electron transport systems. These are largely mediated via oxidoreductase enzymes. Their use in biology has been linked to a host of systems including reprogramming for energy requirements in cancer. Consequently, our ability to modulate membrane redox systems may give rise to opportunities to modulate underlying biology. The current work aimed to develop a wireless bipolar electrochemical approach to form on-demand electron transfer across biological membranes. To achieve this goal, we show that using membrane inserted carbon nanotube porins that can act as bipolar nanoelectrodes, we could control electron flow with externally applied electric fields across membranes. Before this work, bipolar electrochemistry has been thought to require high applied voltages not compatible with biological systems. We show that bipolar electrochemical reaction via gold reduction at the nanotubes could be modulated at low cell-friendly voltages, providing an opportunity to use bipolar electrodes to control electron flux across membranes. Our observations present a new opportunity to use bipolar electrodes to alter cell behavior via wireless control of membrane electron transfer.</p> | Jacqueline M. Hicks; Yun-Chiao Yao; Sydney Barber; Nigel Neate; Julie Watts; Aleksandr Noy; Frankie Rawson | Electrochemical Analysis; Nanocatalysis - Catalysts & Materials; Nanodevices; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757e6bdbb898c33a3acb3/original/electric-field-induced-biomimetic-transmembrane-electron-transport-using-carbon-nanotube-porins-as-bipolar-electrodes.pdf |
66220e8a21291e5d1d27408d | 10.26434/chemrxiv-2024-44ft2 | Cost-Informed Bayesian Reaction Optimization | Bayesian optimization (BO) is an increasingly popular method for optimization and development of chemical reactions. Although effective in guiding experimental design, BO does not account for experimentation costs: testing readily available reagents under different conditions might be more cost and time-effective than synthesizing or buying additional ones. To address this issue, we present cost-informed BO (CIBO), an approach tailored for the rational planning of chemical experimentation that prioritizes the most cost-effective experiments. Reagents are used only when their anticipated improvement in reaction performance sufficiently outweighs their costs. Our algorithm tracks the available reagents, including recently acquired ones, and dynamically updates their cost during the optimization. Using literature data of Pd-catalyzed reactions, we show that CIBO reduces the cost of reaction optimization by up to 90% compared to standard BO. Our approach is compatible with any type of cost, e.g., the cost of buying equipment or compounds, waiting time, and environmental or security concerns. We believe CIBO supersedes BO in chemistry and envision applications in both traditional and self-driving laboratories for experiment planning. | Alexandre Schoepfer; Jan Weinreich; Ruben Laplaza; Jerome Waser; Clemence Corminboeuf | Theoretical and Computational Chemistry; Catalysis; Machine Learning; Artificial Intelligence; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66220e8a21291e5d1d27408d/original/cost-informed-bayesian-reaction-optimization.pdf |
64931faa853d501c00458e0b | 10.26434/chemrxiv-2023-pxfjg | A Union of Distinct Azolium Salts Toward Stereoselective Synthesis of Tertiary Amine Cage Frameworks | The tertiary amine-based cage molecules are high-value intricate synthetic targets and their succinct stereoselective synthesis with broad substrate generality remains rare. Herein, we report for the first time the union of two distinct readily available azolium salts as an efficient synthetic platform to access natural products like tertiary amine cage frameworks under mild conditions. The strategy combines the masked nucleophilic and electrophilic properties of isoquinolinium salts and pyridinium salts, respectively, and avails double dearomatization guided inverse electron demand (4+2) or (3+2) annulation in a highly regio- and diastereoselective manner to materialize the nitrogen cage motifs including the aza-polycyclic core of hetisine-type alkaloids in high yields (50 examples). To streamline further, we delineated a five-component as well as a four-component one-pot sequential addition strategy without compromising the selectivity, emphasizing the efficient utilization of resources and the pot economy. Our methodology harvests two new rings and four new bonds in a single operation and transforms from flat-aromatic compounds into structurally unprecedented three-dimensional architectures with contiguous stereocenters as a single diastereomer. | Koushik Patra; Samiran Deb; Sana Mulani; Sumitava Mallik; Mahiuddin Baidya | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64931faa853d501c00458e0b/original/a-union-of-distinct-azolium-salts-toward-stereoselective-synthesis-of-tertiary-amine-cage-frameworks.pdf |
60c745c3bdbb895962a38acf | 10.26434/chemrxiv.10257686.v1 | Magnesium-Accelerated Maillard Reactions Drive Differences in Adjunct and All-Malt Brewing | Magnesium
impacts key processes in brewing including yeast metabolism and mash pH but is
typically overshadowed in brewing studies, owing to the established centrality
of calcium. Using flame atomic absorption spectroscopy (FAAS), we have
identified a 33.7% average increase in magnesium concentration in commercially
available beers brewed with 100% barley malt versus those brewed with adjunct
grains. Parallel analysis of brewing grains implicates rice in driving this
discrepancy. Given the known catalytic properties of magnesium, we investigated
its role in beer color development via Maillard chemistry using model systems
and wort (unfermented beer). Kinetic data were obtained by ultraviolet-visible
spectrometry and reaction species were identified by electrospray ionization
mass spectrometry. Magnesium accelerated Maillard chemistry in all systems in a
dose-dependent manner. It is proposed that magnesium inhibits water mobility
and serves as a Lewis acid catalyst to facilitate Maillard reactions. | Isaac Omari; Hannah Charnock; Alexa Fugina; Euan Thomson; J Scott McIndoe | Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c3bdbb895962a38acf/original/magnesium-accelerated-maillard-reactions-drive-differences-in-adjunct-and-all-malt-brewing.pdf |
60c752429abda26042f8dda5 | 10.26434/chemrxiv.13275254.v1 | Ultrasound Luminescence Chemical Imaging: A Tool for Detection of Implant Infection via Monitoring of pH Changes at Implant Surface | <p>Using ultrasound
luminescent chemical imaging (ULCI) technique we<i>
</i>imaged changes in the luminescence spectra of the ultrasound luminescent
film modulated by a pH sensitive dye coating in different pH environments through a light
scattering media. Our results show that
high resolution images can be obtained through scattering media, and that the
ultrasound luminescent film could be modulated by the pH sensitive dye.</p> | Sriparna Bhattacharya; Gretchen Schober; Unaiza Uzair; Morgan Reel; Herbert Behlow; LSSN Vigjna Abbaraju; Apparao M. Rao; Jeffrey Anker | Imaging Agents; Optical Materials; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752429abda26042f8dda5/original/ultrasound-luminescence-chemical-imaging-a-tool-for-detection-of-implant-infection-via-monitoring-of-p-h-changes-at-implant-surface.pdf |
60c753c8469df4c73ef44e13 | 10.26434/chemrxiv.13550246.v1 | Extensive Crystallographic Fragment-Based Approach to Design SARS CoV2 3CLpro Main Protease Inhibitors and Related Metadata | <p>3CLpro
is a vital protein for the SARS-CoV-2 replications and its inhibition using
small molecules is a <i>bona fide</i> approach used to develop new drugs
against the virus. In this study, a comprehensive crystallography-guided
fragment-based drug discovery approach was employed to design new inhibitors
for SARS-CoV-2 3CLpro. Protein Data Bank was explored to find small molecules
cocrystallized with SARS-CoV-2 3CLpro. The fragments sitting in the binding
pocket (87) were interactively coupled using various linkers with the intention
to get molecules having the same orientation as those of the constituting
fragments. In total, 1251 couples were prepared and converted to maximum
possible stereoisomers using LigPrep for screening using Glide (standard
precision and extra precision), AutoDock Vina, and Prime MMGBSA. Top 22 hits having
conformations similar to their cocrystallized fragments were selected for MD
simulation on Desmond. MD simulation suggested that 15 hits had conformations
very close to their constituting fragments. Results indicated that these hits
were computationally reliable and could be considered for further development. This
suggests that the study could provide a benchmark starting point for the further
design of SARS-CoV-2 3CLpro inhibitors with improved binding (data provided). <br /></p> | Sarfraz Ahmad; Iskandar Abdullah; Yean Kee Lee; Mamoona Nazir; Muhammad Usman Mirza; John F. Trant; Noorsaadah Binti Abd Rahman | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c8469df4c73ef44e13/original/extensive-crystallographic-fragment-based-approach-to-design-sars-co-v2-3c-lpro-main-protease-inhibitors-and-related-metadata.pdf |
678921316dde43c908d2f05e | 10.26434/chemrxiv-2025-9lf2t | Levodopa Sensing with a Nanosensor Array and a Low-Cost Near Infrared Readout | Near infrared (NIR) signals are beneficial for biomedical applications due to reduced light absorption,
scattering, and autofluorescence in this range, which promises higher signal-to-noise ratios (SNR).
Single-walled carbon nanotubes (SWCNTs) fluoresce in the NIR (800 nm – 1700 nm) and serve as
building blocks for biosensors. To quantify the benefits of NIR fluorescence biosensing, we simulate
the SNR considering wavelength-dependent scattering/absorption, autofluorescence, dark currents, and
excitation background. We also compare Si and InGaAs PIN phototdiodes (pn diode with an additional
intrinsic layer) as detectors for the NIR region. The simulation shows that the SNR of fluorophores in
the NIR is higher but InGaAs detectors are outperformed by Si detectors in the short NIR (< 1050 nm).
This was also validated in experiments with (6,5)-SWCNTs (emission 990 nm), showing a 1.2-fold
higher SNR for Si PIN photodiodes. Next, SWCNTs were chemically modified to create sensor
arrays/barcodes that detect levodopa. Monitoring levodopa blood levels is a crucial step for personalized
Parkinson's disease treatment. We then combine nanosensors and detectors to engineer a portable lowcost
fluorescence reader that scans (6,5)-SWCNT sensor barcodes. It detects levodopa at relevant
concentrations (10 μM) in human blood serum. Thus, we combine NIR fluorescent sensors with high
SNR and low-cost Si detectors to make use of beneficial NIR signals, which opens opportunities for
point-of-care applications. | Jan Stegemann; Matthias Niklas Augustin; Julia Ackermann; Nour el Houda Fizzi; Krisztian Neutsch ; Markus Gregor; Svenja Herbertz; Sebastian Kruss | Biological and Medicinal Chemistry; Analytical Chemistry; Nanoscience; Biochemical Analysis; Spectroscopy (Anal. Chem.); Plasmonic and Photonic Structures and Devices | CC BY 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678921316dde43c908d2f05e/original/levodopa-sensing-with-a-nanosensor-array-and-a-low-cost-near-infrared-readout.pdf |
65b30fa29138d23161c1befd | 10.26434/chemrxiv-2024-xpprm-v2 | Aza-Prilezhaev Aziridination-Enabled Multidimensional Analysis of Isomeric Lipids via High-Resolution U-Shaped Mobility Analyzer-Mass Spectrometry | Unsaturated lipids constitute a significant portion of lipidome, serving as players of multifaceted functions involving cellular signaling, membrane structure and bioenergetics. While derivatization-assisted liquid chromatography tandem mass spectrometry (LC-MS/MS) remains the gold standard technique in lipidome, it mainly faces challenges in efficiently labeling carbon-carbon double bond (C=C) and differentiating isomeric lipids in full dimension. This presents the need for new orthogonal methodologies. Herein, a metal- and additive-free aza-Prilezhaev aziridination (APA)-enabled ion mobility mass spectrometric method is developed for probing multiple levels of unsaturated lipid isomerization with high-sensitivity. Both unsaturated polar and nonpolar lipids can be efficiently labeled in the form of N-H aziridine without significant side reactions. The signal intensity can be increased by up to three orders of magnitude, achieving nM detection limit. Abundant site-specific fragmentation ions indicate C=C location and sn-position in MS/MS spectra. Better yet, stable mono-aziridination product is dominant, simplifying the spectrum for lipids with multiple double bonds. Coupled with a U-shaped mobility analyzer, identification of geometric isomers and separation of different lipid classes can be achieved. Additionally, a unique pseudo MS3 mode with UMA-QTOF MS boosts the sensitivity for generating diagnostic fragments. Overall, the current method provides a comprehensive solution for deep-profiling of lipidome, which is valuable for lipid marker discovery in disease monitoring and diagnosis. | Yuling Li; Yiming Wang; Kang Guo; Kuo-feng Tseng; Xiaoqiang Zhang; Wenjian Sun | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b30fa29138d23161c1befd/original/aza-prilezhaev-aziridination-enabled-multidimensional-analysis-of-isomeric-lipids-via-high-resolution-u-shaped-mobility-analyzer-mass-spectrometry.pdf |
60c751fe0f50db3eb63978ad | 10.26434/chemrxiv.13238996.v1 | A Technoeconomic Evaluation of the Potential of Industrial Biotechnology for the Competitive Production of Commodity and Bulk Chemicals | <div>
<div>
<div>
<p>Fermentation based bioprocesses are routinely developed for higher value products;
however, the development of bioprocesses for larger volume chemicals has lagged. While
electrification of transportation may enable significant reductions in greenhouse gas emissions in
the fuel sector, the production of chemicals, by its very nature, requires a carbon feedstock. The
utilization of more sustainable bioprocessing has unique potential in this sector. Despite the start-
up of several bio-based chemical facilities none of these
technologies have had break-out success, as measured by the construction of multiple follow on
plants. A key barrier to the wide-spread adoption of large scale bio-based processes includes the
potential financial return on capital spent on new facilities and, importantly, the comparative
financial return for bioprocesses vs. incumbent petrochemical technology. A standard metric of a
project’s financial return is the internal rate of return or IRR. Bio-based
chemical processes will likely not be extensively commercialized unless they have an IRR that is
competitive with petrochemical routes.
</p>
</div>
</div>
</div> | Jennifer Hennigan; Phillip Wagner; Chris Burk; John Efromson; Zhixia Ye; Matthew Lipscomb; Michael Lynch | Bioengineering and Biotechnology; Industrial Manufacturing; Petrochemicals | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751fe0f50db3eb63978ad/original/a-technoeconomic-evaluation-of-the-potential-of-industrial-biotechnology-for-the-competitive-production-of-commodity-and-bulk-chemicals.pdf |
60c74d2b469df41d25f44235 | 10.26434/chemrxiv.12592322.v1 | Imine Based Self-Healing Hydrogel Triggered by Periodate | <p>Design of materials with novel
sensitivities and smart behaviour is important for the development of smart
systems with automated responsiveness. We have recently reported the synthesis of
hydrogels, cross-linked by <i>N,N'</i>-diallyltartardiamide (DAT). The covalent
DAT-crosslinking points have vicinal diols which can be easily cleaved with
periodate, generating valuable a-oxo-aldehyde
functional groups, useful for further chemical modification. Based on those
findings, we envisioned that a self-healable hydrogel could be obtained by
incorporation of primary amino functional groups, from <a>2-aminoethyl
methacrylate </a>hydrochloride (AEMA), coexisting with DAT into the same
network. The a-oxo-aldehyde
groups generated after the reaction with periodate would arise in the immediate
environment of amine groups to form imine cross-links. For this purpose, DAT-crosslinked
hydrogels were synthesized and carefully characterized. The cleavage of
DAT-crosslinks with periodate promoted changes in the mechanical and swelling
properties of the materials. As expected, a self-healing behavior was observed,
based on the spontaneous formation of imine covalent bonds. In addition, we
surprisingly found a combination of fast vicinal diols cleavage and a low speed
self-crosslinking reaction by imine formation. Consequently, it was found a
time-window in which a periodate-treated polymer was obtained in a transient
liquid state, which can be exploited to choose the final shape of the material,
before automated gelling. The singular properties attained on these hydrogels
could be useful for developing sensors, actuators, among other smart systems.</p> | Alexis Wolfel; Cecilia Inés Alvarez Igarzabal; Marcelo Ricardo Romero | Hydrogels; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d2b469df41d25f44235/original/imine-based-self-healing-hydrogel-triggered-by-periodate.pdf |
64d12052dfabaf06ffe07a6d | 10.26434/chemrxiv-2023-skm06 | Downsizing Porphyrin Covalent Organic Framework Particles Using Protected Precursors for Electrocatalytic CO2 Reduction | Covalent organic frameworks (COFs) are promising electrocatalyst platforms owing to their designability, porosity, and stability. Recently, COFs with various chemical structures were developed as efficient electrochemical CO2 reduction catalysts. However, controlling the morphology of COF catalysts remains a challenge, which can limit their electrocatalytic performance even if the chemical structure is optimally designed. Especially, while metalated porphyrinoids show great promise as catalytically active COF building blocks, their intermolecular stacking and coordination interactions make it difficult to conduct solution-based COF synthesis which can control the particle size dominated by the aggregation of crystallites. In this work, we report a new synthetic methodology for rationally downsized COF catalyst particles, where a tritylated amine is employed as a novel protected precursor for COF synthesis. Trityl protection provides high solubility to a representative cobalt porphyrin precursor, while its deprotection proceeds in situ under typical solvothermal COF synthesis conditions. This colloidal deprotection–polycondensation process yields smaller COF particles with less crystallite aggregation than a conventional synthesis, maintaining crystallinity and porosity. The downsized COF particles exhibit superior catalytic performance in electrochemical CO2 reduction, with higher CO production rate and faradaic efficiency with similar stability compared to conventional COF particles. The improved performance of downsized COF particles is attributed to the higher contact area with a conductive agent. This study provides a strategy for the preparation of COF electrocatalysts with controlled morphology and enhanced performance and also reveals an important factor in the evaluation of COF electrocatalysts. | Kenichi Endo; Asif Raza; Liang Yao; Samuel Van Gele; Andrés Rodríguez-Camargo; Hugo Vignolo-González; Lars Grunenberg; Bettina Lotsch | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d12052dfabaf06ffe07a6d/original/downsizing-porphyrin-covalent-organic-framework-particles-using-protected-precursors-for-electrocatalytic-co2-reduction.pdf |
62f61df1e650df1eff236aaf | 10.26434/chemrxiv-2022-xlppr | Synthesis and Structural Verification of an ArI(OTf)2 | PhI(OTf)2 and related ArI(OTf)2 species have been incorrectly invoked as intermediates in oxidation reactions for many years. We recently established that such compounds did not yet exist but remain an attractive target. Here we describe the synthesis, isolation and structural characterization of NO2-PhI(OTf)2 which is resistant to decomposition, and also more reactive than PhI(OTf)(OAc), the species previously misidentified as PhI(OTf)2. | Jason Dutton; Tania _; Lachlan Sharp-Bucknall | Organic Chemistry; Organic Compounds and Functional Groups | CC BY NC 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f61df1e650df1eff236aaf/original/synthesis-and-structural-verification-of-an-ar-i-o-tf-2.pdf |
670f0ae3cec5d6c142449f0c | 10.26434/chemrxiv-2024-0c6zk | Accelerated discovery of solid-state electrolytes using Bayesian optimisation | Current lithium batteries do not fully meet the longevity and safety requirements of electric vehicles. Novel solid state lithium ion batteries could be a compelling solution to these problems. In this work we unravel some of these new materials with potentially high lithium conductivity by using a Bayesian optimization approach. This involves exploring the material space for new solid-state electrolyte materials with the objective of maximising - lithium diffusivity. The materials selected by the Bayesian optimisation algorithm are then examined using ab initio molecular dynamics to estimate their diffusion energy barrier. We establish that the materials are electronic insulators, a requirement in electrolyte materials, by computing the electronic bandgaps of each of the selected materials using a hybrid exchange method, and then examine the stability of the materials at the lithium metal anode interface by computing the crystal decomposition energies. Out of the selected materials, we find that Li3YBr6 has a reasonably low diffusion barrier, a high bandgap and is potentially the most stable material at the lithium metal interface. In addition to introducing stable and high-diffusivity solid-state electrolyte materials, our work presents a material discovery method that can be applied for a broad range of applications. | Sherif Tawfik; Julian Berk; Tiffany Walsh; Santu Rana; Svetha Venkatesh | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f0ae3cec5d6c142449f0c/original/accelerated-discovery-of-solid-state-electrolytes-using-bayesian-optimisation.pdf |
62df62168e16072ed6ce18c5 | 10.26434/chemrxiv-2022-thz3c | Catalytic Borylation of Dinitrogen into Borylamines and Borylhydrazines Using Rhenium Complexes under Ambient Reaction Conditions | In the presence of a catalytic amount of a dinitrogen-bridged dirhenium complex bearing PNP-type pincer ligands, an atmospheric pressure of dinitrogen reacted with potassium as a reductant and dicyclohexylchloroborane as a borylating reagent at room temperature to give 14.4 equiv of ammonia and 3.2 equiv of hydrazine based on the rhenium atom of the catalyst upon hydrolysis (20.8 equiv of fixed N atom). This result demonstrates the first successful example of the borylation of dinitrogen into ammonia and hydrazine equivalents under ambient conditions with rhenium complexes as catalysts. | Fanqiang Meng; Shogo Kuriyama; Akihito Egi; Hiromasa Tanaka; Kazunari Yoshizawa; Yoshiaki Nishibayashi | Organometallic Chemistry; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62df62168e16072ed6ce18c5/original/catalytic-borylation-of-dinitrogen-into-borylamines-and-borylhydrazines-using-rhenium-complexes-under-ambient-reaction-conditions.pdf |
67d1b84d81d2151a02225ceb | 10.26434/chemrxiv-2025-b0s6j | Direct Recycling of All-Solid-State Batteries with a Halide Solid Electrolyte via Water-based Separation: Interactions of Electrode Materials in Aqueous Li3InCl6 Solutions | Despite extensive research in the field of all-solid-state batteries, there has been limited attention to their recycling, which is crucial for achieving long-term sustainability. Different electrolyte and electrode combinations must be considered for the recycling of these batteries, each requiring a detailed investigation of potential recycling approaches. The halide-based solid electrolyte, Li3InCl6, has attracted significant attention due to its high room-temperature lithium-ion conductivity and its ability to recover its initial crystal structure after dissolution in water without significant electrochemical deterioration. This structural reversibility could potentially enable a direct recycling approach, allowing for the separation of the electrolyte from active electrode materials when dissolved in H2O. To assess the recycling compatibility, the interactions of Li3InCl6 with different electrode materials (Li4Ti5O12, LiCoO2, LiMn2O4, carbon-coated LiFePO4, LiNi0.8Mn0.1Co0.1O2 and LiNi0.8Co0.15Al0.05O2) are studied during dissolution. Interactions arising from Lewis-acid and Lewis-base reactions can be identified using a combination of X-ray diffraction, X-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry. Depending on the material combination, these interactions significantly impact the electrochemical properties | Martine Jacob; Harol Moreno Fernández; Aaron Haben; Aamir Iqbal Waidha; Simay Özel; Jan Philipp Hofmann; Ralf Kautenburger; Oliver Clemens; Kerstin Wissel | Materials Science; Inorganic Chemistry; Inorganic Acid/Base Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1b84d81d2151a02225ceb/original/direct-recycling-of-all-solid-state-batteries-with-a-halide-solid-electrolyte-via-water-based-separation-interactions-of-electrode-materials-in-aqueous-li3in-cl6-solutions.pdf |
6650a5a491aefa6ce1e38256 | 10.26434/chemrxiv-2024-fm1cl | One-step dispersive solid phase extraction (dSPE) and protein precipitation to streamline high-throughput reversed-phase metabolic phenotyping of blood samples | The chemical analysis of blood products (plasma and serum) is commonplace in metabolic phenotyping studies. The diversity of analytes in blood products characterized by varying physico-chemical properties, stability, and solubility presents an analytical challenge when attempting to achieve comprehensive analyte coverage by liquid chromatography mass spectrometry (LC-MS). While reversed-phase chromatography (RPC) of lipid analytes does not suffer from the presence of small molecules eluting mostly early in the chromatogram, the RPC-based analysis of low-molecular-weight metabolites (LMWMs) in minimally processed blood products is hindered by the presence of proteins and lipid species which fail to cleanly elute and negatively impact the assay. Here, we propose a novel application of dispersive solid phase extraction (dSPE) for the one-step single-phase depletion of proteins and lipids from plasma and serum samples without detrimental effect to the composition of LMWMs, overcoming challenges of conventional SPE. Using this approach, we demonstrate in two clinical studies the paired use of C18 RPC LC-MS for LMWM profiling enabled by dSPE and C8 RPC LC-MS for lipid profiling, providing 650+ annotated LMWMs and lipid species in plasma and serum samples. | Mark David; Elena Chekmeneva; María Gómez-Romero; Stephane Camuzeaux; Benjamin Cooper; Ada Yuen; Ravi Mehta; Shiranee Sriskandan; Miguel Reis Ferreira; Olivier Cloarec; Caroline Sands; Goncalo Correia; Zoltan Takats; Matthew Lewis | Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Separation Science | CC BY 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6650a5a491aefa6ce1e38256/original/one-step-dispersive-solid-phase-extraction-d-spe-and-protein-precipitation-to-streamline-high-throughput-reversed-phase-metabolic-phenotyping-of-blood-samples.pdf |
67611cf1fa469535b9e05258 | 10.26434/chemrxiv-2024-t6khm | Properties of o-Carborane Triads: Non-covalent σ…π Interactions and Intermolecular Charge Transfer | Two ortho-carborane triads, p-BrPh-oCB-PhEPy (3), where p-BrPh is p-bromobenzene, and DMA-oCB-PhEPy (4), where DMA is p-N,N-dimethylaniline, PhEPy is 1-(p-phenylethynyl)pyrene, were studied in solution, as single crystals, and in the solid state (photophysical measurements). Both compounds exhibited aggregation-induced emission (in solution, or in the solid state). The crystal structures of both triads exhibit interactions between pyrene units and the carborane (CB) moiety, resulting in intermolecular charge-transfer between the pyrene units and the o-carborane moiety. This interaction significantly influences crystallization, leading to distinctive crystallographic packing patterns. Remarkably, these molecules display multiple emissive species, positioning them as potential candidates for single molecule white-light emission and thermally-activated delayed fluorescence (TADF). | Yang Zhang; Roger Lalancette; Elena Galoppini | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67611cf1fa469535b9e05258/original/properties-of-o-carborane-triads-non-covalent-interactions-and-intermolecular-charge-transfer.pdf |
6634f60791aefa6ce111fedb | 10.26434/chemrxiv-2024-sfxq8 | Stereoselective N-heterocyclic-carbene-catalyzed spiroannulation as an access towards spirobenzofuranone-fused cyclohexenones | Heterocyclic spirocyclic compounds as structurally unique compounds are present in many natural or bioactive compounds. Not surprisingly, developing novel methodologies that enable stereocontrol access toward spirocyclic compounds represents an important goal in modern synthetic chemistry. The main interest is oriented toward developing methods for accessing spirooxindoles. On the other hand, the development of their oxygen-containing cousins is still overlooked. Here, we report a simple organocatalytic spiroannulation method, which provides access to spirocyclic benzofuran-2-ones. The utility of the protocol was underscored by gram-scale reaction and follow-up transformations. | Ladislav Lóška; Vojtěch Dočekal; Daniel Čermák; Simona Petrželová; Milan Pour; Ivana Císařová; Klára Konečná; Ondřej Janďourek; Jan Veselý | Organic Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6634f60791aefa6ce111fedb/original/stereoselective-n-heterocyclic-carbene-catalyzed-spiroannulation-as-an-access-towards-spirobenzofuranone-fused-cyclohexenones.pdf |
60c74d039abda25c21f8d39f | 10.26434/chemrxiv.12477776.v2 | Under Pressure: Mechanochemical Effects on Structure and Ion Conduction in the Sodium-Ion Solid Electrolyte Na3PS4 | <div>
<p>Fast-ion conductors are critical to
the development of solid-state batteries. The effects of mechanochemical
synthesis that lead to increased ionic conductivity in an archetypical
sodium-ion conductor Na<sub>3</sub>PS<sub>4</sub> are not fully understood. We
present here a comprehensive analysis based on diffraction (Bragg, pair
distribution function), spectroscopy (impedance, Raman, NMR, INS) and <i>ab-initio</i> simulations aimed at
elucidating the synthesis-property relationships in Na<sub>3</sub>PS<sub>4</sub>.
We consolidate previously reported interpretations about the local structure of
ball-milled samples, underlining the sodium disorder and showing that a local tetragonal
framework more accurately describes the structure than the originally proposed
cubic one. Through variable-pressure impedance spectroscopy measurements, we
report for the first time the activation volume for Na<sup>+</sup> migration in
Na<sub>3</sub>PS<sub>4</sub>, which is ~30% higher for the ball-milled samples.
Moreover, we show that the effect of ball-milling on increasing the ionic
conductivity of Na<sub>3</sub>PS<sub>4</sub> to ~10<sup>-4</sup> S/cm can be
reproduced by applying external pressure on a sample from conventional high
temperature ceramic synthesis. We conclude that the key effects of
mechanochemical synthesis on the properties of solid electrolytes can be
analyzed and understood in terms of pressure, strain and activation volume.</p>
</div> | Theodosios Famprikis; O. Ulas Kudu; James Dawson; Pieremanuele Canepa; François Fauth; Emmanuelle Suard; Mohamed Zbiri; Damien Dambournet; Olaf Borkiewicz; Houssny Bouyanfif; Steffen Emge; Clare P. Grey; Sorina Cretu; Jean-Nöel Chotard; Wolfgang Zeier; Saiful Islam; Christian Masquelier | Materials Processing; Solid State Chemistry; Spectroscopy (Inorg.); Energy Storage; Spectroscopy (Physical Chem.); Structure; Transport phenomena (Physical Chem.); Crystallography; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d039abda25c21f8d39f/original/under-pressure-mechanochemical-effects-on-structure-and-ion-conduction-in-the-sodium-ion-solid-electrolyte-na3ps4.pdf |
60cf3b14e2113368fddfdeae | 10.26434/chemrxiv-2021-9gx0c | Is Dissociation of HCl in DMSO Clusters Bistable? | The dissociation of HCl embedded in DMSO clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm–1 along the H–Cl bond. However, a large number of exceptions wherein the electric field values much higher than the critical electric field of 137 MV cm–1 did not result in dissociation of HCl. On the other hand, the MP2 level calculations reveal that the critical electric field for the HCl dissociation is about 181 MV cm–1 with almost no exceptions. The B3LYP-D3 calculations suggest that the dissociation of HCl embedded in DMSO clusters is bistable, which is an artefact. The answer to the question raised as the title of this paper is NO. | Debopriya Sadhukhan; Po-Jen Hsu; Jer-Lai Kuo; G Naresh Patwari | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cf3b14e2113368fddfdeae/original/is-dissociation-of-h-cl-in-dmso-clusters-bistable.pdf |
60c75573bdbb891e79a3a80f | 10.26434/chemrxiv.12917957.v2 | The Permeation Mechanism of Cisplatin through a Dioleoylphosphocholine Bilayer | The investigation of the
intermolecular interactions between platinum-based anticancer drugs and lipid
bilayers is of special relevance to unveil the mechanisms involved in different
steps of the anticancer mode of action of these drugs. We have simulated the
permeation of cisplatin through a model membrane composed of
1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling
classical molecular dynamics simulations. The initial physisorption of
cisplatin into the polar region of the lipid membrane is controlled, in a first
moment, by long-range electrostatic interactions with the choline groups and,
in a second step, by long-range electrostatic and hydrogen bond interactions
with the phosphate groups. The second half of the permeation pathway, in which
cisplatin diffuses through the nonpolar region of the bilayer, is characterized
by the drop of the interactions with the polar heads and the rise of attractive
interactions with the non-polar tails, which are dominated by van der Waals
contributions. | Lorena Ruano; Gustavo Cárdenas; Juan Jose Nogueira | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75573bdbb891e79a3a80f/original/the-permeation-mechanism-of-cisplatin-through-a-dioleoylphosphocholine-bilayer.pdf |
60c74dbbbdbb8963f8a39a43 | 10.26434/chemrxiv.12606377.v2 | Visible Light-Enabled Paternò-Büchi Reaction via Triplet Energy Transfer for the Synthesis of Oxetanes | <div>
<p>One
of the most efficient ways to synthesize oxetanes is the light-enabled [2+2]
cycloaddition reaction of carbonyls and alkenes, referred to as the
Paternò-Büchi reaction. The reaction conditions for this transformation
typically require the use of high energy UV light to excite the carbonyl,
limiting the applications, safety, and scalability. We herein report the
development of a visible light-mediated Paternò-Büchi reaction protocol that
relies on triplet energy transfer from an iridium-based photocatalyst to the
carbonyl substrates. This mode of activation is demonstrated for a variety of aryl
glyoxylates and negates the need for both, visible light-absorbing carbonyl
starting materials or UV light to enable access to a variety of functionalized
oxetanes in up to 99% yield.</p>
</div>
<br /> | Katie Rykaczewski; Corinna Schindler | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dbbbdbb8963f8a39a43/original/visible-light-enabled-paterno-buchi-reaction-via-triplet-energy-transfer-for-the-synthesis-of-oxetanes.pdf |
6601874d9138d2316140b462 | 10.26434/chemrxiv-2023-3bxp0-v2 | Solid-state vibrational circular dichroism for pharmaceutical
applications: polymorphs and cocrystal of sofosbuvir | X-ray diffraction is a commonly used technique in the pharmaceutical industry for the determination of the atomic and molecular structure of crystals. However, it is costly, sometimes time-consuming, and it requires a considerable degree of expertise. Vibrational circular dichroism (VCD) spectroscopy resolves these limitations, while also exhibiting substantial sensitivity to subtle modifications in the conformation and molecular packaging in the solid state. This study showcases VCD's ability to differentiate between various crystal structures of the identical molecule (polymorphs, cocrystals). We examined the most effective approach for producing high-quality spectra and unveiled the intricate link between structure and spectrum via quantum-chemical computations. We rigorously assessed, using alanine as a model compound, multiple experimental conditions on the resulting VCD spectra, with the aim of proposing an optimal and efficient procedure. The proposed approach, which yields reliable, reproducible and artifact-free results with maximum signal-to-noise ratio, was then validated using a set comprising of three amino acids (serine, alanine, tyrosine), one hydroxy acid (tartaric acid), and a monosaccharide (ribose) to mimic active pharmaceutical components. Finaly, the optimized approach was applied to distinguish three polymorphs of the antiviral drug sofosbuvir and its cocrystal with piperazine. Our results indicates that solid-state VCD is a prompt, cost-effective, and easy-to-use technique to identify crystal structures, demonstrating potential for application in pharmaceuticals. We also adapted the cluster and transfer approach to calculate the spectral properties of molecules in a periodic crystal environment. Our findings demonstrate that this approach reliably produces solid-state VCD spectra of model compounds. Although for large molecules with many atoms per unit cell, such as sofosbuvir, this approach has to be simplified and provides only a qualitative match, spectral calculations and energy analysis helped us to decipher the observed differences in the experimental spectra of sofosbuvir. | Jakub Kaminsky; Adam Sklenář; Lucie Růžičková; Lucie Bednárová; Markéta Pazderková; Argyro Chatziadi; Eliška Skořepová; Miroslav Šoóš; Věra Schrenková | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601874d9138d2316140b462/original/solid-state-vibrational-circular-dichroism-for-pharmaceutical-applications-polymorphs-and-cocrystal-of-sofosbuvir.pdf |
64471e4183fa35f8f632b031 | 10.26434/chemrxiv-2023-7w3rz | Oxidative instability of ionomers in hydroxide-exchange-membrane electrolyzers | Hydroxide exchange membrane (HEM) electrolyzers can produce green H2 with only earth-abundant catalysts and electrolyte-free (nominally pure) water feed, significantly decreasing system cost and complexity. However, HEM technology suffers from short lifetimes, attributed in part to poor stability of anion-exchange polymers used in the membrane and catalyst layers. Here, we use electrochemical analysis and ex-situ characterization techniques to study anion exchange polymer degradation in electrolyzers. Using multiple ionomers, catalyst layer additives, and electrolyte feed, we show anode ionomer oxidation is the dominant degradation mechanism for all HEM-based electrolyzers tested. We show improved device stability using oxidation-resistant catalyst layer binders and offer new design strategies for advanced ionomer and catalyst layer development. | Grace Lindquist; Jamie Gaitor; Willow Thompson; Valerie Brogden; Kevin Noonan; Shannon Boettcher | Catalysis; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64471e4183fa35f8f632b031/original/oxidative-instability-of-ionomers-in-hydroxide-exchange-membrane-electrolyzers.pdf |
60c756af337d6c7dece28e88 | 10.26434/chemrxiv.14283788.v1 | Operando SAXS Study of a Pt/C Fuel Cell Catalyst with an X-ray Laboratory Source | Small angle X-ray scattering (SAXS) is a powerful technique to investigate the degradation of catalyst materials. Ideally such investigations are performed <i>operando</i>, i.e., during a catalytic reaction. An example of <i>operando </i>measurements is to observe the degradation of fuel cell catalysts during an accelerated stress test (AST). Fuel cell catalysts consist of Pt or Pt alloy nanoparticles (NPs) supported on a high surface area carbon. A key challenge of operando SAXS measurements is a proper background subtraction of the carbon support to extract the information of the size distribution of the Pt NPs as a function of the AST treatment. Typically, such operando studies require the use of synchrotron facilities. The background measurement can then be performed by anomalous SAXS (aSAXS) or in a grazing incidence con-figuration. In this work we present a proof-of-concept study demonstrating the use of a laboratory X-ray diffractometer for <i>operando </i>SAXS. Data acquisition of <i>operando </i>SAXS with a laboratory X-ray diffractometer is desirable due to the general challenging and limited accessibility of synchrotron facilities. They become even more crucial under the ongoing and foreseen restrictions related to the COVID-19 pandemic. Although, it is not the aim to completely replace synchrotron-based studies, it is shown that the background subtraction can be achieved by a simple experimental consideration in the setup that can ultimately facilitate <i>operando </i>SAXS measurements at a synchrotron facility. <br /> | Johanna Schröder; Jonathan Quinson; Jacob J. K. Kirkensgaard; Matthias Arenz | Electrochemical Analysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756af337d6c7dece28e88/original/operando-saxs-study-of-a-pt-c-fuel-cell-catalyst-with-an-x-ray-laboratory-source.pdf |
6628a410418a5379b0901abd | 10.26434/chemrxiv-2024-wn0cx | Total Synthesis of Carbazomycins E and F | Total synthesis of carbazomycins E and F was achieved by double functionalization of an aryne intermediate generated from a 2-aminobiphenyl derivative. The tethered amino group underwent nucleophilic addition to the aryne intermediate to construct the carbazole skeleton. The resulting carbanion was formylated to give the multiply substituted carbazole. This formyl group caused several problems. For example, it was difficult to perform regioselective demethylation of the methoxy group proximal to the formyl group without protecting the carbazole nitrogen. In addition, the formyl group was unexpectedly reduced to give a methoxymethyl group under heating conditions with copper iodide and sodium methoxide. Oxidation of this compound in the presence of water was effective for obtaining the formylated carbazole, leading to the first total synthesis of carbazomycin F. | Yunosuke Shima; Yuxuan Feng; Atsunori Mori; Kentaro Okano | Organic Chemistry; Organometallic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6628a410418a5379b0901abd/original/total-synthesis-of-carbazomycins-e-and-f.pdf |
643d319373c6563f140899bb | 10.26434/chemrxiv-2023-lgnrm-v2 | Accelerating Reaction Network Explorations with Automated Reaction Template Extraction and Application | Autonomously exploring chemical reaction networks with first-principles methods can generate vast data. Especially autonomous explorations without tight constraints risk getting trapped in regions of reaction networks that are not of interest. In many cases, these regions of the networks are only exited once fully searched. Consequently, the required human time for analysis and computer time for data generation can make these investigations unfeasible. Here, we show how simple reaction templates can facilitate the transfer of chemical knowledge from expert input or existing data into new explorations. This process significantly accelerates reaction network explorations and improves cost-effectiveness. We discuss the definition of the reaction templates and their generation based on molecular graphs. The resulting, simple filtering mechanism for autonomous reaction network investigations is exemplified with a polymerization reaction. | Jan Patrick Unsleber | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d319373c6563f140899bb/original/accelerating-reaction-network-explorations-with-automated-reaction-template-extraction-and-application.pdf |
62ebd00fa05ea11d2b92bf2d | 10.26434/chemrxiv-2022-hq4fc-v2 | Breathing porous liquids based on responsive
metal-organic framework particles | Responsive metal-organic frameworks (MOFs) that display sigmoidal isotherms triggered by discrete gas pressure-induced structural transformations are highly promising materials for energy related applications. However, their lack of transportability via continuous flow hinders their application in systems and designs that rely on liquid agents. We herein present examples of responsive liquid systems which exhibit a breathing behaviour and show step-shaped gas sorption isotherms, akin to the distinct oxygen saturation curve of haemoglobin in blood. Dispersions of flexible MOF nanocrystals in a size-excluded silicone oil form stable porous liquids exhibiting gated uptake for CO2, propane and propylene, as characterized by sigmoidal gas sorption isotherms with distinct transition steps. In situ X-ray diffraction studies show that the sigmoidal gas sorption curve is caused by a narrow pore to large pore phase transformation to the flexible MOF nanocrystals, which respond to gas pressure despite being dispersed in silicone oil. Given the established flexible nature and tunability of a range of MOFs, these results herald the advent of breathing porous liquids whose sorption properties can be tuned rationally for a variety of technological applications. | Athanasios Koutsianos; Roman Pallach; Louis Frentzel-Beyme; Chinmoy Das; Michael Paulus; Christian Sternemann; Sebastian Henke | Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ebd00fa05ea11d2b92bf2d/original/breathing-porous-liquids-based-on-responsive-metal-organic-framework-particles.pdf |
621139e40c0bf04f51ef7ca1 | 10.26434/chemrxiv-2022-q63wc | Fast and accurate quantum mechanical modeling of large molecular systems using small basis set Hartree–Fock methods corrected with atom-centered potentials | There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine-learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bio-organic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*), and the HF-3c method. The new ACPs are trained on a very large set (73832 data points) of non-covalent properties (interaction and conformational energies) and validated additionally on a set of 32048 data points. All reference data is of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for non-covalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set DFT but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and non-covalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms. | Viki Kumar Prasad; Alberto Otero-de-la-Roza; Gino A. DiLabio | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2022-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621139e40c0bf04f51ef7ca1/original/fast-and-accurate-quantum-mechanical-modeling-of-large-molecular-systems-using-small-basis-set-hartree-fock-methods-corrected-with-atom-centered-potentials.pdf |
66d8b30d12ff75c3a167cf89 | 10.26434/chemrxiv-2024-42fn7 | HILIC-LC-MS assisted oxidative three-component on-DNA click reactions | The synthesis of DNA-encoded libraries (DELs) is a critical drug discovery technology that enables the rapid generation of billions of DNA-tagged compounds. However, a barrier to on-DNA reaction development in academic laboratories is the need for dedicated instrumentation for ion-pairing reversed-phased liquid chromatography-mass spectrometry (IP-RP LC-MS), which is required for reaction monitoring and analysis. In this work, we report the use of a hydrophilic interaction chromatography (HILIC) LC-MS method with an MS-friendly mobile phase as a convenient way to desalt and resolve crude mixtures. This approach allows academic labs to easily translate reaction and sample preparation protocols directly from the literature. HILIC-LC-MS analysis was employed in diverse oxidative three-component click reactions on-DNA that display broad substrate tolerance and observable damage to the DNA. This work not only provides access to new heterocyclic compounds libraries, but offers new tools and inspiration for continued on-DNA reaction development by academic labs due to its ease of setup and analysis. | Yun Hu; Hillary Dequina; Minxue Huang; Yun Ding; Martha Vestling; Jing Chai; Jennifer Schomaker | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d8b30d12ff75c3a167cf89/original/hilic-lc-ms-assisted-oxidative-three-component-on-dna-click-reactions.pdf |
60c74990842e658846db2d79 | 10.26434/chemrxiv.12011157.v3 | On the Generation of Novel Ligands for SARS-CoV-2 Protease and ACE2 Receptor via Constrained Graph Variational Autoencoders | SARS-CoV-2 has no known vaccine nor any effective treatment that has been released for clinical trials yet. This has ultimately paved the way for novel drug discovery approaches since although there are multiple efforts focused on drug repurposing of clinically-approved drugs for SARS-CoV-2, it is also worth considering that these existing drugs can be surpassed in effectivity by novel ones. This research focuses on the generation of novel candidate inhibitors via constrained graph variational autoencoders and the calculation of their Tanimoto similarities against existing drugs---repurposing these existing drugs and considering the novel ligands as possible SARS-CoV-2 main protease inhibitors and ACE2 receptor blockers by docking them through PyRx and ranking these ligands. Additionally, this research has successfully generated three novel ligands for the SARS-CoV-2 main protease and four novel ligands for the ACE2 receptor. | Jasper Kyle Catapang; Junie B. Billones | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74990842e658846db2d79/original/on-the-generation-of-novel-ligands-for-sars-co-v-2-protease-and-ace2-receptor-via-constrained-graph-variational-autoencoders.pdf |
60e863610387b16bf8cab482 | 10.26434/chemrxiv-2021-n35tz | Manganese-Catalyzed Dehydrogenative Silylation of Alkenes Following Two Paral-lel Pathways | We report on an additive-free Mn(I)-catalyzed dehydrogenative silylation of terminal alkenes. The most active pre-catalyst is the bench-stable alkyl bisphosphine Mn(I) complex fac-[Mn(dippe)(CO)3(CH2CH2CH3)]. The catalytic pro-cess is initiated by migratory insertion of a CO ligand into the Mn-alkyl bond to yield an acyl intermediate which un-dergoes rapid Si-H bond cleavage of the silane HSiR3 forming the active 16e- Mn(I) silyl catalyst [Mn(dippe)(CO)2(SiR3)] together with liberated butanal. A broad variety of aromatic and aliphatic alkenes was efficient-ly and selectively converted into E-vinylsilanes and allylsilanes, respectively, at room temperature. Mechanistic insights are provided based on experimental data revealing that two parallel reaction pathways are operative: an acceptorless reaction pathway involving dihydrogen release and a pathway requiring an alkene as sacrificial hydrogen acceptor. | Stefan Weber; Manual Glavic; Berthold Stöger; Ernst Pittenauer; Luis Veiros; Karl Kirchner | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e863610387b16bf8cab482/original/manganese-catalyzed-dehydrogenative-silylation-of-alkenes-following-two-paral-lel-pathways.pdf |
67979b91fa469535b90c7ef8 | 10.26434/chemrxiv-2025-wncqj | Identification of metal-organic frameworks for near practical energy limit CO2 capture from wet flue gases: an integrated atomistic and process simulation screening of experimental MOFs | Metal-organic framework (MOF) materials have attracted significant attention as solid sorbents for low energy CO2 capture with adsorption-based gas separation processes. In this work, an integrated screening workflow combining a series of atomistic and process simulations was applied to identify promising MOFs for a 4-step pressure-vacuum swing adsorption (P/VSA) process at three different CO2 flue gas compositions (6%, 15% and 35%). Starting from 55,818 unique experimentally characterized MOFs, ~19k porous MOFs were investigated via atomistic grand canonical Monte Carlo (GCMC) simulations and process optimizations. Thousands of MOFs were identified for each of the CO2 compositions tested that could achieve within 4% of the practical energy limit of dry CO2 capture for the P/VSA process while still meeting the 95% CO2 purity and 90% recovery constraints. From this pool, 526, 536 and 1,527 MOFs were subjected to the multi-component (CO2/N2/H2O) GCMC simulations at 40% relative humidity. Based on these simulations, hundreds of MOFs were identified at each CO2 composition that could retain 90% of their CO2 capture at this humidity while also adsorbing a minimal amount of water. A geometric analysis of these high performing materials revealed that narrow, straight 1D-channels, were a common structural motif for low energy wet flue gas CO2 capture with P/VSA. | Ohmin Kwan; Marco Gibaldi; Kasturi Nagesh Pai; Arvind Rajendran; Tom Woo | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Machine Learning; Process Control; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67979b91fa469535b90c7ef8/original/identification-of-metal-organic-frameworks-for-near-practical-energy-limit-co2-capture-from-wet-flue-gases-an-integrated-atomistic-and-process-simulation-screening-of-experimental-mo-fs.pdf |
63591e0dca86b8b650c41dfc | 10.26434/chemrxiv-2022-2mljk | Engineering Excitonically-Coupled Dimers in an Artificial Protein for Light Harvesting via Molecular Dynamics Simulations | In photosynthesis, pigment – protein complexes achieve outstanding photoinduced charge separation efficiencies through a set of strategies in which excited states delocalisation over multiple pigments (‘excitons’) and charge-transfer states play key roles. These concepts, and their implementation in bioinspired artificial systems, are attracting increasing attention due to the vast potential that could be tapped by realising efficient photochemical reactions. In particular, de novo designed proteins provide a diverse structural toolbox that can be used to manipulate the geometric and electronic properties of bound chromophore molecules. However, achieving excitonic and charge-transfer states requires closely spaced chromophores, a non-trivial aspect since a strong binding with the protein matrix needs to be maintained. Here, we show how a general-purpose artificial protein can be optimised via molecular dynamics simulations to improve its binding capacity of a chlorophyll derivative, achieving complexes in which chromophores form two closely spaced and strongly interacting dimers. Based on spectroscopy results and computational modelling, we propose each dimer is excitonically coupled, and displays signatures of charge-transfer state mixing. This work could open new avenues for the rational design of chromophore – protein complexes with advanced functionalities. | Mariano Curti; Valentin Maffeis; Luís G.T.A. Duarte; Saeed Shareef; Luisa X. Hallado; Carles Curutchet; Elisabet Romero | Physical Chemistry; Biophysical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63591e0dca86b8b650c41dfc/original/engineering-excitonically-coupled-dimers-in-an-artificial-protein-for-light-harvesting-via-molecular-dynamics-simulations.pdf |
60c7508b842e655b46db3a3a | 10.26434/chemrxiv.13053995.v1 | Characterizing the Turbostratic Disorder in COF-5 with NMR Crystallography | Since its initial synthesis in 2005, COF-5 has been known to have intrinsic disorder in the placement of the 2D layers relative to one another (i.e. turbostratic disorder). Prior studies of have demonstrated that the eclipsed layering found in the space group originally assigned to COF-5 (<i>P</i>6<i>/mmm</i>) is inconsistent with energy considerations. Herein it is demonstrated that eclipsed layers are also inconsistent with<sup> 13</sup>C solid-state NMR data. Crystal structure predictions are made in five alternative space groups and good agreement is obtained in <i>P</i>21<i>/m</i>, <i>Cmcm</i>, and <i>C</i>2<i>/m</i>. We posit that all three space groups are present within the stacked 2D layers and show that this conclusion is consistent with evidence from <sup>13</sup>C solid-state NMR linewidths and chemical shifts, powder x-ray diffraction data and energy considerations. An alternative explanation involving a mixture of multiple pure phases is rejected because the observed NMR spectra don’t exhibit the characteristic features of such mixed phase materials. | Giovanna Pope; Demetrius Vazquez; Fernando Uribe-Romo; James
K. Harper | Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7508b842e655b46db3a3a/original/characterizing-the-turbostratic-disorder-in-cof-5-with-nmr-crystallography.pdf |
60c755bb4c8919f3f6ad472b | 10.26434/chemrxiv.13643690.v4 | Chemoinformatic Analysis of Psychotropic and Antihistaminic Drugs in the Light of Experimental Anti-SARS-CoV-2 Activities | <div>
<div>
<div><b>Introduction:</b> There is an urgent need to identify
therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19
patients.
<p><b>Objective:</b> We proposed, before summer 2020, that cationic
amphiphilic psychotropic and
antihistaminic drugs could protect psychiatric patients from SARS-CoV-2
infection based upon clinical observations. At that time, experimental in vitro
data on SARS-CoV-2 were missing.</p>
<p><b>Methods:</b> Open
high-throughput screening results are now available at the NCATS
COVID-19 portal and it is possible to investigate again our initial hypothesis
using simple chemoinformatics approaches but this time with in vitro data on SARS-CoV-2.</p>
<p><b>Results and Discussion:</b>
We here revisit our initial hypothesis in the light of SARS-CoV-2 experimental screening results and
propose that several cationic amphiphilic psychotropic and antihistaminic drugs could protect people from SARS-CoV-2 infection; some of these
molecules have very limited adverse effects and could eventually be used as
prophylactic drugs. Further, recent analyses of electronic health records
reported by several research groups, including drug combinations, indicate that
a small list of molecules could be of interest at different stages of the
disease progression. Taken together, these observations suggest that clinical
trials are now needed to fully evaluate the potentials of these potential small
molecules broad-spectrum antiviral agents. Orally available drugs would indeed
be of outmost importance to deal with COVID-19.</p>
</div>
</div>
</div> | Bruno Villoutreix; Rajagopal Krishnamoorthy; Ryad Tamouza; Marion Leboyer; Philippe Beaune | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755bb4c8919f3f6ad472b/original/chemoinformatic-analysis-of-psychotropic-and-antihistaminic-drugs-in-the-light-of-experimental-anti-sars-co-v-2-activities.pdf |
61fab39b32e10e8988d1ea03 | 10.26434/chemrxiv-2022-vwc6l | Carbon Dioxide-Mediated Desalination | Water is arguably the most important molecule for mankind. It is becoming more critical to secure water supply, which is increasingly difficult. Desalination is an ideal solution – taking abundant seawater and turning it into potable water – however requires energy for distillation and/or membrane-based reverse osmosis (RO) processes even though the technologies were highly optimized. Modern desalination technologies, namely RO membranes, is based on the rejection of ions (mostly sodium and chloride) on the phase boundary is the main mechanism. Meanwhile, the development of supramolecular chemistry showed that selective recognition and sequestration of ions can reduce energy input by taking advantage of pre-organized “host” environments. However, this approach renders difficulties in aqueous media due to high hydration energy of ions. Moreover, a regeneration of the host can be cumbersome due to the high affinity between the host and guest ions, which is prerequisite for the recognition.
We found a completely different approach: stimuli mediated ion-exchange for removing chloride ions. This is based on well-known Solvay process where baking soda is produced from brine (NaCl + H2O), CO2 and ammonia. After ion exchange between ammonium bicarbonate and salt, ammonium chloride is produced, which is water soluble. By employing hydrophobic amines, now we can mediate Solvay-like process while removing in situ generated ammonium chloride from brine solutions and real seawater samples up to 1 L scale. This method can be applied in a continuous flow system with amine-decorated resin, producing desalinated water by using only CO2 and acid treatment to decompose produced NaHCO3. | Anand Sharadha-Ravi Ayyar; Desta Tesfay Aregawi; Allan R. Petersen; Jonas Merlin Ibsgaard Pedersen; Rasmus Refsgaard Kragh; Mohamed M. H. Desoky; Jonas Sundberg; Lars Vinum; Ji-Woong Lee | Organic Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fab39b32e10e8988d1ea03/original/carbon-dioxide-mediated-desalination.pdf |
61e5503fb815cc6726986008 | 10.26434/chemrxiv-2022-tt8fm | Cascade C‒H-Activated Polyannulations toward Ring-Fused Heteroaromatic Polymers for Intracellular pH Mapping and Cancer Cell Killing | The development of straightforward and efficient synthetic methods toward ring-fused heteroaromatic polymers with attractive functionalities has great significance in both chemistry and materials science. Herein, we develop a facile cascade C-H-activated polyannulation route that can in situ generate multiple ring-fused aza-heteroaromatic polymers from readily available monomers in an atom-economical manner. A series of complex polybenzimidazole derivatives with high absolute molecular weights of up to 24000 are efficiently produced in high yields within 2 hours. Benefiting from their unique imidazole-containing ring-fused structures with multiple aryl pendants, the obtained polymers show excellent thermal and morphological stability, good solution processability, high refractive index, small chromic dispersion, as well as remarkable acid-base-responsive fluorescence. Taking advantage of the ratiometric fluorescence response of the triphenylamine-substituted heteroaromatic polymer to pH variations, we successfully apply it as a sensitive fluorescence probe for the mapping and quantitative analysis of intracellular pH changes in live cells. Furthermore, through the simple N-methylation reaction of the ring-fused polybenzimidazoles, diverse azonia-containing polyelectrolytes are readily produced, which can efficiently kill cancer cells via the synergistic effects of dark toxicity and photo-toxicity. | Kang Wang; Saisai Yan; Ting Han; Qian Wu; Neng Yan; Miaomiao Kang; Jinyin Ge; Dong Wang; Ben Zhong Tang | Physical Chemistry; Polymer Science; Organic Polymers; Polymerization (Polymers); Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e5503fb815cc6726986008/original/cascade-c-h-activated-polyannulations-toward-ring-fused-heteroaromatic-polymers-for-intracellular-p-h-mapping-and-cancer-cell-killing.pdf |
63b47348e8047a4fb6ff0466 | 10.26434/chemrxiv-2023-v78q6 | Electrolytic seawater mineralization and how it ensures (net) carbon dioxide removal | We present the mass balances associated with carbon dioxide (CO2) removal (CDR) using seawater as both the source of reactants, and as the reaction medium via electrolysis following the “EquaticTM” (formerly known as “SeaChange”) process. The process involves the application of an overpotential that splits water to form H+ and OH– ions, producing acidity and alkalinity, i.e., in addition to gaseous co-products, at the anode and cathode, respectively. The alkalinity that results, i.e., via the “continuous electrolytic pH pump” results in the instantaneous precipitation of calcium carbonate (CaCO3), magnesium carbonates (Mg–CO3), and/or magnesium hydroxide (Mg(OH)2) depending on the CO32– activity in solution. This results in the trapping, and hence durable and permanent (at least ~10,000–100,000 years) immobilization of CO2 that was originally dissolved in water, and that is additionally drawn down from the atmosphere within: a) mineral carbonates, and/or b) as solvated bicarbonate (HCO3–) and carbonate (CO32–) ions (i.e., due to the absorption of atmospheric CO2 into seawater having enhanced alkalinity). Taken together, these actions result in the net removal of up to ≈4.6 kg of CO2 per m3 of seawater processed. Geochemical simulations quantify the extents of net CO2 removal including the dependencies on the process configuration. It is furthermore indicated that the efficiency of realkalinization of the acidic anolyte using alkaline solids depends on their H+ neutralization capacity and dissolution reactivity. We also assess changes in seawater chemistry resulting from Mg(OH)2 dissolution with emphasis on the change in its alkalinity and saturation state. Overall, this analysis provides direct quantifications of the ability of the EquaticTM process to serve as a means for technological CDR to mitigate the worst effects of accelerating climate change. | Erika La Plante; Xin Chen; Steven Bustillos; Arnaud Bouissonnie; Thomas Traynor; David Jassby; Lorenzo Corsini; Dante Simonetti; Gaurav Sant | Energy | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b47348e8047a4fb6ff0466/original/electrolytic-seawater-mineralization-and-how-it-ensures-net-carbon-dioxide-removal.pdf |
61be5fbf1e13eba7d0fe4352 | 10.26434/chemrxiv-2021-ldzzz-v3 | In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses | Proteolysis targeting chimeras (PROTACs) are bifunctional molecules that induce ubiquitination and subsequent degradation of proteins via formation of ternary complexes between an E3 ubiquitin ligase and a target protein. Rational design of PROTACs requires accurate knowledge of the native configuration of the PROTAC induced ternary complex. This study demonstrates that native and non-native ternary complex poses can be distinguished based on pose occupancy time in MD, where native poses exhibit longer occupancy times than non-native ones at both room and higher temperatures. Candidate poses are generated by MD sampling and pre-ranked by the classic MM/GBSA method. A specific heating scheme is then applied to induce ternary pose departure, generating an occupancy score and temperature score reflecting pose occupancy time and fraction. The scoring approach enables identification of the native pose in all the test systems. Beyond providing a relative rank of hypothetical poses of a given ternary system, the method could also provide empirical guidance to whether a given ternary pose is likely a native one or not. The success of the method is in part attributed to the dynamic nature of the pose departure analysis which accounts for solute entropic effects, typically neglected in the faster static pose scoring methods, while solute entropic contributions play a greater role in protein-protein interactions than in protein-ligand systems. | Junzhuo Liao; Xueqing Nie; Ilona Unarta; Spencer Ericksen; Weiping Tang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61be5fbf1e13eba7d0fe4352/original/in-silico-modeling-and-scoring-of-protac-mediated-ternary-complex-poses.pdf |
64a02bedba3e99daef57a31c | 10.26434/chemrxiv-2023-64h6v | One-pot synthesis of CRBN PROTACs via photoinduced C(sp2)–C(sp3) cross coupling and amide formation for PROTAC library synthesis | In this study, a one-pot synthesis via photoinduced C(sp2)–C(sp3) coupling followed by amide formation to access proteolysis targeting chimeras (PROTACs) was developed. The described protocol was studied on cereblon (CRBN)-based E3-ligase binders and (+)-JQ-1, a bromodomain inhibitor, to generate BET (bromodomain and extra terminal domain) targeting protein degraders. The generated PROTACs were profiled in-vitro and tested for their degradation ability with several potent candidates identified. Upfront, the individual reactions of the one-pot transformation were carefully optimized for CRBN binder functionalization and multiple heterobifunctional linker moieties were designed and synthesized. Separate scopes detailing the C(sp2)–C(sp3) coupling and one-pot PROTAC synthesis are described in this report as well as a library minituarization study showing the high-throughput compatibility. Overall, the developed protocol provides rapid access to PROTACs in a single process thereby allowing efficient generation of CRBN-based PROTAC libraries. | Christine Marie Arndt; Jacqueline Bitai; Jessica Brunner; Till Opatz; Paola Martinelli; Andreas Gollner; Kevin R Sokol; Matthias Krumb | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a02bedba3e99daef57a31c/original/one-pot-synthesis-of-crbn-prota-cs-via-photoinduced-c-sp2-c-sp3-cross-coupling-and-amide-formation-for-protac-library-synthesis.pdf |
66fe82ad12ff75c3a149f123 | 10.26434/chemrxiv-2024-fhnvl-v2 | B-Power: Investigating the Upper Limits of Enhanced Surface Reactivity in Doped MoTe2 | Transition-metal dichalcogenide (TMD) monolayers have recently gained attention, driven by their growing potential for applications in electronics, gas sensing, and electrocatalysis. However, the lack of coordinatively unsaturated surface sites makes TMDs' basal plane chemically inert, leading to technological limitations. One promising approach to increase the activity is single-atom doping. Nevertheless, the optimal doping strategies remain unclear, due to the limited understanding of the extent, selectivity, and underlying mechanisms driving this modulation. Consequently, this study aims to explore the upper limits of TMD reactivity and the underlying mechanisms by investigating boron-doped MoTe2 (B-MoTe2), which was identified as the most active candidate following systematic testing of 22 p-block dopants in our previous work. We employed density functional theory (DFT) methods to simulate the adsorption of 9 molecules: N2O, NO2, NO, N2, CO2, CO, O2, H2O, and H2, chosen to probe the available modes of interaction and their availability. Four distinctive behaviors were observed: (i) dissociation of NO2, O2, and H2, (ii) substitution of B with N atom for NO, (iii) chemisorption of CO, and H2O, and (iv) physisorption of N2 and CO2. This selectivity arises from the molecule's intrinsic bonding affinity with the dopant and the geometric constraints imposed by the sheet. When the potential of doping is effectively harnessed, the enhanced reactivity results from boron adopting more favorable orbital hybridization during molecule adsorption. Thus, B-MoTe2 becomes significantly more reactive than pristine MoTe2, exhibiting adsorption strengths several tens of times greater, which profoundly impacts the structure of the adsorbates. The presented picture is completely different from interactions on pristine MoTe2, governed by van der Waals forces. The demonstrated novel physicochemical properties underscore the potential of MoTe2 to be finely tuned for applications in catalysis and gas sensing. Moreover, the new insights offer a foundation for developing more effective doping strategies. | Piotr Radomski; Dominik Florjan; Maciej Szary | Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fe82ad12ff75c3a149f123/original/b-power-investigating-the-upper-limits-of-enhanced-surface-reactivity-in-doped-mo-te2.pdf |
6760e49cfa469535b9dbbb1d | 10.26434/chemrxiv-2024-gq9sd | An unaccounted pathway for rapid aging of atmospheric soot | Soot is a short-lived climate forcing agent whose warming potential varies significantly during its atmospheric lifetime. The particles of soot have a complex fractal morphology, but in atmospheric aerosol models they are commonly represented as spheres. We show that taking the fractal morphology into consideration significantly accelerates the rate of aging of soot aerosol in the atmosphere because concave surfaces in fractal particles promote rapid capillary condensation of trace gas chemicals produced from the photochemical oxidation of volatile organic compounds, even when vapors of such chemicals are subsaturated. Our results suggest that by capillary condensation alone these chemicals can transform hydrophobic soot particles into cloud condensation nuclei within a few hours. Additionally, capillary condensation induces compaction of fractal soot even at a moderately elevated relative humidity, changing its transport and optical properties. Representing an important mechanism of atmospheric aging, capillary condensation has a profound effect on the evolution of direct and indirect climate impacts of soot, at a higher rate than previously recognized, and hence it must be incorporated into atmospheric aerosol models to improve their predictive power. | Alexei F. Khalizov; Ella V. Ivanova; Egor V. Demidov; Ali Hasani; Jeffrey H. Curtis; Nicole Riemer; Gennady Y. Gor | Physical Chemistry; Nanoscience; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6760e49cfa469535b9dbbb1d/original/an-unaccounted-pathway-for-rapid-aging-of-atmospheric-soot.pdf |
67d9f6aa6dde43c908590f85 | 10.26434/chemrxiv-2024-zvcb4-v4 | 3D2SMILES: Translating Physical Molecular Models into Digital DeepSMILES Notations Using Deep Learning | Physical molecular models are widely used in educational settings for teaching organic and other branches of chemistry, offering an intuitive understanding of molecular structures. Conversely, while less intuitive, virtual models provide additional functionalities, such as retrieving molecular names and other properties. Currently, to the best of our knowledge, there is a gap between 3D molecular models and their digital counterparts. This paper introduces a computer vision model designed to bridge this gap by converting images of physical molecular models into their digital DeepSMILES representations. This conversion facilitates further information retrieval, enhancing educational utility. We developed synthetic and real datasets to train our model and evaluated its performance across various dataset combinations. Additionally, we attempted to improve the model’s accuracy by multi-image input and beam search. We achieved 62.0% top1 accuracy and 80.3% top-3 accuracy with beam search and multi-image input on our validation set. We also explored the model’s characteristics, such as explainability by saliency maps, and examined its calibration. We also discussed the model’s limitations and directions for future research. | Wenqi Guo; Yiyang Du; Mohamed Shehata | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d9f6aa6dde43c908590f85/original/3d2smiles-translating-physical-molecular-models-into-digital-deep-smiles-notations-using-deep-learning.pdf |
60c74065bb8c1aa6173d9dbe | 10.26434/chemrxiv.7322402.v3 | Visible-Light-Induced Oxidative Cleavage of C-C Triple Bond via Hydroamination: Direct Synthesis of Oxamates from Amines and Activated Alkynes | <p>The direct oxidative cleavage of activated
alkynes <i>via</i> hydroamination has been described using organic photocatalyst under visible-light irradiation at room temperature. In
this reaction, the single electron oxidation of an insitu formed enamines
undergo radical coupling with oxidant which finally delivers the oxamates. The key features of this photocatalytic reaction are the
mild reaction conditions, metal-free organic dye as photocatalyst, TBHP plays
dual role as “O” source and for the regeneration of photocatalyst. <br /></p> | Sharada Duddu. S; Sagar Arepally; Arumugavel Murugan; Narenderreddy Katta; Mamata Ojha | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74065bb8c1aa6173d9dbe/original/visible-light-induced-oxidative-cleavage-of-c-c-triple-bond-via-hydroamination-direct-synthesis-of-oxamates-from-amines-and-activated-alkynes.pdf |
64aff58aae3d1a7b0d9c36a9 | 10.26434/chemrxiv-2023-1hhg9-v2 | Molten Salt Synthesis of Multi-Faceted Pure-Phase Spinel LiNi0.5Mn1.5O4 Platelets | The spinel LiNi0.5Mn1.5O4 is largely studied as a positive electrode material for lithium-ion batteries, but further optimization of its properties are required to enable its commercialization. The superior electrochemical performance of the disordered polymorph of LiNi0.5Mn1.5O4 is limited by its traditional method of synthesis. This solid-state route generates impurities that reduce specific capacity and results in the formation of octahedral particles with exposed {111} facets, thus limiting explo-ration of the effects of surface orientation. In this work, we report for the first time the preparation of a disordered impurity-free LiNi0.5Mn1.5O4 with platelet-like morphology via molten salt synthesis. We discovered that these platelets exhibit multi-ple surface orientations, including {111}, {112} and six other high-indexed facets, and deliver equivalent energy storage performance to their octahedral counterpart. Such ability to tune primary particle morphology and orientation will open the gate to investigate mechanisms at the individual particle level using spectroscopy and microscopy techniques. | Gozde Oney; Jacob Olchowka; Arnaud Demortière; François Weill; Laurence Croguennec | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64aff58aae3d1a7b0d9c36a9/original/molten-salt-synthesis-of-multi-faceted-pure-phase-spinel-li-ni0-5mn1-5o4-platelets.pdf |
6363d2ec55a081ac00d0fa24 | 10.26434/chemrxiv-2022-0dknf-v3 | Simulations Explain the Swelling Behavior of Hydrogels with Alternating Neutral and Weakly Acidic Blocks
| We used computer simulations to study the equilibrium swelling of weak (pH-responsive) polyelectrolyte hydrogels as a function of pH and salt concentration in a supernatant solution. Our simulations were designed to represent recently synthesized gels composed of tetrapoly-(acrylic acid) and tetrapoly(ethylene glycol) stars. To model the ionization equilibrium of the weak acid groups and the exchange of small ions with the reservoir, we applied the recently developed Grand-Reaction Monte-Carlo method. We showed that the ionization of these gels as a function of the pH significantly deviates from the ideal Henderson-Hasselbalch equation due to two main contributions: (1) electrostatic interactions and (2) Donnan partitioning of small ions. The first contribution dominates in the gels composed of alternating neutral and acidic blocks, contrasting with our previous observations that both contributions are comparably strong in hydrogels composed of homogeneously distributed weak acid groups. We also critically examined the counterion condensation argument, previously invoked to explain why the experimentally observed swelling was lower than predicted by theory. Thus, a detailed analysis of the simulations allowed us to understand which of the above effects dominates in different systems and why, thereby allowing us to identify the correct physical origin of the deviations from ideal swelling. Such an understanding is important not only for correctly interpreting experimental measurements but also for designing polyelectrolyte gels tailored to exhibit specific swelling response to pH and salt concentration. | David Beyer; Peter Košovan; Christian Holm | Theoretical and Computational Chemistry; Physical Chemistry; Polymer Science; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6363d2ec55a081ac00d0fa24/original/simulations-explain-the-swelling-behavior-of-hydrogels-with-alternating-neutral-and-weakly-acidic-blocks.pdf |
60c747ecbb8c1a6b553dab84 | 10.26434/chemrxiv.11691714.v2 | Engineering High Energy Density Sodium Battery Anodes for Improved Cycling with Superconcentrated Ionic Liquid Electrolytes | <div>
<div>
<div>
<p>Non-uniform metal deposition and dendrite formation in high density energy storage
devices reduces the efficiency, safety, and life of batteries with metal anodes.
Superconcentrated ionic liquid (IL) electrolytes (e.g. 1:1 IL:alkali ion) coupled with
anode preconditioning at more negative potentials can completely mitigate these
issues, and therefore revolutionize high density energy storage devices. However, the
mechanisms by which very high salt concentration and preconditioning potential
enable uniform metal deposition and prevent dendrite formation at the metal anode
during cycling are poorly understood, and therefore not optimized. Here, we use
</p>
</div>
</div>
</div>
<div>
<div>
<div>
<p>atomic-force microscopy and molecular dynamics simulations to unravel the influence
of these factors on the interface chemistry in a sodium electrolyte, demonstrating how
a molten salt like structure at the electrode surface results in dendrite free metal
cycling at higher rates. Such a structure will support the formation of a more
favorable solid electrolyte interphase (SEI) accepted as being a critical factor in
stable battery cycling. This new understanding will enable engineering of efficient
anode electrodes by tuning interfacial nanostructure via salt concentration and high
voltage preconditioning.
</p>
</div>
</div>
</div> | Dmitrii A. Rakov; Fangfang Chen; Shammi A. Ferdousi; Hua Li; Thushan Pathirana; Alexandr Simonov; Patrick
C. Howlett; Rob Atkin; Maria Forsyth | Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747ecbb8c1a6b553dab84/original/engineering-high-energy-density-sodium-battery-anodes-for-improved-cycling-with-superconcentrated-ionic-liquid-electrolytes.pdf |
67a10cc981d2151a0210d70e | 10.26434/chemrxiv-2025-dz1fs | The Effect of Monolayers on Atomic-scale Friction in Aprotic Electrolytes: Underpotential Deposition (UPD) of Silver on I-modified Au(111) | Using lateral force microscopy (LFM), we investigate the frictional behavior on I-modified Au(111) during Ag underpotential deposition (UPD) in aprotic electrolytes. Force-separation (FS) curves clearly show that the solvent forms about 3 ordered layers near the iodine adlayer independent of potential. These ordered layers of solvent can be readily pushed away by the AFM tip. Regardless of solvent, transitions of the lateral adsorbate structure have been observed depending on potential and normal load, respectively. These structural transitions indicate that the structure of adsorbed iodine is very sensitive to the Ag coverage, and the tip penetrates the adsorbed iodine as normal load increases. Friction forces as function of normal load convincingly show the influence of the tip penetration on friction; plowing of the tip in the adsorbate layer leads to an additional friction force depending on potential and solvent. With increasing normal load in Ag+ containing tetraglyme (G4), friction increases steeply as the sliding tip penetrates the iodine adsorbed on Ag adlayers, in agreement with the results in aqueous electrolyte. Furthermore, friction increases more drastically as the concentration of water increases. Considering the high friction on Ag monolayer after the penetration into the iodine, there are two possible causes: 1) the reduced mobility of the iodine on Ag adlayer and 2) the interaction between water adsorbed on the tip and Ag adlayers. However, in Ag+ containing PC, in spite of the penetration of the tip into the iodine adlayer, friction force dependence on load does not show a clear distinction between gold and silver substrates. | Inhee Park; Florian Hausen; Helmut Baltruschat | Physical Chemistry; Nanoscience; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a10cc981d2151a0210d70e/original/the-effect-of-monolayers-on-atomic-scale-friction-in-aprotic-electrolytes-underpotential-deposition-upd-of-silver-on-i-modified-au-111.pdf |
60c74c28bdbb8948fba3970d | 10.26434/chemrxiv.11901996.v3 | Hidden Assumption of Gouy-Chapman-Stern Model | Understanding the double layer at the electrode-electrolyte interface is a long-standing challenge in electrochemistry. The orthodox Gouy-Chapman-Stern (GCS) model and its many derivatives invariably picture the double layer as a serial connection of a compact layer and a diffuse layer. We unravel herein that the serial connection tacitly prescribes a zero potential gradient at the solution-side boundary, which is, rigorously speaking, invalid. The bearing of this problematic assumption is pinpointed by comparing the double-layer impedance, which is analytically solved at the potential of zero charge, derived from the original and amended GCS models. Specifically, in the amended GCS model, the capacitance of the compact layer now shows frequency dispersion. The deviation between the original and amended models is greater when the double layer is confined in narrower space. | Chenkun Li; Jun Huang | Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c28bdbb8948fba3970d/original/hidden-assumption-of-gouy-chapman-stern-model.pdf |
65a3cefa66c13817296a7eaf | 10.26434/chemrxiv-2024-vlxbt | Low-toxicity nanoMolar scaffolds with hundreds of variants generated by computational co-evolution into prokaryotic potassium channel cavities | Human potassium channels (Kir) are implicated in numerous dysfunction diseases genetically affecting cardiovascular, skeletal-muscle and/or synaptic-neuronal functions. Variations in Kir sequences, organ distribution differences and toxicity of some of their known inhibitors, require alternative drugs to interfere specifically with each human Kir molecular species. In this work, a prokaryotic asymmetric transmembrane homotetramer potassium (K+) channel protein highly homologous to Kirs has been used as their model. Computational methods combining molecular parent co-evolutions confirmed by consensus docking, were explored as possible prove-of-concept to generate rather than screen for numerous KcsA docking-ligands. The explorations of the KcsA central cavity and of their interface lipid-binding shallow-grooves, predicted highly specific novel scaffolds with low-toxicity risks, displaying hundreds of molecular variations of new scaffolds within nanoMolar-ranged affinities. Experimental validation and/or additional computational research on human Kirs could be attempted in the future. | julio coll | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a3cefa66c13817296a7eaf/original/low-toxicity-nano-molar-scaffolds-with-hundreds-of-variants-generated-by-computational-co-evolution-into-prokaryotic-potassium-channel-cavities.pdf |
6710691112ff75c3a1a71db4 | 10.26434/chemrxiv-2024-l6k59-v2 | Effects of Germicidal Far-UVC on Indoor Air Quality in a Conference Room | The application of 222 nm light from KrCl excimer lamps (GUV222 or Far-UVC) is a promising approach to reduce the indoor transmission of airborne pathogens, including the SARS-CoV-2 virus. GUV222 inactivates airborne pathogens and is believed to be relatively safe for human skin and eye exposure. However, UV light initiates photochemical reactions which may negatively impact indoor air quality. We conducted a series of experiments to assess the formation of ozone (O3), and resulting formation of secondary organic aerosols (SOA), induced by commercial far-UVC devices in an office environment (small conference room) with an air exchange rate of 1.3 h-1. We studied scenarios with a single far-UVC lamp, corresponding to the manufacturer’s recommendations for disinfection of a space that size, and with four far-UVC lamps, to test conditions of greater far-UVC fluence. The single lamp did not significantly impact O3 or fine particulate matter levels in the room. Consistent with previous studies in the literature, the higher far-UVC fluences lead to increases in O3 of 5 to 10 ppb above background, and minor increases in particulate matter (16% ± 10 % increase in particle number count). The use of far-UVC at minimum intensities required for disinfection, and in conjunction with adequate ventilation rates (e.g. ANSI/ASHRAE recommendations), may allow the reduction of airborne pathogen levels while minimizing the formation of air pollutants in furnished indoor environments. | Farideh Narouei; Zifeng Tang; Shiqi Wang; Raabia Hashmi; David Welch; Sandhya Sethuraman; David Brenner; V. Faye McNeill | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710691112ff75c3a1a71db4/original/effects-of-germicidal-far-uvc-on-indoor-air-quality-in-a-conference-room.pdf |
66a8e186c9c6a5c07a7f6966 | 10.26434/chemrxiv-2024-gt72l | Towards Global Feasibility Prediction and Robustness Estimation of Organic Chemical Reactions with High Throughput Experimentation Data and Bayesian Deep Learning | Predicting organic reaction feasibility and robustness against environmental factors is challenging. We address this issue by integrating high throughput experimentation (HTE) and Bayesian deep learning. Diverging from existing HTE studies focused on niche chemical spaces, in this work, our in-house HTE platform conducted 11,669 distinct acid amine coupling reactions in 156 working hours, yielding the most extensive single HTE dataset at a volumetric scale for industrial delivery. Our Bayesian neural network model achieved a new benchmark for prediction accuracy of 89.48% for reaction feasibility. Furthermore, our fine-grained uncertainty disentanglement enables efficient active learning, reducing 80% of data requirements. Our uncertainty analysis effectively identifies out-of-domain reactions and evaluates reaction robustness for scaling up, offering a practical framework for navigating chemical spaces and designing highly robust industrial processes. | Haowen Zhong; Yilan Liu; Haibin Sun; Yuru Liu; Rentao Zhang; Baochen Li; Yi Yang; Yuqing Huang; Fei Yang; Frankie Mak; Klement Foo; Sen Lin; Tianshu Yu; Peng Wang; Xiaoxue Wang | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8e186c9c6a5c07a7f6966/original/towards-global-feasibility-prediction-and-robustness-estimation-of-organic-chemical-reactions-with-high-throughput-experimentation-data-and-bayesian-deep-learning.pdf |
61adcee3704d055242420481 | 10.26434/chemrxiv-2021-xvcwb | NeuralTPL: a deep learning approach for efficient reaction
space exploration | Computer-aided synthesis planning (CASP) has been helping chemists to synthesize novel molecules
at an accelerated pace. The recent integration of deep learning with CASP has opened up new avenues
for digitizing and exploring the vastly unknown chemical space, and has led to high expectations for
fully automated synthesis plannings using machine-discovered novel reactions in the "future". Despite
many progresses in the past few years, most deep-learning methods only focus on improving few aspects
of CASP (e.g., top-k accuracy). In this work, we target specifically the efficiency of reaction space
exploration and its impact on CASP. We propose NeuralTPL, a template-oriented generative approach,
that performs impressively across a range of evaluation metrics including chemical validity, diversity, and
novelty for various tasks in CASP. In addition, our Transformer-based model bears the potential to learn
the core reaction transformation as it can efficiently explore the reaction space. We then perform several
experiments and conduct a thorough analysis regarding the three metrics and demonstrate its chemical
value for improving the existing deep-learning-driven CASP algorithms. | Yue Wan; Xin Li; Xiaorui Wang; Xiaojun Yao; Benben Liao; Cheng-Yu Hsieh; Shengyu Zhang | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY NC 4.0 | CHEMRXIV | 2021-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61adcee3704d055242420481/original/neural-tpl-a-deep-learning-approach-for-efficient-reaction-space-exploration.pdf |
656cd7d2cf8b3c3cd7b436a5 | 10.26434/chemrxiv-2023-zrgkp | Machine learning assisted hit prioritization for high throughput screening in drug discovery | Efficient prioritization of bioactive compounds from high throughput screening campaigns is a fundamental challenge for accelerating drug development efforts. In this study, we present the first data-driven approach to simultaneously detect assay interferents and prioritize true bioactive compounds. By analyzing the learning dynamics during training of a gradient boosting model on noisy high throughput screening data using a novel formulation of sample influence, we are able to distinguish between compounds exhibiting the desired biological response and the ones producing assay artifacts. Therefore, our method enables false positive and true positive detection without relying on prior screens or assay interference mechanisms, making it applicable to any high throughput screening campaign. We demonstrate that our approach consistently excludes assay interferents with different mechanisms and prioritizes biologically relevant compounds more efficiently than all tested baselines, including a retrospective case study simulating its use in a real drug discovery campaign. Finally, our tool is extremely computationally efficient, requiring less than 30 seconds per assay on low-resource hardware. As such, our findings show that our method is an ideal addition to existing false positive detection tools and can be used to guide further pharmacological optimization after high throughput screening campaigns. | Davide Boldini; Lukas Friedrich; Daniel Kuhn; Stephan Sieber | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656cd7d2cf8b3c3cd7b436a5/original/machine-learning-assisted-hit-prioritization-for-high-throughput-screening-in-drug-discovery.pdf |
60c74128702a9bce7818a1f9 | 10.26434/chemrxiv.7987247.v1 | Revealing the Elemental Distribution Within Latent Fingermarks Using Synchrotron Sourced X-Ray Fluorescence Microscopy | <div><div><div><p>Fingermarks are an important form of crime-scene trace evidence; however, their usefulness may be hampered by a variation in response or a lack of robustness in detection methods. Understanding the chemical composition and distribution within fingermarks may help explain variation in latent fingermark detection with existing methods and identify new strategies to increase detection capabilities. The majority of research in the literature describes investigation of organic components of fingermark residue, leaving the elemental distribution less well understood. The relative scarcity of information regarding the elemental distribution within fingermarks is in part due to previous unavailability of direct, micron resolution elemental mapping techniques. This capability is now provided at third generation synchrotron light sources, where X-ray Fluorescence Microscopy (XFM) provides micron or sub-micron spatial resolution and direct detection with sub-μM detection limits. XFM has been applied in this study to reveal the distribution of inorganic components within fingermark residue, including endogenous trace metals (Fe, Cu, Zn), diffusible ions (Cl-, K+, Ca2+), and exogeneous metals (Ni, Ti, Bi). This study incorporated a multi-modal approach using XFM and Infrared Microspectroscopy (IRM) analyses to demonstrate co-localisation of endogenous metals within the hydrophilic organic components of fingermark residue. Additional experiments were then undertaken to investigate how sources of exogenous metals (e.g. coins and cosmetics) may be transferred to, and distributed within latent fingermarks. Lastly, this study reports a preliminary assessment of how environmental factors such as exposure to aqueous environments may effect elemental distribution within fingermarks. Taken together, the results of this study advance our current understanding of fingermark composition and its spatial distribution of chemical components, and may help explain detection variation observed during detection of fingermarks using standard forensic protocols.</p></div></div></div> | Rhiannon Boseley; Buddhika Dorakumbura; Daryl L. Howard; martin de jonge; Mark J. Tobin; Jitraporn Vongsvivut; tracey ho; Wilhelm van Bronswijk; Mark J. Hackett; Simon W. Lewis | Analytical Chemistry - General; Biochemical Analysis; Imaging; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74128702a9bce7818a1f9/original/revealing-the-elemental-distribution-within-latent-fingermarks-using-synchrotron-sourced-x-ray-fluorescence-microscopy.pdf |
638ed50d14d92d3678a290db | 10.26434/chemrxiv-2022-qn64t | Topologically Engineering of π-Conjugated Macrocycles: Tunable Emissions and Photochemical Reactions | The topology of conjugated macrocycles had significant impacts on their photo-physical and photo-chemical properties. Herein, a series of π-conjugated macrocycles with diverse topology were synthesized via intramolecular McMurry coupling. Their chemical structure and macrocyclic topology were unambiguously confirmed via NMR, MALDI-TOF mass spectra, and scanning tunneling microscopy (STM). Depending on the structural topology and structural rigidity, these macrocyclic luminogens display obviously distinctive emission behavior and photochemical reactions in the solution and in the solid state. Monocyclic MST with lower strain was more susceptible to intramolecular motions, and thus exhibited aggregation-induced emission properties. After UV light irradiation, MST was also vulnerable to undergo photo-cyclization in solution and triplet sensitizer promoted photo-dimerization, and yielded the anti-dimer via triplet excimer on the HOPG surface confirmed by STM investigation. By contrast, highly constrained bis-macrocyclic luminogens DMTPE, featured with high emission quantum yields of 68% both in solution and in the solid state, was relatively inert to photochemical reactions and yield syn-dimer on the surface via singlet excimer involved [2+2] photo-dimerization. | Yi Liu; Yang Feng; Peng Lei; Xindong Liu; Xiaoqing Liu; Siqi Zhang; Bin Tu; Chen Chen; Qing-Dao Zeng; Lei Wang | Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Self-Assembly; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638ed50d14d92d3678a290db/original/topologically-engineering-of-conjugated-macrocycles-tunable-emissions-and-photochemical-reactions.pdf |
60c74822842e655062db2b10 | 10.26434/chemrxiv.11859183.v1 | Probing Competing Relaxation Pathways in Malonaldehyde with Transient X-Ray Absorption Spectroscopy | <p>Excited-state intramolecular hydrogen transfer (ESIHT) is a fundamental reaction relevant to chemistry and biology. Malonaldehyde is the simplest example of ESIHT, yet only little is known experimentally about its excited-state dynamics. Several competing relaxation pathways have been proposed, including internal conversion mediated by ESIHT and C=C torsional motion as well as intersystem crossing. We perform an in silico transient X-ray absorption spectroscopy (TRXAS) experiment at the oxygen K-edge to investigate its potential to monitor the proposed ultrafast decay pathways in malonaldehyde upon photoexcitation to its bright S2(pp*) state. We employ both restricted active space perturbation theory and algebraic diagrammatic construction for the polarization propagator along interpolated reaction coordinates as well as representative trajectories from ab initio multiple spawning simulations to compute the TRXAS signals from the lowest valence states. Our study suggests that oxygen K-edge TRXAS can distinctly fingerprint the passage through the H-transfer intersection and the concomitant population transfer to the S1(np*) state. Potential intersystem crossing to T1(pp*) is detectable from reappearance of the double pre-edge signature and reversed intensities. Moreover, the torsional deactivation pathway induces transient charge redistribution from the enol side towards the central C-atom and manifests itself as substantial shifts of the pre-edge features. Given the continuous advances in X-ray light sources, our study proposes an experimental route to disentangle ultrafast excited-state decay channels in this prototypical ESIHT system and provides a pathway-specific mapping of the TRXAS signal to facilitate the interpretation of future experiments.</p> | Nanna Holmgaard List; Adrian L. Dempwolff; Andreas Dreuw; Patrick Norman; Todd J. Martínez | Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74822842e655062db2b10/original/probing-competing-relaxation-pathways-in-malonaldehyde-with-transient-x-ray-absorption-spectroscopy.pdf |
644c4cb16ee8e6b5ed45944d | 10.26434/chemrxiv-2023-bhl32 | Activating Ru in the pyramidal sites of Ru2P-type structures with earth-abundant transition-metals for achieving extremely high HER activity while minimizing noble metal content | Rational design of efficient pH-universal hydrogen evolution reaction (HER) catalysts to enable large-scale hydrogen production via electrochemical water splitting is of great significance, yet a challenging task. Herein, Ru atoms in the Ru2P structure were replaced with M=Co, Ni, or Mo to produce M2-xRuxP nanocrystals. The metals show strong site preference, with Co and Ni occupying the tetrahedral sites and Ru the square pyramidal sites of the CoRuP and NiRuP Ru2P-type structures. The presence of Co or Ni in the tetrahedral sites leads to charge redistribution for Ru and, according to density functional theory (DFT) calculations, to a significant increase in the Ru d-band centers. As a result, the intrinsic activity of CoRuP and 1 NiRuP increases considerably compared to Ru2P in both acidic and alkaline media. The effect is not observed for MoRuP, in which Mo prefers to occupy the pyramidal sites. In particular, CoRuP shows state-of-the-art activity, outperforming Ru2P with Pt-like activity in 0.5 M H2SO4 (η10=12.3 mV; η100=52 mV; turnover frequency (TOF)=4.7 s-1). It remains extraordinarily active in alkaline conditions (η10=12.9 mV; η100=43.5 mV) with a TOF of 4.5 s-1, which is 4x higher than that of Ru2P and 10x that of Pt/C. Further increase of the Co content does not lead to drastic loss of activity, especially in alkaline medium, where for example the TOF of Co1.9Ru0.1P remains comparable to that of Ru2P and higher than Pt/C, highlighting the viability of the adopted approach to prepare cost efficient catalysts. | Sayed El-Refaei; Patrícia Russo; Thorsten Schultz; Zhe-Ning Chen; Patrick Amsalem; Norbert Koch; Nicola Pinna | Inorganic Chemistry; Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644c4cb16ee8e6b5ed45944d/original/activating-ru-in-the-pyramidal-sites-of-ru2p-type-structures-with-earth-abundant-transition-metals-for-achieving-extremely-high-her-activity-while-minimizing-noble-metal-content.pdf |
60c74496bdbb894a66a3883b | 10.26434/chemrxiv.9724061.v2 | Operando Diffuse Reflectance UV-VIS Spectroelectrochemistry for Investigating Oxygen Evolution Electrocatalysts | <div>This is a complete self-standing study on operando diffuse reflectance UV-vis spectroelectrochemistry for investigating oxygen evolution electrocatalysts.</div> | Sebastian Wahl; Sayed M. El-Refaei; Patrick Amsalem; Ana de Oliveira Guilherme Buzanich; Norbert Koch; Nicola Pinna | Nanostructured Materials - Materials; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74496bdbb894a66a3883b/original/operando-diffuse-reflectance-uv-vis-spectroelectrochemistry-for-investigating-oxygen-evolution-electrocatalysts.pdf |
64a6ab889ea64cc167899575 | 10.26434/chemrxiv-2023-zpgrm | Pore-networked membrane for trace-level molecular separations in environmental water | The wide presence of pharmaceuticals and personal care products (PPCPs) in water is a major concern regarding current emerging pollution and urges their selective monitoring to establish water quality management. Microporous materials have been developed to extract organic contaminants and further embedded as fillers into polymeric composites like matrix-mixed membranes (MMMs) for practical use. Considering the relatively large molecular size of PPCPs and their slow diffusion in the membrane, the MMM configuration is, however, inadequate for liquid-phase separations. Here we report pore-networked membranes (PNMs) based on the concept of interconnecting the microporous fillers within the polymer matrix to form a continuous porous phase. Linked metal-organic polyhedra (MOP) network is designed for the continuous porous phase with tunable micro/mesopores, which are accessible for big PPCP molecules to facilitate their diffusion and adsorption. By contrast to MMMs, PNMs show enhanced stability, capacity and extraction selectivity towards specific pharmaceutical drugs amongst 13 PPCPs in environmental water matrices at trace-level concentrations. | Zaoming Wang; Idaira Pacheco-Fernández; James E. Carpenter; Takuma Aoyama; Guoji Huang; Ali Pournaghshband Isfahani; Behnam Ghalei; Easan Sivaniah; Kenji Urayama; Yamil. J. Colón; Shuhei Furukawa | Materials Science; Inorganic Chemistry; Analytical Chemistry; Composites; Environmental Analysis; Coordination Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2023-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a6ab889ea64cc167899575/original/pore-networked-membrane-for-trace-level-molecular-separations-in-environmental-water.pdf |
664dadb4418a5379b0f19b7e | 10.26434/chemrxiv-2024-38km6 | CuAgNPs-enzyme Biohybrids as Antimicrobial nanomaterials | Multidrug-resistant bacterial infections have become major threats to public health worldwide. Thus, bimetallic Ag-Cu nanoparticles-enzyme biohybrids has been developed. Different bimetallic bionanohybrids were synthesized with different contents of Ag, by the direct incubation of a previous synthesized Cu3(PO4)2NPs-CALB hybrid with silver salt in aqueous media and r.t. They were fully characterized, determining silver phosphate as metal species, and different nanoparticles sizes depending on the amount of silver used. HAADF-STEM analyses demonstrated the formation of individual Ag3PO4 NPs on the Cu-CALB nanoflowers. The catalytic reductase or oxidase-like activities of the bimetallic biohybrids was also affected being higher values when lower amount of silver was used. This effect was corroborated in their antimicrobial efficacy against Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Mycobacterium smegmatis. Results indicate that the presence of small content on silver in the bimetallic hybrids highly enhanced the antibacterial activity compared to initial Cu36@CALB hybrid. Optimal amount of silver has been found corresponding to the bimetallic Ag4Cu32@CALB hybrid which showed the strongest antibacterial effect, with log reductions of 7.6, 4.3 and 3.9 for K. pneumoniae, P. aeruginosa, E. coli, and 1.8 for M. smegmatis. Overall, these novel nanomaterials are a promising alternative for fight against different pathogens. | Clara Ortega-Nieto; Noelia Losada-Garcia; Pilar Domingo-Calap; Miroslawa Pawlyta; Jose Miguel Palomo | Nanoscience; Nanocatalysis - Catalysts & Materials | CC BY NC 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664dadb4418a5379b0f19b7e/original/cu-ag-n-ps-enzyme-biohybrids-as-antimicrobial-nanomaterials.pdf |
64dccb1f69bfb8925a05cd9a | 10.26434/chemrxiv-2023-xmhzg | In Crystallo Reactions with an Engineered Cytochrome P450 Peroxygenase | The cytochrome P450 monooxygenases are a class of heme-thiolate enzymes that are able to insert oxygen into unactivated C-H bonds. These enzymes can be converted into peroxygenases via protein engineering which enables this activity to occur using hydrogen peroxide (H2O2) with-out the requirement for additional nicotinamide co-factors or partner proteins. This offers significant advantages in terms of applications and mechanistic studies. Here, we investigate whether soaking crystals of an engineered P450 peroxygenase with H2O2 enables the enzymatic reactions to occur within the crystal. A designed bacterial P450 peroxy-genase, CYP199A4 (T252E variant), which has enhanced activity for the O-demethylation of 4-methoxybenzoic acid using H2O2 was used. Crystals of T252E-CYP199A4 in complex with 4-methoxybenzoic acid were soaked with different concentrations of H2O2 for varying times to initiate an in crystallo O-demethylation reaction. Crystal structures of T252E-CYP199A4 showed a distinct loss of electron density that was consistent with the O-demethylated metabolite, 4-hydroxybenzoic acid when compared to the crystal structures of the same enzyme with the 4-hydroxybenzoic acid product and the 4-methoxybenzoic acid substrate bound. The visualisation of enzymatic catalysis in action is challenging in structural biology and the ability to start and monitor the reactions of P450 enzymes, or their progress, in crystallo by simply soaking crystals with H2O2 will enable new information on intermediates, such as product bound structures, and the mechanisms of these oxygenase reactions to be obtained. | Joel Lee; John Bruning; Stephen Bell | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Biochemistry; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dccb1f69bfb8925a05cd9a/original/in-crystallo-reactions-with-an-engineered-cytochrome-p450-peroxygenase.pdf |
657212e5cf8b3c3cd70cc2f7 | 10.26434/chemrxiv-2023-qx7tc | Green Light Promoted Iridium(III)/Copper(I)-Catalyzed Addition of Alkynes to Aziridinoquinoxalines Through the Intermediacy of Azomethine Ylides | This manuscript describes the development of alkyne addition to the aziridine moiety of aziridinoquinoxalines using dual Ir(III)/Cu(I) catalytic system under green LED photolysis (lmax = 525 nm). This mild method features high levels of chemo- and regioselectivity and was used to generate 29 highly functionalized substituted dihydroquinoxalines in 44-98% yield. This transformation was also carried asymmetrically using (S,R)-N-PINAP as the chiral ligand to provide 9 chiral addition products in 96:4 to 86:14 e.r. The experimental and quantum chemical explorations of this reaction suggest a mechanism that involves Ir(III)-catalyzed triplet energy transfer mechanism followed by a ring-opening reaction ultimately leading to the formation of azomethine ylide intermediates. These azomethine intermediates undergo sequential protonation/copper(I) acetelide addition to provide the products. | Oleksii Zhelavskyi; Seren Parikh; Richard Staples; Paul Zimmerman; Pavel Nagorny | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Stereochemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657212e5cf8b3c3cd70cc2f7/original/green-light-promoted-iridium-iii-copper-i-catalyzed-addition-of-alkynes-to-aziridinoquinoxalines-through-the-intermediacy-of-azomethine-ylides.pdf |
65a512d09138d23161f68c3f | 10.26434/chemrxiv-2024-8j81v | Scalable Synthesis of Accordion-Like Multilayered Titanium Nitride in Air with Enhanced Performance as Catalytic Support for Oxygen Reduction | MXenes, recognized for their potential in energy storage and conversion, face significant challenges due to severe degradation in oxidative environments, which compromises their functional properties and limits further applications. To address this issue, we have developed an efficient pathway for transforming bulk titanium nitride (TiN) into multilayered titanium nitride (M-TiN). This method integrates the intrinsic properties of MXenes with the enhanced stability of TiN, offering a viable solu-tion to the pressing issue of oxidation stability for practical applications. The synthesis of M-TiN avoids the need for inert gas protection or chemical purification steps, making the process both practical and scalable. Notably, M-TiN exhibits inherent stability and improved performance, particularly in oxygen reduction reaction (ORR) when coupled with iron phthalocyanine (FePc). The oxidized surface layer of M-TiN enhances stability in corrosive and oxidative environments and facilitates the formation of Fe-O-Ti bonds, effectively modulating the spin states of the Fe center from low spin to medium spin, thereby improving ORR performance. M-TiN/FePc also delivers a greater power density of 270.31 mW cm-2 and better cyclability than Pt/C in a zinc-air battery. The simplicity of M-TiN's synthesis, along with the inherent properties of both MXene and TiN, positions it as a promising material for the future of energy conversion and storage technologies | Shuren Zhang; Rui Zhang; Zhiyuan Zhang; Kefan Shi; Genban Sun | Materials Science; Multilayers | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a512d09138d23161f68c3f/original/scalable-synthesis-of-accordion-like-multilayered-titanium-nitride-in-air-with-enhanced-performance-as-catalytic-support-for-oxygen-reduction.pdf |
65784156bec7913d276d467b | 10.26434/chemrxiv-2023-jzd33-v2 | Efficiency Conceptualization Model: A Theoretical Method for Predicting the Turnover of Catalysts | In recent times, the theoretical prediction of catalytic efficiency is of utmost urgency. With the advent of density functional theory (DFT), reliable computations are possible that delineate a quantitative aspect of the study. To this state-of-the-art approach, valuable incorporation would be a tool that can acknowledge the efficiency of a catalyst. In the current work, we developed a method, the efficiency conceptualization model (ECM), that utilizes the quantum mechanical tool to achieve efficiency in terms of turnover frequency (TOF). In the current work, ECM will be executed for the twenty-six experimentally designed transition metal (TM) water oxidation catalysts under similar experimental conditions of temperature, pressure, and pH. The computations conclude that the iron (Fe)-based catalysts (MWOC-16, MWOC-17, and MWOC-18) are highly active catalysts and therefore can endure for more time in the catalytic cycle. Our results conclude that the iridium (Ir) based catalysts MWOC-23 and MWOC-24 report the highest computed turnover number, τ_(computed TON )^0 of 5113 and 5612 against the highest experimental TON, τ_(experimental TON) of 2000 and 1200 respectively, whereas MWOC-19 has the lowest computed TON (τ_(computed TON )^0 = 264, τ_(experimental TON) = 16) among the chosen catalysts and thereby is successful in corroborating the previous experimental results. | Himangshu Pratim Bhattacharyya; Manabendra Sarma | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65784156bec7913d276d467b/original/efficiency-conceptualization-model-a-theoretical-method-for-predicting-the-turnover-of-catalysts.pdf |
60c73dd29abda2411ef8b797 | 10.26434/chemrxiv.6127826.v1 | STK: A Python Toolkit for Supramolecular Assembly | <p>A tool for the automated assembly, molecular optimization and property calculation of supramolecular materials is presented. stk is a modular, extensible and open-source Python library that provides a simple Python API and integration with third party computational codes. stk currently supports the construction of linear polymers, small linear oligomers, organic cages in multiple topologies, and covalent organic frameworks (COFs) in multiple framework topologies, but is designed to be easy to extend to new, unrelated, supramolecules or new topologies. Extension to metal-organic frameworks (MOFs), metallocycles or supramolecules, such as catenanes, would be straightforward. Through integration with third party codes, stk offers the user the opportunity to explore the potential energy landscape of the assembled supramolecule and then calculate the supramolecule’s structural features and properties. stk provides support for high-throughput screening of large batches of supramolecules at a time. The source code of the program can be found at https://github.com/supramolecular-toolkit/stk.</p> | Lukas Turcani; Enrico Berardo; Kim Jelfs | Supramolecular Chemistry (Org.); Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd29abda2411ef8b797/original/stk-a-python-toolkit-for-supramolecular-assembly.pdf |
60c7404b4c8919f1e9ad20e0 | 10.26434/chemrxiv.7689092.v1 | Towards Prediction of Non-Radiative Decay Pathways in Organic Compounds I: The Case of Naphthalene Quantum Yields | <div>Many emerging technologies depend on human’s ability to control and manipulate the excited-state properties of molecular systems. These technologies include fluorescent</div><div>labeling in biomedical imaging, light harvesting in photovoltaics, and electroluminescence in light-emitting devices. All of these systems suffer from non-radiative loss pathways that dissipate electronic energy as heat, which causes the overall system efficiency to be directly linked to quantum yield (Φ) of the molecular excited state. Unfortunately, Φ is very difficult to predict from first principles because the description of a slow non-radiative decay mechanism requires an accurate description of long-timescale excited-state quantum dynamics. In the present study, we introduce an efficient semiempirical method of calculating the fluorescence quantum yield (Φ<sub>fl</sub>) for molecular chromophores, which, based on machine learning, converts simple electronic energies computed using time-dependent density functional theory (TDDFT) into an estimate of Φ<sub>fl</sub>. As with all machine learning strategies, the algorithm needs to be trained on fluorescent dyes for which Φ<sub>fl</sub>’s are known, so as to provide a black-box method which can later predict Φ<sub>fl</sub>’s for chemically similar chromophores that have not been studied experimentally. As a first illustration of how our proposed algorithm can be trained, we examine a family of 25 naphthalene derivatives. The simplest application of the energy gap law is found to be inadequate to explain the rates of internal conversion (IC) or intersystem crossing (ISC) – the electronic properties of at least one higher-lying electronic state (S<i><sub>n</sub></i> or T<i><sub>n</sub></i>) or one far-from-equilibrium geometry are typically needed to obtain accurate results. Indeed, the key descriptors turn out to be the transition state between the Franck–Condon minimum a distorted local minimum near an S<sub>0</sub>/S<sub>1</sub> conical intersection (which governs IC) and the magnitude of the spin–orbit coupling (which governs ISC). The resulting Φ<sub>fl</sub>’s are predicted with reasonable accuracy (±22%), making our approach a promising ingredient for high-throughput screening and rational design of the molecular excited states with desired Φ’s. We thus conclude that our model, while semi-empirical in nature, does in fact extract sound physical insight into the challenge of describing non-radiative relaxations.</div> | Alexander Kohn; Zhou Lin; Troy Van Voorhis | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Radiation | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7404b4c8919f1e9ad20e0/original/towards-prediction-of-non-radiative-decay-pathways-in-organic-compounds-i-the-case-of-naphthalene-quantum-yields.pdf |
65598f412c3c11ed71b0a72d | 10.26434/chemrxiv-2023-tmr8q | Developing Cheap but Useful Machine Learning based Models for Investigating High-Entropy Alloy Catalysts | This work aims to address the challenge of developing interpretable ML-based models when access to large scale computational resources is limited. Using CoMoFeNiCu high-entropy alloy catalysts as an example, we present a cost-effective workflow that synergistically combines descriptor based approaches, machine learning based force fields and low-cost density functional theory (DFT) calculations to predict high-quality adsorption energies for H, N and NHx (x = 1, 2 and 3) adsorbates. This is achieved using three specific modifications to typical DFT workflows including, (1) using a sequential optimization protocol, (2) developing a new-geometry based descriptor, and (3) re-purposing the already-available low-cost DFT optimization trajectories to develop a ML-FF. Taken together, this study illustrates how cheap DFT calculations and appropriately designed descriptors can be used to develop cheap but useful models for predicting high-quality adsorption energies at significantly lower computational costs. We anticipate that this resource-efficient philosophy may be broadly relevant to the larger surface catalysis community. | Chenghan Sun; Rajat Goel; Ambarish Kulkarni | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65598f412c3c11ed71b0a72d/original/developing-cheap-but-useful-machine-learning-based-models-for-investigating-high-entropy-alloy-catalysts.pdf |
646c2473268ed316c93ce527 | 10.26434/chemrxiv-2023-xbjd0-v2 | Glycolipids from the gut symbiont Bacteroides fragilis are agonists for natural killer T cells and induce their regulatory differentiation | Natural Killer T (NKT) cells are a lipid-antigen reactive, CD1d-restricted T cell subset with diverse functional properties that contribute to inflammatory and regulatory immune responses. The most studied lipid antigen target for these cells is alpha-galactosylceramide (GC). The commensal organism Bacteroides fragilis (B. fragilis) produces several forms of GC, but conflicting information exists about the influence of these lipids on NKT cells. Herein, we report the total synthesis of a major form of alpha-GC from B. fragilis (Bf alpha-GC), and several analogues thereof. We confirm the T cell receptor (TCR)-mediated recognition of these glycolipids by mouse and human NKT cells. Despite the natural structure of Bf alpha-GC containing lipid branching that limits potency, we demonstrate that Bf alpha-GC drives mouse NKT cells to proliferate and differentiate into producers of the immunoregulatory cytokine, interleukin-10 (IL-10). These Bf alpha-GC-experienced NKT cells display regulatory function by inhibiting the expansion of naïve NKT cells upon subsequent exposure to this antigen. Moreover, this regulatory activity impacts more than just NKT cells, as demonstrated by the NKT cell-mediated inhibition of antigen-stimulated mucosal-associated invariant T (MAIT) cells. These findings reveal that B. fragilis-derived NKT cell agonists may have broad immunoregulatory activity, providing insight into the mechanisms influencing immune tolerance to commensal bacteria and highlighting a potential means to manipulate NKT cell function for therapeutic benefit. | Garth Cameron; Tram Nguyen; Marcin Cuila; Spencer Williams; Dale Godfrey | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646c2473268ed316c93ce527/original/glycolipids-from-the-gut-symbiont-bacteroides-fragilis-are-agonists-for-natural-killer-t-cells-and-induce-their-regulatory-differentiation.pdf |
6724996d7be152b1d0a7dbfb | 10.26434/chemrxiv-2024-rk6w2 | VeloxChem: GPU-accelerated Fock matrix construction enabling complex polarization propagator simulations of circular dichroism spectra of G-quadruplexes | An automatic code generated C++/HIP/CUDA implementation of the (auxiliary) Fock, or Kohn–Sham, matrix construction for execution in GPU-accelerated hardware environments is presented. The module is developed as part the quantum chemistry software package VeloxChem, employing localized Gaussian atomic orbitals. The per- formance and scaling characteristics are analyzed in view of the specific requirements for self-consistent field optimizations and response theory calculations. As an example, the electronic circular dichroism spectrum of a G-quadruplex is calculated at the level of time-dependent density functional theory in conjunction with the range-separated CAM-B3LYP exchange–correlation functional. Computational issues due to the high- density of states following the adoption of large-scale model systems is here bypassed with use of the complex polarization propagator approach. The origin of the negative Cotton effect in the long-wavelength onset of the experimental spectrum is elucidated in the large-scale modeling and shown to be associated with the TTA nucleobase linkers in the G-quadruplex. | Xin Li; Mathieu Linares; Patrick Norman | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6724996d7be152b1d0a7dbfb/original/velox-chem-gpu-accelerated-fock-matrix-construction-enabling-complex-polarization-propagator-simulations-of-circular-dichroism-spectra-of-g-quadruplexes.pdf |
66d358e620ac769e5f7a61a9 | 10.26434/chemrxiv-2024-zh59c | An insight into the chemical exposome during pregnancy - A non-targeted analysis study | The extensive use of human-made chemicals in our daily lives results in chronic exposure to complex mixtures of potentially harmful substances. We investigated chemical exposures in pregnant women in New York City by applying a non-targeted analysis (NTA) workflow to 95 paired prenatal urine and serum samples (35 pairs of preterm birth) collected as part of the New York University Children’s Health and Environment Study. The goal was to i) study chemical exposures in this population, ii) explore differences in the chemical profiles comparing urine vs. serum samples, and comparing preterm vs. term birth samples, and iii) investigate potential associations between exogenous chemicals and endogenous metabolites. We analyzed all samples using liquid chromatography coupled with Orbitrap high-resolution mass spectrometry (LC-Orbitrap HRMS) in both positive and negative electrospray ionization modes (ESI+ and ESI-), employing full scan and data-dependent MS/MS fragmentation (ddMS2) scans. We detected a total of 1,524 chemical features for annotation, with 12 chemicals confirmed by authentic standards. Two confirmed chemicals dodecyltrimethylammonium and n,n-dimethyldecylamine n-oxide appear to not have been previously reported in human blood samples. We observed a statistically significant differential enrichment between urine and serum samples, as well as between preterm and term birth (p < 0.0001) in serum samples. When comparing between preterm and term births, an exogenous contaminant, 1,4-cyclohexanedicarboxylic acid (tentative), showed a statistical significance difference (p = 0.003) with more abundance in preterm birth in serum. An example of chemical associations (12 associations in total) observed was between surfactants (tertiary amines) and endogenous metabolites (e.g., bioactive lipid mediators and fatty acid amides). | Xiaowen Ji; Mathusa Lakuleswaran; Whitney Cowell; Linda Kahn; Marina Sirota; Dimitri Abrahamsson | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2024-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d358e620ac769e5f7a61a9/original/an-insight-into-the-chemical-exposome-during-pregnancy-a-non-targeted-analysis-study.pdf |
65d4c77fe9ebbb4db9cb893c | 10.26434/chemrxiv-2024-g9lx2-v2 | Temperature-Driven Dissolution of Nanoalloyed Catalyst During Ink Preparation and Membrane Electrode Assembly Fabrication | Platinum (Pt) alloys are excellent oxygen-reduction catalysts used in proton exchange membrane fuel cells, yet their effective integration poses challenges. Through in-situ X-ray diffraction, we investigate the compositional changes during the ink preparation of PtCo and PtNi catalysts and reveal that dissolution is primarily driven by temperature. Comparisons with conventional catalyst-coated membrane (CCM) fabrication methods highlight structural transformations during hot-pressing. Paving the way for advancements in sustainable energy technologies, our findings emphasize the essential need for fundamental knowledge of ink-making and CCM fabrication to unlock Pt-alloy catalyst potential for hydrogen fuel cells. In addition to the academic community, the industry shall benefit from this precise and easy-to-employ methodology.
| Michal Ronovský; Olivia Dunseath; Tomáš Hrbek; Peter Kúš; Matija Gatalo; Shlomi Polani; Jan Kubát; Daniel Götz; Hridya Nedumkulam; Andrea Satori; Enrico Petrucco; Francisco Ruiz Zepeda; Nejc Hodnik; Peter Strasser; Alex Martinez Bonastre; Jakub Drnec | Catalysis; Energy; Electrocatalysis; Fuel Cells; Power; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d4c77fe9ebbb4db9cb893c/original/temperature-driven-dissolution-of-nanoalloyed-catalyst-during-ink-preparation-and-membrane-electrode-assembly-fabrication.pdf |
60c754b6ee301c1d5ec7afe5 | 10.26434/chemrxiv.13713487.v1 | In-Depth Lipidome Annotation Through an Operatively Simple Method Combining Cross-Metathesis Reaction and Tandem Mass Spectrometry | The in-depth knowledge of lipid biological functions calls for a comprehensive lipid structure annotation that implies implementing a method to locate fatty acids unsaturations. To address this challenge we have associated Grubbs' cross metathesis reaction and liquid chromatography hyphenated to tandem mass spectrometry. The pretreatment of lipids containing samples by Grubbs' catalyst and an appropriate alken generates substituted lipids through cross-metathesis reaction under mild, chemoselective and highly reproducible conditions. A systematic LC-MS/MS analysis of the reaction mixture allows locating unambigouslt the double bounds in fatty acid side chains. This method has en successfully applied at a nanomole scale to commerical standard mixtures as well as in lipid extracts from an in vitro model of corneal toxicity.<br /><div><a></a><a></a><a></a><a></a></div><div><a></a><a></a><a></a>
</div> | Romain MAGNY; Anne Regazzetti; Karima Kessal; Christophe Baudouin; Stéphane Mélik-Parsadaniantz; Olivier Laprévote; Françoise Brignole-Baudouin; nicolas auzeil; Emmanuel Roulland | Analytical Chemistry - General; Mass Spectrometry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754b6ee301c1d5ec7afe5/original/in-depth-lipidome-annotation-through-an-operatively-simple-method-combining-cross-metathesis-reaction-and-tandem-mass-spectrometry.pdf |
652e38ce8bab5d205583e98e | 10.26434/chemrxiv-2023-d4nxn | Protecting-Group-Free Mechanosynthesis of Amides from Hydroxycarboxylic Acids: Application to the Synthesis of Imatinib | Mechanochemical methods for assembling carbon-nitrogen bonds play a central role in the ongoing green chemistry-driven renovation of organic synthesis, including the synthesis of active pharmaceutical ingredients (APIs). However, chemoselective issues in these transformations, such as the tolerance of unmasked hydroxyl groups, have not been systematically explored. Screening of various amide coupling conditions revealed that 1 ethyl 3 (3 dimethylaminopropyl)carbodiimide (EDC) in combination with ethyl acetate as a liquid-assisted grinding (LAG) solvent was the most selective amide coupler, delivering 76–94% yields of the respective amide products from unprotected hydroxycarboxylic acids. Boc-protected tyrosine and serine with unmasked hydroxyl functionalities were successfully involved in peptide couplings. By incorporating green chemistry principles as a driver for innovation, the established protocol was applied to the synthesis of imatinib, an anticancer drug included in the World Health Organization’s List of Essential Medicines. The target API was synthesized with an overall yield of 86% and 99% HPLC purity through a two-step mechanochemical C–N bond assembling reaction sequence starting from 4 (hydroxymethyl)benzoic acid. A comparison of green chemistry metrics between the developed mechanochemical approach and similar solution-based approaches revealed reduced waste generation, enhanced eco-friendliness, and a superior safety profile for the proposed strategy. The safety improvement was primarily attributed to the elimination of toxic solvents and a genotoxic intermediate from the production chain. | Tatsiana Nikonovich; Tatsiana Jarg; Jevgenija Martõnova; Artjom Kudrjašov; Danylo Merzhyievskyi; Marina Kudrjašova; Fabrice Gallou; Riina Aav; Dzmitry Kananovich | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e38ce8bab5d205583e98e/original/protecting-group-free-mechanosynthesis-of-amides-from-hydroxycarboxylic-acids-application-to-the-synthesis-of-imatinib.pdf |
665ad87721291e5d1dcee486 | 10.26434/chemrxiv-2024-zf1m7 | Spirocyclic pyrrolidinyl nitroxides with exo-methylene substituents | Nitroxides are stable organic radicals with exceptionally long lifetimes, which render them uniquely suitable as observable probes or polarising agents for spectroscopic investigation of biomolecular structure and dynamics. Radical-based probes for biological applications are ideally characterized by both robustness towards reductive degradation and beneficial electron spin relaxation parameters. These properties are largely influenced by the molecular structure of the nitroxide scaffold, and also by the conformations it prefers to adopt. In this study we present the synthesis of the first nitroxides based on a spirocyclic pyrrolidine scaffold with an exocyclic methylene substituent. The conformations adopted by these nitroxides were evaluated by X-ray crystallography, both with single nitroxide crystals and by inclusion of nitroxides in a microporous crystalline sponge. The kinetic and thermodynamic stability of the new nitroxides towards reduction was investigated by electron paramagnetic resonance (EPR) spectroscopy and cyclic voltammetry (CV). In combination with EPR measurements of electron spin relaxation properties, these results suggest that this new family of nitroxides can provide access to multifunctionalized probes and polarising agents suitable for use in biological environments at elevated temperatures. | Mateusz P. Sowiński; Anna-Luisa Warnke; Bjarte A. Lund; Susann Skagseth; David B. Cordes; Janet E. Lovett; Marius Myreng Haugland | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665ad87721291e5d1dcee486/original/spirocyclic-pyrrolidinyl-nitroxides-with-exo-methylene-substituents.pdf |
625af94debac3aca9ad76f27 | 10.26434/chemrxiv-2022-24jhd | Formation of Keteniminium Salts: Mechanistic Aspects and
Substituent Effects | Keteniminium salts (KIs) are versatile intermediates in synthetic organic chemistry. Elucidation of the mechanistic aspects of KI formation reactions facilitates the design of KI intermediates that give access to complex compounds. In this study, in order to provide a comprehensive understanding of KI formation, various mechanisms were investigated using a density functional theory approach. Particularly, Ghosez’s KI formation mechanism, by activation of an amide with triflic anhydride, was extensively elaborated, since this procedure occurs under mild conditions and is, by far, the most frequently used method. Moreover, a broad range of substituents was examined to give insight on their potential contributions to the ease of formation of KIs. The effect of substituents on the reactivity of the corresponding starting amides was inspected by means of energetics, population analysis, frontier molecular orbitals (FMO) and reactivity descriptors. Computed data shows that electron donating groups lower the activation barrier by increasing the electron density of the amide carbonyl oxygen. Additionally, distortion/interaction model also confirmed the energetic outcomes. In addition, investigation of KI reactivity using FMO, and reactivity descriptors displayed that KI reactivity is inversely correlated with amide reactivity. Lastly, experimental outcomes are in line with computational predictions. We suggest that the reactivity of the amide has a crucial impact on the ease of KI formation and the reactivity of the corresponding KIs. This study gives pivotal insights into mechanistic aspects of KI formation and the role of the substituents. | Zeynep Aktas; Gamze Tanriver; Pierre Quinodoz; Dylan Dagoneau; Amandine Kolleth; Alexandre Lumbroso; Sarah Sulzer-Mossé; Alain De Mesmaeker; Saron Catak | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625af94debac3aca9ad76f27/original/formation-of-keteniminium-salts-mechanistic-aspects-and-substituent-effects.pdf |
60c7436a702a9b6e3e18a5c3 | 10.26434/chemrxiv.9120974.v1 | Global Aromaticity and Antiaromaticity in Porphyrin Nanoring Anions | Doping, through oxidation or reduction, is often used to modify the properties of π-conjugated oligomers. In most cases, the resulting charge distribution is difficult to determine. If the oligomer is cyclic and doping establishes global aromaticity or antiaromaticity, then it is certain that the charge is fully delocalized over the entire perimeter of the ring. Here we show that reduction of a six-porphyrin nanoring using decamethylcobaltocene results in global aromaticity (in the 6– state; [90 π]) and antiaromaticity (in the 4– state; [88 π]), consistent with Hückel’s rules. Aromaticity is assigned by NMR spectroscopy and density-functional theory calculations. <br /> | Martin D. Peeks; Michael Jirasek; Timothy D. W. Claridge; Harry L. Anderson | Physical Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436a702a9b6e3e18a5c3/original/global-aromaticity-and-antiaromaticity-in-porphyrin-nanoring-anions.pdf |
63d2c9bf10cb6a68dfe7c2d7 | 10.26434/chemrxiv-2023-vbjql | Understanding the Unique Optical and Vibrational Signatures of Sequential Infiltration Synthesis Derived Indium Oxyhydroxide Clusters for CO2 Absorption | Sequential infiltration synthesis (SIS) is a vapor phase synthesis technique with potential to exert precise control over metal oxyhydroxide incorporation into polymer scaffolds. We observe strong size-dependent properties of InOx(OH)y few-atom clusters deposited with variable SIS cycle numbers within a polymethylmethacrylate (PMMA) matrix. Infrared and ultraviolet absorption spectroscopy reveal that the metal atom coordination and optical properties of the clusters depend on the number of SIS cycles performed as well as the choice of processing parameters. The incorporation of indium oxyhydroxide in PMMA via SIS improves the gravimetric CO2 absorption capacity, demonstrating a novel platform with potential for CO2 activation. | Thabiso Kunene; Alex B.F. Martinson | Materials Science; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d2c9bf10cb6a68dfe7c2d7/original/understanding-the-unique-optical-and-vibrational-signatures-of-sequential-infiltration-synthesis-derived-indium-oxyhydroxide-clusters-for-co2-absorption.pdf |
67cf1b596dde43c9084b97d7 | 10.26434/chemrxiv-2025-9n401 | Results of IEA Bioenergy Task 34 Round Robin Study: Analysis of Biomass Liquefaction Oil Composition and Role of Sample Homogeneity on Measurements | Accurate composition analysis of biomass liquefaction oils (BLOs) is essential for evaluating process performance and determining their suitability for end-use applications, further processing or upgrading to fungible fuels. In this study, IEA Bioenergy Task 34 conducted a round robin (RR) or interlaboratory study (ILS) to assess the reliability of analytical methods used for BLO characterization. Building on insights from a previous ILS, this study specifically addressed challenges related to representative sampling and homogeneity while also evaluating the performance of methods not previously included in past ILS comparison. The study focused on widely used composition analyses, including CHN and water content, as well as emerging techniques for measuring trace nitrogen (N), trace sulfur (S), and inorganics via inductively couple plasma (ICP). Homogeneity controls were implemented through blind duplicates and prescribed mixing intensities to assess their impact on analytical consistency. Results showed that global averages aligned with the known origins of the oils, and blind duplicates performed similarly under the applied sampling protocol. Moreover, increased mixing had little effect on global averages but improved within-lab repeatability for specific samples, analyses, and analytes. Nitrogen content determined by traditional CHN analysis were consistently higher than those obtained via chemiluminescence. ICP results exhibited high variability, largely influenced by method selection, the analyte of interest, and detection limits, particularly at concentrations around 100 mg/kg and below. These findings highlight the need for continued refinement of BLO analytical methods, particularly of trace element analysis, to improve reproducibility and support broader adoption of these bio-derived oils in industrial and commercial applications. | Philip Bulsink; Leslie Nguyen; Murlidhar Gupta; François-Xavier Collard; Axel Funke; Jawad Jeaidi; Benjamin Bronson | Analytical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Analytical Chemistry - General; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf1b596dde43c9084b97d7/original/results-of-iea-bioenergy-task-34-round-robin-study-analysis-of-biomass-liquefaction-oil-composition-and-role-of-sample-homogeneity-on-measurements.pdf |
6480a62a4f8b1884b7fa036c | 10.26434/chemrxiv-2023-fspxm | Synthesis, crystal structure, and magnetic properties of MgPr9Mo16O35 – structural comparison with the LiR9Mo16O35 (R = La, Ce, Pr, Nd) | Polycrystalline and single crystal specimens of the new quaternary phase MgPr9Mo16O35 were synthesized by direct solid-state reaction. MgPr9Mo16O35 presents a monoclinic unit cell (S.G. C2/m; a = 18.3422 (3) Å, b = 8.6188 (1) Å, c = 9.7276 (4) Å, = 101.9680 (4) and Z = 2). Its crystal structure was solved on a single-crystal by X-ray diffraction and refined to the final values R1 = 0.0281 and wR2 = 0.0473 (3903 independent reflections and 101 variables). For a comparative study the crystal structure of LiPr9Mo16O35 was also determined (a = 18.3422 (3) Å, b = 8.6188 (1) Å, c = 9.7276 (4) Å,= 101.9680 (4) and Z = 2; R1 = 0.0281 and wR2 = 0.0473). The crystal structure of both compounds is based on Mo16O26O10 units containing Mo16 clusters that share some of their O atoms to form infinite Mo-O cluster chains developing in the [010] direction and between which the Mg2+ or Li+ and Pr3+ cations are located. The increase of the charge transfer towards the Mo16 cluster due to the supplementary electron brought by the Mg2+ cations leads to some variations of the Mo-Mo distances. Application of the Mo-O bond-length–bond-strength relationship developed by Brown & Wu leads to a value of 55.1 electrons per Mo16 cluster in good agreement with that calculated from the stoichiometry (55 e-/Mo16). Magnetic susceptibility measurements confirm the presence of one unpaired electron on the Mo16 cluster. | Patrick Gougeon; Philippe Gall | Inorganic Chemistry; Lanthanides and Actinides; Solid State Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6480a62a4f8b1884b7fa036c/original/synthesis-crystal-structure-and-magnetic-properties-of-mg-pr9mo16o35-structural-comparison-with-the-li-r9mo16o35-r-la-ce-pr-nd.pdf |
60c757844c8919f6cdad4a26 | 10.26434/chemrxiv.14411081.v1 | Prediction and Optimization of Ion Transport Characteristics in Nanoparticle-Based Electrolytes Using Convolutional Neural Networks | <pre>We develop a convolutional neural network (CNN) model to predict the diffusivity of cations in nanoparticle-based electrolytes, and use it to identify the characteristics of morphologies which exhibit optimal transport properties. The ground truth data is obtained from kinetic Monte Carlo (kMC) simulations of cation transport parameterized using a multiscale modeling strategy. We implement deep learning approaches to quantitatively link the diffusivity of cations to the spatial arrangement of the nanoparticles. We then integrate the trained CNN model with a topology optimization algorithm for accelerated discovery of nanoparticle morphologies that exhibit optimal cation diffusivities at a specified nanoparticle loading, and we investigate the ability of the CNN model to quantitatively account for the influence of interparticle spatial correlations on cation diffusivity. Finally, using data-driven approaches, we explore how simple descriptors of nanoparticle morphology correlate with cation diffusivity, thus providing a physical rationale for the observed optimal microstructures. The results of this study highlight the capability of CNNs to serve as surrogate models for structure--property relationships in composites with monodisperse spherical particles, which can in turn be used with inverse methods to discover morphologies that produce optimal target properties.</pre> | Sanket Kadulkar; Michael Howard; Thomas Truskett; Venkat Ganesan | Nanostructured Materials - Materials; Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY 4.0 | CHEMRXIV | 2021-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757844c8919f6cdad4a26/original/prediction-and-optimization-of-ion-transport-characteristics-in-nanoparticle-based-electrolytes-using-convolutional-neural-networks.pdf |
65b3cafd9138d23161cc5ea4 | 10.26434/chemrxiv-2024-871mt | Quantifying the hardness of bioactivity prediction tasks for transfer learning | Today, machine learning methods are widely employed in drug discovery. However, the chronic lack of data continues to hamper their further development, validation, and application. Several modern strategies aim to mitigate the challenges associated with data scarcity by learning from data on related tasks. These knowledge-sharing approaches encompass transfer learning, multi-task learning, and meta-learning. A key question remaining to be answered for these approaches is about the extent to which their performance can benefit from the relatedness of available source (training) tasks, in other words, how difficult (“hard”) a test task is to a model, given the available source tasks. This study introduces a new method for quantifying and predicting the hardness of a bioactivity prediction task based on its relation to the available training tasks. The approach involves the generation of protein and chemical representations and the calculation of distances between the bioactivity prediction task and the available training tasks. In the example of meta-learning, we demonstrate that the proposed task hardness metric is inversely correlated with performance. The metric will be useful in estimating the task-specific gain in performance that can be achieved through meta-learning. | Hosein Fooladi; Steffen Hirte; Johannes Kirchmair | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b3cafd9138d23161cc5ea4/original/quantifying-the-hardness-of-bioactivity-prediction-tasks-for-transfer-learning.pdf |
60c742da702a9b612918a4f0 | 10.26434/chemrxiv.8795045.v1 | ChemBioServer 2.0: An Advanced Web Server for Filtering, Clustering and Networking of Chemical Compounds Facilitating Both Drug Discovery and Repurposing | <p>ChemBioServer
2.0 is the advanced sequel of a web-server for filtering, clustering and
networking of chemical compound libraries facilitating both drug discovery and
repurposing. It provides researchers the ability to (i) browse and visualize compounds
along with their physicochemical and toxicity properties, (ii) perform
property-based filtering of chemical compounds, (iii) explore compound
libraries for lead optimization based on perfect match substructure search, (iv)
re-rank virtual screening results to achieve selectivity for a protein of
interest against different protein members of the same family, selecting only
those compounds that score high for the protein of interest, (v) perform clustering
among the compounds based on their physicochemical properties providing
representative compounds for each cluster, (vi) construct and visualize a
structural similarity network of compounds providing a set of network analysis
metrics, (vii) combine a given set of compounds with a reference set of compounds
into a single structural similarity network providing the opportunity to infer
drug repurposing due to transitivity, (viii) remove compounds from a network
based on their similarity with unwanted substances (e.g. failed drugs) and (ix)
build custom compound mining pipelines. The updated web server is available in
the URL: <a href="http://chembioserver.vi-seem.eu/">http://chembioserver.vi-seem.eu/</a>
</p> | Evangelos Karatzas; Juan Eiros Zamora; Emmanouil Athanasiadis; Dimitris Dellis; Zoe Cournia; George Spyrou | Bioinformatics and Computational Biology; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742da702a9b612918a4f0/original/chem-bio-server-2-0-an-advanced-web-server-for-filtering-clustering-and-networking-of-chemical-compounds-facilitating-both-drug-discovery-and-repurposing.pdf |
6552d6c12c3c11ed715658d8 | 10.26434/chemrxiv-2023-plb6m | Strongly Reducing Helical Phenothiazines as Recyclable Organophotoredox Catalysts | Photocatalysts have recently attracted significant interest due to their potential applications in sustainable energy-conversion systems. In organic chemistry, recyclability of photocatalysts are important characteristics with respect to environmental concerns and economic benefits. Metal-based polypyridyl complexes of ruthenium and iridium have been widely used as recyclable homogeneous photoredox catalysts, whereas organophotoredox catalysts are less explored and usually limited to the use of polymer methods. Herein, we report the design and synthesis of recyclable phenothiazine organophotoredox catalysts (PTHS 1–3). These catalysts exhibit relatively high excited-state oxidation potentials (E1/2ox* = −2.34 to −2.40 V vs. SCE) that can efficiently promote photoredox reactions via the one-electron reduction of 1,3-bis(trifluoromethyl)benzene and 4-trifluoromethyliodobenzene, which have high reduction potentials (Ep/2 = −2.07 to −2.16 V vs. SCE). Notably, when the recycling performance was evaluated in the cross-coupling reaction between an aryl halide and triethylphosphite, PTHS-1 can be recovered at least four times without loss of its catalytic activity. The present recyclable and reusable organophotoredox catalysts thus represent a promising tool for sustainable organic synthesis. | Haru Ando; Hiroyoshi Takamura; Isao Kadota; Kenta Tanaka | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6552d6c12c3c11ed715658d8/original/strongly-reducing-helical-phenothiazines-as-recyclable-organophotoredox-catalysts.pdf |
662608f721291e5d1d5b2988 | 10.26434/chemrxiv-2024-l32rb | Surface, Interface, Compression and Formation Energies of Bimetallic Ag/Pt(111) and Ag/Pd(111) Surfaces from First Principles | As an example for bimetallic surfaces in general, we have systematically investigated the thermodynamic surface properties of bimetallic Ag/Pt(111) and Ag/Pd(111) surfaces, including pseudomorphic Ag film covered surfaces and M1Ag3/M(111) (M = Pt, Pd) monolayer surface alloys, by periodic density functional theory calculations. Employing larger, symmetric unit cells and slabs, we could determine the surface energy of the asymmetric surface region without interference with contributions from the bottom side of the slab used in these calculations. In the calculation of formation energies, we distinguish between bulk and slab formation energies. Interface energies are derived from appropriately structured bulk unit cells, and corrected for contributions arising from the compression of pseudomorphic film layers (compression energy). While the general trends for the Pt(111)- and Pd(111)-based systems are rather similar, we also find specific differences. Possible reasons for these trends and the specific discrepancies will be addressed. We propose that the procedures presented here are of general validity and can be applied also to other complex surfaces. | Sung Sakong; Axel Groß; R. Jürgen Behm | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Alloys; Computational Chemistry and Modeling; Surface | CC BY 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662608f721291e5d1d5b2988/original/surface-interface-compression-and-formation-energies-of-bimetallic-ag-pt-111-and-ag-pd-111-surfaces-from-first-principles.pdf |
66753df35101a2ffa82208a9 | 10.26434/chemrxiv-2024-mjmj8 | py.Aroma: An Intuitive Graphical User Interface for Diverse Aromaticity Analyses | The nucleus-independent chemical shift (NICS) criterion plays a significant role in evaluating (anti-)aromaticity. While readily accessible even for non-computational chemists, adding ghost atoms for multi-points NICS evaluations poses a significant challenge. In this note, I introduce py.Aroma, a freely available and open-source Python package designed specifically for analyzing (anti-)aromaticity. Through its user-friendly graphical interface, py.Aroma simplifies and enhances aromaticity analyses by offering key features such as HOMA/HOMER index computation, Gaussian-type input file generation for diverse NICS calculations and corresponding output processing, NMR spectra plotting, and generating computational supporting information (SI) for scientific manuscripts. Additionally, pre-compiled executables for macOS and Windows are available at https://wongzit.github.io/program/pyaroma. Make facilitate accessibility for users lacking programming experience or time constraints. I believe py.Aroma will prove to be a valuable tool for the chemistry community. | Zhe Wang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66753df35101a2ffa82208a9/original/py-aroma-an-intuitive-graphical-user-interface-for-diverse-aromaticity-analyses.pdf |
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