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60c74f60702a9bc57a18bb78 | 10.26434/chemrxiv.12331652.v3 | Resolving the Complexity of Spatial Lipidomics Using MALDI TIMS Imaging Mass Spectrometry | <p>Lipids are a structurally diverse class of molecules with important biological functions including cellular signaling and energy storage. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) allows for direct map-ping of biomolecules in tissue. Fully characterizing the structural diversity of lipids remains a challenge due to the presence of isobaric and isomeric species, which greatly complicates data interpretation when only <i>m/z </i>information is available. Integrating ion mobility separations aids in deconvoluting these complex mixtures and addressing the challenges of lipid IMS. Here we demonstrate that a MALDI quadrupole time-of-flight (Q-TOF) mass spectrometer with trapped ion mobility spectrometry (TIMS) enables approximately a ~270% increase in the peak capacity during IMS experiments. MALDI TIMS-MS separation of lipid isomer standards, including sn-backbone isomers, acyl chain isomers, as well as double bond positional and geometric isomers are demonstrated. As a proof-of-concept, <i>in situ </i>separation and imaging of lipid isomers with distinct spatial distributions was performed using tissue sections from a whole-body mouse pup.</p> | Katerina Djambazova; Dustin R. Klein; Lukasz Migas; Elizabeth Neumann; Emilio Rivera; Raf Van de Plas; Richard
M. Caprioli; Jeffrey Spraggins | Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f60702a9bc57a18bb78/original/resolving-the-complexity-of-spatial-lipidomics-using-maldi-tims-imaging-mass-spectrometry.pdf |
66e32818cec5d6c142e358ef | 10.26434/chemrxiv-2024-xsnqj | Exploring Flavone Reactivity: A Quantum Mechanical Study and TDDFT Benchmark on UV-Vis Spectroscopy | Flavones exhibit a range of pharmacological and diverse biological activities, making them valuable candidates for drug development and complementary medicine. In this study, inclusive investigations of the chemical reactivity, kinetic stability, and biological activity of the flavone molecule are performed using B3LYP/6-311++G(d, p) density functional theory (DFT). The proton affinity (PA), ionisation energy (IE), and electron affinity (EA) along with global reactivity parameters such as chemical potential (µ), chemical hardness (η), softness (σ), electrophilic index (ω), and electronegativity (χ) of flavone molecule are computed. A comparative study with different DFT/correlation functional such as wB97XD, M062X, and MP2 shows that the adopted DFT method is reliable and computationally economical. Benchmark calculations using B3LYP, CAM- B3LYP, PBE0, M06-2X, LC-wHPBE, and wB97XD on the excited electronic states and absorption spectra indicate that CAM-B3LYP, M06-2X, and wB97XD are the most effective for predicting the absorption spectra of Flavone. | MANJEET BHATIA | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e32818cec5d6c142e358ef/original/exploring-flavone-reactivity-a-quantum-mechanical-study-and-tddft-benchmark-on-uv-vis-spectroscopy.pdf |
60c744f7bb8c1a07f03da5ce | 10.26434/chemrxiv.8246498.v2 | Norm-Conserving Pseudopotentials and Basis Sets Optimized for Lanthanide Molecules and Solid-State Compounds | A complete set of pseudopotentials and corresponding basis sets for all lanthanide elements are presented based on the relativistic, norm-conserving, Gaussian-type pseudo potential protocol of Goedecker, Teter, and Hutter (GTH) within the generalized gradient approximation and exchange-correlation functional of Perdew, Burke, and Ernzerhof. The accuracy and reliability of our GTH pseudopotentials and companion basis sets optimized for lanthanides is illustrated by a series of test calculations on lanthanide-containing molecules and solid-state systems. | Junbo Lu; David Cantu; Manh-Thuong Nguyen; Jun Li; Vassiliki-Alexandra Glezakou; Roger Rousseau | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f7bb8c1a07f03da5ce/original/norm-conserving-pseudopotentials-and-basis-sets-optimized-for-lanthanide-molecules-and-solid-state-compounds.pdf |
60c74daebb8c1ad7883db622 | 10.26434/chemrxiv.12646919.v1 | Robust Supramolecular Nano-Tunnels Built from Molecular Bricks | Chemists are always seeking new methods to construct porous lattice frameworks using simple motifs as the impetus. Different from the extensively reported frameworks which were stabilized by extended bonding, porous crystals of discrete organic molecules is an emerging area of porous materials with dynamic and flexible conformation, consisting exclusively of non-covalent interactions. Herein we report geometrically simple linear molecule that assemble into a supramolecular nano-tunnel through synergy of anionic trident and multiple intermolecular pi-pi stacking interactions. The nano-tunnel crystal exhibit exceptional chemical stability in concentrated HCl and NaOH aqueous solutions, which is rarely been seen in supramolecular organic frameworks and often related to designed extensive hydrogen bonding interactions. Upon thermal treatment, the formed nano-tunnel crystals go through multistage single-crystal-to-single-crystal phase transformations accompanied by thermosalient effect. Aggregation-induced emission joins with the adaptive pores render the crystals with responsive fluorescent change from blue to yellow and visible self-healing porosity transformation upon being stimulated. Furthermore, the desolvated pores exhibit highly selective CO2 adsorption at ambient temperature. <br /> | Peifa Wei; Zheng Zheng; Junyi Gong; Jun Zhang; Herman H.-Y. Sung; Ian Duncan Williams; Jacky W. Y. Lam; Ben Zhong Tang | Aggregates and Assemblies; Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74daebb8c1ad7883db622/original/robust-supramolecular-nano-tunnels-built-from-molecular-bricks.pdf |
623c15d75cf71977fc5ed517 | 10.26434/chemrxiv-2022-xwrc7-v2 | Theoretical and Experimental Investigations of Shape Memory Characteristics of Miscible Rubber-Wax Blends | Shape Memory Polymers (SMPs) are smart materials capable of transforming back to their intended shape and therefore, are used to replicate biomimetic functionalities in synthetic materials. Here, we demonstrate that polymer blending can be used as an effective technique to design SMPs. In particular, the blends consists of wax and rubber that signify soft and hard segments of the SMP, respectively. In particular, we use the standard linear viscoelastic model where the two constituents, rubber represented by Hookean spring and wax represented by Maxwellian liquid, are connected in parallel; hence, we assume that the contribution of each component in the total stress is distributed in proportion of the composition. Via simulation, we establish that wax and rubber, individually do not exhibit shape memory behavior but do so upon blending; the shape memory behavior is qualitatively validated from experiments. We also confirm that the shape memory properties of our rubber-wax blends, namely, the shape fixity and shape recovery ratios at different concentrations, is in qualitative agreement with the properties of SMPs. Our findings indicate that polymer blending can be seen as an alternative strategy to design SMPs; the properties of these polymers can be varied directly by changing the composition of the blend. | Surbhi Khewle; Priyanka Nemani; Nikhil Sharma; Pratyush Dayal | Materials Science; Polymer Science; Polymer blends | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623c15d75cf71977fc5ed517/original/theoretical-and-experimental-investigations-of-shape-memory-characteristics-of-miscible-rubber-wax-blends.pdf |
60c74061567dfe1f37ec3b7a | 10.26434/chemrxiv.7712510.v1 | Exploring the stochasticity of chemical processes in an automated robotic crystallization platform to generate random numbers | <p>Random number generators are important in fields which
require non-deterministic input, such as cryptography. One example of a
non-deterministic system is found in chemistry via the crystallization of
chemical compounds, which occurs through stochastic processes. Herein, we
present an automated platform capable of generating random numbers from
observation of crystallizations resulting from multiple parallel one-pot
chemical reactions. From the resulting images, crystals were identified using
computer vision, and binary sequences were obtained by applying a binarization
algorithm to these regions. An assessment of randomness of these sequences was
undertaken by applying a barrage of tests for randomness described by the
National Institute of Standards and Technology (NIST). We find that numbers
generated through this method are able to pass each of the three levels for
each of the NIST tests. We then compare the encryption strength of the random
numbers generated from each of the crystallizing systems to that of a
pseudo-random number generation algorithm (the Mersenne Twister). We find that
messages encrypted using chemically derived random numbers take significantly
longer to decrypt than the algorithmically generated number.</p> | Leroy Cronin; Edward Lee; Juan Manuel Parrilla Gutiérrez; Alon Henson; Euan K. Brechin | Supramolecular Chemistry (Inorg.); Clusters; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74061567dfe1f37ec3b7a/original/exploring-the-stochasticity-of-chemical-processes-in-an-automated-robotic-crystallization-platform-to-generate-random-numbers.pdf |
60c741a8ee301cb49dc78ce8 | 10.26434/chemrxiv.8081945.v1 | On the Relative Resonance-Acceptor Abilities of CN, NO, COMe, CHO and NO2 Groups | <p>The relative resonance-acceptor ability based on ∆G<sup>‡</sup><sub>out</sub> is different from that based on ∆G<sup>‡</sup><sub>in</sub> for the conrotatory ring-opening of 3-carbomethoxycyclobutene bearing CN, NO, COMe, CHO and NO<sub>2</sub> as C1-substituent. In contrast, the relative resonance-acceptor ability based on s<sub>C3C4</sub>-p*<sub>C1C2 </sub>interaction in TS<sub>out</sub> is much the same as in TS<sub>in</sub>. It matches further with the acceptor ability based on the net of s<sub>C3C4</sub>-p*<sub>C1C2 </sub>and p<sub>C1C2</sub>-s*<sub>C3C4 </sub>interactions. The overall resonance-acceptor ability is estimated to be CN < COMe < CHO < NO<sub>2</sub> < NO from calculations at MP2/6-31+G(d,p) level of theory.</p> | Veejendra Yadav; Arpita Yadav | Physical Organic Chemistry; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a8ee301cb49dc78ce8/original/on-the-relative-resonance-acceptor-abilities-of-cn-no-co-me-cho-and-no2-groups.pdf |
65c436f966c13817292e9bfc | 10.26434/chemrxiv-2024-cwnwc | An affordable platform for automated synthesis and electrochemical characterization
| Electrochemical techniques are pivotal for material discovery and renewable energy; however, often the extensive chemical spaces to be explored require high-throughput experimentation (HTE) to ensure timely results, which are costly both for instrument and materials/consumables. While self-driving laboratories (SDL) promise efficient chemical exploration, most contemporary implementations demand significant time, economic investment, and expertise. This study introduces an open and cost-effective autonomous electrochemical setup, comprising a synthesis platform and a custom-designed potentiostat device. We present an SDL platform that offers rapid deployment and extensive control over electrochemical experiments compared to commercial alternatives. Using ChemOS 2.0 for orchestration, we showcase our setup's capabilities through a campaign in which different metal ions reacts with ligands to form coordination compounds., yielding a database of 400 electrochemical measurements. Committed to open science, we provide a potentiostat design, campaign software, and raw data, aiming to democratize customized components in SDLs and ensure transparent data sharing and reproducibility. | Sergio Pablo-García; Ángel García; Gun Deniz Akkoc; Malcolm Sim; Yang Cao; Maxine Somers; Chance Hattrick; Naruki Yoshikawa; Dominik Dworschak; Han Hao; Alán Aspuru-Guzik | Theoretical and Computational Chemistry; Inorganic Chemistry; Analytical Chemistry; Coordination Chemistry (Inorg.); Electrochemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c436f966c13817292e9bfc/original/an-affordable-platform-for-automated-synthesis-and-electrochemical-characterization.pdf |
66b93e5f5101a2ffa806de18 | 10.26434/chemrxiv-2024-xpt6r | Operando electron spin probes for the study of battery processes | Operando electron spin probes, namely magnetometry and electron paramagnetic resonance (EPR), provide real-time insights into the electrochemical processes occurring in battery materials and devices. In this work, we describe the design criteria and outline the development of operando magnetometry and EPR electrochemical cells. Notably, we show that a clamping mechanism, or springs, are needed to achieve sufficient compression of the battery stack and an electrochemical performance on par with that of a standard Swagelok-type cell. The tandem use of operando EPR and magnetometry allows us to identify five distinct and reversible redox processes taking place on charge and discharge of the intercalation-type LiNi0.5Mn0.5O2 Li-ion cathode. While redox processes in conversion-type electrodes are notoriously difficult to investigate using standard characterization methods (e.g. X-ray based) and/or post mortem analysis, due to the formation of poorly crystalline and metastable reaction intermediates and products during cycling, we show that operando magnetometry provides unique insight into the kinetics and reversibility of Fe nanoparticle formation in the Na3FeF6 electrode for Na-based batteries. Step increases in the cell magnetization upon extended cycling indicate the build-up of Fe nanoparticles in the system, hinting at only partially reversible charge-discharge processes. The broad applicability of the tools developed herein to a range of electrode chemistries and structures, from intercalation to conversion electrodes, and from crystalline to amorphous systems, makes them particularly promising for the development of electrochemical energy storage technologies and beyond. | Howie Nguyen; Euan Bassey; Emily Foley; Daniil Kitchaev; Raynald Giovine; Raphaële Clément | Materials Science; Energy; Magnetic Materials; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b93e5f5101a2ffa806de18/original/operando-electron-spin-probes-for-the-study-of-battery-processes.pdf |
6550dbf4dbd7c8b54b1fa875 | 10.26434/chemrxiv-2023-91xf7 | Synthesis and assessment of novel sustainable antioxidants with different polymer systems. | Antioxidants are essential to the polymer industry. The addition of antioxidants delays oxidation and materials degradation during their processing and usage. Sustainable phenolic acids such as 4-hydroxybenzoic acid or 3,4-dihydroxybenzoic acid have been selected. They have been chemically modified by esterification to obtain various durable molecules, which have been tested and then compared to resveratrol, a biobased antioxidant, and Irganox 1076, a well-known and very efficient fossil-based antioxidant. Different sensitive matrices have been used, such as a thermoplastic polyolefin (a blend of PP and PE) and a purposely synthesized thermoplastic polyurethane. Several formulations were then produced, with the different antioxidants in varying amounts. The potential of these different systems has been analyzed using various techniques and processes. In addition to antioxidant efficiency, other parameters were also evaluated, such as the evolution of the sample color. Finally, an accelerated aging protocol was set up to evaluate variations in polymer properties and estimate the evolution of the potential of different antioxidants tested over time and with aging. In conclusion, these environmentally friendly antioxidants make it possible to obtain high-performance materials with efficiency comparable to that of conventional ones, with variations according to the type of matrix considered. | Agathe Mouren; Eric Pollet; Luc Avérous | Materials Science; Polymer Science | CC BY 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6550dbf4dbd7c8b54b1fa875/original/synthesis-and-assessment-of-novel-sustainable-antioxidants-with-different-polymer-systems.pdf |
676f6096fa469535b9072d56 | 10.26434/chemrxiv-2025-jlc89 | Optimizing Solid-Phase Protein Synthesis: A Systematic Study of Solid Supports and Mild Cleavage Techniques | Solid-phase chemical ligation (SPCL) is a powerful method for simplifying protein synthesis, offering streamlined workflows, improved efficiency, and higher yields. However, the broader application of SPCL, particularly for synthesizing larger proteins, is hindered by the complexity of orthogonal protection strategies, suboptimal solid supports, and limited availability of compatible cleavable linkers. In this study, we systematically evaluated solid supports and cleavable linkers to optimize SPCL. By combining the low loading-controlled pore glass (CPG-2000) support with a nickel-cleavable SNAC-tag linker, we developed an optimized system that enabled the successful assembly of five peptide fragments through SPCL. his approach facilitated the efficient synthesis of a 130-amino-acid de novo designed protein with a yield of approximately 25%. | Jianyi Han; Bobo Dang | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676f6096fa469535b9072d56/original/optimizing-solid-phase-protein-synthesis-a-systematic-study-of-solid-supports-and-mild-cleavage-techniques.pdf |
60c74fe0f96a00a72a287d0d | 10.26434/chemrxiv.12951062.v1 | Pouch-Cell Architecture Downscaled to Coin Cells for Electrochemical Characterization of Bilateral Electrodes | <p>We suggest a new technique to assemble coin cells that allows
the use of two unilateral electrodes with a bilateral electrode sandwiched
between them. This method requires no unique tools or materials, and can help
labs with limited resources test their electrodes in more realistic, pouch type
conditions that can better showcase the capabilities of their novel research
products.</p> | Dan Schneier; Nimrod Harpak; Fernando Patolsky; Diana Golodnitsky; Emanuel Peled | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fe0f96a00a72a287d0d/original/pouch-cell-architecture-downscaled-to-coin-cells-for-electrochemical-characterization-of-bilateral-electrodes.pdf |
63f3eb499da0bc6b3343a63d | 10.26434/chemrxiv-2023-ht795 | The preservation of sarin and O,O’-diisopropyl fluorophosphate inside coordination cage hosts | The host-guest chemistry of O,O-diisopropyl fluorophosphate (DFP), a phosphonofluoridate G-series chemical warfare agent simulant, in the presence of a number of octanuclear cubic coordination cages was investigated. The aim was to demonstrate cage-catalysed hydrolysis of DFP at near neutral pH, however, two octanuclear coordination cages, HPEG (containing water solubilising PEG groups) and HW (containing water solubilising hydroxymethyl groups), were actually found to increase the lifetime of DFP in aqueous buffer solution (pH 8.7). Crystallographic analysis of DFP with a structurally related cage revealed that DFP binds to windows in the cage surface, not the internal cavity, with the phosphorus-fluorine bond directed into the cavity rather than towards the external environment, with the cage/DFP association protecting DFP from hydrolysis. Initial studies with the chemical warfare agent (CWA) sarin (GB) with HPEG cage in a buffered solution also drastically reduced the rate of hydrolysis. The ability of these cages to inhibit the hydrolysis of these P-F bond containing organophosphorus guests, by encapsulation, may have applications in forensic sample preservation and analysis. | Jack Dorrat; Rosemary Young; Chris Taylor; Max Tipping; Andrew Blok; David Turner; Alasdair McKay; Simon Ovenden; Michael Ward; Genevieve Dennison; Kellie Tuck | Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f3eb499da0bc6b3343a63d/original/the-preservation-of-sarin-and-o-o-diisopropyl-fluorophosphate-inside-coordination-cage-hosts.pdf |
6311890cbc257b24e1d84247 | 10.26434/chemrxiv-2022-xbjw2 | Confinement effect catalysis with covalent organic frameworks for highly efficient synthesis of lactide | The efficient synthesis of lactide with high purity is the key to poly-lactic acid (PLA) production. Here, we demonstrated a 2D COFs-based catalyst, which could convert L-lactic acid into L-lactide directly in an excellent yield (80%) under mild conditions. Similar to enzymatic catalysis in which the product selectivity is controlled by the enzyme pocket, the precision confinement effect of the highly ordered channels and adjustable structures with functional moieties of the COFs play key roles in converting the monomer to the cyclic dimer directly and avoiding oligomerization. This strategy is sharply different from the current two-stage process for synthesizing lactide and renders COFs materials as an ideal heterogeneous catalyst with confinement effect. | Jinyu Zhao; Guangming Guo; Danbo Wang; Hui Liu; Zhenxiu Zhang; Lishui Sun; Naixiu Ding; Zhibo Li; Yingjie Zhao | Catalysis; Polymer Science; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6311890cbc257b24e1d84247/original/confinement-effect-catalysis-with-covalent-organic-frameworks-for-highly-efficient-synthesis-of-lactide.pdf |
63597b4f2e0c63f4c83d7d32 | 10.26434/chemrxiv-2022-cq1qm | A surrogate based genetic algorithm method for efficient identification of low-energy peptide structures | Identification of the most stable structure(s) of a system is a prerequisite for the calculation of any of its properties from first-principles. However, even for relatively small molecules, exhaustive explorations of the potential energy surface (PES) are severely hampered by the dimensionality bottleneck. In this work, we address the challenging task of efficiently sampling realistic low-lying peptide coordinates by resorting to a surrogate based genetic algorithm (GA)/density functional theory (DFT) approach (sGADFT) in which promising candidates provided by the GA are ultimately optimized with DFT. We provide a benchmark of several computational methods (GAFF, AMOEBApro13, PM6, PM7, DFTB3-D3(BJ)) as possible prescanning surrogates and apply sGADFT to two test case systems that are (i) two isomer families of the protonated Gly-Pro-Gly-Gly tetrapeptide, and (ii) the doubly-protonated cyclic decapeptide gramicidin S. We show that our GA procedure can correctly identify low-energy minima in as little as a few hours. Subsequent refinement of surrogate low-energy structures within a given energy threshold (≤ 10 kcal/mol (i), ≤ 5 kcal/mol (ii)) via DFT relaxation invariably led to the identification of the most stable structures as determined from high-resolution infrared (IR) spectroscopy at low temperature. The sGADFT method therefore constitutes a highly efficient route for the screening of realistic low-lying peptide structures in the gas phase as needed for instance for the interpretation and assignment of experimental IR spectra. | Justin Villard; Murat Kılıç; Ursula Rothlisberger | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2022-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63597b4f2e0c63f4c83d7d32/original/a-surrogate-based-genetic-algorithm-method-for-efficient-identification-of-low-energy-peptide-structures.pdf |
60c741240f50dbe270395a6d | 10.26434/chemrxiv.7949024.v1 | RDChiral: An RDKit Wrapper for Handling Stereochemistry in Retrosynthetic Template Extraction and Application | There is a renewed interest in computer-aided synthesis planning, where the vast majority of approaches require the application of retrosynthetic reaction templates. Here, we introduce an open source Python wrapper for RDKit designed to provide consistent handling of stereochemical information in applying retrosynthetic transformations encoded as SMARTS strings. RDChiral is designed to enforce the introduction, destruction, retention, and inversion of tetrahedral centers as well as the cis/trans chirality of double bonds. We also introduce an open source implementation of a retrosynthetic template extraction algorithm to generate SMARTS patterns from atom-mapped reaction SMILES strings. In this manuscript, we describe the implementation of these two pieces of code and illustrate their use through many examples.<div><br /></div><div>The two .json.gz files can be generated from the open source USPTO data available at https://figshare.com/articles/Chemical_reactions_from_US_patents_1976-Sep2016_/5104873 using the code contained in the rdchiral GitHub repository. They are placed here for convenience if you would prefer to copy them into the templates/data subfolder instead of creating them from the source .rsmi file.</div> | Connor W. Coley; William H. Green; Klavs F. Jensen | Stereochemistry; Chemoinformatics | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741240f50dbe270395a6d/original/rd-chiral-an-rd-kit-wrapper-for-handling-stereochemistry-in-retrosynthetic-template-extraction-and-application.pdf |
61ade8fd772cb28cd4522de9 | 10.26434/chemrxiv-2021-2dz95 | More Than Carbazole Derivative Activates Room Temperature Ultralong Organic Phosphorescence of Benzoindole Derivative | Herein, we report four carbazole/1H-benzo[f]indole (Cz/Bd) derivatives with increasing Bd substitution (Bd number=0~3), which give a general mechanism for Bd-based ultralong organic phosphorescence. To physically isolate Cz and Bd, we synthesized Cz and Bd in the lab, separately. According to experimental results, we draw several important points. The first important point is that Bd and its derivatives commonly possess two groups of intrinsic phosphorescence bands, of which short-lifetime band at ~450 nm is assigned to the molecular phosphorescence of their neutral molecules and of which typical ultralong phosphorescence bands at 560 nm, 610 nm and 660 nm are assigned to their radical cations. Amazingly, PMMA films (1wt.%) of CNCzBdBr and CN2BdBr both demonstrate photo-activated room-temperature ultralong organic phosphorescence while this doesn’t happen to Bd and CN3Bd. The second important point is that activation of ultralong phosphorescence from Bd derivatives involves three factors: well dispersion with limited amount in matrix, generation of Bd derivatives’ radical cations and stabilizing radical cations mediated by matrix. Cz derivative can function as a matrix to activate (room temperature) ultralong organic phosphorescence of Bd derivative but its activation function can be replaced by other methods such as photo-activation. The third important point is that the photo-activated ultralong organic phosphorescence is closely related to molecular structure of Bd derivative and stability of its radical cation. The fourth important point is that for double-carbazole system with trace isomer its room temperature ultralong organic phosphorescence originates at least from synergistic effect of monosubstituted product and disubstituted product of Bd. Furthermore, it is discovered that several other matrixes can also activate room-temperature ultralong organic phosphorescence of Bd derivatives, further verifying the second important point. To our best knowledge, this study is a big breakthrough in ultralong organic phosphorescence and will probably open a new era for its development. | Zhiyong Ma; Chen Qian; Zhimin Ma; Xiaohua Fu; Xue Zhang; Zewei Li; Huiwen Jin; Mingxing Chen; Hong Jiang; Xinru Jia | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ade8fd772cb28cd4522de9/original/more-than-carbazole-derivative-activates-room-temperature-ultralong-organic-phosphorescence-of-benzoindole-derivative.pdf |
6526cdb045aaa5fdbbc8f82b | 10.26434/chemrxiv-2023-v1rbg | Diazene-Catalyzed Oxidative Alkyl Halide-Olefin Metathesis | The first platform for oxidative alkyl halide-olefin metathesis is described. The procedure employs diazenes as catalysts, which effect cyclization of alkenyl alkyl halides to generate cyclic olefins. Mechanistically, the diazene catalyst is converted to a hydrazonium intermediate by alkylation with the alkyl halide component followed by tautomerization. The resulting hydrazonium ion reacts with the olefin component through [3+2] cycloaddition and cycloreversion reactions, leading to new olefin and hydrazonium moieties. Hydrolysis of the newly formed hydrazonium was found to outcompete retro-tautomerization / dealkylation, thus furnishing a carbonyl product instead of an alkyl halide. For this reason, the process is termed oxidative alkyl-halide olefin metathesis. Adventitious O2 and H2O were sufficient for catalyst turnover. The synthesis of phenanthrene, coumarin, and quinolone derivatives is demonstrated, as well as the potential to apply this strategy to other electrophiles. | Julian Kellner-Rogers; Rina Wang; Tristan Lambert | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2023-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6526cdb045aaa5fdbbc8f82b/original/diazene-catalyzed-oxidative-alkyl-halide-olefin-metathesis.pdf |
65a55fe266c1381729832427 | 10.26434/chemrxiv-2024-2v7k1 | A lysate-based TR-FRET approach for the facile quantification of cellular drug concentration | Many pharmacologically relevant drug targets are located inside cells. The development of therapeutically active small molecule modulators for intracellular targets requires that successful drug candidates can efficiently pass through the plasma membrane at higher rates than their metabolic inactivation or expulsion by drug efflux pumps. Such knowledge is invaluable for correlating biochemical and cellular activity, and for guiding ligand optimization. Despite the critical im-portance of this metric, current methodologies for measuring the intracellular concentration of non-fluorescent small molecules have many limitations, significantly restricting the ability of medicinal chemists to readily and routinely measure cellular drug concentration. We here introduce a straightforward, high-throughput TR-FRET assay platform based on CoraFluor technology to readily quantify the abundance of biologically active small molecules in whole cell lysates. Our approach builds on existing homogenous ligand displacement assays and does not require any additional reagents or equipment, enabling the comprehensive biochemical and cellular characterization of small molecule ligands. | N. Connor Payne; Ralph Mazitschek | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a55fe266c1381729832427/original/a-lysate-based-tr-fret-approach-for-the-facile-quantification-of-cellular-drug-concentration.pdf |
613526b890051ea90ae9a733 | 10.26434/chemrxiv-2021-l64kg | Proline transport inhibitors trigger differential responses in Trypanosoma cruzi growth inhibition | Background: Proline is a fundamental amino acid for Trypanosoma cruzi, the etiological agent of Chagas disease. Proline is mainly incorporated from the extracellular medium by amino acid transport systems. Different proline analogues proved to interact with the proline permease TcAAAP069 and inhibit the proline uptake by T. cruzi.
Methods: Decyl- (1), oleyl- (2) and farnesyl- (3) substituted proline analogues were evaluated on six T. cruzi DTUs. Cell death type was determined by flow cytometry, and the effect on the parasite metabolism was analysed by directed NMR exometabolomics. Structural modifications of 1 (compounds 4 – 6) were implemented to have more information on the mode of action (MoA).
Results: The compounds showed broad-spectrum activity against all DTUs. Compound 3 at high concentration (116 µM) induced necrosis. The removal of the triazole from 1 proved to be important for the activity. Compounds 1 and 2 induced deep changes in the exometabolome, diminishing the amounts of succinate, lactate, acetate, and ethanol excreted. The fluorescent labelling and subsequent microscopy showed that compound 1 can be taken up by epimastigotes.
Conclusions: Two different MoA related to proline transport for decyl and farnesyl-substituted proline analogues are proposed. The former presented an in-cell action while the latter was not taken up by the parasites but interacted with the extracellular side of the proline permease.
General Significance: Subtle structural variations in the compounds determine differences in the MoA. This finding opens new perspectives that should be examined on the development of new drugs targeting metabolite permeases.
| María Sol Ballari; Lucía Fargnoli; Lucas Pagura; Julia Cricco; Ariel Silber; Guillermo Labadie | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613526b890051ea90ae9a733/original/proline-transport-inhibitors-trigger-differential-responses-in-trypanosoma-cruzi-growth-inhibition.pdf |
64f1ff7379853bbd78dff313 | 10.26434/chemrxiv-2023-w50m1 | Partially perfluorinated derivatives as powerful tool for the restoration of blanching easel paintings | Perfluorinated oligoamides/amines were prepared and characterized. They were
evaluated then for easel painting restoration by filling pores resulting of the blanching.
They were used on prepared mock-ups analysed by FEG-SEM for morphological
changes and by spectro-colorimetry analysis for the restoration. Compared to
DG6G900 , the new partially perfluorinated products DSTF and DSF are recommended
as restoration products for blanching easel paintings. | Yuqing Zhang; Myriam Eveno; Florian Gallier; Mara Camaiti; Nadège Lubin-Germain; Antonella Salvini; Agnès Lattuati-Derieux | Polymer Science | CC BY NC 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1ff7379853bbd78dff313/original/partially-perfluorinated-derivatives-as-powerful-tool-for-the-restoration-of-blanching-easel-paintings.pdf |
67c10ea5fa469535b93eec48 | 10.26434/chemrxiv-2025-8dmvw-v2 | Gram-scale Synthesis of Dibenzo[a,e]pentalenes from Trialkyl(phenylethynyl)silanes via Organosodium Intermediates | Previous gram-scale synthesis of 5,10-disilyldibenzo[a,e]pentalenes (5,10-disilylDBPs), which are good precursors of 5,10-dihaloDBPs, was accomplished by the reduction of trialkyl(phenylethynyl)silanes with highly pyrophoric potassium metals. Here we report two types of potassium-free and scalable synthesis of 5,10-disilylDBPs: (1) reduction of trialkyl(phenylethynyl)silanes with sodium dispersion (SD), and (2) reduction of trialkyl(phenylethynyl)silanes with lithium in the presence of NaOtBu. Both reactions involve 1,4-disodio-1,3-butadienes with an s-trans conformation as the key intermediates. | Ayane Sato; Takuya Kuwabara | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c10ea5fa469535b93eec48/original/gram-scale-synthesis-of-dibenzo-a-e-pentalenes-from-trialkyl-phenylethynyl-silanes-via-organosodium-intermediates.pdf |
60c74c27f96a004458287722 | 10.26434/chemrxiv.12362333.v2 | Natural Compounds as Inhibitors of SARS-CoV-2 Main Protease (3CLpro): A Molecular Docking and Simulation Approach to Combat COVID-19 | <p></p><p>Recently, the
emergence and dissemination of SARS-CoV-2 has caused high mortality and
enormous economic loss. In the fight against COVID-19, the rapid development of
new drug molecules is the need of hour. However, the conventional approaches of
drug development is time consuming and expensive in nature. In this study, we
have adopted an alternative approach to identify lead molecules from natural
sources using high throughput virtual screening approach. Ligands from natural compounds
library from Selleck Inc (L1400) have been screened to evaluate their ability
to bind and inhibit the main protease (M<sup>pro</sup> or 3CL<sup>pro</sup>) of
SARS-CoV-2, which is a potential drug target. We found that Kaempferol,
Quercetin, and Rutin were able to bind at the substrate binding pocket of 3CL<sup>pro</sup>
with high affinity (10<sup>5</sup>-10<sup>6</sup> M<sup>-1</sup>) and interact
with the active site residues such as His41 and Cys145 through hydrogen bonding
and hydrophobic interactions. In fact, the binding affinity of Rutin was much
higher than Chloroquine (1000 times) and Hydroxychloroquine (100 times) and was
comparable to that of the reference drug Remdesivir, which is in clinical
trials to treat COVID-19 patients. The results suggest that natural compounds
such as flavonoids have the potential to be developed as novel inhibitors of
SARS-CoV-2 with a comparable potency as that of Remdesivir. However, their
clinical usage on COVID-19 patients is a subject of further investigations and
clinical trials.</p><br /><p></p> | Md Tabish Rehman; Mohamed F AlAjmi; Afzal Hussain | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c27f96a004458287722/original/natural-compounds-as-inhibitors-of-sars-co-v-2-main-protease-3c-lpro-a-molecular-docking-and-simulation-approach-to-combat-covid-19.pdf |
6672e42601103d79c5932f33 | 10.26434/chemrxiv-2024-zf81q | Machine-learning prediction of protein function from the portrait of its intramolecular electric field | We introduce a machine learning framework designed to predict enzyme functionality directly from the heterogeneous electric fields inherent to protein active sites. We apply this method to a curated dataset of Heme-Iron Oxidoreductases, spanning three enzyme classes: monooxygenases, peroxidases, and catalases. Conventional analysis, focused on simplistic, point electric fields along the Fe-O bond, are shown to be inadequate for accurate activity prediction. Our model demonstrates that the enzyme's heterogenous 3-D electric field, alone, can accurately predict its function, without relying on additional protein-specific information. Through feature selection, we uncover key electric field components that not only validate previous studies but also underscore the crucial role of multiple components beyond the traditionally emphasized electric field along the Fe-O bond in heme enzymes. Further, by integrating protein dynamics, principal component analysis, clustering, and QM/MM calculations, we reveal that while dynamic complexities in protein structures can complicate predictions, accounting for this increased dynamic variability can substantially enhance model performance. This research significantly advances our understanding of how protein scaffolds possess signature electric fields that are tailored to their functions at the active site. Moreover, it presents a novel electrostatics-based tool to harness these signature electric fields for predicting enzyme function. | Santiago Vargas; Shobhit Chaturvedi; Anastassia Alexandrova | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6672e42601103d79c5932f33/original/machine-learning-prediction-of-protein-function-from-the-portrait-of-its-intramolecular-electric-field.pdf |
65b128c4e9ebbb4db9e1fe32 | 10.26434/chemrxiv-2024-1rw6m | Unveiling the Mechanistic Role of Chiral Palladacycles in Pd(II)-Catalyzed Enantioselective C(sp3)-H Functionalization | Palladium-catalyzed enantioselective C(sp3)-H functionalization reactions has attracted considerable attention due to its ability for the synthesis of enantiomerically enriched molecules and stimulation of novel retrosynthetic disconnections. Understanding the reaction mechanism, especially the stereochemical process of the reaction, is crucial for the rational design of more efficient catalytic systems. Previously, we developed a Pd(II)/sulfoxide-2-hydroxypridine (SOHP) catalytic system for asymmetric C(sp3)-H functionalization reactions. In this study, our focus is on unraveling the chemistry of chiral palladacycles involved in the Pd(II)-catalyzed enantioselective C(sp3)-H functionalization. We have isolated key palladacycle intermediates involved in the enantioselective β-C(sp3)-H arylation of carboxylic acids catalyzed by the Pd(II)/SOHP system. These palladacycles, exhibiting ligand-induced chirality, provided a significant opportunity to investigate the stereochemical process and the ligand effect in this asymmetric C-H functionalization. Our investigation revealed that the C(sp3)-H palladation step is irreversible, representing the enantioselectivity-determining step to form diastereomeric palladacycles. Ligand exchange experiments and DFT calculations provided insights into the chiral induction in palladacycle formation and the preservation of chirality in the functionalization step. This work highlights the value of chiral palladacycle chemistry in offering mechanistic insights into the Pd(II)-catalyzed asymmetric C(sp3)-H functionalization reactions. | Chen-Hui Yuan; Xiao-Xia Wang; Keyun Huang; Lei Jiao | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b128c4e9ebbb4db9e1fe32/original/unveiling-the-mechanistic-role-of-chiral-palladacycles-in-pd-ii-catalyzed-enantioselective-c-sp3-h-functionalization.pdf |
60c754814c89198281ad453f | 10.26434/chemrxiv.13271501.v3 | A General Model to Optimise Copper(II) Labelling Efficiency of Double-Histidine Motifs for Pulse Dipolar EPR Applications | <div>
<p>Electron paramagnetic
resonance (EPR) distance measurements are making increasingly important
contributions to studies of biomolecules underpinning health and disease by
providing highly accurate and precise geometric constraints. Combining
double-histidine (dH) motifs with Cu<sup>II</sup> spin labels shows promise for
further increasing the precision of distance measurements, and for
investigating subtle conformational changes. However, non-covalent coordination-based
spin labelling is vulnerable to low binding affinity. Dissociation constants of
dH motifs for Cu<sup>II</sup>-nitrilotriacetic acid were previously
investigated <i>via </i>relaxation induced dipolar modulation enhancement
(RIDME), and demonstrated the feasibility of exploiting the double histidine
motif for EPR applications at sub-μM protein concentrations. Herein, the
feasibility of using modulation depth quantitation in Cu<sup>II</sup>-Cu<sup>II
</sup>RIDME to simultaneously estimate a pair of non-identical independent <i>K<sub>D</sub></i>
values in such a tetra-histidine model protein is addressed. Furthermore, we
develop a general speciation model to optimise Cu<sup>II </sup>labelling
efficiency, in dependence of pairs of identical or disparate <i>K<sub>D</sub></i>
values and total Cu<sup>II</sup> label concentration. We find the dissociation
constant estimates are in excellent agreement with previously determined values,
and empirical modulation depths support
the proposed model. </p>
</div>
<br /> | Joshua L. Wort; Katrin Ackermann; David G. Norman; Bela E. Bode | Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754814c89198281ad453f/original/a-general-model-to-optimise-copper-ii-labelling-efficiency-of-double-histidine-motifs-for-pulse-dipolar-epr-applications.pdf |
60c75876842e651efcdb486b | 10.26434/chemrxiv.14555355.v1 | A Robust and Efficient Implicit Solvation Model for Fast Semiempirical Methods | We present a robust and efficient method to implicitly account for solvation effects in modern semiempirical quantum mechanics and force-fields. A computationally efficient yet accurate solvation model based on the analytical linearized Poisson--Boltzmann~(ALPB) model is parameterized for the extended tight binding (xTB) and density functional tight binding (DFTB) methods as well as for the recently proposed GFN-FF general force-field. The proposed methods perform well over a broad range of systems and applications, from conformational energies over transition-metal complexes to large supramolecular association reactions of charged species. For hydration free energies of small molecules GFN1-xTB(ALPB) is reaching the accuracy of sophisticated explicitly solvated approaches, with a mean absolute deviation of only 1.4 kcal/mol compared to experiment. Logarithmic octanol--water partition coefficients (log K<sub>ow</sub>) are computed with a mean absolute deviation of about 0.65 using GFN2-xTB(ALPB) compared to experimental values indicating a consistent description of differential solvent effects. Overall, more than twenty solvents for each of the six semiempirical methods are parameterized and tested. They are readily available in the xtb and dftb+ programs for diverse computational applications. | Sebastian Ehlert; Marcel Stahn; Sebastian Spicher; Stefan Grimme | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75876842e651efcdb486b/original/a-robust-and-efficient-implicit-solvation-model-for-fast-semiempirical-methods.pdf |
6745f6027be152b1d0ee4d33 | 10.26434/chemrxiv-2024-v335b-v2 | Solution Thermodynamics of L-Glutamic Acid Polymorphs from Finite-Sized Molecular Dynamics Simulations | Efficiently obtaining atomic-scale thermodynamic parameters characterizing crystallization from solution is key to developing the modeling strategies needed in the quest for digital design strategies of industrial crystallization processes. Based on the thermodynamics of crystal nucleation in confined solutions, we develop a simulation framework to efficiently estimate the solubility and surface tension of organic crystals in solution from a few unbiased molecular dynamics simulations at a reference temperature. We then show that such a result can be extended with minimal computational overhead to capture the whole solubility curve. This enables an efficient and self-consistent estimate of the solubility and limit of solution stability associated with crystal nucleation in molecular systems from equilibrium molecular dynamics without requiring sophisticated free energy calculations. We apply our analysis to investigate the relative thermodynamics stability and aqueous solubility of the α and β polymorphs of L-Glutamic acid. Our analysis enables an efficient appraisal of emergent ensemble properties associated with the thermodynamics of nucleation from solutions against experimental data, demonstrating that while the absolute solubility is still far from being quantitatively captured by an off-the-shelf point charge transferable forcefield, the relative polymorphic stability and solubility obtained from finite temperature simulation are consistent with the experimentally available information on glutamic acid. We foresee the ability to efficiently obtain solubility information from a limited number of computational experiments as a key component of high-throughput computational polymorph screenings. | Fabienne Bachtiger; Aliff Rahimee; Lunna Li; Matteo Salvalaglio | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6745f6027be152b1d0ee4d33/original/solution-thermodynamics-of-l-glutamic-acid-polymorphs-from-finite-sized-molecular-dynamics-simulations.pdf |
60c749b4bdbb89f804a39221 | 10.26434/chemrxiv.12100599.v1 | Caffeinated Interfaces Enhance Alkaline Hydrogen Electrocatalysis | <p>The high Pt loading required for hydrogen oxidation
(HOR) and evolution (HER) reactions in alkaline fuel cells and electrolyzers
adversely impacts the system cost. Here, we demonstrate the use of caffeine as
a ‘double-layer dopant’ to enhance both the HER and HOR of Pt electrodes in
base. HER/HOR rates increase by fivefold on Pt(111) and are accelerated on
Pt(110), Pt(pc), and Pt/C as well. FTIR spectroscopy confirms that caffeine is
adsorbed at the Pt surface, forming a self-limiting film through
electrochemical deposition. Caffeine films are stable up to 1.0 V vs. RHE and
are readily regenerated through caffeine deposition during load/potential
cycling. The findings presented here both identify a potential catalyst
additive that can mitigate high Pt loadings in alkaline fuel cells and
electrolyzers while opening the door to molecular engineering of solid/liquid
interfaces for energy storage and conversion.</p> | Saad Intikhab; Luis Rebollar; Yawei Li; Rahul Pai; Vibha Kalra; Maureen H. Tang; Joshua Snyder | Energy Storage; Fuels - Energy Science; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749b4bdbb89f804a39221/original/caffeinated-interfaces-enhance-alkaline-hydrogen-electrocatalysis.pdf |
60c745be0f50db20c5396308 | 10.26434/chemrxiv.10026932.v2 | Large Scale Indium Tin Oxide (ITO) One Dimensional Gratings for Ultrafast Signal Modulation in the Visible | We present a photophysical study on an indium tin oxide (ITO) one
dimensional grating, realized using femtosecond micromachining technology, a
technology very industrially accessible. The geometries, dimensions and pitch
of the various gratings analyzed are obtained by means of direct ablation in a
controlled atmosphere of a homogeneous thin layer of ITO deposited on a glass
substrate. The pitch has been selected in order to obtain a higher order of the
photonic band gap in the visible. By
means of ultrafast pump-probe spectroscopy we characterize both the plasmon and
inter-band temporal dynamics. We observe a large optical non-linearity of ITO
grating in the visible range, where the photonic band gap occurs, when pumped
at the surface plasmon resonance in the near infrared (1500 nm). All together
we show the possibility of all-optical signal modulation with heavily doped
semiconductors in their transparency window with a picosecond response time
through the formation of ITO grating structures. | Michele Guizzardi; Silvio Bonfadini; Liliana Moscardi; Ilka Kriegel; Francesco Scotognella; Luigino Criante | Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745be0f50db20c5396308/original/large-scale-indium-tin-oxide-ito-one-dimensional-gratings-for-ultrafast-signal-modulation-in-the-visible.pdf |
612d3de990051ec43fe4fbe9 | 10.26434/chemrxiv-2021-2zk2t | Investigating the Transfer of Drug Particulate onto Evidence Packaging During Routine Case Analysis | The presence of drug residue and drug background in a forensic context continues to be of interest for a variety of reasons ranging from its potential use as a means for presumptive identification to ensuring the safety and well-being of drug chemists. While prior work has studied the presence of these residues on laboratory surfaces and on drug evidence, the contribution of residue on the exterior of drug packaging from the analysis process itself has not yet been studied. This work aims to qualitatively and quantitively identify what, if any, effect the analysis of drug evidence has on the drug residue levels on the exterior of the evidence packaging. Using wipe collection techniques, samples from the exterior of drug evidence packaging were taken prior to opening cases and after repackaging to measure changes in residue composition and mass. A total of 64 submissions were analyzed, and an increase in drug residue mass was observed 85.5 % of the time. After analysis and repackaging, 95 % of packages had detectable drug residue on their exterior even though some of the cases were repackaged into new bags. Drug residue masses on the exterior of drug packaging were found to be as high as tens of micrograms. The presence of drug residue on the exterior of drug evidence packaging is expected given the collection and analysis procedures, therefore potential ways to minimize these levels are currently being studied. The presence of these residues is an important factor to consider when developing protocols for the entire evidence handling process and its impact on personnel – from evidence handling technicians to crime scene technicians to submitting officers. | Edward Sisco; Elizabeth L. Robinson; Rebecca Mead; Charles R. Miller IV | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612d3de990051ec43fe4fbe9/original/investigating-the-transfer-of-drug-particulate-onto-evidence-packaging-during-routine-case-analysis.pdf |
63815ea96b4e8140a97fcebb | 10.26434/chemrxiv-2022-4jk6h | Force Decomposition Analysis: A method to
decompose intermolecular forces into physically
relevant component contributions | Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to non-covalent interactions. Herein, we formulate, implement and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis. | Abdulrahman Aldossary; Martí Gimferrer; Yuezhi Mao; Hongxia Hao; Akshaya K. Das; Pedro Salvador; Teresa Head-Gordon; Martin Head-Gordon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63815ea96b4e8140a97fcebb/original/force-decomposition-analysis-a-method-to-decompose-intermolecular-forces-into-physically-relevant-component-contributions.pdf |
6578707d7acf130c3210f6da | 10.26434/chemrxiv-2023-5p4tg | TD GC-MS and UPLC-MS methods to discover differentially expressed metabolites in sebum | Sebum is a lipid-rich biofluid produced by the sebaceous glands which are found in high abundance in areas where hair is present, along the neckline, the ‘T’-area of the face and on the upper back. Recent work has shown that sebum can be used in mass spectrometry-based metabolomics experimental workflows to identify metabolic changes that occur in individuals who are infected with the SARS-CoV-2 virus, Parkinson’s disease and REM-sleep Behavioural Disorders (RBD) when compared to healthy non-disease controls. We describe here standard operating protocols that can be used to analyse sebum that has been collected on gauze or cotton buds using two common and applicable hyphenated mass spectrometry (MS) methods, namely Thermal Desorption Gas Chromatography-Mass Spectrometry (TD GC-MS) and Ultra High Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS). For TD GC-MS the sebum samples are analysed directly with no sample preparation requirements and for UPLC-MS we detail the extraction process for sebum prior to data acquisition. The methods are demonstrated with results from sebum obtained from in-lab healthy volunteers to permit experiments in laboratories with access to either or both of the utilised chromatography-mass spectrometry methods. | Thomas D. Hoare; Caitlin Walton-Doyle; Katherine A. Hollywood; Eleanor Sinclair; Drupad K. Trivedi; Perdita Barran | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6578707d7acf130c3210f6da/original/td-gc-ms-and-uplc-ms-methods-to-discover-differentially-expressed-metabolites-in-sebum.pdf |
656f3bae5bc9fcb5c918caa2 | 10.26434/chemrxiv-2023-3zcfl-v3 | Chemprop: A Machine Learning Package for Chemical Property Prediction | Deep learning has become a powerful and frequently employed tool for the prediction of molecular properties, thus creating a need for open-source and versatile software solutions that can be operated by non-experts. Among current approaches, directed message-passing neural networks (D-MPNNs) have proven to perform well on a variety of property prediction tasks. The software package Chemprop implements the D-MPNN architecture, and offers simple, easy, and fast access to machine-learned molecular properties. Compared to its initial version, we present a multitude of new Chemprop functionalities such as the support of multi-molecule properties, reactions, atom/bond-level properties, and spectra. Further, we incorporate various uncertainty quantification and calibration methods along with related metrics, as well as pretraining and transfer learning workflows, improved hyperparameter optimization, and other customization options concerning loss functions or atom/bond features. We benchmark D-MPNN models trained using Chemprop with the new reaction, atom-level and spectra functionality on a variety of property prediction datasets, including MoleculeNet and SAMPL, and observe state-of-the-art performance on the prediction of water-octanol partition coefficients, reaction barrier heights, atomic partial charges, and absorption spectra. Chemprop enables out-of-the-box training of D-MPNN models for a variety of problem settings in a fast, user-friendly, and open-source software. | Esther Heid; Kevin P. Greenman; Yunsie Chung; Shih-Cheng Li; David E. Graff; Florence H. Vermeire; Haoyang Wu; William H. Green; Charles J. McGill | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f3bae5bc9fcb5c918caa2/original/chemprop-a-machine-learning-package-for-chemical-property-prediction.pdf |
60c7464a337d6c9ac3e27136 | 10.26434/chemrxiv.11301017.v1 | Exogenous Directing Group Free, Ligand-Enabled gamma-C(sp3)–H Arylation of Free Primary Aliphatic Amines and α-Amino Esters | A Pdᴵᴵ-catalyzed, ligand-enabled gamma-C(sp3)–H arylation of free primary aliphatic amines and amino esters without using an exogenous directing group is reported. This reaction is compatible with unhindered free aliphatic amines, and it is also be applicable to the rapid synthesis of biologically and synthetically valuable unnatural α-amino acids. Large scale synthesis is also feasible using this method.<br /> | Yongzheng Ding; Shuai Fan; Xiaoxi Chen; yuzhen gao; Gang Li | Organic Synthesis and Reactions; Catalysis; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7464a337d6c9ac3e27136/original/exogenous-directing-group-free-ligand-enabled-gamma-c-sp3-h-arylation-of-free-primary-aliphatic-amines-and-amino-esters.pdf |
60c757aaee301c33b6c7b5d8 | 10.26434/chemrxiv.14445243.v1 | An Isolable Mononuclear Palladium(I) Amido Complex | Mononuclear Pd(I) species are putative intermediates in Pd-catalyzed reactions, but our
knowledge about them is limited due to difficulties in accessing them. Herein, we report the
isolation of a Pd(I) amido complex, [(BINAP)Pd(NHArTrip )] (BINAP = 2,2′-
bis(diphenylphosphino)-1,1′-binaphthalene, ArTrip = 2,6-bis(2’,4’,6’-triisopropylphenyl)phenyl),
from the reaction of (BINAP)PdCl2 with LiNHArTrip. This Pd(I) amido species has been
characterized by X-ray crystallography, electron paramagnetic resonance, and multi-edge Pd Xray absorption spectroscopy. Theoretical study revealed that, while the 3-electron-2-center π interaction between Pd and N in the Pd(I) complex imposes severe Pauli repulsion in its Pd–N
bond, pronounced attractive inter-ligand dispersion force aids its stabilization. In accord with its
electronic features, reactions of homolytic Pd–N bond cleavage and deprotonation of primary
amines are observed on the Pd(I) amido complex. | jian Liu; Melissa Bollmeyer; Yujeong Kim; Dengmengfei Xiao; Samantha N. Macmillan; qi chen; xuebing leng; Sun Hee Kim; Lili Zhao; Kyle M. Lancaster; Liang Deng | Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757aaee301c33b6c7b5d8/original/an-isolable-mononuclear-palladium-i-amido-complex.pdf |
60c74adf4c89194215ad331e | 10.26434/chemrxiv.12249833.v1 | A Tunable 3D Printed Microfluidic Resistive Pulse Sensor for the Characterisation of Algae and Microplastics | Technologies that can detect and characterise particulates
in liquids have applications in health, food and environmental monitoring. Here
we present a low-cost and high-throughput multiuse counter that classifies a
particle’s size, concentration, porosity and shape. Using an additive
manufacturing process, we have assembled a reusable flow resistive pulse
sensor. The device remains stable for several days with repeat measurements. We
demonstrate its use for characterising algae with spherical and rod structures
as well as microplastics shed from teabags. We present a methodology that results in a specific signal for microplastics, namely a conductive pulse, in contrast to particles with smooth surfaces such as calibration particles or algae, allowing the presence of microplastics to be easily confirmed and quantified. In addition, the shape of the signal and particle are correlated, giving an extra physical property to characterise suspended particulates. The technology can rapidly screen volumes of liquid, 1 mL/ min, for the presence of microplastics and algae.<br /> | Mark Platt; Eugenie Hunsicker; Marcus Pollard | Environmental Analysis; Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74adf4c89194215ad331e/original/a-tunable-3d-printed-microfluidic-resistive-pulse-sensor-for-the-characterisation-of-algae-and-microplastics.pdf |
63c6d13830e3e5924d93aa10 | 10.26434/chemrxiv-2023-928dq | Toward a hydrogen-free reductive catalytic fractionation of wheat straw biomass | The reductive catalytic fractionation (RCF) is an attractive method for the conversion of lignin toward valuable low-molecular weight aromatics during the pretreatment of lignocellulosic biomass. A prominent limitation to the upscaling of such technology is represented by the use of pressurized hydrogen gas. In this contribution, the role of hydrogen gas within the RCF of wheat straw biomass is investigated. The use of H2 was shown to enhance lignin depolymerization, by virtue of an improved hydrogenolysis and hydrogenation of lignin fragments, with a yield of phenolic monomers that increased from ~12 wt% of acid-insoluble lignin in the initial biomass under inert atmosphere, up to ~25 wt% under H2, for a reaction in methanol, at 250 °C, with Ru/C. The adoption of methanol, ethanol and isopropanol as hydrogen-donor solvents was also investigated in the absence of H2, and the use of ethanol was found to give the highest yield of monophenolics (up to ~20 wt%) owing to a better balance between solvolysis, hydrogenolysis, and hydrogenation of lignin. Nevertheless, a substantial loss of the carbohydrate fraction was observed for reactions performed at 250 °C, irrespective of hydrogen pressure and of the solvent employed. The use of a lower temperature of 200 °C in combination with H3PO4 resulted in an improved recovery of cellulose in the pulp and in the solubilization of hemicellulose and lignin, with the formation of monosaccharides (~14 wt% of polysaccharides in the initial biomass) and phenolic monomers (up to 18 wt%, in the absence of H2). Overall, the obtained results show that a tradeoff exists between the removal of H2 from the process and the production of low-MW phenolics during RCF, which can be improved by accurately tuning the process conditions. | Filippo Brienza; Korneel Van Aelst; François Devred; Delphine Magnin; Bert Sels; Patrick Gerin; Iwona Cybulska; Damien Debecker | Catalysis; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c6d13830e3e5924d93aa10/original/toward-a-hydrogen-free-reductive-catalytic-fractionation-of-wheat-straw-biomass.pdf |
6662f395418a5379b04ae157 | 10.26434/chemrxiv-2024-9hxz7 | Synthesis and evaluation of tetrahydropyrrolo[1,2-a]quinolin-1(2H)-ones as new tubulin polymerization inhibitors | Dynamic polymers of tubulin, known as microtubules, are among the most important targets for anti-cancer chemo-therapy. Although several inhibitors of tubulin polymerization are clinically successful, the resistance of cancers to existing drugs urges for the development of novel tubulin-binding substances that can inhibit microtubule dynamics. Here we explored new 1,5-disubstituted pyrrolidin-2-ones 1, 2 and 5-aryl-3,3a,4,5-tetrahydropyrrolo[1,2-a]quinoline-1(2H)-ones 3 as potential binders of the colchicine site of tubulin. We evaluated their effects on microtubules dynamics in vitro and on the proliferation of cultured cancer cell lines. Guided by molecular modeling of the interactions between tubulin and the most active of identified compounds, we designed, synthesized, and tested the 3-hydroxyphenyl-substituted compound 3c, which decreased microtubule growth rate in vitro and arrested cancer cells division in the low micromolar range (IC50 = 6.6 μM). This finding demonstrates that 5-aryltetrahydropyrrolo[1,2-a]quinoline-1(2H)-one is a promising scaffold for the development of novel efficient tubulin polymerization inhibitors. | Mikhail N. Anisimov; Maksim A. Boichenko; Vitaly V. Shorokhov; Julia N. Borzunova; Marina Janibekova; Vadim V. Mustyatsa; Ilya A. Lifshits; Andrey Yu. Plodukhin; Ivan A. Andreev; Nina K. Ratmanova; Sergey S. Zhokhov; Elena A. Tarasenko; Ivan A. Vorobjev; Igor V. Trushkov; Olga A. Ivanova; Nikita Gudimchuk | Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6662f395418a5379b04ae157/original/synthesis-and-evaluation-of-tetrahydropyrrolo-1-2-a-quinolin-1-2h-ones-as-new-tubulin-polymerization-inhibitors.pdf |
667c7ec35101a2ffa895c52b | 10.26434/chemrxiv-2024-vvxlx-v2 | Alkene Isomerization Catalyzed by a Mn(I) Bisphosphine Borohydride Complex | An additive-free manganese-catalyzed isomerization of terminal alkenes to internal alkenes is described. This reaction is atom economic, implementing an inexpensive, non-precious metal catalyst. The most efficient catalyst is the borohydride complex cis-[Mn(dippe)(CO)2(κ2-BH4)]. This catalyst operates at room temperature with a catalyst loading of 2.5 mol %. A variety of terminal alkenes are effectively and selectively transformed to the respective internal E-alkenes. Preliminary results show chain walking isomerization at elevated temperature. Mechanistic studies were carried out including stochiometric reactions and in situ NMR analysis. These experiments are flanked by computational studies. Based on these, the catalytic process is initiated by liberation of “BH3” as a hydroborated alkene. The catalytic process is initiated by double bond insertion into an M–H species leading to an alkyl metal intermediate, followed by β-hydride elimination at the opposite position to afford the isomerization product. | Ines Blaha; Stefan Weber; Robin Dülger; Luis Veiros; Karl Kirchner | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667c7ec35101a2ffa895c52b/original/alkene-isomerization-catalyzed-by-a-mn-i-bisphosphine-borohydride-complex.pdf |
64660c73f2112b41e9c0f70d | 10.26434/chemrxiv-2023-pz3kj-v2 | Cobalt bis(dicarbollide) is a DNA-neutral pharmacophore | Cobalt bis(dicarbollide) (COSAN) is a metallacarborane used as a versatile pharmacophore to prepare biologically active hybrid organic‒inorganic compounds or to improve the pharmacological properties of nucleosides, antisense oligonucleotides, and DNA intercalators. Despite these applications, COSAN interactions with nucleic acids remain unclear, limiting further advances in metallacarborane-based drug development. Although COSAN intercalates into DNA, COSAN-containing intercalators do not, and while COSAN shows low cytotoxicity, intercalators are often highly toxic. The present study aimed at comprehensively characterizing interactions between COSAN and DNA using a wide range of techniques, including UV‒Vis absorption, circular (CD) and linear (LD) dichroism, nuclear magnetic resonance (NMR) spectroscopy, thermal denaturation, viscosity, differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC), and equilibrium dialysis measurements. Our results showed that COSAN has no effect on DNA structure, length, stability, or hybridization, with no or only faint signs of COSAN binding to DNA. Moreover, DNA is not necessary for COSAN to induce cytotoxicity at high concentrations, as shown by in vitro experiments. These findings demonstrate that COSAN is a DNA-neutral pharmacophore, thus confirming the general safety and biocompatibility of metallacarboranes and opening up new opportunities for further developing metallacarborane-based drugs. | Krzysztof Fink; Jakub Cebula; Zdeněk Tošner; Mateusz Psurski; Mariusz Uchman; Tomasz M. Goszczyński | Biological and Medicinal Chemistry; Inorganic Chemistry; Organometallic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64660c73f2112b41e9c0f70d/original/cobalt-bis-dicarbollide-is-a-dna-neutral-pharmacophore.pdf |
648b046c4f8b1884b7547a70 | 10.26434/chemrxiv-2023-xp3qq-v2 | Vapor-phase synthesis of low-valent metal-organic frameworks from metal carbonyl synthons | Incorporating low-valent metals as nodes in metal-organic frameworks (MOFs) is orthogonal to the commonly accepted strategy to robust and porous structures. The electronic structures of low-valent metals are chemically unique and have driven the successes of organometallic chemistry. The translation of these properties into MOFs is largely impeded by the lack of generalizable synthetic approaches. Metal carbonyls are bona fide low-valent and volatile synthons, which, by partial chemical substitution may tether ditopic ligands into MOF architectures. We herein demonstrate the formation of CO2 adsorbing MOFs from the direct vapor-phase substitution of CO by ditopic 4,4′-bipyridine at Mo(0) and W(0) centers, which allows facile coating of low-valent MOFs onto substrates such as indium tin oxide. We envisage this strategy could be generalized to a multitude of mono- and polynuclear metal carbonyls, paralleling the diversity of conventional MOFs. | Carl Emil Andersen; James Neill McPherson; Mónica Giménez-Marqués; Jingguo Li; Mariusz Kubus; Sho Ito; Christian R. Göb; Sascha Ott; René Wugt Larsen; Guillermo Minguez Espallargas; Kasper S. Pedersen | Inorganic Chemistry; Organometallic Chemistry; Transition Metal Complexes (Inorg.); Transition Metal Complexes (Organomet.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648b046c4f8b1884b7547a70/original/vapor-phase-synthesis-of-low-valent-metal-organic-frameworks-from-metal-carbonyl-synthons.pdf |
654ea5a62c3c11ed7129a030 | 10.26434/chemrxiv-2023-27389 | Hydrothermal Destruction and Defluorination of Trifluoroacetic Acid (TFA) | Per- and polyfluoroalkyl substances (PFAS) have received increased attention due to their environmental prevalence and threat to public health. Trifluoroacetic acid (TFA) is an ultra-short-chain PFAS and the simplest perfluorocarboxylic acid (PFCA). While the US EPA does not currently regulate TFA, its chemical similarity to other PFCAs and its simple molecular structure make it a suitable model compound for studying the destruction of PFAS. We show that hydrothermal processing in compressed liquid water degrades TFA at relatively mild conditions (T = 150 – 250 ˚C, P < 30 MPa), initially yielding gaseous products, such as CHF3 and CO2, that naturally aspirate from the solution. Alkali amendment (e.g., NaOH) promotes the mineralization of CHF3, yielding dissolved fluoride, formate, and dissolved carbonate species as final products. Fluorine and carbon balances are closed using Raman spectroscopy and fluoride ion selective electrode measurements for experiments performed at alkaline conditions, where gas yields are negligible. Qualitative FTIR gas analysis allows for establishing the degradation pathways; however, the F-balance could not be quantitatively closed for experiments without NaOH amendment. The kinetics of TFA degradation under hydrothermal conditions are measured, showing little to no dependency on NaOH concentration, indicating that the thermal decarboxylation is a rate-limiting step. A proposed TFA degradation mechanism motivates additional work to generalize the hydrothermal reaction pathways to other PFCAs. | Conrad Austin; Anmol Purohit; Cody Thomsen; Brian Pinkard; Timothy Strathmann; Igor Novosselov | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654ea5a62c3c11ed7129a030/original/hydrothermal-destruction-and-defluorination-of-trifluoroacetic-acid-tfa.pdf |
646259fef2112b41e99cbf64 | 10.26434/chemrxiv-2023-fwgql | Lamellar ionenes with highly dissociative, anionic channels provide low barriers for cation transport | Solid polymer electrolytes have the potential to enable safer and more energy dense batteries; however, a deeper understanding of their ion conduction mechanisms, and how they can be optimized by rational molecular design, is needed to realize this goal. Here, we investigate the impact of anion dissociation energy on ion conduction in solid polymer electrolytes via a novel class of ionenes prepared using acyclic diene metathesis polymerization of highly dissociative, liquid crystalline fluorinated aryl sulfonimide-tagged ("FAST”) anion monomers. These polyanions with various cations (Li+, Na+, K+, and Cs+) form well-ordered lamellae that are thermally stable up to 180 °C and feature domain spacings that correlate with cation size, providing channels lined with dissociative FAST anions. Electrochemical impedance spectroscopy (EIS) and differential scanning calorimetry (DSC) experiments, along with nudged elastic band (NEB) calculations, suggest that cation motion in these materials operates via an ion hopping mechanism. Moreover, the activation energy for Li+ conduction is 59 kJ/mol, which is amongst the lowest for systems that are proposed to operate via an ion conduction mechanism that is decoupled from polymer segmental motion. Furthermore, the addition of a 1 equivalent of a cation-coordinating solvent to these materials led to a >1000-fold increase in ionic conductivity without detectable disruption of the lamellar structure, suggesting selective solvation of the lamellar ion channels. This work demonstrates a novel molecular design strategy to facilitate controlled formation of dissociative anionic channels, which translates to significant enhancements in ion conduction in solid polymer electrolytes. | Michael Stolberg; Benjamin Paren; Pablo Leon; Christopher Brown; Gavin Winter; Kiarash Gordiz; Alberto Concellón; Rafael Gómez-Bombarelli; Yang Shao-Horn; Jeremiah Johnson | Organic Chemistry; Polymer Science; Energy; Physical Organic Chemistry; Polyelectrolytes - Polymers; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646259fef2112b41e99cbf64/original/lamellar-ionenes-with-highly-dissociative-anionic-channels-provide-low-barriers-for-cation-transport.pdf |
6388391328c16426ba5ef3ce | 10.26434/chemrxiv-2022-8zlg4-v3 | Electric Field Induced Release of Guest Molecules from Clathrate Hydrates and Its Consequences for Electrochemical CO2 Conversion | When CO2 is encapsulated in clathrate hydrate, where the concentration is nearly two orders of magnitude greater than in saturated aqueous solution, the rate of the CO2 reduction reaction (CO2RR) increases, and the corresponding Faradaic efficiency becomes up to three times higher than that of the competing hydrogen evolution reaction (HER) at applied potential of -0.5 to -0.7 vs. RHE. The energy efficiency of the CO2RR is correspondingly increased. The enhanced CO2RR in clathrate is ascribed to non-equilibrium release of the CO2 due to the electric field near the electrode, analogous to what has been observed recently for tetrahydrofuran [Li et al. J. Phys. Chem. Letters 125, 13802 (2021)]. This raises the chemical potential of CO2 beyond that of saturated aqueous solution, thereby reversing the relative rates of the CO2RR and the HER. The experimental demonstration of this release mechanism for the application of CO2 up-conversion illustrates how the electric field can not only influence electrochemical reactions at the surface but also the reactant supply from clathrate hydrates to the surface. Experimental focus rests on the low applied-potential regime, where the consequences of the reactant release mechanism are well- observable unobscured by mass-transport effects. | Mengjie Lyu; Ziyue Li; Maxime Bossche; Hannes Jónsson; Christoph Rose-petruck | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6388391328c16426ba5ef3ce/original/electric-field-induced-release-of-guest-molecules-from-clathrate-hydrates-and-its-consequences-for-electrochemical-co2-conversion.pdf |
60c753629abda203ccf8df8f | 10.26434/chemrxiv.13487247.v1 | Programmed Assembly of Bespoke Prototissue Spheroids on a Microfluidic Platform | <p>The precise assembly of protocell building blocks into prototissues that are stable in water, capable of sensing the external environment and which display collective behaviours remains a considerable challenge in prototissue engineering. In this work we explore the use of microfluidic technologies for the programmed assembly of bio-orthogonally reactive protein-polymer protocells into prototissue spheroids of precise size, composition and with unique Janus configurations. We then show that by controlling the number and phenotype of the protocells that compose the prototissue spheroids it is possible to modulate both the amplitude of the thermally induced contractions of the biomaterial and its collective endogenous biochemical reactivity. Overall, our results show that microfluidic technologies enable a new route to the precise and high-throughput fabrication of tissue-like materials with programmable collective properties that can be tuned through a careful assembly of protocell building blocks of different phenotypes. We anticipate that our bespoke prototissues will be a starting point for the development of more sophisticated artificial tissues for use in medicine, soft robotics and environmentally beneficial bioreactor technologies.</p> | Kaitlyn Ramsay; Jae Levy; Pierangelo Gobbo; Katherine Elvira | Biological Materials; Biopolymers; Bioengineering and Biotechnology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753629abda203ccf8df8f/original/programmed-assembly-of-bespoke-prototissue-spheroids-on-a-microfluidic-platform.pdf |
60c75859567dfe3ce0ec6848 | 10.26434/chemrxiv.14541432.v1 | Modular Integration of Hydrogel Neural Interfaces | <p>Thermal drawing has been recently leveraged to yield multi-functional, fiber-based neural probes at near kilometer length scales. Despite its promise, the widespread adoption of this approach has been impeded by (1) material compatibility requirements and (2) labor-intensive interfacing of functional features to external hardware. Furthermore, in multifunctional fibers, significant volume is occupied by passive polymer cladding that so far has only served structural or electrical insulation purposes. In this letter, we report a rapid, robust, and modular approach to creating multi-functional fiber-based neural interfaces using a solvent evaporation or entrapment driven (SEED) integration process. This process brings together electrical, optical, and microfluidic modalities all encased within a co-polymer comprised of water-soluble poly(ethylene glycol) tethered to water-insoluble poly(urethane) (PU-PEG). We employ these devices for simultaneous optogenetics and electrophysiology, and demonstrate that multi-functional neural probes can be used to deliver cellular cargo with high viability. Upon exposure to water, PU-PEG cladding spontaneously forms a hydrogel, which in addition to enabling integration of modalities, can harbor small molecules and nanomaterials that can be released into local tissue following implantation. We also synthesized a custom nanodroplet forming block polymer and demonstrated that embedding such materials within the hydrogel cladding of our probes enables delivery of hydrophobic small molecules in vitro and in vivo. Our approach widens the chemical toolbox and expands the capabilities of multi-functional neural interfaces.</p> | Anthony Tabet; Marc-Joseph Antonini; Atharva Sahasrabudhe; Jimin Park; Dekel Rosenfeld; Florian Koehler; Hyunwoo Yuk; Samuel Hanson; Jordan
A. Stinson; Melissa Stok; Xuanhe Zhao; Chun Wang; Polina Anikeeva | Biocompatible Materials; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75859567dfe3ce0ec6848/original/modular-integration-of-hydrogel-neural-interfaces.pdf |
60c7575f9abda21e1ef8e6e5 | 10.26434/chemrxiv.13636457.v3 | Helical Electronic Transitions of Spiroconjugated Molecules | <div><div><div><div><p>The two pi-systems of allene can mix into helical molecular orbitals (MOs), yet the helicity is lost in the pi-pi∗ transitions. In spiroconjugated molecules the relative orientation of the two π- systems is different as only half the pi-MOs become helical. Consequently, the helicity of the electronic transitions is symmetry protected and thus helical pi-conjugation can manifest in observable electronic and chiroptical properties.</p></div></div></div></div> | Marc Hamilton Garner; Clemence Corminboeuf | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7575f9abda21e1ef8e6e5/original/helical-electronic-transitions-of-spiroconjugated-molecules.pdf |
65ebd7db66c138172996f47f | 10.26434/chemrxiv-2022-zq8x7-v2 | Predicting DNA Reactions with a Quantum Chemistry-Based Deep Learning Model | DNA reactions are crucial in biology, synthetic biology, and DNA computing. Accurate prediction of thermodynamic and kinetic parameters is vital for understanding molecular interactions and designing functional DNA-based systems. Existing models have limitations due to simplifications and approximations that may deviate from experimental measurements. In this study, we propose a quantum chemistry-based deep learning model to enhance accuracy and efficiency in predicting DNA reaction parameters. The model integrates quantum chemistry calculations, new designed descriptor matrices, and deep learning algorithms. It comprehensively describes energy variations by expanding stacks and considering relevant factors. To address limited labeled data, an active learning method selects informative samples iteratively, optimizing data utilization. The results demonstrate the superior predictive capabilities of our model in accurately determining DNA hybridization free energies and strand displacement rate constants. This integration of quantum chemistry and deep learning improves our understanding of DNA reactions and facilitates precise design and optimization of DNA-based systems. | Likun Wang; Na Li; Mengyao Cao; Yun Zhu; Xiewei Xiong; Li Li; Tong Zhu; Hao Pei | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Bioengineering and Biotechnology; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ebd7db66c138172996f47f/original/predicting-dna-reactions-with-a-quantum-chemistry-based-deep-learning-model.pdf |
66a83864c9c6a5c07a715b05 | 10.26434/chemrxiv-2024-0mljv | Installation of Superacidic Carbon Acid Moieties into Polymer Materials via PostPolymerization Modification | In the fields of polymer and material chemistries, strong acid units have mainly included sulfonic acids, which has limited the extension of related material chemistries. Here, a unique carbon acid functionality, namely the bis[(trifluoromethyl)sulfonyl]methyl group, was integrated with polymers via a simple postpolymerization modification with the outstandingly electrophilic 1,1-bis[(trifluoromethyl)sulfonyl]ethylene. The proposed synthesis protocol was verified as an efficient process even for solid-state reactions. The synthesis afforded an organic material with a surface decorated with bis[(trifluoromethyl)sulfonyl]methyl units. The fabricated membranes featuring surface bis[(trifluoromethyl)sulfonyl]methyl units functioned as efficient organocatalysts with high catalytic activity for the Mukaiyama aldol reaction. This study provides a simple method for installing superacidic carbon acid moieties onto the surfaces of materials without tedious chemical treatments. | Ryohei Kakuchi; Takuma Oguchi; Minoru Kuroiwa; Yu Hirashima; Masaaki Omichi; Noriaki Seko; Hikaru Yanai | Materials Science; Polymer Science | CC BY NC 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a83864c9c6a5c07a715b05/original/installation-of-superacidic-carbon-acid-moieties-into-polymer-materials-via-post-polymerization-modification.pdf |
62fc8ac16e379681107e8f60 | 10.26434/chemrxiv-2022-xdlsk | Analysis of Near Infrared-Emitting Bimolecular Excited States in Platinum(II) Complexes with Simple Computational Tools | This work presents a simple computational methodology for analysing and predicting luminescence originating from bimolecular excited states, dimers and excimers, of platinum(II) complexes. Photoluminescence spectrum of said species resembles Gaussian distribution. Gaussian perfectly fits PL spectra in the region of interest from the onset to peak and given its simplicity serves as a perfect model for experimental data. Time-dependent density functional theory (TDDFT) methods provide computational data which are then correlated with the features of the experimental PL spectrum: peak and onset energy. Good linear correlation (r2 = 0.94) between experimental and computational data yields high precision predictions of PL spectra based on the simple computational model. A diverse selection of platinum(II) complexes used for calibration of the model guarantees generality. The study provides an insight into the structure of dimers/excimers of platinum complexes, suggesting that anti or head-to-tail configuration is preferred. | Piotr Pander | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fc8ac16e379681107e8f60/original/analysis-of-near-infrared-emitting-bimolecular-excited-states-in-platinum-ii-complexes-with-simple-computational-tools.pdf |
6317807d49042a7e1ccde60f | 10.26434/chemrxiv-2022-rknwt-v3 | Electrostatic Embedding of Machine Learning Potentials | This work presents a variant of an electrostatic embedding scheme that allows the embedding of arbitrary machine learned potentials trained on molecular systems in vacuo. The scheme is based on physically motivated models of electronic density and polarizability, resulting in a generic model without relying on an exhaustive training set. The scheme only requires in vacuo single point QM calculations to provide training densities and molecular dipolar polarizabilities. As an example, the scheme is applied to create an embedding model for the QM7 dataset using Gaussian Process Regression with only 445 reference atomic environments. The model was tested on SARS-CoV-2 protease complex with PF-00835231, resulting in predicted embedding energy RMSE of 2 kcal/mol, compared to explicit DFT/MM calculations. | Kirill Zinovjev | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2022-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6317807d49042a7e1ccde60f/original/electrostatic-embedding-of-machine-learning-potentials.pdf |
60c74268bb8c1a9d173da108 | 10.26434/chemrxiv.8266733.v1 | BrHgO• + C2H4 and BrHgO• + HCHO in Atmospheric Oxidation of Mercury: Determining Rate Constants of Reactions with Pre-Reactive Complexes and a Bifurcation | Models suggest BrHgONO to be the major Hg(II) species formed in the global oxidation of Hg(0), and BrHgONO undergoes rapid photolysis to produce the thermally stable radical BrHgO•. We previously used quantum chemistry to demonstrate that BrHgO• can, like OH radical, readily can abstract hydrogen atoms from sp<sup>3</sup>-hybridized carbon atoms as well as add to NO and NO<sub>2</sub>. In the present work, we reveal that BrHgO• can also add to C<sub>2</sub>H<sub>4</sub> to form BrHgOCH<sub>2</sub>CH<sub>2</sub>•, although this addition appears to proceed with a lower rate constant than the analogous addition of •OH to C<sub>2</sub>H<sub>4</sub>. Additionally, BrHgO• can readily react with HCHO in two different ways: either by addition to the carbon or by abstraction of a hydrogen atom. The minimum energy path for the BrHgO• + HCHO reaction bifurcates, forming two pre-reactive complexes, each of which passes over a separate transition state to form a different product. | Khoa T. Lam; Curtis J. Wilhelmsen; Theodore Dibble | Atmospheric Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74268bb8c1a9d173da108/original/br-hg-o-c2h4-and-br-hg-o-hcho-in-atmospheric-oxidation-of-mercury-determining-rate-constants-of-reactions-with-pre-reactive-complexes-and-a-bifurcation.pdf |
65a9771b66c1381729c2d289 | 10.26434/chemrxiv-2024-k6wtc | Innovative Integration of Butina Clustering with Ensemble Learning Techniques for the Refined Pharmacophore Modeling of Apelin Receptor Agonists: A High-Impact Computational Approach | 3D pharmacophore models describe the ligand’s chemical interactions in their bioactive conformation. They offer a simple but sophisticated approach to decipher the chemically encoded ligand information, making them a valuable tool in Drug Design. Our research summarized the key studies for applying 3D pharmacophore models in virtual screening for APJ receptor agonists. Recent advances in clustering algorithms and ensemble methods have enabled classical pharmacophore modeling to evolve into more flexible and knowledge-driven techniques. Butina clustering categorizes molecules based on their structural similarity (indicated by the Tanimoto coefficient) to create a structurally diverse training dataset. The ensemble learning method combines various individual pharmacophore models into a set of pharmacophore models for pharmacophore space optimization in virtual screening. This approach was evaluated on Apelin datasets and afforded good screening performance, as proven by receiver operating characteristic, enrichment factor, Güner-Henry score, and F-measure. Although one of the high-scoring models achieved statistically superior results in each dataset, the ensemble learning method including Voting and Stacking method balanced the shortcomings of each model and passed with close performance measures. | Xuan-Truc Dinh Tran; Tieu-Long Phan; Van-Thinh To; Ngoc-Vi Nguyen Tran; Nhu-Ngoc Song Nguyen; Dong-Nghi Hoang Nguyen; Ngoc-Tam Nguyen Tran; Tuyen Ngoc Truong | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a9771b66c1381729c2d289/original/innovative-integration-of-butina-clustering-with-ensemble-learning-techniques-for-the-refined-pharmacophore-modeling-of-apelin-receptor-agonists-a-high-impact-computational-approach.pdf |
60c7463e337d6c9ce3e27106 | 10.26434/chemrxiv.9120635.v2 | Electrocatalytic CO2 Reduction to Formate with Molecular Fe(III) Complexes Containing Pendent Proton Relays | Electrocatalytic performance of two Fe complexes for CO<sub>2</sub> reduction to formate is described. Pendent functional groups are found to enhance the rate and activity of the catalytic response. | Asa W. Nichols; Shelby L. Hooe; Joseph S. Kuehner; Diane A. Dickie; Charles Machan | Electrochemistry; Transition Metal Complexes (Inorg.); Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7463e337d6c9ce3e27106/original/electrocatalytic-co2-reduction-to-formate-with-molecular-fe-iii-complexes-containing-pendent-proton-relays.pdf |
60c74c9f0f50db7568396ebb | 10.26434/chemrxiv.12497834.v1 | Hydrostibination of Alkynes: A Radical Mechanism | The addition of Sb-H bonds to alkynes was reported recently as a new hydroelementation reaction that exclusively yields anti-Markovnikov <i>Z</i>-olefins from terminal acetylenes. We examine four possible mechanisms that are consistent with the observed stereochemical and regiochemical outcomes. A comprehensive analysis of solvent, substituent, isotope, additive, and temperature effects on hydrostibination reaction rates definitively refutes three ionic mechanisms involving closed-shell charged intermediates. Instead the data support a fourth pathway featuring neutral radical Sb<sup>II</sup> and Sb<sup>III</sup> intermediates. Density Functional Theory (DFT) calculations are consistent this model, predicting an activation barrier that is within 1 kcal mol<sup>-1</sup> of the experimental value (Eyring analysis) and a rate limiting step that is congruent with experimental kinetic isotope effect. We therefore conclude that hydrostibination of arylacetylenes is initiated by the generation of stibinyl radicals, which then participate in a cycle featuring Sb<sup>II</sup> and Sb<sup>III</sup> intermediates to yield the observed <i>Z</i>-olefins as products. This mechanistic understanding will enable rational evolution of hydrostibination as a methodology for accessing challenging products such as <i>E</i>-olefins. | Josh MacMillan; Katherine Marczenko; Erin Johnson; Saurabh Chitnis | Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c9f0f50db7568396ebb/original/hydrostibination-of-alkynes-a-radical-mechanism.pdf |
67593934f9980725cfb177c5 | 10.26434/chemrxiv-2024-7bgrw-v2 | The atomic density based tight-binding (aTB) model: A robust and accurate semi-empirical method parameterized for H-Ra; applied to structures, vibrational frequencies, noncovalent interactions, and excited states | This work introduces a semi-empirical method, named aTB, based on the tight-binding model and named for its zero-order Hamiltonian that utilizes density-fitting atomic densities. This method can calculate the molecular structure, vibrational frequencies, non-covalent interactions, and excited states of large molecular systems. The parameters of aTB cover elements from Hydrogen (H) to Radium (Ra), and for ground state calculations, it supports the analysis of first- and second-order derivatives. The Hamiltonian of aTB contains a zero-order Hamiltonian, Coulomb term, an explicit second- and third-order expansion of the exchange-correlation term, and a spin-polarization term with only one additional parameter. A series of extensive tests were conducted to compare aTB with existing semi-empirical methods. | Yingfeng Zhang; Jin Xiao; Shunyu Wang; Tong Zhu; John Z.H. Zhang | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67593934f9980725cfb177c5/original/the-atomic-density-based-tight-binding-a-tb-model-a-robust-and-accurate-semi-empirical-method-parameterized-for-h-ra-applied-to-structures-vibrational-frequencies-noncovalent-interactions-and-excited-states.pdf |
67c58b6d6dde43c90848b127 | 10.26434/chemrxiv-2024-1819d-v4 | On the connection between the Exact Factorization and the Born-Huang representation of the molecular wavefunction | In these Notes we present a new perspective on the exact-factorization expression of a molecular wavefunction, which does not rely of the probabilistic interpretation of the molecular wavefunction as a joint probability amplitude. Instead, we demonstrate a close relation with the traditional Born-Huang representation, as the exact factorization emerges as the representation in the basis the of eigenvectors of the density matrix at nuclear position R. In doing so, the partial normalization condition and gauge freedom arise naturally from the formalism. In a second part, we derive the equation of motion in the here introduced exact factorization basis. | Peter Schürger; Yorick Lassmann; Federica Agostini; Basile Curchod | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c58b6d6dde43c90848b127/original/on-the-connection-between-the-exact-factorization-and-the-born-huang-representation-of-the-molecular-wavefunction.pdf |
60c73dba0f50db65e9395529 | 10.26434/chemrxiv.6057431.v1 | Size Tunable Synthesis and Surface Chemistry of Metastable TiO2-Bronze Nanocrystals | <p>The metastable titania phase, <i>bronze</i>, has great potential as photo-catalyst or as anode material
in Li-ion batteries. Here, we report the first synthesis of colloidally stable,
size-tunable TiO<sub>2</sub>-<i>bronze</i>
(TiO<sub>2</sub>-B) nanocrystals, via a hydrothermal process. By employing
Definitive Screening Design, the experimental parameters affecting the size and
agglomeration of the nanocrystals are identified. The size is mostly determined
by the reaction temperature, resulting in 3 – 8 nm NCs in the range of 130 °C –
180 °C. To avoid irreversible aggregation, short reaction times are desired and
in this respect microwave heating proved essential due to its fast heating and
cooling rates. The resulting nanocrystals are de-aggregated and stabilized in
polar solvents using either positive or negative surface charges. In nonpolar
solvents, steric stabilization is provided by long chain amines and carboxylic
acids. Furthermore, we study this peculiar post-synthetic surface modification
through solution <sup>1</sup>H NMR and elemental analysis. Surprisingly, we
find ion-pairs of alkylammonium carboxylates bound to the surface, contrasting
with earlier reports on carboxylic acid stabilized metal oxide nanocrystals. To
rationalize this, a general framework of acid/base chemistry with metal oxide
nanocrystals is constructed and discussed. </p> | Jonas Billet; Wouter Dujardin; Katrien De Keukeleere; Klaartje De Buysser; Jonathan De Roo; Isabel Van Driessche | Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Photocatalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dba0f50db65e9395529/original/size-tunable-synthesis-and-surface-chemistry-of-metastable-ti-o2-bronze-nanocrystals.pdf |
60c74fba9abda2f39ff8d8e1 | 10.26434/chemrxiv.12935189.v1 | Flexible and Responsive Nature of 2D Layered Conductive Metal-Organic Frameworks Determine Their Catalytic Activity in Oxidative Dehydrogenation of Propane | A multi-faceted approach is introduced for investigating the effects of intrinsic and guest(water)-induced structural transformations/deformations and heterogeneity on catalytic activity of the 2D π-stacked layered Co3(HTTP)2, HTTP = hexathiotriphenylene, metal-organic framework. Through comprehensive molecular dynamics simulations coupled with periodic and cluster electronic structure calculations, we uncover a complex array of catalytically active sites in 2D Co3(HTTP)2 MOF which would have been entirely missed if conventional static electronic structure methods were to be employed. | Mohammad R. Momeni; Zeyu Zhang; Farnaz A. Shakib | Hybrid Organic-Inorganic Materials; Thermal Conductors and Insulators; Theory - Computational; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fba9abda2f39ff8d8e1/original/flexible-and-responsive-nature-of-2d-layered-conductive-metal-organic-frameworks-determine-their-catalytic-activity-in-oxidative-dehydrogenation-of-propane.pdf |
673a23c47be152b1d064213b | 10.26434/chemrxiv-2024-6ts41 | How does the concentration of microplastics in recycled toilet paper compare to non-recycled toilet paper when tested in a shredded state and controlled laboratory conditions? | This paper aims to compare the concentration of microplastics in recycled and non-recycled toilet paper when tested in a shredded state under controlled laboratory conditions. The goal is to determine whether recycled toilet paper contains fewer microplastics than non-recycled toilet paper. By investigating the microplastic content in recycled and non-recycled toilet paper, this investigation aims to shed light on an often-overlooked source of microplastic pollution. The results will not only enhance the understanding of the environmental impact of toilet paper products but also guide consumers and manufacturers towards more sustainable practices in reducing microplastics in everyday items.
| Evan trinh; Kevin Trinh | Materials Science; Polymer Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673a23c47be152b1d064213b/original/how-does-the-concentration-of-microplastics-in-recycled-toilet-paper-compare-to-non-recycled-toilet-paper-when-tested-in-a-shredded-state-and-controlled-laboratory-conditions.pdf |
64f76a0279853bbd7829bf27 | 10.26434/chemrxiv-2023-vsmpx-v4 | MS2Mol: A transformer model for illuminating dark chemical space from mass spectra | The ability to identify small molecules in complex samples from their mass spectra is among the grand challenges of analytical chemistry. Improvements to this ability could significantly advance fields as diverse as drug discovery, diagnostics, environmental science, and synthetic biology. A primary bottleneck is that standard structure elucidation technologies are limited to identifying only those molecules that are contained in databases of known spectra or molecular structures and are therefore not well suited to identifying the vast majority of potentially billions of natural metabolites, whose structures are not yet catalogued. To improve the identification of molecular structures within this vast dark chemical space, we present MS2Mol, a de novo structure prediction model based on a generative sequence to sequence transformer. We also release EnvedaDark, a first-of-its-kind data set for benchmarking identification performance on unknown metabolites. EnvedaDark contains experimental mass spectra from 226 natural products not currently found in major databases. We demonstrate on this challenging dataset that MS2Mol is able to predict 21% of molecular structures to within a close-match accuracy threshold and 62% to within meaningful similarity, both of which are significant improvements over the closest match retrieved using standard database methods. We further present a confidence scorer that enables practical usage for novel molecule discovery and enriches the accuracy on meaningfully-similar and close-match thresholds to 98% and 63%, respectively, for the top 10% most confident predictions. | Thomas Butler; Abraham Frandsen; Rose Lightheart; Brian Bargh; Thomas Kerby; Kiana West; Joseph Davison; James Taylor; Christoph Krettler; TJ Bollerman; Gennady Voronov; Kevin Moon; Tobias Kind; Pieter Dorrestein; August Allen; Viswa Colluru; David Healey | Theoretical and Computational Chemistry; Analytical Chemistry; Mass Spectrometry; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2023-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f76a0279853bbd7829bf27/original/ms2mol-a-transformer-model-for-illuminating-dark-chemical-space-from-mass-spectra.pdf |
677766816dde43c90822bbf0 | 10.26434/chemrxiv-2025-xtxjn | Resolving Three-Dimensional Nanoscale Heterogeneities in Lithium Metal Batteries with Cryogenic Electron Tomography | Current direct observation of sensitive battery materials and interfaces primarily relies on two-dimensional (2D) imaging, leaving out their three-dimensional (3D) relationship. Here, we used cryogenic electron tomography (cryo-ET) to visualize the lithium metal anode in 3D at nanometer resolution and cryogenic electron microscopy (cryo-EM) to reveal atomic details in local regions. We imaged both freshly prepared and calendar aged Li metal anodes to reveal the development of LiH in Li dendrites and the Li-LiH interface, as well as the development of the solid-electrolyte interphase (SEI). Using a convolutional neural network-based technique, the 3D arrangement of Li metal, along with nanoscale LiH and Cu heterogeneities in dendrites were visualized and annotated. In longer-term calendar aging, we observed more substantial LiH growth accompanied by extended SEI growth. Our results show that the growth of LiH and of the extended SEI during battery calendar aging are temporally and spatially separate processes | Zewen Zhang; Yanbin Li; weijiang zhou; Gongher Wu; Jane Lee; Jiayu Wan; Hao Chen; William Huang; Yusheng Ye; Michael Schmid; Wah Chiu; Yi Cui | Materials Science; Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677766816dde43c90822bbf0/original/resolving-three-dimensional-nanoscale-heterogeneities-in-lithium-metal-batteries-with-cryogenic-electron-tomography.pdf |
60c746ee337d6cd4fee27259 | 10.26434/chemrxiv.11441313.v1 | Synthesis, Characterization and Study of DC Electrical Conductivity of Poly[MWCNT/Imidoselenium] Composite | <p>The
chemical functionalization of amino multi-walled carbon nanotubes (MWCNT-NH<sub>2</sub>)
by selenium dioxide (SeO<sub>2</sub>) was used to produce Poly [MWCNT/Imidoselenium] composite. The prepared poly-composite was characterized by FTIR, SEM, TEM, XRD, UV, DSC and TGA. The DC electrical conductivity of poly-composite was 4.3×10<sup>-4</sup>
S/cm due to the interaction between the nanotubes. </p> | Abeer O. Obeid; Fatma Al-Yusufy; Sama A Al-Aghbari; omar alshujaa; Yassin Gaber; Zinab A. Al-Washal | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ee337d6cd4fee27259/original/synthesis-characterization-and-study-of-dc-electrical-conductivity-of-poly-mwcnt-imidoselenium-composite.pdf |
60c7567abdbb895902a3aa24 | 10.26434/chemrxiv.14254109.v1 | Interphase Control in Lithium Metal Batteries Through Electrolyte Design | <p>Future rechargeable Li metal batteries (LMBs) require a rational electrolyte design to stabilize</p><p>the interfaces between the electrolyte and both the lithium metal anode and the high voltage</p><p>cathode. This remains the greatest challenge in achieving high cycling performance in</p><p>LMBs. We report an ether-aided ionic liquid electrolyte which offers superior Li metal</p><p>deposition, high voltage (5 V) stability and non-flammability. High performance cycling of</p><p>LiNi0.8Mn0.1Co0.1O2 (4.4 V) and LiNi0.6Mn0.2Co0.2O2 (4.3 V) cells is demonstrated with high</p><p>coulombic efficiency (>99.5%) at room temperature and elevated temperatures, even at high</p><p>practical areal capacity for the latter of 3.8 mAh/cm2 and with a capacity retention of 91% after</p><p>100 cycles. The ether-ionic liquid chemistry enables desirable plated Li microstructures with</p><p>high packing density, minimal ‘dead’ or inactive lithium formation and dendrite-free long-term</p><p>cycling. Along with XPS studies of cycled electrode surfaces, we use molecular dynamics</p><p>simulations to demonstrate that changes to the electrolyte interfacial chemistry upon addition</p><p>of DME plays a decisive role in the formation of a compact stable SEI.</p> | Urbi Pal; Dmitrii Rakov; Bingyu Lu; Baharak Sayahpour; Fangfang Chen; Binayak Roy; Douglas R. MacFarlane; Michel Armand; Patrick
C. Howlett; Ying Shirley Meng; Maria Forsyth; Dmitrii A. Rakov | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7567abdbb895902a3aa24/original/interphase-control-in-lithium-metal-batteries-through-electrolyte-design.pdf |
6119b73930231a0d710b0715 | 10.26434/chemrxiv-2021-bqtm9 | Effect of Silicone Coating on Atomic Oxygen
Reactivity with Carbon Fiber Preform and
Phenolic Impregnated Carbon Ablator
| We have conducted a comparative study on how the presence of the anti-dust CV-1144-0 silicone coating from NuSil Technology LLC affects the atomic oxygen oxidation and ablation of heat shields, specifically phenolic-impregnated carbon ablator (PICA) and its carbon fiber preform substrate, FiberForm. Using an atomic oxygen beam-surface scattering apparatus, we measured the scattered products from the surface of the materials at temperatures from 1000 K to 1800 K. Results showed higher nonreactive vs. reactive scattering flux on coated materials compared to their uncoated counterparts up to 1500 K, around which point the silicon-oxide layer decomposed. Upon the breakdown of the oxide layer, the reactivity of the sample reverted to that of its underlying substrate, either that of FiberForm or charred PICA. In addition, a subtle influence of underlying impurities, specifically calcium, was observed in the oxidation of both PICA and FiberForm. PICA appeared to retain the presence of these impurities after ablation at 1800 K, which was attributed to a shielding effect that the phenolic resin matrix provides to the material. The data should be useful for the development of an improved PICA ablation model. | David Chen; Chenbiao Xu; Timothy Minton | Physical Chemistry; Interfaces; Physical and Chemical Processes; Surface; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6119b73930231a0d710b0715/original/effect-of-silicone-coating-on-atomic-oxygen-reactivity-with-carbon-fiber-preform-and-phenolic-impregnated-carbon-ablator.pdf |
641c891591074bccd029f24f | 10.26434/chemrxiv-2023-3db0j-v2 | Copper-Phosphido Catalysis: Enantioselective Addition of Phosphines to Cyclopropenes | We describe a copper-catalyst that promotes the addition of phosphines to cyclopropenes at ambient temperature. A range of cyclopropylphosphines bearing different steric and electronic properties can now be accessed in high yields and enantioselectivities. A combined experimental and theoretical mechanistic study supports insertion of a Cu(I)-phosphido intermediate into the strained olefin. Density functional theory calculations reveal migratory insertion as the stereodetermining step of the pathway, with final product formation occurring via a syn-protodemetalation. Enrichment of phosphorus stereocenters is demonstrated via a DyKAT process. | Brian S. Daniel; Xintong Hou; Stephanie A. Corio; Lindsey M. Weissman; Vy M. Dong; Jennifer S. Hirschi; Shaozhen Nie | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Ligand Design; Theory - Organometallic | CC BY 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c891591074bccd029f24f/original/copper-phosphido-catalysis-enantioselective-addition-of-phosphines-to-cyclopropenes.pdf |
60c74dc1702a9b6cc218b8f2 | 10.26434/chemrxiv.12582272.v3 | Characterizing Moisture Uptake and Plasticization Effects of Water on Amorphous Amylose Starch Models Using Molecular Dynamics Methods | <p>Dynamics and thermophysical properties of amorphous starch were explored using molecular dynamics (MD) simulations. Using the OPLS3e force field, simulations of short amylose chains in water were performed to determine force field accuracy. Using well-tempered metadynamics, a free energy map of the two glycosidic angles of an amylose molecule was constructed and compared with other modern force fields. Good agreement of torsional sampling for both solvated and amorphous amylose starch models was observed. Using combined grand canonical Monte Carlo (GCMC)/MD simulations, a moisture sorption isotherm curve is predicted along with temperature dependence. Concentration-dependent activation energies for water transport agree quantitatively with previous experiments. Finally, the plasticization effect of moisture content on amorphous starch was investigated. Predicted glass transition temperature (Tg) depression as a function of moisture content is in line with experimental trends. Further, our calculations provide a value for the dry Tg for amorphous starch, a value which no experimental value is available.</p><div><br /></div> | Jeffrey Sanders; Mayank Misra; Thomas JL Mustard; David J. Giesen; Teng Zhang; John Shelley; Mathew
D. Halls | Biological Materials; Biopolymers; Food; Biophysics; Computational Chemistry and Modeling; Transport Phenomena (Chem. Eng.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dc1702a9b6cc218b8f2/original/characterizing-moisture-uptake-and-plasticization-effects-of-water-on-amorphous-amylose-starch-models-using-molecular-dynamics-methods.pdf |
65a18b9d9138d23161c824ec | 10.26434/chemrxiv-2024-0psx3 | SmartGraph API: Programmatic
Knowledge Mining in Network-
Pharmacology Setting | The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows
with ease in the network-pharmacology paradigm. However, at the time of its publication, we
identified the need for the development of an Application Programming Interface (API) that
could promote biomedical data integration and hypothesis generation in an automated manner.
This need was magnified at the time of the COVID-19 pandemic. This study addresses this
hiatus. Most functionalities of the original platform were implemented in the SmartGraph API.
We demonstrate that by using the API it is possible to transform the original semi-automated
workflow behind the Neo4COVID19 database to a fully automated one. The availability of the
SmartGraph API lends a significant improvement to the programmatic integration of networkpharmacology-
oriented knowledge graphs and analytics, as well as predictive functionalities and
workflows. | Gergely Zahoránszky-Kőhalmi; Brandon Walker; Nathan Miller; Brett Yang; Dhatri V. L. Penna; Jessica Binder; Timothy Sheils; Ke Wang; Jennifer King; Hythem Sidky; Sridhar Vuyyuru; Jeyaraman Soundarajan; Samuel G. Michael; Alexander G. Godfrey; Tudor I. Oprea | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a18b9d9138d23161c824ec/original/smart-graph-api-programmatic-knowledge-mining-in-network-pharmacology-setting.pdf |
65d6b18f9138d23161aee6cb | 10.26434/chemrxiv-2024-nt66h | Tailoring the surface termination of BiVO4 photoanodes using ammonium metavanadate enhances the solar water oxidation performance | Altering the surface stoichiometry of semiconductor electrodes is known to affect the photoelectrochemical (PEC) response. To date, several reports have hinted at the influence of the surface Bi:V ratio on the solar water oxidation performance of BiVO4 photoanodes, but only a handful of strategies have been reported to afford to fine-tune such surface stoichiometry while a comprehensive understanding of an atomic level of the role of the surface termination remains elusive. Herein, we report a new methodology that modulates the surface Bi:V ratio and, in turn, maximizes the PEC performance towards the oxygen evolution reaction (OER). We found that annealing in the presence of ammonium metavanadate drastically reduces the surface recombination while improving the charge separation. Detailed characterization revealed that this treatment filled the native surface vanadium vacancies, which are found to act as recombination centers, while inducing a significant increase in the density of oxygen vacancies, which reinforced the built-in electric field that drives the charge separation. Interestingly, coating with NiFeOx improves, especially, the charge separation in surface V-rich BiVO4. Results suggest that the V-rich surface termination altered the surface energetics of BiVO4 leading to an improved band alignment across the interface. Overall, these results provide a new platform to modulate the surface stoichiometry of BiVO4 thin films while shedding new light on the mechanisms whereby the surface termination governs the PEC response. | Qingjie Wang; Zeyuan Wang; Nan Liao; Salvador Montilla; Maxime Contreras; Néstor Guijarro; Jingshan Luo | Catalysis; Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d6b18f9138d23161aee6cb/original/tailoring-the-surface-termination-of-bi-vo4-photoanodes-using-ammonium-metavanadate-enhances-the-solar-water-oxidation-performance.pdf |
60c750bb567dfec0f7ec58fc | 10.26434/chemrxiv.12982574.v3 | Use of Natural Coagulants/Flocculants in the Treatment of Hospital Laundry Effluents | <p>Water is a fundamental substance for the existence of life on earth.
However, globally there is a freshwater crisis. Hospitals generate exorbitant volumes of
effluents (5 to 15 times more toxic than urban ones). Hospital laundry is known for
demanding the highest volumes of water, generating a proportional amount of complex
effluents with high toxicity and recalcitrance. Adequate treatment for hospital wastewater is
always an essential solution. Among all treatment methods, coagulation/flocculation emerges as one of the best alternatives. However, the use of traditional compounds such
as aluminium sulfate has caused secondary pollution; its residues are harmful to public
and environmental health. In this sense, the present study used natural compounds that
do not cause adverse effects, such as chitosan/hydroxyapatite, to clarify the laundry
effluents of the largest hospital from the Tocantins. The results showed that the
hydroxyapatite associated with chitosan, at pH 6 and dosage of 50 mg/L, reduced the
turbidity and apparent colour of these wastewaters by up to 67 and 55%, respectively.
With lower performance and higher dosage (60 mg/L), the chitosan gel used (pH 6)
promoted a maximum reduction of 35% of the apparent colour and 40% of turbidity.<br /></p> | Maykon Abreu; Adão L. B. Montel; Elisandra Scapin | Biodegradable Materials; Composites; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2020-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750bb567dfec0f7ec58fc/original/use-of-natural-coagulants-flocculants-in-the-treatment-of-hospital-laundry-effluents.pdf |
64df868e00bbebf0e665dc8b | 10.26434/chemrxiv-2023-j76c0 | Making Sunscreen with Household Chemicals - A Frugal Demonstration of the Aldol Clock Reaction | The aldol clock reaction is a classic introductory chemistry demonstration often overlooked in high school classrooms due to the poor availability of its component chemicals. Here, we report a simple and inexpensive way to perform the demonstration using readily available household chemicals. | Jacob Wolfe; Mikaela Luksic; Rebecca Gonda | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Education; Organic Synthesis and Reactions; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64df868e00bbebf0e665dc8b/original/making-sunscreen-with-household-chemicals-a-frugal-demonstration-of-the-aldol-clock-reaction.pdf |
65153bcaa69febde9ed55d25 | 10.26434/chemrxiv-2023-vh02l | Ultrahigh-density superhard hexagonal BN and SiC with quartz topology from crystal chemistry and first principles | Based on superdense C6 with quartz (qtz) topology, new ultrahigh-density hexagonal binary phases, qtz BN and qtz SiC, have been identified from full geometry structure relaxations and ground state energies using calculations based on the quantum density functional theory (DFT) with gradient GGA exchange-correlation XC functional. Like qtz C6 with respect to diamond, the resulting binary qtz BN and qtz SiC were found to be less cohesive than cubic BN and cubic SiC, respectively, but were confirmed to be mechanically (elastic constants) and dynamically (phonon band structures) stable. Higher densities of the new phases correlate with their higher hardness values compared to cubic BN and cubic SiC. In contrast to the regular tetrahedra that characterize the cubic BN and SiC phases, the corner-sharing tetrahedra in the new phases are distorted, which accounts for their exceptional density and hardness. All three qtz phases were found to be semiconducting to insulators with reduced band gaps compared to diamond, cubic BN and cubic SiC. | Samir F. Matar; Vladimir L. Solozhenko | Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65153bcaa69febde9ed55d25/original/ultrahigh-density-superhard-hexagonal-bn-and-si-c-with-quartz-topology-from-crystal-chemistry-and-first-principles.pdf |
664203ea91aefa6ce1dc1645 | 10.26434/chemrxiv-2024-gxvd9-v2 | Describing Chiral Ligands in Palladium-catalyzed Decarboxylative Asymmetric Allylic Allylation: A Critical Comparison of Three Machine Learning Approaches | Despite its current popularity, machine learning (ML) applied to asymmetric catalysis remains underexplored. Present strategies include direct use of existing descriptors (e.g. those originally formulated for medicinal chemistry), the development of new bespoke steric and electronic descriptors, or the use of molecular graphs. This method diversity, in the absence of user guidelines, makes selecting an optimal ML algorithm unclear. The fact that asymmetric catalysis data sets are frequently small also make interpretable ML of chiral ligand understanding difficult to realize. Herein, we present an exhaustive evaluation of reaction representations in combination with different machine learning algorithms (including linear regression, random forests, gradient boosting, and graph neural networks) using a realistic-size database compromising 103 palladium- catalyzed decarboxylative asymmetric allylic alkylation (DAAA). This database consists of the combination of three different Trost-type ligands with 54 different substrates. It is concluded that our new bespoke steric and electronic descriptors offer the best performance, while overcoming the problem of interpretability of using existing topo-electronic descriptors, and the problem of data requirements of Graph Neural Networks. | Declan Galvin; Eduardo Alberto Aguilar Bejarano; David M. Rogers; Simon Woodward; Ender Özcan; Patrick J. Guiry; Grazziela Figueredo | Theoretical and Computational Chemistry; Catalysis; Chemoinformatics - Computational Chemistry; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664203ea91aefa6ce1dc1645/original/describing-chiral-ligands-in-palladium-catalyzed-decarboxylative-asymmetric-allylic-allylation-a-critical-comparison-of-three-machine-learning-approaches.pdf |
6410a9a7e53eff1af31fa9f1 | 10.26434/chemrxiv-2022-ddzv8-v3 | HUB: A method to model and extract the distribution of ice nucleation temperatures from drop-freezing experiments | The heterogeneous nucleation of ice is an important atmospheric process facilitated by a wide range of aerosols. Drop-freezing experiments are key for the determination of the ice nucleation activity of biotic and abiotic ice nucleators (INs). The results of these experiments are reported as the fraction of frozen droplets f_ice (T) as a function of decreasing temperature, and the corresponding cumulative freezing spectra N_m (T) computed using Valis methodology. The differential freezing spectrum n_m (T) is an approximant to the underlying distribution of heterogeneous ice nucleation temperatures P_u (T) that represents the characteristic freezing temperatures of all IN in the sample. However, N_m (T) can be noisy, resulting in a differential form n_m (T) that is challenging to interpret. Furthermore, there is no rigorous statistical analysis of how many droplets and dilutions are needed to obtain a well-converged n_m (T) that represents the underlying distribution P_u (T). Here, we present the HUB method and associated Python codes that model (HUB-forward code) and interpret (HUB-backward code) the results of drop-freezing experiments. HUB-forward predicts f_ice (T) and N_m (T) from a proposed distribution P_u (T) of IN temperatures, allowing its users to test hypotheses regarding the role of subpopulations of nuclei in freezing spectra, and providing a guide for a more efficient collection of freezing data. HUB-backward uses a stochastic optimization method to compute n_m (T) from either N_m (T) or f_ice (T). The differential spectrum computed with HUB-backward is an analytical function that can be used to reveal and characterize the underlying number of IN subpopulations of complex biological samples (e.g. ice nucleating bacteria, fungi, pollen), and quantify the dependence of their subpopulations on environmental variables. By delivering a way to compute the differential spectrum from drop freezing data, and vice-versa, the HUB-forward and HUB-backward codes provide a hub to connect experiments and interpretative physical quantities that can be analysed with kinetic models and nucleation theory. | Ingrid de Almeida Ribeiro; Konrad Meister; Valeria Molinero | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6410a9a7e53eff1af31fa9f1/original/hub-a-method-to-model-and-extract-the-distribution-of-ice-nucleation-temperatures-from-drop-freezing-experiments.pdf |
651b0e5da69febde9e1bd50f | 10.26434/chemrxiv-2023-jnpqg | Building Chemical Intuition About Physicochemical Properties of C8-Per-/Poly-fluoroalkyl Carboxylic Acids Through Computational Means | We have predicted acid dissociation constants (pKa), octanol-water partition coefficients (KOW), and DPMC lipid membrane-water partition coefficients (Klipid-w) of 150 different 8-carbon containing poly-/per-fluoroalkyl carboxylic acids (C8-PFCAs) utilizing COMSO-RS theory. Different trends associated with functionalization, degree of fluorination, degree of saturation, degree of chlorination, and branching are discussed based upon the predicted values for the partition coefficients. In general, functionalization closest to the carboxylic head group had the greatest impact on the value of the predicted physicochemical properties. | Jonathan Antle; Michael Larock; Zackary Falls; Carla Ng; Ekin Atilla-Gokcumen; Diana Aga; Scott Simpson | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651b0e5da69febde9e1bd50f/original/building-chemical-intuition-about-physicochemical-properties-of-c8-per-poly-fluoroalkyl-carboxylic-acids-through-computational-means.pdf |
60c74c64567dfe59aeec5139 | 10.26434/chemrxiv.12473177.v1 | Effect of Secondary Additives on the Properties of Vanadium-Aluminum Mixed Oxide Catalysts Used in the Oxidation of Propane | <div>We investigated how secondary additives for tableting vanadium-aluminum</div><div>mixed-oxides affect the mechanical resistance, surface chemistry, and catalytic performance in</div><div>propane oxidation of tablets based on this material. The secondary additives were magnesium </div><div>oxide, silica, boron nitride, sepiolite, and zinc oxide while graphite was used as the primary</div><div>shaping agent. Our results showed that the changes in mechanical strength and porosity were</div><div>directly related to the softness and ductility of the secondary additive. Overall, we learned that</div><div>when manufacturing catalyst tablets, there is a compromise between mechanical strength and</div><div>loss in mesoporosity and surface area. On the other hand, the components of the formulated</div><div>tablets did not show signs of establishing a chemical interaction with the vanadium-aluminum</div><div>mixed oxide. Therefore, the effects of the additives that we found on the catalytic performance</div><div>were ascribed to the fact that the selected secondary additives may act as co-catalysts during</div><div>propane oxidation. In this sense, boron nitride and sepiolite were best for promoting both the</div><div>reactivity of the catalytic formulations while showing a better productivity of propene. The data</div><div>was interpreted suggesting that the promotion effect may be due to the combination of a redox</div><div>mechanism over the vanadium-aluminum mixed oxide phase and to a surface radical mechanism</div><div>occurring over the active moieties of these secondary additives.</div> | Víctor Gabriel Baldovino Medrano; Benjamin Farin; Eric M. Gaigneaux | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c64567dfe59aeec5139/original/effect-of-secondary-additives-on-the-properties-of-vanadium-aluminum-mixed-oxide-catalysts-used-in-the-oxidation-of-propane.pdf |
60c75032bdbb899487a39eb5 | 10.26434/chemrxiv.12958412.v2 | Ion-specific Adsorption on Bare Gold (Au) Nanoparticles in aqueous Solution: Double-Layer Structure and Surface Potentials | We study the solvation and electrostatic properties of bare gold (Au) nanoparticles (NPs) of 1-2 nm in size in aqueous electrolyte solutions of sodium salts of various anions with large physicochemical diversity (Cl<sup>-</sup>, BF<sub>4</sub><sup>-</sup>, PF<sub>6</sub><sup>-</sup>, Nip<sup>-</sup>(nitrophenolate), 3- and 4-valent hexacyanoferrate (HCF)) using nonpolarizable, classical molecular dynamics computer simulations. We find a substantial facet selectivity in the adsorption structure and spatial distribution of the ions at the Au-NPs: while sodium and some of the anions (e.g., Cl<sup>-</sup>, HCF<sup>3-</sup>) adsorb more at the `edgy' (100) and (110) facets of the NPs, where the water hydration structure is more disordered, other ions (e.g., BF<sub>4</sub><sup>-</sup>, PF<sub>6</sub><sup>-</sup>, Nip<sup>-</sup>) prefer to adsorb strongly on the extended and rather flat (111) facets. In particular, Nip<sup>-</sup>, which features an aromatic ring in its chemical structure, adsorbs strongly and perturbs the first water monolayer structure on the NP (111) facets substantially. Moreover, we calculate adsorptions, radially-resolved electrostatic potentials, as well as the far-field <i>effective</i> electrostatic surface charges and potentials by mapping the long-range decay of the calculated electrostatic potential distribution onto the standard Debye-Hückel form. We show how the extrapolation of these values to other ionic strengths can be performed by an analytical Adsorption-Grahame relation between effective surface charge and potential. We find for all salts negative effective surface potentials in the range from -10 mV for NaCl down to about -80 mV for NaNip, consistent with typical experimental ranges for the zeta-potential. We discuss how these values depend on the surface definition and compare them to the explicitly calculated electrostatic potentials near the NP surface, which are highly oscillatory in the ± 0.5 V range. <br /> | Zhujie Li; Victor G. Ruiz; Matej Kanduč; Joachim Dzubiella | Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75032bdbb899487a39eb5/original/ion-specific-adsorption-on-bare-gold-au-nanoparticles-in-aqueous-solution-double-layer-structure-and-surface-potentials.pdf |
6232be25202c066706d6b6f5 | 10.26434/chemrxiv-2022-b4c3v | Chemical Reaction Spectrum: A Holographic Image for Characterizing Multi-component Chemical Mixtures | Abstract: Multi-component chemical mixtures (MCMs) and their various effects always concerned in analytical chemistry, but current analytical techniques based on test-tube experiments often involves many high-cost and laborious operations. Today’s pop machine-learning (ML) technology has exhibited their successes in dealing with the analysis task of various complex systems. Predictably, the introduction of ML will radically accelerate the exploration of many fields involving mixture analysis. But the biggest challenge ahead for this process is how to provide some intelligible and sufficient data for various algorithms. In this study, we proposed a chemical imaging strategy to visualize various mixtures as some feature images by using ink-jet printing technology based on combinatorial chemistry. Here, these feature images were as a novel data form of chemical reaction spectrum (CRS), which can comprehensively describe and record the reaction characteristics of the complex sample. Compared with common imaging methods, the CRS with high-throughput chemical reaction dots is an efficient and economic information visualization way for the MCM sample. It is expected to be an important data acquisition approach for the application of ML in the field of chemistry in future. | Qiannan Duan; Jiayuan Chen; Jianchao Lee*; Sifan Bi; Run Luo; Fenli Liu; Yunjin Feng | Analytical Chemistry; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6232be25202c066706d6b6f5/original/chemical-reaction-spectrum-a-holographic-image-for-characterizing-multi-component-chemical-mixtures.pdf |
613d4d4327d906556d8523a2 | 10.26434/chemrxiv-2021-26ltj | Evidence of sulfur centered hydrogen bond with sulfur atoms as a donor in aromatic thiols and aliphatic thiols on complexation with water using quantum mechanical methods | It has been more than a century since the discovery of hydrogen bonds, but the knowledge about its impact on day to day life of people is getting enhanced even now. It has a pivotal role in the stabilization of various biomolecules and subsequent bioactivity. Sulfur cantered hydrogen bond (SCHB), which is a weak interaction, has attracted the attention of many scientists in the last few decades. In this work, we report the nature of the SCHB between aliphatic/aromatic thiols and water. B3LYP-D3(BJ) with cc-pVTZ level was used for modeling the hydrogen bonded thiol-water complexes. Domain-based local pair natural orbitals coupled-cluster theory with single, double, and perturbative triple excitation DLPNO-CCSD(T) method was used for local energy decomposition analysis. QTAIM analysis helped to examine hydrogen bonds, weak non-covalent interactions, and the various electron density delocalization. Natural Bond Orbital (NBO) analysis explains the reason for the sulfur atom being the H-bond donor. Second-order perturbation energy from NBO findings supports the data obtained by LED and AIM calculations. Aromatic thiols form stronger hydrogen bonds than aliphatic thiols. The effect of substituents was also explored by studying aromatic systems with electron-withdrawing groups and donating groups. EDG substituted have more vital interaction, and EWG substituted thiols form stronger S-H…O hydrogen bonds. | Arnav Paul; Renjith Thomas | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613d4d4327d906556d8523a2/original/evidence-of-sulfur-centered-hydrogen-bond-with-sulfur-atoms-as-a-donor-in-aromatic-thiols-and-aliphatic-thiols-on-complexation-with-water-using-quantum-mechanical-methods.pdf |
60c742274c8919418cad23d9 | 10.26434/chemrxiv.8217479.v1 | Functionalized Titanium Oxide Nanowire Substrate for Surface-Assisted Laser Desorption/ionization Imaging Mass Spectrometry | Imaging mass
spectrometry (IMS) is
a powerful technique that enables analysis of various molecular species
at a high spatial resolution with low detection limits. In contrast to the standard matrix-assisted laser desorption/ionization mass
spectrometry (MALDI-MS) approach, surface-assisted laser desorption/ionization
(SALDI) is more effective in the detection of small molecules due to the absence
of interfering background signals in low <i>m/z</i>
ranges. We developed a functionalized TiO<sub>2</sub> nanowire as a solid
substrate for IMS of low-molecular-weight species in biological specimens. We
prepared TiO<sub>2</sub> nanowires using the inexpensive modified hydrothermal
process and subsequently functionalized it chemically with various silane
analogs to overcome the problem of superhydrophilicity of the substrate.
Chemical modification changed the selectivity of imprinting of samples
deposited on the surface of the plate and thus improved the detection limits. Due
to the enhanced performance, the functionalized TiO<sub>2</sub> nanowire
substrate could be successfully used for imaging of complex native samples. We
applied our new substrate to image distribution of the secondary metabolites in
(1) petal of the medicinal plant <i>Catharanthus
roseus</i> and (2) microbial co-culture of <i>Burkholderia</i>
<i>cenocepacia </i>869T2 vs <i>Phellinus
noxius</i>. We observed that secondary metabolites are distributed heterogeneously
in a petal, which is consistent with previous results reported for the <i>C. roseus</i> plant leaf and stem. We
verified the semi-quantitative capabilities of the imprinting/imaging approach
by comparing results using standard LC-MS analysis of the plant extracts. Several
bacteria-related metabolites produced by <i>B</i>.
<i>cenocepacia</i> 869T2 in presence of <i>P. noxius</i>, which were unable to be detected by MALDI-MS approach,
were revealed by our newly developed approach. This suggested that the
functionalized TiO<sub>2</sub> nanowire substrates-based SALDI is a powerful technique
complementary to MALDI-MS. | Ewelina P. Dutkiewicz; Han-Jung Lee; Cheng-Chih Hsu; Yu-Liang Yang | Nanostructured Materials - Materials; Imaging; Mass Spectrometry; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742274c8919418cad23d9/original/functionalized-titanium-oxide-nanowire-substrate-for-surface-assisted-laser-desorption-ionization-imaging-mass-spectrometry.pdf |
60c746de469df4779ef4372c | 10.26434/chemrxiv.11421201.v1 | Quantifying Protein-Protein Interactions in Molecular Simulations | <p><a></a></p><p><a></a>We present simple, accurate, and efficient methods to estimate the dissociation constant K<sub>d </sub>and the second osmotic virial coefficient B<sub>2 </sub>from molecular simulations. We show that for simulations of two proteins in a box, K<sub>d </sub>is determined by B<sub>2 </sub>and the fraction of bound protein. We present two different methods to calculate B<sub>2 </sub>from Monte Carlo and molecular dynamics simulations using implicit or explicit solvent. We derive a surprisingly simple expression for B<sub>2</sub>, adding significantly to the understanding of this important quantity. Non-binding interactions of proteins and other macromolecules shape the physicochemical properties of the crowded environments inside cells and of biomolecular condensates. We show how to extract the contributions of non-binding conformations to B<sub>2 </sub>and discuss how these can be determined in analytical ultracentrifugation and SAXS experiments. We expect that our methods will prove to be instrumental in force parameterization efforts and high-throughput studies of large interactomes. </p> | Alfredo Jost Lopez; Patrick K. Quoika; Max Linke; Gerhard Hummer; Juergen Koefinger | Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746de469df4779ef4372c/original/quantifying-protein-protein-interactions-in-molecular-simulations.pdf |
60c74aa74c89193c67ad32d4 | 10.26434/chemrxiv.12091260.v3 | Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? An Answer from All-Atoms Simulations | <p>The latest outbreak of a new pathogenic coronavirus
(SARS-CoV-2) is provoking a global health, economic and societal crisis.
All-atom simulations enabled us to uncover the key molecular traits underlying
the high affinity of SARS-CoV-2 spike glycoprotein towards its human receptor,
providing a rationale to its high infectivity. Harnessing this knowledge can
boost developing effective medical countermeasures to fight the current global
pandemic.</p> | Angelo Spinello; Andrea Saltalamacchia; Alessandra Magistrato | Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa74c89193c67ad32d4/original/is-the-rigidity-of-sars-co-v-2-spike-receptor-binding-motif-the-hallmark-for-its-enhanced-infectivity-an-answer-from-all-atoms-simulations.pdf |
655252c22c3c11ed71516c24 | 10.26434/chemrxiv-2023-wcrv3 | Generative AI-Driven Molecular Design: Combining Predictive Models and Reinforcement Learning for Tailored Molecule Generation | Molecular design is a critical aspect of various scientific and industrial fields, where the properties of molecules hold significant importance. In this study, a three-fold methodology design is presented that leverages the power of generative artificial intelligence (AI), predictive modeling, and reinforcement learning to create tailored molecules with desired properties. This model synergistically combines deep learning techniques with Self-Referencing Embedded Strings (SELFIES) molecular representation to build a generative model which generates valid molecules and a graphical neural network model that accurately forecasts molecular properties. The Variational Autoencoder (VAE) coupled with reinforcement learning, helps refine molecule generation based on targeted attributes. Data from an experimental study involving surfactants was used to test the framework. Saliency maps for the generated surfactants were produced to identify the features explaining the property values. The results showed that the proposed framework can effectively produce valid molecules within the set property threshold value. This approach not only streamlines molecular design for surfactant systems but also augurs transformative advancements across different scientific and industrial landscapes. | Miriam Nnadili; Andrew Okafor; Teslim Olayiwola; David Akinpelu; Jose Romagnoli | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Surfactants; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655252c22c3c11ed71516c24/original/generative-ai-driven-molecular-design-combining-predictive-models-and-reinforcement-learning-for-tailored-molecule-generation.pdf |
60c75218337d6c30f0e2867d | 10.26434/chemrxiv.13100564.v2 | Discovery of Cyanobacterial Natural Products Containing Fatty Acid Residues | Natural products have an important role in several human activities, most notably as sources of new drugs. In recent years, massive sequencing and annotation of bacterial genomes has revealed an unexpectedly large number of secondary metabolite biosynthetic gene clusters whose products are yet to be discovered. For example, cyanobacterial genomes contain a large number of gene clusters that likely incorporate fatty acid-derived moieties, but for most cases we lack the knowledge and tools to effectively predict or detect the encoded natural products. Here, we exploit the apparent lack of a functional beta-oxidation pathway in cyanobacteria to achieve efficient stable-isotope labeling of their fatty acid-derived lipidome. We show that supplementation of cyanobacterial cultures with deuterated fatty acids can be used to easily detect natural product signatures in individual strains. The utility of this strategy is demonstrated in two cultured cyanobacteria by uncovering analogues of the multidrug-resistance reverting hapalosin, and novel, cytotoxic, lactylate-nocuolin A hybrids – the nocuolactylates. | Sandra A. C. Figueiredo; Marco Preto; Gabriela Moreira; Teresa P. Martins; Kathleen Abt; André Melo; Vitor M. Vasconcelos; Pedro Leao | Natural Products; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75218337d6c30f0e2867d/original/discovery-of-cyanobacterial-natural-products-containing-fatty-acid-residues.pdf |
677fbf8081d2151a02705e45 | 10.26434/chemrxiv-2025-vssxt | Enhancing Chemical Synthesis Planning: Automated Quantum Mechanics-Based Regioselectivity Prediction for C-H Activation with Directing Groups | The mild and selective functionalization of carbon-hydrogen (C-H) bonds remains a pivotal challenge in organic synthesis, crucial for developing complex molecular architectures in pharmaceuticals, polymers, and agrochemicals. Despite advancements in directing group (DG) methodologies and computational approaches, predicting accurate regioselectivity in C-H activation poses significant difficulties due to the diversity and complexity of organic compounds. This study introduces a novel quantum mechanics-based computational workflow tailored for the regioselective prediction of C-H activation in the presence of directing groups. Utilizing (semi-empirical) quantum calculations hierarchically, the workflow efficiently predicts outcomes by considering concerted metallation deprotonation mechanisms mediated by common catalysts like Pd(OAc)2. Our methodology not only identifies potential activation sites but also addresses the limitations of existing models by including a broader range of directing groups and reaction conditions while maintaining moderate computational cost. Validation against a comprehensive dataset reveals that the workflow achieves high accuracy, significantly surpassing traditional models in both speed and predictive capability. This development promises substantial advancements in the design of new synthetic routes, offering rapid and reliable regioselectivity predictions that are essential for accelerating innovation in material science and medicinal chemistry. | Julius Seumer; Nicolai Ree; Jan H. Jensen | Theoretical and Computational Chemistry; Catalysis; Chemoinformatics - Computational Chemistry; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677fbf8081d2151a02705e45/original/enhancing-chemical-synthesis-planning-automated-quantum-mechanics-based-regioselectivity-prediction-for-c-h-activation-with-directing-groups.pdf |
60c7599e702a9bdc8118ceff | 10.26434/chemrxiv.14356628.v2 | Evaluating the Anharmonicity Contributions to the Molecular Excited State Internal Conversion Rates with Finite Temperature TD-DMRG | <div>In this work, we propose a new method to calculate the molecular nonradiative electronic relaxation rates based on the numerically exact time-dependent density matrix renormalization group theory (TD-DMRG). This method could go beyond the existing frameworks under the harmonic approximation (HA) of the potential energy surface (PES) so that the anharmonic effect could be considered, which is of vital importance when the electronic energy gap is much larger than the vibrational frequency. We calculate the internal conversion (IC) rates in a two-mode model with Morse potential to investigate the validity of HA. We find that HA is unsatisfactory unless only the lowest several vibrational states of the lower electronic state are involved in the transition process when the adiabatic excitation energy is relatively low. As the excitation energy increases, HA first underestimates and then overestimates the IC rates when the excited state PES shifts towards the dissociative side of the ground state PES. On the contrary, HA slightly overestimates the IC rates when the excited state PES shifts towards the repulsive side. In both cases, higher temperature enlarges the error of HA. As a real example to demonstrate the effectiveness and scalability of the method, we calculate the IC rates of azulene from $S_1$ to $S_0$ on the ab initio anharmonic PES approximated by 1-mode representation. The calculated IC rates of azulene under HA are consistent with the analytically exact results. The rates on anharmonic PES are 30%-40% higher than the rates under HA.</div> | Yuanheng Wang; Jiajun Ren; Zhigang Shuai | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7599e702a9bdc8118ceff/original/evaluating-the-anharmonicity-contributions-to-the-molecular-excited-state-internal-conversion-rates-with-finite-temperature-td-dmrg.pdf |
60c74acebdbb8945aca39428 | 10.26434/chemrxiv.12005994.v2 | Chiral Cyclic [n]Spirobifluorenylenes: Carbon Nanorings Consisting of Helically Arranged Quaterphenyl Rods Illustrating Partial Units of Woven Patterns | Chiral cyclic [n]spirobifluorenylenes consisting of helically arranged quaterphenyl rods, illustrating partial units of woven patterns, were designed and synthesized as a new family of carbon nanorings. The synthesis was accomplished by the Ni(0)-mediated Yamamoto-coupling of chiral spirobifluorene building blocks. The structures of the cyclic 3-, 4-, and 5-mers were determined by X-ray crystallographic analysis. These carbon nanorings exhibited a strong violet colored emission with high quantum yields in solution (95%, 93%, and 94% for 3-, 4-, and 5-mer, respectively). Other spectroscopic properties, including their chiroptical properties, were also investigated. The g-values for circularly polarized luminescence were found to be in the order of 10<sup>-3</sup>, where that of the 4-mer showed a relatively higher value 8.5 x 10<sup>-3</sup>. Characteristic spiroconjugation induced by multiple<br />3) bifluorenyl units, for example the even-odd effect of the number of units in the matching of the sign of the orbitals, were also indicated by DFT calculations.<br /> | Kaige Zhu,; Kosuke Kamochi; Takuya Kodama; Mamoru Tobisu; Toru Amaya | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74acebdbb8945aca39428/original/chiral-cyclic-n-spirobifluorenylenes-carbon-nanorings-consisting-of-helically-arranged-quaterphenyl-rods-illustrating-partial-units-of-woven-patterns.pdf |
60c74aca9abda251aff8cf34 | 10.26434/chemrxiv.12243077.v1 | Systems Microbiology and Engineering of Aerobic-Anaerobic Ammonium Oxidation | Aerobic and anaerobic oxidations of ammonium
are core biological processes driving the nitrogen cycle in natural and
engineered microbial ecosystems. These conversions are tailored in
mixed-culture biotechnology to propel partial nitritation and anammox (PN/A)
for a complete chemolithoautotrophic removal of nitrogen from wastewater at low
resource and energey expenditures. Good practices of microbiome science and
engineering are needed to design microbial PN/A systems and translate them to a
spectrum of wastewater environments. Inter-disciplinary investigations of
systems microbiology and engineering are paramount to harness the microbial
compositions and metabolic performance of complex microbiomes. We propose
“process ecogenomics” as an integration ground to combine community systems
microbiology and microbial systems engineering by establishing a synergy
between the life and physical sciences. It drives a high-resolution analysis,
engineering and management of microbial communities and their metabolic
performance in mixed-culture systems. While addressing the key underpinnings of
the science and engineering of aerobic-anaerobic ammonium oxidations, we
advocate the need to formulate targeted research questions in order to
elucidate and manage microbial ecosystems in wastewater environments. We
propose a systems-level roadmap to investigate and functional engineer
technical microbiomes like PN/A, via: (<i>i</i>)
quantitative biotechnological measurement of stoichiometry and kinetics of
nitrogen turnovers; (<i>ii</i>)
genome-centric metagenomic fingerprinting of the microbiome; (<i>ii</i>) ecophysiological examination of the
main metabolizing lineages; (<i>iii</i>)
multi-omics elucidation of expressed metabolic functionalities across the
microbial network; and (<i>iv</i>)
translation of microbial and functional ecology principles into physical
designs.<br /> | David G. Weissbrodt; George F. Wells; Michele Laureni; shelesh Agrawal; Ramesh Goel; Giancarlo Russo; Yujie Men; David Johnson; Magnus Christensson; Susanne Lackner; Adriano Joss; Jeppe Lund Nielsen; Helmut Bürgmann; Eberhard Morgenroth | Environmental Science; Wastes; Biochemical Analysis; Environmental Analysis; Mass Spectrometry; Microscopy; High-throughput Screening; Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Environmental biology; Microbiology; Natural Resource Recovery; Process Control; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aca9abda251aff8cf34/original/systems-microbiology-and-engineering-of-aerobic-anaerobic-ammonium-oxidation.pdf |
64dcee86dfabaf06ff5fa2d0 | 10.26434/chemrxiv-2023-jnt7m-v2 | Toward Benchmark-quality Ab Initio Predictions for 3d Transition Metal Electrocatalysts - A Comparison of CCSD(T) and ph-AFQMC | Generating accurate ab initio ionization energies for transition metal complexes is an important step towards the accurate computational description of their electrocatalytic reactions. Benchmark-quality data is required for testing existing theoretical methods and for developing new ones but is complicated to obtain for many transition metal compounds due to the potential presence of both strong dynamical and static electron correlation. In this regime, it is questionable whether the so-called gold standard, coupled cluster with singles, doubles, and perturbative triples (CCSD(T)), provides the desired level of accuracy -- roughly 1-3 kcal/mol. In this work, we compiled a test set of 28 3d metal-containing molecules relevant to homogeneous electrocatalysis (termed 3dTMV) and computed their vertical ionization energies (ionization potentials) with CCSD(T) and phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) in the def2-SVP basis set. A substantial effort has been made to converge away the phaseless bias in the ph-AFQMC reference values. We assess a wide variety of multireference diagnostics, and find that spin-symmetry breaking of the CCSD wavefunction and in the PBE0 density functional correlate well with our analysis of multiconfigurational wavefunctions. We propose quantitative criteria based on symmetry breaking to delineate correlation regimes inside of which appropriately-performed CCSD(T) can produce mean absolute deviations from the ph-AFQMC reference values of roughly 2 kcal/mol or less, and outside of which CCSD(T) is expected to fail. We also present a preliminary assessment of DFT functionals on the 3dTMV set. | Hagen Neugebauer; Hung T. Vuong; John L. Weber; Richard A. Friesner; James Shee; Andreas Hansen | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dcee86dfabaf06ff5fa2d0/original/toward-benchmark-quality-ab-initio-predictions-for-3d-transition-metal-electrocatalysts-a-comparison-of-ccsd-t-and-ph-afqmc.pdf |
655337036e0ec7777fe7d9c4 | 10.26434/chemrxiv-2023-pcfjc | QUANTUM STATES OF THE ‘ENIGMATIC’ 1-D HYDROGEN ATOM: DO THEY EXIST? | The quantum states of hydrogen atom in one dimension can be obtained by a careful application of the well-known Frobenius method. The exercise is highly educative and brings to focus the subtle aspects of quantum mechanics. The allowed states turn out to be only of odd parity and non-degenerate, having energy given by E_n=-ⅇ^2/(2n^2 a_0 ) , n= 1, 2, 3,..., and a_0 being the first Bohr radius, in exact correspondence with energy levels of 3-D H-atom. In view of odd parity of all states the spectrum of 1-D H-atom is expected to be dominated by weak electric quadrupole transitions. | Sucheta Ghosh; Shankar Prasad Bhattacharyya | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education | CC BY 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655337036e0ec7777fe7d9c4/original/quantum-states-of-the-enigmatic-1-d-hydrogen-atom-do-they-exist.pdf |
67322011f9980725cfdc747c | 10.26434/chemrxiv-2024-wkdpf | Antiadhesive glycoconjugate metal complexes targeting pathogens Pseudomonas aeruginosa and Candida albicans | Glycoconjugates are known to interact with carbohydrate-binding proteins involved in adhesion by pathogens, and offer opportunities for designing antimicrobial agents. Metal complexes with Eu(III), Ni(II) and Zn(II) were prepared from glycoconjugate ligand 1Gal, which binds to P. aeruginosa’s lectin LecA. In vitro anti-adhesive activity of these compounds was evaluated for both P. aeruginosa and C. albicans. Choice of metal ion played a crucial role in modulating anti-adhesive activity of these complexes, with Eu(III) complexes most effective: [Eu⋅(1Gal)](CF3SO3)3 inhibits 47% biofilm formation by P. aeruginosa and [Eu⋅(1Gal)3](CF3SO3)3 inhibits 62% of C. albicans adhesion to buccal epithelial cells (both at 0.1 mM). The results presented demonstrate the potential for metal coordination for enhancing biological activity of glycoconjugates. | Karolina Wojtczak; Emilie Gillon; Diana Bura; Karen Richmond; Megan Joyce; Emma Caraher; Keela Kessie; Trinidad Velasco-Torrijos; Cristina Trujillo; Anne Imberty; Kevin Kavanagh; Gordon Cooke; Joseph P. Byrne | Biological and Medicinal Chemistry; Organic Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Microbiology | CC BY 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67322011f9980725cfdc747c/original/antiadhesive-glycoconjugate-metal-complexes-targeting-pathogens-pseudomonas-aeruginosa-and-candida-albicans.pdf |
673f37d85a82cea2fa37b388 | 10.26434/chemrxiv-2024-r7xbm | Facile and Versatile Mechanochemical Synthesis of Indigoid Photoswitches | We demonstrate the application of mechanochemistry in the synthesis of indolone-based photoswitches (hemiindigos, hemithioindigos, and oxindoles) via Knoevenagel condensation reactions. Utilizing ball-milling and an organic base (piperidine) acting as catalyst and solvent for liquid assisted grinding (LAG) conditions, we achieve rapid, solvent-free transformations, obtaining a set of known and previously unreported photoswitches, including highly functional amino acid–based photoswitches, multichromophoric derivatives and photoswitchable cavitands based on resorcin[4]arenes. The reaction under mechanochemical conditions gives moderate-to-high yields and is highly stereoselective leading to Z-isomers of hemiindigos and hemithioindigos and E-isomers of oxindoles. For selected examples, reversible visible-light photoswiching properties have been demonstrated. | Arturo Llamosí Fornés; Oksana Danylyuk; Agnieszka Szumna | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f37d85a82cea2fa37b388/original/facile-and-versatile-mechanochemical-synthesis-of-indigoid-photoswitches.pdf |
60c750cd337d6c1721e283e8 | 10.26434/chemrxiv.13072100.v1 | Estradiol Determine Liver Lipid Deposition in Ratsfed Standard Diets Unbalanced with Excess Lipid or Protein | <p>The ingestion of excess fat often produces an increased body weight, because of
higher adiposity and accumulation of fat in the liver. However, modulation of
diet energy partition may affect differently the body metabolic responses and
the extent of lipid deposition. Ten-week-old male and female rats were fed with
either standard rat chow (SD), standard diet enriched with coconut oil
(high-fat diet, HF), standard diet enriched with protein (high-protein diet,
HP) or a self-selected “cafeteria” diet (CAF) for one month. Both HF and CAF
diets provided the same lipid-derived percentage of energy (40%) HP diet
protein-energy derived was twice (40%) than those of the SD diet. After the
treatment, CAF groups showed significant weight increases. Hepatic lipid
content also showed sex-related differences; triacylglycerol accumulation was
significant in HF and CAF fed males. Cholesterol content was higher only in the
CAF male group. Plasma estradiol in HF and HP males was higher than in CAF.
Circulating cholesterol was inversely correlated with estradiol levels, which
were proportional to lactate levels. These changes agreed with the differences
found in the expression of key hepatic enzymes of lipid and energy metabolism.
The protective effect of estrogens preventing excess liver lipid deposition, is
also effective in males with ‘normal’ diets
unbalanced by lipid or protein, but is not sufficient to protect males
from the massive changes produced by a markedly obesogenic cafeteria-type diet.
Estradiol protective effects are exerted at the root of energy metabolism, on
the partition of substrates distributed from or entering the liver. </p> | Laia Oliva; Marià Alemany; José-Antonio Fernández-López; Xavier Remesar | Food | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750cd337d6c1721e283e8/original/estradiol-determine-liver-lipid-deposition-in-ratsfed-standard-diets-unbalanced-with-excess-lipid-or-protein.pdf |
65cdfb889138d231612c2727 | 10.26434/chemrxiv-2024-18bg6 | Quantum chemical and molecular modeling studies of twenty therapeutic nucleosides and nucleoside analogues | Naturally occurring and synthetic, chemically modified nucleosides and nucleoside analogues are suggested to be effective therapeutic agents against different diseases, especially viral diseases, and cancer. Theoretical studies including molecular dynamics simulations are often necessary for the determination of the stability, conformational characteristics, binding efficiency, etc. of such residues. Here, we report AMBER force field parameters and topologies, including glycosidic torsion parameters and partial atomic charges for a set of twenty therapeutically important nucleosides/nucleoside analogues most of which are known/potential antiviral and antitumor agents. These parameter sets would be useful for future simulation studies involving these residues and for further improvements. We also report molecular properties observed from quantum mechanical calculations and conformational characteristics extracted from molecular dynamics simulations of these residues using the newly derived parameter sets. Our results would enrich the understanding of their functional characteristics, activity, and efficacy as therapeutic agents and possibly for their repurposing against other similar diseases. | Nivedita Dutta; Indrajit Deb; Joanna Sarzynska; Ansuman Lahiri | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cdfb889138d231612c2727/original/quantum-chemical-and-molecular-modeling-studies-of-twenty-therapeutic-nucleosides-and-nucleoside-analogues.pdf |
67ceae83fa469535b9b3ebeb | 10.26434/chemrxiv-2025-3kfcf | A Digital Tool for Liquid-Liquid Extraction Process Design | Aqueous liquid-liquid extractions are crucial for purifying compounds and removing impurities in the pharmaceutical industry. However, the extensive solvent space involved in such operations highlights the need for an informed approach in solvent selection. We present a digital tool designed to leverage data-driven experimentation to enhance process efficiency and sustainability, aligning with industry trends towards digitalisation. It allows users to input various parameters, retrieve relevant data, and visualise extraction efficiencies, thereby improving process understanding and reducing process development lead times. By providing interactive visualisations and facilitating rapid hypothesis generation, the tool supports informed decision-making and streamlines workflows. The tool's application is demonstrated through representative complex scenarios involving the separation of compounds in a chemical reaction. Overall, this digital tool represents a significant advancement in chemical process design, promoting more sustainable and efficient practices in the industry. | George Karageorgis; Simone Tomasi; Elliot Farrar; Maxime Tarrago; Tabassum Malik | Physical Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Compounds and Functional Groups; Pharmaceutical Industry; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ceae83fa469535b9b3ebeb/original/a-digital-tool-for-liquid-liquid-extraction-process-design.pdf |
63591d36cf6de9238123097a | 10.26434/chemrxiv-2022-zs4wh | Chitin-binding function and glycosyl hydrolysis/motor-like system facilitate the spread of the wheat mosaic virus | Infecting cereals and grasses worldwide, wheat mosaic disease poses a serious risk to food security. The major grain producing regions have been threatened by major crop diseases and insect pests. The wheat curl mite was previously thought to be the primary vector for the spread of the wheat mosaic virus. However, recent research has shown that soil may actually be more influential. In this present study,we used domain search of the bioinformatics method to study the coat protein of the Chinese wheat mosaic virus. The wheat mosaic virus's binding regions to chitin, chitosan, and cellulose, as well as the active region of cell wall degrading enzymes, and the related domains of endocytotic entry, were determined through the domain search.There are Ca2+ and Mg2+-ATP binding sites in the wheat mosaic virus coat protein. It demonstrates that wheat mosaic virus can complete its transmission by binding chitin via its coat protein. By binding Ca2+ via an EF-hand, the coat protein is capable of inducing the binding of Mg2+-ATP, which is essential for initiating serine-threonine kinase activity. A coating containing serine kinase activity facilitates the capacity of proteins to bind chitin, collagen, or fibrillar cellulose. Upon activation of the PPM enzyme domain that binds Mg2+-ATP, glycosyl hydrolases and swelling enzymes become active. This process necessitates the hydrolysis of glycosyl chains contained in proteins, which contributes to the enlargement of the cell wall. As they continue to move, the motor domains of the coat protein rotate and puncture holes in the cell wall. Using phospholipid transporter domains, it creates membrane fusion pores on the cell membrane. At the same time, the coat protein inserts viral genetic material into plant cells. | wenzhong liu; hualan li | Biological and Medicinal Chemistry; Agriculture and Food Chemistry; Food; Biochemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63591d36cf6de9238123097a/original/chitin-binding-function-and-glycosyl-hydrolysis-motor-like-system-facilitate-the-spread-of-the-wheat-mosaic-virus.pdf |
677c4f7f6dde43c9088a354c | 10.26434/chemrxiv-2025-4mbsk | Wiggle150: Benchmarking Density Functionals And Neural Network Potentials On Highly Strained Conformers | Accurate benchmarks are key to assessing the accuracy and robustness of computational methods, yet most available benchmark sets focus on equilibrium geometries, limiting their utility for applications involving non-equilibrium structures such as ab initio molecular dynamics and automated reaction-path exploration. To address this gap, we introduce Wiggle150, a benchmark comprising 150 highly strained conformations of adenosine, benzylpenicillin, and efavirenz. These geometries—generated via metadynamics and scored using DLPNO-CCSD(T)/CBS reference energies—exhibit substantially larger deviations in bond lengths, angles, dihedrals, and relative energies than other conformer benchmarks. We evaluate a diverse array of computational methods, including density-functional theory, composite quantum chemical methods, semiempirical models, neural network potentials, and force fields, on predicting relative energies for this challenging benchmark set. The results highlight multiple methods along the speed–accuracy Pareto frontier and identify AIMNet2 as particularly robust among the NNPs surveyed. We anticipate that Wiggle150 will be used to validate computational protocols involving non-equilibrium systems and guide the development of new density functionals and neural network potentials. | Joseph Gair; Corin Wagen; Rebecca Brew; Ian Nelson; Meruyert Binayeva; Amlan Nayak; Wyatt Simmons | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c4f7f6dde43c9088a354c/original/wiggle150-benchmarking-density-functionals-and-neural-network-potentials-on-highly-strained-conformers.pdf |
60c750029abda253caf8d95d | 10.26434/chemrxiv.12977678.v1 | Force-Modulated Reductive Elimination from Platinum(II) Diaryl Complexes | <div><p>Coupled mechanical forces are known to drive a range of covalent chemical reactions, but the interplay of mechanical force applied to a spectator ligand and transition metal reactivity is relatively unexplored. Here we report the effect of mechanical force on the rate of C(sp<sup>2</sup>)-C(sp<sup>2</sup>) reductive elimination from platinum(II) diaryl complexes containing macrocyclic bis(phosphine) force probe ligands. Compressive forces decreased the rate of reductive elimination whereas extension forces increased the rate of reductive elimination relative to the strain-free MeOBiphep complex with a 3.4-fold change in rate over a ~290 pN range of restoring forces. The natural bite angle of the free ligand changes with force, but <sup>31</sup>P NMR analysis strongly suggests no significant force-induced perturbation of the ground state geometry of the (P–P)PtAr<sub>2</sub> complexes. Rather, the force/rate behavior observed across this range of forces (from ca. 65 pN in compression to >200 pN in extension) for reductive elimination is attributed to the coupling of force to the elongation of the O<b><sup>…</sup></b>O distance in the transition state for reductive elimination. The results suggest opportunities to experimentally map geometry changes associated with reactions in transition metal complexes and potential strat-egies for force-modulated catalysis. </p></div><br /> | Yichen Yu; Liqi Wang; Chenxu Wang; Yancong Tian; Roman Boulatov; Ross Widenhoefer; Stephen Craig | Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750029abda253caf8d95d/original/force-modulated-reductive-elimination-from-platinum-ii-diaryl-complexes.pdf |
6703c87651558a15ef5a09c3 | 10.26434/chemrxiv-2024-1kbcw | Catalysis-driven active transport across a liquid membrane | Biology masters energy transduction, converting energy between various forms, and employing it to drive its vital processes. Central to this is the ability to use chemical energy for the active transport of substances, pumping ions and molecules across hydrophobic lipid membranes between aqueous (sub)cellular compartments. Biology employs information ratchet mechanisms, where kinetic asymmetry in the fuel-to-waste (i.e., substrate-to-product) conversion results in catalysis-driven active transport. Here, we report an artificial system for catalysis-driven active transport across a liquid hydrophobic membrane, pumping a maleic acid cargo between aqueous compartments. We employ two strategies to differentiate the conditions in either compartment, showing that transmembrane active transport can be driven either by adding fuel to a single compartment, or by differentiating the rates of activation and/or hydrolysis when fuel is present in both compartments. We characterize the nonequilibrium system through complete kinetic analysis. Finally, we quantify the energy transduction achieved by the catalysis-driven active transport, and establish the emergence of positive and negative feedback mechanisms within the system. | Kaiyuan Liang; Federico Nicoli; Shaymaa Al Shehimy; Emanuele Penocchio; Simone Di Noja; Yuhan Li; Claudia Bonfio; Stefan Borsley; Giulio Ragazzon | Physical Chemistry; Organic Chemistry; Catalysis; Supramolecular Chemistry (Org.); Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703c87651558a15ef5a09c3/original/catalysis-driven-active-transport-across-a-liquid-membrane.pdf |
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