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62acd26d6124c209db1de405 | 10.26434/chemrxiv-2022-vh7m3 | The Carbodiimide Click Reaction Provides Rapid and Conver-gent Access to Aminotriazoloquinazolines | A novel, convergent synthesis of aminotriazoloquinazolines is reported. These heterocycles are reliably prepared via a “click” reaction between readily available aryl carbodiimides and acyl hydrazides. Such products are of particular interest with respect to their inhibitory activity against the A2A and A2B adenosine receptors and the title “click” reaction has greatly accelerated the discovery of potent/selective chemical matter in this space. | Elisabeth Hennessy; Maximilian Palkowitz; Josep Saurí; Aaron Sather | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62acd26d6124c209db1de405/original/the-carbodiimide-click-reaction-provides-rapid-and-conver-gent-access-to-aminotriazoloquinazolines.pdf |
643d594673c6563f140a7012 | 10.26434/chemrxiv-2023-31393-v2 | Cu(II)-Catalyzed Aerobic Synthesis of Sulfinamidines from Sulfenamides | Inhere, the first instance of copper-catalyzed oxidative amination of sulfenamides for the synthesis of sulfinamidines was documented. Employing air as the terminal oxidant, a variety of secondary and primary amines can be effectively transformed into their target products. This reaction boasts excellent chemoselectivity, mild conditions, straightforward operation, and broad substrate compatibility, which has significant implications for the fields of pharmaceuticals and organic synthesis. | Xunbo Lu; Guoling Huang; Jianlin Ye; Yuetong Chen; Minxi Tan | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643d594673c6563f140a7012/original/cu-ii-catalyzed-aerobic-synthesis-of-sulfinamidines-from-sulfenamides.pdf |
60c7545c702a9b9f6e18c4f0 | 10.26434/chemrxiv.13580519.v1 | How to Organize a Photocatalysis Conference Online (on a Budget) | Originally planned as an on-site meeting, the inaugural CataLight Young Scientist Symposium (CYSS) took place as a fully online conference in November 2020. Dedicated to various aspects of photocatalysis, namely synthesis, theory, characterization, and application, CYSS aimed to provide a stage for early-career scientists to connect to each other and present their research to peers in the field. While still keeping a traditional on-site conference format including both plenary and poster sessions, several minor and major changes had to be applied to the format to deliver a full experience. In this report, we highlight key steps in the organization of such an online conference, laying a focus on using mostly open source software to minimize costs, and discuss differences to both on-site and other online conference formats.<br /> | Mathias Micheel; Julian Hniopek; Elisabeth Hofmeister; Carolin Müller; Miftahussurur Hamidi Putra; Ludwig Schwiedrzik; Pascal Wintergerst | Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2021-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7545c702a9b9f6e18c4f0/original/how-to-organize-a-photocatalysis-conference-online-on-a-budget.pdf |
6222bb3bc45c0b1af525a491 | 10.26434/chemrxiv-2022-czsx6 | Home-built spinning apparatus for drying agarose-based imaging mass spectrometry samples | Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a
useful technique for mapping the spatial distribution of molecules across biological samples.
Sample preparation is crucial for MALDI-IMS; samples must be flat, dry, and co-crystallized with
a matrix prior to analysis. Agar and agarose-based samples can be difficult to consistently
prepare as they are susceptible to environmental changes, which can lead to inconsistent drying
and wrinkling on the sample surface. Small height differences may cause low ionization of target
analytes, or introduce artifacts in imaging data. To overcome the variations, a home-built robotic
spinner was constructed and applied to agarose-based samples. This robotic-spinner is
inexpensive, easy to assemble; and when applied to agarose-based samples, accelerated the
drying process and reduced wrinkles, improving the overall quality of the resulting IMS data. | Hannah Lusk; Sarah Levy; Tova Bergsten; Joanna Burdette; Laura Sanchez | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Imaging; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6222bb3bc45c0b1af525a491/original/home-built-spinning-apparatus-for-drying-agarose-based-imaging-mass-spectrometry-samples.pdf |
670642b212ff75c3a1efcf8b | 10.26434/chemrxiv-2024-k5j3x | Thiol-Thiol Cross-Clicking Using Bromo-Ynone Reagents | Thiols are used in many click reactions, and are also excellent platforms for biomolecular click or bioconjugation reactions. The direct cross-coupling of two thiols is an attractive biomimetic concept for click chemistry, but leads to statistical mixtures of homo- and heterodimers. Here, we introduce a novel class of thiol-click reagents, bromo-ynones, where the kinetic differentiation between the first and second thiol addition onto these reagents facilitates a stepwise one-pot “cross-clicking” of two distinct thiols in aqueous media, without the need for intermediate isolation or purification. The two thiols are linked through a single carbon atom, mimicking a disulfide bridge. We demonstrate the use of bromo-ynones in the synthesis of various cross-coupled thiols, including small molecule drugs, fluorophores, carbohydrates, peptides and proteins. The resulting adducts are robust under physiological conditions and by judicious choice of the bromo-ynone reagent, the adducts can be stable even in the presence of excess free thiols. | Marvin Nicque; Jan Meffert; Diederick Maes; Kevin Bevernaege; Mehwish Iftikhar; Annemieke Madder; Johan Winne | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670642b212ff75c3a1efcf8b/original/thiol-thiol-cross-clicking-using-bromo-ynone-reagents.pdf |
62fb227a21350107783a93cf | 10.26434/chemrxiv-2022-fzj5w-v2 | Solution-Phase Synthesis of the Chalcogenide Perovskite Barium Zirconium Sulfide as Colloidal Nanomaterials | Chalcogenide perovskites such as BaZrS3 have promising optoelectronic properties. Methods to produce these materials at low temperatures, especially in the solution phase, are currently scarce. We describe a solution-phase synthesis of colloidal nanoparticles of BaZrS3 using reactive metal amide precursors. The nanomaterials are crystallographically and spectroscopically characterized. | Daniel Zilevu; Omri Parks; Sidney Creutz | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fb227a21350107783a93cf/original/solution-phase-synthesis-of-the-chalcogenide-perovskite-barium-zirconium-sulfide-as-colloidal-nanomaterials.pdf |
63595357311072ffa5f0c3d1 | 10.26434/chemrxiv-2022-2t32g-v2 | Quantum versus Classical Unimolecular Fragmentation Rate Constants and Activation Energies at Finite Temperature from Direct Dynamics Simulations | In the present work, we investigate how nuclear quantum effects modify the temperature dependent rate constants and, consequently, the activation energies in unimolecular reactions. In the reactions under study, nuclear quantum effects mainly stem from the presence of a large zero point energy. Thus, we investigate the behavior of methods compatible with direct dynamics simulations, the Quantum Thermal Bath (QTB) and Ring Polymer Molecular Dynamics (RPMD). To this end, we first compare them with quantum reaction theory for a model Morse potential before extending this comparison to molecular models. Our results show that, in particular in the temperature range comparable with or lower than the zero point energy of the system, the RPMD method is able to correctly capture nuclear quantum effects on rate constants and activation energies. On the other hand, although the QTB provides a good description of equilibrium properties including zero-point energy effects, it largely overestimates the rate constants. The origin of the different behaviours is in the different distance distributions provided by the two methods and in particular how they differently describe the tails of such distributions. | Federica Angiolari; Simon Huppert; Riccardo Spezia | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63595357311072ffa5f0c3d1/original/quantum-versus-classical-unimolecular-fragmentation-rate-constants-and-activation-energies-at-finite-temperature-from-direct-dynamics-simulations.pdf |
60c747069abda2999af8c84f | 10.26434/chemrxiv.11475291.v1 | Seeking Magneto-Structural Correlations in Easily Tailored Pentagonal Bipyramid Dy(III) Single-Ion Magnets | <p><a></a>Controlling molecular magnetic anisotropy via structural engineering is delicate and fascinating, especially for single-molecule magnets (SMMs). Herein a family of dysprosium single-ion magnets (SIMs) sitting in pentagonal bipyramid geometry have been synthesized with the variable-size terminal ligands and counter anions, through which the subtle coordination geometry of Dy(III) can be finely tuned based on the size effect. The effective energy barrier (Ueff) successfully increases from 439 K to 632 K and the magnetic hysteresis temperature (under a 200 Oe/s sweep rate) raises from 11 K to 24 K. Based on the crystal-field theory, a semi-quantitative magneto-structural correlation deducing experimentally for the first time is revealed that the Ueff is linearly proportional to the structural-related value S2<sup>0</sup> corresponding to the axial coordination bond lengths and the bond angles. Through the evaluation of the remanent magnetization from hysteresis, quantum tunneling of magnetization (QTM) is found to exhibit negative correlation with the structural-related value S<sub>tun</sub> corresponding to the axial coordination bond angles.<br /></p> | Guo-Zhang Huang; Ze-Yu Ruan; Jie-Yu Zheng; Yan-Cong Chen; Si-Guo Wu; Jun-Liang Liu; Ming-Liang Tong | Lanthanides and Actinides; Magnetism; Solid State Chemistry | CC BY NC 4.0 | CHEMRXIV | 2019-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747069abda2999af8c84f/original/seeking-magneto-structural-correlations-in-easily-tailored-pentagonal-bipyramid-dy-iii-single-ion-magnets.pdf |
661bd38821291e5d1dd0f10b | 10.26434/chemrxiv-2024-mpl8l-v6 | Graph-Text Contrastive Learning of Inorganic Crystal Structure toward a Foundation Model of Inorganic Materials | Developing foundation models for materials science has attracted attention. However, there is a lack of studies on inorganic materials due to the difficulty in the comprehensive representation of geometric concepts composing crystals: local atomic environments, their connections, and the global symmetries. We present a contrastive learning of inorganic crystal structure (CLICS) for embedding the geometric concepts, which contrasts texts representing the contextual patterns of geometries with the crystal graphs. We demonstrate that the geometric concepts are integrally embedded on the CLICS feature space, through experiments of concept retrieval from crystal graphs, similar structure search, and few-shot/imbalanced crystal structure classification. | Keisuke Ozawa; Teppei Suzuki; Shunsuke Tonogai; Tomoya Itakura | Materials Science; Inorganic Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661bd38821291e5d1dd0f10b/original/graph-text-contrastive-learning-of-inorganic-crystal-structure-toward-a-foundation-model-of-inorganic-materials.pdf |
633d84e6fee74e15f7568efe | 10.26434/chemrxiv-2022-mhs5z-v2 | Teaching FAIR in Computational Chemistry: Managing and publishing data using the twin tools of Compute Portals and Repositories. | The history of the development of two tools for managing research resources and the data produced from them is summarised. These tools are a portal or electronic laboratory notebook for computational chemistry interfaced in one direction to a high-performance computing resource and in the other direction to a modern research data repository. The essential features of both these tools are described over two generations of each, with examples of student work cited as examples using persistent identifiers or PIDs, better known as DOIs. Underpinning this is metadata describing the data being processed. The evolution of managing data in this manner over almost two decades and its progress towards what can now be summarised by the acronym FAIR data is outlined. | Henry Rzepa | Theoretical and Computational Chemistry; Chemical Education; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633d84e6fee74e15f7568efe/original/teaching-fair-in-computational-chemistry-managing-and-publishing-data-using-the-twin-tools-of-compute-portals-and-repositories.pdf |
66e6edafcec5d6c142236a2d | 10.26434/chemrxiv-2024-p8fz6 | Droplet deformation in steady fluidic flows enables robust, accessible, high-throughput surface tension measurements | Impressive improvements in the ability of microfluidic devices to reliably fabricate a wide variety of droplet, capsule, and particle architectures necessitate comparable improvements in techniques to measure and characterize these materials in line. Measurement and control of droplet surface tension are needed to ensure droplet stability while minimizing excess use of surfactants. Standard techniques to measure surface tension typically measure one droplet at a time. Fluidics can be leveraged to measure surface tension in-line with droplet formation. Typically, this requires channel geometries that enable extensional flow. Transient relaxation of deformed droplets is then measured at the exit of a constriction. We propose an alternative approach, in which a single value of steady deformation within a constriction is used to measure surface tension. We flow aqueous droplets in mineral oil through a series of increasingly narrow constrictions and measure steady deformation. In a subset of experiments, droplets contain varying concentrations of polyethylene glycol diacrylate, a common blank-slate hydrogel polymer. We calculate surface tension using Taylor’s small deformation theory, which describes the relationship between steady deformation in shear flows and the Capillary number, the ratio of the applied viscous stress to restoring surface tension stress. We measure surface tension over a wide range of surfactant concentration. Validation using both the transient deformation fluidic approach and pendant droplet measurements demonstrates the viability of our approach. Importantly, our results suggest that steady state measurements of deformation in pressure driven flows provide accurate assessments of surface tension, even when droplets are slightly confined. The use of multiple constrictions allows measurement of hundreds of droplets at several distinct shear rates without the need to vary control parameters. This steady deformation approach represents a readily-accessible option for measuring surface tension of micro-scale droplets in pressure driven flow through rectangular channels. | Evyatar Shaulsky; Sabrina Marnoto; Avi J. Patel; Sara M. Hashmi | Materials Science; Chemical Engineering and Industrial Chemistry; Surfactants; Fluid Mechanics; Transport Phenomena (Chem. Eng.) | CC BY NC 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e6edafcec5d6c142236a2d/original/droplet-deformation-in-steady-fluidic-flows-enables-robust-accessible-high-throughput-surface-tension-measurements.pdf |
62850d7170876788a156d97d | 10.26434/chemrxiv-2022-fxg8s | Direct evidence of exfoliation efficiency and graphene dispersibility of green solvents towards sustainable graphene production | Achieving sustainable production of pristine high-quality graphene and other layered materials at low cost is one of the bottlenecks that needs to be overcome for reaching 2D materials applications at scale. Liquid Phase Exfoliation (LPE) in conjunction with N-methyl-2-pyrrolidone (NMP) is recognised as the most efficient method for both the exfoliation and dispersion of graphene. Unfortunately, NMP is neither sustainable nor suitable for up-scaling production due to its adverse impact on the environment. Here we show the real potential of green solvents by revealing the independent contributions of their exfoliation efficiency and graphene dispersibility to the graphene yield. By experimentally separating these two factors we show that the exfoliation efficiency of a given solvent is independent of its dispersibility. Here we show that isopropanol can be used to exfoliate graphite as efficiently as NMP. This finding is corroborated by the matching ratio between the polar and dispersive energy of graphite and that of the solvent surface tension. This direct evidence of exfoliation efficiency and dispersibility of solvents paves the way to developing a deeper understanding of the real potential of sustainable graphene manufacturing at scale. | Kai Ling Ng; Barbara M Maciejewska; Ling Qin; Colin Johnston; Jesus Barrio; Maria-Magdalena Titirici; Iakovos Tzanakis; Dmitry Eskin; Kyriakos Porfyrakis; Jiawei Mi; Nicole Grobert | Materials Science; Nanoscience; Carbon-based Materials; Materials Processing; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62850d7170876788a156d97d/original/direct-evidence-of-exfoliation-efficiency-and-graphene-dispersibility-of-green-solvents-towards-sustainable-graphene-production.pdf |
6340dd33975e94ae1a98b279 | 10.26434/chemrxiv-2022-8c7kn | Machine learning prediction of open metal sites in metal-organic framework catalysts | Metal-organic frameworks (MOF) have garnered much attention as promising catalysts due to their tunable porosity, high surface area, and diversity of catalytic metal clusters and organic linkers as building blocks. The presence of open metal sites (OMS) significantly influences the catalytic, adsorption, and separation capabilities of MOFs. However, common laboratory methods are indirect and can suffer from structural heterogeneity. Computational methods, including machine learning, play a central role in the rational design of MOFs, yet in silico detection of OMS still relies heavily on computationally expensive simulations. In this work, we use extreme gradient boosting (XGboost) and random forest (RF) methods to predict the existence of OMS in various MOF compounds based on structural and chemical features. RF provided a higher prediction accuracy of 0.891 compared to 0.865 of XGBoost. Average ionization energy, average electron affinity, and fraction of electrons in d orbitals exhibited the highest importance scores across the two models. These prediction models not only provide novel insights into the structural-property relationship between MOFs and OMS, but also would enable accurate and efficient exploration of MOFs that would give rise to OMS, facilitating the engineering of sorption, separation, and catalytic properties. | Huixuan Guo; Jiahao Ma; Yueshan Zhong; Yuhui Yin; Mingcan Chen | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6340dd33975e94ae1a98b279/original/machine-learning-prediction-of-open-metal-sites-in-metal-organic-framework-catalysts.pdf |
647e3cafe64f843f41614465 | 10.26434/chemrxiv-2022-5v86b-v2 | Photonic Enhancement in Photoluminescent Metal Halide Perovskite–Photonic Crystal Bead Hybrids | The integration of photonic materials with semiconductor nanocrystals by correlating the photonic stopband and the photoluminescence maximum is expected to afford hybrid materials with enhanced optoelectronic properties. Here, we report two photonic crystal–perovskite nanocrystal microbead hybrids synthesized through simple vacuum drying techniques. Photonic polystyrene microbeads combined with metal halide perovskite (CsPbBr3 and CsPbBr1.5Cl1.5) nanocrystals yield hybrids with photoluminescence matching that of the parent nanocrystals and increased photoluminescence quantum yields. Time-resolved photoluminescence spectroscopy quantifies the radiative enhancement afforded by the photonic environment of the microbeads. These nanocrystal–microbead hybrids also demonstrate markedly better resistance to degradation in water over 30 days of immersion compared to their colloidal counterparts. | Victoria Lapointe; Christian Imperiale; Sollavi Chengadu; Cristina Pomilio; Meera Ganesh; Stéphane Kéna-Cohen; Marek Majewski | Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647e3cafe64f843f41614465/original/photonic-enhancement-in-photoluminescent-metal-halide-perovskite-photonic-crystal-bead-hybrids.pdf |
6547b97fa8b423585aff76f1 | 10.26434/chemrxiv-2023-k1q81-v2 | Predictive Thermodynamic Model for Intrusion of Electrolyte Aqueous Solutions in Nanoporous Materials | We performed Monte Carlo simulations in the osmotic ensemble in three representative hypothetical pure-silica zeolites that are silicalite-1, chabazite and faujasite for which adsorption isotherm of water has been calculated from grand canonical Monte Carlo simulations. Monte Carlo moves in the osmotic ensemble to insert electrolyte reveal that ions do not penetrate the zeosils at water intrusion pressure because they are better solvated in the bulk for low-diameter pore zeosils, which is associated to a lower ion solvation. Then, Chemical potential of water in electrolyte solutions has been calculated and highlight the same dependency in pressure as the chemical potential of pure water. From these conclusions, we propose a thermodynamic model that revisit the law of osmotic pressure in order to predict the intrusion pressure in zeosils taking account of the nature of electrolytes in solution. | Ambroise de Izarra; François-Xavier Coudert; Alain H. Fuchs; Anne Boutin | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6547b97fa8b423585aff76f1/original/predictive-thermodynamic-model-for-intrusion-of-electrolyte-aqueous-solutions-in-nanoporous-materials.pdf |
60c75770bb8c1aeccc3dc833 | 10.26434/chemrxiv.14208287.v3 | A Study with Peptide Dendrimers Reveals an Extreme pH Dependence of Antibiotic Activity Above pH 7.4 | The presence of ionizable groups in antimicrobial peptides (AMPs)
often induces a pH-dependent activity. Herein we report that removing eight low
p<i>K</i><sub>a</sub> amino termini
in antimicrobial peptide dendrimer (AMPD) <b>G3KL</b> provides dendrimer <b>XC1</b>
with a broader pH-activity range. Furthermore, raising the pH to 8.0 reveals
strong activities against <i>Klebsiella pneumoniae</i> and methicillin
resistant <i>Staphylococcus aureus</i> (MRSA) against which these AMPDs are
inactive at pH 7.4. We observe a similar effect with polymyxin B on MRSA. Binding
experiments with
a fluorescent AMPD and the effect of high salt concentration
suggest that the activity increase reflects stronger
electrostatic binding to the bacteria at
high pH. pH-profiling of other
polycationic antimicrobials (polymers, peptidomimetics, foldamers, dendrimers)
might similarly enhance their activity range,
with possible use for topical treatments. | Xingguang Cai; Sacha Javor; Bee-Ha Gan; Thilo Köhler; Jean-Louis Reymond | Bioorganic Chemistry; Biopolymers; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75770bb8c1aeccc3dc833/original/a-study-with-peptide-dendrimers-reveals-an-extreme-p-h-dependence-of-antibiotic-activity-above-p-h-7-4.pdf |
668ea219c9c6a5c07ae16e4f | 10.26434/chemrxiv-2024-4q3nn | Amino acid-based, sustainable organic nanozyme for allergic biomolecule detection | The newly emerged organic nanozymes overcome the chronic issues associated with inorganic nanozymes due to their sustainable properties. However, several limitations have been identified from recently developed agricultural-centered, organic compound-based nanozymes, including a narrow variety of constituent materials and a relatively larger physical diameter due to the monotonous fabrication strategy hurdling its diverse application. To mitigate these limitations, a novel organic compound-based nanozyme with smaller physical dimensions and a wide range of materials is desired. Herein, the amino acid-based, sustainable organic nanozyme (OA nanozyme) is introduced, which exhibits peroxidase-like catalytic activity. A modified fabrication process based on single chelation/polymer entanglement was developed for fast (up to 3 hours) nanozyme fabrication resulting in a smaller physical diameter with homogenous morphology (within 100nm, D90), and a designated surface charge (negatively charged in neutral pH). This OA nanozyme exhibits decent kinetic profiles (Km = 0.009 mM, H2O2), and has been successfully used for detecting allergic biomolecules using surface charge interaction and achieved a limit of detection (LOD) of 21.37 pgmL-1, for histamine with higher selectivity, capable of sensing molecule within 3 minutes. It is envisioned that this amino acid-based organic nanozyme will be utilized for further sustainable applications. | DONG HOON LEE; Mohammed Kamruzzaman | Analytical Chemistry; Nanoscience; Agriculture and Food Chemistry; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ea219c9c6a5c07ae16e4f/original/amino-acid-based-sustainable-organic-nanozyme-for-allergic-biomolecule-detection.pdf |
60c74f6af96a002a64287c38 | 10.26434/chemrxiv.12899432.v1 | Standard Molar Enthalpies of Formation of Halomethanes Based on Quantum Chemical Computations | Accurate calculations of standard molar enthalpies of formation (ΔΗf°)m(g) and carbon-halogen bond dissociation enthalpies, BDE, of a variety of halomethanes with relevance on several atmospheric chemical processes and particularly to ozone destruction, were performed in the gas phase at 298.15 K. The (ΔΗf°)m(g) of the radicals formed through bond dissociations have also been computed. Ab initio computational methods and isodesmic reaction schemes were used. It is found that for the large majority of these species, the gold standard method of quantum chemistry (CCSD(T)) and even MP2 are capable to predict enthalpy values nearing chemical accuracy provided that isodesmic reaction schemes are used. New estimates for standard molar enthalpies of formation and BDE are suggested including for species that to our knowledge there are no experimental (ΔΗf°)m(g) (CHCl2Br, CHBr2Cl, CHBrCl, CHICl, CHIBr) or BDE values (CHCl2Br, CHBr2Cl, CHBrCl, CHICl, CHIBr) available in the literature. The method and calculational procedures presented may profitably be used to obtain accurate (ΔΗf°)m(g) and BDE values for these species. | Konstantinos Kalamatianos | Atmospheric Chemistry; Environmental Science; Theory - Computational; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f6af96a002a64287c38/original/standard-molar-enthalpies-of-formation-of-halomethanes-based-on-quantum-chemical-computations.pdf |
612645438e38a31d31405734 | 10.26434/chemrxiv-2021-snn5p | A microelectrode-based sensor for measuring operando active species concentrations in redox flow cells | The assessment of candidate materials for redox flow batteries requires effective diagnostic techniques for monitoring the evolution of electrolyte state of charge and state of health to interrogate time-dependent changes in system behavior. Further, such tools can be applied in practical embodiments to inform maintenance schedules and optimize energy utilization. In this work, we develop and test a flow-through, microelectrode-based electrochemical sensor to continuously measure active species concentrations in redox flow cells. A gold microelectrode (working electrode) and platinum wire (pseudo-reference electrode) are sealed into a stainless-steel fitting (counter electrode), and three-electrode electroanalytical techniques (i.e., voltammetry, chronoamperometry) are performed to correlate steady-state current to concentration. To validate transport and thermodynamics that govern the sensing mechanism, we combine multiphysics simulation with ex situ experimental testing, confirming the device is capable of accurately determining individual species concentrations. We then evaluate the microelectrode sensor in a symmetric redox flow cell, demonstrating the utility of this approach for measuring operando concentrations, and discuss additional considerations for successful implementation (e.g., measurement protocol, material selection, flow cell design). Assembled from commercially available, off-the-shelf components, the sensor can be readily adopted by research laboratories and integrated into existing experimental workflows, making it a promising tool for studying novel flow battery materials. | Bertrand Neyhouse; Kevin Tenny; Yet-Ming Chiang; Fikile Brushett | Analytical Chemistry; Energy; Electrochemical Analysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612645438e38a31d31405734/original/a-microelectrode-based-sensor-for-measuring-operando-active-species-concentrations-in-redox-flow-cells.pdf |
64215860647e3dca9993d052 | 10.26434/chemrxiv-2023-m6zbz | Selenourea as a hydrogen bond donor catalyst and source of selenium for metal-, activator-free synthesis of selenoesters in a batch and flow reactor | A new metal- and activator-free method for the synthesis of selenoesters from carboxylic acids, Michael acceptors, and selenourea is reported. This is the first reported method for the synthesis of selenoesters directly from carboxylic acids, using selenourea as a nucleophile, source of selenium, and an activator of carbonyl group. A new multifunctional selenourea (source of selenium, activator, base) has been synthesized, tried in a flow reactor to reduce impurity and reaction time. | Mouzma Mhate; Chandra Sekhara Mahanta; Kankanala Naveen Kumar; Devendra K. Dhaked; V. Ravichandiran; Sharada Prasanna Swain | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64215860647e3dca9993d052/original/selenourea-as-a-hydrogen-bond-donor-catalyst-and-source-of-selenium-for-metal-activator-free-synthesis-of-selenoesters-in-a-batch-and-flow-reactor.pdf |
61dd55906be42029402a6f35 | 10.26434/chemrxiv-2022-b1qp5 | Protonation-Induced Charge Transfer and Polaron Formation in Organic Semiconductors Doped by Lewis
Acids | Lewis acid doping of organic semiconductors (OSCs) opens up new ways of p-type doping and has
recently become of significant interest. As for the mechanistic understanding, it was recently proposed
that upon protonation of the OSC backbone, electron transfer occurs between the protonated polymer
chain and a neutral chain nearby, inducing a positive charge carrier in the latter [Nat. Mater. 18,
1327 (2019)]. To further clarify the underlying microscopic processes on a molecular level, in the
present work, we analyze the influence of protons on the electronic properties of the widely used
PCPDT–BT copolymer. We find that single protonation of the polymer chain leads to the formation
of a polaron coupled to the position of the proton. Upon protonation of the same chain with a
second proton, an intrachain electron transfer occurs, leaving behind a polaron largely decoupled
from the proton positions. We also observe the possibility of an interchain electron transfer from
a neutral chain to a double protonated chain in agreement with the mechanism recently proposed
in the literature. The simulated vertical excitation spectra for an ensemble of protonated species
with different amounts of protons enable a detailed interpretation of experimental observation on
PCPDT–BT doped with the Lewis acid BCF. Our results further suggest that multi-protonation plays
an important role for completing the mechanistic picture of Lewis acid doping of OSCs. | Fabian Bauch; Chuanding Dong; Stefan Schumacher | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dd55906be42029402a6f35/original/protonation-induced-charge-transfer-and-polaron-formation-in-organic-semiconductors-doped-by-lewis-acids.pdf |
60c740e30f50db34bd395a12 | 10.26434/chemrxiv.7862456.v1 | Copper-Catalyzed Hydrocarboxylation of Allenes | The addition of carboxylic acids to allenes was performed for the first time with copper catalysis. The hydrocarboxylation reaction is totally regio- and stereoselective, ligand-free and used catalytic amounts of copper and base. | Rémi blieck; Marc Taillefer; Florian Monnier | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e30f50db34bd395a12/original/copper-catalyzed-hydrocarboxylation-of-allenes.pdf |
60c7518a567dfe1bd8ec5a95 | 10.26434/chemrxiv.12906035.v3 | Theoretical Estimates of Equilibrium Carbon and Hydrogen Isotope Effects in Microbial Methane Production and Anaerobic Oxidation of Methane | Microbial production and consumption of methane are widespread in natural and artificial environments, with important economic and climatic implications. Attempts to use the isotopic composition of methane to constrain its sources are complicated by incomplete understanding of the mechanisms of variation in methane's isotopic composition. Knowledge of the equilibrium isotope fractionations among the large organic intracellular intermediates in the microbial pathways of methane production and consumption must form the basis of any exploration of the mechanisms of isotopic variation, but estimates of these equilibrium isotope fractionations are currently unavailable. To address this gap, we calculated the equilibrium isotopic fractionation of carbon (<sup>13</sup>C/<sup>12</sup>C) and hydrogen (D/H) isotopes among compounds in anaerobic methane metabolisms, as well as the abundance of multiple isotope substitutions ("clumping," e.g., <sup>13</sup>C--D) in these compounds. The Density Functional Theory calculations employed the M06-L/def2-TZVP level of theory and the SMD implicit solvation model, which we have recently optimized for large organic molecules and tested against measured equilibrium isotope fractionations. The computed <sup>13</sup>beta and <sup>2</sup>beta values decrease with decreasing average oxidation state of the carbon atom in the molecules, resulting in a preference for enrichment of the molecules with more oxidized carbon in <sup>13</sup>C and D. Using the computed $\beta$ values, we calculated the equilibrium isotope fractionation factors in the prominent methanogenesis pathways (hydrogenotrophic, methylotrophic and acetoclastic) and in the pathway for anaerobic oxidation of methane (AOM) over a temperature range of 0-700 degrees Celsius. Our calculated equilibrium fractionation factors compare favorably with experimental constrains, where available, and we used them to investigate the relation between the apparent isotope fractionation during methanogenesis and AOM and the thermodynamic drive for these reactions. We show that a detailed map of the equilibrium fractionation factors along these metabolic pathways allows an evaluation of the contribution of equilibrium and kinetic isotope effects to apparent isotope fractionations observed in laboratory, natural and artificial settings. The comprehensive set of equilibrium isotope fractionation factors calculated in this study provides a firm basis for future explorations of isotope effects in methane metabolism. | Jonathan Gropp; Mark Iron; Itay Halevy | Geochemistry; Microbiology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7518a567dfe1bd8ec5a95/original/theoretical-estimates-of-equilibrium-carbon-and-hydrogen-isotope-effects-in-microbial-methane-production-and-anaerobic-oxidation-of-methane.pdf |
60c74bd8ee301c08f0c79f51 | 10.26434/chemrxiv.12382580.v1 | Antibody-Inspired Affinity Measurements of Fluorescein-Linked Small Molecule Ligands | The availability of reliable methods for the characterization of the binding of small molecule ligands to protein targets is crucially important for Drug Discovery. We have adapted a method, routinely used for the characterization of monoclonal antibodies (Enzyme-linked immunosorbent assay, or “ELISA”), to small molecule ligands, using fluorescein conjugates and anti-fluorescein antibodies as detection reagents. The new small molecule-ELISA methodology was tested using a panel of binders specific to carbonic anhydrase II, with dissociation constants ranging between 6 uM and 14 nM. An excellent agreement was found between ELISA measurements and fluorescence polarization results. The methodology was also extended to BIAcore measurements and implemented for ligands coupled to oligonucleotides. Small molecule-ELISA procedures are particularly useful in the context of DNA-encoded libraries, for which hit validation procedures need to be performed on dozens of candidate molecules and hit compounds can be conveniently resynthesized on DNA. | Marco Catalano; Sebastian Oehler; Luca Prati; Nicholas Favalli; Gabriele Bassi; Jörg Scheuermann; Dario Neri | Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bd8ee301c08f0c79f51/original/antibody-inspired-affinity-measurements-of-fluorescein-linked-small-molecule-ligands.pdf |
6784bc0581d2151a02dfbcd3 | 10.26434/chemrxiv-2025-hc64q | Induced bifunctionality by mechanical blending of OER and ORR active 3D perovskite electrocatalysts for zinc-air batteries | Bifunctional electrocatalysts for oxygen electrocatalysis are typically developed by combining separate OER and ORR electrocatalysts to form composites, often requiring complex synthesis methods. In this study, we present a simplified approach by mechanical blending of BaSr2CoTiSbO9 (BSCTS), an OER catalyst, with BaSr2MnTiSbO9 (BSMTS), an ORR catalyst, to construct a composite bifunctional electrocatalyst. The DFT calculation supports superior ORR activity of BSMTS due to an uplifted Mn d-band center than the Co d-band and its proximity to the Fermi level, whereas the greater OER activity of BSCTS is due to the uplifted O 2p band center. While microstructural similarity of BSCTS and BSMTS facilitates efficient mixing for composite formation, the mechanical blending avoids intervention of complex synthesis procedures. The resulting bifunctional composite electrocatalyst demonstrates excellent performance with a bifunctional index of 0.72 V and a peak power density of 125 mW/cm2 when used as an air cathode electrocatalyst in Zn-air battery (ZAB). This approach underscores the importance of mechanical blending of microstructurally compatible OER and ORR catalysts in designing practical bifunctional electrocatalysts for zinc-air batteries. | Sujan Sen; Anil Kumar; Sounak Roy; Tapas Kumar Mandal | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6784bc0581d2151a02dfbcd3/original/induced-bifunctionality-by-mechanical-blending-of-oer-and-orr-active-3d-perovskite-electrocatalysts-for-zinc-air-batteries.pdf |
60c7426ebdbb890e61a384d7 | 10.26434/chemrxiv.8292362.v1 | Machine Learning Guided Approach for Studying Solvation Environments | <div><div><div><p>Toward practical modeling of local solvation effects of any solute in any solvent, we report a static and all-quantum mechanics based cluster-continuum approach for calculating single ion solvation free energies. This approach uses a global optimization procedure to identify low energy molecular clusters with different numbers of explicit solvent molecules and then employs the Smooth Overlap for Atomic Positions (SOAP) kernel to quantify the similarity between different low energy solute environments. From these data, we use sketch-map, a non-linear dimensionality reduction algorithm, to obtain a two-dimensional visual representation of the similarity between solute environments in differently sized microsolvated clusters. Without needing either dynamics simulations or an a priori knowledge of local solvation structure of the ions, this approach can be used to calculate solvation free energies with errors within five percent of experimental measurements for most cases.</p></div></div></div> | Yasemin Basdogan; Mitchell
C. Groenenboom; Ethan Henderson; Sandip De; Susan Rempe; John Keith | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426ebdbb890e61a384d7/original/machine-learning-guided-approach-for-studying-solvation-environments.pdf |
6709247951558a15efc7aff8 | 10.26434/chemrxiv-2024-x62zz | Rapid quantification of methane in water with parts-per-billion sensitivity using a metal-organic framework-functionalized quartz crystal resonator | Wetlands and water bodies are essential sources of methane emissions, a greenhouse gas that is roughly 25 times more potent than carbon dioxide. However, the biological production, fluxes, and interplay between methane and carbon dioxide due to microbial activity must be better understood. This is primarily attributed to the lack of sensor technology that can provide the required spatial and temporal resolution. Herein, we demonstrate how a porous metal-organic framework material can be used to create a sensor to quantify dissolved methane. The sensor is based on a quartz crystal microbalance, which measures methane adsorption using a quartz resonator functionalised with the material. Combining quartz crystal microbalance and the porous material yields fast response rates and high sensitivity. This is due to a favourable partitioning coefficient between the empty pores of the material and the aqueous phase, promoting rapid migration of dissolved methane into the material. The result is a sensor system that achieves equilibration and response times below 60 seconds with parts-per-billion sensitivity. A fully functioning prototype has been designed, built and evaluated to demonstrate real-life applicability, demonstrating sense response using spiked lake water. The modular nature of metal-organic frameworks opens possibilities for designing materials for selective sensing of other aqueous analytes. Thus, our study showcases the importance of new materials for methane sensing and general environmental monitoring. | Jaskaran Singh Malhotra; Clara Davila Duarte; Per Reichert; Deepthy Krishnan; Jonas Sundberg | Materials Science; Analytical Chemistry; Thin Films; Environmental Analysis; Separation Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6709247951558a15efc7aff8/original/rapid-quantification-of-methane-in-water-with-parts-per-billion-sensitivity-using-a-metal-organic-framework-functionalized-quartz-crystal-resonator.pdf |
678df39cfa469535b9bf1540 | 10.26434/chemrxiv-2025-p0rj1 | Molecular Glue-Augmented E2-Ubiquitin Recognition from A Computational Approach | Ubiquitin (Ub) is a small regulatory protein that tags unwanted or misfolded proteins for degradation by the proteasome. Molecular glues as small molecules stabilizing and augmenting protein-protein interactions have gained increasing attention in ubiquitination. Highly efficient computational approaches for the investigation of thermodynamics of molecular glue (MG)-Ub-protease systems remain absent. In this work, we introduced a cost-effective computational framework for all-atom characterization of the thermodynamics driving force in the cooperativity or molecule glue-induced enhancement of Ub-E2 recognition. Based on the testing bed involving the CDC34A-Ub protein-protein system and 18 unique molecule glues, we illustrate that our method could satisfactorily decoding the interaction thermodynamics inside the multimeric system. Specifically, our method enables both the ranking the protein-ligand MG-(E2-Ub) affinity and qualitatively capture the MG-induced E2-Ub interaction strengthening, which are generally unachievable with standard methods such as MM/GBSA and commonly applied scoring functions (e.g., AutoDock Vina). We additionally explore the general picture of the interfacial interactions in the multimeric complex, identifying important residues in the binding of molecular glue to Ub-E2 complex and also in Ub-E2 binding. Our computational approach could facilitate high-throughput virtual screening of potent molecular glues in assisting protein-protein recognition and ubiquitination. | Danial Muhammad; Wei Xia; Musheng Wang; Zhaoxi Sun; John Z. H. Zhang | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678df39cfa469535b9bf1540/original/molecular-glue-augmented-e2-ubiquitin-recognition-from-a-computational-approach.pdf |
6725dc987be152b1d0bce046 | 10.26434/chemrxiv-2024-c6m5r | Unveiling Drug Discovery Insights through Molecular Electrostatic Potential Analysis | Molecular Electrostatic Potential (MESP) analysis has emerged as a pivotal tool in drug discovery, providing insights into molecular reactivity and noncovalent interactions essential for drug function. While widely used MESP-on-isodensity surface analysis offers interpretations of electron-rich or deficient regions of a drug molecule, the MESP topology parameters such as spatial minimum (Vmin) and MESP at nuclei (Vn) provide a quantitative understanding. The investigation into the correlation between MESP parameters and various molecular properties such as lipophilicity, pKa (acidity/basicity), conformations, and tautomeric forms is crucial for understanding the impact on biological activity of drugs and facilitating drug design. Moreover, MESP topology analysis serves as a fundamental tool in elucidating the pharmacological behavior of compounds and optimizing their therapeutic efficacy. A quantitative study utilizing Vn parameters to assess the hydrogen bond propensity of a drug presents a novel strategy for investigating drug-receptor interactions with increased precision. The qualitative and quantitative analysis of the MESP features of various drugs, including their applications in cancer, tuberculosis, tumors, inflammation, and infectious diseases such as malaria, bacterial infections, fungal infections, and viral infections, is conducted in this review. | Cherumuttathu Suresh; Mambatta Haritha | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6725dc987be152b1d0bce046/original/unveiling-drug-discovery-insights-through-molecular-electrostatic-potential-analysis.pdf |
67de18be6dde43c908cce66d | 10.26434/chemrxiv-2025-ql49v-v2 | Germanium-based long-conjugation xanthene fluorophores for bioimaging in optimal NIR-II sub-window | Abstract
The near-infrared-IIx (NIR-IIx, 1,400-1,500 nm) sub-window theoretically surpasses the conventional near-infrared-II (NIR-II) region in optical imaging fidelity but requires luminophores with high brightness and stability. Herein, we present a germanium-engineered xanthene fluorophore (EGe5) featuring extended π-conjugation and a planarized pentagonal core, as unequivocally resolved by single-crystal X-ray analysis. The vertically aligned methyl groups sterically hinder molecular vibration, while germanium's heavy-atom effect enhances radiative decay, collectively resulting in a 3.3% quantum yield in the NIR-II window and high NIR-IIx brightness. In addition, EGe5 retains nearly unchanged fluorescence intensity for over 12 hours under harsh oxidative and reductive conditions. In vivo studies confirms its prolonged circulation time (> 60 min) is enough for persistent NIR-IIx fluorescent angiography, which helps to identify the intestinal obstruction by tracing the diseased intestinal wall blood vessels. Furthermore, PEGylated EGe5 (EGe5-PEG45) achieves rapid renal clearance and enables high-contrast excretory urography, dynamically tracking hydronephrosis progression in ureteral obstruction models. This work provides a molecular design paradigm for NIR-IIx probes and a versatile tool for minimally invasive diagnosis of gastrointestinal/urological diseases.
| Jin Li; Qiming Xia; Jiayi Li; Xiaoming Yu; Zhe Feng; Yuhuang Zhang; Tianxiang Wu; Zhongmin Xu; Hui Lin; Jun Qian | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67de18be6dde43c908cce66d/original/germanium-based-long-conjugation-xanthene-fluorophores-for-bioimaging-in-optimal-nir-ii-sub-window.pdf |
662a41dc418a5379b0b03c26 | 10.26434/chemrxiv-2024-vfp2c | Directed Evolution of an Artificial Hydroxylase Based on a Thermostable Human Carbonic Anhydrase Protein | The assembly of artificial metalloenzymes provides a second coordination sphere around a metal catalyst. Such a well-defined microenvironment can lead to enhancing the activities and selectivity of the catalyst. Herein, we present the development of artificial hydroxylase (ArHase) by embedding a Fe-TAML (TAML = Tetra Amide Macrocyclic Ligand) catalyst into a human carbonic anhydrase II (hCAII). Incorporation of the Fe-TAML catalyst ([BS-Fe-bTAML]–) within hCAII enhanced the Total TurnOver Number (TTON) for the hydroxylation of benzylic C–H bonds. After engineering a thermostable variant of hCAII (hCAIITS), the resulting ArHase, [BS-Fe-bTAML]– · hCAIITS, was subjected to directed evolution using cell lysates in a 384-well format. After three rounds of laboratory evolution, the best-performing variants exhibited 36-fold enhancement in the initial rate (124.4 min-1) and 2.8-fold enhancement in the TTON (2629 TTON) for the hydroxylation of benzylic C–H bonds compared to the free cofactor. We surmise that an arginine residue introduced in the course of directed evolution engages in hydrogen bonding with [BS-Fe-bTAML]–. This study highlights the potential of relying on a thermostable host protein to improve the catalytic performance of the hCAII-based ArMs. | Iori Morita; Adriana Faraone; Kailin Zhang; Roman P. Jakob; Timm Maier; Thomas R. Ward | Catalysis; Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662a41dc418a5379b0b03c26/original/directed-evolution-of-an-artificial-hydroxylase-based-on-a-thermostable-human-carbonic-anhydrase-protein.pdf |
675c89fb7be152b1d0e6fcdc | 10.26434/chemrxiv-2024-z75dw | Mutual Information Informed Novelty Estimation of Materials Along Chemical and Structural Axes | This work presents a parameter-free method for estimating materials novelty along chemical and structural axes using mutual information informed density functions. The approach quantifies novelty by analyzing how MI changes with distance between materials, establishing objective criteria for determining meaningful neighborhoods without requiring predetermined parameters. We demonstrate the method's effectiveness using two case studies: a control dataset of materials with varying degrees of similarity and a practical application analyzing lithium-containing compounds from the GNOME dataset relative to known materials. The method successfully identifies meaningful patterns of novelty in both chemical and structural domains while providing interpretable results that align with materials science intuition. This framework offers researchers a quantitative tool for assessing candidate materials against existing knowledge bases and could support more informed selection of synthesis targets in materials discovery campaigns. | Andrew Falkowski; Taylor Sparks | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c89fb7be152b1d0e6fcdc/original/mutual-information-informed-novelty-estimation-of-materials-along-chemical-and-structural-axes.pdf |
6595739d9138d231611a30fe | 10.26434/chemrxiv-2024-dmvk9-v2 | PFAS destruction and near complete defluorination of undiluted aqueous film-forming foams at ambient conditions by piezoelectric ball milling | The non-thermal destruction of aqueous film-forming foam (AFFF) stockpiles, one of the major culprits responsible for water and soil contamination by per- and polyfluoroalkyl substances (PFAS), is extremely challenging because of the coexistence of mixed recalcitrant PFAS and complicated organic matrices at extremely high concentrations. To date, the complete defluorination of undiluted AFFF at ambient conditions has not been demonstrated. This study reports a novel piezoelectric ball milling (BM) approach for treating AFFF with a total organic fluorine concentration of 9,080 mg/L and total organic carbon of 234 g/L. Near-complete defluorination (> 95% conversion of organofluorine to fluoride) of undiluted AFFF was achieved by co-milling with boron nitride (BN). By carefully examining the experimental data, we identified AFFF liquid film thickness (Z) at the collision interface as a descriptor of treatment performance. We further validated that effective defluorination proceeded when Z was less than a criteria value of 2.3 μm. In light of this new understanding, the addition of SiO2 as a dispersant and the pre-evaporation solvents to reduce Z have been validated as effective strategies to promote AFFF treatment capacity. | Nanyang Yang; Yunqiao Guan; Shasha Yang; Caitlyn Olive; Sujan Fernando; Thomas Holsen; Yang Yang | Earth, Space, and Environmental Chemistry; Wastes | CC BY 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6595739d9138d231611a30fe/original/pfas-destruction-and-near-complete-defluorination-of-undiluted-aqueous-film-forming-foams-at-ambient-conditions-by-piezoelectric-ball-milling.pdf |
60c74de8ee301c9e5fc7a3bc | 10.26434/chemrxiv.12662690.v1 | Further SAR on the (Phenylsulfonyl)piperazine Scaffold as Inhibitors of the Aedes Aegypti Kir1 (AeKir) Channel and Larvicides | We have discovered new chemical compounds that are characterized as Kir channel inhibitors of the Aedes aegypti mosquito. This is important as the Ae. aegypti mosquito is the primary vector for Zika virus (ZIKV), Dengue virus (DENV) and chikungunya virus (CHIKV). Traditional mosquitocides are plagued with significant resistance and developing new compounds with novel mechanisms of action are vitally important. Lastly, we show that our compounds are potent larvicides against pyrethroid-susceptible and pyrethroid-resistant strains. | Christopher
D. Aretz; Sujay V. Kharade; Keagan S. Chronister; Erick J. Martinez Rodriguez; Peter M. Piermarini; Jerod S. Denton; Corey Hopkins; Renata Rusconi Trigueros | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de8ee301c9e5fc7a3bc/original/further-sar-on-the-phenylsulfonyl-piperazine-scaffold-as-inhibitors-of-the-aedes-aegypti-kir1-ae-kir-channel-and-larvicides.pdf |
60c74f6f4c89193296ad3bcb | 10.26434/chemrxiv.12905633.v1 | Harnessing Deep Neural Networks to Solve Inverse Problems in Quantum Dynamics: Machine-Learned Predictions of Time-Dependent Optimal Control Fields | Inverse problems continue to garner immense interest in the physical sciences, particularly in the context of controlling desired phenomena in non-equilibrium systems. In this work, we utilize a series of deep neural networks for predicting time-dependent optimal control fields, <i>E(t)</i>, that enable desired electronic transitions in reduced-dimensional quantum dynamical systems. To solve this inverse problem, we investigated two independent machine learning approaches: (1) a feedforward neural network for predicting the frequency and amplitude content of the power spectrum in the frequency domain (i.e., the Fourier transform of <i>E(t)</i>), and (2) a cross-correlation neural network approach for directly predicting <i>E(t)</i> in the time domain. Both of these machine learning methods give complementary approaches for probing the underlying quantum dynamics and also exhibit impressive performance in accurately predicting both the frequency and strength of the optimal control field. We provide detailed architectures and hyperparameters for these deep neural networks as well as performance metrics for each of our machine-learned models. From these results, we show that machine learning approaches, particularly deep neural networks, can be employed as a cost-effective statistical approach for designing electromagnetic fields to enable desired transitions in these quantum dynamical systems. | Xian Wang; Anshuman Kumar; Christian Shelton; Bryan Wong | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Quantum Computing; Optics; Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics; Quasiparticles and Excitations; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f6f4c89193296ad3bcb/original/harnessing-deep-neural-networks-to-solve-inverse-problems-in-quantum-dynamics-machine-learned-predictions-of-time-dependent-optimal-control-fields.pdf |
60c7551c4c89198d52ad4622 | 10.26434/chemrxiv.14043434.v1 | Compatible Ferroelectricity, Antiferroelectricity and Broadband Emission for a Multi-Functional 2D Organic-Inorganic Hybrid Perovskite | Two-dimensional (2D)
organic-inorganic hybrid perovskites with multifunctional characteristics have
potential applications in many fields, such as, solar cells, microlasers and
light-emitting diodes (LEDs), etc. Here, a 2D organic-inorganic lead halide
perovskite, [Br(CH<sub>2</sub>)<sub>3</sub>NH<sub>3</sub>]<sub>2</sub>PbBr<sub>4</sub>
(<b>BPA-PbBr<sub>4</sub></b>, BPA = Br(CH<sub>2</sub>)<sub>3</sub>NH<sub>3</sub>,
3-Bromopropylamine), is examined for its photophysical properties.
Interestingly, <b>BPA-PbBr<sub>4</sub></b>
reveals five successive phase transitions with decreasing temperature,
including successive paraelectric-ferroelectric-antiferroelectric phases.
Besides, <b>BPA-PbBr<sub>4</sub></b>
displays ferroelectricity and antiferroelectricity throughout a wide
temperature range (<376.4 K) with accompanying saturation polrization (<i>P</i><sub>s</sub>) values of 4.35 and 2.32
μC/cm<sup>2</sup>, respectively, and energy storage efficiency of 28.2%, and
also exhibits superior second harmonic generation (SHG) with maximum value
accounts for 95 % of the standard KDP due to the great deformation of structure
(3.2302*10<sup>-4</sup>). In addition, the photoluminescence (PL) of the <b>BPA-PbBr<sub>4</sub></b> exhibits abnormal
red-shift and blue-shift in different phases due to a consequence of competition
between electron-phonon interaction and the lattice expansion. Further, <b>BPA-PbBr<sub>4</sub></b> reveals a
broadband emission accompanied by bright white light at room temperature (293
K), which is supposed to be due to self-trapped excitons. In short, the versatility
of <b>BPA-PbBr<sub>4</sub></b> originates
from molecular reorientation of dynamic organic cations, as well as significant
structural distortion of PbBr<sub>6</sub> octahedra. This work paves an avenue
to design new hybrid multifunctional perovskites for potential applications in the
photoelectronic field. | Wenjuan Wei; Hongqiang Gao; Yuhui Tan; Yunzhi Tang | Hybrid Organic-Inorganic Materials; Hydrogen Storage Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7551c4c89198d52ad4622/original/compatible-ferroelectricity-antiferroelectricity-and-broadband-emission-for-a-multi-functional-2d-organic-inorganic-hybrid-perovskite.pdf |
64f1dd813fdae147fa43d4c0 | 10.26434/chemrxiv-2023-s0hvf | Visible light-driven dearomatization of tryptamine-derived isocyanides through aggregation-based charge transfer | Aggregation-based charge transfer has emerged as an attractive concept in organic chemistry. In this work, we have demonstrated the ability of tryptamine-derived isocyanides to form aggregates, which enable a single electron transfer step to generate carbon-based-radical intermediates. The developed protocol is operationally simple, robust and demonstrates a novel approach to generate constrained spirocyclic scaffolds. Mechanistic and computational studies have elucidated key aspects associated with radical generation and photophysical properties of tryptamine-derived isocyanides. | Minghui Wu; Jordy M. Saya; Peiliang Han; Rajat Walia; Bapi Pradhan; Maarten Honing; Romano V. A. Orru; Prabhat Ranjan | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f1dd813fdae147fa43d4c0/original/visible-light-driven-dearomatization-of-tryptamine-derived-isocyanides-through-aggregation-based-charge-transfer.pdf |
612e9afbb817b4aa240fa13d | 10.26434/chemrxiv-2021-h71p5 | Bias corrections for speciated and source-resolved PM2.5 chemical transport model simulations using a geographically weighted regression | The ability to provide speciated and source-resolved PM2.5 estimates make chemical transport models a potentially valuable tool for exposure assessments. However, epidemiological studies often require unbiased estimates, which can be challenging for chemical transport models. We use geographically weighted regression to predict and correct the bias in source-resolved PM2.5 species (elemental carbon, organic aerosol, ammonium, nitrate, and sulfate) across the continental U.S. for 2001 and 2010. The regression models are trained using speciated ground-level monitors from the CSN and IMPROVE networks. A 10-fold cross-validation shows minimal bias across all simulated PM2.5 species (0 – 3%) and improved agreement with ground-level monitors (R2 = 0.53 – 0.97). Corrections also improve the agreement between simulated and observed species mixtures on a fractional basis. The source-resolved exposure estimates developed in this study are suitable for use in health analyses of PM2.5 toxicity. | Carlos Hernandez; Ksakousti Skyllakou; Pablo Garcia Rivera; Brian Dinkelacker; Julian Marshall; Arden Pope; Allen Robinson; Spyros Pandis; Peter Adams | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e9afbb817b4aa240fa13d/original/bias-corrections-for-speciated-and-source-resolved-pm2-5-chemical-transport-model-simulations-using-a-geographically-weighted-regression.pdf |
60d4e352e211334430e0a008 | 10.26434/chemrxiv-2021-2n6jh | Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking | Screening already approved drugs for activity against a novel pathogen can be an important part of global rapid-response strategies in pandemics. Such high-throughput
repurposing screens have already identified several existing drugs with potential to combat SARS-CoV-2. However, moving these hits forward for possible development into drugs specifically against this pathogen requires unambiguous identification of their corresponding targets, something the high-throughput screens are not typically designed to reveal. We present here a new computational inverse-docking protocol that uses all-atom protein structures and a combination of docking methods to rank-order targets for each of several existing drugs for which a plurality of recent high-throughput screens detected anti-SARS-CoV-2 activity. We demonstrate validation of this method with known drug-target pairs. We subjected 152 distinct drugs potentially suitable for repurposing to the inverse docking procedure. Detailed structural analysis revealed important insights and could potentially lead to more rational design of new drugs against these targets. | Sergio P. Ribone; S. Alexis Paz; Cameron F. Abrams; Marcos A. Villarreal | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d4e352e211334430e0a008/original/target-identification-for-repurposed-drugs-active-against-sars-co-v-2-via-high-throughput-inverse-docking.pdf |
60c746694c8919cedcad2b41 | 10.26434/chemrxiv.11319860.v1 | Schrodinger-ANI: An Eight-Element Neural Network Interaction Potential with Greatly Expanded Coverage of Druglike Chemical Space | We have developed a neural network potential energy function for use in drug discovery, with chemical element support extended from 41% to 94% of druglike molecules based on ChEMBL. We expand on the work of Smith et al., with their highly accurate network for the elements H, C, N, O, creating a network for H, C, N, O, S, F, Cl, P. We focus particularly on the calculation of relative conformer energies, for which we show that our new potential energy function has an RMSE of 0.70 kcal/mol for prospective druglike molecule conformers, substantially better than the previous state of the art. The speed and accuracy of this model could greatly accelerate the parameterization of protein-ligand binding free energy calculations for novel druglike molecules. | James Stevenson; Leif D. Jacobson; Yutong Zhao; Chuanjie Wu; Jon Maple; Karl Leswing; Edward Harder; Robert Abel | Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746694c8919cedcad2b41/original/schrodinger-ani-an-eight-element-neural-network-interaction-potential-with-greatly-expanded-coverage-of-druglike-chemical-space.pdf |
64df4b6e00bbebf0e6639ff0 | 10.26434/chemrxiv-2023-zwcw4-v2 | Searching for the Rules of Electrochemical Nitrogen Fixation | Li-mediated ammonia synthesis is – thus far – the only electrochemical method to decentralised ammonia production, an alternative to one of the largest thermal heterogeneous catalytic processes, for its unique selectivity on a solid electrode. However, it is burdened with intrinsic energy losses, operating at Li plating potential. In this work, we survey the periodic table to understand the fundamental features that make Li stand out. Through density functional theory calculations and experimentation on chemistries analogous to lithium (e.g. Na, Mg, Ca), we find that lithium is unique in several ways. It combines a stable nitride that readily decomposes to ammonia, with an ideal solid electrolyte interphase, balancing reagents at the reactive interface. We propose descriptors based on simulated formation and binding energies of key intermediates, and further on hard and soft acids and bases (HSAB principle) to generalize such features. The survey will help the community towards new electrochemical systems for nitrogen fixation. | Romain Tort; Alexander Bagger; Olivia Westhead; Yasuyuki Kondo; Artem Khobnya; Anna Winiwarter; Bethan J. V. Davies; Aron Walsh; Mary P. Ryan; Maria-Magdalena Titirici; Ifan E. L. Stephens | Theoretical and Computational Chemistry; Catalysis; Energy; Theory - Computational; Electrocatalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64df4b6e00bbebf0e6639ff0/original/searching-for-the-rules-of-electrochemical-nitrogen-fixation.pdf |
637661dabe365e5b732322d5 | 10.26434/chemrxiv-2022-fk22p | Accelerating Organic Electronic Materials Design with Low-Cost, Robust Molecular Reorganization Energy Predictions | A critical bottleneck for the design of high-conductivity organic materials is finding molecules with low reorganization energy. The development of low-cost machine-learning-based models for calculating the reorganization energy has proven to be challenging. Here we combine a graph-based neural network recently benchmarked for drug design applications, ChIRo, with low-cost conformational features and show the feasibility of reorganization energy predictions on the benchmark QM9 dataset without needing DFT geometries. | Cheng-Han Li; Daniel Tabor | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637661dabe365e5b732322d5/original/accelerating-organic-electronic-materials-design-with-low-cost-robust-molecular-reorganization-energy-predictions.pdf |
62c70af7244ce062963e07b7 | 10.26434/chemrxiv-2022-9pjmw-v2 | Electrocatalytic Radical-Polar Crossover Hydroetherification of Alkenes with Phenols | We disclose a general electrocatalytic hydroetherfication for modular synthesis of alkyl aryl ethers by utilizing a wide range of alkenes and phenols. The integration of the two involves an electrochemically instigated cobalt-hydride catalyzed radical–polar crossover of alkenes that enables the generation of key cationic intermediates, which could readily be entrapped by challenging nucleophilic phenols. We highlight the importance of precise control of the reaction potential by electrochemistry to obtain optimal chemoselectivity. Notably, this reaction system is pertinent to late-stage functionalization of pharmacophores that contain alkyl aryl ethers which has constantly been challenged since traditionally unconventional methods. | Steve Park; Jieun Jang; Kwangmin Shin; Hyunwoo Kim | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c70af7244ce062963e07b7/original/electrocatalytic-radical-polar-crossover-hydroetherification-of-alkenes-with-phenols.pdf |
60c74c60f96a003b712877ae | 10.26434/chemrxiv.12373262.v3 | Silver-Catalyzed Enantioselective Propargylic C–H Bond Amination Through Rational Ligand Design | Asymmetric C–H amination via nitrene transfer (NT) is a powerful tool for the preparation of enantioenriched amine building blocks from abundant C–H bonds. Herein, we report a highly regio- and enantioselective synthesis of -alkynyl -amino alcohol motifs via a silver-catalyzed propargylic C–H amination. The protocol was enabled by development of a new bis(oxazoline) (BOX) ligand through a rapid structure-activity relationship (SAR) analysis. The method utilizes readily accessible carbamate ester substrates bearing -propargylic C–H bonds and furnishes versatile products in good yields and with excellent enantioselectivity (90–99% ee). A putative Ag–nitrene intermediate is proposed to undergo an enantiodetermining hydrogen-atom transfer (HAT) during the C–H amination event. Density functional theory (DFT) calculations were performed to investigate the origin of enantioselectivity in the HAT step. | minsoo ju; Emily Zerull; Jessica Roberts; Minxue Huang; Jennifer Schomaker | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c60f96a003b712877ae/original/silver-catalyzed-enantioselective-propargylic-c-h-bond-amination-through-rational-ligand-design.pdf |
60c74e6bee301c3a24c7a4bf | 10.26434/chemrxiv.12752312.v1 | Congener-Specific Partition Properties of Chlorinated Paraffins Evaluated with COSMOtherm and Gas Chromatographic Retention Indices | <p>Chlorinated Paraffins (CPs) are high
volume production chemicals and have been found in various organisms including
humans and in environmental samples from remote regions. It is thus of great importance
to understand the physical-chemical properties of CPs. In this study, gas
chromatographic (GC) retention indexes (RIs) of 26 CP congeners were measured
on various polar and nonpolar columns to investigate the relationships between
the molecular structure and the partition properties. Retention measurements
show that analytical standards of individual CPs often contain several
stereoisomers. RI values show that chlorination pattern have a large influence
on the polarity of CPs. Single Cl substitutions (-CHCl-, -CH<sub>2</sub>Cl)
generally increase polarity of CPs. However, many consecutive -CHCl- units
(e.g., 1,2,3,4,5,6-C<sub>11</sub>Cl<sub>6</sub>) increase polarity less than
expected from the total number of -CHCl- units. Polyparameter linear free
energy relationship descriptors show that polarity difference between CP
congeners can be explained by the H-bond donating properties of CPs. RI values
of CP congeners were predicted using the quantum chemically based prediction
tool COSMO<i>thermX</i>. Predicted RI values correlate well with the experimental
data (R<sup>2</sup>, 0.975–0.995), indicating that COSMO<i>thermX</i> can be
used to accurately predict the retention of CP congeners on GC columns. </p> | Jort Hammer; Hidenori Matsukami; Satoshi Endo | Environmental Science; Wastes; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e6bee301c3a24c7a4bf/original/congener-specific-partition-properties-of-chlorinated-paraffins-evaluated-with-cosm-otherm-and-gas-chromatographic-retention-indices.pdf |
60c741ecee301c7efdc78d75 | 10.26434/chemrxiv.6552743.v2 | Colloidal Plasmonic Nanostar Antennas with Wide Range Resonance Tunability | <div>Gold nanostars display exceptional field enhancement properties and tunable resonant modes that can be leveraged to create effective imaging tags or phototherapeutic agents, or to design novel hot-electron based photocatalysts. From a fundamental standpoint, they represent important tunable platforms to study the dependence of hot carrier energy and dynamics on plasmon band intensity and position. Toward the realization of these platforms, holistic approaches taking into account both theory and experiments to study the fundamental behavior of these</div><div>particles are needed. Arguably, the intrinsic difficulties underlying this goal stem from the inability to rationally design and effectively synthesize nanoparticles that are sufficiently monodispersed to be employed for corroborations of the theoretical results without the need of single particle experiments. Herein, we report on our concerted computational and experimental effort to design, synthesize, and explain the origin and morphology-dependence of the plasmon modes of a novel gold nanostar system, with an approach that builds upon the well-known plasmon hybridization model. We have synthesized monodispersed samples of gold nanostars with finely tunable morphology employing seed-mediated colloidal protocols, and experimentally observed narrow and spectrally resolved harmonics of the primary surface plasmon resonance mode both at the single particle level (via electron energy loss spectroscopy) and in ensemble (by UV-Vis and ATR-FTIR spectroscopies). Computational results on complex anisotropic gold nanostructures are validated experimentally on samples prepared colloidally, underscoring their importance as ideal testbeds for the study of structure-property relationships in colloidal nanostructures of high structural complexity.</div> | Theodoros Tsoulos; Supriya Atta; Maureen Lagos; Michael Beetz; Philip Batson; George Tsilomelekis; Laura Fabris | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ecee301c7efdc78d75/original/colloidal-plasmonic-nanostar-antennas-with-wide-range-resonance-tunability.pdf |
639723ff04bc66a663131ae2 | 10.26434/chemrxiv-2022-mr4tk | Regulation of the Liquid–liquid Phase-Separated Droplets of Biomacromolecules by Butterfly-Shaped Gold Nanomaterials | Liquid–liquid phase-separated (LLPS) droplets play key roles in regulating protein behaviors, such as enzyme compart-mentalization, stress response, and disease pathogenesis, in living cells. The manipulation of the droplet for-mation/deformation dynamics is the next target of nano-biotechnology, although the required nanodevices for controlling the dynamics of liquid–liquid phase separation, LLPS, have not been invented. Here, we propose a butterfly-shaped gold nanobutterfly (GNB) as a nanodevice for manipulating the droplet-formation/deformation dynamics of LLPS. GNBs are moderate, symmetrical gold nanomaterials (average diameter = ~30 nm) bearing two concaves and resembling a butter-fly. Their growth process is analyzed via their time-lapse electroscopic images and time-lapse ultraviolet/visible/near-infrared (NIR) spectroscopy, as well as the application of solution additives in protein science. These nanomaterials are synthesized via the seed-mediated method with an efficiency of ~70%. Interestingly, the GNBs stabilized the LLPS droplet of adenosine triphosphate (ATP)/poly-L-lysine, whereas other two gold nanoparticles with different shapes (spherical and rod-shaped) did not, indicating that the concave of the GNBs interacts with the precursor of the droplets. The NIR-laser irradiation of the GNBs facilitates the on-demand deformation of the droplets via the localized-heat effect. This but-terfly-shaped nanodevice represents a future strategy for manipulating the dynamics of LLPS. | Tomohiro Nobeyama; Koji Takata; Megumi Mori; Tatsuya Murakami; Kentaro Shiraki | Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639723ff04bc66a663131ae2/original/regulation-of-the-liquid-liquid-phase-separated-droplets-of-biomacromolecules-by-butterfly-shaped-gold-nanomaterials.pdf |
60c756409abda2488df8e4d4 | 10.26434/chemrxiv.14222303.v1 | High Yielding Flow Synthesis of a Macrocyclic Molecular Hinge | ABSTRACT: Many molecular machines are built from modular components with well-defined motile capabilities, such as axles and wheels. Hinges are particularly useful, as they provide the minimum flexibility needed for a simple and pronounced conformational change. Compounds with multiple stable conformers are common, but molecular hinges almost exclusively operate via dihedral rotations rather than truly hinge-like clamping mechanisms. An ideal molecular hinge would better reproduce the behavior of hinged devices, such as gates and tweezers, while remaining soluble, scalable and synthetically versatile. Herein, we describe two isomeric macrocycles with clamp-like open and closed geometries, which crystallize as separate polymorphs but interconvert freely in solution. An unusual one-pot addition cyclization reaction was used to produce the macrocycles on a multigram scale from inexpensive reagents, without supramolecular templating or high-dilution conditions. Using mechanistic information from NMR kinetic studies and at-line mass spectrometry, we developed a semi-continuous flow synthesis with maximum conversions of 85-93% and over 80% selectivity for a single isomer. The macrocycles feature voids that are sterically protected from guests, including reactive species such as fluoride ions, and could therefore serve as chemically inert hinges for adaptive supramolecular receptors and flexible porous materials. | Christopher Jones; Laurence
J. Kershaw Cook; David Marquez-Gamez; Konstantin V. Luzyanin; Jonathan Steed; Anna Slater | Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.); Computational Chemistry and Modeling; Reaction Engineering; Self-Assembly; Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756409abda2488df8e4d4/original/high-yielding-flow-synthesis-of-a-macrocyclic-molecular-hinge.pdf |
60c756460f50db08a439806a | 10.26434/chemrxiv.14224148.v1 | Revealing the Surface Structure of CdSe Nanocrystals by Dynamic Nuclear Polarization-Enhanced 77Se and 113Cd Solid-State NMR Spectroscopy | <p>Dynamic nuclear polarization (DNP) solid-state NMR (SSNMR) spectroscopy was used to obtain detailed surface structures of zinc blende CdSe nanocrystals (NCs) with plate or spheroidal morphologies and which are capped by carboxylic acid ligands. 1D <sup>113</sup>Cd and <sup>77</sup>Se cross-polarization magic angle spinning (CPMAS) NMR spectra revealed distinct signals from Cd and Se atoms on the surface of the NCs, and those residing in bulk-like environments below the surface. <sup>113</sup>Cd cross-polarization magic-angle-turning (CP-MAT) experiments identified CdSe<sub>3</sub>O, CdSe<sub>2</sub>O<sub>2</sub>, and CdSeO<sub>3</sub> Cd coordination environments on the surface of the NCs, where the oxygen atoms are presumably from coordinated carboxylate ligands. The sensitivity gain from DNP enabled natural isotopic abundance 2D homonuclear <sup>113</sup>Cd-<sup>113</sup>Cd and <sup>77</sup>Se-<sup>77</sup>Se and heteronuclear <sup>113</sup>Cd-<sup>77</sup>Se scalar correlation solid-state NMR experiments that reveal the connectivity of the Cd and Se atoms. Importantly, <sup>77</sup>Se{<sup>113</sup>Cd} scalar heteronuclear multiple quantum coherence (<i>J</i>-HMQC) experiments were used to selectively measure one-bond <sup>77</sup>Se-<sup>113</sup>Cd scalar coupling constants (<sup>1</sup><i>J</i>(<sup>77</sup>Se, <sup>113</sup>Cd)). With knowledge of <sup>1</sup><i>J</i>(<sup>77</sup>Se, <sup>113</sup>Cd), heteronuclear <sup>77</sup>Se{<sup>113</sup>Cd} spin echo (<i>J</i>-resolved) NMR experiments were then used to determine the number of Cd atoms bonded to Se atoms and vice versa. The <i>J</i>-resolved experiments directly confirmed that major Cd and Se surface species have CdSe<sub>2</sub>O<sub>2</sub> and SeCd<sub>4</sub> stoichiometries, respectively. Considering the crystal structure of zinc blende CdSe, and the similarity of the solid-state NMR data for the platelets and spheroids, we conclude that the surface of the spheroidal CdSe NCs is primarily composed of {100} facets. The methods outlined here will generally be applicable to obtain detailed surface structures of various main group semiconductors.</p> | Yunhua Chen; Rick Dorn; Michael Hanrahan; Lin Wei; Rafael Blome-Fernandez; Alan Medina-Gonzalez; Marquix Adamson; Anne Flintgruber; Javier Vela; Aaron Rossini | Nanostructured Materials - Materials; Interfaces; Spectroscopy (Physical Chem.); Structure; Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756460f50db08a439806a/original/revealing-the-surface-structure-of-cd-se-nanocrystals-by-dynamic-nuclear-polarization-enhanced-77se-and-113cd-solid-state-nmr-spectroscopy.pdf |
67ab86b56dde43c9086af885 | 10.26434/chemrxiv-2025-1bkrg | Synthesis of radical-bridged lanthanide heterobimetallic complexes | Heteromultimetallic lanthanide (Ln) molecules are used in sensing and imaging, and have recently demonstrated Ln to-Ln energy transfer and potential as quantum logic processors. However, the selective synthesis of molecular Ln heteromultimetallics is challenging, limiting further investigation of their properties and applications. For example, redox active ligands mediate f-block reactivity with small molecules and have applications in molecular magnetics in homometallic Ln systems, yet have not been incorporated into heteromultimetallic complexes. Herein, we utilise the chemically distinct binding sites and redox chemistry of 1,10-phenanthroline-5,6-dione (pd) to synthesise radical-bridged Ln heterobimetallic complexes. In a stepwise, modular, and extendable synthesis, we tailor the ancillary ligand environment to generate selectivity within the non-directional ionic bonding regime typical for Ln ions. The selectivity of binding for two lanthanide combinations with different ionic radius ratios is demonstrated by solution-state spectroscopy (NMR, UV-vis, photoluminescence), and confirmed in the solid-state by crystallographic determination of the molecular structures. In preliminary photoluminescence studies, we observe complex, selective energy transfer unusually involving the radical ligand. Our synthetic strategy enables any pair of lanthanide ions to be combined and will be widely applicable in the preparation of heteromultimetallic complexes of otherwise non-selective metal ions. | Samuel Horsewill; Tajrian Chowdhury; Anna Bailey; William Peveler; Gordon Hedley; Claire Wilson; Joy Farnaby | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab86b56dde43c9086af885/original/synthesis-of-radical-bridged-lanthanide-heterobimetallic-complexes.pdf |
6606c3a4e9ebbb4db9e79931 | 10.26434/chemrxiv-2024-6rps5 | Highly Enantiomerically Enriched Secondary Alcohols via Epoxide Hydrogenolysis | In this paper, we report the development of ruthenium-catalyzed hydrogenolysis of epoxides to selectively give the branched (Markovnikov) alcohol products. In contrast to previously reported catalysts, the use of Milstein’s PNN-pincer-ruthenium complex at room temperature allows the conversion of enantiomerically enriched epoxides to secondary alcohols without racemization of the product. The catalyst is effective for a range of aryl epoxides, alkyl epoxides and glycidyl ethers, and is the first homogenous system to selectively promote hydrogenolysis of glycidol to 1,2-propanediol without loss of enantiomeric purity. A detailed mechanistic study was conducted, including experimental observations of catalyst speciation under catalytically relevant conditions, comprehensive kinetic characterization of the catalytic reaction, and computational analysis via density functional theory. Heterolytic hydrogen cleavage is mediated by the ruthenium center and exogenous alkoxide base. Epoxide ring-opening occurs through opposite-side attack of the ruthenium hydride on the less-hindered epoxide carbon, giving the branched alcohol product selectively. | Olivia J. Borden; Benjamin T. Joseph; Marianna C. Head; Obsidian Ammons; Diane Eun Kim; Abigail C. Bonino; Jason M. Keith; Anthony Chianese | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6606c3a4e9ebbb4db9e79931/original/highly-enantiomerically-enriched-secondary-alcohols-via-epoxide-hydrogenolysis.pdf |
62102a090aec1af9462299d8 | 10.26434/chemrxiv-2022-wc2gr | Spectroscopic characterization of rare events in colloidal particle stochastic thermodynamics | Given the remarkable developments in synthetic control over colloidal particle chemical and physical properties, it is interesting to see how stochastic thermodynamics studies may be performed with new, surrogate, or hybrid model systems. In the present work, we apply stochastic dynamics and nonlinear optical light-matter interaction simulations to study non-equilibrium trajectories of individual Yb(III):Er(III) co-doped colloidal and nanoparticles driven by two-dimensional dynamic optical traps. We characterize the role of fluctuations at the single particle level by analyzing position trajectories as well as time-dependent upconversion and downconversion emission intensities. By integrating these two complementary perspectives, we show how the methods developed here can be used to characterize rare events. | René Nome; Sandro Otani; Thalyta Martins; Sérgio Muniz; Paulo Cesar de Sousa Filho; Fernando Sigoli | Physical Chemistry; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62102a090aec1af9462299d8/original/spectroscopic-characterization-of-rare-events-in-colloidal-particle-stochastic-thermodynamics.pdf |
63c14932553889a2f17f8147 | 10.26434/chemrxiv-2023-vc2dl | Benzophenone as a Cheap and Effective Photosensitizer for the Photocatalytic Synthesis of Dimethyl Cubane-1,4-dicarboxylate | The key intramolecular [2+2] photochemical cycloaddition step in the synthesis of dimethyl cubane-1,4-dicarboxylate is performed with substoichiometric amounts of the photosensitizer benzophenone. The reaction proceeds via a Dexter energy transfer process between the triplet excited state benzophenone and a well-known cubane precursor diene. The use of the cheap and widely available benzophenone as the photosensitizer enables lower energy light to be used than the traditional photochemical process. | Callum Prentice; Alice Martin; James Morrison; Andrew Smith; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c14932553889a2f17f8147/original/benzophenone-as-a-cheap-and-effective-photosensitizer-for-the-photocatalytic-synthesis-of-dimethyl-cubane-1-4-dicarboxylate.pdf |
63c6eb6f5ab313638caace49 | 10.26434/chemrxiv-2022-w0jzh-v2 | Five Years of ChemRxiv: Where We Are and Where We Go From Here | ChemRxiv was launched on August 15, 2017 to provide researchers in chemistry and related fields a home for the immediate sharing of their latest research. In the past five years, ChemRxiv has grown into the premier preprint server for the chemical sciences, with a global audience and a wide array of scholarly content that helps advance science more rapidly. On the service’s fifth anniversary, we would like to reflect on the past five years and take a look at what is next for ChemRxiv. | Benjamin Mudrak; Sara Bosshart; Wolfram Koch; Allison Leung; Donna Minton; Mitsuo Sawamoto; Sarah Tegen | Chemical Education; Chemical Education - General | CC BY 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c6eb6f5ab313638caace49/original/five-years-of-chem-rxiv-where-we-are-and-where-we-go-from-here.pdf |
655235c62c3c11ed714f241b | 10.26434/chemrxiv-2023-p5gsr | Laser induced temperature-jump time resolved IR spectroscopy of zeolites | Combining pulsed laser heating and time-resolved infrared (TR-IR) absorption spectroscopy provides a means of initiating and studying thermally activated chemical reactions and diffusion processes in heterogeneous catalysts on timescales from nanoseconds to seconds. To this end, we investigated single pulse and burst laser heating in zeolite catalysts under realistic conditions using TR-IR spectroscopy. 1 ns, 70 µJ, 2.8 µm laser pulses from a Nd:YAG-pumped optical parametric oscillator were observed to induce temperature-jumps (T-jumps) in zeolite pellets in nanoseconds, with the sample cooling over 1 – 3 ms. By adopting a tightly focused beam geometry, T-jumps as large as 145 °C from the starting temperature were achieved, demonstrated through comparison of the TR-IR spectra with temperature dependent IR absorption spectra and three dimensional heat transfer modelling using realistic experimental parameters. The simulations provide a detailed understanding of the temperature distribution within the sample and its evolution over the cooling period, which we observe to be bi-exponential. These results provide foundations for determining the magnitude of a T-jump in a catalyst/adsorbate system from its absorption spectrum and physical properties, and for applying T-jump TR-IR spectroscopy to the study of reactive chemistry in heterogeneous catalysts. | Alexander P. Hawkins; Amy E. Edmeades; Christopher D.M. Hutchison; Mike Towrie; Russell F. Howe; Gregory M. Greetham; Paul M. Donaldson | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655235c62c3c11ed714f241b/original/laser-induced-temperature-jump-time-resolved-ir-spectroscopy-of-zeolites.pdf |
60c74e57567dfe18e4ec54db | 10.26434/chemrxiv.12605207.v2 | Online in No Time: Design and Implementation of a Remote Learning First Quarter General Chemistry Laboratory and Second Quarter Organic Chemistry Laboratory | The instruction of high enrollment general and organic chemistry laboratories at a large public
10 university always have curricular, administrative, and logistical challenges. Herein, we describe how
we met these challenges in the transition to remote teaching during the COVID-19 pandemic. We
discuss the reasoning behind our approach, the utilization of our existing web-based course content,
the additions and alterations to our curriculum, replacement of experimental work with videos, the
results of both student and TA surveys, and lessons learned for iterations of these courses in the near
15 future. | William J. Howitz; Taylor A. Thane; Taylor Frey; Xinran S. Wang; Joe C. Gonzales; Chase A. Tretbar; Daniel D. Seith; Shannon S. Saluga; Simon Lam; Melanie M. Nguyen; Peter Tieu; Renee Link; Kimberly D. Edwards | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e57567dfe18e4ec54db/original/online-in-no-time-design-and-implementation-of-a-remote-learning-first-quarter-general-chemistry-laboratory-and-second-quarter-organic-chemistry-laboratory.pdf |
63addd6604902a1fac13cdc0 | 10.26434/chemrxiv-2022-mg53z | Photoactivable WAY-161503 and Desmethylclozapine for Tight Regulation of Serotonin Receptor 2C Signaling. | Recreating the signaling profile a chemical synapse to analyze serotonin receptor activation is a challenge. This is due in part to the kinetics of the synapse, where neurotransmitters are rapidly released and quickly cleared by active reuptake machinery. One strategy to produce a rapid rise in a bio-orthogonally controlled signal is via photocaged compounds. In this work, a complementary pair of BODIPY photoremovable protecting groups was conjugated to a 5HT2C subtype selective agonist, WAY-161503, and antagonist, N-desmethylclozapine, to generate “caged” versions of these drugs. These conjugates can release their bioactive drug upon stimulation with green light (agonist) or red light (antagonist). We report on the synthesis, characterization, and bioactivity testing of the conjugates against the 5HT2C receptor. We then characterize the kinetics of photolysis quantitatively using HPLC and qualitatively in cell culture conditions stimulating live cells. The compounds are shown to be stable under dark conditions for 48 hours at room temperature, yet photolyze readily when irradiated with visible light. In live cells expressing the 5HT2C receptor, precise spatiotemporal control of the degree and length of calcium signaling is demonstrated. By loading both compounds in tandem and leveraging spectral multiplexing as a non-invasive method to control local small molecule drug availability, we can reproducibly initiate and suppress intracellular calcium flux on a timescale not possible by traditional methods of drug dosing. These tools enable a greater spatiotemporal control of 5HT2C modulation and will allow for more detailed studies of the receptors signaling, interactions with other proteins, and native physiology. | Spencer Kim; Dylan Gray; Michelle Shanguhyia; Rachel Steinhardt | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2022-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63addd6604902a1fac13cdc0/original/photoactivable-way-161503-and-desmethylclozapine-for-tight-regulation-of-serotonin-receptor-2c-signaling.pdf |
60c74169f96a0012ee286438 | 10.26434/chemrxiv.7977131.v2 | Penalized Variational Autoencoder for Molecular Design | Variational autoencoders have emerged as one of the most common approaches for automating molecular generation. We seek to learn a cross-domain latent space capturing chemical and biological information, simultaneously. To do so, we introduce the Penalized Variational Autoencoder which directly operates on SMILES, a linear string representation of molecules, with a weight penalty term in the decoder to address the imbalance in the character distribution of SMILES strings. We find that this greatly improves upon previous variational autoencoder approaches in the quality of the latent space and the generalization ability of the latent space to new chemistry. Next, we organize the latent space according to chemical and biological properties by jointly training the Penalized Variational Autoencoder with linear units. Extensive experiments on a range of tasks, including reconstruction, validity, and transferability demonstrates that the proposed methods here substantially outperform previous SMILES and graph-based methods, as well as introduces a new way to generate molecules from a set of desired properties, without prior knowledge of a chemical structure. | Sadegh Mohammadi; Bing O'Dowd; Christian Paulitz-Erdmann; Linus Goerlitz | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74169f96a0012ee286438/original/penalized-variational-autoencoder-for-molecular-design.pdf |
64472eaf83fa35f8f6332a07 | 10.26434/chemrxiv-2023-dcch9 | Resolving the structural complexity of gamma-Al2O3: the nature of vacancy ordering and the structure of complex antiphase boundaries | The structure of gamma-Al2O3 remains largely undetermined despite decades of research. This is due to the high degree of disorder, which poses significant challenges for structural analysis using conventional crystallographic approaches. Herein, we study the structure of gamma-Al2O3 with Scanning Transmission Electron Microscopy (STEM) and ab-initio calculations to provide a complete structural description. We show that the microstructure can be understood in terms of two key structural features of nanoscale spinel domains and finite thickness segments termed as complex antiphase boundaries (cAPB) that provide the domain interconnectivity. The spinel domains have a distinctive preference for vacancy ordering, which can be rationalized in terms of a structure with a stacking disorder. Tetragonal P41212 or monoclinic P21 models, all based on the identical motif, can be considered as representative ordered forms. Individual spinel domains are interconnected via cAPBs, which adopt a distinct non-spinel bonding environment of gamma-Al2O3. The most common cAPB consists of a single delta motif with thickness of just 0.6 nm on (001), with the resulting displacement a/4 [101]. Remarkably, the cAPBs are shown to energetically stabilize the spinel domains of gamma-Al2O3 explaining their high abundance. We demonstrate how the tetragonal distortions naturally arise in this intricate microstructure and place the proposed model in the context of phase transformations to high temperature transition aluminas. | Libor Kovarik; Mark Bowden; Konstantin Khivantsev; Ja Hun Kwak; Janos Szanyi | Physical Chemistry; Materials Science; Catalysts; Structure; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64472eaf83fa35f8f6332a07/original/resolving-the-structural-complexity-of-gamma-al2o3-the-nature-of-vacancy-ordering-and-the-structure-of-complex-antiphase-boundaries.pdf |
60c7513a702a9bba6a18bee9 | 10.26434/chemrxiv.13138427.v1 | Cellular Uptake and Magneto-Hyperthermia Induced Cytotoxicity using Photoluminescent Fe3O4 Nanoparticle/Si Quantum Dot Hybrids | <p>The design and fabrication
of Si-based multi-functional nanomaterials for biological and biomedical
applications is an active area of research. The potential benefits of using
Si-based nanomaterials are not only due to their size/surface-dependent optical
responses but also the high biocompatibility and low-toxicity of silicon
itself. Combining these characteristics with the magnetic properties of Fe<sub>3</sub>O<sub>4</sub>
nanoparticles (NPs) multiplies the options available for real-world
applications. In the current study, biocompatible magnetofluorescent
nano-hybrids have been prepared by covalent linking of Si quantum dots to
water-dispersible Fe<sub>3</sub>O<sub>4</sub> NPs <i>via</i> dicyclohexylcarbodiimide (DCC) coupling. We explore some of the
properties of these magnetofluorescent nano-hybrids as well as evaluate uptake,
the potential for cellular toxicity, and the induction of acute cellular
oxidative stress in a mast cells-like cell line (RBL-2H3) by heat induction
through short-term radio frequency modulation (10 min @ 156 kHz, 500 A). We
found that the NPs were internalized readily by the cells and also penetrated
the nuclear membrane. Radio frequency
activated nano-hybrids also had significantly increased cell death where >
50% of the RBL-2H3 cells were found to be in an apoptotic or necrotic state,
and that this was attributable to increased triggering of oxidative cell stress
mechanisms. </p> | Morteza Javadi; Van A. Ortega; Alyxandra Thiessen; Maryam Aghajamali; Muhammad Amirul Islam; Jenna M. Drummond; Greg G. Goss; Jonathan G.C. Veinot | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7513a702a9bba6a18bee9/original/cellular-uptake-and-magneto-hyperthermia-induced-cytotoxicity-using-photoluminescent-fe3o4-nanoparticle-si-quantum-dot-hybrids.pdf |
622b8d933599deea00fc1f95 | 10.26434/chemrxiv-2022-j2rnd | Lithium-Ion Battery Degradation: Measuring Rapid Loss of Active Silicon in Silicon-Graphite Composite Electrodes | In an effort to increase the specific energy of lithium-ion batteries, silicon additives are often blended with graphite (Gr) in the negative electrode of commercial cells. However, due to the large volumetric expansion of silicon upon lithiation, these Si-Gr composites are prone to faster rates of degradation than conventional graphite electrodes. Understanding the effect of this difference is key to controlling degradation and improving cell lifetimes. Here, we investigate the effects of state of charge and temperature on the ageing of a commercial cylindrical cell with a Si-Gr electrode (LG M50T). Using degradation mode analysis, we were able to quantify the rates of degradation for Si and Gr separately. Loss of active Si is shown to be worse than Gr under all operating conditions, but especially at low state of charge and high temperature, with up to 80% loss in Si capacity after 4 kA h of charge throughput (~400 equivalent full cycles). The results indicate cell lifetimes can be improved by limiting the depth of discharge of cells containing Si-Gr, which suggests Si is not beneficial for all applications. The degradation mode analysis methods developed here provide valuable new insight into the causes of cell ageing by separating the effects of the two active materials in the composite electrode. These methods provide a suitable framework for data analysis of any experimental investigations on cells involving composite electrodes. | Niall Kirkaldy; Mohammad Amin Samieian; Gregory J. Offer; Monica Marinescu; Yatish Patel | Materials Science; Inorganic Chemistry; Energy; Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622b8d933599deea00fc1f95/original/lithium-ion-battery-degradation-measuring-rapid-loss-of-active-silicon-in-silicon-graphite-composite-electrodes.pdf |
60c74524702a9b2d6018a96e | 10.26434/chemrxiv.9975389.v1 | Elucidating the Drug Release from Metal-Organic Framework Nanocomposites via in Situ Synchrotron Microspectroscopy and Theoretical Modelling | Nanocomposites comprising metal-organic frameworks (MOFs) embedded in a polymeric matrix are promising carriers for drug delivery applications. While understanding the chemical and physical transformations of MOFs during the release of confined drug molecules is challenging, this is central to devising better ways for controlled release of therapeutic agents. Herein we demonstrate the efficacy of synchrotron microspectroscopy to track the in situ release of 5-fluorouracil (5-FU) anticancer drug molecules from a drug@MOF/polymer composite (5-FU@HKUST-1/polyurethane). Using experimental time-resolved infrared spectra jointly with newly developed density functional theory calculations, we reveal the detailed dynamics of vibrational motions underpinning the dissociation of 5-FU bound to the framework of HKUST-1 upon water exposure. We discover that HKUST-1 creates hydrophilic channels within the hydrophobic polyurethane matrix hence helping to tune drug release rate. The synergy between a hydrophilic MOF with a hydrophobic polymer can be harnessed to engineer a tunable nanocomposite that alleviates the unwanted burst effect commonly encountered in drug delivery.<br /> | Barbara Souza; Lorenzo Dona; Kirill Titov; Paolo Bruzzese; Zhixin Zeng; Yang Zhang; Arun Babal; Annika Moslein; Mark Frogley; Magda Wolna; Gianfelice Cinque; Bartolomeo Civalleri; Jin-Chong Tan | Biocompatible Materials; Biodegradable Materials; Composites; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Chemical Kinetics; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74524702a9b2d6018a96e/original/elucidating-the-drug-release-from-metal-organic-framework-nanocomposites-via-in-situ-synchrotron-microspectroscopy-and-theoretical-modelling.pdf |
668ef2c65101a2ffa803c5a0 | 10.26434/chemrxiv-2024-d515q | Decarbonizing Specialty Chemical Manufacturing: Opportunities for Electrochemists | To meet global decarbonization goals, the chemical industry faces the challenge of dramatically reducing greenhouse gas emissions even as demand for chemical products continues to grow. This challenge is amplified by the sector's reliance on petroleum-based hydrocarbons as both fuel and feedstock. Electrochemical synthesis is widely viewed as an attractive method to decarbonize chemical manufacturing through the use of low-carbon electricity to drive redox reactions. Presently, much of the work in this area is focused on electrochemical strategies to produce commodity chemicals. In this work, we make the case that developing electrosynthetic methods for specialty chemical manufacturing is another attractive entry point for electrochemical process design. We further outline the results of a scoping study aimed at assessing the potential to decarbonize the production of several organic compounds that are widely used in specialty chemical manufacturing by using electrochemical reactors. Our approach entails mapping the supply chain for each compound back to its petrochemical feedstock, identifying opportunities to incorporate electrochemical transformations along the supply chain, and estimating the potential for decarbonization through the adoption of electrosynthetic schemes. The results show there already exist significant opportunities to decarbonize specialty chemical transformations today, even under very conservative assumptions about process efficiency and the carbon intensity of the input electricity. | Robert Hacku; Thomas Henry; Michael Kane; Maxwell Vance; Zachary Sebastian; Glenn Cormack; Tyler Petek; Elisa Seddon; James McKone | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Petrochemicals; Reaction Engineering | CC BY NC 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668ef2c65101a2ffa803c5a0/original/decarbonizing-specialty-chemical-manufacturing-opportunities-for-electrochemists.pdf |
675317ff085116a133949ddc | 10.26434/chemrxiv-2024-3zd08 | Novel Tet3 enzymes for next generation epigenetic sequencing | Epigenetic regulation of gene expression is essential for cellular development and differentiation processes in higher eukaryotes. Modifications of cytidine, in particular 5-methylcytidine (5mdC) in DNA plays a central role through impacting on chromatin structure, repression of transposons and regulation of transcription. DNA methylation is actively installed by DNA methyltransferases and reversed through Tet-dioxygenase-mediated oxidation of 5mdC to 5-hydroxylmethylcytosine (5hmdC), formylcytosine (5fdC) and 5-carboxycytosine (5cadC). In order to understand the role of these epigenetic DNA modification in cellular differentiation and developmental processes, as well as disease states mapping and tracing of 5mdC and its oxidized forms is crucial. Bisulfite sequencing, the benchmark for mapping 5mdC for the last decades, suffers from degradation of the majority of genetic material through the harsh chemical treatment. Alternative, sequencing methods often utilize Tet-enzyme-mediated oxidation of 5mdC to locate 5mdC and 5hmdC in genomic DNA. Here we report the development of novel Tet3-variants for oxidation-based bisulfite free 5mdC- sequencing. | Özge Simsir; Tobias Walter; Hanife Sahin; Thomas Carell; Sabine Schneider | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675317ff085116a133949ddc/original/novel-tet3-enzymes-for-next-generation-epigenetic-sequencing.pdf |
60c74c16469df43dbef43fff | 10.26434/chemrxiv.12385577.v1 | Pd/FER vs Pd/SSZ-13 Passive NOx Adsorbers: Adsorbate-controlled Location of Atomically Dispersed Pd(II) in FER Determines High Activity and Stability | <p>Pd-loaded FER and SSZ-13 zeolites as
low-temperature passive NOx adsorbers (PNA) are compared under practically relevant
conditions. Vehicle cold-start exposes the material to CO under a range of concentrations,
necessitating a systematic exploration of the effect of CO on the performance
of isolated Pd ions for PNA. NO release temperature of both adsorbers decreases
gradually with the increase of CO concentration from a few hundred to a few
thousand ppm. This beneficial effect results from local nano-“hot spots”
formation during CO oxidation. Dissimilar to Pd/SSZ-13, increasing the CO
concentration above ~1,000 ppm improves the NOx storage significantly for
Pd/FER, attributed to the presence of a Pd ions in FER γ-site that is shielded from NO<sub>x</sub>. CO mobilizes
this Pd atom to the NO<sub>x</sub> accessible position where it becomes active
for PNA. This behavior explains the very high resistance of Pd/FER to
hydrothermal aging: Pd/FER materials survive hydrothermal aging at 800⁰C in 10% H<sub>2</sub>O
vapor for 16 hours with no deterioration in NOx uptake/release behavior. Thus,
by allocating Pd ions to the specific microporous pockets in FER, we have
produced very hydrothermally stable and active PNA materials with immediate practical
applications.<br /></p> | Konstantin Khivantsev; Xinyi Wei; Libor Kovarik; Nicholas
R. Jaegers; Eric D. Walter; Pascaline Tran; Yong Wang; János Szanyi | Nanocatalysis - Catalysts & Materials; Industrial Manufacturing; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c16469df43dbef43fff/original/pd-fer-vs-pd-ssz-13-passive-n-ox-adsorbers-adsorbate-controlled-location-of-atomically-dispersed-pd-ii-in-fer-determines-high-activity-and-stability.pdf |
60c743b14c8919d703ad26a1 | 10.26434/chemrxiv.8639942.v2 | Randomized SMILES Strings Improve the Quality of Molecular Generative Models | Recurrent Neural Networks (RNNs) trained with a set of molecules
represented as unique (canonical) SMILES strings, have shown the capacity to
create large chemical spaces of valid and meaningful structures. Herein we
perform an extensive benchmark on models trained with subsets of GDB-13 of
different sizes (1 million , 10,000 and 1,000), with different SMILES variants
(canonical, randomized and DeepSMILES), with two different recurrent cell types
(LSTM and GRU) and with different hyperparameter combinations. To guide the
benchmarks new metrics were developed that define the generated chemical space with
respect to its uniformity, closedness and completeness. Results show that
models that use LSTM cells trained with 1 million randomized SMILES, a
non-unique molecular string representation, are able to generate larger
chemical spaces than the other approaches and they represent more accurately
the target chemical space. Specifically, a model was trained with randomized
SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform
probability. Models trained with smaller samples show an even bigger improvement
when trained with randomized SMILES models. Additionally, models were trained
on molecules obtained from ChEMBL and illustrate again that training with
randomized SMILES lead to models having a better representation of the
drug-like chemical space. Namely, the model trained with randomized SMILES was
able to generate at least double the amount of unique molecules with the same
distribution of properties comparing to one trained with canonical SMILES. | Josep Arús-Pous; Simon Viet Johansson; Oleksii Prykhodko; Esben Jannik Bjerrum; Christian Tyrchan; Jean-Louis Reymond; Hongming Chen; Ola Engkvist | Chemoinformatics; Machine Learning | CC BY 4.0 | CHEMRXIV | 2019-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b14c8919d703ad26a1/original/randomized-smiles-strings-improve-the-quality-of-molecular-generative-models.pdf |
60c74573f96a00c53c286bb2 | 10.26434/chemrxiv.10013090.v1 | Robot-Accelerated Perovskite Investigation and Discovery (RAPID): 1. Inverse Temperature Crystallization | Metal halide perovskites are a promising class of materials for next-generation photovoltaic and optoelectronic devices. The discovery and full characterization of new perovskite-derived materials are limited by the difficulty of growing high quality crystals needed for single-crystal X-ray diffraction studies. We present the first automated, high-throughput approach for metal halide perovskite single crystal discovery based on inverse temperature crystallization (ITC) as a means to rapidly identify and optimize synthesis conditions for the formation of high quality single crystals. Using this automated approach, a total of 1928 metal halide perovskite synthesis reactions were conducted using six organic ammonium cations (methylammonium, ethylammonium, n-butylammonium, formamidinium, guanidinium, and acetamidinium), increasing the number of metal halide perovskite materials accessible by ITC syntheses by three and resulting in the formation of a new phase, [C<sub>2</sub>H<sub>7</sub>N<sub>2</sub>][PbI<sub>3</sub>]. This comprehensive dataset allows for a statistical quantification of the total experimental space and of the likelihood of large single crystal formation. Moreover, this dataset enables the construction and evaluation of machine learning models for predicting crystal formation conditions. This work is a proof-of-concept that combining high throughput experimentation and machine learning accelerates and enhances the study of metal halide perovskite crystallization. This approach is designed to be generalizable to different synthetic routes for the acceleration of materials discovery. | Zhi Li; Mansoor Ani Najeeb; Liana Alves; Alyssa Sherman; Peter Cruz Parrilla; Ian M. Pendleton; Matthias Zeller; Joshua Schrier; Alexander
J. Norquist; Emory Chan | Hybrid Organic-Inorganic Materials; Materials Processing; High-throughput Screening; Machine Learning; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74573f96a00c53c286bb2/original/robot-accelerated-perovskite-investigation-and-discovery-rapid-1-inverse-temperature-crystallization.pdf |
6616c60a91aefa6ce145f4c1 | 10.26434/chemrxiv-2023-c14r3-v3 | Transferable prediction of formation energy across lattices of increasing size | In this study, we show the transferability of graph convolutional neural network (GCNN) predictions of the formation energy of the nickel-platinum (NiPt) solid solution alloy across atomic structures of increasing sizes. The original dataset was generated with the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) using the second nearest-neighbor modified embedded-atom method (2NN MEAM) empirical interatomic potential. Geometry optimization was performed on the initially randomly generated face centered cubic (FCC) crystal structures and the formation energy has been calculated at each step of the geometry optimization, with configurations spanning the whole compositional range. Using data from various steps of geometry optimization, we first trained the GCNN on a lattice of 256 atoms, which accounts well for the short-range interactions. Using this data, we predicted the formation energy for lattices of 864 atoms and 2,048 atoms, which resulted in lower-than-expected accuracy due to the long-range interactions present in these larger lattices. We accounted for the long-range interactions by including a small amount of training data representative for those two larger sizes, whereupon the predictions of the GCNN scaled linearly with the size of the lattice. Therefore, our strategy ensured scalability while reducing significantly the computational cost of training on larger lattice sizes. | Massimiliano Lupo Pasini; Mariia Karabin; Markus Eisenbach | Materials Science; Inorganic Chemistry; Alloys; Solid State Chemistry; Transition Metal Complexes (Inorg.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6616c60a91aefa6ce145f4c1/original/transferable-prediction-of-formation-energy-across-lattices-of-increasing-size.pdf |
67582b35f9980725cf99b0ae | 10.26434/chemrxiv-2025-r2ph8 | Atomic layer deposition on spray-dried supraparticles to rationally design catalysts with ultralow noble metal loadings | This document is the unedited not peer-reviewed Author’s version of a Submitted Work to Chemistry of Materials.
The controlled assembly of supraparticles using spray-drying enables the synthesis of nanoporous materials. Changing the size of the constituent nanoparticles or their agglomeration states provides access to a diverse range of pore frameworks. This turns supraparticles into ideal scaffolds in heterogeneous catalysis. The combination of supraparticles with atomic layer deposition (ALD) as a surface functionalization technique offers excellent control over the deposition of a functional material and its distribution over the scaffold on the nanoscale. This work reports the combination of SiO2 supraparticles as tunable scaffolds and their loading with a platinum-based ALD catalyst. The deliberate adjustment of the scaffold pore framework via spray-drying and its effects on the catalyst deposition are highlighted. Furthermore, varying numbers of Pt ALD cycles are applied to explore the capability of the combinational approach with respect to catalyst loading and Pt efficiency. High-resolution electron microscopy reveals ultra-small Pt clusters deposited on the supraparticles after the very first ALD cycle. Using the hydrogenation of 4-nitrophenol as a demonstration, the impact of the pore framework and the Pt deposition variation in ALD on the catalytic functionality is investigated. | Philipp Groppe; Valentin Müller; Johannes Will; Xin Zhou; Kailun Zhang; Jörg Libuda; Tanja Retzer; Erdmann Spiecker; Julien Bachmann; Karl Mandel; Susanne Wintzheimer | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67582b35f9980725cf99b0ae/original/atomic-layer-deposition-on-spray-dried-supraparticles-to-rationally-design-catalysts-with-ultralow-noble-metal-loadings.pdf |
6694790901103d79c508aaea | 10.26434/chemrxiv-2024-23v3c | DOPtools: a Python platform for descriptor calculation and model optimization. Overview and usage guide | DOPtools (Descriptors and Optimization tools) platform is a Python library for calculation of chemical descriptors and hyperparameters optimization, building and validation of QSPR models. While a variety of existing tools and libraries can calculate various molecular de- scriptors, their output format is often unique, which complicates their connection to standard machine learning libraries. DOPtools provides a unified API for the calculated descriptors as an input for the scikit-learn library. Moreover, DOPtools has a command line interface for automatic calculation of various descriptors on server side and for eventual hyperparameters optimization of statistical models. The modular nature of the code allows easy additions of algorithms if required by the end user. The code for the platform is freely available at GitHub: https://github.com/POSidorov/DOPtools. | Said Byadi; Philippe Gantzer; Timur Gimadiev; Pavel Sidorov | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6694790901103d79c508aaea/original/do-ptools-a-python-platform-for-descriptor-calculation-and-model-optimization-overview-and-usage-guide.pdf |
670979c3cec5d6c142e2980b | 10.26434/chemrxiv-2024-lq0m0 | Racial Diversity in Cancer Models: A Call to Action for Nanomedicine Researchers | Global cancer incidence is projected to surge by 47% from 2020 to 2040, exacerbating existing healthcare
disparities, particularly among ethnically diverse women. This article examines the urgent need for equitable
therapeutic innovation in cancer care, focusing on the lack of diversity in preclinical cancer models. Our analysis
of the top 50 cited papers on gynecological cancers in nanomedicine reveals an overreliance on cell lines
predominantly of European origin, raising questions about the generalizability of findings. Using the Estimated
Cell Line Ancestry database, we further explore the underrepresentation of equity deserving groups in available
cancer cell lines while highlighting challenges and strategies that can be employed to address this growing issue. | Lucy Wang; Oluwatomilayo Ejedenawe; Stephanie Lheureux; Danielle Rodin; Christine Allen | Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670979c3cec5d6c142e2980b/original/racial-diversity-in-cancer-models-a-call-to-action-for-nanomedicine-researchers.pdf |
60c74c48702a9b46c418b630 | 10.26434/chemrxiv.12055440.v2 | Disentangling Second Harmonic Generation from Multiphoton Photoluminescence in Halide Perovskites using Multidimensional Harmonic Generation | Metal halide perovskites are an intriguing class of semiconductor materials being explored for their linear and non-linear optical, and potentially ferroelectric properties. In particular, layered two-dimensional Ruddlesden-Popper (RP) halide perovskites have shown non-linear optoelectronic properties. Optical second harmonic generation (SHG) is commonly used to screen for non-centrosymmetric and ferroelectric materials, however, SHG measurements of perovskites are complicated by their intense multiphoton photoluminescence (mPL) which can be mistaken for SHG signal. In this work, we introduce multidimensional harmonic generation as a method to eliminate the complications caused by mPL. By scanning and correlating both excitation and emission frequencies, we un-ambiguously assess whether a material supports SHG by examining if an emission feature scales as twice the excitation frequency. Careful multidimensional harmonic generation measurements of a series of n=2 and n=3 RP perovskites reveal that, contrary to previous belief, n-butylammonium (BA) RP perovskites display no SHG, thus they have inversion symmetry; but RP perovskites with phenylethylammonium (PEA) and 2-thiophenemethylammonium (TPMA) spacer cations display SHG. Multidimensional harmonic generation is also able to confirm the SHG and thus non-centrosymmetry of a recently reported ferroelectric RP perovskite even in the presence of an obscuring mPL background. This work establishes multidimensional harmonic generation as a definitive method to measure the SHG properties of materials and demonstrates that tuning organic cations can allow the design of new non-centrosymmetric or even ferroelectric RP perovskites.<br /> | Darien Morrow; Matthew Hautzinger; David Lafayette; Jason Scheeler; Lianna Dang; Meiying Leng; Daniel Kohler; Amelia Wheaton; yongping fu; Ilia Guzei; Jiang Tang; Song Jin; John Wright | Hybrid Organic-Inorganic Materials | CC BY 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c48702a9b46c418b630/original/disentangling-second-harmonic-generation-from-multiphoton-photoluminescence-in-halide-perovskites-using-multidimensional-harmonic-generation.pdf |
64c2a636658ec5f7e547f72b | 10.26434/chemrxiv-2023-cgv0c | Total Synthesis of Psammaplysins A, M, O, and Q, and Ceratinamide A | The psammaplysins are a unique class of brominated marine alkaloids bearing a signature 5/7-spiroisoxazoline-oxepine core linked to a variable tyramine-derived unit. Here, we report the total synthesis of several members of this family via a dipolar cycloaddition between an in situ generated nitrile oxide and an unusual 7-membered enediol diether dipolarophile. Carefully orchestrated oxidative transformation towards the fully functionalized spirocycle and direct coupling with tyramine-derived amines provides access to five representative family members, psammaplysins A, M, O, and Q, and ceratinamide A, the latter four for the first time. | Andrew Morrow; Myles Smith | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c2a636658ec5f7e547f72b/original/total-synthesis-of-psammaplysins-a-m-o-and-q-and-ceratinamide-a.pdf |
60c74f300f50db1ee539736b | 10.26434/chemrxiv.12860852.v1 | Multiweek Experiments for an Inorganic Chemistry Laboratory Course: Synthesis of Nickel Complexes Supported by a Tetradentate Ligand with an N2O2 Donor Set | <div>Inorganic Chemistry teaches students the concept that modifications to ligand structures, especially
the donor properties, can have a drastic impact on the reactivity and stability of the metal complexes. Experiments described here reinforce this concept through the investigation of two tetradentate
ligands derived from o-phenylenediamine and salicylaldehyde. The Schiff base ligand, H2salophen,
reacts with Ni(OAc)2•4H2O to yield a maroon colored, square planar complex, Ni(salophen). Under the
same conditions, the amine-type ligand, H2salophan, forms a light-blue compound with a formula
Ni(salophan)(HOAc). Complex Ni(salophan) free of acetate may be produced from the reaction of H2salophan with Ni(OAc)2•4H2O in the presence of NaOH, but undergoes ligand dehydrogenation to
yield Ni(salophen). Students conducting these experiments have the opportunity to learn synthetic
techniques and various characterization methods. Most importantly, the inquiry-guided experimental
design helps them develop critical thinking skills and apply acquired knowledge to solving a research
problem in a laboratory course. <br /></div> | Joel Collett; Jeanette Krause; Hairong Guan | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f300f50db1ee539736b/original/multiweek-experiments-for-an-inorganic-chemistry-laboratory-course-synthesis-of-nickel-complexes-supported-by-a-tetradentate-ligand-with-an-n2o2-donor-set.pdf |
60c7517bf96a009d2d28800c | 10.26434/chemrxiv.12456146.v3 | Ensemblization of density-functional theory: Insight from the fluctuation-dissipation theorem | Density functional theory can be generalized to mixtures of ground and excited states, for the purpose of determining energies of excitations using low-cost density functional approximations. Adapting approximations originally developed for ground states to work in the new setting would fast-forward progress enormously. But, previous attempts have stumbled on daunting fundamental issues. Here we show that these issues can be prevented from the outset, by using a fluctuation dissipation theorem (FDT) to dictate key functionals. We thereby show that existing exchange energy approximations are readily adapted to excited states, when combined with a rigorous exact Hartree term that is different in form from its ground state counterpart, and counterparts based on ensemble ansatze. Applying the FDT to correlation energies also provides insights into ground state-like and ensemble-only correlations. We thus provide a comprehensive and versatile framework for ensemble density functional approximations. | Tim Gould; Gianluca Stefanucci; Stefano Pittalis | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517bf96a009d2d28800c/original/ensemblization-of-density-functional-theory-insight-from-the-fluctuation-dissipation-theorem.pdf |
61ea3d39eab6ef3548e8d9e7 | 10.26434/chemrxiv-2022-ss450 | Modelling mercury sorption of a polysulfide coating made from sulfur and limonene | A polymer made from sulfur and limonene was used to coat silica gel and then evaluated as a mercury sorbent. A kinetic model of mercury uptake was established for a range of pH values and concentrations of sodium chloride. Mercury uptake was generally rapid from pH = 3 to pH = 11. At neutral pH, the sorbent (500 mg with a 10:1 ratio of silica to polymer) could remove 90% of mercury within one minute from a 100 mL solution 5 ppm in HgCl2 and 99% over 5 minutes. It was found that sodium chloride, at concentrations comparable to seawater, dramatically reduced mercury uptake rates and capacity. It was also found that the spent sorbent was stable in acidic and neutral media, but degraded at pH 11 which led to mercury leaching. These results help define the conditions under which the sorbent could be used, which is an important advance for using this material in remediation processes. | Max Worthington; Ismi Yusrina Muhti; Maximilian Mann; Zhongfan Jia; Anthony Miller; Justin Chalker | Polymer Science; Earth, Space, and Environmental Chemistry; Organic Polymers; Environmental Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ea3d39eab6ef3548e8d9e7/original/modelling-mercury-sorption-of-a-polysulfide-coating-made-from-sulfur-and-limonene.pdf |
61d68c155015ebbf56af40f0 | 10.26434/chemrxiv-2022-f4p0c | Visualization and monitoring of damaging-healing processes of polymers by AIEgen-loaded multifunctional microcapsules | Polymeric materials play an essential and ubiquitous role in modern societies, but they are inevitably damaged during service, which can lead to compromised performance or even direct failure. The sensitive detection and dynamic monitoring of the health states of polymers is thus crucial to increase their reliability, safety, and lifetime. Herein, a facile fluorescence-based approach that can achieve the nondestructive, on-site, real-time, full-field, and sensitive visualization and monitoring of damaging-healing processes of polymers is demonstrated. By embedding novel UV-blocking microcapsules containing a diisocyanate solution of aggregation-induced emission luminogens (AIEgens) into a polymer matrix, the damaged regions of the composite show turn-on fluorescence and dual signal changes in both fluorescence intensity and fluorescence color can be observed during the healing processes. The invisible information of the static health states and dynamic healing processes can be directly and semi-quantitatively visualized by naked eyes based on the collective effects of AIE and twisted intramolecular charge transfer. In addition to the autonomous damage-reporting, self-healing, and health indication functionalities, the microcapsule-embedded polymeric coatings possess excellent photo- and water-protection capabilities, which are appealing to various practical applications. | Shusheng Chen; Ting Han; Junkai Liu; Xinting Liang; Jinglei Yang; Ben Zhong Tang | Materials Science; Polymer Science; Aggregates and Assemblies; Coating Materials; Core-Shell Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d68c155015ebbf56af40f0/original/visualization-and-monitoring-of-damaging-healing-processes-of-polymers-by-ai-egen-loaded-multifunctional-microcapsules.pdf |
62b384101278ae34f8ebe4a8 | 10.26434/chemrxiv-2022-x9flv | Copper(I) Donor-Chromophore-Acceptor Assembly for Light-Driven Oxidation on a Zinc Oxide Nanowire Electrode | Dye-sensitized photoelectrochemical cells have emerged as a potential candidate for solar-to-fuels conversion. Herein, we report a Cu(I)-based donor-chromophore-acceptor triad comprising a triphenylamine electron donor and dipyrido[3,2-a:2',3'-c]phenazine electron acceptor as the active material for photoanodes. Energy levels of this triad are carefully aligned for thermodynamically favorable photoinduced electron transfer. Once this triad is surface grafted onto zinc oxide nanowires, photoelectrochemical studies confirm the utility of this architecture for oxidative processes such as alcohol oxidation with modest yields. | Zujhar Singh; Saeid Kamal; Marek Majewski | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b384101278ae34f8ebe4a8/original/copper-i-donor-chromophore-acceptor-assembly-for-light-driven-oxidation-on-a-zinc-oxide-nanowire-electrode.pdf |
61aa62f963557c744495b4c3 | 10.26434/chemrxiv-2021-8gthw | An open-source framework for fast-yet-accurate calculation of quantum mechanical features | We present the open-source framework kallisto that enables the efficient and robust calculation of quantum mechanical features for atoms and molecules.
For a benchmark set of 49 experimental molecular polarizabilities, the predictive power of the presented method competes against second-order perturbation theory in a converged atomic-orbital basis set at a fraction of its computational costs.
Robustness tests within a diverse validation set of more than 80,000 molecules show that the calculation of isotropic molecular polarizabilities has a low failure-rate of only 0.3 %.
We present furthermore a generally applicable van der Waals radius model that is rooted on atomic static polarizabilites.
Efficiency tests show that such radii can even be calculated for small- to medium-size proteins where the largest system (SARS-CoV-2 spike protein) has 42,539 atoms.
Following the work of Domingo-Alemenara et al. [Domingo-Alemenara et al., Nat. Comm., 2019, 10, 5811],
we present computational predictions for retention times for different chromatographic methods and describe how physicochemical features improve the predictive power of machine-learning models that otherwise only rely on two-dimensional features like molecular fingerprints.
Additionally, we developed an internal benchmark set of experimental super-critical fluid chromatography retention times.
For those methods, improvements of up to 17 % are obtained when combining molecular fingerprints with physicochemical descriptors.
Shapley additive explanation values show furthermore that the physical nature of the applied features can be retained within the final machine-learning models.
We generally recommend the kallisto framework as a robust, low-cost, and physically motivated featurizer for upcoming state-of-the-art machine-learning studies. | Eike Caldeweyher; Christoph Bauer; Ali Soltani Tehrani | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aa62f963557c744495b4c3/original/an-open-source-framework-for-fast-yet-accurate-calculation-of-quantum-mechanical-features.pdf |
670f483acec5d6c1424860fc | 10.26434/chemrxiv-2024-rplpq | The Synthesis of Acenes by Mechanochemical Reductive Aromatization | A Sn-mediated mechanochemical reductive aromatization of 1,4-dihydroxy- and 1,4-dimethoxy-cyclohexadienes has been used to form ten acenes, including derivatives of benzene, anthracene, tetracene, and pentacene. This method has been developed to overcome issues faced during the formation of electron-deficient 1,4-dihydroxy- or 1,4-dimethoxy-cyclohexadienes under homogeneous conditions. While this method does not tolerate trimethylsilyl protecting groups for alkynes, it can provide a fast, easy to set up alternative to homogeneous reductive aromatization. | Zachary W. Schroeder; Madeline Lietz; Michael J. Ferguson; Rik R. Tykwinski | Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Carbon-based Materials; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f483acec5d6c1424860fc/original/the-synthesis-of-acenes-by-mechanochemical-reductive-aromatization.pdf |
60c75283ee301c509cc7ac12 | 10.26434/chemrxiv.13308458.v1 | Characterization of a Modular Flow Cell System for Electrocatalytic Experiments and Comparison to a Commercial RRDE System | Generator-collector
experiments offer insights into the mechanisms of electrochemical reactions by
correlating the product and generator currents. Most commonly, these
experiments are performed using a rotating ring-disk electrode (RRDE). We
developed a double electrode flow cell (DEFC) with exchangeable generator and
detector electrodes where the electrode width equals the channel width.
Commonalities and differences between the RRDE and DEFC are discussed based on
analytical solutions, numerical simulations and measurements of the
ferri-/ferrocyanide redox couple on Pt electrodes in a potassium chloride
electrolyte. The analytical solutions agree with the measurements using
electrode widths of 5 and 2 mm. Yet, we find an unexpected dependence on the
exponent of the width so that wider electrodes cannot be analysed using the
conventional analytical solution. In contrast, all the investigated electrodes
show a collection efficiency of close to 35.4% above a minimum rotation speed
or flow rate, where the narrowest electrode is most accurate at the cost of
precision and the widest electrode the least accurate but most precise. Our
DEFC with exchangeable electrodes is an attractive alternative to commercial RRDEs
due to the flexibility to optimize the electrode materials and geometry for the
desired reaction. | Frederik J. Stender; Keisuke Obata; Max Baumung; Fatwa
F. Abdi; Marcel Risch | Analytical Apparatus; Electrochemical Analysis; Theory - Computational; Electrochemistry - Mechanisms, Theory & Study; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75283ee301c509cc7ac12/original/characterization-of-a-modular-flow-cell-system-for-electrocatalytic-experiments-and-comparison-to-a-commercial-rrde-system.pdf |
62790702d555507e7f9397c5 | 10.26434/chemrxiv-2022-mghvd | High-field NMR, reactivity, and DFT modeling reveal the gamma-Al2O3 surface hydroxyl network. | Aluminas are strategic materials used in many major industrial processes, either as catalyst supports or as catalysts in their own right. The transition alumina gamma-Al2O3 is a privileged support, whose reactivity can be tuned by thermal activation. This study provides an qualitative and quantitative assessment of the hydroxyl groups present on the surface of gamma-Al2O3 at three different dehydroxylation temperatures. The principal [AlOH] configurations are identified and described in unprecedented detail at the molecular level. The structures were established by combining information from high-field 1H and 27Al solid-state NMR, IR spectroscopy and DFT calculations, as well as selective reactivity studies. Finally, the relationship between the hydroxyl structures and the molecular-level structures of the active sites in catalytic alkane metathesis is discussed. | Nicolas Merle; Tarnuma Tabassum; Susannah Scott; Alessandro Motta; Kai Szeto; Mostafa Taoufik; Régis Gauvin; Laurent Delevoye | Theoretical and Computational Chemistry; Catalysis; Analytical Chemistry; Spectroscopy (Anal. Chem.); Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62790702d555507e7f9397c5/original/high-field-nmr-reactivity-and-dft-modeling-reveal-the-gamma-al2o3-surface-hydroxyl-network.pdf |
613a6a45abeb637ccecde35c | 10.26434/chemrxiv-2021-tt6sx | Low Energy Carbon Capture via Electrochemically Induced pH Swing with Electrochemical Rebalancing |
We demonstrate a carbon capture system based on pH swing cycles driven through proton-coupled electron transfer of sodium (3,3’-(phenazine-2,3-diylbis(oxy))bis(propane-1-sulfonate)) (DSPZ) molecules. Electrochemical reduction of DSPZ causes an increase of hydroxide concentration, which absorbs CO2; subsequent electrochemical oxidation of the reduced DSPZ consumes the hydroxide, causing CO2 outgassing. The measured electrical work of separating CO2 from a binary mixture with N2, at CO2 inlet partial pressures ranging from 0.1 to 0.5 bar, and releasing to a pure CO2 exit stream at 1.0 bar, was measured for electrical current densities of 20 to 150 mA/ cm2. The work for separating CO2 from a 0.1 bar inlet and concentrating into 1 bar exit is 61.3 kJ/molCO2 at a current density of 20 mA/cm2 and extrapolates to 57.1 kJ/molCO2 in the low-current-density limit. At this limit, the cycle work for capture from 0.4 mbar extrapolates to 108-212 kJ/ molCO2 depending on the initial composition of the electrolyte. We also introduce an electrochemical rebalancing method that extends cell lifetime by recovering the initial electrolyte composition after it is perturbed by side reactions. We discuss the implications of these results for future low-energy electrochemical carbon capture devices.
| Shijian Jin; Min Wu; Yan Jing; Roy Gordon; Michael Aziz | Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a6a45abeb637ccecde35c/original/low-energy-carbon-capture-via-electrochemically-induced-p-h-swing-with-electrochemical-rebalancing.pdf |
60c757ef337d6c4944e29104 | 10.26434/chemrxiv.13560260.v2 | Routes involving no free C2 in a DFT-computed mechanistic model for the reported room-temperature chemical synthesis of C2. | <p>Recent lively debates about the nature of the quadruple bonding in the diatomic species C<sub>2</sub> have been heightened by recent suggestions of molecules in which carbon may be similarly bonded to other elements. The desirability of having methods for generating such species at ambient temperatures and in solution in order to study their properties may have been realized by a recent report of the first chemical synthesis of free C<sub>2</sub> itself under mild conditions. The method involved unimolecular fragmentation of an alkynyl zwitterion<b> 2</b> as generated from the precursor <b>1</b>, resulting in production and then trapping of free C<sub>2</sub> at ambient temperatures rather than the high temperature gas phase methods normally employed for C<sub>2</sub> generation. Here, alternative mechanisms are proposed for this reaction based on DFT calculations involving bimolecular 1,1- or 1,2-iodobenzene displacement reactions from <b>2</b> directly by galvinoxyl radical, or hydride transfer from 9,10-dihydroanthracene to <b>2</b>. These mechanisms result in the same trapped products as observed experimentally, but unlike that involving unimolecular generation of free C<sub>2</sub>, exhibit calculated free energy barriers commensurate with the reaction times observed at room temperatures. The relative energies of the transition states for 1,1 <i>vs</i> 1,2 substitution provide a rationalisation for the observed isotopic substitution patterns. The same mechanism also provides an energetically facile path to polymeric synthesis of carbon rich species by extending the carbon chain attached to the iodonium group, eventually resulting in formation of amorphous carbon and discrete molecules such as C<sub>60</sub>.</p><div><div><p><br /></p></div></div> | Henry Rzepa | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757ef337d6c4944e29104/original/routes-involving-no-free-c2-in-a-dft-computed-mechanistic-model-for-the-reported-room-temperature-chemical-synthesis-of-c2.pdf |
60c757d5f96a00cb01288d44 | 10.26434/chemrxiv.14460153.v1 | A Molecular Dynamics Approach to Calculate the Thermodiffusion (Soret and Seebeck) Coefficients of Salts in Aqueous Solutions | <div><div><div><p>An approach to investigate the physical parameters related to the ions thermodiffusion in aqueous solution is proposed herein by calculating the equilibrium hydration free energy and the self-diffusion coefficient as a function of temperature, ranging from 293 to 353 K, using molecular dynamics simulations of infinitely diluted ions in aqueous solutions. Several ion force field parameters are used in the simulations and new parameters are proposed for some ions to better describe their hydration free energy. Such a theoretical framework enables the calculation of some single-ion properties, such as heat of transport, Soret coefficient and mass current density, as well as properties of salts, such as effective mass and thermal diffusion, Soret and Seebeck coefficients. These calculated properties are compared with experimental data available from optical measurements and showed good agreement revealing an excellent theoretical predictability of salt thermodiffusion properties. Differences in single-ion Soret and self-diffusion coefficients of anions and cations give rise to a thermoelectric field, which affects the system response that is quantified by the Seebeck coefficient. The fast and slow Seebeck coefficients are calculated and discussed, resulting in values with mV/K order-of-magnitude, as observed in experiments involving several salts, such as K+Cl−, Na+Cl−, H+Cl−, Na+OH−, TMA+OH− and TBA+OH−. The present approach can be adopted for any ion or charged particle dispersed in water with the aim of predicting the thermoelectric field induced through the fluid. It has potential applications in designing electrolytes for ionic thermoelectric devices in order to harvest energy and thermoelectricity in biological nanofluids.</p></div></div></div> | Leandro Rezende Franco; André Luiz Sehnem; Antônio Martins Figueiredo Neto; Kaline Coutinho | Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757d5f96a00cb01288d44/original/a-molecular-dynamics-approach-to-calculate-the-thermodiffusion-soret-and-seebeck-coefficients-of-salts-in-aqueous-solutions.pdf |
60c74df4702a9b176818b94c | 10.26434/chemrxiv.12646613.v2 | Identification of Putative Plant Based Antiviral Compounds to Fight Against SARS-CoV-2 Infection | <p><i>Background:
</i>This
study aimed to examine the efficacy of some natural compounds and their
derivatives in inhibiting the nucleocapsid protein N-terminal RNA binding
domain (NSP-NTD), of SARS-CoV-2 virus by using the molecular doacking approach.</p>
<p><i>Methods:</i>
Physiochemical and drug likeness properties of the compounds were characterized
by using SWISS ADME server tool. ADMET and TOPKAT modules of Discovery studio
4.0 were used for prediction of pharmacokinetic properties and toxicity of the
compounds. Molecular docking of the ligands with the target protein (NSP-NTD)
was carried out using the receptor-ligand interactions module of DS 4.0. The
CDOCKER energy, CDOCKER interaction energy and binding energy of the
interactions were calculated to identify the best interacting compounds.</p>
<p><i>Results:</i>
Four compounds including 4-hydroxybenzoic acid, benzoic acid, 4-aminobenzoic
acid and salicylic acid have been predicted as effective compounds to inhibit
the NSP-NTD (responsible for packing the viral RNA into the crown like capsid) <i>vis-à-vis</i> combat the SARS-Cov-2 virus
infection. </p>
<p><i>Conclusions:</i> <i>In vitro</i> and <i>in vivo</i> evaluation of these compounds against SARS-CoV-2 virus is required prior to assuring their potential roles
in SARS-CoV-2 infection control.</p> | Sujit Kumar Mishra; Rajguru Rajesh Raman Mishra; Saumya Dash; Jogeswar Panigrahi | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df4702a9b176818b94c/original/identification-of-putative-plant-based-antiviral-compounds-to-fight-against-sars-co-v-2-infection.pdf |
63be4dabcac3180e2d9c4568 | 10.26434/chemrxiv-2023-kx6gp | A fluorescent molecular probe for live-cell imaging of starch granules | Plants accumulate photosynthetic product as starch, which is also a major carbohydrate source for human. Herein, we report the development of a fluorescent molecular probe for starch. Through a in vivo screening-based approach, we identified fluorescein-5-methy thiocarbamate as a candidate of starch probe that works in living plants. We synthesized 19 derivatives for the structural optimization of the starch probe and discovered that fluorescein-5-tert-butyl carbamate is the most specific probe with the brightest fluorescence among them. Analysis using Arabidopsis thaliana mutants of starch metabolism and in vitro NMR experiments revealed that the probe forms a complex with starch and illuminates starch granules in leaf chloroplasts and root amyloplasts within 10 minutes after the probe infiltration into living plant tissues. The starch probe is applicable to track the changes in intracellular starch contents in response to circadian cycle or light conditions. We concluded that fluorescein-5-tert-butyl carbamate can be used as a probe for live-cell and quantitative imaging of starch granules. The probe could be a useful imaging tool to facilitate finding novel phenomena linked with starch metabolism in crop plants. | Shuhei Kusano; Sakuya Nakamura; Masanori Izumi; Shinya Hagihara | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63be4dabcac3180e2d9c4568/original/a-fluorescent-molecular-probe-for-live-cell-imaging-of-starch-granules.pdf |
60c741204c8919c3f8ad2235 | 10.26434/chemrxiv.7934987.v1 | Missing Reactivity of Trimethylsilyl Reagents: Dehalogenative Activation Enabling One-Pot Generation of Aryne from 2-Iodophenol | Herein we present a missing reactivity of trimethylsilyl reagents; dehalogenative activation, which involves abstracting a halogen atom and anionically activating the substrate similar to the halogen-metal exchange reaction in classical carbanion species. This missing reactivity allowed for the one-pot generation of aryne from 2-iodophenol. | Koichiro Mikami; Takaaki Hirano; Hanamura Hitoshi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741204c8919c3f8ad2235/original/missing-reactivity-of-trimethylsilyl-reagents-dehalogenative-activation-enabling-one-pot-generation-of-aryne-from-2-iodophenol.pdf |
657b105e9138d23161a20a7b | 10.26434/chemrxiv-2023-j2s14 | Arylsulfonylacetate as Bifunctional Reagent for Photoredox Catalytic Alkylarylation of Alkynes | The radical difunctionalization of alkynes represents a powerful and straightforward approach for the synthesis of sophisticated molecules. However, the difunctionalization of alkynes mediated by bifunctional reagents remains unexplored, despite significant progress having been made in alkene difunctionalization. Here, we report a novel arylsulfonylacetate skeleton in which aryl rings are attached to acetates through SO2, serving as a powerful bifunctional reagent for the alkylarylation of alkynes under photoredox conditions. This modular bifunctional reagent enables the simultaneous incorporation of a wide range of functional groups, including (hetero)aryl ring and alkyl carboxylate into alkynes, resulting in synthetic valuable all-carbon tetrasubstituted alkene derivatives. This transformation is distinguished by its redox-neutral nature, readily accessible starting materials, compatibility with diverse functional groups and its capacity to facilitate convergent synthesis. The utility of this approach was further demonstrated though the late-stage functionalization of complex molecules, the preparation of fluorescent molecules and anti-cancer drugs | Chonglong He; Min Wang; Yulong Wang; Lirong Zhao; Youkang Zhou; Keyuan Zhang; Shenyu Shen; Yaqiong Su; Xin-hua Duan; Le Liu | Catalysis | CC BY 4.0 | CHEMRXIV | 2023-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b105e9138d23161a20a7b/original/arylsulfonylacetate-as-bifunctional-reagent-for-photoredox-catalytic-alkylarylation-of-alkynes.pdf |
60c74368bb8c1a3b4c3da2e3 | 10.26434/chemrxiv.8937017.v2 | Rh(III)-Catalyzed Coupling of N-Chloroimines with α-Diazo-α-Phosphonoacetates for Skeleton-Oriented Synthesis of 2H-Isoindoles | A major hurdle for realizing the full potential of transition metalcatalyzed, directed C-H functionalization synthesis of heterocycles is the blockingof ability for designated structural elaboration by the reactivity-assisting groupderived, unintended appendages. We communicate herein Rh(III)-catalyzed coupling of N-chloroimines with α-diazo-α-phosphonoacetates for skeletonoriented synthesis (SOS) of 2H-Isoindoles. Comprehensive mechanistic studies with rhodacycle intermediates support an associative covalent relay mechanism for this first reported N-chloroimine-directed C-H functionalization reaction. Theinitial dechlorination/dephosphonation under Rh(III) catalysis and subsequent deesterification under Ni(II) catalysis allow the complete elimination of unintended appendages and full exposure of reactivity for C3 and N2 ring atoms. The proofof - concept utility has been demonstrated with electrophilic substitution at the C3 site (formylation, azo derivatization) and nucleophilic reaction (methylation) at the N2 site, showcasing the enormous synthetic potential of SOS for attaching structurally unrelated appendages and enabling entry to distinct chemical space. | Bing Qi; Lei Li; Qi Wang; Wenjing Zhang; Lili Fang; Jin Zhu | Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2019-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74368bb8c1a3b4c3da2e3/original/rh-iii-catalyzed-coupling-of-n-chloroimines-with-diazo-phosphonoacetates-for-skeleton-oriented-synthesis-of-2h-isoindoles.pdf |
60c746a8567dfe2d6cec4679 | 10.26434/chemrxiv.11322860.v1 | Aza-BODIPY Platform: Towards an Efficient Water-Soluble Bimodal Imaging Probe for MRI and Near-Infrared Fluorescence | <p>In this study, an original aza-BODIPY
system comprising two Gd<sup>3+</sup> complexes has been designed and
synthesized for magnetic resonance imaging/optical imaging application, by
functionalization of the boron center. This strategy enabled to obtain a
positively-charged bimodal probe, which displays an increased water-solubility,
optimized photophysical properties in the near-infrared region, and very
promising relaxometric properties. The absorption and emission wavelengths are
705 and 741 nm respectively, with a quantum yield of around 10 % in aqueous
media. Moreover, the system does not produce singlet oxygen upon excitation,
which would be toxic for tissues. The relaxivity obtained is high at
intermediate fields (16.1 mM<sup>-1</sup>.s<sup>-1</sup> at 20 MHz and 310
K) and competes with that of bigger or more rigid systems. A full relaxometric
and <sup>17</sup>O NMR study and fitting of the data using the
Lipari-Szabo approach showed that this high relaxivity can be explained by the
size of the system and the presence of some small aggregates. These optimized
photophysical and relaxometric properties highlight the potential use of such
systems for future bimodal imaging studies.</p> | Oceane Flores; Jacques Pliquett; Laura Abad Galan; Robin Lescure; Franck Denat; Olivier Maury; Agnès Pallier; Pierre-Simon Bellaye; Bertrand Collin; Sandra Même; Celia S. Bonnet; Ewen Bodio; Christine Goze | Bioorganic Chemistry; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a8567dfe2d6cec4679/original/aza-bodipy-platform-towards-an-efficient-water-soluble-bimodal-imaging-probe-for-mri-and-near-infrared-fluorescence.pdf |
60c753bf337d6c654be288e2 | 10.26434/chemrxiv.13547459.v1 | Multiplexed Affinity Measurements of Extracellular Vesicles Binding Kinetics | <p>Extracellular vesicles (EVs) have attracted significant attention as impactful diagnostic biomarkers, since their properties are closely related to specific clinical conditions. However, designing experiments that involve EVs phenotyping is usually highly challenging and time-consuming, due to laborious optimization steps that require very long or even overnight incubation durations. In this work, we demonstrate label-free, real-time detection and phenotyping of extracellular vesicles binding to a multiplexed surface. With the ability of label-free kinetic binding measurements using the Interferometric Reflectance Imaging Sensor (IRIS) in a microfluidic chamber, we successfully optimize the capture reaction by tuning various assay conditions (incubation time, flow conditions, surface probe density and specificity). A single (less than 1 hour) experiment allows for characterization of binding affinities of the EVs to multiplexed probes. We demonstrate kinetic characterization of 18 different probe conditions, namely three different antobodies, each spotted at six different concentrations, simultaneously. The affinity characterization is then analyzed through a model which considers the complexity of multivalent binding of large structures to a carpet of probes, and therefore introduces a combination of fast and slow association and dissociation parameters. Additionally, our results confirm higher affinity of EVs to aCD81 with respect to aCD9 and aCD63. Single-vesicle imaging measurements corroborate our findings, as well as confirming the EVs nature of the captured particles through fluorescence staining of the EVs membrane and cargo. </p> | Elisa Chiodi; George G. Daaboul; Allison Marn; M. Selim Ünlü | Imaging; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753bf337d6c654be288e2/original/multiplexed-affinity-measurements-of-extracellular-vesicles-binding-kinetics.pdf |
660fa13a21291e5d1d1dc8ff | 10.26434/chemrxiv-2024-c7tn9 | Differentiation of species and provenance of palm leaf manuscripts using Fourier-Transform infrared spectrocopy and chemometrics | For the authentication and interpretation of palm leaf manuscripts, material analyses are required that enable the identification of specific characteristics of the written artefacts. In this study we apply infrared spectroscopy (DRIFTS) in combination with chemometrics as a fingerprinting technique for the analysis of palm leaf manuscripts. We demonstrate that manuscript specific information is obtained and that a differentiation regarding the taxonomic species of the palm leaves used for production and their geographical origin in South and Southeast Asia is possible. The results show the potential of infrared spectroscopy for fingerprinting and authentication of written artefacts. | Lucas F. Voges; Nils Horn; Giovanni Ciotti; Stephan Seifert | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660fa13a21291e5d1d1dc8ff/original/differentiation-of-species-and-provenance-of-palm-leaf-manuscripts-using-fourier-transform-infrared-spectrocopy-and-chemometrics.pdf |
60c742ab9abda2de8af8c05e | 10.26434/chemrxiv.8325251.v1 | Cyclopropanation of Terminal Alkenes via Sequential Atom Transfer Radical Addition – 1,3-Elimination | An operationally simple protocol to affect an atom transfer radical addition (ATRA) of commercially available ICH<sub>2</sub>Bpin to terminal alkenes has been developed. The intermediate iodide can be transformed in a one-pot process into the corresponding cyclopropane upon treatment with tetrabutylammonium fluoride (TBAF). This method is highly selective for the cyclopropanation of unactivated terminal alkenes over non-terminal alkenes and electron deficient alkenes. Due to the mildness of the procedure, a wide range of functional groups such as esters, amides, alcohols, ketones, and vinylic cyclopropanes are well tolerated. The whole reaction sequence relies on simple reagents such dilauroyl peroxide (DLP) and TBAF and can be run on multi-gram scales in ethyl acetate as a solvent. | Nicholas D. C. Tappin; Weronika Michalska; Simon Rohrbach; Philippe Renaud | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ab9abda2de8af8c05e/original/cyclopropanation-of-terminal-alkenes-via-sequential-atom-transfer-radical-addition-1-3-elimination.pdf |
65d5f3b5e9ebbb4db9dfa25e | 10.26434/chemrxiv-2024-4hhmd | The eXact integral simplified time-dependent density functional theory (XsTD-DFT) | In the framework of simplified quantum chemistry methods, we introduce the eXact integral simplified time-dependent density functional theory (XsTD-DFT). This method is based on the simplified time-dependent density functional theory (sTD-DFT) where all semi-empirical two-electron integrals are replaced by exact one- and two-center atomic orbital (AO) two-electron integrals while all other approximations from sTD-DFT are kept. The performance of this new parameter-free XsTD-DFT method was benchmarked to evaluate excited state and (non)linear response properties, including ultra-violet/visible absorption, first hyperpolarizability, and two-photon absorption. For a set of 77 molecules, results from the XsTDA approach (or XsTD-DFT considering the Tamm-Dancoff approximation) were compared to corresponding TDA data. XsTDA/B3LYP excitation energies only deviate absolutely by 0.14 eV in average from those obtained from standard TDA while drastically cutting computational costs by a factor of 20 or more depending on the single energy threshold chosen. The absolute deviations of excitation energies with respect to the full scheme are decreasing when the system size is increasing, showing the suitability of XsTDA/XsTD-DFT to treat large systems. Comparing XsTDA and its predecessor sTDA, the new scheme globally improves excitation energies and oscillator strengths. Particularly, the XsTDA scheme can faithfully reproduce TDA results for charge transfer states. Among the various results, TD-DFT first hyperpolarizability frequency dispersions for a set of push-pull $\pi$-conjugated molecules are faithfully reproduced by XsTD-DFT while the sTD-DFT method always provides red-shifted resonance energy positions. Excellent performance with respect to experiment is observed for the 2PA spectrum of the enhanced green fluorescent protein (eGFP). The generally excellent results with an accuracy similar to TD-DFT but at a fraction of its computational cost opens the way for a plethora of applications considering large systems as well as high throughput screening studies. | Marc de Wergifosse; Stefan Grimme | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d5f3b5e9ebbb4db9dfa25e/original/the-e-xact-integral-simplified-time-dependent-density-functional-theory-xs-td-dft.pdf |
670cd17712ff75c3a15cfea6 | 10.26434/chemrxiv-2024-lrkln | Synthesis, antiproliferative activity, and biological profiling of C-19 trityl and silyl ether andrographolide analogs in colon cancer and breast cancer cells
| Andrographolide, a natural product, putatively functions through covalent inhibition of NF-κB, a transcription factor that modulates tumor survival and metastasis. Previous studies found that functionalization of the C-19 hydroxyl alters the primary mode of action from inhibition of NF-κB to the modulation of the Wnt1/β-catenin signaling pathway. Here, we synthesized a series of C-19 trityl and silyl ether analogs. MTT assays reveal cell line selectivity between colorectal and breast cancer cells, which is consistent with known mechanisms of β-catenin-driven cell proliferation in colorectal cancer cell lines. Through a TNF-α dependent NF-κB reporter assay, we observed that our analogs generally exhibit greater activity than andrographolide. Fluorescence imaging demonstrated that cells treated with andrographolide and its C-19 analogs retained similar distributions of active β-catenin, but notable differences in antiproliferative potency upon co-delivery with GSK-3β inhibitor CHIR99021 suggest several analogs have a greater dependence on β-catenin signaling for antiproliferative activity in HT-29 cells.
| Tiffany Gu; Rushika Raval; Zachary Bashkin; Carina Zhou; Sanghyuk Ko; Natalie Kong; Seoyeon Hong; Aditya Bhaskara; Samarth Shah; Aditi Joshi; Samahith Thellakal; Kaitlyn Rim; Anushree Marimuthu; Srishti Venkatesan; Emma Wang; Sophia Li; Aditi Jayabalan; Alice Tao; Yilin Fang; Lorelei Xia; Aidan Chui; Emily Shu; Tracy Zhang; Zhan Chen; Edward Njoo | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670cd17712ff75c3a15cfea6/original/synthesis-antiproliferative-activity-and-biological-profiling-of-c-19-trityl-and-silyl-ether-andrographolide-analogs-in-colon-cancer-and-breast-cancer-cells.pdf |
632df2fffee74ebf3247eb76 | 10.26434/chemrxiv-2022-wv4f5 | New Salt Hydrates for Thermal Energy Storage | Thermal energy storage (TES) has the potential to improve the efficiency of many applications, but has not been widely deployed. The viability of a TES system depends upon the performance of its underlying storage material; improving the energy density of TES materials is an important step in accelerating the adoption of TES systems. Salt hydrates are a promising class of TES materials due to their relatively high energy densities and their reversibility. Despite their promise, relatively few salt hydrates have been characterized, presenting the possibility that new hydrate compositions with superior properties may exist. Here, the energy densities, turning temperatures, and thermodynamic stabilities of 5292 hypothetical salt hydrates are predicted using high-throughput density functional theory calculations. The hydrates of several metal-fluorides, including CaF2, VF2, and CoF3, are identified as new, stable TES materials with class-leading energy densities and operating temperatures suitable for use in domestic heating and intermediate-temperature applications. The promising performance of these materials is demonstrated at the system level by parameterizing an operating model of a solar thermal TES system with data from the new hydrates. Finally, machine learning models for salt hydrate thermodynamics are developed and used to identify design guidelines for maximizing energy density. In total, the new materials and design rules reported here are expected to foster the adoption of TES systems. | Steven Kiyabu; Patrick Girard; Donald Siegel | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632df2fffee74ebf3247eb76/original/new-salt-hydrates-for-thermal-energy-storage.pdf |
678a5e2bfa469535b9668173 | 10.26434/chemrxiv-2025-77hg5 | Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design | Integrated understanding of pharmacokinetics (PK) and pharmacodynamics (PD) is a key aspect of successful drug discovery. Yet in generative computational drug design, the focus often lies on optimizing potency. Here we integrate PK property predictions in DrugEx, a generative drug design framework and we explore the generated compounds’ PD through simulations with a quantitative systems pharmacology (QSP) model. Quantitative structure-property relationship models were developed to predict molecule PK (clearance, volume of distribution and unbound fraction) and affinity for the Adenosine A2AR receptor (A2AR), a drug target in immuno-oncology. These models were used to score compounds in a reinforcement learning framework to generate molecules with a specific PK profile and high affinity for the A2AR. We predicted the expected tumor growth inhibition profiles using the QSP model for selected candidate molecules with varying PK and affinity profiles. We show that optimizing affinity to the A2AR, while minimizing or maximizing a PK property, shifts the type of molecular scaffolds that are generated. The difference in physicochemical properties of the compounds with different predicted PK parameters was found to correspond with the differences observed in the PK dataset. We demonstrated the use of the QSP model by simulating the effect of a broad range of compound properties on the predicted tumor volume. In conclusion, our proposed integrated workflow incorporating affinity predictions with PKPD may provide a template for the next generation of advanced generative computational drug design. | Helle W. van den Maagdenberg; Jikke de Mol van Otterloo; J. G. Coen van Hasselt; Piet H. van der Graaf; Gerard J. P. van Westen | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a5e2bfa469535b9668173/original/integrating-pharmacokinetics-and-quantitative-systems-pharmacology-approaches-in-generative-drug-design.pdf |
66d1e134f3f4b05290a2444d | 10.26434/chemrxiv-2024-hdgr5 | Non-Targeted Assessment of Environmental Contaminants and their Correlations with Semen Health Factors in New York City | Characterizing chemical composition of semen can provide valuable insights into the exposome and environmental factors that directly affect seminal and overall health. In this study, we compared molecular profiles of 45 donated semen samples from general population New York City participants and examined the correlation between the chemical profiles in semen vs. fertility parameters, i.e., sperm count, sperm morphology, sperm motility and semen volume. Samples were prepared using a protein precipitation procedure and analyzed using liquid chromatography (LC) and high-resolution mass spectrometry (HRMS). Non-targeted analysis (NTA) revealed eighteen chemicals not previously reported in human exposome studies, with 3-hydroxyoctanedioic acid, a cosmetic additive, emerging as a plausible candidate found to be at higher levels in cases vs. controls (p < 0.01) and associated with adverse sperm motility and morphology.
This study aims to be the first of its kind to utilize NTA to understand the association of contaminants of emerging concern (CECs) along with a full chemical profile to find trends separating poor and normal semen health parameters from each other chemically. Our results suggest that the collective effects of many CECs could adversely affect semen quality. | Trevor A Johnson; Sarah Adelman; Bobby B Najari; Joshua F Robinson; Linda G Kahn; Dimitri P Abrahamsson | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d1e134f3f4b05290a2444d/original/non-targeted-assessment-of-environmental-contaminants-and-their-correlations-with-semen-health-factors-in-new-york-city.pdf |
6452167607c3f02937233f09 | 10.26434/chemrxiv-2023-8jzsp | Understanding chiral proton organocatalysis using cinchonium derivatives | This work presents a detailed mechanistic study of a quininium-catalyzed aza-Michael reaction, providing essential infor-mation for the development of reactions in chiral proton organocatalysis (CPO). The use of cinchona derivatives as chiral proton catalysts demonstrates their potential beyond their conventional roles as base-promoted and phase-transfer cata-lysts. Competitive reaction pathways are studied using density functional theory (DFT), wavefunction theory, and microki-netic simulations. Additionally, theoretical studies are complemented with experimental titration and kinetic techniques to verify the intrinsic details of the reaction. The mechanistic study reveals a complex hydrogen bond network formed in the rate- and selectivity-determining step (hydrazide addition), involving four noncovalently attached components that favor a more efficient substrate docking in the R transition state. Notably, while counteranions are often considered innocent reac-tion components, carboxylic anions are crucial in understanding reaction yield and enantioselectivity, as they act as nucleo-phile-activating bases. Overall, this study introduces cinchonium derivatives as new options for CPO and provides a thor-ough mechanistic analysis that may be critical in expanding this underdeveloped type of catalysis. | Fernando Auria-Luna; Eugenia Marqués-López; M. Concepción Gimeno; Juan V. Alegre-Requena; Raquel P. Herrera | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Theory - Computational; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6452167607c3f02937233f09/original/understanding-chiral-proton-organocatalysis-using-cinchonium-derivatives.pdf |
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