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60c750b6337d6c765de283b7 | 10.26434/chemrxiv.13073153.v1 | Efficient Interlayer Exciton Transport in Two-Dimensional Metal-Halide Perovskites. | We present transient microscopy measurements of interlayer energy transport in (PEA)<sub>2</sub>PbI<sub>4</sub> perovskite. We find efficient interlayer exciton transport (0.06 cm<sup>2</sup>/s), which translates into a diffusion length that exceeds 100 nm and a sub-ps timescale for energy transfer. While still slower than in-plane exciton transport (0.2 cm<sup>2</sup>/s), our results show that excitonic energy transport is considerably less anisotropic than charge-carrier transport for 2D perovskites. | Alvaro J Magdaleno; Michael Seitz; Michel Frising; Ana Herranz de la Cruz; Antonio I. Fernández-Domínguez; Ferry Prins | Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b6337d6c765de283b7/original/efficient-interlayer-exciton-transport-in-two-dimensional-metal-halide-perovskites.pdf |
60c756f2bdbb899612a3ab1c | 10.26434/chemrxiv.14347265.v1 | Calcium Bridging Drives Polysaccharide Co-Adsorption to a Proxy Sea Surface Microlayer | Saccharides comprise a significant mass fraction of
organic carbon in sea spray aerosol (SSA), but the mechanisms through which
saccharides are transferred from seawater to the ocean surface and eventually
into SSA are unclear. It is hypothesized that saccharides cooperatively adsorb
to other insoluble organic matter at the air/sea interface, known as the sea
surface microlayer (SSML). Using a combination of surface-sensitive infrared
reflection-absorption spectroscopy and all-atom molecular dynamics simulations,
we demonstrate that the marine-relevant, anionic polysaccharide alginate
co-adsorbs to an insoluble palmitic acid monolayer via divalent cationic
bridging interactions. Ca<sup>2+</sup> induces the greatest extent of alginate
co-adsorption to the monolayer, evidenced by the ~30% increase in surface
coverage, whereas Mg<sup>2+</sup> only facilitates one-third the extent of
co-adsorption at seawater-relevant cation concentrations due to its strong hydration
propensity. Na<sup>+</sup> cations alone do not facilitate alginate co-adsorption,
and palmitic acid protonation hinders the formation of divalent cationic
bridges between the palmitate and alginate carboxylate moieties. Alginate
co-adsorption is largely confined to the interfacial region beneath the monolayer
headgroups, so surface pressure, and thus monolayer surface coverage, only
changes the amount of alginate co-adsorption by less than 5%. Our results
provide physical and molecular characterization of a potentially significant
polysaccharide enrichment mechanism within the SSML. | Kimberly Carter-Fenk; Abigail Dommer; Michelle E Fiamingo; Jeongin Kim; Rommie Amaro; Heather Allen | Atmospheric Chemistry; Environmental Science; Computational Chemistry and Modeling; Interfaces; Self-Assembly; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756f2bdbb899612a3ab1c/original/calcium-bridging-drives-polysaccharide-co-adsorption-to-a-proxy-sea-surface-microlayer.pdf |
60c742090f50db75d4395c15 | 10.26434/chemrxiv.8204654.v1 | β-NaVP2O7 as a Superior Electrode Material for Na-Ion Batteries | <p>Herein,
we present a novel <i>β</i>-polymorph of sodium vanadium pyrophosphate NaVP<sub>2</sub>O<sub>7</sub>
with the KAlP<sub>2</sub>O<sub>7</sub>-type
structure obtained via hydrothermal synthesis and further thermal dehydration
of a hydrophosphate intermediate. <i>β</i>-NaVP<sub>2</sub>O<sub>7</sub> demonstrates attractive electrochemical
behavior as a Na-ion positive electrode (cathode) material with practically achieved
reversible capacity of 104 mAh/g at C/10 current density, average operating
voltage of 3.9 V vs. Na/Na<sup>+ </sup>and only 0.5% volume change between the charged
and discharged states. Electrode material exhibits excellent C-rate capability
and cycling stability, providing the capacity of 90 mAh/g at 20C
discharge rate and < 1% capacity loss after 100 charge-discharge cycles. At
low voltage region (≈1.5 V vs. Na/Na<sup>+</sup>), <i>β</i>-NaVP<sub>2</sub>O<sub>7</sub>
reversibly intercalates additional sodium cations leading to unprecedented overall
Na-ion storage ability exceeding 250 mAh/g within the 1.5 – 4.4 V vs. Na/Na<sup>+</sup>
voltage region. This material is one of only a few materials that exhibits
reversible sodium ion storage capabilities over such a large potential window. </p> | Oleg Drozhzhin; Ilya Tertov; Anastasia Alekseeva; Dmitry A. Aksyonov; Keith Stevenson; Artem M. Abakumov; Evgeny Antipov | Electrochemistry; Solid State Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742090f50db75d4395c15/original/na-vp2o7-as-a-superior-electrode-material-for-na-ion-batteries.pdf |
60c73d900f50db1d2f3954cc | 10.26434/chemrxiv.5856825.v1 | Global and Local Reactivity Descriptors Based on Quadratic and Linear Energy Models for α,β-Unsaturated Organic Compounds | <div>Global and local descriptors of chemical reactivity can be derived from conceptual density functional theory. Their explicit form, however, depends on how the energy is defined as a function of the number of electrons. Within the existing interpolation models, here, the quadratic and the linear energy model were used to derive global descriptors as the electrophilicity and nucleophilicity (defined as the negative of the ionization potential) and local descriptors employing either the corresponding condensed fukui function in the linear model or the local response of the global descriptor in the quadratic model. The ability of these descriptors to predict the reactivity of molecules with more than one reactive site was first studied on a set of α ,β -unsaturated ketones, where experimental rate constants for the nucleophilic attack is known. With the validated descriptors the reactivity of α ,β -unsaturated carboxylic compounds with different heteroatoms as α ,β -unsaturated thioesters, esters and amides as alternative substrates for the enzymatic CO<sub>2</sub> fixation studied experimentally by Erb <i>et al.</i> was addressed. The carbon dioxide fixation involves the reduction of the neutral α ,β -unsaturated carboxylic compounds by a nucleophilic attack of a hydride anion from NADPH and the following electrophilic attack by carbon dioxide. It was found that condensed values of the linear fukui function within the fragment of molecular response approximation describe best the reactivity of α ,β -unsaturated ketones. For the two relevant processes involved in CO<sub>2</sub> fixation the amides present the largest reactivity in vacuum and in aqueous solution compared to the esters and thioesters and may, therefore, serve as alternative sustrates of carboxylases.</div> | Javier Oller; Patricia Perez; Paul W. Ayers; Esteban Vöhringer-Martinez | Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d900f50db1d2f3954cc/original/global-and-local-reactivity-descriptors-based-on-quadratic-and-linear-energy-models-for-unsaturated-organic-compounds.pdf |
60c746794c8919c904ad2b4f | 10.26434/chemrxiv.11328173.v1 | Assembly and Characterization of Polyelectrolyte Complex Micelles | We provide protocols and representative data for designing, assembling, and characterizing polyelectrolyte complex micelles (core-shell nanoparticles formed by polyelectrolytes and hydrophilic charged-uncharged block copolymers). | Alexander Marras; Jeffrey Vieregg; Matthew Tirrell | Biopolymers; Drug delivery systems; Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746794c8919c904ad2b4f/original/assembly-and-characterization-of-polyelectrolyte-complex-micelles.pdf |
6176a0580c04803d03442c1a | 10.26434/chemrxiv-2021-tgvjk | Acetate Facilitated Nickel Catalyzed Coupling of Aryl Chlorides and Alkyl Thiols | We report a mild, fast and convenient catalytic system for the coupling of aryl chlorides with primary, secondary, as well as previously challenging tertiary alkyl thiols using an air-stable nickel(II) precatayst in combination with the low-cost base potassium acetate at room temperature. This new catalytic system tolerates a variety of functional groups and enables the generation of thioethers for a wide range of substrates, including pharmaceutical compounds in excellent yields. Chemoselec-tive functionalization of disubstituted substrates was demonstrated. Kinetic and NMR-studies, as well as DFT computations support a Ni(0)/Ni(II) catalytic cycle and identify the oxidative addition product as the resting state. Acetate coordination and subsequent acetate facilitated formation of a thiolate complex via internal deprotonation play a key role in the catalytic cycle. | Regina M. Oechsner; J. Philipp Wagner; Ivana Fleischer | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6176a0580c04803d03442c1a/original/acetate-facilitated-nickel-catalyzed-coupling-of-aryl-chlorides-and-alkyl-thiols.pdf |
613a227265db1e3f14b1ab27 | 10.26434/chemrxiv-2021-f6n9j | Adding colour to mass spectra: Charge Determination Analysis (CHARDA) assigns charge state to every ion peak | Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for individual peaks their charge states z, starting from z=1, and colour-coding z in m/z spectra. CHARDA combines the analysis of ion signal decay rates in the time-domain data (transients) in Fourier transform (FT) MS with the interrogation of mass defects of biopolymers. Being applied to individual isotopic peaks in a complex protein tandem (MS/MS) dataset, CHARDA facilitates charge state deconvolution of large ionic species in crowded regions, estimating z even in the absence of isotopic distribution (e.g., for monoisotopic mass spectra). CHARDA is fast, robust and consistent with conventional FT MS and FT MS/MS data acquisition procedures. An effective charge state resolution Rz≥6 is obtained, with potential for further improvements.
| Yaroslav Lyutvinskiy; Konstantin O. Nagornov; Anton N. Kozhinov; Natalia Gasilova; Laure Menin; Zhaowei Meng; Xuepei Zhang; Amir Ata Saei; Yury O. Tsybin; Alexander Makarov; Roman Zubarev | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613a227265db1e3f14b1ab27/original/adding-colour-to-mass-spectra-charge-determination-analysis-charda-assigns-charge-state-to-every-ion-peak.pdf |
631aedb65351a31dd0f420f3 | 10.26434/chemrxiv-2022-q4ck3-v2 | Dissecting transmembrane bicarbonate transport by 1,8-di(thio)amidocarbazoles | Synthetic ionophores able to transport bicarbonate and chloride anions across lipid bilayers are appealing for their wide range of potential biological applications. We have studied the bicarbonate and chloride transport by carbazoles with two amido/thioamido groups using a bicarbonate-sensitive europium(III) probe in liposomes and found a highly remarkable concentration dependence. This can be explained by a combination of two distinct transport mechanisms: HCO3−/Cl− exchange and a combination of unassisted CO2 diffusion and HCl transport, of which the respective contributions were quantified. The compounds studied were found to be highly potent HCl transporters. Based on the mechanistic insights on anion transport, we have tested the antimicrobial activity of these compounds and found good correlation with their ion transport properties and a high activity against Gram-positive bacteria. | Krystyna Maslowska-Jarzyna; Alessio Cataldo; Anna Marszalik; Ilona Ignatikova; Stephen Butler; Radosław Stachowiak; Michał J. Chmielewski; Hennie Valkenier | Biological and Medicinal Chemistry; Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631aedb65351a31dd0f420f3/original/dissecting-transmembrane-bicarbonate-transport-by-1-8-di-thio-amidocarbazoles.pdf |
61a650198029910fbff80a21 | 10.26434/chemrxiv-2021-d77zd | Revisiting the chevrel phase: Impact of dispersion corrections on the properties of Mo6S8 for cathode applications | While the Mo6S8 chevrel phase is frequently used as cathode material in Mg--ion batteries, theoretical studies on this material are comparatively scarce. The particular structure of the Mo6S8 phase, with rather loosely connected cluster entities, points to the important role of dispersion forces in this material. However, so far this aspect has been completely neglected in the discussion of Mo6S8 as cathode material for mono- and multivalent-ion batteries. In this work we therefore have studied the impact of dispersion forces on stability and kinetics of Mo6S8 intercalation compounds. For this purpose, a series of charge carriers (Li, Na, K, Mg, Ca, Zn, Al) has been investigated. Interestingly, dispersion forces are observed to only slightly affect the lattice spacing of the chevrel phase, nevertheless having a significant impact on insertion voltage and in particular on the charge carrier mobility in the material. Moreover, upon varying the charge carriers in the chevrel phase, their diffusion barriers are observed to scale linearly with the ion size, almost independent of the charge of the considered ions. This indicates a rather unique and geometry dominated diffusion mechanism in the chevrel phase. The consequences of these findings for the ion mobility in the chevrel phase will be carefully discussed. | Katharina Helmbrecht; Holger Euchner; Axel Gross | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a650198029910fbff80a21/original/revisiting-the-chevrel-phase-impact-of-dispersion-corrections-on-the-properties-of-mo6s8-for-cathode-applications.pdf |
6439659d08c86922fff8d260 | 10.26434/chemrxiv-2023-thnhv | A step towards correct interpretation of XPS results in metal oxides: a case study aided by first-principles method in ZnO | Metal oxide semiconductors constitute a vast group of materials whose physical properties are greatly affected by native defects. For decades, X-ray photoelectron spectroscopy (XPS) has been widely used in defect analysis. However, correct interpretation of XPS results remains a difficult task. In this work, we present a detailed first-principles study on the core-level shift (CLS) of the most stable and commonly cited crystal imperfections in ZnO, including O and -OH species at surface with different coverages and bulk defects, including O interstitial (Oi), O vacancy in the +2 charge state (Vo2+) and the neutral vacancy (Vo0). The O1s core level spectrum is simulated and compared with experiments, to understand the correlation between specific local structures and features in the O1s spectrum. In particular, our results indicate that the widely adopted assignment in the defect analysis of ZnO, which links the defect peak in XPS to Vo, the most stable defect, is very likely a misinterpretation. Theoretical analysis indicates that there are no distinguishable XPS features arising from the Vo defect. Furthermore, we show that the commonly observed defect-related peak instead arises due to Oi or specific surface configurations. Given the importance of native defects in materials performance, misinterpretation of XPS results may lead to erroneous conclusions regarding materials properties. This work provides a first-principles basis for the analysis of oxides defects through XPS. | Jin Li; Michael Nolan; Christophe Detavernier | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6439659d08c86922fff8d260/original/a-step-towards-correct-interpretation-of-xps-results-in-metal-oxides-a-case-study-aided-by-first-principles-method-in-zn-o.pdf |
621853da011b5866dab38def | 10.26434/chemrxiv-2021-bsk4b-v2 | The Anomalies and Local Structure of Liquid Water from Boiling to the Supercooled Regime as Predicted by the Many-Body MB-pol Model | For the last 50 years, researchers have sought molecular models that can accurately reproduce water’s microscopic structure and thermophysical properties across broad ranges of its complex phase diagram. Herein, molecular dynamics simulations with the many-body MB-pol model are performed to monitor the thermodynamic response functions and local structure of liquid water from the boiling point down to deeply supercooled temperatures at ambient pressure. The isothermal compressibility and isobaric heat capacity show maxima near 223 K, in excellent agreement with recent experiments, and the liquid density exhibits a minimum at ~208 K. A local tetrahedral arrangement, where each water molecule accepts and donates two hydrogen bonds, is found to be the most probable hydrogen-bonding topology at all temperatures. This work suggests that MB-pol may provide predictive capability for studies of liquid wa- ter’s physical properties across broad ranges of thermodynamic states, including the so-called water’s “no man’s land” which is difficult to probe experimentally.
| Thomas E. Gartner III; Kelly M. Hunter; Eleftherios Lambros; Alessandro Caruso; Marc Riera; Gregory R. Medders; Athanassios Z. Panagiotopoulos; Pablo G. Debenedetti; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621853da011b5866dab38def/original/the-anomalies-and-local-structure-of-liquid-water-from-boiling-to-the-supercooled-regime-as-predicted-by-the-many-body-mb-pol-model.pdf |
60c74a519abda27ff7f8ce0a | 10.26434/chemrxiv.12176865.v1 | Behavior of Volatile Compounds in Membrane Distillation: The Case of Carboxylic Acids | <p>
</p><p>Thanks to
its unique features, membrane distillation (MD) has been particularly applied
for desalination but also for niches applications with feed solutions
containing a mixture of volatile molecules. For such solutions, the complex
interplay of the solutes and solvent physicochemical and operating parameters
makes it challenging to predict the separation efficiency by MD. There is thus
a need for a better understanding of the behavior of volatile compounds in MD
as well as the influence of their physicochemical environment. This study aimed
at investigating the influence of different operating parameters on rejection
efficiency of air-gap MD towards carboxylic acids (formic, acetic and succinic
acids). Acid rejection was found to be highly dependent on the carboxylic acid
structure. In addition, it increased with the acid concentration, which could
be related to the formation of acid dimers in the feed solution. This behavior
is opposite to what is classically observed for pressure-driven membrane
processes thus suggesting that MD can be a suitable alternative to these
techniques for the concentration/separation of carboxylic acids. On the other
hand, acid rejection decreased with the increase of feed temperature which
could be explained by the calculation of the apparent energies of activation of
both the water and carboxylic acids using an Arrhenius-type model. Finally, the
acid dissociation rate played a key role in the acid rejection. Taking
advantage of this observation, it was demonstrated how a simple pH adjustment
can be used to successfully achieve the selective separation of ethanol
(compared to acetic acid) from an acetic acid/ethanol aqueous mixture (typical
case of the extraction of bioethanol from a fermentation broth).</p>
<p></p> | Abdelaziz Khiter; Béatrice Balannec; Anthony Szymczyk; Omar Arous; Noureddine Nasrallah; Patrick LOULERGUE | Transport Phenomena (Chem. Eng.); Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a519abda27ff7f8ce0a/original/behavior-of-volatile-compounds-in-membrane-distillation-the-case-of-carboxylic-acids.pdf |
65dfa68466c1381729ca0cc4 | 10.26434/chemrxiv-2024-8cmgq | FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation | Developing production quality CHARMM force-field (FF) parameters is a very detailed process involving a variety of calculations many of which are specific for the molecule of interest. The first version of FFParam was developed as a standalone python package designed for optimization of electrostatic and bonded parameters of the CHARMM additive and polarizable Drude FFs using quantum mechanical (QM) target data. The new version of FFParam has multiple new capabilities for FF parameter optimization and validation, with emphasis on the ability to use condensed phase target data in the optimization. FFParam-v2 allows optimization of Lennard-Jones (LJ) parameters using potential energy scans of interactions between selected atoms in a molecule and noble gases viz. He, Ne and through condensed phase calculations from which experimental observables such as heats of vaporization and free energies of solvation may be obtained. This functionality serves as a gold-standard for both optimizing parameters and validating the performance of the final parameters. A new bonded parameter optimization algorithm has been introduced to account for simultaneously optimizing multiple molecules sharing parameters. FFParam-v2 also supports comparison of normal modes and the percent contribution of internal coordinates towards each normal mode obtained from QM and molecular mechanics calculations. Such comparison capability is vital to validate the balance amongst various bonded parameters that contribute to the complex normal modes of molecules. User interaction has been extended beyond the original graphical user interface (GUI), to include command line interface capabilities that allows for integration of FFParam in workflows thereby facilitating automation of parameter optimization. With these new functionalities, FFParam is a more comprehensive parameter optimization tool for both beginner and advanced users. | Anmol Kumar; Alexander D. MacKerell Jr. | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dfa68466c1381729ca0cc4/original/ff-param-v2-0-a-comprehensive-tool-for-charmm-additive-and-drude-polarizable-force-field-parameter-optimization-and-validation.pdf |
60c756c6f96a00bff5288b68 | 10.26434/chemrxiv.14320907.v1 | Img2Mol - Accurate SMILES Recognition from Molecular Graphical Depictions | <p>Automatic recognition of the molecular content of a molecule’s graphical depiction is an extremely challenging problem that remains largely unsolved despite decades of research. Recent advances in neural machine translation enable the auto-encoding of molecular structures in a continuous vector space of fixed size (latent representation) with low reconstruction errors. In this paper, we present a fast and accurate model combining a deep convolutional neural network learning from molecule depictions and a pre-trained decoder that translates the latent representation into the SMILES representation of the molecules. This combination allows to precisely infer a molecular structure from an image. Our rigorous evaluation show that Img2Mol is able to correctly translate up to 88% of the molecular depictions into their SMILES representation. A pretrained version of Img2Mol is made publicly available on GitHub for non-commercial users.</p> | Djork-Arné Clevert; Tuan Le; Robin Winter; Floriane Montanari | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756c6f96a00bff5288b68/original/img2mol-accurate-smiles-recognition-from-molecular-graphical-depictions.pdf |
62ceb38d4689332fca5570e0 | 10.26434/chemrxiv-2022-npnrs | Biodegradable Polymer Nanocomposites: A Review of Properties | Biodegradable polymers exhibit shortcomings, including low thermal stability and electrical conductivity. These challenges limit the broad applications of several applications, such as electronic devices. They show suitable dielectric, thermal, and electrical conductivity compared to the biodegradable polymer alone. Several methods can improve biodegradable polymers' dielectric, thermal, and electric conductivity, including co-polymerization, blending, and cross-linking with other polymers. Furthermore, the formation of nanocomposites seems to be the most effective method to improve the properties and performance of biodegradable polymers. This book chapter summarized biodegradable polymers' dielectric, thermal, and electrical conductivity. Biodegradable polymers nanocomposites consisting of polymers blend, inorganic, and other nanomaterials were discussed. | Hani Nasser Abdelhamid | Materials Science | CC BY 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ceb38d4689332fca5570e0/original/biodegradable-polymer-nanocomposites-a-review-of-properties.pdf |
64649714f2112b41e9b2957e | 10.26434/chemrxiv-2023-j5kkt | Data-Driven Tailoring of Molecular Dipole Polarizability and Frontier Orbital Energies in Chemical Compound Space | Understanding correlations - or lack thereof - between molecular properties is crucial for enabling fast and accurate molecular design strategies. In this contribution, we explore the relation between two key quantities describing the electronic structure and chemical properties of molecular systems: the energy gap between the frontier orbitals and the dipole polarizability. Based on the recently introduced QM7-X dataset, augmented with accurate molecular polarizability calculations as well as analysis of functional group compositions, we show that polarizability and HOMO-LUMO gap are uncorrelated when considering sufficiently extended subsets of the chemical compound space. The relation between these two properties is further analyzed on specific examples of molecules with similar composition as well as homooligomers. Remarkably, the freedom brought by the lack of correlation between molecular polarizability and HOMO-LUMO gap enables the design of novel materials, as we demonstrate on the example of organic photodetector candidates. | Szabolcs Góger; Leonardo Medrano Sandonas; Carolin Müller; Alexandre Tkatchenko | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64649714f2112b41e9b2957e/original/data-driven-tailoring-of-molecular-dipole-polarizability-and-frontier-orbital-energies-in-chemical-compound-space.pdf |
60e21312e7f2bf5f7f8196a3 | 10.26434/chemrxiv-2021-mlbwv | JigCell: A New Environment to Simulate the Dynamics of Memory Formation
| Since their initial discovery, long-term potentiation (LTP), and long-term depression (LTD) are accepted as the main biomolecular mechanism that controls memory acquisition. In doing this, both mechanisms are fairly complex and involve specific triggers and many cascades reactions that cross-talk and communicate with others. Thus, they are very complex. To reveal how these mechanisms operate and instruct the brain to remember and forget, one judicious approach is developing the mathematical models of processes. However, this notion requires some basic knowledge regarding ordinary differential equations and writing codes. To this respect, it can be postulated that tools, which can be utilized rather by everyone, would certainly expedite and facilitate the formulation of such models. With this rationale in mind, we demonstrate that JigCell offers the perfect platform to develop such models of LTP. Our choice for this tool stems from the fact that it is designed to simulate complex biological systems in a modular way. Thus, this manuscript is crafted to illustrate how this model was constructed in the JigCell environment and to give an idea of how this tool works. | Onur Alpturk | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e21312e7f2bf5f7f8196a3/original/jig-cell-a-new-environment-to-simulate-the-dynamics-of-memory-formation.pdf |
648c963bbe16ad5c57073b27 | 10.26434/chemrxiv-2023-nw1hs | Combined Imaging and Chromatic Confocal Microscopy Technique to Characterize Size and Shape of Ensembles of Cuboidal Particles | The presence of needle- and plate-like particles has detrimental consequences on their downstream processing in the fine chemicals sector. Therefore, the ability to accurately characterize the particle size and shape of the powder is essential to quantify and predict their impact on the product processability. Nonetheless, tools able to characterize the size and -- most importantly -- the shape, of ensembles of cuboidal crystals are seldom available. Thus, the overarching goal of this work is to provide a fast and accurate offline size and shape characterization tool. To this aim, we have designed and experimentally validated a combined imaging and chromatic confocal microscopy technique. We propose two modes of operation: one that facilitates the 3D reconstruction of particles at the expense of characterization time; and the other that facilitates rapid characterization without the need to 3D reconstruct the particles. We evaluate and validate the performance of our technique, using a commercial technique as a reference, by characterizing particles that exhibit differences in size and shape characteristics and optical properties. We show that our technique can be used to accurately obtain three characteristic lengths (length, width, and thickness) for thousands of particles, making it a valuable addition to existing process analytical technology. | Petros Neoptolemou; Thomas Vetter; Aurora Cruz-Cabeza; Ashwin Kumar Rajagopalan | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Pharmaceutical Industry; Quality Control | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648c963bbe16ad5c57073b27/original/combined-imaging-and-chromatic-confocal-microscopy-technique-to-characterize-size-and-shape-of-ensembles-of-cuboidal-particles.pdf |
6721dd695a82cea2fa4d4662 | 10.26434/chemrxiv-2024-g2p6z | Quantum Spin Sensor for Open-shell Molecules | Zig-zag graphene nanoribbons (ZGNRs) exhibit symmetric spin distributions on their edges, making them susceptible to perturbations due to molecular adsorption. This study investigates the impact of adsorption of closed-shell (e.g. N2, CO, CO2) and open-shell paramagnetic (e.g. O2, NO, NO2) molecules on the spin-polarized quantum transport properties of zig-zag graphene nanoribbons using density functional theory and nonequilibrium Green’s function (NEGF-DFT) methods. We found that closed-shell molecules physisorbed on graphene nanoribbons, while open-shell molecules chemisorbed strongly at the edges. This chemisorption disrupts the symmetric spin distribution, leading to spin-polarized transmission. The underlying mechanism for spin-polarized transmission in open-shell molecule adsorbed cases is quantum interference between the localized states of the molecule and the delocalized states of the graphene nanoribbons. The bond current, the current between a pair of two atoms, analysis shows that physisorbed closed-shell molecules act as a scattering center, which reduces the current through graphene nanoribbons. We showed that the interaction of open-shell molecules with the graphene nanoribbons depends on the electronic properties of adsorbed molecules. Thus a variation in destructive quantum interference pattern is observed for different open-shell molecules resulting in different spin current. This phenomenon can be used for molecular recognition of open-shell paramagnetic species, providing avenue for quantum spin sensors technology. | SHAHJAD ALI; Md. Ehesan Ali | Physical Chemistry; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6721dd695a82cea2fa4d4662/original/quantum-spin-sensor-for-open-shell-molecules.pdf |
668c817d01103d79c56be637 | 10.26434/chemrxiv-2024-hlvjr-v2 | Picosecond MLCT Deactivation in Co(ppy)3 via Jahn‐Teller Distortion | The excited‐state dynamics of fac‐Co(ppy)3, where ppy = 2‐[2‐(pyridyl)phenyl], are measured with femtosecond UV‐Vis transient absorption spectroscopy. The initial state is confirmed with spectroelectrochemistry to have significant metal‐to‐ligand charge transfer (MLCT) character, unlike other Co complexes that generally have ligand‐to‐metal charge transfer or ligand‐field transitions in this energy range. Ground‐state recovery occurs in 8.65 ps in dichloromethane. Density functional theory (DFT) calculations show that the MLCT state undergoes Jahn‐Teller distortion and converts to a 5‐ coordinate 3MC state in which one Co‐N bond is broken. The results highlights a potential pitfall of heteroleptic‐bidentate ligands when designing strong‐field ligands for transition metal chromophores. | Justin Malme; Jenelle Weaver; Gregory Girolami; Josh Vura-Weis | Physical Chemistry; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c817d01103d79c56be637/original/picosecond-mlct-deactivation-in-co-ppy-3-via-jahn-teller-distortion.pdf |
60c73f5c469df461aaf42a79 | 10.26434/chemrxiv.7326491.v1 | A Full Additive QM/MM Scheme for the Computation of Molecular Crystals with Extension to Many-Body Expansions | An additive quantum mechanics/molecular mechanics (QM/MM) model for the theoretical investigation of molecular crystals (AC-QM/MM) is presented. At the one-body level, a single molecule is chosen as the QM region. The MM region around it consists of a finite cluster of explicit MM atoms, represented by point charges and Lennard-Jones potentials, with additional background charges to mimic periodic electrostatics. Cluster charges are QM-derived and calculated self-consistently to ensure a polarizable embedding. We have also considered the extension to many-body QM corrections, calculating the interactions of a central molecule to neighbouring units in the crystal. Full gradient expressions have been derived, also including symmetry information. The scheme allows for the calculation of molecular properties as well as unconstrained optimisations of the molecular geometry and cell parameters with respect to the lattice energy. Benchmarking the approach with the X23 reference set confirms the convergence pattern of the many-body extension, although comparison to plane wave DFT reveals a systematic overestimation of cohesive energies by 6-16 kJ·mol<sup>−1</sup> . While the scheme primarily aims to provide an inexpensive and flexible way to model a molecule in a crystal environment, it can also be used to reach highly accurate cohesive energies by the straightforward application of wave function correlated approaches. Calculations with local coupled cluster with singles, doubles, and perturbative triples, albeit limited to numerical gradients, show an impressive agreement with experimental estimates for small molecular crystals.<br /><br /> | Thorsten Teuteberg; Marco Eckhoff; Ricardo A. Mata | Computational Chemistry and Modeling; Theory - Computational; Quantum Computing | CC BY 4.0 | CHEMRXIV | 2018-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5c469df461aaf42a79/original/a-full-additive-qm-mm-scheme-for-the-computation-of-molecular-crystals-with-extension-to-many-body-expansions.pdf |
60c754f50f50db7a3d397df6 | 10.26434/chemrxiv.13917179.v1 | An Ultrafast and Flexible LC-MS/MS System Paves the Way for Machine Learning Driven Sample Processing and Data Evaluation in Early Drug Discovery | Rationale: Low speed and flexibility of most LC-MS/MS approaches in early drug discovery
delays sample analysis from routine in vivo studies within the same day of measurements. A highthroughput platform for the rapid quantification of drug compounds in various in vivo assays was
developed and established in routine bioanalysis.
Methods: Automated selection of an efficient and adequate LC method was realized by
autonomous sample qualification for ultrafast batch gradients (9 s/sample) or for fast linear
gradients (45 s/sample) if samples require chromatography. The hardware and software
components of our Rapid and Integrated Analysis System (RIAS) were streamlined for increased
analytical throughput via state-of-the-art automation while keeping high analytical quality.
Results: Online decision-making was based on a quick assay suitability test (AST) based on a
small and dedicated sample set evaluated by two different strategies. 84% of the acquired data
points were within ±30% accuracy and 93% of the deviations between the lower limit of
quantitation (LLOQ) values were ≤2-fold compared to standard LC-MS/MS systems while speed,
flexibility and overall automation was significantly improved.
Conclusions: The developed platform provided an analysis time of only 10 min (batch-mode) and
50 min (gradient-mode) per standard pharmacokinetic (PK) study (62 injections). Automation,
data evaluation and results handling were optimized to pave the way for machine learning based
decision-making regarding the evaluation strategy of the AST | Tim Häbe; Christian Späth; Steffen Schrade; Wolfgang Jörg; Roderich Süssmuth; Daniel Bischoff; Andreas Luippold | Analytical Apparatus; Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f50f50db7a3d397df6/original/an-ultrafast-and-flexible-lc-ms-ms-system-paves-the-way-for-machine-learning-driven-sample-processing-and-data-evaluation-in-early-drug-discovery.pdf |
648a6129be16ad5c57f0cee0 | 10.26434/chemrxiv-2023-rkm7t | Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host--guest challenge | As part of the SAMPL9 community-wide blind host--guest challenge, we implemented an expanded ensemble workflow to predict absolute binding free energies for 13 small molecules against pillar[6]arene. Notable features of our protocol include consideration of a variety of protonation and enantiomeric states for both host and guests, optimization of alchemical intermediates, and analysis of free energy estimates and their uncertainty using large numbers of simulation replicates performed using distributed computing. Our predictions of absolute binding free energies resulted in a mean absolute error of 2.29 kcal mol$^{-1}$ and an $\text{R}^{2}$ of 0.54. Overall, results show that expanded ensemble calculations using all-atom molecular dynamics simulations are a valuable and efficient computational tool in predicting absolute binding free energies. | Matthew F. D. Hurley; Robert M. Raddi; Jason G. Pattis; Vincent Voelz | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648a6129be16ad5c57f0cee0/original/expanded-ensemble-predictions-of-absolute-binding-free-energies-in-the-sampl9-host-guest-challenge.pdf |
644155fd83fa35f8f6f6668b | 10.26434/chemrxiv-2023-9n5s0-v2 | Antibody-based Imaging of Bioreductive Prodrug Release in Hypoxia | Regions of hypoxia occur in most tumors and predict for poor patient prognosis. Hypoxia-activated prodrugs provide an ideal strategy to target the aggressive, hypoxic fraction of a tumor while protecting the normal tissue from toxicity. A key challenge associated with the development of novel hypoxia-activated prodrugs, however, is the ability to visualize the delivery of the prodrug to hypoxic regions and determine where it has been activated. Here we report a modified version of the commonly used nitroimidazole bioreductive group that incorporates the fluoroethyl epitope of the antibody-based hypoxia imaging agent, EF5. Attachment of this group to the red fluorescent dye, DCM, enabled us to correlate release of the DCM dye with imaging of the reduced bioreductive group using the EF5 antibody. This study confirmed that the antibody was imaging reduction and fragmentation of the pro-fluorophore. We next employed the modified bioreductive group to synthesize a new prodrug of the KDAC inhibitor Panobinostat, EF5-Pano. Release of EF5-Pano in hypoxic multiple myeloma cells was imaged using the EF5 antibody, and the presence of an imaging signal correlated with apoptosis and a reduction in cell viability. Therefore, EF5-Pano is an imageable hypoxia-activated prodrug with proven cytotoxic effect in multiple myeloma, which could be utilized in future in vivo experiments. | Cagla Tosun; Maxim Mallerman; Antoine Wallabregue; Sarah Phillips; Claire Edwards; Stuart Conway; Ester Hammond | Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644155fd83fa35f8f6f6668b/original/antibody-based-imaging-of-bioreductive-prodrug-release-in-hypoxia.pdf |
626064e4d048ed48ad4b48a5 | 10.26434/chemrxiv-2022-vbtk8 | Hydrogen evolution mitigation in iron-chromium redox flow batteries via electrochemical
purification of the electrolyte | The redox flow battery (RFB) is a promising electrochemical energy storage solution that has seen limited deployment due, in part, to the high capital costs of current offerings. While the search for lower-cost chemistries has led to exciting expansions in available material sets, recent advances in RFB science and engineering may revivify older chemistries with suitable property profiles. One such system is the iron-chromium (Fe-Cr) RFB, which utilizes a low-cost, high-abundance chemistry, but the poor Cr redox reaction kinetics and high hydrogen evolution reaction (HER) rates challenge efficient, long-term operation. Of late, renewed efforts have focused on HER mitigation through materials innovation including electrocatalysts and electrolyte additives. Here, we show electrochemical purification, where soluble contaminants are deposited onto a sacrificial electrode prior to cell operation, can lead to a ca. 5× reduction in capacity fade rates. Leveraging data harvested from prior literature, we identify an association between coulombic efficiency and discharge capacity decay rate, finding that electrochemical purification can enable cell performance equivalent to that with new and potentially-expensive materials. We anticipate this method of mitigating HER may reduce capacity maintenance needs and, in combination with other advances, further durational Fe-Cr RFBs. | Charles Wan; Kara Rodby; Mike Perry; Yet-Ming Chiang; Fikile Brushett | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626064e4d048ed48ad4b48a5/original/hydrogen-evolution-mitigation-in-iron-chromium-redox-flow-batteries-via-electrochemical-purification-of-the-electrolyte.pdf |
673dfb63f9980725cffb30d7 | 10.26434/chemrxiv-2024-s2jgl | Benchmarking of Vibrational Exciton Models Against Quantum-Chemical Localized-Mode Calculations | Vibrational exciton models are widely used for the simulation of biomolecular vibrational spectra, in particular of two-dimensional infrared (2D-IR) spectra. The parameters entering such models, specifically local-mode frequencies and coupling constants, are provided by vibrational maps, which have been parametrized agains computational data for small molecules as well as experimental data. Here, we put forward a novel approach for assessing the quality of these vibrational maps against quantum-chemical reference data. For a test set consisting of molecular dynamics snapshots of polypeptides and small proteins, covering different secondary structure motifs, we we performed full quantum-chemical calculations of harmonic vibrational frequencies and normal modes, and applied a localization of normal modes to obtain localized-mode frequencies and coupling constants. These can be directly compared to those predicted by vibrational maps. We find that while there is a good correlation for the coupling constants and for local-mode frequencies of isolated polypeptides, there is hardly any correlation for the local-mode frequencies of solvated polypeptides. This striking finding calls into question the accuracy of the electrostatic maps that are used to model the effect of the solvent molecules on local-mode frequencies. | Anna M. van Bodegraven; Kevin Focke; Mario Wolter; Christoph Jacob | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673dfb63f9980725cffb30d7/original/benchmarking-of-vibrational-exciton-models-against-quantum-chemical-localized-mode-calculations.pdf |
63b6ea5c1f2403642f174d0f | 10.26434/chemrxiv-2023-6mc4f | Food Thermal Labels are a Source of Dietary Exposure to Bisphenol S and Other Color Developers | To test the hypothesis that migration from the thermal labels on plastic film packaging is a major source of exposure to bisphenols and alternative color developers in food, we analyzed 140 packaging materials from packaged fresh food purchased in North America. No bisphenol A (BPA) was detected in either the packaging samples or thermal labels. However, significant amounts of bisphenol S (BPS) and alternative color developers (up to 214 μg/cm2) were present in thermal labels; their relative occurrence varied among stores. In a controlled experiment, we wrapped fish in film with a thermal label for five days at 4℃. The fish in contact with the label contained BPS (≤ 1140 ng/g wet weight [ww]), 4-hydroxyphenyl 4-isoprooxyphenylsulfone (D-8) (≤ 230 ng/g ww), bis(2-chloroethyl)ether-4,400-dihydroxydiphenyl sulfone monomer (D-90) (≤ 3.41 ng/g ww), and Pergafast-201 (≤ 1.87 ng/g ww). This study provides evidence, for the first time, that BPS and alternative thermal label color developers migrate from packaging materials into food. Further, BPS migration significantly exceeded the European Union Specific Migration Limit (50 ng/g ww), suggesting that further risk assessment studies are warranted. | Ziyun Xu; Lei Tian; Lan Liu; Cindy Gates Goodyer; Barbara Hales; Stephane Bayen | Analytical Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b6ea5c1f2403642f174d0f/original/food-thermal-labels-are-a-source-of-dietary-exposure-to-bisphenol-s-and-other-color-developers.pdf |
6263af30bdc9c2a677dfcd74 | 10.26434/chemrxiv-2022-8s68d | Polyester-Tethered Near-Infrared Fluorophores Confined in Colloidal Nanoparticles: Tunable Excitonic Coupling and Biomedical Applications | Intricate assembly of multiple molecular chromophores assisted by protein scaffolds is essential in tuning the optical absorption and energy transfer in the light-harvesting complexes of the photosynthetic systems in nature. However, it remains a challenge to achieve such structural complexity and functionality in synthetic polymer-chromophore systems. Here we report a series of polyester-tethered pyrrolopyrrole cyanine derivatives and their colloidal nanoparticles dispersed in water, which show tunable J- or H-aggregation excitonic coupling and near-infrared fluorescence by precise control of the polymer chain lengths, composition, and temperature. Moreover, the optimal fluorescence or photothermal effect of the J-aggregates nanoparticles enables broad applications in fluorescence or photoacoustic bioimaging and phototherapy. | Mingfeng Wang; Cangjie Yang; Wei Zhang; Xin Pang; Fan Xiao; Sandeep Kumar Kalva; Yipeng Zhang; Manojit Pramanik; Leilei Tian; Gang Liu | Polymer Science; Nanoscience; Organic Polymers; Polymerization (Polymers); Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6263af30bdc9c2a677dfcd74/original/polyester-tethered-near-infrared-fluorophores-confined-in-colloidal-nanoparticles-tunable-excitonic-coupling-and-biomedical-applications.pdf |
6726fe68f9980725cfec6195 | 10.26434/chemrxiv-2024-gq4tk | Computational Simulations of PROTAC as a BRD4 Inhibitor in Neuroblastoma
| Neuroblastoma (NB) is the most common tumor of nerve tissue and is the most common cancer in babies. The oncogene MYCN gets amplified in the disease, which can be inhibited by targeting the BRD4 protein.[1] PROTAC, a protein degradation tool, is an emerging therapeutic strategy that targets disease-causing proteins.[2] The current research work focuses on two proteins: BRD4 protein and E3 ubiquitin (E3) ligase protein. The BRD4 protein plays an important role in gene regulation and cell functioning, and its malfunction can lead to Neuroblastoma. On the other hand, the E3 protein acts as a cancer suppressor and can inhibit BRD4 protein activity. To destroy the BRD4 protein, the E3 protein should come into proximity to each other. We hypothesize that the aptamers used in this study will bind strongly at the interface between the BRD4 and E3 ligase protein. This is facilitated by a chemical compound known as PROTAC, which binds to both the BRD4 and E3 proteins, bringing them close together to form a BRD4-PROTAC-E3 complex. In the current work, we have used molecular docking to understand the BRD4-PROTAC-E3 interactions, and based on this knowledge, we have designed novel 30 PROTACs and computed their pharmaceutical properties and based on our analysis Aptamer II formed strong interactions with both the proteins. Finding novel PROTACs will aid in computer-aided designing of potent, cost-effective, and less side-effect PROTACs against cancer. | Diya Agarwal; Gaurav Sharma | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6726fe68f9980725cfec6195/original/computational-simulations-of-protac-as-a-brd4-inhibitor-in-neuroblastoma.pdf |
60c75434ee301c0479c7af10 | 10.26434/chemrxiv.13633958.v1 | Strategic Synthesis of ‘Picket Fence’ Porphyrins Based on Nonplanar Macrocycles | Traditional ‘picket fence’ porphyrin systems have been a topic of interest for their capacity to direct steric shielding effects selectively to one side of the macrocycle. Sterically overcrowded porphyrin systems that adopt macrocycle deformations have recently drawn attention for their applications in organocatalysis and sensing. Here we explore the combined benefits of nonplanar porphyrins and the old molecular design to bring new concepts to the playing field. The challenging ortho-positions of meso-phenyl residues dodecasubstituted porphyrin systems led us to transition to less hindered para- and meta-sites and develop selective demethylation based on the steric interplay. Isolation of the symmetrical target compound [2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(3,5-dipivaloyloxyphenyl)porphyrin] was investigated under two synthetic pathways. The obtained insight was used to isolate unsymmetrical [2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetrakis(2-nitro-5-pivaloyloxyphenyl)porphyrin]. Upon separation of the atropisomers, a detailed single-crystal X-ray crystallographic analysis highlighted intrinsic intermolecular interactions. The nonplanarity of these systems in combination with ‘picket fence’ motifs provides an important feature in the design of supramolecular ensembles.<br /> | Karolis Norvaisa; Kathryn Yeow; Brendan Twamley; Marie Roucan; Mathias O.. Senge | Bioorganic Chemistry; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75434ee301c0479c7af10/original/strategic-synthesis-of-picket-fence-porphyrins-based-on-nonplanar-macrocycles.pdf |
6635102c21291e5d1d5c7a2d | 10.26434/chemrxiv-2024-05d56 | Reproducibility of electrochemical measurements with ionic liquids: Is the water content the decisive parameter? | Studying the potential dependent interaction of non-aqueous electrolytes, such as ionic liquids (ILs), with model electrode surfaces plays a crucial role not only in the field of battery-related research. These electrolytes bear the advantage that their electrochemical stability windows often exceed that of water. Comparing results using ILs as electrolytes reported in the literature reveals strong discrepancies in the reproducibility of the data. In this study, we show that parameters such as the supplier, the supplied batch, and the purification steps can have a huge impact on the electrochemical properties. As a reference system, these properties are studied by cyclic voltammetry on a Au(111) single crystal electrode in N-methyl-N-propylpiperidinium bis(trifluoromethane)sulfonimide ([MPPip][TFSI]). Analysing the different features observed in the cyclic voltammograms, we were able to deconvolute (to some extent) the features that are related to the interaction of ILs with the substrate, impurities added from the pre-treatment due to the influence of residual water and oxygen. | Maren-Kathrin Heubach; Fabian M. Schuett; Jerome Mayer; Omar W. Elkhafif; Albert K. Engstfeld; Timo Jacob | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6635102c21291e5d1d5c7a2d/original/reproducibility-of-electrochemical-measurements-with-ionic-liquids-is-the-water-content-the-decisive-parameter.pdf |
617143b545f1ee1d3334e17d | 10.26434/chemrxiv-2021-q6133 | Ligand assisted hydrogenation of levulinic acid on Pt(111) from first principles calculations | In this study, we investigate the hydrogenation reaction of levulinic acid to 4-hydroxypentanovic acidon a ligand-modified Pt(111) using DFT. Modifying nanoparticle surfaces with ligands can havebeneficial effects on the desired reaction such as improved selectivity or lower activation energies.The N3,N3-dimethyl-N2-(quinolin-2-yl)propane-1,2-diamine (AQ) ligand was selected to modify thesurface, since it combines good surface adsorption properties with functional groups that can influencethe reaction. The adsorption geometry of the AQ ligand was studied as well as the co-adsorptionof a second AQ for the possibility of self-assembly. We find that dissociated hydrogen from thePt(111) surface can protonate the AQ ligand and discuss the role this plays on the mechanism ofthe hydrogenation reaction of levulinic acid (LA). By comparing the ligand-modified Pt(111) surfaceto the bare Pt(111) surface we show that the reaction changes from a step-wise to a concertedmechanism due to the influence of the ligand molecule. This demonstrates the effect ligand-modifiedsurfaces can have in catalyzing reactions and shows that desired reactions can be achieved by tuningthe reaction environment. | Lars Gell; Karoliina Honkala | Theoretical and Computational Chemistry; Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617143b545f1ee1d3334e17d/original/ligand-assisted-hydrogenation-of-levulinic-acid-on-pt-111-from-first-principles-calculations.pdf |
679956dbfa469535b939679c | 10.26434/chemrxiv-2025-hmhvn | Predator-prey behavior of droplets propelling through self-generated channels in crystalline surfactant layers. | Motile droplets provide an attractive platform for liquid matter-based applications and protocell analogues displaying life-like features. The functionality of collectively operating droplets increases by the advance of well-designed (physico)chemical systems directing droplet-droplet interactions. Here, we report a strategy based on crystalline surfactant layers at air/water interfaces, which sustain the propulsion of floating droplets and at the same time shape the paths for other droplets attracted by them. First, we show how decylamine forms a closed, crystalline layer that remains at the air/water interface. Second, we demonstrate how aldehyde-based oil droplets react to decylamine in the crystalline layer by forming an imine, causing the droplets to move through the layer while leaving behind an open channel (comparable to “Pacman”). Third, we introduce tri(ethylene glycol) monododecylether (C12E3) droplets in the crystalline layer. Whereas the crystalline layer suppresses the motion of the C12E3 droplets, the aldehyde droplets create surface tension gradients upon depletion of surfactants from the air/water interface, thereby driving Marangoni flows that attract the C12E3 droplets as well as the myelin filaments they grow: Causing the C12E3 droplets to chase, and ultimately catch, the aldehyde droplets along the channels they have created, featuring a predator-prey analogy established at an air/water interface. | Priyanshu Singh; Peter A. Korevaar | Physical Chemistry; Interfaces; Self-Assembly; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679956dbfa469535b939679c/original/predator-prey-behavior-of-droplets-propelling-through-self-generated-channels-in-crystalline-surfactant-layers.pdf |
62459801739db107551f3e08 | 10.26434/chemrxiv-2022-mstv5 | Benzylic fluorination induced by N–F bond activation of Selectfluor® with a solvent-dependent selectivity switch | We present a divergent radical strategy for the fluorination of phenylacetic acid derivatives through N–F bond activation of Selectfluor® with 4-(dimethylamino)pyridine. Comprehensive reaction investigation revealed the critical role of reaction media on selectivity. In presence of water, decarboxylative fluorination through a single electron oxidation is dominant. Non-aqueous conditions result in the clean formation of α-fluoro-α-arylcarboxylic acids through hydrogen atom transfer. | Amiera Madani; Lucia Anghileri; Matthias Heydenreich; Heiko M. Möller; Bartholomäus Pieber | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62459801739db107551f3e08/original/benzylic-fluorination-induced-by-n-f-bond-activation-of-selectfluor-with-a-solvent-dependent-selectivity-switch.pdf |
6295c110e2ef7a0097f27687 | 10.26434/chemrxiv-2022-f2lsd | Light-Driven Ecological-Evolutionary Dynamics in a Synthetic Replicator System | Natural selection is the cornerstone of Darwinian evolution and acts on reproducing entities exhibiting variations that can be inherited and selected for based on, among others, interactions with the environment. Conversely, the replicating entities can also affect their environment generating a two-way feedback on evolutionary dynamics. The onset of such ecological-evolutionary dynamics marks a stepping stone in the transition from chemistry to biology. Yet the bottom-up creation of a molecular system that exhibits ecological-evolutionary dynamics has remained elusive. Here, we describe the onset of such dynamics in a minimal system containing two synthetic self-replicators. The replicators are capable of binding and activating a cofactor, enabling them to change the oxidation state of their environment through photoredox catalysis. The replicator distribution adapts to this change and, depending on light intensity, one or the other replicator prevails. In both cases the replicator distribution evolves towards higher dynamic kinetic stability, rooted in a faster replication rate under the specific environmental conditions. This study opens the world of chemistry to evolutionary dynamics that has until now been restricted to biology. | Kai Liu; Alex W. P. Blokhuis; Chris van Ewijk; Armin Kiani; Juntian Wu; Wouter H. Roos; Sijbren Otto | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6295c110e2ef7a0097f27687/original/light-driven-ecological-evolutionary-dynamics-in-a-synthetic-replicator-system.pdf |
60c74de1842e652458db3532 | 10.26434/chemrxiv.12640760.v1 | Vibrational Couplings and Energy Transfer Pathways of Water’s Bending Mode | <p>Coupling between vibrational modes is essential for
energy transfer and dissipation in condensed matter. For water, different O-H
stretch modes are known to be very strongly coupled both within and between
water molecules, leading to ultrafast dissipation and delocalization of
vibrational energy. In contrast, the information on the vibrational coupling of
the H-O-H bending mode of water is lacking, even though the bending mode is an
essential intermediate for the energy relaxation pathway from the stretch mode
to the heat bath. By combining static and femtosecond infrared, Raman, and hyper-Raman
spectroscopy with<i> ab initio </i>molecular
dynamics simulations, we find the vibrational coupling of the bending mode
differs significantly from the stretch mode: the intramode intermolecular
coupling of the bending mode is very weak, in stark contrast to the stretch
mode. Our results elucidate the vibrational energy transfer pathways of water.
Specifically, the librational motion is essential for the vibrational energy
relaxation and orientational dynamics of H-O-H bending mode.</p> | Chun-Chieh Yu; Kuo-Yang Chiang; Masanari Okuno; Takakazu Seki; Tatsuhiko Ohto; Xiaoqing Yu; Vitaly Korepanov; Hiro-o Hamaguchi; Mischa Bonn; Johannes Hunger; Yuki Nagata | Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de1842e652458db3532/original/vibrational-couplings-and-energy-transfer-pathways-of-water-s-bending-mode.pdf |
60c74e6df96a006a2c287af8 | 10.26434/chemrxiv.12753539.v1 | In Silico Study on Spice-Derived Antiviral Phytochemicals Against SARS-CoV-2 TMPRSS2 Target | We predicted the structure of TMPRSS2 (transmembrane protease serine 2), a host protein that truncates spike protein of SARS-CoV-2. Then we docked 18 anti-viral compounds found in Indian spices against the catalytic domain of TMPRSS2. We then performed rigorous molecular simulation dynamics simulation to screen the best natural phytochemical which could act as a potential inhibitor of TMPRSS2 activation. <br /> | Pradeep Kumar Yadav; Amit Jaiswal; Rajiv Kumar Singh | Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e6df96a006a2c287af8/original/in-silico-study-on-spice-derived-antiviral-phytochemicals-against-sars-co-v-2-tmprss2-target.pdf |
635e6609ac45c788bb9e44d7 | 10.26434/chemrxiv-2022-m025c | On accelerating reaction optimization using computational Gibbs energy barriers: A numerical consideration utilizing a computational dataset | Reaction optimization is a time- and resource-consuming step in organic synthesis. Recent advances in chemo- and materials-informatics provide systematic and efficient procedures utilizing tools like Bayesian optimization (BO). This study explores the possibility of reducing the required experiments further utilizing computational Gibbs energy barriers. To thoroughly validate the impact of using computational Gibbs energy barriers in BO-assisted reaction optimization, this study employs a computational Gibbs energy barrier dataset in the literature and performs an extensive numerical investigation virtually regarding the Gibbs energy barriers as experimental reactivity and those with systematic and random noises as computational reactivity. The present numerical investigation shows that even the computational reactivity affected by noises as much as 20 kJ/mol helps reduce the number of required experiments. | Hiroaki Okada; Satoshi Maeda | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635e6609ac45c788bb9e44d7/original/on-accelerating-reaction-optimization-using-computational-gibbs-energy-barriers-a-numerical-consideration-utilizing-a-computational-dataset.pdf |
60c741670f50db17cc395ada | 10.26434/chemrxiv.7797719.v2 | Quantum vs Thermal Effects in Formic Acid Adsorption on (101) TiO2 Anatase Surfaces | <p>Carboxylic acids adsorption on
anatase TiO<sub>2</sub> is a key process in circular economy and
sustainability. Yet, in spite of several decades of investigations, its
intimate working mechanisms still remain elusive. In particular, the behavior
of the acid proton and its localization – either on the molecule or on the
surface – are still open issues. By modeling the adsorption of formic acid on
top of regular (101) anatase TiO<sub>2</sub> surfaces, we found that, in the 0
K limit, the acid proton is shared between a carboxylic oxygen and a surface oxygen.
In this regime, the proton behavior is mainly governed by quantum
delocalization effects in a single potential well. Nonetheless, as temperature
is raised to room conditions, simulations evidenced a rapid “classical”
shuttling of the proton due to the onset of a two-wells free energy profile
separated by a free energy barrier of the order of <i>kT</i>. This picture, supported by the agreement between simulated and
experimental IR spectra, shows that the titania surface acts like a protecting
group for the carboxylic acid functionality. Such a conceptual insight might
help rationalize the chemical processes of carboxylic species on TiO<sub>2</sub>
surfaces.</p><div>
<div>
<div><a></a>
<p> </p>
</div>
</div>
</div> | gloria tabacchi; Ettore Fois; Marco Fabbiani; Lorenzo Mino; Gianmario Martra | Theory - Computational; Interfaces; Quantum Mechanics; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741670f50db17cc395ada/original/quantum-vs-thermal-effects-in-formic-acid-adsorption-on-101-ti-o2-anatase-surfaces.pdf |
67a3bf5f81d2151a024c36cc | 10.26434/chemrxiv-2025-q3mwr | AlphaFold2-RAVE: Protein Ensemble Generation with Physics-Based Sampling | We introduce AlphaFold2-RAVE (af2rave), an open-source Python package that integrates machine learning-based structure prediction with physics-driven sampling to generate alternative protein conformations efficiently. Protein structures are not static but exist as ensembles of conformations, many of which are functionally relevant yet challenging to resolve experimentally. While deep learning models like AlphaFold2 can predict structural ensembles, they lack explicit physical validation. af2rave addresses this limitation by combining reduced multiple sequence alignment (MSA) AlphaFold2 predictions with molecular dynamics (MD) simulations to efficiently explore local conformational space. A feature selection module identifies key structural degrees of freedom, and the State Predictive Information Bottleneck (SPIB) method uncovers the underlying conformational topology, classifying functionally relevant states. Under the Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE) protocol, either unbiased or biased sampling can be performed to further explore the conformation ensembles. We validate af2rave on multiple systems, including E. coli adenosine kinase (ADK) and human DDR1 kinase, successfully identifying distinct functional states with minimal prior biological knowledge. Furthermore, we demonstrate that af2rave achieves conformational sampling efficiency comparable to long unbiased MD simulations on the SARS-CoV-2 spike protein receptor-binding domain while significantly reducing computational cost. The af2rave package provides a streamlined workflow for researchers to generate and analyze alternative protein conformations, offering an accessible tool for drug discovery and structural biology. | Da Teng; Vanessa J. Meraz; Akashnathan Aranganathan; Xinyu Gu; Pratyush Tiwary | Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Biophysics | CC BY 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a3bf5f81d2151a024c36cc/original/alpha-fold2-rave-protein-ensemble-generation-with-physics-based-sampling.pdf |
66183ae091aefa6ce15e0263 | 10.26434/chemrxiv-2024-5b2fn | Determining aluminium co-ordination of kaolinitic clays before and after calcination with electron energy loss spectroscopy | Developing a greater understanding of kaolinite dehydroxylation upon calcination is crucial for several industrial applications, including cements. Aluminium coordination in meta-kaolinite indicates the extent of its dehydroxylation and its potential chemical reactivity, and it is typically determined using 27Al magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. This technique however presents limitations for Fe-rich materials, given the magnetic properties of Fe ions and minerals containing Fe. In this study, the effect of calcination on Al coordination was assessed in a low-Fe clay used as a reference system, and a Fe-rich clay. Al coordination in the low-Fe clay was quantified via 27Al MAS NMR spectra deconvolution, using data collected at 9.4 T and 11.7 T. Energy dispersive X-ray spectroscopy (EDX) maps and electron energy loss spectroscopy (EELS) measurements were carried out in a scanning transmission electron microscope (STEM) on both clays. Al K-edge EEL spectra showed distinguishable 4/5-fold Al and 6-fold Al sites in both clay types. Differences in line-profile indicated a higher proportion of 4/5-fold Al in kaolinite in the Fe-rich clay compared to the low-Fe clay. Conversely, the Fe-rich clay contained a lower proportion of 4/5-fold Al in meta-kaolinite after calcination, relative to the low-Fe clay. These differences are consistent with the greater structural disorder of the meta-kaolinite identified in the Fe-rich clay by X-ray diffraction and the geological origins of both clays. Overall, this study demonstrates the potential of EELS to provide information about Al coordination for individual kaolinite and meta-kaolinite particles. | Alastair Marsh; Andy Brown; Helen Freeman; Brant Walkley; Helen Pendlowski; Susan Bernal | Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Minerals; Spectroscopy (Inorg.); Natural Resource Recovery; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66183ae091aefa6ce15e0263/original/determining-aluminium-co-ordination-of-kaolinitic-clays-before-and-after-calcination-with-electron-energy-loss-spectroscopy.pdf |
61543a4346030a5552c1d3f5 | 10.26434/chemrxiv-2021-hljbh | Sustainable nitrate production out of thin air:
The photocatalytic oxidation of molecular nitrogen | Novel processes for the sustainable production of fertilizers are highly sought after to combat climate change. Herein, we demonstrate that by irradiating with strong UVA-light, TiO2 is able to photocatalytically oxidize molecular nitrogen in the gas phase under ambient conditions to NOx and nitrate. The reaction produces predominantly nitrogen dioxide with a high selectivity of up to 93% which could be captured afterwards to produce nitric acid or nitrates and used as sustainable (solar) fertilizer. | Aneta Pashkova; Bastien Burek; Jonathan Bloh | Catalysis; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61543a4346030a5552c1d3f5/original/sustainable-nitrate-production-out-of-thin-air-the-photocatalytic-oxidation-of-molecular-nitrogen.pdf |
60c756664c8919558ead483c | 10.26434/chemrxiv.14178212.v2 | High Throughput in Silico Identification of Novel Phytochemical Inhibitors for the Master Regulator of Inflammation (TNFα) | <p><a>The over expression of Tumor
necrosis factor-α (TNFα) has been implicated in a variety of disease and is
classified as a therapeutic target for inflammatory diseases (Crohn disease,
psoriasis, psoriatic arthritis, rheumatoid arthritis).Commercially available
therapeutics are biologics which are associated with several risks and
limitations. Small molecule inhibitors and natural compounds (saponins) were
identified by researchers as lead molecules against TNFα, however, </a>they
were often associated with high IC50 values which can lead to their failure in clinical trials. This
warrants research related to identification of better small molecule inhibitors
by screening of large compound libraries. Recent developments have demonstrated
power of natural compounds as safe therapeutics, hence, in this work, we have
identified TNFα phytochemical inhibitors using high throughput <i>in silico </i>screening approaches of 6000
phytochemicals followed by 200 ns molecular dynamics simulations and relative binding
free energy calculations. The work yielded potent hits that bind to TNFα at its
dimer interface. The mechanism targeted was inhibition of oligomerization of TNFα
upon phytochemical binding to restrict its interaction with TNF-R1 receptor. MD
simulation analysis resulted in identification of two phytochemicals that showed
stable protein-ligand conformations over time. The two compounds were
triterpenoids: Momordicilin and Nimbolin A with relative binding energy-
calculated by MM/PBSA to be -190.5 kJ/Mol and -188.03 kJ/Mol respectively. Therefore,
through this work it is being suggested that these phytochemicals can be used
for further <i>in vitro</i> analysis to confirm their inhibitory action against
TNFα or can be used as scaffolds to arrive at better drug candidates.</p> | Pratap Kumar Parida; Dipak Paul; Debamitra Chakravorty | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756664c8919558ead483c/original/high-throughput-in-silico-identification-of-novel-phytochemical-inhibitors-for-the-master-regulator-of-inflammation-tnf.pdf |
61f8b9da360c842812b1d6c2 | 10.26434/chemrxiv-2022-z4wg2 | (CAAC)Copper Catalysis Enables Regioselective Three-Component Carboboration of Terminal Alkynes | Cyclic(alkyl)(amino)carbene (CAAC) ligands are found to perturb regioselectivity of the copper-catalyzed carboboration of terminal alkynes, favoring the less commonly observed internal alkenylboron regiosomer through an α-selective borylcupration step. A variety of carbon electrophiles participate in the reaction, including allyl alcohols derivatives and alkyl halides. The method provides a straightforward and selective route to versatile tri-substituted alkenylboron compounds that are otherwise challenging to access. | Yang Gao; Nana Kim; Sima Yazdani; Mingyu Liu; Aaron Kendrick; Douglas Grotjahn; Guy Bertrand; Rodolphe Jazzar; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f8b9da360c842812b1d6c2/original/caac-copper-catalysis-enables-regioselective-three-component-carboboration-of-terminal-alkynes.pdf |
64f0c61479853bbd78cfc30a | 10.26434/chemrxiv-2023-gxf3q | Electrochemical sulfate production from sulfide-containing wastewaters and integration with electrochemical nitrogen recovery | Electrochemical methods can help manage sulfide in wastewater, which poses environmental and health concerns due to its toxic, odorous, and corrosive nature. Yet, as a crucial element for agriculture and chemical manufacturing processes, sulfur could be recovered as fertilizer and commodity chemicals from sulfide-containing wastewaters. Wastewater characteristics vary widely and even within one type of wastewater over time; however, it remains unclear how these characteristics affect electrochemical sulfate production. In this study, we evaluated how four characteristics of influent wastewaters (electrolyte pH, composition, sulfide concentration, and buffer strength) affect sulfide removal metrics (sulfide removal rate, sulfide removal efficiency) and sulfate production metrics (sulfate production rate, sulfate production selectivity). We identified that electrolyte pH (3x differences in sulfide removal rate within the studied pH range) and sulfide concentration (16x difference in removal rate) were the most influential factors for electrochemical sulfide removal. Sulfate production was most sensitive to buffer strength (6x difference in sulfate production rate) and insensitive to electrolyte composition. Together, these results provide recommendations for the design of wastewater treatment trains and the feasibility of applying electrochemical methods to varying sulfide-containing wastewaters. In addition, we investigated a simultaneous multi-nutrient recovery (i.e., sulfur and nitrogen) process that leverages electrochemical stripping to further enhance the versatility and compatibility of electrochemical nutrient recovery methods. | Xiaohan Shao; Yixuan Huang; Robert Wood; William Tarpeh | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0c61479853bbd78cfc30a/original/electrochemical-sulfate-production-from-sulfide-containing-wastewaters-and-integration-with-electrochemical-nitrogen-recovery.pdf |
67c842cafa469535b90a493e | 10.26434/chemrxiv-2025-fv7hk | Upcycling Waste Polyoxymethylene to Value-added Chemicals Using Reusable Polymeric Acid Catalysts at ppm Levels | Waste polyoxymethylene (POM) plastic was upcycled using m-phenolsuflonic acid-formaldehyde resin, a polymeric heterogeneous catalyst, to afford multiple value-added chemicals, including solvents, insecticides, and pillar[5]arenes using biomass-derived alcohols or water as reactants. The acid catalyst exhibited stable and reliable performance at a 260 mol ppm loading and remained active after five reuse cycles without any loss of catalytic efficiency. The upcycling process was effective even at a 166 mmol (5-gram) scale. Under acid-catalyzed conditions, the POM moiety in carbon-fiber-reinforced polymers (CFRPs; 360 mg-5 g scale) was selectively depolymerized, yielding carbon fibers free of POM residues, as confirmed by solid-state NMR. This process also mitigates environmental concerns by converting microplastics into value-added chemicals. Additionally, microwave irradiation proved more effective (99% upcycling) than conventional heating methods (73%). This upcycling process offers a sustainable approach to plastic waste management, enabling the synthesis of valuable chemicals and materials while reducing environmental pollution. | Abhijit Sen; Yoichi M. A. Yamada | Organic Chemistry; Catalysis; Polymer Science; Organic Polymers; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c842cafa469535b90a493e/original/upcycling-waste-polyoxymethylene-to-value-added-chemicals-using-reusable-polymeric-acid-catalysts-at-ppm-levels.pdf |
60c744fd842e6517efdb2579 | 10.26434/chemrxiv.9945083.v1 | Electrochemical Synthesis of Sulfinic Esters from Alcohols and Thiophenols | Electrochemical oxidative couplings between S–H and O–H bonds are achieved herein directly from readily-available alcohols and thiophenols, affording a series of diverse sulfinic esters.<br /> | Yang He; Yu Wei; Liang Xu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fd842e6517efdb2579/original/electrochemical-synthesis-of-sulfinic-esters-from-alcohols-and-thiophenols.pdf |
64888025be16ad5c57dfc786 | 10.26434/chemrxiv-2023-vhlgg-v2 | CONFPASS: fast DFT re-optimizations of structures from conformation searches | CONFPASS (Conformer Prioritizations & Analysis for DFT re-optimisations) has been developed to extract dihedral angle descriptors from conformational searching outputs, perform clustering and return a priority list for DFT re-optimisations. Evaluations were conducted with DFT data of the conformers for 150 structurally diverse molecules, most of which are flexible CONFPASS gives a confidence estimate that the global minimum structure has been found, and based on our dataset, we can have 90% confidence after optimizing half of the FF structures. Re-optimizing conformers in order of the FF energy often generates duplicate results; using CONFPASS, the duplication rate is reduced by a factor of two for the first 30% of the re-optimisations, which includes the global minimum structure about 80% of the time. | Ching Ching Lam; Jonathan M. Goodman | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64888025be16ad5c57dfc786/original/confpass-fast-dft-re-optimizations-of-structures-from-conformation-searches.pdf |
60c752ecee301c7eedc7acd5 | 10.26434/chemrxiv.13366274.v1 | Synthesis of Deuterated Surrogate Standards for the Analysis of Legally Regulated Substances in Cosmetics | <p>The presence of harmful substances in cosmetic
products is regulated in most countries. In the European Union the Regulation
(EC) No. 1223/2009 lays down the requirements for the marketing of cosmetic
products. Among others, important families of compounds restricted in the
Regulation are musks, allergenic fragrances and phthalates. To ensure product
safety, improved analytical methods capable of reliably
and reproducibly detecting the presence of traces of prohibited and/or restricted
ingredients in raw materials and finished products are required. </p>
<p>For the continuous improvement of the reliability of the analytical methods
developed to check the compliance of cosmetic products with the Regulation, the
use of appropriate surrogate standards or contaminants (substances that are
added to the samples to be analyzed to establish the recovery and the
reproducibility of the quantification of the analytes) are of utmost
importance. One of the best kinds of
surrogate standards are isotopically labeled analogs of the analytes of
interest. In this work, several synthetic methods have been developed to prepare
isotopically labeled analogs of atranol, chloroatranol, di-n-octylphthalate,
musk xylene, and musk ambrette, which are restricted substances in cosmetic
articles.</p> | Fariña Beatriz; Carlos González; Manuel Lolo; F. Javier Sardina | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752ecee301c7eedc7acd5/original/synthesis-of-deuterated-surrogate-standards-for-the-analysis-of-legally-regulated-substances-in-cosmetics.pdf |
678bdf4e81d2151a02a89cb3 | 10.26434/chemrxiv-2025-484mk-v2 | Process Characterization of Epitaxial SiP [100] and [110] Films | Epitaxial SiP films are necessary to enable semiconductor scaling. One of the key problems arising from highly doped epitaxial growth is the difference in growth rate for different crystal orientations. In this paper, we analyze the impact of different process parameters on the [100] and [110] oriented Si substrates. We characterized the thickness and substitutional doping by using high resolution X-ray diffraction (HRXRD) and reciprocal space maps (RSM). We look at every single independent process variable, i:e temperature, pressure and all the gas flows and characterize how the changes in each variable affects the overall [100]/[110] thickness and doping ratio. We also analyze the chemical kinetics o Si:P deposition on [100] and [110] substrate individually. | Protyush Sahu; Madhana Sunder; Jesse Wensel; Silvia Borsari | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678bdf4e81d2151a02a89cb3/original/process-characterization-of-epitaxial-si-p-100-and-110-films.pdf |
6438035473c6563f14caa401 | 10.26434/chemrxiv-2023-04d1g-v2 | Teaching Old Presumptive Tests New Digital Tricks with Computer Vision for Forensic Applications | Presumptive (or 'spot') tests have served forensic scientists, law enforcement, and legal practitioners for over a hundred years. Yet, the intended design of such tests, enabling quick identification of drugs by-eye, also hides their full potential. Here, we report the development and application of time-resolved imaging methods of reactions attending spot tests for amphetamines, barbiturates, and benzodiazepines. Analysis of the reaction videos helps distinguish drugs within the same structural class that, by-eye, are judged to give the same qualitative spot test result. It is envisaged that application of these results will bridge the existing suite of field and lab-based confirmatory forensic tests, and support a broader range of colorimetric sensing technologies. | Nathalie Bugeja; Cameron Oliver; Nicole McGrath; Jake McGuire; Chunhui Yan; Felicity Carlysle-Davies; Marc Reid | Organic Chemistry; Analytical Chemistry; Organometallic Chemistry; Analytical Apparatus; Imaging; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438035473c6563f14caa401/original/teaching-old-presumptive-tests-new-digital-tricks-with-computer-vision-for-forensic-applications.pdf |
66fcc79e12ff75c3a11ec5a5 | 10.26434/chemrxiv-2024-4drz1-v5 | Mutual Interactions of Silymarin and Colon Microbiota in Healthy Young and Healthy Elder Subjects | Scope
This multi-omic study investigates the bidirectional interactions between gut microbiota and silymarin metabolism, highlighting the differential effects across various age groups. Silymarin, the extract from Silybum marianum (milk thistle), is commonly used for its hepatoprotective effects.
Methods and results
An in vitro fermentation colon model was used with microbiota from 20 stool samples obtained from healthy donors divided into two age groups. A combination of three analytical advanced techniques namely next-generation sequencing, 1H-NMR and LC-MS was used to determine silymarin microbial metabolites over 24 h, overall metabolome and microbiota composition.
Silymarin at a low diet-relevant dose of 50 µg/mL significantly altered gut microbiota metabolism, reducing short-chain fatty acid (acetate, butyrate, propionate) production, glucose utilization, and increasing alpha-diversity. Notably, the study revealed age-related differences in silymarin catabolism. Healthy elderly donors (70–80 years) exhibited a significant increase in a specific catabolite associated with Oscillibacter sp., whereas healthy young donors (12–45 years) showed a faster breakdown of silymarin components, particularly isosilybin B, which was associated with higher abundance of Faecalibacterium and Erysipelotrichaceae UCG-003.
Conclusion
This study provides insights into microbiome functionality in metabolizing dietary flavonolignans, highlighting implications for age-specific nutritional strategies and advancing our understanding of dietary (poly)phenol metabolism. | Katerina Tomisova; Veronika Jarosova; Petr Marsik; Anna Mascellani Bergo; Ondrej Cinek; Lucie Hlinakova; Pavel Kloucek; Vaclav Janousek; Kateřina Valentová; Jaroslav Havlik | Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fcc79e12ff75c3a11ec5a5/original/mutual-interactions-of-silymarin-and-colon-microbiota-in-healthy-young-and-healthy-elder-subjects.pdf |
64d3f2af69bfb8925aa95709 | 10.26434/chemrxiv-2023-9fgdt-v2 | CoPi-modified mesoporous titania photoelectrodes for water splitting: why less is more | Solar technologies have emerged as a clean and sustainable source of energy towards the mitigation of climate change. In the last years, an increasing interest has been devoted to obtaining solar fuels such as hydrogen through photoelectrochemistry. In this framework, titanium dioxide is a sound and promising platform for photoelectrochemical water splitting; however, its performance is limited due to the sluggish oxygen evolution reaction (OER). In this work, a photoactive electrode was developed by combining ordered mesoporous TiO2 thin films with a cobalt oxo-phosphate OER catalyst (CoPi). We conducted a detailed structural and electrochemical characterization of the TiO2-CoPi nanocomposite. We compared the performance of dense and mesoporous TiO2 films on different substrates as photoelectrodes for water splitting. All studied photoelectrodes exhibit high stability, reproducibility and cycling durability, with consistent photocurrent densities. Controlled amounts of CoPi were deposited on this matrix. Low loadings resulted in a 20% increase in photocurrent, whereas higher loadings suppressed the photocurrent due to recombination with the TiO2 matrix or the underlying FTO. In this study, we demonstrate the importance of optimizing the co-catalyst loading based on the interactions between different components in a nanocomposite photoanode, with a focus on understanding the recombination pathways that appear when working with nanostructured semiconductors. | Priscila Vensaus; Lucas Nahuel Mendioroz; Facundo Carlos Herrera; Mark Patrick Kreuzer; Federico Andres Viva ; Galo Juan de Ávila Arturo Soler Illia | Catalysis; Nanoscience; Nanostructured Materials - Nanoscience; Electrocatalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d3f2af69bfb8925aa95709/original/co-pi-modified-mesoporous-titania-photoelectrodes-for-water-splitting-why-less-is-more.pdf |
635aa16b2e0c63ae373eb220 | 10.26434/chemrxiv-2022-xmg75 | Data-centric heterogeneous catalysis: identifying rules and materials genes of alkane selective oxidation | Artificial intelligence (AI) can accelerate materials design by identifying the key parameters correlated with the performance. However, widely used AI methods require big data, and only the smallest part of the available data in
heterogeneous catalysis meets the quality requirement for data-efficient AI. Here, we use rigorous experimental procedures, designed to consistently take into account the kinetics of the catalyst active states formation, in order to measure 55 physicochemical parameters as well as the reactivity of 12 catalysts towards ethane, propane, and n-butane oxidation. These catalyst materials are based on vanadium or manganese redox-active elements (RAEs) and present diverse phase compositions, crystallinities, and catalytic behaviors. By applying the sure-independence-screening-and-sparsifying-operator (SISSO) approach to the consistent data set, we identify nonlinear property-function relationships depending on several key parameters, reflecting the intricate interplay of underlying processes governing selective oxidation. This approach indicates the most relevant characterization techniques and shows how the catalyst properties may be tuned in order to achieve the
desired performance. For example, to achieve high olefin yields, the catalyst must have a high specific surface area, a low concentration of surface RAE, and the ability to change the surface RAE oxidation states under reaction conditions with respect to vacuum. These parameters are measured by N2 adsorption, x-ray photoelectron spectroscopy (XPS), and near-ambient-pressure in situ XPS. They reflect the relevance of local transport, site isolation, surface redox activity, and the materials dynamical restructuring under reaction conditions. Although the relationship describing the even more challenging oxygenate yields shares similarities with that for olefin yields, a parameter reflecting the importance of specific surface sites, derived from the analysis of the carbon 1s XPS spectra, is additionally identified as key for high selectivity to oxygenates. | Lucas Foppa; Frederik Rüther; Michael Geske; Gregor Koch; Frank Girgsdies; Pierre Kube; Spencer Carey; Michael Hävecker; Olaf Timpe; Andrey Tarasov; Matthias Scheffler; Frank Rosowski; Robert Schlögl; Annette Trunschke | Catalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635aa16b2e0c63ae373eb220/original/data-centric-heterogeneous-catalysis-identifying-rules-and-materials-genes-of-alkane-selective-oxidation.pdf |
639a21cc963bf37a33999909 | 10.26434/chemrxiv-2022-k7n1b-v2 | Large interactive touchscreens as an opportunity for synchronous hybrid teaching during COVID-19 pandemic and beyond | The year 2020 will be remembered as the year of COVID-19 and its subsequent lockdowns. The time to return to face-to-face teaching has arrived, but the shadow of the disease still hangs over teachers, students and society. Disruption in teaching can still occur for students, or even teachers, if they are either diagnosed as COVID-19 positive or as a contact case and forced to self-isolate. In order to limit the impact of self-isolation on learning, synchronous hybrid teaching (i.e. teaching face-to-face to students in a classroom and to students online at the same time) was successfully implemented owing to the combination of a videoconference software and a large interactive touchscreen. The setup presented in this paper allows courses to be broadcasted to students at-home (i.e. voice, visual pedagogic support and, more interestingly, indications handwritten by the teacher) as well as simultaneously teaching to students in the classroom face-to-face. It also allows self-isolated teachers to teach tutorials from their home to students in the classroom. This paper focuses on the use of large interactive touchscreens for synchronous hybrid teaching and its evaluation by students using a questionnaire. The key findings of this study are that students prefer synchronous hybrid teaching rather than missing a course and that synchronous hybrid teaching should only be used in case of absolute necessity. | Pierre-Edouard Danjou; Saâd Bouhsina; Sylvain Billet; Francine Cazier-Dennin | Chemical Education; Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639a21cc963bf37a33999909/original/large-interactive-touchscreens-as-an-opportunity-for-synchronous-hybrid-teaching-during-covid-19-pandemic-and-beyond.pdf |
64f192433fdae147fa3efade | 10.26434/chemrxiv-2023-x3rps | Contilisant+Tubastatin A hybrids, as new multi-target-directed polyfunctionalized indole derivatives able to inhibit histone deacetylase/cholinesterase/monoamine oxidase enzymes, and modulate histamine 3/sigma 1/5-HT6/dopamine 3 receptors for the treatment of cancer | Herein we describe the design and synthesis of Contilisant+Tubastatin A hybrids as polyfunctionalized indole derivatives for the treatment of a broad diversity of cancers, such as glioblastoma. The new Contilisant+Tubastatin A hybrids have been designed as a Multi-Target-Directed (MTD) small molecules, able to inhibit HDAC6, cholinesterase and monoamine oxidase enzymes, and modulate histamine 3, sigma 1, 5-HT6, and dopamine 3 receptors. Contilisant+Tubastatin A hybrids have been submitted to biological evaluation in suitable in vitro and vivo glioblastoma models. | José Luis Marco-Contelles; Mireia Toledano-Pinedo; Fernando Romero; Abdelouahid Samadi; Alicia Porro; Pedro Almendros; Isabel I Iriepa; M. Mercedes Rodríguez-Fernández; Francisco López-Muñoz; Aizpea Artetxe-Zurutuza; Ander Matheu | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f192433fdae147fa3efade/original/contilisant-tubastatin-a-hybrids-as-new-multi-target-directed-polyfunctionalized-indole-derivatives-able-to-inhibit-histone-deacetylase-cholinesterase-monoamine-oxidase-enzymes-and-modulate-histamine-3-sigma-1-5-ht6-dopamine-3-receptors-for-the-treatment-.pdf |
60c7426b0f50db3364395cd5 | 10.26434/chemrxiv.8277392.v1 | Total Synthesis of (±)-Illisimonin A, a Neuroprotective Sesquiterpenoid from the Fruits of Illicium simonsii | <p>Illisimonin A was isolated from Illicium simonsii and has a previously unreported tricyclic carbon framework. It displayed neuroprotective effects against oxygen-glucose deprivation-induced cell injury in SH-SY5Y cells. It incorporates a highly strained trans-pentalene ring system. We report the first synthesis of illisimonin A. Notable steps in the route include a 1,3-dioxa-2-silacyclohexenetemplated Diels-Alder cycloaddition and type-3 semipinacol rearrangement to generate the trans-pentalene. The final step is an iron-catalyzed C-H oxidation. The synthetic route is robust, with 94 mg prepared in a single pass.</p> | Alexander S. Burns; Scott Rychnovsky | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426b0f50db3364395cd5/original/total-synthesis-of-illisimonin-a-a-neuroprotective-sesquiterpenoid-from-the-fruits-of-illicium-simonsii.pdf |
65b76b5266c13817297df04d | 10.26434/chemrxiv-2024-f93fr | Water-Soluble Soft Nylons: Novel Class of Soft Matter Exhibiting LCST-type Thermo-Responsiveness | High crystallinity and low solubility are inherent characteristics of polyamides. Research efforts have primarily focused on exploring their bulk properties as fibers, with less emphasis on their solution properties. Herein, we report on the synthesis and properties of soft and soluble N-methylated nylons as a novel class of soft polymer matter. Surprisingly, N-methylated nylons have scarcely been reported and are almost not registered with CAS SciFindern, while their unit structure is very simple. The N-methylation of nylons resulted in softness and high solubility by eliminating hydrogen bonds between polymer backbones and generating two conformers (cis and trans) of the tertiary amide group. Remarkably, some of them exhibit lower critical solution temperature (LCST)-type phase separation in water. By manipulating the carbon number within polymer backbones, we have found that the quantitative hydrophilic/hydrophobic balance for LCST is its unit formula per amide group equal to C6H11NO, which aligns with typical LCST polymers like poly(N-isopropylacrylamide) (PNIPAM). Despite the structural similarity to PNIPAM, polymer scientists have never found LCST-type behavior of N-methylated nylons during over 50 years of soft polymer matter research. The long-standing assumption that polyamides are inherently rigid and cannot exhibit softness and solubility has impeded their application to soft polymer matter. | Akari Sugano; Natsuki Inaba; Keitaro Matsuoka; Kazuki Sada | Polymer Science; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b76b5266c13817297df04d/original/water-soluble-soft-nylons-novel-class-of-soft-matter-exhibiting-lcst-type-thermo-responsiveness.pdf |
60c74e3cbb8c1a04123db704 | 10.26434/chemrxiv.11475300.v4 | Nucleation and Structural Identification in Gold Particles of High Aspect Ratios Developed through Mechanistic Approach | <p>A
structural identification in different geometrical shapes of gold particles is presented
here. Nucleation mechanisms of particles having geometrical shapes are
discussed here, which have never been reported before. Dimensional regularity
of particles in geometrical shapes incites a new insight. At electronically
flat solution surface, different zones have been found dealing with the developing
tiny-shaped particles in less elongation of atoms and more elongation of atoms.
Tiny-shaped particles in less elongation of atoms nucleate particles of one-dimensional
(1D) shapes due to developing in a zone consisting of regions rearward to north-pole
at solution surface. Tiny-shaped particles in more elongation of atoms nucleate
multi-dimensional (MD) shapes due to developing in a zone consisting of
east-west regions at solution surface. To assemble at a common point forming at
the centre of concave meniscus, structures of smooth elements at electronically
decreasing level solution surface experience force in immersing format. A force
exerting in the immersing format is related to the simultaneous actions of four
forces to a structure of smooth element coming to assemble. In addition to the acquired
orientation of an electron and the position of its atom at solution surface, a manner
of energy knot clamping to electron in an atom also varies exertion of force
for it. Particles of geometrical shapes show different structures in 1D and MD shapes.
On identifying structure, a mechanism of photon reversion is disclosed. In the
selected area patterns of particles, printing spots of reverted force in
photons reflected from the laterally orientated electrons of less and more elongated
atoms validates that photons are not carried by the electrons, so it is a
photon reflection instead of an electron diffraction.<br /></p> | Mubarak Ali; I-Nan Lin | Nanostructured Materials - Materials; Microscopy; Nanocatalysis - Catalysts & Materials; Nanodevices; Nanostructured Materials - Nanoscience; Interfaces; Self-Assembly; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3cbb8c1a04123db704/original/nucleation-and-structural-identification-in-gold-particles-of-high-aspect-ratios-developed-through-mechanistic-approach.pdf |
6412c42fdab08ad68f32db80 | 10.26434/chemrxiv-2023-b7ph8 | Additive Manufacturing of Hierarchically Porous Silicon-based Ceramics: 3D Printing Black Glass with Unimodal, Bimodal, and Trimodal Porosity. | Silicon-based ceramics offer unique chemical and mechanical properties, gaining their hierarchically porous structures considerable attention over the years to advance various fields. Hence, a new resin system has been developed to precisely control the size and distribution of pores in silicon-based ceramics while allowing their high-resolution photopolymerisation-based 3D printing. The ability to control pore size and distribution of 3D printed ceramics by simply incorporating one or more of the above-mentioned resin components was explored by 3D printing silicon oxycarbide micro-structures, such as microneedles, with unimodal (micropores), bimodal (micro- and mesopores), and trimodal (micro-, meso-, and macropores) porosity. The resin system allowed precise modulation of pore sizes ranging from 1 nm to 200 nm and their three-dimensional distribution. Their elemental analysis suggested a total carbon content of 24.7% and an empirical formula of SiO2.05C1.06S0.04. The structures were found to be amorphous as per their X-ray diffraction. | Ahmad Norouzi; Brett Paull; Vipul Gupta | Materials Science; Biocompatible Materials; Ceramics; Materials Processing; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6412c42fdab08ad68f32db80/original/additive-manufacturing-of-hierarchically-porous-silicon-based-ceramics-3d-printing-black-glass-with-unimodal-bimodal-and-trimodal-porosity.pdf |
60c75734ee301ccefac7b4cb | 10.26434/chemrxiv.14381378.v1 | Sol-Gel Processing of a Covalent Organic Framework for the Generation of Hierarchically Porous Monolithic Adsorbents | Covalent organic frameworks (COFs) have emerged as a versatile materials platform for applications including chemical separations, water purification, chemical reaction engineering and energy storage. Their inherently low mechanical stability, however, frequently renders existing methods of pelletisation ineffective contributing to pore collapse, pore blockage or insufficient densification of crystallites. Here, we present a general process for the shaping and densifying of COFs into centimetre-scale porous monolithic pellets without the need for templates, additives or binders. This process minimises mechanical damage from shear-induced plastic deformation and further provides a network of interparticle mesopores that we exploit in accessing analyte capacities above those achievable from the intrinsic porosity of the COF framework. Using a lattice-gas model, we accurately capture the monolithic structure across the mesoporous range and tie pore architecture to performance characteristics in both gas storage and separation applications. Collectively, these findings represent a substantial step in the practical applicability of COFs and other mechanically weak porous materials. | Mark Carrington; Nakul Rampal; David G. Madden; Daniel O'Nolan; Nicola Pietro Maria Casati; Giorgio Divitini; Ritums Cepitis; Jesus A. Martin Ilan; Ceren Camur; Joaquin Silvestre-Albero; Felix Zamora; Sergei Taraskin; Karena W. Chapman; David Fairen-Jimenez | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75734ee301ccefac7b4cb/original/sol-gel-processing-of-a-covalent-organic-framework-for-the-generation-of-hierarchically-porous-monolithic-adsorbents.pdf |
667f10de5101a2ffa8d0702e | 10.26434/chemrxiv-2024-zn0hx | A simulation study of the water ordering effect of callose | Callose, a polysaccharide closely related to cellulose, is a minority component of the plant cell wall, playing a crucial role, among others, in plants' development and resistance to environmental stress. These functions are often attributed to the enhancement by callose of the mechanical properties of semi-ordered assemblies of cellulose nanofibres, that represent the majority component of the plant cell wall. A recent study (Gensler, W. {\it Plant Signal. Behav.} {\bf 2019}, {\it 14}, e1548878), however, suggested that the enhancement of mechanical properties by callose might be partly due to its ability to order neighboring water molecules, resulting in the formation, up to room temperature and beyond, of solid-like water-callose domains. This hypothesis is tested by atomistic molecular dynamics simulations, using ad-hoc models consisting of callose and cellulose chains forming networks (gels) in water, spanning a wide range of polysaccharide-water concentrations. The simulation results highlight systematic differences in the coordination and H-bonding of callose and cellulose by water. These structural differences are reflected in the different dynamical properties of water in samples made of callose or cellulose in water, to some extent validating the water-ordering hypothesis. However, mechanical properties, characterised by the computation of the Young's modulus of the polysaccharide / water gels, are nearly the same in the callose/water and in the cellulose/water samples, lending support to the view that callose's ability to link cellulose nanofibres into networks is the main mechanism underlying the strengthening of the plant cell wall. | Robinson Cortes-Huerto; Nancy C. Forero-Martinez; Pietro Ballone | Physical Chemistry; Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Cellulosic materials; Biophysics | CC BY NC 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667f10de5101a2ffa8d0702e/original/a-simulation-study-of-the-water-ordering-effect-of-callose.pdf |
6408d4f9cc600523a3df8c87 | 10.26434/chemrxiv-2023-9678k | Broadening the scope of binding free energy calculations using a Separated Topologies approach | Binding free energy calculations predict the potency of compounds to protein binding sites in a physically rigorous manner and see broad application in prioritizing the synthesis of novel drug candidates. Relative binding free energy calculations (RBFE) have emerged as an industry standard approach to achieve highly accurate rank-order predictions of the potency of related compounds; however, this approach requires that the ligands share a common scaffold and a common binding mode, restricting the methods' domain of applicability. This is a critical limitation, since complex modifications to the ligands, especially core hopping, are very common in drug design. Absolute Binding Free Energy calculations (ABFE) are an alternate method, which can be used for ligands that are not congeneric. However, ABFE suffer from a known problem of long convergence times, due to the need to sample additional degrees of freedom within each system, such as sampling rearrangements necessary to open and close the binding site. Here, we report on an alternative method for RBFE, called Separated Topologies (SepTop), which overcomes the issues in both of the aforementioned methods, by enabling large scaffold changes between ligands with a convergence time comparable to traditional RBFE. Instead of only mutating atoms that vary between two ligands, this approach performs two absolute free energy calculations at the same time in opposite directions, one for each ligand. Defining the two ligands independently allows the comparison of binding of diverse ligands without the artificial constraints of identical poses or a suitable atom-atom mapping. This approach also avoids the need to sample the unbound state of the protein, making it more efficient than absolute binding free energy calculations. Here, we introduce an implementation of SepTop. We developed a general and efficient protocol for running SepTop, and we demonstrated the method on four diverse, pharmaceutically relevant systems. Here we report the performance of the method, as well as our practical insights into strengths, weaknesses, and challenges of applying this method in an industrial drug design setting. We find that the accuracy of the approach is sufficiently high to rank order ligands with an accuracy comparable to traditional RBFE calculations, while maintaining the additional flexibility of SepTop. | Hannah M. Baumann; Eric Dybeck; Christopher Lee McClendon; Frank C. Pickard IV; Vytautas Gapsys; Laura Pérez-Benito; David F. Hahn; Gary Tresadern; Alan M. Mathiowetz; David L. Mobley | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6408d4f9cc600523a3df8c87/original/broadening-the-scope-of-binding-free-energy-calculations-using-a-separated-topologies-approach.pdf |
64e8f5b73fdae147fad3c87f | 10.26434/chemrxiv-2023-z657t | Cooperative Fe Sites on Transition Metal (Oxy)hydroxides for High Oxygen Evolution Activity | Fe-containing transition-metal (oxy)hydroxides are record-activity oxygen-evolution reaction (OER) electrocatalysts in alkaline media and ubiquitously form as the active surface phase across many materials systems. The complexity, heterogeneity, and dynamics of the Fe sites within the (oxy)hydroxide has slowed mechanistic understanding of how and where the Fe-based active sites form—information critical for designing catalysts and electrolytes with higher activity and stability. We show that where Fe species in the electrolyte incorporate into host Ni or Co (oxy)hydroxides depends on the electrochemical history and the structural properties of host material. Substantially less Fe is incorporated from Fe-spiked electrolyte into Ni (oxy)hydroxide at anodic potentials, past the nominally Ni2+/3+ redox wave, compared to during potential cycling. The Fe adsorbed under constant anodic potentials leads to high OER activity which we attribute to under-coordinated “surface” Fe. By systematically controlling the concentration of surface Fe, we discover that the per-Fe OER turn-over frequency (TOF-Fe) increases linearly with the Fe concentration, suggesting a changing OER mechanism with increased Fe concentration. We propose a mechanism involving multiple, cooperative Fe sites in FeOx clusters. The magnitude of TOF-Fe depends on the host material, with new Fe:NiOxHy showing record-high TOF-Fe of ~ 40 s-1 at 350 mV overpotential. | Yingqing Ou; Liam Twight; Bipasa Samanta; Lu Liu; Santu Biswas; Jessica Fehrs; Nicole Sagui; Javier Villalobos; Joaquín Morales-Santelices; Denis Antipin; Marcel Risch; Maytal Caspary Toroker; Shannon Boettcher | Catalysis; Electrocatalysis; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e8f5b73fdae147fad3c87f/original/cooperative-fe-sites-on-transition-metal-oxy-hydroxides-for-high-oxygen-evolution-activity.pdf |
6765b51afa469535b948e1d7 | 10.26434/chemrxiv-2024-n5213 | Sustainable D/L-Lactate Production from Methane and Carbon Dioxide via Acetylenedicarboxylate | Lactic acid (LA), a high-value chemical with extensive applications, is currently produced either from petrochemical sources, which are economically unviable or through fermentation of sugars with laborious pretreatment steps. We present acetylenedicarboxylate (ADCA), obtained from methane and carbon dioxide through commercial processes, as an alternative feedstock for LA production. In this study, we developed both in vitro and in vivo enzymatic routes for converting ADCA to LA employing FumA, MaeB, and LDH. We achieved LA yields of 0.96 mol/mol and 0.61 mol/mol for in vitro and in vivo approaches, respectively. We observed the complete conversion of 25 mM ADCA to lactate within 30 minutes, with 0.1 units of each enzyme. The in vivo approach involved using ALE isolates, strains harboring deletions in dcuC, and a fumA knockout mutant as a plasmid addiction strategy. These findings demonstrate the feasibility of using ADCA as a sustainable feedstock for LA production, offering a promising alternative for the production of commodity chemicals. | Bismarck Amaniampong; Elizabeth Courthright; Noor Saber; Reuben Swart; Karen Draths | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6765b51afa469535b948e1d7/original/sustainable-d-l-lactate-production-from-methane-and-carbon-dioxide-via-acetylenedicarboxylate.pdf |
67658a776dde43c908cc8749 | 10.26434/chemrxiv-2024-07h4m | Simplified carbonylation catalyst based on [Co2(CO)8] and coordinating solvents for the carbonylation of β-lactones and α,β-unsaturated acids to cyclic anhydrides | Cyclic anhydrides are valuable chemical intermediates and monomers that can be synthesized through the carbonylation of oxygenated substrates like β-lactones and unsaturated acids. Sophisticated cobalt-based catalysts, which require the addition of ligands or presynthesis of a metal cation, have been extensively used to promote such reactions. Herein, we show that the commercial complex [Co2(CO)8] is a suitable catalytic precursor for the carbonylative ring expansion of β-lactones in a wide range of conditions and even at low CO pressure. In particular, succinic anhydride is formed quantitatively from β-propiolactone in the presence of only [Co2(CO)8] in acetonitrile under a moderate CO pressure. The carbonylation of acrylic acid in these conditions is also possible, and provides quantitative yields of product when the gas phase includes H2. This work reinvestigates the potential of [Co2(CO)8] as a catalyst precursor: its disproportionation in the presence of a coordinating solvent (including MeCN and acetone) yields active catalytic species and thus paves the way toward the design of simpler catalytic systems for carbonylation reactions. | Marie-Hélène Pietraru; Antonin Homassel; Emmanuel Nicolas; Thibault Cantat | Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67658a776dde43c908cc8749/original/simplified-carbonylation-catalyst-based-on-co2-co-8-and-coordinating-solvents-for-the-carbonylation-of-lactones-and-unsaturated-acids-to-cyclic-anhydrides.pdf |
6152e3e478257b34612daba2 | 10.26434/chemrxiv-2021-p8twj | Diversifying databases of metal organic frameworks for high-throughput computational screening | By combining metal nodes and organic linkers, an infinite number of metal organic frameworks (MOFs) can be designed in silico. When making new databases of such hypothetical MOFs, we need to assure that they not only contribute towards the growth of the count of structures but also add different chemistry to existing databases. In this study, we designed a database of ~20,000 hypothetical MOFs which are diverse in terms of their chemical design space—metal nodes, organic linkers, functional groups and pore geometries. Using Machine Learning techniques, we visualized and quantified the diversity of these structures. We find that on adding the structures of our database, the overall diversity metrics of hypothetical databases improve, especially in terms of the chemistry of metal nodes. We then assessed the usefulness of diverse structures by evaluating their performance, using grand-canonical Monte Carlo simulations, in two important environmental applications—post combustion carbon capture and hydrogen storage. We find that many of these structures perform better than widely used benchmark materials such as Zeolite-13X (for post combustion carbon capture) and MOF-5 (for hydrogen storage). | Sauradeep Majumdar; Seyed Mohamad Moosavi; Kevin Maik Jablonka; Daniele Ongari; Berend Smit | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6152e3e478257b34612daba2/original/diversifying-databases-of-metal-organic-frameworks-for-high-throughput-computational-screening.pdf |
67b74f386dde43c908b9a627 | 10.26434/chemrxiv-2024-rcx7n-v2 | AI-driven de-novo design and development of non-toxic DYRK1A inhibitors | (DYRK1A) plays a key role in various diseases, including DYRK1A syndrome, cancer, diabetes, and neurodegenerative disorders such as Alzheimer’s disease (AD), making it a compelling therapeutic target. This work integrates multiple Artificial Intelligence (AI) methods, including predictive models and generative algorithms, to design non-toxic DYRK1A inhibitors. A dual-target drug discovery framework is constructed by combining AI-driven approaches with classical techniques. An ensemble Quantitative Structure-Activity Relationship (QSAR) model predicts compound affinities, while Directed Message Passing Neural Networks (DMPNN) assess toxicity. In the generative phase, a Hierarchical Graph Generation (HGG) model facilitates the design of potential inhibitors, which are further refined through docking studies, synthesized, and experimentally validated. This approach led to the identification of the pyrazolyl-1H-pyrrolo[2,3-b]pyridine 1 as a potent DYRK1A inhibitor, prompting the synthesis of a novel derivative series. Enzymatic assays confirmed nanomolar-level inhibitory activity, while ORAC assays and LPS-induced pro-inflammatory response evaluations in BV2 microglial cells demonstrated antioxidant and anti-inflammatory properties. Overall, these compounds exhibit strong DYRK1A inhibition alongside promising pharmacological effects. | Eduardo González; Pablo Varas; Pedro González-Naranjo; Eugenia Ulzurrun; Guillermo Marcos-Ayuso; Concha Pérez; Juan A. Páez; David Rios-Insua; Simón Rodríguez Santana; Nuria E. Campillo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b74f386dde43c908b9a627/original/ai-driven-de-novo-design-and-development-of-non-toxic-dyrk1a-inhibitors.pdf |
632c364de61502aece221e82 | 10.26434/chemrxiv-2022-lg6qs | Detection of tobacco consumers using 4-hydroxycoumarin as chromogenic agent in Konig’s reaction | The purpose of this study was to develop and standardize a protocol for the novel use of a benzopyrone derivative, namely 4-hydroxycoumarin (4-HC), for the estimation of cotinine to identify tobacco consumers using Konig’s reaction. 4-HC was soluble in 2-propanol and 1-butanol at a concentration of 100 mg/mL and 80 mg/mL, respectively. Cotinine was estimated by Konig’s reaction using three different formats in which the physical nature of primarily two reagents, potassium thiocyanate and Chloramine-T, was varied. The three formats included dry format, semi-dry format and liqiuid format. The use of 4-HC disssolved in 2-propanol was found to quantitatively estimate cotinine at a lower detection limit of 50 μM in all three formats at 500 nm. A quantitative lower limit of detection of 3.2 μM of cotinine was obtained when 4-HC was dissolved in 1-butanol in semi-dry format wherein potassium thiocyanate and Chloramine-T were used in a combination of liquid and solid form, respectively, at Abs (525 nm)-Abs (750 nm). Besides, quantitative detection, use of 4-HC in 1-butanol results in a biphasic reaction which credits its use for cotinine estimation in a qualitative visual format with the development of a pink polymethine product in the upper 1-butanol layer against the colorless lower aqeous layer. | Serena DSouza; INN Namboothiri; Santosh Noronha | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632c364de61502aece221e82/original/detection-of-tobacco-consumers-using-4-hydroxycoumarin-as-chromogenic-agent-in-konig-s-reaction.pdf |
60c749079abda23737f8cb47 | 10.26434/chemrxiv.12012720.v1 | State Dependent Photochemical and Photophysical Behavior of Dithiolate Ester and Trithiocarbonate RAFT Polymerization Agents. | The rise in popularity of photochemically initiated RAFT polymerization (photoRAFT) along with the broad spectrum of proposed, and possible, initiation mechanisms results in the need for careful characterization of the photophysical properties of some common RAFT agents. Direct irradiation of the RAFT agent as a means to generate radicals, also known as the photoiniferter mechanism, is one commonly proposed mechanism. The current study shows that the dithioesters and trithiocarbonates have lowest singlet, and triplet excited state energy levels that are close to, or lower then C-S bond dissociation energies. Excitation of these agents into their S<sub>1</sub> band results in negligible radical production, while excitation into S<sub>2</sub> or higher results in the decomposition of dithioesters and trithiocarbonates resulting in radical formation, but with low quantum yields. Likewise, there is significant literature precedence for an electron transfer initiation mechanism, PET-RAFT. It is shown that the dithioesters and trithiocarbonates all show peak reduction potentials at ca. -1.0 V (vs. SCE). However, transient absorption spectroscopy studies of the electron transfer from a mediator shows that theses reactions occur rapidly only when the mediator potential is more negative than -1.2 V (vs. SCE). | Daniel Falvey; Matthew Thum; Steven Wolf | Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749079abda23737f8cb47/original/state-dependent-photochemical-and-photophysical-behavior-of-dithiolate-ester-and-trithiocarbonate-raft-polymerization-agents.pdf |
60c73e99469df45c97f428c9 | 10.26434/chemrxiv.7057913.v1 | Molecular Iodine-Catalyzed Carbonyl-Olefin Metathesis | The carbonyl-olefin metathesis reaction is a
synthetically valuable transformation that could facilitate rapid functional
group interconversion and construction of new organic structures. Herein we
demonstrate that elemental iodine, a very simple and mild catalyst, can
efficiently promote this chemical transformation under mild reaction conditions
with excellent outcomes. Our mechanistic studies revealed intriguing aspects of
iodine activation mode that could change the previously established perception
of catalyst and substrate design for the carbonyl-olefin metathesis reaction. | Thanh Vinh Nguyen; Uyen P. N. Tran; Giulia Oss; Martin Breugst; Eric Detmar; Kevin Liyanto | Organic Synthesis and Reactions; Acid Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e99469df45c97f428c9/original/molecular-iodine-catalyzed-carbonyl-olefin-metathesis.pdf |
61953348a831ec6f51d2c065 | 10.26434/chemrxiv-2021-xdh0x-v4 | Disparities in Air Pollution Exposure in the United States by Race-Ethnicity and Income, 1990 – 2010 | All data used are publicly available. Demographic data are available via IPUMS National Historic Geographic Information Systems [<a href="http://www.nhgis.org/" target="_blank">www.nhgis.org</a>]; air pollution estimates are available via the EPA CACES project [<a href="http://www.caces.us/" target="_blank">www.caces.us</a>]). | Jiawen Liu; Lara P. Clark; Matthew Bechle; Anjum Hajat; Sun-Young Kim; Allen Robinson; Lianne Sheppard; Adam A. Szpiro; Julian D. Marshall | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61953348a831ec6f51d2c065/original/disparities-in-air-pollution-exposure-in-the-united-states-by-race-ethnicity-and-income-1990-2010.pdf |
65e4f5ef66c13817292028ad | 10.26434/chemrxiv-2024-9gm62 | Solubilization and Photostabilization in a Sodium Deoxycholate Hydrogel of a Neutral Conjugated Thiophene Oligomer and Polymer | Oligo(3-hexylthiophene-co-1,4-phenylene) and poly(3-hexylthiophene) were solubilized in sodium deoxycholate self-assemblies in water solutions and hydrogels. The oligomer and polymer were incorporated as monomers into the self-assemblies with sodium deoxycholate aggregates, leading to the photoprotection of these neutral conjugated and water insoluble molecules. Dynamic light scattering, rheology and fluorescence experiments established that the deoxycholate aggregation and gel formation properties were not altered with the incorporation of the oligomer or polymer into the deoxycholate self-assemblies, showing that this adaptable host system with some molecular recognition elements is a viable strategy to incorporate neutral conjugated molecules into hydrogels. | Alessandra S. Menandro; Laura O. Péres; Cornelia Bohne | Physical Chemistry; Polymer Science; Hydrogels; Organic Polymers; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e4f5ef66c13817292028ad/original/solubilization-and-photostabilization-in-a-sodium-deoxycholate-hydrogel-of-a-neutral-conjugated-thiophene-oligomer-and-polymer.pdf |
668495ce5101a2ffa8363d93 | 10.26434/chemrxiv-2024-tx50z | An integrated framework for the detection and filtration of perfluoroalkyl substances from surface water in the Thames Basin | PFAS pollution is a growing concern worldwide, with no equitable solution in the Thames Basin. We developed a geospatial neural network, predicting PFAS values to within 10% of experimentally validated values. With those predictions, we designed and tested a point-of-use filtration device to be installed on taps. Observing a 93% reduction in PFAS concentration, we reduce PFAS to below health limits of 4 ng/l. Further, we optimised the design, where a 10mm depth of activated carbon allows for 2.5 months of usage, with minimal impact on flow rate and introducing no impurities. Not only do we reduce the devastating impacts of PFAS pollution, but we present a potential solution that is accessible for all. | Wenqi Zhao; Christopher Whitfeld | Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668495ce5101a2ffa8363d93/original/an-integrated-framework-for-the-detection-and-filtration-of-perfluoroalkyl-substances-from-surface-water-in-the-thames-basin.pdf |
6507e694b6ab98a41ca54f7a | 10.26434/chemrxiv-2023-mvc6g | Improving Wastewater-Based Epidemiology for New Psychoactive Substance Surveillance by Combining a High-Throughput In Vitro Metabolism Assay and LC−HRMS Metabolite Identification | One of the primary criteria for a suitable drug biomarker for wastewater-based epidemiology (WBE) is having a unique source representing human metabolism. For WBE studies, this means it is important to identify and monitor metabolites rather than parent drugs, to capture consumption of drugs and not fractions that could be directly disposed. In this study, a high-throughput workflow based on a human liver S9 fraction in vitro metabolism assay was developed to identify human transformation products of new chemicals, using α-pyrrolidino-2-phenylacetophenone (α-D2PV) as a case study. Analysis by liquid chromatography coupled to high resolution mass spectrometry identified four metabolites. Subsequently, a targeted liquid chromatography – tandem mass spectrometry method was developed for their analysis in wastewater samples collected from a music festival in Australia. The successful application of this workflow opens the door for future work to better understand the metabolism of chemicals and their detection and application for wastewater-based epidemiology. | Richard Bade; Julia Huchthausen; Carolin Huber; Pradeep Dewapriya; Benjamin Tscharke; Rory Verhagen; Cheneal Puljevic; Beate Escher; Jake O'Brien | Analytical Chemistry; Environmental Analysis; Separation Science | CC BY NC 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6507e694b6ab98a41ca54f7a/original/improving-wastewater-based-epidemiology-for-new-psychoactive-substance-surveillance-by-combining-a-high-throughput-in-vitro-metabolism-assay-and-lc-hrms-metabolite-identification.pdf |
60c745ef842e656e64db26fb | 10.26434/chemrxiv.10288547.v1 | Highly Specific, Fluorescent Cannabinoid Type 2 Receptor Probes Enable Applications in Microscopy, Flow Cytometry and FRET-based Binding Assays | Pharmacological modulation of cannabinoid type 2 receptor (CB2R) holds promise for the treatment of numerous conditions including inflammatory diseases, autoimmune disorders, pain, and cancer. Despite its significance, researchers lack reliable tools to address questions concerning the complex mechanism of CB2R signaling and its downstream consequences, especially in cell-type and tissue-dependent contexts. Herein, we report highly specific CB2R fluorescent probes and their use in a variety of applications: flow cytometry with overexpressing as well as endogenously expressing cells, real-time confocal microscopy of living cells, and a novel FRET-based, CB2R binding assay amenable to high throughput screening.<br /> | Roman Sarott; Matthias Westphal; Patrick Pfaff; Claudia Korn; David Sykes; Gazzi, Thais; Benjamin Brennecke; Kenneth Atz; Marie Weise; Yelena Mostinski; Pattarin Hompluem; Tamara Miljuš; Nicolas Roth; Hermon Asmelash; Man Vong; Wolfgang Guba; Arne C. Rufer; Eric A. Kusznir; Sylwia Huber; Catarina Raposo; Elisabeth A. Zirwes; Anja Osterwald; Anto Pavlovic; Svenja Moes; Jennifer Beck; Irene Benito-Cuesta; Teresa Grande; Alexei Yeliseev; Faye Drawnel; Gabriella Widmer; Daniela Holzer; Tom van der Wel; Harpreet Mandhair; Chen-Yin Yuan; Wiliam Drobyski; Yurii Saroz; Natasha Grimsey; Michael Honer; Jürgen Fingerle; Klaus Gawrisch; Julian Romero; Cecilia J. Hillard; Zoltan V. Varga; Mario van der Stelt; Pal Pacher; Jürg Gertsch; Peter J. McCormick; Christoph Ullmer; Sergio Oddi; Mauro Maccarrone; Dmitry B. Veprintsev; Marc Nazare; Uwe Grether; Erick Carreira | Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745ef842e656e64db26fb/original/highly-specific-fluorescent-cannabinoid-type-2-receptor-probes-enable-applications-in-microscopy-flow-cytometry-and-fret-based-binding-assays.pdf |
64cb9ab74a3f7d0c0d8649dc | 10.26434/chemrxiv-2023-rz9mc-v3 | A New Method for Determining Aromaticity through Comparison of Inclusive vs. Non-Inclusive Steric Number Calculation in Conjunction with an Alternative Approach to Reveal Conjugated Pi Systems in Alkyne-Containing Compounds | A required aspect for the classification of a compound as aromatic is it must have a conjugated pi system, which is constituted by a region of overlapping p-orbitals or, in other words, a continuous system of sp2-hybridized atoms. This is usually determined by drawing a valid resonance structure (one with no more than 2 formal charges) where all atoms are sp2-hybridized for the compound of interest, but we propose a new method intuitively suggesting resonance (if the atom of interest is determined to be sp2-hybridized) involving the comparison of inclusive vs. non-inclusive steric number calculation. We define inclusive steric number calculation as the number of sigma bonds plus the number of lone pairs bonded to the atom (both localized and delocalized), and define non-inclusive as the number of sigma bonds plus the number of localized lone pairs only. In the non-inclusive steric number calculation, the delocalized lone pairs count towards the Huckel number of pi electrons in the compound (4n+2 where n is an integer). Once both are calculated for the atom of interest and the rest of the following requirements for aromaticity are evaluated (i.e. compound is planar, cyclic, and has Huckel number of electrons) the version of the compound with the most stable aromatic configuration is selected as the correct configuration. For alkyne-containing compounds, we devised an alternative method for determining sp2-hybridization of atoms involved in an alkyne to ultimately reveal a conjugated pi system in the compound that agrees with our inclusive vs. non-inclusive steric number calculation. This approach involves the idea that the pi electrons of a pi bond within an alkyne that are not involved in the conjugated pi system (due to these p-orbitals being perpendicular relative to the parallel p-orbitals contributing to conjugation) can occupy a single atom in the alkyne, but the specific atom they occupy is unclear. Therefore, we present a “lone pair hybrid” that accounts for both atoms being equally able to receive the pi electrons as a lone pair. These hypothetical lone pairs are localized due to an alkene still bonding the atoms and makes the steric number calculation for both the inclusive and non-inclusive approach 2 sigma bonds + 1 lone pair = 3, sp2, making the atoms sp2-hybridized and thus revealing the conjugated pi system. | Dylan Amiri | Organic Chemistry; Chemical Education | CC BY 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cb9ab74a3f7d0c0d8649dc/original/a-new-method-for-determining-aromaticity-through-comparison-of-inclusive-vs-non-inclusive-steric-number-calculation-in-conjunction-with-an-alternative-approach-to-reveal-conjugated-pi-systems-in-alkyne-containing-compounds.pdf |
66b11a7901103d79c5d1a7fd | 10.26434/chemrxiv-2024-g127v | Emergence of New Nitrogen-rich Compounds
in Lead-Nitrogen Phase Diagram under
Pressure | In this study, we employed a variable-composition evolutionary algorithm in conjunction
with first-principles calculations to perform a comprehensive structural search for the Pb-N binary system under pressure and to determine a hyperfine
pressure composition phase diagram. The findings revealed the existence of eleven new pressurestabilized
structures in the pressure range of 0-100 GPa and at 0 K. Six nitrogen-rich compositions, PbNz (z = 2-4, 6, 8 and 10), and seven thermodynamically stable phases were identified. The most prevalent nitrogen motif observed in the predicted PbNz phases is the N2 dumbbell (z = 2-4, 6, and 8). As z increases, the lowest N-N vibrational frequencies decrease from 2076 cm−1 in Im-3 Pb(N2)4 to 1302 cm−1 in I 4/mcm
Pb(N2) at 25 GPa. This finding is related to the lowering of the charge transfer from Pb to N2 dimers. The νN−N frequencies act as a clear signature of the existence of
high-pressure PbNz phases containing N2 dumbbells. In addition to N2 dimers, the aromatic pentazolate unit N−5 is stabilized in the I 4/m Pb(cyclo-N5)2 phase which becomes thermodynamically stable at 25 GPa. This nitrogen-rich phase can be recoverable to ambient pressure and exhibits a high detonation velocity of 10.2 km/s. Additionally, one- and two-dimensional covalent nitrogen nets are also observed in PbNz (z = 6 and 8). Infinite polymeric chains are found in PbN6 and a two-dimensional nitrogen covalent net is encountered in Cc Pb@2D-N8, which is composed of fused aromatic 18-rings. | Sylvain PITIE; Ken Niwa; Gilles FRAPPER | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Quantum Computing; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b11a7901103d79c5d1a7fd/original/emergence-of-new-nitrogen-rich-compounds-in-lead-nitrogen-phase-diagram-under-pressure.pdf |
654a9b52a8b423585a29763e | 10.26434/chemrxiv-2023-cljn3 | Keeping an “eye” on the experiment: computer vision for
real-time monitoring and control | This work presents a generalizable computer vision (CV) and machine learning model that is used for automated real-time monitoring and control of a diverse array of workup processes. Our system simultaneously monitors multiple physical parameters (e.g., liquid level, homogeneity, turbidity, solid, residue, and color), offering a method for rapid data acquisition and deeper analysis from multiple visual cues. We demonstrate a single platform (consisting of CV, machine learning, real-time monitoring techniques, and flexible hardware) to monitor and control vision-based experimental techniques, including solvent exchange distillation, antisolvent crystallization, evaporative crystallization, cooling crystallization, solid ̶ liquid mixing, and liquid ̶ liquid extraction. Both qualitative (video capturing) and quantitative data (parameters measurement) were obtained which provided a method for data cross-validation. Our CV model's ease of use, generalizability, and non-invasiveness make it an appealing complementary option to in situ and real-time analytical monitoring tools and mathematical modeling. Additionally, our platform is integrated with Mettler-Toledo’s iControl software, which acts as a centralized system for real-time data collection, visualization, and storage. With consistent data representation and infrastructure, we were able to efficiently transfer the technology and reproduce results between different labs. This ability to easily monitor and respond to the dynamic situational changes of the experiments is pivotal to enabling future flexible automation workflows. | Rama El-khawaldeh; Mason Guy; Finn Bork; Nina Taherimakhsousi; Kris Jones; Joel Hawkins; Lu Han; Robert Pritchard; Sebastien Monfette; Jason Hein | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Process Chemistry; Process Control; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2023-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654a9b52a8b423585a29763e/original/keeping-an-eye-on-the-experiment-computer-vision-for-real-time-monitoring-and-control.pdf |
67936bd581d2151a02c12efa | 10.26434/chemrxiv-2025-wv370-v2 | Evans-Polanyi-like models for rapidly predicting
barriers in xylopyranoses: Accelerating the
development of kinetic models for hemicellulose
pyrolysis | This work elucidates Evans-Polanyi-like (EPL) relations to rapidly estimate the standard activation enthalpy of three ubiquitous reaction classes playing a central role in hemicellulose pyrolysis: ring-opening, ring contraction, and elimination. These models leverage computationally cheap local and global electron-density-based chemical reactivity descriptors, such as Fukui’s functions (f), electron population of CO bonds (N), and the gross intrinsic strength bond index (Δgpair), evaluated for reactants solely. More than 270 reactions observed in twenty-eight functionalized β-D-xylopyranoses, the hemicellulose building block, are used under the 20-80 % partition scheme for validating-deriving purposes. By using the relatively simple multilinear regression analysis, four EPL are proposed for informing barriers at the M06-2X/6-311++G(d,p), CBS-QB3, G4, and DLPNO-CCSD(T)-F12/cc-pVTZ-F12//M06-2X/6-311++G(d,p), namely, ΔHDFT = –168.82f ̅– 66.28N ̅ + 328.10Δ ̅gpair – 18.80, ΔHCBS = –189.01(f ) ̅– 65.11N ̅ + 266.44Δ ̅gpair + 13.96, ΔHG4 = –184.99f ̅ – 64.85N ̅ + 275.10Δ ̅gpair + 8.52, and ΔHDLPNO = –187.82f ̅ – 72.45N ̅ + 296.14Δ ̅gpair + 7.72, respectively. An adjusted coefficient of determination of 0.80 characterizes all these parametric polynomials. Moreover, MAE and RMSE equal to ≈3.3 and ≈4.1 kcal mol-1 describe the performance of the best-fitting models at DFT and G4. Conversely, the highest values, MAE = 3.6 and RMSE = 4.7 kcal mol-1, are associated with the CBS-QB3 level. The benchmarking of the computed activation enthalpies at 298 K yields simple functions for high-level estimations from low levels of theory: ΔHCBS = 0.96ΔHDFT + 1.67, ΔHG4 = 0.96ΔHDFT + 1.72, ΔHDLPNO = 1.02ΔHDFT – 1.57, ΔHG4 = 0.96ΔHCBS + 2.86, ΔHDLPNO = 1.01ΔHCBS – 0.14, and ΔHDLPNO = 1.05ΔHG4 – 2.77. R2 ranges from 0.94 to 0.98 across these polynomials. Extrapolating the DPLNO barriers to the complete basis set limit tends to lower them by 0.63 kcal mol-1. EPL expressions are tailored to facilitate the development of chemical kinetic models for hemicellulose pyrolysis, as the reactant structure is the only input required, thereby contributing to the faster deployment of bioproducts at a commercial level. | Leandro Ayarde-Henríquez; Jacopo Lupi; Bernardo Ballotta; Stephen Dooley | Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67936bd581d2151a02c12efa/original/evans-polanyi-like-models-for-rapidly-predicting-barriers-in-xylopyranoses-accelerating-the-development-of-kinetic-models-for-hemicellulose-pyrolysis.pdf |
64b77248b053dad33a809652 | 10.26434/chemrxiv-2023-wkjpg | Combined Data-driven and Mechanism-based Approaches for Human-Intestinal-Absorption Prediction in Early Drug-Discovery Stage | It is important to precisely predict the intestinal absorption ratio (Fa) at an early stage in the discovery of orally available drugs because it directly influences drug efficacy. Gastrointestinal unified theoretical framework (GUTFW) and machine learning (ML) are commonly used to predict the percentage of Fa. In GUTFW, the Fa of a drug is estimated using an equation based on the mechanism of human intestinal absorption, dose, solubility, membrane permeability, and dispersion of the drug. The experimental values of these in vitro parameters are required to accurately predict Fa. However, most of these values are unavailable at early stages of development. ML uses a dataset of the observed Fa values of many drugs in humans. In most previously published ML approaches, the dose information for each drug has been ignored. However, Fa can vary in a dose-dependent manner through changes in solubility, membrane permeability, and dispersion. To overcome these problems, we combined GUTFW and ML to compensate for each defect. We collected published data on the chemical structures of 460 drugs, including Fa and dose amounts. The key parameters of the GUTFW (Do, dose number; Dn, dispersion number; Pn, permeation number), solubility, membrane permeability, and structural descriptors were calculated and used as explanatory variables for ML. ML algorithms, namely, the random forest (RF) and message-passing neural network (MPNN; Chemprop), were investigated. The GUTFW model was compared to the conventional ML method, which uses only structural descriptors, and combined ML method, which uses both structural descriptors and GUTFW parameters. In addition, using the Chemprop framework, we investigated important substructures of Fa. Our result suggested that combinational ML produced higher predictivity than the GUTFW model and conventional ML model in the test dataset (20% of the dataset) [R2 value and RMSE in combinational ML method: 0.611 and 19.7 (RF), 0.520 and 21.6 (Chemprop); in conventional ML: 0.339 and 25.4 (RF), 0.497 and 22.1 (Chemprop); in GUTFW: 0.353 and 31.9]. Additionally, most of the substructures indicated by the Chemprop framework were consistent with the common knowledge of medicinal chemistry. We developed an accurate prediction method for human Fa using a combination of data-driven ML and mechanism-based GUTFW, where the parameters could be calculated without experimental data, enabling the model to efficiently promote early drug discovery. Furthermore, some of the important substructures identified here were previously unknown and require further investigation. | Koichi Handa; Sakae Sugiyama; Michiharu Kageyama; Takeshi Iijima | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b77248b053dad33a809652/original/combined-data-driven-and-mechanism-based-approaches-for-human-intestinal-absorption-prediction-in-early-drug-discovery-stage.pdf |
60c752af567dfe60c6ec5cef | 10.26434/chemrxiv.13337072.v1 | Biosynthesis of Triangular-Shape ZnO Nanoparticles Using Tecoma Stans and Its Antimicrobial Activity | <div>The present work reports the first green synthesis of zinc oxide nanoparticles (ZnO-NPs) using Tecoma stans leaf extract. The ZnO-NPs have been investigated by X-Ray Diffraction (XRD), Ultra Violet-Visible (UV-Vis), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM) and Fourier Transform-Infra Red (FT-IR) analysis. XRD investigation confirms the crystalline structure of ZnO. The TEM images show triangular shape ZnO-NPs with sizes running from 15-20 nm. The XPS spectrum revealed the presence of Zn and O in the sample. Photoluminescence studies of ZnO-NPs displayed a sharp emission of blue band at 447 nm which is attributed to the defect structures in ZnO crystal. The presence of alcoholic, phenolic amide groups in the plant extracts is responsible for the formation of ZnO-NPs. The synthesized ZnO-NPs showed a very high antibacterial property against five bacterial strains such as Bacillus cereus,</div><div>Acinetobacter johnsonii, Achromobacter xylosoxidans, Achromobacter spanius and Chromobacterium pseudoviolaceum, with the highest zone of inhibition (ZOI) of 24 mm being shown against Achromobacter spanius strain. Further, the synthesized nanoparticles displayed excellent activities against four fungal strains, where a highest ZOI of 30 mm was observed against Penicillium citirinum, hence proving its high efficacy as antimicrobial agents.</div> | Samuel Lalthazuala Rokhum; Aayushi Biswas; Bishwajit Changmai; Vanlalveni Chhangte; R. Lalfakzuala; Soumitra Nath | Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752af567dfe60c6ec5cef/original/biosynthesis-of-triangular-shape-zn-o-nanoparticles-using-tecoma-stans-and-its-antimicrobial-activity.pdf |
67aad15a81d2151a02ec74a6 | 10.26434/chemrxiv-2025-0dlbs | Reversibly photocontrolled polyacrylamide hydrogels for mechanobiology | We report the development of polyacrylamide hydrogels with photoswitchable stiffness using solely visible light and their application to cell culture. We have previously shown that azobenzenes can control the binding constants of dynamic covalent boronic ester bonds (Chem. Sci. 2018, 9, 5987; J. Am. Chem. Soc. 2020, 42, 19969). Here we show that these photoswitchable dynamic bonds can be incorporated into polyacrylamide hydrogels that are stable for at least 10 days in buffer without changes in stiffness or photoresponse. Reversible stiffening and softening are achieved with green and blue irradiation, respectively. We prepared soft (877 ± 79 Pa) and stiff (8.4 ± 0.3 kPa) hydrogels that undergo photoreversible changes in modulus over at least 3 light irradiation cycles. In vitro studies show that the hydrogels are nontoxic to HepG2 cells. The cells undergo the expected changes in morphology, actin stress fiber formation, and Yes-associated protein (YAP) subcellular localization upon stiffening and softening the hydrogel substrate with visible light. These results validate the suitability of our visible-light-controlled hydrogel as a versatile platform for cellular mechanotransduction studies. | Eric Abenojar; Ekta Minocha; Emmanuel Garcia Villatoro; Viraj Kirinda; Ashwani Gupta; Boyeong Kang; IkSung Cho; Vivian Zhang; Jae-Won Shin; Jason Wertheim; Julia Kalow | Biological and Medicinal Chemistry; Polymer Science; Hydrogels; Bioengineering and Biotechnology | CC BY NC 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67aad15a81d2151a02ec74a6/original/reversibly-photocontrolled-polyacrylamide-hydrogels-for-mechanobiology.pdf |
616443b5a3d2c9f07dd30e3d | 10.26434/chemrxiv-2021-bhb1j-v2 | Improving Ligand-Ranking of AutoDock Vina by Changing the Empirical Parameters | AutoDock Vina (Vina) achieved a very high docking-success rate, p ̂, but give a rather low correlation coefficient, R, for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. R is affected more by changing the gauss2 and rotation than other terms. The docking-success rate p ̂ is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment R_set1=0.556±0.025 compared with R_Default=0.493±0.028 obtained by the original Vina and R_(Vina 1.2)=0.503±0.029 by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving R≥0.500 for 32/48 targets, compared with the default package, giving R≥0.500 for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient (R_set1=0.621±0.016) than the default package (R_Default=0.552±0.018) and Vina version 1.2 (R_(Vina 1.2)=0.549±0.017). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina. The outcomes would enhance the ranking of ligand-binding affinity using Autodock Vina. | T. Ngoc Han Pham; Trung Hai Nguyen; Nguyen Minh Tam; Thien Y Vu; Nhat Truong Pham; Nguyen Truong Huy; Binh Khanh Mai; Nguyen Thanh Tung; Minh Quan Pham; Van V. Vu; Son Tung Ngo | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616443b5a3d2c9f07dd30e3d/original/improving-ligand-ranking-of-auto-dock-vina-by-changing-the-empirical-parameters.pdf |
60c744fabdbb896478a3891e | 10.26434/chemrxiv.9929885.v1 | Divalent Cobalt and Copper Coordination Complexes of κ2-N, O-Derivatives of (Z)-1-R-2-(2’-oxazolin-2’-yl)-eth-1-en-1-ates: Structure and Reactivity Patterns | The synthesis and characterisation of a small library of Co and Cu derivatives (29 examples) incorporating the (Z)-1-R1-2-(4’,4’-R2-2’-oxazolin-2’-yl)-eth-1-en-1-ate (L: R1 = alkyl or aryl; R2 = H or Me) skeleton is described. This work includes six new derivatives of “Tohda’s Ligands”. In the case where R2 = H, solid-state stable Co(II) materials of formula Co(κ2-N,O-L)2 could, in some cases, be obtained following base-induced deprotonation of L+H and treatment with hydrated CoX2 salts. These complexes display redox induced solution decomposition behaviour giving Co(κ2-N,O-L)3 as one isolable product. Stable Cu(II) complexes could only be obtained in the case of for R1 = Ph and R2 = H. In the case of R2 = Me, distorted tetrahedral Co(II) compounds (also Co(κ2-N,O-L)2) are obtained as above (twelve examples). Square planar derivatives of Cu(II), of similar stoichiometry, are likewise isolated (eleven new examples). In contrast to the R2 = H reactions, all of these latter materials were found to be air-stable in solution or the solid phase. In total, 18 complexes have been characterised by single crystal X-ray diffraction. Molecular modelling (PM6(tm) and DFT) are also used to elucidate the molecular properties of selected complexes. Only a single Co complex (R1 = t-butyl and R2 = Me) of the library displays reversible one-electron redox properties.<br /> | Kathleen L. May; Sanja Resanović; Maja W. Chojnacka; Khrystyna Herasymchuk; Douglas G. Vaughan; Jianfeng Zhu; J. Wilson Quail; Alan J. Lough; Robert Gossage | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fabdbb896478a3891e/original/divalent-cobalt-and-copper-coordination-complexes-of-2-n-o-derivatives-of-z-1-r-2-2-oxazolin-2-yl-eth-1-en-1-ates-structure-and-reactivity-patterns.pdf |
61f2b3d6360c8437d9ac968d | 10.26434/chemrxiv-2022-cggpz | Enantioselective Synthesis of [3]-Ladderanol through a Late-Stage Organocatalytic Desymmetrization | Ladderane phospholipids, with their unusual ladder-like arrangement of fused cyclobutane rings, represent an architecturally unique class of natural products. However, despite their fascinating structure and other necessary impetus, only a few synthetic studies of these molecules have been reported so far. We have now devised a concise synthesis of [3]-ladderanol, a component of ladderane phospholipids, using an organocatalytic enantioselective desymmetrizing formal C(sp2)‒H alkylation. Our synthetic strategy rests on a late-stage introduction of chirality, thus allowing facile access to both the enantiomers of [3] ladderanol as well as its analog. This is the first time a desymmetrization strategy is applied to the synthesis of [3]-ladderanol. The scope of this desymmetrizing C(sp2)‒H alkylation of meso cyclobutane fused cyclohexenediones is also presented. | Sayan Ray; Subhajit Mondal; Santanu Mukherjee | Organic Chemistry; Catalysis; Natural Products; Photochemistry (Org.); Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f2b3d6360c8437d9ac968d/original/enantioselective-synthesis-of-3-ladderanol-through-a-late-stage-organocatalytic-desymmetrization.pdf |
6273dbfa7087671ea146dcf8 | 10.26434/chemrxiv-2022-pm4zp | Tailoring CsPbBr3 Growth Via Non-Polar Solvent Choice and Heating Method | This study describes an investigation of the role of non-polar solvents on the growth of cesium lead halide (CsPbX3 X = Br, I) nanoplatelets. We employed two solvents, benzyl ether (BE), and 1-octadecene (ODE), as well as two nucleation and growth mechanisms, one-pot, facilitated by microwave irradiation (MWI) based heating, and hot-injection, using conventional heating. Using BE and MWI, large mesoscale CsPbBr3 nanoplatelets were produced, whereas use of ODE produced thin small crystallites. Differences between the products were observed by optical spectroscopies, which showed first band edge absorptions consistent with thicknesses of ~ 9 nm (~15 monolayer (ML)) for the BE-CsPbBr3, and ~5 nm (~9 ML) for ODE-CsPbBr3. Both products had orthorhombic crystal structure, with the BE-CsPbBr3 revealing significant preferred orientation diffraction signals consistent with the asymmetric and two-dimensional (2D) platelet morphology. The differences in final morphology were also observed for products formed via hot-injection, with BE-CsPbBr3 showing thinner square platelets with thicknesses of ~2 ML, and ODE-CsPbBr3 showing similar morphologies and small crystallite sizes. To understand the role solvent plays in crystal growth, we studied lead plumbate precursor (PbBrn2-n) formation in both solvents, as well as solvent plus ligand solutions. The findings suggest that BE dissolves PbBr2 salts to a higher degree than ODE, and that this BE to precursor affinity persists during growth. | Hediyeh Zamani; Tsung-Hsing Chiang; Kaylie R. Klotz; Annie J. Hsu; Mathew M. Maye | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Solid State Chemistry; Solvates; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6273dbfa7087671ea146dcf8/original/tailoring-cs-pb-br3-growth-via-non-polar-solvent-choice-and-heating-method.pdf |
64a609c76e1c4c986be342f8 | 10.26434/chemrxiv-2023-z0vxs | Optical Properties of Neutral F Centers in Bulk MgO with Density Matrix Embedding | The optical spectra of neutral oxygen vacancies ($F^0$ centers) in the bulk MgO lattice was investigated using density matrix embedding theory. The impurity Hamiltonian was solved with the complete active space self-consistent field (CAS-DMET) and second-order n-electron valence state perturbation theory (NEVPT2-DMET) multireference methods. To estimate defect-localized vertical excitation energies at the non-embedding and thermodynamic limits, a double extrapolation scheme was employed. The extrapolated NEVPT2-DMET vertical excitation energy value of 5.24 eV agrees well with the experimental absorption maxima at 5.03 eV, whereas the excitation energy value of 2.89 eV at the relaxed triplet defect localized state geometry overestimates the experimental emission at 2.4 eV by only nearly 0.5 eV, indicating the involvement of triplet-singlet decay pathway. | Shreya Verma; Abhishek Mitra; Yu Jin; Soumi Haldar; Christian Vorwerk; Matthew R. Hermes; Giulia Galli; Laura Gagliardi | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a609c76e1c4c986be342f8/original/optical-properties-of-neutral-f-centers-in-bulk-mg-o-with-density-matrix-embedding.pdf |
61438dfd87a02d39703d2551 | 10.26434/chemrxiv-2021-dz2d8 | Predicting Solvation Thermodynamics in Water and Ionic Liquids using the Multi-Scale Solvation Layer Interface Condition (SLIC) | We highlight the most recent developments of the solvation-layer interface condition (SLIC) continuum dielectric model in predicting solvation thermodynamics of neutral small molecules in water and multiple ionic liquids. We demonstrate that a simple temperature-dependent solvent-accessible-surface-area (SASA) correlation and a cavity-dispersion-combinatorial (CDC) theory, combined with the SLIC electrostatics model, provide highly accurate predictions of Gibbs solvation energies, solvation entropies, and solvation heat capacities. The SLIC/SASA model parameters are temperature dependent, whereas the SLIC/CDC parameters are constant. To address the lack of experimental data pertaining to the accuracy of the models, we conducted an extensive literature search and data compilation to obtain credible experimental solvation data. This yielded 159 and 123 data points for hydration entropies and heat capacities of neutral small molecules, respectively.
Compared to experimental data, the SLIC/SASA and SLIC/CDC models, respectively, achieve an RMS error 1.39 (1.24) and 1.15 (1.76) kcal/mol for hydration free energy (hydration entropy) predictions. Solvation heat capacities are predicted with RMS errors 24.42 and 46.17 cal/mol/K. Most remarkably, the SLIC/CDC predictions of solvation entropies and heat capacities are made without apriori knowledge of experimental solvation entropies. In addition, the SLIC/SASA predictions of Gibbs solvation energies (solvation entropies) of 12 amino acid side-chain analogs in seven (three) ionic liquids are compared to the available explicit-solvent simulation data from Paluch et al.~\cite{Paluch12} and Latif~\cite{Latif14} et al. | Ali Mehdizadeh Rahimi; Safa Jamali; Jaydeep Bardhan; Steve Lustig | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61438dfd87a02d39703d2551/original/predicting-solvation-thermodynamics-in-water-and-ionic-liquids-using-the-multi-scale-solvation-layer-interface-condition-slic.pdf |
60c74be6bb8c1a47633db2f6 | 10.26434/chemrxiv.12397910.v1 | CO2 Assisted Ethane Oxidative Dehydrogenation over MoO3 and V2O5 Catalysts Supported on Reducible CeO2-TiO2 | <p>Supported MO<sub>x</sub> (M= Mo, V) on
mixed CeO<sub>2</sub>-TiO<sub>2</sub> were investigated for the oxidative
dehydrogenation of ethane (ODHE) using CO<sub>2</sub> as a mild oxidant. Raman spectroscopic
characterization of the synthesized catalysts under dehydrated conditions
suggest that surface MoO<sub>x</sub> species prefer to anchor on the crystalline
domains of TiO<sub>2</sub>. Upon increasing the amount of CeO<sub>2</sub> in
the mixed oxide support, an intense and broad band at ~930cm<sup>-1</sup>
underscored that the prevalent species tend to be polymeric (MoO<sub>x</sub>)<sub>n</sub>
domains. On the other hand, in the case of VO<sub>x</sub> catalysts, a gradual
shift in the symmetric stretching of the vanadyl (V=O) Raman band with increasing
CeO<sub>2</sub> content was observed that points at the gradual anchoring of
the surface vanadia species on both TiO<sub>2</sub> and CeO<sub>2</sub> thus
highlighting the possible existence of the amorphous VO<sub>x</sub> to be
located at the interface of the two mixed oxides. The catalytic behavior of Mo
and V were distinct. As the ceria content in the support increased, MoO<sub>x</sub>
catalysts promoted the ODHE via Mars van Krevelen mechanism while VO<sub>x</sub>
catalysts appeared to favor ethane direct dehydrogenation. Investigation of
structure-function relationships via in-situ Raman spectroscopic efforts
revealed that adding ceria not only changed the redox properties of the support
but also improved those of the deposited metal oxide. We also show that upon
incorporation of ceria into the support, CO<sub>2</sub> directly participates in
the reoxidation of the dispersed MoO<sub>x</sub> species during catalysis. This
effect was distinct from the reaction of CO<sub>2</sub> in the reverse water
gas shift reaction. Operando Raman spectra revealed that the presence of CO<sub>2</sub>
enhances the stability of the bridging Mo–O–Mo bond of polymeric molybdena
domains, which is proposed to affect the relative contribution of oxidative
versus non-oxidative pathways in ethane dehydrogenation.</p> | Thu D. Nguyen; Fuat E. Celik; George Tsilomelekis | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74be6bb8c1a47633db2f6/original/co2-assisted-ethane-oxidative-dehydrogenation-over-mo-o3-and-v2o5-catalysts-supported-on-reducible-ce-o2-ti-o2.pdf |
674ed35c7be152b1d0c7fa85 | 10.26434/chemrxiv-2024-08l0l-v2 | Sex Classification from Human Scent Using Image Interpretation of 2D Gas Chromatography-Mass Spectrometry Data | Two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GCxGC ToF-MS) is a powerful technique for analyzing complex chemical mixtures, capturing rich chemical information valuable for applications from environmental monitoring to medical diagnostics. One promising application is sex classification based on human scent, where subtle differences in chemical compounds can indicate biological sex. In this paper, we propose the first pattern recognition approach to sex classification that interprets raw GCxGC ToF-MS data as images, moving beyond traditional compound-based analysis. Furthermore, we introduce a new, publicly available dataset of GCxGC ToF-MS measurements specifically curated for this task. We evaluate our method on the proposed dataset, achieving state-of-the-art results of $\approx 95\%$ cross-validation accuracy with a dataset of $200$ identities, advancing the analysis of GCxGC ToF-MS data. The results show that applying computer vision techniques to chemical data analysis has significant potential for interdisciplinary research. | Jan Hlavsa; Radim Spetlik; Jana Čechová; Petra Pojmanová; Jiří Matas; Štěpán Urban | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674ed35c7be152b1d0c7fa85/original/sex-classification-from-human-scent-using-image-interpretation-of-2d-gas-chromatography-mass-spectrometry-data.pdf |
6266f7001033887a20fa7917 | 10.26434/chemrxiv-2022-x30vr-v2 | Impact of Nanoparticle Size and Surface Chemistry on Peptoid Self-Assembly | Self-assembled organic nanomaterials can be generated by bottom-up assembly pathways where the structure is controlled by the organic sequence and altered using pH, temperature, and solvation. In contrast, self-assembled structures based on inorganic nanoparticles typically rely on physical packing and drying effects to achieve uniform superlattices. By combining these two chemistries to access inorganic-organic nanostructures, we aim to understand the key factors that govern the assembly pathway and structural outcomes in hybrid systems. In this work, we outline two assembly regimes between quantum dots (QDs) and reversibly binding peptoids. These regimes can be accessed by changing the solubility and size of the hybrid (peptoid-QD) monomer unit. The hybrid monomers are prepared via ligand exchange, assembled, and the resulting assemblies are studied using ex-situ transmission electron microscopy as a function of assembly time. In aqueous conditions, QDs were found to stabilize certain morphologies of peptoid intermediates and generate a final product consisting of multilayers of small peptoid sheets linked by QDs. The QDs were also seen to facilitate or inhibit assembly in organic solvents based on the relative hydrophobicity of the surface ligands, which ultimately dictated the solubility of the hybrid monomer unit. Increasing the size of the QDs led to large hybrid sheets with regions of highly ordered square packed QDs. A second, smaller QD species can also be integrated to create binary hybrid lattices. These results create a set of design principles for controlling the structure and structural evolution of hybrid peptoid-QD assemblies and contribute to the predictive synthesis of complex hybrid matter. | Madison Monahan; Micaela Homer; Shuai Zhang; Renyu Zheng; Chun-Long Chen; James DeYoreo; Brandi Cossairt | Materials Science; Nanoscience; Aggregates and Assemblies; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6266f7001033887a20fa7917/original/impact-of-nanoparticle-size-and-surface-chemistry-on-peptoid-self-assembly.pdf |
6669b20ae7ccf7753a9a5449 | 10.26434/chemrxiv-2024-qjjnv | C-H Functionalisation by Iron Ligand-to-Metal Charge Transfer in Water | Functionalisation of partially water-soluble C-H precursors through Fe(III)Cl3 Ligand-to-Metal charge transfer catalysis in aqueous solution is achieved under near UV-light irradiation. The light-driven bond-homolysis of the Fe-Cl bond within the iron complex results in the generation of highly reactive chlorine radicals, facilitating hydrogen atom abstraction from a furane-derived starting material. Sugars or cinchonidine derivatives promote the interaction between metal salt and organic substrates. Lowering the reaction temperature to 4°C can modulate the reaction kinetics, resulting in a shorter induction period of the photoreaction. | Jessica Stahl; Burkhard Koenig | Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6669b20ae7ccf7753a9a5449/original/c-h-functionalisation-by-iron-ligand-to-metal-charge-transfer-in-water.pdf |
60c74f1bbdbb89a6f5a39ce9 | 10.26434/chemrxiv.12808526.v1 | Can We See the Energy Densities? II. Insights from Linear-Response Time-Dependent Density Functional Theory Calculations | Inspired by the analysis of Kohn-Sham energy densities by Nakai et al, we extended the energy density analysis to linear-response time-dependent density functional theory (LR-TDDFT) calculations. Using ethylene-tetrafluoroethylene and oxyluciferin–water complexes as examples, distinctive distribution patterns were demonstrated for the excitation energy densities of local excitations (within a molecular fragment) and charge-transfer excitations (between molecular fragments). It also provided a simple way to compute the effective energy of both hot carriers (particle and hole) from charge-transfer excitations via an integration of the excitation energy density over the donor<br />and acceptor grid points. | Zheng Pei; junjie yang; Jingheng Deng; Yuezhi Mao; Qin Wu; Zhibo Yang; bin wang; Christine
M. Aikens; Wanzhen Liang; Yihan Shao | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f1bbdbb89a6f5a39ce9/original/can-we-see-the-energy-densities-ii-insights-from-linear-response-time-dependent-density-functional-theory-calculations.pdf |
60c74b2b469df45b04f43e83 | 10.26434/chemrxiv.12277046.v1 | Screening of Anticancer Drugs as Potential Candidates to Target COVID-19 Disease | The current work was focused on predicting the potential of several anticancer drugs as potential inhibitors of COVID-19 disease. The work was accoplished using molecular docking performed using SwissDock tool. Information about COVID-19 proteins and anticancer drugs from databases like PDB, PubChem and Drugbank has been incorporated appropriately in the manuscript. Data analysis has revealed some highly promising anticancer drugs which can further be critically analyzed through both computational and biological validation methods.<div>This work was intended to support the urgent need of finding drugs/remedies against COVID-19. The results can be a foundation for other researchers around the world to further validate/test these anticancer agents against the pathogen. </div> | Gayatri Gurjar | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b2b469df45b04f43e83/original/screening-of-anticancer-drugs-as-potential-candidates-to-target-covid-19-disease.pdf |
60c74a4b842e65c186db2ee6 | 10.26434/chemrxiv.9978539.v2 | Kinetic Control over Droplet Ripening in Fuel-Driven Active Emulsions | Active droplets are made of phase-separated molecules that are activated and deactivated by a metabolic reaction cycle. Such droplets play a crucial role in biology as a class of membrane-less organelles. Moreover, theoretical studies show that active droplets can evolve to the same size or spontaneously self-divide when energy is abundant. All of these exciting properties, i.e., emergence, decay, collective behavior, and self-division, are pivotal to the functioning of life. However, these theoretical predictions lack experimental systems to test them quantitively. Here, we describe the synthesis of synthetic active droplets driven by a metabolic chemical cycle and we find a surprising new behavior, i.e., the dynamics of droplet-growth is regulated by the kinetics of the fuel-driven reaction cycle. Consequently, these droplets ripen orders of magnitude faster compared to Ostwald ripening. Combining experiments and theory, we elucidate the underlying mechanism, which could help better understand how cells regulate the growth of membrane-less organelles.<br /> | Marta Tena-Solsona; Jacqueline Janssen; Caren Wanzke; Fabian Schnitter; Hansol Park; Benedikt Rieß; Julianne M. Gibbs; Christoph A. Weber; Job Boekhoven | Supramolecular Chemistry (Org.); Aggregates and Assemblies; Biophysics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a4b842e65c186db2ee6/original/kinetic-control-over-droplet-ripening-in-fuel-driven-active-emulsions.pdf |
60c759af4c8919954cad4e04 | 10.26434/chemrxiv.14721477.v1 | Thiazolidine Deprotection by 2-Aminobenzamide-Based Aldehyde Scavenger for One-Pot Multiple Peptide Ligation | Strategies for one-pot peptide ligation enable chemists to access synthetic proteins at a high yield in a short time. Herein, we report a new one-pot multi-segments ligation strategy using N-terminal thiazolidine (Thz) peptide and a formaldehyde scavenger. Among our designed 2-aminobenzamide-based aldehyde scavengers, 2-amino-5-methoxy-N’,N’-dimethylbenzohydrazide showed a good ability to capture formaldehyde from Thz at pH 4.0. This scavenger had compatibility with the conditions of native chemical ligation at pH 7.5. Using this scavenger for a model peptide ligation system, we performed one-pot four-segment ligation at a high yield without significant side reactions. | Koki Nakatsu; Hitoshi Murakami; Gosuke Hayashi; Akimitsu Okamoto | Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759af4c8919954cad4e04/original/thiazolidine-deprotection-by-2-aminobenzamide-based-aldehyde-scavenger-for-one-pot-multiple-peptide-ligation.pdf |
6633f75621291e5d1d47e734 | 10.26434/chemrxiv-2024-67xzs | Highly Stereoselective Radical Cyclopropanation of Olefins via Cobaloxime-Based Metalloradical Catalysis | Metalloradical catalysis (MRC), predominantly exemplified by metalloporphyrin complexes, has emerged as a promising strategy for regulating radical reactions and broadening their synthetic applications. In this paper, we report that cobaloxime complexes, functioning as a surrogate for metalloporphyrin systems, can mediate radical cyclopropanation of olefins using donor/acceptor-type carbene precursor α-aryl diazoacetates through the MRC process. The reaction proceeds under mild conditions, yielding cyclopropane derivatives in good yields with high stereoselectivity. The reaction exhibits extensive substrate tolerance, encompassing gram-scale transformations and the synthesis of pharmaceutical compounds. Our discoveries underscore the potential of cobaloxime-catalyzed cyclopropanation as a valuable asset in organic syntheses and further expand the repertoire of metalloradical systems in catalysis. | Liming Tan; McKay Boehme; Lorenzo Papworth; Keyang Wu; Gang Li | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6633f75621291e5d1d47e734/original/highly-stereoselective-radical-cyclopropanation-of-olefins-via-cobaloxime-based-metalloradical-catalysis.pdf |
63d6e9526606948a7d428c69 | 10.26434/chemrxiv-2022-fjqz8-v2 | Reversible Chlorite/Chlorine Dioxide Anion Redox Couple for Low-Cost Energy Storage | The ClO2-/ClO2 electrochemical reaction is shown to be highly reversible in acidic, near-neutral, and alkaline electrolytes while using low-cost carbon electrodes. Its equilibrium potential (0.954 V vs SHE) is pH-independent and enables high aqueous cell voltages of 1.38-2.15 V when used as a positive electrode with negative electrodes such as Zn, Fe, or S. This anion redox couple may enable low-cost aqueous rechargeable batteries free of resource-constrained metals, here demonstrated in prototype Zn-NaClO2 full cells. The rapid reaction kinetics and stability of the ClO2 phase at low temperatures also suggests that chlorite-based batteries may be favorable for applications in cold environments. | Merrill K. Chiang; Liang Su; Kailash Raman; Yet-Ming Chiang; William H. Woodford | Energy; Energy Storage; Power; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d6e9526606948a7d428c69/original/reversible-chlorite-chlorine-dioxide-anion-redox-couple-for-low-cost-energy-storage.pdf |
60c749c1337d6c5ec4e2777d | 10.26434/chemrxiv.12090426.v1 | Computational Evaluation of the COVID-19 3c-like Protease Inhibition Mechanism, and Drug Repurposing Screening | <p>The rapid spread of the COVID-19 outbreak is now a global threat with over a million diagnosed cases and more than 70 thousand deaths. Specific treatments and effective drugs regarding such disease are in urgent need. To contribute to the drug discovery against COVID-19, we performed computational study to understand the inhibition mechanism of the COVID-19 3c-like protease, and search for possible drug candidates from approved or experimental drugs through drug repurposing screening against the DrugBank database. Two novel computational methods were applied in this study. We applied the “Consecutive Histogram Monte Carlo” (CHMC) sampling method for understanding the inhibition mechanism from studying the 2-D binding free energy landscape. We also applied the “Movable Type” (MT) free energy method for the lead compound screening by evaluating the binding free energies of the COVID-19 3c-like protease – inhibitor complexes. Lead compounds from the DrugBank database were first filtered using ligand similarity comparison to 19 published SARS 3c-like protease inhibitors. 70 selected compounds were then evaluated for protein-ligand binding affinities using the MT free energy method. 4 drug candidates with strong binding affinities and reasonable protein-ligand binding modes were selected from this study, <i>i.e.</i> Enalkiren (DB03395), Rupintrivir (DB05102), Saralasin (DB06763) and TRV-120027 (DB12199). </p> | Hao Liu; Tao Jiang; Wenlang Liu; Zheng Zheng | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c1337d6c5ec4e2777d/original/computational-evaluation-of-the-covid-19-3c-like-protease-inhibition-mechanism-and-drug-repurposing-screening.pdf |
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