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658a7cee66c13817291062d6 | 10.26434/chemrxiv-2023-83j5j | Unlocking the Genetic Mysteries of SARS-CoV-2: A Deep Dive into the Sequence, Structure, and Dynamics of Mpro Mutations | Abstract
A global challenge is presented by the continuous surge in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), leading to the COVID-19 pandemic. A major concern arises as SARS-CoV-2 undergoes mutations, potentially increasing its lethality for humans. Mutations in crucial replication enzymes, particularly the main protease (Mpro), add complexity to disease progression and impact the effectiveness of existing COVID-19 treatments. In this study, the thermodynamic stability of Mpro mutants was predicted using nine structure-based methods. Gibbs free energy for 109 Mpro mutants was predicted, and the top three recurrently destabilizing mutants (I106T, F140L, and A173S) across multiple methods were discovered. Analysis of secondary structure changes revealed diverse alterations and a dynamics study highlighted increased rigidity in A173S and heightened flexibility in I106T and F140L. This study sheds light on the evolving SARS-CoV-2 landscape and emphasises the potential functional consequences of specific mutants
| MOHD KHAN | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658a7cee66c13817291062d6/original/unlocking-the-genetic-mysteries-of-sars-co-v-2-a-deep-dive-into-the-sequence-structure-and-dynamics-of-mpro-mutations.pdf |
60c745ee842e653443db26f7 | 10.26434/chemrxiv.10295546.v1 | Opening up Connectivity Between Documents, Structures and Bioactivity | This article assesses a key aspect of data sharing that has the
potential to accelerate the progress and impact of medicinal chemistry. To achieve
this the community needs to increase the
outward flow of experimental results locked-up in millions of published PDFs
into structured open databases that explicitly capture the connectivity between
structures, documents and bioactivity results. | Christopher Southan | Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745ee842e653443db26f7/original/opening-up-connectivity-between-documents-structures-and-bioactivity.pdf |
60c747214c8919300dad2c47 | 10.26434/chemrxiv.11537913.v1 | Labeling of Proteins for Single-Molecule Fluorescence Spectroscopy | Single-molecule fluorescence spectroscopy has become an important technique for studying the conformational dynamics and folding of proteins. A key step for performing such experiments is the availability of high-quality samples. Here we describe the practical details of a simple and widely applicable strategy for preparing proteins that are site-specifically labeled with a donor and an acceptor dye for single-molecule Förster resonance energy transfer (FRET) experiments. The method is based on introducing two cysteine residues that are labeled with maleimide-functionalized fluorophores, combined with high-resolution chromatography. We discuss how to optimize site-specific labeling even in the absence of orthogonal coupling chemistry and present purification strategies that are suitable for samples ranging from intrinsically disordered proteins to large folded proteins. We also discuss common problems in protein labeling, how to avoid them, and how to stringently control sample quality.<br /> | Franziska Zosel; Andrea Holla; Benjamin Schuler | Biochemistry; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747214c8919300dad2c47/original/labeling-of-proteins-for-single-molecule-fluorescence-spectroscopy.pdf |
67a4098381d2151a0251522c | 10.26434/chemrxiv-2025-9bh5d | Nickel-Catalyzed Gas-Free Reductive Carbonylation of Aryl Thianthrenium Salts to Access Aryl Amides and Aryl Thioesters | A nickel-catalyzed site-selective reductive carbonylation of arenes via aryl thianthrenium salts is described.
Using Mo(CO)6 as a convenient solid CO source and reductant, and employing nitroarenes and sulfonyl chlorides as readily
available nitrogen and sulfur sources, a range of aryl amides and aryl thioesters were successfully synthesized in moderate
to good yields. The utility of this transformation is demonstrated through the synthesis of antimicrobial agents and the latestage
functionalization of biorelevant molecules. | Chen Chen; Lu-Yao Ding; Xiao-Xu Zhang; Guan-shen Chen; Yan-Ping Zhu; Chunjie Ni; Bolin Zhu | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a4098381d2151a0251522c/original/nickel-catalyzed-gas-free-reductive-carbonylation-of-aryl-thianthrenium-salts-to-access-aryl-amides-and-aryl-thioesters.pdf |
6659ccd7418a5379b0c0461f | 10.26434/chemrxiv-2024-llc6t-v2 | Partial to Total Generation of 3D Transition Metal Complexes | The design of transition metal complexes has drawn much attention over the years because of their important applications as metallodrugs and functional materials. In this work, we present an extension of our recently reported approach, LigandDiff. The new model, which we call multi-LigandDiff, is more flexible and greatly outperforms its predecessor. This scaffold-based diffusion model allows de novo ligand design either with existing ligands or without any ligand. Moreover, it allows users to predefine the denticity of the generated ligand. Our results indicate that multi-LigandDiff can generate well-defined ligands and has great transferability with regard to transition metals and coordination geometries. In terms of its application, multi-LigandDiff successfully designs 338 Fe(II) SCO complexes from only 47 experimentally validated SCO complexes. And these generated complexes are configurationally diverse and experimentally reasonable. Overall, the results show that multi-LigandDiff is an ideal tool to design novel transition metal complexes from scratch. | Hongni Jin; Kenneth M. Merz | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659ccd7418a5379b0c0461f/original/partial-to-total-generation-of-3d-transition-metal-complexes.pdf |
60c758c59abda2c9a9f8e984 | 10.26434/chemrxiv.14578320.v1 | Electron-Deficient Heteroacenes that Contain Two Boron Atoms: Near-Infrared Fluorescence Based on a Push–Pull Effect | Electron-deficient heteroacenes that contain two tricoordinate boron atoms in their acene skeletons and planarized phenyl ether moieties at their periphery were synthesized via the borylation of the corresponding silicon-bridged precursors. X-ray crystallographic analysis revealed quinoidal structures, which give rise to two-step reversible redox processes for both the reduction and oxidation. These compounds exhibit intense absorption and sharp fluorescence bands with vibronic structures in the near-infrared (NIR) region. These properties originate from the push–pull effect along the long axis of the molecule derived from the electron-donating ether moiety and the electron-accepting boron moieties. Of particular note is the NIR emission of the thienothiophene-centered heteroacene, which has a maximum at 952 nm with a narrow band width of 309 cm–1 in cyclohexane. A Franck–Condon analysis revealed the crucial role of the sterically less-hindered thienothiophene spacer in achieving this sharp emission band. | Masato Ito,; Mika Sakai; Naoki Ando; Shigehiro Yamaguchi | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758c59abda2c9a9f8e984/original/electron-deficient-heteroacenes-that-contain-two-boron-atoms-near-infrared-fluorescence-based-on-a-push-pull-effect.pdf |
6578032fbec7913d27697585 | 10.26434/chemrxiv-2023-frlnl | Size and Shape Tunability of Cesium Lead Bromide Nanocrystals by Pb(II) Counter Anions | The size modulation of perovskite nanocrystals is a well-established practice in existing literature, achieved through adjustments in reaction temperature or ligand chain lengths. However, our study introduces a novel approach, aiming to govern the dimensions (including shape, size, and phase) of these nanocrystals by manipulating the counter anions of Pb(II) during the synthesis by hot-injection method. We utilize diethyl 2-bromomalonate as the bromide precursor for this purpose. The resulting tunability is ascribed to the specific counter anion present in the Pb(II) salts. For instance, lead acetate, lead bromide, lead oxide, and lead nitrate resulted in the formation of 1D (nanorods), 2D (nanoplatelets), 3D (nanocubes), and quantum dots, respectively. Despite the diverse range of sizes and shapes achieved, all CsPbBr3 nanocrystals consistently exhibit a high photoluminescence quantum yield (PLQY > 90%) with considerable excited state lifetimes (τ ~ 18-20 ns). Moreover, these nanocrystals remain highly stable when exposed to air in colloidal solutions. | Anupam Manna; Pravat Nayek; Prasenjit Mal | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6578032fbec7913d27697585/original/size-and-shape-tunability-of-cesium-lead-bromide-nanocrystals-by-pb-ii-counter-anions.pdf |
60c74b95702a9bf38418b482 | 10.26434/chemrxiv.12355934.v1 | Frequency Selective Phase-Optimized Recoupling for Protons in Ultra-Fast Solid-State Magic-Angle Spinning NMR | <p>We propose a new category of homonuclear frequency-selective recoupling
methods for protons under ultra-fast MAS ranging from 40 kHz to 150 kHz. The
methods, named as Selective Phase-optimized Recoupling (SPR) are simple in the
form with defined phase schemes and RF amplitudes. SPR are robust to RF
variations and efficient in frequency-selective recoupling. We demonstrated
that SPR can provide a sensitivity gain of ~ 3 over the widely-used RFDR for
selective <sup>1</sup>H<sub>N</sub>-<sup>1</sup>H<sub>N</sub> correlations
under 150 kHz MAS using a protonated tripeptide N-formyl-Met-Leu-Phe (fMLF). Moreover,
SPR requires small ratios (~ 0.5) of RF power with respect to MAS frequency,
making it perfect to probe long-range <sup>1</sup>H-<sup>1</sup>H distance
under ultra-fast MAS up to 150 kHz.</p> | Zhengfeng Zhang; Andres Oss; Mai-Liis Org; Ago Samoson; Huan Tan; Jun Yang | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b95702a9bf38418b482/original/frequency-selective-phase-optimized-recoupling-for-protons-in-ultra-fast-solid-state-magic-angle-spinning-nmr.pdf |
6760b43efa469535b9d92fbb | 10.26434/chemrxiv-2024-ctb9h | NaCl Ion Pairing at Liquid-Insulator and Liquid-Conductor Interfaces | We study the formation and dissociation of NaCl ion pairs at water-insulator and water-conductor interfaces, a crucial process in determining the structure and compo- sition of interfacial electrolytes. Using Molecular Dynamics simulations, we show that both ions remain strongly hydrated and excluded from the interfacial region where wa- ter layering is significant. This enables a successful treatment of ion pairing at the water-insulator interface with a simple dielectric continuum theory with no free param- eters. However, in contradiction to this simple theory, the water-electrode interface acts as a water-insulator interface from the perspective of the NaCl ion pairing we consider here. | Amro Dodin | Theoretical and Computational Chemistry; Physical Chemistry; Interfaces; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6760b43efa469535b9d92fbb/original/na-cl-ion-pairing-at-liquid-insulator-and-liquid-conductor-interfaces.pdf |
6706f25212ff75c3a1fe1f7a | 10.26434/chemrxiv-2024-gj19b | Z-Selective Alkyne Transfer Semihydrogenation in Drug-Like Molecules via an Organic Photoreductant | The deactivation of transition metal catalysts poses a significant challenge when applying synthetic methods to medicinal chemistry, where Lewis-basic functional groups based on nitrogen and sulfur are prevalent. C–C multiple bond reduction reactions usually depend on Lewis-acidic metal hydrides with open coordination sites that render them incompatible with such functional groups. Reduction mechanisms that replace the Lewis-acidic transition metal with an organic reductant offer a potential solution to this issue. Indeed, reactions via organic hydrides and photoredox catalysts have shown a broad tolerance of Lewis-basic motifs but remain restricted to the reduction of highly electrophilic Michael acceptors. Herein, we report the development of a mechanistically distinct transformation using an organic photoreductant that can be applied to the reduction of unpolarized alkynes. The reaction tolerates most medicinally relevant functional groups including highly Lewis-basic motifs like tetrazoles, guanidines, and triazoles, which have never been tolerated in an alkyne semihydrogenation before. Overreduction is minimized by controlling the redox potential and the high Z-selectivity is ensured by steric matching during association between reduced intermediates and reductant thus mimicking the transition metal mediated mechanism. | Benjamin R. G. Bissinger; Dang H. Vu; Henric F. Janning; Mario Patrick Wiesenfeldt | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706f25212ff75c3a1fe1f7a/original/z-selective-alkyne-transfer-semihydrogenation-in-drug-like-molecules-via-an-organic-photoreductant.pdf |
61b9009f75c572a26aeb37b2 | 10.26434/chemrxiv-2021-26xgh | Experimental validation of an adsorbent-agnostic artificial neural network (ANN) framework for the design and optimization of cyclic adsorption processes | The efficacy of an adsorbent agnostic machine-learning surrogate model for rapid design and optimization of a Skarstrom cycle vacuum swing adsorption (VSA) process is experimentally validated. The surrogate model is trained to predict the process performance using adsorbent features that include hypothetical Langmuir adsorption isotherm parameters, particle density, porosity and bed voidage, and process variables such as pressure, step duration and feed velocity. The training data was generated from a detailed process model for 20,000 unique combinations of the training variables. The model shows high accuracy of R2adj>0.99 for predicting key performance parameters such as product purity, recovery and productivity. The ability of this surrogate to predict the experimental performance for the purification of O2 from the air on two adsorbents, namely 13X and LiX zeolites, was studied. Two separate multi-objective optimization studies, to maximize purity and recovery, and to maximize productivity and purity were performed. For these optimization studies, the volumetrically measured isotherms of N2 and O2 were used as inputs to the surrogate model. Note that these isotherms were not a part of the dataset used to train the model. Nine points were chosen from the Parteo curves and the corresponding decision variables were used as set-points in a two-column lab-scale rig. The average difference between the calculated and experimentally measured purity, recovery and productivity was 3%, 5% and 9%, respectively. This study provides the necessary confidence to use surrogate-based process models for adsorbent screening and adsorption process optimization. | Kasturi Nagesh Pai; Tai T.T. Nguyen; Vinay Prasad; Arvind Rajendran | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Petrochemicals; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b9009f75c572a26aeb37b2/original/experimental-validation-of-an-adsorbent-agnostic-artificial-neural-network-ann-framework-for-the-design-and-optimization-of-cyclic-adsorption-processes.pdf |
673f30f3f9980725cf47b8ba | 10.26434/chemrxiv-2024-2xcsq | PubChemLite plus Collision Cross Section (CCS) values for enhanced interpretation of non-target environmental data | Finding relevant chemicals in the vast (known) chemical space is a major challenge for environmental and exposomics studies leveraging non-target high resolution mass spectrometry (NT-HRMS) methods. Chemical databases now contain hundreds of millions of chemicals, yet many are not relevant. This article details an extensive collaborative, open science effort to provide a dynamic collection of chemicals for environmental, metabolomics and exposomics research, along with supporting information about their relevance to assist researchers in the interpretation of candidate hits. The PubChemLite for Exposomics collection is compiled from ten annotation categories within PubChem, enhanced with patent, literature and annotation counts, predicted partition coefficient (logP) values, as well as predicted collision cross section (CCS) values using CCSbase. Monthly versions are archived on Zenodo under a CC-BY license, supporting reproducible research, and a new interface has been developed, including the chemical stripes on patent and literature data, for researchers to browse the collection. This article further describes how PubChemLite can support researchers in environmental/exposomics studies, describes efforts to increase the availability of experimental CCS values, and explores known limitations and potential for future developments. The data and code behind these efforts are openly available. PubChemLite content can be explored at https://pubchemlite.lcsb.uni.lu. | Anjana Elapavalore; Dylan Ross; Valentin Groues; Dagny Aurich; Allison Krinsky; Sunghwan Kim; Paul Thiessen; Jian Zhang; James Dodds; Erin Baker; Evan Bolton; Libin Xu; Emma Schymanski | Biological and Medicinal Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Chemoinformatics; Environmental Analysis; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f30f3f9980725cf47b8ba/original/pub-chem-lite-plus-collision-cross-section-ccs-values-for-enhanced-interpretation-of-non-target-environmental-data.pdf |
678fc8a26dde43c9088d4900 | 10.26434/chemrxiv-2025-23z17 | Purification of Pharmaceuticals via Retention Time Prediction: Leveraging Graph Invariant Networks, Limited Data, and Transfer Learning | The design-make-test cycle for drug discovery is highly dependent on the purification of synthesized compounds. Prior to evaluation of suitability, ultrahigh performance liquid chromatography is used for an initial standard analysis, where retention times of analytes are measured with a shorter standard gradient method and used to select the appropriate gradients for a final purification method. To circumvent this preliminary screening experiment for small molecule libraries, retention time prediction had been achieved previously by use of commercial modeling methods. However, these retention time prediction models can have limited applicability when built from smaller datasets and are less effective when constructed from disparate data collected under differing chromatography conditions. Having thousands of measured retention times from high-throughput physiochemical screening, we sought to leverage these data for the construction of predictive models for a standard preliminary method enabling high-throughput purification of macrocyclic peptide libraries. Utilizing 4549 analytes and their retention times from high-throughput physiochemical screening, a structure to retention time model was built using a graph invariant network, a form of artificial neural network architecture. Once fitted to high-throughput screening data, the model was re-trained with standard gradient method data, a technique known as transfer learning. Through transfer learning, a training set of 80 analytes yielded a neural network model, that when evaluated against a test set of 24 analytes, displays high performance metrics with a coefficient of determination (R2) of 0.82 and mean average error of 0.088 minutes, or 1.26% of the gradient time. This model has been deployed internally as a dash-app to help democratize the use of the developed models and is being used for selecting purification methods based on analyte structure. | Armen G. Beck; Rojan Shrestha; Jun Wang; Jonathan Fine; Erik L. Regalado; Kanaka Hettiarachchi; Katharine B. Williams; Edward C. Sherer; Pankaj Aggarwal | Theoretical and Computational Chemistry; Analytical Chemistry; Chemoinformatics; Separation Science; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678fc8a26dde43c9088d4900/original/purification-of-pharmaceuticals-via-retention-time-prediction-leveraging-graph-invariant-networks-limited-data-and-transfer-learning.pdf |
60c75076ee301c0358c7a88e | 10.26434/chemrxiv.13047818.v1 | SoluProt: Prediction of Soluble Protein Expression in Escherichia coli | <p><b>Motivation:</b> Poor protein
solubility hinders the production of many therapeutic and industrially useful proteins.
Experimental efforts to increase solubility are plagued by low success rates
and often reduce biological activity. Computational prediction of protein
expressibility and solubility in <i>Escherichia
coli</i> using only sequence information could reduce the cost of experimental
studies by enabling prioritisation of highly soluble proteins.</p>
<p><b>Results:</b> A new
tool for sequence-based prediction of soluble protein expression in <i>Escherichia coli, </i>SoluProt, was created
using the gradient boosting machine technique with the TargetTrack database as
a training set. When evaluated against a balanced independent test set derived
from the NESG database, SoluProt’s accuracy of 58.4% and AUC of 0.60 exceeded those of a suite of alternative solubility prediction tools.
There is also evidence that it could significantly increase the success rate of
experimental protein studies. SoluProt is freely available as a standalone program
and a user-friendly webserver at <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a>.</p>
<p> </p>
<p>Availability
and Implementation: <a href="https://loschmidt.chemi.muni.cz/soluprot/">https://loschmidt.chemi.muni.cz/soluprot/</a></p>
<p>Contact:
[email protected]</p>
Supplementary Information: Supplementary data are
available at Bioinformatics online | Jiri Hon; Martin Marusiak; Tomas Martinek; Antonin Kunka; Jaroslav Zendulka; David Bednar; Jiri Damborsky | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75076ee301c0358c7a88e/original/solu-prot-prediction-of-soluble-protein-expression-in-escherichia-coli.pdf |
6188beb8f9f05be1e7f11159 | 10.26434/chemrxiv-2021-pk7m6-v3 | Flexible boundary layer using exchange for embedding theories. I. Theory and implementation | Embedding theory is a powerful computational chemistry approach to exploring the electronic structure and dynamics of complex systems, with QM/MM being the prime example. A challenge arises when trying to apply embedding methodology to systems with diffusible particles, e.g. solvents, if some of them must be included in the QM region, for example in the description of solvent-supported electronic states or reactions involving proton transfer or charge-transfer-to-solvent: without a special treatment, inter-diffusion of QM and MM particles will lead eventually to a loss of QM/MM separation. We have developed a new method called Flexible Boundary Layer using Exchange (FlexiBLE) that solves the problem by adding a biasing potential to the system that closely maintains QM/MM separation. The method rigorously preserves ensemble averages by leveraging their invariance to exchange of identical particles. With a careful choice of the biasing potential, and the use of a tree algorithm to include only important QM and MM exchanges, we find the method has an MM-forcefield-like computational cost and thus adds negligible overhead to a QM/MM simulation. Furthermore, we show that molecular dynamics with the FlexiBLE bias conserves total energy and remarkably, dynamical quantities in the QM region are unaffected by the applied bias. FlexiBLE thus widens the range of chemistry that can be studied with embedding theory. | Zhuofan Shen; William Glover | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6188beb8f9f05be1e7f11159/original/flexible-boundary-layer-using-exchange-for-embedding-theories-i-theory-and-implementation.pdf |
63932c2692f084eab92e480f | 10.26434/chemrxiv-2022-nhnk6 | New ionic liquids constructed on complexation of Aluminum chloride anhydrous and Chloroacetamide | A new kind of ionic liquid was prepared by reacting chloroacetamide (CA) and AlCl3 at the best mole ratio (1:2) respectively. The resulting clear brown ionic liquid showed good heat stability at room temperature in a nitrogen gas-filled glove box, having an ionic conductivity of 0.34 mS/cm. FT-IR was used to establish its coordination. Other physical properties, such as viscosity and cyclic voltammetry have been measured. | Bassam Hasan; Taghried Salman | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63932c2692f084eab92e480f/original/new-ionic-liquids-constructed-on-complexation-of-aluminum-chloride-anhydrous-and-chloroacetamide.pdf |
65af381d66c13817290d5404 | 10.26434/chemrxiv-2024-gs6zn | Dynamic Promotion of the Oxygen Evolution Reaction via Programmable Metal Oxides | Hydrogen gas is a promising renewable energy storage medium when produced via water electrolysis, but this process is limited by the sluggish kinetics of the anodic oxygen evolution reaction (OER). Herein, we used a microkinetic model to investigate promoting the OER using programmable oxide catalysts (i.e., forced catalyst dynamics). We found that programmable catalysts could increase current density at a fixed overpotential (100X to 600X over static rates) or reduce the overpotential required to reach a fixed current density of 10 mA/cm^2 (45 – 140% reduction vs. static). In our kinetic parameterization, the key parameters controlling the quality of the catalytic ratchet were the O*-to-OOH* and O*-to-OH* activation barriers. Our findings indicate that programmable catalysts may be a viable strategy for accelerating the OER or enabling lower-overpotential operation, but a more accurate kinetic parameterization is required for precise predictions of performance, ratchet quality, and resulting energy efficiency. | Sallye Gathmann; Christopher Bartel; Lars Grabow; Omar Abdelrahman; C. Daniel Frisbie; Paul Dauenhauer | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65af381d66c13817290d5404/original/dynamic-promotion-of-the-oxygen-evolution-reaction-via-programmable-metal-oxides.pdf |
649ca6886e1c4c986b822da9 | 10.26434/chemrxiv-2023-90d5t | Associating Molecular Physicochemical Properties with Ionization Efficiency for Compounds in Aprotic, Polar Solvent Using Field-free and Field-enabled cVSSI Techniques | The relationship between separate molecular physicochemical properties and ionization efficiency has been investigated for the new ionization technique capillary vibrating sharp-edge spray ionization (cVSSI). Intensity values have been recorded for both positively- and negatively-charged ions arising from various compounds in the aprotic, polar acetonitrile (ACN) solvent environment. These have been recorded for field-free cVSSI as well as field-enabled cVSSI and compared to results obtained from standard ESI. In general, the strongest correlating factors include the logarithm of the octanol/water partition coefficient (log P) and the compound proton affinity (PA) in both positive and negative ion mode. This is contrasted with results for the polar, protic solvents water and methanol where the log of the base dissociation constant (pKb) often produced the strongest correlation. The results suggest that, in the absence of abundant protonating reagent, pre-formed ions do not govern the ionization process for samples in the ACN solvent systems. Another notable result is the increased ion signal levels observed for the majority of the ions in positive ion mode upon their production by a field-free source; that is, remarkably, the application of a DC voltage to the solution serves to decrease the overall ion signal level. Overall, it appears that, regardless of whether or not ions are produced by the charged residue model or the ion evaporation model, gas-phase proton transfer reaction is the major process by which they are produced. | Kinkini Jayasundara; Stephen Valentine | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649ca6886e1c4c986b822da9/original/associating-molecular-physicochemical-properties-with-ionization-efficiency-for-compounds-in-aprotic-polar-solvent-using-field-free-and-field-enabled-c-vssi-techniques.pdf |
66466ce4418a5379b0788547 | 10.26434/chemrxiv-2024-4052q | Heteroaryl derivatives of suvorexant as OX1R selective PET ligand candidates: Cu-mediated 18F-fluorination of boroxines, in vitro and initial in vivo evaluation | Background: The orexin receptor (OXR) plays a role in drug addiction and appears as a tumor marker in colon carcinoma. Subtype-selective OXR PET ligands have not yet been reported. The present work deals with the development of 18F-labeled OXR ligands dervived from selective OX1R antagonist JH112.
Methods: Applying computational analysis, medicinal chemistry, integrated OXR binding studies, Cu-mediated 18F-fluorination and initial small animal PET studies, we evaluated a series of OXR ligands (1a-1f), varying the heteroarene scaffold of FH112 by 5-fluorobenzoxazole, 5-/6-fluorobenzthiazole and 6-fluoroquinoxaline. Receptor binding studies were preformed on HEK293T cells transiently expressing the OX1R and OX2R. Cu-mediated 18F-fluorination was performed on BPin and boroxine precursors. In vitro assays for logD7.4, stability in plasma, plasma-protein binding and potential P-gp-mediated transport in the Caco-2 monolayer model were performed. The brain uptake of 18F-labeled ligands was studied by dynamic PET imaging in rats.
Results: Computational analysis predicted that fluorine substitution (1e) and introduction of the fluorobenzothiazole scaffold (1f) would be suitable for maintaining high OX1R affinity. After multi-step synthesis of 1a-1f, in vitro OXR binding studies confirmed molecular dynamics calculations and revealed single-digit nanomolar OX1R affinities for 1a-f, ranging from 0.69 nM-2.5 nM. The benzothiazole 1f showed high OX1R affinity (Ki = 0.69 nM), along with 77-fold subtype selectivity over OX2R. Cu-mediated 18F-fluorination of the nonselective OXR ligands benzothiazole [18F]1c and quinoxaline [18F]1d yielded RCY of 44% and 56%, respectively, after 10 min, compared to low RCY for benzoxazole [18F]1a of 12% after 20 min. The nonselective OXR ligand [18F]1c and the selective OX1R ligand [18F]1f gave total activity yields of 14% and 22%, respectively, using boroxine precursors for Cu-mediated 18F-fluorination with 5 min reaction time and a total synthesis time of 50-60 min. [18F]1c and [18F]1f were stable in plasma and serum in vitro, with logD7.4 of 2.28 ([18F]1c) and 2.37 ([18F]1f), and high plasma-protein binding of 66% and 77%, respectively, reflecting only marginal differences in brain uptake of [18F]1c (0.17 %ID/g) and [18F]1f (0.15 %ID/g). 1c showed higher passive permeability than 1f in vitro, which was consistent with the faster brain clearance of [18F]1c compared to [18F]1f. However, preinjection of the OXR antagonist suvorexant did not significantly block [18F]1c or [18F]1f uptake in the rat brain. Pretreatment with cyclosporin A to study the role of P-gp in limiting brain accumulation moderately increased brain uptake of [18F]1c and [18F]1f. Accordingly, in vitro experiments demonstrated that the P-gp inhibitor zosuquidar only moderately inhibited polarized, basal to apical transport of 1c (p<0.05) and had no influence on transport of 1f (n.s.), indicating that P-gp does not play a relevant role in brain accumulation of [18F]1c and [18F]1f in vivo.
Conclusions: The in vitro and in vivo results of [18F]1c and [18F]1f provide a solid basis for further development of suitable OXR PET ligands for brain imaging. This could be achieved through structural changes that would result in lower blood protein binding and 18F labeling methods that would allow for improved molar activities.
| Kim-Viktoria Bolik; Jan Hellmann; Simone Maschauer; Eduard Neu; Jürgen Einsiedel; Patrick Riss; Nora Vogg; Jörg König; Martin Fromm; Harald Hübner; Peter Gmeiner; Olaf Prante | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66466ce4418a5379b0788547/original/heteroaryl-derivatives-of-suvorexant-as-ox1r-selective-pet-ligand-candidates-cu-mediated-18f-fluorination-of-boroxines-in-vitro-and-initial-in-vivo-evaluation.pdf |
60c7422a702a9bf66b18a3d1 | 10.26434/chemrxiv.8229158.v1 | Atomic Partitioning of the MPn (N=2,3,4) Dynamic Electron Correlation Energy by the Interacting Quantum Atoms (IQA) Method: A Fast and Accurate Electrostatic Potential Integral Approach | The calculation of Moller-Plesset electron correlation energy of a topological atom interacting with its environment is now sped up by about an order of magnitude. Secondly, the proposed algorithm generates much more accurate energies for modest quadrature grids. Thus it becomes now possible to provide the training of the force field FFLUX with electron correlation energies. | Mark A. Vincent; arnaldo silva; Paul Popelier | Computational Chemistry and Modeling; Machine Learning; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422a702a9bf66b18a3d1/original/atomic-partitioning-of-the-m-pn-n-2-3-4-dynamic-electron-correlation-energy-by-the-interacting-quantum-atoms-iqa-method-a-fast-and-accurate-electrostatic-potential-integral-approach.pdf |
60c74f009abda207d4f8d77e | 10.26434/chemrxiv.12551867.v2 | Benchmark Assessment of Molecular Geometries and Energies from Small Molecule Force Fields | <div>Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. </div><div>Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1 and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared these to reference quantum mechanical (QM) data. We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94s and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Our molecule set and results are available for other researchers to use in testing.</div> | Victoria T. Lim; David
F. Hahn; Gary Tresadern; Christopher I. Bayly; David Mobley | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f009abda207d4f8d77e/original/benchmark-assessment-of-molecular-geometries-and-energies-from-small-molecule-force-fields.pdf |
66cdd5e2a4e53c4876caa9dc | 10.26434/chemrxiv-2024-dwwwj | A classical force field for selenium oxyanions in aqueous solutions and minerals | Selenium species are highly soluble in water and also occur in cement structures. In this study, we develop a classical force field for selenate (SeO42−) and selenite (SeO32−) oxyanions. The force field is fitted to the ab initio calculations, including the hydrated properties and equilibrium geometries. It allows to study mobility of selenium ions in aqueous solutions and mineral nanopores using classical molecular dynamics. | Artem Glushak; Evgeny Tararushkin; Grigory Smirnov | Theoretical and Computational Chemistry; Inorganic Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cdd5e2a4e53c4876caa9dc/original/a-classical-force-field-for-selenium-oxyanions-in-aqueous-solutions-and-minerals.pdf |
65373b3d87198ede0723d1f8 | 10.26434/chemrxiv-2023-rmj8t | In-situ effects on vinyl ester resin’s flammability and mechanical properties after adding maleated epoxy resin/epoxidized corn oil thermoset blend additive | With a global annual output of over 65 million tons and accounting for over 20% of all polymeric materials made today, thermoset polymers serve a significant role in modern industrial applications such as plastic and rubber. The high-density crosslinks not only give useful properties like as chemical and thermal resistance to the thermoset, but also make it difficult to modify. Here, using a maleated eco-thermoset blend additive (50% v/v) synthesized from epoxidized corn oil and epoxy resins (MEPECO), we show that adding an optimal amount of 5% MEPECO to vinyl ester (VE) resin improved flammability properties as analyzed by microcalorimeter, contact angle, and thermogravimetric analyzer. Using flexural testing and spectral analysis, the mechanical properties enhanced considerably in terms of strength and modulus with the same optimal amount of MEPECO. However, impact energy is much lower during digestion of the eco-thermoset resin due to shear yielding localization, as demonstrated by morphological analysis. The utility of these aliphatic polymers derived from epoxidised corn oil as a precursor of effective synergistic effects over petroleum-based epoxy resins was demonstrated in various engineering approaches for their potential application to green composites manufacturing. | Maurelio Jr Cabo; Manoj Prabhakar; Dong-Woo Lee; Ruiwen Yu; Vinista Chanthavong ; Jung-Il Song | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Composites; Fire-Resistant Materials; Polymer blends | CC BY 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65373b3d87198ede0723d1f8/original/in-situ-effects-on-vinyl-ester-resin-s-flammability-and-mechanical-properties-after-adding-maleated-epoxy-resin-epoxidized-corn-oil-thermoset-blend-additive.pdf |
60c74479bb8c1a51e93da500 | 10.26434/chemrxiv.9833909.v1 | Catalytic Enantioselective Pyridine N-Oxidation | The catalytic, enantioselective N-oxidation of substituted pyridines is described. The approach is predicated on a biomolecule-inspired catalytic cycle wherein high levels of asymmetric induction are provided by aspartic acid containing peptides as the aspartyl side chain shuttles between free acid and peracid forms. Desymmetrizations of bis(pyridine) substrates bearing a remote pro stereogenic center are demonstrated, presenting a new entry into chiral pyridine frameworks in a heterocycle-rich molecular environment. Representative functionalizations of the enantioenriched pyridine N-oxides further document the utility of this approach. Demonstration of the asymmetric N-oxidation in two venerable drug-like scaffolds, Loratadine and Varenicline, show the likely generality of the method for highly variable and distinct chiral environments, while also revealing that the approach is applicable to both pyridines and 1,4-pyrazines. <br /><br /> | Sheng-Ying Hsieh; Yu Tang; Simone Crotti; Elizabeth Stone; Scott Miller | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479bb8c1a51e93da500/original/catalytic-enantioselective-pyridine-n-oxidation.pdf |
651592aca69febde9ed8d6a6 | 10.26434/chemrxiv-2023-9gch7 | notes on Generalized Configuration-Interaction in python | In this work we construct a detailed understanding of the distribution of electrons as described by the Full-Configuration-Interaction (FCI) and for a generalized active-space. These results are presented at an introductory level for beginning practitioners or non-experts. Suitable background are a knowledge of linear-algebra and basic NumPy and Python principles of array manipulation. | Julio Candanedo | Theoretical and Computational Chemistry; Chemical Education; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651592aca69febde9ed8d6a6/original/notes-on-generalized-configuration-interaction-in-python.pdf |
676003226dde43c90856d699 | 10.26434/chemrxiv-2024-j30fr | Triplet state reactivity of iminium ions in organocatalytic asymmetric [2 + 2] photocycloadditions | Enantioselective iminium-ion catalysis has demonstrated significant synthetic potential for constructing chiral molecules. The photochemistry of iminium ions has experienced a recent renaissance. While singlet-state (S₁) reactivity has been widely used for diverse synthetic applications, triplet-state (T₁) reactivity remains largely reliant on external sensitizers. In this study, we explored the ability of chiral iminium ions embedded within an indole core to directly access the elusive T₁ reactivity, enabling organocatalytic enantioselective [2 + 2] photocycloadditions. Optical and transient spectroscopic techniques, complemented by DFT and TD-DFT calculations, revealed the pivotal role of the T₁ state intermediate. The broad applicability of our findings is demonstrated by the synthesis of various chiral cyclobutane-containing polycyclic scaffolds with high yields and excellent optical purity. | Vasco Corti; Gianluca Simionato; Lorenzo Rizzo; Stefano Serapian; Giorgio Pelosi; Mirco Natali; Luca Dell'Amico | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Photochemistry (Org.); Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676003226dde43c90856d699/original/triplet-state-reactivity-of-iminium-ions-in-organocatalytic-asymmetric-2-2-photocycloadditions.pdf |
6621433121291e5d1d1ad9c8 | 10.26434/chemrxiv-2024-lh7lv | Synthesis of Ti1-xWx Solid Solution MAX Phases and Derived MXenes for Sodium-Ion Battery Anodes | One of the distinguishing features of MAX phases and their MXene derivatives is their remarkable chemical diversity. This diversity, coupled with the two-dimensional nature of MXenes, positions them as outstanding candidates for a wide range of electrochemical applications. In this study, we report the synthesis of M site T1-xWx solid solution MAX phases, specifically (Ti1-xWx)2AlC and (Ti1-xWx)3AlC2. The 211-type phase exhibited a disordered solid solution, whereas the 312-type phase displayed a more ordered structure, resembling an o-MAX arrangement, with W atoms preferentially occupying the outer planes. This specific ordering in the 312-type MAX phase is attributed to the unique electronic structure and atomic radius of W, indicating that these characteristics are crucial for the preferential occupation of the outer planes.
Moreover, corresponding solid-solution MXenes, Ti2.4W0.6C2Tz and Ti1.6W0.4CTz, were synthesized via selective etching of MAX powder precursors containing 20% W. These MXenes were evaluated as sodium-ion battery anodes, with Ti1.6W0.4CTz showing exceptional capacity, outperforming existing multilayer MXene chemistries. This work not only demonstrates the successful integration of W in meaningful quantities into a double transition metal solid solution MAX phase, but also paves the way for the development of cost-effective MXenes containing W. Such advancements significantly widen their application spectrum by fine-tuning their physical, electronic, mechanical, electrochemical, and catalytic properties.
| Barak Ratzker; Bar Favelukis; Mark Baranov; Yugal Rathod; Avia Greenberg; Or Messer; Dor Goldstein; Alexander Upcher; Vladimir Ezersky; Nitzan Maman; Ido Biran; Varun Natu; Maxim Sokol | Materials Science; Ceramics; Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6621433121291e5d1d1ad9c8/original/synthesis-of-ti1-x-wx-solid-solution-max-phases-and-derived-m-xenes-for-sodium-ion-battery-anodes.pdf |
60c746ccbb8c1a04b33da974 | 10.26434/chemrxiv.10026701.v2 | Chemical Vapor Deposition of Metallic Films Using Plasma Electrons as Reducing Agents | Metallic thin films are key components in electronic devices and catalytic applications. Deposition of a conformal metallic thin film require using volatile precursor molecules in a chemical vapor deposition (CVD) process. The metal centers in such molecules typically have a positive valence, meaning that reduction of the metal centers is required on the film surface. Powerful molecular reducing agents for electropositive metals are scarce and hampers the exploration of CVD of electropositive metals. We present a new CVD method for depositing metallic films where free electrons in a plasma discharge are utilized to reduce the metal centers of chemisorbed precursor molecules. We demonstrate this method by depositing Fe, Co and Ni from their corresponding metallocenes using electrons from an argon plasma as a reducing agent. | Hama Nadhom; Daniel Lundin; Polla Rouf; Henrik Pedersen | Coating Materials; Magnetic Materials; Materials Processing; Nanostructured Materials - Materials; Thin Films; Interfaces; Physical and Chemical Processes; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ccbb8c1a04b33da974/original/chemical-vapor-deposition-of-metallic-films-using-plasma-electrons-as-reducing-agents.pdf |
6525efdf45aaa5fdbbbc4986 | 10.26434/chemrxiv-2023-swb13 | Can Mesoscopic Persistent Currents Thrive in Metal Nanoparticles at Room Temperature? | Mesoscopic persistent current phenomena have sought significant attention, initially observed in metal micro-ring structures at cryogenic temperatures and subsequently in metal nanoparticles at room temperature. This paper explores the underlying physics of this intriguing phenomenon and explores potential explanations proposed by various research groups. Specifically, we focus on two major theoretical approaches, each shedding light on the unique characteristics of mesoscopic persistent currents. The first approach draws upon Fermi-Dirac statistics to elucidate the behaviour of electrons in mesoscopic systems. This classical framework has provided valuable insights into the quantum mechanical aspects of persistent currents in confined metal structures. In contrast, a very recent and promising theoretical avenue incorporates the concept of spin-orbit coupling, which has emerged as a novel explanation for mesoscopic persistent currents. This approach highlights the role of intrinsic spin properties of electrons and their interactions with the crystal lattice, offering a fresh perspective on this phenomenon. Moreover, this paper underscores the important role played by geometry in shaping mesoscopic persistent currents. By examining the intricate interplay between material properties and structural design, we establish a clear link between the geometry of the system and the manifestation of persistent currents. In summary, this paper presents a comprehensive overview of mesoscopic persistent currents in metal microstructures, offering a comparative analysis of two major theoretical approaches—Fermi-Dirac statistics and spin-orbit coupling. Through this exploration, we enhance our understanding of the fascinating interplay between quantum physics, material science, and geometry in the manifestation of persistent currents in mesoscopic systems. | Siddharth Ghosh | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6525efdf45aaa5fdbbbc4986/original/can-mesoscopic-persistent-currents-thrive-in-metal-nanoparticles-at-room-temperature.pdf |
60e8e7e4551cb02a05ae0c32 | 10.26434/chemrxiv-2021-4624n-v2 | Bayesian optimization of nanoporous materials | Nanoporous materials (NPMs) could be used to store, capture, and sense many different gases. Given an adsorption task, we often wish to search a library of NPMs for the one with the optimal adsorption property. The high cost of NPM synthesis and gas adsorption measurements, whether these experiments are in the lab or in a simulation, often precludes exhaustive search.
We explain, demonstrate, and advocate Bayesian optimization (BO) to actively search for the optimal NPM in a library of NPMs-- and find it using the fewest experiments. The two ingredients of BO are a surrogate model and an acquisition function. The surrogate model is a probabilistic model reflecting our beliefs about the NPM-structure--property relationship based on observations from past experiments. The acquisition function uses the surrogate model to score each NPM according to the utility of picking it for the next experiment. It balances two competing goals: (a) exploitation of our current approximation of the structure-property relationship to pick the highest-performing NPM, and (b) exploration of blind spots in the NPM space to pick an NPM we are uncertain about, to improve our approximation of the structure-property relationship. We demonstrate BO by searching an open database of ~70,000 hypothetical covalent organic frameworks (COFs) for the COF with the highest simulated methane deliverable capacity. BO finds the optimal COF and acquires 30% of the top 100 highest-ranked COFs after evaluating only ~120 COFs. More, BO searches more efficiently than evolutionary and one-shot supervised machine learning approaches. | Aryan Deshwal; Cory Simon; Janardhan Rao Doppa | Theoretical and Computational Chemistry; Materials Science; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e8e7e4551cb02a05ae0c32/original/bayesian-optimization-of-nanoporous-materials.pdf |
61b38e7002d90d84695cc1fb | 10.26434/chemrxiv-2021-dl7mg-v2 | Highly ordered N-heterocyclic carbene monolayers on Cu(111) | The benzannulated N-heterocyclic carbene, 1,3-dibenzylbenzimidazolylidene (NHCDBZ) forms large, highly ordered domains when adsorbed on a Cu(111) surface under ultrahigh vacuum conditions. A combination of scanning tunneling microscopy (STM), high resolution electron energy loss spectroscopy (HREELS) and density functional theory (DFT) calculations reveals that the overlayer consists of vertical benzannulated NHC moieties coordinating to Cu adatoms. Long range order results from the placement of the two benzyl units from a single NHC on opposite sides of the benzimidazole moiety, with the planes of their aromatic rings approximately parallel to the surface. The organization of three surface-bound benzyl substituents from three different NHCs into a triangular array controls the formation of a highly ordered Kagome-like lattice on the surface. This study illustrates the importance of dispersive interactions to control the binding geometry and self-assembly of the NHC. | Eloise Angove; Federico Grillo; Herbert Früchtl; Alex Veinot; Ishwar Singh; Hugh Horton; Cathleen Crudden; Christopher Baddeley | Physical Chemistry; Organometallic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b38e7002d90d84695cc1fb/original/highly-ordered-n-heterocyclic-carbene-monolayers-on-cu-111.pdf |
63695dff8e0d355e6d1006f3 | 10.26434/chemrxiv-2022-2wq2c | The Contribution of Hyperconjugation and Inductive Effects to the Pseudo-Anomeric Effect in 4-Substituted Methoxycyclohexanes | The importance of electrostatic non-conventional hydrogen bonds (NCHBs) to the pseudo-anomeric effect of 4-substituted methoxycyclohexanes is evaluated using theory (NBO) to deconvolute electrostatic from other contributing effects. There is an interesting interplay between σCH → σ*CX hyperconjugation and the electropositive charge on the 3,5-axial hydrogens (Hax). In essence better σ*CX (or 𝜋*CO) acceptors increase the charge on 3,5-CHax, which in turn strengthens Cδ⁺Hax···δ⁻OMe NCHB interactions. | Bruno Piscelli; David O'Hagan; Rodrigo Cormanich | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63695dff8e0d355e6d1006f3/original/the-contribution-of-hyperconjugation-and-inductive-effects-to-the-pseudo-anomeric-effect-in-4-substituted-methoxycyclohexanes.pdf |
60c74af49abda2142df8cf96 | 10.26434/chemrxiv.12234564.v2 | Text and Network-Mining for COVID-19 Intervention Studies | <div><b>Background</b>: The COVID-19 pandemic has led to a massive and collective pursuit by the research community to find effective diagnostics, drugs and vaccines The large and growing body of literature present in MEDLINE and other online resources including various self-archive sites are invaluable for these efforts. MEDLINE has more than 30 million abstracts and an additional corpus related to COVID-19, SARS and MERS has more than 40,000 literature articles, and these numbers are growing. Automated extraction of useful information from literature and automated generation of novel insights is crucial for accelerated discovery of drug/vaccine targets and re-purposing drug candidates.</div><div><br /></div><div><b>Methods</b>: We applied text-mining on MEDLINE abstracts and the CORD-19 corpus to extract a rich set of pair-wise correlations between various biomedical entities. We built a comprehensive pair-wise entity association network involving 15 different entity types using both text-mined associations as well as novel associations obtained using link prediction. The resulting network, which we call CoNetz, also contains a specialized COVID-19 subnetwork that provides a network view of COVID-19 related literature. Additionally, we developed a set of network exploration utilities and user-friendly network visualization utilities using NetworkX and PyVis.</div><div><br /></div><div><b>Results</b>: CoNetz consisted of pair-wise associations involving 174,000 entities covering 15 different entity types. The specialized COVID-19 subnetwork consisted of 7.8 million pair-wise associations involving 43,000 entities. The network captured several of the well-known COVID-19 drug re-purposing candidates and also predicted novel candidates including ingavirin, laninamivir, nevirapine, paritaprevir, pranlukast and peficitinib.</div><div><br /></div><div><b>Conclusions</b>: Our automated text and network-mining approach builds an up-to-date and comprehensive knowledge network from literature for COVID-19 studies. The wide range of entity types captured in CoNetz provides a rich neighborhood context around the relations of interest. The approach avoids multiple drawbacks associated with manual curation including cost and effort involved, lack of up-to-date information and limited coverage. Amongst the novel repurposing drugs predicted, laninamivir and paritaprevir are possible COVID-19 anti-viral drugs while pranlukast was postulated to be a candidate for managing severe respiratory symptoms in COVID-19 patients. CoNetz is available for download and use from https://web.rniapps.net/tcn/tcn.tar.gz</div> | Aditya Rao; VG Saipradeep; Thomas Joseph; Sujatha Kotte; Naveen Sivadasan; Rajgopal Srinivasan | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74af49abda2142df8cf96/original/text-and-network-mining-for-covid-19-intervention-studies.pdf |
60c74d62bdbb890e4ba3997b | 10.26434/chemrxiv.12609398.v1 | Principles for Self-Assembly of Cyanine Dyes into 2-Dimensional Excitonic Aggregates Across the Visible and Near-Infrared | <div>Cyanine dyes show a remarkable tendency to form non-covalent supramolecular aggregates with diverse morphologies (dimers, sheets, tubes and bundles). Specific molecular arrangements within these H- or J-aggregates dictate the extraordinary photophysical properties, including long-range exciton delocalization, extreme redshifts, and excitonic superradiance. Despite extensive literature on cyanine dye aggregates, design principles that drive the solution self-assembly to a preferred H- or J-aggregated state are unknown. We present a general approach to tune the thermodynamics of self-assembly, selectively stabilizing H- or J-aggregates and thereby achieving supramolecular control over aggregate photophysics. A simple interplay of solvent to non-solvent ratio, ionic strength or dye concentration yields a broad range of conditions that predictably and preferentially stabilize the monomer, H- or J-aggregate species that can be easily monitored using absorption spectroscopy. Diffusion ordered spectroscopy, cryo-electron microscopy and atomic force microscopy together reveal a dynamic equilibrium between monomers, H-aggregated dimers, and extended J-aggregated 2-dimensional monolayers. This structural information informs a three-component equilibrium model that describes the observed concentration dependence of spectral signatures, showing excellent fit with experimental data and yields the Gibb’s free energies of self-assembly for dimerization and 2D aggregate assembly. We further demonstrate the universality of this approach among several sheet forming cyanine dyes including the benzothiazole and benzimidazole families with absorptions spanning visible, near and shortwave infrared wavelengths.</div> | Arundhati Deshmukh; Austin Bailey; Leandra Forte; Xingyu Shen; Niklas Geue; Ellen Sletten; Justin Caram | Aggregates and Assemblies; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Quasiparticles and Excitations; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d62bdbb890e4ba3997b/original/principles-for-self-assembly-of-cyanine-dyes-into-2-dimensional-excitonic-aggregates-across-the-visible-and-near-infrared.pdf |
66754d4501103d79c5c31dd2 | 10.26434/chemrxiv-2024-fnpc7 | Proteome selectivity profiling of photoaffinity probes derived from imidazopyrazine-kinase inhibitors | Kinases are attractive drug targets, but the design of highly selective kinase inhibitors remains challenging. Selectivity may be evaluated against a panel of kinases, or – preferred – in a complex proteome. Probes that allow photoaffinity-labeling of their targets can facilitate this process. Here, we report photoaffinity probes based on the imidazopyrazine scaffold, which is found in several kinase inhibitors and drugs or drug candidates. By chemical proteomics experiments, we find a range of off-targets, which vary between the different probes. In silico analysis suggests that differences between probes may be related to the size, spatial arrangement and rigidity of the imidazopyrazine and its substituent at the 1-position. | Dimitris Korovesis; Christel Merillat; Rita Derua; Steven Verhelst | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66754d4501103d79c5c31dd2/original/proteome-selectivity-profiling-of-photoaffinity-probes-derived-from-imidazopyrazine-kinase-inhibitors.pdf |
62ff5114521cb73fd59e60d8 | 10.26434/chemrxiv-2022-gn3fm | Evolution of the oxygen vacancy order during oxidation and reduction of SrFeOx followed by in situ 3D electron diffraction | For oxygen conducting materials applied in solid oxide fuel cells and chemical-looping processes, the understanding of the oxygen diffusion mechanism and the materials’ crystal structure at different stages of the redox reactions is a key parameter to control their performance. In this paper we report the first ever in situ 3D ED experiment in a gas environment and with it uncover the structure evolution of SrFeO2.5 as notably different from that reported from in situ X-ray and in situ neutron powder diffraction studies in gas environments. Using in situ 3D ED on submicron sized single crystals obtained from a high quality monodomain SrFeO2.5 single crystal, we observe the transformation under O2 flow of SrFeO2.5 with an intra- and interlayer ordering of the left and right twisted (FeO4) tetrahedral chains (space group Pcmb) into consecutively SrFeO2.75 (space group Cmmm) and SrFeO3- (space group Pm3 ̅m). Upon reduction in H2 flow, the crystals return to the brownmillerite structure with intralayer order, but without regaining the interlayer order of the pristine crystals. Therefore, redox cycling of SrFeO2.5 crystals in O2 and H2 introduces stacking faults into the structure, resulting in an I2/m(0βγ)0s symmetry with variable β. | Maria Batuk; Daphne Vandemeulebroucke; Monica Ceretti; Werner Paulus; Joke Hadermann | Materials Science; Inorganic Chemistry; Ceramics; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ff5114521cb73fd59e60d8/original/evolution-of-the-oxygen-vacancy-order-during-oxidation-and-reduction-of-sr-fe-ox-followed-by-in-situ-3d-electron-diffraction.pdf |
63d41eef10cb6a2949e8eb42 | 10.26434/chemrxiv-2023-19369 | Handling Fluorinated Gases as Solid Reagents Using Metal–Organic Frameworks | Fluorine is ubiquitous in the pharmaceutical and agrochemical industries because it improves the bioavailability and metabolic stability of molecules. However, most modern fluoroalkylation and fluorovinylation protocols rely on reagents that are expensive, explosive, or otherwise challenging to use. Fluorinated gaseous reagents are promising alternatives that are overlooked for late-stage functionalization because they require specialized equipment. Herein, we report a general strategy for safely handling inexpensive fluorinated gaseous building blocks as benchtop-stable solid reagents using porous metal–organic frameworks (MOFs). Gas–MOF reagents are employed to facilitate novel fluorovinylation and fluoroalkylation reactions, which represent safe, efficient, and atom-economical alternatives to current methods. Our approach enables high-throughput reaction development with any gaseous reagent, opening the door for the development of myriad new synthetic transformations. | Kaitlyn Keasler; Mary Zick; Emily Stacy; Jaehwan Kim; Jung-Hoon Lee; Lida Aeindartehran; Tomce Runcevski; Phillip Milner | Organic Chemistry; Organic Synthesis and Reactions; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d41eef10cb6a2949e8eb42/original/handling-fluorinated-gases-as-solid-reagents-using-metal-organic-frameworks.pdf |
663cce9921291e5d1dd9824c | 10.26434/chemrxiv-2024-rfq9d | Dual Ligand Enabled Pd-Catalyzed Ortho-Alkylation of Iodoarenes | The synthesis of complex polysubstituted aromatic molecules from simple precursors is a central goal in organic chemistry. In this study, we developed an approach for the ortho-alkylation of iodoarenes utilizing a dual ligand catalytic system. By combining Pd/olefin ligand cooperative catalysis with bulky trialkylphosphine ligand-promoted C(sp2)-I reductive elimination, we have established an ortho-alkylative Catellani-type reaction with the aryl-iodine bond reconstruction as the final step, which opens new synthetic opportunities within the Catellani-type reactions. Through in-depth mechanistic investigations, we have isolated and characterized key organopalladium intermediates, revealing the synergistic interaction of the dual ligands in merging the Catellani-type process with C(sp2)-I reductive elimination. The present study showcases the unique advantages of Pd/olefin ligand catalysis and emphasizes the effectiveness of the dual ligand system in expanding the chemical space of the Catellani chemistry. | Xiao-Xia Wang; Lei Jiao | Organometallic Chemistry; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663cce9921291e5d1dd9824c/original/dual-ligand-enabled-pd-catalyzed-ortho-alkylation-of-iodoarenes.pdf |
62bc466552acb76d26779f6b | 10.26434/chemrxiv-2022-jc55l | A Sulfonative rearrangement of N-Aryl Sulfamates to para-Sulfonyl Anilines | The C(sp2)-aryl sulfonate functional group is widely found in bioactive scaffolds but can often only be accessed under forcing temperatures (>190 °C) and corrosive reaction conditions. Inspired by the Tyrer process to sulfa dyes that involves an aniline N(sp2)-SO3 intermediate en route to a C(sp2)-SO3 rearranged product - we deployed tributylsulfoammonium betaine (TBSAB) as an initiating mild sulfamating agent to sulfonate relay reagent.
A range of aniline and heterocyclic scaffolds were sulfonated in high conversions (6 examples of N(sp2)-sulfamates up to 99% isolated yield and 16 examples of C(sp2)-sulfonate in up to 80% isolated yield) with the ability to change the ortho-para selectivity of the products obtained under thermal control. Isolation of the N(sp2)-SO3 intermediates for a two-step procedure was significantly lower yielding than a direct one-pot procedure.
Furthermore, we explore counterion effects on the N- to C- sulfate rearrangement and discovered the reversibility of the TBSAB reagent. Investigation of the N- to C- mechanism through designed examples with variation at the heteroatom position, and kinetic isotope experiments (KIEH/D) confirmed the formation of a key N(sp2)-SO3 intermediate and further supporting evidence of an intermolecular mechanism. Compounds without an accessible nitrogen (or hydroxyl) lone pair did not undergo sulfonation under these reaction conditions.
| Yifei Zhou; Alan Jones | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bc466552acb76d26779f6b/original/a-sulfonative-rearrangement-of-n-aryl-sulfamates-to-para-sulfonyl-anilines.pdf |
67dbd29881d2151a022328d7 | 10.26434/chemrxiv-2025-m441k | Quantification of Reaction Barriers under Diffusion Controlled Conditions | In quantum chemistry, diffusion-controlled reactions are typically characterised by a monotonous rise in electronic energy, indicative of a barrierless process. In reality, this change in electronic energy is accompanied by an increase in entropy, thereby introducing a barrier in free energy. While standard quantum chemical models fall short in capturing this phenomenon, we have developed a cost-efficient method to address this challenge. By tracking changes in covalent bonding based on quantum chemical descriptors, we can model the onset of entropy along the reaction path, by defining a cutoff which indicates the halfway point in the entropy gain. Utilizing a sigmoid fit function to model the entropy change, we obtain a a transition state in the free energy surface for such reactions. Our methodology is robust and suitable for diverse complexes within both organic and inorganic chemistry. | Martin M. Maehr; Radu A Talmazan; Maren Podewitz | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dbd29881d2151a022328d7/original/quantification-of-reaction-barriers-under-diffusion-controlled-conditions.pdf |
66d6942a12ff75c3a13aadbd | 10.26434/chemrxiv-2024-10n14 | Brownian Dynamics Simulation of Microscale Thermophoresis in Liquid | Microscale thermophoresis (MST) has garnered significant attention as a manipulation method for chemical species ranging from nanometers to micrometers in liquids. Despite the substantial increase in experimental reports on MST, a comprehensive theoretical model remains elusive due to its intricate mechanism. Consequently, experimental research into MST faces two primary challenges: (i) predicting the outcomes of experiments before their execution at a practical level and (ii) quantitatively interpreting experimental results by comparing them with numerical calculation results, such as evaluating the thermophoretic force acting on nanomaterials. To address these challenges, we have developed a numerical method for the thermophoresis of individual nanoparticles diffusing in a liquid by combining the finite element method for steady-state heat conduction with Brownian dynamics simulations. The scripts for the finite element method and Brownian dynamics calculations used in the present simulations are uploaded in the Supporting Information and freely available. The numerical results demonstrated satisfactory agreement with the experimental results of laser-induced thermophoresis performed on polystyrene nanoparticles with a diameter of 500 nm in water. This numerical method is expected to be invaluable for predicting and interpreting MST phenomena in liquids. | Koki Ide; Tetsuro Tsuji; Takayuki Suzuki; Kenji Setoura | Physical Chemistry; Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d6942a12ff75c3a13aadbd/original/brownian-dynamics-simulation-of-microscale-thermophoresis-in-liquid.pdf |
60c74b6f842e650c15db3161 | 10.26434/chemrxiv.12333251.v1 | Gymnema Sylvestre A- Potential Inhibitor of COVID-19 Main Protease by MD Simulation Study | Gymnema sylvestre (GS) is one of the herbal plant used since in ancient times. The present study aimed to assess bioactive compounds GS mainly gymnemic acids as potential inhibitors for COVID-19 against Mpro enzyme using a molecular docking study. The docking score observed between -53.4 to - 42.4 of all gymnemic acids and its derivatives. Molecular Dynamics (MD) simulation studies carried out at 100ns supported the stability of GS molecules within the binding pocket. RMSD score of less than 3.6. mainly, our results supported that these GS molecules bind to the domain I & II, and domain II-III linker of 3CLpro enzyme, suggesting its suitability as strong candidate for therapeutic against COVID-19. <br /> | Senthil Kumar Subramani; Yash Gupta; Manish Manish; GBKS Prasad | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b6f842e650c15db3161/original/gymnema-sylvestre-a-potential-inhibitor-of-covid-19-main-protease-by-md-simulation-study.pdf |
663e808121291e5d1df402d9 | 10.26434/chemrxiv-2024-mn1h9 | Molecular Shuttles with a Photoresponsive Macrocycle:
Investigating Interactions and Operation within Lipid Membranes | Rotaxane-based molecular shuttles using their motion to move cargo within lipid bilayers could be used to position probes and actuators at specific membrane regions, enabling new ways to study and modulate biological and artificial membranes. As an initial step towards that goal, we designed a rotaxane whose ring is decorated with two azobenzene photoswitches. We investigated its operation in solution and within lipid bilayers of large unilamellar vesicles. In solution, two-dimensional exchange spectroscopy showed that the photoswitches can be stochastically shuttled along the axle at 0.114 Hz. Remarkably, the azobenzene units retain their photoreversibility and fatigue resistance when integrated into the rotaxane. Moreover, a 55% increase in the hydrodynamic radius (RH) of the vesicles was induced by consecutive cycles of azobenzene photoswitching at a 10 mol% concentration of rotaxane. Initial molecular dynamic simulations suggest water accumulates near the rotaxanes in the bilayer. Therefore, it is plausible that continuous rearrangement of the lipid packing induced by each azobenzene photoisomerization could facilitate further water penetration and vesicle swelling. However, other mechanisms could also contribute to the increase in RH. Future large-scale simulations and complementary experimental techniques will offer a better understanding of the observed phenomenon and determine if shuttling occurs within the bilayer. Our findings provide new insights into the interaction of rotaxanes with the surrounding lipids and their impact on membrane properties, aiding in developing systems for precise manipulation of lipid membranes for applications in biomedicine and bioengineering. | Udyogi N. K. Conthagamage; Rajitha T. Rajeshwar; Nasim Akthar; Macallister Lauren Davis; Senuri G. Jayawardana; Lilia Lopez; Jeremy Smith; Micholas Dean Smith; Víctor García-López | Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Photochemistry (Org.); Supramolecular Chemistry (Org.); Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663e808121291e5d1df402d9/original/molecular-shuttles-with-a-photoresponsive-macrocycle-investigating-interactions-and-operation-within-lipid-membranes.pdf |
66d9d22a51558a15ef24863a | 10.26434/chemrxiv-2024-769n0 | Dimolybdenum paddlewheel complexes with cation binding sites as electrolyte additives to manipulate the solid-electrolyte interphase at lithium metal anodes | Use of electrolyte additives at mM loadings to control the surface chemistry of lithium metal anodes (LMAs) is a leading strategy to improve safety, efficiency, and reliability of lithium metal batteries and promote various types of electrosynthetic reactions. Whereas previous studies employed either inorganic or organic additives, in this study we report the first organometallic additive, Mo2(mea)4 [1, mea = 2-(2- methoxyethoxy)acetate], a dimolybdenum paddlewheel complex that is stable under Li plating conditions. Unlike more classically used crown ether additives, complex 1 features cation binding sites in the second coordination sphere that promote reversible Li+ coordination. Furthermore, binding of Li+ ions to 1 induces aggregation of cationically charged coordination oligomers/polymers that assemble at the LMA surface due to electrostatic attraction. Upon surface immobilization and incorporation into the solid- electrolyte interphase (SEI), the additive serves multiple beneficial functions. It was found to protect the LMA against parasitic side reactions by chemical passivation, produce modest but measurable improvements to Li plating properties (e.g. overpotential, surface structure, Coulombic efficiency), and modulate the composition and thickness of the SEI. The latter effect translates to significantly decreased resistance in battery settings due to improved interfacial charge transport properties. The most notable benefit to battery cycling performance comes from calendar aging tests, which show that the presence of the additive protects the LMA from parasitic side reactions that would otherwise decrease overall cell cycling efficiency Collectively, these data disclose a new tactic for designing electrolyte additives using principles of organometallic synthesis. | Simon Gersib; Erik Askins; Matthew Li; Supundrika Subasinghe; Biki Behera; Dan McElheny; Seoung-Bum Son; Khalil Amine; Ksenija Glusac; Neal Mankad | Inorganic Chemistry; Organometallic Chemistry; Energy; Coordination Chemistry (Inorg.); Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d9d22a51558a15ef24863a/original/dimolybdenum-paddlewheel-complexes-with-cation-binding-sites-as-electrolyte-additives-to-manipulate-the-solid-electrolyte-interphase-at-lithium-metal-anodes.pdf |
6340505ccf3829cd5bc18471 | 10.26434/chemrxiv-2022-hs9lp | Constructive Ozonolysis: Capturing Primary Ozonides | Ozonolysis is a widely used and practical synthetic technique for the deconstructive oxidation of olefins using ozone. While there are numerous ozonolysis reactions that give myriad products and functionality, almost all of them involve scission at the olefin double bond. Utilizing ozone as a constructive reagent rather than a deconstructive one would open new domains of chemical reactivity and amplify molecular complexity in synthetic methodology. We report here the first instance of primary ozonides as preparative synthetic intermediates for a safe and green olefin syn-dihydroxylation reaction. Additionally, we have demonstrated this method using a continuous flow reactor that virtually eliminates peroxide accumulation and extended these applications towards the synthesis of pharmaceutically relevant small molecules including guaifenesin, the active ingredient in Mucinex and a precursor to ponesimod, a drug to treat multiple sclerosis. | Danniel Arriaga ; Andy Thomas | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6340505ccf3829cd5bc18471/original/constructive-ozonolysis-capturing-primary-ozonides.pdf |
646b8d46268ed316c9389d63 | 10.26434/chemrxiv-2023-r8wjl-v2 | Ultrafast Transient Vibrational Action Spectroscopy of Cryogenically Cooled Ions | Ultrafast transient vibrational action spectra of cryogenically cooled Re(CO)3(CH3CN)3+ ions are presented. Nonlinear spectra were collected in the time domain by monitoring the photodissociation of a weakly-bound N2 messenger tag as a function of delay times and phases between a set of three infrared pulses. Frequency-resolved spectra in the carbonyl stretch region show relatively strong bleaching signals that oscillate at the difference frequency between the two observed vibrational features as a function of the pump-probe waiting time. This observation is consistent with the presence of nonlinear pathways resulting from underlying cross-peak signals between the coupled symmetric asymmetric C≡O stretch pair. The successful demonstration of frequency resolved ultrafast transient vibrational action spectroscopy of dilute molecular ion ensembles provides an exciting new framework for the study of molecular dynamics in isolated, complex molecular ion systems. | Liangyi Chen; Zifan Ma; Joseph Fournier | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b8d46268ed316c9389d63/original/ultrafast-transient-vibrational-action-spectroscopy-of-cryogenically-cooled-ions.pdf |
60c7494fbdbb899c70a39150 | 10.26434/chemrxiv.12048738.v1 | Solution chemistry effects on the solvation shell of metal ions | <div>
<p>As natural aqueous solutions are far from
being pure water, being rich in ions, the properties of solvated ions are of
relevance for a wide range of systems, including biological and geochemical
environments. We conducted ab initio and classical MD simulations of the
alkaline earth metal ions Mg<sup>2+</sup> and Ca<sup>2+</sup> and of the alkali
metal ions Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup> and Cs<sup>+</sup> in
pure water and electrolyte solutions containing the counterions Cl<sup>–</sup>
and SO<sub>4</sub><sup>2–</sup>. Through a detailed analysis of these
simulations, this study reports on the effect of solution chemistry
(composition and concentration of the solution) to the ion–water structural
properties and interaction strength, and to the dynamics, hydrogen bond
network, and low-frequency dynamics of the ionic solvation shell. Except for
the ion–water radial distribution function, which is weakly dependent on the
counter-ions and concentrations, we found that all other properties can be
significantly influenced by the chemical characteristics of the solution.
Calculation of the velocity autocorrelation function of magnesium ions, for
example, shows that chlorine ions located in the second coordination shell of
Mg<sup>2+</sup> weaken the Mg(H<sub>2</sub>O)<sub>6</sub><sup>2+</sup>
hydration ‘cage’ of the cation. The result reported in this study suggest that
ionic solvation shell can be significantly influenced by the interactions
between other ions present in solution ions, especially those of opposite
charge. In more general terms, the chemical characteristics of the solution,
including the balance between ion-solvent and ion-ion interactions, could
result in significant differences in behavior and function of the ionic
solvation shell.</p>
</div> | Xiangwen Wang; Dimitrios Toroz; Seonmyeong Kim; Simon Clegg; Gun-Sik Park; Devis Di Tommaso | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7494fbdbb899c70a39150/original/solution-chemistry-effects-on-the-solvation-shell-of-metal-ions.pdf |
675783b4085116a133e25ebe | 10.26434/chemrxiv-2024-f0w08 | Chemoenzymatic Diazo Synthesis Enabled by Enzymatic Halide Recycling with Vanadium-Dependent Haloperoxidases | Diazo compounds are privileged carbene precursors in synthetic organic chemistry. Despite their versatility in both chemo- and biocatalytic synthesis, their preparation typically requires the use of reagents that are expensive, toxic, and unsustainable. Herein, we describe a chemoenzymatic strategy for the preparation of stabilized diazo compounds enabled by enzymatic halide recycling by vanadium-dependent haloperoxidase (VHPO) enzymes. The process involves the conversion of a carbonyl-containing compound to an intermediate hydrazone that is subjected directly to a VHPO-catalyzed nitrogen-nitrogen (N-N) bond oxidation to the corresponding diazo compound. The protocol is applied to a broad range of benzoylformate and isatin derivatives. Molecular docking experiments provide insight into reactivity rate differences between (E)- and (Z)-configured hydrazones in the VHPO-mediated oxidation process. Finally, the developed method is interfaced with lipase-mediated transacylation to produce a collection of diazo derivatives starting from a single benzoylformate starting material. | Manik Sharma; Yue Li; Lorenzo Layug; Katherine M. Davis; Kyle F. Biegasiewicz | Organic Chemistry; Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675783b4085116a133e25ebe/original/chemoenzymatic-diazo-synthesis-enabled-by-enzymatic-halide-recycling-with-vanadium-dependent-haloperoxidases.pdf |
65f868f666c13817293fd18c | 10.26434/chemrxiv-2024-sqjtp | Ti-Catalyzed 1,2-Diamination of Alkynes using 1,1-Disubstituted Hydrazines | Ti-catalyzed alkyne diamination and Ti- catalyzed alkyne hydrohydrazination proceed through a common N-aminoazatitanacyclobutene intermediate. Previously, these reactions have existed as processes catalyzed by distinct catalysts, where there are many reports (and catalysts) for hydrohydrazination, and only a single example (and catalyst) for diamination. Here, we demonstrate that a diamidoamine Ti catalyst, (NNN)Ti(=NNR2) (1, (NNN)H2 = N-methyl-N',N"-bis(trimethylsilyl)diethylenetriamine; R = alkyl, aryl), is capable of catalyzing both diamination and hydrohydrazination, where the selectivity is dictated by simple changes to the reaction conditions, capitalizing on Ph the fact that there are entropic differences at the selectivity branch point between diamination (unimolecular) and hydrohydrazination (bimolecular). This discovery leads to an expanded substrate scope for alkyne diamination, and an understanding of how structure-activity relationships can impact the relative rates (selectivity) of diamination and hydrohydrazination. More broadly, these results suggest that this strategy may be more generally applied to Ti hydrohydrazination catalysts to uncover new catalysts capable of alkyne diamination with 1,1-disubstituted hydrazines. | Partha Sarathi Karmakar; Ian Tonks | Catalysis; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f868f666c13817293fd18c/original/ti-catalyzed-1-2-diamination-of-alkynes-using-1-1-disubstituted-hydrazines.pdf |
64791a18be16ad5c5750d75a | 10.26434/chemrxiv-2023-80fg1 | Fluorosulfate as a Latent Sulfate in Peptides and Proteins | Sulfation widely exists in the eukaryotic proteome. However, understanding of the biological functions of sulfation in peptides and proteins has been hampered by the lack of methods to control its spatial or temporal distribution in the proteome. Herein, we report that fluorosulfotyrosine can serve as a latent precursor of sulfotyrosine in peptides and proteins, which can be efficiently converted into sulfotyrosine residues by hydroxamic acid activators under physiologically relevant conditions. Photocaging the hydroxamic acid activators further allowed for light-controlled activation of functional sulfopeptides. This work provides a valuable tool for probing functional roles of sulfation in the peptides and proteins. | Chao Liu; Xueyi Liu; Mi Zhou; Chaoshuang Xia; Chintan Soni; Zefeng Zhou; Yujia Wu; Abhishek Chatterjee; Cheng Lin; Jia Niu | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64791a18be16ad5c5750d75a/original/fluorosulfate-as-a-latent-sulfate-in-peptides-and-proteins.pdf |
60c74f8f842e65e6d7db3863 | 10.26434/chemrxiv.12921734.v1 | Calculation of the Detonation State of HN3 with Quantum Accuracy | <div>HN<sub>3</sub> is a unique liquid energetic material that exhibits ultrafast detonation chemistry and a transition to metallic states during detonation. We combine the ChIMES many-body reactive force field and the extended-Lagrangian multiscale shock technique (MSST) molecular dynamics method to calculate the detonation properties of HN<sub>3</sub> with the accuracy of Kohn-Sham density-functional theory. ChIMES is based on a Chebyshev polynomial expansion and can accurately reproduce density-functional theory molecular dynamics (DFT-MD) simulations for a wide range of unreactive and decomposition conditions of liquid HN<sub>3</sub>. We show that addition of random displacement configurations and the energies of gas-phase equilibrium products in the training set allows ChIMES to efficiently explore the complex potential energy surface. Schemes for selecting force field parameters and the inclusion of stress tensor and energy data in the training set are examined. Structural and dynamical properties, as well as chemistry predictions for the resulting models are benchmarked against DFT-MD. We demonstrate that the inclusion of explicit four-body energy terms is necessary to capture the potential energy surface across a wide range of conditions. The present force field, which was fit to a balance of forces, energies, and stress tensors yields excellent agreement with DFT, while exhibiting an orders-of-magnitude increase in computational efficiency over DFT-MD. Our results generally retain the accuracy of DFT-MD while yielding a high degree of computational efficiency, allowing simulations to approach orders of magnitude larger time and spatial scales. The techniques and recipes for MD model creation we present allow for direct simulation of nanosecond shock compression experiments and calculation of the detonation properties of materials with the accuracy of Kohn-Sham density-functional theory.</div> | Cong Huy Pham; Rebecca Lindsey; Laurence E. Fried; Nir Goldman | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f8f842e65e6d7db3863/original/calculation-of-the-detonation-state-of-hn3-with-quantum-accuracy.pdf |
641e30a491074bccd03cab4d | 10.26434/chemrxiv-2023-xppmb | A Förster Resonance Energy Transfer Assay for Investigating the Reactivity of Thioesters | The sulfur–carbonyl bond in a thioester is an “energy-rich” functionality but is hydrolytically stable, while susceptible to attack by thiolate and amine nucleophiles, enabling thioester chemistry to take place in aqueous medium. In this work, we developed a fluorogenic assay format for the direct and continuous investigation of the rate of reaction between thioesters and nucleophiles under various conditions. We designed three different substrates, mimicking the chemical environment in acyl-CoA, S-acylcysteine, and an activated thioester commonly used in chemical protein synthesis by native chemical ligation. The data resulting from monitoring of the reaction of these substrates with a series of nucleophiles at varying pH values generally recapitulated previously reported reactivity of thioesters. We investigated key aspects of native chemical ligation reaction conditions. Our data revealed a profound effect of the tris-(2-carboxyethyl)phosphine (TCEP) commonly used in systems where thiol–thioester exchange occurs, including a potentially harmful hydrolysis side reaction. These data provide insight for potential optimization of native chemical ligation chemistry. | Bengt Gless; Sabrina Schmied; Christian Adam Olsen | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641e30a491074bccd03cab4d/original/a-forster-resonance-energy-transfer-assay-for-investigating-the-reactivity-of-thioesters.pdf |
640aee1f0e6a36faba0c9473 | 10.26434/chemrxiv-2022-q8hhp-v2 | Ultrafast spin crossover photochemical mechanism in [Fe(2,2'−bipyridine)3]2+ revealed by quantum dynamics | The role of triplet intermediates in the photoinduced spin crossover reaction of [FeII(2,2'-bipyridine)3]2+ is still under debate. Employing quantum dynamics, we show that the metal-centered (MC) triplets are responsible for the transfer to the quintet high-spin state. This photochemical pathway is made possible thanks to bipyridine stretching vibrations, facilitating the transfer between the initial metal-ligand charge transfer (MLCT) states to the MC triplets. These results show the central role of ligands in modulating the excited state spectrum and the photochemical mechanism, opening the route for increased metal-centered lifetime that increases the effciency of iron-based photocatalysts. | Marc Alias-Rodriguez; Swarnendu Bhattacharyya; Miquel Huix-Rotllant | Theoretical and Computational Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640aee1f0e6a36faba0c9473/original/ultrafast-spin-crossover-photochemical-mechanism-in-fe-2-2-bipyridine-3-2-revealed-by-quantum-dynamics.pdf |
60dfb73be7f2bf5b4e8110d6 | 10.26434/chemrxiv-2021-vjbh3 | Computational Scaling Relationships Predict Experimental Activity and Rate Limiting Behavior in Homogenous Water Oxidation | While computational screening with first-principles density functional theory (DFT) is essential for evaluating mechanisms of candidate catalysts, limitations in accuracy typically prevent prediction of experimentally relevant activities. Exemplary of these challenges are homogeneous water oxidation catalysts (WOCs) where differences in experimental conditions along with small changes in ligand structure can alter rate constants by over an order of magnitude. To leverage computational screening for homogeneous WOC design, a distinct approach is needed. Here, we compute mechanistically-relevant electronic and energetic properties for 19 mononuclear Ru transition metal complexes (TMCs) from three experimental water oxidation catalysis studies. We discover that 15 of these TMCs have experimental activities that can be correlated to a single property, the ionization potential of the Ru(II)-O2 catalytic intermediate. This scaling parameter is well correlated with experimentally-reported rate constants, allowing quantitative understanding activity trends and insight into rate-limiting behavior. We use this approach to rationalize differences in activity with differing experimental conditions, and we qualitatively analyze the source of distinct behavior for differing electronic states in the other four catalysts. Comparison to closely related single-atom catalysts and modified WOCs enables rationalization of the source of rate enhancement in these experimental WOC catalysts. | Daniel Harper; Heather Kulik | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dfb73be7f2bf5b4e8110d6/original/computational-scaling-relationships-predict-experimental-activity-and-rate-limiting-behavior-in-homogenous-water-oxidation.pdf |
60c75876469df4e150f4566d | 10.26434/chemrxiv.14555706.v1 | Autonomous Exploration and Identification of High Performing Adsorbents using Active Learning | <div>MOFs and COFs are porous materials with a large variety of applications including gas</div><div>storage and separation. Synthesised in a modular fashion from distinct building blocks, a</div><div>near in?nite number of structures can be constructed and the properties of the material can</div><div>be tailored for a speci?c application. While this modularity is a very attractive feature it also</div><div>poses a challenge. Attempting to identify the best performing material(s) for a given appli-</div><div>cation is experimentally intractable. Current research e?orts combine molecular simulations</div><div>and machine learning techniques to evaluate the simulated performance of hundreds of thou-</div><div>sands of materials to identify top performing MOFs and COFs for a given application. These</div><div>approaches typically rely on moderated brute-force screening which is still resource-intensive</div><div>as typically between 70 - 100 % of the hundreds of thousands of materials must be simulated</div><div>to create a training set for the machine learning models used, restricting screening to rela-</div><div>tively simple molecules. In this work we demonstrate our novel Bayesian mining approach</div><div>to materials screening which allows 62 - 92 % of the top 100 porous materials for a range of</div><div>applications to be readily identi?ed from large materials databases after only assessing less</div><div>than one percent of all materials. This is a stark contrast to the 0 - 1 % achieved by conven-</div><div>tional brute-force screening where porous materials are just chosen at random during a high</div><div>throughput screening. Through this accelerated virtual screening process, the identi?cation of</div><div>high performing materials can be used to more rapidly inform experimental e?orts and hence</div><div>lead to an acceleration of the entire research and development pipeline of porous materials.</div> | Gael Donval; Calum Hand; James Hook; Emiko Dupont; Malena Sabate Landman; Malina Freitag; Matthew Lennox; Tina Düren | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75876469df4e150f4566d/original/autonomous-exploration-and-identification-of-high-performing-adsorbents-using-active-learning.pdf |
63d63670246f1674d6d0c065 | 10.26434/chemrxiv-2023-njj75 | Decoding the assembly of Mixed and Branched heterotypic Ubiquitin chains | In eukaryotes, post-translational modification (PTMs) creates a proteome diversity that is essential for cellular processes. The PTM ubiquitination regulates cell signaling, immune response, protein processing, molecular trafficking, and DNA repair. While molecular trafficking typically relies on substrate monoubiquitination, the other functions require the assembly of polymeric Ubiquitin chains on the substrate. The chains are linked through lysine amino acids of Ubiquitin, and depending on which lysine is linked, the chains could be heterotypic or homotypic. The heterotypic Ubiquitin chains generate myriad cellular signals whose functions are distinct from the homotypic Ubiquitin chains. Heterotypic chains can be mixed, branched, or a combination of both. The molecular rules of heterotypic chain assembly are poorly understood. While several techniques exist to detect these chains, few exist to study their assembly. Here we describe a new technique based on isotopic labeling and mass spectrometry to study the assembly of mixed and branched heterotypic chains. The technique is demonstrated using multiple Ubiquitin enzymes and Ubiquitin chains as substrates and will be instrumental in studying the assembly of large Ubiquitin polymeric chains. | Gajendra Singh; Sanjeev Kumar; Ranabir Das | Biological and Medicinal Chemistry; Biochemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d63670246f1674d6d0c065/original/decoding-the-assembly-of-mixed-and-branched-heterotypic-ubiquitin-chains.pdf |
61c42697203b404f2696e82b | 10.26434/chemrxiv-2021-w8brg-v3 | Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist | The overwinding and underwinding of duplex segments between junctions have been used in designing both left-handed and right-handed DNA origami nanostructures. For a variety of DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the DNA tile (specified as the intrinsic tile curvature) has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile curvature and its evolution in DNA tubes by the coupling of the twist of the inter-tile arm (specified as the arm twist) have never been addressed. In this work, we designed three types of tile cores built around a circular 128 nucleotide scaffold by using longitudinal weaving (LW), bridged longitudinal weaving (bLW) and transverse weaving (TW). Joining the tiles with inter-tile arms having the length of an odd number of DNA half-turns (termed O-tiling) almost resulted into planar 2D lattices, whereas joining the tiles with the arms having the length of an even number of DNA half-turns (termed E-tiling) nearly generated tubes. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the E-tiling tubes and thereby the conformations of their component tiles with addressable concave and convex curvatures. When the arms have the normal winding at the relaxed B-form of DNA, the intrinsic tile curvature deter-mines the chirality of the E-tiling tubes. By regulating the arm length and the sticky end length of the bLW-Ep/q (E-tiling of the bLW cores with the arm length of p-bp and the sticky end length of q-nt) assemblies, the arm can be overwound, resulting in a left-handed twist, and can also be underwound, resulting in a right-handed twist. Chiral bLW-Ep/q tubes with either a right-handed curvature or a left-handed curvature can also be formed by the coupling of the intrinsic tile curvature and the arm twist. We were able to assign the chiral indices (n,m) to each tube using high-resolution AFM images, and therefore were able to estimate the tile curvature using a regular polygon model that approximated the transverse section of the tube. A deeper understanding of the integrated actions of dif-ferent types of twisting forces on the DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future. | Chuan Jiang; Biao Lu; Wei Zhang; Yoel P. Ohayon; Feiyang Feng; Shou-Jun Xiao; Shijie Li; Nadrian C. Seeman | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c42697203b404f2696e82b/original/regulation-of-2d-dna-nanostructures-by-the-coupling-of-intrinsic-tile-curvature-and-arm-twist.pdf |
60c74b844c8919b0bdad347a | 10.26434/chemrxiv.12344258.v1 | Donor Acceptor Copolymers from Cyclopentannulation Polymerizations with Dicyclopenta[cd,jk]pyrene and Dicyclopenta[cd,lm]perylene Acceptors | A series of donor-acceptor copolymers with dicyclopenta[cd,jk]pyrene and dicyclopenta[cd,lm]perylene acceptor units was prepared via palladium catalyzed cyclopenta-annulation reactions. The acceptor units were paired with diethynyl containing donor groups based on benzo[1,2-b:4,5-b']dithiophene, thieno[3,2-b]thiophene, and 4-octyl-4H-dithieno[3,2-b:2',3'-d]pyrrole to create six polymer variants. The cyclopentannulation polymerization resulted in copolymers with molecular weights (Mn) of 6-14 kDa and broad light absorption in the visible region with band gaps of 1.38-1.85 eV. The synthetic methodology, as well as optoelectronic properties, including thin-film absorption and cyclic voltammetry, of the donor-acceptor copolymers are presented.<br /> <br /><br /> | Ain Uddin; Kyle Plunkett | Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b844c8919b0bdad347a/original/donor-acceptor-copolymers-from-cyclopentannulation-polymerizations-with-dicyclopenta-cd-jk-pyrene-and-dicyclopenta-cd-lm-perylene-acceptors.pdf |
619cc1a0836f654deb7a3d92 | 10.26434/chemrxiv-2021-2kxxt | Impedance-based forecasting of battery performance amid uneven usage | Accurate forecasting of lithium-ion battery performance is important for easing consumer concerns about the safety and reliability of electric vehicles. Most research on battery health prognostics focuses on the R&D setting where cells are subjected to the same usage patterns, yet in practice there is great variability in use across cells and cycles, making forecasting much more challenging. Here, we address this challenge by combining electrochemical impedance spectroscopy (EIS), a non-invasive measurement of battery state, with probabilistic machine learning. We generated a dataset of 40 commercial lithium-ion coin cells cycled under multistage constant current charging/discharging, with currents randomly changed between cycles to emulate realistic use patterns. We show that future discharge capacities can be predicted with calibrated uncertainties, given the future cycling protocol and a single EIS measurement made just before charging, and without any knowledge of usage history. Our method is data-efficient, requiring just eight cells to achieve a test error of less than 10%, and robust to dataset shifts. Our model can forecast well into the future, attaining a test error of less than 10% when projecting 32 cycles ahead. Further, we find that model performance can be boosted by 25% by augmenting EIS with additional features derived from historical capacity-voltage curves. Our results suggest that battery health is better quantified by a multidimensional vector rather than a scalar State of Health, thus deriving informative electrochemical `biomarkers' in tandem with machine learning is key to predictive battery management and control. | Penelope Jones; Ulrich Stimming; Alpha Lee | Theoretical and Computational Chemistry; Energy; Machine Learning; Chemoinformatics - Computational Chemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619cc1a0836f654deb7a3d92/original/impedance-based-forecasting-of-battery-performance-amid-uneven-usage.pdf |
64ac10c26e1c4c986b24155b | 10.26434/chemrxiv-2023-bfhnh | Cyclic(Alkyl)(Amino)Carbene Stabilized Gold Nanoparticles: Efficient Catalyst for Selective Electrochemical Reduction of CO2 to CO | Electrochemical reduction of CO2 to value-added products is an important area for sustainable energy research. The nanomaterials offer a wide variety of catalysts for this task. In this work, we have synthesized an extremely electron-rich cyclic(alkyl)(amino)carbene (CAAC) stabilized gold nanoparticles (AuNPs) and utilized them for the electrochemical reduction of CO2. This newly prepared CAAC functionalized AuNP catalyst demonstrates a remarkable faradaic efficiency (FE) of 94% towards selective carbon monoxide (CO) formation (at pH 6.3, 2 hr of controlled potential electrolysis at -0.7 V vs NHE). Our results establish CAAC as a promising ligand for surface functionalization of AuNPs through the strong σ-donation, which enhances the electrocatalytic properties and set a platform for further developing persistent carbenes as the universal ligands. | Moushakhi Ghosh; Paramita Saha; Sumit Roy; Pramod Pillai; Abhishek Dey; Shabana Khan | Inorganic Chemistry; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrochemistry; Main Group Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ac10c26e1c4c986b24155b/original/cyclic-alkyl-amino-carbene-stabilized-gold-nanoparticles-efficient-catalyst-for-selective-electrochemical-reduction-of-co2-to-co.pdf |
62a08f9b804dbe03323e9a74 | 10.26434/chemrxiv-2022-r228j | Hydrogen Bonding-Induced Oxygen Clusters and Long-Lived Room Temperature Phosphorescence from Amorphous Polylols | The study of non-conjugated luminescent polymers (NCLPs) with fluorescence and long-lived room-temperature phosphorescence is of great significance for revealing the essence of NCLPs luminescence, which has gradually attracted the attention of researchers in recent years. Herein, polymethylol (PMO) and poly(3-butene-1,2-diol) (PBD) with polyhydroxyl structures were prepared and their luminescence behaviors were investigated to further reveal the clusteroluminescence (CL) mechanism. Compared with the weak or even non-luminescent behavior of polyvinyl alcohol, PMO and PBD exhibit cyan-blue fluorescence with quantum yields of ca. 12% and green room-temperature phosphorescence with lifetimes of ca. 89 ms in the solid state. Both fluorescence and phosphorescence exhibit typical excitation-dependent CL behavior. Experimental and theoretical analyses show that the strong hydrogen-bonding interaction of PMO and PBD greatly promotes the formation of oxygen clusters and the through-space n-n interaction of oxygen atoms, enabling fluorescence and phosphorescence emission. The results of this work have important implications for understanding the clusteroluminescence mechanism of NCLPs and provide a new polymer design strategy for the rational design of novel NCLPs materials. | Bin Liu; Kang Chen; Ya-Ling Wang; Hai-Ru Li; Bo Chu; Zi-Shan Yan; Hao-Ke Zhang; Yong-Zhen Yang; Shengliang Hu; Xing-Hong Zhang | Organic Chemistry; Polymer Science; Photochemistry (Org.); Fluoropolymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a08f9b804dbe03323e9a74/original/hydrogen-bonding-induced-oxygen-clusters-and-long-lived-room-temperature-phosphorescence-from-amorphous-polylols.pdf |
63e30ee55c37ece322b90e9a | 10.26434/chemrxiv-2023-hqk71 | Defect-Free Synthesis of a Fully π-Conjugated Helical Ladder Polymer and Resolution into a Pair of Enantiomeric Helical Ladders | Fully π-conjugated ladder polymers with a spiral geometry represent a new class of helical polymers with great potential for organic nanodevices, but there is no precedent for an optically-active helical ladder polymer totally composed of achiral units. We now report the defect-free synthesis and resolution of a fully π-conjugated helical ladder polymer with a rigid helical cavity, which has been achieved by quantitative and chemoselective acid-promoted alkyne benzannulations of a rationally designed, random-coil achiral polymer followed by chromatographic enantioseparation. Because of a sufficiently high helix-inversion barrier, the isolated excess one-handed helical ladder polymer with the degree of polymerization of more than 15 showed a strong circular dichroism with the dissymmetry factor of up to 1.7 x 102 and is thermally stable, maintaining its optical activity in solution even at 100 °C, as well supported by molecular dynamics simulation. | Tomoyuki Ikai; Sayaka Miyoshi; Kosuke Oki; Ranajit Saha; Yuh Hijikata; Eiji Yashima | Organic Chemistry; Polymer Science; Conducting polymers; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e30ee55c37ece322b90e9a/original/defect-free-synthesis-of-a-fully-conjugated-helical-ladder-polymer-and-resolution-into-a-pair-of-enantiomeric-helical-ladders.pdf |
60c73e150f50dba0733955b9 | 10.26434/chemrxiv.6394409.v1 | Synthesis of a Novel Bicyclic Scaffold Inspired by the Antifungal Natural Product Sordarin | A simplified bicyclic scaffold inspired by the antifungal natural product sordarin was designed and synthesized which maintains the carboxylic acid/aldehyde (or nitrile) pharmacophore. A densely functionalized chiral cyclopentadiene was constructed in 8 steps and utilized in a Diels-Alder reaction with acrylonitrile. The resulting [2.2.1]cycloheptene was transformed into a scaffold possessing vicinal carboxylic acid and nitrile groups, with orientations predicted to provide high affinity for the fungal protein eukaryotic elongation factor 2 (eEF2). | Yibiao Wu; Chris Dockendorff | Natural Products; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e150f50dba0733955b9/original/synthesis-of-a-novel-bicyclic-scaffold-inspired-by-the-antifungal-natural-product-sordarin.pdf |
635264951db0bd1bd1335a08 | 10.26434/chemrxiv-2022-5qf36 | New Nucleic Base-tethered Trithiolato-bridged Dinuclear Ruthenium(II)-Arene Compounds: Synthesis and Antiparasitic Activity | Aiming to generate novel compounds with improved antitoxoplama activity by exploiting the parasite auxotrophies, a library of nucleic base-tethered trithiolato-bridged dinuclear ruthenium(II)-arene conjugates - was synthesized and evaluated. Various structural features as the nucleobase (adenine, uracil, cytosine, thymine, and xanthine) and the linker between the two units were progressively modified. To substantiate the concept, hybrid molecules comprising the diruthenium moiety and other type of pendant molecules were also synthesized and assessed. The use of the CuAAC (copper catalyzed azide-alkyne cycloaddition) approach for the obtainment of conjugates bearing the trithiolato diruthenium scaffold was validated. 37 Compounds (diruthenium conjugates and corresponding intermediates) were assessed in a primary screening for in vitro activity against transgenic Toxoplasma gondii tachyzoites constitutively expressing β-galactosidase (T. gondii β-gal) at 0.1 and 1 μM. In parallel the cytotoxicity in non-infected host cells (human foreskin fibroblasts, HFF) was determined by alamarBlue assay. 20 Compounds strongly impairing parasite proliferation with little effect on HFF viability were subjected to T. gondii β-gal dose-response studies (IC50, half maximal inhibitory concentration determination) and their toxicity for HFF was assessed at 2.5 μM. Two compounds showing promise for further development were identified: 14, ester conjugate with 9-(2-oxyethyl)adenine, and 36, a click conjugate bearing a 2-(4-(hydroxymethyl)-1H-1,2,3-triazol-1-yl)methyl substituent, with IC50 values of 0.059 and 0.111 μM respectively, significantly lower compared to the standard drug pyrimethamine (IC50 = 0.326 μM). Both 14 and 36 exhibited low toxicity against HFF when applied at 2.5 μM and are candidates as potential treatment options in a suitable in vivo model. | Oksana Desiatkina; Martin Mösching; Nicoleta Anghel; Ghalia Boubaker; julien Furrer; Yosra Amdouni; Andrew Hemphill; Emila Păunescu | Inorganic Chemistry; Bioinorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635264951db0bd1bd1335a08/original/new-nucleic-base-tethered-trithiolato-bridged-dinuclear-ruthenium-ii-arene-compounds-synthesis-and-antiparasitic-activity.pdf |
6797b722fa469535b90feb5a | 10.26434/chemrxiv-2025-qr0hk | EvolvedComplexity as a Total Synthesis Assessment Metric: Strychnine as a Case Study of Scoring Functions | The selection of synthetic routes to a small molecule of interest is enabled by the use of various tools to assess the chemical complexity of a given intermediate. While prior approaches assess the intrinsic molecular complexity or the facility with which an intermediate can be synthesized, in this study we introduce an alternative approach that tracks the progress towards the target structure in a given synthesis. A simple metric, EvolvedComplexity, was developed that compares the chemical similarity of a pair of molecules on the basis of the Tanimoto distance between chemical fingerprints. This complementary approach to assessing progress in synthesis may prove to be a useful tool for planning synthetic routes and for developing novel chemistries. | Abbigayle Cuomo; John-Paul Webster; H. Ray Kelly; Sumon Sarkar; Yu Shee; Sanil Sreekumar; Haote Li; Frederic Buono; Victor Batista; Timothy Newhouse | Theoretical and Computational Chemistry; Organic Chemistry; Natural Products; Process Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6797b722fa469535b90feb5a/original/evolved-complexity-as-a-total-synthesis-assessment-metric-strychnine-as-a-case-study-of-scoring-functions.pdf |
638ddb56e6f9a1946f2c9ccb | 10.26434/chemrxiv-2022-5ck0s | Glolloc: Mixture of Global and Local Experts for Molecular Activity Prediction | Quantitative structure-activity relationships (QSAR) models have been used for decades to predict the activity of small molecules, using encodings of the molecular structure, for which simple 2D descriptors of the molecular graph are still most commonly used. One of the recurrent problems of QSAR is that relationships observed for a specific scaffold (pruned molecular skeleton) are often not transferable to another; this is often addressed by building several local models from subsets of the chemical space. Similarly, single task models sometimes outperform large multi-task models in predicting the activity of small molecules against specific proteins. In this paper, we introduce Glolloc, a global-local MoE-QSAR architecture, based on a Mixture of Experts (MoE) framework. Glolloc combines predictions from global and local experts, provides a built-in model introspection tool, can enhance model performance, and removes the need to maintain several local models. Published at the MLDD workshop, ICLR 2022. | Héléna Alexandra Gaspar; Matthew Seddon | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638ddb56e6f9a1946f2c9ccb/original/glolloc-mixture-of-global-and-local-experts-for-molecular-activity-prediction.pdf |
61004da07bf0c93ed261416f | 10.26434/chemrxiv-2021-0mjmt | A Low-cost Sulfate-based All Iron Redox Flow Battery | Redox flow batteries (RFBs) are promising choices for stationary electric energy storage. Nevertheless, commercialization is impeded by high-cost electrolyte and membrane materials. Here, we report a low-cost all-iron RFB that features inexpensive FeSO4 electrolytes, microporous membrane along with a glass fiber separator. The addition of 0.1 м 1-ethyl-3-methylimidazolium chloride (EMIC) overcomes the low solubility of FeSO4 in water which is raised to 2.2 м. DFT calculations demonstrate that EMI+ can strengthen the interaction between sulfate anions and water molecules. This electrolyte composition also allows both anode and cathode reactions to operate without actively maintaining a pH gradient between them, thus eliminating the need for expensive ion exchange membranes. The all-iron RFB demonstrates stable operation at a current density of 20 mA cm−2 for more than 800 cycles via a simple, periodic regeneration process. Furthermore, the system cost of FeSO4/EMIC RFBs is projected to be $ 50 per kWh due to its low-cost active materials and the inexpensive microporous membrane. This low-cost, high-concentration all-iron RFB is a promising stationary energy‐storage system for storing renewable energy. | Sicen Yu; Xiujun Yue; John Holoubek; Xing Xing; Eric Pan; Tod Pascal; Ping Liu | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61004da07bf0c93ed261416f/original/a-low-cost-sulfate-based-all-iron-redox-flow-battery.pdf |
676d39296dde43c90862eca2 | 10.26434/chemrxiv-2024-bjx6t | Practical synthesis of Csp3 Chlorinated Compounds from Cyclopropanes, Olefins and C-H Bonds via photolysis of Willgerodt-type reagents | Csp3-Cl bonds are essential as diversification handles in organic synthesis and are found in many natural products and bioactive molecules. In this work, we introduce a general protocol for the selective chlorination of aryl cyclopropanes, olefins, and activated C-H bonds using the direct photoexcitation of Willgerodt-type reagents to generate chlorine radicals. Preliminary results on an iodine(I/III) catalytic process starting from abundant chloride salts are also presented. Furthermore, a one-pot protocol has been developed for the telescoped functionalization of benzylic chlorides with C, N, O, and S nucleophiles. Especially, this approach provides a platform to access 1,1-diaryl motifs, which are important building blocks for the synthesis of pharmacophores. | Tin V. T. Nguyen; Trinh T. H. Tran; Thanh V. Q. Nguyen; Jerome Waser | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676d39296dde43c90862eca2/original/practical-synthesis-of-csp3-chlorinated-compounds-from-cyclopropanes-olefins-and-c-h-bonds-via-photolysis-of-willgerodt-type-reagents.pdf |
675aff077be152b1d0bff705 | 10.26434/chemrxiv-2024-5hzqf | A Data-Science Approach to Experimental Catalyst Discovery: Integrating Exploration, Exploitation, and Serendipity | Predicting the performance of heterogeneous catalysts is difficult because it involves complex interactions and unknown elementary reactions; hence, traditional catalyst development relies on trial and error. Machine learning offers a structured approach to address these issues. However, this approach is limited by challenges such as descriptor design, sparse data, and context-dependent interactions. In this study, two machine learning systems were developed to address these challenges in catalyst discovery: a recommender system that balances exploration and exploitation, and a "serendipiter" that detects unexpected discoveries. These systems were tested on the oxidative coupling of methane, and the results demonstrated a promising improvement in the efficiency of catalyst discovery. The recommender, based on evidence theory, uses binary combinations of catalyst components as descriptors to predict performance. It handles incomplete data by quantifying contradictions and uncertainty, facilitating a balance between exploration (testing unevidenced catalysts) and exploitation (refining known high-performing ones). The recommender efficiently identified a diverse range of high-performing catalysts through adaptive sampling with 160 catalysts. The serendipiter, a meta-learner, identifies unexpected high-performing catalysts by leveraging different machine learning models. It increased the occurrence of serendipitous discoveries to 50%, compared to 3% with the recommender alone. In summary, these systems improve the efficiency and reproducibility of catalyst discovery by balancing exploitation, exploration, and serendipity. | Sunao Nakanowatari; Keisuke Takahashi; Dam Hieu-Chi; Toshiaki Taniike | Theoretical and Computational Chemistry; Materials Science; Catalysis; Machine Learning; Artificial Intelligence; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675aff077be152b1d0bff705/original/a-data-science-approach-to-experimental-catalyst-discovery-integrating-exploration-exploitation-and-serendipity.pdf |
674c85d45a82cea2fa9fb297 | 10.26434/chemrxiv-2024-3ld27 | Advancing Aqueous Solubility Prediction: A Machine Learning Approach for Organic Compounds Using a Curated Dataset | Aqueous solubility is one key property of a chemical compound that determines its possible use in different applications from drug development to materials sciences. In this work, we present an aqueous solubility prediction study that leverages a curated dataset merged from four distinct sources. This unified dataset encompasses a diverse range of organic compounds, providing a robust foundation for our investigation of solubility prediction. Our approach involves employing a variety of machine learning and deep learning models that combine an extensive array of chemical descriptors, fingerprints, and functional groups. This methodology is designed to address the complexities of solubility prediction, and it is tailored to achieve high accuracy and generalization. We tested the finalized model on a diverse dataset of 1282 unique organic compounds from the Husskonnen dataset. The results of our analysis demonstrate the success of our model, which, given an R2 value of 0.92 and an MAE value of 0.40, outperforms existing prediction methods for aqueous solubility on one of the most diverse datasets in the field. | Mushtaq Ali; Sylvia Vanderheiden; Christoph W. Grathwol; Pascal Friederich; Nicole Jung; Stefan Bräse | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674c85d45a82cea2fa9fb297/original/advancing-aqueous-solubility-prediction-a-machine-learning-approach-for-organic-compounds-using-a-curated-dataset.pdf |
66d04fbbf3f4b052907a9b38 | 10.26434/chemrxiv-2024-f5tq3-v2 | A field-portable technology for illicit drug discrimination via deep learning of hybridized reflectance/fluorescence spectro-scopic fingerprints | Novel Psychoactive Substances (NPS) pose one of the greatest challenges across the illicit drug landscape. They can be highly potent, and coupled with rapid changes in structure, tracking and identifying these drugs is difficult, and presents users with a ‘Russian roulette’ if used. Benzodiazepines, synthetic opioids, synthetic cannabinoids and synthetic cathi-nones account for the majority of NPS related deaths and harm. Detecting these drugs with existing field-portable technol-ogies is challenging and has hampered the development of community harm reduction services and interventions. Herein, we demonstrate that hybridizing fluorescence and reflectance spectroscopies can accurately identify NPS and provide concentration information, with a focus on benzodiazepines and nitazenes. The discrimination is achieved through a deep learning algorithm trained on a library of pre-processed spectral data. We demonstrate the potential for these measure-ments to be made using a low-cost, portable device that requires minimal user training. Using this device, we demon-strate the discrimination of 11 benzodiazepines and from ‘street’ tablets that include bulking agents and other excipients. We show the detection of complex mixtures of multiple drugs, with the key example of nitazene + benzodiazepine (metonitazene + bromazolam), fentanyl + xylazine and heroin + nitazene (etonitazene) combinations. These samples represent current drug trends and associated with drug related deaths. When combined with the implementation of detection technology in a portable device, these data point to the immediate potential to support harm reduction work in community-based settings. Finally, we demonstrate that the approach may be more broadly generalized to other drug classes outside of NPS discrimination. | Alexander Power; Matthew Gardner; Rachael Andrews; Gyles Cozier; Ranjeet Kumar; Tom Freeman; Ian Blagbrough; Jennifer Scott; Anca Frinculescu; Trevor Shine; Gillian Taylor; Caitlyn Norman; Herve Menard; Niamh Nic Daeid; Oliver Sutcliffe; Stephen Husbands; Richard Bowman; Tom Haines; Christopher Pudney | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d04fbbf3f4b052907a9b38/original/a-field-portable-technology-for-illicit-drug-discrimination-via-deep-learning-of-hybridized-reflectance-fluorescence-spectro-scopic-fingerprints.pdf |
60c75811469df47fc4f4558e | 10.26434/chemrxiv.14496015.v1 | Synthesis of Cardiotonic Steroids Oleandrigenin and Rhodexin B | This article describes a concise synthesis of cardiotonic steroids oleandrigenin (7) and its subsequent
elaboration into the natural product rhodexin B (2) from the readily available intermediate (8) that could be derived from
the commercially available steroids testosterone or DHEA via 3 step sequences. These studies feature an expedient
installation of the β16-oxidation based on β14-hydroxyl directed epoxidation and subsequent epoxide rearrangement. The
following singlet oxygen oxidation of the C17 furan moiety provides access to oleandrigenin (7) in 12 steps (LLS) and 3.9%
overall yield from 8. The synthetic oleandrigenin (7) was successfully glycosylated with L-rhamnopyranoside-based donor
using Pd(II)-catalyst, and the subsequent deprotection under acidic conditions provided cytotoxic natural product rhodexin
B (2) in 68% yield (2 steps). <br /> | Zachary Fejedelem; Nolan Carney; Pavel Nagorny | Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75811469df47fc4f4558e/original/synthesis-of-cardiotonic-steroids-oleandrigenin-and-rhodexin-b.pdf |
60c745849abda27e0cf8c5c9 | 10.26434/chemrxiv.10052531.v1 | Total Synthesis and Structural Verification of Isatindigotindoline C | Total synthesis of the polycyclic alkaloid isatindigotindoline C is achieved in two steps using an exo-selective [3+2]-dipolar cycloaddition. The synthesis verifies the originally computationally assigned relative stereochemistry. | Juha Siitonen; Muhammed Yousufuddin; Laszlo Kurti | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745849abda27e0cf8c5c9/original/total-synthesis-and-structural-verification-of-isatindigotindoline-c.pdf |
677e78676dde43c908b95e43 | 10.26434/chemrxiv-2024-kq9wl-v3 | Oxide’s Acidity Prediction in Smith Scale Using a Simple Linear Model | A numeric scale of acidity and basicity, developed by D.W. Smith, allows for quantitative comparison between different oxides and has been useful in explaining various oxide behaviors. In this study, we aim to predict oxide acidity on the Smith scale using a machine learning approach. Previous attempts using a linear fit based on electronegativity showed a clear trend but lacked precision due to the simplicity of the model and the multi-valent nature of metal oxides. We propose a multi-parameter model incorporating four features: electronegativity, metal valence (raised to the power of 1/3), ionic radius, and dipole polarizability. A simple linear neural network outperformed a more complex 1D convolutional neural network, demonstrating superior accuracy and interpretability. Our model significantly improved predictive performance as compared to the single-parameter model. These results were validated through predictions of testing data and unknown oxides acidity were predicted in this work. | Wen Xing; Yngve Larring; Kai Bao | Inorganic Chemistry; Inorganic Acid/Base Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e78676dde43c908b95e43/original/oxide-s-acidity-prediction-in-smith-scale-using-a-simple-linear-model.pdf |
67afd4e4fa469535b95b9d44 | 10.26434/chemrxiv-2025-f87x3 | Atomically Precise Single-Site Pt Catalyst via Dual-Confinements for Enhanced Low-Temperature Exhaust Oxidation | Developing single-site catalysts (SSCs) with thermal stability and high activity towards exhaust oxidation is crucial yet challenging, due to sintering at severe reaction temperature and limited activity. Here, we report a Pt SSC with atomic-precision structures confined by both polyoxometalate (POM) and Zr-based Metal-Organic Frameworks (MOF) NU1K, exhibits high oxidation activity and stability towards exhaust oxidation. Difference envelope density (DED) and pair distribution function (PDF) analyses showed that isolated PtV9O28 clusters are well-maintained in the c-pores of NU1K. The node-bound formate facilitates partial reduction of isolated Pt (IV) species in single crystals to Pt (II) species in isolated PtV9O28 clusters after encapsulation in NU1K with the generation of oxygen vacancy as demonstrated by 1H Nuclear Magnetic Resonance (NMR) and X-ray Photoelectron Spectroscopy (XPS). When the simultaneous oxidation of CO, C3H6, and C3H8 was performed on these fully exposed single-Pt sites, the T100 (temperature at 100% conversion) for CO and C3H6 oxidation significantly decreased by 100 °C on PtV9O28@NU1K compared to that of PtV9O28/ZrO2. Meanwhile, it completely oxidizes C3H8 at 260 °C, but C3H8 oxidation does not occur on PtV9O28/ZrO2 until 470 °C. Theoretical calculation shows C3H8 molecules are easily absorbed to Pt sites on isolated PtV9O27 cluster with the adsorption energy of -1.84eV. These molecularly defined SSCs structures facilitate understanding the origins of catalyst activity and designing fully dispersed catalysts with maximum atom efficiency. | Qin Liu; Zhenhao Hou; Yanghong Yu; Zhihengyu Chen; Yucheng Huang; Chuanqiang Wu; Wentuan Bi; Karena W. Chapman; Joseph T. Hupp | Inorganic Chemistry; Catalysis; Coordination Chemistry (Inorg.); Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67afd4e4fa469535b95b9d44/original/atomically-precise-single-site-pt-catalyst-via-dual-confinements-for-enhanced-low-temperature-exhaust-oxidation.pdf |
656415e029a13c4d47123ccf | 10.26434/chemrxiv-2023-x3w8t | Photoswitching of arylazopyrazoles upon S1 (nπ*) excitation studied by transient absorption and ab-initio molecular dynamics | Arylazopyrazoles (AAPs) are an important class of molecular photoswitches with high photostationary states (PSS) and long thermal lifetimes. The ultrafast photoisomerization of four water-soluble arylazopyrazoles, all of them featuring an ortho-dimethylated pyrazole ring, is studied by narrowband femtosecond transient absorption spectroscopy and ab-initio molecular dynamics calculations. Upon S1 (nπ*) photoexcitation of the planar E-isomers (E-AAPs), excited-state bi-exponential decays with time constants τ1 in the 220–440 fs range and τ2 in the 1.4–1.8 ps range are observed, comparable to those reported for azobenzene (AB). This is indicative of the same bottleneck for completing the photoisomerization which was reported for ABs. In contrast to the planar E-AAPs, a twisted E-AAP with two methyl groups in ortho-position of the phenyl ring displays faster initial photoswitching with τ1=170 ± 10 fs and τ2=1.6 ± 0.1 ps. Our DFT calculations and ab-initio molecular dynamics simulations of E-AAPs on the S0 and S1 potential energy surfaces suggest that twisted E-isomer azo photoswitches exhibit faster initial photoisomerization dynamics out of the Franck-Condon region due to a weaker π-coordination of the central CNNC unit to the aromatic ligands. | Till Reichenauer; Marcus Böckmann; Katharina Ziegler; Vikas Kumar; Bart Jan Ravoo; Nikos Doltsinis; Sebastian Schlücker | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Chemical Kinetics; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656415e029a13c4d47123ccf/original/photoswitching-of-arylazopyrazoles-upon-s1-n-excitation-studied-by-transient-absorption-and-ab-initio-molecular-dynamics.pdf |
6132ea0627d90625437d3f4a | 10.26434/chemrxiv-2021-fq3mg | Insights into the Binding and Covalent Inhibition Mechanism of PF-07321332 to SARS-CoV-2 Mpro | The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been causing the COVID-19 pandemic resulting in several million death were reported. Numerous investigations have been carried out to discover a compound that can inhibit the biological activity of SARS-CoV-2 main protease, which is an enzyme related to the viral replication. Among these, PF-07321332 is currently under clinical trial for COVID-19 therapy. Therefore, in this work, atomistic and electronic simulations were performed to unravel the binding and covalent inhibition mechanism of the compound to Mpro. Initially, 5 µs of steered-molecular dynamics simulations were carried out to evaluate the ligand-binding process to SARS-CoV-2 Mpro. Successfully generated bound state between two molecules showed the important role of the PF-07321332 pyrrolidinyl group and the residues Glu166 and Gln189 in the ligand-binding process. Moreover, from the MD-refined structure, quantum mechanics/molecular mechanics (QM/MM) calculations were carried out to unravel the reaction mechanism for the formation of thioimidate product from SARS-CoV-2 Mpro and PF07321332 inhibitor. We found that the catalytic triad Cys145–His41–Asp187 of SARS-CoV-2 Mpro plays important role in the activation of PF-07321332 covalent inhibitor, which renders the deprotonation of Cys145 and, thus, facilitates further reaction. Our results are definitely beneficial for better understanding on the inhibition mechanism and designing new effective inhibitors for SARS-CoV-2 Mpro. | Son Tung Ngo; Trung Hai Nguyen; Nguyen Thanh Tung; Binh Khanh Mai | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6132ea0627d90625437d3f4a/original/insights-into-the-binding-and-covalent-inhibition-mechanism-of-pf-07321332-to-sars-co-v-2-mpro.pdf |
679008b7fa469535b9117aed | 10.26434/chemrxiv-2025-cgp0s | ‘Innocent’ Hexafluorophosphate Salts Induce Capacity Fade in Non-Aqueous Redox Flow Batteries | The use of organic active materials in redox flow batteries (RFBs) presents a promising approach to sustainable large-scale energy storage. However, the cycling stability of non-aqueous organic RFB electrolytes is generally limited by the occurrence of degradation reactions that cause capacity fade. These reactions are commonly thought to form products that are no longer electrochemically active. Here we study capacity fade in non-aqueous RFBs using the bipolar 1,2,4-benzotriazin-4-yl radical (1) in a symmetric cell (10/-║10/+). Active material crossover does not contribute to capacity fade in these symmetric RFBs, allowing the determination of intrinsic electrolyte stability. We show that the negative redox reaction (10/-) acts as a ‘reporter’ of electrolyte degradation, which reveals that capacity fade occurs in a non-linear (autocatalytic) fashion caused by acid-induced decomposition of the commonly used supporting salt anion PF6- in the posolyte solution. This is shown to be a universal degradation reaction in non-aqueous RFBs with PF6- supporting salts. Although the posolyte is not negatively affected by acidic degradation products, crossover of acid to the opposite compartment leads to capacity-limiting protonation of the negolyte active material. By replacing PF6- with other anions, the stability of these non-aqueous electrolytes was substantially improved. This allowed the construction of a symmetrical RFB based on 0.38M of active material 1 that can be cycled for >43 days with very high capacity retention. | Wenlong Tang; Jelte Steen; Jurjen Hettinga; Johan Hjelm; Edwin Otten | Organic Chemistry; Inorganic Chemistry; Energy; Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679008b7fa469535b9117aed/original/innocent-hexafluorophosphate-salts-induce-capacity-fade-in-non-aqueous-redox-flow-batteries.pdf |
632e22362984c91d4d6aa766 | 10.26434/chemrxiv-2022-7hgbk | The Influence of Sintering Condition on Microstructure, Phase Composition, and Electrochemical Performance of the Scandia- Ceria- Co-Doped Zirconia for SOFCs | Samples of 6 mol% Sc2O3- 1 mol% CeO2 co-doped ZrO2 were fabricated by conventional ceramic processing methods and sintered at various temperatures from 1000 °C to 1650 °C in air. The sintering conditions on microstructure and phase content are investigated using various characterization methods, including pycnometry, diffraction, and spectroscopy. The electrical conductivity of samples was investigated using electrochemical impedance spectroscopy (EIS). The effect of inductive load (measured from room temperature to 800 °C) is discussed in low to high-temperature regimes. At T<400 °C since the arc is not a complete semicircle, the high-frequency arc could be fit using a constant phase element (CPE), while by subtraction of inductive load, a good fit is achieved using a capacitor element instead of CPE. The Arrhenius conductivity plot of samples reveals that the specimen sintered at 1600 °C for 6 hours exhibits the highest conductivity. The activation energy (Ea) and conductivity pre-exponential (σ0) factor are calculated from a linear fit to data that decreases by the increase in sintering temperature. | POOYA ELAHI; Elizabeth Winterholler; Taylor Sparks | Materials Science; Inorganic Chemistry; Energy; Ceramics; Electrochemistry; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632e22362984c91d4d6aa766/original/the-influence-of-sintering-condition-on-microstructure-phase-composition-and-electrochemical-performance-of-the-scandia-ceria-co-doped-zirconia-for-sof-cs.pdf |
66928754c9c6a5c07a2e7ee9 | 10.26434/chemrxiv-2024-1j2wb | A Reusable Non-Complementary-DNA-Based Neural Network | The emulation of intelligence across diverse domains of the human brain has spurred the development of neural network based artificial intelligence. The computation of the DNA-based neural network has recently emerged as a focal point of research due to its versatility, scalability, energy efficiency and potentially other huge benefits and implications, as compared to electronic computation. Despite notable advancements, the development of the current DNA neural networks, based on the complementary pairing of DNA nucleobases, is restricted by the lack of reusability of the DNA computing materials, one of key bottlenecks impeding their progression towards neural network learning and evolution. As a result, even the state-of-the-art DNA neural network computations are limited to one-time use currently. Here we report the design of an unprecedented, reusable DNA based non-complementary perceptron (NCP) strategy that implements thresholding and weighted summation functions like neurons and the corresponding neural networks capable of 4-bit molecular pattern recognition. To facilitate the scaling-up of the non-complementary circuits, a modulated concept employing “tagging” domains is also coined. We demonstrate that non-complementary “winner-take-all” circuit can be rationally constructed with a non-complementary annihilator strand. Such NCP based neural network architecture is capable of 4-bit pattern recognition, evidenced by its success in playing the “I Spy” game. Most importantly, when removable input strands (lipid-oligonucleotide conjugates) are utilized, this NCP-based pattern recognition neural network shows high fidelity in multiple-cycle computing. This suggests a reusable DNA based NCP computation strategy as a potential conceptual breakthrough for the design of next-generation DNA computers. | Chengjie Sun; Xiaoyang Liu; Jiafeng Zhong; Qin Zhou; Jianjun Cheng | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66928754c9c6a5c07a2e7ee9/original/a-reusable-non-complementary-dna-based-neural-network.pdf |
65cacaa266c1381729813b06 | 10.26434/chemrxiv-2024-82644 | Can we achieve atmospheric chemical environments in the laboratory? An integrated model-measurement approach to chamber SOA studies | Secondary organic aerosol (SOA), atmospheric particulate matter formed from low-volatility products of volatile organic compound (VOC) oxidation, impacts both air quality and climate. Current 3D models, however, cannot reproduce the observed variability in atmospheric organic aerosol. Because many SOA model descriptions are derived from environmental chamber experiments, our ability to represent atmospheric conditions in chambers directly impacts our ability to assess the air quality and climate impacts of SOA. Here, we develop a new approach that leverages global modeling and detailed mechanisms to design chamber experiments that mimic the atmospheric chemistry of organic peroxy radicals (RO2), a key intermediate in VOC oxidation. Drawing on decades of laboratory experiments, we develop a framework for quantitatively describing RO2 chemistry and show that no previous experimental approaches to studying SOA formation have accessed the relevant atmospheric RO2 fate distribution. We show proof-of-concept experiments that demonstrate how SOA experiments can access a range of atmospheric chemical environments and propose several directions for future studies. | Hannah Kenagy; Colette Heald; Nadia Tahsini; Matthew Goss; Jesse Kroll | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cacaa266c1381729813b06/original/can-we-achieve-atmospheric-chemical-environments-in-the-laboratory-an-integrated-model-measurement-approach-to-chamber-soa-studies.pdf |
64c75f7ace23211b20d99109 | 10.26434/chemrxiv-2023-qv6d2 | Theoretical Insight into the Effect of Phosphorus Oxygenation on Nonradiative Decays: Comparative Analysis of P-Bridged Stilbene Analogs | Incorporation of phosphorus element into a 𝜋-conjugated skeleton offers valuable prospects for adjusting the electronic structure of the resulting functional 𝜋-electron systems. The trivalent phosphorus has the potential to decrease the LUMO level through the 𝜎∗-𝜋∗ interaction, which is further enhanced by its oxygenation to the pentavalent P center. This study shows that utilizing our computational analysis to examine excited-state dynamics based on radiative/nonradiative rate constants and fluorescence quantum yield (ΦF) is effective for analyzing the photophysical properties of P-containing organic dyes. We theoretically investigate how the trivalent phosphanyl group and pentavalent phosphine oxide moiety affect radiative and nonradiative decay processes. We evaluate four variations of P-bridged stilbene analogs. Our analysis reveals that the primary decay pathway for photo-excited bis-phosphanyl-bridged stil- bene is the intersystem crossing (ISC) to the triplet state and nonradiative. The oxidation of the phosphine moiety, however, suppresses the ISC due to the relative destabilization of the triplet states. The calculated rate constants match an increase in experimental ΦF from 0.07 to 0.98, as simulated from 0.23 to 0.94. The reduced HOMO–LUMO gap supports a red shift in the fluorescence spectra relative to the phosphine analog. The thiophene-fused variant with the non-oxidized trivalent P cen- ter exhibits intense emission with a high ΦF, 0.95. Our prediction indicates that the ISC transfer is obstructed owing to relatively destabilized triplet state induced by the thiophene substitution. Conversely, the thiophene-fused analog with the phosphine ox- ide moieties triggers a high-rate internal conversion mediated by conical intersection, leading to a decreased ΦF. | Naoto Inai; Shigehiro Yamaguchi; Takeshi Yanai | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c75f7ace23211b20d99109/original/theoretical-insight-into-the-effect-of-phosphorus-oxygenation-on-nonradiative-decays-comparative-analysis-of-p-bridged-stilbene-analogs.pdf |
66fa233a12ff75c3a1e6b304 | 10.26434/chemrxiv-2024-x1hfm-v3 | The NanoSIMS-HR: the next generation of high spatial resolution dynamic SIMS | The high lateral resolution and sensitivity of the NanoSIMS 50 and 50L series of dynamic SIMS instruments has enabled numerous scientific advances over the past 25 years. Here we report on the NanoSIMS-HR, the first major upgrade to the series, and analytical tests in a suite of sample types, including an aluminum sample containing silicon crystals, microalgae and plant roots colonized with arbuscular mycorrhizal fungi. Significant improvements have been made in the Cs+ ion source, high voltage (HV) control, stage reproducibility, and other aspects of the instrument that affect performance. The modified design of the NanoSIMS-HR thermal-ionization Cs+ source enables a 5-pA primary ion beam to be focused into a 100 nm spot, a ~2.5-fold increase compared to Cs+ sources on previous instruments (~2 pA at 100 nm). The brightness of the new Cs+ source enables an ultimate lateral resolution as high as 30 nm and improved detection limits for a given analysis area. Sample stage movement accuracy is higher than 500 nm, enabling many-fold higher throughput automated analyses. With the new HV control, the primary ion beam impact energy can be reduced from 16 keV to 2 keV, which enables higher depth resolution during depth profiling (a 2-fold improvement), albeit with a 5-fold decrease in lateral resolution. In the NanoSIMS-HR, the secondary ion column and detection system are identical to those used in the previous series, and isotopic analysis performance is as precise as in previous NanoSIMS instruments. | Peter K Weber; Marc Debliqui; Céline Defouilloy; Xavier Mayali; Ming-Chang Liu; Rachel Hestrin; Jennifer Pett-Ridge; Rhona Stuart; Megan Morris; Christina Ramon; Danielle M Jorgens; Reena Zalpuri; Laurent Arnoldi; Jérôme Farcy; Nicolas Saquet; Sarah Vitcher Fichou; Ludovic Renaud; Aurélien Thomen | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa233a12ff75c3a1e6b304/original/the-nano-sims-hr-the-next-generation-of-high-spatial-resolution-dynamic-sims.pdf |
67b2204481d2151a02bce374 | 10.26434/chemrxiv-2025-46wkb | Grafted Coiled-coil Peptides as Multivalent Scaffolds for Protein Recognition | Self-assembled peptides are promising templates for the design of inhibitors of protein-protein interaction (PPI) because they can be endowed with affinity- and selectivity-defining amino ac-ids alongside favorable physicochemical properties such as solubility and stability. Here we describe a tunable coiled-coil scaffold and its interaction with MCL-1, an α helix-binding anti-apoptotic protein and important target in oncology. We explore the role of oligomerization, multivalency and co-operativity in PPI inhibition. Hot-spot residues from an MCL-1 binding peptide (NOXA B) are grafted onto the outer surfaces of homo- and hetero-dimeric coiled-coil peptides to obtain inhibitors with mid-nM potency and selectivity over BCL-xL. Binding of ho-modimeric coiled coils to MCL-1 is positively co-operative resulting in stabilization of both part-ners. Homodimeric coiled coils support binding of two copies of the target protein. Modification of the coiled-coil sequence to favor assembly of higher-order scaffolds (trimer and tetramer), negatively impacts inhibitory potency, with AlphaFold2 modelling and biophysical data indicat-ing a complex interplay between coiled-coil oligomerization and target binding. Together, these data establish dimeric coiled coils as the most-promising of such scaffolds to develop inhibitors of α helix-mediated PPIs. | Amanda Acevedo-Jake; Bram Mylemans; Danielle Kay; Peiyu Zhang; Boguslawa Korona; Guto Rhys; Aneika Leney; Danny Huang; Thomas Edwards; Laura Itzhaki; Derek Woolfson; Wilson Andrew | Biological and Medicinal Chemistry; Organic Chemistry; Bioinformatics and Computational Biology; Biophysics; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b2204481d2151a02bce374/original/grafted-coiled-coil-peptides-as-multivalent-scaffolds-for-protein-recognition.pdf |
60c748570f50dbbb1e39676b | 10.26434/chemrxiv.11897157.v1 | Azetidinimines as a Novel Series of Non-Covalent Broad-Spectrum Inhibitors of β-Lactamases with Submicromolar Activities Against Carbapenemases of Classes A, B and D | The increasingly worrisome situation of antimicrobial resistances has pushed synthetic chemists to design original molecules that can fight these resistances. To do so, inhibiting β-lactamases, one of the main modes of resistance to β-lactam antibiotics, is one of the most sought-after strategies, as recently evidenced by the development and approval of avibactam, relabactam and vaborbactam. Yet molecules able to inhibit simultaneously β-lactamases belonging to different molecular classes remain scarce and currently there is no metallo-β-lactamase inhibitor approved for clinical use. Having recently developed a synthetic methodology to access imino-analogues of β-lactams (Chem. – Eur. J. 2017, 23, 12991,see ref) we decided to evaluate them as potential β-lactamase inhibitors and specifically against carbapenemases, which can hydrolyze and inactivate penicillins, cephalosporins and carbapenems. Herein we eport our findings that show that our newly developed family of molecules are indeed excellent β-lactamase inhibitors and that our lead compound can inhibit NDM-1 (0.1 µM), KPC-2 (0.4 µM), and OXA-48 (0.6 µM) even though these three enzymes belong to three different molecular classes of carbapenemases. This lead compound also inhibits the ESBL CTX-M-15 and the cephalosporinase CMY-2, it is metabolically stable, and can repotentiate imipenem against a resistant strain of Escherichia coli expressing NDM-1.<br /><br /><br /> | Eugénie Romero; Saoussen Oueslati; Mohamed Benchekroun; Agathe C. A. D’Hollander; Sandrine Ventre; Kamsana Vijayakumar; Corinne Minard; Cynthia Exilie; Linda Tlili; Pascal Retailleau; Agustin Zavala; Eddy Elisée; Edithe Selwa; Laetitia A. Nguyen; Alain Pruvost; Thierry Naas; Bogdan I. Iorga; Robert Dodd; Kevin Cariou | Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748570f50dbbb1e39676b/original/azetidinimines-as-a-novel-series-of-non-covalent-broad-spectrum-inhibitors-of-lactamases-with-submicromolar-activities-against-carbapenemases-of-classes-a-b-and-d.pdf |
661f70a191aefa6ce1babd20 | 10.26434/chemrxiv-2024-qhtkh | Interface-Engineered Atomic Layer Deposition of 3D Li4Ti5O12 for High-Capacity Lithium-Ion 3D Thin-Film Batteries | Upcoming energy-autonomous mm-scale Internet-of-things devices require high-energy and high-power microbatteries. On-chip 3D thin-film batteries (TFBs) are the most promising option but lack available high-rate anode materials. Here, Li4Ti5O12 thin films fabricated by atomic layer deposition (ALD) are electrochemically evaluated on 3D substrates for the first time. The 3D Li4Ti5O12 reveals an excellent footprint capacity of 20.23 µAh cm-2 at 1 C. The outstanding high-rate capability is demonstrated with 7.75 µAh cm-2 at 5 mA cm-2 (250 C) while preserving a remarkable capacity retention of 97.4 % after 500 cycles. Planar films with various thicknesses exhibit electrochemical nanoscale effects and are tuned to maximize performance. The developed ALD process enables conformal high-quality spinel (111)-textured Li4Ti5O12 films on Si substrates with an area enhancement of 9. Interface engineering by employing ultrathin AlOx on the current collector facilitates a required crystallization time reduction which ensures high film and interface quality and prospective on-chip integration. This work demonstrates that 3D Li4Ti5O12 by ALD can be an attractive solution for the microelectronics-compatible fabrication of scalable high-energy and high-power Li-ion 3D TFBs. | Jan Speulmanns; Sascha Bönhardt; Wenke Weinreich; Philipp Adelhelm | Materials Science; Nanoscience; Energy; Nanostructured Materials - Materials; Thin Films; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661f70a191aefa6ce1babd20/original/interface-engineered-atomic-layer-deposition-of-3d-li4ti5o12-for-high-capacity-lithium-ion-3d-thin-film-batteries.pdf |
6334b044e665bd5395161f64 | 10.26434/chemrxiv-2022-4rffg | High resolution membrane structures within hybrid lipid-polymer vesicles revealed by combining x-ray scattering and electron microscopy | Hybrid vesicles consisting of phospholipids and block-copolymers are increasingly finding applications in science and technology. Herein, small angle X-ray scattering (SAXS) and cryo-electron tomography (cryo-ET) were used to obtain detailed structural information about hybrid vesicles with different ratios of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and poly(1,2-butadiene-block-ethylene oxide) (PBd22-PEO14, Ms = 1800 gmol-1) . Using single particle analysis (SPA) we were able to further interpret the information gained from SAXS and cryo-ET experiments, showing that increasing PBd22-PEO14 mole fraction increases the membrane thickness from 52 Å for a pure lipid system to 97 Å for pure PBd22-PEO14 vesicles. We find two vesicle populations with different membrane thicknesses in hybrid vesicle samples. As these lipids and polymers are known to homogeneously mix, bistability is inferred between weak and strong interdigitation regimes of PBd22-PEO14 within the hybrid membranes. It is hypothesized that membranes of intermediate structure are not energetically favourable. Therefore, upon formation, each vesicle selects one of these two membrane structures, which are assumed to have comparable free energies. We conclude that, by combining biophysical methods, an accurate determination of the influence of composition on the structural properties of hybrid membranes is achieved, revealing that two distinct membranes structures can coexist in homogeneously mixed lipid-polymer hybrid vesicles. | Rashmi Seneviratne; Georgina Coates; Zexi Xu; Caitlin Cornell; Rebecca Thompson; Amin Sadeghpour; Daniel Maskell; Lars Jeuken; Michael Rappolt; Paul Beales | Physical Chemistry; Materials Science; Polymer Science; Polymer blends; Interfaces; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6334b044e665bd5395161f64/original/high-resolution-membrane-structures-within-hybrid-lipid-polymer-vesicles-revealed-by-combining-x-ray-scattering-and-electron-microscopy.pdf |
6576eee5fd283d7904bf4cd4 | 10.26434/chemrxiv-2023-v6hns | Towards sustainable reprocessable structural composites: benzoxazines as biobased matrices for natural fibers | In this work, we synthesized and investigated three fully biobased benzoxazine matrices containing exchangeable ester bonds for natural fiber composites. The thermoset properties were investigated and the transesterification behavior was assessed. The obtained polymers show high tunability. Using isosorbide as the starting building block, the thermoset exhibits a glass transition of 130 °C, a bending modulus of 2.5 GPa, and thermal stability leading to degradation occurring after 270 °C with 31% char at 800 °C. All formulations stress relax under catalyst-free conditions within an hour with properties recovery superior to 80%. Finally, flax composites were manufactured. We highlight strong affinities between the matrices and the fibers through high mechanical performances with a modulus over 30 GPa and stress at break of 400 MPa in the longitudinal direction. 5 GPa modulus and 47 MPa stress at break were found in the transverse direction. Excellent fire retardancy properties, with self-extinguishment and UL-94 V1 classification were obtained for the isosorbide-based/flax composite. The obtained composites were able to be welded with comparable results to glued ones, paving the way to processable laminates and stable cured prepreg perfectly suited for transportation-engineered applications. | Guillem Seychal; Louis Van Renterghem; Connie Ocando; Leila Bonnaud; Jean-Marie Raquez | Materials Science; Polymer Science; Composites; Fire-Resistant Materials; Cellulosic materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6576eee5fd283d7904bf4cd4/original/towards-sustainable-reprocessable-structural-composites-benzoxazines-as-biobased-matrices-for-natural-fibers.pdf |
60cb4a6d403d99fdffbb07a9 | 10.26434/chemrxiv-2021-qqbs1 | A Luminescent 1D Silver Polymer Containing [2.2]Paracyclophane Ligands | [2.2]Paracyclophane scaffolds have seen limited use as building blocks in supramolecular chemistry. Here, we report the synthesis and characterization of a 1D coordination polymer consisting of silver(I) ions bound to a [2.2]paracyclophane scaffold functionalized with two 4-pyridyl units. The structure of the polymer has been determined from single crystal X-ray diffraction analysis and reveals two different silver coordination motifs that alternate along the 1D coordination polymer. The coordination polymer exhibits strong blue and sky-blue fluorescence in solution and in the crystalline solid state, respectively. | Campbell Mackenzie; Lucie Delforce; Diego Rota Martir; David Cordes; Alexandra Slawin; Eli Zysman-Colman | Inorganic Chemistry; Spectroscopy (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cb4a6d403d99fdffbb07a9/original/a-luminescent-1d-silver-polymer-containing-2-2-paracyclophane-ligands.pdf |
658e41d866c13817293fd1d7 | 10.26434/chemrxiv-2023-cbkqh | Optimization of Liquid Handling Parameters for Viscous Liquid Transfers with Pipetting Robots, a “Sticky Situation” | Automated air-displacement pipettes have become a standard equipment for the transfer of liquids in laboratory settings. However, these tools fail to perform accurate and precise transfers for liquids with viscosities higher than 100 cP. In this study, we report a systematic protocol for optimizing liquid-handling parameters of automated pipettes to achieve accurate and precise transfers of viscous liquids (within 5% of percentage transfer error) with viscosities as high as 1275 cP using minimal transfer times. The protocol is based on the iterative gravimetric testing of different combinations of aspiration and dispense rates obtained by a Multi-Objective Bayesian Optimization (MOBO) algorithm. We demonstrate that optimal solutions obtained through MOBO can match or outperform solutions derived from human intuition, showing a consistent performance even when different pipetting equipment and tip geometries are used. Finally, we demonstrate that the protocol can be performed in fully automated closed-loop fashion by integrating an automated mass balance, increasing the manpower efficiency of the method. This offers a valuable advancement in the accurate manipulation of highly viscous liquids, with broad applications for the automation of various laboratory experiments. | Pablo Quijano Velasco; Andre Low; Chang Jie Leong; Wan Ting Ng; Selina Qiu; Shivam Jhunjhunwala; Bryant Li; Anne Qian; Kedar Hippalgaonkar; Jayce Cheng | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2023-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658e41d866c13817293fd1d7/original/optimization-of-liquid-handling-parameters-for-viscous-liquid-transfers-with-pipetting-robots-a-sticky-situation.pdf |
651051d4ed7d0eccc32252ea | 10.26434/chemrxiv-2023-k3tf2-v2 | Directional Multiobjective Optimization of Metal Complexes at the Billion-Scale with the tmQMg-L Dataset and PL-MOGA Algorithm | Transition metal complexes (TMCs) play a key role in several areas of high interest, including medicinal chemistry, renewable energies, and nanoporous materials. The development of TMCs enabling these technologies remains challenged by the need to optimize multiple properties within very large chemical spaces, in which the thirty transition metals can be combined with a virtually infinite number of ligands. In this work, we provide the open tmQMg-L dataset including 30K TMC ligands, which combines large chemical diversity with synthesizability. The charge and metal-coordination mode of the ligands were robustly defined with a novel algorithm based on graph and natural bond orbital theories. The tmQMg-L dataset was leveraged in the automated generation of 1.37M TMCs resulting from all possible combinations between a square planar palladium(II) scaffold and a pool of 50 different ligands. This TMC space was used to benchmark a multiobjective genetic algorithm (MOGA) that optimized two properties over a Pareto front; namely the polarizability (alpha) and the HOMO-LUMO gap (epsilon). The MOGA evolved 130 TMC hits with maximal (alpha, epsilon) values in a way that could be easily rationalized by analyzing the nature of the ligands selected. Instead of the traditional mutation and crossover of fragments within a single ligand, this MOGA implemented full-ligand genetic operations acting on all coordination sites, maximizing chemical diversity. Further, we extended this MOGA algorithm with the Pareto-Lighthouse functionality (PL-MOGA), which allows for controlling both the aim and scope of the multiobjective optimization over the Pareto front. In explicit spaces containing billions of TMCs, the PL-MOGA enabled the explainable generation of thousands of novel and highly diverse TMC hits. We believe that the combined use of the tmQMg-L dataset and PL-MOGA algorithm will facilitate the discovery of TMCs with optimal properties within untapped chemical spaces. | Hannes Kneiding; Ainara Nova; David Balcells | Theoretical and Computational Chemistry; Materials Science; Organometallic Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651051d4ed7d0eccc32252ea/original/directional-multiobjective-optimization-of-metal-complexes-at-the-billion-scale-with-the-tm-q-mg-l-dataset-and-pl-moga-algorithm.pdf |
65707ec65bc9fcb5c92b8f6a | 10.26434/chemrxiv-2023-rp320 | Ratiometric imaging of catecholamine neurotransmitters with nanosensors | Neurotransmitters are important signaling molecules in the brain and relevant in many diseases. Measuring them with high spatial and temporal resolution in biological systems is challenging. Here, we develop a ratiometric fluorescent sensor/probe for catecholamine neurotransmitters based on near-infrared (NIR) semiconducting single wall carbon nanotubes (SWCNTs). Phenylboronic acid (PBA)-based quantum defects are incorporated into them to interact selectively with catechol moieties. These PBA-SWCNTs are further modified with polyethylene glycol phospholipids (PEG-PL) for biocompatibility. Catecholamines including dopamine do not affect the intrinsic E11 fluorescence (990 nm) of these (PEG-PL-PBA-SWCNT) sensors. In contrast, the defect-related E11* emission (1130 nm) decreases by up to 35%. Furthermore, this dual-functionalization allows tuning selectivity by changing the charge of the PEG-polymer. These sensors are not taken up by cells, which is beneficial for extracellular imaging and they are functional in brain slices. In summary, we use dual-functionalization of SWCNTs to create a ratiometric biosensor for dopamine. | Chen Ma; Jennifer M. Mohr; German Lauer; Justus T. Metternich; Krisztian Neutsch; Tim Ziebarth; Andreas Reiner; Sebastian Kruss | Materials Science; Nanoscience; Biocompatible Materials; Biological Materials; Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65707ec65bc9fcb5c92b8f6a/original/ratiometric-imaging-of-catecholamine-neurotransmitters-with-nanosensors.pdf |
66425714418a5379b02a4f7e | 10.26434/chemrxiv-2024-fgvst | Statistical Mechanics of Kevlar® KM2® Plus Nanostructure: Deformations and High-Rate Impact | A detailed understanding of all phenomena that determine high-rate impact response of woven polyaramid systems is needed to design more effective materials and save lives. This study investigates the detailed nanostructures of Kevlar® KM2® Plus fibers from woven systems subjected to controlled rheometric deformations and high-rate impact. The rheometric tension, axial compression following tensile failure, and transverse compression are basic deformations not previously studied by our methods and hypothesized in high-rate impact. The impact of a high-rate object causes significant, layer-dependent nanostructural changes to woven systems. Multichannel AM-FM atomic force microscopy characterizes interior fiber nanostructure with spatially-resolved topological and viscoelastic property measurements of pleat lengths, crystal misorientation angles, fibril widths, and void widths. Statistical analyses were developed to assess convergence of nanostructure feature measurement distributions and compare the correlated nanostructure feature distributions between samples. The data and analyses indicate that tension is not the only mechanism of energy transfer from the impact of a high-rate object and that compressions, both in the axial and transverse directions, are also significant. The varying localized responses to high-rate impact and the presence of both tension and compression imply better systems can be created by improving tensile and compressive properties, tailoring fabric layers to perform to specific types of mechanical deformations. | Michael Ploch; Michael Roenbeck; Jacob Pretko; Christopher Seay; Kenneth Strawhecker; Steven Lustig | Materials Science; Polymer Science; Nanoscience; Nanostructured Materials - Materials; Polymer morphology; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66425714418a5379b02a4f7e/original/statistical-mechanics-of-kevlar-km2-plus-nanostructure-deformations-and-high-rate-impact.pdf |
60c7491e567dfeedcdec4b3a | 10.26434/chemrxiv.7965152.v3 | Developing an Amorphous Kerogen Molecular Model Based on Gas Adsorption Isotherms | <div>(1) Development of molecular models based on Bakken kerogen experiments using molecular dynamics and quantum mechanics software.<br /></div><div>(2) CO2 and N2 gas molecules adsorption simulation on the models was a good agreement with experiments.</div> | Hyeonseok Lee; kouqi liu; Farnaz A. Shakib; Bailey Bubach; Mehdi Ostadhassan | Geochemistry; Computational Chemistry and Modeling; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7491e567dfeedcdec4b3a/original/developing-an-amorphous-kerogen-molecular-model-based-on-gas-adsorption-isotherms.pdf |
64124fe92bfb3dc251d4b15e | 10.26434/chemrxiv-2023-q5wbw | Development of electrochemical cells for spatially resolved analysis using a multi-technique approach: from conventional experiments to X-ray nanoprobe beamlines | Real (electro-)catalysts are often heterogeneous, and their activity and selectivity depend on the properties of specific active sites. Therefore, unveiling the so-called structure-activity relationship is essential for a rational search for better materials and, consequently, for the development of the field of (electro-)catalysts. Thus, spatially resolved techniques are powerful tools as they allow us to characterize and/or measure the activity and selectivity of different regions of heterogeneous catalysts. To take full advantage of that, we have developed spectroelectrochemical cells (SEC) to perform spatially resolved analysis using X-ray nanoprobe synchrotron beamlines, and conventional pieces of equipment. Here, we describe the techniques available at the Carnaúba beamline at Sirius-LNLS storage ring, then we show how our SECs enable obtaining X-ray (XRF, XRD, XAS, etc.) and vibrational spectroscopy (FTIR and Raman) contrast images. Through some proof-of-concept experiments, we demonstrate how using a multi-technique approach could render a complete and detailed analysis of an (electro-)catalyst overall performance. | Rafael Vicente; Swathi Raju; Heloisa Gomes; Itamar Neckel; Hélio Tolentino; Pablo Sebastián Fernández | Materials Science; Catalysis; Energy; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64124fe92bfb3dc251d4b15e/original/development-of-electrochemical-cells-for-spatially-resolved-analysis-using-a-multi-technique-approach-from-conventional-experiments-to-x-ray-nanoprobe-beamlines.pdf |
60c73d51702a9b33f1189b68 | 10.26434/chemrxiv.5702233.v1 | pH-Controlled Assembly of 3D and 2D Zinc-based Metal-Organic Frameworks with Tetrazole Ligands | <div>
<div>
<div>
<p>We report the synthesis and structural diversity of Zn(II) MOF with in situ formation of
tetrazole ligand 3-ptz [3-ptz = 5-(3-pyridyl)tetrazolate], as a function pH. By varying the
initial reaction pH, we obtain high-quality crystals of the non-centrosymmetric 3D MOF
Zn(3-ptz)2, mixed phases involving the zinc-aqua complex [Zn(H2O)4(3-ptz)2]·4H2O, and
2D MOF crystals Zn(OH)(3-ptz) with a tunable micro-rod morphology, keeping reaction
time, temperature and metal-ligand molar ratio constants. Structures are
characterized by X-ray diffraction, scanning electron microscopy, FTIR and UV-Vis
spectroscopy. We discuss the observed structural diversity in terms of the relative
abundance of hydroxo-zinc species in solution for different values of pH. </p>
</div>
</div>
</div> | Felipe Herrera; Ignacio Chi-Duran; Javier Enriquez; Carolina Manquian; Kerry Wrighton-Araneda; Walter Cañon-Mancisidor; Diego Venegas-Yazigi; Dinesh Pratap Singh | Hybrid Organic-Inorganic Materials; Materials Processing; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51702a9b33f1189b68/original/p-h-controlled-assembly-of-3d-and-2d-zinc-based-metal-organic-frameworks-with-tetrazole-ligands.pdf |
676acca881d2151a02c71391 | 10.26434/chemrxiv-2024-jxph9 | Catalysis in Protein Bioconjugation | Advancement of catalytic transformations in traditional synthetic organic chemistry have made significant impacts on development of novel bioconjugation technologies. While a wide range of applications have become possible through catalytic protein bioconjugation approaches, there has been a lack of literature collectively reviewing advances of chemical modification of proteins through the lens of catalysis. This review article is focused on design principles and chemical strategies of nonenzymatic catalysis for targeting natural protein substrates by identifying seven catalysis patterns as organizing topics: Electrocatalysis, photocatalysis, metal catalysis, acid catalysis, organocatalysis, supramolecular catalysis, and heterogeneous catalysis. Many literature examples demonstrated possibility of simple translation of small molecule-based catalysis into protein bioconjugation methodologies whereas others demonstrated unique approaches such as dual catalytic systems and polypeptide structure-specific catalysis design. With a series of successful examples, the survey of catalytic approaches for protein bioconjugation also highlighted the remaining challenges and potential future directions of the area of catalytic bioconjugation. | Seiya Ishizawa; Koki Fujimura; Kounosuke Oisaki; Shinichi Sato; Jun Ohata | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676acca881d2151a02c71391/original/catalysis-in-protein-bioconjugation.pdf |
64f0ad643fdae147fa33a108 | 10.26434/chemrxiv-2023-rjj1f | Rashba effect: a chemical physicist's approach | Understanding the mechanisms underlying the emergence of giant spin splitting (GSS) is fundamental in the pursuit of more robust strategies for designing materials with desired spin splitting. This drive for material innovation continues to captivate a burgeoning community of early-career researchers with backgrounds in chemistry and material science. However, new to the field, they are often equipped only with the insight provided by the original Bychkov-Rashba model. Furthermore, daunted by the tight-binding perspective on the non-vanishing orbital angular momentum (OAM), they struggle to accurately account for the atomic spin-orbit iteration (SOI) in the formation of GSS. To address these challenges and equip young chemists with better-suited tools, this review aims to provide a more intuitive perspective on atomic interactions (orbital hybridization), structure symmetry, and atomic SOI in the formation of GSS. In pursuit of this goal, the review explores the Bychkov-Rashba model, its advantages, and limitations. Subsequently, it introduces the orbital framework, wherein GSS is modulated by atomic SOI and the interplay of OAM with the surface electrostatic field. Given the explicit dependence of both these factors on OAM, the review examines why OAM is typically quenched in crystal structures and how chemical bonds involving different orbital types can lead to its non-zero values in the presence of inversion symmetry breaking. Finally, with this chemistry-focused perspective, the review examines the rise of GSS in selected examples in selected materials. | Maciej Jan Szary | Theoretical and Computational Chemistry; Materials Science; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0ad643fdae147fa33a108/original/rashba-effect-a-chemical-physicist-s-approach.pdf |
652980b98bab5d20554b070c | 10.26434/chemrxiv-2023-s83vq | Knot data analysis using multiscale Gauss link integral | In the past decade, topological data analysis (TDA) has emerged as a powerful approach in data science. The main technique in TDA is persistent homology, which tracks topological invariants over the filtration of point cloud data using algebraic topology. Although knot theory and related subjects are a focus of study in mathematics, their success in practical applications is quite limited due to the lack of localization and quantization. We address these challenges by introducing knot data analysis (KDA), a new paradigm that incorporating curve segmentation and multiscale analysis into the Gauss link integral. The resulting multiscale Gauss link integral (mGLI) recovers the global topological properties of knots and links at an appropriate scale but offers multiscale feature vectors to capture the local structures and connectivities of each curve segment at various scales. The proposed mGLI significantly outperforms other state-of-the-art methods in benchmark protein flexibility analysis, including earlier persistent homology-based methods. Our approach enables the integration of artificial intelligence (AI) and KDA for general curve-like objects and data. | Li Shen; Hongsong Feng; Fengling Li; Fengchun Lei; Jie Wu; Guo-wei Wei | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652980b98bab5d20554b070c/original/knot-data-analysis-using-multiscale-gauss-link-integral.pdf |
66b56ee75101a2ffa8a47886 | 10.26434/chemrxiv-2024-xkb96 | Synthesis of head-to-tail-type poly(1,3-phenylene) with high degrees of polymerization catalyzed by Nickel(II)-(N-heterocyclic Carbene) complex | Poly(1,3-phenylene)s with high degree of polymerization were synthesized in a regioregular manner. The reaction of 2-bromo-4-chloro-hexyloxybenzene with a Grignard reagent and following cross-coupling catalyzed by a nickel(II) complex underwent polymerization in good to excellent yields. The use of bidentate phosphines as a ligand, which were shown to be suitable for poly(1,4-phenylene) synthesis, only afforded the polymer with relatively low degree of polymerization (DP), while the polymerization with N-heterocyclic carbene as a ligand showed a high degree of polymerization (DP) of up to >100 in excellent yield. | Seiha Yamaoka; Koki Susami; Shuichi Ikeda; Masaki Horie; Hideto Minami; Nozomu Suzuki; Kentaro Okano; Atsunori Mori | Catalysis; Organometallic Chemistry; Polymer Science; Polymerization catalysts; Homogeneous Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b56ee75101a2ffa8a47886/original/synthesis-of-head-to-tail-type-poly-1-3-phenylene-with-high-degrees-of-polymerization-catalyzed-by-nickel-ii-n-heterocyclic-carbene-complex.pdf |
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