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6317025003e27d90a4cac858 | 10.26434/chemrxiv-2022-kgxfk-v2 | Atomistic insights into the mechanical anisotropy and fragility of monolayer fullerene networks using quantum mechanical calculations and machine-learning molecular dynamics simulations | In this work, we comprehensively study the mechanical properties of the newly synthesised monolayer quasi-hexagonal-phase fullerene (qHPF) membrane [Nature \textbf{606}, 507-510 (2022)] under uniaxial tension by using quantum mechanical density-functional-theory (DFT) calculations and molecular dynamics (MD) simulations with a machine-learned neuroevolution potential (NEP). The elastic properties and fracture behaviours of monolayer qHPF are found to be strongly anisotropic due to the
different properties between the inter-fullerene C-C single bonds and [2 + 2] cycloaddition bonds. Moreover, the tensile strength and fracture strain of monolayer qHPF are much smaller than those of any other existing two-dimensional (2D) carbon crystals. The very small tensile strength or fracture strain is ascribed to the inhomogeneous deformation of the stretched monolayer qHPF, which originates from the stiffness difference between the soft inter-fullerene bonds and the rigid intra-fullerene bonds. Compared with DFT calculations at the ground state, the NEP-based extensive MD simulations predict a much smaller tensile strength and fracture strain for monolayer qHPF due to their consideration of the effects of temperature and membrane size. Our work not only reveals the underlying mechanism of the fracture behaviours of monolayer fullerene networks from an atomistic perspective, but also shows the effectiveness and accuracy of the NEP approach in determining the mechanical properties of 2D materials in the realistic situations. | Penghua Ying; Haikuan Dong; Ting Liang; Zheyong Fan; Zheng Zhong; Jin Zhang | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6317025003e27d90a4cac858/original/atomistic-insights-into-the-mechanical-anisotropy-and-fragility-of-monolayer-fullerene-networks-using-quantum-mechanical-calculations-and-machine-learning-molecular-dynamics-simulations.pdf |
629304972f3a05788108a0a8 | 10.26434/chemrxiv-2022-fdxzn | Membrane-based TBADT recovery: increasing the sustainability of continuous-flow photocatalytic HAT transformations | Photocatalytic hydrogen atom transfer (HAT) processes have been the object of numerous studies showcasing the potential of the homogeneous photocatalyst tetrabutylammonium decatungstate (TBADT) for the functionalization of C(sp3)–H bonds. However, to translate these studies into large-scale industrial processes, careful considerations of catalyst consumption, cost, and removal are required. This work presents organic solvent nanofiltration (OSN) as the answer to reduce TBADT consumption, to increase its turnover number and to lower its concentration in the product solution, thus enabling large-scale photocatalytic HAT-based transformations. The operating parameters for a suitable membrane for TBADT recovery in acetonitrile were optimized. Continuous photocatalytic C(sp3)-H alkylation reactions were carried out with in-line TBADT recovery via two OSN steps. Promisingly, the observed product yields for the reactions with in-line catalyst recycling are comparable to those of reactions performed with pristine TBADT, therefore highlighting that not only catalyst recovery (>99%, TON > 6500) is a possibility, but also that it does not happen at the expense of reaction performance. | Zhenghui Wen; Diego Pintossi; Manuel Nuno; Timothy Noel | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629304972f3a05788108a0a8/original/membrane-based-tbadt-recovery-increasing-the-sustainability-of-continuous-flow-photocatalytic-hat-transformations.pdf |
60c74626469df473b3f435e4 | 10.26434/chemrxiv.10830143.v1 | Relative and Absolute Structure Assignments of Alkenes Using Crystalline Osmate Derivatives for X-Ray Analysis | <div><div><p>Osmium tetroxide and TMEDA form stable crystalline adducts with alkenes. The structure of liquid alkenes can be determined through X-ray analysis of these derivatives. Osmium, a heavy atom, facilitates the crystallographic analysis and the determination of the absolute configuration using common Mo X-ray sources. The utility of this method for assigning structures and absolute configurations was demonstrated on a number of unsaturated substrates that include simple alkenes, enones, enol ethers, and silyl enol ethers.</p></div></div> | Alexander S. Burns; Charles dooley; Paul R. Carlson; Joseph W. Ziller; Scott Rychnovsky | Natural Products; Stereochemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74626469df473b3f435e4/original/relative-and-absolute-structure-assignments-of-alkenes-using-crystalline-osmate-derivatives-for-x-ray-analysis.pdf |
62b54a90486c981373b15d57 | 10.26434/chemrxiv-2022-6wgzk | QCforever: Quantum chemistry for everyone | To obtain observable physical or molecular properties like ionization potential and fluo- rescent wavelength with quantum chemical (QC) computation, multi-step computation manip- ulated by a human is required. Hence, automating the multi-step computational process and making it a black box that can be handled by anybody, are important for effective database con- struction and fast realistic material design through the framework of black-box optimization where machine learning algorithms are introduced as a predictor. Here, we propose a python library, QCforever, to automate the computation of some molecular properties and chemical phenomena induced by molecules. This tool just requires a molecule file for providing its ob- servable properties, automating the computation process of molecular properties (for ionization potential, fluorescence, etc) and output analysis for providing their multi-values for evaluating a molecule. Incorporating the tool in black-box optimization, we can explore molecules that have properties we desired within the limitation of QC. | Masato Sumita; Kei Terayama; Ryo Tamura; Koji Tsuda | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b54a90486c981373b15d57/original/q-cforever-quantum-chemistry-for-everyone.pdf |
60c753a7702a9b38c118c3cc | 10.26434/chemrxiv.13523939.v1 | Tuning the Magnetic Properties of Two-Dimensional MXenes by Chemical Etching | Two-dimensional materials based on transition metal carbides have been intensively studied due to their unique properties including metallic conductivity, hydrophilicity, and structural diversity and have shown great potential in several applications. While MXenes based on magnetic transition elements show interesting magnetic properties, not much is known about the magnetic properties of titanium-based MXenes. Here, we measured magnetic properties of Ti<sub>3</sub>C<sub>2</sub>T<sub>x </sub>MXenes synthesized by different chemical etching conditions. Our measurements indicate that there is a paramagnetic–antiferromagnetic (PM-AFM) phase transition, and the transition temperature depends on the synthesis procedure of MXenes. Our observation indicates that the magnetic properties of these MXenes can be tuned by the extent of chemical etching which can be beneficial for the design of MXene-based spintronic devices. | Kemryn Allen-Perry; Weston Straka; Danielle Keith; Shubo Han; C. Lewis Reynolds; Bhoj Gautam; Daniel Autrey | Nanostructured Materials - Materials; Magnetism | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a7702a9b38c118c3cc/original/tuning-the-magnetic-properties-of-two-dimensional-m-xenes-by-chemical-etching.pdf |
6380bd380949e12fc255cfea | 10.26434/chemrxiv-2022-kls5q | AiZynthTrain: robust, reproducible, and extensible pipelines for training synthesis prediction models | We introduce the AiZynthTrain Python package for training synthesis models in a robust, reproducible, and extensible way. It contains two pipelines that create a template-based one-step retrosynthesis model and a RingBreaker model that can be straightforwardly integrated in retrosynthesis software. We train such models on the publicly available reaction dataset from the US Patent and Trademark Office (USPTO), and these are the first retrosynthesis models created in a completely reproducible end-to-end fashion, starting with the original reaction data source and ending with trained machine-learning models. In particular, we show that employing the pipeline greatly improves the ability of the RingBreaker model for disconnecting ring systems. Furthermore, we demonstrate the robustness of the pipeline by training on a more diverse but proprietary dataset. We envisage that this framework will be extended with other synthesis models in the future. | Samuel Genheden; Per-Ola Norrby; Ola Engkvist | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6380bd380949e12fc255cfea/original/ai-zynth-train-robust-reproducible-and-extensible-pipelines-for-training-synthesis-prediction-models.pdf |
60c74e674c891985a1ad3a05 | 10.26434/chemrxiv.12097683.v2 | Strain-Based Chemical Sensing Using Metal-Organic Framework Nanoparticles | <div><div><p>Metal-organic frameworks (MOFs) have received much attention for their potential as chemical sensors, owing to unparalleled tunability of their host-guest response, high uptake and structural flexibility. However, because of the limited compatibility between MOF properties and sensor transduction mechanisms, very few MOFs have successfully been integrated into practical devices. We report the fabrication of the first strain-based sensor constructed from MOF nanoparticles deposited directly onto a membrane-type surface stress sensing architecture, which exhibits unprecedented response times on the order of seconds and ppm-level sensitivity towards volatile organic compounds (VOCs). Finite element analysis is used to demonstrate that the sensor response is a result of analyte-induced strain in the MOF receptor layer. We show that an array of four types of MOF nanoparticles allows for clear discrimination between different classes of VOCs and even individual gases, using principal component analysis of their response profiles. This work opens up the possibility of VOC sensing using a wide range of MOFs, beyond those that are electrically conducting or those that form oriented thin films, with the added advantages of high sensitivity and rapid response compared to existing MOF strain-based sensors.</p></div><p></p></div> | Hamish Yeung; Genki Yoshikawa; Kosuke Minami; Kota Shiba | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Sensors | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e674c891985a1ad3a05/original/strain-based-chemical-sensing-using-metal-organic-framework-nanoparticles.pdf |
67c221956dde43c908e8de13 | 10.26434/chemrxiv-2025-jxbs0 | A 3D Hepatocyte Model with Composite Nanofibers that Reproduced Human in vivo Drug Clearance Profiles | This study presents a novel in vitro 3D hepatocyte model that contains a nanofibrous scaffold designed to mimic the extracellular matrix (ECM) of the human liver, both structurally and biochemically. A modular 3D-printed device housing the ECM scaffold was also developed, readily fitting in well plates. HepaRG hepatocytes cultured on the scaffold exhibited enhanced metabolic activity compared to traditional 2D cultures, indicating improved hepatocyte functionality. Drug clearance studies with lidocaine, clozapine, and fluoxetine demonstrated significantly faster clearance rates on the scaffold, closely aligning with in vivo results from literature, while 2D cultures showed limited metabolic capacity. This model offers a physiologically relevant platform for hepatocyte studies. The findings underscore the model’s potential to advance preclinical drug development by replicating liver-specific functions in vitro. | Rudolph Park; Chengpeng Chen | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c221956dde43c908e8de13/original/a-3d-hepatocyte-model-with-composite-nanofibers-that-reproduced-human-in-vivo-drug-clearance-profiles.pdf |
60c748a5f96a00e02a2870ca | 10.26434/chemrxiv.11573337.v2 | Internal Fragments Generated by Electron Ionization Dissociation Enhances Protein Top-down Mass Spectrometry | Top-down proteomics by mass spectrometry (MS)
involves the mass measurement of an intact protein followed by subsequent
activation of the protein to generate product ions. Electron-based
fragmentation methods like electron capture dissociation (ECD) and electron
transfer dissociation (ETD) are widely used for these types of analysis,
however these fragmentation methods can be inefficient due to the low energy
electrons fragmenting the protein without the dissociation products; that is no
detection of fragments formed. Recently, electron ionization dissociation (EID),
which utilizes higher energy electrons (> 20 eV) has been shown to be more
efficient for top-down protein fragmentation compared to other electron-based
dissociation methods. Here we demonstrate that the use of EID enhances protein
fragmentation and subsequent detection of protein fragments. Protein product
ions can form by either single cleavage events, resulting in terminal fragments
containing the C-terminus or N-terminus of the protein, or by multiple cleavage
events to give rise to internal fragments that do not contain the C-terminus or
N-terminus of the protein. Conventionally, internal fragments have been
disregarded as reliable assignments of these fragments were limited. Here, we
demonstrate that internal fragments generated by EID can account for ~20-40% of
the mass spectral signals detected by top-down EID-MS experiments. By including
internal fragments, the extent of the protein sequence that can be explained
from a single tandem mass spectrum increases from ~50% to ~99% for 29 kDa
carbonic anhydrase II and 8.6 kDa ubiquitin. By including internal fragments in
the data analysis, previously unassigned peaks can be readily and accurately
assigned to enhance the efficiencies of top-down protein sequencing
experiments. | Muhammad Zenaidee; Carter Lantz; Taylor Perkins; Janine Fu; Wonhyuek Jung; Rachel R. Ogorzalek Loo; Joseph A. Loo | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748a5f96a00e02a2870ca/original/internal-fragments-generated-by-electron-ionization-dissociation-enhances-protein-top-down-mass-spectrometry.pdf |
625bfead742e9fb1ed60c71e | 10.26434/chemrxiv-2022-gvpxz-v2 | Advanced Kinetic Characterization | Microkinetic analysis that assumes the steady-state approximation are ubiquitous in the modelling and simulations of redox and non-redox reactions. Operando studies such as photoemission electron microscopic investigations have, however, provided evidence for (a)periodic surface concentration profiles and adspecie mobility. Consequently, the ubiquitous steady-state approximation used in nearly all (micro)-kinetic models may not be universally applicable. Furthermore, on unsupported and unpromoted catalyst surfaces, variations in the nature, quantity, and mobility of active sites are observed leading to various forms of site heterogeneity, induced heterogeneity, or both, as well as (a)periodic heterogeneity in the form of oscillatory waves and self-organised patterns. The relationship between surface-site distribution and the ensuing homogeneity and/or heterogeneity and product distribution and the resulting modelling tools used for analysis have not been explored comprehensively. Consequently, we provide a framework for cataloguing catalysts for advanced kinetic characterisation and modelling. The catalogue has two functions: (1) it relates surface models with reactor models, and (2) for any specific reaction, it shows (visually) the dynamicity of adspecie formation and evolution on the catalyst surface. Indeed, this second advantage has been exemplified by archived studies of carbon monoxide oxidation over Pd(111) catalysts. Using the homotattic patch model that leads to the adsorption integral equation, we catalogue catalysts according to evolving active sites on catalyst surfaces with varied homogeneity. We observe that the conventional microkinetic models are only accurate for a very small subset of chemical reactions where the standard model of catalysis applies. However, for many redox catalytic transformations, these models lose their applicability with respect to the dynamics of the active site, catalyst surface, and reaction. As a substitute, we present microdynamic models which not only account for every elementary reaction step but incorporate a multi-scale approach within kinetic models allowing for changing catalyst states, charge transport, as well as active site, catalyst surface, reaction, and reactor dynamics. | Toyin Omojola | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Reaction Engineering; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625bfead742e9fb1ed60c71e/original/advanced-kinetic-characterization.pdf |
64b7cff5b053dad33a87ab43 | 10.26434/chemrxiv-2023-vsgpb | A Gaussian process regression (GPR) quest to predict HOMO-LUMO energy | Machine learning methods employ statistical algorithms and pattern recognition techniques to learn patterns and make predictions based on statistical patterns. Global reactivity descriptors, such as HOMO-LUMO energy, chemical potential (µ), chemical hardness (η), softness (σ) and electrophilic index (ω) are predicted using Gaussian process regression (GPR) machine learning method. GPR predicted values are in close agreement with the values obtained via ab initio methods. Over 85% prediction accuracy in HOMO energies and reactivity parameters is observed, while LUMO energies were in good range with the DFT evaluations. An appropriate kernel combination with proper tuning of parameters and the selection of quality correlated data can make the GPR model robust and powerful. Machine learning models like GPR could play a pivotal role in assisting and accelerating ab initio calculations and providing insights for highly complex molecular systems. | MANJEET BHATIA | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b7cff5b053dad33a87ab43/original/a-gaussian-process-regression-gpr-quest-to-predict-homo-lumo-energy.pdf |
60c7562df96a00743a288a04 | 10.26434/chemrxiv.14204231.v1 | Key Factors During the Milling Stage of the Seed Assisted and Solvent-Free Synthesis of MFI and Catalytic Behavior in the Alkylation of Phenol with Tert-Butyl Alcohol | The so-called mechanochemical method for the synthesis of zeolites reduces the generation of liquid residues and gaseous pollutants as compared to the conventional solvothermal method. Different types of zeolites have been synthesized at the laboratory scale with this method using mostly pestle and mortar. However, such an approach hinders both the systematic comprehension of the effects of the input variables of the milling process and its further scale-up towards the synthesis of the zeolites and their catalytic application. This work investigates the influence of key factors involved in the ball milling stage of the mechanochemical route for the synthesis of MFI done with the assistance of a commercial MFI seed and in the absence of solvents over the most salient physicochemical properties of this type of materials, i.e. the recovery percentage, production cost, morphology, surface area and porosity, crystallinity, acidity of the protonated MFI and catalytic performance. The synthesis of the materials was planned and executed following a full 24 factorial experiment whose input variables were the Na2O/SiO2 and H2O/SiO2 molar ratios and the milling time and speed. The effects of both main and interaction factors over key physicochemical properties, and catalytic behavior of the synthesized materials on the alkylation of phenol with tert-butyl alcohol were established within the explored sampling space. Results showed that the Na2O/SiO2 molar ratio plays a key role for the mechanochemical synthesis of MFI, since this variable may direct the synthesis to the preferential production of MOR instead of MFI. On the other hand, it was found that the milling time and speed and their interactions markedly impact the textural properties of MFI. Furthermore, the triple interaction between the input variables affected the concentration of Lewis acid sites of the produced materials. These effects were rationalized by considering that sodium can act as a structure directing agent during the mechanochemical synthesis of MFI and also can promote the incorporation of aluminum to its structure. On the other hand, the milling time and speed are non-linearly correlated to the milling energy required for forming the aluminosilicate precursor that crystallizes during the hydrothermal stage of the process. Overall, all the zeolites synthesized by the mechanochemical route were less crystalline than both the MFI used as seed and an MFI synthesized by sol-gel. This was associated to the formation of amorphous agglomerates around the zeolitic crystals. Finally, the catalytic behavior of the mechanochemical MFI zeolites in the studied reaction was found to be linearly and positively correlated with both the concentration of BrØnsted of sites and with the density of acid sites. The catalytic tendencies were consistent with the proposal of a stepwise Langmuir-Hinshelwood mechanism for the alkylation of phenol with tert-butyl alcohol. | Julieth García-Sánchez; Iván Darío Mora-Vergara Vergara; Daniel R. Molina V.; José Antonio Henao-Martínez; Víctor Gabriel Baldovino Medrano | Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7562df96a00743a288a04/original/key-factors-during-the-milling-stage-of-the-seed-assisted-and-solvent-free-synthesis-of-mfi-and-catalytic-behavior-in-the-alkylation-of-phenol-with-tert-butyl-alcohol.pdf |
67b30661fa469535b9b327b7 | 10.26434/chemrxiv-2025-qznlf | Light-Activated Nanobumps: Photoresponsive Low-Density Azobenzene Self-Assembled Monolayers | Controlling the interfacial properties of organic materials using external stimuli is crucial for applications in adhesion, tribology, and electrochemistry. In particular, light irradiation provides a precise, non-contact method for dynamically manipulating molecular structures and surface morphology. Azobenzene-based photoresponsive self-assembled monolayers (SAMs) undergo reversible trans–cis isomerization, inducing conformational changes. However, conventional SAMs form densely packed structures that restrict the free volume required for efficient isomerization. To address this limitation, reducing molecular packing density is essential to achieving functional surface responses to light irradiation. This study addressed the challenge of constructing azobenzene-based photoresponsive low-density SAMs by controlling their formation kinetics. We demonstrate that combining bulky substituents in azobenzenethiol with kinetic control of SAM formation enables the creation of low-density SAMs capable of dynamic surface morphological changes upon photoisomerization. Unlike conventional densely packed SAMs, where the azobenzene moieties remain static, the proposed approach facilitates the reversible emergence and disappearance of nanoscale "nanobumps.” X-ray photoelectron spectroscopy and atomic force microscopy analyses confirm this behavior results from a combination of molecular packing density and thiolate binding states, which are absent in conventional high-density SAMs. This study offers new insights into the design of functional photoresponsive surfaces and presents a strategy for developing light-controllable interfacial systems with potential applications in molecular switches and adaptive coatings. | Daisuke Ishikawa; Masahiko Hara | Physical Chemistry; Materials Science; Nanoscience; Thin Films; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b30661fa469535b9b327b7/original/light-activated-nanobumps-photoresponsive-low-density-azobenzene-self-assembled-monolayers.pdf |
60c74d82bdbb894487a399ef | 10.26434/chemrxiv.12629858.v1 | Prioritization of Potential Drugs Targeting the SARS-CoV-2 Main Protease | <p>
Since
its outbreak in 2019, the acute respiratory syndrome caused by
SARS-Cov-2 has become a severe global threat to human. The lack of
effective drugs strongly limits the therapeutic treatment against
this pandemic disease. Here we employed a computational approach to
prioritize potential inhibitors that directly target the core enzyme
of SARS-Cov-2, the main protease, which is responsible for processing
the viral RNA-translated polyprotein into functional proteins for
viral replication. Based on a large-scale screening of over 13, 000
drug-like molecules, we have identified the most potential drugs that
may suffice drug repurposing for SARS-Cov-2. Importantly, the second
top hit is Beclabuvir, a known replication inhibitor of hepatitis C
virus (HCV), which is recently reported to inhibit SARS-Cov-2 as
well. We also noted several neurotransmitter-related ligands among
the top candidates, suggesting a novel molecular similarity between
this respiratory syndrome and neural activities. Our approach not
only provides a comprehensive list of prioritized drug candidates for
SARS-Cov-2, but also reveals intriguing molecular patterns that are
worth future explorations.</p> | Yanjin Li; Yu Zhang; Yikai Han; Tengfei Zhang; Ranran Du | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d82bdbb894487a399ef/original/prioritization-of-potential-drugs-targeting-the-sars-co-v-2-main-protease.pdf |
614c74b6aeaa6e3a00f73c1c | 10.26434/chemrxiv-2021-3hwfv | Transient Absorption of DNA bases in the gas phase
and in chloroform solution: a comparative quantum
mechanical study | We study the excited state absorption (ESA) properties of the four DNA bases (thymine, cytosine, adenine, and guanine) by different single reference quantum mechanical methods, i.e. equation of motion coupled cluster singles and doubles (EOM-CCSD), singles, doubles and perturbative
triples (EOM-CC3), and time-dependent density functional theory (TD-DFT), with the long-range corrected CAM-B3LYP functional. Preliminary results at the Tamm-Dancoff (TDA) CAM-B3LYP level using the maximum overlap method (MOM) are reported for Thymine. In the gas phase,
the three methods predict similar One Photon Absorption (OPA) spectra, which are also consistent
with the experimental results and with the most accurate computational studies available in the
literature. The ESA spectra are then computed for the pp states (one for pyrimidine, two for
purines) associated with the lowest energy absorption band, and for the close-lying np state. The
EOM-CC3, EOM-CCSD and CAM-B3LYP methods provide similar ESA spectral patterns, which are
also in qualitative agreement with literature RASPT2 results. Once validated in the gas phase,
TD-CAM-B3LYP has been used to compute the ESA in chloroform, including solvent effect by the
polarizable continuum model (PCM). The predicted OPA and ESA spectra in chloroform are very
similar to those in the gas phase, most of the bands shifting by less than 0.1 eV, with a small increase of the intensities and a moderate destabilization of the np state. Finally, ESA spectra have been computed from the minima of the lowest energy pp state, and are consistent with the
available experimental transient absorption spectra of the nucleosides in solution, providing a final validation of our computational approach. | Daniil A. Fedotov; Alexander C. Paul; Henrik Koch; Fabrizio Santoro; Sonia Coriani; Roberto Improta | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614c74b6aeaa6e3a00f73c1c/original/transient-absorption-of-dna-bases-in-the-gas-phase-and-in-chloroform-solution-a-comparative-quantum-mechanical-study.pdf |
658559c466c1381729c83ebf | 10.26434/chemrxiv-2023-sjqz5-v2 | Exploring the Mechanism of the Electrochemical Polymerization of CO2 to hard carbon over CeO2 (110) | Conversion of CO2 to hard carbon is an interesting technology for the removal of carbon dioxide from the atmosphere. Recently, it was shown that CeO2 can selectively catalyse this reaction but we still lack information regarding the reaction mechanism. Using density functional theory (DFT) modelling we explore possible reaction mechanisms that allow for the polymerization of CO2. According to our computations the reaction is initialized by the adsorption of CO2 in an oxygen vacancy. Owing to the rich defect chemistry of ceria a large number of suitable sites are available at the surface. C-C bond formation is achieved through an aldol condensation type mechanism which comprises the electrochemical elimination of water to form a carbene. This carbene then performs a nucleophilic attack on CO2 . The reaction mechanism possesses significant similarities to the corresponding reaction in synthetic organic chemistry. Since the mechanism is completely generic it allows for all relevant steps of the formation of hard carbon like chain growth, chain linkage and the formation of side chains or aromatic rings. Surprisingly, ceria mainly serves as an anchor for CO2 in an oxygen vacancy while all other subsequent reaction steps are almost completely independent from the catalyst. These insights are important for the development of novel catalysts for CO2 reduction and may also lead to new reactions for the electrosynthesis of organic molecules. | Florian Keller; Johannes Döhn; Axel Gross; Michael Busch | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658559c466c1381729c83ebf/original/exploring-the-mechanism-of-the-electrochemical-polymerization-of-co2-to-hard-carbon-over-ce-o2-110.pdf |
6777dba26dde43c9082adfa8 | 10.26434/chemrxiv-2025-rcrq6 | Chemical Termination and Interfacial Redox Behavior of Freestanding SrTiO3 | Tailoring oxide heterointerfaces has sparked the search for electronic and ionic phenomena in low-dimensional, confined systems. The fabrication of freestanding oxide membranes has further expanded the possible fields of application. Based on the structural vulnerability and physical confinement of such membranes, it remains a great challenge to achieve atomically defined and single-terminated surfaces by the typical chemical treatments and to induce interfacial redox-reactions in these nanoscopic transition metal oxides. To address this, we use the sacrificial layer exfoliation route, involving an all-perovskite epitaxial layer structure to fabricate freestanding SrTiO3 membranes with high crystallinity and defined surface morphology. To study the interfacial redox-behavior of the singly TiO2-terminated, annealed membrane, we employ the formation of oxygen vacancies in SrTiO3, triggered by the low-pressure deposition of a thin LaAlO3 layer epitaxially grown on the transferred SrTiO3 layer. A mixed Ti3+/4+ valence state is indicative of the induced transfer of oxygen ions from the confined SrTiO3 membrane into the LaAlO3 overlayer, resulting in an oxygen vacancy concentration around 1021 cm−3 in the confined SrTiO3 membrane. Our results highlight that interfacial redox-reactions can be induced in SrTiO3 membranes, which enables the ionic engineering of confined oxides heterointerfaces based on the freestanding oxide approach. | Marcus Wohlgemuth; Kapil Nayak; Anton Kaus; Lisa Heymann; Lee-Kang Huang; Alexandros Sarantopoulos; Joachim Thomsen; Rafal Dunin-Borkowski; Victor Rouco; Jacobo Santamaria; Regina Dittmann; Felix Gunkel | Materials Science; Nanostructured Materials - Materials; Thin Films | CC BY NC 4.0 | CHEMRXIV | 2025-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6777dba26dde43c9082adfa8/original/chemical-termination-and-interfacial-redox-behavior-of-freestanding-sr-ti-o3.pdf |
627f77833f1e7c21edbdb1cb | 10.26434/chemrxiv-2022-zcvlg | Dynamics and biomedical application of novel superparamagnetic helical nanorobots | The magnetic nanorobots, primarily composed of ferromagnetic materials, have been extensively investigated for their potential applications in cellular diagnostics and therapy. However, because of the substantial magnetic remanence exhibited by ferromagnetic materials, the magnetic stability of these nanorobots is a matter of serious concern. Here, we have designed and developed superparamagnetic iron oxide nanoparticles’(SPIONs) functionalized nanorobots (SPIONs-NR), a unique system that is highly stable against magnetic agglomeration. This kind of arrangement of random magnetic moments adhering to the nanorobot’s surface is relatively new and has not been previously explored in terms of fundamental physics and biomedical applications. We have carefully analyzed the various dynamical aspects of these functionalized nanorobots by studying their precession angle as a function of applied frequency at different magnetic fields. Furthermore, these functionalized nanorobots can be controllably maneuvered in the extracellular matrix by the application of rotating magnetic fields of comparatively lower magnitudes (usually < 50 G) to selectively target and annihilate malignant tissues via magnetic hyperthermia-induced localized heating, and therefore, making SPIONs-NR promising candidates in modernizing advanced nanomedicine research. | Suvra S. Laha; Debayan Dasgupta; Reshma V. R.; Ramray Bhat; Deepak K. Saini; Ambarish Ghosh | Materials Science; Nanoscience; Magnetic Materials; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627f77833f1e7c21edbdb1cb/original/dynamics-and-biomedical-application-of-novel-superparamagnetic-helical-nanorobots.pdf |
60c752f6bb8c1ade323dbf62 | 10.26434/chemrxiv.13333952.v2 | Controlling the Heterodimerisation of the Phytosulfokine Receptor 1 (PSKR1) via Island Loop Modulation | Phytosulfokine (PSK) is a phytohormone responsible for cell-to-cell communication in plants, playing pivotal role in plant development and growth. The binding of PSK to its cognate receptor, PSKR1, is modulated by the formation of a binding site located between leucine-rich repeat (LRR) domain of PSKR1 and the loop located in the receptor’s island domain (ID). The atomic resolution structure of the extracellular PSKR1 bound to PSK has been reported, however, the intrinsic dynamics of PSK binding and the architecture of PSKR1 binding site remain to be understood. In this work, we used atomistic molecular dynamics (MD) simulations and free energy calculations to elucidate how the PSKR1 island domain (ID) loop forms and binds PSK. Moreover, we report a novel “druggable” binding site which could be exploited for the targeted modulation of the PSKR1-PSK binding by small molecules. We expect that our results will open new ways to modulate the PSK signalling cascade via small molecules, which can result in new crop control and agricultural applications. | Joao Victor de Souza Cunha; Matthew Kondal; Piotr Zaborniak; Ryland Cairns; Agnieszka K. Bronowska | Food; Plant Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752f6bb8c1ade323dbf62/original/controlling-the-heterodimerisation-of-the-phytosulfokine-receptor-1-pskr1-via-island-loop-modulation.pdf |
62a7477870f8a7859001081a | 10.26434/chemrxiv-2022-2l1fp-v2 | An Orbital Weak Interaction Theory of Catalytic Activity in Ammonia Synthesis and Hydrogen Evolution Reaction | In the research for a quantitative correlation between catalytic activity and the property of various catalysts, the electronic configuration, at each catalytic atom in solid-state materials, is considered as an important factor. Comparing the reported experimental results of various pure metal catalysts for Ammonia Synthesis (AS) and Hydrogen Evolution Reaction 10 (HER), we find that the elements having suitable electronegativity and sufficient accessible half-filled orbitals are most positive for catalytic activity. It is, therefore, proposed that the half-filled orbitals interaction between reactant species and the catalytic active atom plays a decisive role in catalytic activity. The theoretical significance of this discrimination of the orbitals’ interaction in relation to the catalytic behaviors is discussed.
| Youyi Sun | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a7477870f8a7859001081a/original/an-orbital-weak-interaction-theory-of-catalytic-activity-in-ammonia-synthesis-and-hydrogen-evolution-reaction.pdf |
60c740699abda2761ff8bcc6 | 10.26434/chemrxiv.7746266.v1 | Influence of Interpenetration on the Flexibility of MUV-2 | <p>The crystal structure of an interpenetrated tetrathiafulvalene(TTF)- based metal-organic framework (MOF) is reported. This MOF, denoted MUV-2-i, is the interpenetrated analogue of the hierarchical and flexible MUV-2. Interestingly, the large flexibility exhibited by MUV-2 upon polar solvent adsorption is considerably reduced in the interpenetrated form which can be explained by short S···S interactions between adjacent TTF-based ligands ensuring more rigidity to the framework. In addition, porosity of MUV-2-i significantly decreased in comparison to MUV-2 as shown by the reduced free volume in the crystal structure.</p> | María Vicent-Morales; Iñigo J. Vitórica-Yrezábal; Manuel Souto; Guillermo Minguez Espallargas | Coordination polymers; Nanostructured Materials - Nanoscience; Ligands (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740699abda2761ff8bcc6/original/influence-of-interpenetration-on-the-flexibility-of-muv-2.pdf |
65780ebd7acf130c320b12f5 | 10.26434/chemrxiv-2022-rk7pv-v2 | Phasor-Fluorescence Lifetime Imaging Correlates Dynamics of in-situ Amyloid Nanostructures to Respiratory Dysfunction | The complex dynamics and transience of molecular aggregation pathways leading to amyloid-based neurodegeneration complicate the mechanistic understanding of these fatal diseases. Current technologies are unable to track the molecular processes leading to the onset of amyloidogenesis where real-time information is imperative to correlate its rich biology. Using a chemically-designed amyloidogenic molecule, we map its molecular transformation into amyloids and the resultant fusion with endosomes to form discrete, hollow plaque clusters. Tracked by phasor-fluorescence lifetime imaging (phasor-FLIM) in epithelial cells (L929, A549, MDA-MB 231) and correlative light-electron microscopy/tomography (CLEM), spatiotemporal splicing of the aggregation events shows time-correlated respiratory failure. We reveal that the initial dynamics of aggregation invokes cellular responses on a systemic level. | Yong Ren; Zhixuan Zhou; Konrad Maxeiner; Anke Kaltbeitzel; Iain Harley; Jiaqi Xing; Yingke Wu; Manfred Wagner; Katharina Landfester; Ingo Lieberwirth; Tanja Weil; David Y.W. Ng | Polymer Science; Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65780ebd7acf130c320b12f5/original/phasor-fluorescence-lifetime-imaging-correlates-dynamics-of-in-situ-amyloid-nanostructures-to-respiratory-dysfunction.pdf |
67573a2cf9980725cf89cbe6 | 10.26434/chemrxiv-2024-7gs4p | Linear Discriminant Analysis Based Machine Learning and All-Atom Molecular Dynamics Simulations for Probing Electroosmotic Transport in Cationic-Polyelectrolyte-Brush-Grafted Nanochannels | Deciphering the correct mechanism governing certain phenomenon in polyelectrolyte (PE) brush grafted systems, revealed through atomistic simulations, is an extremely challenging problem. In a recent study, our all-atom molecular dynamics (MD) simulations revealed a non-linearly large electroosmotic flow (in the presence of an applied electric field) in nanochannels grafted with PMETAC [Poly(2-(methacryloyloxy)ethyl trimethylammonium chloride] brushes. Given the lack of any formal mechanism that would have directed us to identify the correct factors responsible for such an occurrence, we needed to spend several months and devote significant analysis to unravel the involved mechanism. In this paper, we propose a Linear Discriminant Analysis (LDA) based ML approach to address this gap. At first, we obtain data on certain basic features from the all-atom MD data for a reference case (case with a smaller electric field) and the perturbed case in bins in which the nanochannel half height has been divided into. These datasets are high-dimensional dataset, to which the LDA is applied. This leads to the projection of the data (between the reference and the perturbed states) in a highly separated form on a 1D line. From such LDA calculations, we are able to identify the importance scores for the different features, which in turn tell us what to study and where to study. Such knowledge enables us to rapidly identify the key factors responsible for the non-linearly large EOS transport in PMETAC-brush-grafted nanochannels. | Raashiq Ishraaq; Siddhartha Das | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67573a2cf9980725cf89cbe6/original/linear-discriminant-analysis-based-machine-learning-and-all-atom-molecular-dynamics-simulations-for-probing-electroosmotic-transport-in-cationic-polyelectrolyte-brush-grafted-nanochannels.pdf |
63bbd7542840d838ebaa0a7d | 10.26434/chemrxiv-2023-hgp7b | Near infrared fluorescence lifetime imaging of
biomolecules with carbon nanotubes | Single wall carbon nanotubes (SWCNTs) are versatile building blocks for biosensors. Their near infrared (NIR) fluorescence enables detection of biomolecules in the optical tissue transparency window. The fluorescence intensity of SWCNTs changes in response to an analyte and this interaction can be chemical tailored by the surface chemistry. However, optical signals based on intensity are affected by external factors such as sample movement or fluctuations in excitation light. Here, we demonstrate fluorescence lifetime imaging microscopy (FLIM) of SWCNT-based sensors in the NIR as calibration-free method.
For this purpose, we tailored a confocal laser scanning microscope (CLSM) for NIR signals (>800 nm) and employed time correlated single photon counting (TCSPC). (GT)10-DNA functionalized SWCNTs are then used as sensors because they increase their fluorescence (995 nm) in response to the important neurotransmitter dopamine. Their fluorescence lifetime (> 900 nm) follows a biexponential decay and the longer lifetime component (370 ps) changes with dopamine concentration. It increases by up to 25 % with detection limits in the nM range. These sensors serve as paint to cover cells and report extracellular dopamine in 3D via FLIM. We therefore show the potential of using fluorescence lifetime in combination with confocal microscopy as readout for SWCNT-based sensors.
| Linda Sistemich; Phillip Galonska; Jan Stegemann; Sebastian Kruss | Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2023-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bbd7542840d838ebaa0a7d/original/near-infrared-fluorescence-lifetime-imaging-of-biomolecules-with-carbon-nanotubes.pdf |
67204e5883f22e42147e4d99 | 10.26434/chemrxiv-2024-7j7cn | MnO2 decorated N-doped mesoporous carbon electrodes boost enhanced removal of Cu2+ and Pb2+ ions from wastewater via a hybrid capacitive deionization platform | Integrating Faradaic (charge transfer) materials with carbon has been proven extensively to be a valid strategy to prepare highly efficient electrodes for electrochemical desalination or removal of heavy metal ions from wastewater via a capacitive deionization (CDI) platform. However, the influences of preliminary functionalization of the carbon component (e.g., nitrogen doping, hydroxyl grafting) and pairing of cathodes and anodes on the desalination performance have yet to be thoughtfully explored. Herein, we prepared a group of MnO2-decorated mesoporous carbon composites with nitrogen as a dopant (i.e., MK-NMCS, K-NMCS, NMCS, and CS), and systematically evaluated the desalination performance of various cathode//anode pairs in a hybrid capacitive deionization (HCDI) for capturing Na+, Cu2+, and Pb2+, respectively. Of all electrodes, the MK-NMCS//K-NMCS pair demonstrates the optimum desalination performance based on salt adsorption capacity (SAC) and cycling stability, offering a SAC of 25.4 mg g−1 and a SAC retention of 102.4% after 50 consecutive charge-discharge cycles at 1.2 V in 500 ppm NaCl solution. In addition, the MK-NMCS//K-NMCS electrodes also show the maximum ion adsorption capacity (IAC) toward Cu2+ and Pb2+ ions compared to other cathode//anode pairs, attaining an IAC of 37.0 and 30.0 mg Cu2+ per gram electrode materials at 1.2 V in 500 and 200 ppm Cu2+ solutions, respectively (cf. 32.2 mg Pb2+ per gram electrode materials in 200 ppm Pb2+ solution). Besides, these electrodes exhibit excellent cycling stability when applied in removing each heavy metal ion separately, with an IAC retention of 90.0% and 98.5% after 50 cycles toward Cu2+ and Pb2+ ions, respectively. Mechanical analysis reveals that both heavy metals are likely to be sequestered via capacitive electrosorption by carbon, intercalation with the MnO2, and surface complexation at the external surface of the [MnO6] octahedral layers. These findings underscore the pivotal roles of pre-functionalization of the original carbon and pairing of cathodes and anodes in the configuration of HCDI cells with improved performance and provide valuable insight into the optimization of Faradaic/carbon composite electrodes for remediation of wastewater with heavy metals via CDI platforms. | Jie Jin; Feihu Li | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67204e5883f22e42147e4d99/original/mn-o2-decorated-n-doped-mesoporous-carbon-electrodes-boost-enhanced-removal-of-cu2-and-pb2-ions-from-wastewater-via-a-hybrid-capacitive-deionization-platform.pdf |
60c73d93ee301ccf1ac785cd | 10.26434/chemrxiv.5993326.v1 | Protein-Protein Interaction Network Analysis and Identification of Key Players in nor-NOHA and NOHA Mediated Pathways for Treatment of Cancer through Arginase Inhibition: Insights from Systems Biology | <p>L-arginine
is involved in a number of biological processes in our bodies. Metabolism of
L-arginine by the enzyme arginase has been found to be associated with cancer
cell proliferation. Arginase inhibition has been proposed as a potential therapeutic
means to inhibit this process. N-hydroxy-nor-L-Arg (nor-NOHA) and N (omega)-hydroxy-L-arginine
(NOHA) has shown promise in inhibiting cancer progression through arginase
inhibition. In this study, nor-NOHA and NOHA-associated genes and proteins were
analyzed with several Bioinformatics and Systems Biology tools to identify the associated
pathways and the key players involved so that a more comprehensive view of the
molecular mechanisms including the regulatory mechanisms can be achieved and more
potential targets for treatment of cancer can be discovered. Based on the
analyses carried out, 3 significant
modules have been identified from the PPI network. Five pathways/processes have
been found to be significantly associated with nor-NOHA and NOHA associated
genes. Out of the 1996 proteins in the PPI network, 4 have
been identified as hub proteins- SOD, SOD1, AMD1, and NOS2. These 4 proteins have been implicated
in cancer by other studies. Thus, this study provided further validation into
the claim of these 4 proteins being potential targets for cancer treatment.</p> | Ishtiaque Ahammad | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d93ee301ccf1ac785cd/original/protein-protein-interaction-network-analysis-and-identification-of-key-players-in-nor-noha-and-noha-mediated-pathways-for-treatment-of-cancer-through-arginase-inhibition-insights-from-systems-biology.pdf |
62e7688f8e1607ff37d71d6f | 10.26434/chemrxiv-2022-5tlrz | Towards predictive design of electrolyte solutions by accelerating ab initio simulation with neural networks.
| Electrolyte solutions play a vital role in a vast range of important materials chemistry applications. For example, they are a crucial component in batteries, fuel cells, supercapacitors, electrolysis and carbon dioxide conversion/capture. Unfortunately, the determination of even their most basic properties from first principles remains an unsolved problem. As a result, the discovery and optimisation of electrolyte solutions for these applications largely relies on chemical intuition, experimental trial and error or empirical models. The challenge is that the dynamic nature of liquid electrolyte solutions require long simulation times to generate trajectories that sufficiently sample the configuration space; the long range electrostatic interactions require large system sizes; while the short range quantum mechanical (QM) interactions require an accurate level of theory. Fortunately, recent advances in the field of deep learning, specifically neural network potentials (NNPs), can enable significant accelerations in sampling the configuration space of electrolyte solutions. Here, we outline the implications of these recent advances for the field of materials chemistry and identify outstanding challenges and potential solutions. | Junji Zhang; Joshua Pagotto; Timothy Duignan | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e7688f8e1607ff37d71d6f/original/towards-predictive-design-of-electrolyte-solutions-by-accelerating-ab-initio-simulation-with-neural-networks.pdf |
6391dbaae6f9a14ab730f8b5 | 10.26434/chemrxiv-2022-qkd7j | Enantioselective diversification of alkene radical anions | Alkene radical ions constitute an integral and unique class of reactive intermediates for the synthesis of valuable compounds, because they have both unpaired spins and charge. However, relatively few synthetic applications of alkene radical anions have emerged, due to a dearth of generally applicable and mild radical anion generation approaches. Precise control over the chemo- and stereoselectivity in alkene radical anion-mediated processes represents another long-standing challenge due their high reactivity. To overcome these issues, here, we develop a new redox-neutral strategy that seamlessly merges photoredox and copper catalysis to enable the controlled generation of alkene radical anions and their orthogonal enantioselective diversification via distonic-like species. This new strategy enables highly regio-, chemo- and enantioselective hydrocyanation, deuterocyanation, and cyanocarboxylation of alkenes without stoichiometric reductants or oxidants under visible light irradiation. This work demonstrates the power of photochemistry in expanding new chemical space and overcoming persistent challenges in radical anion chemistry. | Bin Zhang; Min Jiang; Zhi-Han Zhang; Ke Zhao; Wen-Yuan Qu; Wen-Jing Xiao; Jia-Rong Chen | Organic Chemistry; Catalysis; Photochemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6391dbaae6f9a14ab730f8b5/original/enantioselective-diversification-of-alkene-radical-anions.pdf |
60c7523b842e65187edb3ccc | 10.26434/chemrxiv.13270124.v1 | On the Use of Catalysis to Bias Reaction Pathways in out Of-Equilibrium Systems | <p>Catalysis is an essential function in living systems and provides a way to control complex reaction networks. In natural out-of-equilibrium chemical reaction networks (CRNs) driven by the consumption of chemical fuels, enzymes provide catalytic control over pathway kinetics, giving rise to complex functions. Catalytic regulation of man‑made fuel‑driven systems is far less common and mostly deals with enzyme catalysis instead of synthetic catalysts. Here, we show via simulations, illustrated by literature examples, how any catalyst can be incorporated in a non-equilibrium CRN and what their effect is on the behavior of the system. Alteration of the catalysts’ concentrations in batch and flow gives rise to responses in product yield, lifetime and steady states. <i>In-situ</i> up or downregulation of catalysts’ levels temporarily changes the product steady state, whereas feedback elements can give unusual concentration profiles as a function of time and self-regulation in a CRN. We show that simulations can be highly effective in predicting CRN behavior and mapping parameter space, for complex processes that can proceed counterintuitively. In the future, shifting the focus from enzyme catalysis towards small molecule and metal catalysis in out-of-equilibrium systems can provide us with new reaction networks and enhance their application potential in synthetic materials, overall advancing the design of man‑made responsive and interactive systems.</p> | Michelle van der Helm; Tuanke de Beun; Rienk Eelkema | Homogeneous Catalysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7523b842e65187edb3ccc/original/on-the-use-of-catalysis-to-bias-reaction-pathways-in-out-of-equilibrium-systems.pdf |
637feac9ebc1c765cfd1d543 | 10.26434/chemrxiv-2022-g92t8 | Improving Efficiency Roll-off in Multi-Resonant Thermally Activated Delayed Fluorescent OLEDs Through Modulation of the Energy of the T2 State | The S1 state and high-lying triplet excited states (𝚫ES1Tn) offers insight into clarifying the mechanism of efficiency roll-off of organic light-emitting diodes (OLEDs). However, experimental detection of the 𝚫ES1Tn is challenging due to Kasha’s rule. Here, we report two emitters, PhCz-O-DiKTa and PhCz-DiKTa, showing multi-resonant thermally activated delayed fluorescence (MR-TADF). By modulating the conjugation between the MR-TADF DiKTa emissive center and donor substituent, emission directly from the T2 state was for the first time observed in MR-TADF emitters. Single crystal and reduced density gradient (RDG) analyses reveal that the origin of the reduced observed concentration-quenching results from weak CH and slipped stacking interactions, which suppress nonradiative transitions. Theoretical and photophysical investigations reveal that the 𝚫ES1T2 difference influences the reverse intersystem crossing (RISC) rate. The OLEDs employing PhCz-O-DiKTa and PhCz-DiKTa as emitters show maximum external quantum efficiencies (EQEmax) of over 20%, but very different efficiency roll-off behavior (54.5% vs 13.6% at 100 cd m-2). Thus, this design provides a possible solution to mitigating device efficiency roll-off by designing MR-TADF emitters with degenerate S1 and T2 states. | Tao Wang; Abhishek Kumar Gupta; David Cordes; Alexandra Slawin; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical Organic Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637feac9ebc1c765cfd1d543/original/improving-efficiency-roll-off-in-multi-resonant-thermally-activated-delayed-fluorescent-ole-ds-through-modulation-of-the-energy-of-the-t2-state.pdf |
657aff0366c138172929afc2 | 10.26434/chemrxiv-2024-crr79 | Functionalized polysaccharides improve sensitivity of tyramide/peroxidase proximity labeling assays through electrostatic interactions | High-throughput assays that efficiently link genotype and phenotype with high fidelity are key to successful enzyme engineering campaigns. Among these assays, the tyramide/peroxidase proximity labeling method converts the product of an enzymatic reaction of a surface expressed enzyme to a highly reactive fluorescent radical, which labels the cell surface. In this context, maintaining the proximity of the readout reagents to the cell surface is crucial to prevent crosstalk and ensure that short-lived radical species react before diffusing away. Here we investigated improvements to tyramide/peroxidase proximity labeling for enzyme screening. We modified chitosan (Cs) chains with horseradish peroxidase (HRP), and evaluated the effects of these conjugates on the efficiency of proximity labeling reactions on yeast cells displaying D-amino acid oxidase. By tethering HRP to chitosan through different chemical approaches, we localized the auxiliary enzyme close to the cell surface and enhanced the sensitivity of tyramide/peroxidase labeling reactions. We found that immobilizing HRP onto chitosan through a 5 kDa PEG-linker improved labeling sensitivity by over 3.5-fold for substrates processed with low turnover rate (e.g., D-lysine), while the sensitivity of the labeling for high activity substrates (e.g., D-Alanine) was enhanced by over 0.6-fold. Such improvements in labeling efficiency broaden the range of enzymes and conditions that can be studied and screened with tyramide/peroxidase proximity labeling. | Malvina Heiniger; Rosario Vanella; Zarah Walsh-Korb; Michael A. Nash | Materials Science; Catalysis; Polymer Science; Biopolymers; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657aff0366c138172929afc2/original/functionalized-polysaccharides-improve-sensitivity-of-tyramide-peroxidase-proximity-labeling-assays-through-electrostatic-interactions.pdf |
652f05cd45aaa5fdbb38811f | 10.26434/chemrxiv-2023-3823q | Thioimidate Solutions to Thioamide Problems during Peptide Synthesis | Thioamides have structural and chemical similarity to peptide bonds, and therefore offer valuable insights when probing peptide backbone interactions, including hydrogen bonding, stereoelectronic, and hydrophobicity effects. There is a perception that methods to install thioamides within peptides are sufficient, yet anecdotal reports indicate that many labs have sought to employ thioamides in a variety of studies but the results of many synthetic campaigns do not yield the intended products, leading researchers to abandon such projects and any information these structural probes would provide. We catalogue and provide evidence for the major pitfalls associated with current methods to synthesize thioamide-containing peptides during each stage of solid-phase peptide synthesis (SPPS), including (A) thioamide coupling, (B) peptide elongation, and (C) peptide cleavage from resin. We then demonstrate the utility of thioimidate protecting groups as a means to side-step each of these problematic synthetic difficulties. Our approach is generally applicable to all peptides and ultimately permits access to an important benchmark $\alpha$-helical peptide that had previously eluded synthesis and isolation. With the process of thionopeptide synthesis demystified, a broader range of researchers should find it easier to employ thioamides in the study of peptide-based biomolecules. | Jacob Byerly-Duke; Aaron Donovan; Krishna Sharma; Rida Ibrahim; Brett VanVeller | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652f05cd45aaa5fdbb38811f/original/thioimidate-solutions-to-thioamide-problems-during-peptide-synthesis.pdf |
60c75353702a9b026e18c337 | 10.26434/chemrxiv.12834977.v3 | B-Cell Epitope Discovery: The First Protein Flexibility-Based Algorithm – Zika Virus Conserved Epitope Demonstration | <p></p><p>Antibody-antigen interaction –
at antigenic local environments called B-cell epitopes – is a prominent
mechanism for neutralization of infection. Effective mimicry, and display, of
B-cell epitopes is key to vaccine design. Here, a
physical approach is evaluated for the discovery of epitopes which evolve slowly
over closely related pathogens (conserved epitopes). The approach is 1) protein
flexibility-based and 2) demonstrated with clinically relevant enveloped
viruses, simulated via molecular dynamics. The approach is validated against 1)
seven structurally characterized enveloped virus epitopes which evolved the
least (out of thirty-eight enveloped virus-antibody structures) and 2) eight
preexisting epitope and peptide discovery algorithms. Rationale for a new benchmarking
scheme is presented. A data-driven epitope clustering algorithm is introduced.
The prediction of eleven Zika virus epitopes (for future exploration on
recombinant vaccine technologies) is demonstrated. For the first time, protein
flexibility is shown to outperform solvent accessible surface area as an epitope
discovery metric.</p><p></p> | Daniel W. Biner; Jason S. Grosch; Peter J. Ortoleva | Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75353702a9b026e18c337/original/b-cell-epitope-discovery-the-first-protein-flexibility-based-algorithm-zika-virus-conserved-epitope-demonstration.pdf |
60c74ce34c8919734bad3704 | 10.26434/chemrxiv.12553673.v1 | Automated Stirring Device for Continuous Stirring While Sampling in Liquid Chromatography Systems | A device is presented, which enables continuous stirring of samples whilst inside an ultra-performance liquid chromatography system. Utilizing standard magnetic stirring bars that fit standard vials, the device allows for the automation of experimental setups that require stirring. The device is designed such that it can replace the standard sample holder and fits in its place, while being battery operated. The use of 3D printing and commercially available parts enables low-effort and low-cost device production, as well as easy modifications. Various tests were performed by following the kinetics of a dynamic combinatorial library that is known for exhibiting self-replication under mechanical agitation, via fiber growth-breakage mechanism. Design files and schematics are available.<br /> | Omer Markovitch; Jim Ottelé; Obe Veldman; Sijbren Otto | Analytical Chemistry - General; Analytical Apparatus | CC BY 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce34c8919734bad3704/original/automated-stirring-device-for-continuous-stirring-while-sampling-in-liquid-chromatography-systems.pdf |
67adcda96dde43c908b2b220 | 10.26434/chemrxiv-2025-hzxjv | Impact of Fermentation Duration on the Nutritional, Anti-Nutritional, and Functional Characteristics of Colocasia Esculenta. | This study investigated the effect of fermentation on the nutrient, anti-nutrient, and functional properties of cocoyam (Colocasia esculenta) flour at different time intervals. The tubers of
Colocasia esculenta were processed and fermented at varying durations (24, 48, 72, and 96 hours), while an unfermented sample was retained as a control for comparative analysis. Subsequently, the fermented tubers were oven-dried at 65°C for 8 hours and milled into flour. Proximate composition, anti-nutritional factors and functional properties of the fermented and unfermented cocoyam flours were then evaluated. Results revealed an increase in Crude protein (15.11 to 19.81%) and carbohydrate levels (71.57 to 75.9%) with corresponding increase in fermentation time. While there was a reduction in moisture content (8.56 to 3.18%), crude fat (1.20 to 0.40%), fibre (0.73 to 0.21%) and ash content (2.87 to 0.49%) with corresponding increase in fermentation time. Anti-nutritional factors of fermented samples also reduced in a time-dependent manner. The result of the functional properties showed increase in water absorption capacity (0.27 to 0.87g/g), while a decrease was observed in bulk density (0.68 to 0.56g/ml), oil absorption capacity (3.47 to 1.04g/g), gelation temperature (85.35 to 83.92°C) and foaming capacity (15.54 to 9.52%). These changes suggest that fermentation can improve the nutritional quality and functionality of cocoyam flour, making it suitable for various food applications. | Oyiyechukwu Elizabeth Chikelu; Juliet Nnenna Udeh ; Chiamaka Vivian Ugwu | Agriculture and Food Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67adcda96dde43c908b2b220/original/impact-of-fermentation-duration-on-the-nutritional-anti-nutritional-and-functional-characteristics-of-colocasia-esculenta.pdf |
61d4d4709efae70a7731a9b4 | 10.26434/chemrxiv-2022-zkfsp | Multi-active Site Dynamics on a Molecular Cr/Co/Se Cluster Catalyst | This study provides detailed insights into the interconnected reactivity of the three catalytically active sites of an atomically precise nanocluster Cr3(py)3Co6Se8L6 (Cr3(py)3, L = Ph2PNTol–, Ph = phenyl, Tol = 4-tolyl). Catalytic and stoichiometric studies into tosyl azide activation and carbodiimide formation enabled the isolation and crystallographic characterization of key metal-nitrenoid catalytic intermediates, including the tris(nitrenoid) cluster Cr3(NTs)3, the catalytic resting state Cr3(NTs)3(CNtBu)3, and the mono(nitrenoid) cluster Cr3(NTs)(CNtBu)2. Nitrene transfer proceeds via a stepwise mechanism, with the three active sites engaging sequentially to produce carbodiimide. Comparative structural analysis and CNtBu bind-ing studies reveal that the chemical state of neighboring active sites regulates the affinity for substrates of an individual Cr-nitrenoid edge site, intertwining their reactivity through the inorganic support. | Jonathan Kephart; Benjamin Mitchell; Werner Kaminsky; Alexandra Velian | Inorganic Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Kinetics and Mechanism - Inorganic Reactions; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d4d4709efae70a7731a9b4/original/multi-active-site-dynamics-on-a-molecular-cr-co-se-cluster-catalyst.pdf |
63dc38175c37ece322a6df84 | 10.26434/chemrxiv-2023-hx311 | The Indenyl Effect: Accelerated C-H Amidation of Arenes via Weakly-Coordinating Group Directed Nitrene Transfer Catalysis | Investigations into C-H amidation reactions using electron-deficient cationic half-sandwich d6 metal complexes revealed that the indenyl-derived catalyst [Ind*RhCl2]2 significantly accelerated the directed ortho C-H amidation of benzoyl silanes using 1,4,2-dioxazol-5-ones. Ring slippage involving a haptotropic rearrangement of the indenyl complex proposedly enables ligand substitution at the metal centre to proceed via associative, rather than dissociative pathways, leading to significant rate and yield enhancements. Intriguingly, this phenomenon appears specific for C-H amidation reactions involving weakly coordinating carbonyl-based directing groups with no acceleration observed for the corresponding reactions involving strongly coordinating nitrogen-based directing groups. | Liselle Atkin; Daniel Priebbenow | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dc38175c37ece322a6df84/original/the-indenyl-effect-accelerated-c-h-amidation-of-arenes-via-weakly-coordinating-group-directed-nitrene-transfer-catalysis.pdf |
60c73f1a842e65ae53db1a00 | 10.26434/chemrxiv.7234826.v1 | Mechanical Properties and Processing Techniques of Bulk Metal-Organic Framework Glasses | Glasses formed by melt quenching metal–organic frameworks (MOFs) are attracting growing attention because they exhibit an improved processability compared with their crystalline counterparts. Melt quenched MOF glasses also define a new category of glass, distinct from metallic, organic and inorganic glasses, owning to the role that metal-ligand coordination bonding plays in their three-dimensional structures. The mechanical properties of glasses in general are of importance given their application in protective coatings, display technologies and screens. Little, however, is known about the mechanical behavior of MOF-glasses, and experimental elucidation of key properties such as their scratch resistance has been limited by the lack of processing methodologies capable of producing bulk glass samples. Here, nanoindentation was used to investigate the Young’s modulus and hardness of four melt-quenched glasses formed from zeolitic imidazolate frameworks (ZIF): agZIF-4, agZIF-62, agZIF-76 and agZIF-76-mbIm. The creep resistance of the melt-quenched glasses was studied via strain-rate jump (SRJ) tests, and through constant load and hold (CLH) indentation creep experiments. Values for the strain-rate sensitivity were found to be close to those for other glassy polymers and Se-rich GeSe chalcogenide glasses. One glass, agZIF-62, was used to explore two strategies for the preparation of bulk glass samples, i.e. (i) vacuum hot-pressing and (ii) remelting and annealing. Vacuum hot-pressing resulted in an inhomogeneous bulk sample containing the glass and amorphous, non-melt quenched aZIF-62. Remelting and annealing however, resulted in the fabrication of a transparent, bubble-free, bulk specimen, which allowed the first scratch testing experiments to be performed on a MOF-glass. The results are of high significance for potential applications of MOF-glasses. | Thomas Bennett; Shichun Li; Rene Limbach; Louis Longley; Amir Shirzadi; John C. Walmsley; Duncan Johnstone; Paul A. Midgley; Lothar Wondraczek | Hybrid Organic-Inorganic Materials; Coordination polymers; Ligands (Inorg.); Organometallic Compounds; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1a842e65ae53db1a00/original/mechanical-properties-and-processing-techniques-of-bulk-metal-organic-framework-glasses.pdf |
60c74decf96a005279287a1d | 10.26434/chemrxiv.12674345.v1 | Molecular Modeling of Structures and Interaction of Short Peptides and Sortase Family Protein of Enterococcus Faecalis: Basis for Developing Peptide-Based Therapeutics Against Multidrug Resistant Strains | <p>The <i>Enterococcus faecalis</i> (<i>E.
faecalis</i>) infection starts with initial adhesion to a host cell or abiotic
surface by multiple adhesions on its cell membrane. The pathogenicity is due to
virulence factors SrtA, SrtC, EbpA, EbpB, EbpC, and Aggregation Substance. <i>E. faecalis</i> developed resistance to the
majority of standard therapies. Additionally, a notable key feature of <i>E. faecalis</i> is its ability to form
biofilm <i>in vivo</i>. <i>E. faecalis</i> strains show resistance to aminoglycosides and β-lactam
antibiotics with different degree of susceptibility. Sortases (SrtA and SrtC)
are enzymes spatially localized at the septal region in majority of
gram-positive bacteria during the cell cycle, which in-turn plays an important
role in proper assembling of adhesive surface proteins and pilus on cell
membrane. The studies have also proved that the both SrtA and SrtC were focally
localized in <i>E. faecalis</i> and
essential for efficient bacterial colonization and biofilm formation on the
host tissue surfaces Using homology modeling and protein-peptide flexible
docking methods, we report here the detailed interaction between peptides and <i>Ef</i>Srt (Q836L7) enzyme. Plausible binding
modes between <i>Ef</i>Srt and the selected
short biofilm active peptides were revealed from protein-peptide flexible
docking. The simulation data further revealed critical residues at the complex
interface and provided more details about the interactions between the peptides
and <i>Ef</i>Srt. The flexible docking simulations
showed that the peptide-<i>Ef</i>Srt binding
was achieved through hydrogen bonding, hydrophobic, and van der Waals
interaction. The strength of interactions between peptide-<i>Ef</i>Srt complexes were calculated using standard energy calculations
involving non-bonded interactions like electrostatic, van der Waals, and
hydrogen bonds.</p> | Muthusaravanan S; Ram Kothandan; Kumaravel Kandaswamy; Cashlin Anna Suveetha Gnana Rajan; Janamitra Arjun; Rejoe Raymond | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74decf96a005279287a1d/original/molecular-modeling-of-structures-and-interaction-of-short-peptides-and-sortase-family-protein-of-enterococcus-faecalis-basis-for-developing-peptide-based-therapeutics-against-multidrug-resistant-strains.pdf |
6750b06e7be152b1d0f69017 | 10.26434/chemrxiv-2024-hxdbt | Particulates and Gaseous Emission from Indian Agricultural Sector and Health Burden Attributable to Agricultural PM2.5 | The agricultural sector significantly contributes to atmospheric pollution, impacting air quality through activities such as tillage, planting, fertilizer application, harvesting, crop residue burning (CRB), and grain handling. The outcome of this work is the docu- mentation of emission inventory of particulates (PM10 and PM2.5) and gaseous emission (SO2, CO, NOx, NH3, and volatile organic compounds (VOCs)) from the agricultural industry. Further the emission of EC, OC, and (Polycyclic Aromatic Hydrocarbons) PAHs, which are part of particulate matter (PM), were calculated along with green- house gases (CO2, CH4 and N2O) coming from the agricultural sector for 2021, with projections for 2051. Total greenhouse gas emission in 2021 were 377 Tg, while PM10 and PM2.5 emissions were approximately 2.5 Tg and 1.1 Tg, respectively. The health impact of agricultural PM2.5 was quantified, revealing an estimated approximately 4 million Disability-Adjusted Life Years (DALYs) and 0.14 million deaths attributable to these emissions in 2021. The findings highlight the urgent need for technological advancements to reduce emissions at their source, ensuring sustainable agricultural practices. This study provides critical data for policymakers to address air quality and health challenges. Furthermore, the emission inventory developed will serve as a valuable resource for researchers conducting air quality modeling and environmental impact assessments.
Synopsis: Emission inventory for various agricultural activities is not yet available for India. This study of aggregation of emission inventory for India supports efforts to improve public health, reduce pollution, and promote long-term sustainability in agriculture. | Roshan Kumar Singh; Seema Prajapati; Indra Mohan Nigam; Ran Zhao; Tarun Gupta | Analytical Chemistry; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6750b06e7be152b1d0f69017/original/particulates-and-gaseous-emission-from-indian-agricultural-sector-and-health-burden-attributable-to-agricultural-pm2-5.pdf |
65f630efe9ebbb4db9da50e8 | 10.26434/chemrxiv-2024-wl1bg | The role of organic cations in the electrochemical reduction of CO2 in aprotic solvents | The electrochemical reduction of CO2 is sensitive to the microenvironment surrounding catalytic active sites. Although the impact of changing electrolyte composition on CO2 reduction kinetics in aqueous electrolytes has been studied intensively, less is known about the influence of the electrochemical environment in non-aqueous solvents. Here, we present data demonstrating that organic alkyl ammonium cations influence catalytic performance in non-aqueous media and describe a physical model that rationalizes these observations. Using results from a combination of kinetic, spectroscopic, and computational techniques, we argue that the interfacial electric field present at the catalyst surface is sensitive to the molecular identity of the organic cation in the aprotic electrolyte. This is true irrespective of solvent, electrolyte ionic strength, or the supporting electrolyte counter anion. Our results suggest that changes in the interfacial field can be attributed to differences in the cation-electrode distance. Changes in the electric field strength are consequential to CO2R to CO as they modify the energetics of the kinetically relevant CO2 activation step. | Jon-Marc McGregor; Jay Bender; Amanda Petersen; Louise Canada; Jan Rossmeisl; Joan Brennecke; Joaquin Resasco | Catalysis; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f630efe9ebbb4db9da50e8/original/the-role-of-organic-cations-in-the-electrochemical-reduction-of-co2-in-aprotic-solvents.pdf |
6367ec49ac45c71d90a8bc61 | 10.26434/chemrxiv-2022-ghjbk | Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerisation | The misincorporation of a non-complimentary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling first-principles quantum chemistry calculations to an open quantum systems master equation. This methodology allows us to accurately calculate the proton transfer between bases, allowing the misincorporation and formation of mutagenic tautomeric forms of DNA bases. Our quantum mechanic model predicts the existence of a short-lived ``tunnelling-ready" configuration along the wobble reaction pathway, effectively compressing the energy barrier for this reaction and dramatically increasing the rate of mismatch formation by a hundredfold. Further, we calculate rates of genetic error formation that are in excellent agreement with experimentally observed mutation rates, demonstrating that quantum tunnelling plays a critical role in determining the transcription error frequency of the polymerase. | Louie Slocombe; Jim Al-Khalili; Marco Sacchi | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Cell and Molecular Biology; Chemical Biology; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6367ec49ac45c71d90a8bc61/original/quantum-tunnelling-effects-in-the-guanine-thymine-wobble-misincorporation-via-tautomerisation.pdf |
60c749dfbdbb89240aa3929e | 10.26434/chemrxiv.12084822.v2 | Computational Target-Based Drug Repurposing of Elbasvir, an Antiviral Drug Predicted to Bind Multiple SARS-CoV-2 Proteins | Coronavirus disease 19 (COVID-19) is a severe acute respiratory syndrome caused by SARS-CoV-2 (2019-nCoV). While no drugs have yet been approved to treat this disease, small molecules effective against other viral infections are under clinical evaluation for therapeutic abatement of SARS-CoV-2 infections. Ongoing clinical trials include Kaletra (a combination of two protease inhibitors approved for HIV treatment), remdesivir (an investigational drug targeting RNA-dependent RNA polymerase [RdRP] of SARS-CoV-2), and hydroxychloroquine (an approved anti-malarial and immuno-modulatory drug). Since SARS-CoV-2 replication depends on three virally encoded proteins (RdRP, papain-like proteinase, and helicase), we screened 54 FDA-approved antiviral drugs and ~3300 investigational drugs for binding to these proteins using targeted and unbiased docking simulations and computational modeling. Elbasvir, a drug approved for treating hepatitis C, is predicted to bind stably and preferentially to all three proteins. At the therapeutic dosage, elbasvir has low toxicity (liver enzymes transiently elevated in 1% of subjects) and well-characterized drug-drug interactions. We predict that treatment with elbasvir, alone or in combination with other drugs such as grazoprevir, could efficiently block SARS-CoV-2 replication. The concerted action of elbasvir on at least three targets essential for viral replication renders viral mutation to drug resistance extremely unlikely. | Meenakshisundaram Balasubramaniam; Robert Shmookler Reis | Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749dfbdbb89240aa3929e/original/computational-target-based-drug-repurposing-of-elbasvir-an-antiviral-drug-predicted-to-bind-multiple-sars-co-v-2-proteins.pdf |
60c750f2ee301c70b1c7a973 | 10.26434/chemrxiv.12758474.v2 | Prediction of Chemical Reaction Yields using Deep Learning | <div>Artificial intelligence is driving one of the most important revolutions in organic chemistry. </div><div>Multiple platforms, including tools for reaction prediction and synthesis planning based on machine learning, successfully became part of the organic chemists' daily laboratory, assisting in domain-specific synthetic problems. Unlike reaction prediction and retrosynthetic models, the prediction of reaction yields has received less attention in spite of the enormous potential of accurately predicting reaction conversion rates. Reaction yields models, describing the percentage of the reactants converted to the desired products, could guide chemists and help them select high-yielding reactions and score synthesis routes, reducing the number of attempts. So far, yield predictions have been predominantly performed for high-throughput experiments using a categorical (one-hot) encoding of reactants, concatenated molecular fingerprints, or computed chemical descriptors. Here, we extend the application of natural language processing architectures to predict reaction properties given a text-based representation of the reaction, using an encoder transformer model combined with a regression layer. We demonstrate outstanding prediction performance on two high-throughput experiment reactions sets. An analysis of the yields reported in the open-source USPTO data set shows that their distribution differs depending on the mass scale, limiting the dataset applicability in reaction yields predictions. </div> | Philippe Schwaller; Alain C. Vaucher; Teodoro Laino; Jean-Louis Reymond | Organic Synthesis and Reactions; Chemoinformatics; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750f2ee301c70b1c7a973/original/prediction-of-chemical-reaction-yields-using-deep-learning.pdf |
6504426c99918fe537fe131d | 10.26434/chemrxiv-2023-z90vv | Strain-promoted cycloadditions in lipid bilayers triggered by liposome fusion | Due to the variety of roles served by the cell membrane, its composition and structure are complex, making it difficult to study. Bioorthogonal reactions, such as the strain promoted azide–alkyne cycloaddition (SPAAC), are powerful tools for exploring the function of biomolecules in their native environment but have been largely unexplored within the context of lipid bilayers. Here, we developed a new approach to study the SPAAC reaction in liposomal membranes using azide- and strained alkyne-functionalized Förster resonance energy transfer (FRET) dye pairs. This study represents the first characterization of the SPAAC reaction between diffusing molecules inside liposomal membranes. Potential applications of this work include in situ bioorthogonal labeling of membrane proteins, improved understanding of membrane dynamics and fluidity, and the generation of new probes for biosensing assays. | Coline Jumeaux; Christopher Spicer; Patrick Charchar; Philip Howes; Margaret Holme; Li Ma; Nicholas Rose; Harunur Rashid; Irene Yarovsky; Molly Stevens | Biological and Medicinal Chemistry; Nanoscience; Nanodevices; Bioengineering and Biotechnology; Chemical Biology; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6504426c99918fe537fe131d/original/strain-promoted-cycloadditions-in-lipid-bilayers-triggered-by-liposome-fusion.pdf |
60c745f9f96a0053ec286c7d | 10.26434/chemrxiv.10293395.v1 | Sniff Olfactometry: Temporal effects on odorant mixture perception in humans | There is evidence in mice and honeybees that signals initiated by odorants at the olfactory epithelium arrive downstream in the olfactory bulb between 10 and 200ms later and that these latencies are ligand dependent. It has recently been proposed that these latencies could be used by mice to identify or classify. Here we demonstrate that humans are sensitive to the timing of individual of odorant presentation. Using a two-alternate forced choice (2AFC) paradigm—subjects chose which odorant they recognized first after they experienced two 70ms puffs separated in time by some interval in the range of -450ms to +450ms. All subject recognition probabilities yielded the same linear function of latency (p<0.05) even though they differed in their recognition thresholds for the components and their recognition probability to detect them in binary mixtures. These results indicate that temporal structure of odor delivery affects human odor perception and sniff olfactometry (SO) has the temporal resolution necessary to measure these effects. <div><br /></div> | Kaifeng Ding; Xiaoyuan Wang; Dmitry Rinberg; Terry Acree | Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745f9f96a0053ec286c7d/original/sniff-olfactometry-temporal-effects-on-odorant-mixture-perception-in-humans.pdf |
6724fa585a82cea2fabc3461 | 10.26434/chemrxiv-2024-lp619 | Green Pudovik Addition/Cyclization/Aromatization to Isobenzofuran-Based AIEgens with Color Tunability for Lipid Droplets Imaging and Photodynamic Therapy | Aggregation-induced emission luminogens (AIEgens) have gained significant attention in science and manufacture due to its potential application in photoelectric materials and biomedical materials. Thus, development of new organic reactions to synthesize novel AIEgens is highly essential. Due to their unique electronic structures and distinctive optoelectronic properties, the formation of main group heterocycle-based AIEgens is becoming a research hotspot. Herein, we develop a one-pot metal-free Pudovik addition/cyclization/aromatization reaction between o-propargyl alcohol benzaldehydes and diarylphosphine oxides to generate isobenzofuran-based AIEgens. Such reaction possesses green synthesis, simple operation, high skeletal stability, satisfactory quantum yields and tunable emission covering the entire visible region. Moreover, these isobenzofuran-substituted phosphine oxides (IBFPO) can be used as bioprobes for cell imaging of lipid droplets in HeLa cells. Notably, quantitative evaluation of phototherapy effect demonstrates that one of these presented AIEgens, namely IBFPO-3j, displays high Type-I reactive oxygen species (ROS) generation efficiency, enabling its effective application for photodynamic therapy in hypoxic environment. Benefiting from the easy preparation and the tunable emission, versatile IBFPO-based AIEgens provide a new platform toward advanced materials for extensive applications in biological systems. | Xin Chang; Xiao-Wen Han; Ni-Ni Zhou; Hai-Tao Zhu; Nan Yang; Chen-Ping Shen; Chunxuan Qi; An-Xi Zhou; Hai-Tao Feng; Ben Zhong Tang | Biological and Medicinal Chemistry; Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6724fa585a82cea2fabc3461/original/green-pudovik-addition-cyclization-aromatization-to-isobenzofuran-based-ai-egens-with-color-tunability-for-lipid-droplets-imaging-and-photodynamic-therapy.pdf |
675554fe7be152b1d04f84d9 | 10.26434/chemrxiv-2024-r0r1z | Fluorescence from pentacyanopropenide aggregates in melamine | Aggregation-induced optical properties of molecules are at the forefront of materials sciences. Here, tetracyanoethylene (TCNE) is reacted and encapsulated in melamine. Crystallization in aqueous tetrahydrofuran solutions of melamine and TCNE at different concentrations yields colorful crystals with fluorescence emission at multiple wavelengths. Combined infrared spectroscopy and mass spectrometry reveal that the crystals are melamine doped with a trace amount of 1,1,2,3,3,-pentacyanopropenide. The fluorescence excitation-emission spectral mapping elucidates concentration dependences of the fluorescence emission in both precursor solutions and crystals. Based on density functional theory calculations the multi-wavelength emissions can be attributed to aggregates of the pentacyanopropenide. Highly stable doped melamines have the potential as multifunctional optical materials in optielectronics. | Hanen Mechi; Arthur Mantel; Vipin Mishra; Yuto Urano; Ryo Kitaura; Hidetsugu Shiozawa | Materials Science; Aggregates and Assemblies; Optical Materials | CC BY 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675554fe7be152b1d04f84d9/original/fluorescence-from-pentacyanopropenide-aggregates-in-melamine.pdf |
60c743ae842e655807db22e4 | 10.26434/chemrxiv.9445202.v1 | Deeper Insight into the Protease-Mediated Formation of Pyronin Dyes and Possible Implications in the Design of Fluorogenic Probes for Bioimaging and Theranostic Prodrugs | We report a rational and systematic study devoted to structural optimisation of a novel class of protease-sensitive fluorescent probes recently reported by us (<i>Org. Biomol. Chem.</i>, 2017, <b>15</b>, 2575-2584), based on the "covalent-assembly" strategy and using the targeted enzyme (penicilin G acylase as model protease) to build a fluorescent pyronin dye by triggering a biocompatible domino cyclisation-aromatisation reaction. The aim is to identify <i>ad hoc</i> probe candidate(s) that might combine fast/reliable fluorogenic "turn-on" response, full stability in complex biological media and ability to release a second molecule of interest (drug or second fluorescent reporter), for applications in disease diagnosis and therapy. We base our strategy on screening a set of active methylene compounds (C-nucleophiles) to convert the parent probe to various pyronin caged precursors bearing Michael acceptor moieties of differing reactivity. <i>In vitro</i> stability and fluorescent enzymatic assays combined to HPLC-fluorescence analyses provide data useful to define the most appropriate structural features for these fluorogenic scaffolds depending on the specifications required by the biomedical application (<i>e.g.</i>, <i>in vivo</i> molecular imaging, image-guided drug delivery and theranostics) for which they will be used. | Kévin RENAULT; Sylvain DEBIEU; Jean-Alexandre RICHARD; Anthony ROMIEU | Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ae842e655807db22e4/original/deeper-insight-into-the-protease-mediated-formation-of-pyronin-dyes-and-possible-implications-in-the-design-of-fluorogenic-probes-for-bioimaging-and-theranostic-prodrugs.pdf |
60c74b994c8919c129ad348c | 10.26434/chemrxiv.12357302.v1 | Predicting Glycosylation Stereoselectivity Using Machine Learning | Predicting the stereochemical outcome of chemical reactions is challenging in mechanistically ambiguous transformations. The stereoselectivity of glycosylation reactions is influenced by at least eleven factors across four chemical participants and temperature. A random forest algorithm was trained using a highly reproducible, concise dataset to accurately predict the stereoselective outcome of glycosylations. The steric and electronic contributions of all chemical reagents and solvents were quantified by quantum mechanical calculations. The trained model accurately predicts stereoselectivities for unseen nucleophiles, electrophiles, acid catalyst, and solvents across a wide temperature range (overall root mean square error 6.8%). All predictions were validated experimentally on a standardized microreactor platform. The model helped to identify novel ways to control glycosylation stereoselectivity and accurately predicts previously unknown means of stereocontrol. By quantifying the degree of influence of each variable, we discovered that environmental factors influence the stereoselectivity of glycosylations more than the coupling partners in this area of chemical space. <br /> | Soo-Yeon Moon; Sourav Chatterjee; Peter H. Seeberger; Kerry Gilmore | Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b994c8919c129ad348c/original/predicting-glycosylation-stereoselectivity-using-machine-learning.pdf |
60c745789abda256a1f8c57a | 10.26434/chemrxiv.9758558.v2 | From Desktop to Benchtop – A Paradigm Shift in Asymmetric Synthesis | The organic chemist’s toolbox is vast with
technologies to accelerate the synthesis of novel chemical matter. The field of
asymmetric catalysis is one approach to access new areas of chemical space and
computational power is today sufficient to assist in this exploration.
Unfortunately, existing techniques generally require computational expertise
and are therefore under-utilized in synthetic chemistry. We present herein our
platform Virtual Chemist that
allows bench chemists to predict outcomes of asymmetric chemical reactions
ahead of testing in the lab, in just a few clicks. Modular workflows facilitate
the simulation of various sets of experiments, including the four realistic
scenarios discussed: one-by-one design, library screening, hit optimization,
and substrate scope evaluation. Catalyst candidates are screened within hours
and the enantioselectivity predictions provide substantial enrichments compared
to random testing. The achieved accuracies within ~1 kcal/mol provide new
opportunities for computational chemistry in asymmetric catalysis. | Mihai Burai Patrascu; Joshua Pottel; Sharon Pinus; Michelle Bezanson; Per-Ola Norrby; Nicolas Moitessier | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745789abda256a1f8c57a/original/from-desktop-to-benchtop-a-paradigm-shift-in-asymmetric-synthesis.pdf |
62446a06437a066df1ecbfe3 | 10.26434/chemrxiv-2022-w10gs | Milliwatt Three- and Four-Pulse Double Electron Electron Resonance for Protein Structure Determination. | Electron paramagnetic resonance (EPR) experiments for protein structure determination using double electron-electron resonance (DEER) spectroscopy rely on very high incident microwave powers (>300 W) to create the short pulse lengths needed to excite a sizable portion of the spectrum. The recently introduced self-resonant microhelix combines a high B1 conversion efficiency with an intrinsically large bandwidth (low Q-value) and a high absolute sensitivity. We report dead times as low as 14±2 ns achieved using less than 1 W of power at X-band (nominally 9.5 GHz) on a molecular ruler and a T4-lysozyme sample. These low-power experiments were performed using an active volume 120 times smaller than that of a standard pulse EPR resonator, while only a sixfold decrease in the signal-to-noise ratio was observed. Small build sizes, as realized with the microhelix, give access to volume-limited samples, while shorter dead times allow the investigation of fast relaxing spin species. With the significantly reduced dead times, the 3-pulse DEER experiment can be revisited. Here, we show experimentally that 3-pulse DEER offers superior sensitivity over the 4-pulse DEER. We assert that the microhelix paves the road for low-cost benchtop X-band pulse EPR spectrometers by eliminating the need for high-power amplifiers, accelerating the adoption of pulse EPR to a broader community. | Markus Teucher; Jason Sidabras; Alexander Schnegg | Physical Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62446a06437a066df1ecbfe3/original/milliwatt-three-and-four-pulse-double-electron-electron-resonance-for-protein-structure-determination.pdf |
6695b30801103d79c51c4ce2 | 10.26434/chemrxiv-2024-n1928 | High Throughput Parallel Reaction Monitoring with Computer Vision | We report the development and applications of a computer vision based reaction monitoring method for high throughput experimentation (HTE). Whereas previous efforts reported methods to extract bulk kinetics from a single video, this new approach enables one video to capture bulk kinetics of multiple reactions running in parallel. Case studies in and beyond well-plate high throughput settings are described. Analysis of parallel dye-quenching hydroxylations, DMAP-catalysed esterification, solid-liquid sedimentation dynamics, metal catalyst degradation, and biologically-relevant sugar-mediated nitro reduction reactions have each provided insight into the scope and limitations of camera-enabled high throughput kinetics as a means of widening known analytical bottlenecks in HTE for reaction discovery, mechanistic understanding, and optimisation. It is envisaged that the nature of the multi-reaction time-resolved datasets made available by this analytical approach will later serve a broad range of downstream efforts in machine learning approaches towards exploring chemical space. | Henry Barrington; Timothy J.D. McCabe; Kristin Donnachie; Calum Fyfe; Aaron McFall; Marina Gladkikh; Jake McGuire; Chunhui Yan; Marc Reid | Physical Chemistry; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Analytical Apparatus; High-throughput Screening; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6695b30801103d79c51c4ce2/original/high-throughput-parallel-reaction-monitoring-with-computer-vision.pdf |
60c746a69abda26247f8c785 | 10.26434/chemrxiv.11365943.v1 | Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field | <p>We studied by molecular dynamic (MD)
simulations systems including the inward<sub>closed</sub> state of influenza A
M2 protein in complex with aminoadamantane drugs in membrane bilayers. We
varied the M2 construct and performed MD simulations in M2TM or M2TM with
amphipathic helices (M2AH). We also varied the lipid bilayer by changing either
the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer
size, 10x10 Å<sup>2 </sup>or 20x20 Å<sup>2</sup>. We aimed to suggest optimal
system conditions for the computational description of this ion channel and
related systems. Measures performed include quantities that are available experimentally
and include: (a) the position of ligand, waters and chlorine anion inside the M2
pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in
complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the
AHs conformation and structure which is affected from interactions with lipids
and chol and is important for membrane curvature and virus budding. In several
cases we tested OPLS2005, which is routinely applied to describe drug-protein
binding, and CHARMM36 which describes reliably protein conformation. We found
that for the description of the ligands position inside the M2 pore, a 10x10 Å<sup>2</sup>
lipids buffer in DMPC is needed when M2TM is used but 20x20 Å<sup>2</sup>
lipids buffer of the softer POPC; when M2AH is used all 10x10 Å<sup>2</sup> lipid
buffers with any of the tested lipids can be used. For the passage of waters at
least M2AH with a 10x10 Å<sup>2</sup> lipid buffer is needed. The folding
conformation of AHs which is defined from hydrogen bonding interactions with
the bilayer and the complex with chol is described well with a 10x10 Å<sup>2</sup>
lipids buffer and CHARMM36. </p> | Dimitrios Kolokouris; Iris Kalenderoglou; Panagiotis Lagarias; Antonios Kolocouris | Biochemistry; Bioinformatics and Computational Biology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746a69abda26247f8c785/original/spotting-differences-in-molecular-dynamic-simulations-of-influenza-a-m2-protein-ligand-complexes-by-varying-m2-construct-lipid-bilayer-and-force-field.pdf |
6518cdbca69febde9e00a3a8 | 10.26434/chemrxiv-2023-2tcvb | Resolving metal binding properties within subunits of a multimeric enzyme Mnx by surface induced dissociation and native ion mobility mass spectrometry | Multi-subunit enzymes function as coordinated assemblies. Yet most enzymatic assays measure the summed output of all populations in solution and cannot easily differentiate contributions of individual subunits. Native mass spectrometry detects intact protein complexes in the gas phase. Surface induced dissociation further releases subunits from protein complexes while retaining compact conformations and bound ligands. Combined with ion mobility, the released subunits can then be carefully monitored for more in-depth structural analysis. Mnx is a unique bacterial multicopper oxidase complex that oxidizes Mn(II) to form MnO2 minerals, and is composed of three subunits: MnxG, a multicopper oxidase containing the active site, and two accessory proteins, MnxE and MnxF which also bind copper ions. Other known multicopper oxidases do not require accessory proteins, therefore the functions of MnxE and MnxF are not well understood. Here, we use native mass spectrometry with surface induced dissociation and ion mobility to characterize the metal binding properties of Mnx with two metals, catalytic Cu(II) and Mn(II) substrate. We demonstrate our assay can detect subtle structural changes within each subunit, which are presumably related to the allosteric mechanism. We also noticed that ionic strength and solution composition can impact metal binding and must be carefully investigated for such experiments. | Deseree Reid; Stephanie Thibert; Jesse Wilson; Alexandra Soldatova; Bradley Tebo; Thomas Spiro; Mowei Zhou | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6518cdbca69febde9e00a3a8/original/resolving-metal-binding-properties-within-subunits-of-a-multimeric-enzyme-mnx-by-surface-induced-dissociation-and-native-ion-mobility-mass-spectrometry.pdf |
60c75875842e65700ddb4862 | 10.26434/chemrxiv.14495388.v2 | Using ATR-FTIR Spectra and Convolutional Neural Networks for Characterizing Mixed Plastic Waste | <p>We present a convolutional neural network
(CNN) framework for classifying different types of plastic materials that are
commonly found in mixed plastic waste (MPW) streams. The CNN framework uses
experimental ATR-FTIR (attenuated total reflection-Fourier transform infrared
spectroscopy) spectra to classify ten different plastic types. We show that the
approach reaches accuracies of over 87% and that some plastic types can be perfectly
classified.</p> | Shengli Jiang; Zhuo Xu; Medhavi Kamran; Stas Zinchik; Sidike Paheding; Armando McDonald; Ezra Bar-Ziv; Victor Zavala | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75875842e65700ddb4862/original/using-atr-ftir-spectra-and-convolutional-neural-networks-for-characterizing-mixed-plastic-waste.pdf |
60e5e9e98a469b9739783b6c | 10.26434/chemrxiv-2021-fhcv5 | The Impact of Surface Chemistry on Gold Nanorods Uptake in Stem Cell-derived Therapeutic Cells | Gold nanorods (AuNRs) hold tremendous potential to improve the diagnosis and therapeutic options across the blood-retinal barrier to treat retinal diseases. For clinical ophthalmological translation, a fundamental understanding of how their physicochemical properties such as size, shape, charge, surface chemistry, and concentration, impact their stability biological environments, mechanism and efficiency of uptake, and toxicity is a necessity. Here we interrogated the uptake efficiency, biocompatibility, and stability of two subtypes of AuNRs with different types of surface coatings and varying charges, including a commercially available set of AuNRs with a 5 nm mSiO2-polymer coating and hybrid lipid-coated AuNRs developed in-house. Confocal and bright field microscopy images showed uptake of both subtypes of AuNRs in retinal pigment epithelium (RPE), neural progenitor (NP), and baby hamster kidney (BHK) cells. Transmission electron microscopy (TEM) confirms both types of AuNRs are taken up into the cytoplasm of the cells; however, larger aggregates of AuNRs are observed with the more positive and “sticky” AuNRs with a 5 nm mSiO2-polymer coating than the slightly negative hybrid lipid-coated AuNRs. Inductively Coupled Mass Spectroscopy (ICP-MS) confirm that ~3,000 of the slightly negative hybrid lipid-coated AuNRs cells and ~5,400 of the positively charged AuNRs with a 5 nm mSiO2-polymer coating (+35 mV) are taken up into RPE and BHK cell lines. Stability studies in a variety of cellular media showed that hybrid lipid-coated AuNRs are stable and disaggregated in water, 10 mM PBS buffer pH 7, and BHK media except for NP media. In contrast, the positively charged AuNRs with a 5 nm mSiO2-zeta polymer coating aggregated in all media, indicating more interactions with each other and components of the media. Bright-field and TEM confirm the presence of large aggregates of AuNRs on the surface and within the cytoplasm. Cytotoxicity studies both subtypes of AuNRs have an 80 ± 8 % cell viability, indicating mild toxicity. The hybrid lipid-coated AuNR with the cell-penetrating peptide had the least toxicological impact with a > 92 ± 7 % cell viability. Our study highlights the importance of evaluating the impact of the physicochemical features of each new nanoparticle design on their stability in biologically relevant environments and their impact on cellular uptake and toxicity in stem cell-derived therapeutic cells. Here we also provide a simple design strategy for tuning the surface chemistry of robust hybrid lipid-coated AuNRs to enhance cellular uptake to label stem cells with minimal aggregation and toxicity. | Marilyn Mackiewicz; Grant Marquart; Jonathan Stoddard; Trevor McGill; Karen Kinnison; Richard Hugo; Renee Ryals; Scott Schubert; Felicia Zhou | Biological and Medicinal Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Cell and Molecular Biology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e5e9e98a469b9739783b6c/original/the-impact-of-surface-chemistry-on-gold-nanorods-uptake-in-stem-cell-derived-therapeutic-cells.pdf |
67a52ef1fa469535b94e9a96 | 10.26434/chemrxiv-2025-mkjvl | Metal nano clusters on TiO2: catalytic activity in CH4 coupling | The TiO2 nano clusters have absorption in visible region for effective photo catalytic conversion of methane to ethane. The mechanistic study different steps involved in the ethane formation reaction, their calculated reaction energies and energy of activation confirm the successful conversion on methane to ethane on TiO2 nano cluster under normal conditions. The introduction of gold nano cluster as co-catalyst with TiO2 nano cluster reduces the energy gap for C-C coupling reaction step in ethane formation reaction. The C-H activation reaction on Au6-TiO2 nano cluster, the reaction energy is almost the same as that on the bare TiO2 nano cluster. The final desorption energy of free ethane from the adsorbed surface is less in case Au6-TiO2 nano cluster compared to TiO2 nano cluster. | Vidya Kaipanchery; Dorota Rutkowska-Zbik | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a52ef1fa469535b94e9a96/original/metal-nano-clusters-on-ti-o2-catalytic-activity-in-ch4-coupling.pdf |
61f0fc40c18d67e82084eb58 | 10.26434/chemrxiv-2022-1c4qh | Does Explicit Polarizability Improve Molecular Dynamics Predictions of Glass Transition Temperatures of Ionic Liquids? | Molecular-dynamics simulations are used for predictions of the glass transition temperatures for a test set of 5 aprotic ionic liquids. Glass transitions are localized with the trend-shift method analyzing volumetric and transport properties of bulk amorphous phases. Classical non-polarizable all-atom OPLS force-field model developed by Canongia Lopes and Pádua (CL&P) is employed as the starting level of theory for all calculations. Alternative approaches of charge scaling and Drude oscillator model, accounting for atomic polarizability either implicitly or explicitly, respectively, are used to investigate the sensitivity of the glass transition temperatures to induction effects. The former non-polarizable model overestimates the glass transition temperature by tens of Kelvins (37 K in average).
The charge scaling technique yields a significant improvement, and the best estimations were achieved
using polarizable simulations with the Drude model, which yielded an average deviation of 11 K. Although the volumetric data usually exhibit a lesser trend shift upon vitrification, their lower statistical uncertainty enables to predict the glass transition temperature with a lower uncertainty than the ionic self-diffusivities, the temperature dependence of which is usually more scattered. Additional analyses of the simulated data were also performed, revealing that the Drude model predicts lower densities for
most sub-cooled liquids, but higher densities for the glasses than the original CL&P, and that the Drude model also invokes some longer-range organization of the sub-cooled liquid, greatly impacting the temperature trend of ionic self-diffusivities in the low-temperature region.
| Martin Klajmon; Ctirad Cervinka | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f0fc40c18d67e82084eb58/original/does-explicit-polarizability-improve-molecular-dynamics-predictions-of-glass-transition-temperatures-of-ionic-liquids.pdf |
60c74b1fbdbb89f300a394ee | 10.26434/chemrxiv.12213398.v2 | E. coli Nickel-Iron Hydrogenase 1 Catalyses Non-native Reduction of Flavins: Demonstration for Alkene Hydrogenation by Old Yellow Enzyme | <p>Robust
[NiFe] hydrogenase 1 (Hyd1) from <i>Escherichia
coli</i> is shown to have non-native, H<sub>2</sub>-dependent activity for FMN
and FAD reduction, and to function as a promising recycling system for FMNH<sub>2</sub>
supply to flavoenzymes for chemical synthesis, giving a total turnover number
over 10 thousand when coupled with an Old Yellow Enzyme ene reductase. </p> | Shiny Joseph Srinivasan; Sarah Cleary; Caroline Paul; Miguel A. Ramirez; Kylie Vincent | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b1fbdbb89f300a394ee/original/e-coli-nickel-iron-hydrogenase-1-catalyses-non-native-reduction-of-flavins-demonstration-for-alkene-hydrogenation-by-old-yellow-enzyme.pdf |
630f5ea1d858fb5700635756 | 10.26434/chemrxiv-2022-vjl32 | Formation, Reactivity and Decomposition of Aryl Phospha-Enolates | Two lithium phospha-enolates [RP=C(SiiPr3)OLi]2 were prepared by reduction of triisopropyl silyl phosphaethynolate, iPr3SiPCO, with aryl lithium reagents LiR (R = Mes: 1,3,5-trimethyl phenyl; or Mes*: 1,3,5,-tri-tert-butyl phenyl). Monomer/dimer aggregation of the enolates can be modulated by addition of 12-crown-4. Substitution of lithium for a heavier alkali metal was achieved through initial formation of a silyl enol ether, followed by reaction with KOtBu to form the corresponding potassium phospha-enolate [MesP=C(SiiPr3)OK]2. On addition of water, the enolates are protonated to afford RP=C(SiiPr3)(OH). For the sterically less demanding system (R = Mes), this phospha-enol rapidly tautomerises to the corresponding acyl phosphine MesP(H)C(SiiPr3)(O), which on heating extrudes CO. In contrast, bulkier phospha-enol (R = Mes*) is stable to rearrangement at room temperature and thermally decomposes to RH and iPr3SiPCO. | Stephanie Urwin; Jose Goicoechea | Inorganic Chemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630f5ea1d858fb5700635756/original/formation-reactivity-and-decomposition-of-aryl-phospha-enolates.pdf |
60c759a0337d6c080fe2943f | 10.26434/chemrxiv.14714895.v1 | Designing Asymmetrically Modified Nanochannel Sensors Using Virtual EIS | We devised an approach to capture the physics of localized charge modulation and its effect on ionic transport across asymmetrically charged nanopores by combining computational and experimental strategies. A virtual EIS tool has been developed to compute the impedance across nanopores. Nanoporous anodic alumina membrane (NAA) is employed for thrombin detection with thrombin binding aptamer to experimentally validate the computed impedance results. Using the approach proposed in this work, a novel biosensor is designed and a way to enhance the sensitivity of the sensor is established. | Sivaranjani Devarakonda; Sungu Kim; Baskar Ganapathysubramanian; Pranav Shrotriya | Nanodevices; Bioengineering and Biotechnology; Microbiology; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759a0337d6c080fe2943f/original/designing-asymmetrically-modified-nanochannel-sensors-using-virtual-eis.pdf |
6583b659e9ebbb4db9652720 | 10.26434/chemrxiv-2023-pwtlp | Crucial Effect of Surface Oxygen Species on CO2 Electroreduction Performance in Ti@Cu Single Atom Alloys | Here, we theoretically screened and explored the catalytic mechanism of electrocatalytic CO2 reduction reaction (eCO2RR) on Ti@Cu single atom alloy (SAA) and its oxidized variants (O-Ti@Cu and OH-Ti@Cu), focuseing on the effect of surface oxygen species on catalytical activity and selectivity under varying acidity and applied potential. Thermodynamically, Ti@Cu can be easily synthesized and oxidized in an aqueous solvent, as indicated by its low formation energy (-1.60 eV) and free energy (-0.92 eV) for oxidation. Catalytically, the introduction of bystander oxygen species facilitates the hydrogenation of residual *O after the generation of C2 products in eCO2RR on the Ti@Cu surface. This results in an inclination for eCO2RR on Ti@Cu to predominantly produce C1 product CH4 (ΔGRDS = 0.51 eV), while on the O-Ti@Cu and OH-Ti@Cu surfaces, there is a respective tendency towards the production of C2 products CH2CH2 (ΔGRDS = 0.51 eV) and CH3COOH (ΔGRDS=0.45 eV). Importantly, the potential required for eCO2RR on pure Ti@Cu is 0.70 V, notably lower than the 0.86 V needed for the *O hydrogenation. This confirms the stability of oxygen species (*O and *OH) on Ti@Cu under electrochemical conditions. Furthermore, the catalytic mechanism under varying electrochemical conditions (different potential and acidity) revealed that Ti@Cu favored CH4 production at pH = 1, 7, and 13, whereas both O-Ti@Cu and OH-Ti@Cu surfaces tended to produce CH2CH2 and CH3COOH at pH 1 and CH4 at pH = 7 and 13. This study contributes to our understanding of the catalytic mechanism of eCO2RR under realistic electrochemical conditions. | Xue-long Zhang; Zhi-jun Wu; Wei Zhang; Fu-li Sun; Cun-biao Lin; Wen-xian Chen; Gui-lin Zhuang | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6583b659e9ebbb4db9652720/original/crucial-effect-of-surface-oxygen-species-on-co2-electroreduction-performance-in-ti-cu-single-atom-alloys.pdf |
60c73ed7337d6c6c80e263eb | 10.26434/chemrxiv.7108631.v1 | Cooperative Adsorption of Carbon Disulfide in Diamine-Appended Metal– Organic Frameworks | <p>Over one million tons of carbon disulfide are produced globally each year for an array of applications, and emissions of this highly volatile and toxic liquid, known to generate acid rain, remain poorly controlled. As such, materials capable of reversibly capturing this commodity chemical in an energy-efficient manner are of interest. Recently, we detailed a family of diamine-appended metal–organic frameworks capable of selectively capturing carbon dioxide through a cooperative insertion mechanism that promotes efficient adsorption–desorption cycling. We therefore sought to explore the fundamental ability of these materials to capture CS<sub>2 </sub>through a similar mechanism. Employing crystallography, spectroscopy, and gas adsorption analysis, we demonstrate that CS<sub>2</sub> is indeed cooperatively adsorbed in <i>N,N</i>-dimethylethylenediamine-appended M<sub>2</sub>(dobpdc) (M = Mg, Mn, Zn; dobpdc<sup>4− </sup>= 4,4′-dioxidobiphenyl-3,3′-dicarboxylate), via the formation of electrostatically paired ammonium dithiocarbamate chains. Notably, in the weakly thiophilic Mg congener, chemisorption is cleanly reversible with mild thermal input. Importantly, this work demonstrates that the hitherto CO<sub>2</sub>-specific cooperative insertion mechanism can be generalized to other high-impact target molecules.</p> | C. Michael McGuirk; Rebecca L. Siegelman; Walter S. Drisdell; Tomče Runčevski; Phillip J. Milner; Julia Oktawiec; Liwen F. Wan; Gregory M. Su; Henry Z. H. Jiang; Douglas A. Reed; Miguel I. Gonzalez; David Prendergast; Jeffrey R. Long | Coordination Chemistry (Inorg.); Inorganic Acid/Base Chemistry; Main Group Chemistry (Inorg.); Solid State Chemistry; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed7337d6c6c80e263eb/original/cooperative-adsorption-of-carbon-disulfide-in-diamine-appended-metal-organic-frameworks.pdf |
60c7422abb8c1aea253da07a | 10.26434/chemrxiv.7637081.v2 | Bio-Copolyesters of Poly(butylene succinate)(PBS) Containing Long Chain Bio-Based Glycol | <p>Poly(butylene succinate) (PBS) is a thermoplastic and biodegradable polyester characterized by high rigidity due to its high crystallinity. However, the use of long chain biobased monomers to produce segmented copolymers is an effective strategy to tailor the properties of PBS, such as greater flexibility. In this paper, a series of aliphatic bio-copolyesters of poly(butylene succinate-dilinoleic succinate) (PBS-DLS) were successfully synthesized <i>via </i>a direct two-step polycondensation method using a semi-pilot scale reactor for melt polymerization and titanium dioxide/silicon dioxide coprecipitate catalyst (C-94). In this study, the thermal and mechanical properties were investigated and compared, focusing on the effect of varying the amount of biobased dilinoleic diol in the structure. With increasing amount of long chain diol, a decrease in molecular weight, density, and melt flow index was observed. The semicrystalline nature of the copolymers was confirmed using differential scanning calorimetry (DSC) and dynamic mechanical thermal analysis (DMTA) methods. These copolymers exhibit two main transition temperatures and vary in softness and processing flexibility. Furthermore, in the DSC data a linear trend was observed with increasing wt.% of hard PBS segments, which can be described by the Gordon-Taylor equation. Increasing the soft DLS segment content in the copolymer series resulted in an increase in the elastic behavior of the polymers. The broad range of crystallization temperatures and melt flow index values indicates that a polyester library with customizable properties that spans PBS applications has been successfully obtained.</p> | Karolina Stępień; Cathrine Miles; Andrew McClain; Ewa Wiśniewska; Peter Sobolewski; Joachim Kohn; Judit E. Puskas; H. Daniel Wagner; Miroslawa El Fray | Biodegradable Materials; Elastic Materials; Biopolymers; Polymerization (Polymers); Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422abb8c1aea253da07a/original/bio-copolyesters-of-poly-butylene-succinate-pbs-containing-long-chain-bio-based-glycol.pdf |
60c7401c9abda284f7f8bbe9 | 10.26434/chemrxiv.7594982.v1 | Dust Fall Monitoring In University of Ibadan, University of Ilorin and Kwara State University Motor Parks, Nigeria | The study was carried out for five months from November, 2014 to April, 2015 during which dust fall (particulate matter) was monitored in University of Ilorin, University of Ibadan and Kwara State University motor parks. Dust fall monitoring was carried out using Single open bucket sampler based on American Standard Test Method (ASTM D1739). The average dust fall depositions were found to be 1122.15 ± 50, 627.648 ± 34, and 316.322 ± 16 mgm-2day-1 for University of Ilorin (Un), Kwara State University (Kw) and University of Ibadan (UI) sites respectively. It was observed that unpaved surface and number of moving vehicles were the main factors for increased or decreased in dust fall concentrations. There was correlation between some meteorological parameters (rain fall, wind speed, temperature and relative humidity) and dust fall depending on the site.<br /> | Zaccheus Shehu | Atmospheric Chemistry; Analytical Chemistry - General; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401c9abda284f7f8bbe9/original/dust-fall-monitoring-in-university-of-ibadan-university-of-ilorin-and-kwara-state-university-motor-parks-nigeria.pdf |
624171c3202c065d31e45660 | 10.26434/chemrxiv-2022-2sqgf | Identical Spin Multi-State Reactivity Towards C-H Bond Activation in High-valent Fe/Mn-Oxo/Hydroxo Species | Activation of C-H bonds using an earth-abundant metal catalyst is one of the top challenges of chemistry where high-valent Fe/Mn-O/OH biomimic species play an important role. There are several open questions related to the comparative oxidative abilities of these species, and a unifying concept that could accommodate various factors influencing the reactivity is lacking. To shed light on these open questions, here we have used a combination of the DFT (B3LYP-D3/def2-TZVP) and ab initio (DLPNO-CCSD(T); CASSCF/NEVPT2) calculations to study a series of high-valent metal-oxo/hydroxo species, [Mn+H3buea(X)] (M = Fe and Mn, n = II to V, X = O/OH; H3buea = tris[(N'-tert-butylureaylato)-N-ethylene)]aminato) towards the activation of dihydroanthracene (DHA). Detailed analysis unveils the following reactivity trend FeV=O > MnIII=O > MnIV=O > FeIII=O > MnV=O > FeII-OH > MnII-OH > MnIV-OH > FeIV-OH > FeIV=O > FeIII-OH > MnIII-OH and suggests that neither higher oxidation nor high-spin ground state yields superior reactivity. The secondary coordination sphere is found to play a vital role in controlling the reactivity wherein the H-bonding interactions reduce the crystal field strength, and this brings several excited states of the same spin multiplicity closer to the ground state resulting in the observation of identical spin multistate reactivity (ISMR) in MnIII/IV=O and FeII-OH species. For FeV=O species, strong ligand spin polarization was detected, diminishing the crystal field leading to the exhibition of ISMR reactivity. The ISMR is found to control the basicity of the oxo/hydroxo group as well as the redox potentials. Further, when pKa > 15, a PT-ET mechanism for C-H bond activation is detected, and a higher E1/2 value directs the reaction via the concerted HAT/PCET mechanism. On the other hand, for species that exhibit classical SSR/TSR reactivity, such as MnII-OH, FeIV=O, the secondary coordination sphere effect is found to be lethal. As the multireference character is absent in these species, they lack the electronic flexibility that ISMR species enjoy during the reaction, leading to sluggish/no reactivity for many species, including the popular FeIV=O species. As metalloenzymes' active sites have several H-bonding networks resembling the species studied here, this unlocks the possibility of having ISMR type reactivity for metalloenzymes to rationalize their superior catalytic abilities. | Gopalan Rajaraman; Asmita Sen; Abinash SWAIN; Bhawana Pandey; Azaj Ansari | Theoretical and Computational Chemistry; Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624171c3202c065d31e45660/original/identical-spin-multi-state-reactivity-towards-c-h-bond-activation-in-high-valent-fe-mn-oxo-hydroxo-species.pdf |
6418648a2bfb3dc2511106a4 | 10.26434/chemrxiv-2023-b39lw | Increasing the resolution of field flow fractionation with increasing crossflow gradients | The resolution of flow field flow fractionation (flow FFF) depends primarily on the crossflow rate and its change over time. In this work we demonstrate a method for modulation of the crossflow rate during separation increases the peak-to-peak resolution of the resulting fractograms. In classical FFF methods, the crossflow rate is either maintained constant or decreased during separation of the different species. In this work, higher resolution between peaks was achieved by a novel gradient method in which the crossflow is increased briefly during separation to allow stronger retention of the later eluting peaks. We first outline the theoretical basis by which the improved separation is achieved. We confirm our hypothesis by quantifying the impact of increasing crossflow on the resolution between a monoclonal antibody monomer and its high molecular weight (HMW) aggregate. We then demonstrate that this method is applicable to two different FFF methods (AF4 and HF5) and various pharmaceutically relevant samples (monoclonal antibodies (mAbs) and adeno-associated viruses (AAV)). Finally, we hypothesize that increasing the force perpendicular to laminar flow as described here is broadly applicable to all FFF methods and improve the quality of FFF-based separations. | Nicholas Larson; George Bou-Assaf | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Separation Science; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6418648a2bfb3dc2511106a4/original/increasing-the-resolution-of-field-flow-fractionation-with-increasing-crossflow-gradients.pdf |
6533cd7887198ede07f38366 | 10.26434/chemrxiv-2023-m0mqh | Dynamics of Methyl Radical Formation Following 266 nm Dissociative Photoionization of Dimethyl- and Trimethyl- Pyridines | The 266 nm photolysis of various positional isomers of dimethylpyridines (DMPs) and trimethylpyridine (TMP) was investigated by measuring the translational energy distribution of methyl radical following {sp2}C−C{sp3} bond dissociation. The observed translational energy distribution is attributed to the dissociative photoionization in the cationic ground state following [1+1+1] three-photon absorption. The translational energy distribution profiles of the methyl radical were broad with the maximum translation energy in the excess of 2 eV, which originates due to the dissociation of {sp2}C−C{sp3} bond ortho to nitrogen atom in the ring. The dynamics of {sp2}C−C{sp3} bond dissociation in the cationic ground state of methyl pyridines is marginally dependent on the number and position of the methyl groups, however is site selective with preferential cleavage of the C−C bond in the ortho position to the pyridinic nitrogen atom. | Sumitra Singh; Monali Kawade; G Naresh Patwari | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6533cd7887198ede07f38366/original/dynamics-of-methyl-radical-formation-following-266-nm-dissociative-photoionization-of-dimethyl-and-trimethyl-pyridines.pdf |
60c743b60f50db4cab395fb5 | 10.26434/chemrxiv.9619823.v1 | Improved GPCR Ligands Based on Genetically Impossible Nanobody-Peptide Fusions | Here we describe a new method for improving signalling potency and selectivity for suboptimal GPCR ligands through conjugation with receptor-targeting nanobodies<br /> | Ross Cheloha; Fabian A. Fischer; Andrew W. Woodham; Eileen Daley; Naomi Suminski; Thomas
J. Gardella; Hidde L. Ploegh | Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b60f50db4cab395fb5/original/improved-gpcr-ligands-based-on-genetically-impossible-nanobody-peptide-fusions.pdf |
678ef43981d2151a02028d16 | 10.26434/chemrxiv-2025-29gd5 | Influence of substitution pattern on the dynamics of internal conversion and intersystem crossing in thiopyridone isomers | We report a combined experimental and theoretical investigation of the ultrafast internal conversion (IC) and intersystem crossing (ISC) dynamics of two thiopyridone isomers in solution. Our study used sulfur K-edge ultrafast transient x-ray absorption spectroscopy (XAS), in conjunction with electronic excited state surface hopping molecular dynamics and simulations of the excited state XAS, to investigate the impact of the functional group substitution pattern and solvent on the dynamics of IC and ISC. The combination of the localized x-ray probe and the simulation results enables, in part, the differentiation between ππ∗ and nπ∗ character excited states, as well as singlet and triplet states. Access to nπ∗ character excitations has particular value since they often prove challenging to assess with optical spectroscopy. The results point to the key role of these nπ∗ intermediates in mediating the intersystem crossing of these systems. Varying the substitution pattern of the molecule can stabilize or destabilize these intermediates leading to an increase in the rate of ISC in the ortho isomer as compared to the para isomer, while changing the solvent from acetonitrile to water had minimal effect on the electronic excited state relaxation mechanism. | Douglas Garratt; Sambit K. Das; Kacie J. Nelson; Jessica Harich; Antonia Freibert; Camila Bacellar; Claudio Cirelli; Philip J. M. Johnson; Rebeca G. Castillo; Marija R. Zoric; Ru-Pan Wang; Hyeongtaek Lim; Amy A. Cordones; Nils Huse; Michael Odelius; Kelly Gaffney | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ef43981d2151a02028d16/original/influence-of-substitution-pattern-on-the-dynamics-of-internal-conversion-and-intersystem-crossing-in-thiopyridone-isomers.pdf |
64c120529ed5166e93800edd | 10.26434/chemrxiv-2023-j0lms | Morphologies of proteinoids | Proteinoids, or thermal proteins, are aminoacid polymers formed at high temperatures by non-biological processes. Proteinoids form microspheres in liquids. The microspheres exhibit electrical activity similar to that of neurons. The electrically spiking microspheres are seen as proto-neurons capable of forming networks and carrying out information transmission and processing. Previously, we demonstrated that ensembles of proteinoid microspheres can respond to optical and electrical stimulation, implement logical gates, recognise arbitrary wave forms, and undergo learning. Thus, the ensembles of proteinoid microspheres can be seen as proto-brains. In present we decided to uncovering morphologies of these proto-brains. We utilise a supersaturated solution of calcium carbonate to facilitate the crystallisation of proteinoids and subsequently generate proteinoid brain structures. Our hypothesis suggests that calcium carbonate crystals have the potential to serve as scaffolds and connectors for proteinoid microspheres, thereby improving their electrical properties and facilitating communication. In this section, we outline the experimental methods and techniques used in our study. We share our findings and results regarding the morphology, composition, stability, and functionality of proteinoid brain structures. We discuss the implications and applications of our work in the fields of bio-inspired computing, artificial neural networks, and origin of life research. | Panagiotis Mougkogiannis; Andrew Adamatzky | Materials Science; Biological Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c120529ed5166e93800edd/original/morphologies-of-proteinoids.pdf |
60c74bacf96a00444b287668 | 10.26434/chemrxiv.12369461.v1 | A Single-Step Synthesis of 1,3,4,6-Tetraaryl-5-Aryliminopiperazin-2-One | We report here novel reaction that we found unprecedented, up to our knowledge. In a single step, we obtained unusual result. After magnificent efforts we could deduce the structure. We confirmed the structure of this product by reproducing the reaction using other substrates. The reaction therefore resulted in a piperazine ring that is functionalized on every atom in the ring. This was stage 1. We almost finished making this reaction more utilizable (stage 2) in a future paper. Enjoy it because you won't see a new chemistry everyday. | Moustafa El-Araby; Abdelsattar Omar | Organic Synthesis and Reactions; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bacf96a00444b287668/original/a-single-step-synthesis-of-1-3-4-6-tetraaryl-5-aryliminopiperazin-2-one.pdf |
6246121d855ee57605deda10 | 10.26434/chemrxiv-2022-3vgqt | Bioactive Fibronectin-III10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading | Integrating proteins with DNA nanotechnology would enable materials with diverse applications in biology, medicine, and engineering. Here, we describe a method for incorporating bioactive fibronectin domain proteins with DNA nanostructures using two orthogonal coiled-coil peptides. One peptide from each coiled-coil pair is attached to a DNA origami cuboid in a multivalent fashion by attaching the peptides to DNA handles. These structures can then be assembled into one-dimensional arrays through the addition of a fibronectin domain linker genetically fused with the complementary peptides to those on the origami. We validate array formation using two different self-assembly protocols and characterize the fibers by atomic force and electron microscopy. Finally, we demonstrate that surfaces coated with the protein-DNA nanofibers can serve as biomaterial substrates for fibroblast adhesion and spreading, with the nanofibers enhancing bioactivity compared with the monomeric protein. | Alex Buchberger; Kyle Riker; Julio Bernal-Chanchavac; Raghu Pradeep Narayanan; Chad R. Simmons; Nour Eddine Fahmi; Ronit Freeman; Nicholas Stephanopoulos | Biological and Medicinal Chemistry; Polymer Science; Nanoscience; Nanostructured Materials - Nanoscience; Bioengineering and Biotechnology; Cell and Molecular Biology | CC BY NC 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6246121d855ee57605deda10/original/bioactive-fibronectin-iii10-dna-origami-nanofibers-promote-cell-adhesion-and-spreading.pdf |
6385685894ff60608f430f2f | 10.26434/chemrxiv-2022-bwc99 | Comprehensive COSMO-RS Exploration of Highly CO2 Selective Hydrogen-bonding Binary Absorbents even under Humid Conditions | Improving the carbon capture efficiency with reducing the cost is mandatory for popularizing carbon capture, utilization, and storage (CCUS). Considering the objectives of green chemistry and engineering, here we show a theoretical exploration of the CO2-absorbing capacity of a set of 1,527,030 deep eutectic solvents (DESs). Comprehensive statistical thermodynamic calculations followed the previous experiments that DESs, including choline chloride, would have better CO2-absorbing capacity than those composed of non-ionic hydrogen bonding species in the case that choline chloride is used as a hydrogen-bonding acceptor. Quantitative evaluation of hydrogen-bonding interaction also indicated that the CO2-absorbing capacity would increase further when choline chloride is used as a hydrogen- bonding donor. | Shiori Watabe; Nahoko Kuroki; Hirotoshi Mori | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6385685894ff60608f430f2f/original/comprehensive-cosmo-rs-exploration-of-highly-co2-selective-hydrogen-bonding-binary-absorbents-even-under-humid-conditions.pdf |
678e95eb6dde43c90862581e | 10.26434/chemrxiv-2025-1s8h1 | Serine Octamer Clusters Direct the Chirality of Peptides Formed in Water Microdroplets | The chemistry underlying biological homochirality remains challenging. We propose that non-covalent clusters may have served as the means through which homochiral biochemistry emerged. Serine has long been known to exhibit a chiral preference in clustering to form the octamer; we extend this finding by reporting the effects of a non-zero e.e. in serine on the chiral preference seen in the formation of non-covalent clusters with other amino acids and in the formation of their covalent condensation products, peptides. We show (i) enantiopure serine directs racemic leucine and proline toward enantioselective dipeptide formation in water microdroplets and (ii) likely intermediates are seen as amino acid substitution products into the serine octamer cluster. This work indicates the relevance of microdroplet sprays, such as those found in natural aerosols, to molecular clustering phenomena and to homochirality. | R Graham Cooks; Brison Shira | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678e95eb6dde43c90862581e/original/serine-octamer-clusters-direct-the-chirality-of-peptides-formed-in-water-microdroplets.pdf |
648818f4be16ad5c57dbe9b7 | 10.26434/chemrxiv-2023-c68fc | Synthesis of Enantioenriched Substituted (Hetero)Cycloalkanes by Convergent NiH Catalysis | Enantioenriched alkyl-substituted cycloalkanes and azacyclic compounds constitute an essential class of compounds in pharmaceuticals, natural products and agrochemicals. Here we report an NiH-catalyzed asymmetric migratory hydroalkylation process for the efficient and selective construction of such compounds. Through a dynamic kinetic asymmetric transformation (DYKAT), easily accessible racemic and isomeric mixtures of cycloalkenes could be directly utilized as starting materials, convergently producing thermo-dynamically disfavored chiral 1,2-cis disubstituted cycloalkanes bearing vicinal stereocenters with high levels of regio-, diastereo- and enantioselectivity. Alternatively, N-heterocyclic alkenes can be employed, and deliver a variety of enantioenriched α-alkylated cyclic amines. The synthetic utility of this transformation is further demonstrated by the facile synthesis of two alkaloids, (+)-connine and (R)-pipecoline. | Changpeng Chen; Wenqing Guo; Deyong Qiao; Shaolin Zhu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648818f4be16ad5c57dbe9b7/original/synthesis-of-enantioenriched-substituted-hetero-cycloalkanes-by-convergent-ni-h-catalysis.pdf |
653207ca87198ede07d918b3 | 10.26434/chemrxiv-2023-09rcb | A Combined Experimental and Computational Investigation of Hydrogen-Bonded 2,7-Diazaindole-(Water)1,2 Complexes Isolated in the Gas Phase | We have presented a detailed experimental and computational analysis on the 1:1 and 1:2 complexes of 2,7-diazaindole (27DAI) with water in the gas phase. The complexes were characterized using two-color-resonant two-photon ionization (R2PI), laser induced fluorescence (LIF), single vibronic level fluorescence (SVLF), and photoionization efficiency spectroscopic methods. The 0_0^0 band of the S1←S0 electronic transition of 27DAI-H2O complex was observed at 33074 cm-1, largely red shifted by 836 cm-1 compared to that of the bare 27DAI. From the R2PI spectrum, the detected modes at 141 (v’Tx), 169 (v’Ty) and 194 (v’Ry) cm-1 were identified as the internal motions of H2O molecule in the complex. However, these modes were detected at 115 (v’’Tx), 152 (v’’Ty) and 190 (v’’Ry) cm-1 in the ground state which suggested a stronger hydrogen bonding interaction in the photo-excited state. The structural determination was aided by the detection of νNH and νOH values in the ground and excited state complex using the FDIR and IDIR spectroscopies. The detection of νNH at 3414 and νOH at 3447 cm-1 in 27DAI-H2O have shown an excellent correlation with the most stable structure consisting of N(1)-H‧‧‧O and OH‧‧‧N(7) hydrogen bonded bridging water molecule in the ground state. The structure of the complex in the electronic excited state (S1) were confirmed by corresponding bands at 3210 (νNH) and 3265 cm-1 (νOH). The IR-UV hole burning spectroscopy confirmed the presence of only one isomer in the molecular beam. The ionization energy (IE) of the 27DAI-H2O complex was obtained as 8.7890.001 eV, which was significantly higher than the 7AI-H2O complex. The 1:2 complex 27DAI-(H2O)2 was identified by a strong transition at 32565 cm-1, which was red shifted by 1345 cm-1. The corresponding FDIR spectrum resulted three bands at 3207, 3261 and 3385 cm-1, which are assigned as the hydrogen bonded νNH of 27DAI and two νOH vibrations from solvent-bridge connecting N(1)H and N(7) groups. The obtained structures of 27DAI-H2O and 27DAI-(H2O)2 have explicitly shown the formation of cyclic one- and two-solvent bridges incorporating N(1)-H‧‧‧O and O-H‧‧‧N(7) hydrogen bonds upon micro solvation. The lower excitation and higher ionization energies of the 27DAI-H2O complex compared to 7AI-H2O established higher stabilization of N-rich molecules. The solvent clusters forming linear bridge between the hydrogen/proton acceptor and donor sites in the complex can be considered a stepping stone to investigate the photoinduced tautomerization of N-bearing biologically relevant molecules. | Simran Baweja; Bhavika Kalal; surajit Maity | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653207ca87198ede07d918b3/original/a-combined-experimental-and-computational-investigation-of-hydrogen-bonded-2-7-diazaindole-water-1-2-complexes-isolated-in-the-gas-phase.pdf |
63d240821fe142b7cf5a6f48 | 10.26434/chemrxiv-2023-vwfnd | Cooperativity between the Silver(I) and Iodine(III) Centers in Electrophilic Activation of Organic Substrates | Kinetic data and computational study indicate that in the solution, pyrazole-containing iodolium salts and silver(I) center bind each other, and such interplay significantly affect the total catalytic activity of mixture of these Lewis acids compared with separate catalysis of the reactions required electrophilic activation of carbonyl, imino group, or triple CC bond. Moreover, the kinetic data and 1H NMR monitoring indicate that such cooperation results in prevention of decomposition of the organocatalysts by the silver(I) center during the reaction progress. XRD study indicates that in the solid state, the iodolium triflates and silver(I) triflate associate each other to give the complex species featuring triflate-bridged iodine(III) and silver(I) centers: a rare example of square-planar silver(I) complex and pentacoordinated trigonal bipyramidal dinuclear silver(I) complex. | Mikhail V. Il’in; Denis A. Polonnikov; Alexander S. Novikov; Alexandra A. Sysoeva; Yana V. Safinskaya; Sevilya N. Yunusova; Dmitrii S. Bolotin | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d240821fe142b7cf5a6f48/original/cooperativity-between-the-silver-i-and-iodine-iii-centers-in-electrophilic-activation-of-organic-substrates.pdf |
60c7473ebb8c1a1d543da9ea | 10.26434/chemrxiv.11560224.v1 | Process Intensification of Photochemical Oxidations using a High Throughput Rotor-Stator Spinning Disk Reactor: A Strategy for Scale Up | <div>This paper presents a novel high-throughput reactor for intensification of photochemical conversion processes. The photocatalyzed gas-liquid oxidation of α-terpinene to the drug ascaridole with rose-bengal was achieved with throughputs of over 1 kg∙day-1 (71 kg∙day-1∙m-2) under visible light irradiation. The performance of the reactor is correlated to rotation speed, liquid flowrate, gas flowrate, catalyst concentration, substrate concentration, gas holdup, gas bubble size, and energy dissipation rate. The conversion and selectivity increase from 37% to 97% and 75% to 90% respectively with an increase of rotation speed from 100 to 2000 RPM. Compared to conventional photochemical reactors such as the batch reactor or the microreactor, the photo-rotor-stator spinning disk reactor has much higher productivity (270 mmol∙h-1 or 19.2 mol∙h-1∙m-2) and higher selectivity (> 90%), with the latter illustrating the impact of mixing on selectivity. The findings of this study can be used to study, design, optimize and scale photochemical processes using the rotor-stator spinning disk reactor.</div> | Arnab Chaudhuri; Koen P. L. Kuijpers; Raoul Hendrix; Jasper Hacking; Parimala Shivaprasad; Emma A. C. Emanuelsson; Timothy Noel; John van der Schaaf | Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2020-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7473ebb8c1a1d543da9ea/original/process-intensification-of-photochemical-oxidations-using-a-high-throughput-rotor-stator-spinning-disk-reactor-a-strategy-for-scale-up.pdf |
640a74bc0e6a36faba079ec8 | 10.26434/chemrxiv-2023-v6x4f | Bridging Field Theory and Ion Pairing in the Theory of Polymer Complex Coacervation | Complex coacervation is a phase separation phenomenon, driven by the electrostatic attraction between oppositely-charged macromolecular species. A recent surge of interest in coacervation between polyelectrolytes has been driven by both fundamental advances in experimental characterization of these systems, along with recognition of their relevance for both biological systems such as biomolecular condensates as well as industrially-relevant consumer products. Concomitantly, there have been several theories capable of predicting complex coacervation that are used to explain these experimental observations. While there has been a general conceptual consensus on the underlying physics of coacervation, these theoretical approaches have so far remained distinct. Polymer field theory, liquid state theory, ion pairing theories, and scaling theories all provide useful insights, but how the assumptions of each candidate theory are interrelated remains largely unexplored. In this manuscript, we attempt to show how two such classes of models can be derived from a single starting point, using cluster expansions as the basis for discussing which interactions are included in both field theory and ion pairing theory. This allows us to compare and contrast these approaches, evaluate conditions where each model should be relevant, and suggest ways in which existing models can be improved or parameterized. | Charles Sing; Jian Qin | Polymer Science; Polyelectrolytes - Polymers | CC BY 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640a74bc0e6a36faba079ec8/original/bridging-field-theory-and-ion-pairing-in-the-theory-of-polymer-complex-coacervation.pdf |
60c73cc9702a9bc5dd189aa8 | 10.26434/chemrxiv.14769873.v1 | Chloromethyl Acryl Reagents for Simple and Site-Selective Cysteine and Disulfide Modification | The generation of protein biotherapeutics with improved features compared to the synthetic drugs has received emerging interest. The conjugation of various synthetic functionalities to proteins provides access to new classes of protein conjugates, where the advantages from both the synthetic world and Nature can be combined in a synergistic fashion. Here, we reported that 2-chloromethyl acryl scaffold can serve as a simple yet versatile platform for synthesizing acrylamide or acrylate derivatives by coupling with different end-group functionalities (amino group or hydroxyl group) via a one-pot reaction. The chemical properties of the amide or ester linkage influence their inherent reactivity as bioconjugation reagents, which in turn allows synthetic customization of their features to achieve selective protein modification at cysteine or disulfide sites on demand. 2-Chloromethyl acrylamide reagents with amide linkage favors selective modification at cysteine site with high efficiency and the resultant bioconjugates exhibit superior stability compared to commonly employed maleimide-thiol conjugates. In contrast, 2-chloromethyl acrylate reagents bearing ester linkage can undergo two successive Michael reaction, allowing the selective modification of disulfides with high labelling efficiency and conjugate stability. These reagents could outperform widely applied maleimide reagents in terms of stability of the resultant bioconjugates without compromising on the ease of reagent preparation, reactivity and reaction speed. <br /> | Lujuan Xu; Seah Ling Kuan; Tanja Weil | Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9702a9bc5dd189aa8/original/chloromethyl-acryl-reagents-for-simple-and-site-selective-cysteine-and-disulfide-modification.pdf |
60c757ed567dfe2b98ec6779 | 10.26434/chemrxiv.14481855.v1 | Multiscale Structural Control of Linked Metal-Organic Polyhedra Gel by Aging-Induced Linkage-Reorganization | Assembly of permanently porous metal-organic cages with functional polymers forms soft supramolecular networks featuring both porosity and processability. However, the amorphous nature of such soft materials complicates their characterization and thus limits structural control. Here we demonstrated that aging is an effective strategy to control the hierarchical network of supramolecular gels, which are assembled from organic ligands as linkers and metal-organic polyhedra (MOP) as junctions. Normally, the initial gel formation by rapid gelation leads to a kinetically trapped structure with low controllability. Through a controlled post-synthetic aging process, we show that it is possible to tune the network of the linked MOP gel over multiple length scales. This process allows control on the molecular-scale rearrangement of interlinking MOPs, mesoscale fusion of colloidal particles and macroscale densification of the whole colloidal network. In this work we elucidate the relationships between the gel properties, such as porosity and rheology, and their hierarchical structures, which suggest that porosity measurement can be used as a powerful tool to characterize the microscale structural transition of the amorphous gels. This aging strategy can be applied in other supramolecular polymer systems particularly containing kinetically controlled structures and shows an opportunity to engineer the structure and porosity of amorphous porous soft materials for further applications. | Zaoming Wang; Christian Villa Santos; alexandre legrand; Frederik Haase; Yosuke Hara; Kazuyoshi Kanamori; Takuma Aoyama; Kenji Urayama; Cara M. Doherty; Glen-Jacob Smales; Brian R. Pauw; Yamil J. Colon; Shuhei Furukawa | Supramolecular Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2021-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757ed567dfe2b98ec6779/original/multiscale-structural-control-of-linked-metal-organic-polyhedra-gel-by-aging-induced-linkage-reorganization.pdf |
675f8491f9980725cf306daf | 10.26434/chemrxiv-2024-0n73z-v2 | Schedule Optimization for Chemical Library Synthesis | Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the scheduling problem for chemical library synthesis, where operations from interdependent synthetic routes are scheduled to minimize the makespan---the total duration of the synthesis campaign. We formalize this problem as a flexible job-shop scheduling problem with chemistry-relevant constraints in the form of a mixed integer linear program (MILP), which we then solve in order to design an optimized schedule. The scheduler's ability to produce valid, optimal schedules is demonstrated by 720 simulated scheduling instances for realistically accessible chemical libraries. Reductions in makespan up to 58%, with an average reduction of 20%, are observed compared to the baseline scheduling approach. | Qianxiang Ai; Fanwang Meng; Runzhong Wang; J. Cullen Klein; Alexander G. Godfrey; Connor W. Coley | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Process Control | CC BY 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675f8491f9980725cf306daf/original/schedule-optimization-for-chemical-library-synthesis.pdf |
60c7523c0f50db2dbf397931 | 10.26434/chemrxiv.13270469.v1 | Vibrational Excitation Initiates Biomimetic Charge-Coupled Motions in the Electronic Ground State | <p>The concerted interplay between reactive nuclear and electronic motions in molecules actuates chemistry. Manipulating reaction pathways to
achieve product selectivity via precise control of light-molecule interactions
has allured chemists for decades. Yet it remains an elusive challenge in the
electronic ground state, where conventional thermally-driven chemistry occurs. Here, we demonstrate that
ground-state vibrational excitation of localised bridge modes initiates charge
transfer in a donor-bridge-acceptor molecule in solution. The
vibrationally-induced change in the ground-state electronic configuration is
visualised by transient absorption spectroscopy, involving a mid-infrared pump
and a visible probe, and detailed <i>ab initio </i>molecular dynamics simulations. Mapping the potential
energy landscape unravels a hitherto undocumented charge-transfer-assisted
double-bond isomerization channel in the electronic ground state. The reaction
pathway bears remarkable parallels with the thermal isomerization process in
rhodopsin, the retinal protein responsible for scotopic vision. Our results
illustrate a generic protocol for activating key vibrational modes to drive
photo-triggered ground-state reactions and motivate synthetic and catalytic
strategies to achieving potentially new chemistry. </p> | Gourab Chatterjee; Ajay Jha; Alejandro Blanco-Gonzalez; Vandana Tiwari; Madushanka Manathunga; Hong-Guang Duan; Friedjof Tellkamp; Valentyn I. Prokhorenko; Nicolas Ferré; Jyotishman Dasgupta; Massimo Olivucci; R. J. Dwayne Miller | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7523c0f50db2dbf397931/original/vibrational-excitation-initiates-biomimetic-charge-coupled-motions-in-the-electronic-ground-state.pdf |
64770891e64f843f41127b92 | 10.26434/chemrxiv-2023-9lk05-v3 | Aggregation characteristics of non-aromatic polar amino acids and its association to amyloids | Aggregation of amino acids to amyloid like structures is known to have implications in the pathophysiology of single amino acid based inborn-errors of metabolism (IEMs). Studying the aggregation properties of amino acids is of crucial interest also to understand the etiology of these IEMs from an amyloid perspective. Hence, herein we have studied the self-assembly of different non-aromatic charged/uncharged polar amino acids namely L-Glutamine (Gln), L-Aspartic acid (Asp) L-Glutamic acid (Glu) L-Histidine (His), L-Arginine (Arg), L-Serine (Ser) and L-Threonine (Thr) whose amyloid characteristics have still not been explored by ageing them in aqueous solution for varying time intervals from 0-15 days.. Notably, of all amino acids glutamine revealed amyloid like fibrillar morphologies as observed in case of aromatic amino acids reported previously after ageing. Further, aspartic acid and glutamic acids also revealed uniform self-assembled morphologies after 10 days of ageing. The MTT assay also corroborated with microscopic observations and a relatively more cytotoxic nature of glutamine assemblies as compared to other amino acids could also be envisaged. The Thioflavin T binding assays suggest the structures formed by Gln, Asp and Glu may have amyloid nature. Hence, the results presented in this manuscript may have crucial implications in understanding the patho-physiology of IEMs caused by the excess of Gln, Asp and Glu and suggest a possible extension of generic amyloid hypothesis to these diseases. | Nidhi Gour; Ankita Jaiswal; , Monisha Patel; Neeraja Revi ; Aravind Rengan; Sandeep Verma | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64770891e64f843f41127b92/original/aggregation-characteristics-of-non-aromatic-polar-amino-acids-and-its-association-to-amyloids.pdf |
635162f41db0bd1b8a322c7a | 10.26434/chemrxiv-2022-b7s7m | PyrroTriPol: a Semi-rigid Trityl-Nitroxide for High Field Dynamic Nuclear Polarization | Magic angle spinning (MAS) dynamic nuclear polarization (DNP) has significantly broadened the scope of solid-state NMR to study biomolecular systems and materials. In recent years, the advent of very high field DNP combined with fast MAS has brought new challenges in the design of polarizing agents (PA) used to enhance nuclear spin polarization. Here, we present a trityl-nitroxide PA family based on a piperazine linker, named PyrroTriPol, for both aqueous and organic solutions. These new radicals have similar properties to that of TEMTriPol-I and can be readily synthesized, and purified in large quantities thereby ensuring widespread application. The family relies on a rigid bridge connecting the trityl and the nitroxide offering a better control of the electron spin-spin interactions thus providing improved performance across a broad range of magnetic fields and MAS frequencies while requiring reduced microwave power compared to bis-nitroxides. We demonstrate the efficiency of the PyrroTriPol family under a magnetic field of 9.4, 14.1 and 18.8 T with respect to TEMTriPol-I. In particular, the superiority of PyrroTriPol was demonstrated on γ-Al2O3 nanoparticles which enabled the acquisition of a high signal-to-noise surface-selective 27Al multiple-quantum MAS experiment at 18.8 T and 40 kHz MAS frequency | Thomas Halbritter; Rania Harrabi; Subhradip Paul; Johan van Tol; Daniel Lee; Sabine Hediger; Snorri Th. Sigurdsson; Frederic Mentink-Vigier; Gaël De Paëpe | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635162f41db0bd1b8a322c7a/original/pyrro-tri-pol-a-semi-rigid-trityl-nitroxide-for-high-field-dynamic-nuclear-polarization.pdf |
63a5dbf7a53ea62753556945 | 10.26434/chemrxiv-2022-wnnz4 | Characterization of peptide O∙∙∙HN hydrogen bonds via multidimensional 1H-detected 15N/17O solid-state nuclear magnetic resonance spectroscopy | Solid-state NMR methods with high resolution and sensitivity are presented for identification and charaterization of hydrogen-bonded 15N/17O atomic pairs in peptide samples. Indirect 1H detection under fast magic-angle spinning, and the stronger 1H-15N and 1H-17O couplings are leveraged to significantly improve sensitivity over previous methods that use direct 15N-17O interactions. | Ivan Hung; Wenping Mao; Eric G. Keeler; Robert G. Griffin; Peter L. Gor'kov; Zhehong Gan | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a5dbf7a53ea62753556945/original/characterization-of-peptide-o-hn-hydrogen-bonds-via-multidimensional-1h-detected-15n-17o-solid-state-nuclear-magnetic-resonance-spectroscopy.pdf |
60c75139ee301cbd56c7a9f8 | 10.26434/chemrxiv.13083224.v2 | Identification of Small-Molecule Inhibitors of FGF23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho | <p>Fibroblast growth factor 23 (FGF23) is a therapeutic target for treating hereditary and acquired hypophosphatemic disorders, such as X-linked hypophosphatemic (XLH) rickets and tumor-induced osteomalacia (TIO), respectively. FGF23-induced hypophosphatemia is mediated by signaling through a ternary complex formed by FGF23, FGF receptor (FGFR), and α-Klotho. Currently, disorders of excess FGF23 are treated with an FGF23-blocking antibody, Burosumab. Small-molecule drugs that disrupt protein:protein interactions necessary for the ternary complex formation offer an alternative to disrupt FGF23 signaling. In this study, the FGF23:α-Klotho interface was targeted to identify small-molecule protein:protein interaction inhibitors. We computationally identified “hot spots” in the FGF23:α-Klotho interface of the ternary complex and performed <i>in silico</i> docking of ~5.5 million compounds from the ZINC database to the interface region of α-Klotho from the ternary crystal structure. Following docking, 23 and 18 compounds were chosen based on the lowest binding free energies to α-Klotho and the largest number of contacts with Tyr433, a predicted hot spot, respectively. 5 compounds available were assessed experimentally by their FGF23-mediated extracellular signal-regulated kinase (ERK) activities <i>in vitro</i>, and two of these reduce activities significantly. Both these compounds have a favorable predicted binding affinity, but not a large number of contacts with the hot spot residues. ZINC12409120 was found experimentally to reduce FGF23-mediated ERK activities by 70% and have a half maximal inhibitory concentration (IC<sub>50</sub>) of 5.0 ± 0.23 uM. ZINC12409120 exhibits contacts with residues on KL1 and KL2 domains and on the linker between the two domains of α-Klotho in <i>in silico</i> binding poses, thereby possibly disrupting the regular function of α-Klotho and impeding FGF23 binding. ZINC12409120 is a candidate for lead optimization.</p> | Shih-Hsien Liu; Zhousheng Xiao; Sambit K. Mishra; Julie C. Mitchell; Jeremy C. Smith; L. Darryl Quarles; Loukas Petridis | Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75139ee301cbd56c7a9f8/original/identification-of-small-molecule-inhibitors-of-fgf23-signaling-via-in-silico-hot-spot-prediction-and-molecular-docking-to-klotho.pdf |
6315e936bada38a3b9ba078c | 10.26434/chemrxiv-2022-clbrk | Periodic system converges and is affected by wars | The periodic system emerges by intertwining order and similarity relationships among chemical elements, which in turn arise from known substances at a given time that constitute the chemical space. Although the system has been adjusted to accommodate new elements, the connection with the chemical space has been largely forgotten and the question that arises is about the effect of the exponentially growing chemical space upon the periodic system. To what extent advances in chemistry have confirmed or distorted the periodic system? Is the system --icon of chemistry-- a traversal feature of the chemical space? Here we solve these questions by computationally analysing the effect of the chemical space upon the periodic system from the dawn of the 19th century until the present. We found that although the system has undergone several and significant changes across history, it converges towards a stable structure. This dynamics results from advances in chemistry such as the discovery of elements, of forms of chemical combination and the incorporation of new theoretical frameworks. Interestingly, the periodic system is also influenced by socio-political events such as wars. Given the nature of the chemical space, which holds the inertia of more than 200 years of chemical practice, and the limited chemical possibilities for the remaining elements to be synthesised, we hypothesise that the periodic system is going to remain largely untouched in the years to come. We expect our results and methods trigger further research and discussion in the history, pedagogy, philosophy, and ultimately, in the practice of chemistry. | Andres M. Bran; Peter F. Stadler; Juergen Jost; Guillermo Restrepo | Theoretical and Computational Chemistry; Inorganic Chemistry; Chemical Education; Chemical Education - General; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6315e936bada38a3b9ba078c/original/periodic-system-converges-and-is-affected-by-wars.pdf |
6719bd0912ff75c3a15a7fbb | 10.26434/chemrxiv-2024-lzq9j | Direct Correlation of the Crystalline Phases of La0.9Sr0.1Co1-yFeyO3-δ with the Partial Oxidation of Methane Via In Situ Neutron and Synchrotron Diffraction | Oxygen transport membranes find broad usage in many technologies but, due to the harsh conditions that such technologies operate under, detailed structural analysis under operational conditions has been limited. This work details the in situ neutron and synchrotron diffraction of the industrially relevant family of compounds, La0.9Sr0.1Co1-yFeyO3-δ (y = 0, 0.25, 0.75, 1), under reductive and oxidative conditions at elevated temperatures, 723 K-1123 K. Quantitative Rietveld refinements determines the molar fraction of all crystalline intermediates and products that form during the reactions of La0.9Sr0.1Co1-yFeyO3-δ (y = 0, 0.25, 0.75, 1) with methane and then air. Coupling in situ diffraction analysis with catalytic product analysis of the partial oxidation of methane allows for the catalytically active phases to be determined. This work shows the strength of in situ diffraction under extreme conditions and the insight it can give about reactions in the solid state that have been previously elusive. | Dennis D. Nguyen; Mara J. Milhander; Elizabeth M. Hitch; Dmitri Leo M. Cordova; Jose L. Gonzalez Jimenez; Juana Mora; Daniel Sandoval; Maxx Q. Arguilla; Allyson M. Fry-Petit | Inorganic Chemistry; Catalysis; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6719bd0912ff75c3a15a7fbb/original/direct-correlation-of-the-crystalline-phases-of-la0-9sr0-1co1-y-fey-o3-with-the-partial-oxidation-of-methane-via-in-situ-neutron-and-synchrotron-diffraction.pdf |
6280d5bf809e32427890631a | 10.26434/chemrxiv-2022-6dd6n | Revealing Structure-Property Relationships in Polybenzenoid Hydrocarbons with Interpretable Machine-Learning | The structure-property relationships of polybenzenoid hydrocarbons (PBHs) were investigated with interpretable machine learning, for which two new tools were developed and applied. First, a novel textual molecular representation, based on the annulation sequence of PBHs was defined and developed. This representation can be used either in its textual form or as a basis for a curated feature-vector; both forms show improved interpretability over the standard SMILES representation, and the former also has increased predictive accuracy. Second, the recently-developed model, CUSTODI, was applied for the first time as an interpretable model and identified important structural features that impact various electronic molecular properties. The resulting insights not only validate several well-known “rules of thumb” of organic chemistry but also reveal new behaviors and influential structural motifs, thus providing guiding principles for rational design and fine-tuning of PBHs. | Shachar Fite; Alexandra Wahab; Eno Paenurk; Zeev Gross; Renana Gershoni-Poranne | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6280d5bf809e32427890631a/original/revealing-structure-property-relationships-in-polybenzenoid-hydrocarbons-with-interpretable-machine-learning.pdf |
60c75027bdbb8960eea39ea9 | 10.26434/chemrxiv.12994004.v1 | In Vitro and In Vivo Sequestration of Phencyclidine by Me4Cucurbit[8]uril | This work describes the in vitro binding of CB[8] and Me4CB[8] toward a panel of 10 drugs of abuse, and in vitro and in vivo assays to demonstrate the biocompatibility of Me4CB[8]. In vivo efficacy studies show that Me4CB[8] can control the hyper locomotion of animals treated with PCP. | Steven Murkli; Jared Klemm; Adam T. Brockett; Michael Shuster; Volker Briken; Matthew R. Roesch; Lyle Isaacs | Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75027bdbb8960eea39ea9/original/in-vitro-and-in-vivo-sequestration-of-phencyclidine-by-me4cucurbit-8-uril.pdf |
65553da02c3c11ed71789206 | 10.26434/chemrxiv-2022-bk73l-v3 | Characterization of an N-Allylglyoxylamide Based Bioorthogonal Nitrone Trap | Aldehydes are attractive bioorthogonal coupling partners. The ease of manipulation of aldehydes and their orthogonality to other classes of bioorthogonal reactions has inspired the exploration of chemistries which generate irreversible conjugates. Similarly, nitrones have been shown to be potent 1,3 dipoles in bioorthogonal reactions when paired with strained alkynes. Here we combine the reactivity of nitrones with the simplicity of aldehydes using an N-allyl glyoxylamide, in a cascade reaction with an N-alkylhydroxylamine to produce a bicyclic isoxazolidine. The reaction is found to be catalyzed by 5-methoxyanthranilic acid and proceeds at pH 7 with favorable kinetics. Using the HaloTag7 protein bearing a hydroxylamine we show the reaction to be bioorthogonal in a complex cell lysate and to proceed well at the surface of a HEK293 cell. Furthermore, the reaction is orthogonal to a typical strain-promoted alkyne-azide click reaction. The characteristics of this reaction suggest it will be a useful addition to the pallet of bioorthogonal reactions revolutionizing chemical biology. | Daniel Lee; Simon Latour; Michael Emblem; Hunter Clark; Jobette Santos; Jaewan Jang; Alison McGuigan; Mark Nitz | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65553da02c3c11ed71789206/original/characterization-of-an-n-allylglyoxylamide-based-bioorthogonal-nitrone-trap.pdf |
6102099e40c8bd5fc1994632 | 10.26434/chemrxiv-2021-hr2n9 | Antagonistic Role of Aqueous Complexation in the Solvent Extraction and Separation of Rare Earth Ions | During solvent extraction of rare earth ions, an aqueous electrolyte solution is placed in contact with an immiscible organic solution of extractants to enable extractant-facilitated transport of ions into the organic solvent. Although ex-perimental methodologies such as x-ray and neutron scattering have been applied to characterize ion-extractant complexes, identifying the site of ion-extractant complexation has proven challenging. Here, we use tensiometry and surface-sensitive x-ray scattering to study the surface of aqueous solutions of lanthanide chlorides and the water-soluble extractant bis(2-ethylhexyl) phosphate (HDEHP), in the absence of a coexisting organic solvent. These studies restrict interactions of HDEHP with trivalent lanthanide ions to the aqueous phase and the liquid-vapor interface, allowing us to explore the consequences that one or the other is the site of ion-extractant complexation. Unexpectedly, we find that light lanthanides preferentially occupy the liquid-vapor interface, with an overwhelming preference for a light lanthanide, Nd, when present in a mixture with a heavy lanthanide, Er. This contradicts our expectation that heavy lanthanides should have a higher interfacial density since they are preferentially extracted by HDEHP in the presence of an organic phase. These results reveal the antagonistic role played by ion-extractant complexation within the aqueous phase and clarify the potential advantages of water-insoluble extractants that interact with ions primarily at the interface during the process of solvent extraction. | Pan Sun; Erik A. Binter; Zhu Liang; M. Alex Brown; Artem V. Gelis; Ilan Benjamin; Mrinal K. Bera; Binhua Lin; Wei Bu; Mark L. Schlossman | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Interfaces; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6102099e40c8bd5fc1994632/original/antagonistic-role-of-aqueous-complexation-in-the-solvent-extraction-and-separation-of-rare-earth-ions.pdf |
60c74ddc567dfe0ff5ec53f7 | 10.26434/chemrxiv.12357284.v2 | Direct Epitaxial Nanometer-Thin InN of High Structural Quality on 4H-SiC by Atomic Layer Deposition | <div>Indium nitride (InN) is a highly promising material for high frequency electronics given its</div><div>low band gap and high electron mobility. The development of InN-based devices is hampered</div><div>by the limitations in depositing very thin InN films of high quality. We demonstrate growth of</div><div>high-structural-quality nanometer thin InN films on 4H-SiC by atomic layer deposition (ALD).</div><div>High resolution X-ray diffraction and transmission electron microscopy show epitaxial growth</div><div>and an atomically sharp interface between InN and 4H-SiC. The InN film is fully relaxed already after a few atomic layers and shows a very smooth morphology where the low surface</div><div>roughness (0.14 nm) is found to reproduced sub-nanometer surface features of the substrate. Raman measurements show an asymmetric broadening caused by grains in the InN film. Our results show the potential of ALD to prepare high quality nanometer-thin InN films for subsequent formation of heterojunctions.</div> | Chih-Wei Hsu; Petro Deminskyi; Ivan Martinovic; Ivan G. Ivanov; Justinas Palisaitis; Henrik Pedersen | Coating Materials; Materials Processing; Nanostructured Materials - Materials; Thin Films; Nanostructured Materials - Nanoscience; Main Group Chemistry (Inorg.); Interfaces; Surface; Crystallography | CC BY 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ddc567dfe0ff5ec53f7/original/direct-epitaxial-nanometer-thin-in-n-of-high-structural-quality-on-4h-si-c-by-atomic-layer-deposition.pdf |
6765465481d2151a025b6804 | 10.26434/chemrxiv-2024-l7fl9-v2 | Diffusion Generative Models for Designing Efficient Singlet Fission Dimers | Diffusion generative models, a class of machine learning techniques, have shown remarkable promise in materials science and chemistry by enabling the precise generation of complex molecular structures. In this paper, we propose a novel application of diffusion generative models for stabilizing reactive molecular structures identified through quantum mechanical screening. Specifically, we focus on the design challenge presented by Singlet Fission (SF), a phenomenon crucial for advancing solar cell efficiency beyond theoretical limits. While theoretical chemistry has been successful in predicting intermolecular arrangements with enhanced SF coupling, the practical implementation of these configurations faces challenges due to discrepancies between favorable and stabilized structures. To address this gap, we introduce a three-step strategy combining quantum mechanical screening for identifying optimal molecular arrangements and diffusion generative models for predicting stabilizing linkers. Through a case study on cibalackrot dimers, a promising SF material, we demonstrate the efficacy of our approach in enhancing SF efficiency by stabilizing the desired molecular arrangements. | Lasse Kreimendahl; Mikhail Karnaukh; Merle I. S. Röhr | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6765465481d2151a025b6804/original/diffusion-generative-models-for-designing-efficient-singlet-fission-dimers.pdf |
63186cc7faf4a484d8095c54 | 10.26434/chemrxiv-2022-cpjsj | 1,3 dipolar cycloaddition of münchnones: Factors behind the regio-selectivity | The 1,3 dipolar cycloaddition reactions of münchnones and alkenes provide an expedite synthetic way to substituted pyrroles, an exceedingly important structural motif in the pharmaceutical and material science fields of research. The factors governing their regio-selectivity rationalization are not well understood. Using several approaches, we investigate a set of 14 reactions (featuring two münchnones, 12 different alkenes, and two alkynes). The Natural Bond Theory and the Non-Covalent Interaction Index analyses of the non-covalent interaction energies fail to predict the experimental major regio-isomer. Employing global cDFT descriptors or local ones such as the Fukui function and dual descriptor yields similarly inaccurate predictions. Only the local softness pairing, withing Pearson's Hard and Soft Acids and Bases principle, constitutes a reliable predictor for the major reaction product. By taking into account an estimator for the steric effects, the correct regio-isomer is predicted. Steric effects play a major role in driving the regio-selectivity, as was corroborated by energy decomposition analysis of the transition states. | Meylin Bocalandro; Juan J. González Armesto; Luis A. Montero-Cabrera; Marco Martínez González | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63186cc7faf4a484d8095c54/original/1-3-dipolar-cycloaddition-of-munchnones-factors-behind-the-regio-selectivity.pdf |
67658fe4fa469535b944984b | 10.26434/chemrxiv-2025-mwspf | A new perspective on aqueous electrolyte solutions | Aqueous electrolyte solutions are central to many natural phenomena and industrial applications. This leads to the continuous development of increasingly complex analytical models to predict their chemical properties. These are all based on an explicit, atomistic description of ion-ion electrostatic interactions combined with mean-field approaches for the dielectric response of water. Such approaches approximate the complex multi-body ion-ion correlations to pair interactions, introducing the concept of ion-pairs. Despite many achievements, these concepts fail to describe situations where ion-ion correlation and specific solvation become relevant, such as for concentrated electrolyte solutions. Here, we propose a change of perspective, by introducing a statistical, coarse-grained view that bypasses the need to define ion pairs, and does not require any prior knowledge of specific solvation. We base our concept on separating the solution into a spherical observation droplet whose size and average composition are fully determined by the solution parameters and the environment of the remaining solution. This allows us to express the droplet-environment interaction in terms of a generalized multipole expansion, i.e. in a convenient, additive way. We applied this approach to 139 electrolytes including some ionic liquids and notoriously complex electrolytes, such as LiCl or ZnCl2. Our model yields a set of analytical functions sharing the same parameters that simultaneously model the activity coefficient, the osmotic coefficient, and water activity, Those parameters give direct access to the radius-dependent partition function around the observation droplet. The functions predict electrolyte behavior over the whole electrolyte mole fraction range, paving the road toward understanding super-saturated and water-in-salt solutions and electrolyte nucleation. | Gerhard Schwaab; Simone Pezzotti | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Physical and Chemical Properties; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67658fe4fa469535b944984b/original/a-new-perspective-on-aqueous-electrolyte-solutions.pdf |
60c74cbf469df4a6a8f44133 | 10.26434/chemrxiv.12535913.v1 | Computational Identification of Drug Lead Compounds for COVID-19 from Moringa Oleifera | <div>COVID-19 which is caused by the virus SARS-CoV-2, has now been declared a global pandemic by the World Health Organization. At present, no specific vaccines or drugs are available to treat COVID-19. Therefore, there is an urgent need for the identification of novel drug lead compounds</div><div>to treat COVID-19. The SARS-CoV-2 main protease (Mpro also known as 3CLpro) and RNA-dependent RNA polymerase (RdRp also known as nsp12) are the best-characterized drug targets among corona viruses. In order to discover the natural lead compounds for SARS-CoV-2, we</div><div>performed molecular docking with the compounds from <i>Moringa Oleifera</i> that target the Mpro and RdRp. The molecular docking studies were carried out using AutoDock Vina through PyRx. Drug-likeness property of the selected compounds was checked by applying the ‘Lipinski’s rule of five’ using Swiss ADME. The top four compounds with most favourable binding affinity were selected for each of the targets. The results indicated that the compounds kaempferol, pterygospermin, morphine and quercetin exhibited best binding energy towards Mpro and RdRp. This study suggests that these natural compounds could be promising candidates for further evaluation of COVID-19 prevention.</div> | Dr. Divya Shaji | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cbf469df4a6a8f44133/original/computational-identification-of-drug-lead-compounds-for-covid-19-from-moringa-oleifera.pdf |
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