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60c750b9842e65630ddb3a8b | 10.26434/chemrxiv.13073048.v1 | Acetaminophen Metabolism Revisited Using Non-Targeted Analyses: Implications for Human Biomonitoring | The analgesic paracetamol (N-acetyl-4-aminophenol, APAP) is commonly used to relieve pain, fever and malaise. While sales have increased worldwide, a growing body of experimental and epidemiological evidence has suggested APAP as a possible risk factor for various health disorders. To perform internal exposure-based risk assessment, the use of accurate and optimized biomonitoring methods is criticical. However, retrospectively assessing pharmaceutical use of APAP in humans is challenging because of its short half-life. The objective of this study was to address the key biomonitoring issues with APAP using current standard analytical methods based on urinary analyses of free APAP and its phase II conjugates. Using non-targeted analyses based on high-resolution mass spectrometry, we identified in a controlled longitudinal exposure study with male volunteers, unrecognized APAP metabolites with delayed formation and excretion rates. We postulate that these metabolites are formed via the thiomethyl shunt after the enterohepatic circulation as already observed in rodents. Importantly, the conjugated thiomethyl metabolites were (i) of comparable diagnostic sensitivity as the free APAP and its phase II conjugates detected by current methods; (ii) had delayed peak levels in blood and urine compared to other APAP metabolites and therefore potentially extend the window of exposure assessment; and (iii) provide relevant information regarding metabolic pathways of interest from a toxicological point of view. Including these metabolites in future APAP biomonitoring methods provide an option to decrease potential underestimation of APAP use and challenges the notion that the standard methods in biomonitoring based exclusively on the parent compound and its phase II metabolites are adequate for human biomonitoring of non-persistant chemical such as APAP. <br /> | Arthur David; Jade Chaker; Thibaut Léger; Raghad Al-Salhi; Marlene Danner Dalgaard; Bjarne Styrishave; Daniel Bury; Holger M. Koch; Bernard Jégou; David M. Kristensen | Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b9842e65630ddb3a8b/original/acetaminophen-metabolism-revisited-using-non-targeted-analyses-implications-for-human-biomonitoring.pdf |
60c7401f337d6c3630e2664a | 10.26434/chemrxiv.7628771.v1 | Doping in Garnet-Type Electrolytes: Kinetic and Thermodynamic Effects from Molecular Dynamics Simulations | Molecular modeling using polarizable force fields of W-doped lithium containing garnets to understand the various aspect of the impact of doping on the lithium dynamics and conductivity.<br /> | Matthieu Mottet; Aris Marcolongo; Ivano Tavernelli; Teodoro Laino | Solid State Chemistry; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401f337d6c3630e2664a/original/doping-in-garnet-type-electrolytes-kinetic-and-thermodynamic-effects-from-molecular-dynamics-simulations.pdf |
63f8047b32cd591f12630ba1 | 10.26434/chemrxiv-2023-3fkt9 | Solid-state Graft Polymer Electrolytes with Conductive Backbones and Side-chains for Lithium Batteries | Graft polymers have been widely investigated as solid polymer electrolytes (SPEs) in the past decades. However, the presence of insulating backbones in the conventional graft polymers damps the overall Li+ conductivity and transport number (tLi+). Herein, a series of polycarbonates (PCs) possessing ethylene oxide (EO) side-chains were designed and synthesized through ring-opening polymerization (ROP), and their ionic conductivities were evaluated as SPEs with LiTFSI. The synergy of conductive backbones and side-chains gives a high tLi+ value of 0.67, while having an ionic conductivity of 210-5 S cm-1 at 30 C. This work provides new insights into the development of high-performance SPEs by combining different conductive polymers. | Guangjian Zeng; Shuqi Dai; Xiupeng Chen; Lu Qiu; Xian Kong; Mingjun Huang; Tao Wen | Polymer Science; Polyelectrolytes - Polymers; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f8047b32cd591f12630ba1/original/solid-state-graft-polymer-electrolytes-with-conductive-backbones-and-side-chains-for-lithium-batteries.pdf |
65988766e9ebbb4db983b1c2 | 10.26434/chemrxiv-2024-hm6vh | Giant Band Degeneracy via Orbital Engineering Enhances Thermoelectric Performance from Sb2Si2Te6 to Sc2Si2Te6 | The complex interrelationships among thermoelectric parameters mean that a priori design of high-performing materials is difficult. However, band engineering can allow the power factor to be optimized through enhancement of the Seebeck coefficient. Herein, using layered Sb2Si2Te6 and Sc2Si2Te6 as model systems, we comprehensively investigate and compare their thermoelectric properties by employing density functional theory combined with semiclassical Boltzmann transport theory. Our simulations reveal that Sb2Si2Te6 exhibits superior electrical conductivity compared to Sc2Si2Te6 due to lower scattering rates and more pronounced band dispersion. Remarkably, despite Sb2Si2Te6 exhibiting a lower lattice thermal conductivity, the introduction of Sc-d orbitals dramatically increases conduction band degeneracy in Sc2Si2Te6, yielding a significantly improved Seebeck coefficient relative to Sb2Si2Te6. As a result, Sc2Si2Te6 is predicted to achieve an extraordinary dimensionless figure of merit (ZT) of 3.51 at 1000 K, which significantly surpasses the predicted maximum ZT of 2.76 for Sb2Si2Te6 at 900 K. This work suggests that engineering band degeneracy through compositional variation is an effective strategy for improving the thermoelectric performance of layered materials. | Wenzhen Dou; Kieran Spooner; Seán Kavanagh; Miao Zhou; David O. Scanlon | Materials Science; Energy; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65988766e9ebbb4db983b1c2/original/giant-band-degeneracy-via-orbital-engineering-enhances-thermoelectric-performance-from-sb2si2te6-to-sc2si2te6.pdf |
660d2a8c21291e5d1df4f21d | 10.26434/chemrxiv-2024-znfw5 | “Naked Nickel”-Catalyzed Amination of Heteroaryl Bromides | In this article we report that the air-stable “naked nickel” [Ni(4-tBustb)3] is a competent catalyst in thermal C–N bond formation between (hetero)aryl bromides and N-based nucleophiles. The catalytic system is characterized by a “naked nickel” complex and Zn, the absence of external light sources, photocatalysts, exogeneous ligands, as well as electrical setups. By applying this method, various heteroaryls bearing Lewis-basic heteroatoms can be accommodated and directly aminated with a set of primary and secondary amines. | Rakan Saeb; Bryan Boulenger; Josep Cornella | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660d2a8c21291e5d1df4f21d/original/naked-nickel-catalyzed-amination-of-heteroaryl-bromides.pdf |
60c748a50f50dbf31e3967c2 | 10.26434/chemrxiv.11954403.v1 | The Limits of Inelastic Tunneling Spectroscopy for Identifying Transport Pathways | Inelastic Electron Tunneling Spectroscopy (IETS) is a powerful tool to study the properties of molecular junctions. In particular, it is considered useful for extracting information on electron transport pathways. We explore the limits of this approach by comparing computed interatomic transmission pathways with IETS intensities for different molecular junctions, employing a new efficient implementation for evaluating IETS intensities via the mode-tracking algorithm. We find that while a correlation be- tween pathways and IETS intensities indeed holds when vibrations are clearly localized on atoms off the transport pathway, there is no such correlation for molecules with less localized vibrations, even if transport pathways only sample part of the molecule, and even if a statistical analysis over the vibrational modes is made. This could indicate that the significance of IETS signals for transport pathways is limited to molecules with localized vibrational modes. | Michael Deffner; Carmen Herrmann | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748a50f50dbf31e3967c2/original/the-limits-of-inelastic-tunneling-spectroscopy-for-identifying-transport-pathways.pdf |
66c0d0b3f3f4b05290336ed3 | 10.26434/chemrxiv-2024-8q9bd | Ligand solid-solution tuning of magnetic and mechanical properties of the van der Waals metal-organic magnet NiCl2(btd)1–x(bod)x | Van der Waals (vdW) magnets offer unique opportunities for exploring magnetism in the 2D limit. Metal-organic magnets (MOM) are of particular interest because functionalising the organic ligands allows for control over their physical properties. Here, we demonstrate tuning of mechanical and magnetic functionality of a recently reported non-collinear vdW ferromagnet, NiCl2(btd) (btd = 2,1,3-benzothiadiazole), through creating solid-solutions with the oxygen-substituted analogue ligand 2,1,3-benzoxadiazole (bod). We synthesise solid-solutions, NiCl2(btd)1-x(bod)x, up to x=0.33 above which we find mixtures form, primarily composed of a new 1D coordination polymer NiCl2(bod)2. Magnetometry on this series shows that bod incorporation reduces the coercivity significantly (up to 60%), without significantly altering the ordering temperatures. Our high pressure synchrotron diffraction measurements up to 0.4 GPa demonstrate that the stiffest axis is the b axis, through the Ni-N-(O/S)-N-Ni bonds, and the softest is the interlayer direction. Doping with bod fine-tunes this compressibility, softening the layers, but stiffening the interlayer axis. This demonstrates how mixed-ligand strategy can be used to realise targeted magnetic and mechanical properties in vdW MOMs. | Emily Myatt; Simrun Lata; Jem Pitcairn; Dominik Daisenberger; Silva M. Kronawitter; Sebastian Hallweger; Gregor Kieslich; Stephen P. Argent; Jeremiah P. Tidey; Matthew J. Cliffe | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c0d0b3f3f4b05290336ed3/original/ligand-solid-solution-tuning-of-magnetic-and-mechanical-properties-of-the-van-der-waals-metal-organic-magnet-ni-cl2-btd-1-x-bod-x.pdf |
679753856dde43c9089081ee | 10.26434/chemrxiv-2025-hn77r | Developing red and NIR thermally activated delayed fluorescence emitters based on dibenzo[f,h]pyrido[2,3-b]quinoxaline acceptor | Recently, there has been growing interest in deep red (DR) and near-infrared (NIR) thermally activated delayed fluorescence (TADF) emitters due to their potential use in applications in bioimaging and night-vision displays. However, the performance of long wavelength TADF emitters is inherently limited by the energy gap law, which reduces their photoluminescence quantum yields (ΦPL), making a robust design strategy challenging. Herein, we designed and synthesized a series of red/NIR TADF emitters. The emission wavelengths were rationally tuned by modulating the strength of the electron-donating groups, DMAC, PXZ, and DPACz, that are coupled to the same electron-accepting PyBP (dibenzo [f, h] pyrido [2,3-b]quinoxaline) moiety. These compounds emit with photoluminescence maxima (λPL) at 643 nm for DMACPyBP, 722 nm for DPACz PyBP, and 743 nm for PXZPyBP in toluene solution, while their thin films singlet-triplet energy gaps (ΔEST) are < 0.1 eV. DMACPyBP, with the weakest donor, has the highest ΦPL of 62.3%, the smallest ΔEST of 0.03 eV, and a fast reverse intersystem crossing rate constant (kRISC) of 0.5 × 105 s-1 in a 1 wt% doped film in CBP. In contrast, PXZPyBP, containing the strongest donor, has a lower ΦPL (21.2%), a relatively larger ΔEST (0.10 eV), and a slower kRISC (0.04 × 105 s-1). Thus, our work highlights the molecular design challenges involved in pushing emission into the NIR region while maintaing both TADF and high PL in PyBP-based donor-acceptor emitters. | Falak Naz; Changfeng Si; Suela Kellici; Tariq Sajjad; 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 | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679753856dde43c9089081ee/original/developing-red-and-nir-thermally-activated-delayed-fluorescence-emitters-based-on-dibenzo-f-h-pyrido-2-3-b-quinoxaline-acceptor.pdf |
60c741689abda24e73f8be83 | 10.26434/chemrxiv.8046938.v1 | Bioinspired Oxidative Cyclization of the Geissoschizine Skeleton for the Enantioselective Total Synthesis of Mavacuran Alkaloids | We report the
enantioselective total syntheses of mavacurans alkaloids, (+)-taberdivarine H, (+)-16-hydoxymethyl-pleiocarpamine,
(+)-16-epi-pleiocarpamine, and their postulated biosynthetic precursor
16-formyl-pleiocarpamine. This family of monoterpene indole alkaloids is a
target of choice since some of its members are subunits of intricate bisindole
alkaloids such as bipleiophylline. Inspired by the biosynthetic hypothesis, we
explored an oxidative coupling approach from the geissoschizine framework to
form the N1-C16 bond. Quaternization of the aliphatic nitrogen was key to achieve
the oxidative coupling induced by KHMDS/I<sub>2 </sub>since<sub> </sub>it hides
the nucleophilicity of the aliphatic nitrogen and locks the required cis conformation. | Maxime Jarret; Victor Turpin; Aurélien Tap; Jean-Francois Gallard; Cyrille Kouklovsky; Erwan Poupon; Guillaume Vincent; Laurent Evanno | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741689abda24e73f8be83/original/bioinspired-oxidative-cyclization-of-the-geissoschizine-skeleton-for-the-enantioselective-total-synthesis-of-mavacuran-alkaloids.pdf |
65e641319138d23161aa2a22 | 10.26434/chemrxiv-2024-4kttp | Synthesis of Alcohols: Streamlined C1 to Cn Hydroxyalkylation through Photoredox Catalysis | Naturally occurring and readily available α-hydroxy carboxylic acids (AHAs) are utilized as platforms for visible light-mediated oxidative CO2-extrusion furnishing α-hydroxy radicals proved to be versatile C1 to Cn hydroxyalkylating agents. The decarboxylative direct Giese reaction (DDGR) is operationally simple, not requiring activator or sacrificial oxidants, and enables the synthesis of a diverse range of hydroxylated products, introducing connectivity typically precluded from conventional polar domains. Notably, the methodology has been extended to widely used glycolic acid resulting in a highly efficient and unprecedented C1 hydroxyhomologation tactic. The use of flow technology further facilitates scalability and adds green credentials to this synthetic methodology. | Francesco Pasca; Yuri Gelato; Michael Andresini; Giuseppe Romanazzi; Leonardo Degennaro; Marco Colella; Renzo Luisi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e641319138d23161aa2a22/original/synthesis-of-alcohols-streamlined-c1-to-cn-hydroxyalkylation-through-photoredox-catalysis.pdf |
60c747039abda278ecf8c841 | 10.26434/chemrxiv.11462160.v1 | Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation | Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system. | Liqun Cao; Jinzhe Zeng; Mingyuan Xu; Chih-Hao Chin; Tong Zhu; John ZH Zhang | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747039abda278ecf8c841/original/combustion-driven-by-fragment-based-ab-initio-molecular-dynamics-simulation.pdf |
66d1202cf3f4b05290933a88 | 10.26434/chemrxiv-2024-7k67q | Roles of Water Molecules in STING Activation: A Computational Perspective | The cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) pathway is crucial in the innate immune response, particularly in cancer immunotherapy. Despite promising preclinical results, 5,6-dimethylxanthenone-4-acetic acid (DMXAA) showed limited efficacy in human clinical trials due to species-specific differences in STING activation. This study investigates these differences by analyzing the binding dynamics and affinities of various STING-ligand complexes using molecular dynamics (MD) simulations and binding free energy calculations. We confirmed that specific point mutations, notably G230I and S162A/Q266I, significantly improve DMXAA’s binding affinity to human STING (hSTING), replicating the behavior observed in mouse STING (mSTING). Explicit solvent MD simulations revealed the essential role of water molecules in the binding site. Bridge water molecules, forming hydrogen bonds between the ligand and the protein, were significant in stabilizing the cyclic GMP-AMP (cGAMP) system, influencing local dielectric constants. Additionally, for DMXAA systems, we found that the mutations lowered the interaction energies required for ligand binding by reducing the number of water molecules and localizing them to specific locations within the binding site. These findings deepen our understanding of STING-DMXAA interactions and highlight potential pharmacological modifications required to enhance STING-targeted therapies. Integrating structural biology, computational simulations, and thermodynamic analyses offers a robust framework for advancing STING-based therapeutic development. | Hannah Gates; Rachel Payne; Haley Pfeifer; Lyly Le; Silvia Crivelli; Masakatsu Watanabe | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d1202cf3f4b05290933a88/original/roles-of-water-molecules-in-sting-activation-a-computational-perspective.pdf |
60c748e3567dfe4a65ec4ac6 | 10.26434/chemrxiv.11955174.v1 | Artificial Biosynthetic Pathway for an Unnatural Terpenoid with an Iridiumcontaining P450 | <div>Synthetic biology enables microbial hosts to produce complex molecules that are</div><div>otherwise produced by organisms that are rare or difficult to cultivate, but the structures of these</div><div>molecules are limited to chemical reactions catalyzed by natural enzymes. The integration of</div><div>artificial metalloenzymes (ArMs) that catalyze abiotic reactions into metabolic networks could</div><div>broaden the cache of molecules produced biosynthetically by microorgansms. We report the</div><div>assembly of an ArM containing an iridium-porphyrin complex in the cytoplasm of a terpene</div><div>producing Escherichia coli by a heterologous heme transport machinery, and insertion of this ArM</div><div>into a natural biosynthetic pathway to produce an unnatural terpenoid. This work shows that</div><div>synthetic biology and synthetic chemistry, incorporated together in whole cells, can produce</div><div>molecules previously inaccessible to nature.</div> | Jing Huang; Zhennan Liu; brandon bloomer; Douglas Clark; Aindrila Mukhopadhyay; Jay Keasling; John Hartwig | Biocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748e3567dfe4a65ec4ac6/original/artificial-biosynthetic-pathway-for-an-unnatural-terpenoid-with-an-iridiumcontaining-p450.pdf |
60c75394bb8c1adb1d3dc099 | 10.26434/chemrxiv.13514816.v1 | A Size-Matching Strategy to Differentiate Flexible Conformers for the Discovery of Novel Cages with Twin Cavities | <p>Considerable efforts have been made to characterize the meaningful conformers that a molecule can adopt, which is of great significance for understanding the structure-property correlation in the fileds of molecular biology, drug discovery, catalysis, materials science, etc. It is however challenging to differentiate and make use of the flexible conformers in solution, as they often experience rapid interconversion due to low isomerization barrier. We herein present a novel yet simple size-matching strategy for conformation identification. As a proof of concept, we rationally designed a three-dimensional model compound, namely hexaformyl molecule <b>1 </b>exhibiting two types of conformers, <i>i.e.</i> <b>Conformer-1</b> and -<b>2</b> with different cleft positions and sizes. Aided by DFT calculations, we selected two triamino conformation capturers (denoted CC). Small-sized <b>CC-1</b> selectively captured <b>Conformer-1</b> by matching its cleft size, while large-sized <b>CC-2</b> was able to match and capture both conformers. It therefore allowed facile differentiation of the two conformations by conventional NMR and X-ray analyses. These two erstwhile inverconverting and indistinguishable conformational isomers were made use of, leading to the discovery of two novel configurational isomers, namely two novel cage-like compounds with twin cavities, one exhibiting a sandglass-shaped and another with a dumbbell form, which we coined <i>diphane.</i></p> | Zhenyu Yang; Chunyang Yu; Lihua Chen; Pan Li; Jiaolong Chen; Kim Jiayi Wu; Qiangyu Zhu; Yuquan Zhao; Xiaoning Liu; Shaodong Zhang | Aggregates and Assemblies; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75394bb8c1adb1d3dc099/original/a-size-matching-strategy-to-differentiate-flexible-conformers-for-the-discovery-of-novel-cages-with-twin-cavities.pdf |
60c74bea337d6ccb3be27b68 | 10.26434/chemrxiv.12361238.v2 | How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer | <p>The SARS-CoV-2 coronavirus pandemic is certainly the most important public health concern today. Until now there are no vaccines or treatments available, despite intensive international efforts. One of the targets for new drugs is the Coronavirus Spike Protein, responsible for its binding and entry into the host cells. The Receptor Binding Domain (RBD) found at the Spike Protein recognizes the human angiotensin-converting enzyme 2 (hACE2). The present in silico study discuss structural and thermodynamic aspects of the protein complexes involving the RBD’s from the 2002 SARS-CoV and 2019 SARS-CoV-2 with the hACE2. Molecular docking and molecular dynamics simulations of the complexes and isolated proteins were performed, providing insights on their detailed pattern of interactions, and estimating the free energy of binding. The obtained results support previous studies indicating that the chemical affinity of the new SARS-CoV-2 for the hACE2 enzyme virus is much higher than the 2002 SARS-CoV. The herein calculated Gibbs free energy of binding to the hACE2 enzyme is, depending on the technique, from 5.11 kcal/mol to 8.39 kcal/mol more negative in the case of the new coronavirus’ RBD. In addition, within each employed technique, this free energy is consistently 61±2% stronger for SARS-CoV-2 than for SARS-CoV. This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus using drugs targeting its Spike Protein, as well as helps to explain its infectivity, while defining a minimum free energy of binding for new drugs to be designed against this disease.<br /></p> | Jones de Andrade; Paulo Fernando Bruno Gonçalves; Paulo Augusto Netz | Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bea337d6ccb3be27b68/original/how-does-the-novel-coronavirus-interact-with-the-human-ace2-enzyme-a-thermodynamic-answer.pdf |
67254b49f9980725cfd0d5fa | 10.26434/chemrxiv-2024-5xrn9 | Modeling, screening, and techno-economic evaluation of metal-organic frameworks for boil-off gas capture during intercontinental transportation of LNG | Intercontinental transportation of liquefied natural gas (LNG) relies on the energy-intensive re-liquefaction process to minimize boil-off gas (BOG) losses during trips. Previous research efforts have focused on improving and optimizing the existing process designs to treat BOGs. In this work, we developed an energy-efficient high-pressure and low-temperature (HPLT) adsorption process using nanoporous materials, such as metal-organic frameworks (MOFs), for boil-off gas treatment. A high-throughput, multiscale modeling campaign was carried out to discover high-performance nanoporous materials. Our analyses show that the developed HPLT adsorption process with the optimal adsorbent is more economical than the current state-of-the-art processes for 8-day and 13-day trips, with annualized savings of $1.0–2.0 million per ship. We discuss related challenges and opportunities based on adsorbed storage tank for international energy transportation. | Sunghyun Yoon; Haneul Mun; Seongbin Ga; Jinwoo Park; Inkyu Lee; YONGCHUL CHUNG | Theoretical and Computational Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Thermodynamics (Chem. Eng.); Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67254b49f9980725cfd0d5fa/original/modeling-screening-and-techno-economic-evaluation-of-metal-organic-frameworks-for-boil-off-gas-capture-during-intercontinental-transportation-of-lng.pdf |
634aec0786473a713f144c2e | 10.26434/chemrxiv-2022-n3tjf | Bioceramics for medical applications: a computational view | Bio ceramics have enormous applications in the medical field as being used as implants. The base material in bioceramics is mostly calcium phosphate which comes in the form of hydroxyapatite (HAp) or Beta-tricalcium phosphate (β-TCP). The other materials are silica and alumina. The different blends of these bioceramics as well as bioglass are in use for medical implants. The use of simulation and modeling in determining and analysing the structure and function of these bioceramics is used for developing implants, scaffolds, and prosthetics as well as for analysing complex molecular interactions. The use of different molecular dynamics modeling techniques, Density Functional Theory, Finite Element Modeling, Artificial Neural Networks, etc is done in this regard. The results of these modeling and simulations are used for bone grafting, making scaffolds, making dental implants, healing damaged bones, 3D modeling, stress analysis, As removal, nanoindentation, etc. Some software like GROMACS, MEGACELL, and ANOVA is used for this purpose. Hydroxyapatite (HAp) was prepared from egg shells by various routes using hexane and acetic acid followed by heat treatment. Hap has a wide application in water treatment by removal of metal ions. XRD of the samples showed use of acetic acid followed by high temperature sintering leads to formation crystalline phases of HAp. Strong evidence of CaCO3 in calcite phase was obtained in other samples. | Ritambhara Dash; Abhay Kumar Rajak; Ramagiri Praveen Kumar; Parameshwar Kommu; Shruti Sharma; Mukesh Gurjar; Arnab Bhattacharyya | Materials Science; Biocompatible Materials; Ceramics | CC BY 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634aec0786473a713f144c2e/original/bioceramics-for-medical-applications-a-computational-view.pdf |
679a3d85fa469535b94f68bb | 10.26434/chemrxiv-2025-w64t8 | Importance of self-absorption correction for HERFD-XAS of concentrated samples | High energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD-XAS) can dramatically reduce core-hole lifetime broadening that smears out spectroscopic detail in conventional X-ray absorption spectroscopy (XAS). This increased spectroscopic resolution can directly translate to increased speciation capabilities in analysis of complex mixtures. However, spectral distortions due to fluorescence self-absorption are inherent in the HERFD-XAS method and can negate improvements. We discuss a method for correcting self-absorption. | Ben Huntsman; Linda Vogt; Clinton Kidman; Julien Cotelesage; Dimosthenis Sokaras; Thomas Kroll; Ingrid Pickering; Graham George | Physical Chemistry; Inorganic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Inorg.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679a3d85fa469535b94f68bb/original/importance-of-self-absorption-correction-for-herfd-xas-of-concentrated-samples.pdf |
624feb9f505f63d6e06ee71a | 10.26434/chemrxiv-2022-hn3hd-v2 | High-voltage dilute ether electrolytes enabled by regulating interfacial structure | Poor oxidation stability of ether solvents at the cathode restricts the use of dilute ether electrolytes with conventional concentrations around 1 M in high-voltage lithium metal batteries. Here we develop an anion-adsorption approach to altering the ether solvent environment within the electrical double layer (EDL) at the cathode, by adding a small amount of nitrate, so that the oxidation tolerance of nitrate-containing dilute ether electrolytes is enhanced up to 4.4 V (versus Li/Li+), leading to complete compatibility with high-voltage cathodes and exhibiting superior cycling stability. Constant-potential molecular dynamics simulations reveal that ether molecules are mostly excluded from the cathode because of nitrate occupation in the inner layer of the EDL, thus suppressing ether oxidative decomposition. This work highlights that regulating the interfacial structure by adding surface adsorbates, rather than passivating cathode-electrolyte interphase or changing ion solvation, can help to enhance the oxidation stability of ether solvents. It also provides design criteria for adsorption-type additives to achieve high-voltage dilute ether electrolytes. | Huwei Wang; Jinkai Zhang; Haodong Zhang; Wei Li; Ming Chen; Qing Guo; Kah Chun Lau; Liang Zeng; Guang Feng; Dengyun Zhai; Feiyu Kang | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624feb9f505f63d6e06ee71a/original/high-voltage-dilute-ether-electrolytes-enabled-by-regulating-interfacial-structure.pdf |
60c758a44c8919d85bad4c0e | 10.26434/chemrxiv.14571573.v1 | High Shear in Situ Exfoliation of 2D Gallium Oxide Sheets from Centrifugally Derived Thin Films of Liquid Gallium | Herein, we have explored the use of a microfluidics platform for the exfoliation and oxidation of liquid gallium into ultrathin sheets of gallium oxide under continuous flow condition. The novel method developed here takes advantage of the high mass transfer in liquids and has the potential for creating high yielding thin sheets of oxidised gallium with insulating properties as well as acts as an active catalyst in hydrogen evolution reactions. This highlights the potential utility of the sheets as an alternative to the expensive and scarce noble metal based electrocatalysts | Kasturi Vimalanathan; Timotheos Palmer; Zoe Gardner; Irene Ling; Soraya Rahpeima; Sait Elmas; Qiang Sun; Jason R. Gascooke; Christopher T Gibson; Jin Zou; Mats R. Anderson; Nadim Darwish; Colin Raston | Materials Processing; Nanostructured Materials - Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758a44c8919d85bad4c0e/original/high-shear-in-situ-exfoliation-of-2d-gallium-oxide-sheets-from-centrifugally-derived-thin-films-of-liquid-gallium.pdf |
638ddfb414d92d318ba19ce0 | 10.26434/chemrxiv-2022-4645x | Molecular engineering to tune functionality: the case of Cl substituted [Fe(terpy)2]2+ | The properties of transition metal complexes and their chemical dynamics can be effectively modified with ligand substitutions, and theory can be a great aid to such molecular engineering. In this paper we first theoretically explore how substitution with a Cl atom at different positions of the terpyridine ligand affects the electronic structure of the [Fe(terpy)2]2+ complex. We found that besides the substitution at position 4’, the next most promising candidate to cause substantial electronic effects is that where the side pyridine ring is substituted at position 5 (beta). Therefore, next we examine in detail the Fe(II) complexes of the 5- chloro and 5,5”-di-chloro derivatives of terpy, theoretically and experimentally, to reveal how these substitutions modify the ground state properties and the lifetime of the excited quintet state in such complexes. In addition, we extend the investigation to the complexes of the analogously substituted derivatives of 4’-SMe-terpy. The substitution at position(s) 5 (and 5”) with Cl lowers the energy of the quintet state and increases its lifetime; the results on the 4’-SMe substituted complexes show similar changes with these two substitutions, verifying that these effects are more or less additive. This study contributes to the enhancement of our molecular engineering toolset for modifying the potential energy landscape of similar complexes. | Mariann Papp; Tamás Keszthelyi; Andor Vancza; Éva G. Bajnóczi; Éva Kováts; Zoltán Németh; Csilla Bogdán; Gábor Bazsó; Tamás Rozgonyi; György Vankó | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Ligands (Inorg.); Transition Metal Complexes (Inorg.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638ddfb414d92d318ba19ce0/original/molecular-engineering-to-tune-functionality-the-case-of-cl-substituted-fe-terpy-2-2.pdf |
60c741e7bb8c1ae1513da029 | 10.26434/chemrxiv.8100152.v1 | 16-Step Synthesis of the Isoryanodane Diterpene (+)-Perseanol | (+)-Perseanol is an isoryanodane diterpene with potent antifeedant and insecticidal properties isolated from the tropical shrub <i>Persea indica</i>. Here we report the first chemical synthesis of (+)-perseanol, which proceeds in 16 steps from commercially available (<i>R</i>)-pulegone. The synthesis features a two-step annulation process that rapidly assembles the tetracyclic core from readily accessible cyclopentyl building blocks. This work demonstrates how convergent fragment coupling, when combined with strategic oxidation tactics, can enable the concise synthesis of complex and highly oxidized diterpene natural products. <br /> | Arthur Han; Yujia Tao; Sarah Reisman | Natural Products; Organic Synthesis and Reactions; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e7bb8c1ae1513da029/original/16-step-synthesis-of-the-isoryanodane-diterpene-perseanol.pdf |
60c74b5af96a00973b2875b6 | 10.26434/chemrxiv.12148572.v2 | van der Waals Potential: An Important Complement to Molecular Electrostatic Potential in Studying Intermolecular Interactions | Electrostatic and van der Waals (vdW) interactions are two major components of intermolecular weak interactions. Electrostatic potential has been a very popular function in revealing electrostatic interaction between the system under study and other species, while the role of vdW potential is less recognized and has long been ignored. In this paper, we explicitly present definition of vdW potential, describe its practical implementation, and demonstrate its important value by visual analysis and comparing it with spatial distribution function obtained via molecular dynamics simulation. We hope this work can arouse researchers' attention to van der Waals potential and promote its application in practical studies of weak interaction. Calculation, visualization and quantitative analysis of the vdW potential have been supported by our freely available code Multiwfn (http://sobereva.com/multiwfn). | Tian Lu; Qinxue Chen | Computational Chemistry and Modeling; Theory - Computational; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b5af96a00973b2875b6/original/van-der-waals-potential-an-important-complement-to-molecular-electrostatic-potential-in-studying-intermolecular-interactions.pdf |
6304aab50187d9a18c9e24e2 | 10.26434/chemrxiv-2022-nz9kt-v2 | The Effect of Fibrous Tows and Weave Pattern on Carbon Cloths as Electrodes in Redox Flow Batteries | The electrochemical and fluid dynamic performance of redox flow batteries is strongly influenced by the microstructure of the porous electrodes. Carbon cloths are a potential candidate whose hierarchical structure affects length scales associated with electrolyte flow; however, few studies have investigated the electrochemical behavior spanning from the fibrous tow to the bulk weave pattern. Here, we explore commercially activated weave patterns (plain, 8-harness satin, 2×2 basket) in an aqueous environment while quantifying reactive transport for individual tows and simulating fiber bundle electrochemical activity through multiphysics modeling. We then evaluate each woven electrode in a redox flow cell, measuring the pressure loss, polarization, and galvanostatic cycling behavior before comparing the mass-transfer relationships. We find the weave pattern strongly correlates with flow cell pressure drop, while the carbon fibers per tow influence electrochemistry and mass-transport scaling. Collectively, these results offer new insights into how advanced carbon cloths structures impact flow cell performance. | Kevin Tenny; Yet-Ming Chiang; Fikile Brushett | Energy; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Reaction Engineering; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6304aab50187d9a18c9e24e2/original/the-effect-of-fibrous-tows-and-weave-pattern-on-carbon-cloths-as-electrodes-in-redox-flow-batteries.pdf |
623a26b5a4ed95dbed29dc02 | 10.26434/chemrxiv-2022-j39b0 | Trends in Research and Development for CO2 Capture and Sequestration | Technological and medical advances over the past few decades epitomize human capabilities. However, the increased life expectancies and concomitant land-use changes have significantly contributed to the release of ~830 gigatons of CO2 into the atmosphere over the last three decades, an amount comparable to the prior two and a half centuries of CO2 emissions. The United Nations has adopted a pledge to achieve “net zero”, i.e., yearly removing as much CO2 from the atmosphere as the amount emitted due to human activities, by the year 2050. Attaining this goal will require a concerted effort by scientists, policy makers and industries all around the globe. Design of novel industrial-scale materials to selectively remove CO2 from other atmospheric gases has meant that it is now possible to adopt a multi-pronged approach towards atmospheric CO2 remediation. Broadly, the CO2 present in the atmosphere can be captured using materials and processes for biological, chemical, and geological technologies that can sequester CO2 while also reducing our dependence on fossil-fuel reserves. In this review, we used the curated literature available in the CAS Content Collection to present a systematic analysis of the various approaches taken by scientists and industrialists to restore carbon balance in the environment. Our analysis highlights the latest trends alongside the associated challenges. | Xiang Yu; Carmen Otilia Catanescu; Robert Bird; Sriram Satagopan; Zachary J. Baum; Qiongqiong Angela Zhou | Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science | CC BY 4.0 | CHEMRXIV | 2022-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623a26b5a4ed95dbed29dc02/original/trends-in-research-and-development-for-co2-capture-and-sequestration.pdf |
65303aec2431cc1dacd6c83b | 10.26434/chemrxiv-2023-t0x61 | Adjusting the Operational Potential Window as a Tool for Prolonging the Durability of Carbon-supported Pt-alloy Nanoparticles as Oxygen Reduction Reaction Electrocatalysts | A current trend in the investigation of the state-of-the-art Pt-alloys as the proton exchange membrane fuel cells (PEMFCs) electrocatalysts is to study their long-term stability as a bottleneck for their full commercialization. Although many parameters have been appropriately addressed, there are still certain issues that must be considered. Here, the stability of an experimental Pt-Co/C electrocatalyst is investigated by high-temperature accelerated degradations tests (HT-ADTs) in a high-temperature disc electrode (HT-DE) setup, allowing the imitation of close-to-real operational conditions in terms of temperature (60 ℃). Whereas the US Department of Energy (DoE) protocol has been chosen as the basis of the study (30 000 trapezoid-wave cycling steps between 0.6–0.95 VRHE with a 3 s hold time at both the lower potential limit (LPL) and the upper potential limit (UPL)), this works demonstrates that limiting both the LPL and UPL (from 0.6–0.95 VRHE to 0.7–0.85 VRHE) can dramatically reduce the degradation rate of state-of-the-art Pt-alloy electrocatalysts. This has been additionally confirmed with the use of an electrochemical flow cell coupled to an inductively coupled plasma mass spectrometry (EFC-ICP-MS), which enables real-time monitoring of the dissolution mechanisms of Pt and Co. In line with the HT-DT methodology observations, a dramatic decrease in the total dissolution of Pt and Co has once again been observed upon narrowing the potential window to 0.7–0.85 VRHE rather than 0.6–0.95 VRHE. Additionally, the effect of the potential hold time at both LPL and UPL on the metal dissolution has also been investigated. The findings demonstrate that the dissolution rate of both metals is proportional to the hold time at UPL, regardless of the applied potential window, while the hold time at the LPL does not appear to be as detrimental to the stability of metals. Nevertheless, the total dissolution of metals has been once again significantly lower for the narrower potential window of 0.7–0.85 VRHE rather than 0.6–0.95 VRHE. | Tina Đukić; Léonard Jean Moriau; Iva Klofutar; Martin Šala; Luka Pavko; Francisco Javier González López; Francisco Ruiz-Zepeda; Andraž Pavlišič; Miha Hotko; Matija Gatalo; Nejc Hodnik | Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Electrocatalysis; Fuel Cells | CC BY 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65303aec2431cc1dacd6c83b/original/adjusting-the-operational-potential-window-as-a-tool-for-prolonging-the-durability-of-carbon-supported-pt-alloy-nanoparticles-as-oxygen-reduction-reaction-electrocatalysts.pdf |
60c746b1842e658158db2856 | 10.26434/chemrxiv.11369061.v1 | Electronic Band Contraction Induced Low Temperature Methane Activation on Metal Alloys | The catalytic conversion of methane under mild conditions is an appealing approach to selectively produce value-added products from natural gas. Catalysts which can chemisorb methane can potentially overcome challenges associated with its high stability and achieve facile activation. Although transition metals can activate C-H bonds, chemisorption and low-temperature conversion remains elusive on these surfaces. The broad electronic bands of metals can only weakly interact with the methane orbitals, in contrast to specific transition metal oxide and supported metal cluster surfaces which are now recognized to form methane σ-complexes. Here, we report methane chemisorption can, remarkably, occur on metal surfaces via electronic band contraction and localization from metal alloying. From a broad screening including single atom and intermetallic alloys in various substrates, we find early transition metals as promising metal solutes for methane chemisorption as well as low-temperature activation. These findings demonstrate a combinatorial diversity of possible candidates in earth abundant metal alloys with this attractive catalytic behavior. | Victor Fung; Guoxiang Hu; Bobby Sumpter | Alloys; Catalysts; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Machine Learning; Petrochemicals; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746b1842e658158db2856/original/electronic-band-contraction-induced-low-temperature-methane-activation-on-metal-alloys.pdf |
61cca090a53f1b0b86ac318b | 10.26434/chemrxiv-2021-jv2wp | Inverse Molecular Design of Alkoxides and Phenoxides
for Aqueous Direct Air Capture of CO2 | Aqueous direct air capture (DAC) is a key technology toward a carbon negative infrastructure. Developing sorbent molecules with water- and oxygen-tolerance and high CO2 binding capacity is therefore highly desired. In this work, we analyze the CO2 absorption chemistries on amines, alkoxides, and phenoxides with density functional theory (DFT) calculations and search for the optimal sorbent using an inverse molecular design strategy. The alkoxides and phenoxides are found to be more suitable for aqueous DAC than amines thanks to their water-tolerance and capture stoichiometry of 1:1 (2:1 for amines). All three molecular systems are found to obey the same linear scaling relationship (LSR) between pK_(CO_2 ) and pK_a, since both CO2 and proton are bonded to the nucleophilic binding site through a majorly σ bonding orbital. Several high-performance alkoxides are proposed from the computational screening. In contrast, phenoxides have relatively poor correlation between pK_(CO_2 ) and pK_a, showing promise for optimization. We apply genetic algorithm (GA) to search the chemical space of substituted phenoxides for the optimal sorbent. Several promising candidates that break the LSR are discovered. The most promising off-LSR candidate phenoxides feature bulky ortho substituents forcing the CO2 adduct into a perpendicular configuration with respect to the aromatic ring. In this configuration, CO2 utilizes a different molecular orbital for binding than does the proton, and the pK_(CO_2 ) and pK_a are thus decoupled. The pK_(CO_2 )-pK_a trend and off-LSR behaviors are then confirmed by experiments, validating the inverse molecular design framework. This work not only extensively studies the chemistry of the aqueous DAC, but also presents a transferrable computational workflow for understanding and optimization of other functional molecules. | Zisheng Zhang; Amanda L. Kummeth; Jenny Y. Yang; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cca090a53f1b0b86ac318b/original/inverse-molecular-design-of-alkoxides-and-phenoxides-for-aqueous-direct-air-capture-of-co2.pdf |
66ba34dc01103d79c5bf07a4 | 10.26434/chemrxiv-2024-5s3zt | Reactivity of Acceptor-Acceptor Diazo-Pyrazolones with Allyl Thioethers under Visible Light: Access to Homoallyl and Bis-Homoallyl Sulfides, Spiropyrazolones-Pesticide Analogues and Photo-Flow Synthesis | Pyrazolone framework has been greatly explored for various applications owing to their presence in many
bioactive compounds. The novel reactivity of less selective and more reactive acceptor-acceptor kind of diazo pyrazolone (DIPOL) has been explored under visible light for the first time. We have successfully demonstrated the reaction of DIPOL and different allyl thioethers under blue light to construct a wide variety of products including pesticidal analogue exclusively in excellent chemo-selectivities in good to excellent yields. Moreover, the possible side products emanating from ketene were
not observed. This protocol works smoothly in environmentally benign solvent under inert free condition. The practicality of the protocol has been extended to photo-flow reaction and also the reaction works smoothly under the direct exposure of sunlight. | Onkar S. Bankar; Chhabi Pal; Debasish Laha; Abhijeet S. Sabale; Dr. Ramakrishna G. Bhat | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ba34dc01103d79c5bf07a4/original/reactivity-of-acceptor-acceptor-diazo-pyrazolones-with-allyl-thioethers-under-visible-light-access-to-homoallyl-and-bis-homoallyl-sulfides-spiropyrazolones-pesticide-analogues-and-photo-flow-synthesis.pdf |
659d2f53e9ebbb4db9c28bb6 | 10.26434/chemrxiv-2024-g7swp | Ion Mobility Mass Spectrometry for Synthetic Molecules: Expanding the Analytical Toolbox | Understanding the composition, structure and stability of synthetic molecules is crucial for their design, yet currently the analytical tools commonly used do not readily provide this information, particularly for larger complex analytes above M = 500 Da. In this perspective, we show how ion mobility mass spectrometry (IM-MS), in combination with tandem mass spectrometry, computational methods and other complementary techniques, can be used to structurally characterise new synthetic molecules, make and predict new complexes, monitor disassembly processes and determine stability. Using IM-MS, we present an experimental and computational framework for the analysis and design of complex molecular architectures such as (metallo)supramolecular cages, interlocked molecules, rotaxanes, dendrimers, polymers and host-guest complexes. | Niklas Geue; Richard E.P. Winpenny; Perdita Barran | Inorganic Chemistry; Analytical Chemistry; Organometallic Chemistry; Mass Spectrometry; Separation Science; Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659d2f53e9ebbb4db9c28bb6/original/ion-mobility-mass-spectrometry-for-synthetic-molecules-expanding-the-analytical-toolbox.pdf |
639b24dae9d0fd62f41df5f7 | 10.26434/chemrxiv-2022-25q9h-v4 | Understanding the emergence of the boson peak in molecular glasses | A common feature of glasses is the “boson peak”, observed as an excess in the heat capacity over the crystal or as an additional peak in the terahertz vibrational spectrum. The microscopic origins of this peak are not well understood; the emergence of locally ordered structures has been put forward as a possible candidate. Here, we show that depolarised Raman scattering in liquids consisting of highly symmetric molecules can be used to isolate the boson peak, allowing its detailed observation from the liquid into the glass. The boson peak in the vibrational spectrum matches the excess heat capacity. As the boson peak intensifies on cooling, wide-angle x-ray scattering shows the simultaneous appearance of a pre-peak due to molecular clusters consisting of circa 20 molecules. Atomistic molecular dynamics simulations indicate that these are caused by over-coordinated molecules. These findings represent an essential step toward our understanding of the physics of vitrification. | Mario González-Jiménez; Trent Barnard; Ben Russell; Nikita Tukachev; Uroš Javornik; Laure-Anne Hayes; Andrew Farrell; Sarah Guinane; Hans Senn; Andrew Smith; Martin Wilding; Gregor Mali; Motohiro Nakano; Yuji Miyazaki; Paul McMillan; Gabriele Sosso; Klaas Wynne | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Physical and Chemical Properties; Structure; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b24dae9d0fd62f41df5f7/original/understanding-the-emergence-of-the-boson-peak-in-molecular-glasses.pdf |
60c747de4c891984ffad2e22 | 10.26434/chemrxiv.11812371.v1 | Plasma CVD of B-C-N Thin Films Using Triethylboron in Argon-Nitrogen Plasma | <div>
<p>Amorphous
boron-carbon-nitrogen (B-C-N) films with low density are potentially
interesting as alternative low-dielectric-constant (low-κ) materials for future
electronic devices. Such applications require deposition at temperatures below
300 °C, making plasma chemical vapor deposition (plasma CVD) a preferred
deposition method. Plasma CVD of B-C-N films is today typically done with
separate precursors for B, C and N or with precursors containing B–N bonds and
an additional carbon precursor. We present an approach to plasma CVD of B-C-N
films based on triethylboron (B(C<sub>2</sub>H<sub>5</sub>)<sub>3</sub>) a
precursor with B-C bonds in an argon-nitrogen plasma. From quantitative
analysis with Time-of-Flight Elastic Recoil Detection Analysis (ToF-ERDA), we
find that the deposition process can afford B-C-N films with a B/N ratio
between 0.98 and 1.3 and B/C ratios between 3.4 and 8.6 and where the films
contain between 3.6 and 7.8 at. % H and 6.6 and 20 at. % of O. The films have
low density, from 0.32 to 1.6 g/cm<sup>3</sup> as determined from cross-section
scanning electron micrographs and ToF-ERDA
with morphologies ranging from smooth films to separated nanowalls. Scaning
transmission electron microscopy shows that C and BN does not phase seperarte
in the film. The static dielectric constant κ, measured by capacitance–voltage
measurements<b>,</b> varies with the Ar concentration in the range from 3.3 to
35 for low and high Ar concentrations, respectively. We
suggest that this dependence is caused by the energetic bombardment of plasma species during film deposition.</p>
</div>
<br /> | Laurent Souqui; Justinas Palisaitis; Hans Högberg; Henrik Pedersen | Ceramics; Coating Materials; Nanostructured Materials - Materials; Thin Films; Nanostructured Materials - Nanoscience; Main Group Chemistry (Inorg.); Organometallic Compounds; Spectroscopy (Inorg.); Main Group Chemistry (Organomet.); Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747de4c891984ffad2e22/original/plasma-cvd-of-b-c-n-thin-films-using-triethylboron-in-argon-nitrogen-plasma.pdf |
60c7422cee301c7456c78dea | 10.26434/chemrxiv.8234147.v1 | MasterMSM: A Package for Constructing Master Equation Models of Molecular Dynamics | <div>Markov state models (MSMs) have become one of the most important
techniques for understanding biomolecular transitions from classical
molecular dynamics (MD) simulations. MSMs provide a systematized way
of accessing the long time kinetics of the system of interest from
the short-timescale microscopic transitions observed in simulation
trajectories. At the same time, they provide a consistent description
of the equilibrium and dynamical properties of the system of interest,
and they are ideally suited for comparisons against experiment. A few
software packages exist for building MSMs, which have been widely
adopted. Here we introduce MasterMSM, a new Python package
that uses the master equation formulation of MSMs and provides a
number of new algorithms for building and analyzing these models.
We demonstrate some of the most distinctive features of the package,
including the estimation of rates, definition of core-sets for
transition based assignment of states, the estimation of committors
and fluxes, and the sensitivity analysis of the emerging networks.
The package is available at https://github.com/daviddesancho/MasterMSM.</div> | David De Sancho; Anne Aguirre | Computational Chemistry and Modeling; Biophysical Chemistry; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422cee301c7456c78dea/original/master-msm-a-package-for-constructing-master-equation-models-of-molecular-dynamics.pdf |
60c73f22ee301c3a2ec78868 | 10.26434/chemrxiv.7235555.v1 | Hypergolic Zeolitic Imidazolate Frameworks (ZIFs) as Next-Generation Solid Fuels: Unlocking the Latent Energetic Behavior of ZIFs | We present the first strategy to induce hypergolic behavior, i.e. spontaneous ignition and combustion in contact with an external oxidizer, into metal-organic frameworks (MOFs). The strategy uses trigger acetylene or vinyl substituents to unlock the latent hypergolic properties of linkers in zeolitic imidazolate frameworks, illustrated here by six hypergolic MOFs of zinc, cobalt and cadmium. Varying the metal and linker enabled the modulation of ignition and combustion properties, leading to ultrashort ignition delays (down to 2 ms), on par with popular propellants, but without requiring highly energetic or carcinogenic hydrazine components found in conventional hypergols.<br /> | Tomislav Friscic; Hatem M. Titi; Mihails Arhangelskis; Dayaker Gandrath; Cristina Mottillo; Andrew Morris; Robin Rogers; Joseph Marrett; Giovanni Rachiero | Fuels - Materials; Hybrid Organic-Inorganic Materials; Ligands (Inorg.); Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f22ee301c3a2ec78868/original/hypergolic-zeolitic-imidazolate-frameworks-zi-fs-as-next-generation-solid-fuels-unlocking-the-latent-energetic-behavior-of-zi-fs.pdf |
60c74bbdbb8c1a3c6e3db28c | 10.26434/chemrxiv.12369353.v1 | Controlling the Alignment of 1D Nanochannel Arrays in Oriented Metal-Organic Framework Films for Host-Guest Materials Design | Here, we successfully prepared macroscopically oriented films of Cu-based pillar-layered MOFs (Cu<sub>2</sub>(Linker)<sub>2</sub>DABCO) having regularly ordered 1D nanochannels. The direction of 1D nanochannels was controllable by optimizing the crystal growth process; 1D nanochannels either perpendicular or parallel to substrates, which offer molecular-scale pore arrays for a macroscopic alignment of functional guest molecules in the desired direction. We also showed the fabrication of oriented Cu<sub>2</sub>(Linker)<sub>2</sub>DABCO MOF patterns, where the direction of 1D nanochannels is controllable on individual locations on the same substrate. These Cu<sub>2</sub>(Linker)<sub>2</sub>DABCO MOF films and patterns with controlled orientation are importante steps towards the development of MOF film-based applications such as sensors and electrical/optical devices because functionalities derived from the accommodated guest species in their 1D nanochannels are optimized for the rational direction on the desired substrate for the device fabrication.<br /> | Kenji Okada; Miharu Nakanishi; Ken Ikigaki; Yasuaki Tokudome; paolo falcaro; Christian Doonan; Masahide Takahashi | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bbdbb8c1a3c6e3db28c/original/controlling-the-alignment-of-1d-nanochannel-arrays-in-oriented-metal-organic-framework-films-for-host-guest-materials-design.pdf |
67410c6a7be152b1d06b430f | 10.26434/chemrxiv-2024-5j7gx | Anions in corrosion: Influence of polymer electrolytes on the interfacial ion transfer kinetics of Cu at Au(111) surfaces | The corrosion kinetics of metals in the presence of polymer electrolytes—which are frequently used in devices for the electrochemical production of hydrogen, hydrocarbons, and alcohols—is convoluted by transport and ill-defined reactive interfaces which mask the fundamental reaction kinetics. Underpotential-deposited monolayers of Cu at Au(111) surfaces provide a structurally well-defined active site for interfacial ion transfer, with a fixed number of sites available for adsorption. Here, we investigate the adsorption behavior of Cu at Au(111) surfaces across a series of sulfate and sulfonate electrolytes, to understand how anion structure influences the kinetics of elementary interfacial ion-transfer reactions. The influence of anion structure is most significant at high adsorbate coverage, with similar adsorption isotherms and kinetics observed for all three molecular sulfates and sulfonates. In contrast, a suspended perfluorosulfonic acid ionomer reduced both the equilibrium coverage of Cu as well as the standard exchange rate at Au(111) at low coverages of Cu. These results suggest that electrocatalyst corrosion is inhibited for metal nanoparticles supported at polymer electrolytes due to changes in adsorbate coverage as well as suppressed kinetics for interfacial ion transfer. | Kira Thurman; Caitlyn Cannan; Raj Shekhar; Yang Zhao; Shannon Boettcher; Paul Kempler | Physical Chemistry; Catalysis; Energy; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67410c6a7be152b1d06b430f/original/anions-in-corrosion-influence-of-polymer-electrolytes-on-the-interfacial-ion-transfer-kinetics-of-cu-at-au-111-surfaces.pdf |
635460b9aca198c66be1097d | 10.26434/chemrxiv-2022-39dc0 | The Relation Between the Bond Angle and Carbon-Oxygen Stretching Frequencies of Carboxylato Complexes | The symmetric (νs) and antisymmetric (νas) OCO stretching modes of carboxylate containing compounds encode structural information that can be difficult to decipher due to the sensitivity of these spectral features to small shifts in charge distribution and structure, as well as the anharmonicities of these two vibrational modes. In this work, we discuss the relation between the frequency of these modes and the geometry of the carboxylate group, showing that the splitting between νs and νas (νs-a) can be predicted based only on the OCO bond angle obtained from quantum chemical calculations with reasonable accuracy (± 58 cm-1, R2 = 0.992). The relationship is shown to hold for infrared spectra of carboxylato groups in a variety of molecules measured in vacuo. The physical origins of this model are discussed in the framework of normal mode analysis. | Madison M. Foreman; John F Stanton; J. Mathias WEBER | Physical Chemistry; Clusters; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635460b9aca198c66be1097d/original/the-relation-between-the-bond-angle-and-carbon-oxygen-stretching-frequencies-of-carboxylato-complexes.pdf |
641e4470647e3dca9975b2a4 | 10.26434/chemrxiv-2023-zdt5s | Rational design, synthesis, and characterization of a solid Δ9-tetrahydrocannabinol (THC) nanoformulation suitable for “microdosing” applications | Background: This paper highlights the formulation of a solid THC-loaded ingestible prepared from pure THC distillate. A THC ethanol-assisted cannabinoid nanoemulsion (EACNE) was created without the need for specialized emulsification equipment such as a high-pressure homogenizer or a microfluidizer. Stress-testing was performed on the EACNE to evaluate its chemical and colloidal stability under the influence of different environmental factors, encompassing both physical and chemical stressors. Subsequently, the EACNE was converted to a solid powdery material while still retaining its THC potency, and suited for “microdosing” applications.
Methods: An ethanol-assisted emulsification method was used to generate a THC nanoemulsion. The EACNE was fully characterized, imaged, and subjected to stress-tests. The EACNE was then mixed with a solid matrix material post facto and lyophilized to create a solid ingestible substance. Upon ball-milling, a dense powdery material was obtained. Flow properties and thermal properties of this material were recorded. Potency of the material was evaluated in triplicate using HPLC and correlated with the potency of the starting EACNE.
Results: EACNE had an average lipid droplet size of ca. 190 nm, with a polydispersity index (PDI) of 0.15, and an average droplet zeta potential of -49±10 mV. The nanoemulsion was colloidally stable for at least 6 weeks, with no meaningful change in cannabinoid potency over the experimental period, as determined by HPLC analysis. The EACNE remained stable when subjected to physical stresses such as heat, freeze/thaw cycles, carbonation, dilution to beverage concentrations, high sucrose concentrations, and a pH range between 5-8. The effect of undesirable events during the lyophilization of the EACNE were minimized by ball-milling the resulting solid. The microencapsulated EACNE demonstrated limited free-flowing behaviour but was freely redispersible in water without any visible phase separation.
Conclusions: A solvent-mediated emulsification protocol creates a THC-loaded nanoemulsion that can subsequently be converted to a water-soluble powder. These materials are particularly suited for THC “microdosing”, a practice that
might decouple the health benefits of THC from its psychotropic effects. | Abhinandan Banerjee; William Hosie; Ana Carolina Terso Ventura; Kasra Razmkhah; Joseph Bautista; Afeson Beyene; Justin Binder; John Trant | Nanoscience; Agriculture and Food Chemistry; Nanostructured Materials - Nanoscience; Food | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641e4470647e3dca9975b2a4/original/rational-design-synthesis-and-characterization-of-a-solid-9-tetrahydrocannabinol-thc-nanoformulation-suitable-for-microdosing-applications.pdf |
63e2a4a81f23f0032d4880f5 | 10.26434/chemrxiv-2023-6d253 | Multimodal Nonlinear Vibrational Hyperspectral Imaging | Linescanning vibrational sum-frequency generation (VSFG) hyperspectral microscopy was developed into an inverted microscope design. The geometry enables seamless collection of brightfield, second-harmonic generation (SHG), and VSFG images of a given sample area. The new vertical configuration also enables future application to biologically relevant environments. The instrument is capable of simultaneously reporting on spatially resolved chemical and geometric specific sample characteristics. This capability is demonstrated with three samples: lyophilized collagen, a molecular self-assembly of sodium dodecyl sulfate and -cyclodextrin (SDS@2-BCD), and a L-phenylalanyl-L-phenylalanine (FF) self-assembly. Hyperspectral analysis showed that the FF samples have anisotropic structural alignment, which is uniform along the long axis and structurally evolving along the short radial axis. Because all three samples represent protein and molecular hierarchically organized materials in the biomaterial and biomimetic fields, this work highlights the chemical-physical information VSFG microscopy can reveal to help in the bottom-up design and characterization of biomaterials. | Jackson Wagner; Zishan Wu; Wei Xiong | Physical Chemistry; Biological and Medicinal Chemistry; Biophysical Chemistry; Self-Assembly; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e2a4a81f23f0032d4880f5/original/multimodal-nonlinear-vibrational-hyperspectral-imaging.pdf |
62cf1461b464faa5cf5f91f3 | 10.26434/chemrxiv-2022-gtmk1 | The burden of city’s pain treatment – a longitudinal one year study of two cities via wastewater-based epidemiology | This paper explores Wastewater-Based Epidemiology (WBE) as a tool enabling understanding of city’s pain treatment in an intercity longitudinal study. An intensive 13-month monitoring programme was undertaken in two adjacent urban areas in South-West England: a small commuter town Keynsham and the city of Bath. The study has shown a great potential of using triangulated WBE and National health Service (NHS) prescription data in understanding pain treatment in two contrasting communities with strong apparent seasonal patterns of short pain medications vs chronic pain treatment as well as the type of treatment used (e.g. oral vs topical). Community-wide usage of NSAIDs and paracetamol in the intercity study is population size and season driven with the highest usage recorded in winter months. This contrasts with other pain pharmaceuticals, especially those used for chronic pain, where no/limited seasonal usage was recorded. Unmetabolized NSAIDs are, to a large extent, directly disposed of into the sewerage system bypassing metabolism due to their preferred topical application. This is particularly apparent in winter months with naproxen showing the highest seasonal variability. Pharma/met analysis allows for tracking topical (non-metabolic) application/down-the-drain disposal of pharmaceuticals with frequent instances of direct disposal of NSAIDs into the sewerage system observed. Normalisation of pharma markers to population size shows comparable estimates of pharma usage in the two cities confirming population as the main driver of pharma loads in wastewater. Variable application patterns of pain pharmaceuticals make back-calculation of intake more convoluted. Intake calculated using percentage of urinary/faecal excretion of metabolites or parent compounds as consumption markers leads to likely underestimation of NSAIDs usage due their both oral and topical application. Prescription data indicates cumulative internal and topical usage. | Andrew Kannan; Natalie Sims; Angus Hold; Kishore Jagadeesan; Richard Standerwick; Ruth Barden; Barbara Kasprzyk-Hordern | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Wastes; Environmental Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2022-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cf1461b464faa5cf5f91f3/original/the-burden-of-city-s-pain-treatment-a-longitudinal-one-year-study-of-two-cities-via-wastewater-based-epidemiology.pdf |
6573d29129a13c4d47072346 | 10.26434/chemrxiv-2023-px3t6-v2 | Discovery of red-shifting mutations in firefly luciferase using high-throughput biochemistry | The Photinus pyralis luciferase (FLuc) has proven a valuable tool for bioluminescence imaging, but much of the light emitted from the native enzyme is absorbed by endogenous biomolecules. Thus, luciferases displaying red-shifted emission enable higher resolution during deep-tissue imaging. A robust model of how protein structure determines emission color would greatly aid the engineering of red-shifted mutants, but no consensus has been reached to date. In this work, we apply deep mutational scanning to systematically assess twenty functionally important amino acid positions on FLuc for red-shifting mutations, predicting that an unbiased approach would enable novel contributions to this debate. We report dozens of red-shifting mutations as a result, a large majority of which have not been previously identified. Further characterization revealed that mutations L286V and T352M, in particular, cause pure red emission with much of the light being >600 nm. The red-shifting mutations identified by this high-throughput approach provide strong biochemical evidence for the multiple-emitter mechanism of color determination, and point to the importance of a water network in the enzyme binding pocket for altering the emitter ratio. This work provides a broadly applicable mutational data set tying FLuc structure to emission color that informs our mechanistic understanding of emission color determination and should facilitate the further engineering of improved probes for deep-tissue imaging. | Clair M. Colee; Nicole M. Oberlag; Marcell Simon; Owen S. Chapman; Lyndsey C. Flanagan; Edison S. Reid-McLaughlin; Jordan A. Gewing-Mullins; Synaida Maiche; Devi F. Patel; Andre R.O. Cavalcanti; Aaron M. Leconte | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6573d29129a13c4d47072346/original/discovery-of-red-shifting-mutations-in-firefly-luciferase-using-high-throughput-biochemistry.pdf |
60c74153337d6cd696e268a0 | 10.26434/chemrxiv.8010962.v1 | Monophosphine Ligands Promote Pd-Catalyzed C–S Cross-Coupling Reactions at Room Temperature with Soluble Bases | <div>
<p>The Pd-catalyzed cross-coupling of thiols
with aromatic electrophiles is a reliable method for the synthesis of aryl
thioethers, which are important compounds for pharmaceutical and agricultural
applications. Since thiols and thiolates strongly bind late transition metals,
previous research has focused on catalysts supported by chelating, bisphosphine
ligands, which were considered less likely to be displaced during the course of
the reaction. We show that by using monophosphine ligands instead, more effective
catalysis can be achieved. Notably, compared to previous methods, this
increased reactivity allows for the use of much lower reaction temperature,
soluble bases, and base-sensitive substrates. In contrast to conventional
wisdom, our mechanistic data suggest that the extent of displacement of
phosphine ligands by thiols is, firstly, not correlated with the ligand bulk or
thiol nucleophilicity, and secondly, not predictive of the effectiveness of a
given ligand in combination with palladium.</p>
</div> | Jessica Xu; Richard Liu; Charles Yeung; Stephen L. Buchwald | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74153337d6cd696e268a0/original/monophosphine-ligands-promote-pd-catalyzed-c-s-cross-coupling-reactions-at-room-temperature-with-soluble-bases.pdf |
60c746c8f96a004e5a286e06 | 10.26434/chemrxiv.11403804.v1 | Mesoporous Carbon Structure-Based Glass Nanopipettes as Micro pH Probes | <p>Nanopore-based nanomaterials have been widely used to prepare the biosensor due to the unique structure, and the high sensitivity to the external stimuli under different environmental conditions. In this report, we ingeniously designed and prepared mesoporous carbon structure-based quartz nanopipettes. The mesoporous carbon was in situ grown in the tip working area of a single quartz nanopipette through the method of evaporation induced self-assembly (EISA). The mesoporous carbon could reduce the effective aperture of the nanopipette, while the surface area of nanopipette tip could be increased by the mesoporous carbon structure as well. The negative charges on the inner surface of the nanopipette increased significantly, which made the ionic current rectification of the nanopore more remarkable, with the ionic current rectification ratio increasing from 2.3 to 34.8. The mesoporous carbon-based glass nanopipette with good response to pH has been used for the probe of pH value of micro-volume solution. The test results were consistent with those obtained by using a commercial pH meter.<br /></p> | Haili He; Dongyuan Zhao | Analytical Chemistry - General | CC BY NC 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c8f96a004e5a286e06/original/mesoporous-carbon-structure-based-glass-nanopipettes-as-micro-p-h-probes.pdf |
6752c918085116a1338f5ae8 | 10.26434/chemrxiv-2024-b5vgf | Testing the acceleration of the flavin-N(5)-hydroperoxide formation by O2 binding in monooxygenase EncM by QM/MM MD simulations | In monooxygenase EncM, the reduced flavin cofactor binds O2 to form an uncommon oxygenating species – flavin-N(5)-oxide. Here we present the results of QM/MM MD demonstrating that the regioselective O2 activation is driven by the O2 binding pose in EncM. We report the free-energy of the superoxide radical binding to the flavin N(5) and C(4a) positions and link these energies and distances of O2 binding returned by the QM/MM MD simulations. | Konstantin Odintsov; Tatiana Domratcheva | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6752c918085116a1338f5ae8/original/testing-the-acceleration-of-the-flavin-n-5-hydroperoxide-formation-by-o2-binding-in-monooxygenase-enc-m-by-qm-mm-md-simulations.pdf |
63620304ee3186c73f7bce8a | 10.26434/chemrxiv-2022-pxnv9-v2 | Deciphering O-glycoprotease substrate preferences with O-Pair Search | O-glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylated sequence motifs, such as those found in mucin domains. Their utility for multiple glycoproteomic applications is driving the search to both discover new O-glycoproteases and to understand how structural features of characterized O-glycoproteases influence their substrate specificities. One challenge of defining O-glycoprotease specificity restraints is the need to characterize O-glycopeptides with site-specific analysis of O-glycosites. Here, we demonstrate how O-Pair Search, a recently developed O-glycopeptide-centric identification platform that enables rapid searches and confident O-glycosite localization, can be used to determine substrate specificities of various O-glycoproteases de novo from LC-MS/MS data of O-glycopeptides. Using secreted protease of C1 esterase inhibitor (StcE) from enterohemorrhagic Escherichia coli and O-endoprotease OgpA from Akkermansia mucinophila, we explore numerous settings that effect O-glycopeptide identification and show how non-specific and semi-tryptic searches of O-glycopeptide data can produce candidate cleavage motifs that can be used to define new protease cleavage settings that lower search times and improve O-glycopeptide identifications. We use this platform to generate a consensus motif for the recently characterized immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa and show that IMPa is a favorable O-glycoprotease for characterizing densely O-glycosylated mucin-domain glycoproteins. | Nicholas M. Riley; Carolyn R. Bertozzi | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63620304ee3186c73f7bce8a/original/deciphering-o-glycoprotease-substrate-preferences-with-o-pair-search.pdf |
60c742d2bdbb8981a7a3856c | 10.26434/chemrxiv.8787311.v1 | Electrochemical Characterization of Low-Temperature Direct Ethanol Fuel Cells Using Direct and Alternate Current Methods | Here we report for the first time the results of systematic characterization of a low-temperature polymer electrolyte membrane direct ethanol fuel cell using DC and AC electrochemical methods. Model catalysts (carbon supported Pt nanoparticles) painted on carbon paper are used as anode and cathode. Influence of physical parameters, such as cell temperature, current density, ethanol concentration and anode fuel flow rate on overall cell impedance is studied. Analysis of the obtained impedance spectra in connection with DC measurements allows us to comment on cell properties and to separate different contributions to the overall cell polarization. Our results suggest that the cell impedance is dominated by anode faradaic impedance, with negligible contribution from cathode faradaic impedance. The anode impedance depends strongly on current density and cell temperature, but is not significantly influenced by ethanol concentration. Presence of anode mass-transfer impedance, even when ethanol was fed to the cell in high excess, is confirmed. Based on the results we conclude that changes in ethanol electro-oxidation mechanism might manifest themselves on the impedance spectra in the low-frequency inductive loop. Nonetheless, further studies involving equivalent circuit modelling are needed to determine the exact influence of the cell parameters on the anode kinetics. | Paweł Wnuk; Rafal Jurczakowski; Adam Lewera | Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Fuel Cells; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742d2bdbb8981a7a3856c/original/electrochemical-characterization-of-low-temperature-direct-ethanol-fuel-cells-using-direct-and-alternate-current-methods.pdf |
669a316cc9c6a5c07aceb782 | 10.26434/chemrxiv-2024-qzrlv | Nickel Dynamics Switch the Selectivity of CO2 Hydrogenation | The dynamic properties of catalysts under reaction conditions are difficult to characterize and thus their contribution to performance has traditionally been overlooked. Herein, we uncover the mechanism behind the selectivity switch in the hydrogenation of CO2 on Nickel catalysts. The swap between methanation and the Reverse Water Gas-Shift reaction (CO2+H2 <=> CO+H2O) is driven by dynamics induced by some of the reaction intermediates. In particular, at low temperatures, CO accumulates on the Ni surface promoting the formation of Ni adatoms, which enhances further CO conversion to methane. At elevated temperatures, the adatom population decreases, and the selectivity towards CO increases. In the present example, the lack of understanding of the materials under operando conditions leads to poor representativeness of the structural models in the calculations. This introduces an error that accumulates with the energy evaluation error of Density Functional Theory simulations. Our work paves the way for including dynamic aspects of the materials under reaction conditions in microkinetic simulations. | José Manuel González-Acosta; Albert Sabadell-Rendón; Kamila Kaźmierczak; Florian Euzenat; Nicolas Montroussier; Daniel Curulla-Ferré; Núria López | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a316cc9c6a5c07aceb782/original/nickel-dynamics-switch-the-selectivity-of-co2-hydrogenation.pdf |
676ab844fa469535b9a55400 | 10.26434/chemrxiv-2024-p9fvc | CrossMat: Integrating Material Databases for Multi-Domain Cross-Application | Big data and artificial intelligence (AI) have emerged as a transformative force in materials science. However, the field still faces significant challenges, primarily the scarcity of comprehensive material datasets and the inefficiencies in utilizing existing data to its full potential. In this work, we propose the CrossMat platform, integrating material databases to accelerate material discovery across diverse applications. Currently encompassing fields such as electrocatalysis, thermocatalysis, photocatalysis, solid-state electrolyte materials, hydrogen storage materials, lithium battery electrolytes, thermoelectric materials, and superconducting materials, CrossMat is driven by large language models and machine learning algorithms to significantly broaden the scope of material prediction. By systematically identifying synthesizable, cost-effective, and environmentally stable materials, CrossMat facilitates their adaptation to previously unexplored domains. This approach not only addresses critical limitations in current methodologies but also opens up innovative avenues for the discovery and development of advanced materials. | Di Zhang; Xue Jia; Hung Ba Tran; Fangling Yang; Qian Wang; Hanghui Liu; Yaping Qi; Eric Jianfeng Cheng; Hao Li | Materials Science; Catalysts; Nanostructured Materials - Materials | CC BY NC 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676ab844fa469535b9a55400/original/cross-mat-integrating-material-databases-for-multi-domain-cross-application.pdf |
6772ca42fa469535b946809b | 10.26434/chemrxiv-2024-n73fc | New prospects in the inhibition of monoamine oxidase-B (MAO-B) utilizing propargylamine derivatives for the treatment of Alzheimer’s disease: a review | It is well known that monoamine oxidase (MAO) plays a pivotal role in neurodegeneration and the inhibition of this enzyme can manifest anti-depressant properties as well as have a positive impact in Alzheimer’s and Parkinson’s diseases. Specifically, the MAO enzyme catalyzes the oxidative deamination of a variety of monoamines. This reaction leads to the formation of aldehydes, together with H2O2 and ammonia. Hydrogen peroxide can generate additional reactive oxygen species (ROS), this way leading to neurotoxicity. When MAO is activated, it induces the amyloid-beta (Aβ) deposition via abnormal cleavage of the amyloid precursor protein (APP) and contributes to the generation of neurofibrillary tangles and cognitive impairment due to neuronal loss. MAO has two isoforms: MAO-A and MAO-B. The main hMAO-B inhibitors used for the treatment of Alzheimer’s and Parkinson’s diseases, encompass a terminal triple bond in their structure, which provides their potency. Recently, a new class of inhibitors has emerged, bearing the carbon-carbon triple bond not necessarily at the end of the chain. In this review, the structure and physiological function of the MAO enzymes is discussed, as well as their mechanism of inhibition via terminal propargylamines. Moreover, it is highlighted the current development and discovery of potential hMAO-B inhibitors from propargylamine scaffolds and docking studies are performed to four of them by our group, in order to assess their binding energy with the enzyme. Finally, molecules which do not contain a propargylamine moiety in their structure were studied and compared against a known hMAO-B inhibitor, deprenyl. From the superimposition results of these molecules with deprenyl, as well as the interactions of the molecules with the amino acids of the active site of hMAO-B, it appears that these compounds have several similarities with deprenyl, opening new paths for the creation of novel molecules against Alzheimer’s disease. | Filippos Panteleimon Chatzipieris; Athanasios Kokkalis; Nikitas Georgiou; Errikos Petsas; Ektoras Vasileios Apostolou; Georgios C. Vougioukalakis; Thomas Mavromoustakos | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6772ca42fa469535b946809b/original/new-prospects-in-the-inhibition-of-monoamine-oxidase-b-mao-b-utilizing-propargylamine-derivatives-for-the-treatment-of-alzheimer-s-disease-a-review.pdf |
612e43f042198e340e68fb89 | 10.26434/chemrxiv-2021-t9vkz-v3 | Structure determination of small molecule compounds by an electron diffractometer for 3D ED/MicroED
| 3D electron diffraction (3D ED)/Micro electron diffraction (MicroED) has extended the limits of crystallography by enabling the determination of three dimensional molecular structures from sub-μm microcrystals. However, 3D ED/microED measurements using current state-of-the-art electron microscopes require experts in both electron microscopy and crystallography making the method rather difficult for researchers who simply need structures. Here, we present a diffractometer specifically designed for 3D ED/microED and show how it works for determining crystal structures. The newly developed electron diffractometer will provide many researchers with an easy path to structure determination of crystals that are less than 1 μm in size. | Sho Ito; Fraser White; Eiji Okunishi; Yoshitaka Aoyama; Akihito Yamano; Hiroyasu Sato; Joseph Ferrara; Michał Jasnowski; Mathias Meyer | Organic Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e43f042198e340e68fb89/original/structure-determination-of-small-molecule-compounds-by-an-electron-diffractometer-for-3d-ed-micro-ed.pdf |
63765c0553ab805310294075 | 10.26434/chemrxiv-2022-2cl7z | One-Bond 13C-13C Spin-Coupling Constants in Saccharides: A Comparison of Experimental and Calculated Values By Density Functional Theory Using Solid-State 13C NMR and X-Ray Crystallography | Methyl aldohexopyranosides were 13C-labeled at contiguous carbons, crystallized, and studied by single-crystal X-ray crystallography and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy to examine the degree to which density functional theory (DFT) can calculate one-bond 13C-13C spin-coupling constants (1JCC) in saccharides with sufficient accuracy to permit their use in MA’AT analysis (J. Chem. Inf. Model., 2022, 62, 3135–3141). Experimental 1JCC values in crystalline samples of the doubly 13C-labeled compounds were measured by solid-state 13C NMR and compared to those calculated from four different DFT models: (1) 1JCC values calculated from a single structure identical to that observed in crystalline samples by X-ray crystallography; (2) 1JCC values calculated from the same single structure in (1) but allowing all C–H bonds to optimize during the DFT calculations; and (3 and 4) 1JCC values calculated in rotamers of torsion angle theta 2 (C1–C2–O2–O2H) or omega (C4–C5–C6–O6) from which either specific or generalized parameterized equations were obtained and used to calculate 1JCC values in the specific theta 2 or omega rotamer observed in crystalline samples. Good qualitative agreement was observed between calculated 1JCC values and those measured by solid-state 13C NMR regardless of the DFT model, but in no cases were calculated 1JCC values quantitative, differing on average by 4–5% from experimental values. Calculated 1JCC values were consistently larger than experimental values. These findings, and those reported in recent solution NMR studies (Tetrault et al., J. Phys. Chem. B 2022, in press), indicate that improvements in DFT calculations are needed before calculated 1JCC values can be used as reliable constraints in MA’AT analyses of saccharides in solution. | Timothy Tetrault; Reagan Meredith; Mi-Kyung Yoon; Christopher Canizares; Allen Oliver; Ian Carmichael; Anthony Serianni | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63765c0553ab805310294075/original/one-bond-13c-13c-spin-coupling-constants-in-saccharides-a-comparison-of-experimental-and-calculated-values-by-density-functional-theory-using-solid-state-13c-nmr-and-x-ray-crystallography.pdf |
60c74477567dfe033bec42ae | 10.26434/chemrxiv.9809834.v1 | Wetting Properties of the CO2–Water–Calcite System via Molecular Simulations: Shape and Size Effects | <p>Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO<sub>2</sub> and the pore fluids. In this context, the interfacial tension (IFT) between CO<sub>2</sub> and the aqueous fluid and the contact angle, theta, with the pore mineral surfaces are the two key parameters that control the capillary pressure in the pores of the candidate host rock. Knowledge of these two parameters and their dependence on the local conditions of pressure, temperature and salinity is essential for the correct prediction of structural and residual trapping. We have performed classical molecular dynamics simulations to predict the CO<sub>2</sub>–water IFT and the CO<sub>2</sub>–water–calcite contact angle. The IFT results are consistent with previous simulations, where simple point charge water models have been shown to underestimate the water surface tension, thus affecting the simulated IFT values. When combined with the EPM2 CO<sub>2</sub> model, the SPC/Fw water model indeed underestimates the IFT in the low pressure region at all temperatures studied. On the other hand, at high pressure and low temperature, the IFT is overestimated by ~5 mN/m. Literature data regarding the water contact angle on calcite are contradictory. Using our new set of force field parameters, we performed NVT simulations at 323 K and 20 MPa to calculate the contact angle of a water droplet on the calcite {10.4} surface in a CO<sub>2</sub> atmosphere. We performed simulations for both spherical and cylindrical droplet configurations for different initial radii, to study the size dependence of the water contact angle on calcite in the presence of CO<sub>2</sub>. Our results suggest that the contact angle of a cylindrical water droplet on calcite {10.4}, in the presence of CO<sub>2</sub>, is independent of droplet size, for droplets with a radius of 50 Å or more. On the contrary, spherical droplets make a contact angle that is strongly influenced by their size. At the largest size explored in this study, both spherical and cylindrical droplets converge to the same contact angle, 38 degrees, indicating that calcite is strongly wetted by water.</p> | Alessandro Silvestri; Evren Ataman; Akin Budi; Susan Stipp; Julian D Gale; Paolo Raiteri | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74477567dfe033bec42ae/original/wetting-properties-of-the-co2-water-calcite-system-via-molecular-simulations-shape-and-size-effects.pdf |
66925c7a5101a2ffa8468b77 | 10.26434/chemrxiv-2024-b6qj8 | Electrochemical and digital simulation analyses of two-proton-coupled electron transfer between superoxide and hydroquinone | Electrochemical reduction of dioxygen (O2) in the presence of benzene-1,4-diol (hydroquinone) in N,N-dimethylformamide (DMF) was investigated using cyclic voltammetry and digital simulation techniques. Along the electrochemical reduction, a quasireversible cyclic voltammogram (CV) of O2 forming superoxide radical anion (O2•−) was modified in the presence of hydroquinone, where electrogenerated O2•− was scavenged by hydroquinone forming quinone radical anion and hydroperoxide with superior reaction kinetics via two-proton-coupled electron transfer (2PCET). Digital simulations of the CVs were conducted to clarify the details of 2PCET, where heterogeneous electrochemical reactions and homogeneous solution reactions between electrogenerated O2•− and hydroquinone are involved. As a result of the simulation analyses, thermodynamic and kinetic parameters for the 2PCET were obtained, which involved three elementary steps, (i) formation of the prereactive complex from the free reactants, (ii) intra-complex 2PCET forming the product complex via a transition state, and (iii) dissociation of the product complex yielding the free products. The obtained parameters provide fundamental and prerequisite information for the development of artificial electron transfer catalysts and electron transfer carriers using H2Q derivatives. | Tatsushi Nakayama | Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66925c7a5101a2ffa8468b77/original/electrochemical-and-digital-simulation-analyses-of-two-proton-coupled-electron-transfer-between-superoxide-and-hydroquinone.pdf |
636ed15ddcecb4bd852814e8 | 10.26434/chemrxiv-2022-s6z4k | Influence of transition metal electron configuration on the structure of metal-EDTA complexes | The vibrational spectra of cold complexes of ethylenediaminetetraacetic acid (EDTA) with transition metal dications in vacuo show how the electronic structure of the metal provides a geometric template for interaction with the functional groups of the binding pocket. The OCO stretching modes of the carboxylate groups of EDTA serve as structural probes, informing on the spin state of the ion as well as the coordination number in the complex. The results highlight the flexibility of EDTA in accepting a large range of metal cations in its binding site. | Madison M. Foreman; Maristella Alessio; Anna I. Krylov; J. Mathias WEBER | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636ed15ddcecb4bd852814e8/original/influence-of-transition-metal-electron-configuration-on-the-structure-of-metal-edta-complexes.pdf |
6483c81bbe16ad5c57b83059 | 10.26434/chemrxiv-2023-h4qz5 | Acetal Formation of Flavoring Agents with Propylene Glycol in E-cigarettes: Impacts on Indoor Partitioning and Thirdhand Exposure | The widespread use of flavored e-cigarettes has led to a significant rise in teenage nicotine use. In e-liquids, the flavor carbonyls can form acetals with unknown chemical and toxicological properties. These acetals can cause adverse health effects on both smokers and non-smokers through thirdhand exposure. This study aims to explore the impacts of these acetals formed in e-cigarettes on indoor partitioning and thirdhand exposure. Specifically, the acetalization reactions of commonly-used flavor carbonyls in laboratory-made e-liquids were monitored using proton nuclear magnetic resonance (1H NMR) spectroscopy. EAS-E Suite and Poly-Parameter Linear Free Energy Relationships (ppLFERs) were employed to estimate the partitioning coefficients for species. Further, a chemical two-dimensional (2D) partitioning model was applied to visualize the indoor equilibrium partitioning and estimate the distribution of flavor carbonyls and their acetals in the gas phase, aerosol phase, and surface reservoirs. Our results demonstrate that a substantial fraction of carbonyls were converted into acetals in e-liquids, and their chemical partitioning was significantly influenced. This study shows that acetalization is a determinant factor in the exposure and toxicology of harmful carbonyl flavorings, with its impact extending to both direct exposure to smokers and involuntary exposure to non-smokers. | Shuang Wu; Erica Kim; Ran Zhao | Analytical Chemistry; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6483c81bbe16ad5c57b83059/original/acetal-formation-of-flavoring-agents-with-propylene-glycol-in-e-cigarettes-impacts-on-indoor-partitioning-and-thirdhand-exposure.pdf |
6722ee537be152b1d0869f99 | 10.26434/chemrxiv-2024-rs0d6 | Electronic spectroscopy and excited state mixing of OThF | Electronic spectra for OThF have been recorded using fluorescence excitation and two-photon resonantly enhanced ionization techniques. Multiple vibronic bands were observed in the 340 – 460 nm range. Dispersed fluorescence spectra provided ground state vibrational constants and evidence of extensive vibronic state mixing at higher excitation energies. Two-photon ionization measurements established an ionization energy for OThF of 6.283(5) eV. To guide the assignment of the OThF spectra, electronic structure calculations were carried out using relativistic equation-of-motion coupled-cluster singles and doubles methods. These calculations indicated that spin-orbit induced mixing of the 3A" and 4A' states was mediated by a seam of potential energy surface intersections. | Arianna Rodriguez; Jiande Han; Jiarui Yan; Michael Heaven; Lan Cheng | Physical Chemistry; Structure | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6722ee537be152b1d0869f99/original/electronic-spectroscopy-and-excited-state-mixing-of-o-th-f.pdf |
62fa600cd0c5cb353465329f | 10.26434/chemrxiv-2022-0zrdl-v2 | DeepStruc: Towards structure solution from pair distribution function data using deep generative models | Structure solution of nanostructured materials that have limited long-range remains a bottleneck in materials development. We present a deep learning algorithm, DeepStruc, that can solve a simple nanoparticle structure directly from a Pair Distribution Function obtained from total scattering data by using a conditional variational autoencoder (CVAE). We first apply DeepStruc to PDFs from seven different structure types of monometallic nanoparticles, and show that structures can be solved from both simulated and experimental PDFs, including PDFs from nanoparticles that are not present in the training distribution. We also apply DeepStruc to a system of hcp, fcc and stacking faulted nanoparticles, where DeepStruc recognizes stacking faulted nanoparticles as an interpolation between hcp and fcc nanoparticles and is able to solve stacking faulted structures from PDFs. Our findings suggests that DeepStruc is a step towards a general approach for structure solution of nanomaterials. | Emil Thyge Skanning Kjær; Andy Sode Anker; Marcus Nørgaard Weng; Simon J. L. Billinge; Raghavendra Selvan; Kirsten Marie Ørnsbjerg Jensen | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fa600cd0c5cb353465329f/original/deep-struc-towards-structure-solution-from-pair-distribution-function-data-using-deep-generative-models.pdf |
60c74b59469df45660f43ece | 10.26434/chemrxiv.12213125.v2 | Targeting TMPRSS2 and Cathepsin B/L Together May Be Synergistic Against SARS-CoV-2 Infection | <p>The entry of SARS-CoV-2 into target cells requires the activation of its surface
spike protein, S, by host proteases. The host serine protease TMPRSS2 and
cysteine proteases Cathepsin B/L can activate S, making two independent entry
pathways accessible to SARS-CoV-2. Blocking the proteases prevents SARS-CoV-2
entry <i>in vitro</i>. This blockade may be achieved <i>in vivo</i> through
‘repurposing’ drugs, a potential treatment option for COVID-19 that is now in
clinical trials. Here, we found, surprisingly, that drugs targeting the two
pathways, although independent, could display strong synergy in blocking virus
entry. We predicted this synergy first using a mathematical model of SARS-CoV-2
entry and dynamics <i>in vitro</i>. The model considered the two pathways
explicitly, let the entry efficiency through a pathway depend on the
corresponding protease expression level, which varied across cells, and let inhibitors
compromise the efficiency in a dose-dependent manner. The synergy predicted was
novel and arose from effects of the drugs at both the single cell and the cell population
levels. Validating our predictions, available <i>in vitro</i> data on SARS-CoV-2
and SARS-CoV entry displayed this synergy. Further, analysing the data using
our model, we estimated the relative usage of the two pathways and found it to
vary widely across cell lines, suggesting that targeting both pathways <i>in
vivo</i> may be important and synergistic given the broad tissue tropism of
SARS-CoV-2. Our findings provide insights into SARS-CoV-2 entry into target
cells and may help improve the deployability of drug combinations targeting host
proteases required for the entry. <br /></p> | Pranesh Padmanabhan; Rajat Desikan; Narendra Dixit | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b59469df45660f43ece/original/targeting-tmprss2-and-cathepsin-b-l-together-may-be-synergistic-against-sars-co-v-2-infection.pdf |
64f8b69279853bbd783cd1fb | 10.26434/chemrxiv-2023-lc6pn | Relationships between Defectivity and Porosity in High Surface Area Porous Aromatic Frameworks | Porous aromatic framework microporosity is known to be strongly dependent on synthetic approach, but little is known about why certain reactions consistently yield significantly more porous materials than other methods. This paper explores the connections between synthetic pathway, polymer defectivity, and microporosity. Using a network disassembly strategy, we show that defectivity is highly dependent on synthetic approach and that more defective polymers are associated with lower surface areas and pore volumes. This empirical association is corroborated through systematic introduction of defects to a model polymer, which results in significant reduction of apparent surface area and pore volumes. Taken together, these data suggest that only highly efficient coupling reactions should be targeted for the synthesis of ultra-high surface area organic polymers. | Anthony Porath; Tony Lybrand; James Bour | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f8b69279853bbd783cd1fb/original/relationships-between-defectivity-and-porosity-in-high-surface-area-porous-aromatic-frameworks.pdf |
67ab5f486dde43c9086648c9 | 10.26434/chemrxiv-2025-srlvk | Taming Distonic Radical Cations for Precise gamma-C–H Functionalization of Alkylamines | Alkylamines are crucial structural motifs found in 43% of pharmaceuticals, where they interact with biological targets such as receptors and enzymes. Consequently, C–H functionalization of alkylamines serves as a powerful strategy for accelerating drug development. Especially, remote C–H functionalization enables selective modification of the periphery of the active nitrogen site, improving bioactivity and pharmacokinetics properties. While remote functionalization of primary and secondary alkylamines is well-established, analogous transformations of tertiary amines remain highly challenging, despite their prevalence in 60% of alkylamine-containing pharmaceuticals. This study unveils the new reactivity of α-ammonio radicals, a class of distonic radical cations, to achieve g-selective functionalization of tertiary amines. Our approach leverages halomethylammonium salts as precursors to α-ammonio radicals, facilitating precise radical transfer to the g-position. The resulting g-radicals enable a diverse range of gamma-selective functionalizations, including thioetherification, amination, alkylation, (hetero)arylation, and alkenylation. This method offers a broad substrate scope and facilitates late-stage functionalization of complex pharmaceutical molecules, highlighting its potential for drug development. Furthermore, this research expands the synthetic utility of distonic radical cations, broadening the methodological landscape for selective radical transformations and inspiring future advancements in radical chemistry. | Yota Sakakibara; Takumi Kinoshita; Kazuki Hirate; Kosuke Hamawaki; Shoma Chiba; Kosuke Terada; Kei Murakami | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab5f486dde43c9086648c9/original/taming-distonic-radical-cations-for-precise-gamma-c-h-functionalization-of-alkylamines.pdf |
6541721bc573f893f1889f75 | 10.26434/chemrxiv-2023-nlvw0 | Dual Catalytic C(sp2)–H Activation of Azaheterocycles towards C–N Atropisomers | We describe a PdII-catalyzed enantioselective C(heteroaryl)–H activation method enabled by a chiral transient directing group (cTDG) to gain access to C–N atropisomers. Reversible condensation between the aldehyde-containing substrate and a chiral amino acid facilitates coordination of the metal catalyst and subsequent atroposelective C–H activation. Various N-heterocycles, including 2-imidazolone, indole, pyrrole, and 2-pyridone, and diverse alkene coupling partners participate in the reaction in moderate to good yields and enantioselectivity. The utility of this method is demonstrated by several downstream transformations that rapidly build up molecular complexity. | Juntao Sun; Yiyao Hu; Chen-Xi Liao; Wen-Ji He; Quynh Wong; Keary Engle | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6541721bc573f893f1889f75/original/dual-catalytic-c-sp2-h-activation-of-azaheterocycles-towards-c-n-atropisomers.pdf |
60dad7f766f2c443ed1435e3 | 10.26434/chemrxiv-2021-87hpz | Structural and Electronic Effects of X-ray Irradiation on Prototypical [M(COD)Cl]2 Catalysts | X-ray characterisation techniques are invaluable for probing material characteristics and properties, and have been instrumental in discoveries across materials research. However, there is a current lack of understanding of how X-ray induced effects manifest in small molecular crystals. This is of particular concern as new X-ray sources with ever increasing brilliance are developed. In this paper, systematic studies of X-ray-matter interactions are reported on two industrially important catalysts, [Ir(COD)Cl]2 and [Rh(COD)Cl]2, exposed to radiation in X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS) experiments. From these complimentary techniques, changes to structure, chemical environments, and electronic structure are observed as a function of X-ray exposure, allowing comparisons of stability to be made between the two catalysts. Radiation dose is estimated using recent developments to the RADDOSE-3D software for small molecules and applied to powder XRD and XPS experiments. Further insights into the electronic structure of the catalysts and changes occurring as a result of the irradiation are drawn from density functional theory (DFT). The techniques combined here offer much needed insight into the X-ray induced effects in transition metal catalysts and consequently, their intrinsic stabilities. There is enormous potential to extend the application of these methods to other small molecular systems of scientific or industrial relevance. | Nathalie Fernando; Andrew B. Cairns; Claire A. Murray; Amber L. Thompson; Joshua L. Dickerson; Elspeth F. Garman; Nayera Ahmed; Laura E. Ratcliff; Anna Regoutz | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Radiation; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dad7f766f2c443ed1435e3/original/structural-and-electronic-effects-of-x-ray-irradiation-on-prototypical-m-cod-cl-2-catalysts.pdf |
67d1ef0d6dde43c90892c2d0 | 10.26434/chemrxiv-2025-h5v4s | Structural and thermodynamic properties of La3+ in chloride-bearing hydrothermal fluids - Insights from a new ab initio-based polarizable force field | Rare earth elements (REEs) are an important group of elements both geologically and economically. The ability of hydrothermal fluids to mobilize REEs in natural, ore-forming environments depends on the chemical composition and the presence of suitable ligands such as chloride and fluoride. Here, we use molecular dynamics (MD) simulations to study the molecular structure and thermodynamic stability of La3+ species in Cl-bearing hydrothermal fluids. We develop a new polarizable force field for this system optimized by reference to density functional theory (DFT) calculations. The structural and thermodynamic data obtained with the new potential using the well-tempered metadynamics (WMetaD) technique reproduce experimental and ab initio MD simulation data well. Polarization effects are shown to be essential for predicting realistic association and stability constants, which was not achieved with simpler non-polarizable interaction potentials. Simulations with different box sizes indicate that the effects of simulation box sizes on calculated thermodynamic quantities are almost negligible at high temperatures. | Rajorshi Chattopadhyay; Sandro Jahn | Earth, Space, and Environmental Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1ef0d6dde43c90892c2d0/original/structural-and-thermodynamic-properties-of-la3-in-chloride-bearing-hydrothermal-fluids-insights-from-a-new-ab-initio-based-polarizable-force-field.pdf |
654e8a6adbd7c8b54b07feee | 10.26434/chemrxiv-2023-dvmvq | Diabolus in Chemistry? | This article explores the possible presence of a pentacle valence bond structure in C$_5$ cyclic molecules. At this end, we have used quantum chemistry tools to elucidate the possible arrangement and the nature of chemical bonds within linear, cyclic, and three-dimensional structures only formed by five carbon atoms. While the linear structure is clearly the most stable one, local minima were obtained for both bi- and three-dimensional structures. Beyond the historical satanic symbol, the pentacle arrangement corresponds to an unusual formal structure with five crossing between C-C bonds. Our calculations show that this diabolic cyclic C$_5$ scheme is a relevant resonant structure and, furthermore, it is also present in the more known cyclo-pentadienyl molecule. | Julien Pilmé; Riccardo Spezia | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e8a6adbd7c8b54b07feee/original/diabolus-in-chemistry.pdf |
662ba11e21291e5d1dc86479 | 10.26434/chemrxiv-2024-s0tcv-v3 | Emerging conformational-analysis protocols from
the RTCONF-16K reaction thermochemistry
conformational benchmark set | Here, we provide a new, realistic reactive conformational analysis benchmark set (RTCONF-16) based on state-of-the-art and cost-efficient methods to assess different protocols. Our comprehensive reference calculations were used to underpin the accuracy of the CENSO (JPCA, 2021, 125, 4039) procedure and to provide alternative recipes with different cost-accuracy compromises. Our general-purpose and economical protocols (CENSO-light and zero, respectively), were found to be 10-30 times faster than the original algorithm while adding only 0.4-0.7 kcal/mol absolute error to the relative free energy estimates. | Bence Balázs Mészáros; Károly Kubicskó; Dávid Dorián Németh; János Daru | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662ba11e21291e5d1dc86479/original/emerging-conformational-analysis-protocols-from-the-rtconf-16k-reaction-thermochemistry-conformational-benchmark-set.pdf |
61f541218d70c36f2311b874 | 10.26434/chemrxiv-2022-x3mh6 | Doping-induced modulation of electronic, optical and wetting properties of CeO2 | Recently, CeO2 as well as other Rare-Earth Oxides (REOs) have become known as water repelling materials which enables their usage in glass industry. In this study, we investigate electronic, optical and wetting properties of pure and doped CeO2 by first-principles calculations. It is established that introduction of tetravalent doping atoms (Zr, Ti, Sn and Si) significantly modifies the optical response of CeO2 in the visible range by shifting the absorption edge which also effects on the refractive index of the material. For these systems, the water contact angle has been computed through adsorption energy of water layers. We report the intrinsic hydrophilicity of the low-index surfaces of CeO2, which is enhanced by introduction of the impurity atom. Influence of the dopants on the oxygen vacancy formation energy E_f (V_O ) is considered and discussed with respect to its possible effect on the hydrophobic behavior of CeO2. It is found out that all the considered doping atoms reduce E_f (V_O ) , resulting in enhanced adsorption of the air hydrocarbons at the surface, which leads to an increased water contact angle. Based on the obtained results, an assessment on the applicability of doped CeO2 in glass industry is made. It is concluded that Zr-doped CeO2 possesses the most prominent properties among considered systems for the application as transparent layer. | Damir Mamedov; Smagul Karazhanov | Theoretical and Computational Chemistry; Materials Science; Coating Materials; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f541218d70c36f2311b874/original/doping-induced-modulation-of-electronic-optical-and-wetting-properties-of-ce-o2.pdf |
64bb9a88b605c6803b28be94 | 10.26434/chemrxiv-2023-8f5g4 | Essential Insight of Direct Electron Transfer-Type Bioelectrocatalysis by Membrane-bound D-Fructose Dehydrogenase with Structural Bioelectrochemistry | Flavin adenine dinucleotide-dependent D-fructose dehydrogenase (FDH) from Gluconobacter japonicus NBRC3260, a membrane-bound heterotrimeric flavohemoprotein capable of direct electron transfer (DET)-type bioelectrocatalysis, was investigated from the perspective of structural biology, bioelectrochemistry, and protein engineering. DET-type reactions offer several benefits in biomimetics (e.g., biofuel cells, bioreactors, and biosensors) owing to their mediator-less configuration. FDH provides an intense DET-type catalytic signal; therefore, extensive research has been conducted on the fundamental principles and applications of biosensors. Structural analysis using cryo-electron microscopy and single-particle analysis has revealed the entire FDH structures with resolutions of 2.5 and 2.7 Å for the reduced and oxidized forms, respectively. The electron transfer (ET) pathway during the catalytic oxidation of D-fructose was investigated using both thermodynamic and kinetic approaches. Structural analysis has shown the localization of the electrostatic surface charges around heme 2c in Subunit II, and experiments using functionalized electrodes with a controlled surface charge support that heme 2c is the electrode-active site. Furthermore, two aromatic amino acid residues (Trp427 and Phe489) were located in a possible long-range ET pathway between heme 2c and the electrode. Two variants (W427A and F489A) were obtained by site-directed mutagenesis, and their effects on DET-type activity were elucidated. The results have shown that Trp427 plays an essential role in accelerating long-range ET and triples the standard rate constant of heterogeneous ET based on bioelectrochemical analysis. | Yohei Suzuki; Fumiaki Makino; Tomoko Miyata; Hideaki Tanaka; Keiichi Namba; Kenji Kano; Keisei Sowa; Yuki Kitazumi; Osamu Shirai | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bb9a88b605c6803b28be94/original/essential-insight-of-direct-electron-transfer-type-bioelectrocatalysis-by-membrane-bound-d-fructose-dehydrogenase-with-structural-bioelectrochemistry.pdf |
6380825d94ff60197f3ef00a | 10.26434/chemrxiv-2022-pglv8 | Automated semiquantitative analysis of protein macroarrays | Protein arrays are systematically arranged, large collections of annotated proteins on planar surfaces commonly used for the characterisation of protein binding events against a wide range of possible probes. These may include analyses of protein-protein, peptide-protein, enzyme-substrate or antibody-antigen interactions from simple reagents to complex mixtures. Absence of appropriate image analysis and data processing software may bestow a substantial hurdle limiting the uptake of protein arrays in research. We developed a first, automated semiquantitative open source software package for the analysis of widely used protein macroarrays. The software allows accurate single array and inter-array comparative studies through the tackling of intra-array inconsistencies arising from experimental disparities. The innovative and automated image analysis process includes adaptive positioning, background identification and subtraction, removal of null signals, robust statistical analysis, and protein pair validation. The normalized values allow a convenient semiquantitative data analysis of different samples or timepoints, enabling accurate characterisation of sample series to identify relative changes for instance in clinical samples in response to diseases and treatment. | Chin Hong Ooi; Nam-Trung Nguyen; Gregor Kijanka | Biological and Medicinal Chemistry; Analytical Chemistry; High-throughput Screening; Bioinformatics and Computational Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6380825d94ff60197f3ef00a/original/automated-semiquantitative-analysis-of-protein-macroarrays.pdf |
652438e9bda59ceb9a30feef | 10.26434/chemrxiv-2023-wjnpj | Tolman Electronic Parameter Predictions from a Fast, Accurate, and Robust Machine Learning Model Provide Insight into Phosphine Ligand Electronic Effects | Phosphines are extremely important ligands in organometallic chemistry and their donor or acceptor ability can be measured through the Tolman electron parameter (TEP). Here we describe the development of a TEP machine learning model (called TEPid) that provides nearly instantaneous calculation of experimentally calibrated CO vibrational stretch frequencies for (R)3P-Ni0(CO)3 complexes. This machine learning model with an error of less than 1 cm-1 was developed using >4,000 DFT calculated (R)3P-Ni0(CO)3 TEP values and 19 key connectivity-based descriptors associated with SMILES strings. We also built a web-based interface to run the machine learning model where SMILES strings can be entered and TEP values returned. We applied this TEPid model to examine the donor and acceptor capability of phosphines in the large Kraken phosphine database. Surprisingly, this showed that the Kraken database is skewed towards donor phosphines. In the same spirit of the Kraken database, we generated tens of thousands of new experimentally based phosphines that when combined with Kraken phosphines provide a more electronically balanced ligand library. | Daniel Ess; Justin Kirkland; Harlan Stevens; Jeffrey Olsen | Theoretical and Computational Chemistry; Organometallic Chemistry; Chemoinformatics - Computational Chemistry; Coordination Chemistry (Organomet.); Theory - Organometallic | CC BY 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652438e9bda59ceb9a30feef/original/tolman-electronic-parameter-predictions-from-a-fast-accurate-and-robust-machine-learning-model-provide-insight-into-phosphine-ligand-electronic-effects.pdf |
64710aa64f8b1884b7557bc5 | 10.26434/chemrxiv-2023-w5l6k | Chemoselective C(sp)-H Borylation of Terminal Alkynes Catalyzed by a Bis(N-heterocyclicsilylene) Manganese Complex | The manganese(II) complex [Mn(SiNSi)Cl2] (SiNSi = 2,6-[EtNSi(NtBu)2CPh]2C5H3N) was an efficient catalyst for the chemoselective C(sp)-H borylation of terminal alkynes. Aliphatic as well as aromatic alkynes containing electron-withdrawing and -donating substituents in different positions have been efficiently borylated. In all cases, the cata-lyst showed an excellent chemoselectivity towards C-H borylation and the reactions proceeded without additives or in-situ activators. Paramagnetic Mn complexes are involved in catalytic turnover which is proposed to occur by a re-dox-neutral Mn(II) cycle. Stoichiometric reactions support that the [Mn(SiNSi)Cl2] precatalyst enters the catalytic cycle by reaction with HBPin. KIE experiments point toward C-H activation of the alkyne as not being involved in the rate-determining step. | Himani Ahuja; Harleen Kaur; Rebeca Arevalo | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64710aa64f8b1884b7557bc5/original/chemoselective-c-sp-h-borylation-of-terminal-alkynes-catalyzed-by-a-bis-n-heterocyclicsilylene-manganese-complex.pdf |
60c74e84567dfecd22ec550c | 10.26434/chemrxiv.12770468.v1 | Direct β- and γ-C(sp3)–H Alkynylation of Free Carboxylic Acids | In this study we report the identification of a novel class of ligands for palladium-catalyzed C(sp3)–H activation that enables the direct alkynylation of free carboxylic acid substrates. In contrast to previous synthetic methods no introduction/removal of an exogenous directing group is required. A broad scope of acids including both α-quaternary and challenging α-non-quaternary can be used as substrates. Additionally, the alkynylation in the distal γ-position is reported. Finally, this study encompasses preliminary findings on an enantioselective variant of the title transformation as well as synthetic applications of the products obtained. | Francesca Ghiringhelli; Manuel van Gemmeren | Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation; Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e84567dfecd22ec550c/original/direct-and-c-sp3-h-alkynylation-of-free-carboxylic-acids.pdf |
634e5dd2e79b3fac2ced5893 | 10.26434/chemrxiv-2022-fdh5d | MLRNet: Combining physics-motivated potential model with neural network for intermolecular potential energy surface construction | A physics-based machine learning model called MLRNet has been developed to construct the high-accuracy two-body intermolecular potential energy surface (IPES). The outputs of the neural network are integrated into the physically realistic Morse/Long Range (MLR) function, which ensures that the MLRNet has meaningful extrapolation at both short and long ranges and solves the asymptotic problem in common neural network potential (NNP) models. The neural network representation of the MLR parameters is more flexible and more efficient than the polynomials expansion in the conventional mdMLR model, especially for systems containing non-rigid monomer(s). The present work illustrates the basic framework of the current MLRNet model, including (i) how to combine the physically meaningful MLR function with different possible NN structures, (ii) the preservation of permutation symmetry, and (iii) the predetermination of the long-range function uLR. We choose two realistic systems to demonstrate the performance of MLRNet: the 3-dimensional IPES of CO2-He including CO2 anti-symmetric vibration Q3, and the 6-dimensional IPES of H2O-Ar system. In both cases, the fitting errors of the MLRNet are several times smaller than those of the conventional mdMLR model. Both the short-range and long-range extrapolation tests have been performed to illustrate the extrapolation ability of the MLRNet and its damping function version. Moreover, for the 6-D H2O-Ar system, the MLRNet only needs 1596 trainable parameters which are almost equal 5-D mdMLR model (1509) and half of the PIP-NN model (3501) with similar accuracy, which illustrates the model efficiency in high-dimensional IPES fitting. | You Li; Yu Zhai; Hui Li | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634e5dd2e79b3fac2ced5893/original/mlr-net-combining-physics-motivated-potential-model-with-neural-network-for-intermolecular-potential-energy-surface-construction.pdf |
6511b32260c37f4f766ee3b4 | 10.26434/chemrxiv-2023-nt5rj-v2 | Scaling the Process Chemistry of a COVID-19 Antiviral Pharmaceutical Down for a Multi-Step Synthesis Experiment in the Undergraduate Teaching Laboratory | Molnupiravir is an orally bioavailable direct acting antiviral agent that received emergency use authorization in late 2021 from the FDA for the treatment of patients with mild, moderate, or severe COVID-19. This prodrug is metabolized into a ribonucleoside that that is incorporated into the viral RNA during replication. Its tautomerization between cytidine- and uridine-like forms ultimately causes multiple irreversible errors in the genetic code of the virus, which prevents successful viral replication. There are multiple process chemistry routes for molnupiravir synthesis published in the literature that attempt to maximize synthetic yield while minimizing cost and waste. In this way, the goals of a successful process scale route are similar to those of an implementable educational laboratory experiment for the teaching laboratory. We have developed a multi-week laboratory module for undergraduate students in which students conduct a multi-step synthesis of molnupiravir. Specifically, our Organic Chemistry II Laboratory course section comprised chemistry and biochemistry majors performed the final two steps of molnupiravir synthesis using procedures derived directly from the published process chemistry literature. We utilized this opportunity to introduce students to reading and interpreting these primary experimental sources. Students obtained authentic characterization data via high pressure liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) spectroscopy to assess the conversion and purity of their products at each synthetic step. The relevance of this laboratory experience to the pandemic, which has had a direct effect on their daily lives, motivates the students to a high level of engagement with this experimental module. We report our in-lab activities and student generated data as well as suggestions for how this laboratory experiment could be tailored to meet similar learning objectives in other courses, such as medicinal chemistry or capstone laboratory courses, and as a function of available instrumentation. | Andrew J. Wommack; Aaliyah B. Holloway; Kaitlyn A. Stallings; Pamela M. Lundin | Organic Chemistry; Chemical Education; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511b32260c37f4f766ee3b4/original/scaling-the-process-chemistry-of-a-covid-19-antiviral-pharmaceutical-down-for-a-multi-step-synthesis-experiment-in-the-undergraduate-teaching-laboratory.pdf |
65610a1acf8b3c3cd70b6fca | 10.26434/chemrxiv-2023-90tb6 | A Quantitative Measurement Technique for Anodic Corrosion of BDD Advanced
Oxidation Electrodes | Electrochemical advanced oxidation (EAO) systems are of significant interest due to their ability to treat a wide range of organic contaminants in water. Despite their popularity, all studies to date that examine anodic corrosion of BDD electrodes are qualitative, using techniques such as scanning electron microscopy, electrochemistry, and spectroscopy. In this work we present a new method to quantify anodic corrosion and determine average corrosion rates as a function of solution composition, current density and BDD material. The method uses white light interferometry (WLI), in conjunction with BDD electrodes integrated into 3D-printed flow cells, to measure three-dimensional changes in surface structure pre- and post-anodic corrosion over a 72-hr period. It is equally applicable to both thin film BDD and much thicker, freestanding BDD. As WLI lends itself to large area measurements, data are collected over geometric areas of 0.5 cm2. In particular it is shown that the addition of 1 M acetic acid to a 0.5 M potassium sulfate solution results in an increase in the average corrosion rate of ~×60 (for freestanding polished BDD). In the same solution, thin film BDD is found to corrode ~×2 faster than freestanding polished BDD. This methodology also represents an important step forward for the prediction of BDD electrode lifetimes in a laboratory setting for a wide range of EAO applications. | Joshua Tully; Daniel Houghton; Ben Breeze; Tim Mollart; Julie Macpherson | Materials Science; Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Electrochemical Analysis; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65610a1acf8b3c3cd70b6fca/original/a-quantitative-measurement-technique-for-anodic-corrosion-of-bdd-advanced-oxidation-electrodes.pdf |
67366db2f9980725cf37c0e1 | 10.26434/chemrxiv-2024-r7kmt | Development of an Optimized Extraction Method to Recover Drug Material from Used Test Strips for Comprehensive Drug Checking | Drug checking programs use point-of-need testing (e.g., test strips) and laboratory-based analysis to rapidly identify emerging drug threats, but each have limitations. Test strips are quick but have high specificity, whereas laboratory testing can identify more compounds but have lengthy turnaround times. To address these limitations, it was proposed that compounds could be extracted from used test strips for additional analyses allowing for rapid onsite information followed by comprehensive laboratory results.
The method development process involved four parts: determining the optimal extraction approach, assessing the feasibility of performing direct analysis in real time mass spectrometry (DART-MS) analysis on extracts, determining the limits of detection (LODs) for a range of analytes, and evaluating the method using used test strips submitted by harm reduction sites. The optimized method consisted of extracting analytes of interest from a cut test strip using 0.5 mL methanol while vortexing for 10 s. DART-MS successfully identified compounds of interests and successfully identified potential false positives from chemical background. LODs were found to be as low as a mass fraction of 0.005 in a mixture. For the samples submitted by harm reduction sites, concordance between extracts and test strip results was 96 % and the agreement in compound identification between used test strip extracts and authentic drug collection samples was approximately 80% regardless of test strip type and preparation.
This work shows that additional analyses of extracted test strips can provide a low-barrier way for high-quality testing that can be used to increase data on the drug landscape.
| Meghan Appley; Elise Pyfrom; Rae Elkasabany; Rick Rousch; Edward Sisco | Analytical Chemistry; Mass Spectrometry; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67366db2f9980725cf37c0e1/original/development-of-an-optimized-extraction-method-to-recover-drug-material-from-used-test-strips-for-comprehensive-drug-checking.pdf |
60c74857337d6c11d6e2753f | 10.26434/chemrxiv.11897241.v1 | Theoretical and Experimental Investigation on the Intersystem Crossing Kinetics in Benzothioxanthene Imide Luminophores, and Their Dependence on Substituents Effects | <p><i>In
spite of their remarkable luminescence properties, benzothioxanthene imide (BTXI
an imide containing rylene chromophores) derivatives have been largely overlooked
compared to their perylene bisimide and naphthalene bisimide counterparts. Thus
their detailed photophysics are much less understood. In this paper, we show
how relatively simple structural modifications of the backbone of BTXIs can
lead to impressive variations in their Inter-System Crossing kinetics. Thus,
through rational engineering of their structure, it is possible to obtain a
triplet formation quantum yield that reaches unity, making BTXI a promising
class of compounds for triplet-based applications (photodynamic therapy,
electroluminescence, etc.).</i></p> | Laura Abad Galan; Jose Maria Andrés Castán; Clement Dalinot; Pablo Simon Marques; Philippe Blanchard; Olivier MAURY; Clement Cabanetos; Tangui Le Bahers; Cyrille Monnereau | Organic Compounds and Functional Groups; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74857337d6c11d6e2753f/original/theoretical-and-experimental-investigation-on-the-intersystem-crossing-kinetics-in-benzothioxanthene-imide-luminophores-and-their-dependence-on-substituents-effects.pdf |
668eaa4c01103d79c59ceaf6 | 10.26434/chemrxiv-2024-g76xl | Insights from techno-economic analysis can guide the design of low-temperature CO₂ electrolyzers towards industrial scaleup | The field of CO₂ reduction has identified several challenges that must be overcome to realize its immense potential to simultaneously close the carbon cycle, replace fossil-based chemical feedstocks, and store renewable electricity. However, frequently cited research targets were set without quantitatively predicting their impact on the economic viability of CO₂ reduction. Using a physics-informed techno-economic assessment, we offer guidance on the most pressing research priorities for CO₂ reduction based on state-of-the-art electrolyzer performance. We find that the levelized product cost is dominated by the cost of electricity used to drive electrolysis, and the capital cost of the process mostly arises from separations, especially of unreacted CO₂ to be recycled. At a cell resistance as low as 1 Ω·cm² and retail electricity prices, operating at a total current density >475 mA/cm² drives up electricity demands and increases the cost of producing CO. High current density operation is therefore undesirable unless low cell voltages can be maintained. Although wholesale wind and solar electricity are cheaper than retail electricity, their capacity factors are too low for economical process operation. Adding energy storage to increase the capacity factor of solar electricity triples the capital cost from $34.4 million to $112.6 million for a plant making 50 tCO/day. Improving single-pass conversion is not a priority because it leads to selectivity loss in contemporary membrane electrode assemblies, giving an optimum conversion at <15%. To overcome this limitation, we identify the opportunity to modify reactor design to improve CO₂ availability to the catalyst. Decoupling selectivity and single-pass conversion by moving away from a plug flow reactor design, without adding cell voltage, would reduce the base case levelized cost of $1.22/kgCO to $0.97/kgCO and save 36% on capital cost. Finally, we conclude that resolving the “carbonate crossover problem” in neutral electrolytes is not a priority for improving the levelized cost of product. | Shashwati da Cunha; Joaquin Resasco | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Petrochemicals; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668eaa4c01103d79c59ceaf6/original/insights-from-techno-economic-analysis-can-guide-the-design-of-low-temperature-co2-electrolyzers-towards-industrial-scaleup.pdf |
60c757344c891974b8ad4984 | 10.26434/chemrxiv.14378897.v1 | A Soft On/Off Switch Based on the Electrochemically Reversible H-J Interconversion of a Floating Porphyrin Membrane | <p>Soft molecular assemblies that respond reversibly to external stimuli are attractive materials as on/off switches, in optoelectronic, memory and sensor technologies. In this article, we present the reversible structural rearrangement of a soft porphyrin membrane under an electrical potential stimulus in the absence of solid-state architectures. The free-floating porphyrin membrane lies at the interface between immiscible aqueous and organic electrolyte solutions and is formed through interfacial self-assembly of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrins (ZnPor). A potential difference between the two immiscible electrolyte solutions induces the intercalation of bis(triphenylphosphoranylidene)ammonium cations from the organic electrolyte that exchange with protons in the porphyrin membrane. In situ UV/vis absorbance spectroscopy shows that this ionic intercalation and exchange induces a structural interconversion of the individual porphyrin molecules in the membrane from an H- to a J-type molecular configuration. These structural rearrangements are reversible over 30 potential cycles. In situ polarisation-modulation fluorescence spectroscopy further provides clear evidence of structural interconversion of the porphyrin membrane, as intercalation of the organic electrolyte cations significantly affects the latter’s emissive properties. By adjusting the pH of the aqueous phase, additional control of the electrochemically reversible structural interconversion can be achieved, with total suppression at pH 3.<br /></p> | Andrés F. Molina-Osorio; Sho Yamamoto; Alonso Gamero-Quijano; Hirohisa Nagatani; Micheal D. Scanlon | Electrochemistry - Mechanisms, Theory & Study; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757344c891974b8ad4984/original/a-soft-on-off-switch-based-on-the-electrochemically-reversible-h-j-interconversion-of-a-floating-porphyrin-membrane.pdf |
66b4b4345101a2ffa88b5e42 | 10.26434/chemrxiv-2024-3nmrr | Structure and transport properties of LiTFSI-based deep eutectic electrolytes from machine learning interatomic potential simulations | Deep Eutectic Solvents have recently gained significant attention as versatile and inexpensive materials with many desirable properties and a wide range of applications. In particular, their similar characteristics to ionic liquids, make them a promising class of liquid electrolytes for electrochemical applications. In this study, we utilized a local equivariant neural network interatomic potential model to study a series of deep eutectic electrolytes based on lithium bis(trifluoromethanesulfonyl)imide (LiTFSI) by molecular dynamics (MD) simulations. The use of equivariant features combined with the strict locality result in highly accurate, data-efficient and scalable interatomic potentials enabling large-scale MD simulations of these liquids with first-principles accuracy. Comparing the structure of the liquids to reported results from classical force field (FF) simulations indicates that ion–ion interactions are not accurately characterized by FFs. Furthermore, close contacts between lithium ions bridged by oxygen atoms of two amide molecules are observed. The computed cationic transport numbers and the estimated ratios of Li–amide lifetime (τ[Li–amide]) to the amide’s rotational relaxation time (τ[R]), combined with the ionic conductivity trend, suggest a more structural Li+ transport mechanism in the LiTFSI:urea mixture through exchange of amide molecules. However, a vehicular transport could have a larger contribution to Li+ ion transport in the LiTFSI:N-methylacetamide electrolyte. Moreover, comparable diffusivities of Li+ cation and TFSI – anion and a τ[Li–amide]/τ[R] close to unity, indicate that vehicular and solvent-exchange mechanisms have rather equal contributions to Li+ ion transport in the LiTFSI:acetamide system. | Omid Shayestehpour; Stefan Zahn | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b4b4345101a2ffa88b5e42/original/structure-and-transport-properties-of-li-tfsi-based-deep-eutectic-electrolytes-from-machine-learning-interatomic-potential-simulations.pdf |
66f70cc7cec5d6c1427070d7 | 10.26434/chemrxiv-2024-lxg2w | Precise Synthesis of Ultra-Dense Bottlebrush Polymers Unearths Unique Trends in Lyotropic Ordering | Biomacromolecular networks with multiscale fibrillar structures are characterized by exceptional mechanical properties, mak-ing them attractive architectures for synthetic materials. However, there is a dearth of synthetic polymeric building blocks capable of forming similarly structured networks. Bottlebrush polymers (BBPs) are anisotropic graft polymers with the po-tential to mimic and replace biomacromolecules such as tropocollagen for the fabrication of synthetic fibrillar networks; however, a longstanding limitation of BBP’s has been the lack of rigidity necessary to access the lyotropic ordering that underpins the formation of collagenous networks. While the correlation between BBP rigidity and grafting density is well-established, synthetic approaches to rigidify BBPs by increased grafting density are underdeveloped. To address this gap in synthetic capability, we report the synthesis of novel macroinitiators that provide well-defined BBPs with unprecedentedly high grafting density. A suite of light scattering techniques are used to correlate macromolecular rigidity with grafting archi-tecture and density, and demonstrate for the first time that poly(norbornene) BBPs exhibit long-range lyotropic ordering as a result of their rod-like character. Specifically, the newly reported ultra-densely grafted structures, preparable on multigram scale, form hexagonal arrays while conventional BBPs do not, despite showing long range spatial correlations. These results implicate the central role of density and entanglement in the solution phase assembly of BBPs and provides new fundamen-tal insight that is broadly relevant to the fabrication and performance of BBP derived materials, spanning biomedical research to photonic materials and thermal management technologies. Furthermore, these newly reported liquid crystalline BBPs pro-vide a structural template to explore the untapped potential of the bottom-up assembly of semiflexible networks and are ul-timately intended to provide a modular route to hierarchically structured biomimetic materials. | Timea Kolozsvary; Phillip Kohl; Tianyu Li; David Gillespie; Youli Li; Ben McDonald | Polymer Science; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f70cc7cec5d6c1427070d7/original/precise-synthesis-of-ultra-dense-bottlebrush-polymers-unearths-unique-trends-in-lyotropic-ordering.pdf |
658fcdcf9138d23161cd4482 | 10.26434/chemrxiv-2024-dv24j | A Closed Bipolar Electrochemical Cell for the Interrogation of BDD Single Particles: Electrochemical Advanced Oxidation | A closed bipolar electrochemical cell containing two conductive boron-doped diamond (BDD) particles of size 250 – 350 um, produced by high-pressure high-temperature (HPHT) synthesis, has been used to demonstrate the applicability of single BDD particles for electrochemical oxidative degradation of the dye, methylene blue (MB). The cell is fabricated using stereolithography 3D printing and the BDD particles are located at either end of a solution excluded central channel. Platinum wire electrodes placed in each of the two outer solution compartments are used to drive electrochemical reactions at the two BDD particles, which, under bipolar conditions do not require direct electrical connection to a potential source. Experiments using ultra high-performance liquid chromatography coupled with mass spectrometry (UHPLC-MS) show that the anodic pole BDD particle is able to electrochemically remove > 99% of the dye (originally present at 1 x 10-4 M) to undetectable UHPLC-MS products in 600 s. Monitoring of the time dependant change in MB peak area, from the UHPLC chromatograms, enables a pseudo first order rate constant of 0.54 min-1 to be determined for MB removal. Given the large scale at which such particles can be produced (tonnes), such data bodes well for scale up opportunities using HPHT-grown BDD particles, where the particles can be assembled into high surface area electrode formats. | Anna Dettlaff; Joshua Tully; Georgia Wood; Deep Chauhan; Ben Breeze; Lijiang Song; Julie Macpherson | Physical Chemistry; Materials Science; Analytical Chemistry; Carbon-based Materials; Analytical Chemistry - General; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658fcdcf9138d23161cd4482/original/a-closed-bipolar-electrochemical-cell-for-the-interrogation-of-bdd-single-particles-electrochemical-advanced-oxidation.pdf |
6728f9ef5a82cea2fa046f8e | 10.26434/chemrxiv-2024-gt89f | Exploring the Synthesis and Properties of Fluorinated Cationic Triangulenes and Their Precursors | Fluorination of tris(2,6-dimethoxyphenyl)-methylium ((DMP)3C+) was achieved through the partial defluorination of the methyl 2,3,5,6-tetrafluorobenzoate via nucleophilic aromatic substitution. Using the fluorinated 2F((DMP)3C+) as a precursor, fluorinated tetramethoxy- and dimethoxyquin- acridinium salts (2F4 and 2F5 respectively) and trioxo-, azadioxo-, and diazaoxo- triangulenium salts (2F6, 2F7 and 2F8 respectively) were synthesized successfully in good to moderate yields. Fluorination induced significant red shifts in absorption (16 to 29 nm) and emission (13 to 41 nm) maxima, and increased electrophilicity as evidenced by lower reduction potentials. X-ray structural analysis showed distinct packing patterns compared to the non-fluorinated analogues, indicating the presence of molecular dipoles. | Ramandeep Kaur; Jules Moutet; Thomas L. Gianetti | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6728f9ef5a82cea2fa046f8e/original/exploring-the-synthesis-and-properties-of-fluorinated-cationic-triangulenes-and-their-precursors.pdf |
658646989138d231614e7cde | 10.26434/chemrxiv-2023-w19vx | Computational Insights into Water Oxidation Mechanisms on Rutile SnO2(110) that Form Ozone | Electrochemical ozone production (EOP) is intriguing as a sustainable route for gen- erating powerful chemical oxidants and disinfectants, but atomic scale details of EOP mechanisms on nickel and antimony doped SnO2 (NATO) electrocatalysts have been unclear. We used computational quantum chemistry to evaluate the thermodynamic feasibility of six-electron water oxidation steps based on 1) the adsorbate evolving mech- anism (AEM) and the lattice oxygen mechanism (LOM). This work provides atomic scale insights into the atomic scale nature of tin oxide-based electrocatalysts under highly oxidizing potentials and how and why dopants would influence EOP catalysis on NATO. Importantly, we identify that EOP adsorbates are significantly stabilized by explicit hydrogen bonding networks that arise from H* and OH* intermediates that form from dissociated water molecules, likely over the entire SnO2 surface. The disso- ciated water network is essential to developing computational catalysis model for EOP that is qualitatively consistent with experimental observations. | Lingyan Zhao; Rayan Alaufey; Qin Wu; Maureen Tang; John Keith | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658646989138d231614e7cde/original/computational-insights-into-water-oxidation-mechanisms-on-rutile-sn-o2-110-that-form-ozone.pdf |
61007116171fc77d77b93785 | 10.26434/chemrxiv-2021-b9vg4 | Biological evaluation and spectral characterization of novel tetracenomycin X congener | The aromatic polyketide tetracenomycin X (TcmX) was recently found to be a potent inhibitor of protein synthesis, whose binding site is located in a unique locus within the tunnel of the large ribosomal subunit. The distinct mode of action makes this relatively narrow class of macrolides promising for drug development, in our quest to prevent the spread of drug resistant pathogens. Here we report the isolation and structure elucidation of novel natural tetracenomycin X congener – 6-hydroxytetraceonomycin X (6-OH-TcmX). In contrast to TcmX, 6-OH-TcmX exhibited lower antimicrobial and cytotoxic activity, but comparable in vitro protein synthesis inhibition ability. A survey on spectral properties of tetracenomycins showed profound differences in both UV-absorption and fluorescence spectra of TcmX and 6-OH-TcmX, suggesting the significant influence of 6-hydroxylation on tetracenomycin chromophore. Nonetheless, characteristic spectral properties of tetracenomycins make them suitable candidates as a foundation for semi-synthetic drug development (e.g., for targeted delivery, theranostics or cell imaging). | Vera A. Alferova; Tinashe P. Maviza; Mikhail B. Biryukov; Yuliya B. Zakalyukina; Dmitrii A. Lukianov; Dmitry A. Skvortsov; Lilia A. Vasilyeva; Vadim N. Tashlitsky; Vladimir I. Polshakov; Olga A. Dontsova; Petr V. Sergiev; Vladimir A. Korshuna; ILya A. Osterman | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61007116171fc77d77b93785/original/biological-evaluation-and-spectral-characterization-of-novel-tetracenomycin-x-congener.pdf |
670fade151558a15ef3f0015 | 10.26434/chemrxiv-2024-xkxd5 | Efficient Training of Neural Network Potentials for Chemical and Enzymatic Reactions by Continual Learning | The machine learning (ML) method has emerged as an efficient surrogate for high-level electronic structure theory, offering precision and computational efficiency. However, the construction of a general force field remains challenging due to the vast conformational and chemical space. Training data sets typically cover only a limited region of this space, resulting in poor extrapolation performance. Traditional strategies inadequately address this problem by training models from scratch using both old and new datasets. In addition, model transferability is crucial for general force field construction. Existing ML force fields, designed for closed systems with no external environmental potential, exhibit limited transferability to complex condensed phase systems such as enzymatic reactions, resulting in inferior performance and high memory costs. Our ML/MM model based on the Taylor expansion of the electrostatic operator showed high transferability between reactions in several simple solvents. In this work, we extend the strategy to enzymatic reactions to explore transferability between more complex heterogeneous environments. In addition, we also apply continual learning strategies based on memory datasets to enable autonomous and on-the-fly training on a continuous stream of new data. By combining these two methods, we can construct a more general force field more efficiently. | Yao-Kun Lei; Kiyoshi Yagi; Yuji Sugita | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670fade151558a15ef3f0015/original/efficient-training-of-neural-network-potentials-for-chemical-and-enzymatic-reactions-by-continual-learning.pdf |
62704c0eef2ade2756464264 | 10.26434/chemrxiv-2022-9v4j1 | Biocatalytic Carbene Transfer Using Diazirines | Biocatalytic carbene transfer from diazo compounds is a versatile strategy in asymmetric synthesis. However, the limited pool of stable diazo compounds constrains the variety of accessible products. To overcome this restriction, we have engineered variants of Aeropyrum pernix protoglobin (ApePgb) that use diazirines as carbene precursors. While the enhanced stability of diazir- ines relative to their diazo isomers enables access to a diverse array of carbenes, they have previously resisted catalytic activation. Our engineered ApePgb variants represent the first example of catalysts for selective carbene transfer from these species at room temperature. The structure of an ApePgb variant, determined by microcrystal electron diffraction (MicroED), reveals that evolution has enhanced access to the heme active site to facilitate this new-to-nature catalysis. Using readily prepared aryl diazirines as model substrates, we demonstrate the application of these highly-stable carbene precursors in biocatalytic cyclopropanation, N–H insertion, and Si–H insertion reactions. | Nicholas Porter; Emma Danelius; Tamir Gonen; Frances Arnold | Catalysis; Chemical Engineering and Industrial Chemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62704c0eef2ade2756464264/original/biocatalytic-carbene-transfer-using-diazirines.pdf |
60c7513c702a9b6f9818bef0 | 10.26434/chemrxiv.13140053.v1 | Hole-Mediated PhotoRedox Catalysis: Tris(p-Substituted)biarylaminium Radical Cations as Tunable, Precomplexing and Potent Photooxidants | <p>Electrochemically-mediated
Photoredox Catalysis emerged as a powerful synthetic technique in recent years,
overcoming fundamental limitations of electrochemistry and photoredox catalysis
in the single electron transfer activation of small organic molecules. However,
the mechanism of how photoexcited radical ion species with ultrashort
(picosecond-order) lifetimes could ever undergo productive photochemistry has
eluded synthetic chemists. We report tri(<i>para</i>-substituted)biarylamines as
a tunable class of electroactivated photocatalysts that become superoxidants in
their photoexcited states, even able to oxidize molecules (such as
dichlorobenzene and trifluorotoluene) beyond the solvent window limits of
cyclic voltammetry. Furthermore, we demonstrate that precomplexation not only
permits the excited state photochemistry of tris(<i>para</i>-substituted)biarylaminium
cations, but enables and rationalizes the surprising photochemistry of their <i>higher-order</i>
doublet (D<i><sub>n</sub></i>) excited states.</p> | Shangze Wu; Jonas Zurauskas; Michal Domanski; Patrick Hitzfeld; Valeria Butera; Daniel Scott; Julia Rehbein; Ajeet Kumar; Erling Thyrhaug; Jürgen Hauer; Joshua Barham | Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2020-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7513c702a9b6f9818bef0/original/hole-mediated-photo-redox-catalysis-tris-p-substituted-biarylaminium-radical-cations-as-tunable-precomplexing-and-potent-photooxidants.pdf |
643e535208c86922ff355db1 | 10.26434/chemrxiv-2023-zshqp | Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs | Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide represent the most typical cereblon (CRBN) recruiters that are frequently utilized in proteolysis-targeting chimera (PROTAC) design. These CRBN binders, however, cause degradation of IMiD neosubstrates and are innately unstable as they undergo hydrolytic degradation under mild conditions. Here we present the systematic approach towards novel non-phthalimide CRBN binders that were obtained via the simultaneous optimization of their physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features. Our efforts led to the discovery of conformationally-locked benzamide-type derivatives that mimic the interactions of the natural CRBN degron, displayed improved chemical stability, and showed a favorable selectivity profile with respect to the recruitment of neosubstrates. The usefulness of the most potent ligands was demonstrated by their conversion into potent degraders of BRD4 and HDAC6 that displayed superiority compared to previously described benchmark PROTACs. We show that our diversified CRBN ligands offer opportunities to design chemically inert proximity-inducing compounds with reduced neomorphic E3 ligase activity of CRBN. | Christian Steinebach; Izidor Sosič; Aleša Bricelj; Arunima Murgai; Luca Bischof; Yuen Lam Dora Ng; Christopher Heim; Samuel Maiwald; Matic Proj; Rabea Voget; Felix Feller; Janez Košmrlj; Annika Schmidt; Patricia Lemnitzer; Finn K. Hansen; Michael Gütschow; Jan Krönke; Marcus D. Hartmann | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643e535208c86922ff355db1/original/leveraging-ligand-affinity-and-properties-discovery-of-novel-benzamide-type-cereblon-binders-for-the-design-of-prota-cs.pdf |
644f43b56ee8e6b5ed62cfea | 10.26434/chemrxiv-2023-dlv5t | Computational Prediction of Stacking Mode in Conductive Two-Dimensional Metal-Organic Frameworks: An Exploration of Chemical and Electrical Property Changes | Conductive two-dimensional metal-organic frameworks (2D MOFs) have attracted interest as they induce strong charge delocalization and improve charge carrier mobility and concentration. However, no clear explanation has been put forth on why the stacking mode varies for each 2D MOF, and characterizing their stacking mode depends on expensive and time-consuming experimental measurements. Here, we construct a potential energy surface (PES) map database for 36 2D MOFs using density functional theory (DFT) for the experimentally synthesized and non-synthesized 2D MOFs to predict their stacking mode. The DFT PES results successfully predict the experimentally synthesized stacking mode with an accuracy of 92.9% and explain the coexistence mechanism of dual stacking modes in a single compound. Furthermore, we analyze the chemical (i.e. host-guest interaction) and electrical (i.e. electronic structure) property changes affected by stacking mode. The DFT results show that the host-guest interaction can be enhanced by the transition from AA to AB stacking, taking H2S gas as a case study. The electronic band structure calculation confirms that as AB stacking displacement increases, in-plane charge transport pathway is reduced while the out-of-plane charge transport pathway is maintained or even increased. These results indicate that there is a trade-off between chemical and electrical properties in accordance with the stacking mode. | Mingyu Jeon; Minhyuk Kim; Joon-Seok Lee; Honghui Kim; Seon-Jin Choi; Hoi Ri Moon; Jihan Kim | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644f43b56ee8e6b5ed62cfea/original/computational-prediction-of-stacking-mode-in-conductive-two-dimensional-metal-organic-frameworks-an-exploration-of-chemical-and-electrical-property-changes.pdf |
67647707fa469535b91fac66 | 10.26434/chemrxiv-2024-d8jv1 | Potential of sorption-enhanced ammonia synthesis – An equilibrium and reactor modeling study | Ammonia production is one of the most important industrial chemical processes, but the synthesis reaction is strongly limited by chemical equilibrium. This is commonly compensated by applying high pressures, but large recycle ratios and purging losses are still unavoidable. Equilibrium limitations can alternatively be evaded by sorption-enhancement, where NH3 is selectively removed from the reaction mixture by a solid sorbent material. One material class commonly applied in this approach are metal halides like MgCl2, as they typically show high NH3 capacity even at elevated temperatures. In this study, a thermodynamic equilibrium model based on Gibbs energy minimization was established that is able to predict the simultaneous NH3 synthesis and sorption equilibrium. After parameterization for metal chloride-based sorbents, the model is used to estimate the potential extent of sorption-enhancement of the NH3 synthesis in equilibrium. For kinetic studies under realistic operation conditions, a reactor model was established using kinetics for both iron and ruthenium-based catalysts. Simulations reveal that near-full conversion is possible in sorption-enhanced NH3 synthesis under a wide range of realistic operating conditions. In that way the integration of a sorbent material into the NH3 synthesis reaction results in increased conversion, but at the same time also allows for a higher NH3 productivity. While it has been demonstrated experimentally before, these findings quantify and emphasize the vast potential of sorption-enhanced NH3 synthesis under a wide range of conditions. | Theresa Kunz; Thomas Cholewa; Robert Güttel | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Thermodynamics (Chem. Eng.); Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67647707fa469535b91fac66/original/potential-of-sorption-enhanced-ammonia-synthesis-an-equilibrium-and-reactor-modeling-study.pdf |
660c40239138d23161f97a2a | 10.26434/chemrxiv-2024-q1n61-v2 | Molecular Glues & Bifunctional Compounds:
Therapeutic Modalities Based on Induced Proximity
| This Perspective explores molecular glues and bifunctional compounds – proximity-inducing compounds – and offers a framework to understand and exploit their similarity to hot spots, missense mutations, and posttranslational modifications (PTMs). | Stuart Schreiber | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660c40239138d23161f97a2a/original/molecular-glues-bifunctional-compounds-therapeutic-modalities-based-on-induced-proximity.pdf |
628a576987d01f33ddee159b | 10.26434/chemrxiv-2022-t1xn4 | N-(N-Morpholindithio)phthalimide: A Shelf-Stable, Bilateral Platform Molecule for Accessing Diverse Unsymmetrical Disulfides | A new, shelf-stable, and odorless bilateral disulfurating platform molecule, N-(N-morpholindithio)phthalimide, was developed. This reagent can be easily prepared in high yields on a gram scale in a single step from the readily available N,N'-dithiobis(phthalimide). The two leaving groups bound to sulfur were selectively transformed: the morpholino and phthalimide groups were transformed in the presence and absence of H+, respectively. The platform molecule enabled the facile replacement of the morpholino moiety with various substituents, such as allyl (Csp3), aryl (Csp2), and alkynyl (Csp) groups, affording the products in high yields. The wide substrate scope of these transformations and the transformability of the resulting dithiophthalimide moiety provided rapid access to divergent multi-functionalized unsymmetrical disulfides. These results demonstrate the utility of this method for structural expansion in drug discovery and efficient conjugation in linker chemistry. | Hayato Asanuma; Kazuya Kanemoto; Tokiharu Watanabe; Shin-ichi Fukuzawa | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628a576987d01f33ddee159b/original/n-n-morpholindithio-phthalimide-a-shelf-stable-bilateral-platform-molecule-for-accessing-diverse-unsymmetrical-disulfides.pdf |
616fc2b3f718df5f1ae4afe4 | 10.26434/chemrxiv-2021-v2rcx | Development and Application of ReaxFF Methodology for Understanding the Chemical Dynamics of Metal Carbonates in Aqueous Solutions | A new ReaxFF reactive force field has been developed for metal carbonate systems including Na+, Ca2+, and Mg2+ cations and the CO32- anion. This force field is fully transferable with previous ReaxFF water and water/electrolyte descriptions. The Me-O-C three-body valence angle parameters and Me-C non-reactive parameters of the force field have been optimized against quantum mechanical calculations including equations of states, heats of formation, heats of reaction, angle distortions and vibrational frequencies. The new metal carbonate force field has been validated using molecular dynamics simulations to study solvation and reactivity of metal and carbonate ions in water at 300 K and 700 K. The coordination radius and self-diffusion coefficient show good consistency with existing experiments and simulations results. The angular distribution analysis explains the structural preference of carbonate ions to form carbonates and bicarbonates, where Na+ predominantly forms carbonates due to lesser angular strain, while Ca2+ and Mg2+ prefer to form bicarbonates monodentate in nature. Residence time distribution analyses on different systems reveal the role of ions in accelerating and decelerating dynamics of water and carbonate ions under different thermodynamic conditions. The formation and dissolution of bicarbonates and carbonates in the solution were explored on the basis of protonation capability in different systems. The nucleation phenomenon of metal carbonates at ambient and supercritical conditions is explained from the perspective of clusters formation over time: Ca2+ ions can form prenucleation clusters at ambient temperature but shows a saturation with temperature, whereas Na+ and Mg2+ ions show rapid increase in cluster size and amount upon increasing time and temperature. | Nabankur Dasgupta; Chen Chen; Adri van Duin | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study; Statistical Mechanics | CC BY NC 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616fc2b3f718df5f1ae4afe4/original/development-and-application-of-reax-ff-methodology-for-understanding-the-chemical-dynamics-of-metal-carbonates-in-aqueous-solutions.pdf |
66340e29418a5379b04b2c07 | 10.26434/chemrxiv-2024-nxrfz | Carbon Dioxide Capture by Niobium Polyoxometalate Fragments | High oxidation state metal cations have diverse roles in carbon dioxide removal (direct air capture and at-the-source) includ-ing providing basic oxygens for chemisorption reactions, direct binding of carbonate, and low-temperature release of CO2 for regeneration of capture media. Moreover, metal oxide systems and aqueous metal-oxo species are stable in harsh condi-tions. Here we demonstrate the carbon capture ability of niobium polyoxometalates (POMs) as aqueous solutions, specifi-cally [Nb6O19]8-, Nb6. Upon exposure of Nb6 solutions to CO2, Nb6 fragments and binds carbonate, evidenced by crystalliza-tion of Nb-carbonate POMs including [Nb22O53(CO3)16]28-and [Nb10O25(CO3)6]12−. While Rb/Cs+ counter cations yielded crystal structures to understand the chemisorption processes, K+ counter cations enabled higher capture efficiency (based on CO3:Nb ratio), as determined by CHN analysis and thermogravimetry-mass spectrometry of the isolated solids. Sum fre-quency generation (SFG) spectroscopy also showed higher carbon capture efficiency of the K-Nb6 solutions at the air-water interface, while small-angle X-ray scattering (SAXS) provided insight into the role of the alkalis in influencing these process-es. Tetramethylammonium counter cations (TMA), like K+, demonstrated high efficiency of carbonate chemisorption at the interface, but SAXS and Raman of the bulk showed a predominance of a Nb24-POM (HxNb24O72, x~9) that can bind car-bonate only minimally, and any carbonate present is likely free bicarbonate instead of Nb-bound. Control experiments show that all carbonate present at the interface is Nb-bound, and the Nb-carbonate species are stabilized by alkalis, demon-strating a synergistic role of alkalis and high oxidation state metal cations in chemisorption of CO2. Of fundamental im-portance, this study presents rare examples of directing POM speciation with a gas, instead of liquid phase acid or base. | Zhiwei Mao; Mokhtar Rashwan; Eduard Garrido-Ribo; Makenzie Nord; Lev Zakharov; Wesley Surta; Ahmet Uysal; May Nyman | Inorganic Chemistry; Coordination Chemistry (Inorg.); Kinetics and Mechanism - Inorganic Reactions; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66340e29418a5379b04b2c07/original/carbon-dioxide-capture-by-niobium-polyoxometalate-fragments.pdf |
60c744344c89195503ad2766 | 10.26434/chemrxiv.8874404.v2 | Highly Anisotropic Thermal Transport in LiCoO2 | <div>LiCoO<sub>2</sub> is the prototype cathode in lithium ion batteries. It adopts a crystal structure with alternating Li<sup>+</sup> and CoO<sub>2</sub><sup>-</sup> layers along the hexagonal <0001> axis. It is well established that ionic and electronic conduction is highly anisotropic; however, little is known regarding heat transport. We analyse the phonon dispersion and lifetimes of LiCoO<sub>2</sub> using anharmonic lattice dynamics based on quantum chemical force constants. Around room temperature, the thermal conductivity in the hexagonal ab plane of the layered cathode is ≈ 6 times higher than that along the c axis based on the phonon Boltzmann transport. The low thermal conductivity (< 10Wm<sup>-1</sup>K<sup>-1</sup>) originates from a combination of short phonon lifetimes associated with anharmonic interactions between the octahedral face-sharing CoO<sub>2</sub><sup>-</sup> networks, as well as grain boundary scattering. The impact on heat management and thermal processes in lithium ion batteries based on layered positive electrodes is discussed.</div> | Hui Yang; Jia-Yue Yang; Christopher Savory; Jonathan Skelton; Benjamin Morgan; David Scanlon; Aron Walsh | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744344c89195503ad2766/original/highly-anisotropic-thermal-transport-in-li-co-o2.pdf |
66a76fcac9c6a5c07a656f83 | 10.26434/chemrxiv-2024-q5fwg | Wetting of a dynamically patterned surface is a time-dependent matter | Wetting of a dynamically patterned surface is a time-dependent matter
In nature and many technological applications, aqueous solutions are in contact with patterned surfaces, which are dynamic over timescales spanning from ps to μs. In biology, exposed polar and apolar residues of biomolecules form a pattern, which fluctu- ates in time due to sidechain and conformational motions. At metal/ and oxide/water interfaces the pattern is formed by surface topmost atoms, and fluctuations are due to, e.g., local surface polarization and rearrangements in the adsorbed water layer. All these dynamics have the potential to influence key processes such as wetting, energy relaxation, and biological function. Yet, their impact on the water H-bond network remains elusive. Here, we leverage on molecular dynamics to address this fundamental question at a Self-Assambled Monolayer (SAM)/water interface, where ns dynamics is induced by frustrating SAM-water interactions via methylation of the terminal -OH groups. We find that surface dynamics couples to the water H-bond network, inducing a response on the same ns timescale. This leads to time fluctuations of local wetting, oscillating from hydrophobic to hydrophilic environments. Our results suggest that more than average properties, it is the local—both in time and space—solvation that determines the chemical-physical properties of dynamically patterned surfaces in water. | Wanlin Chen; Ondrej Kroutil; Milan Predota; Simone Pezzotti; Marie-Pierre Gaigeot | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a76fcac9c6a5c07a656f83/original/wetting-of-a-dynamically-patterned-surface-is-a-time-dependent-matter.pdf |
656d87a629a13c4d479c2eec | 10.26434/chemrxiv-2023-vk4f4 | A Unique strategy for probing in-situ NO for screening the neuroinflammatory phenotypes against SARS-CoV-2 RNA in phagocytotic microglia | The severe acute respiratory (SARS-CoV-2) jeopardized public health by causing significant morbidity and mortality among people with pre-existing physiological dysfunction caused by aging, diabetes, hypertension, and obesity. Besides, patients with severe infections are more likely to have neuro-inflammation and higher mortality risk. Neuroinflammation is majorly caused by activating the brain’s residential macrophage cells called microglia, which increases the generation of reactive species including nitric oxide via the iNOS pathway. In addition, NO regulates lysosomal functions and exhibits complex effects on lysosomal machinery to neutralize foreign pathogens through phagocytosis and improve host-defense inflammatory response. To date, lack of efficient probes to monitor lysosomal NO and phagocytosis processes in the least explored human microglia during SARS-CoV-2 infection. Herein, a unique design strategy was adopted for the first time by avoiding the conventional control amination reaction approach to develop lysosomal specific-NO probe, PDM-NO, which can discriminate activated microglia from its resting state. The non-fluorescent probe at physiological pH exhibits turn-on response towards NO only at lysosomal pH (4.5-5.5). PDM-NO demonstrated lysosomal specificity in activated HMC3 cells and enabled monitoring phagocytosis process with a several advantages compared to commercial E. coli bio-particles. Moreover, this probe can effectively map the overexpression and dynamics of lysosomal NO levels against SARS-CoV-2 RNA virus-induced neuroinflammation in HMC3. Thus, lysosome-specific PDM-NO is a potential fluorescent marker for detecting RNA virus infection in human microglia and excellent molecular probe for monitoring phagocytosis during neuroinflammation. It could be a useful commercial probe in future for screening viral activity and neuro-inflammation for diagnosis of neurological diseases. | Subrata Munan; Abir Mondal; Shailja Singh; Soumya Pati; Animesh Samanta | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Imaging; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656d87a629a13c4d479c2eec/original/a-unique-strategy-for-probing-in-situ-no-for-screening-the-neuroinflammatory-phenotypes-against-sars-co-v-2-rna-in-phagocytotic-microglia.pdf |
60c7586c567dfea58aec685b | 10.26434/chemrxiv.14544555.v1 | Internal Conversion of the Anionic GFP Chromophore: In and Out of the I-twisted S1/S0 Conical Intersection Seam | <p>The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic <i>p</i>-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI<sup>–</sup>). Its propensity to undergo <i>Z/E</i> photoisomerization following excitation to the S<sub>1</sub>(pp<sup>*</sup>) state is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. However, key dynamical aspects of this process and its range of tunability still remain elusive. Here, we investigate the internal conversion behavior intrinsic to HBDI<sup>–</sup> with focus on competing deactivation pathways, rate and yield of photoisomerization. Based on non-adiabatic dynamics simulations, we confirm that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways can account for the three decay constants reported experimentally, leading to competing ultrafast relaxation along the I-twisted pathway and S<sub>1 </sub>trapping along the P-torsion. The majority of the population (~70%) is transferred to S<sub>0</sub> in the vicinity of two near-symmetry-related minima on the I-twisted intersection seam (MECI-Is). Despite their reactant-biased topographies, our account of inertial effects suggests that isomerization not only occurs as a thermal process on the vibrationally hot ground state but also as a direct photoreaction with a total quantum yield of ~40%.</p><p>By comparing the non-adiabatic dynamics to a photoisomerization committor analysis, we provide a detailed mapping of the intrinsic photoreactivity and dynamical behavior of the two MECI-Is. Our work offers new insight into the internal conversion process of HBDI<sup>–</sup> that enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.</p> | Nanna Holmgaard List; Chey Marcel Jones; Todd J. Martínez | Photochemistry (Physical Chem.); Physical and Chemical Processes; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7586c567dfea58aec685b/original/internal-conversion-of-the-anionic-gfp-chromophore-in-and-out-of-the-i-twisted-s1-s0-conical-intersection-seam.pdf |
62ec0b03659a3f5825343355 | 10.26434/chemrxiv-2022-h5j16 | Intercepting Hydrogen Evolution with Hydrogen-Atom Transfer: Electron-Initiated Hydrofunctionalization of Alkenes | Hydrogen-atom transfer mediated by earth-abundant transition-metal hydrides (M-Hs) has emerged as a powerful tool in organic synthesis. Current methods to generate M-Hs most frequently rely on oxidatively initiated hydride transfer. Herein, we report a reductive approach to generate Co-H, which allows for canonical hydrogen evolution reactions to be intercepted by hydrogen-atom transfer to an alkene. Electroanalytical and spectroscopic studies provided mechanistic insights into the formation and reactivity of Co-H, which enabled the development of two new alkene hydrofunctionalization reactions. | Xiangyu Wu; Cara N. Gannett; Jinjian Liu; Rui Zeng; Luiz F. T. Novaes; Hongsen Wang; Héctor D. Abruña; Song Lin | Organic Chemistry; Catalysis; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec0b03659a3f5825343355/original/intercepting-hydrogen-evolution-with-hydrogen-atom-transfer-electron-initiated-hydrofunctionalization-of-alkenes.pdf |
60c75549bdbb89aa50a3a7cd | 10.26434/chemrxiv.14068094.v1 | Rapid and Accurate Discrimination Between Pure and Adulterated Commercial Indian Honey Brands Using FTIR Spectroscopy and Principal Component Analysis | <p>Four leading commercial Indian honey brands were investigated
using FTIR spectroscopy and principal component analysis for a rapid and
accurate differentiation of pure, mildly adulterated, and highly adulterated
honey brand samples. This study is first of its kind investigating
commercial Indian honey brands using
FTIR and PCA, hence can be used for investigating adulterations in bulk commercial
honey brand samples where sophisticated instrumentations and facilities are not
available.</p> | Bipin Singh; Sanmitra Barman | Spectroscopy (Anal. Chem.); Food; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75549bdbb89aa50a3a7cd/original/rapid-and-accurate-discrimination-between-pure-and-adulterated-commercial-indian-honey-brands-using-ftir-spectroscopy-and-principal-component-analysis.pdf |
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