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65f4089c66c1381729098d48 | 10.26434/chemrxiv-2024-tq22r | AutoTemplate: Enhancing Chemical Reaction Datasets for
Machine Learning Applications in Organic Chemistry | This paper presents AutoTemplate, an innovative data preprocessing protocol, addressing the
crucial need for high-quality chemical reaction datasets in the realm of machine learning
applications in organic chemistry. Recent advances in artificial intelligence have expanded the
application of machine learning in chemistry, particularly in yield prediction, retrosynthesis, and
reaction condition prediction. However, the effectiveness of these models hinges on the integrity
of chemical reaction datasets, which are often plagued by inconsistencies like missing reactants,
incorrect atom mappings, and outright erroneous reactions. AutoTemplate introduces a twostage
approach to refine these datasets. The first stage involves extracting meaningful reaction
transformation rules and formulating generic reaction templates using a simplified SMARTS
representation. This simplification broadens the applicability of templates across various chemical
reactions. The second stage is template-guided reaction verification, where these templates
are systematically applied to validate and correct the reaction data. This process effectively
amends missing reactant information, rectifies atom-mapping errors, and eliminates incorrect
data entries. A standout feature of AutoTemplate is its capability to concurrently identify and
correct false chemical reactions. It operates on the premise that most reactions in datasets are
accurate, using these as templates to guide the correction of flawed entries. The protocol demonstrates
its efficacy across a range of chemical reactions, significantly enhancing dataset quality.
This advancement provides a more robust foundation for developing reliable machine learning
models in chemistry, thereby improving the accuracy of forward and retrosynthetic predictions.
AutoTemplate marks a significant progression in the preprocessing of chemical reaction datasets,
bridging a vital gap and facilitating more precise and efficient machine learning applications in
organic synthesis. Scientific contribution: The proposed automated preprocessing tool for chemical
reaction data aims to identify errors within chemical databases. Specifically, if the errors
involve atom mapping or the absence of reactant types, corrections can be systematically applied
using reaction templates, ultimately elevating the overall quality of the database. | Lung-Yi Chen; Yi-Pei Li | Theoretical and Computational Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f4089c66c1381729098d48/original/auto-template-enhancing-chemical-reaction-datasets-for-machine-learning-applications-in-organic-chemistry.pdf |
65f0819566c1381729db3175 | 10.26434/chemrxiv-2024-r9c2g | Lewis Acid Catalysis Enables Switch from [2π+2σ] to Hetero-[4π+2σ] Cycloaddition Reactivity of Bicyclo[1.1.0]butanes for Spiro- and Bridged-Heterocycle Synthesis | The exploration of the complex chemical diversity of bicyclo[n.1.1]alkanes and their use as benzene bioisosteres has attracted considerable interest in the past 20 years. Regiodivergent syntheses of thiabicyclo[4.1.1]octanes (S-BCOs) and highly substituted bicyclo[2.1.1]hexanes (BCHs) through a Lewis acid-catalyzed formal cycloaddition of bicyclobutanes (BCBs) and 3-benzylideneindoline-2-thione derivatives are established. By using Zn(OTf)2 as the catalyst, the first hetero-(4+3) cycloaddition of BCBs was achieved with broad substrate scope under mild reaction conditions. In contrast, the less electrophilic BCB ester undergo a Sc(OTf)3-catalyzed formal [2π+2σ] reaction with 1,1,2-trisubstituted alkenes to generate BCHs featuring a spirocyclic quaternary carbon center. Furthermore, this innovative protocol has been proven to be useful in the efficient synthesis of an analogue of the lipid-lowering agent Lomitapide. | Ji-Jie Wang; Lei Tang; Yuanjiu Xiao; Wen-Biao Wu; Jian-Jun Feng | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f0819566c1381729db3175/original/lewis-acid-catalysis-enables-switch-from-2-2-to-hetero-4-2-cycloaddition-reactivity-of-bicyclo-1-1-0-butanes-for-spiro-and-bridged-heterocycle-synthesis.pdf |
677eb43afa469535b935c3b6 | 10.26434/chemrxiv-2025-v596v | Enantioselective Total Synthesis of Griseocazine D2 & D3 | The first enantioselective and biomimetic total syntheses of neuroprotective multiprenylated pyrroloindoline-DKP Griseoca-zine D2, and its diastereomeric congener D3, are reported. The 4-step synthetic route is scalable and convergent, resulting in 24% & 32% overall yields of the congeners, respectively. One of the key features of the synthesis is the installation of both C3 and C3´ normal isoprenyl substituents through a catalytic and highly enantioselective dearomative n-isoprenylation of L-tryptophan. Use of this enantioselective strategy overrides the innate substrate selectivities and thereby requires L-tryptophan as a common precursor for both prenylation and farnesylation steps. DKP formation through the coupling of the two halves occurred without epimerization of the stereogenic alpha center of the amino acids. | Subhasish Pradhan; Rajesh Viswanathan | Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677eb43afa469535b935c3b6/original/enantioselective-total-synthesis-of-griseocazine-d2-d3.pdf |
66c79806a4e53c487644c72b | 10.26434/chemrxiv-2024-wrp5z | Defect diffusion graph neural networks for materials discovery in high-temperature, clean energy applications | The migration of crystallographic defects dictates material properties and performance for a plethora of technological applications. Density functional theory (DFT)-based nudged elastic band (NEB) calculations are a powerful computational technique for predicting defect migration activation energy barriers, yet they become prohibitively expensive for high-throughput screening of defect diffusivities. Without introducing hand-crafted (i.e., chemistry- or structure-specific) descriptors, we propose a generalized deep learning approach to train surrogate models for NEB energies of vacancy migration by hybridizing graph neural networks with transformer encoders and simply using pristine host structures as input. With sufficient training data, computationally efficient and simultaneous inference of vacancy defect thermodynamics and migration activation energies can be obtained to compute temperature-dependent vacancy diffusivities and to down-select candidates for more thorough DFT analysis or experiments. Thus, as we specifically demonstrate for potential water-splitting materials, candidates with desired defect thermodynamics, kinetics, and host stability properties can be more rapidly targeted from open-source databases of experimentally validated or hypothetical materials. | Lauren Way; Catalin Spataru; Reese Jones; Dallas Trinkle; Andrew Rowberg; Joel Varley; Robert Wexler; Christopher Smyth; Tyra Douglas; Sean Bishop; Elliot Fuller; Anthony McDaniel; Stephan Lany; Matthew Witman | Theoretical and Computational Chemistry; Materials Science; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c79806a4e53c487644c72b/original/defect-diffusion-graph-neural-networks-for-materials-discovery-in-high-temperature-clean-energy-applications.pdf |
60c7514c842e657c46db3b79 | 10.26434/chemrxiv.13146782.v1 | Quantitative Criterion for AIEgens | We defined two novel descriptors to demonstrate the flexibility<br />of both chemical and electronic structures of organic<br />fluorescence compounds upon excitation. Classification<br />algorithms were introduced to predict the aggregationinduced<br />emission behavior from the chemical structures<br />based on the new descriptors. A dataset was built to train<br />the classifier, which is optimized to 87.3% accuracy finally. | Junyi Gong; Jacky W. Y. Lam; Ben Zhong Tang | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7514c842e657c46db3b79/original/quantitative-criterion-for-ai-egens.pdf |
60c749bd842e650e3ddb2dc9 | 10.26434/chemrxiv.12089415.v1 | Efficacy of an Asynchronous Online Preparatory Chemistry Course: A Post-hoc Analysis | <p>In an ongoing effort to increase
student retention and success in the undergraduate general chemistry course
sequence, a fully online preparatory chemistry course was developed and
implemented at a large public research university. To gain insight about the
efficacy of the online course, post-hoc analyses were carried out in which
student performance on final exams, and performance in the subsequent general
chemistry course were compared between the online cohort and a previous student
cohort who completed the preparatory chemistry course in a traditional lecture format.
Because the retention of less academically prepared students in STEM majors is
a historical problem at the institution in which the online preparatory
chemistry course was implemented, post-hoc analyses were also carried out to
determine if this at-risk group demonstrated similar achievement relative to
the population at large. Multiple linear regression analyses were used
to compare final exam scores and general chemistry course grades between the
online and in-person student cohorts, while statistically controlling for
incoming student academic achievement. Results from these analyses suggest the
fully online course led to increased final exam scores in the preparatory
course (unstandardized <i>B</i> = 8.648, <i>p</i> < 0.001) and higher grades
in the subsequent general chemistry course (unstandardized <i>B</i> = 0.269, <i>p</i>
< 0.001). Notably, students from the lowest
quartile of incoming academic preparation appear to have been more positively
impacted by the online course experience (preparatory chemistry final exam
scores: unstandardized <i>B</i> = 11.103, <i>p</i> < 0.001; general chemistry
course grades: unstandardized <i>B</i> = 0.323, <i>p</i> = 0.002). These
results suggest a fully online course can help improve student preparation for
large populations of students, without resulting in a negative achievement gap
for less academically prepared students. The structure and implementation of
the online course, and the results from the post-hoc analyses will be described
herein. </p> | Jack Eichler; Grace Henbest; Kiana Mortezaei; Teresa Alvelais; Courtney Murphy | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749bd842e650e3ddb2dc9/original/efficacy-of-an-asynchronous-online-preparatory-chemistry-course-a-post-hoc-analysis.pdf |
67dd853e81d2151a0254085e | 10.26434/chemrxiv-2025-3f6br | Topology-Enforced Synthesis of Atomically-Precise Silver Nanoclusters in 3D DNA Lattices | DNA nanotechnology leverages the molecular design resolution of the DNA double helix to fold and tile matter into designer architectures. Recent advances in bioinorganic chemistry have exploited the affinity of soft nucleobase functional groups for silver ions in order to template the growth of silver nanoclusters by templated reduction. The coupling of the spatial resolution of DNA nanotechnology and the atomic precision of DNA-based nanocluster synthesis has not been realized. Here we develop a method using 3D DNA crystals to employ silver-ion-mediated base pairs as nucleation sites for atomically-precise nanocluster growth. By leveraging the topology of DNA tensegrity triangles, we provide a mesoporous 3D lattice that is robust to reducing conditions, enabling precise spatial templating. Use of in situ confocal fluorescence microscopy allows for the direct observation of reaction kinetics and reconstruction of the optical bandgap. Control over reaction time and stoichiometry, base pair identity, and buffer composition enable precise tuning of the atomic composition and optical properties of the ensuing nanoclusters. The resulting crystals are of diffraction quality, yielding molecular structures of Ag4 and Ag6 in 3D. Inter-cluster distances of less than 2 nm show strong plasmonic coupling, with red shifting observed relative to literature standards. We anticipate that these results will yield advances in materials synthesis, DNA-based plasmonic crystals, and optically-active nanoelectronics. | Lara Perren; Karol Woloszyn; Jordan Janowski; Laibah Faiaz; Vidya R. Singh; Mara Jaffe; Chengde Mao; James W. Canary; Yoel P. Ohayon; Ruojie Sha; Simon Vecchioni | Materials Science; Inorganic Chemistry; Nanoscience; Optical Materials; Nanostructured Materials - Nanoscience; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd853e81d2151a0254085e/original/topology-enforced-synthesis-of-atomically-precise-silver-nanoclusters-in-3d-dna-lattices.pdf |
6503fdae99918fe537fb5820 | 10.26434/chemrxiv-2023-004rm-v2 | Pseudo-equilibrium equations for calcium phosphate precipitation with multi-unit particles | In the reaction of calcium phosphate precipitation from a near-neutral solution, an amorphous phase and hydroxyapatite nanoparticles appear successively, and the reaction system containing either of the two kinds of precipitates is in a non-equilibrium state. Here, we report an extension of our previous study on the relationship between a precipitate and the corresponding ionic product in pseudo-equilibrium states. We employed two series of reaction systems, collected samples at various stages, and analyzed the solution chemistry data on the basis of a simplified model of reaction. We derived two types of pseudo-equilibrium equations from the two series, respectively. These equations reveal the multiple structural units in a precipitate particle and correlate the ionic product with the surface proportion of a structural unit (m). By means of a particle-surface equation, we further related the surface proportion to the whole particle. Notably, the two types of pseudo-equilibrium constants have the common expression of “Kd = ionic product” if the number of the structural units (u) gets large enough. The concept of the multi-unit particle may shed new light on the study of precipitation reactions of other slightly soluble salts. Moreover, the relationship between the ionic product and the surface proportion of a structural unit is not only fundamental in chemistry, but may also apply to the non-equilibrium systems in nature and biology, such as marine sedimentation and human vascular calcification. | Tian-Lan ZHANG | Physical Chemistry; Inorganic Chemistry; Theory - Inorganic; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6503fdae99918fe537fb5820/original/pseudo-equilibrium-equations-for-calcium-phosphate-precipitation-with-multi-unit-particles.pdf |
61da1f94636cc93b7d438223 | 10.26434/chemrxiv-2022-s0p9c | Dynamics of small molecules within the F127 PEO-PPO-PEO triblock copolymer gel and sol phases studied at the molecular scale | The dynamics of naphthalene derivatives with different hydrophobicities bound to F127 polyethyleneoxide-polypropyleneoxide-polyethyleneoxide (PEO-PPO-PEO) micelles in the gel and sol phases were studied using a quenching methodology for the triplet excited states of the naphthalenes. Studies with triplet excited states probe a larger reaction volume than the volumes accessible when using fluorescent singlet excited states. The use of triplet excited states enables the determination of the dynamics between different compartments of a supramolecular system, which in the case of F127 micelles are the micellar core, the micellar corona and the aqueous phase. This report includes laser flash photolysis studies for the four naphthalene derivatives in the F127 gel and sol phases. The triplet excited states were quenched using the nitrite anion as the quenchers. The association and dissociation rate constants of the naphthalenes from the micelles and the quenching rate constants for the naphthalenes bound to the micelles were determines from the curved quenching plot (observed decay rate constant vs. nitrite concentration). | Suma S. Thomas; Helia Hosseini-Nejad; Cornelia Bohne | Physical Chemistry; Chemical Kinetics; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61da1f94636cc93b7d438223/original/dynamics-of-small-molecules-within-the-f127-peo-ppo-peo-triblock-copolymer-gel-and-sol-phases-studied-at-the-molecular-scale.pdf |
6116e7d830231ae1fc0997cd | 10.26434/chemrxiv-2021-3hs3t | Light-Driven Reduction of Aromatic Olefins in Aqueous Media Catalysed by Aminopyridine Cobalt Complexes. | A catalytic system based on earth-abundant elements that efficiently hydrogenates aryl olefins using visible light as driving-force and H2O as the sole hydrogen atoms source is reported. The catalytic system involves a robust and well-defined aminopyridine cobalt complex and a heteroleptic Cu photoredox catalyst. The system shows the reduction of styrene in aqueous media with a remarkable selectivity (> 20000) versus water reduction (WR). Reactivity and mechanistic studies support the formation of a [Co-H] intermediate, which reacts as a hydrogen transfer agent (HAT). Synthetically useful deuterium-labelled compounds can be straightforwardly obtained by replacing H2O with D2O and using only catalysts based on earth-abundant elements. Moreover, the dual photocatalytic system and the photocatalytic conditions can be rationally designed to tune the selectivity for aryl olefin vs aryl ketone reduction; not only by changing the structural and electronic properties of the cobalt catalysts, but also by modifying the reduction properties of the light-harvesting system | Julio Lloret-Fillol; Carla Casadevall; David Pascual; Jordi Aragón; Arnau Call; Alicia Casitas; Irene Casademont-Reig | Organic Chemistry; Inorganic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6116e7d830231ae1fc0997cd/original/light-driven-reduction-of-aromatic-olefins-in-aqueous-media-catalysed-by-aminopyridine-cobalt-complexes.pdf |
60c74ed8bdbb89508fa39c7a | 10.26434/chemrxiv.12813254.v1 | Inhibition of Protease of Novel Corona Virus by Designed Noscapines: Molecular Docking and ADMET Studies | <p>Nowadays, many people were dying due to infectious
coronavirus diseases (COVID-19). It belongs to the betacoronavirus family and
also known as SARS-CoV-2. However, COVID-19 is a new form that has some basic
difference in the genome which makes it more lethal and infectious. In
transmitted in human in late December 2019 and it infected about 20 million till
date. Its genome is composed of positive-sense single-stranded RNA, which
encodes for the poly-protein. This poly-protein further cleaved into various
components of the virus to make the numerous copy of the virus. There are many
more similarities in their genome among the SARS-CoV-2, SARS-CoV, MERS-CoV.
However, protease proteins are responsible for the cleavage and hence, COVID-19
main protease is a prime therapeutic target. To date, no medicine/ vaccine can
fully cure their infection. To inhibit the activity of protease of COVID-19,
molecular docking and ADMET studies of 116 noscapine derivatives were performed
and the result was compared with 14 reputed antiviral drugs including
chloroquine and hydroxychloroquine. The molecular docking result indicates a
better binding in comparison of 14 reputed drugs. Further, the top six
noscapines was taken into consideration for the pose analysis and ADMET
studies. Finally, the top six noscapine was refined by ADMET properties to get
the most potent one.</p> | Vijay Kumar Vishvakarma; Kamlesh Kumari; PRASHANT SINGH | Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ed8bdbb89508fa39c7a/original/inhibition-of-protease-of-novel-corona-virus-by-designed-noscapines-molecular-docking-and-admet-studies.pdf |
60c7441a567dfe287fec420d | 10.26434/chemrxiv.9745289.v1 | Molecular Design Realizing Very Fast Reverse Intersystem Crossing in Purely Organic Emitter | Reverse intersystem
crossing (RISC), originally considered forbidden in purely organic materials,
has been recently enabled by minimizing the energy gap between the lowest
singlet excited state (S<sub>1</sub>) and lowest triplet state (T<sub>1</sub>) in
thermally activated delayed
fluorescence (TADF) systems.
However, direct spin-inversion between S<sub>1</sub> and T<sub>1</sub> is still
inefficient when both states are of the same charge transfer (CT) nature (i.e. <sup>1</sup>CT
and <sup>3</sup>CT, respectively). Intervention of locally excited triplet
states (<sup>3</sup>LE) between <sup>1</sup>CT and <sup>3</sup>CT is expected
to trigger fast spin-flip. Here, we report on the systematic-design of the
ideal TADF molecules
with near-degenerate <sup>1</sup>CT, <sup>3</sup>CT and <sup>3</sup>LE states
by controlling the through-space distance between the donor and acceptor
segments in a molecule with tilted intersegment angles. The new system realizes
very fast RISC with a rate constant (<i>k</i><sub>RISC</sub>) of 1.2×10<sup>7</sup> s<sup>−1</sup>. The large <i>k</i><sub>RISC</sub>
of the emitter resulted in great device performance in the applications to blue
TADF assisted fluorescence organic light-emitting diodes (OLEDs) as well as
TADF-emitter OLEDs.<br /> | Yoshimasa Wada; Hiromichi Nakagawa; Soma Matsumoto; Yasuaki Wakisaka; Hironori Kaji | Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7441a567dfe287fec420d/original/molecular-design-realizing-very-fast-reverse-intersystem-crossing-in-purely-organic-emitter.pdf |
60c7401ebb8c1a82903d9d1c | 10.26434/chemrxiv.7613027.v1 | Cyclic Alkyne Approach to Heteroatom-Containing Polycyclic Aromatic Hydrocarbon Scaffolds | We report a modular synthetic strategy for accessing heteroatom-containing polycyclic aromatic hydrocarbons (PAHs) that relies on the controlled generation of transient heterocyclic alkynes and arynes. The strained intermediates undergo in situ trapping with readily accessible oxadiazinones. Four sequential pericyclic reactions occur, namely two Diels–Alder / retro-Diels–Alder sequences, which can be performed in a stepwise or one-pot fashion to assemble four new carbon–carbon (C–C) bonds. | Evan Darzi; Joyann Barber; Neil Garg | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7401ebb8c1a82903d9d1c/original/cyclic-alkyne-approach-to-heteroatom-containing-polycyclic-aromatic-hydrocarbon-scaffolds.pdf |
62a1cb84f85b59fa6102e10d | 10.26434/chemrxiv-2022-8d6p7 | Surfactant Effects on Hydrogen Evolution by Small Molecule Non-Fullerene Acceptor Nanoparticles | Organic donor:acceptor semiconductor nanoparticles (NPs) formed through the miniemul- sion method have been shown to be active photocatalysts. Here we report photocatalytic hydrogen (H2) evolution under sacrificial conditions with Pt as a co-catalyst by NPs comprising only the non-fullerene acceptor Y6, stabilized by either sodium dodecyl sulfate (SDS) or the thiophene-containing surfactant 2-(3-thienyl)ethyloxybutylsulfonate sodium salt (TEBS). Typically, changes in the photocatalytic activity of donor:acceptor NPs are associated with differences in morphology due to the use of surfactants. However, as these NPs are single-component, their photocatalytic activity has a significantly lower dependence on morphology than two-component donor:acceptor NPs. Results from ultrafast transient absorption spectroscopy show a minor difference between the photophysics of the TEBS- and SDS-stabilized Y6 NPs, with free charges present with either surfactant. The similar photophysics suggest that both TEBS- and SDS-stabilized Y6 NPs would be expected to have similar rates of H2 evolution. However, the results from photocatalysis show that Y6 NPs stabilized by TEBS have a H2 evolution rate 21 times higher than that of the SDS- stabilized NPs under broadband solar-like illumination (400–900 nm). Transmission electron microscopy images of the Y6 NPs show effective photodeposition of Pt on the surface of the TEBS-stabilized NPs. In contrast, photodeposition of Pt is inhibited when SDS is used. Furthermore, the zeta potential of the NPs is higher in magnitude when SDS is present. Hence, we hypothesize that SDS forms a dense, insulating layer on the NP surface which hinders the photodeposition of Pt and reduces the rate of H2 evolution. This insulating effect is absent for TEBS-stabilized Y6 NPs, allowing a high rate of H2 evolution. The TEBS-stabilized Y6 NPs have a H2 evolution rate higher than most single-component organic photocatalysts, signaling the potential use of the Y-series acceptors for H2 evolution in Z-scheme photocatalysis. | Andrew Dolan; Jessica de la Perrelle; Emily Milsom; Thomas Small; Gregory Metha; Xun Pan; Mats Andersson; David Huang; Tak W. Kee | Physical Chemistry; Catalysis; Energy; Photocatalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a1cb84f85b59fa6102e10d/original/surfactant-effects-on-hydrogen-evolution-by-small-molecule-non-fullerene-acceptor-nanoparticles.pdf |
655ab54d6e0ec7777f4b00dd | 10.26434/chemrxiv-2023-dgf39 | Steam adsorption equilibrium data at 110°C on an activated carbon, Lewatit VP OC 1065, and CALF-20 using a microscale dynamic column breakthrough apparatus | Steam adsorption equilibrium data is important for many carbon capture applications, including direct-air capture, point-source, and pre-combustion carbon capture. However, there is a dearth of concentrated unary equilibrium data for H2O at temperatures greater than 100°C. In this study, unary steam adsorption equilibrium data was measured at 110°C and up to approximately 1.0 bar partial pressure with a steam microscale dynamic column breakthrough (μDCB) apparatus using a milligram quantities of adsorbent. These partial pressures are equivalent to those used in industrial carbon capture processes. The construction of the apparatus is detailed, along with the necessary calibrations and validations to ensure accurate equilibrium measurement. Three adsorbents were considered in this study: an activated carbon (Calgon BPL), an amine-functionalized polymer (Lewatit VP OC 1065), and a metal-organic framework (CALF-20). It was observed that steam adsorbs strongly on all three materials at 110°C. Activated carbon and Lewatit displayed type-3 isotherm shapes, and CALF-20 displayed a type-5 isotherm shape. Activated carbon and Lewatit were modeled with the GAB isotherm, and CALF-20 was modeled with the cubic-Langmuir isotherm. The 110°C data was compared against H2O equilibrium data collected at 25°C as a function of relative pressure. An in-house dynamic column breakthrough simulator coded in MATLAB was able to predict the μDCB composition breakthrough curves well for all three materials. The data obtained from the steam breakthrough experiments has important process implications and highlights the need to measure steam adsorption data for any proposed carbon capture material. | Nicholas Stiles Wilkins; James A. Sawada; Arvind Rajendran | Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Analytical Apparatus; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655ab54d6e0ec7777f4b00dd/original/steam-adsorption-equilibrium-data-at-110-c-on-an-activated-carbon-lewatit-vp-oc-1065-and-calf-20-using-a-microscale-dynamic-column-breakthrough-apparatus.pdf |
65b820369138d23161ff9eae | 10.26434/chemrxiv-2024-6f9cq | Improved Rate Capability for Dry Thick Electrodes Through Finite Elements Method and Machine-Learning Coupling | A coupled Finite Elements Method (FEM) and Machine-Learning (ML) workflow is presented to optimize the rate capability of thick positive electrodes (ca. 150 µm and 8 mAh/cm²). An ML model is trained based on the geometrical observables of individual LiNi0.8Mn0.1Co0.1O2 particles and their average state of discharge (SOD) predicted from FEM modeling. This model not only bypasses lengthy FEM simulations, but also provides deeper insights on the importance of pore tortuosity and the active particles size, identified as the limiting phenomenon during the discharge. Based on these findings, a bi-layer configuration is proposed to tackle the identified limiting factors for the rate capability. The benefits of this structured electrode are validated through FEM by comparing its performance to a pristine mono-layer electrode. Finally, experimental validation using dry processing demonstrates a 40% higher volumetric capacity of the bi-layer electrode when compared to the previously reported thick NMC electrodes. | Mehdi Chouchane; Weiliang Yao; Ashley Cronk; Minghao Zhang; Shirley Meng | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Artificial Intelligence; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b820369138d23161ff9eae/original/improved-rate-capability-for-dry-thick-electrodes-through-finite-elements-method-and-machine-learning-coupling.pdf |
65983a5be9ebbb4db980ece4 | 10.26434/chemrxiv-2024-vnxns | A quantitative active template click reaction (AT-CuAAC) for the synthesis of mechanically interlocked nanohoops | Mechanically interlocked molecules (MIMs) represent an exciting yet underexplored area of research in the context of carbon nanoscience. Recently, work from our group and others has shown that small carbon nanotube fragments—[n]cycloparaphenylenes ([n]CPPs) and related nanohoop macrocycles—may be integrated into mechanically interlocked architectures by leveraging supramolecular interactions, covalent tethers, or metal-ion templates. Still, available synthetic methods are typically difficult and low yielding and general methods that allow for the creation of a wide variety of these structures are limited. Here we report an efficient route to interlocked nanohoop structures via active template Cu-catalyzed azide-alkyne cycloaddition (AT-CuAAC) reaction. With the appropriate choice of substituents, a macrocyclic precursor to 2,2’-bipyridyl embedded [9]CPP (bipy[9]CPP) participates in the AT-CuAAC reaction to provide [2]rotaxanes in near-quantitative yield, which can then be converted to the fully pi-conjugated catenane structures. Through this approach two nanohoop[2]catenanes are synthesized which consist of a bipy[9]CPP catenated with either Tz[10]CPP or Tz[12]CPP (where Tz denotes a 1,2,3-triazole moiety replacing one phenylene ring in the [n]CPP backbone). | James May; Julia Fehr; Jacob Lorenz; Lev Zakharov; Ramesh Jasti | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65983a5be9ebbb4db980ece4/original/a-quantitative-active-template-click-reaction-at-cu-aac-for-the-synthesis-of-mechanically-interlocked-nanohoops.pdf |
6761c4e881d2151a020c40a9 | 10.26434/chemrxiv-2024-g6bsl-v2 | A systematic and general machine learning approach to build a consistent data set from different experiments: application to the thermal conductivity of methane | Experimental data from different sources present challenges due to variability and noise from various experimental conditions, apparatuses, and environmental factors. In this work, we propose a general method to address these challenges to build a consistent data set. As a case study, we analyze experimental data sets of methane’s thermal conductivity across the liquid, vapor, and supercritical phases. The method is based on machine learning (ML) techniques, which consistently integrate data from various experimental sources compiled by the National Institute of Standards and Technology (NIST) database. Different ML algorithms are used for this purpose. Our findings indicate that ML models yield predictions closer to the NIST’s processed data than to the original raw experimental data used to train the models. This demonstrates the models’ generalization ability from heterogeneous, noisy, and untreated data sets. While our approach does not eliminate preprocessing, it suggests that ML can autonomously handle noisy data, providing a faster and cost-effective alternative to traditional pre- and postprocessing methods. By guiding the refinement of labor-intensive methods, ML proves adaptable for real-time data, enabling immediate adjustments and revolutionizing industrial and scientific optimizations. Therefore, the proposed ML approach is general and efficient in handling complex and heterogeneous data to deliver reliable predictions without extensive preprocessing. | Matheus Máximo-Canadas; Julio Cesar Duarte; Jakler Nichele; Leonardo Alves; Luiz Octavio Pereira; Rogerio Ramos; Itamar Borges | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Fluid Mechanics; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6761c4e881d2151a020c40a9/original/a-systematic-and-general-machine-learning-approach-to-build-a-consistent-data-set-from-different-experiments-application-to-the-thermal-conductivity-of-methane.pdf |
65791094bec7913d277803cc | 10.26434/chemrxiv-2023-cl8tr | Differentiating the yield of chemical reactions using parameters in first-order kinetic equations to identify elementary steps that control the reactivity from complicated reaction path networks | The yield of a chemical reaction is obtained by solving the rate equation. This study introduces an approach for differentiating the yields using the parameters of the rate equation, which is expressed as a first-order linear differential equation. The yield derivative for a specific pair of reactant and product is derived by mathematically expressing the rate constant matrix contraction method, which is a simple kinetic analysis method. The parameters of the rate equation are the Gibbs energies of the intermediates and transition states in the reaction path network used to formulate the rate equation. Thus, the differentiating yield allows the numerical evaluation of the contribution of energy variation to the yield for each intermediate and transition state in the reaction path network. In other words, a comparison of these values automatically extracts the factors affecting the yield from a complicated reaction path network consisting of numerous reaction paths and intermediates. This study verifies the behavior of the proposed approach through numerical experiments on the reaction path networks of a model system and the Rh-catalyzed hydroformylation reaction. Moreover, the possibility of using this approach for designing organometallic catalyst ligands is discussed. | Yu Harabuchi; Tomohiko Yokoyama; Wataru Matsuoka; Taihei Oki; Satoru Iwata; Satoshi Maeda | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2023-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65791094bec7913d277803cc/original/differentiating-the-yield-of-chemical-reactions-using-parameters-in-first-order-kinetic-equations-to-identify-elementary-steps-that-control-the-reactivity-from-complicated-reaction-path-networks.pdf |
66746b965101a2ffa816b473 | 10.26434/chemrxiv-2024-80klb | Chemically transferable electronic coarse graining for polythiophenes | Recent advances in machine-learning-based electronic coarse graining (ECG) methods have
demonstrated the potential to enable electronic predictions in soft materials at mesoscopic length
scales. However, previous ECG models have yet to confront the issue of chemical transferability. In
this study, we develop chemically transferable ECG models for polythiophenes using graph neural
networks. Our models are trained on a dataset that samples over the conformational space of random
polythiophene sequences generated with 15 different monomer chemistries and three different
degrees of polymerization. We systematically explore the impact of coarse-grained (CG) representation
at multiple resolutions on ECG accuracy, highlighting the significance of preserving the C-beta
coordinates in thiophene. We also find that integrating unique polymer sequences into training enhances
model performance more efficiently than augmenting conformational sampling for sequences
already in the training dataset. Moreover, our ECG models, developed initially for one property
and one level of quantum chemical theory, can be efficiently transferred to related properties and
higher levels of theory with minimal additional data. The chemically transferable ECG model introduced
in this work will serve as a foundation model for new classes of chemically transferable
ECG predictions across a broader chemical space. | Zheng Yu; Nicholas Jackson | Theoretical and Computational Chemistry; Polymer Science; Conducting polymers; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66746b965101a2ffa816b473/original/chemically-transferable-electronic-coarse-graining-for-polythiophenes.pdf |
67cbd71f6dde43c908031135 | 10.26434/chemrxiv-2024-00f19-v2 | Electric Field’s Dueling Effects through Dehydration and Ion Separation in Driving NaCl Nucleation at Charged Nanoconfined Interfaces | Investigating nucleation in charged nanoconfined environments under electric fields is crucial for many scientific and engineering applications. Here we study the nucleation of NaCl from aqueous solution near charged surfaces using machine-learning-augmented enhanced sampling molecular dynamics simulations. Our simulations successfully drive phase transitions between liquid and solid phases of NaCl. The solid phase is stabilized under electric fields, particularly at an intermediate surface charge density. We examine which physical characteristics drive the nucleation of NaCl from aqueous solutions and find that the removal of solvent water from Cl- at the solid precursor surface plays a more critical role than the accumulation of ions. Our simulations reveal the competing effects of electric fields on nucleation processes: they facilitate the removal of water, promoting nucleation, but also promote the separation of ion pairs thereby hindering nucleation. This work provides a framework for studying nucleation processes in nanoconfined environments under electric fields and physical insights for the design of electrochemistry materials. | Ruiyu Wang; Pratyush Tiwary | Theoretical and Computational Chemistry; Physical Chemistry; Artificial Intelligence; Interfaces; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cbd71f6dde43c908031135/original/electric-field-s-dueling-effects-through-dehydration-and-ion-separation-in-driving-na-cl-nucleation-at-charged-nanoconfined-interfaces.pdf |
6172b202ff3ba9b4899d464a | 10.26434/chemrxiv-2021-440t2-v2 | A Reliable and Sustainable Multicomponent Access to Protein Degraders | The use of small molecules to induce targeted protein degradation is increasingly growing in the drug discovery landscape and protein degraders have progressed rapidly through the pipelines. Despite the advances made so far, their synthesis still represents a significant burden and new approaches are urgently demanded. Herein, we report an unprecedented platform that leverages the modular nature of both multicomponent reactions and degraders to enable the preparation of highly decorated PROTACs and hydrophobic tag-mediated degraders. Compared to the existing methods, our approach offers a versatile and cost-effective means to access libraries of protein degraders and increase the chance of identifying successful clinical candidates. | Irene Preet Bhela; Alice Ranza; Marta Serafini ; Tracey PIRALI | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6172b202ff3ba9b4899d464a/original/a-reliable-and-sustainable-multicomponent-access-to-protein-degraders.pdf |
64b45930b605c6803bd6cdd4 | 10.26434/chemrxiv-2023-4c69m | Deciphering the existence of hexagonal sodium zirconate CO2 sorbent | Sodium zirconate (sodium zirconium oxide; Na2ZrO3) is amongst the most investigated carbon dioxide (CO2) sorbent. Na2ZrO3 is renowned for its high capture capacity and cyclic stability. It can effectively capture CO2 at temperatures that are found in industrial processes such as the manufacture of steel or cement. Na2ZrO3 is reported to adopt monoclinic, hexagonal, and cubic structures since it was first discussed in the 1960s. Researchers relied on the differences in the relative intensities between two peaks (2θ ~ 16.2 and 38.7 °) in the powder X-ray diffraction (PXRD) pattern to determine the phase of this compound. It is also widely believed that the CO2 capture performance of Na2ZrO3 is related to the crystal structure, yet the crystal structure of hexagonal Na2ZrO3 has remained elusive. With the use of 3D electron diffraction (3D ED), X-ray photoelectron spectroscopy (XPS), and PXRD, we show that the hexagonal Na2ZrO3 does not exist. The so-called hexagonal Na2ZrO3 is Na2ZrO3 with three different types of disorder. Furthermore, the two PXRD peaks (2θ ~ 16.2 and 38.7 °) cannot be used to distinguish the different phases of Na2ZrO3, as the changes in the PXRD pattern are related to the extent of structure disorder. Finally, we also show that the CO2 capture properties of Na2ZrO3 are related to the Na+ site occupancy between different Na2ZrO3 samples, and not differences in crystal structures. The findings from our work shows that the current literature discussion on the structure of Na2ZrO3 is misleading. In order to further develop Na2ZrO3 as well as other mixed-metal oxides for applications, their structures, as well as any disorder, needs be understood using the methods shown in this study. | Ribooga Chang; Ocean Cheung; Ashok Menon; Erik Svensson Grape; Peter Broqvist; Andrew Ken Inge | Materials Science; Inorganic Chemistry; Nanostructured Materials - Materials; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b45930b605c6803bd6cdd4/original/deciphering-the-existence-of-hexagonal-sodium-zirconate-co2-sorbent.pdf |
6195296a64a70792d373598a | 10.26434/chemrxiv-2021-mhgfz | Dynamic Molecular Switches Drive Negative Memristance Mimicking Synaptic Behavior | To realize molecular scale electrical operations beyond the von Neumann bottleneck, new types of multi-functional switches are needed that mimic self-learning or neuromorphic computing by dynamically toggling between multiple operations that depend on their past. Here we report a molecule that switches from high to low conductance states with massive negative memristive behavior that depends on the drive speed and the number of past switching events. This dynamic molecular switch emulates synaptic behavior and Pavlovian learning and can provide all of the fundamental logic gates because of its time-domain and voltage-dependent plasticity. This multi-functional switch represents molecular scale hardware operable in solid-state devices opening a pathway to dynamic complex electrical operations encoded within a single ultra-compact component. | christian nijhuis; Yulong Wang; Qian Zhang; Hippolyte Astier; Cameron Nickle; Ziyu Zhang; Andrea Leoncini; Dong-Cheng Qi; Yingmei Han; Enrique del Barco; Damien Thompson | Physical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6195296a64a70792d373598a/original/dynamic-molecular-switches-drive-negative-memristance-mimicking-synaptic-behavior.pdf |
66c60ebcf3f4b052909e194d | 10.26434/chemrxiv-2024-x3n3k | Accurately computed dimerization fraction of ALD precursors and their impact on surface reactivity in area-selective atomic layer deposition | The Lewis acidic nature of aluminum atoms in common precursors for the atomic layer deposition (ALD) of Al2O3 can lead to dimerization. This study investigates whether these compounds predominantly exist as monomers or dimers under ALD conditions. Understanding dimerization is crucial for discussing precursor reactivities and other properties, especially in the context of area-selective ALD (AS-ALD). We employed a theoretical approach, incorporating conformer search, density functional theory, and coupled cluster calculations, to determine the dissociated dimer fraction for a range of precursors under typical ALD pressures and temperatures. The precursors studied include aluminum alkyls, chlorinated aluminum alkyls, dimethylaluminumisopropoxide (DMAI), and trisdimethylamidoaluminum (TDMAA). Our findings indicate that aluminum alkyls are completely dissociated over the whole parameter range, while DMAI and TDMAA form stable dimers. Chlorinated precursors were found to exist in both monomeric and dimeric forms depending on temperature and pressure. | Patrick Maue; Émilie Chantraine; Fabian Pieck; Ralf Tonner-Zech | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c60ebcf3f4b052909e194d/original/accurately-computed-dimerization-fraction-of-ald-precursors-and-their-impact-on-surface-reactivity-in-area-selective-atomic-layer-deposition.pdf |
60c74060bdbb898596a38156 | 10.26434/chemrxiv.7712258.v1 | Local Structure and Orientational Ordering in Liquid Bromoform | <p>The neutron
diffraction data of liquid bromoform (CHBr<sub>3</sub>) at 25°C was analysed using
the Empirical Potential Structure Refinement technique in combination with H/D
isotopic substitution. Compared to liquid chloroform (CHCl<sub>3</sub>), CHBr<sub>3</sub>
displays more spatially defined intermolecular contacts. A preference for polar
stacking with collinear alignment of dipole moments is observed for the most
closely approaching CHBr<sub>3</sub> molecules, although to a lesser extent
than in chloroform. Consistent with this and in line with dielectric
spectroscopy, the Kirkwood correlation factor from the structural model of CHBr<sub>3</sub>
is smaller than that of CHCl<sub>3</sub>. The net antiparallel alignment of
dipole moments in CHBr<sub>3</sub>, as suggested by dielectric spectroscopy,
must be due to weak but persistent long-range orientation correlations in CHBr<sub>3</sub>,
which counteract the local polar stacking.</p> | Jacob J. Shephard; John S. O. Evans; Christoph Salzmann | Computational Chemistry and Modeling; Solution Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74060bdbb898596a38156/original/local-structure-and-orientational-ordering-in-liquid-bromoform.pdf |
60c74f13bdbb89358ba39cd3 | 10.26434/chemrxiv.12846602.v1 | Improving Small Molecule Force Fields by Identifying and Characterizing Small Molecules with Inconsistent Parameters | Many molecular simulation methods use force fields to help model and simulate molecules and their behavior in various environments. Force fields are sets of functions and parameters used to calculate the potential energy of a chemical system as a function of the atomic coordinates. Despite the widespread use of force fields, their inadequacies are often thought to contribute to systematic errors in molecular simulations. Furthermore, different force fields tend to give varying results on the same systems with the same simulation settings. Here, we present a pipeline for comparing the geometries of small molecule conformers. We aimed to identify molecules or chemistries that are particularly informative for future force field development because they display inconsistencies between force fields. We applied our pipeline to a subset of the eMolecules database, and highlighted molecules that appear to be parameterized inconsistently across different force fields. We then identified over-represented functional groups in these molecule sets. The molecules and moieties identified by this pipeline may be particularly helpful for future force field parameterization. | Jordan Ehrman; Victoria T. Lim; Caitlin C. Bannan; Nam Thi; Daisy Kyu; David Mobley | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2020-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f13bdbb89358ba39cd3/original/improving-small-molecule-force-fields-by-identifying-and-characterizing-small-molecules-with-inconsistent-parameters.pdf |
60c756aa9abda25e61f8e585 | 10.26434/chemrxiv.13340939.v1 | Inhibition Mechanism of SARS-CoV-2 Main Protease with Ketone-Based Inhibitors Unveiled by Multiscale Simulations | <p>We present the results of combined classical and QM/MM simulations for the inhibition of SARS-CoV-2 3CL protease by a recently proposed ketone-based covalent inhibitor, PF-00835231, that is under clinical trial. In the noncovalent complex formed after binding into the active site the carbonyl group of this inhibitor is accommodated into the oxyanion hole formed by the NH main chain groups of residues 143 to 145. The P1-P3 groups of the inhibitor establish similar interaction with the enzyme to those of equivalent groups in the natural peptide substrate, while the hydroxymethyl moiety of the inhibitor partly mimics the interactions established by the P1’ group of the peptide in the active site. Regarding the formation of the covalent complex, the reaction is initiated after the proton transfer from Cys145 to His41. Formation of the covalent hemithioacetal complex takes place by means of the nucleophilic attack of the Sg atom of Cys145 on the electron deficient carbonyl carbon atom and a proton transfer from the catalytic His41 to the carbonyl oxygen atom mediated by the hydroxyl group. Our findings can be used as a guide to propose modifications of the inhibitor in order to increase its affinity by the 3CL protease.</p> | Carlos A. Ramos-Guzmán; J. Javier Ruiz-Pernía; Iñaki Tuñón | Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756aa9abda25e61f8e585/original/inhibition-mechanism-of-sars-co-v-2-main-protease-with-ketone-based-inhibitors-unveiled-by-multiscale-simulations.pdf |
60c7598d567dfe1a19ec6a76 | 10.26434/chemrxiv.14377361.v4 | Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant | <div>
<p><a>Understanding
thermodynamics and kinetics of the binding process of an antibody to SARS-CoV-2
receptor-binding domain (RBD) of Spike protein is very important for the
development of COVID19 vaccines. Especially, it is essential to understand how
the binding mechanism may change under the effects of RBD mutations. In this
context, we have demonstrated that the South African variant (B1.351 or
501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD
including K417N, E484K, and N501Y alters the free energy landscape, binding
pose, binding free energy, binding kinetics, hydrogen bond, nonbonded contacts,
and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb
to 501Y.V2 RBD confirms the antibody resistance of the South African variant.</a> Moreover, the fragment of NAb + RBD can be used as an affordable
model to investigate the change of the binding process between mutations RBD
and antibodies.</p></div> | Son Tung Ngo; Trung Hai Nguyen; Duc-Hung Pham; Nguyen
Thanh Tung; Pham Cam Nam | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Biophysical Chemistry; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7598d567dfe1a19ec6a76/original/thermodynamics-and-kinetics-in-antibody-resistance-of-the-501y-v2-sars-co-v-2-variant.pdf |
64a70d3a6e1c4c986bedaf00 | 10.26434/chemrxiv-2023-9jgs9 | A Review of Emerging Photo-Induced Degradation Methods for Per- and Polyfluoroalkyl Substances (PFAS) in Water | The remediation of per- and polyfluoroalkyl substances (PFAS) in water continues to garner significant attention due to their environmental persistence and adverse health effects. Among the various PFAS remediation methods, photo-induced approaches have recently emerged as promising techniques for the degradation of these persistent contaminants. However, many questions remain unanswered regarding the detailed mechanisms in these photo-induced methods as well as the best ways to leverage these approaches for PFAS degradation. In this review, we provide an update on recent experimental and theoretical developments in photo-induced PFAS degradation techniques over the past 2 - 5 years. We conclude with a perspective of promising research directions in this vibrant area and give recommendations on future experimental and computational approaches needed to further advance these photo-induced remediation capabilities. | Zulfikhar Ali; Sharma Yamijala; Bryan Wong | Theoretical and Computational Chemistry; Catalysis; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a70d3a6e1c4c986bedaf00/original/a-review-of-emerging-photo-induced-degradation-methods-for-per-and-polyfluoroalkyl-substances-pfas-in-water.pdf |
62264891c6bb55c37b8027c1 | 10.26434/chemrxiv-2021-0nmwt-v2 | Localized Quantum Chemistry on Quantum Computers | Quantum chemistry calculations of large, strongly correlated systems are typically limited by the computation
cost that scales exponentially with the size of the system. Quantum algorithms, designed specifically for
quantum computers, can alleviate this, but the resources required are still too large for today’s quantum devices.
Here we present a quantum algorithm that combines a localization of multireference wave functions of chemical
systems with quantum phase estimation (QPE) and variational unitary coupled cluster singles and doubles
(UCCSD) to compute their ground state energy. Our algorithm, termed “local active space unitary coupled
cluster” (LAS-UCC), scales linearly with system size for certain geometries, providing a polynomial reduction
in the total number of gates compared with QPE, while providing accuracy above that of the variational quantum
eigensolver using the UCCSD ansatz and also above that of the classical local active space self-consistent
field. The accuracy of LAS-UCC is demonstrated by dissociating (H2)2 into two H2 molecules and by breaking
the two double bonds in trans-butadiene and resources estimates are provided for linear chains of up to 20 H2
molecules. | Matthew Otten; Matthew Hermes; Riddhish Pandharkar; Yuri Alexeev; Stephen Gray; Laura Gagliardi | Theoretical and Computational Chemistry; Theory - Computational; Quantum Computing | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62264891c6bb55c37b8027c1/original/localized-quantum-chemistry-on-quantum-computers.pdf |
6625693121291e5d1d53cc7b | 10.26434/chemrxiv-2024-3phh7 | Quantification of temperature-dependent CO2 adsorption kinetics in Lewatit VP OC 1065, Purolite A110, and TIFSIX-3-Ni for direct air capture | One of the critical factors affecting the performance of an adsorption-based direct air capture (DAC) process is the CO2 adsorption kinetics. Yet, this data is not currently available in the literature for many DAC adsorbents, particularly at the relevant conditions for DAC (i.e. ~ 0.04%vol or 400 ppm). In this study, we report temperature-dependent linear driving force constants (kLDF(T)) measured at 400 ppm CO2 between 20 °C and 70 °C for three promising DAC adsorbents: Lewatit VP OC 1065, Purolite A110, and TIFSIX-3-Ni. TIFSIX-3-Ni exhibits the fastest adsorption kinetics across the whole temperature range, while Purolite A110 has faster adsorption kinetics compared to Lewatit VP OC 1065 at temperatures greater than 40 °C. Overall, the kLDF(T) values determined in this work can be used for initial process scale modelling to assess the process performance of these adsorbents for DAC, while additional experiments would have to be conducted to determine kLDF constants outside this temperature range and at different CO2 concentrations. | May-Yin (Ashlyn) Low; David Danaci; Callum Sturman; Camille Petit | Materials Science; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625693121291e5d1d53cc7b/original/quantification-of-temperature-dependent-co2-adsorption-kinetics-in-lewatit-vp-oc-1065-purolite-a110-and-tifsix-3-ni-for-direct-air-capture.pdf |
61841d4cf9f05b9689ec9c2b | 10.26434/chemrxiv-2021-1lcbx | Contra-Thermodynamic Positional Isomerization of Olefins | A light-driven method for the contra-thermodynamic positional isomerization of olefins is described. In this work, stepwise PCET activation of a more substituted and more thermodynami-cally stable olefin substrate is mediated by an excited-state oxi-dant and a Brønsted base to afford an allylic radical that is cap-tured by a Cr(II) co-catalyst to furnish an allylchromium(III) intermediate. In situ protodemetalation of this allylchromium complex by methanol is highly regioselective and affords an isomerized and less thermodynamically stable alkene product. The higher oxidation potential of the less substituted olefin isomer renders it inert to further oxidation by the excited-state oxidant, enabling it to accumulate in solution over the course of the reaction. A broad range of isopropylidene substrates is ac-commodated, including enol ethers, enamides, styrenes, 1,3-dienes, and tetrasubstituted alkyl olefins. Mechanistic investiga-tions of the protodemetalation step are also presented. | Kuo Zhao; Robert Knowles | Organic Chemistry; Catalysis; Organometallic Chemistry; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61841d4cf9f05b9689ec9c2b/original/contra-thermodynamic-positional-isomerization-of-olefins.pdf |
6449acd883fa35f8f64d330d | 10.26434/chemrxiv-2023-n20f0 | Spatial Transcriptomics: Emerging Technologies in Tissue Gene Expression Profiling | Spatial transcriptomics technologies are providing new insights to study gene expression, allowing researchers to investigate the spatial organization of transcriptomes in cells and tissues. This approach enables the creation of high-resolution maps of gene expression patterns within their native spatial context, adding an extra layer of information to bulk sequencing data. Spatial transcriptomics has expanded significantly in recent years and is making a notable impact on a range of fields, including tissue architecture, developmental biology, cancer, neurodegenerative and infectious diseases. The latest advancements in spatial transcriptomics have resulted in the development of highly multiplexed methods, transcriptomic-wide analysis, and single-cell resolution, utilizing diverse technological approaches. In this perspective, we provide a detailed analysis of the molecular foundations behind the main spatial transcriptomics technologies, including methods based on microdissection, in situ sequencing, single-molecule FISH, spatial capturing, selection of regions of interest and single-cell or nuclei dissociation. We contextualize the detection and capturing efficiency, strengths, limitations, tissue compatibility, and applications of these techniques, as well as provide information on data analysis. In addition, this perspective discusses future directions and potential applications of spatial transcriptomics, highlighting the importance of the continued development to promote widespread adoption of these techniques within the research community. | Agustín Robles-Remacho*; Rosario M. Sanchez-Martin; Juan J. Diaz-Mochon* | Analytical Chemistry; Analytical Chemistry - General; Imaging; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6449acd883fa35f8f64d330d/original/spatial-transcriptomics-emerging-technologies-in-tissue-gene-expression-profiling.pdf |
60c752690f50db9d3c3979a3 | 10.26434/chemrxiv.13296323.v1 | Kinetics of Hydride Transfer from Metal-Free Hydride Donors to CO2 | Selective reduction of CO<sub>2</sub> to formate
represents an ongoing challenge in photoelectrocatalysis. To provide
mechanistic insights, we investigate the kinetics of hydride transfer (HT) from
a series of metal-free hydride donors to CO<sub>2</sub>. The observed
dependence of experimental and calculated HT barriers on the thermodynamic
driving force was modeled using the Marcus hydride transfer formalism to obtain
the insights into the effect of reorganization energies on the reaction
kinetics. Our results indicate that, even if the most ideal hydride donor were
discovered, the HT to CO<sub>2</sub> would exhibit sluggish kinetics (less than
100 turnovers at 0.1 eV driving force), indicating that the conventional HT may
not be an appropriate mechanism for Solar conversion of CO<sub>2</sub> to
formate. We propose that the conventional HT mechanism should not be considered
for CO<sub>2</sub> reduction catalysis and argue that the orthogonal HT
mechanism, previously proposed to address thermodynamic limitations of this
reaction, may also lead to lower kinetic barriers for CO<sub>2</sub> reduction
to formate. | Ravindra Weerasooriya; Jonathan L. Gesiorski; Abdulaziz Alherz; Stefan Ilic; George Hargenrader; Charles B. Musgrave; Ksenija Glusac | Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752690f50db9d3c3979a3/original/kinetics-of-hydride-transfer-from-metal-free-hydride-donors-to-co2.pdf |
67d2f3ae81d2151a023d64f8 | 10.26434/chemrxiv-2025-ggp8n | How to generalize machine learning models to both canonical and non-canonical peptides | Bioactive peptides are an important class of natural products with great functional diversity. Chemical modifications can improve their pharmacology, yet their structural diversity presents unique challenges for computational modeling. Furthermore, data for canonical peptides (non-modified) is more abundant than for non-canonical (chemically modified). We explored whether current methods are sufficient to generalize from canonical data to non-canonical datasets. To do this, we first considered two critical aspects of the modeling problem, namely choice of similarity function for guiding dataset partitioning and choice of molecular representation. Similarity-based dataset partitioning is an evaluation technique that divides the dataset into train and test subsets, such that the molecules in the test set are different from those used to fit the model. We demonstrate, across four peptide function prediction tasks, that chemical fingerprint-based similarity measures outperform traditional sequence alignment-based metrics for partitioning canonical peptide datasets, challenging standard practices. We have also found that the deep-learned embeddings from Chemical Language Models (CLMs) generally outperform chemical fingerprints and other peptide-specific pre-trained models, performing best for non-canonical peptides and second best for canonical. Despite this, models trained on only one of the two peptide classes fail to properly extrapolate to the other. However, by enriching the canonical datasets with a small proportion of non-canonical peptides, we are able to build robust joint models that generalise adequately to both canonical and non-canonical data. All code and data necessary for reproducing the experiments are available in Github (https://github.com/IBM/AutoPeptideML/tree/peptide-rep-gen). | Raúl Fernández-Díaz; Rodrigo Ochoa; Thanh Lam Hoang; Vanessa Lopez; Denis Shields | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d2f3ae81d2151a023d64f8/original/how-to-generalize-machine-learning-models-to-both-canonical-and-non-canonical-peptides.pdf |
619b75ede0ea841896a2c579 | 10.26434/chemrxiv-2021-q1f7k | Which bridge to cross, which mountain to climb – Supramolecular
Photocatalysis Outpacing Conventional Catalysis | Unequivocal assignment of rate limiting steps in supramolecular photocatalysts is of utmost
importance to rationally optimize photocatalytic activity. By spectroscopic and catalytic analysis of a
series of three structurally similar [(tbbpy) 2 Ru-BL-Rh(Cp*)Cl] 3+ photocatalysts just differing in the
central part (alkynyl, triazole or phenazine) of the bridging ligand (BL) we were able to derive design
strategies for improved photocatalytic activity of this class of compounds (tbbpy = 4,4´-tert-butyl-
2,2´-bipyridine, Cp* = pentamethylcyclopentadienyl). Most importantly, not the rate of the transfer
of the first electron towards the Rh III center but rather the rate at which a two-fold reduced Rh I
species is generated can directly be correlated with the observed photocatalytic formation of NADH
from NAD + . Interestingly, the complex which exhibited the fastest intramolecular electron transfer
kinetics for the first electron is not the one that allowed the fastest photocatalysis. With the
photocatalytically most efficient alkynyl linked system, it was even possible to overcome the rate of
thermal NADH formation. Moreover, for this photocatalyst loss of the alkynyl functionality under
photocatalytic conditions was identified as an important deactivation pathway. | Linda Zedler; Pascal Wintergerst; Alexander Mengele; Carolin Müller; Chunyu Li; Benjamin Dietzek-Ivanšić; Sven Rau | Physical Chemistry; Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.); Photocatalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619b75ede0ea841896a2c579/original/which-bridge-to-cross-which-mountain-to-climb-supramolecular-photocatalysis-outpacing-conventional-catalysis.pdf |
67a5044481d2151a026864f1 | 10.26434/chemrxiv-2025-5b5vd | NMR structure of chromeraxanthin - a unique allenic carotenoid of the apicomplexan alga Chromera velia | Chromera velia is photosynthetic alga that is evolutionary closest to the group of het- erotrophic apicomplexan parasites. The main light harvesting carotenoid of C. velia has been described as isofucoxanthin-like pigment, however its structure remained unknown. Here, we purified this pigment from a 5 L culture of C. velia using a two-step HPLC procedure and its structure determined using combination of tandem mass spectrometry and 2D- and 3D-NMR techniques. The data identified this pigment as a new allenic xanthophyll which we denoted chromeraxanthin. Although previously predicted to be structurally similar to isofucoxanthin, chromeraxanthin possess different arrangement of the terminal cycles and thus it likely not derived directly from fucoxanthin biosynthe- sis pathway. The six membered ring connected to the carotenoid backbone via allenic bond is identical to that of fucoxanthin including its O-acetylation. However, the second six-membered ring bearing epoxy group in fucoxanthin is replaced by a capsanthin-like cyclopentane ring in chromeraxanthin. Notably, similar structure lacking only the O- acetylation has been previously described as allenicmytiloxanthin isolated from Pacific oyster. | Zoltan Takacs; Pavel Hrouzek; Jan Hájek; Kumar Saurav; Jan Pilny; Ulrika Brath; Roman Sobotka | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a5044481d2151a026864f1/original/nmr-structure-of-chromeraxanthin-a-unique-allenic-carotenoid-of-the-apicomplexan-alga-chromera-velia.pdf |
6277b12bd555506f509263d9 | 10.26434/chemrxiv-2022-476ct | Effect of lipophilicity in oxyanions responsive Eu(III) complexes | Responsive lanthanide(III) complexes—europium(III) complexes in particular—has been the focus of studies for several decades. The response, in the form of changes of photophysical and electronic properties of the lanthanide(III) ion, arises through supramolecular interactions between a guest or analyte molecule, and the lanthanide(III) complex which acts as host. While responsive lanthanide complexes have been reported and investigated frequently, the supramolecular aspects and linear free-energy relationship have had less attention. Here, we are revising five europium(III) complexes and investigating their binding to nine different guests, all with a primary interaction between europium(III) ion and a bidentate carboxylate anion. The media effect was investigated, and by eliminating the impact of hydrophobic effects, we can show that selectivity in these host-guest systems can be tuned by the secondary lipophilic interactions. | Laura Grenier; Lea G Nielsen; Thomas Just Sørensen | Inorganic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Lanthanides and Actinides; Sensors | CC BY NC 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6277b12bd555506f509263d9/original/effect-of-lipophilicity-in-oxyanions-responsive-eu-iii-complexes.pdf |
63bd66ec3af973599e62fe43 | 10.26434/chemrxiv-2023-fgsdf | Brønsted Acid Catalyzed Asymmetric Synthesis of cis-Tetrahydrocannabinoids | We report herein the catalytic asymmetric cyclization of 1-aryl terpenols to afford enantiomerically highly enriched cis-tetrahydrocannabinoid scaffolds in a single step. As powerful chiral catalysts strongly acidic imidodiphosphorimidates (IDPis) have been identified which furnish the products with good yields and excellent enantioselectivity. Upon MOM-deprotection some naturally occurring cannabimimetica such as (-)-cis-Δ9-tetrahydrocannabinol and ( )-perrotettinene as well as some unnatural analogues were made accessible along a merely 3-step biomimetic sequence. | Caroline Dorsch; Christoph Schneider | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bd66ec3af973599e62fe43/original/br-nsted-acid-catalyzed-asymmetric-synthesis-of-cis-tetrahydrocannabinoids.pdf |
61c320d7d6dcc2437a4139c8 | 10.26434/chemrxiv-2021-ndmfl | Functionalization and Hydrogenation of Carbon Chains
Derived from CO
| Selective reactions that combine H2, CO and organic electrophiles (aldehyde, ketones, isocyanide) to form hydrogenated C3 and C4 carbon chains are reported. These reactions proceed by CO homologation mediated by [W(CO)6] and an aluminum(I) reductant, followed by functionalization and hydrogenation of the chain ends. A combination of kinetics (rates, KIEs) and DFT calculations has been used to gain insight into a key step which involves hydrogenation of a metallocarbene intermediate. These findings expand the extremely small scope of systems that combine H2 and CO to make well-defined products with complete control over chain length and functionality. | Maria Batuecas; Richard Kong; Andrew White; Mark Crimmin | Organometallic Chemistry; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2021-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c320d7d6dcc2437a4139c8/original/functionalization-and-hydrogenation-of-carbon-chains-derived-from-co.pdf |
641e349891074bccd03cc4e5 | 10.26434/chemrxiv-2023-322s3 | Degradation of Perfluorooctanoic Acid (PFOA) on Aluminum Oxide Surfaces: New Mechanisms from Ab Initio Molecular Dynamics Simulations | Perfluorooctanoic acid (PFOA) is a part of a large group of anthropogenic, persistent, and bio-accumulative contaminants known as per- and polyfluoroalkyl substances (PFAS) that can be harmful to human health. In this work, we present the first ab initio molecular dynamics (AIMD) study for systematically investigating a wide range of temperature-dependent degradation dynamics of PFOA on (100) and (110) surfaces of gamma-Al2O3. Our results show that PFOA degradation does not occur on the pristine (100) surface, even when carried out at high temperatures. However, introducing an oxygen vacancy on the (100) surface facilitates an ultra-fast (< 100 fs) defluorination of C-F bonds in PFOA. We also examined degradation dynamics on the (110) surface and found that PFOA interacts strongly with Al(III) centers on the surface of gamma-Al2O3, resulting in a stepwise breaking of C-F, C-C, and C-COO bonds. Most importantly, at the end of the degradation process, strong Al-F bonds are formed on the mineralized gamma-Al2O3 surface, which prevents further dissociation of fluorine into the surrounding environment. Taken together, our AIMD simulations provide critical reaction mechanisms at a quantum level of detail and highlight the importance of temperature effects, defects, and surface facets for PFOA degradation on reactive surfaces, which have not been systematically explored or analyzed. | Sohag Biswas; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641e349891074bccd03cc4e5/original/degradation-of-perfluorooctanoic-acid-pfoa-on-aluminum-oxide-surfaces-new-mechanisms-from-ab-initio-molecular-dynamics-simulations.pdf |
65085ce7b338ec988ab31715 | 10.26434/chemrxiv-2023-r53mf-v3 | Analyzing the Accuracy of Critical Micelle Concentration Predictions using Deep Learning | This paper presents a novel approach to predicting critical micelle concentrations (CMCs) using graph neural networks (GNNs) augmented with Gaussian processes (GPs). The proposed model uses learned latent space representations of molecules to predict CMCs and estimate uncertainties. The performance of the model on a dataset containing nonionic, cationic, anionic and zwitterionic molecules is compared against a linear model that works with extended-connectivity fingerprints (ECFPs). The GNN-based model performs slightly better than the linear ECFP model, when there is enough well-balanced training data, and achieves predictive accuracy that is comparable to published models that were evaluated on a smaller range of surfactant chemistries. We illustrate the applicability domain of our model using a molecular cartogram to visualize the latent space, which helps identify molecules for which predictions are likely to be erroneous. In addition to accurately predicting CMCs for some surfactant classes, the proposed approach can provide valuable insights into the molecular properties that influence CMCs. | Alexander Moriarty; Takeshi Kobayashi; Matteo Salvalaglio; Panagiota Angeli; Alberto Striolo; Ian McRobbie | Theoretical and Computational Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65085ce7b338ec988ab31715/original/analyzing-the-accuracy-of-critical-micelle-concentration-predictions-using-deep-learning.pdf |
67a780e06dde43c90812d9fe | 10.26434/chemrxiv-2025-340h4 | Drug Repurposing by Virtual Screening: identification of new already approved ROCK inhibitors as promising drugs to target neurodegeneration | Rho-associated protein kinases (ROCK) play a pivotal role in various cellular processes and have emerged as therapeutic targets for neurodegenerative diseases such as Alzheimer's disease (AD). Inhibition of ROCK affects the production of key AD pathophysiological markers and reduces neuroinflammation. This study aims to accelerate the identification of effective candidates for neurodegeneration by drug repurposing. By conducting chemical space and crystallographic structure analyses, we developed a pharmacophoric map and optimized it to perform a virtual screening campaign. This approach led to the discovery of novel 6 already approved ROCK inhibitors: ruxolitinib (hROCK1IC50 = 0.025 µM; hROCK2IC50 = 0.007 µM), baricitinib (hROCK1IC50 = 0.019 µM; hROCK2IC50 = 0.011 µM), ponatinib (hROCK1IC50 = 0.197 µM; hROCK2IC50 = 0.056 µM), tivozanib (hROCK1IC50 = 12.86 µM; hROCK2IC50 = 0.856 µM), nialamide (hROCK1IC50 = 18.8 µM; hROCK2IC50 = 29.2 µM) and tucatinib (hROCK1IC50 = 51.45 µM; hROCK2IC50 = 18.62 µM). The results of this study highlight ruxolitinib and baricitinib as potent ROCK inhibitors with IC50 values in the low nanomolar range. Tivozanib showed 15-fold selectivity for ROCK2 over ROCK1. Molecular dynamics simulations with ruxolitinib revealed a tight binding with the ATP-binding site of ROCK1 and ROCK2, with stable bidentate hydrogen bonding interactions with the main chain of amino acid residues in the hinge region of ROCK1 and ROCK2. In addition, ruxolitinib showed selectivity for ROCK enzymes across AGC kinase family, highlighting its interesting ROCK/JAK multitarget profile, which can open new avenues in the discovery of novel multitarget-directed ligands for the treatment of neurodegenerative disorders. Biological validation revealed ruxolitinib’s safety profile against different neuronal and glial cell lines. Further, ruxolitinib reduced the immunolabeling for C3, a glial inflammation marker, in LPS-treated astrocytes. This work highlights ruxolitinib as a promising therapeutic option for Alzheimer's disease and other neurodegenerative conditions and pave the way for the new in vitro/in vivo studies for its repurposing. | Lucas Franco; Daniel Rodrigues; Gabriela Baumart; Flavia Gomes; Lídia Lima; Carlos Alberto Fraga; Pedro Pinheiro | Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a780e06dde43c90812d9fe/original/drug-repurposing-by-virtual-screening-identification-of-new-already-approved-rock-inhibitors-as-promising-drugs-to-target-neurodegeneration.pdf |
610cf54f4cb479f729299249 | 10.26434/chemrxiv-2021-313b1 | Don’t help them to bury the light. The interplay between intersystem crossing and hydrogen transfer in photoexcited curcumin revealed by state-hopping dynamics. | Curcumin is a natural compound extracted from turmeric (curcuma longa), which has shown remarkable antiinflammatory, antibacterial, and possibly anticancert properties. The intense absorption in the visible domain, and the possibility of intersystem crossing make curcumin attractive also for photodynamic therapy purposes. In the present contribution we unravel, thanks to non-adiabatic state hopping dynamics, the competition between intersystem crossing and hydrogen transfer within enol, the most stable tautomer of curcumin. Most notably, we show that while hydrogen-transfer is ultrafast and happens in the sub-ps regime, intersystem crossing is still present, as shown by the non-negligible population of the triplet state manifold after 2 ps. Hence, while the hydrogen transfer channel can act as an unfavorable deactivating channel, curcumin, also in the red-shifted absorption enol form, can still be regarded as potentially favorable for photodynamic therapy applications. | Raul Losantos ; Andreea Pasc; Antonio Monari | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610cf54f4cb479f729299249/original/don-t-help-them-to-bury-the-light-the-interplay-between-intersystem-crossing-and-hydrogen-transfer-in-photoexcited-curcumin-revealed-by-state-hopping-dynamics.pdf |
62e7a293d131b7b0ea0871cc | 10.26434/chemrxiv-2022-qhc16 | Energy Transfer-Enabled Unsymmetrical Diamination Using Unprecedented Bifunctional Nitrogen-Radical Precursors | Vicinal diamines, especially unsymmetrical ones, are among the most common structural motifs in biologically active molecules, natural products, and pharmaceuticals. While the catalytic diamination of carbon–carbon double bonds provides rapid access to diamines, these reactions are often limited to installing undifferentiated amino functionalities through transition-metals or hyper-valent iodine reagents catalysis. Herein, we disclose a metal-free, photosensitized dearomative unsymmetrical diamination of various electron-rich (hetero)arenes with bifunctional diamination reagents, producing a series of previously inaccessible vicinal diamines with excellent regio- and diastereoselectivity. A class of unprecedented bifunctional nitrogen-radical precursors was developed for the first time to simultaneously generate two N-centered radicals with different reactivities via an energy transfer (EnT) process. In addition, the protocol was also suitable for a wide range of alkenes. Notably, the formed vicinal diamines bear two differentiated amino functionalities, and either imine or amide units could be easily and orthogonally convertedconverted converted converted into unprotected amines, thereby facilitating the selective downstream transformations. | Frank Glorius; Guangying Tan; Mowpriya Das; Roman Kleinmans; Felix Katzenburg; Constantin Daniliuc | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e7a293d131b7b0ea0871cc/original/energy-transfer-enabled-unsymmetrical-diamination-using-unprecedented-bifunctional-nitrogen-radical-precursors.pdf |
665122fc21291e5d1d32266c | 10.26434/chemrxiv-2024-8fxl9 | Dynamic cycling enhances battery lifetime | Laboratory aging campaigns benchmark and elucidate the complex degradation behavior of lithium-ion batteries, and are critical not only for developing new battery chemistries and cell designs but also for engineering reliable battery management systems. Critically, these laboratory experiments aim to quantify and capture realistic aging mechanisms. In this study, we systematically compare dynamic discharge profiles representative of electric vehicle driving to the well-accepted constant-current profiles. Surprisingly, we discovered that dynamic discharge enhances lifetime substantially compared to constant current discharge. Specifically, for the same average current and voltage window, varying the dynamic discharge profile leads to an increase of up to 38 % in equivalent full cycles at end-of-life. Explainable machine learning reveals the importance of low-frequency current pulses as well as time-induced aging under these realistic discharge conditions. Our work quantifies the importance of evaluating new battery chemistries and designs with realistic load profiles, and highlights the opportunities to revisit our understanding of aging mechanisms at the chemistry, materials, and cell levels. | Alexis Geslin; Le Xu; Devi Ganapathi; Kevin Moy; William Chueh; Simona Onori | Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665122fc21291e5d1d32266c/original/dynamic-cycling-enhances-battery-lifetime.pdf |
6728fe5cf9980725cf14a6b4 | 10.26434/chemrxiv-2024-vf8bj | Catching Fullerenes: Synthesis of Molecular Nanogloves | Herein, we report the synthesis of a new series of rigid, all meta-phenylene, conjugated deep-cavity molecules, displaying high binding affinity towards buckyballs. A facile two-step synthetic approach with an overall yield of approximately 54% has been developed using a templating strategy that combines the general structure of resorcin[4]arene and [12]cyclo-meta-phenylene. These two moieties are covalently linked via four acetal bonds resulting in a glove-like architecture. 1H NMR titration experiments reveal fullerene binding affinities (Ka) ex-ceeding >10^6 M–1. The size complementarity between fullerenes and these scaffolds maximizes CH⋯π and π⋯π interactions and their host:guest adduct resemble a ball in a glove, hence their name as nanogloves. Fullerene recognition is tested by suspending carbon soot in a solution of nanoglove in 1,1,2,2-tetrachloroethane, where more than a dozen fullerenes are observed ranging from C60 to C96. | Saber Mirzaei; Xiangquan Hu; M. Saeed Mirzaei; Victor M. Espinoza Castro; Xu Wang; Nicholas Figueroa; Tieyan Chang; Ying-Pin Chen; Gabriella Prieto Rios; Natalia Isabel Gonzalez-Pech; Yu-Sheng Chen; Raúl Hernández Sánchez | Organic Chemistry; Analytical Chemistry; Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6728fe5cf9980725cf14a6b4/original/catching-fullerenes-synthesis-of-molecular-nanogloves.pdf |
652961d78bab5d2055483e20 | 10.26434/chemrxiv-2023-lvj76 | The role of helicity in PFAS resistance to degradation:
DFT simulation of electron capture and defluorination
| Defluorination of perfluorinated alkyl substances (PFASs) via the direct capture of excess electrons poses a promising path to environmental decontamination. Herein we show that ab initio model optimization methods can be adapted to simulate the changes to molecular geometry that result from electron capture. These reaction pathways demonstrate that the introduction of an additional electron causes a loss of the helical arrangement along linear carbon tail chains. Regaining helicity is sufficiently favourable to enable fluoride release in C7-C10 carboxylate or sulfonate PFAS chains; shorter chains are enthalpically hindered from degradation while the additional charge is stabilized on longer chains by the greater entropy their flexibility permits. These results suggest that reductive PFAS treatment processes could be made more effective under high pressure or confined conditions. | Matt McTaggart; Cecile Malardier-Jugroot | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Computational Chemistry and Modeling; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652961d78bab5d2055483e20/original/the-role-of-helicity-in-pfas-resistance-to-degradation-dft-simulation-of-electron-capture-and-defluorination.pdf |
60c74361567dfe6bacec40c2 | 10.26434/chemrxiv.8206349.v2 | Rapid Visualization of Chemically Related Compounds Using Kendrick Mass Defect as a Filter in Mass Spectrometry Imaging | <div>
<p>Kendrick mass defect (KMD) analysis is widely used for
helping the detection and identification of chemically related compounds based
on exact mass measurements. We report here the use of KMD as a criterion for
filtering complex mass spectrometry dataset. The method enables an automated, easy
and efficient data processing, enabling the reconstruction of 2D distributions
of family of homologous compounds from MSI images. We show that the KMD filtering,
based on an in-house software, is suitable and robust for high resolution (full
width at half-maximum, FWHM, at <i>m/z</i>
410 of 20 000) and very high-resolution (FWHM, at <i>m/z</i> 410 of 160 000) MSI data. This method has been successfully
applied to two different types of samples, bacteria co-cultures and brain
tissue section</p>
</div> | Christopher Kune; Andréa Mc Cann; Raphaël La Rocca; Anthony Arguelles Arias; Mathieu Tiquet; Daan van Kruining; Pilar Martinez-Martinez; Marc Ongena; Gauthier Eppe; Loïc Quinton; Johann Far; Edwin De Pauw | Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74361567dfe6bacec40c2/original/rapid-visualization-of-chemically-related-compounds-using-kendrick-mass-defect-as-a-filter-in-mass-spectrometry-imaging.pdf |
6352382e55a08126fcbee875 | 10.26434/chemrxiv-2022-03m5q | Predicting Propellant Properties of Boron-Based Hypergolic Ionic Liquids via Machine Learning | Boron-based hypergolic ionic liquids (HILs) have gained increasing attention in the field of propellants due to the low toxicity, high energy density, and short ignition delay time. However, the performance of propellants based on boron-based HILs is still inferior to hydrazine derivatives, restricting their widespread applications as a rocket propellant. To boost the propellant performance of boron-based HILs, constantly engineering their chemical structures is highly necessary. The conventional approaches modify the anions and cations of the ionic liquids based on experiences and heuristics, and then experimentally verify the physicochemical properties of the synthesized compounds. However, such a trial-and-error design cycle is biased by practitioners’ preferences and the variations of experimental conditions. Meanwhile, it is expensive and tedious to measure all relevant properties of the ionic liquids by experiments. To solve these problems, we propose a protocol of combining machine learning and density functional theory (DFT) calculations to predict boron-based HILs’ properties such as ignition delay time, thermal stability, and energy storage capacity. With well-curated data, the experimental results show that the machine learning approaches can satisfactorily predict the chemical properties of boron-based HILs. We also use the Shapley value to find that (1) the thermal correction to enthalpy is critical for ignition delay, (2) HOMO, electronic energy and entropy values have a major impact on decomposition temperature, and (3) electronic energy also has a significant impact on the specific impulse. | Yang Xiao; Hang-Cheng Dong; Tieyong Zeng; Tinghao Ma; Feng-Lei Fan; Deng-Tao Yang | Theoretical and Computational Chemistry; Energy; Earth, Space, and Environmental Chemistry; Space Chemistry; Machine Learning; Fuels - Energy Science | CC BY NC 4.0 | CHEMRXIV | 2022-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6352382e55a08126fcbee875/original/predicting-propellant-properties-of-boron-based-hypergolic-ionic-liquids-via-machine-learning.pdf |
6392fa530fd99207553ebad1 | 10.26434/chemrxiv-2022-r5kct-v4 | Optical tactile sensor using scattering inside sol–gel-derived flexible macroporous monoliths | Tactile sensors are an essential technology for robots, and various types have been developed. This paper reports on a new optical tactile sensor based on multiple scattering in a porous material with a viscoelastic phase-separated structure fabricated by a sol–gel method. When a macroporous silicone monolith with a few micrometer diameter skeletons was compressed, the diffuse light intensity near the light source was reduced due to Mie multiple scattering. This light intensity change was opposite to the behavior of conventional polymer foams (cellular structures), which have a large structural scale. A simple tactile sensor using a macroporous monolith and a photo reflector was fabricated based on this finding. The skeleton diameter was an important factor for the sensor. In the case of macroporous silicones, the voltage-strain curve showed an almost hysteresis-free clear response. However, the response of macroporous polymethylmethacrylate monolith with a smaller skeleton diameter was weak due to low Mie scattering intensity. Sensors using sol–gel derived macroporous materials have the potential to be thinner and provide improved surface tactile sensation compared to foam materials. | Gen Hayase | Physical Chemistry; Optics | CC BY NC 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6392fa530fd99207553ebad1/original/optical-tactile-sensor-using-scattering-inside-sol-gel-derived-flexible-macroporous-monoliths.pdf |
61c5f63c7284d010ccf723e1 | 10.26434/chemrxiv-2021-8nlfl | Concise syntheses of GB22, GB13 and himgaline by cross-coupling and complete reduction | Class III neuroactive metabolites from the bark of Galbu-limima belgraveana occur in variable distribution and are not easily procured by chemical synthesis. Here we decrease the synthetic burden of himgaline to nearly one-third of the prior best (7–9 vs. 19–31 steps) by cross-coupling high fraction aromatic (FAr) building blocks followed by com-plete, stereoselective reduction to high-fraction sp3 (Fsp3) products. This short entry into GB alkaloid space allows its extensive exploration and biological interrogation. | Eleanor Landwehr; Meghan Baker; Takuya Oguma; Hannah Burdge; Takahiro Kawajiri; Ryan Shenvi | Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c5f63c7284d010ccf723e1/original/concise-syntheses-of-gb22-gb13-and-himgaline-by-cross-coupling-and-complete-reduction.pdf |
64c7badf658ec5f7e57d966e | 10.26434/chemrxiv-2023-fjllf-v2 | Interlaboratory Study Assessing the Analysis of Supercapacitor Electrochemistry Data | Supercapacitors are fast-charging energy storage devices of great importance for developing robust and climate-friendly energy infrastructures for the future. Research in this field has seen rapid growth in recent years. Therefore, consistent reporting practices must be implemented to enable reliable comparison of device performance. Although several studies have highlighted the best practices for analysing and reporting data from such energy storage devices, there is yet to be an empirical study investigating whether researchers in the field are correctly implementing these recommendations, and which assesses the variation in reporting between different laboratories. Here, we address this deficit by carrying out the first interlaboratory study of the analysis of supercapacitor electrochemistry data. We find that the use of incorrect formulae and researchers having different interpretations of key terminologies are the primary causes of variability in data reporting. Furthermore, we highlight the more significant variation in reported results for electrochemical profiles showing non-ideal capacitive behaviour. From the insights gained through this study, we make additional recommendations to the community to help ensure consistent reporting of performance metrics moving forward. | Jamie W. Gittins; Yuan Chen; Stefanie Arnold; Veronica Augustyn; Andrea Balducci; Thierry Brousse; Elzbieta Frackowiak; Pedro Gómez-Romero; Archana Kanwade; Lukas Köps; Plawan Kumar Jha; Dongxun Lyu; Michele Meo; Deepak Pandey; Le Pang; Volker Presser; Mario Rapisarda; Daniel Rueda-García; Saeed Saeed; Parasharam M. Shirage; Adam Ślesiński; Francesca Soavi; Jayan Thomas; Maria-Magdalena Titirici; Hongxia Wang; Zhen Xu; Aiping Yu; Maiwen Zhang; Alexander C. Forse | Energy; Energy Storage; Power | CC BY 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c7badf658ec5f7e57d966e/original/interlaboratory-study-assessing-the-analysis-of-supercapacitor-electrochemistry-data.pdf |
60c75194567dfe7b9fec5ab8 | 10.26434/chemrxiv.11447775.v3 | In situ small angle X-ray scattering reveals solution phase discharge of Li-O2 batteries with weakly solvating electrolytes | Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and dissolved LiO2 governs whether Li2O2 grows as a conformal surface film or larger particles, leading to low or high capacities, respectively. However, governing factors for Li2O2 packing density and capacity need better understanding, requiring in situ metrologies with structural sensitivity from the atomic to sub-micron scale. Here, we establish in situ small and wide angle X-ray scattering as a suitable method to record the Li2O2 phase evolution with atomic to sub-micrometer resolution during cycling a custom-built in situ Li-O2 cell. Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative structural information from complex multi-phase systems. Surprisingly, we find that features are absent that would point at a Li2O2 surface film formed via two consecutive electron transfers, even in poorly solvating electrolytes thought to be prototypical for surface growth. All scattering data can be modeled by stacks of thin Li2O2 platelets eventually forming large toroidal particles. Higher discharge overpotentials (high currents) lead to smaller Li2O2 particles, but there is no transition to an electronically passivating, conformal Li2O2 coating. This implies that mass transport of reactive species rather than electronic transport through a Li2O2 film limits the discharge capacity. Provided that species mobilities and carbon surface areas are high, this allows for high discharge capacities even in poorly solvating electrolytes. The currently accepted Li-O2 reaction mechanism ought to be reconsidered.<br /> | Christian Prehal; Aleksej Samojlov; Manfred Nachtnebel; Manfred Kriechbaum; Heinz Amenitsch; Stefan Freunberger | Energy Storage | CC BY 4.0 | CHEMRXIV | 2020-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75194567dfe7b9fec5ab8/original/in-situ-small-angle-x-ray-scattering-reveals-solution-phase-discharge-of-li-o2-batteries-with-weakly-solvating-electrolytes.pdf |
630496fcf9e99c2d7086ab3a | 10.26434/chemrxiv-2022-v1bvb | Shape and stability matter: enhanced catalytic reactions via sol-gel entrapped catalysts | The morphology and the unique chemical and physical stability of organosilica-entrapped sol-gel catalysts allow to apply them to successfully mediate the synthesis of a wide variety of valued molecules, including polymers, manufactured by the fine chemical industry. Referring to selected independent research achievements, in this study we offer a practically oriented insight on these catalytic materials that will hopefully be useful in renewed, unified catalysis education aimed to foster practically relevant innovation and uptake of heterogeneous catalysis in the fine chemical industry. | Rosaria Ciriminna; Mario Pagliaro | Catalysis; Chemical Education; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC 4.0 | CHEMRXIV | 2022-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630496fcf9e99c2d7086ab3a/original/shape-and-stability-matter-enhanced-catalytic-reactions-via-sol-gel-entrapped-catalysts.pdf |
64f58f4679853bbd780f09d7 | 10.26434/chemrxiv-2023-d22qx | Atroposelective Chan-Evans-Lam Amination | The synthetic control of atropoisomerism along C─N bonds is a major challenge, and methods that allow C─N atroposelective bond formation are rare. This is a problem because each atropoisomer can feature starkly differentiated biological properties. Yet, among the three most practical and applicable classical amination methods available: 1) the Cu-catalyzed Ullmann-Goldberg reaction, 2) the Pd-catalyzed Buchwald-Hartwig reaction, and 3) the Cu-catalyzed Chan-Evans-Lam reaction, none has truly been rendered atroposelective at the newly formed C─N bond. The first ever Chan-Evans-Lam atroposelective amination is herein described with a simple copper catalyst and new PyrOx chiral ligand. This method constitutes a change of paradigm in the field. | Vinzenz Thönnißen; Johannes Westphäling; Iuliana Atodiresei; Frederic Patureau | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f58f4679853bbd780f09d7/original/atroposelective-chan-evans-lam-amination.pdf |
60c74648702a9bfeaf18aba8 | 10.26434/chemrxiv.11298398.v1 | A General Convergent Strategy for the Synthesis of Tetrasubstituted Furan Fatty Acids (FuFAs) | Synthetic route for the synthesis of tetrasubstituted furan fatty acids; including experimental details, characterisation, and spectral data of all intermediates. | Yamin Wang; Gareth Pritchard; Marc Kimber | Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74648702a9bfeaf18aba8/original/a-general-convergent-strategy-for-the-synthesis-of-tetrasubstituted-furan-fatty-acids-fu-f-as.pdf |
60c750644c8919a1adad3d84 | 10.26434/chemrxiv.9970571.v3 | Site-selective Protonation of the One-electron Reduced Cofactor in [FeFe]-Hydrogenase | Hydrogenases are microbial redox enzymes
that catalyze H2 oxidation and proton reduction (H2 evolution). While
all hydrogenases show high oxidation activities, the majority of
[FeFe]-hydrogenases are excellent H2 evolution catalysts as well. Their
active site cofactor comprises a [4Fe-4S] cluster covalently linked to a
diiron site equipped with carbon monoxide and cyanide ligands that
facilitate catalysis at low overpotential. Distinct proton transfer
pathways connect the active site niche with the solvent, resulting in a
non-trivial dependence of hydrogen turnover and bulk pH. To analyze the
catalytic mechanism of [FeFe]-hydrogenase, we employ in situ infrared
spectroscopy and infrared spectro-electrochemistry. Titrating the pH
under H2 oxidation or H2 evolution conditions reveals the influence of
site-selective protonation on the equilibrium of reduced cofactor
states. Governed by pKa differences across the active site niche and
proton transfer pathways, we find that individual electrons are
stabilized either at the [4Fe-4S] cluster (alkaline pH values) or at the
diiron site (acidic pH values). This observation is discussed in the
context of the natural pH dependence of hydrogen turnover as catalyzed
by [FeFe]-hydrogenase.<br /> | Konstantin Laun; Iuliia Baranova; Jifu Duan; Leonie Kertess; Florian Wittkamp; Ulf-Peter Apfel; Thomas Happe; Moritz Senger; Sven T. Stripp | Electrochemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Biophysics; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750644c8919a1adad3d84/original/site-selective-protonation-of-the-one-electron-reduced-cofactor-in-fe-fe-hydrogenase.pdf |
60c74f9fbb8c1a75393db971 | 10.26434/chemrxiv.12925295.v1 | Probing Folded Proteins and Intact Protein Complexes by Desorption Electrospray Ionization Mass Spectrometry | Native mass spectrometry (Native MS) enables the
study of intact proteins as well as non-covalent protein-protein and
protein-ligand complexes in their biological state. In this work we present the
application of a prototype Waters DESI source for rapid surface measurements of
folded and native protein structures. Ions with narrow charge state
distribution (CSD), i.e. folded structures are observed in the spectra of protein
samples with the molecular weight ranging from 8.6 kDa up to 66.4 kDa. Intact
protein complexes of holo-myoglobin and tetrameric hemoglobin are also successfully
detected from a surface. These results reveal that DESI could be gentle enough
to detect compact structures and noncovalent bond interactions. We also examine
whether unfolded proteins and protein complexes can refold during transient spray
solvent-sample interactions during DESI. Our results from ion mobility
experiments of standards of ubiquitin, cytochrome c and protein complex
myoglobin indicate that such phenomenon may occur, presenting artificial
native-like spectra. Nevertheless, the observation of hemoglobin tetramer is
promising as it demonstrates the capability of DESI to maintain truly native
structures. | Bin Yan; Josephine Bunch | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f9fbb8c1a75393db971/original/probing-folded-proteins-and-intact-protein-complexes-by-desorption-electrospray-ionization-mass-spectrometry.pdf |
60c74b1b0f50db64e9396ba3 | 10.26434/chemrxiv.12287879.v1 | Site-Specific Electrodeposition Enables Self-Terminating Growth of Atomically Dispersed Metal Catalysts | <p>The growth of atomically dispersed metal catalysts (ADMCs) remains a great challenge owing to the thermodynamically driven atom aggregation. Here we report a surface-limited electrodeposition technique that uses site-specific substrates for the rapid and room-temperature synthesis of ADMCs. We obtained ADMCs by the underpotential deposition (UPD) of a single-atom nonnoble metal onto the chalcogen atoms of chemically exfoliated transition metal dichalcogenides and subsequent galvanic displacement with a more-noble single-atom metal. The site-specific electrodeposition (SSED) enables the formation of energetically favorable metal–support bonds, and then automatically terminates the sequential formation of metallic bonding. The self-terminating effect restricts the metal deposition to the atomic scale. The modulated ADMCs exhibit remarkable activity and stability in the hydrogen evolution reaction compared to state-of-the-art single-atom electrocatalysts. We demonstrate that this SSED methodology could be extended to the synthesis of a variety of ADMCs (for example, Pt, Pd, Rh, Cu, Pb, Bi, and Sn single atoms), showing its general scope for the large-scale production of functional ADMCs in heterogenous catalysis. </p> | Yi Shi; Wenmao Huang; Jian Li; Yue Zhou; Zhongqiu Li; Yunchao Yin; Xinghua Xia | Nanocatalysis - Catalysts & Materials; Electrochemistry; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b1b0f50db64e9396ba3/original/site-specific-electrodeposition-enables-self-terminating-growth-of-atomically-dispersed-metal-catalysts.pdf |
66b5d740c9c6a5c07a986922 | 10.26434/chemrxiv-2024-b8hqh | What is the exchange-repulsion energy? Insight by partitioning into physically meaningful contributions | Exchange repulsion, the dominant repulsive contribution to intermolecular interaction energies, is caused by the Pauli principle, which enforces that electrons with the same spin must not be located at the same place. Starting from the Heitler-London expression of the exchange-repulsion energy, Exr, we investigate how it can be partitioned into physically relevant and comprehensible contributions. We demonstrate that a division of Exr into a positive kinetic and a negative potential part is possible. However, these contributions correlate only poorly with the actual exchange-repulsion energy. A meaningful partitioning of Exr is derived, where the kinetic energy contribution belongs to a term that vanishes for exact Hartree-Fock wave functions. The remaining pure potential energy terms are distinguished into an exchange integral contribution, Exi, as well as contributions to the repulsion-energy with two, three and four orbital indices (Exr2, Exr3, and Exr4). Qualitative explanations of these terms and their physical origin are proposed. The forms, relationships and absolute sizes of the four parts of Exr suggest an intuitive partitioning of the exchange-repulsion energy into orbital-pair contributions. Insight into the analytic form and quantitative size of the contributions to Exr is provided by considering the 3Sigma+u (1sigma g 1sigma u) state of the H2 molecule, the water dimer, as well as an argon atom interacting with Cl2 and N2. It is demonstrated that Exr is best described as a contribution due to the potential energy and that its leading contribution, Exr2, provides an intuitive qualitative and quantitative approach towards the exchange-repulsion energy. | Johannes Henrichsmeyer; Michael Thelen; Reinhold F. Fink | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5d740c9c6a5c07a986922/original/what-is-the-exchange-repulsion-energy-insight-by-partitioning-into-physically-meaningful-contributions.pdf |
641b37052bfb3dc25130e17d | 10.26434/chemrxiv-2023-rknfd-v2 | A scalable crystal representation for reverse engineering of novel inorganic materials using deep generative models | The efficient search for crystals with targeted properties is a significant challenge in materials discovery. The rapidly growing field of materials informatics has so far primarily focused on the application of AI/ML models to predict the properties of known crystals from their fundamental and derived properties as descriptors. In the last few years, deep learning-based approaches have spawned a slew of innovative data-driven materials research applications. Materials scientists have used these techniques for the reverse engineering of crystal structures for target applications. However, one of the challenges has been the representation of the crystal structures in the machine readable format. Proposed representations in the literature lack in generality and scalability. In this paper, we train a conditional variational autoencoder with a scalable and invertible representation along with the elemental properties of the constituents as descriptors to inverse-design new crystal structures with specified attributes. When targeting formation energy, we show that our model predicts structures that are not in the complete OQMD database. Finally, we use first-principles density functional theory calculations to validate our findings and show that the developed model is able to generate novel crystal structures for targeted property, i.e. formation energy in this case. | Rochan Bajpai; Atharva Shukla; Janish Kumar; Abhishek Tewari | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641b37052bfb3dc25130e17d/original/a-scalable-crystal-representation-for-reverse-engineering-of-novel-inorganic-materials-using-deep-generative-models.pdf |
64fbd8e3b6ab98a41c1c0412 | 10.26434/chemrxiv-2023-g6t3m | CatScore: A High-Efficiency Evaluation Metric for Asymmetric Catalyst Design | Asymmetric catalysis plays a crucial role in advancing medicine and materials science. However, the prevailing experiment-driven methods for catalyst evaluation are both resource-heavy and time-consuming. To address this challenge, we present CatScore - a learning-centric metric designed for the automatic evaluation of catalyst design models at both instance and system levels. This approach harnesses the power of deep learning to predict product selectivity as a function of reactants and the proposed catalyst. The predicted selectivity serves as a quantitative score, enabling a swift and precise assessment of a catalyst’s activity. On an instance level, CatScore’s predictions correlate closely with experimental outcomes, demonstrating a Spearman’s ρ = 0.84, which surpasses the density functional theory (DFT) with ρ = 0.54 and round-trip accuracy metrics at ρ = 0.24. Importantly, when ranking catalyst candidates, CatScore achieves a mean reciprocal ranking significantly superior to traditional DFT methods, marking a considerable reduction in labor and time investments needed to find top-performing catalysts. | Bing Yan; Kyunghyun Cho | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fbd8e3b6ab98a41c1c0412/original/cat-score-a-high-efficiency-evaluation-metric-for-asymmetric-catalyst-design.pdf |
63862f6c6b4e814dbd83e36f | 10.26434/chemrxiv-2022-zcqtq | Mechanocatalytic partial depolymerization of lignocellulosic feedstock towards oligomeric glycans | The depolymerization of lignocellulosic feedstock with a heterogeneous composition is a major challenge and usually leads to the formation of monosaccharides as main
products. Our work aims to convert such feedstock into oligomeric glycans as more valuable products compared to sugars, by using mechanocatalysis in a planetary ball mill in a cost-efficient and resource-saving manner. Herein, we utilized raw materials such as wheat straw, beet pulp, cocoa shells and apple pomace as residual natural raw materials from food and feed production. Reaction parameters such as rotational speed, acid content and milling duration were investigated and optimized towards a maximum amount of soluble species and a minimum of monosaccharides. The optimization for cellulose as substrate resulted in a nearly full-soluble fraction containing oligomeric glycans. Based on these results the reaction parameters were transferred and further optimized for lignocellulosic feedstock. For wheat straw a solubility of over 90 % was achieved comprising a mixture of oligomeric glycans as well as partially depolymerized lignin. | Gregor Meyer; Marius Wolf; Stefan Hanstein; Marcus Rose | Catalysis; Chemical Engineering and Industrial Chemistry; Natural Resource Recovery; Reaction Engineering; Acid Catalysis | CC BY 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63862f6c6b4e814dbd83e36f/original/mechanocatalytic-partial-depolymerization-of-lignocellulosic-feedstock-towards-oligomeric-glycans.pdf |
60c7523f469df43e6ef44b26 | 10.26434/chemrxiv.13271594.v1 | Salt Dependent Mesoscopic Model for RNA with Multiple Strand Concentrations | Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength. | Izabela Ferreira; Tauanne Dias Amarante; Gerald Weber | Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7523f469df43e6ef44b26/original/salt-dependent-mesoscopic-model-for-rna-with-multiple-strand-concentrations.pdf |
6557f9a0dbd7c8b54b7c014d | 10.26434/chemrxiv-2023-v99p5 | Coagulation and crystallinity in Sn (II, IV) oxide as an electron transfer layer | Stannic oxide (SnO2) synthesized by the sol-gel method showed efficient optoelectronic mobility due to high
crystallinity and coagulation involved in the morphology. These properties are applicable for SnO2 to be used as an
electron transfer layer (ETL) in perovskite solar cells. The structure and morphology were determined by XRD and
SEM which also indicated formation of Sn (II) O with p-type doping. The optical properties were reflected in the
UV-Vis and PL studies. A coagulation factor was determined based on the polynomial fits of the surface and linear
profiles | N Usharani; Ramagiri Praveen Kumar; Arnab Bhattacharyya; A Raju | Materials Science; Nanoscience; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6557f9a0dbd7c8b54b7c014d/original/coagulation-and-crystallinity-in-sn-ii-iv-oxide-as-an-electron-transfer-layer.pdf |
670c86f251558a15effc4c65 | 10.26434/chemrxiv-2024-3b53q | Equilibrium Driven Ring Expansion Metathesis Polymerization via Tunable Chain Transfer Processes | Ring expansion metathesis polymerization (REMP) is a robust and versatile method used to access polymeric cyclic architectures for applications in biomedicine, electronics, and performance engineering. Cyclic Ru-benzylidene REMP catalyst CB6 demonstrates higher stability and polymerization rates compared to other Ru-based systems. However, CB6 also exhibits an unusual molar mass evolution profile where high molar mass cyclic polymers are produced at early time points followed by a gradual decrease in molar mass. For broad cyclic polymer applications to be fully realized, a mechanistic understanding of REMP is crucial. In this work, we investigate the polymerization profiles of CB6 using a series of mechanistic studies to probe the requisite chain transfer steps envisaged for such a polymerization profile. Furthermore, our studies reveal an intricate relationship between reaction concentration and equilibrium molar mass. These collective studies demonstrate CB6’s role not only as an initiator, but also as a catalytic chain transfer agent. Overall, we showcase a new toolkit by which to control REMP that will allow further optimization of catalyst design and the creation of novel cyclic materials. | Meredith Pomfret; Nicholas Serck; Lucy Miller; Matthew Golder | Polymer Science; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c86f251558a15effc4c65/original/equilibrium-driven-ring-expansion-metathesis-polymerization-via-tunable-chain-transfer-processes.pdf |
6660d0d6418a5379b02a13aa | 10.26434/chemrxiv-2024-n2v36 | Evolutionary Optimization of the Reduced Gas-phase Isoprene Oxidation Mechanism | Atmospheric chemistry is highly complex, and significant reductions in the size of the chemical mechanism are required to simulate the atmosphere. One of the bottlenecks in creating reduced models is identifying optimal numerical parameters. This process has been difficult to automate, and often relies on manual testing. In this work, we present the application of particle swarm optimization (PSO) towards optimizing the stoichiometric coefficients and rate constants of a reduced isoprene atmospheric oxidation mechanism. Using PSO, we are able to achieve up to 27% improvement in our accuracy metric when compared to a manually tuned reduced mechanism, leading to a significantly optimized final mechanism. This work demonstrates PSO as a promising and thus far underutilized tool for atmospheric chemical mechanism development. | Arijit Chakraborty; Forwood Wiser; Siddhartha Sen; V. Faye McNeill; Venkat Venkatasubramanian | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6660d0d6418a5379b02a13aa/original/evolutionary-optimization-of-the-reduced-gas-phase-isoprene-oxidation-mechanism.pdf |
6319e53e5351a3607cf32527 | 10.26434/chemrxiv-2022-hs89d | A Modular and Efficient Synthetic Platform for the Construction of Supramolecular Mono-telechelic Polymers | Supramolecular telechelic polymers are intriguing macromolecular systems for the construction of complex supramolecular systems and responsive soft materials. In this work, we report a practical synthetic approach to preparing supramolecular mono-telechelic polymers with high efficiency and modularity. With a combination of in situ catalyst functionalization, ring- opening metathesis polymerization, and post-polymerization modification, a series of supramolecular mono-telechelic polymers with different supramolecular end-groups and sidechains are synthesized. Several selected examples are then discussed in detail to demonstrate their potential in constructing hierarchical supramolecular architectures, adaptive materials, and supramolecular biomaterials. It is highly anticipated that the synthetic approach reported here will provide rapid and controlled access to complex supramolecular telechelic polymers with tailored functions. | Jiaxiong Liu; Fang Huang; Yiliu Liu | Polymer Science; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6319e53e5351a3607cf32527/original/a-modular-and-efficient-synthetic-platform-for-the-construction-of-supramolecular-mono-telechelic-polymers.pdf |
64e34fe400bbebf0e68bcfb8 | 10.26434/chemrxiv-2023-qdvmm | Expanding the chemical space using a Chemical Reaction Knowledge Graph | In this work, we present a new molecular de novo design approach which utilizes a knowledge graph encoding of chemical reactions, extracted from the publicly available USPTO (United States Patent and Trademark Office) dataset. Our proposed method can be used to expand the chemical space by performing forward synthesis prediction on the knowledge graph and can generate libraries of de novo compounds along with a valid synthetic route. The forward synthesis prediction of novel compounds involves two steps. In a first step, a graph neural network-based link prediction model is used to suggest pairs of existing reactant nodes in the graph that are likely to react. In a second step, product prediction is performed using a molecular transformer model to obtain the potential products for the suggested reactant pairs. We achieve a ROC-AUC score of 0.861 for link prediction in the knowledge graph and for the product prediction a top-1 accuracy of 0.924. The method’s utility is demonstrated by generating a set of de novo compounds by predicting high probability reactions in USPTO. The generated compounds are diverse in nature and many exhibits drug-like properties. Further, evaluation of the potential activity using a quantitative structure–activity relationship (QSAR) model suggested presence of potential dopamine receptor D2 (DRD2) modulators among the proposed compounds. In summary, our results suggest that the proposed method can expand the easily accessible chemical space and identify novel drug-like compounds for a specific target. | Emma Rydholm; Tomas Bastys; Emma Svensson; Christos Kannas; Ola Engkvist; Thierry Kogej | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e34fe400bbebf0e68bcfb8/original/expanding-the-chemical-space-using-a-chemical-reaction-knowledge-graph.pdf |
60c74b56ee301cef4ec79dee | 10.26434/chemrxiv.12320504.v1 | Near-Infrared AIE Dots with Chemiluminescence for Deep-Tissue Imaging | A novel AIEgen named TBL was
designed based on the classic CL emitter luminol. The NIR CL emission of TBL
dots could penetrate through 3 cm-thick pork ham, which is much better than NIR
fluorescence and blue CL emission. Moreover, the successful differentiation of
tumor and normal tissue makes this system promising for CL-guided tumor
diagnosis and surgery. | Chenchen LIU; Xiuxia Wang; Junkai Liu; Qiang Yue; Jacky W. Y. Lam; Liang Luo; Ben Zhong Tang | Aggregates and Assemblies; Imaging | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b56ee301cef4ec79dee/original/near-infrared-aie-dots-with-chemiluminescence-for-deep-tissue-imaging.pdf |
67ab0c866dde43c9085fb9b5 | 10.26434/chemrxiv-2025-9k50r | Temperature-Dependent Mechanistic Control of Nonadiabatic Tunnelling in Triplet
Carbenes | Experiments on three chemically similar triplet carbenes observed the reaction of one at 10 K, another only when heated to 65 K, whereas the third remained stable despite heating. As the products are singlets, it is clear that the reactions involve intersystem crossing in addition to intramolecular hydrogen transfer. Here, instanton theory is used to study various possible reaction mechanisms, including sequential and concerted pathways. The latter describes a new reaction mechanism which involves changing spin state (a nonadiabatic process) while heavy atoms tunnel underneath a barrier (an adiabatic process). In each case, we find that the concerted pathway dominates the rate at low temperatures, but at higher temperatures it switches to a sequential process. The existence of a crossover temperature is the key to explaining the experimental observations and demonstrates that temperature can control the reactivity of triplet carbenes via nonadiabatic tunnelling. | Meghna A. Manae; Jeremy O. Richardson | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab0c866dde43c9085fb9b5/original/temperature-dependent-mechanistic-control-of-nonadiabatic-tunnelling-in-triplet-carbenes.pdf |
6231d4c95c8dae62b4eb89e3 | 10.26434/chemrxiv-2022-p6kp9 | Nonacethrene Unchained: A Cascade to Chiral Contorted Conjugated Hydrocarbon with Two sp3-Defects | A dihydro precursor of helical diradicaloid nonacethrene undergoes a reaction cascade triggered by an oxidant to a chiral contorted polycyclic aromatic hydrocarbon named hypercethrene. In this ten-electron-oxidation process, four σ bonds, one π bond, and three six-membered rings are formed in a reaction sequence of up to nine steps to yield a 72-carbon-atom warped framework, comprising two configurationally locked [7]helicene units, fluorescent peropyrene unit, and two precisely installed sp3-defects.The key intermediate in this cascade is a closed nonacethrene derivative with one quaternary center, presumably formed via an electrocyclic ring closure of nonacethrene, which—
when activated by oxidation—undergoes an oxidative dimerization of phenalenyl to peropyrene. By controlling the amount oxidant used, two intermediates and one side product could be isolated and fully characterized, including single-crystal X-ray diffraction analysis, and one intermediate was detected by electron paramagnetic resonance spectroscopy. In concert with density functional theory calculations, these intermediates support the proposed reaction mechanism. Compared to peropyrene, the absorption and emission of hypercethrene are slightly red-shifted on account of extended conjugation and the fluorescence quantum yield of 0.45 is decreased by a factor of ~2. Enantiomerically enriched hypercethrene displays circularly polarized luminescence with a CPL brightness value of 8.3 M–1cm–1. This unexpected reaction cascade demonstrates that the reactivity of “unchained”diradicaloid compounds, which is typically considered an undesired feature, can be well-defined and employed as a useful, step-economic synthetic tool toward novel carbon nanostructures. | Daniel Čavlović; Daniel Häussinger; Olivier Blacque; Prince Ravat; Michal Juríček | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231d4c95c8dae62b4eb89e3/original/nonacethrene-unchained-a-cascade-to-chiral-contorted-conjugated-hydrocarbon-with-two-sp3-defects.pdf |
60c74e6af96a007614287aec | 10.26434/chemrxiv.12047103.v2 | SAMPL7 TrimerTrip Host-Guest Binding Poses and Binding Affinities from Spherical-Coordinates-Biased Simulations | Host-guest binding remains
a major challenge in modern computational modelling. The newest 7<sup>th</sup>
statistical assessment of the modeling of proteins and ligands (SAMPL)
challenge contains a new series of host-guest systems. The TrimerTrip host
binds to 16 structurally diverse guests. Previously, we have successfully employed
the spherical coordinates as the collective variables coupled with the enhanced
sampling technique metadynamics to enhance the sampling of the
binding/unbinding event, search for possible binding poses and predict the
binding affinities in all three host-guest binding cases of the 6<sup>th</sup>
SAMPL challenge. In this work, we employed the same protocol to investigate the
TrimerTrip host in the SAMPL7 challenge. As no binding pose is provided by the
SAMPL7 host, our simulations initiate from randomly selected configurations and
are proceeded long enough to obtain converged free energy estimates and search
for possible binding poses. The predicted binding affinities are in good agreement
with the experimental reference, and the obtained binding poses serve as a nice
starting point for end-point or alchemical free energy calculations. | Zhaoxi Sun | Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e6af96a007614287aec/original/sampl7-trimer-trip-host-guest-binding-poses-and-binding-affinities-from-spherical-coordinates-biased-simulations.pdf |
60c744f8bb8c1a18be3da5d7 | 10.26434/chemrxiv.8311865.v3 | Computationally Generated Maps of Surface Structures and Catalytic Activities for Alloy Phase Diagrams | <p>To facilitate the rational design of
alloy catalysts, we introduce a method for rapidly calculating the structure
and catalytic properties of a substitutional alloy surface that is in
equilibrium with the underlying bulk phase. We implement our method by developing
a way to generate surface cluster expansions that explicitly account for the
lattice parameter of the bulk structure. This approach makes it possible to
computationally map the structure of an alloy surface and statistically sample
adsorbate binding energies at every point in the alloy phase diagram. When
combined with a method for predicting catalytic activities from adsorbate binding
energies, maps of catalytic activities at every point in the phase diagram can
be created, enabling the identification of synthesis conditions likely to result
in highly active catalysts. We demonstrate our approach by analyzing Pt-rich Pt–Ni
catalysts for the oxygen reduction reaction, finding two regions in the phase
diagram that are predicted to result in highly active catalysts. Our analysis
indicates that the Pt<sub>3</sub>Ni(111) surface, which has the highest known
specific activity for the oxygen reduction reaction, is likely able to achieve
its high activity through the formation of an intermetallic phase with L1<sub>2</sub>
order. We use the generated surface structure and catalytic activity maps to
demonstrate how the intermetallic nature of this phase leads to high catalytic
activity and discuss how the underlying principles can be used in catalysis
design. We further discuss the importance of surface phases and demonstrate how
they can dramatically affect catalytic activity.</p> | Liang Cao; Le, Niu; Tim Mueller | Alloys; Catalysts; Computational Chemistry and Modeling; Theory - Computational; Electrocatalysis; Heterogeneous Catalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f8bb8c1a18be3da5d7/original/computationally-generated-maps-of-surface-structures-and-catalytic-activities-for-alloy-phase-diagrams.pdf |
60c749b5567dfee0a3ec4c3d | 10.26434/chemrxiv.12090423.v1 | Discovery of Potent Covid-19 Main Protease Inhibitors Using Machine Learning Based Virtual Screening Strategy | <p>The emergence and rapid spreading of
novel SARS-CoV-2 across the globe represent an imminent threat to public
health. Novel antiviral therapies are urgently needed to overcome this
pandemic. Given the great role of main protease of Covid-19 for virus
replication, we performed drug repurposing study using recently deposited main protease
structure, 6LU7. For instance, pharmacophore- and e-pharmacophore-based
hypotheses such as AARRH and AARR respectively were developed using available
small molecule inhibitors and utilized in the screening of DrugBank repository.
Further, hierarchical docking protocol was implemented with the support of Glide
algorithm. The resultant compounds were then examined for its binding free
energy against main protease of Covid-19 by means of Prime-MM/GBSA algorithm. Most
importantly, the resultant compounds antiviral activities were further predicted
by machine learning-based model generated by AutoQSAR algorithm. Finally, the
hit molecules were examined for its drug likeness and its toxicity parameters through
QikProp algorithm. Overall, the present analysis yielded four potential inhibitors (DB07800, DB08573, DB03744 and DB02986) that are
predicted to bind with main protease of Covid-19 better than currently used
drug molecules such as N3 (co-crystallized native ligand), Lopinavir and
Ritonavir. </p> | Muthu Kumar T; Rohini K; Nivya James; Shanthi V; Ramanathan Karuppasamy | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749b5567dfee0a3ec4c3d/original/discovery-of-potent-covid-19-main-protease-inhibitors-using-machine-learning-based-virtual-screening-strategy.pdf |
622112a5c6bb55074f7b9244 | 10.26434/chemrxiv-2022-sgc5w | Dynamic Catalysis Fundamentals: II. Consequences of scaling relationships on mechanisms and kinetics | Dynamic catalysis proffers a new strategy for leveraging linear free energy (LFE) relationships in catalysis to increase reaction rate, conversion, and selectivity by high-frequency, forced kinetic oscillations. This work explicates two dynamic catalysis mechanisms—“resonance” and quasi-static, characterized by finite frequency bands and high frequency limits, respectively—and details the necessary LFE parameters necessary for each dynamic catalysis phenomena to arise. Detailed analytical and numerical analyses reveal that under quasi-static mechanisms, Sabatier limits on reaction rates and thermodynamic limits on conversion can be completely subverted with sufficiently large kinetic oscillation amplitudes. In resonance mechanisms, reaction rates and conversion are still limited by Sabatier volcanos and thermodynamic equilibrium constants, respectively; however, these imposed limitations are those for a subset of elementary steps, rather than for the entire overall reaction. An investigation of dynamic catalysis for reaction schemes with multiple products reveals that quasi-static dynamic catalysis can drive selectivities of any intermediate or product to 100%, provided the appropriate LFE relationships. | Brandon Foley; Neil Razdan | Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622112a5c6bb55074f7b9244/original/dynamic-catalysis-fundamentals-ii-consequences-of-scaling-relationships-on-mechanisms-and-kinetics.pdf |
655e2c325bc9fcb5c922e8d0 | 10.26434/chemrxiv-2023-knlzg | Investigation of extraneous peak reveals ethylene oxide in food supplements | The global food supplement market is growing rapidly and so as the concerns on their quality, safety, and product efficacy. Product monitoring is challenging due to lenient regulation across the globe when compared to pharmaceutical counterparts. As part of quality and safety compliance of food supplements, products are being tested randomly in the Emirate of Abu Dhabi, UAE. This study is the part of routine monitoring of supplements during which an extraneous peak was observed and characterized. Analysis was performed using a Gas chromatography coupled to mass spectrometry and headspace extraction sampler. The extraneous peak with signal to noise ratio (S/N) of 140 was identified as ethylene oxide. Since traces were observed in active product formulation, it is worthwhile to monitor the levels in a higher number of supplements to elucidate its significance. | Abdulla Siddiqui; Ahmed Jaber Al Shareef; Premanandh Jagadeesan | Organic Chemistry; Analytical Chemistry; Agriculture and Food Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655e2c325bc9fcb5c922e8d0/original/investigation-of-extraneous-peak-reveals-ethylene-oxide-in-food-supplements.pdf |
61254027e65e2d5abb1f3590 | 10.26434/chemrxiv-2021-zkmmk-v2 | On the dynamics in chemical vapor deposition of InN | Epitaxial, nanometer-thin indium nitride (InN) films are considered as promising active layers in various device applications but remains challenging to deposit. We compare the morphological evolution and characterizations of InN films with various growth conditions in chemical vapor deposition (CVD), by both a plasma atomic layer deposition (ALD) approach and a conventional metalorganic CVD approach. Our results, and previous literature, show that a time-resolved precursor supply is highly beneficial for deposition of smooth and continuous InN nanometer-thin films. We show that the time for purging the reactor between the precursor pulses and low deposition temperature are key factors to achieve homogeneous InN. Our study suggests that 320 °C is the upper temperature where the dynamics of the deposition chemistry can be controlled to involve only surface reactions with surface species. The results highlight the promising role of the ALD technique in realizing electronic devices based on nanometer-thin InN layers. | Chih-Wei Hsu; Petro Deminskyi; Anton Persson; Matts Karlsson; Henrik Pedersen | Physical Chemistry; Materials Science; Materials Processing; Nanostructured Materials - Materials; Thin Films; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61254027e65e2d5abb1f3590/original/on-the-dynamics-in-chemical-vapor-deposition-of-in-n.pdf |
6741ab42f9980725cf92b079 | 10.26434/chemrxiv-2024-38nl4-v2 | Divergent Activity Shifts of Sn-Based Catalysts for Electrochemical CO2 Reduction: pH-Dependent Behavior of Single-Atom vs. Polyatomic Structures | Tin (Sn)-based catalysts have been widely studied for electrochemical CO2 reduction reaction (CO2RR) to produce formic acid, but the intricate influence of the structural sensitivity in single-atom Sn (e.g., Sn-N-C) and polyatomic Sn (e.g., SnOx and SnSx; x=1,2) on their pH-dependent performance remains enigmatic. Herein, we integrate large-scale data mining (with >2,300 CO2RR catalysts from available experimental literature during the past decade), ab initio computations, machine learning force field accelerated molecular dynamic simulations, and pH-field coupled microkinetic modelling to unravel their pH dependence. We reveal a fascinating contrast: the electric field response of the binding strength of *OCHO on Sn-N4-C and polyatomic Sn exhibits opposite behaviors due to their differing dipole moment changes upon *OCHO formation. Such response leads to an intriguing opposite pH-dependent volcano evolution for Sn-N4-C and polyatomic Sn. Subsequent experimental validations of turnover frequency and current density under both neutral and alkaline conditions well aligned with our theoretical predictions. Most importantly, our analysis suggests the necessity of distinct optimization strategies for *OCHO binding energy on different types of Sn-based catalysts. | Yuhang WANG; Di Zhang; Bin Sun; Xue Jia; Linda Zhang; Hefeng Cheng; Jun Fan; Hao Li | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6741ab42f9980725cf92b079/original/divergent-activity-shifts-of-sn-based-catalysts-for-electrochemical-co2-reduction-p-h-dependent-behavior-of-single-atom-vs-polyatomic-structures.pdf |
638f60e50fd99286863a677b | 10.26434/chemrxiv-2022-81lj6 | Paper Powered Pharmaceutical Manufacturing | Programmable multistep syntheses can be useful tools in molecule discovery and process optimization, and have recently been bolstered by advances in computational chemistry and machine learning applications to molecule design. Current approaches rely on advanced liquid handling and reactor design that can reliably create fractions and aliquots of reagents and products. Here we report on the use of non-aqueous synthesis programming of pharmaceutically relevant molecules using reconfigurable paper comprising an Ampli chemical plug and play construction set. Liquid fractions and reactions are replaced with paperfluidic membranes on blocks that can be snapped together and disconnected for real time design of experiments. Reagents are embedded into the paper membranes of each block, and reactions are synthesized by snapping together blocks and allowing solution to run through them in a sequence. We explored the use of Ampli to synthesize two pharmaceutically relevant species, gold nanoparticles and the antibiotic metronidazole. Reaction products were characterized by different spectroscopic techniques (Raman spectroscopy, optical absorption spectroscopy, dynamic light scattering). The resulting products were extracted to form functional nanoparticles used in diagnostic immunoassays, and our paper synthesized metronizadole was functional in an anti-bacterial disk diffusion assay. We investigated how to map off-the-shelf reactions onto individual Ampli blocks and how to successfully generate and extract these products. This paper based pharmaceutical synthesis was faster, significantly more affordable, and lighter than traditional methods with important implications for local and distributed manufacturing. | Josselyn Mata Calidonio; Jose Gomez-Marquez; Kimberly Hamad-Schifferli | Materials Science; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638f60e50fd99286863a677b/original/paper-powered-pharmaceutical-manufacturing.pdf |
650a8de0b927619fe778766b | 10.26434/chemrxiv-2023-tp55l | Olefination of Aromatic Carbonyls via Site-Specific Activation of Cycloalkanone Ketals | Skeletal editing is an important strategy in organic synthesis as it modifies the carbon backbone to tailor molecular structures with precision, enabling access to compounds with specific desired properties. Skeletal editing empowers chemists to transform synthetic approaches of target compounds across diverse applications from drug discovery to materials science. Herein, we introduce a new skeletal editing method to convert readily available aromatic carbonyl compounds into valuable unsaturated carboxylic acids with extended carbon chains. Our reaction setup enable a cascade reaction of enolization-[2+2]cycloaddition-[2+2]cycloreversion between aromatic carbonyl compounds and ketals of cyclic ketones to generate unsaturated carboxylic acids as ring-opening products. Through a simple design, our substrates are specifically activated to react at predetermined positions to enhance selectivity and efficiency. This practical method offers convenient access to versatile organic building blocks as well as provides fresh insights into manipulating traditional reaction pathways for new synthetic applications. | Tuong Anh To; Thanh Vinh Nguyen | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650a8de0b927619fe778766b/original/olefination-of-aromatic-carbonyls-via-site-specific-activation-of-cycloalkanone-ketals.pdf |
63818c5928c1643855587edf | 10.26434/chemrxiv-2022-9rx0m | Beyond Tafel Analysis for Electrochemical CO2 Reduction | The development and characterization of active and selective catalysts is critical for the simulation and optimization of electrochemical synthesis of chemicals and fuels using renewable energy. The rate of electrochemical generation of a specific product as a function of electrode potential can be described by a Tafel equation, which depends on two parameters: the Tafel slope (or the related transfer coefficient) and the exchange current density. However, common methods for calculating Tafel slopes are subjective and limited by data insufficiency resulting from challenges associated with product quantification, and, as shown here, the effects of mass transport, bulk reaction occurring in the mass-transfer boundary layer, and the occurrence of competitive surface reactions. Errors in the Tafel slope extracted from experimental data can also lead to errors in the exchange current density estimation. To address these issues, we present a technique that leverages statistical learning methods informed by physics-based modeling to calculate kinetic parameters (the transfer coefficient and exchange current density) with quantified uncertainty. The method is applied to 21 sets of data for the electrochemical reduction of CO2 to CO and H2 on Ag catalysts acquired under similar experimental conditions. We find that fitted values for the transfer coefficient and exchange current density do not converge to a unique set of values, and that there is an apparent correlation of these parameters; however, the most probable value of the exchange coefficient for CO and H2 formation correspond reasonably well with the DFT-predicted values of this parameter. While the system explored is relatively simple, the techniques developed can be used to evaluate the transfer coefficient and exchange current density for many other electrochemical processes. | Kaitlin Rae M. Corpus; Justin C. Bui; Aditya M. Limaye; Lalit M. Pant; Karthish Manthiram; Adam Z. Weber; Alexis T. Bell | Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Electrocatalysis; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2022-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63818c5928c1643855587edf/original/beyond-tafel-analysis-for-electrochemical-co2-reduction.pdf |
6635b99c21291e5d1d63bd3e | 10.26434/chemrxiv-2024-61vv7 | Synthesis and Reactivity of Rhodium Complex Bearing a PNiP Pincer Ligand | Rhodium complexes bearing a pincer-type ligand containing nickel were successfully synthesized. Through single-crystal X-ray diffraction analyses and theoretical calculations, the electronic structures of the bimetallic complexes were elucidated. Notably, this represents the inaugural synthesis of a bimetallic complex featuring a distinct nickel–rhodium bond. The reactivity of these synthesized complexes was probed through catalytic arene C–H borylation reactions. | Kouki Fujita; Kazuhiko Semba; Yoshiaki Nakao | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Coordination Chemistry (Organomet.); Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6635b99c21291e5d1d63bd3e/original/synthesis-and-reactivity-of-rhodium-complex-bearing-a-p-ni-p-pincer-ligand.pdf |
6707a95c51558a15efafa915 | 10.26434/chemrxiv-2024-73fhj | Exploring Halide Perovskite Nanocrystal Decomposition: Insight by In-Situ Electron Paramagnetic Resonance Spectroscopy | Zero-dimensional (0D) and three-dimensional (3D) halide perovskite nanocrystals (HP-NCs), owing to their unique optoelectronic properties, are extensively studied for photocatalytic activity. However, HPs are highly sensitive to light, humidity, and other environmental factors, which accelerate their decomposition. Understanding the decomposition process is crucial for gaining insights into how to stabilize HP-NCs. Here, we investigate the radical-driven decomposition process and dynamics of the 0D C4PbBr6 and 3D CsPbBr3 NCs under the influence of visible light and a polar solvent by electron paramagnetic resonance (EPR) spectroscopy. Our findings indicate that light accelerates radical formation over time, making the decomposition of HP-NCs a self-sustaining process. Upon illumination of the NCs, hydroperoxyl radicals are formed first, followed by unconventional Br, Cs, and Pb-related radicals, indicating the initiation of NC decomposition. The decomposition of CsPbBr¬3 NCs starts after 3 min of light exposure, while C4PbBr6 NCs take 18 min, indicating the greater stability of the latter. Additionally, we evaluated the photocatalytic activity of the HPs toward degrading organic dyes. The 3D CsPbBr3 NCs performed as superior photocatalysts compared to their 0D Cs4PbBr6 NCs counterparts. Yet, linking the results of EPR measurements with the photocatalytic efficacy suggests that the CsPbBr3 NCs undergo degradation during the photocatalytic process, thereby serving as a sacrificial agent to enhance photocatalytic activity. The understanding derived from EPR spectroscopy in tracking radical formation and dynamics can be extended to enhance the stability and efficiency of various nanomaterials in optoelectronic and photocatalytic applications, thus contributing to advancements beyond the HP family. | Anastasiya Sedova; Philip Nathaniel Immanuel; Raanan Carmieli; Hila Shalom; Achiad Goldreich; Alen Sam Thomas; Jonathan Prilusky; Akshay Puravankara; Ido Bar-On; Lena Yadgarov | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Nanocatalysis - Reactions & Mechanisms; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707a95c51558a15efafa915/original/exploring-halide-perovskite-nanocrystal-decomposition-insight-by-in-situ-electron-paramagnetic-resonance-spectroscopy.pdf |
650a7a65b927619fe776da85 | 10.26434/chemrxiv-2023-0xkv1-v3 | MLQD: A package for machine learning-based
quantum dissipative dynamics | Machine learning has emerged as a promising paradigm to study the quantum dissipative dynamics of open quantum systems. To facilitate the use of our recently published ML-based approaches for quantum dissipative dynamics, here we present an open-source Python package MLQD (https://github.com/Arif-PhyChem/MLQD), which currently supports the three ML-based quantum dynamics approaches: (1) the recursive dynamics with kernel ridge regression (KRR) method, (2) the non-recursive artificial-intelligence-based quantum dynamics (AIQD) approach and (3) the blazingly fast one-shot trajectory learning (OSTL) approach, where both AIQD and OSTL use the convolutional neural networks (CNN). This paper describes the features of the MLQD package, the technical details, optimization of hyperparameters, visualization of results, and the demonstration of the MLQD's applicability for two widely studied systems, namely the spin-boson model and the Fenna--Matthews--Olson (FMO) complex. To make MLQD more user-friendly and accessible, we have made it available on the Python Package Index (PyPi) platform and it can be installed via pip install mlqd. In addition, it is also available on the XACS cloud computing platform (https://XACScloud.com) via the interface to the MLATOM package (http://MLatom.com) | Arif Ullah; Pavlo O. Dral | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Machine Learning; Optics; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2023-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650a7a65b927619fe776da85/original/mlqd-a-package-for-machine-learning-based-quantum-dissipative-dynamics.pdf |
6691336601103d79c5d1aada | 10.26434/chemrxiv-2024-hbsbj | Facile Access to Hindered Ethers via Photoinduced O-H Bond Insertions | The synthesis of the hindered and polyfluorinated dialkyl ethers poses challenges owing to the bulkiness of tertiary alcohols and the low nucleophilicity of polyfluorinated alcohols. Additionally, associated competitive side reactions always provide poor reactivities. Although certain strategies, such as the electrocatalytic decarboxylation and hydroalkoxylation, have been explored, a straightforward method for obtaining ethers with structural diversity remains elusive. In this study, we proposed a photoinduced approach that involved the in-situ formation of singlet carbenes followed by O-H insertions to access the hindered and polyfluorinated ethers. This method successfully converted diverse congested alcohols and polyfluorinated alcohols into their corresponding challenging ethers. Moreover, other nucleophiles such as phenols, H2O, thiols, silanols, tributyltin hydride etc. were tolerable to obtain valuable products. The gram-scale synthesis of marketed drugs and the modification of complex molecules demonstrated the practicality of this approach. The detailed mechanistic studies have elucidated the key intermediates and reaction mechanisms. | Yu Zhang; Xinyu Han; Dong Li; Dinggang Wang; Jinxin Wang; Xin Luan; Shao-Fei Ni; Shoubhik Das; Wei-Dong Zhang | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2024-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6691336601103d79c5d1aada/original/facile-access-to-hindered-ethers-via-photoinduced-o-h-bond-insertions.pdf |
673e14ecf9980725cf01ad8c | 10.26434/chemrxiv-2024-6v6j0 | Hybrid Materials: Next-Generation Engineering Materials | Hybrid organic-inorganic materials represent a fascinating class of compounds that combine the unique properties of both organic compounds and inorganic materials. These hybrids leverage the versatility of organic molecules - such as their flexibility and functionality - alongside the robustness and stability of inorganic components through to coordination between components. This synergy leads to innovative applications across various fields, including optoelectronics, gas storage and separation, and catalysis. By tailoring the composition and structure of these materials, researchers can create multifunctional systems that exhibit enhanced performance, such as improved mechanical strength, conductivity, and thermal stability, making them pivotal in advancing technology and materials science. This review will provide an overview of two classes of hybrid materials: metal−organic frameworks and hybrid organic-inorganic perovskites, with their structures, applications and responses to external stimuli discussed. The emerging field of hybrid glasses will also be discussed as it represents a novel frontier in the design of hybrid materials, combining the nature of glasses with the functional properties of hybrid materials. This review aims to highlight not only the current advancements but to also provide an insight into potential future applications. | Jay McCarron; Bethan Turner; Lauren McHugh | Materials Science; Hybrid Organic-Inorganic Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e14ecf9980725cf01ad8c/original/hybrid-materials-next-generation-engineering-materials.pdf |
60c74ff4bb8c1a3c403dba3f | 10.26434/chemrxiv.12971831.v1 | A Quantum-Based Approach to Predict Primary Radiation Damage in Polymeric Networks | <div>Initial atomistic-level radiation damage in chemically reactive materials is thought
to induce reaction cascades that can result in undesirable degradation of macroscale
properties. Ensembles of quantum-based molecular dynamics (QMD) simulations can
accurately predict these cascades, but extracting chemical insights from the many underlying trajectories is a labor-intensive process that can require substantial a priori
intuition. We develop here a general and automated graph-based approach to extract
all chemically distinct structures sampled in QMD simulations and apply our approach
to predict primary radiation damage of polydimethylsiloxane (PDMS), the main constituent of silicones. A post-processing protocol is developed to identify underlying
polymer backbone structures as connected components in QMD trajectories. These
backbones form a repository of radiation-damaged structures. A scheme for extracting
and updating a library of isomorphically distinct structures is proposed to identify the
spanning set and aid chemical interpretation of the repository. The analyses are applied
to ensembles of cascade QMD simulations in which the four element types in PDMS
are selectively excited in primary knock-on atom events. Our approach reveals a much
higher degree of combinatorial complexity in this system than was inferred through radiolysis experiments. Probabilities are extracted for radiation-induced network changes
including formation of branch points, carbon linkages, cycles, bond scissions, and carbon uptake into the Si-O siloxane backbone network. The general analysis framework
presented here is readily extendable to modeling chemical degradation of other polymers
and molecular materials and provides a basis for future quantum-informed multiscale
modeling of radiation damage. <br /></div> | Matthew Kroonblawd; Nir Goldman; Amitesh Maiti; James Lewicki | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff4bb8c1a3c403dba3f/original/a-quantum-based-approach-to-predict-primary-radiation-damage-in-polymeric-networks.pdf |
678ae367fa469535b97246ba | 10.26434/chemrxiv-2025-vvfzs | A new, literature-informed critical mineral life cycle assessment framework: an essential foundation for the energy transition | In this paper, we demonstrate that life cycle assessment (LCA) is a valuable tool for evaluating the trade-offs between critical mineral acquisition and its resulting environmental impacts, but the applications of LCA to critical mineral mining are inconsistent and limited. These inconsistencies inhibit fair comparison of mines’ effects and decision-making. To illustrate these limitations, we analyzed the four LCA phases for 56 peer-reviewed or grey literature critical mineral mining LCAs. Additionally, we compiled reported environmental impacts of critical mining from the Environmental Justice Atlas (EJAtlas) to guide impact category selection. We elaborate a framework with recommendations for each LCA phase. This framework provides an opportunity to standardize critical mineral mining LCAs and enable better comparison, decision-making, and mining policy. | Jenna Trost; Jennifer Dunn; Kimberly Marion Suiseeya | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ae367fa469535b97246ba/original/a-new-literature-informed-critical-mineral-life-cycle-assessment-framework-an-essential-foundation-for-the-energy-transition.pdf |
635931d718a8cc30a95226c6 | 10.26434/chemrxiv-2022-sgb2d | Photocatalytic treatment of organoselenium in synthetic mine-impacted effluents | Biological selenium reduction processes are commonly employed as the best available technology (BAT) for selenium removal, however, as a by-product they produce trace amounts of organoselenium compounds with orders of magnitude greater bioaccumulation potential and toxicity. Here we assessed buoyant photocatalysts (BPCs) as a potential passive advanced oxidation process (P-AOP) for organoselenium treatment. Using a synthetic mine-impacted water solution, spiked with selenomethionine (96 µg/L) as a representative organoselenium compound, photocatalysis with BPCs fully eliminated selenomethionine to <0.01 µg/L with conversion to selenite and selenate. A theoretical reaction pathway was inferred, and a kinetics model developed to describe the treatment trends and intermediates. Given the known toxic responses of Lepomis macrochirus and Daphnia magna to organoselenium, it was estimated that photocatalysis could effectively eliminate organoselenium acute toxicity within a UV dose of 8 kJ/L (1-2 days solar equivalent exposure), by transformation of selenomethionine to less hazardous oxidized Se species. Solar photocatalysis may therefore be a promising passive treatment technology for selenium-impacted mine water management. | Jeffrey Martin; Tia Chai; Timothy Leshuk; Zachary Young; Frank Gu | Catalysis; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Water Purification; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635931d718a8cc30a95226c6/original/photocatalytic-treatment-of-organoselenium-in-synthetic-mine-impacted-effluents.pdf |
641d1c9e91074bccd030ccf4 | 10.26434/chemrxiv-2023-8f0mx | Piezochromism in Dynamic Three-Dimensional Covalent Organic Frameworks | Piezochromic materials with pressure-dependent photoluminescence-tuning properties are important in many fields, such as mechanical sensors, security papers, and storage devices. Covalent organic frameworks (COFs), as an emerging class of crystalline porous materials (CPMs), feature structural dynamics and tunable photophysical properties, which are suitable for designing piezochromic materials, but related research is scarce. Herein, we report two dynamic three-dimensional COFs based on aggregation-induced emission (AIE) or aggregation-caused quenching (ACQ) chromophores, termed JUC-635 and JUC-636, and for the first time, study their piezochromic behavior by diamond anvil cell technique. Due to the various luminescent groups, JUC-635 has completely different solvatochromism and molecular aggregation behavior in the solvents. More importantly, JUC-635 with AIE effect exhibited a maintained fluorescence with increasing pressure (~3 GPa), and a reversible sensitivity with high-contrast emission differences (Δλem = 187 nm) up to 12 GPa, which is superior to other CPMs reported so far. Therefore, this research will open a new gate for expanding the potential applications of COFs as exceptional piezochromic materials in pressure sensing, barcoding, and signal switching. | Jing Fang; Zhiyuan Fu; Xiaohong Chen; Yaozu Liu; Fengqian Chen; Yujie Wang; Hui Li; Yusran Yusran; Kai Wang; Valentin Valtchev; Shilun Qiu; Bo Zou; Qianrong Fang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641d1c9e91074bccd030ccf4/original/piezochromism-in-dynamic-three-dimensional-covalent-organic-frameworks.pdf |
60c745770f50db65bc39627d | 10.26434/chemrxiv.9941948.v2 | Site-Specific Generation of Protein-Protein Conjugates Using Native Amino Acids | <p>Chimeric protein-protein
conjugates provide platforms for immunotherapy, targeted drug delivery, and
vaccine development. However, many desirable constructs cannot be produced through
direct expression, and the targeted coupling of two proteins is chemically
challenging. Here we present a new approach for the rapid and site-specific coupling
of proteins using native amino acids. Tyrosinase oxidizes exposed tyrosine
residues on polypeptides, generating <i>ortho</i>-quinones that react rapidly
with strategically placed cysteine residues in other proteins. This approach was
used to modify CRISPR-Cas9 and other substrates with small molecules, peptides
and even intact proteins. The conjugation of cell penetrating peptides to
CRISPR-Cas9 was shown to increase cellular genome editing efficiency by 20-fold
relative to unmodified Cas9. This technology represents a new paradigm for
biomolecular coupling, and paves the way to an unprecedented range of
multifunctional bioconjugates.</p> | Marco Lobba; Christof Fellmann; Alan Marmelstein; Johnathan Maza; Elijah Kissman; Stephanie A. Robinson; Brett T. Staahl; Cole Urnes; Rachel J. Lew; Jennifer A. Doudna; Matthew Francis; Casey S. Mogilevsky | Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745770f50db65bc39627d/original/site-specific-generation-of-protein-protein-conjugates-using-native-amino-acids.pdf |
656f25305bc9fcb5c917a18c | 10.26434/chemrxiv-2023-xmxs6 | On the performance of second-order approximate coupled-cluster singles and doubles methods for non-valence anions | We investigate the capability of several variants of the second-order approximate coupled-cluster singles and doubles (CC2) method to describe dipole-bound, quadrupole-bound, and correlationbound molecular anions. The binding energy of anions formed by electron attachment to closed-shell molecules is computed using the electron attachment variant of CC2 (EA-CC2), whereas anions with a closed-shell ground state are treated with the standard CC2 method that preserves the number of particles. We find that EA-CC2 captures the binding energies of dipole-bound radical anions quite well, whereas results for other types of non-valence anions are less reliable.
We also test the performance of semi-empirical spin-scaling factors for all types of non-valence anions and observe that the spin-scaled CC2 variants generally do not provide more accurate binding energies for dipole-bound anions, while the binding energies of quadrupole-bound and correlation-bound anions are improved.
As exemplary applications of EA-CC2, we investigate the dipole-bound anions of the steroids cortisol, progesterone, and testosterone. In addition, we characterize electron attachment to symtetracyanonaphthalene, a molecule that supports five anionic states, two of which can be interpreted as hitherto unobserved pi-type quadrupole states. | Garrette Pauley Paran; Cansu Utku; Thomas Jagau | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f25305bc9fcb5c917a18c/original/on-the-performance-of-second-order-approximate-coupled-cluster-singles-and-doubles-methods-for-non-valence-anions.pdf |
622ec68710d14310fccefeb0 | 10.26434/chemrxiv-2022-sk6r0-v2 | The Behavior of Methane-Water Mixtures Under Elevated Pressures Using Many-Body Potentials | Non-polarizable empirical potentials have been shown not to be able to capture the mixing of methane–water mixtures at elevated pressures. Although DFT-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here we show that the many-body MB-nrg potential, designed to reproduce methane–water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentration. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane–water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. We find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis. | Victor Naden Robinson; Raja Ghosh; Colin K. Egan; Marc Riera; Christopher Knight; Francesco Paesani; Ali Hassanali | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Statistical Mechanics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622ec68710d14310fccefeb0/original/the-behavior-of-methane-water-mixtures-under-elevated-pressures-using-many-body-potentials.pdf |
63fc3fba32cd591f128880c7 | 10.26434/chemrxiv-2023-3kk16 | Systematic search for thermal decomposition pathways of formic acid on anatase TiO2 (101) surface | This study systematically investigates the reaction pathways for the thermal decomposition of formic acid on the anatase TiO2 (101) surface. The investigation was conducted using a single-component artificial force induced reaction method that combines density functional theory calculations. To uncover the entire mechanism at low surface coverage, we explored reaction path networks for three different conditions of the anatase TiO2 (101) surfaces: clean, protonated, and oxygen-deficient surfaces. Previous temperature programmed desorption (TPD) experiments have shown that H2O desorption starts at a low temperature of around 300 K, while CO and formaldehyde desorption begin to occur at high temperatures of around 500 K. The present reaction path networks are consistent with the overall trend observed in the TPD experiments. By using the reaction paths extracted from these networks, the entire dissociation mechanism was discussed. | Hitoshi Nabata; Satoshi Maeda | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fc3fba32cd591f128880c7/original/systematic-search-for-thermal-decomposition-pathways-of-formic-acid-on-anatase-ti-o2-101-surface.pdf |
60c7488d9abda23914f8cac4 | 10.26434/chemrxiv.11926860.v1 | Hydrogen-Bond Driven Chemical Separations: Elucidating the Inter-facial Steps of Self-Assembly in Solvent Extraction | Chemical separations, particularly liquid extractions,
are pervasive in academic and industrial laboratories, yet a mechanistic
understanding of the events governing their function are obscured by
interfacial phenomena that are notoriously difficult to measure. In this work, we
investigate the fundamental steps of ligand self-assembly as driven by changes
in the interfacial H-bonding network using vibrational sum frequency
generation. Our results show how the bulk pH modulates the interfacial structure
of extractants at the buried oil/aqueous interface via the formation of unique
H-bonding networks that order and bridge ligands to produce self-assembled aggregates.
These extended H-bonded structures are key to the subsequent extraction of Co<sup>2+</sup>
from the aqueous phase in promoting micelle formation and subsequent ejection
of said micelle into the oil phase. The combination of static and time resolved
measurements reveals the mechanisms underlying complexities of liquid extractions
at high [Co<sup>2+</sup>]:[DEHPA] ratios by showing an evolution of interfacially
assembled structures that are readily tuned on a chemical basis by altering the
compositions of the aqueous phase. The results of this work point to new mechanistic
principles to <i>design</i> separations
through the manipulation of surface charge, electrostatic screening, and the
associated H-bonding networks that arise at the interface to facilitate
organization and subsequent extraction | Azhad U. Chowdhury; Lu Lin; Benjamin Doughty | Interfaces; Physical and Chemical Processes; Self-Assembly; Spectroscopy (Physical Chem.); Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488d9abda23914f8cac4/original/hydrogen-bond-driven-chemical-separations-elucidating-the-inter-facial-steps-of-self-assembly-in-solvent-extraction.pdf |
60c746c7ee301c3a3bc7958e | 10.26434/chemrxiv.11380980.v1 | Photoredox of Gem-Diborylalkenes: A Novel Reactivity Toward Diverse 1,1-Bisborylalkanes | The use of <i>gem-bis</i>-metalated-alkenes, i.e.,
vinyl <i>gemdi</i>boron-compound, as light-labile substrates is explored for
the first time. The knowledge gained provided us with an in-depth understanding
of the reactivity of novel radical intermediates of <i>geminal</i>-metalated
ethane. This methodology can serve as the late-stage diversification of
bioactive molecules and simple organic molecules in which it drives the synthesis
of gemdiborylalkanes. | Nivesh Kumar; Nadim Eghbarieh; Tamar Stein; Alexander Shames; Ahmad Masarwa | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c7ee301c3a3bc7958e/original/photoredox-of-gem-diborylalkenes-a-novel-reactivity-toward-diverse-1-1-bisborylalkanes.pdf |
60c73d50bb8c1a643a3d971d | 10.26434/chemrxiv.5659576.v1 | Reversible Silver Electrodeposition from Boron Cluster Ionic Liquid (BCIL) Electrolytes | Electrochemical systems offer a versatile means for creating adaptive devices. However, the utility of electrochemical deposition is inherently limited by the properties of the electrolyte. The development of ionic liquids enables electrodeposition in high-vacuum environments and presents opportunities for creating electrochemically adaptive and regenerative spacecraft components. In this work we developed a silver-rich, boron cluster ionic liquid (BCIL) for reversible electrodeposition of silver films. This air and moisture stable electrolyte was used to deposit metallic films in an electrochemical cell to tune the emissivity of the cell <i>in situ</i>, demonstrating a proof-of-concept design for spacecraft thermal control. | Alexander Spokoyny; Rafal M. Dziedzic; Mary A. Waddington; Sarah E. Lee; Jack Kleinsasser; John B. Plumley; William C. Ewing; Beth D. Bosley; Vincent Lavallo; Thomas L. Peng | Coating Materials; Composites; Optical Materials; Surfactants; Thin Films; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d50bb8c1a643a3d971d/original/reversible-silver-electrodeposition-from-boron-cluster-ionic-liquid-bcil-electrolytes.pdf |
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