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6666fd6a409abc034513fa40
|
10.26434/chemrxiv-2024-d4lpr
|
Heterologous Biosynthesis of Cotylenol and Concise Synthesis of Fusicoccane Diterpenoids
|
Fusicoccane diterpenoids have attracted intensive attention due to their complex structures as well as diverse biological activities. Here we report a novel strategy for the synthesis of cotylenol and other fusicoccane diterpenoids. By harnessing the biosynthetic pathways of brassicicenes and fusicoccins, cotylenol was produced in an engineered Aspergillus oryzae strain. We further achieved the concise synthesis of three fusicoccane diterpenoids, including alterbrassicicene E and brassicicenes A and R in 4 or 5 chemical steps from brassicicene I. Our strategy may facilitate the preparation of fusicoccane diterpenoids and their synthetic analogues for biological studies.
|
Zhenhua Guan; Ye Yuan; Xue-Jie Zhang; Nanyu Yao; Wenling Yuan; Yonghui Zhang; Ying Ye; Zheng Xiang
|
Organic Chemistry; Natural Products
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6666fd6a409abc034513fa40/original/heterologous-biosynthesis-of-cotylenol-and-concise-synthesis-of-fusicoccane-diterpenoids.pdf
|
60c742af702a9b806e18a4db
|
10.26434/chemrxiv.8427047.v1
|
Investigation of Charge-Transfer Interactions Induced by Encapsulating Fullerene in a Mesoporous Tetrathiafulvalene-Based Metal-Organic Framework
|
<p>The design of Metal-Organic Frameworks (MOFs) incorporating electroactive guest molecules in the pores has become a subject of great interest in order to install additional electrical functionalities within the framework while maintaining porosity. In this direction, understanding the charge-transfer (CT) process between the framework and the guest molecules is crucial towards the design of new electroactive MOFs. Herein, we present the encapsulation of fullerenes (C<sub>60</sub>) in a mesoporous tetrathiafulvalene(TTF)-based MOF. The CT process between the electron-acceptor C<sub>60 </sub>guest and the electron-donor TTF ligand is studied in detail by means of different spectroscopic techniques and density functional theory calculations. Importantly, gas sorption measurements demonstrate that sorption capacity is maintained after encapsulation of fullerenes, whereas the electrical conductivity is increased by two orders of magnitude due to the CT interactions between C<sub>60</sub>and the TTF-based framework. </p>
|
Manuel Souto; Joaquín Calbo; Samuel Mañas-Valero; Aron Walsh; Guillermo Minguez Espallargas
|
Hybrid Organic-Inorganic Materials; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af702a9b806e18a4db/original/investigation-of-charge-transfer-interactions-induced-by-encapsulating-fullerene-in-a-mesoporous-tetrathiafulvalene-based-metal-organic-framework.pdf
|
65c213d79138d231618a92dd
|
10.26434/chemrxiv-2024-t6680
|
Impact of the potential dependent surface adlayer composition on the ORR activity and H2O2 formation on Ru(0001) in acid electrolytes
|
Stimulated by the increasing interest in ion adsorption effects on electrocatalytic reactions and by recent more detailed reports on the potential dependent adlayer structures formed on Ru(0001) in pure HClO4 and H2SO4 electrolytes, we revisited the oxygen reduction reaction (ORR) on structurally well-defined Ru(0001) single crystal surfaces prepared under ultrahigh vacuum conditions. We demonstrate that the complex, potential-dependent activity both for the ORR and for H2O2 formation is closely related to potential-dependent changes in the composition and structure of the adlayer. Our results demonstrate the enormous effects adsorbed species can have on the ORR reaction characteristics, either by surface blocking, e.g., by (co-)adsorbed bisulfate species, or by participation in the reaction, e.g., by *H transfer from adsorbed H or OH to O2. The comparison with results obtained on polycrystalline Ru, which differ significantly from Ru(0001) data, furthermore underlines the importance of using structurally well-defined surfaces as a reference system for future theoretical studies.
|
Albert K. Engstfeld; Stephan Beckord; Stefan Fuchs; R. Jürgen Behm
|
Catalysis; Electrocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c213d79138d231618a92dd/original/impact-of-the-potential-dependent-surface-adlayer-composition-on-the-orr-activity-and-h2o2-formation-on-ru-0001-in-acid-electrolytes.pdf
|
67436fdc5a82cea2faaaaf70
|
10.26434/chemrxiv-2024-2b0w3
|
Transport characterization of solid-state Li2FeS2 cathodes from a porous electrode theory perspective
|
The abundance and cost of resources for current state-of-the-art cathode active materials makes the search for alternative cell chemistries inevitable. Nonetheless, especially in solid-state batteries, establishing new cell chemistries comes at the challenge of optimizing the transport of both charge carriers, electrons and ions, through the electrode. Limitations in transport of either species lead to underutilization of the electrode caused by insufficiently contacted particles and/or nonuniform reaction rates and state-of-charge gradients through the electrode. In this work, we investigate the capabilities of Li2FeS2 as alternative active material in all-solid-state cathodes by thorough investigation of the initial utilization and rate capability as a function of the cathode loading. The cathode loading is increased from 1.8 to 7.3 mAh·cm−2 by increasing the fraction of active material from 32 to 74 vol.%, and the thickness of the composite electrode from 73 to 145 μm. Careful characterization of the effective electronic and ionic transport, and consideration of the δ-parameter from porous electrode theory, guides the understanding of the electrode performances. With that, this work shows that Li2FeS2 solid-state cathodes with high areal loadings and gravimetric energy densities can be realized.
|
Tim Bernges; Lukas Ketter; Bianca Helm; Marvin Kraft; Kimberly See; Wolfgang Zeier
|
Energy; Energy Storage
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67436fdc5a82cea2faaaaf70/original/transport-characterization-of-solid-state-li2fe-s2-cathodes-from-a-porous-electrode-theory-perspective.pdf
|
650f37c960c37f4f7651d6b8
|
10.26434/chemrxiv-2023-jk33z
|
Carbodiimide and Isocyanate Hydroboration by a Cyclic Carbodiphosphorane Catalyst
|
We report hydroboration of carbodiimide and isocyanate substrates catalyzed by a cyclic carbodiphosphorane catalyst. The cyclic carbodiphosphorane outperformed the other Lewis basic carbon species tested, including other zerovalent carbon compounds, phosphorus ylides, an N-heterocyclic carbene, and an N-heterocyclic olefin. Hydroborations of seven carbodiimides and nine isocyanates were performed at room temperature to form N-boryl formamidine and N-boryl formamide products. Intermolecular competition experiments demonstrated the selective hydroboration of alkyl isocyanates over carbodiimide and ketone substrates. DFT calculations support a proposed mechanism involving activation of pinacolborane by the carbodiphosphorane catalyst, followed by hydride transfer and B–N bond formation.
|
Ben Janda; Julie Tran; Daniel Chang; Gabriela Nerhood; O. Maduka Ogba; Allegra Liberman-Martin
|
Organic Chemistry; Inorganic Chemistry; Catalysis; Main Group Chemistry (Inorg.); Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650f37c960c37f4f7651d6b8/original/carbodiimide-and-isocyanate-hydroboration-by-a-cyclic-carbodiphosphorane-catalyst.pdf
|
60c75379567dfe15b7ec5e82
|
10.26434/chemrxiv.13166774.v3
|
Real-time Sensing of Trace Biomarkers from Viruses with a Microfluidic Immunosensor: A Case Study of SARS-CoV-2 Detection in Cold-chain Food
|
<div>Utilizing an interdigitated microelectrode chip modified with an antibody probe, and integrating dielectrophoresis enrichment with interfacial capacitance sensing, a real-time immunosensor is presented for detection of trace level biomarkers from virus. <br /></div>
|
Haochen Qi; Jian Zhang; Jayne Wu; Xin Fang; Fangshuo You; Wenci Zhao; Xiaoru Liu; Ying Chen; Lei Zheng
|
Analytical Chemistry - General; Analytical Apparatus; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75379567dfe15b7ec5e82/original/real-time-sensing-of-trace-biomarkers-from-viruses-with-a-microfluidic-immunosensor-a-case-study-of-sars-co-v-2-detection-in-cold-chain-food.pdf
|
60c743f6469df47531f4328f
|
10.26434/chemrxiv.9725186.v1
|
Cocrystal Trimorphism as a Consequence of Orthogonality of Halogen- and Hydrogen-Bonding
|
True trimorphic cocrystals, i.e. multi-component molecular crystals of identical composition that exhibit three polymorphic structures, are exceedingly rare and so far no halogen-bonded cocrystal system was reported to exhibit trimorphism. Here, we describe a unique example of a trimorphic cocrystal exhibiting both hydrogen and halogen bonds in which the difference between polymorphs arises from their orthogonality evident by apparently independent variation of hydrogen- and halogen-bonded motifs.<br />
|
Filip Topic; Katarina Lisac; Mihails Arhangelskis; Kari Rissanen; Dominik Cincic; Tomislav Friscic
|
Supramolecular Chemistry (Org.); Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f6469df47531f4328f/original/cocrystal-trimorphism-as-a-consequence-of-orthogonality-of-halogen-and-hydrogen-bonding.pdf
|
67b8619581d2151a026bd82d
|
10.26434/chemrxiv-2025-96kzg-v2
|
Integrating Machine Learning-Based Pose Sampling with Established Scoring Functions for Virtual Screening
|
Physics-based docking methods have long been the cornerstone of structure-based virtual screening (VS). However, the emergence of machine learning (ML)-based docking approaches has opened up new possibilities for enhancing VS technologies. In this study, we explore the integration of DiffDock-L, a leading ML-based pose sampling method, into VS workflows by combining it with the well-established Vina and Gnina scoring functions. We assess this integrated approach in terms of its VS effectiveness, pose sampling quality, and complementarity to traditional physics-based docking methods, such as AutoDock Vina. Our findings from the DUDEZ benchmark dataset show that DiffDock-L performs competitively in both VS performance and pose sampling in cross-docking settings. In most cases, it generates physically plausible and biologically relevant poses, establishing itself as a viable alternative to physics-based docking algorithms. Additionally, we found that the choice of scoring function significantly influences VS success.
|
Thi Ngoc Lan Vu; Hosein Fooladi; Johannes Kirchmair
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8619581d2151a026bd82d/original/integrating-machine-learning-based-pose-sampling-with-established-scoring-functions-for-virtual-screening.pdf
|
647103cabe16ad5c57f7281a
|
10.26434/chemrxiv-2023-n6p86
|
Accurate Prediction of HSE06 Band Structures for a Diverse Set of Materials Using ∆-learning
|
We used machine learning (ML) to accurately predict eigenvalues of the hybrid HSE06 functional using eigenvalues computed by the less computationally expensive PBE and associated electronic features based on the k-point resolved atomic band char- acter. The ML model was trained using eigenvalues from only one k-point for each of the 168 compounds in the training set. The HSE06 eigenvalues across all k-points were then predicted for a separate set of 169 compounds with a mean absolute error (MAE) of 0.13 eV, representing a significant improvement over the error of PBE-computed eigenvalues relative to HSE06 (0.96 eV). These accurately predicted eigenvalues result in remarkably accurate predictions for the band structures, projected density of states and band gaps, even though the model was not explicitly trained on these other prop- erties. Finally, we demonstrate that our ML model has a similar accuracy for both ternary and quaternary compounds well outside the initial training set and on systems with 112 and 160 atoms, demonstrating its potential to rapidly predict HSE06-quality electronic structures of complex materials that are practically unfeasible for HSE06.
|
Santosh Adhikari; Jacob Clary; Ravishankar Sundararaman; Charles Musgrave; Derek Vigil-Fowler; Christopher Sutton
|
Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-05-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647103cabe16ad5c57f7281a/original/accurate-prediction-of-hse06-band-structures-for-a-diverse-set-of-materials-using-learning.pdf
|
60c74126bb8c1aa9683d9ed8
|
10.26434/chemrxiv.7970879.v1
|
Lanthanoid Coordination with a Tetrazole-Substituted Calix[4]diquinone and Calix[4]dihydroquinone
|
<div><div><div><p>The tetrazole-functionalised calixdiquinone 5,17-di-tert-butyl-26,28-bis-(tetrazol-5-ylmethoxy)- calix[4]-25,27-diquinone Q was synthesised by chemical oxidation of the bis-tetrazole calix[4]arene precursor using PbO2/HClO4. The single crystal X-ray structure determination of Q confirmed the structure and showed binding of a water molecule in the solid state. Chemical reduction of Q to the dihydroquinone QR was achieved using N,N-diethylhydroxylamine. Comparison of the solution phase photophysical properties of Q or QR in the presence of terbium ions showed significant excitation only with QR, suggesting redox switching of the photophysical response may be possible with this or similar receptors.</p></div></div></div>
|
Lee Cameron; Aswin Rajagopalam; Laura
Abad Galán; Rene Phe; Brian Skelton; Massimiliano Massi; Mark Ogden
|
Lanthanides and Actinides; Supramolecular Chemistry (Inorg.); Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74126bb8c1aa9683d9ed8/original/lanthanoid-coordination-with-a-tetrazole-substituted-calix-4-diquinone-and-calix-4-dihydroquinone.pdf
|
66c378fb20ac769e5f169f9e
|
10.26434/chemrxiv-2024-wk4bn-v3
|
Sequence-defined structural transitions by calcium-responsive proteins
|
Biopolymer sequences dictate their functions, and protein-based polymers are a promising platform to establish sequence–function relationships for novel biopolymers. To efficiently explore vast sequence spaces of natural proteins, sequence repetition is a common strategy to tune and amplify specific functions. This strategy is applied to repeats-in-toxin (RTX) proteins with calcium-responsive folding behavior, which stems from tandem repeats of the nonapeptide GGXGXDXUX in which X can be any amino acid and U is a hydrophobic amino acid. To determine the functional range of this nonapeptide, we modified a naturally occurring RTX protein that forms β-roll structures in the presence of calcium. Sequence modifications focused on calcium-binding turns within the repetitive region, including either global substitution of nonconserved residues or complete replacement with tandem repeats of a consensus nonapeptide GGAGXDTLY. Some sequence modifications disrupted the typical transition from intrinsically disordered random coils to folded β rolls, despite conservation of the underlying nonapeptide sequence. Proteins enriched in smaller, hydrophobic amino acids adopted secondary structures in the absence of calcium and underwent structural rearrangement in calcium-rich environments. In contrast, proteins with bulkier, hydrophilic amino acids maintained intrinsic disorder in the absence of calcium. These results indicate a significant role of nonconserved amino acids in calcium-responsive folding, thereby revealing a strategy to leverage sequence in the design of tunable, calcium-responsive biopolymers.
|
Marina Chang; Winnie Huang; Gatha Shambharkar; Kenny Hernandez; Danielle Mai
|
Physical Chemistry; Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Bioengineering and Biotechnology; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c378fb20ac769e5f169f9e/original/sequence-defined-structural-transitions-by-calcium-responsive-proteins.pdf
|
637e770fc567539c1c94219d
|
10.26434/chemrxiv-2022-sk9z3
|
Structure, Properties, and Reactivity of Polyoxocationic Zirconium and Hafnium Clusters
|
Hexameric tetravalent zirconium and hafnium molecular metal oxides clusters are key building blocks of many metal-organic frameworks; however, the chemical space to form all possible MOF nodes is vast, containing many potential new clusters. Our computational study provides a complete picture of the structure, properties, and reactivity of two tetrameric zirconium and hafnium [M4(μ2-η2:η2-O2)x(μ2-OH)8-2x(H2O)16]8+ polycationic clusters. The electronic structure of the studied species has the characteristic polyoxometalate oxygen-based and metal-based bands in the valence region. The energetics for the evolution of pure metal clusters into mixed-metal clusters revealed that only the incorporation of zirconium into hafnium clusters is thermodynamically favorable. We confirmed that the incorporation of up to four peroxide ligands is thermodynamically favorable; however, the experimental absence of rich peroxide species with three or more peroxides is attributed to their thermal degradation. The mechanism for peroxide incorporation involves the partial dissociation of the cluster rather than complete dissociation.
|
Rameswar Bhattacharjee; Ethan Hare; Pere Miro
|
Theoretical and Computational Chemistry; Inorganic Chemistry; Theory - Inorganic; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637e770fc567539c1c94219d/original/structure-properties-and-reactivity-of-polyoxocationic-zirconium-and-hafnium-clusters.pdf
|
65c0b17c66c13817290058e3
|
10.26434/chemrxiv-2024-drcrc
|
Ion-specific effects in polyelectrolyte solutions: chain-chain interactions, chain rigidity and dynamics
|
Ion-specific effects in aqueous solutions of polyelectrolytes are addressed here. We focus on ionene cationic chains, featuring simple structure, absence of side-groups and very regular chain charge density. Ion-specific effects in ionene solutions are demonstrated using a series of monovalent (halide) counterions. The study combines both static and dynamic measurements by small angle neutron scattering, neutron spin echo and PFG-NMR. Ion-specific effects are a phenomenon at high polyelectrolyte concentration and the nature of the counterion is seen to influence drastically the ionene chain-chain interactions. The origin lies in the closer approach of large, highly polarisable counterions to the chain backbone, leading to more constricted counterion clouds. Equally affected is the local chain rigidity, as well as collective and self-diffusion coefficients at larger scales. Small, nonpolarizable, strongly hydrating counterions, here F− ions, lead to locally rigid chains. For such chains, the nm-scale collective dynamics as seen by neutron spin echo, is the fastest, while the self-diffusion seen at μm scale by PFG-NMR is the slowest. In other words, the loss of charge on the chain due to ion-specific counterion ”condensation” has the opposite effect on collective diffusion and self-diffusion of the chains.
|
Claire Hotton; Yasine Sakhawoth; Anne-Laure Rollet; Juliette Sirieix-Plenet; Lingsam Tea; Sophie Combet; Melissa Sharp; Ingo Hoffmann; Frederic Nallet; Natalie Malikova
|
Physical Chemistry; Polymer Science; Polyelectrolytes - Polymers; Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0b17c66c13817290058e3/original/ion-specific-effects-in-polyelectrolyte-solutions-chain-chain-interactions-chain-rigidity-and-dynamics.pdf
|
634bf6b1339972c8468cd049
|
10.26434/chemrxiv-2022-h9x2q
|
Enantioselective hydroalkoxylation of 1, 3-dienes via Ni-catalysis
|
As an advance in hydrofunctionalization, we herein report that alcohols add to 1,3-dienes with high regio- and enantioselectivity. Using a Ni-DuPhos, we access enantioenriched allylic ethers. Through the choice of solvent-free conditions, we control the reversibility of C-O bond formation. This work showcases a rare example of methanol as a reagent in asymmetric synthesis
|
Qi Li; Zhen Wang; Vy Dong; Xiao-Hui Yang
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634bf6b1339972c8468cd049/original/enantioselective-hydroalkoxylation-of-1-3-dienes-via-ni-catalysis.pdf
|
6266cd10d048ed285d50a3df
|
10.26434/chemrxiv-2022-hf3gd
|
Co-Immobilization of Enzymes and Aptamers to create Self-Regenerating Ultrafiltration Membranes for Toxin Removal
|
Aptamer-functionalized membranes offer a promising platform for toxin removal, but regeneration of binding capacity requires heat and washing. Moreover, bound molecules can be eluted, resulting in recontamination. Here we report the tandem use of aptamers and enzymes to trap and degrade small-molecule contaminants, resulting in an autonomously self-regenerating purification system.
|
Misael A. Romero-Reyes; Kristen Patterson; Jennifer Heemstra
|
Biological and Medicinal Chemistry; Earth, Space, and Environmental Chemistry; Hydrology and Water Chemistry; Chemical Biology; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-04-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6266cd10d048ed285d50a3df/original/co-immobilization-of-enzymes-and-aptamers-to-create-self-regenerating-ultrafiltration-membranes-for-toxin-removal.pdf
|
6234982b8ab37335ad68fe1c
|
10.26434/chemrxiv-2022-gtpzw
|
Anionically-functionalized glycogen encapsulates melittin by multivalent interactions
|
We developed acid-functionalized glycogen conjugates as supramolecular carriers for efficient encapsulation
and inhibition of a model cationic peptide melittin - the main component of honeybee venom. For this purpose,
we synthesized and characterized a set of glycogens, functionalized to various degrees by several different
acid groups. These conjugates encapsulate melittin up to a certain threshold amount, beyond which they
precipitate. Computer simulations showed that sufficiently functionalized conjugates electrostatically attract
melittin, resulting in its efficient encapsulation in a broad pH range around the physiological pH. Hemolytic
assays confirmed in vitro that the effective inhibition of melittin’s hemolytic activity occurs for highly
functionalized samples, whereas no inhibition is observed when using low-functionalized conjugates. It can
be concluded that functional glycogens are promising carriers for cationic molecular cargos or antidotes against
animal venoms under conditions, in which suitable properties such as biodegradability and biocompatibility
are crucial.
|
Hanna Zhukouskaya; Pablo Blanco; Zulfiya Černochová; Lucie Čtveráčková; Roman Staňo; Ewa Pavlova; Miroslav Vetrík; Peter Černoch; Marcela Filipová; Miroslav Štěpánek; Martin Hurbý; Peter Košovan; Jiří Pánek
|
Physical Chemistry; Polymer Science; Biopolymers; Polyelectrolytes - Polymers; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6234982b8ab37335ad68fe1c/original/anionically-functionalized-glycogen-encapsulates-melittin-by-multivalent-interactions.pdf
|
60c7499fbdbb89c26fa391e7
|
10.26434/chemrxiv.12085083.v1
|
Identification of Potential Inhibitors of SARS-CoV-2 Main Protease via a Rapid In-Silico Drug Repurposing Approach
|
An
in-silico drug repurposing study was carried out to search for
potential COVID-19 antiviral agents. A dataset of 1615 FDA-approved
drugs was docked in the active site of SARS CoV-2 Main protease. A
subset of the top scoring hit compounds was subjected to follow-up
molecular dynamics simulations to further characterise the predicted
binding modes. The main findings are that the drugs Aliskiren,
Capreomycin, Isovuconazonium, emerge as novel potential inhibitors.
We also observed that Ceftolozane, Cobicistat, Carfilzomib and
Saquinavir are well-ranked by our protocol, in agreement with other
recent in silico drug repurposing studies, however MD simulations
shows only potential for the three first, as Saquinavir exhibited an
unstable binding mode. As many HIV-protease inhibitors has been
reported as active and not active, Atazanavir and Lopinavir were
included in the data set in order to rationalize the findings. In
addition, our protocol ranked favourably Dronedarone suggesting that
this recently reported SARS-CoV-2 inhibitor targets SARS-CoV-2 Main
protease.
|
Cesar Mendoza-Martinez; Alejandro Rodriguez-Lezama
|
Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7499fbdbb89c26fa391e7/original/identification-of-potential-inhibitors-of-sars-co-v-2-main-protease-via-a-rapid-in-silico-drug-repurposing-approach.pdf
|
6508cd75b6ab98a41cb12235
|
10.26434/chemrxiv-2023-c9hst
|
Deductive Machine Learning Challenges and Opportunities in Chemical Applications
|
Contemporary machine learning algorithms have largely succeeded in automating the development of mathematical models from data. Although this is a striking accomplishment, it leaves unaddressed the multitude of scenarios, especially across the chemical sciences and engineering, where deductive, rather than inductive, reasoning is required and still depends on manual intervention by an expert. This perspective describes the characteristics of deductive reasoning that are helpful for understanding the role played by expert intervention in problem-solving and why such interventions are often relatively resistant to disruption by typical machine learning strategies. The perspective then covers what factors contribute to creating a deductive bottleneck, how deductive bottlenecks are currently addressed in several application areas, and how machine learning models capable of deduction can be designed. The perspective concludes with a tutorial case-study that illustrates the challenges of deduction problems and a notebook for readers to experiment with on their own.
|
Tianfan Jin; Brett M Savoie
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence
|
CC BY 4.0
|
CHEMRXIV
|
2023-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6508cd75b6ab98a41cb12235/original/deductive-machine-learning-challenges-and-opportunities-in-chemical-applications.pdf
|
674728735a82cea2fa1d5c5a
|
10.26434/chemrxiv-2024-wk36x
|
Mechanometallaphotoredox catalysis: utilizing increased throughput mechanochemistry to develop air-tolerant solvent-minimized metallaphotoredox dual catalysis reactions
|
Photocatalysis as a tool used in organic synthesis has predominantly relied on the use of solvents, be it under homogeneous or heterogeneous conditions. In particular, metallaphotoredox catalysis reactions typically use toxic organic solvents such as DMA and DMF. Herein, we demon-strate how mechanophotocatalysis, the synergistic union of mechanochemistry and photocatalysis, is compatible with this class of dual catalysis reactions involving both photocatalyst and nickel(II) co-catalysts. Using ball milling, these mechanistically complex reactions can be conducted in the ab-sence of bulk solvent and under air, affording high yielding aryl aminations and C(sp2)-C(sp3) cross-couplings. These advances are facilitated by the introduction of a novel reaction vessel design for conducting four mechanophotocatalysis reactions simultaneously. This works highlights the promise of solvent-minimized photocatalysis reactions, demonstrating that in these examples bulk solvent is redundant, thus significantly reducing this waste stream.
|
Francis Millward; Eli Zysman-Colman
|
Organic Chemistry; Catalysis; Photocatalysis
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CC BY 4.0
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CHEMRXIV
|
2024-11-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674728735a82cea2fa1d5c5a/original/mechanometallaphotoredox-catalysis-utilizing-increased-throughput-mechanochemistry-to-develop-air-tolerant-solvent-minimized-metallaphotoredox-dual-catalysis-reactions.pdf
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670ddd8e51558a15ef17efb4
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10.26434/chemrxiv-2023-f6l23-v2
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Comprehensive sampling of coverage effects in catalysis by leveraging generalization in neural network models
|
Sampling high-coverage configurations and predicting adsorbate-adsorbate interactions on surfaces are highly relevant to understand realistic interfaces in heterogeneous catalysis. However, the combinatorial explosion in the number of adsorbate configurations among diverse site environments presents a considerable challenge in accurately estimating these interactions. Here, we propose a strategy combining high-throughput simulation pipelines and a neural network-based model with the MACE architecture to increase sampling efficiency and speed. By training the models on unrelaxed structures and energies, which can be quickly obtained from single-point DFT calculations, we achieve excellent performance for both in-domain and out-of-domain predictions, including generalization to different facets, coverage regimes and low-energy configurations. From this systematic understanding of model robustness, we exhaustively sample the configuration phase space of catalytic systems without active learning. In particular, by predicting binding energies for over 14 million structures within the neural network model and the simulated annealing method, we predict coverage-dependent adsorption energies for CO adsorption on six Cu facets (111, 100, 211, 331, 410 and 711) and the co-adsorption of CO and CHOH on Rh(111). When validated by targeted post-sampling relaxations, our results for CO on Cu correctly reproduce experimental interaction energies reported in the literature, and provide atomistic insights on the site occupancy of steps and terraces for the six facets at all coverage regimes. Additionally, the arrangement of CO on the Rh(111) surface is demonstrated to substantially impact the activation barriers for the CHOH bond scission, illustrating the importance of comprehensive sampling on reaction kinetics. Our findings demonstrate that simplified data generation routines and evaluating generalization of neural networks can be deployed at scale to understand lateral interactions on surfaces, paving the way towards realistic modeling of heterogeneous catalytic processes.
|
Daniel Schwalbe-Koda; Nitish Govindarajan; Joel Varley
|
Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis
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CC BY NC 4.0
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CHEMRXIV
|
2024-10-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670ddd8e51558a15ef17efb4/original/comprehensive-sampling-of-coverage-effects-in-catalysis-by-leveraging-generalization-in-neural-network-models.pdf
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652d84928bab5d20557c5443
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10.26434/chemrxiv-2023-pg6pq
|
Kraft lignin-derived micro- and mesoporous nitrogen-doped carbon adsorbent for air and water purification
|
The study presents a streamlined one-step process for producing highly porous, metal-free, N-doped activated carbon (N-AC) for CO2 capture and herbicide removal from simulated industrially polluted and real environmental systems. N-AC was prepared from kraft lignin - a carbon-rich and abundant by-product of the pulp industry, using nitric acid as the activator and urea as the N-dopant. The reported carbonization process under a nitrogen atmosphere renders a product with a high yield of 30% even at high temperatures up to 800 °C. The N-AC exhibited a substantial high N content (4–5 %), the presence of aliphatic and phenolic OH groups, and a notable absence of carboxylic groups, as confirmed by Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy and Boehm’s titration. Scanning electron microscopy revealed the presence of mesopores with an average diameter of 3 nm. Porosity analysis indicated that micropores constituted the majority of the pore structure, with 86% of pores having diameters less than 0.6 nm. According to BET adsorption analysis, the developed porous structure of N-AC boasted a substantial specific surface area of 1000 m2 g−1. N-AC proved to be a promising adsorbent for air and water purification. Specifically, N-AC exhibited a strong affinity for CO2, with an adsorption capacity of 1.4 mmol g−1 at 0.15 bar, and 20 °C and it demonstrated the highest selectivity over N2 from the simulated flue gas system (27.3 mmol g−1 for 15:85 v:v CO2:N2 at 20 °C) among all previously reported nitrogen-dopped AC materials from kraft lignin. Moreover, N-AC displayed excellent reusability and efficient CO2 release, maintaining an adsorption capacity of 3.1 mmol g−1 (at 1 bar and 25 °C) over ten consecutive adsorption-desorption cycles, confirming N-AC as a useful material for CO2 storage and utilization. The unique cationic nature of N-AC enhanced the adsorption of herbicides in neutral and weakly basic environments, which is relevant for real waters. It exhibited an impressive adsorption capacity for the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) at 96 ± 6 mg g−1 under pH 6 and 25 °C according to the Langmuir-Freundlich model. Notably, N-AC preserves its high adsorption capacity towards 2,4-D from simulated groundwater and runoff from tomato greenhouse, while performance in real samples from Fyris river in Uppsala, Sweden, causes a decrease of only 4-5%. Owing to the one-step process, high yield, the annual abundance of kraft lignin, and the use of environmentally friendly activating agents, N-AC has substantial potential for large-scale industrial applications.
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Oleg Tkachenko; Alina Nikolaichuk; Nataliia Fihurka; Andreas Backhaus; Julie B. Zimmerman; Maria Strømme; Tetyana Budnyak
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Physical Chemistry; Nanoscience; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-10-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d84928bab5d20557c5443/original/kraft-lignin-derived-micro-and-mesoporous-nitrogen-doped-carbon-adsorbent-for-air-and-water-purification.pdf
|
60e70bb78825822d8fa627d8
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10.26434/chemrxiv-2021-clq4h
|
A close-up look at the chemical space of commercially available building blocks for medicinal chemistry
|
The ability to efficiently synthesize desired compounds can be a limiting factor for chemical space exploration in drug discovery. This ability is conditioned not only by the existence of well-studied synthetic protocols but also by the availability of corresponding reagents, so-called building blocks (BB). In this work, we present a detailed analysis of the chemical space of 400K purchasable BB. The chemical space was defined by corresponding synthons – fragments contributed to the final molecules upon reaction. They allow an analysis of BB physicochemical properties and diversity, unbiased by the leaving and protective groups in actual reagents. The main classes of BB were analyzed in terms of their availability, rule-of-two-defined quality, and diversity. Available BBs were eventually compared to a reference set of biologically relevant synthons derived from ChEMBL fragmentation, in order to illustrate how well they cover the actual medicinal chemistry needs. This was performed on a newly constructed universal generative topographic map of synthon chemical space, allowing to visualize both libraries and analyze their overlapping and library-specific regions.
|
Yuliana Zabolotna ; Dmitriy Volochnyuk; Sergey Ryabukhin; Dragos Horvath; Kostiantyn Gavrylenko ; Gilles Marcou ; Yurii Moroz; Olexandr Oksiuta; Alexandre Varnek
|
Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-07-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e70bb78825822d8fa627d8/original/a-close-up-look-at-the-chemical-space-of-commercially-available-building-blocks-for-medicinal-chemistry.pdf
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624dd93254b5d92bf4ec3795
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10.26434/chemrxiv-2022-zdz5b-v2
|
Exciton Effects in Low-Strain GaN/AlGaN Quantum Wells
|
Solid state light sources irradiating in the UV spectral region are key components in today technologies as they can replace conventional mercury vapor gas-discharge lamps. Ultrathin GaN layers in AlGaN barriers are of great interest for UV-emitting photonic devices, but a detailed understanding of the exciton features of these systems is still lacking. In this work, GaN layers, grown by metal organic chemical vapour deposition, were deeply investigated in AlGaN barriers with different Al amount, in order to correlate excitonic effects with structural features.
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Arianna Cretì; David Maria Tobaldi; Mauro Lomascolo; Iolena Tarantini; Adriana Passaseo; Vittorianna Tasco
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Materials Science; Multilayers; Optical Materials; Thin Films
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CC BY NC ND 4.0
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CHEMRXIV
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2022-04-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624dd93254b5d92bf4ec3795/original/exciton-effects-in-low-strain-ga-n-al-ga-n-quantum-wells.pdf
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60c752d4567dfe2309ec5d51
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10.26434/chemrxiv.13353434.v1
|
Inhibition of SARS-CoV-2 Main Protease: A Repurposing Study That Targets the Dimer Interface of the Protein
|
Coronavirus disease-2019 (COVID-19) was firstly reported in Wuhan, China, towards the end of 2019, and, unfortunately, within a short period of time, emerged as a pandemic. The spread and lethality rates of the COVID-19 have ignited studies that focus on the development of therapeutics for either treatment or prophylaxis purposes. In parallel, drug repurposing studies have also come into prominence. In this study, we aimed at having a holistic understanding of <br />conformational and dynamical changes induced by an experimentally characterized inhibitor on main protease (M-pro) which would enable the discovery of novel inhibitors. To this end, we performed molecular dynamics simulations using crystal structures of <i>apo</i> and α-ketoamide-13b-bound M-pro homodimer. Analysis of trajectories pertaining to <i>apo</i> M-pro revealed a new target site, which is located at the homodimer interface, next to the catalytic dyad. Thereafter, we performed ensemble-based virtual screening by exploiting the ZINC and DrugBank databases and identified three candidate molecules, namely eluxadoline, diosmin, and ZINC02948810 that could invoke local and global conformational rearrangements which were also elicited by α-ketoamide-13b on the catalytic dyad of M-pro. Furthermore, ZINC23881687 was also discerned as a promising candidate due to its interaction with catalytically important residues Glu166 and Ser1. Last but not least, we could find another candidate, namely ZINC20425029, whose mode of action was different. It modulated the dynamical properties of catalytically important residue, Ala285 rather than the catalytic dyad. As such, this study presents valuable findings that might be used in the development of novel therapeutics against SARS-CoV-2 M-pro. <br />
|
Hanife Pekel; Metehan Ilter; Ozge Sensoy
|
Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2020-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752d4567dfe2309ec5d51/original/inhibition-of-sars-co-v-2-main-protease-a-repurposing-study-that-targets-the-dimer-interface-of-the-protein.pdf
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64ec042bdd1a73847fabeb7b
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10.26434/chemrxiv-2023-9g0fr-v3
|
GFN-xTB Based Computations Provide Comprehensive Insights into Emulsion Radiation-Induced Graft Polymerization
|
In this article, a deep insight into emulsion radiartion-induced graft polymerization (RIGP) was obtained by computing explicit solvation free energies, conformational entropy, monomer radius and dipole moments with the state-of-the-art Conformer-Rotamer Ensemble Sampling Tool (CREST) package primalily at semiempirical GFN-xTB level. By leveraging the robustness of the CREST package, above parameters provided dynamic nature of methacrylate monoers with the consideration of realistic emulsion conditions. With the chemical and physical importance of the above results, CREST-determined explanatory variables sufficiently led to the building of the prediction models for the RIGP of methacrylate monomers. The machine learning model building resulted in effective reactivity predictions and unveiled important factors for the radiation-induced graft polymerization in a chemically interpretable fashion.
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Kiho Matsubara; Kei Takahashi; Takeshi Matsuda; Yuji Ueki; Noriaki Seko; RYOHEI KAKUCHI
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Chemical Engineering and Industrial Chemistry; Reaction Engineering; Materials Chemistry
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CC BY NC 4.0
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CHEMRXIV
|
2023-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ec042bdd1a73847fabeb7b/original/gfn-x-tb-based-computations-provide-comprehensive-insights-into-emulsion-radiation-induced-graft-polymerization.pdf
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60c756e8469df4e7e9f453ad
|
10.26434/chemrxiv.14346194.v1
|
Morphology Control in 2D Carbon Nitrides: Impact of Particle Size on Optoelectronic Properties and Photocatalysis
|
The carbon nitride poly(heptazine imide), PHI, has recently emerged as a powerful 2D carbon nitride photocatalyst with intriguing charge storing ability. Yet, insights into how morphology, particle size and defects influence its photophysical properties are virtually absent. Here, ultrasonication is used to systematically tune the particle size as well as concentration of surface functional groups and study their impact. Enhanced photocatalytic activity correlates with an optimal amount of those defects that create shallow trap states in the optical band gap, promoting charge percolation, as evidenced by time-resolved photoluminescence spectroscopy, charge transport studies, and quantum-chemical calculations. Excessive amounts of terminal defects can act as recombination centers and hence, decrease the photocatalytic activity for hydrogen evolution. Re-agglomeration of small particles can, however, partially restore the photocatalytic activity. The type and amount of trap states at the surface can also influence the deposition of the co-catalyst Pt, which is used in hydrogen evolution experiments. Optimized conditions entail improved Pt distribution, as well as an enhanced wettability and colloidal stability. A description of the interplay between these effects is provided to obtain a holistic picture of the size–property–activity relationship in nanoparticulate PHI-type carbon nitrides that can likely be generalized to related photocatalytic systems.<br />
|
Julia Kröger; Alberto Jiménez-Solano; Gökcen Savasci; Vincent Wing-hei Lau; Viola Duppel; Igor Moudrakovski; Kathrin Küster; Tanja Scholz; Andreas Gouder; Marie Luise Schreiter; Filip Podjaski; Christian Ochsenfeld; Bettina Lotsch
|
Aggregates and Assemblies; Carbon-based Materials; Catalysts; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Energy Storage; Fuels - Energy Science
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-04-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e8469df4e7e9f453ad/original/morphology-control-in-2d-carbon-nitrides-impact-of-particle-size-on-optoelectronic-properties-and-photocatalysis.pdf
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60c74047567dfea74eec3b42
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10.26434/chemrxiv.7685651.v1
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Why Electrochromism in Li4ti5o12 Differs in the Visible and Infrared Spectrum
|
Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> (LTO) has been experimentally proven as a promising electrochromic material in applications of smart windows, thermal management and infrared camouflage. However, the fundamental mechanism on these phenomena is still lacking. For the first time, we fill this knowledge gap via quantitative matching the LTO's optical properties and electronic structure during charging/discharging using density functional theory. Our study suggests that the absorption of infrared is highly sensitive to intercalation of Li in the LTO lattice, in contrast with the adsorption of visible wavelengths. This unique property of LTO offers the practical ability in controlling infrared-induced heating with minimal effect on transmission of visible light. Furthermore, we also conclude that electrochemically controlled intercalation of Li causes donor states to appear, expand and move to deeper levels in the forbidden band, leading to better conductivity and lower transmittance, which is in line with the experimental results in the literature.
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MENG LI; Tim Gould; Zhong Su; Shanqing Zhang
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Theory - Computational; Optics
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-02-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74047567dfea74eec3b42/original/why-electrochromism-in-li4ti5o12-differs-in-the-visible-and-infrared-spectrum.pdf
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60c74e3b842e659dbddb35e1
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10.26434/chemrxiv.12727787.v1
|
Potential Compounds for the Inhibition of TMPRSS2
|
<p>The ongoing search to contain and
control the spread of COVID-19 disease focuses on discovering drugs or vaccines
that can play an essential role in treating this contagious disease. This paper
focuses on natural compounds that can play a vital role in the treatment of
Covid-19. The study spans over the chemicals that have the potential to bind
with the key residues of type II Transmembrane Protease Serine (TMPRSS2).
TMPRSS2 can be termed as the catalyst that cleaves the spike glycoproteins of
Sars-Cov-2, which causes the replication and spread of virus inside the human
body by facilitating virus-cell fusions. Drugs like Camostat Mesylate, Aprotinin,
and Rimantadine have been proposed as potential inhibitors of TMPRSS2. After
screening large sets of phytochemicals and flavonoids extracted from plants,
potential compounds have been tested, and a set of most effective and suitable
compounds are chosen for further studies. These selected compounds are further
analyzed in terms of binding with key residues as well as high binding affinity
with TMPRSS2. The in silico analysis of possible chemical compounds is carried
out by using docking, screening analysis, Molecular Dynamics, and Electrostatic
Potential Simulations. Chemicals extracted from different plants are
comparatively analyzed with drugs like Aprotinin, Camostat Mesylate, and
Rimantadine.</p>
|
Muhammad Roomi; Yaser Khan
|
Biochemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e3b842e659dbddb35e1/original/potential-compounds-for-the-inhibition-of-tmprss2.pdf
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60c7453f337d6c1d6fe26f53
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10.26434/chemrxiv.9999572.v1
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Overcoming Crystallinity Limitations of Aluminium Metal–Organic Frameworks by Oxalic Acid Modulated Synthesis
|
A modulated synthesis approach based on the chelating properties of oxalic acid (H<sub>2</sub>C<sub>2</sub>O<sub>4</sub>) is presented as a robust and versatile method to achieve highly crystalline Al-based metal–organic frameworks (MOFs). A comparative study on this method and the already established modulation by hydrofluoric acid was conducted using MIL-53 as test system. The superior performance of oxalic acid modulation in terms of crystallinity and absence of undesired impurities is explained by assessing the coordination modes of the two modulators and the structural features of the product. The validity of our approach was confirmed for a diverse set of Al-MOFs, namely X-MIL-53 (X = OH, CH<sub>3</sub>O, Br, NO<sub>2</sub>), CAU-10, MIL-69, and Al(OH)ndc (ndc = 1,4-naphtalenedicarboxylate), highlighting the potential benefits of extending the use of this modulator to other coordination materials.<br />
|
Stefano Canossa; Adrian Gonzalez-Nelson; Leonid Shupletsov; María del Carmen Martín; Monique van der Veen
|
Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
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CHEMRXIV
|
2019-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453f337d6c1d6fe26f53/original/overcoming-crystallinity-limitations-of-aluminium-metal-organic-frameworks-by-oxalic-acid-modulated-synthesis.pdf
|
644ac2cc80f4b75b5337ce4e
|
10.26434/chemrxiv-2023-fjcxd-v2
|
Scalable Extraction of Information from Spatio-Temporal Patterns of Chemoresponsive Liquid Crystals Using Topological Data Analysis
|
Chemoresponsive liquid crystals (LCs) can be engineered to generate information-rich optical responses upon exposure to gas contaminants. We investigate the use of topological descriptors to extract information from these complex responses and with this facilitate sensor design and understand physical phenomena that govern responses. We provide a holistic view of topological descriptors using Minkowski functionals and fractal analysis and show how descriptors can be used for unsupervised (clustering, visualization) and supervised (regression, classification) machine learning (ML) tasks. Specifically, by using high-throughput, experimental data for LC films exposed to diverse contaminants, we show that topological descriptors can be used to effectively detect outliers and predict contaminant concentrations using simple ML models. Notably, these models achieve comparable accuracies to those of powerful convolutional neural networks, but with much lower computational times (from hours to seconds) and using less sophisticated computing hardware. This scalability enables high-resolution, space-time data analysis.
|
Shengli Jiang; Nanqi Bao; Alexander D. Smith; Shraddha Byndoor; Reid C. Van Lehn; Manos Mavrikakis; Nicholas L. Abbott; Victor M. Zavala
|
Theoretical and Computational Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Analytical Chemistry - General; Theory - Computational; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644ac2cc80f4b75b5337ce4e/original/scalable-extraction-of-information-from-spatio-temporal-patterns-of-chemoresponsive-liquid-crystals-using-topological-data-analysis.pdf
|
630e14b4eadd9a71ee873a40
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10.26434/chemrxiv-2022-449g7
|
Inviting Trifluoromethylated Pseudoprolines into Collagen Model Peptides
|
Numerous Collagen Model Peptides (CMPs) have been engineered using proline derivatives substituted at their C(3) and/or C(4) position in order to stabilize or to functionalize collagen triple helix mimics. However, no example has been reported so far with C(5) substitutions. Here, we introduce a fluorinated CMP incorporating trifluoromethyl groups at the C(5) position of pseudoproline residues. In tripeptide models, our NMR and Molecular Dynamics (MD) studies have shown that, when properly arranged, these residues meet the structural requirements for triple helix assembly. A host-guest CMP could be synthesized and its NMR analysis in solution confirmed the presence of structured homotrimers that we interpret as triple helices. MD calculations showed that the triple helix model remained stable throughout the simulation, with all six trifluoromethyl groups pointing outwards from the triple helix. Pseudoprolines substituted at the C(5) positions appeared as valuable tools for the design of new fluorinated collagen mimicking peptides.
|
Anaïs Terrien; Keyvan Rahgoshay; Emelyne Renaglia; Nathalie Lensen; Yves Jacquot; Rodrigue Marquant; Thierry Brigaud; Claire Loison; Grégory Chaume; Emeric Miclet
|
Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Spectroscopy (Anal. Chem.); Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630e14b4eadd9a71ee873a40/original/inviting-trifluoromethylated-pseudoprolines-into-collagen-model-peptides.pdf
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6675c34301103d79c5ca25f3
|
10.26434/chemrxiv-2024-51t11
|
Analysis of protein-glycan recognition using absolute binding free energies
|
Carbohydrates are key biological mediators of molecular recognition and signalling processes. In this work, we explore the ability of absolute binding free energy (ABFE) calculations to predict the affinities of a set of five related carbohydrate ligands for the lectin protein, concanavalin A, ranging from 27-atom monosaccharides to a 120-atom complex-type N-linked glycan core pentasaccharide. ABFE calculations quantitatively rank and estimate the affinity of the ligands in relation to microcalorimetry, with a mean signed error in binding free energy of -0.63 ± 0.04 kcal/mol. Consequently, the diminished binding efficiencies of the larger carbohydrate ligands are closely reproduced: the ligand efficiency values from isothermal titration calorimetry for the glycan core pentasaccharide and its constituent trisaccharide and monosaccharide compounds are respectively -0.14 ± 0.00, -0.22 ± 0.00 and -0.41 ± 0.00 kcal/mol per heavy atom. ABFE calculations predict these ligand efficiencies to be -0.14 ± 0.02, -0.24 ± 0.03 and -0.46 ± 0.06 kcal/mol per heavy atom respectively. Consequently, the ABFE method correctly identifies the high affinity of the key anchoring mannose residue and the negligible contribution to binding of both β-GlcNAc arms of the pentasaccharide. While challenges remain in sampling the conformation and interactions of these polar, flexible and weakly bound ligands, we nevertheless here find that the ABFE method performs well. The method shows excellent promise as a quantitative tool for predicting and deconvoluting carbohydrate-protein interactions, with potential application to design of therapeutics, vaccines and diagnostics.
|
Richard Bryce; Irfan Alibay; Philip Biggin; Sondos Musleh
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6675c34301103d79c5ca25f3/original/analysis-of-protein-glycan-recognition-using-absolute-binding-free-energies.pdf
|
60c7424f4c89196920ad2423
|
10.26434/chemrxiv.8242871.v1
|
Brain-Penetrating Peptide Shuttles Across the Blood-Brain Barrier and Extracellular-like Space
|
Here, we describe a combinatorial approach to identify peptide shuttles that successfully traverse the multiple barriers to systemic drug delivery to the brain--1. the blood-brain barrier (BBB) and the 2. extracellular space (ECS) of the brain. Leveraging the excellent molecular diversity of M13 phage libraries, we identified peptides that actively transport across the BBB and diffuse through the extracellular matrix of the ECS in cell culture and in mice. These peptides demonstrate higher accumulation in the brain than gold standard peptides used in clinical trials. Importantly, these findings suggest that different sized therapeutics that were previous poorly permeable into the brain can accumulate at higher concentrations, thereby improving the therapeutic index and ultimate efficacy of drugs into the brain.
|
Xiujuan Peng; Xinquan Liu; Yen-Liang Liu; Jae You Kim; Yuan-I Chen; Phyllis Ang; Alex Nguyen; Jasmim Leal; Hsin-Chih Yeh; Debadyuti Ghosh
|
Bioengineering and Biotechnology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-06-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7424f4c89196920ad2423/original/brain-penetrating-peptide-shuttles-across-the-blood-brain-barrier-and-extracellular-like-space.pdf
|
61712092d7e1ee92092bf495
|
10.26434/chemrxiv-2021-vfkqb-v3
|
Engineering a Cytidine Aminotransferase for Biocatalytic Production of the Antiviral Molnupiravir
|
The COVID-19 pandemic highlights the urgent need for cost-effective processes to rapidly manufacture antiviral drugs at scale. Here we report a concise biocatalytic process for Molnupiravir, a nucleoside analogue currently in phase 3 clinical trials as an orally available treatment for SARS-CoV-2. Key to the success of this process was the development of a cytidine aminotransferase for the production of N-hydroxy-cytidine through evolutionary adaption of the hydrolytic enzyme cytidine deaminase. This engineered biocatalyst performs >100,000 turnovers in less than 30 minutes, operates at 180 g/L substrate loading and benefits from in situ crystallization of the N-hydroxy-cytidine product (>90% yield), which can be converted to Molnupiravir by a selective 5’-acylation using Novozym® 435.
|
Ashleigh Burke; William Birmingham; Ying Zhuo; Bruna Zuculoto da Costa; Rebecca Crawshaw; Thomas Thorpe; Ian Rowles; James Finnigan; Simon J. Charnock; Sarah Lovelock; Nicholas Turner; Anthony Green; Carl Young
|
Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Biocatalysis
|
CC BY 4.0
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CHEMRXIV
|
2021-10-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61712092d7e1ee92092bf495/original/engineering-a-cytidine-aminotransferase-for-biocatalytic-production-of-the-antiviral-molnupiravir.pdf
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60c750e80f50db343639767a
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10.26434/chemrxiv.13096157.v1
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A Cloud Computing Platform for Scalable Relative and Absolute Binding Free Energy Prediction: New Opportunities and Challenges for Drug Discovery
|
<p>Free energy
perturbation (FEP) has become widely used in drug discovery programs for
binding affinity prediction between candidate compounds and their biological
targets. Simultaneously limitations of FEP applications also exist, including
but not limited to, the high cost, long waiting time, limited scalability and
application scenarios. To overcome these problems, we have developed a scalable
cloud computing platform (XFEP) for both relative and absolute free energy
predictions with refined simulation protocols. XFEP enables large-scale FEP
calculations in a more efficient, scalable and affordable way, e.g. the evaluation
of 5,000 compounds can be performed in one week using 50-100 GPUs with a
computing cost approximately corresponding to the cost for one new compound
synthesis. Together with artificial intelligence (AI) techniques for
goal-directed molecule generation and evaluation, new opportunities can be
explored for FEP applications in the drug discovery stages of hit
identification, hit-to-lead, and lead optimization with R-group substitutions,
scaffold hopping, and
completely different molecule evaluation. We anticipate scalable FEP applications will become widely
used in more drug discovery projects to speed up the drug discovery process
from hit identification to pre-clinical candidate compound nomination. </p>
|
Zhixiong Lin; Junjie Zou; Chunwang Peng; Shuai Liu; Zhipeng Li; Xiao Wan; Dong Fang; Jian Yin; Gianpaolo Gobbo; Yongpan Chen; Jian Ma; Shuhao Wen; Peiyu Zhang; Mingjun Yang
|
Biochemistry; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e80f50db343639767a/original/a-cloud-computing-platform-for-scalable-relative-and-absolute-binding-free-energy-prediction-new-opportunities-and-challenges-for-drug-discovery.pdf
|
60c755014c89194a09ad45f2
|
10.26434/chemrxiv.13853345.v1
|
Liquiritin from Glycirrhyza Glabra L (Fabaceae) - a Natural Derived Drug, as a Potential Inhibitor for SARS-CoV-2
|
<p>Novel Corona virus-2 (Covid-19) is spreading and
causing major damage around the globe and constantly increasing daily. There is
a prerequisite of expeditious development of safe and efficient drugs for such
a contagious disease. In this regard, utilization of a computational approach
with an aim to provide potential enzyme inhibitors derived from natural
resources will give a providential therapy. The present study investigated one
of the promising plants namely Glycyrrhiza glabra L. It has various medicinal
properties viz. anti-inflammatory, anti-cancer, anti-demulcent, expectorant,
etc. <i>In-Silico</i> Analysis of liquiritin
against SARS-CoV-2 Mpro was carried out using Autodock 4.2.6 and results were
compared with presently prescribed drugs i.e. dexamethasone, remdesivir,
hydroxychloroquine, and azithromycin. The binding energy of liquiritin was
found to be -6.62 kcal/mol. It shows presence of hydrogen bond, hydrophobic
interaction and electrostatic interaction with six active residues THR26,
GLY143, CYS145, HIS 164, GLU166, and GLN189. Comparative studies investigated
that dexamethasone, remdesivir, hydroxychloroquine, and azithromycin have four
(THR26, GLY143, CYS145, GLU166), three (CYS145, GLU166, GLN189), four (GLY143,
CYS145, HIS 164, GLN189) and two (GLU166, GLN189) identical active residues,
respectively. The present study recommended liquiritin as a potential candidate
against SARS-CoV-2 as it is naturally derived and has tremendous traditional
usage against various diseases. However, in-vitro and in-vivo studies are
required to prove its efficacy.</p>
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Akash Vanzara; Ravi Patel; Amisha Patel; Nimisha Patel; Kapil Yadav; Padamnabhi Nagar
|
Bioinformatics and Computational Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-02-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755014c89194a09ad45f2/original/liquiritin-from-glycirrhyza-glabra-l-fabaceae-a-natural-derived-drug-as-a-potential-inhibitor-for-sars-co-v-2.pdf
|
659e2e88e9ebbb4db9d3f94a
|
10.26434/chemrxiv-2024-xn4k3
|
Aggregative Luminescence from Perovskite Precursors
|
In this work, we conducted a detailed investigation into the optical properties of all-inorganic perovskite (CsPbBr3) precursors. The absorption, photoluminescence (PL), and photoluminescence excitation spectra of the precursors were analyzed in a broad concentration and various solvents. In specific solvents (such as DMSO, DMF, and NMP), the CsPbBr3 precursor gradually transformed from solution into a colloid and exhibited aggregation-induced emission (AIE) as the concentration increased, and the luminescence intensity and color of the colloid could be controlled by changing the solvent and precursor ratio. Understanding the optoelectronic properties of the precursor may provide deeper insight into the mechanisms that govern the formation and crystallization processes of perovskites, which is vital for the solution-process device performance. Besides, we discussed the difference between the aggregates in the organic system (such as TPE) and the inorganic system (such as CsPbBr3).
|
Siwei Zhang; Fulong Ma; Jinhui Jiang; Zijie Qiu; Zheng Zhao; Jacky Lam; Ben Zhong Tang
|
Materials Science; Inorganic Chemistry; Nanoscience; Dyes and Chromophores; Coordination Chemistry (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659e2e88e9ebbb4db9d3f94a/original/aggregative-luminescence-from-perovskite-precursors.pdf
|
6509cee9b927619fe76fde7a
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10.26434/chemrxiv-2023-nwn3x-v4
|
One-pot Reduction of Nitrostyrenes to Phenethylamines using Sodium Borohydride and Copper(II) chloride
|
The preparation of phenethylamines and phenylisoproylamines of scientific relevance can be achieved with a NaBH4/CuCl2 system in 10 to 30 minutes via reduction of substituted β-nitrostyrenes. The method also reduces nitrobenzene and methyl benzoate in 92 to 97% yields, respectively, while has no effect on benzoic acid, benzamide, and aromatic halides. This one-pot procedure allows the isolation of substituted β-nitrostyrene scaffolds up to 83% yield under mild conditions, without the need for special precautions, inert atmosphere, and time-consuming purification techniques.
|
Laura d'Andrea; Jesper L. Kristensen
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-09-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509cee9b927619fe76fde7a/original/one-pot-reduction-of-nitrostyrenes-to-phenethylamines-using-sodium-borohydride-and-copper-ii-chloride.pdf
|
62815f556cae1c6c6c0b5d05
|
10.26434/chemrxiv-2022-7bdb0
|
A molecular-locked organic crystal imitating the connection mode of base pairs
|
At present, the biggest challenge for the development of organic electronic devices is the uncontrollable molecular structure of organic materials. For small molecule organic electronic materials, due to the lack of design, the arrangement between molecules is often uncontrollable and the formed crystals lack thermal stability. For polymer electronic materials, it is difficult to form ordered lattice, which greatly limits the improvement of its mobility. In this paper, we first proposed the strategy of ‘adjacent molecules can be locked to each other’ (TML) and designed and synthesized a TML molecule with bio-simulating the structure of DNA. Experiments show that TML molecules have good thermodynamic stability and electron beam radiation robustness. PL Spectrum and calculation verified that TML molecules had strong electron coupling, revealing its application potential in organic electronics. More importantly, TML molecules verify the feasibility of bottom-up construction of all-crystalline organic electronic materials.
|
XiaoNan Wung; Humin Chen; xiaojing song; di wang
|
Theoretical and Computational Chemistry; Organic Chemistry; Materials Science; Nanostructured Materials - Materials
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-05-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62815f556cae1c6c6c0b5d05/original/a-molecular-locked-organic-crystal-imitating-the-connection-mode-of-base-pairs.pdf
|
657b19289138d23161a27b0b
|
10.26434/chemrxiv-2023-3cwjs
|
Large-scale validation of a plasmonic sensor for SARS-CoV-2 pseudo-neutralization with a cohort of food and retail workers
|
Plasmonic sensors are candidates for numerous clinical applications, but few examples demonstrate their performance on large sample cohorts, a necessary step for clinical translation. The COVID-19 pandemic provided an unprecedented opportunity to validate a surface plasmon resonance (SPR) sensor for SARS-CoV-2 inhibition with a cohort of over 1,000 clinical samples from the longitudinal study of a food and retail worker population. The SPR sensor provided an in vitro model to assess the level of neutralizing antibodies by measuring the inhibition of the SARS-CoV-2 spike protein interaction with ACE-2 following exposure of the spike protein to naive and immune sera (from vaccination and/or infection). In conjunction with population data on vaccination and infection, and epidemiological data from the local jurisdiction of the study cohort, it is shown that the SPR sensor performed well in assessing the level of “pseudo-neutralization” of participant sera and that the response of the SPR sensor correlates (r = 0.74) with a live virus microneutralization assay as well as with metadata of relevant events (vaccination, waves of infection, etc.) that occurred during the study period. Using these data, the article details the challenges and opportunities of using plasmonic sensors in clinical practice.
|
Julien Coutu; Pierre Ricard; Abdelhadi Djaïleb; Etienne Lavallée; Henintsoa Rabazanaha; Matthew Stuible; Yves Durocher; Caroline Gilbert; Nicholas Brousseau; Kim Santerre; Mathieu Thériault; Sylvie Trottier; Denis Boudreau; Marc-André Langlois; Joelle Pelletier; Mariana Baz Etchebarne; Jean-Francois Masson
|
Analytical Chemistry; Biochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b19289138d23161a27b0b/original/large-scale-validation-of-a-plasmonic-sensor-for-sars-co-v-2-pseudo-neutralization-with-a-cohort-of-food-and-retail-workers.pdf
|
65b3fdeb66c138172957b43f
|
10.26434/chemrxiv-2024-dnbgj
|
Teaching statistics and chemometrics using an open source, free and graphical user interface software.
|
This report aims to introduce the fundamental features of the JAMOVI software to academics in the chemistry field for use in undergraduate and graduate-level research. It is freeware with a graphical user interface (GUI) and it is written in the R language. The discussion began on descriptive statistics ( mean, median, range, skewness how to check data normality using hypothesis tests (Shapiro-Wilk, Kolmogorov-Smirnov and Anderson-Darling tests). Then, some visual tools for checking data normality were presented (histograms, Q-Q plots, and boxplots). When the data normality was checked, two and more dependent means were compared using parametric tests (t test and ANOVA; Fisher’s). When the data was not normally distributed, nonparametric tests were used (Mann-Whitney and Kruskal-Wallis tests). When the data was paired and normally distributed, two and more than two group means were compared using the paired t-test and RMANOVA, respectively. Their nonparametric versions were also used (Wilcoxon and Friedman tests). Means comparisons were also carried out using boxplots and discriminant plots, which provide a visual interpretation beyond the p-values interpretation. In addition, principal component analysis (PCA) was carried out using JAMOVI's plugin MEDA, which builds scores and loading plots. All tests and plots were done easily using JAMOVI's click-and-go interface.
|
Roberto Silva de Souza Junior; ENDLER MARCEl Borges
|
Analytical Chemistry; Chemical Education; Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b3fdeb66c138172957b43f/original/teaching-statistics-and-chemometrics-using-an-open-source-free-and-graphical-user-interface-software.pdf
|
60c74a220f50db5b6c396a00
|
10.26434/chemrxiv.12155499.v1
|
Determining the Geographical Origin of Crude Palm Oil with the Combined Use of GC-IMS Fingerprinting and Chemometrics
|
<p>Current administrative controls used to verify geographical provenance within palm oil supply chains require enhancement and strengthening by more robust analytical methods. In this study, the application of volatile organic compound fingerprinting, in combination with five different analytical classification models, has been used to verify the regional geographical provenance of crude palm oil samples. For this purpose, 108 crude palm oil samples were collected from two regions within Malaysia, namely Peninsular Malaysia (32) and Sabah (76). Samples were analysed by gas chromatography-ion mobility spectrometry (GC-IMS) and the five predictive models (Sparse Logistic Regression, Random Forests, Gaussian Processes, Support Vector Machines, and Artificial Neural Networks) were built and applied. Models were validated using 10-fold cross-validation. The Area Under Curve (AUC) measure was used as a summary indicator of the performance of each classifier. All models performed well (AUC 0.96) with the Sparse Logistic Regression model giving best performance (AUC = 0.98). This demonstrates that the verification of the geographical origin of crude palm oil is feasible by volatile organic compound fingerprinting, using GC-IMS supported by chemometric analysis. </p>
|
Kirstie Goggin; Emma Brodrick; Alfian Nur Wicaksono; James Covington; Antony N Davies; Denis J. Murphy
|
Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a220f50db5b6c396a00/original/determining-the-geographical-origin-of-crude-palm-oil-with-the-combined-use-of-gc-ims-fingerprinting-and-chemometrics.pdf
|
6759b06df9980725cfbc8cef
|
10.26434/chemrxiv-2024-7w6g6
|
Accelerating CO₂ Direct Air Capture Screening for Metal-Organic Frameworks with a Transferable Machine Learning Force Field
|
Direct air capture (DAC) of CO₂ is necessary for climate change mitigation, but it faces challenges from low atmospheric CO₂ concentrations and competition from water vapor. Metal-organic frameworks (MOFs) are attractive candidates for DAC owing to their exceptionally high surface area, tunable porosity, and potential for adsorption-based capture processes with relatively low regeneration cost. Identifying optimal MOFs is hindered by their structural complexity, the vastness of their chemical space, and the expense of accurate simulations. Here, we present a machine learning force field (MACE-DAC) tailored for CO2 and H2O interactions in MOFs by finetuning the foundation model MACE-MP-0. To address smoothing issues and catastrophic forgetting, we curated the diverse GoldDAC dataset and introduced a continual learning loss function. To efficiently sample gas configurations, we developed the DAC-SIM package that uses MLFFs to achieve ab initio quality thermodynamics based on Widom insertion at computational speeds comparable to classical force fields. High-throughput screening on more than 8,000 synthesized MOF structures was performed to identify optimal MOFs and extract important chemical features. This approach overcomes prior limitations in describing CO2/MOF and H₂O/MOF interactions, providing a scalable and accurate framework for accelerating DAC research for porous materials.
|
Yunsung Lim; Hyunsoo Park; Aron Walsh; Jihan Kim
|
Theoretical and Computational Chemistry; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6759b06df9980725cfbc8cef/original/accelerating-co2-direct-air-capture-screening-for-metal-organic-frameworks-with-a-transferable-machine-learning-force-field.pdf
|
64f0492f3fdae147fa2c9b8b
|
10.26434/chemrxiv-2023-rxtk7
|
3,3-Bis[1-(trifluoromethylsulfonyl)-1,4-dihydropyridin-4-yl]benzofuran-2(3H)-one
|
This paper describes the preparation and characterisation of an a,a-bis(N-sulfonyldihydropyrid-4- yl)-substituted lactone, the first reported example containing this functionality and only the second a,a-bis(dihydropyrid-4-yl)-substituted carbonyl compound to be reported.
|
Jeremy Robertson; Linden Schrecker
|
Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0492f3fdae147fa2c9b8b/original/3-3-bis-1-trifluoromethylsulfonyl-1-4-dihydropyridin-4-yl-benzofuran-2-3h-one.pdf
|
60c74eea337d6c0514e2804f
|
10.26434/chemrxiv.12818327.v1
|
A Concise Route to MK-4482 (EIDD-2801)
|
A two-step route to MK-4482 (EIDD-2801, <b>1</b>) was developed consisting of an
esterification and hydroxamination of cytidine.
The reactions can be conducted in either order with overall yields of
67% (first step—esterification) and 37% (first step—hydroxamination). Selective
esterification of the nucleoside’s primary alcohol by enzymatic means
eliminated the need for diol protection/deprotection, and direct transamination
with hydroxylamine precluded the necessity of activating the nucleobase for
amine coupling. This results in a significant
advancement over the reported synthesis which is formed in at best 17%
yield. The step count is reduced from
five transformation to two, and the more expensive uridine is replaced with the
more available cytidine.
|
Natarajan Vasudevan; Grace P. Ahlqvist; Catherine P. McGeough; Dinesh
J. Paymode; Flavio
S. P. Cardoso; Tobias Lucas; Jule-Phillip Dietz; Till Opatz; Timothy F. Jamison; B. Frank Gupton; David Snead
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Process Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eea337d6c0514e2804f/original/a-concise-route-to-mk-4482-eidd-2801.pdf
|
62320b528ab373032066c896
|
10.26434/chemrxiv-2022-1279d
|
Synthesis of 2-BMIDA indoles via heteroannulation: Applications in drug scaffold and natural product synthesis
|
A Pd-catalyzed heteroannulation approach for the synthesis of C2 borylated indoles is reported. The process allows access to highly functionalized 2-borylated indole scaffolds with complete control of regioselectivity. The utility of the process is demonstrated in the synthesis of borylated sulfa drugs and in the concise synthesis of the Aspidosperma alkaloid Goniomi-tine.
|
George Bell; James Fyfe; Eva Israel; Alexandra Slawin; Matthew Campbell; Allan Watson
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62320b528ab373032066c896/original/synthesis-of-2-bmida-indoles-via-heteroannulation-applications-in-drug-scaffold-and-natural-product-synthesis.pdf
|
6411c6f8dab08ad68f27de51
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10.26434/chemrxiv-2023-7bzfq-v2
|
Tailored Lewis Acid Sites for High-Temperature Supported Single-Molecule Magnetism
|
Generating or even retaining slow magnetic relaxation in surface immobilized single-molecule magnets (SMMs) from promising molecular precursors remains a great challenge. Illustrative examples are organolanthanide compounds that show promising SMM properties in molecular systems while surface immobilization generally diminishes their magnetic performance. Here, we show how tailored Lewis acidic Al(III) sites on silica surface enable the synthesis of a material with SMM characteristics via chemisorption of (Cpttt)2DyCl ((Cpttt)= 1,2,4-tri(tert-butyl)- cyclopentadienide). Detailed studies of this system that also include its diamagnetic Y analogue indicate that the interaction of the metal chloride with surface Al sites results in a change of the coordination sphere around the metal center inducing for the dysprosium-containing material slow magnetic relaxation up to 51 K with hysteresis till 8 K and an effective energy barrier (Ueff) of 449 cm-1, the highest reported thus far for a supported SMM.
|
Moritz Bernhardt; Maciej Damian Korzyński; Zachariah James Berkson; Fabrice Pointillart ; Boris Le Guennic ; Olivier Cador ; Christophe Copéret
|
Inorganic Chemistry; Organometallic Chemistry; Lanthanides and Actinides; Magnetism; Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6411c6f8dab08ad68f27de51/original/tailored-lewis-acid-sites-for-high-temperature-supported-single-molecule-magnetism.pdf
|
60c74d4b9abda2f4b7f8d413
|
10.26434/chemrxiv.12611459.v1
|
Divergent Photocatalytic Reactions of α-Ketoesters Under Triplet Sensitization and Photoredox Conditions
|
The long-lived triplet excited states of transition metal photocatalysts can activate organic substrates via either energy- or electron-transfer pathways, and the rates of these processes can be influenced by rational tuning of the reaction conditions. The characteristic reactive intermediates that are generated by each of these activation modalities, however, are distinct and can exhibit very different reactivity patterns. Herein, we show that the photocatalytic reactions of benzoylformate esters with alkenes can be directed towards either Paternò–Büchi cycloadditions under conditions that favor energy transfer or allylic functionalization reactions under superficially similar conditions that favor electron transfer. These studies provide a framework for designing other divergent photocatalytic methods that produce different sets of reaction outcomes under photoredox and triplet sensitization conditions.
|
Jian Zheng; Xiao Dong; Tehshik Yoon
|
Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d4b9abda2f4b7f8d413/original/divergent-photocatalytic-reactions-of-ketoesters-under-triplet-sensitization-and-photoredox-conditions.pdf
|
6655685921291e5d1d703a63
|
10.26434/chemrxiv-2024-n0pd7-v2
|
Photoexcitation and One-Electron Reduction Processes of a CO2 Photoreduction Dyad Catalyst Having a Zinc(II) Porphyrin Photosensitizer
|
We have explored the photophysical properties and one electron reduction process in the dyad photocatalyst for CO2 photoreduction, ZnP-phen=Re, in which the catalyst of fac-[Re(1,10-phenanthoroline)(CO)3Br] (phen=Re) is directly connected with the photosensitizer of zinc (II) porphyrin (ZnP), using time-resolved infrared spectroscopy, transient absorption spectroscopy, and quantum chemical calculations. We revealed the photophysical properties that (1) the intersystem crossing occurs with a time constant of ~20 ps, which is more than 50 times faster than that of zinc (II) porphyrin, and (2) the charge density in the excited singlet and triplet states is mainly localized on ZnP, which means the excited state is assignable to the π -π* transition in ZnP. The one electron reduction using the reductant, 1,3-dimethyl-2-,3-dihydro-1H-benzo[d]imidazole (BIH), occurs via the triplet excited state with time constant of ~170 ns and directly from the ground state by the deprotonated BIH with the time constant of ~3 μs. The charge in the one electron reduction species spans ZnP and the phenanthroline ligand and the dihedral angle between ZnP and the phenanthroline ligand is rotated by ~24° with respect to that in the ground state, which presumably offers an advantage for proceeding to the next CO2 reduction reaction step. These findings on the initial processes of CO2 photoreduction would help us to design novel dyad photocatalysts using porphyrin photosensitizers.
|
Teruyuki Honda; Takumi Ehara; Ren Sato; Tomohiro Ogawa; Yusuke Kuramochi; Akiharu Satake; Kiyoshi Miyata; Ken Onda
|
Inorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6655685921291e5d1d703a63/original/photoexcitation-and-one-electron-reduction-processes-of-a-co2-photoreduction-dyad-catalyst-having-a-zinc-ii-porphyrin-photosensitizer.pdf
|
614011e0abeb6399c2d21773
|
10.26434/chemrxiv-2021-gh6gf
|
Truly Random Degradable Vinyl Copolymers via Photocontrolled Radical Ring-Opening Cascade Copolymerization
|
Degradable vinyl polymers by radical ring-opening polymerization have become a promising solution to the challenges caused by the widespread use of non-degradable vinyl plastics. However, achieving even distribution of labile functional groups in the backbone of degradable vinyl polymers remains challenging. Herein, we report a photocatalytic approach to truly random degradable vinyl copolymers with tunable main-chain composition via radical ring-opening cascade copolymerization (rROCCP). The rROCCP of the macrocyclic allylic sulfone and acrylates or acrylamides mediated by visible light at ambient temperature achieved near-unity reactivity ratios of both comonomers over the entire range of the comonomer compositions and afforded truly random vinyl copolymers with degradable units evenly distributed in the polymer backbone. Experimental and computational evidence revealed an unusual reversible inhibition of chain propagation by in situ generated sulfur dioxide, which was successfully overcome by reducing the solubility of sulfur dioxide in the reaction mixture. This study provided a powerful approach to truly random degradable vinyl copolymers with tunable main-chain labile functionalities and comparable thermal and mechanical properties to traditional non-degradable vinyl polymers.
|
Wenqi Wang; Zefeng Zhou; Xuanting Tang; Stephanie Moran; Jing Jin; Fredrik Haeffner; Jia Niu
|
Organic Chemistry; Polymer Science; Photochemistry (Org.); Organic Polymers; Polymerization (Polymers); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614011e0abeb6399c2d21773/original/truly-random-degradable-vinyl-copolymers-via-photocontrolled-radical-ring-opening-cascade-copolymerization.pdf
|
61273fb565636913ba1a3774
|
10.26434/chemrxiv-2021-36lzf
|
A thermally/chemically robust and easily regenerable anilato-based ultramicroporous 3D MOF for CO2 uptake and separation
|
The combination of the properly designed novel organic linker, 3,6-N-ditriazoyil-2,5-dihydroxy-1,4-benzoquinone (trz2An), with CoII ions results in a 3D ultramicroporous MOF with high CO2 uptake capacity and separation efficiency, with particular attention to CO2/N2 and CO2/CH4 gas mixtures. This material consists of 1D chains of octahedrally coordinated CoII ions linked through the anilato ligands in the equatorial positions and to the triazole substituents from two neighbouring chains in the two axial positions. This leads to a 3D microporous structure with voids with an affinity for CO2 molecules and channels that enable the selective entrance of CO2 but not of molecules with larger kinetic diameter such as N2 or CH4. The adsorption studies revealed that i) the MOF presents a remarkable carbon dioxide uptake, above 20% in weight; ii) CO2 adsorptive separation is successfully performed in CO2:N2 and CO2:CH4 gas mixtures, exhibiting high selectivity in a large operation range; iii) regeneration is easily achieved at mild conditions.
|
Noemi Monni; Eduardo Andrés-García; Katia Caamaño; Víctor García-López; Juan Modesto Clemente-Juan; Mónica Giménez-Marqués; Mariangela Oggianu; Enzo Cadoni; Guillermo Mínguez Espallargas; Miguel Clemente-León; Maria Laura Mercuri; Eugenio Coronado
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61273fb565636913ba1a3774/original/a-thermally-chemically-robust-and-easily-regenerable-anilato-based-ultramicroporous-3d-mof-for-co2-uptake-and-separation.pdf
|
60c749d1ee301c246dc79b35
|
10.26434/chemrxiv.12111138.v1
|
Computational Guided Drug Repurposing for Targeting 2'-O-Ribose Methyltransferase of SARS-CoV-2
|
<p>The
recent outbreak of pandemic severe acute respiratory syndrome
coronavirus-2 (SARS-CoV-2) has led the world towards global health emergency. Currently no proper medicine or effective
treatment strategies are available, therefore repurposing may play an important
role in overcoming the situation. The SARS-CoV-2 genome encodes for 2-O-methyltransferase (2’OMTase) which plays a key
role in methylation of viral RNA for evading host immune system. In the present
study, the protein sequence of 2’OMTase of SARS-CoV-2 was analysed and its structure was modeled
by comparative modeling approach and validated. The modeled structure displayed
the conserved characteristic fold of class I MTase family. The library of 3000
drugs was screened against the active site of 2’OMTase. The docking analysis
displayed that the active site of 2’OMTase accommodates an array of drugs which
includes alkaloids, antivirals, cardiac glycosides, anticancer, steroids and
other drugs. The results suggested that these drugs may be used potential
inhibitors for 2’OMTase for combating the SARS-CoV-2 infection.</p>
|
Kedar Sharma; Sudhir Morla; Arun Goyal; Sachin Kumar
|
Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d1ee301c246dc79b35/original/computational-guided-drug-repurposing-for-targeting-2-o-ribose-methyltransferase-of-sars-co-v-2.pdf
|
65b2c9a666c138172946c4d2
|
10.26434/chemrxiv-2024-pj4h6
|
Digital Light 3D Printing of Double Thermoplastics with Customizable Mechanical Properties and Versatile Reprocessability
|
Digital light processing (DLP) is a 3D printing technology offering high resolution and speed. Printable materials are usually based on multifunctional monomers, resulting in the formation of thermosets that cannot be reprocessed or recycled. Some efforts have been made in DLP 3D printing of thermoplastic materials. However, these materials exhibit limited and poor mechanical properties. Here, we present a new strategy for DLP 3D printing of thermoplastics using two polymers with contrasting mechanical properties, where stiff and flexible linear polymers are sequentially constructed. The inks consist of two vinyl monomers, which lead to the stiff linear polymer, and α-lipoic acid to form the flexible linear polymer via thermal ring-opening polymerization in a second step. By varying the ratio of stiff and flexible polymers, the mechanical properties can be tuned with Young's modulus ranging from 1.1 GPa to 0.7 MPa, while the strain at break increased from 4% to 574%. Furthermore, these 3D-printed thermoplastics allow for a variety of reprocessability pathways including self-healing, solvent casting, reprinting, and closed-loop recycling of the flexible polymer, contributing to the development of a sustainable materials economy. Last, we demonstrate the potential of the new material in applications ranging from soft robotics to electronics.
|
Guangda Zhu; Nadine von Coelln; Yi Hou; Clara Vazquez-Martel; Christoph A. Spiegel; Petra Tegeder; Eva Blasco
|
Materials Science; Polymer Science; Polymer blends
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b2c9a666c138172946c4d2/original/digital-light-3d-printing-of-double-thermoplastics-with-customizable-mechanical-properties-and-versatile-reprocessability.pdf
|
65b7053a9138d23161f08010
|
10.26434/chemrxiv-2024-sc3fd
|
Selectively dissolving CO2 in highly fluorinated non-porous crystalline materials
|
Separation of CO2 from gas mixtures is important is specific applications such as purification of CH4 gas and blue hy-drogen production and more generally in the separation and processing of greenhouse effect gases to mitigate the hazardous effects of global warming. Herein, we report the selective CO2 sorption by a family of isoreticular, flexible silver coordination polymers (AgCPs) that are ostensibly non-porous but exhibit latent porosity to CO2 above a gate pressure, through a mechanism akin to dissolution in fluoroalkanes. The CO2 sorption properties are rationally modified by changing the length of the perfluorocarboxylate ligands. The AgCPs show an absence of CH4 adsorption due to the lack of pores and channels in their structure and the failure of the dissolution mechanism due to alkane-perfluoroalkane immiscibility. In situ single-crystal and powder X-ray diffraction enable the direct visualization of the binding domains of adsorbed CO2 molecules as well as the associated structural changes of the AgCPs and confirming the gating of CO2 uptake. The deployment of perfluoroalkylcarboxylate ligands combined with the flexibility of the silver(I) coordination sphere to generate highly fluorinated but mobile regions of the crystals plays an integral role in the selective sorption of CO2 over CH4.
|
Iñigo Vitórica-Yrezábal; Craig McAnally; Ashleigh Fletcher; Mark Warren; Adrian Hill; Stephen Thompson; Martin Quinn; Sam Mottley; Stephen Mottley; Lee Brammer
|
Inorganic Chemistry; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b7053a9138d23161f08010/original/selectively-dissolving-co2-in-highly-fluorinated-non-porous-crystalline-materials.pdf
|
656a0aec5bc9fcb5c9d62cfc
|
10.26434/chemrxiv-2023-9mxxc
|
Unexpected Photo-driven Linker-to-Node Hole Transfer in a Zirconium-Based Metal–Organic Framework
|
Zr6(µ3-O)4(µ3-OH)4 node cores are indispensable building blocks for almost all zirconium-based metal–organic frameworks. Consistent with the insulating nature of zirconia, they are generally considered electronically inert. Contrasting this viewpoint, we present spectral measurements and calculations indicating that emission from photoexcited NU-601, a six-connected Zr-based MOF, comes from both linker-centric locally-excited and linker-to-node charge-transfer (CT) states. The CT state originates from a hole transfer process enabled by favorable energy alignment of the HOMOs of the node and linker. This alignment can be manipulated by changing the pH of the medium, which alters the protonation state of multiple oxy groups on the Zr-node. Thus, the acid-base chemistry of the node has a direct effect on the photophysics of the MOF following linker-localized electronic excitation. These new findings open opportunities to understand and exploit, for energy conversion, unconventional mechanisms of exciton formation and transport in MOFs.
|
Boris Kramar; Anna Bondarenko; Benjamin Diroll; Xiaodan Wang; Kirk Schanze; Lin Chen; Roel Tempelaar; Joseph Hupp
|
Physical Chemistry; Inorganic Chemistry; Inorganic Acid/Base Chemistry; Photochemistry (Physical Chem.); Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-12-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656a0aec5bc9fcb5c9d62cfc/original/unexpected-photo-driven-linker-to-node-hole-transfer-in-a-zirconium-based-metal-organic-framework.pdf
|
60c752ed702a9bb99f18c276
|
10.26434/chemrxiv.13366316.v1
|
Exploring the Utility of Compound-Specific Isotope Analysis for Assessing Ferrous Iron-Mediated Reduction of RDX in the Subsurface
|
This work determines isotope enrichment factors for RDX during reduction by iron minerals. The values determined are used to assess the transformation of RDX at a site with groundwater contamination and in laboratory column reactors simulating in situ chemical reduction treatment.
|
Yiran Tong; Matthew J. Berens; Bridget A. Ulrich; Jakov Bolotin; Jennifer
H. Strehlau; Thomas Hofstetter; William Arnold
|
Environmental Science; Geochemistry; Hydrology and Water Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752ed702a9bb99f18c276/original/exploring-the-utility-of-compound-specific-isotope-analysis-for-assessing-ferrous-iron-mediated-reduction-of-rdx-in-the-subsurface.pdf
|
6756f02a7be152b1d06a8ca8
|
10.26434/chemrxiv-2024-jjns1-v2
|
Tensor Train Optimization for Conformational Sampling of Organic Molecules
|
Exploring the conformational space of molecules remains a challenge of fundamental importance to quantum chemistry: identification of relevant conformers at ambient conditions enables predictive simulations of almost arbitrary properties. Here, we propose a novel approach to enable conformational sampling of large organic molecules where the combinatorial explosion of possible conformers prevents the use of a brute-force systematic conformer search. We employ tensor trains as a highly efficient dimensionality reduction algorithm, effectively reducing the scaling from exponential to polynomial. In our approach, the conformational search is expressed as global energy minimization task in a high-dimensional grid of dihedral angles. Dimensionality reduction is achieved through a tensor train representation of the high-dimensional torsion space. The performance of the approach is assessed on a variety of drug-like molecules in direct comparison to the state-of-the-art metadynamics based conformer rotamer ensemble sampling tool (CREST). The comparison shows significant acceleration of up to an order of magnitude, while maintaining comparable accuracy. More importantly, the presented approach allows treatment of larger molecules than typically accessible with metadynamics.
|
Christopher Zurek; Ruslan A. Mallaev; Alexander Paul; Nils van Staalduinen; Philipp Pracht; Roman Ellerbrock; Christoph Bannwarth
|
Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756f02a7be152b1d06a8ca8/original/tensor-train-optimization-for-conformational-sampling-of-organic-molecules.pdf
|
64ca649d69bfb8925a3cd875
|
10.26434/chemrxiv-2023-fq4hv
|
A First-in-Class β-Glucuronidase Responsive Conjugate for Selective Dual Targeted and Photodynamic Therapy of Bladder Cancer
|
In this report, we present a novel prodrug strategy that can significantly improve the efficiency and selectivity of combined therapy for bladder cancer. Our approach involved the synthesis of a conjugate based on a chlorin-e6 photosensitizer and a derivative of the tyrosine kinase inhibitor cabozantinib, linked by a β-glucuronidase-responsive linker. Upon activation by β-glucuronidase, which is overproduced in various tumors and localized in lysosomes, this conjugate released both therapeutic modules within targeted cells. This activation was accompanied by the recovery of its fluorescence and the generation of reactive oxygen species. Investigation of photodynamic and dark toxicity in vitro revealed that the novel conjugate had an excellent safety profile and was able to inhibit tumor cells proliferation at submicromolar concentrations. Additionally, combined therapy effects were also observed in 3D models of tumor growth, demonstrating synergistic suppression through the activation of both photodynamic and targeted therapy.
|
Vasilii F. Otvagin; Lubov V. Krylova; Nina N. Peskova; Natalia S. Kuzmina; Ekaterina A. Fedotova; Alexander V. Nyuchev; Yuliya V. Romanenko; Oscar I. Koifman; Sergey Z. Vatsadze; Hans-Günther Schmalz; Irina V. Balalaeva; Alexey Yu. Fedorov
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca649d69bfb8925a3cd875/original/a-first-in-class-glucuronidase-responsive-conjugate-for-selective-dual-targeted-and-photodynamic-therapy-of-bladder-cancer.pdf
|
60c758849abda23993f8e90f
|
10.26434/chemrxiv.14191862.v1
|
Benzothiazole Carboxylate Diester Bifunctional Chelators for 64Cu PET Imaging in Alzheimer’s Disease
|
Herein we report a new series of bifunctional chelators (BFCs) with high
affinity for amyloid β aggregates, strong binding affinity towards Cu(II), and
favorable lipophilicity for potential blood-brain barrier (BBB) penetration.
The alkyl carboxylate ester pendant arms enable high binding affinity towards
Cu(II). The BFCs form stable <sup>64</sup>Cu-radiolabeled complexes and exhibit
favorable partition coefficient (log D) values of 0.75-0.95. Among the five
compounds tested, the <b><sup>64</sup>Cu-YW-1</b> and <b><sup>64</sup>Cu-YW-13</b>
complexes exhibit significant staining of amyloid plaques in <i>ex vivo</i>
autoradiography studies.
|
Yujue Wang; Truc T. Huynh; Nilantha Bandara; Hong-Jun Cho; Buck E. Rogers; Liviu M. Mirica
|
Bioinorganic Chemistry; Nuclear Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758849abda23993f8e90f/original/benzothiazole-carboxylate-diester-bifunctional-chelators-for-64cu-pet-imaging-in-alzheimer-s-disease.pdf
|
60c74d3abdbb89575aa39946
|
10.26434/chemrxiv.12278237.v2
|
Exploring the Influence of Substitution on the Structure and Transport Properties in the Sodium Superionic Conductor Na11+xSn2+x(Sb1−yPy)1−xS12
|
<p>Sulfidic sodium ion conductors are currently investigated for the possible use in all-solid-state sodium ion batteries. The design of high performing electrolytes in terms of temperature-dependent ionic transport is based upon the fundamental understanding of structure – transport relationships within the given structural phase boundaries inherent to the investigated materials class. In this work, the Na<sup>+</sup> superionic structural family of Na<sub>11</sub>Sn<sub>2</sub>PS<sub>12</sub> is explored by using the systematic antimony substitution with phosphorous in Na<sub>11+<i>x</i></sub>Sn<sub>2+<i>x</i></sub>(Sb<sub>1-<i>y</i></sub>P<i><sub>y</sub></i>)<sub>1-<i>x</i></sub>S<sub>12</sub>. A combination of Rietveld refinements against X-ray synchrotron diffraction data with electrochemical impedance spectroscopy is used to monitor the changes in the anionic framework, the Na<sup>+</sup> substructure and the ionic transport. A new simplified descriptor for the average Na<sup>+</sup> diffusion pathways, the average Na<sup>+</sup> polyhedral volume is introduced, which is used to correlate the contraction of the overall lattice and the found activation barriers in the system. This study exemplifies how substitution affects diffusion pathways in ionic conductors and widens the knowledge about the related structural motifs and their influence on the ionic transport in this novel class of ionic conductors.</p>
|
Marvin Kraft; Lara Gronych; Theodosios Famprikis; Saneyuki Ohno; Wolfgang Zeier
|
Solid State Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d3abdbb89575aa39946/original/exploring-the-influence-of-substitution-on-the-structure-and-transport-properties-in-the-sodium-superionic-conductor-na11-x-sn2-x-sb1-y-py-1-x-s12.pdf
|
60c74035469df4480ff42bf3
|
10.26434/chemrxiv.7667495.v1
|
Controlling Quantum Interference by Regulating Charge on the Bridging N Atom of Pyrrolodipyridine Molecular Junctions
|
<b>Control of quantum interference features</b>: molecular junctions incorporating pyrrolodipyridine-based molecular wires were fabricated by scanning probe methods. Quantum interference effects were introduced by employing <i>meta</i>-connected molecules, and modulated in magnitude by changing the substituent on the pyrrolic N. Dramatic changes in molecular conductance and DFT transport calculations demonstrate the storng effect that small changes in electronic density can have on the overall conductance of a molecular wire.
|
Saman Naghibi; Ali K. Ismael; Andrea Vezzoli; Mohsin K. Al-Khaykanee; Xijia Zheng; Iain Grace; Donald Bethell; Simon Higgins; Colin Lambert; Richard Nichols
|
Organic Synthesis and Reactions; Physical Organic Chemistry; Nanodevices; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74035469df4480ff42bf3/original/controlling-quantum-interference-by-regulating-charge-on-the-bridging-n-atom-of-pyrrolodipyridine-molecular-junctions.pdf
|
6425e104647e3dca99c4319b
|
10.26434/chemrxiv-2023-3949g-v2
|
Studies About A biocompatible Maleimide-modified Dextran And Hyaluronic Acid Hydrogel System
|
This article discussed a novel hydrogel, which was created through Michael addition. Two precursors dextran functionalized maleimide groups and hyaluronic acid functionalized thiol groups were designed, prepared, and characterized by NMR. The formed hydrogels were investigated by gelation time, swelling studies, viscoelastic properties, degradation rate. Based on gelation time observation, we detected that the hydrogel gelation time could be varied with diffident weight percentage of precursors. Based on previous research, we measured that 2% dextran with maleimide groups and 2% hydronic acid with thiol groups is the optimal formular for the biomedical application and this formular was also investigated by other studies. The swelling study indicated hydrogel has good flexibility and the degradation test indicated hydrogel is biodegradable. The viscoelastic test indicated hydrogel is elastic solid. From these studies, this a novel hydrogel could be potential for biomedical applications.
|
Song Jiang; Tianjin Zhang
|
Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6425e104647e3dca99c4319b/original/studies-about-a-biocompatible-maleimide-modified-dextran-and-hyaluronic-acid-hydrogel-system.pdf
|
67d7e5126dde43c908181f5f
|
10.26434/chemrxiv-2025-0tw95
|
Evolutionary Machine Learning of Physics-Based Force Fields in High-Dimensional Parameter-Space
|
This work presents the Alexandria Chemistry Toolkit (ACT), an open-source software for machine learning of physics-based force fields (FFs) from scratch, based on user-specified potential functions. In this approach, a set of FF parameters for molecular simulation is described as a chromosome consisting of atom and bond genes. The accuracy of a FF, that is how well quantum chemical train- ing data are reproduced, determines the fitness of the chromosome. The ACT implements a hierarchical parallel scheme that iterates between a genetic algorithm and Monte-Carlo steps for global and local search, to find “genomes” with high fitness. As a sample appli- cation, genome evolution is performed to create physical models that allow the prediction of properties of organic molecules in the gas and liquid phases. Evaluation of the prediction accuracy of different models showcases how Force Field Science can contribute to system- atically improve prediction accuracy of physicochemical observables.
|
David van der Spoel; Julian Marrades; Kristian Kriz; A. Najla Hosseini; Alfred Nordman; Joao Paulo Ateide Martins; Marie-Madeleine Walz; Paul J. van Maaren; Mohammad Mehdi Ghahremanpour
|
Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Statistical Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d7e5126dde43c908181f5f/original/evolutionary-machine-learning-of-physics-based-force-fields-in-high-dimensional-parameter-space.pdf
|
62b396b658b3d64e4e5afd68
|
10.26434/chemrxiv-2022-rph65
|
Passive Permeate-Side-Heated Solar Thermal Membrane Distillation: Single-Stage Tubular and Multistage Planar Systems
|
Scarcity of drinking water is a global problem and especially serious in rural areas of developing countries. Passive permeate-side-heated interfacial-heating solar membrane distillation has been shown recently as a promising system for off-grid distributed water and wastewater treatment. In this study, single-stage tubular systems were developed by giving the poly(vinylidene fluoride) (PVDF) membrane (pore size: 0.45 µm) a tubular structure with the outer surface (i.e., the permeate side) coated with carbon black NPs which absorbed solar thermal energy and evaporated the feedwater inside the membrane tube. Under natural sunlight, the vertical tubular system had a production rate of distilled water per footprint as 0.67‒2.06 kg/(m2·day) throughout the year, 71% higher than the single-stage planar system on average. The three-stage planar systems were developed by overlapping three single-stage modules. Two adjacent modules shared a common copper sheet that serves as both the top of condensation chamber of the preceding stage and the bottom of the feedwater chamber of the following stage. The copper sheet can partially transfer the condensation heat of the preceding stage to the feedwater of the following stage, thus enhancing the system energy efficiency (ƞsys) in producing distilled water. The ƞsys and distillate flux of the three-stage systems were 62% and 5.01 kg/(m2·day) at the average daytime irradiance of 422 W/m2, 34% higher than the single-stage systems.
|
Shahin Ahmed Sujon; Peng Yi
|
Earth, Space, and Environmental Chemistry; Environmental Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b396b658b3d64e4e5afd68/original/passive-permeate-side-heated-solar-thermal-membrane-distillation-single-stage-tubular-and-multistage-planar-systems.pdf
|
60c73f9d842e65c978db1b16
|
10.26434/chemrxiv.7427345.v1
|
Dienamine-Induced Divinylcyclopropane-Cycloheptadiene Rearrangements
|
Sigmatropic rearrangements constitute an important group
of pericyclic reactions. In contrast to cycloaddition reactions,
examples of catalytic variants of electrocyclic reactions and sigmatropic
rearrangements are still scarce in the chemical literature. Herein,
we report the first organocatalytic Cope rearrangement of in situgenerated
divinylcyclopropanes. The reactive motif is generated by
condensation of 4-(2-vinylcyclopropyl)but-2-enal derivatives and a
secondary amine catalyst to form a transient dienamine. The
cycloheptadiene products can be obtained in high yield and excellent
diastereoselectivity. Importantly, the reaction was demonstrated to be
stereospecific, proceeds under mild conditions, and shows broad
functional group tolerance. <br />
|
Caroline Apel; Sven Sören Hartmann; Dieter Lentz; Mathias Christmann
|
Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-12-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9d842e65c978db1b16/original/dienamine-induced-divinylcyclopropane-cycloheptadiene-rearrangements.pdf
|
67afa4e26dde43c908e28784
|
10.26434/chemrxiv-2025-tm4ff
|
An Efficient Workflow for Generation of Conformational Ensembles of Density Functional Theory Quality: Dimers of Polycyclic (Hetero-)Aromatics
|
Several composite density functional theory (DFT) methods, namely HF-3c, B97- 3c, PBEh-3c, r2SCAN-3c, and ωB97X-3c, were tested for accuracy and efficiency in computing binding energies of seven low-lying conformers of the pyrene homodimer, both in the gas phase and in toluene solution. The most promising method was B97-3c, with a Mean Absolute Deviation (MAD) for binding energies of 0.5 kJ/mol, relative to ωB97X-V/def2-TZVP results. Thus, B97-3c was used in a multi-tiered approach for generating conformational ensembles for a series of homodimers. The workflow involves six steps: (i) generate an initial ensemble, using the conformer-rotamer ensemble sam- pling tool (CREST), and its underlying GFN2-xTB method; (ii) reoptimize each mem- ber of the ensemble using B97-3c; (iii) discard duplicates and high-energy conformers; (iv) reoptimize the remaining conformers using ωB97X-D4/def2-SVP; (v) if needed, discard any high energy or duplicate conformers; (vi) compute vibrational frequencies using ωB97X-D4/def2-SVP and final single point energies using ωB97X-V/def2- QZVPP. The six-step workflow allows the generation of large DFT-quality ensembles efficiently, as demonstrated on the known pyrene dimer ensemble, and then applied to the homodimers of eight small polycyclic (hetero-)aromatic molecules related to asphaltenes: anthracene, phenanthrene, fluorenone, dibenzofuran, dibenzothiophene, dibenzothiophene oxide, N -methylcarbazole, and benzo[h]quinoline. The refined ensembles enabled an analysis of trends in dimerization structures and energies for these monomers, revealing a strong dependence for binding energy upon the magnitude of dipole cancellation.
|
Jessica J Ortlieb; Nathanael J King; Alex Brown
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67afa4e26dde43c908e28784/original/an-efficient-workflow-for-generation-of-conformational-ensembles-of-density-functional-theory-quality-dimers-of-polycyclic-hetero-aromatics.pdf
|
66f4108b51558a15ef12b939
|
10.26434/chemrxiv-2024-sk258
|
Controlled Synthesis of Cluster Mimics of Nitrogenase FeMo-cofactor
|
Catalytic conversion of atmosphere dinitrogen into ammonia by nitrogenase is one of the most important chemical processes in nature. FeMo-cofactor (FeMoco), the key active site of this conversion in the Mo-based nitrogenase, is one of the most complicated metalloenzyme molecules. The synthesis of FeMoco cluster holds the key to elucidating the mechanism of nitrogen fixation, but the complex framework with a unique sextuply-bridged carbide in FeMoco cluster dictates its synthesis to be an extreme challenge that remains unsolved for several decades. In this work, two cluster models have been synthesized as the first highly analogous mimics of FeMoco using a precisely-designed cluster-coupling strategy. A carbide ligand has been introduced into M-Fe-S (M = Mo or W) clusters and the characteristic triangular prismatic [Fe6(µ6-C)] moiety of FeMoco has been synthesized for the first time. The structural parameters of the two mimics match well with those of FeMoco identified in natural nitrogenase. Quantum chemical studies reveal that the electronic ground states of the mimics resemble those observed for FeMoco, with maximized antiferromagnetic coupling among the iron centers. The clusters synthesized in this work represent the only highly analogous synthetic mimics of FeMoco. The cluster-coupling reaction is a versatile strategy that allows the synthesis of more analogous mimics of FeMoco. These mimics and the cluster-coupling strategy provide an excellent platform for studying the function and behavior of FeMoco, and also pave the way for elucidating the mechanism of nitrogen fixation by nitrogenase.
|
Yun-Yu Xu; Xue-Lian Jiang; Jia-Lu Chai; Shu-Juan Qiu; Juan He; Gan Xu; Jia Wei; Qiu-Xiang Yu; Hong-Ying Zhang; Yue Li; Xiao-Wen Zhang; Guo-Liang Cao; Yong Li; Yun-Shu Cui; Cong-Qiao Xu; Jun Li; Xu-Dong Chen
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Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bioinorganic Chemistry; Bioorganometallic Chemistry; Coordination Chemistry (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
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2024-09-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f4108b51558a15ef12b939/original/controlled-synthesis-of-cluster-mimics-of-nitrogenase-fe-mo-cofactor.pdf
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650bf0df60c37f4f762e5917
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10.26434/chemrxiv-2023-ts9qr
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Using the phospha-Michael reaction for making phosphonium phenolate zwitterions
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The reactions of 2,4-di-tert-butyl-6-(diphenylphosphino)phenol and various Michael acceptors (acrylonitrile, acrylamide, methyl vinyl ketone, several acrylates, methyl vinyl sulfone) yield the respective phosphonium phenolate zwitterions at room temperature. Nine different zwitterions were synthesized and fully characterized. Zwitterions with the poor Michael acceptors methyl methacrylate and methyl crotonate formed, but could not be isolated in pure form. The solid-state structures of two phosphonium phenolate molecules were determined by single-crystal X-ray crystallography. The bonding situation in the solid state together with NMR data suggests an important contribution of an ylidic resonance structure in these molecules. The phosphonium phenolates are characterized by UV-Vis absorptions peaking around 360 nm and exhibit a negative solvatochromism. An analysis of the kinetics of the zwitterion formation was performed for three Michael acceptors (acrylonitrile, methyl acrylate and acrylamide) in two different solvents (chloroform and methanol). Results revealed the proton transfer step necessary to stabilize the initially formed carbanion as the rate determining step. A preorganization of the carbonyl bearing Michael acceptors allowed for reasonable fast direct proton transfer from the phenol in aprotic solvents. In contrast, acrylonitrile not capable of forming a similar preorganization, is hardly reactive in chloroform solution, while in methanol the corresponding phosphonium phenolate is formed.
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Matthias Steiner; Max Schmallegger; Larissa Donner; Johann A. Hlina; Christoph Marschner; Judith Baumgartner; Christian Slugovc
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Organic Chemistry
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CC BY NC 4.0
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CHEMRXIV
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2023-09-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650bf0df60c37f4f762e5917/original/using-the-phospha-michael-reaction-for-making-phosphonium-phenolate-zwitterions.pdf
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670fe96351558a15ef458cf8
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10.26434/chemrxiv-2024-gh05j-v2
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From Reverse Phase Chromatography to HILIC: Graph Transformers Power Method-Independent Machine Learning of Retention Times
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Liquid chromatography (LC) is a cornerstone of analytical separations, but comparing the retention times (RTs) for different LC methods is difficult because of variations in experimental parameters such as column type and solvent gradient. Nevertheless, RTs are powerful metrics in tandem mass spectrometry (MS2) that can reduce false positive rates for metabolite annotation, differentiate isobaric species, and improve peptide identification. Here, we present Graphormer-RT, a novel graph transformer that performs the first “method-independent” prediction of RTs. We use the RepoRT dataset, containing 142,688 reverse phase (RP) RTs (191 methods) and 4,373 HILIC RTs (49 methods). Our best RP model achieved a test set mean average error (MAE) of 29.3±0.6 s, a significant improvement over the previous record (1 method). Our best performing HILIC model achieved a test MAE=42.4±2.9 s. Extending this proof-of-concept work could enable machine-optimization of automated LC workflows and in silico annotation of unknown analytes in LC-MS2 measurements.
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Cailum Stienstra; Emir Nazdrajić; W. Scott Hopkins
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Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Chemoinformatics; Machine Learning
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CC BY 4.0
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CHEMRXIV
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2024-10-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670fe96351558a15ef458cf8/original/from-reverse-phase-chromatography-to-hilic-graph-transformers-power-method-independent-machine-learning-of-retention-times.pdf
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678eb989fa469535b9dd69c3
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10.26434/chemrxiv-2025-blb4g
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One-Pot Synthesis of Alpha-Diimines from Alkylammonium Salts
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A one-pot synthesis of alkyl-containing diazabutadienes from primary alkylamine-HCl salts is presented. This synthesis avoids halogenated solvents, and the need for a separate free-basing step for commercially available or synthesized amine-HCl salts. Since amine HCl salts are conveniently handled, and diazabutadienes are commonly used as either ligands, or precursors for heterocycles including N-heterocyclic carbenes and diazaphospholenes, this route will be of convenience to many researchers in multiple areas of catalysis.
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Emily Burke; Shay Heans Moreyra; Erin Welsh; Izabella Krug; Katherine Robertson; Alex Speed
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Organic Chemistry; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
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2025-01-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678eb989fa469535b9dd69c3/original/one-pot-synthesis-of-alpha-diimines-from-alkylammonium-salts.pdf
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6228bd28daa4fb1d6c85aee5
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10.26434/chemrxiv-2022-v492x
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Intra-Lattice Inverse Charge Transfer in Bimetallic Electrocatalysts
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The prevalence of intermetallic charge transfer is a marvel for fine-tuning the electronic structure of the active centers in the electrocatalysts. Although, Pauling electronegativity is the primary deciding factor for the direction of charge transfer, we report an unorthodox intra-lattice ‘inverse’ charge transfer from Mo to Ni in two systems, Ni73Mo alloy electrodeposited on Cu nanowires and NiMo-hydroxide (Ni:Mo = 5:1) on Ni foam. The inverse charge transfer deciphered by X-ray absorption fine structure studies and X-ray photoelectron spectroscopy has been understood by the Bader charge and projected density of state analyses. The undercoordinated Mo-center pushes the Mo 4d-orbitals close to the Fermi energy in the valence band region while Ni 3d-orbitals lie in the conduction band. Since, electrons are donated from the electron-rich Mo-center to the electron-poor Ni-center, the inverse charge transfer effect navigates the Mo-center to become positively charged and vice versa. The reverse charge distribution in Ni73Mo accelerates the electrochemical hydrogen evolution reaction in alkaline and acidic media with 0.35 and 0.07 s-1 turnover frequency at -33 and -54 mV versus reversible hydrogen electrode, respectively. The mass activities are 12.5 and 67 A g-1 at 100 mV overpotential, respectively. Anodic potential oxidizes the Ni-center of NiMo-hydroxide for alkaline water oxidation with 0.43 O2 s-1 turnover frequency at 290 mV overpotential. This extremely durable homologous couple achieves water and urea splitting with cell voltages of 1.48 and 1.32 V, respectively at 10 mA cm-2.
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Sahanaz Parvin; Neha Bothra; Ashwani Kumar; Maglu Mura; Dhirendra K. Chaudhary; Parasmani Rajput; Manvendra Kumar; Swapan K. Pati; Sayan Bhattacharyya
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Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-03-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6228bd28daa4fb1d6c85aee5/original/intra-lattice-inverse-charge-transfer-in-bimetallic-electrocatalysts.pdf
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6354c904ee31861d716e7392
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10.26434/chemrxiv-2022-b4t49
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Ni/Co@NDC Modulates the Highly Selective Conversion of Vanillin in Flow Reactor under Mild Conditions
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Vanillin is currently the most abundant aromatic molecule produced from lignin on an industrial scale and one of the few renewable resources that can be readily catalyzed to obtain alkanes. The hydrogenation of vanillin as a lignin model has been a hot research topic in the catalytic community. Vanillin has the potential to be upgraded to value-added compounds by catalytic hydrogenation, and its valuable hydrogenation products are usually vanillinol (VA) and 4-methylguaiacol (MMP). The difficulty of this reaction lies in the selectivity control of the hydrogenation products. Complete conversion of both products cannot be achieved with either noble or non-precious metal catalysts in the same catalytic system. For the hydrogenation of vanillin, the usual catalysts can achieve complete conversion of one product or partial conversion of both products. In our work, we developed a novel bimetallic catalyst encapsulated in nitrogen-rich carbon to achieve, for the first time, the selective and regulated conversion of two products, i.e., 96.06% vanillin and 99.99% MMP, in the same system. The use of nitrogen-doped carbon (NDC) as a carrier for Ni nanoparticles allows the charge transfer from Ni to the carrier, i.e., NDC, resulting in the oxidation potential is corrected. Combined with the more favorable deoxidation activity of Co, our catalysts are inexpensive, simple to prepare, stable in performance, easy to separate, high in activity, and have the advantage of being tunable to the target product. Due to the synergistic effect of Ni and Co bimetals, the vanillin hydrogenation reaction can be almost completely stopped at the step of VA generation and the catalytic activity of the active center can be adjusted by controlling the temperature in a continuous flow to achieve the conversion of the other product MMP at 99.99%, which has never been reported before.
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Jianguo liu; Shanshan Lin; Lungang Chen; Xinghua Zhang; Qi Zhang; Longlong Ma
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Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis
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CC BY 4.0
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CHEMRXIV
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2022-10-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6354c904ee31861d716e7392/original/ni-co-ndc-modulates-the-highly-selective-conversion-of-vanillin-in-flow-reactor-under-mild-conditions.pdf
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635b86322e0c6312263fbda6
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10.26434/chemrxiv-2022-n4fbb
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Structure and Bonding Patterns in Heterometallic Organometallics with Short and Rare Ln-Pd Distances
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Complexes with short intermetallic distances between transition metal fragments and lanthanide (Ln) fragments are fascinating objects of study, owing to the ambiguity of the nature of the interaction. The addition of the divalent lanthanide fragments Cp*2Ln(OEt2) (Ln = Sm or Yb) to a redox-active, non-symmetrical ligand, 2-pyrimidin-2-yl-1H-benzimidazole (Hbimpm), leads to two isostructural complexes, of the general formula (Cp*2Ln)2[μ-Pd(pyridyl)2] (Ln = Sm (4) and Yb (5)). These adducts have interesting features, such as unique linear Ln-Pd-Ln arrangements and short Ln-Pd distances, which deviate from the expected lanthanide contraction. A mixed computational and spectroscopic study into the formation of these adducts gathers important clues as to their formation. At the same time, a thorough characterization of these complexes establishes the +3 oxidation state of all the involved Ln centers. Detailed theoretical computations demonstrate that the apparent deviation from the lanthanide contraction is not due to any difference in the intermetallic interaction between the Pd and the Ln, but that the fragments are joined together by electrostatic interactions and dispersive forces. This conclusion is in contrast with the findings about a third complex, Cp*2Yb(μ-Me)2PdCp* (6), formed during the reaction, which also possesses a short Yb-Pd distance. Studies at the CASSCF level of theory on this complex show several orbitals containing significant interactions between the 4f and 4d manifolds of the metals. This demonstrates the need for methodical and careful analyses in gauging the intermetallic interaction and the inadequacy of empirical metrics in describing such phenomena.
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Valeriu Cemortan; Thomas Simler; Jules Moutet; Arnaud Jaoul; Carine Clavaguera; Gregory Nocton
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Organometallic Chemistry; Bond Activation; Coordination Chemistry (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
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2022-10-31
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b86322e0c6312263fbda6/original/structure-and-bonding-patterns-in-heterometallic-organometallics-with-short-and-rare-ln-pd-distances.pdf
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61213c69fa49ac5c3357b4a0
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10.26434/chemrxiv-2021-r2nd2
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Donor-Acceptor Pyridinium Salts for Photo-Induced Electron Transfer Driven Modification of Tryptophan in Peptides, Proteins, and Proteomes using Visible Light
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Tryptophan (Trp) plays a variety of critical functional roles in protein biochemistry however, owing to its low natural frequency and poor nucleophilicity, the design of effective methods for both single protein bioconjugation at Trp as well as for in situ chemoproteomic profiling re-mains a challenge. Here, we report a method for covalent Trp modification that is suitable for both scenarios by invoking photo-induced electron transfer (PET) as a means of driving efficient reactivity. We have engineered biaryl N-carbamoyl pyridinium salts that possess a donor-acceptor relationship enabling optical triggering with visible light whilst simultaneously attenuating the probe’s photo-oxidation potential in order to prevent photodegradation. This probe was assayed against a small bank of eight peptides and proteins, where it was found that micromolar concentrations of probe and short irradiation times (10-60 min) with violet light enabled efficient reactivity towards surface exposed Trp residues. The carbamate transferring group can be used to transfer useful functional groups to proteins including affinity tags and click handles. DFT calculations and other mechanistic analyses reveal correlations between excited state lifetimes, relative fluorescent quantum yields, and chemical reactivity. Biotinylated and azide-functionalized pyridinium salts were used for Trp profiling in HEK293T lysates and in situ in HEK293T cells using 450 nm LED irradiation. Peptide level enrichment from live cell labelling experiments identified 290 Trp modifications, with an 82% selectivity for Trp modification over other π-amino acids; demonstrating the ability of this method to identify and quantify reactive Trp residues from live cells.
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Caleb Hoopes; Francisco Garcia; Akash Sarkar; Nicholas Kuehl; David Barkan; Nicole Collins; Chien-Hsang Hsu; Michael Jones; Markus Schirle; Michael Taylor
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Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Chemical Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-10-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61213c69fa49ac5c3357b4a0/original/donor-acceptor-pyridinium-salts-for-photo-induced-electron-transfer-driven-modification-of-tryptophan-in-peptides-proteins-and-proteomes-using-visible-light.pdf
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637cb1fee474bf16f74c5bf3
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10.26434/chemrxiv-2022-vqd9b
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Reformulation of the neutron Dirac equation & neutron proton fusion
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In this paper the topic will be how mathematical Dirac equation representations can work out in fusion physics. The Dirac equation under study represents a neutron outside the nucleus but in an external magnetic field. We claim such a description is refering to a real neutron, i.e. we are allowed to employ such a representation here. With a new approach to the computation of the vector wave function solution, it is possible to obtain a sinusoidal time f luctuation in the neutron probability density. This sinusoidal form is applied in neutron- proton fusion.
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Han Geurdes
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Energy; Power
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CC BY 4.0
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CHEMRXIV
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2022-11-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637cb1fee474bf16f74c5bf3/original/reformulation-of-the-neutron-dirac-equation-neutron-proton-fusion.pdf
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60d0750db912f882fd5acad5
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10.26434/chemrxiv-2021-3g3d1
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Tailoring the Reactivity of the Langlois Reagent and Styrenes with Cyanoarenes Organophotocatalysts under Visible-Light.
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The unprecedented selective and straightforward one-step access to fluoroalkylated hexestrol derivatives, nonsteroidal estrogens, is achieved in good to excellent isolated yields under organophotoredox conditions by using the stable and easy to handle Langlois reagent. Furthermore, the challenging selective hydrotrifluoromethylation of styrenes proceeds under mild reaction conditions without the requirement of any additive. We assume that the solvent drives the reaction pathway towards either the reduction or the dimerization of the radical intermediate generated after initial addition of the fluoroalkyl radical to the styrene. The versatility of the developed system is also extended to encompass radical-radical cross-coupling as exemplified here using cyanopyridine. Mechanistic investigations including luminescence and EPR spectroscopy allow to shed the light on the different mechanisms.
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Dan Louvel; Amel Souibgui; ALEXIS TAPONARD; Jean Rouillon; Mongi ben mosbah ; younes moussaoui; GUILLAUME PILET ; Lhoussain Khrouz ; Cyrille MONNEREAU; Anis Tlili
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Organic Chemistry; Photochemistry (Org.)
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CC BY 4.0
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CHEMRXIV
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2021-06-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d0750db912f882fd5acad5/original/tailoring-the-reactivity-of-the-langlois-reagent-and-styrenes-with-cyanoarenes-organophotocatalysts-under-visible-light.pdf
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636d4595afea7fcd1c9f5f67
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10.26434/chemrxiv-2022-f7dfv
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Tiered Leak Detection and Repair Programs at Oil and Gas Production Facilities
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Methane emission rates originating from oil and gas production facilities are highly skewed and span 6-8 orders of magnitude. Traditional leak detection and repair programs have relied on surveys with handheld detectors at intervals of 2 to 4 times a year to find and fix emissions, however this approach leads to leaks being active for the same interval independently of their magnitude. In addition, manual surveys are labor intensive. Novel methane detection technologies offer opportunities to further reduce emissions by quickly detecting the high-emitters, which account for a disproportionate fraction of total emissions. In this work, combinations of methane detection technologies were simulated in a tiered approach for facilities representative of the Permian Basin, a region with skewed emission rates and large numbers of high-emitters, which include sensors on satellites, aircraft, continuous monitors and Optical Gas Imaging (OGI) cameras, with variations on survey frequency, detection thresholds and repair times. Results show that in oil and gas production regions with skewed emission rates and large numbers of high-emitters, strategies that increase the frequency of surveys targeting high-emitters while decreasing the frequency of OGI inspections, which find the smaller emissions, achieve higher reductions than quarterly OGI and, in some cases, reduce emissions further than monthly OGI.
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Felipe J. Cardoso-Saldaña
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Chemical Engineering and Industrial Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-11-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636d4595afea7fcd1c9f5f67/original/tiered-leak-detection-and-repair-programs-at-oil-and-gas-production-facilities.pdf
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60c7499b702a9bec8a18b170
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10.26434/chemrxiv.12058872.v1
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Stimuli-Induced Non-Equilibrium Phase Transitions in Polyelectrolytesurfactant Complex Coacervates
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Polyelectrolyte-surfactant complexes (PESCs) are important soft colloids with applications in the field of personal care, cosmetics, pharmaceutics and much else. If their phase diagrams have long been studied under pseudo-equilibrium conditions, and often inside the micellar or vesicular regions, understanding the effect of non-equilibrium conditions, applied at phase boundaries, on the structure of PESCs generates an increasing interest. In this work we cross the micelle-vesicle and micelle-fiber phase boundaries in an isocompositional surfactantpolyelectrolyte aqueous system through a continuous and rapid variation of pH. We employ two microbial glycolipid biosurfactants in the presence of polyamines, both systems being characterized by their responsiveness to pH. We show that complex coacervates (Co) are always formed in the micellar region of both glycolpids’ phase diagram and that their phase behaviour drives the PESCs stability and structure. However, for glycolipid forming single-wall vesicles, we observe an isostructural and isodimensional transition between complex coacervates and a multilamellar walls vesicle (MLWV) phase. For the fiber-forming glycolipid, on the contrary, the complex coacervate disassembles into free polyelecrolyte coexisting with the equilibrium fiber phase. Last but not least, this work also demonstrates the use of microbial glycolipid biosurfactants in the development of sustainable PESCs.<p>
</p>
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Chloé Seyrig; Patrick Le Griel; Nathan Cowieson; Javier PErez; Niki Baccile
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Interfaces; Self-Assembly
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CC BY NC ND 4.0
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CHEMRXIV
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2020-04-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7499b702a9bec8a18b170/original/stimuli-induced-non-equilibrium-phase-transitions-in-polyelectrolytesurfactant-complex-coacervates.pdf
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6171a07064e2af19560cb469
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10.26434/chemrxiv-2021-qslj3
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Study of Ruthenium-Contamination Effect on Oxygen Reduction Activity of Platinum-based PEMFC and DMFC Cathode Catalyst
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We outline a systematic experimental and theoretical study on the influence of ruthenium contamination on the oxygen reduction activity (ORR) of a Pt/C catalyst at potentials relevant to a polymer electrolyte fuel cell cathode. A commercial Pt/C catalyst was contaminated by different amounts of ruthenium, equivalent to 0.15-4 monolayers. The resulting ruthenium-contaminated Pt/C powders were characterized by Energy–Dispersive X–ray Spectroscopy (EDS), X–ray Photoelectron Spectroscopy (XPS) and Scanning Transmission Electron Microscopy (STEM) to verify ruthenium contamination. A rotating disk electrode (RDE) technique was used to study the influence of ruthenium on oxygen reduction kinetics. Density functional theory (DFT) calculations were performed to estimate the oxygen reduction activity of the platinum surface with increasing ruthenium coverage, simulating ruthenium-contaminated Pt/C. The binding energies of O and OH on the surfaces were used for activity estimations.
It was found that the specific activity of the ORR at 0.85V vs RHE exhibited a pseudo-exponential decay with increased ruthenium contamination, decreasing by ~45% already at 0.15 monolayer-equivalent contamination. The results of the DFT calculations were qualitatively in line with experimental findings, verifying the effect of O and OH binding energies and the oxophilic nature of ruthenium on ORR and the ability of the chosen approach to predict the effect of ruthenium contamination on ORR on platinum.
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Dima Kaplan; Polina Tereshchuk; Chen Olewsky; Liz Keinan; Ohad Ben Yehuda; Meital Shviro; Amir Natan; Emanuel Peled
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Physical Chemistry; Catalysis; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2021-10-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6171a07064e2af19560cb469/original/study-of-ruthenium-contamination-effect-on-oxygen-reduction-activity-of-platinum-based-pemfc-and-dmfc-cathode-catalyst.pdf
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60c74a4f469df441d3f43d18
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10.26434/chemrxiv.12180006.v1
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Artificial, Photoinduced Activation of Nitrogenase Using Directed and Mediated Electron Transfer Processes
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Nitrogenase, a bacteria-based enzyme, is the sole enzyme able to generate ammonia by atmospheric nitrogen fixation. Thus, improved understanding of its mechanism and developing methods to artificially activate it may contribute greatly to basic research, as well as to the design of future artificial systems. Here, we present methods to artificially activate nitrogenase using photoinduced reactions. Two nitrogenase variants originating from Azotobecotor vinelinii were examined using photoactivated CdS nanoparticles (NPs) capped with thioglycolic acid (TGA) or 2-mercaptoethanol (ME) ligands. The effect of methyl viologen (MV) as a redox mediator of hydrogen and ammonia generation was tested and analyzed. We further determined the NPs conductive band edges and their effect on nitrogenase photo-activation. The nano-bio hybrid systems comprising CdS NPs and nitrogenase were further imaged by transmission electron microscopy, confirming their formation for the first time. Our results show that the ME-capped CdS NPs–nitrogenase enzyme biohybrid system with added MV as redox mediator, leads to a five-fold increase in the production of ammonia compared with the non-mediated biohybrid system.
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Matan Moshe Meirovich; Oren Bachar; Omer Yehezkeli
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Nanocatalysis - Catalysts & Materials; Biocatalysis; Photocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2020-04-24
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a4f469df441d3f43d18/original/artificial-photoinduced-activation-of-nitrogenase-using-directed-and-mediated-electron-transfer-processes.pdf
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60c74ff39abda28373f8d94c
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10.26434/chemrxiv.12967832.v1
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In silico Antibody Mutagenesis for Optimizing its Binding to the Spike Protein of SARS-CoV-2
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<p>Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic and there are currently no FDA approved medicines for treatment or prevention. Inspired by promising outcomes for convalescent plasma treatment, developing antibody drugs (biologics) to block SARS-CoV-2 infection has been the focus of drug discovery, along with tremendous efforts in repurposing small-molecule drugs. In the last several months, experimentally, many human neutralizing monoclonal antibodies (mAbs) were successfully extracted from plasma of recovered COVID-19 patients. Currently, several mAbs targeting the SARS-CoV-2's spike protein (Spro) are in clinical trials. With known atomic structures of mAb-Spro complex, it becomes possible to <i>in silico</i> investigate the molecular mechanism of mAb's binding with Spro and design more potent mAbs through protein mutagenesis studies, complementary to existing experimental efforts. Leveraging superb computing power nowadays, we propose a fully automated <i>in silico</i> protocol for quickly identifying possible mutations in a mAb (e.g.~CB6) to enhance its binding affinity with Spro for the design of more efficacious therapeutic mAbs.</p>
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Binquan Luan; Tien Huynh
|
Biophysical Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-09-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff39abda28373f8d94c/original/in-silico-antibody-mutagenesis-for-optimizing-its-binding-to-the-spike-protein-of-sars-co-v-2.pdf
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649c73ce9ea64cc1671ff5db
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10.26434/chemrxiv-2022-3gxlh-v2
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Amphiphilic Molecules Exhibiting Zwitterionic Excited-State Intramolecular Proton Transfer and Near-Infrared Emission for the Detection of Amyloid β Aggregates in Alzheimer’s Disease
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Chromophores with zwitterionic excited-state intramolecular proton transfer (ESIPT) have been shown to have larger Stock shifts and red-shifted emission wavelengths compared to the conventional π-delocalized ESIPT molecules. However, there is still a dearth of design strategies to expand the current library of zwitterionic ESIPT compounds. Herein, we report a novel zwitterionic excited-state intramolecular proton transfer system enabled by addition of triazamacrocycle (TACN) fragments on a dicyanomethylene-4H-pyran (DCM) scaffold. The solvent-dependent steady-state photophysical studies and pKa measurements strongly support that the ESIPT process is more efficient with two TACN groups attached to the DCM scaffold and not affected by polar protic solvents. Impressively, compound DCM-OH-2-DT emits with a near-infrared (NIR) emission wavelength at 740 nm along with an uncommonly large Stokes shift of ~ 280 nm. Moreover, DCM-OH-2-DT shows high affinity towards soluble amyloid β (Aβ) oligomers in vitro and in 5xFAD mouse brain sections, and we have successfully applied DCM-OH-2-DT for the NIR fluorescence in vivo imaging of Aβ aggregates and demonstrated its potential use as an early diagnostic agent for AD. Overall, this study can provide a general molecular design strategy for developing new zwitterionic ESIPT compounds with NIR emission for further in vivo imaging applications.
|
Liviu Mirica; Zhengxin Yu; Yusuff Moshood; Marcin K. Wozniak; Shrey Patel; Karna Terpstra; Daniel A. Llano; Lawrence W. Dobrucki
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Photochemistry (Org.); Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649c73ce9ea64cc1671ff5db/original/amphiphilic-molecules-exhibiting-zwitterionic-excited-state-intramolecular-proton-transfer-and-near-infrared-emission-for-the-detection-of-amyloid-aggregates-in-alzheimer-s-disease.pdf
|
60c74999ee301c0467c79ab9
|
10.26434/chemrxiv.12085791.v1
|
Natural Heterogeneous Catalysis with Immobilised Oxidase Biocatalysts
|
Characterisation of immobilised oxidase biocatalysts allowing
multifunctional oxidation of valuable chemicals is described.
Engineered galactose oxidase (GOase) variants M1 and M3-5, an
engineered choline oxidase (AcCO6) and monoamine oxidase
(MAO-N D9) displayed long-term stability and reusability over
several weeks when covalently attached on solid support,
outperforming their free counterparts in terms of stability,
resistance to heat, and tolerance to neat organic solvents. While
immobilisation of oxidase biocatalysts improves properties that are
critical for industrial implementation, they additionally showed
versatility as the biocatalyst batches can be recovered, washed and
reused multiple times for the oxidation of different substrates.
|
Ashley P. Mattey; Jack J. sangster; Christopher Baldwin; Jeremy I. Ramsden; William R. Birmingham; Rachel S. Heath; antonio angelastro; Nicholas J. Turner; Sebastian Cosgrove; Sabine Flitsch
|
Organic Synthesis and Reactions; Process Chemistry; Biocatalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74999ee301c0467c79ab9/original/natural-heterogeneous-catalysis-with-immobilised-oxidase-biocatalysts.pdf
|
60c73e1f567dfe6b55ec3797
|
10.26434/chemrxiv.6708554.v1
|
Improving Solvation Energy Predictions Using The SMD Solvation Method and Semiempirical Electronic Structure Methods
|
The PM6 implementation in the GAMESS program is extended to elements requiring d-integrals and interfaced with the conducter-like polarized continuum model (C-PCM) of solvation, in- cluding gradients. The accuracy of aqueous solvation energies computed using AM1, PM3, PM6, and DFTB and the SMD continuum solvation model is tested using the MNSOL data set. The errors in SMD solvation energies predicted using NDDO-based methods is considerably larger than when using DFT and HF, with RMSE values of 3.4-5.9 (neutrals) and 6-15 kcal/mol (ions) compared to 2.4 and ca 5 kcal/mol for HF/6-31G(d). For the NDDO-based methods the errors are especially large for cations and considerably higher than the corresponding COSMO results, which suggests that the NDDO/SMD results can be improved by re-parameterizing the SMD parameters focusing on ions. We found the best results are obtained by changing only the radii for hydrogen, carbon, oxygen, nitrogen, and sulfur and this leads to RMSE values for PM3 (neutrals: 2.8/ions: ca 5 kcal/mol), PM6 (4.7/ca 5 kcal/mol), and DFTB (3.9/ca 5 kcal/mol) that are more comparable to HF/6-31G(d) (2.4/ca 5 kcal/mol). Though the radii are optimized to reproduce aqueous solvation energies, they also lead more accurate predictions for other polar solvents such as DMSO, acetonitrile, and methanol, while the improvements for non-polar solvents are negligible.
|
Jimmy C. Kromann; Casper Steinmann; Jan Halborg Jensen
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2018-06-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e1f567dfe6b55ec3797/original/improving-solvation-energy-predictions-using-the-smd-solvation-method-and-semiempirical-electronic-structure-methods.pdf
|
67ca9a2181d2151a0272c971
|
10.26434/chemrxiv-2025-b8k48
|
Electro-Inductive Effects Control the Yield and Stereoselectivity of Brønsted Acid Catalyzed Reactions
|
The electro-inductive effect offers a novel approach to modulating the chemical properties of molecules, potentially eliminating the need for laborious synthesis of derivatives with varying functional groups. By transmitting voltage-induced charge polarization from an electrode to molecules covalently attached to its surface, this method mimics the inductive effect of functional groups. Proof-of-principle studies with self-assembled monolayers of thiols on gold electrodes highlighted the transformative potential of this approach to reaction control. However, such demonstrations have so far been limited to single-molecule scales. In this study, we show that the electro-inductive effect can fine-tune the catalytic behavior of arylsulfonic acid immobilized on porous carbon electrodes for Brønsted acid-catalyzed organic reactions at millimolar scales. Applying voltages between –0.9 and +0.8 V relative to the open circuit voltage modulated the yield of acid-catalyzed esterification by a factor of ~3. Furthermore, in the intramolecular nucleophilic substitution of an alcohol bound to a chiral carbon, the stereochemical outcome of the carbocyclization was altered by adjusting the applied voltage. These results establish the electro-inductive effect as a viable alternative to functional group modification for controlling catalytic organic reactions at practically relevant scales.
|
Jisuk Bang; Seung Hyun Lee; Jun-Hyeong Kim; Johannes Westphäling; Mu-Hyun Baik
|
Catalysis; Acid Catalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca9a2181d2151a0272c971/original/electro-inductive-effects-control-the-yield-and-stereoselectivity-of-br-nsted-acid-catalyzed-reactions.pdf
|
61a88b0bf666652d53903320
|
10.26434/chemrxiv-2021-ggjfx-v4
|
An Efficient GaMD Multi-Level Enhanced
Sampling Strategy: Application to Polarizable
Force Fields Simulations of Large Biological
Systems
|
We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field.By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups thanks to the use of fast multiple--timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual--water approach is tested on the 1D Potential of Mean Force (PMF) of the solvated CD2--CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling--US--GaMD (ASUS-GaMD) scheme. The highly parallel ASUS--GaMD setup decreases time to convergence by respectively 10 and 20 times compared to GaMD-US and US. Overall, beside the acceleration of PMF computations, Tinker-HP now allows for the simultaneous use of Adaptive Sampling and GaMD-"dual water" enhanced sampling approaches increasing the applicability of polarizable force fields to large scale simulations of biological systems.
|
Fréderic Célerse; Theo Jaffrelot-Inizan; Louis Lagardère; Olivier Adjoua; Pierre Monmarché; Yinglong Miao; Etienne Derat; Jean-Philip Piquemal
|
Theoretical and Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-12-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a88b0bf666652d53903320/original/an-efficient-ga-md-multi-level-enhanced-sampling-strategy-application-to-polarizable-force-fields-simulations-of-large-biological-systems.pdf
|
6155d1aa9e3840f83545b650
|
10.26434/chemrxiv-2021-nl537
|
NIR-Emitting Benzene-Fused Oligo-BODIPYs for Bioimaging
|
Near-infrared (NIR) fluorophores are emerging tools for biophotonics because of their reduced scattering, increased tissue penetration and low phototoxicity. However, the library of NIR fluorophores is still limited. Here, we report the NIR fluorescence of two benzene-fused oligo-BODIPYs in their hexameric (H) and octameric (O) forms. These dyes emit bright NIR fluorescence (H: maxima 943/1075 nm, O: maxima 976/1115 nm) that can be excited in the NIR (H = 921 nm, O = 956 nm) or non-resonantly over a broad range in the visible region. The emission bands of H show a bathochromic shift and peak sharpening with increasing dye concentration suggesting the presence of J-aggregates. Furthermore, the emission maxima of both H and O shift up to 20 nm in solvents of different polarity. These dyes can be used as NIR ink and imaged remotely on the macroscopic level with a stand-off distance of 20 cm. We furthermore demonstrate their versatility for biophotonics by coating microscale beads and performing microrheology via NIR video particle tracking (NIR-VPT) in biopolymer (F-actin) networks. No photodamaging of the actin filaments takes place, which is typically observed for visible fluorophores and highlights the advantages of these NIR dyes.
|
Gabriele Selvaggio; Robert Nißler; Peter Nietmann; Atanu Patra; Lukas Jacek Patalag; Andreas Janshoff; Daniel Bodo Werz; Sebastian Kruss
|
Physical Chemistry; Organic Chemistry; Materials Science; Dyes and Chromophores; Optics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6155d1aa9e3840f83545b650/original/nir-emitting-benzene-fused-oligo-bodip-ys-for-bioimaging.pdf
|
60c74acc0f50db8ffe396afe
|
10.26434/chemrxiv.12210290.v2
|
Steering Polymer Growth by Molding Nanochannels: 1,5-Hexadiene Polymerization in High Silica Mordenite
|
<p><a>Zeolites are known as scaffolds for the assembly of
molecules via non-covalent interactions, yielding organized supramolecular
materials. Yet their potential in driving the growth of low-dimensional systems
requiring covalent bond formation is still uncharted. We incorporated 1,5-hexadiene
in the channels of a high‑silica mordenite and analyzed the material by
infrared spectroscopy, X-Ray powder diffraction, thermogravimetric and modeling
techniques. Thanks to the few zeolite acid sites, 1,5‑hexadiene experiences a
slow conversion to a polymer, mainly formed by cyclopentane units and featuring
short side chains able to fit the channels. The shape-directing abilities of
zeolite framework play a two-fold role, involving first the organization of the
monomers inside the void-space and then the linear growth of the chain,
dictated by the channel geometry. These findings highlight the molding action
of zeolites in directing transformations of covalent bonds under ambient conditions
and may provide insights for obtaining confined polymers with intriguing
perspective applications.</a></p>
|
Marco Fabbiani; Giorgia Confalonieri; sara morandi; Rossella Arletti; Simona Quartieri; Mario Santoro; Francesco Di Renzo; Julien Haines; Riccardo Fantini; gloria tabacchi; Ettore Fois; Giovanna Vezzalini; Gianmario Martra
|
Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Organic Polymers; Polymer morphology; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Heterogeneous Catalysis; Spectroscopy (Physical Chem.); Crystallography
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74acc0f50db8ffe396afe/original/steering-polymer-growth-by-molding-nanochannels-1-5-hexadiene-polymerization-in-high-silica-mordenite.pdf
|
60c74f124c8919eafdad3b3a
|
10.26434/chemrxiv.12844733.v1
|
Predicting Aqueous Stability of Solid with Computed Pourbaix Diagram using SCAN Functional
|
In this work, using the SCAN functional, we develop a simple method on top of the Materials Project (MP) Pourbaix diagram framework to accurately predict the aqueous stability of solids. We extensively evaluate the SCAN functional’s performance in computed formation enthalpies for a broad range of oxides and develop Hubbard U corrections for transition metal oxides where the standard SCAN functional exhibits large deviations. The performance of the calculated Pourbaix diagram using the SCAN functional is validated with comparison to the experimental and the MP PBE Pourbaix diagrams for representative examples. Benchmarks indicate the SCAN Pourbaix diagram systematically outperforms the MP PBE in aqueous stability prediction. We further show applications of this method in accurately predicting the dissolution potentials of the state-of-the-art catalysts for oxygen evolution reaction in acidic media.
|
Zhenbin Wang; Xingyu Guo; Joseph H. Montoya; Jens Kehlet Nørskov
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f124c8919eafdad3b3a/original/predicting-aqueous-stability-of-solid-with-computed-pourbaix-diagram-using-scan-functional.pdf
|
659c3b1766c1381729fed4e3
|
10.26434/chemrxiv-2024-0x0bt
|
Converting Heat to Electrical Energy Using Highly Charged Polyoxometalate Electrolytes
|
Thermally regenerative electrochemical cycles and thermogalvanic cells harness redox entropy changes (Src) to interconvert heat and electricity, with applications in heat harvesting and energy storage. Their efficiencies depend on Src because it relates directly to the Seebeck coefficient, yet few approaches exist for controlling reaction entropy. Here, we demonstrate the use of highly charged molecular species in thermogalvanic devices. As a proof-of-concept, the highly charged Wells-Dawson ion [P2W18O62]6- exhibits large ΔSrc (-195 J mol-1 K-1) and a Seebeck coefficient comparable to state-of-the-art electrolytes (1.1 mV K-1), demonstrating the potential of linking the rich chemistry of polyoxometalates to thermogalvanic technologies.
|
Erik Svensson Grape; Jiawei Huang; Dwaipayan Roychowdhury; Tekalign Debela; Haeun Chang; Andrew Jenkins; Alina Schimpf; Christopher Hendon; Carl Brozek
|
Inorganic Chemistry; Energy; Electrochemistry; Supramolecular Chemistry (Inorg.); Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659c3b1766c1381729fed4e3/original/converting-heat-to-electrical-energy-using-highly-charged-polyoxometalate-electrolytes.pdf
|
60c744a0842e653872db24c1
|
10.26434/chemrxiv.9868196.v1
|
Functional Poly(p-Xylylene)s via Chemical Reduction of Poly(p-Phenylene Vinylene)s
|
The synthesis of poly(p-xylylene)s (PPXs) with sidechains containing alkyl bromide functionality, and their post-polymer modification, is described. The PPXs were prepared by a diimide hydrogenation of poly(p-phenylene vinylene)s (PPVs) that were originally synthesized by a Gilch polymerization. The polymer backbone reduction was carried out with hydrazine hydrate in toluene at 80 °C to provide polymers with the sidechain-containing bromide functionality intact. To demonstrate post-polymer modification of the sidechains, the resulting PPX polymers were modified with trimethylamine to form tetraalkylammonium ion functionality and were evaluated as anion conducting membranes. While PPX homopolymers containing tetralkylammonium ions were completely water soluble and not able to form valuable films, PPX copolymers containing mixed tetraalkylammonium ions and hydrophobic chains were capable of film formation and alkaline stability. In addition, an in situ crosslinking process that used N,N,N',N'-tetramethyl-1,6-hexanediamine during the tetraalkylammonium formation of brominated PPX polymers was also evaluated and gave reasonable films with conductivities of ~10 mS-cm-1.
|
Ain Uddin; Weifan Sang; Yong Gao; Kyle Plunkett
|
Organic Polymers; Polyelectrolytes - Polymers; Polymerization (Polymers)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744a0842e653872db24c1/original/functional-poly-p-xylylene-s-via-chemical-reduction-of-poly-p-phenylene-vinylene-s.pdf
|
649c69cdba3e99daef31fba9
|
10.26434/chemrxiv-2023-h1dxg
|
Metal Site-Specific Electrostatic Field Effects on a Tricopper(I) Cluster Probed by Resonant Diffraction Anomalous Fine Structure (DAFS)
|
Studies of multinuclear metal complexes are greatly enhanced by resonant diffraction measurements, which probe X-ray absorption profiles of crystallographically independent metal sites within a cluster. In particular, X-ray diffraction anomalous fine structure (DAFS) analysis provides data that can be interpreted akin to site-specific XANES, allowing for differences in metal K-edge resonances to be deconvoluted even for different metal sites within a homometallic system. Despite the prevalence of Cu-containing clusters in biology and energy science, DAFS has yet to be used to analyze multicopper complexes of any type until now. Here, we report benchmarking studies using a series of strategically chosen Cu(I) and Cu(II) complexes to determine how energy dependences of anomalous scattering factors are impacted by coordination geometry, ligand shell, cluster nuclearity, and oxidation state. This calibration data is used to analyze a formally tricopper(I) complex that was found by DAFS to be site differentiated due to the unsymmetrical influence on different Cu sites of the electrostatic field from a proximal K+ cation.
|
Pinar Alayoglu; Tieyan Chang; Victoria Ocampo; Leslie Murray; Yu-Sheng Chen; Neal Mankad
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649c69cdba3e99daef31fba9/original/metal-site-specific-electrostatic-field-effects-on-a-tricopper-i-cluster-probed-by-resonant-diffraction-anomalous-fine-structure-dafs.pdf
|
675c5781085116a1334c0cef
|
10.26434/chemrxiv-2024-w0dxw
|
Designing single polymer chain nanoparticles to
mimic biomolecular hydration frustration
|
Native folded proteins rely on sculpting the local chemical environment of their active
or binding sites, as well as their shapes. In particular, proteins exhibit a phenomenon known
as “hydration frustration”, i.e. the ability to control the dehydration of hydrophilic and the
hydration of hydrophobic residues, respectively, to amplify their chemical or binding activity. Here, we uncover that single polymer chain nanoparticles formed by random
heteropolymers composed of three or more components can display similar levels of hydration
frustration. We categorize these nanoparticles into three types: i) fully-frustrated
globules, where both types of residues display frustrated states, ii) semi-frustrated, with
either hydrophobic or hydrophilic residues in a frustrated state, and iii) core-shell nonfrustrated
globules. Based on our results, we propose a series of physicochemical rules that
determine the state of these nanoparticles. The rules have been tested in both atomistic and
simplified Monte Carlo models of single polymer chain nanoparticles with different backbones
and residues to show their generality. Our work provides critical insights into the
design of single chain nanoparticles, an emerging polymer modality that achieves the ease
and cost of fabrication of polymeric material with the functionality of biological proteins.
|
Tianyi Jin; Connor Coley; Alfredo Alexander-Katz
|
Theoretical and Computational Chemistry; Materials Science; Polymer Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c5781085116a1334c0cef/original/designing-single-polymer-chain-nanoparticles-to-mimic-biomolecular-hydration-frustration.pdf
|
635a9b18cf6de97abb24ccc2
|
10.26434/chemrxiv-2022-1w1q3
|
Allosteric Modulation of PCSK9-LDLR Interaction: Can Structureless Loops be Drug Targets?
|
While most of the drugs available in the market are competitive inhibitors, there is a rapidly growing interest in development of allosteric drugs, particularly to inhibit protein-protein interactions (PPI) with large interaction surface area. However, it remains a challenge to identify a distal binding site that would be allosterically linked to the canonical ligand/substrate binding site. Such allosteric hotspots are often cryptic sites with a less populated excited conformational state of the protein. In this work we present a general strategy based on thermodynamic arguments to identify such distal cryptic sites as potential targets for allosteric drugs. We demonstrate this on allosterically modulating the PPI between PCSK9 (proprotein convertase subtilisin/Kexin type 9) and LDLR (low density lipoprotein receptor), which is a challenging and therapeutically important target towards treatment of hypercholesterolemia (elevated plasma level of LDL). Using several µs long molecular dynamics (MD) simulations, we demonstrate that on binding with the EGF-A domain of LDLR, there is a significant conformational change (population shift) in a distal loop (residues 211-222) region of PCSK9. We have identified several (meta)stable and kinetically resolved conformational states of this loop and demonstrated that there exists a clear correlation between the loop conformation and the binding affinity with LDLR. Using a thermodynamic argument, we establish that the loop conformations predominantly present in the apo state of PCSK9 would have lower binding affinity with LDLR and they would be potential targets for designing allosteric inhibitors. We also elucidate the molecular origin of the allosteric coupling between this loop and PCSK9-LDLR binding interface in terms of population shift in several specific pair-wise interactions consisting of salt bridges and hydrogen bonds. Overall, our work provides a general strategy towards identifying allosteric hotspots, where one should compare the conformational ensemble between the apo and substrate bound states of the protein and identify distal differences, if any. Subsequently the apo-like conformations should be targeted for designing inhibitors that would specifically bind to those conformations and stabilise them.
|
Ipsita Basu; Krishnendu Sinha; Zacharia Shah; Salim Shah; Suman Chakrabarty
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635a9b18cf6de97abb24ccc2/original/allosteric-modulation-of-pcsk9-ldlr-interaction-can-structureless-loops-be-drug-targets.pdf
|
60c7589a0f50db61863984a1
|
10.26434/chemrxiv.14566656.v1
|
A Study of Two-Dimensional Single Atom-Supported MXenes as Hydrogen Evolution Reaction Catalysts Using DFT and Machine Learning
|
<p></p><p>Enclosed you will find the article entitled “A study
of two-dimensional single atom-supported MXenes as hydrogen evolution reaction
catalysts using DFT and machine learning”.<br /></p>
<p> </p>
<p>Existing
studies predominantly focused on the hydrogen evolution reaction (HER) activities
and stabilities of oxygen-terminated MXenes with single-atom loading. However,
to the best of our knowledge, two-dimensional (2D) MXenes with different
terminations (e.g. Br, I, Se, Te, B, Si, P, and NH) have not yet been
investigated for the purposes of HER catalysis. Therefore, in this work, we
considered the combined effect of the different surface terminations (B, NH, O,
F, Si, P, S, Cl, Se, Br, Te, and I) and single atom loading (Ti, V, Fe, Co, Ni,
Cu, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Hf, Ta, W, Re, Os, Ir, Pt, and Au) using
DFT calculation. Gibbs
free energy of hydrogen adsorption (reflecting activity) and the cohesive energy
(a proxy for thermal stability) of these structures (264 in total) were calculated.
We demonstrate that 21 uninvestigated 2D single-atom MXene catalysts, among 264
promising candidates, show an electrocatalytic activity surpassing that of platinum
and a thermal stability surpassing those of synthesized borophene sheet and MoS<sub>2</sub>.
Moreover, all catalysts examined in this work were
further randomly separated into training and test sets with a ratio of 7:3. The HER
electrocatalytic performance and thermal stability of the catalysts in the test
set were predicted by machine learning algorithms. Most importantly, we present a way
to provide a comparable precision (root mean square error values for the
activity and thermal stability predictions are 0.158 eV and 0.02 eV,
respectively) to the published machine learning works by avoiding their
adoption of complex electronic features and the associated high computational
cost, and <i>by only using features that are </i><i>easily available in chemical
repositories</i>. The algorithms used in this work are expected to help future
researchers quickly screen single atom loaded MXenes HER catalysts at the
initial design stage in a cost-effective manner. </p>
<p> </p>
<p>We have no
financial interest in the subject or instrumentation used and there is no known
conflict of interest. </p><br /><p></p>
|
HONGXING LIANG; Min Xu; Edouard Asselin
|
Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7589a0f50db61863984a1/original/a-study-of-two-dimensional-single-atom-supported-m-xenes-as-hydrogen-evolution-reaction-catalysts-using-dft-and-machine-learning.pdf
|
66c4c82aa4e53c4876fb368e
|
10.26434/chemrxiv-2024-dhtx9
|
Understanding activity trends in electrochemical dinitrogen oxidation over transition metal oxides
|
Nitric acid (HNO3) is a critical commodity chemical produced on enormous scale via oxidation of ammonia (NH3) in the Ostwald process and, as such, is responsible for a significant fraction of global greenhouse gas emission. Formation of nitric acid by directly oxidizing dinitrogen via the electrochemical nitrogen oxidation reaction (N2OR) is an attractive alternative, but has so far largely remained elusive. Towards advancing our fundamental understanding of the limitations of the N2OR, in this work we investigated the competitive adsorption dynamics of nitrogen (N2) and water oxidation intermediates such as hydroxide (OH) on a range of transition metal oxides. Using density functional theory (DFT) calculations, we explore three possible N2OR mechanisms: direct adsorption and dissociative adsorption of N2, and a Mars-van Krevelen (MvK) type mechanism involving adsorption of N2 on a surface-bound atomic oxygen. We observed a strong linear scaling relation between the adsorption energy of N2 and OH on the metal-terminated transition metal oxide, suggesting that under typical highly oxidizing operating conditions for the N2OR (U<sub>RHE</sub>>1.24 V), water oxidation intermediates such as OH are likely to dominate the surface, leading to vanishingly small coverage of adsorbed N2. From this result, we find that direct or dissociative adsorption of N2 is unlikely, suggesting a MvK type mechanism for the N2OR. Probing this mechanism further using DFT, we find that the reaction energetics are largely less favorable than water oxidation due to the high activation barrier for N2 adsorption, which we find to be the rate-determining step for the process. Our experimental findings corroborate these findings, demonstrating that the majority of tested catalysts exhibited poor N2OR selectivity with a rate-determining step involving N2 (g), primarily facilitating the oxygen evolution reaction (OER). However, dynamic potential control emerged as a possible strategy to enhance N2OR activity, as it may limit OER and promote N2 adsorption. This work underscores the challenges in achieving efficient N2OR, highlighting the need for novel catalyst designs and operational strategies, such as electrolyte engineering and dynamic potential control, to overcome the inherent kinetic and thermodynamic barriers.
|
Samuel Olusegun; Yancun Qi; Nishithan Kani; Meenesh Singh; Joseph Gauthier
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Catalysis; Electrocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2024-08-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c4c82aa4e53c4876fb368e/original/understanding-activity-trends-in-electrochemical-dinitrogen-oxidation-over-transition-metal-oxides.pdf
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64967e771dcbb92a5e7b5a4f
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10.26434/chemrxiv-2023-mgqg3
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Giving the green light to photochemical uncaging of large biomolecules in high vacuum
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The isolation of biomolecules in high vacuum enables experiments on fragile species in the absence of a perturbing environment. Since many molecular properties are influenced by local electric fields, here we seek to gain control over the number of charges on a biopolymer. Here, we present the design, modelling and synthesis of photoactive molecular tags, their labelling to peptides and proteins as well as their photochemical validation in solution and in the gas phase. The tailored tags can be selectively cleaved off, at a well-defined time and without the need for any external charge transferring agents. The energy of a single or two green photons can already trigger the process and it is soft enough to ensure the integrity of the released biomolecular cargo. We exploit differences in the cleavage pathways in solution and in vacuum, and observe a surprising robustness in upscaling the approach from a model system to genuine proteins. The interaction wavelength of 532 nm is compatible with various biomolecular entities such as oligonucleotides or oligosaccharides.
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Yong Hua; Marcel Strauss; Sergey Fisher; Martin F. X. Mauser; Pierre Manchet; Martina Smacchia; Philipp Geyer; Armin Shayeghi; Michael Pfeffer; Tim Henri Eggenweiler; Steven Daly; Jan Commandeur; Marcel Mayor; Markus Arndt; Tomáš Šolomek; Valentin Köhler
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Physical Chemistry; Organic Chemistry; Analytical Chemistry; Photochemistry (Org.); Biochemical Analysis; Mass Spectrometry
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CC BY NC ND 4.0
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CHEMRXIV
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2023-06-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64967e771dcbb92a5e7b5a4f/original/giving-the-green-light-to-photochemical-uncaging-of-large-biomolecules-in-high-vacuum.pdf
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60c756e7469df4250df453a6
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10.26434/chemrxiv.14345318.v1
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Organic Photovoltaic Behaviour with Centimeter-long Lateral Junctions
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In the field of organic solar cells, lateral junction is a new concept. Moreover, the photovoltaic behavior is firstly observed for surprising long organic lateral junctions reaching 1.8 cm and the new operation mechanism dominated by trap-assisted recombination is proposed. <div><br /></div>
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Jaseela Palassery Ithikkal; Adrien Girault; Mitsuru Kikuchi; Yusuke Yabara; Seiichiro Izawa; Masahiro Hiramoto
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Thin Films
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CC BY NC ND 4.0
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CHEMRXIV
|
2021-04-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756e7469df4250df453a6/original/organic-photovoltaic-behaviour-with-centimeter-long-lateral-junctions.pdf
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64276814a029a26b4cb628d3
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10.26434/chemrxiv-2023-lnxwm
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Vernonia amygdalina Extract Reverts Hematological and Biochemical Alterations in Rats Exposed to N-Nitroso-N-ethyl urea
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35 Sprague Dawley rats were exposed to carcinogen and treated with different concentrations of Vernonia amygdalina aqueous extracts. 3 doses of 50mg/kg doses of N-Nitroso-N-ethyl urea (NEU) was given intraperitoneally at two weeks interval. Changes in hematological and biochemical parameters were determined in blood and serum samples. NEU exposed rats treated group showed significant alterations in several hematological and biochemical parameters. In comparison to the control group, the carcinogen exposed rats showed significantly increased Blood Glucose, Serum Total Cholesterol: Low Density Lipoprotein (LDL-Cholesterol), Triacylglycerol's levels and High Density Lipoprotein (HDL-Cholesterol) level. After treatment with V. amygdalina aqueous extract, hematological and biochemical parameters in the carcinogen exposed rats treated group were approximately similar to control group. The V. amygdalina extract significantly restored the hematological and biochemical parameters in N-Nitroso-N-ethyl urea carcinogen exposed rats
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Olufunke Olugbenga; Joy Okpuzor
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Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
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CC BY 4.0
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CHEMRXIV
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2023-04-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64276814a029a26b4cb628d3/original/vernonia-amygdalina-extract-reverts-hematological-and-biochemical-alterations-in-rats-exposed-to-n-nitroso-n-ethyl-urea.pdf
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65240a83bda59ceb9a2e078f
|
10.26434/chemrxiv-2023-207wl
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Solvent-base mismatch enables the deconstruction of epoxy polymers and bisphenol A recovery
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Fiber-reinforced epoxy composites are key materials for the construction of wind turbine blades and airplanes due to their remarkable mechanical strength properties. On the flipside, their physical and chemical inertness also results in a lack of viable recycling technologies. Recently, tailored resins have been introduced, which allow controlled fragmentation of the polymer matrix and thus the recovery of embedded fibres. However, for the separated thermoset epoxy fragments there is no recycling solution available, resulting in loss of complex molecular structures at their disposal. Here we report a chemical process for recovering bisphenol A (BPA) from epoxy resins, using a mismatched base-solvent system at an elevated temperature. We demonstrate a combinatory disassembly processes / chemical deconstruction strategy on a commercial tailored composite sample, isolating both fibres and the polymer building block. The recovered BPA could potentially be reused in established polymer production chains, thus closing the recycling loop and reducing the need for virgin resources.
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Hongwei Sun; Alexander Aahrens; Gabriel Batista; Bjarke Donslund; Anne Ravn; Emil Schwibinger; Ainara Flores; Troels Skrydstrup
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Organic Chemistry; Polymer Science; Organic Polymers
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-10-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65240a83bda59ceb9a2e078f/original/solvent-base-mismatch-enables-the-deconstruction-of-epoxy-polymers-and-bisphenol-a-recovery.pdf
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