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60c758e0ee301c7eadc7b7df
|
10.26434/chemrxiv.14604294.v1
|
High-throughput Computational Evaluation of Low Symmetry Pd2L4 Cages to Aid in System Design
|
<p>The use of unsymmetrical
components in metallo-supramolecular chemistry allows for low-symmetry
architectures with anisotropic cavities toward guest-binding with high
specificity and affinity. Unsymmetrical ditopic ligands mixed with Pd(II) have
the potential to self-assemble into reduced symmetry Pd<sub>2</sub>L<sub>4</sub>
metallo-architectures. Mixtures of isomers can form, however, resulting in
potentially undesirable heterogeneity within a system. Therefore it is
paramount to be able to design components that preferentially form a single
isomer. Previous data suggested that computational methods could predict with
reasonable accuracy whether unsymmetrical ligands would preferentially
self-assemble into a single isomer under constraints of geometrical mismatch. We
successfully apply a collaborative computational and experimental workflow to
mitigate costly trial-and-error synthetic approaches. Our low-cost
computational workflow rapidly constructs new unsymmetrical ligands (and Pd<sub>2</sub>L<sub>4</sub>
cage isomers) and ranks their likelihood for forming <i>cis</i>-Pd<sub>2</sub>L<sub>4</sub> assemblies. From
this narrowed search space, we successfully synthesised four new low-symmetry, <i>cis</i>-Pd<sub>2</sub>L<sub>4</sub>
cages, with cavities of different shapes and sizes.</p>
|
Andrew Tarzia; James Lewis; Kim Jelfs
|
Ligands (Inorg.); Supramolecular Chemistry (Inorg.); Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758e0ee301c7eadc7b7df/original/high-throughput-computational-evaluation-of-low-symmetry-pd2l4-cages-to-aid-in-system-design.pdf
|
60c74336702a9b091018a599
|
10.26434/chemrxiv.8985716.v1
|
Copper Hydride-Catalyzed Enantioselective Synthesis of Axially Chiral 1,3-Disubstituted Allenes
|
The general enantioselective synthesis of axially chiral disubstituted allenes from prochiral starting materials remains a long-standing challenge in organic synthesis. Here, we report an efficient enantio- and chemoselective copper hydride-catalyzed semi-reduction of conjugated enynes to furnish 1,3-disubstituted allenes using water as the proton source. This protocol is sufficiently mild to accommodate an assortment of functional groups including keto, ester, amino, halo, and hydroxyl groups. Additionally, applications of this method for the selective synthesis of mono-deuterated allenes and chiral 2,5-dihydropyrroles are described.
|
Liela Bayeh; Stephen L. Buchwald
|
Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-07-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74336702a9b091018a599/original/copper-hydride-catalyzed-enantioselective-synthesis-of-axially-chiral-1-3-disubstituted-allenes.pdf
|
6231004ed6d3ed72949325f5
|
10.26434/chemrxiv-2022-v3t03
|
Directed evolution of a bright variant of mCherry:
Suppression of non-radiative decay by fluorescence lifetime
selections
|
The approximately linear scaling of fluorescence quantum yield (QY) with fluorescence lifetime (τ) in
fluorescent proteins (FPs) has inspired engineering of brighter fluorophores based on screening for
increased lifetimes. Several recently developed FPs such as mTurquoise2, mScarlet and FusionRed-MQV
which have become useful for live cell imaging are products of lifetime selection strategies. However, the
underlying photophysical basis of the improved brightness has not been scrutinized. In this study, we
focused on understanding the outcome of lifetime-based directed evolution of mCherry, which is a popular
red-FP (RFP). We identified four positions (W143, I161, Q163, and I197) near the FP chromophore that
can be mutated to create mCherry-XL (eXtended Lifetime: QY = 0.70; τ =3.9 ns). The threefold higher
quantum yield of mCherry-XL is on par with that of the brightest RFP to date, mScarlet. We examined
selected variants within the evolution trajectory and found a near-linear scaling of lifetime with quantum
yield and consistent blue-shifts of the absorption and emission spectra. We find that the improvement in
brightness is primarily due to a decrease in the non-radiative decay of the excited state. In addition, our
analysis revealed the decrease in non-radiative rate is not limited to the blue-shift of the energy gap and
changes in the excited state reorganization energy. Our findings suggest that non-radiative mechanisms
beyond the scope of energy-gap models such the Englman-Jortner are suppressed in this lifetime evolution
trajectory.
|
Srijit Mukherjee; Premashis Manna; Sheng-Ting Hung; Felix Vietmeyer; Pia Friis; Amy Palmer; Ralph Jimenez
|
Physical Chemistry; Biophysical Chemistry; Physical and Chemical Processes; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231004ed6d3ed72949325f5/original/directed-evolution-of-a-bright-variant-of-m-cherry-suppression-of-non-radiative-decay-by-fluorescence-lifetime-selections.pdf
|
6744ecfef9980725cfec5804
|
10.26434/chemrxiv-2024-f2n88
|
Design of Novel MagnetoPlasmonic Absorbers as MRI Contrast and Photothermal Therapy Agents
|
This study presents a detailed investigation into the photothermal therapy (PTT) performance of single heterogeneous gold (Au) and iron (III) oxide (Fe3O4) nanoparticles, as well as heterogeneous Au@Fe3O4 and Fe3O4@Au core-shell nanoparticles, using PyMieLab and COMSOL Multiphysics simulations. Through a comprehensive parametric analysis, we elucidate the impact of core-shell configurations on the photothermal conversion efficiency and heat generation of these nanoparticles. Our results reveal that Fe3O4@Au core-shell nanoparticles with a core radius of 100 nm and shell thickness of 70 nm exhibit superior heat generation efficiency compared to Au@Fe3O4 and their single-component counterparts, with Fe3O4 demonstrating higher photothermal efficiency than Au. The enhanced thermal response observed in the core-shell structures, particularly Fe3O4@Au, is attributed to the synergistic interaction between the core and shell materials, optimizing light absorption and thermal conversion.
|
Seda Aygül Akyüz; Zeliha Cansu Canbek Ozdil
|
Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6744ecfef9980725cfec5804/original/design-of-novel-magneto-plasmonic-absorbers-as-mri-contrast-and-photothermal-therapy-agents.pdf
|
61b2bdc525f39a5318d4138e
|
10.26434/chemrxiv-2021-xhxtc
|
Conformational Sampling for Transition State Searches on a Computational Budget
|
Transition state searches are the basis for characterizing reaction mechanisms and activation energies, and are thus central to myriad chemical applications. Nevertheless, common search algorithms are sensitive to molecular conformation and the conformational space of even medium-sized reacting systems are too complex to explore with brute force. Here we show that it is possible to train a classifier to learn the features of conformers that conduce successful transition state searches, such that optimal conformers can be down-selected before incurring the cost of a high-level transition state search. To this end, we have benchmarked the use of a modern conformational generation algorithm with our reaction prediction methodology, Yet Another Reaction Program (YARP), for reaction prediction tasks. We demonstrate that neglecting conformer contributions leads to qualitatively incorrect activation energy estimations for a broad range of reactions, whereas a simple random forest classifier can be used to reliably down-select low-barrier conformers. We also compare the relative advantage of performing conformational sampling on reactant, product, and putative transition state geometries. The robust performance of this relatively simple machine learning classifier mitigates cost as a factor when implementing conformational sampling into contemporary reaction prediction workflows.
|
Qiyuan Zhao; Hsuan-Hao Hsu; Brett Savoie
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-12-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b2bdc525f39a5318d4138e/original/conformational-sampling-for-transition-state-searches-on-a-computational-budget.pdf
|
60c74d2e469df4f744f4423a
|
10.26434/chemrxiv.12595184.v1
|
Equation-of-Motion Coupled-Cluster Theory to Model L-edge X-Ray Absorption and Photoelectron Spectra
|
We present an extension of the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) theory for computing x-ray L-edge spectra, both in the absorption
(XAS) and photoelectron (XPS) regimes. The approach is based on the perturbative evaluation of spin-orbit couplings using the Breit-Pauli Hamiltonian and nonrelativistic wave-functions described by the fc-CVS-EOM-CCSD ansatz (EOM-CCSD
within the frozen-core core-valence separated (fc-CVS) scheme). The formalism is
based on spinless one-particle density matrices. The approach is illustrated by modeling
XAS and XPS of several model systems ranging from argon atoms to small molecules
containing sulfur and silicon.
|
Marta L. Vidal; Pavel Pokhilko; Anna Krylov; Sonia Coriani
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d2e469df4f744f4423a/original/equation-of-motion-coupled-cluster-theory-to-model-l-edge-x-ray-absorption-and-photoelectron-spectra.pdf
|
670f2aa712ff75c3a18e2975
|
10.26434/chemrxiv-2024-z11nk-v2
|
An Economic Fluorescent Method for Microplastics Detection in Soil Samples
|
Microplastics from urban and industrial waste are threatening ecosystems worldwide. Quantification methods for soil samples have been proposed but typically require complex and expensive laboratory procedures, which are not accessible to the public. Therefore, we developed a simplified Nile red fluorescent dye method with low-budget materials that can be readily used as lone-standing demonstrations or implemented in environmental education modules. The method was validated on commercial coarse-grain sand spiked with microplastics (1-5 mm). Following incubation with Nile red dye, the analytes were visually inspected using blue light and orange filter glasses and counted by two independent masked assessors. Detection of particles was close to 100 percent. Four different types of environmental analytes were subsequently tested with this method: urban lake shore sediment, agricultural soil, gardening soil, and soil from a state park. Urban lake shore and garden soil samples showed the highest density of microplastic particles. Large numbers of smaller particles (<1 mm) were also identified and counted in these analytes, with very good reproducibility by the same assessor and replication of the rank order of analytes between two assessors. Visualizing microplastic pollution with this low-cost, scalable method can reach broad sections of educational settings and the broader public and thus raise awareness of the problem of microplastic pollution.
|
Madalena Ritz-Meuret; Alexander R Lippert; Thomas Ritz
|
Earth, Space, and Environmental Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670f2aa712ff75c3a18e2975/original/an-economic-fluorescent-method-for-microplastics-detection-in-soil-samples.pdf
|
66325b3b91aefa6ce1e30ba7
|
10.26434/chemrxiv-2024-32t9j
|
Selective and efficient detoxification of sulfur mustard gas analogues with H2O2 using bioinspired Mo and W dithiolene catalysts
|
Efficient and selective decomposition of chemical warfare agents (CWAs) is immensely important to cope with threats from accidental or intentional releases from stockpiles. One of the most stockpiled CWAs is sulfur mustard (SM) gas. The most effective way to detoxify stockpiled SM is to oxidize the thioether functionality to its benign sulfoxide (SMO) state. However, overoxidation to the corresponding sulfone (SMO2), itself a potent toxin, should be avoided. Thus, cat-alysts for SM detoxification must be precisely tuned to promote the sluggish oxidation of SM while avoiding overoxi-dation of SMO to SMO2. In this study, Mo and W dithiolene catalysts, [MO2(dithiolene)2]2- (M = Mo or W), inspired by the active site structures of oxotransferase enzymes such as DMSO reductase were used as catalysts for oxidation of the SM research analogue, 2-chloroethyl ethyl sulfide (CEES), with aqueous H2O2 as a green oxidant. Under optimized conditions, [WO2(mnt)2]2- and [MoO2(bdt)2]2- (mnt = maleonitriledithiolate, bdt = 1,2-benzenedithiolate) were found to promote selective CEES oxidation to sulfoxide CEESO without overoxidation to sulfone CEESO2 in as little as 5-15 min with catalyst loadings as low as 0.015 mol%. The W catalyst was also found to be reusable without measurable loss of activity. Experimental and computational studies indicate the involvement of 𝜂2-peroxo species, [M(O)(𝜂2-O2)(dithiolene)2]2-, as the active oxidants formed in situ. Overall, the bioinspired catalysts in this study are shown to be promising candidates for developing convenient, inexpensive, efficient, and selective mustard gas detoxification technologies.
|
Beria Tanriover; S. M. Supundrika Subasinghe; Neal Mankad
|
Inorganic Chemistry; Catalysis; Organometallic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66325b3b91aefa6ce1e30ba7/original/selective-and-efficient-detoxification-of-sulfur-mustard-gas-analogues-with-h2o2-using-bioinspired-mo-and-w-dithiolene-catalysts.pdf
|
6761148d81d2151a020075f5
|
10.26434/chemrxiv-2024-gd816
|
Light-Triggered Reversible Helicity Switching of a Guest by a Photo-Responsive Plier
|
Controlling synchronized motion and transmission of molecular motion to a remotely located guest is not trivial. Here, we demonstrate a light-triggered, scissor-like conformational change in a molecular plier to reversibly alter the conformation and helical chirality of a noncovalently bound rotor guest. The plier comprises three building blocks: an azobenzene unit that controls the open-close motion of the plier upon light-activated isomerization from E to Z, a BINOL unit that serves as both a hinge and a chiral inducer and two pyridine moieties that can form a complex with the rotor guest. The light-induced conformational alteration of the plier was unequivocally demonstrated by 1H NMR, UV-Vis, and CD spectroscopy. The open-close motion of the plier was translated to the rotor via a 1:1 host-guest complex. Indeed, CD spectroscopy, NMR spectroscopy, thermal back isomerization studies, and molecular modelling confirm that the light-triggered conformational alterations of the host can induce mechanical twisting and helicity switching in the guest.
|
Diptiprava Sahoo; Anshuman Bera; Sivaranjana Reddy Vennapusa; Soumen De
|
Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6761148d81d2151a020075f5/original/light-triggered-reversible-helicity-switching-of-a-guest-by-a-photo-responsive-plier.pdf
|
6129244a90051e47f3e259be
|
10.26434/chemrxiv-2021-2x1d1
|
Computer-aided design, synthesis, and biological evaluation of [4.3.0] bicyclic prolyl oligopeptidase and fibroblast activation protein-α dual inhibitors
|
We have previously described several different chemical series of bicyclic prolyl oligopeptidase (POP) inhibitors as probes for neurodegenerative diseases that demonstrated nanomolar activity in vitro and submicromolar activity in cellulo. The more recent implication of POP in cancer, together with homologous fibroblast activation protein α (FAP), implicated in tumor growth, led us to consider developing POP/FAP dual inhibitors as a promising strategy for the development of cancer therapeutics. We report herein docking-guided design of a new bicyclic scaffold and synthesis of both covalent and non-covalent bicyclic inhibitors. Biological evaluation of first-of-their-kind [4.3.0] bicyclic compounds confirmed that reactive groups, or covalent warheads, are required for inhibitor activity. This work ultimately led to a dual inhibitor equipotent to the only anti-POP/FAP drug that ever-reached clinical trials.
|
Nicolas Moitessier; Jessica Plescia; Damien Hedou; Maud Pousse; Anne Labarre; Caroline Dufresne; Anthony Mittermaier
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2021-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6129244a90051e47f3e259be/original/computer-aided-design-synthesis-and-biological-evaluation-of-4-3-0-bicyclic-prolyl-oligopeptidase-and-fibroblast-activation-protein-dual-inhibitors.pdf
|
62a2b940bb751943ab48db01
|
10.26434/chemrxiv-2022-kh1qq
|
Monofluoro-ether electrolyte design with reduced Li+-anion coordination enables fast-charging ultrahigh-voltage lithium metal batteries
|
Ether-based electrolytes are particularly useful for lithium metal batteries (LMBs) and have shown improved anodic stability with the high concentration design. Nevertheless, the vaunted anion-reinforced solvation in concentrated electrolytes has non-negligible adverse effect on ion conduction and battery rate performance. Here, we propose a new solvent design strategy of ether monofluorination to tune the Li+-anion interaction for fast-charging LMBs. With the highly polar monofluoro functional groups, the ether-based electrolyte not only exhibits excellent high oxidation stability due to the strong electron-withdrawing effect of F, but also has a greatly increased ionic conductivity because of reduced anion coordination. The unique solvation structure also enables the formation of robust and highly conductive interphases at both the Li anode and NMC811 surfaces. High Li CEs (~99.4%) and stable long-term cycling with low overpotential under ultrahigh current densities (10 mA cm-2) could be achieved for Li anode. Li||NMC811 cells exhibit outstanding cycling performance under ultrahigh cut-off voltages of 4.6 V and 4.7 V, or at high current densities (5.1 mA cm-2). This work provides critical insights into the ion-solvent interactions in the solvation complex and their profound influence on the battery electrochemical performances.
|
Digen Ruan; Lijiang Tan; Shunqiang Chen; Jiajia Fan; Qingshun Nian; Li Chen; Zihong Wang; Xiaodi Ren
|
Materials Science; Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a2b940bb751943ab48db01/original/monofluoro-ether-electrolyte-design-with-reduced-li-anion-coordination-enables-fast-charging-ultrahigh-voltage-lithium-metal-batteries.pdf
|
6387c4d894ff60d87445e688
|
10.26434/chemrxiv-2022-hcnng
|
Rapid Planning and Analysis of High-Throughput Experiment Arrays for Reaction Discovery
|
High throughput experimentation (HTE) is an increasingly important tool in reaction discovery. While the hardware for running HTE in the chemical laboratory has evolved significantly in recent years, there remains a need for software solutions to navigate data-rich experiments. Here we have developed phactor™, a software that facilitates the performance and analysis of HTE in a chemical laboratory. phactor™ allows experimentalists to rapidly design arrays of chemical reactions or direct-to-biology experiments in 24, 96, 384, or 1,536 wellplates. Users can access online reagent data, such as a chemical inventory, to virtually populate wells with experiments and produce instructions to perform the reaction array manually, or with the assistance of a liquid handling robot. After completion of the reaction array, analytical results can be uploaded for facile evaluation, and to guide the next series of experiments. All chemical data, metadata, and results are stored in machine-readable formats that are readily translatable to various software formats. We also demonstrate the use of phactor™ in the discovery of several chemistries, including a light-enabled reagent-free sp2–sp2 deaminative–decarboxylative carbon–carbon coupling and a low micromolar inhibitor of the SARS-CoV-2 main protease. Furthermore, phactor™ has been made available for free academic use in 24 and 96 well formats via an online interface.
|
Babak Mahjour; Rui Zhang; Yuning Shen; Andrew McGrath; Ruheng Zhao; Osama G. Mohamed; Yingfu Lin; Zirong Zhang; James L. Douthwaite; Ashootosh Tripathi; Tim Cernak
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6387c4d894ff60d87445e688/original/rapid-planning-and-analysis-of-high-throughput-experiment-arrays-for-reaction-discovery.pdf
|
636477e5ecdad55405f9749c
|
10.26434/chemrxiv-2022-zmnmz
|
Distal Mutations in the Beta-clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity
|
DNA polymerases are responsible for the replication and repair of DNA found in all DNA-based organisms. DNA Polymerase III is the main replicative polymerase of E coli and is composed of over 10 proteins. A subset of these proteins (Pol III*) includes the polymerase (alpha), exonuclease (epsilon), clamp (beta) and accessory protein (theta). Mutations of residues in, or around the active site of the catalytic subunits (alpha and epsilon) can have significant impact on catalysis. However, the effects of
distal mutations in non-catalytic subunits on the activity of catalytic subunits are less well characterized. Here, we investigate the effects of two Pol III* variants: beta-L82E/L82'E and beta-L82D/L82'D, on the proofreading reaction catalyzed by epsilon. MD simulations reveal major changes in the dynamics of Pol III*, that extend throughout the complex. These changes are mostly induced by a shift in the position of the DNA substrate inside the beta-clamp, although no major structural changes are observed in the protein complex. QM/MM calculations indicate that the
beta-L82E/L82'D variant has reduced catalytic proficiency due to highly endoergic reaction energies resulting from
structural changes in the active site and differences in the electric field at the active site arising from the protein and substrate. Conversely, the beta-L82E/L82'E variant is predicted to maintain proofreading activity, exhibiting a similar reaction barrier for nucleotide excision compared
with the WT system. However, significant differences in the reaction mechanism are obtained due to the changes induced by the mutations on the beta-clamp.
|
Madison B Berger; G. Andrés Cisneros
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636477e5ecdad55405f9749c/original/distal-mutations-in-the-beta-clamp-of-dna-polymerase-iii-disrupt-dna-orientation-and-affect-exonuclease-activity.pdf
|
678789ca6dde43c908a7138b
|
10.26434/chemrxiv-2024-05299-v2
|
The wins and failures of current docking methods tested on the flexible active site of cytochromes P450
|
In this work, we benchmark 4 selected open source docking engines for use in the cytochrome P450 protein family. The key enzymes family of phase I metabolism is characterized by a wide variety of accepted substrates due to flexible active site. This work is a benchmark study which aims to evaluate the capabilities of current rigid and induced-fit docking methods for prediction of correct heme-ligand orientation. To asses it, we use two unique distances to heme iron and a SuCOS score to quantify reconstruction of orientation and chemical features. We selected three rigid protein docking engines: GNINA, AutoDock VINA, GalaxyDock2 HEME and a flexible docking model, RosettaFold-All-Atoms to test them on a dataset of 128 CYP-binding ligands.
We report mean absolute error for RosetttaFold-All-Atom on key distance, to the atom closest to heme iron in experimental reference structure, 3 times lower than AutoDock VINA engine in the same simulation. Our results indicate that induced fit method is a significant improvement over rigid methods for flexible active site, but still offer limited predictivity. During crossdocking, RosettaFold-All-Atoms was able to recreate over a quarter of distances up to 20 percent difference from experiment. Further analysis indicates a low overlap in the distribution of ligand chemical features, based on a SuCOS score, which suggests a space for further improvement.
|
Dominik Suwała; Eugen Hruška
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678789ca6dde43c908a7138b/original/the-wins-and-failures-of-current-docking-methods-tested-on-the-flexible-active-site-of-cytochromes-p450.pdf
|
61270e70fc08e3dd0882aa17
|
10.26434/chemrxiv-2021-l755t-v2
|
Retrosynthesis Prediction using Grammar-based Neural Machine Translation: An Information-Theoretic Approach
|
Retrosynthetic prediction is one of the main challenges in chemical synthesis because it requires a search over the space of plausible chemical reactions that often results in complex, multi-step, branched synthesis trees for even moderately complex organic reactions. Here, we propose an approach that performs single-step retrosynthesis prediction using SMILES grammar-based representations in a neural machine translation framework. Information-theoretic analyses of such grammar-representations reveal that they are superior to SMILES representations and are better-suited for machine learning tasks due to their underlying redundancy and high information capacity. We report the top-1 prediction accuracy of 43.8% (syntactic validity 95.6%) and maximal fragment (MaxFrag) accuracy of 50.4%. Comparing our model’s performance with previous work that used character-based SMILES representations demonstrate significant reduction in grammatically invalid predictions and improved prediction accuracy. Fewer invalid predictions for both known and unknown reaction class scenarios demonstrate the model’s ability to learn the underlying SMILES grammar efficiently.
|
Vipul Mann; Venkat Venkatasubramanian
|
Theoretical and Computational Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61270e70fc08e3dd0882aa17/original/retrosynthesis-prediction-using-grammar-based-neural-machine-translation-an-information-theoretic-approach.pdf
|
60c74e97bb8c1a40eb3db790
|
10.26434/chemrxiv.12776000.v1
|
Interfacial Electro-Epoxidation in Electrospray Ionization Mass Spectrometry for Simultaneous Analysis of Negatively and Positively Charged Unsaturated Glycerophospholipids
|
In this study, we developed an AC-induced interfacial electro-epoxidation reaction for localization of double-bonds in nega-tively and positively charged forms of lipids simultaneously. An AC voltage plays multiple roles in this method, including initiation of the electrochemical epoxidation of double-bonds in both charge states of lipids, and protonation and deprotona-tion of lipid for detection in both ion modes. The advantages of simultaneous detection of negatively changed and positively charged unsaturated lipids, voltage-controlled electrochemical derivatization, and the low sample consumption allow its wide applications in a broad range of lipid-related research.
|
Shuli Tang; Licheng Fan; Heyong Cheng; Xin Yan
|
Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e97bb8c1a40eb3db790/original/interfacial-electro-epoxidation-in-electrospray-ionization-mass-spectrometry-for-simultaneous-analysis-of-negatively-and-positively-charged-unsaturated-glycerophospholipids.pdf
|
60c73e14f96a000fb9285e70
|
10.26434/chemrxiv.6144413.v2
|
Identification of Key Proteins Involved in Axon Guidance Related Disorders: A Systems Biology Approach
|
<p>Axon
guidance is a crucial process for growth of the central and peripheral nervous
systems. In this study, 3 axon guidance
related disorders, namely- Duane Retraction Syndrome (DRS) , Horizontal Gaze
Palsy with Progressive Scoliosis (HGPPS) and Congenital fibrosis of the
extraocular muscles type 3 (CFEOM3) were studied using various Systems Biology
tools to identify the genes and proteins involved with them to get a better
idea about the underlying molecular mechanisms including the regulatory
mechanisms. Based on the analyses carried out, 7 significant modules have been identified from the PPI
network. Five pathways/processes have been found to be significantly associated
with DRS, HGPPS and CFEOM3 associated genes. From the PPI network, 3 have
been identified as hub proteins- DRD2, UBC and CUL3. </p>
|
Ishtiaque Ahammad
|
Bioinformatics and Computational Biology
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CC BY NC ND 4.0
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CHEMRXIV
|
2018-04-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e14f96a000fb9285e70/original/identification-of-key-proteins-involved-in-axon-guidance-related-disorders-a-systems-biology-approach.pdf
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60c73e15469df4b308f427f0
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10.26434/chemrxiv.6384065.v1
|
Self-Assembly of α-Tocopherol Transfer Protein Nanoparticles – a Patchy-Protein Model
|
<p>We describe the mechanism of self-aggregation of α-tocopherol transfer protein into a spherical nano-cage employing by Monte Carlo simulations. The protein is modelled by a patchy coarse-grained representation, where the protein-protein interfaces, determined in the past by x-ray diffraction, are represented by simplified two-body interaction potentials. Our results show that the oligomerization kinetics proceeds in two steps, with the formation of meta-stable trimeric units, and the subsequent assembly into the spherical aggregates. Data are in agreement with experimental observations regarding the prevalence of different aggregation states at specific ambient conditions. Finally, our results indicate a route for the experimental stabilization of the trimer, crucial for the understanding of the physiological role of such aggregates in vitamin E body trafficking.</p>
|
Raphael
M. Peltzer; Hima Bindu Kolli; Achim Stocker; Michele Cascella
|
Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Self-Assembly
|
CC BY NC ND 4.0
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CHEMRXIV
|
2018-05-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e15469df4b308f427f0/original/self-assembly-of-tocopherol-transfer-protein-nanoparticles-a-patchy-protein-model.pdf
|
6422634291074bccd066d0fe
|
10.26434/chemrxiv-2023-9nv60
|
Electrochemical synthesis of poly(trisulfides)
|
With increasing interest in high sulfur content polymers, there is a need to develop new methods for their synthesis that feature better safety and control of structure. In this report, electrochemically-initiated ring-opening polymerization of norbornene-based cyclic trisulfide monomers delivered well-defined, linear poly(trisulfides), which were solution processable. Electrochemistry provided a controlled initiation step that obviates the need for hazardous chemical initiators. The high temperatures required for inverse vulcanization are also avoided resulting in an improved safety profile. Density functional theory calculations revealed a reversible ‘self-correcting’ mechanism that ensures trisulfide linkages between monomer units. This control over sulfur rank is a new benchmark for high sulfur content polymers and creates opportunities to better understand the effects of sulfur rank on polymer properties. Thermogravimetric analysis coupled with mass spectrometry revealed the ability to recycle the polymer to the cyclic trisulfide monomer by thermal depolymerization. The featured poly(trisulfide) is an effective gold sorbent, with potential applications in mining and electronic waste recycling. A water-soluble poly(trisulfide) containing a carboxylic acid group was also produced and found to be effective in the binding and recovery of copper from aqueous media.
|
Jasmine Pople; Thomas Nicholls; Le Nhan Pham; Witold Bloch; Lynn Lisboa; Michael Perkins; Christopher Gibson; Michelle Coote; Zhongfan Jia; Justin Chalker
|
Physical Chemistry; Organic Chemistry; Polymer Science; Polymerization (Polymers); Electrochemistry - Mechanisms, Theory & Study
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422634291074bccd066d0fe/original/electrochemical-synthesis-of-poly-trisulfides.pdf
|
672a37245a82cea2fa1ebf99
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10.26434/chemrxiv-2024-8gvxg
|
Dissolution-DNP enables the detection of 13C hyperpolarized NMR spectra of Li-ion battery electrolytes
|
Dissolution Dynamic Nuclear Polarization (dDNP) is a powerful hyperpolarization technique enabling sensitivity gains beyond four orders of magnitude in solution nuclear magnetic resonance (NMR). Over the last decades, researchers’ efforts have led to an extension of dDNP applications in fields such as imaging, metabolomics, and drug discovery.
Lithium-ion batteries are one of the most widespread types of rechargeable batteries, which calls for a deeper understanding of the various physicochemical mechanisms involved in making them more efficient, safe, and sustainable. One of the key challenges lies in better understanding and limiting the degradation of the battery electrolyte, which can significantly impact the battery’s performance. While NMR has been used in attempts to understand these mechanisms, notably by investigating the degradation products, the intrinsic lack of sensitivity of this technique, combined with the limited accessible volume of such compounds, makes its application often challenging.
In this work, we combine several state-of-the-art dDNP methodologies to acquire with high sensitivity solution 13C NMR spectra of battery electrolytes. We show that we can successfully detect hyperpolarized 13C signals on formulated battery electrolyte solutions on a 600 MHz spectrometer with sensitivity gains of up to 3 orders of magnitude. This work paves the way for studying lithium-ion battery electrolyte degradation under real usage conditions (cycling, thermal aging, air exposure…) with a 13C detection limit below the micromolar range. This methodology has the potential to provide new insights into degradation mechanisms and the role and effectiveness of additives to mitigate electrolyte degradation.
|
Chloé GIOIOSA; Ekaterina V. Pokochueva; James Tolchard; Charlotte Bocquelet; Mohamed Ayman Ennachet ; Nghia H. Le; Laurent Veyre; Anne Lesage; Ségolène Laage; Simon Pondaven; Sami Jannin
|
Analytical Chemistry; Energy; Analytical Chemistry - General; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a37245a82cea2fa1ebf99/original/dissolution-dnp-enables-the-detection-of-13c-hyperpolarized-nmr-spectra-of-li-ion-battery-electrolytes.pdf
|
6744a5757be152b1d0bc3d0d
|
10.26434/chemrxiv-2024-2c12c
|
Direct Electrochemical Conversion of Carbon Dioxide into Methanol in Water with High Faradaic Efficiency by Mo-Functionalized Electrode
|
We developed a new electrocatalysts for hybrid homogeneous / heterogeneous conversion of CO2 in water. A Molybdenum-based organometallic compound has been linked by covalent C-C bond to a carbon-cloth electrode surface. This technique allows using the Mo catalyst in water, a solvent in which the catalyst is not soluble, for the direct electrocatalytic conversion of CO2 to methanol. Although the system displays moderate current density (1÷4 mA/cm2), the very high faradaic efficiency of the CO2-to-methanol conversion (65%), the good selectivity (H2 is the only other reduction product), the simply experimental setup and the potential industrial scale-up of the technique makes this approach of great interest. Chronoamperometric measurement carried in water for 21 hours show a stable and constant catalytic performance with no other carbon-reduced products. Spectroelectrochemistry and detailed DFT calculations shed light on the catalytic process, which consists of six protons coupled electron transfer (PCET) steps. We propose the catalytic cycle that converts CO to methanol in which the first step is a PCET localized on the CO coordinated to the metal.
|
Carlo Nervi; Alice Barbero; Federico Pezzano; Federico Calderaro; Roberto Gobetto; Chiara Reviglio; Asia Porceddu; Victoria Nikitina; Jian-Feng Li; Hua Zhang; Zhuo Huang; Jia Liu; Artem Oganov
|
Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry; Electrocatalysis; Small Molecule Activation (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6744a5757be152b1d0bc3d0d/original/direct-electrochemical-conversion-of-carbon-dioxide-into-methanol-in-water-with-high-faradaic-efficiency-by-mo-functionalized-electrode.pdf
|
60c74bf6702a9be51118b57d
|
10.26434/chemrxiv.12408839.v1
|
Direct Synthesis of Cyclopropanes from Gem-Dialkyl Groups Through Double C–H Activation
|
Cyclopropanes are important structural motifs found in numerous bioactive molecules, and a number of methods are available for their synthesis. However, one of the simplest cyclopropanation reactions involving the intramolecular coupling of two C–H bonds on <i>gem</i>-dialkyl groups has remained an elusive transformation. We demonstrate herein that this reaction is accessible using aryl bromide or triflate precursors and the 1,4-Pd shift mechanism. The use of pivalate as the base was found to be crucial to divert the mechanistic pathway toward the cyclopropane instead of the previously obtained benzocyclobutene product. Stoichiometric mechanistic studies allowed the identification of aryl- and alkylpalladium pivalates, which are in equilibrium via a five-membered palladacycle. With pivalate, a second C(sp<sup>3</sup>)–H activation leading to the four-membered palladacycle intermediate and the cyclopropane product is favored. A catalytic reaction was developed and showed a broad scope for the generation of diverse arylcyclopropanes, including valuable bicyclo[3.1.0] systems.
|
Antonin Clemenceau; Pierre Thesmar; Maxime Gicquel; Alexandre Le Flohic; Olivier Baudoin
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf6702a9be51118b57d/original/direct-synthesis-of-cyclopropanes-from-gem-dialkyl-groups-through-double-c-h-activation.pdf
|
6215233bdaa4fb604772b158
|
10.26434/chemrxiv-2021-nxvdr-v3
|
Modulating Electronic Properties of Dinitrosoarene Polymers
|
Using the dinitrosobenzene polymer (1) as an example, we explore how the electronic, transport, and optical properties of a conjugated organic semiconductor can be modulated. Combining computational and experimental tools, we explore the effects of solid-state packing, backbone torsion, surface adsorption, the conjugation in the aromatic core, and substituents. The band gap (Eg) and optical spectrum of 1 are calculated using both GW-BSE with zero-gap renormalization (ZGR) and hybrid TD-DFT, with the former method predicting a value (2.41 eV) in excellent agreement with our diffuse reflectance spectroscopy measurements (2.39 eV). Using GW-BSE-ZGR, changes occurring upon solid-state packing are separated into a contribution arising from (i) the change in the torsional angle and (ii) the change in the screened Coulombic interaction, which strongly affects the exciton binding energies. Comprehensive hybrid TD-DFT calculations find that the effects of substituents on Eg and on transport properties can mostly be explained through changes in the torsional angle t, and predict a linear dependence between t and Eg. Extending the conjugation in the aromatic core is found to enhance transport properties and narrow Eg, identifying future synthetic targets. Atomic force microscopy and spectroscopic ellipsometry are used to study 1 adsorbed to a (111) gold surface (1@Au), with the latter method showing a significant narrowing of the band gap to 0.68 eV, in good agreement with TD-DFT predictions.
|
Lujo Matasović; Barbara Panić; Matej Bubaš; Hrvoj Vančik; Ivana Biljan; Igor Rončević
|
Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-02-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6215233bdaa4fb604772b158/original/modulating-electronic-properties-of-dinitrosoarene-polymers.pdf
|
6537d2ebc3693ca99304382e
|
10.26434/chemrxiv-2023-80vjz-v2
|
Photochemically driven peptide formation in supersaturated aerosol droplets
|
The condensation of amino acids into peptides plays a crucial role in protein synthesis and is thus essential for understanding the origins of life. However, the spontaneous formation of peptides from amino acids in bulk aqueous media is energetically unfavorable, posing a challenge for elucidating plausible abiotic mechanisms. In this study, we investigate the formation of amide bonds between amino acids within highly supersaturated aerosol droplets containing dicyandiamide (DCD), a cyanide derivative potentially present on primordial Earth. Metastable states, i.e. supersaturation, within individual micron-sized droplets are studied using both an optical trap and a linear quadrupole electrodynamic balance. When irradiated with intense visible light, amide bond formation is observed to occur and can be monitored using vibrational bands in Raman spectra. The reaction rate is found to be strongly influenced by droplet size and kinetic modelling suggests that it is driven by the photochemical product of a DCD self-reaction. Our results highlight the potential of atmospheric aerosol particles as reaction environments for peptide synthesis and have potential implications for the prebiotic chemistry of early Earth.
|
Alexander Logozzo; Benjamin Vennes; Ravleen Kaur Kohli; James Davies; Durbis Castillo-Pazos; Chao-Jun Li; Catherine Neish; Thomas Preston
|
Physical Chemistry; Organic Chemistry; Earth, Space, and Environmental Chemistry; Physical Organic Chemistry; Atmospheric Chemistry; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6537d2ebc3693ca99304382e/original/photochemically-driven-peptide-formation-in-supersaturated-aerosol-droplets.pdf
|
60c745cf567dfe4e4aec4512
|
10.26434/chemrxiv.10266635.v1
|
Molar Volume Mismatch: A Malefactor for Irregular Metallic Electrodeposition in Solid Electrolytes
|
Regularizing metallic electrodeposition has been a long-standing challenge in energy storage. Leveraging mechanical stresses, solid ion conductors have been proposed to stabilize the evolving interface. Paradoxically softer electrodepositing metals are often found to form penetration fronts under the hypothesized stable conditions. We find that mechanical contributions to energy of the interacting species (i.e., metal and cation) relate to respective molar volumes. The stresses at the electrodepositing interface are correlated, and consequently, localized deposition is energetically favored for larger cationic molar volumes. Electrolyte stresses cause a stress-driven ionic flux away from compressed locations, which proves to be a stabilizing influence. Stability is found to be nonlinearly related to electrolyte stiffness. Material complexities such as interphases, interlayer, and grain boundaries are also examined to proffer guidelines for a stabilized growth.
|
Aashutosh Mistry; Partha P. Mukherjee
|
Ceramics; Elastic Materials; Theory - Computational; Energy Storage; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Physical and Chemical Properties; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745cf567dfe4e4aec4512/original/molar-volume-mismatch-a-malefactor-for-irregular-metallic-electrodeposition-in-solid-electrolytes.pdf
|
67b70afc6dde43c908b07f20
|
10.26434/chemrxiv-2024-8tqvn-v3
|
Stabilization of the Ferryl=oxoheme Form of Staphylococcus aureus IsdG by Electron Transfer from a Second-Sphere Tryptophan
|
The ferryl heme forms of Staphylococcus aureus IsdG and IsdI have novel UV/Vis absorption spectra that are distinct from those of the three forms of ferryl heme typically found in biological systems: compound I, compound II, and com-pound ES. In this work, the ferryl heme form of IsdG was characterized because it is an analogue for the immediate product of enzyme-catalyzed heme hydroxylation. The ferryl heme form of IsdG generated following the addition of meta-chloroperoxybenzoic acid to the ferric heme form of IsdG has a half-life of 4.0 ± 0.2 min, which is more than 100 times longer than the half-life for the ferryl heme form of human heme oxygenase (hHO). Magnetic circular dichroism characterization of the IsdG species yielded spectral data and zero-field splitting parameters consistent with either a compound II- or compound ES-like ferryl heme. Further characterization of isotopically-enriched samples with elec-tron paramagnetic resonance spectroscopy revealed the presence of a protein-based organic radical, as would be ex-pected for compound ES. Finally, multi-scale quantum mechanics / molecular mechanics and time-dependent density functional theory strongly suggest that the ferryl heme form of IsdG has a ruffled porphyrin ligand and an oxo ligand. Thus, the ferryl heme form of IsdG is assigned to a compound ES-like species with a Trp67-based radical. Electron transfer from Trp67 to porphyrin will stabilize the immediate product of heme hydroxylation and provide a thermodynamic driving force for the reaction. Furthermore, the ability to transfer an electron between Trp67 and the substrate may explain the differential reactivity of meso-hydroxyheme in IsdG and hHO.
|
Aarzoo Grover; Matthew A Conger; Matthew D Liptak
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b70afc6dde43c908b07f20/original/stabilization-of-the-ferryl-oxoheme-form-of-staphylococcus-aureus-isd-g-by-electron-transfer-from-a-second-sphere-tryptophan.pdf
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6615f53e91aefa6ce1385fc2
|
10.26434/chemrxiv-2024-85rxf-v2
|
A General Nitrene Transfer to Sulfides Enabled by Visible-Light-Mediated Triplet Energy Transfer to Sulfonyl Azides
|
Sulfilimines and their derivatives have garnered considerable interest in both synthetic and medicinal chemistry. Photochemical nitrene transfer to sulfides is known as a conventional synthetic approach to sulfilimines. However, the existing methods have a limited substrate scope stemming from the incompatibility of singlet nitrene intermediates with nucleophilic functional groups. Herein, we report a general nitrene transfer for the synthesis of N-sulfonyl sulfilimines enabled by visible-light-mediated energy transfer to sulfonyl azides, uncovering the neglected reactivity of triplet nitrenes with sulfides. The unprecedented mechanism involving single electron transfer enabled broad functional group tolerance, water compatibility, and amenability to use for the late-stage functionalization of drugs.
|
Norihito Arichi; Tsuyoshi Amano; Shuhan Wu; Shinsuke Inuki; Hiroaki Ohno
|
Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615f53e91aefa6ce1385fc2/original/a-general-nitrene-transfer-to-sulfides-enabled-by-visible-light-mediated-triplet-energy-transfer-to-sulfonyl-azides.pdf
|
62ec75e93b834e8e78e55ff9
|
10.26434/chemrxiv-2022-62zdk
|
Accelerated Short Circuiting in Anode-Free Solid-State Batteries Driven by Local Lithium Depletion
|
“Anode-free” solid-state batteries (SSBs), which have no active material at the anode and undergo in situ lithium plating during the first charge, can exhibit extremely high energy density (~1500 Wh L-1). However, there is a lack of understanding of lithium plating/stripping mechanisms at bare solid-state electrolyte (SSE) interfaces since excess lithium is often used. Here, we demonstrate that commercially relevant quantities of lithium (> 5 mAh cm-2) can be reliably plated at relatively high current densities (1 mA cm-2) using the sulfide SSE Li6PS5Cl. Investigations of lithium plating/stripping mechanisms, in conjunction with cryo-focused ion beam (FIB) and ex situ synchrotron tomography, reveal that the cycling stability of these cells is intrinsically limited by spatially uneven plating/stripping. Local lithium depletion toward the end of stripping decreases electrochemically active area, which results in high local current densities and void formation, accelerating subsequent filament growth and short circuiting compared to lithium-excess cells. Despite this governing degradation mode, we show that anode-free cells exhibit comparable Coulombic efficiencies to lithium-excess cells before short circuiting, and improved resistance to short-circuiting is achieved by avoiding local lithium depletion through retention of lithium at the interface. These new insights provide a foundation for engineering future high-energy anode-free SSBs.
|
John Lewis; Stephanie Sandoval; Yuhgene Liu; Douglas Nelson; Sun Geun Yoon; Mengkun Tian; Pavel Shevchenko; Matthew McDowell
|
Materials Science; Energy; Energy Storage
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-08-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec75e93b834e8e78e55ff9/original/accelerated-short-circuiting-in-anode-free-solid-state-batteries-driven-by-local-lithium-depletion.pdf
|
6626e07591aefa6ce1210b7c
|
10.26434/chemrxiv-2024-26mkp
|
Short catalytic peptides with tunable activity: Cys confers functionality and adaptability
|
This study explores the catalytic potential of short peptides containing Cys, a potent nucleophile, able to hydrolyze a variety of ester substrates, including p-NPP and ATP, while enabling control and direction of catalytic activity through thiol oxidation. We identified Ac-CTLGLGSHCGG-Am (CG11), as a potential tunable catalyst capable of hydrolyzing ester and phosphoester substrates. We synthesized multiple analogues with varying sequence compositions and lengths and determined the effect of these changes on the catalytic efficiency. We showed that cyclization through disulfide bridge formation offered tunability and reversibility, while head-to-side chain cyclization conferred excellent resistance to proteases. Additionally, we demonstrated the ability of inactive cy-CG11 to undergo reduction and ring opening to its linear functional form in a physiological setting, specifically in the presence of elevated glutathione levels. These findings provide valuable insights for fine-tuning the characteristics of peptide-based catalysts and pave the way to their potential applicability in a biological context such as targeting glutathione disbalance and providing phosphatase activity.
|
Patrizia Janković; Daniela Kalafatovic
|
Biological and Medicinal Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Biocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6626e07591aefa6ce1210b7c/original/short-catalytic-peptides-with-tunable-activity-cys-confers-functionality-and-adaptability.pdf
|
667de5805101a2ffa8be1193
|
10.26434/chemrxiv-2024-6xnfk
|
Spectroelectrochemical studies of TDMQ20: a potential drug against Alzheimer’s Disease
|
Alzheimer's Disease (AD), reported for the first time in 1906, is a common disease that remains incurable to this day. In the past, a family of treatments using Cu(II) chelators failed during clinical trials, evidencing the importance of pre-clinical studies. In this work, we performed a complete characterisation of TDMQ20, a new potential drug against AD, using electrochemistry and spectroelectrochemistry. On the basis of voltammetry, we determined that TDMQ20 undergoes a two-step irreversible oxidation process and a one-step irreversible reduction process. Both oxidation and reduction reactions are pH-sensitive. Bidimensional UV-Vis spectroelectrochemistry (UV-Vis-SEC) allowed us to confirm that oxidation of TDMQ20 can occur both on the aliphatic chain and on the aromatic ring. The results expand the knowledge of the TDMQ20 redox activity in the human body which is important from the point of view of the toxicity of the proposed therapy.
|
Magdalena Wiloch; Martin Perez-Estebanez; Natalia Baran; Aranzazu Heras; Martin Jönsson-Niedziółka; Alvaro Colina
|
Physical Chemistry; Inorganic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Inorg.); Electrochemistry - Mechanisms, Theory & Study
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667de5805101a2ffa8be1193/original/spectroelectrochemical-studies-of-tdmq20-a-potential-drug-against-alzheimer-s-disease.pdf
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617be48e7a002113943eb032
|
10.26434/chemrxiv-2021-726hl
|
Immobilized cellulose nanospheres in lateral flow immunoassay enable rapid nucleocapsid antigen-based diagnosis of SARS-CoV-2 from salivary samples
|
Rapid and efficient diagnostic systems are essential in controlling the spread of viral pathogens and efficient patient management. The available technologies for low-cost viral antigen testing have several limitations, including lack of accuracy and sensitivity. Here, we develop sensitive antigen tests based on recently introduced, oppositely charged cellulose II nanoparticles (NPan and NPcat) that are effective in controlling surface protein interactions. Passivation against non-specific adsorption and augmented immobilization of sensing antibodies are achieved by adjusting the electrostatic charge of the nanoparticles. The interactions affecting the performance of the system are investigated by microgravimetry and confocal imaging. We further demonstrate SARS-CoV-2 nucleocapsid rapid sensing by saliva-wicking channels stencil-printed on flexible paper supports. Therein, NPcat inkjet printed on the channels elicit distinctive optical signals, visible after only a few minutes, allowing faster diagnosis compared to current microfluidic devices designed for saliva sampling.
|
Katariina Solin; Marco Beaumont; Maryam Borghei; Hannes Orelma; Pascal Mertens; Orlando J. Rojas
|
Biological and Medicinal Chemistry; Materials Science; Nanostructured Materials - Materials; Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617be48e7a002113943eb032/original/immobilized-cellulose-nanospheres-in-lateral-flow-immunoassay-enable-rapid-nucleocapsid-antigen-based-diagnosis-of-sars-co-v-2-from-salivary-samples.pdf
|
60c74b250f50db9652396bac
|
10.26434/chemrxiv.12281078.v1
|
In Silico Exploration of Repurposing and Optimizing Traditional Chinese Medicine Rutin for Possibly Inhibiting SARS-CoV-2's Main Protease
|
<div>Coronavirus disease 2019 (COVID-19) is an ongoing global pandemic with very limited specific treatments. To fight COVID-19, various traditional antiviral medicines haveb been prescribed in China to infected patients with mild to moderate symptoms and received unexpected success in controlling the disease. However, the molecular mechanisms of how these herbal medicines interact with the virus have remained elusive. It is well known that the main protease (Mpro) of SARS-CoV-2 plays an important role in maturation of many viral proteins such as the RNA-dependent RNA polymerase. Here,we explore the underlying molecular mechanisms of the computationally determined top candidate–rutin, a key component in many traditional antiviral medicines such as Lianhuaqinwen and Shuanghuanlian, for inhibiting the viral target–Mpro. Using in silico methods (docking and molecular dynamics simulations), we revealed the dynamics and energetics of rutin when interacting with the Mpro of SARS-CoV-2, suggesting that the highly hydrophilic rutin molecule can be bound inside the Mpro’ pocket (active site) and possibly inhibit its biological functions. In addition, we optimized the structure of rutin and designed a more hydrophobic analog which satisfies the rule of five for western medicines and demonstrated that it possesses a much stronger binding affinity to the SARS-COV-2’s Mpro.<br /></div>
|
Tien Huynh; Haoran Wang; Wendy Cornell; Binquan Luan
|
Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b250f50db9652396bac/original/in-silico-exploration-of-repurposing-and-optimizing-traditional-chinese-medicine-rutin-for-possibly-inhibiting-sars-co-v-2-s-main-protease.pdf
|
63244fdf0e3c6a824b1cfda8
|
10.26434/chemrxiv-2022-jcdpn
|
Heterogenized Molecular Rhodium Phosphine Catalyst within Metal-Organic Framework for Ethylene Hydroformylation
|
Molecularly-defined organometallic rhodium phosphine complexes were efficiently heterogenized within a MOF structure without affecting neither their molecular nature nor their catalytic behavior. Phosphine-functionalized MOF-808 served as solid ligand in a series of eight rhodium phosphine catalysts. These MOF-heterogenized molecular catalysts showed activity up to 2100 h-1 for ethylene hydroformylation towards pro-pionaldehyde as sole carbon-containing product. Combined experimental and computational methods applied to this unique MOF-based molecular system allowed unravelling structure and evolution of the Rh active species within the MOF under catalytic conditions, in line with molecular mechanisms at play during the hydroformylation reaction. The MOF-808 designed as a porous crystalline macroligand for well-defined molecular catalysts allows benefiting from molecular-scale understanding of interactions and mechanisms as well as from stabilization through site-isolation and recycling ability.
|
Partha Samanta; Albert Solé-Daura; Remy Rajapaksha; Florian M. Wisser; Frederic Meunier; Yves Schuurman; Capucine Sassoye; Caroline Mellot-Draznieks; Jerome Canivet
|
Materials Science; Catalysis; Organometallic Chemistry; Hybrid Organic-Inorganic Materials; Heterogeneous Catalysis; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63244fdf0e3c6a824b1cfda8/original/heterogenized-molecular-rhodium-phosphine-catalyst-within-metal-organic-framework-for-ethylene-hydroformylation.pdf
|
60c7453dee301c4b17c7929a
|
10.26434/chemrxiv.8792177.v4
|
Rapid Online Buffer Exchange: A Method for Screening of Proteins, Protein Complexes, and Cell Lysates by Native Mass Spectrometry
|
It is important to assess the identity and purity of proteins and protein complexes during and after protein purification to ensure that samples are of sufficient quality for further biochemical and structural characterization, as well as for use in consumer products, chemical processes, and therapeutics. Native mass spectrometry (nMS) has become an important tool in protein analysis due to its ability to retain non-covalent interactions during measurements, making it possible to obtain protein structural information with high sensitivity and at high speed. Interferences from the presence of non-volatiles are typically alleviated by offline buffer exchange, which is timeconsuming and difficult to automate. We provide a protocol for rapid online buffer exchange (OBE) nMS to directly screen structural features of pre-purified proteins, protein complexes, or clarified cell lysates. Information obtained by OBE nMS can be used for fast (<5 min) quality control and can further guide protein expression and purification optimization.
|
Zachary VanAernum; Florian Busch; Benjamin J. Jones; Mengxuan Jia; Zibo Chen; Scott E. Boyken; Aniruddha Sahasrabuddhe; David Baker; Vicki Wysocki
|
Biochemical Analysis; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7453dee301c4b17c7929a/original/rapid-online-buffer-exchange-a-method-for-screening-of-proteins-protein-complexes-and-cell-lysates-by-native-mass-spectrometry.pdf
|
6206de03a6fb4d3b3152d363
|
10.26434/chemrxiv-2022-j78kp
|
Synthesis and styrene copolymerization of dimethyl, dimethoxy, and halogen ring-substituted isopropyl cyanophenylacrylates
|
Novel trisubstituted ethylenes, dimethyl, dimethoxy, and halogen ring-substituted isopropyl cyanophenylacrylates, RPhCH=C(CN)CO2CH(CH3)2 (where R is 2,3-dimethyl, 2,4-dimethyl, 2,5-dimethyl, 2,6-dimethyl, 3,4-dimethyl, 3,5-dimethyl, 2,3-dimethoxy, 2,4-dimethoxy, 2,5-dimethoxy, 2-Br, 3-Br, 4-Br, 2-Cl, 3-Cl, 4-Cl, 2-F, 3-F, 4-F) were prepared and copolymerized with styrene. The monomers were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and isopropyl cyanoacetate and characterized by CHN elemental analysis, IR, 1H- and 13C-NMR. All the ethylenes were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The composition of the copolymers was calculated from nitrogen analysis, and the structures were analyzed by IR, 1H and 13C-NMR, GPC, DSC, and TGA. Decomposition of the copolymers in nitrogen occurred in two steps, first in the 219-500C range with residue (0.9-5.6 % wt), which then decomposed in the 500-800ºC range.
|
Charles M. Rubert Pérez; Rachel L. Pride; Benjamin Y. Killam; Sara Rocus; William Schjerven; Gregory Kharas
|
Organic Chemistry; Polymer Science
|
CC BY 4.0
|
CHEMRXIV
|
2022-02-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6206de03a6fb4d3b3152d363/original/synthesis-and-styrene-copolymerization-of-dimethyl-dimethoxy-and-halogen-ring-substituted-isopropyl-cyanophenylacrylates.pdf
|
6183dec792abe0f24734a106
|
10.26434/chemrxiv-2021-nvcx9
|
Organic Photovoltaic Efficiency Predictor: Data-Driven Predictions of Power Conversion Efficiencies of Non-Fullerene Acceptor Organic Solar Cells
|
In the fabrication of organic solar cells, there has been a need for materials with high power conversion efficiencies (PCE). Scharber’s model is commonly used to predict efficiency, however it exhibits poor performance with new non-fullerene acceptor (NFA) devices (RMSE=2.53%). In this work, an empirical model is proposed that can be a more accurate alternative for NFA organic solar cells. Additionally, many screening studies use computationally expensive methods. A model based on using the semi-empirical simplified time-dependent density functional theory (sTD-DFT) as an alternative method can accelerate the calculations and yields similar accuracy. The models presented in this paper, referred to as Organic Photovoltaic Efficiency Predictor (OPEP) models, have shown significantly lower errors than previous models, with OPEP/B3LYP yielding errors of 1.53% and OPEP/sTD-DFT of 1.55%. The proposed computational models can be utilized for fast and accurate screening of new high-efficiency NFAs and donor polymer pairs.
|
Brianna Greenstein; Geoffrey Hutchison
|
Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Photovoltaics; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-11-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6183dec792abe0f24734a106/original/organic-photovoltaic-efficiency-predictor-data-driven-predictions-of-power-conversion-efficiencies-of-non-fullerene-acceptor-organic-solar-cells.pdf
|
633472d9f764e619950683c3
|
10.26434/chemrxiv-2022-mkw1d-v2
|
Absolute Binding Free Energy Calculations for Buried Water Molecules
|
Water often plays a key role in mediating protein-ligand interactions. Understanding contributions from active-site water molecules to binding thermodynamics of a ligand is important in predicting binding free energies for ligand optimization. In this work, we tested a nonequilibrium switching method for absolute binding free energy calculations on water molecules in binding sites of 13 systems. We discuss the lessons we learned about identified issues that affected our calculations and ways to address them. This work fits with our larger focus on how to do accurate ligand binding free energy calculations when water rearrangements are very slow, such as rearrangements due to ligand modification (as in relative free energy calculations) or ligand binding (as in absolute free energy calculations). The method studied in this work can potentially be used to account for limited water sampling via providing endpoint corrections to free energy calculations using our calculated binding free energy of water.
|
Yunhui Ge; Hannah Baumann; David Mobley
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633472d9f764e619950683c3/original/absolute-binding-free-energy-calculations-for-buried-water-molecules.pdf
|
60c74893bdbb896136a38fe2
|
10.26434/chemrxiv.11927283.v1
|
Short-Chained Anthracene Strapped Porphyrins and Their Endoperoxides
|
The synthesis of short-chained anthracene-strapped porphyrins and their Zn(II)complexes are reported. The key synthetic step employed was a [2+2] condensation between a dipyrromethane and 2,2'-((anthracene-9,10-diylbis(methylene))bis(oxy))dibenzaldehyde. Following exposure to polychromatic light, self-sensitized singlet oxygen and the anthracene moieties underwent [4+2] cycloaddition reactions to yield the corresponding endoperoxides. 1H NMR studies demonstrate that the endoperoxide readily formed in chloroform-d and decayed at 85 °C. X-ray crystallography and absorption spectroscopy were used to confirm macrocyclic distortion in the parent strapped porphyrins and endoperoxides. Additionally, X-ray crystallography indicated that endoperoxide formation occurred exclusively on the outside face of the anthracene moiety.<br />
|
Susan Callaghan; Keith Flanagan; John E. O'Brien; Mathias O.. Senge
|
Photochemistry (Org.); Physical Organic Chemistry; Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74893bdbb896136a38fe2/original/short-chained-anthracene-strapped-porphyrins-and-their-endoperoxides.pdf
|
60c74bf90f50db1c7a396d5f
|
10.26434/chemrxiv.12408905.v1
|
Kinetic Modeling of Ammonia Decomposition at CVD Conditions
|
Kinetic modeling has been used to study the decomposition chemistry of ammonia at a wide range of temperatures, pressures, concentrations, and carrier gases mimicking the conditions in chemical vapor deposition (CVD) of metal nitrides. The modeling show that only a small fraction of the ammonia molecules will decompose at most conditions studied. This suggests that the high NH<sub>3</sub> to metal ratios often employed in CVD is due to the very low amount of reactive decomposition products rather than due to rapid decomposition of ammonia into stable dinitrogen and dihydrogen as suggested by purely thermodynamic models.
|
Karl Rönnby; Henrik Pedersen; Lars Ojamäe
|
Coating Materials; Main Group Chemistry (Inorg.); Chemical Kinetics; Physical and Chemical Processes; Thermodynamics (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2020-06-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bf90f50db1c7a396d5f/original/kinetic-modeling-of-ammonia-decomposition-at-cvd-conditions.pdf
|
671ca3911fb27ce124a46cf5
|
10.26434/chemrxiv-2024-j4hcs
|
Solid electrolyte interphase (SEI) triggered electrochemical hydrogenation of nitrobenzene with an undivided cell
|
The hydrogenation of nitrobenzene is a vital route to obtain industrially valuable aniline. Strategies have been developed to accomplish this transformation sustainably and efficiently corresponding to the green requirement of modern chemistry. The study explores an electrochemical protocol to obtain the expected product in an undivided cell without loading heterogeneous catalysts on electrodes. An additive, tripyrolidinophosphine (TPPA), forming a solid electrolyte interphase (SEI), inspired by a lithium battery technology, triggers this reaction that would otherwise not occur in a LiBr/THF system. δ-valerolactam (2-piperidone), a unique hydrogen donor, provides the H species and elevates the aniline selectivity to 75.48%. Two reductive paths are discovered existing in this system where aniline is produced from both the direct hydrogenation of phenylhydroxylamine and the indirect hydrolysis of azobenzene. Gram scale reactions are performed under batch and flow conditions, respectively, to make this protocol applicable in practice.
|
Shenghao Pan; Jianguo Liu
|
Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ca3911fb27ce124a46cf5/original/solid-electrolyte-interphase-sei-triggered-electrochemical-hydrogenation-of-nitrobenzene-with-an-undivided-cell.pdf
|
673630c2f9980725cf342e4d
|
10.26434/chemrxiv-2024-g9pt8-v3
|
Understanding the Finite Size and Surface Relaxation Effects on the Surface States of Bi2Se3 Family Topological Insulators
|
Topological insulators (TIs) of the Bi2Se3 family exhibit topological phase transition from three dimensional (3D) to two dimensional (2D) TIs in thin films with decreasing thickness. Understanding the driving force of this transition is critical for the applications of TIs in nanodevices. Herein, we investigate the finite-size effects on the bulk band inversion and the structural relaxation effects on the surface states within the Bi2Se3 family via first-principles calculations. Thin films exposing the three lowest-energy surfaces are modeled by 2D slabs with tunable thicknesses. We propose that the thickness dependence of the topological phase originates from electron confinement created by surface cuts. The increase in film thickness then counteracts these confinement effects, resulting in a monotonically decreasing band gap evaluated at the spin−orbit decoupled level. This dependence of the bulk gap on the thickness is found consistent for various surface slabs. We utilize this relationship to predict the required thickness for maintaining the 3D TI phase and 2D surface states. Our findings underscore the importance of electron delocalization in determining the topological phase of TI thin films. In addition, the actual manifestation of topological surface states on the side surfaces is affected significantly by the co-existing dangling bonds produced by surface cuts. Therefore, surface relaxation plays a crucial role in disentangling the trivial and nontrivial surface states.
|
Guorong Weng; Anastassia N. Alexandrova
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Surface; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673630c2f9980725cf342e4d/original/understanding-the-finite-size-and-surface-relaxation-effects-on-the-surface-states-of-bi2se3-family-topological-insulators.pdf
|
66ade7a35101a2ffa8fde7be
|
10.26434/chemrxiv-2024-5pp4t
|
Catalytic synthesis of one-dimensional nanomaterials in seconds
|
Rapid Joule heating (RJH) has shown its great power and rapid development in the synthesis of nanomaterials due to its simple procedure and extremely high reaction speed and energy efficiency. However, the morphology and structure controllable RJH preparation, for instance, the synthesis of one-dimensional (1D) nanomaterials, is still challenging. Inspired by the widely recognized vapor-liquid-solid (VLS) mechanism in many high temperature synthesis pathways, we develop a catalyzed RJH route for the synthesis of 1D nanomaterials. By introducing suitable metal catalysts, nanowires of refractory carbides, high entropy carbides, II-VI and III-V group semiconductors, as well as multi-walled and single-walled carbon nanotubes are catalytic grown in seconds. With a general applicability to various material types, a short synthesis time and a low energy consumption of kilojoules per gram of nanomaterials, this strategy presents great potential in material synthesis and production.
|
Jian Sheng; Yifan Xu; Zhen Han; Xinrui Zhang; Hai-Gang Lu; Sidian Li; Yan Li
|
Nanoscience; Nanofabrication; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ade7a35101a2ffa8fde7be/original/catalytic-synthesis-of-one-dimensional-nanomaterials-in-seconds.pdf
|
60c7422b567dfe6f56ec3f03
|
10.26434/chemrxiv.8233460.v1
|
Controlling Molecular Weight Distributions Through the Mixing of Low Dispersity Polymer Samples: A Predictive Framework
|
<div>The physical properties of polymer samples are dependent on the overall shape and breadth of the molecular weight distribution (MWD). A small number of methods are available to tune the shape and characteristics of MWDs based on influencing controlled radical polymerizations and on mixing of individual distributions. However, no systematic framework exists to date to predict the characteristics and shapes of artificial MWDs prior the experiments. In this work we present such framework based on interpolation of individual distributions.</div>
|
Maarten Rubens; Tanja Junkers
|
Polymerization (Polymers); Computational Chemistry and Modeling; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422b567dfe6f56ec3f03/original/controlling-molecular-weight-distributions-through-the-mixing-of-low-dispersity-polymer-samples-a-predictive-framework.pdf
|
652cfa658bab5d205573bd37
|
10.26434/chemrxiv-2023-ph1mf
|
A COMPARATIVE STUDY ON THE EFFECTS OF Camellia sinensis EXTRACT AND SALICYLIC ACID TOPICAL FORMULATION ON SELECTED STUDENTS WITH ACNE VULGARIS
|
This research work was carried out to determine the effect and extent of activity of Camellia sinensis and Salicylic acid in the treatment of Acne vulgaris. In the present study, the bioactive compounds of leaves extract of Camellia sinensis were extracted using distilled water and formulated into a serum for topical appliciation. Salicylic acid was also formulated into a gel based cream for topical application and the effect on Acne investigated in the course of two weeks. This involves a longitudinal, open-label and randomized treatment study to determine between the camellia sinensis extract gel based cream and salicylic acid gel based cream which has the highest efficacy against Acne vulgaris.
The Camellia sinensis gel based cream was found to be effective in the treatment of certain types of Acne vulgaris . The salicylic acid gel based cream (standard) was also found to be effective in all types of acne. The effect of Salicylic acid on various forms of acne as presented on test subjects of Group A didn’t peak until the second week, with visible reduction in blackheads (open comedones). Where as that of Camellia sinensis peaked in the first week of treatment, there was little to no reduction in black heads but there was visible reduction in pore size which indicates that there may be preventive properties of Camellia sinensis against the formation of acne. Subjects put on Camellia sinensis experienced no adverse effect while some experienced slight tinging, dryness and irritation while using salicylic acid.
Based on this study, the treatment which showed faster results within the short period allocated to the study shows promising use as a standard form of treatment for acne vulgaris as compared to Salicylic acid because no adverse effect was experienced with camellia sinensis.
|
Onyeka Asumah; Nathan Oparaeche
|
Biological and Medicinal Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652cfa658bab5d205573bd37/original/a-comparative-study-on-the-effects-of-camellia-sinensis-extract-and-salicylic-acid-topical-formulation-on-selected-students-with-acne-vulgaris.pdf
|
60c749d19abda20bc2f8ccea
|
10.26434/chemrxiv.12111309.v1
|
Synthesis of Quaternary -Amino Esters: A Remarkably Broad Substrate Scope in Aza-Friedel−Crafts Alkylation
|
A versatile synthetic protocol of aza-Friedel−Crafts alkylation
has been developed for the synthesis of quaternary a-amino
esters. This operationally simple alkylation proceeds under ambient conditions
with high efficiency, regioselectivity, and an exceptionally broad scope of
arene nucleophiles. A key feature of this alkylation is the role associated
with the silver(I) salt counteranions liberated during the reaction. Taking
advantage of a phase-transfer counteranion/BrØnsted acid pair mechanism,
a catalytic enantioselective version of the reaction is also reported.
|
Stephane Roche; Guangkuan zhao; Shyam Samanta; Jessica Michieletto
|
Organic Synthesis and Reactions; Stereochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d19abda20bc2f8ccea/original/synthesis-of-quaternary-amino-esters-a-remarkably-broad-substrate-scope-in-aza-friedel-crafts-alkylation.pdf
|
656c34ab29a13c4d478b2a12
|
10.26434/chemrxiv-2023-05v1b-v2
|
Automatic extraction of FAIR data from publications using LLM
|
Since the beginning of modern science, researchers have used a specific format to communicate their findings in a standardized language. Such formats help to ensure that results can be replicated and published. With the rise of digitalization, artificial intelligence has become increasingly important in combination with the scientific literature sources of data. This synergy serves as a foundation of robust models following central principles of FAIR (Findable, Accessible, Interoperable, Reusable) data. By having access to more precise data, it is reasonable to anticipate the development of improved models. Specifically, large neural networks have demonstrated a high level of responsiveness to the quality of the data used. Therefore, enhancing the data quality can potentially lead to a reduction in the size of neural networks. Large Language Models (LLMs) have proven to be incredibly effective at replicating human tasks. This is a significant improvement that not only automatizes process but also leads to better results. By combining human and LLM assistance, we can produce higher-quality content and solve repetitive tasks that would otherwise take years to complete. Those generative AI assistants can follow instructions to transform and extrapolate existing text. Our contribution outlines a method for automatically extracting experimental data of molecules from literature. Essentially by our prompt engineering, we demonstrate that this process can be made more cost-effective. Secondly, we use automated fact checking principles to ensure the original data quality as well as the data retrieval by LLM. Ultimately, our aim is to provide guidance for the publication of organic chemical experimental data to assist researchers and enhance FAIR data.
|
Luc Patiny; Guillaume Godin
|
Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656c34ab29a13c4d478b2a12/original/automatic-extraction-of-fair-data-from-publications-using-llm.pdf
|
60c741eb842e6508bedb1fae
|
10.26434/chemrxiv.8191190.v1
|
If You Cannot Win Them, Join Them: Understanding New Ways to Target STAT3 by Small Molecules
|
<p>Signal transducer activator of transcription 3 (STAT3) is among the most investigated oncogenic transcription factors, as it is highly associated with cancer initiation, progression, metastasis, chemoresistance, and immune evasion. The recent evidence from both preclinical and clinical studies have demonstrated that STAT3 plays a critical role in several malignancies associated with poor prognosis such as glioblastoma and triple-negative breast cancer (TNBC), and STAT3 inhibitors have shown efficacy in inhibiting cancer growth and metastasis. Constitutive activation of STAT3 by mutations occurs frequently in tumour cells, and directly contributes to many malignant phenotypes. Unfortunately, detailed structural biology studies on STAT3 as well as target-based drug discovery efforts have been hampered by difficulties in the expression and purification of the full length STAT3 and a lack of ligand-bound crystal structures.</p><p>Considering these, molecular modelling and simulations offer an attractive strategy for the assessment of “druggability” of STAT3 dimers and allow investigations of reported activating and inhibiting STAT3 mutants at the atomistic level of detail. In the present study, we focused on the effects exerted by reported STAT3 mutations on the protein structure, dynamics, DNA binding and dimerisation, thus linking structure, dynamics, energetics, and the biological function. By employing atomistic molecular dynamics (MD) and umbrella sampling (US) simulations to a series of human STAT3 dimer, which comprised wild-type protein and four mutations; we explained the modulation of STAT3 activity by these mutations. Counter-intuitively, our results show that D570K inhibitory mutation exerts its effect by enhancing rather than weakening STAT3-DNA interactions, which interferes with the DNA release by the protein dimer and thus inhibits STAT3 function as a transcription factor. We mapped the binding site and characterised the binding mode of a clinical candidate napabucasin/BBI-608 at STAT3, which resembles the effect of D570K mutation. We also discovered a novel binding site at STAT3 DNA binding domain, amenable to bind small molecule ligands.</p><p>Our results contribute to understanding the activation/inhibition mechanism of STAT3, to explain the molecular mechanism of STAT3 inhibition by napabucasin/BBI-608. In this study, alongside the characterisation of the BBI-608 binding mode, we mapped a novel binding sites amenable to bind small molecule ligands, which may pave the way to design novel STAT3 inhibitors and to suggest new strategies for pharmacological intervention to combat cancers associated with poor prognosis.</p>
|
Francesc Sabanés; Joao Victor de Souza Cunha; Roger Estrada-Tejedor; Agnieszka K Bronowska
|
Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741eb842e6508bedb1fae/original/if-you-cannot-win-them-join-them-understanding-new-ways-to-target-stat3-by-small-molecules.pdf
|
64ddd10b4a3f7d0c0d4e08c1
|
10.26434/chemrxiv-2023-wcr6n
|
Molecular Plastics Programming: Squaramide as a Building Block
|
The plastics structure-property correspondence has been conventionally identified through either forward discovery chemistry approach or reverse analysis physics approach. The viewing of each monomer unit as a non-divisible entity limits these approaches as an inherently non-programmable tool. Herein, molecular plastics programming is reported as an effective prescriptive strategy for achieving programmable molecular-macroscopic correspondence. With each monomer envisioned as a divisible entity, constituted with building blocks (rigid, flexible, spacer coupling, linker), a set of guiding principles has been established for the predictive mapping of polymer chain architecture to physical properties (thermal; mechanical, brittle, ductile). Polymer main-chain rigid-flexible-building-block coupling is established as a feasible route toward mechanical activation and therefore ductility. Squaramide has been utilized as a building block for the design and synthesis of an amorphous-phased, ductile, and degradable plastic, showcasing molecular plastics programming as a promising platform for precision plastics engineering and sustainable polymer development.
|
Tielei Li; Baochen Wang; Benfa Chu; Jin Zhu
|
Polymer Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ddd10b4a3f7d0c0d4e08c1/original/molecular-plastics-programming-squaramide-as-a-building-block.pdf
|
6613d8e121291e5d1d61a628
|
10.26434/chemrxiv-2024-9rhnd-v3
|
Delving into Theoretical and Computational Considerations
for Accurate Calculation of Chemical Shifts in Paramagnetic
Transition Metal Systems using Quantum Chemical Methods
|
The chemical shielding tensor for a paramagnetic system has been derived from the macroscopically
observed magnetization using the perturbation theory. An approach to calculate the paramagnetic chemical
shifts in transition metal systems based on the spin-only magnetic susceptibility directly evaluated from the
ab initio Hilbert space of the electronic Zeeman Hamiltonian has been discussed. Computationally, several
advantages are associated with this approach: (a) it includes the state-specific paramagnetic Curie (firstorder)
and Van Vleck (second-order) contributions of the paramagnetic ion to the paramagnetic chemical
shifts; (b) thus it avoids the system-specific modeling and evaluating effectively in terms of the electron
paramagnetic resonance (EPR) spin Hamiltonian parameters of the magnetic moment of the paramagnetic
ion formulated previously; (c) it can be utilized both in the point-dipole (PD) approximation (in the longrange)
and with the quantum chemical (QC) method based the hyperfine tensors (in the short-range).
Additionally, we have examined the predictive performance of various DFT functionals of different families
and commonly used core-augmented basis sets for nuclear magnetic resonance (NMR) chemical shifts. A
selection of transition metal ion complexes with and without first-order orbital contributions, namely the
[M(AcPyOx)3(BPh)]+ complexes of M=Mn2+, Ni2+ and Co2+ ions and CoTp2 complex and their reported
NMR chemical shifts are studied from QC methods for illustration.
|
Ashraful Islam; Andrew Pell
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Computing; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6613d8e121291e5d1d61a628/original/delving-into-theoretical-and-computational-considerations-for-accurate-calculation-of-chemical-shifts-in-paramagnetic-transition-metal-systems-using-quantum-chemical-methods.pdf
|
60c74a88bdbb893c46a393be
|
10.26434/chemrxiv.11910948.v2
|
Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces
|
<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>
|
Shi Jun Ang; Wujie Wang; Daniel Schwalbe-Koda; Simon Axelrod; Rafael Gomez-Bombarelli
|
Physical Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a88bdbb893c46a393be/original/active-learning-accelerates-ab-initio-molecular-dynamics-on-pericyclic-reactive-energy-surfaces.pdf
|
61ba298f203b404ea38e8b60
|
10.26434/chemrxiv-2021-n8hlc-v2
|
Enhancing the Inhomogeneonus Photodynamics of
Canonical Bacteriophytochrome
|
The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.
|
Jakub Rydzewski; Katarzyna Walczewska-Szewc; Sylwia Czach; Wiesław Nowak; Krzysztof Kuczera
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ba298f203b404ea38e8b60/original/enhancing-the-inhomogeneonus-photodynamics-of-canonical-bacteriophytochrome.pdf
|
673ede1c5a82cea2fa180729
|
10.26434/chemrxiv-2024-25th6
|
Revealing Water Structure at Neutral and Charged Graphene/Water Interfaces through Quantum Simulations of Sum Frequency Generation Spectra
|
The structure and dynamics of water at charged graphene interfaces fundamentally influence molecular responses to electric fields, with implications for applications in energy storage, catalysis, and surface chemistry. Leveraging the realism of the MB-pol data-driven many-body potential and advanced path-integral quantum dynamics, we analyze the vibrational sum-frequency generation (vSFG) spectrum of graphene/water interfaces under varying surface charges. Our quantum simulations reveal a distinctive dangling OH peak in the vSFG spectrum at neutral graphene, consistent with recent experimental findings yet markedly different from earlier studies. As the graphene surface becomes positively charged, interfacial water molecules reorient, decreasing the intensity of the dangling OH peak as the OH groups turn away from the graphene. In contrast, water molecules orient their OH bonds toward negatively charged graphene, leading to a prominent dangling OH peak in the corresponding vSFG spectrum. This charge-induced reorganization generates a diverse range of hydrogen-bonding topologies at the interface, driven by variations in the underlying electrostatic interactions. Re- markably, these structural changes extend into deeper water layers, creating an unequal distribution of molecules with OH bonds pointing toward and away from the graphene sheet. This imbalance amplifies bulk spectral features, underscoring the complexity of many-body interactions that shape the molecular structure of water at charged graphene interfaces.
|
Richa Rashmi; Toheeb O Balogun; Golam Azom; Henry Agnew; Revati Kumar; Francesco Paesani
|
Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Machine Learning; Interfaces; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ede1c5a82cea2fa180729/original/revealing-water-structure-at-neutral-and-charged-graphene-water-interfaces-through-quantum-simulations-of-sum-frequency-generation-spectra.pdf
|
60f338f210531732f1413d6e
|
10.26434/chemrxiv-2021-gh36l
|
Learning H-Coupled 13C NMR in the First Month of Sophomore Organic Lecture
|
Using 13C NMR data that includes 1H coupling allows sophomore organic students to solve simple structural problems, even early in the first semester of the sophomore organic course.
|
Douglass Taber
|
Organic Chemistry; Chemical Education
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f338f210531732f1413d6e/original/learning-h-coupled-13c-nmr-in-the-first-month-of-sophomore-organic-lecture.pdf
|
61a7d3e0f35d4ca9794de71d
|
10.26434/chemrxiv-2021-bj205
|
Electrophilic Sulfur Reagent Design Enables Catalytic syn-Carbosulfenylation of Unactivated Alkenes
|
A multi-component approach to structurally complex organosulfur products is described via the nickel-catalyzed 1,2-carbosulfenylation of unactivated alkenes with organoboron nucleophiles and tailored organosulfur electrophiles. Key to the development of this transformation is the identification of a modular N-alkyl-N-(arylsulfenyl)arenesulfonamide family of sulfur electrophiles. Tuning the electronic and steric properties of the leaving group in these reagents controls pathway selectivity, favoring three-component coupling and suppressing side reactions, as examined via computational studies. The unique syn-stereoselectivity differs from traditional electrophilic sulfenyl transfer processes involving a thiiranium ion intermediate and arises from the directed arylnickel(I) migratory insertion mechanism, as elucidated through reaction kinetics and control experiments. Reactivity and regioselectivity are facilitated by a collection of monodentate, weakly coordinating native directing groups, including sulfonamides, alcohols, amines, amides, and azaheterocycles.
|
Zi-Qi Li; Yilin Cao; Taeho Kang; Keary Engle
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a7d3e0f35d4ca9794de71d/original/electrophilic-sulfur-reagent-design-enables-catalytic-syn-carbosulfenylation-of-unactivated-alkenes.pdf
|
60c74c369abda28ac4f8d23f
|
10.26434/chemrxiv.12459404.v1
|
Statement on Diversity & Inclusion at ChemRxiv [Editorial]
|
Recent events including the publication of troubling remarks in <i>Angewandte Chemie</i> have made clear that many in the
scientific community and broader society continue to face systemic racism and discrimination in their daily personal
and professional lives. As these events unfold, we must take personal responsibility and commit to supporting all
members of our community, regardless of race, culture, national origin, creed or sexual orientation.<div><br /></div><div>In this editorial we detail our commitment to supporting diversity and inclusion on ChemRxiv.</div>
|
Marshall Brennan; Jessica Rucker; Roheena Anand; Wolfram Koch; Donna Minton; Fumio Nakamura; Mitsuo Sawamoto; Irina Sens; Zhigang Shuai; Sarah Tegen; Emma WIlson
|
Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c369abda28ac4f8d23f/original/statement-on-diversity-inclusion-at-chem-rxiv-editorial.pdf
|
64103372e53eff1af31b2d3e
|
10.26434/chemrxiv-2023-rskwt
|
Cycling stability of lithium-ion batteries based on Fe-Ti doped LiNi0.5Mn1.5O4 cathodes, graphite anodes and the cathode additive Li3PO4
|
This study addresses the improved cycling stability of Li-ion batteries based on Fe-Ti doped LiNi0.5Mn1.5O4 (LNMO) high voltage cathode active material and graphite anodes. By using 1 wt.% Li3PO4 as cathode additive, over 90% capacity retention for 1000 charge-discharge cycles and
remaining capacities of 109 mAh∙g-1 were reached in a cells with an areal capacity of 2.3 mAh∙cm-² (potential range: 3.5 V - 4.9 V). Cells without the additive, in contrast, suffered from accelerated capacity loss and increased polarization, resulting in capacity retention of only 78% over 1000 cycles. An electrolyte consisting of ethylene carbonate, dimethyl carbonate and LiPF6 was used without additional additives. The significantly improved cycling stability of the full cells is mainly due to two factors, namely the low MnIII content of the Fe-Ti-doped LNMO active material and the use of the cathode additive Li3PO4. Crystalline Li3PO4 yields a drastic reduction of transition metal deposition on the graphite anode and prevents Li loss and the propagation of cell polarization. Li3PO4 was added to the cathode slurry which makes it a very simple and scalable process, firstly reported herein. The positive effects of crystalline Li3PO4 as electrode additive, however, should apply to other cell chemistries as well.
|
Pirmin Stüble; Marcus Müller; Thomas Bergfeldt; Joachim R. Binder; Andreas Hofmann
|
Energy; Energy Storage; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64103372e53eff1af31b2d3e/original/cycling-stability-of-lithium-ion-batteries-based-on-fe-ti-doped-li-ni0-5mn1-5o4-cathodes-graphite-anodes-and-the-cathode-additive-li3po4.pdf
|
65c627ba66c13817294944b0
|
10.26434/chemrxiv-2024-stdjf
|
Influence of chemical modifications of the crystallophore on protein nucleating properties and supramolecular interactions network.
|
Crystallophores are lanthanide complexes that have demonstrated outstanding induction of crystallization for various proteins. This article explores the effect of tailored modifications of the crystallophore first generation and studies their impact on the nucleating properties, and protein crystal structures. Through high-throughput crystallization experiments and dataset analysis, we evaluated the effectiveness of these variants, in comparison to the first crystallophore generation G1. In particular, the V1 variant, featuring a propyl-3-ol pendant arm, demonstrated the ability to produce new crystallization conditions for the proteins tested (hen-egg white lysozyme, proteinase K and thaumatin). Structural analysis performed in the case of hen egg-white lysozyme along with Molecular Dynamics simulations, highlights V1's unique behavior, taking advantage of the flexibility of its propyl-3-ol arm to explore different protein surfaces and form versatile supramolecular interactions.
|
Amandine Roux; Zaynab Alsalman; Tao Jiang; Jean-Christophe Mulatier; Delphine Pitrat; Elise Dumont; François Riobé; Natacha Gillet; Eric Girard; Olivier Maury
|
Biological and Medicinal Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Supramolecular Chemistry (Inorg.); Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c627ba66c13817294944b0/original/influence-of-chemical-modifications-of-the-crystallophore-on-protein-nucleating-properties-and-supramolecular-interactions-network.pdf
|
60c740a20f50db4c9f395992
|
10.26434/chemrxiv.7777112.v1
|
Dual-Function Fluorescent Probe for the Detection of Peroxynitrite and Adenosine Triphosphate
|
<p>A novel
dual-function fluorescent probe (<b>ATP-LW</b>) was developed for the detection of ONOO<sup>-</sup>
and ATP. </p>
|
Luling Wu; Hai-Hao Han; Yang Wang; Xue Tian; Adam Sedgwick; Steven Bull; Xiao-Peng He; Chusen Huang; Tony James; Jonathan L. Sessler
|
Photochemistry (Org.); Supramolecular Chemistry (Org.); Biochemical Analysis; Sensors
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a20f50db4c9f395992/original/dual-function-fluorescent-probe-for-the-detection-of-peroxynitrite-and-adenosine-triphosphate.pdf
|
670cd07d12ff75c3a15cea2d
|
10.26434/chemrxiv-2024-kw7c9
|
Towards industrially-relevant liquid-phase flow oxidations of secondary alcohols over spinel cobaltites
|
Selective partial oxidation of alcohols is a straightforward synthetic pathway to access aldehydes and ketones, important building blocks for the chemical industry. The catalytic oxidation of higher secondary alcohols is challenging, which entails the need for low temperatures to preserve the selectivity or, in practice, the use of a liquid phase. In this work, we explored the applicability of Co-based spinel oxides as alternatives to noble metal-based supported catalysts for the oxidation of alcohols such as 2-butanol and 2-propanol. We developed a small-scale tri-phasic process in flow for consecutive weeks and using technical grade microporous catalysts, en route to more industrially-relevant systems, focussing on the practical aspects of the process. Co3O4, MnCo2O4, NiCo2O4, ZnCo2O4, and CoFe2O4 were synthesised by combustion and characterised by XRD, SEM, EDX, XPS, N2-physisorption and FT-IR spectroscopy. The same catalysts were tested in batch in the liquid phase to explore the impact of the reaction conditions on the reaction outcome and to rule out flow-specific effects. Gas phase reactions unveiled the different behaviour of the same catalysts in different environments, highlighting phase-specific effects such as the beneficial (liquid phase) vs inhibiting (gas phase) impact of Mn doping.
|
Alberto Tampieri; Federica Romanelli; Michael Pittenauer; Thomas Lederer; Karin Föttinger
|
Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670cd07d12ff75c3a15cea2d/original/towards-industrially-relevant-liquid-phase-flow-oxidations-of-secondary-alcohols-over-spinel-cobaltites.pdf
|
670d1aac12ff75c3a163d130
|
10.26434/chemrxiv-2024-hv6m7
|
Simple and Versatile Electrochemical Synthesis of Highly Substituted 2,1-Benzisoxazoles
|
A sustainable, general and scalable electrochemical protocol for the direct access to 3-(acylamidoalkyl)-2,1-benzisoxazoles by cathodic reduction of widely accessible nitro arenes is established. The method is characterised by a simple undivided set-up under constant current conditions, inexpensive and reusable carbon-based electrodes, and environmentally benign reaction conditions. The versatility of the developed protocol is demonstrated on 38 highly diverse examples with up to 81% yield. A 50-fold scale-up electrolysis highlights its relevance for preparative applications.
|
Marola S. Lenhard; Johannes Winter; Alexander Sandvoß; María de Jesús Gálvez-Vázquez; Dieter Schollmeyer; Siegfried R. Waldvogel
|
Organic Chemistry; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d1aac12ff75c3a163d130/original/simple-and-versatile-electrochemical-synthesis-of-highly-substituted-2-1-benzisoxazoles.pdf
|
60c75272469df4402cf44b6d
|
10.26434/chemrxiv.13297919.v1
|
Intramolecular Oxidative Coupling between Unactivated Aliphatic C-H and Aryl C-H Bonds
|
Direct oxidative coupling
of different inert C-H bonds is the most straightforward and
environmentally benign method to construct C-C bonds. In this article, we
developed a Pd-catalyzed
intramolecular oxidative coupling between unactivated aliphatic and aryl C-H
bonds. This chemistry showed great potential to build up fused cyclic scaffolds
from linear substrates through oxidative couplings. Privileged chromane and
tetralin scaffolds were constructed from readily available linear starting
materials in the absence of any organohalides and organometallic partners.<br />
|
Yang Liao; Yi Zhou; Zhen Zhang; Junzhen Fan; Feng Liu; Zhangjie Shi
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75272469df4402cf44b6d/original/intramolecular-oxidative-coupling-between-unactivated-aliphatic-c-h-and-aryl-c-h-bonds.pdf
|
6374064fe70b0a38e79e3fe8
|
10.26434/chemrxiv-2022-qn6dq-v2
|
The new era of high throughput nanoelectrochemistry
|
Scanning electrochemical probe microscopies (SEPMs) have played a key role in advancing small-scale electrochemistry. SEPMs use an electrochemical probe (micro/nanoelectrode or pipet) to quantify and map local interfacial fluxes of electroactive species and have found increasingly wide applications. Our contribution to the Fundamental and Applied Reviews in Analytical Chemistry 2019 discussed how advances in SEPMs converged towards nanoscale electrochemical mapping. This inflection in experimental capability has opened up myriad opportunities for SEPMs in many types of systems, from material and energy sciences to the life sciences. The enhancement in the spatial resolution of imaging techniques, and instrumental developments, have resulted in significant increases in the size of electrochemical datasets from a typical experiment and served to speed up measurement throughput. Next generation nanoelectrochemistry will thus see an emphasis on “big data”, its analysis, storage and curation, high throughput analysis and parallelization, “intelligent” instruments and experiments, active control of nanoscale systems, and the integration of nanoelectrochemistry and nanoscale micro(spectro)scopy. For this review article, we focus on recent advances in frontier nanoscale electrochemistry, analysis and imaging techniques that are already addressing some of these key targets, and are well-placed to embrace other aspects in the near future. Our goal is to provide an overview of the present state-of-the-art in high throughput nanoelectrochemistry and imaging, and signpost promising new avenues for nanoscale electrochemical methods.
|
Xiangdong Xu; Dimitrios Valavanis; Paolo Ciocci; Samuel Confederat; Fabio Marcuccio; Jean-François Lemineur; Paolo Actis; Frédéric Kanoufi; Patrick Unwin
|
Physical Chemistry; Analytical Chemistry; Nanoscience; Electrochemical Analysis; Imaging; Electrochemistry - Mechanisms, Theory & Study
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-11-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6374064fe70b0a38e79e3fe8/original/the-new-era-of-high-throughput-nanoelectrochemistry.pdf
|
60c7499e337d6ca8cbe2774f
|
10.26434/chemrxiv.12090954.v1
|
Plasmonic-Based Impedance Microspectroscopy of Optically Heterogeneous Samples
|
<p>An optical label-free microscopy technique for
high resolution imaging of electrical impedance is presented. To achieve this,
surface plasmon resonance sensors are used to detect surface charge density
modulation optically. Therefore, they provide the basis for computing electrical
current and impedance. However, one of the major challenges of plasmonic-based
impedance imaging is the contribution from the optical properties of the sample. Here, a correction
method is presented as an effective way for isolating the effect of the optical
heterogeneity. Using this technique, capacitance of bovine serum albumin
(BSA) patterns was mapped with submicroscopic resolution. The work reported will enable electrical characterisation of cells and biomolecules with promising biophysical
applications.</p>
|
Sidahmed Abayzeed
|
Imaging; Microscopy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7499e337d6ca8cbe2774f/original/plasmonic-based-impedance-microspectroscopy-of-optically-heterogeneous-samples.pdf
|
61e1d157eab6ef22e3e175fe
|
10.26434/chemrxiv-2022-vxh1x
|
Augmented Magnetic Response and Spin-Transfer in Copper Corrole/Graphene Hybrids - A DFT Study
|
The search for hybrid materials with outstanding electronic performance is highly demanding Since copper corroles have emerged as versatile building blocks providing outstanding electronic, and reactivity properties, a new series of non-covalent hybrid materials were computationally investigated based on pristine graphene and A3-type copper corrole complexes. The corrole complexes contain strong electron-withdrawing fluorinated substituents at the meso positions. Our results show that the non-innocent character of corrole moiety modulates the structural, electronic, and magnetic properties of the hybrid systems. The graphene-corrole hybrids display outstanding stability via the interplay of dispersion and electrostatic driving forces while graphene act as an electron reservoir for more conductive cases. Furthermore, the hybrid structures display an intriguing magneto-chemical performance since a detailed analysis of magnetic properties evidence how structural and electronic changes contribute to the amplification of the magnetic response also for ferromagnetic and antiferromagnetic cases. This amplification is accompanied by the spin transfer which characterized by a directional spin polarization from the corrole through the graphene surface. Main results suggest that graphene-corrole hybrids are excellent candidates for technologic applications due to the ferromagnetic tendency, the augmented magnetic response, the tunability due to substituents, and the potential conductive properties. Finally, a statistical analysis of magnetic properties suggests correlations between spin transfer, augmented magnetic response, and the geometrical distortion of the copper ligand field, offering exciting hints about how to modulate the magnetic response in the studied hybrid systems.
|
Kerry Wrighton-Araneda; Diego Cortés-Arriagada; Paulina Dreyse; Simon Pascal; Gabriel Canard; Luis Sanhueza
|
Theoretical and Computational Chemistry; Materials Science; Magnetic Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e1d157eab6ef22e3e175fe/original/augmented-magnetic-response-and-spin-transfer-in-copper-corrole-graphene-hybrids-a-dft-study.pdf
|
60c74f55567dfe705bec5672
|
10.26434/chemrxiv.12888383.v1
|
Practical Notes on Building Molecular Graph Generative Models
|
<p>Here are presented technical notes
and tips on developing graph generative models for molecular design. This work
stems from the development of GraphINVENT, a Python platform for graph-based molecular
generation using graph neural networks. In this work, technical details that
could be of interest to researchers developing their own molecular generative
models are discussed, including strategies for designing new models. Advice on development and debugging tools
which were helpful during code development is also provided. Finally, methods that were tested but which ultimately
didn’t lead to promising results in the development of GraphINVENT are
described here in the hope that this will help other researchers avoid pitfalls
in development and instead focus their efforts on more promising strategies for
graph-based molecular generation.</p>
|
Rocío Mercado; Tobias Rastemo; Edvard Lindelöf; Günter Klambauer; Ola Engkvist; Hongming Chen; Esben Jannik Bjerrum
|
Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f55567dfe705bec5672/original/practical-notes-on-building-molecular-graph-generative-models.pdf
|
65e0585966c1381729d62705
|
10.26434/chemrxiv-2024-jncnf
|
Screening of organoboron compounds as potential ionophores in a miniaturized ITIES cell.
|
Screening ionophores for potentiometric ion-selective electrodes is arduous as the interaction between the ion and the recognition molecule might be obscured by improper selection of the plasticizer, lipophilic salt or its concentration. Ion transfer voltammetry at the interface of two immiscible solutions (ITIES) allows for evaluating ionophores in a less complex environment. However, standard four electrode cells require up to 10 mL of organic phase for each experiment, thus, a considerable quantity of ionophores is consumed. The latter are usually expensive or synthetically demanding. In this work, we have developed a miniaturized four-electrode cell that can be easily fabricated in any laboratory from a spectrophotometric cuvette without the need for glassblower services. The cell allows evaluation of ionophore-ion interactions in volumes of organic phase as low as 200 µL. It exhibits a sym-metric diffusion profile, which facilitates the interpretation of the results compared to other low-volume setups like capillaries. It is also easier to assemble and does not need specific surface preparation (e.g. silanisation). In the initial step the electrochemical per-formance of the minaturized cell was tested using solution of tetramethylammonium chloride, and the results were compared to those obtained with a standard macroscopic setup. Next, the device was used to screen through a wide range of organoboron compounds towards their ability to recognize fluoride anions.
|
Martyna Durka; Krzysztof Durka; Sergiusz Luliński; Emilia Witkowska Nery
|
Physical Chemistry; Analytical Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0585966c1381729d62705/original/screening-of-organoboron-compounds-as-potential-ionophores-in-a-miniaturized-ities-cell.pdf
|
67c0e43e6dde43c908c6da25
|
10.26434/chemrxiv-2025-clc28
|
The interplay between carbonate phases in promoted carbonation of MgO
|
Magnesium oxide serves as promising sorbent for CO2 capture, storage and release. The CO2 uptake can be enhanced through the addition of molten alkali nitrate- and bicarbonate promoters, such as NaNO3 and Na2CO3. The mechanisms through which these promotors affect the kinetics of CO2 uptake have so far not been fully uncovered.
Here, using a combination of scanning electron microscopy and X-ray diffraction techniques we unravel the sequence of carbonation processes taking place inside the liquid NaNO3 promotor in the presence of CO2 gas and a single crystalline MgO substrate. We identify the key role that Na2Mg(CO3)2 plays as precursor phase which forms as dominant phase in the early stages of carbonation and remains throughout the carbonation process as intermediate phase that supplies the thermodynamically more stable MgCO3 product with growth species.
The insight into the interplay between CO2 uptake, MgO dissolution, supersaturation and precipitation of phases with different stability regimes provided by this study contributes to a general understanding of the dynamical interplay between phases under chemical gradients.
|
Elena Willinger; Felix Donat; Claudiu Colbea; Marta Mirolo; Marc Willinger
|
Materials Science; Controlled-Release Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c0e43e6dde43c908c6da25/original/the-interplay-between-carbonate-phases-in-promoted-carbonation-of-mg-o.pdf
|
657b9c7a9138d23161ab1a0f
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10.26434/chemrxiv-2023-n6tx4
|
Does trapped O2 form in the bulk of LiNiO2 during charging?
|
LiNiO2 remains a critical archetypal material for high energy density Li-ion batteries, forming the basis of Ni-rich cathodes in use today. Nevertheless, there are still uncertainties surrounding the charging mechanism at high states of charge and the potential role of oxygen redox. We show that oxidation of O2- across the 4.2 V plateau forms O2 trapped in the particles and is accompanied by the formation of 8% Ni vacancies on the transition metal sites of previously fully dense transition metal layers. Such Ni vacancy formation on charging activates O-redox by generating non-bonding O 2p orbitals and is necessary to form vacancy clusters to accommodate O2 in the particles. Ni accumulates at and near the surface of the particles on charging, forming a Ni-rich shell approximately 5 nm thick, enhanced by loss of O2 from the surface, the resulting shell composition is Ni2.3+1.75O2. The overall Ni oxidation state of the particles measured by XAS in fluorescence yield mode after charging across the plateau to 4.3 V is approximately +3.8; however, taking account of the shell thickness and the shell Ni oxidation state of +2.3, this indicates a Ni oxidation state in the core closer to +4 for compositions beyond the plateau.
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Mikkel Juelsholt; Jun Chen; Miguel A. Pérez-Osorio; Gregory J. Rees; Sofia De Sousa Coutinho; Helen E. Maynard-Casely; Jue Liu; Michelle Everett; Stefano Agrestini; Mirian Garcia-Fernandez; Ke-Jin Zhou; Robert A. House; Peter Bruce
|
Materials Science; Energy; Energy Storage; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-12-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b9c7a9138d23161ab1a0f/original/does-trapped-o2-form-in-the-bulk-of-li-ni-o2-during-charging.pdf
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62afb3d4448398b2e47c5e09
|
10.26434/chemrxiv-2022-7vkvz
|
Decarboxylative Cross-Coupling: A Radical Tool In Medicinal Chemistry
|
Carboxylic acids, the most versatile and ubiquitous diversity input used in medicinal chemistry for canonical polar bond constructions such as amide synthesis, can now be employed in a fundamentally different category of reaction to make C–C bonds by harnessing the power of radicals. This outlook serves as a user guide to aid practitioners in both the design of syntheses that leverage the simplifying power of this disconnection and the precise tactics that can be employed to enable them. Taken together this emerging area holds the potential to rapidly accelerate access to
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Gabriele Laudadio; Maximilian Palkowitz; Tamara Ewing; Phil Baran
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Organic Chemistry
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CC BY 4.0
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CHEMRXIV
|
2022-06-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62afb3d4448398b2e47c5e09/original/decarboxylative-cross-coupling-a-radical-tool-in-medicinal-chemistry.pdf
|
60c748ef4c8919dbe6ad2fd0
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10.26434/chemrxiv.11996703.v1
|
Enantioselective Lewis Base Catalyzed Phosphonyldifluoromethylation of Allylic Fluorides Using C-Silyl Latent Pronucleophile
|
The first enantioselective phosphonyldifluoromethylation is enabled by the use of diethyl (difluoro(trimethylsilyl)methyl)pho-sphonate reagent as a latent pronuclephile in Lewis base catalyzed substitution of allylic fluorides. The reactions proceed as kinetic resolution to produce both the difluoromethylphosphonate products and the remaining fluorides in good yields and with high stereoselectivity. The use of cinchona based alkaloid catalysts enables the facile synthesis of both enantiomers of the difluoromethylphosphonate products.
|
You Zi; Markus Lange; Ivan Vilotijevic
|
Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry; Base Catalysis; Homogeneous Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ef4c8919dbe6ad2fd0/original/enantioselective-lewis-base-catalyzed-phosphonyldifluoromethylation-of-allylic-fluorides-using-c-silyl-latent-pronucleophile.pdf
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66a6fbe201103d79c519c9db
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10.26434/chemrxiv-2024-djt5s
|
Asymmetric pathways for lithium extraction and recovery based on the two-phase equilibrium of layered oxides
|
Electrochemical intercalation offers a promising platform for Li+ extraction. However, only limited types of electrode materials have been investigated. The challenge to broaden and tailor materials for electrochemical intercalation-based Li+ extraction lies in the lack of understanding of material’s response upon co-intercalation of multiple ions, therefore, paired process design to enable reversible Li+ extraction and recovery. Here, we showcase the design of asymmetric ion pathways for Li+ extraction and recovery for host material with complex Li+ and Na+ interaction using layered cobalt oxide as a model material, which could enable the large class of layered oxides for Li+ extraction. The two-phase equilibrium of Na0.48CoO2 and Li0.94CoO2 governs record high Li+ selectivity when a high depth of intercalation is achieved (low vacancy level). We show that the relative rate between ion exchange and intercalation is critical to determine the ion pathways. The relationship can be quantitatively compared using the average pseudo ion exchange rate (CpseudoIX) and the intercalation rate (Cinter). The ion pathways at the three regimes with CpseudoIX > Cinter, CpseudoIX ~ Cinter, and CpseudoIX < Cinter are constructed. By selecting the optimized ion pathway and particle size, we demonstrated 9.7×104 Li+ selectivity with 99% purity Li+ recovery from an initial 1:1000 Li: Na molar ratio solution using 115 mAh/g capacity with good reversibility.
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Grant Hill; Raphael Stone; Yu Han; Jiadong Liu; Siqi Zou; Hua Zhou; Chong Liu
|
Materials Science; Ceramics
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CC BY 4.0
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CHEMRXIV
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2024-07-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a6fbe201103d79c519c9db/original/asymmetric-pathways-for-lithium-extraction-and-recovery-based-on-the-two-phase-equilibrium-of-layered-oxides.pdf
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670fa4e551558a15ef3e3b43
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10.26434/chemrxiv-2024-gh7fq
|
Semisynthesis of aged histone H4 reveals robustness and vulnerability of chromatin towards molecular "wear-and-tear"
|
Proteins are subject to molecular “wear-and-tear” in the form of spontaneous, non-enzymatic post-translational modifications (PTMs). One such PTM is the formation of the β-linked isomer L-isoaspartic acid (isoAsp) from aspartic acid (Asp) or asparagine residues, which tends to occur in long-lived proteins. Histones can exhibit half-lives on the order of 100 days, and unsurprisingly, isoAsp formation has been observed in nearly every histone family. Delineating the molecular consequences of isoAsp formation in histones is challenging due to the multitude of processes that occur on such time scales. To isolate the effect of specific isoAsp modification thus necessitates precise in vitro characterisation with well-defined substrates. Here, we adapt a protein semisynthesis approach to generate full-length variants of histone H4 in which the canonical Asp at position 24 is replaced by its isoAsp isomer (H4isoD24). This variant was incorporated into chromatin templates, and the resulting constructs were used to interrogate key parameters of chromatin integrity and maintenance in vitro: compaction, nucleosome remodelling, and methylation of H4 lysine 20 (H4K20). Remarkably, despite its disruptive changes to the backbone’s spacing and direction, isoD24 did not dramatically disrupt Mg2+-mediated chromatin self-association or nucleosome repositioning by the remodeller Chd1. In contrast, H4isoD24 significantly inhibited both Set8- and Suv4-20h1-catalysed methylation at H4K20. These results suggest that H4isoD24 gives rise to a complex reorganisation of the chromatin functional landscape, in which macroscopic processes show robustness and local mechanisms exhibit vulnerability to the presence of this mark.
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Tianze Zhang; Luis Guerra; Yana Berlina; Jon Wilson; Beat Fierz; Manuel Müller
|
Biological and Medicinal Chemistry; Biochemistry; Chemical Biology
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CC BY NC ND 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/670fa4e551558a15ef3e3b43/original/semisynthesis-of-aged-histone-h4-reveals-robustness-and-vulnerability-of-chromatin-towards-molecular-wear-and-tear.pdf
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67311c9e7be152b1d0a55de2
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10.26434/chemrxiv-2024-s7z77
|
Azide- and Transition-Metal-Free Access to Sulfonyl Amidines via C(sp2)-N Coupling of Trifluoroborate-Iminiums with N-Fluorobenzenesulfonimide
|
Amidines are an important class of organic compounds with widespread application as superbases, nucleophilic cata-lysts, and building blocks of heterocyclic compounds in organic synthesis. Moreover, they represent an important struc-tural motif in medicinal chemistry. This work describes an application of primary trifluoroborate‐iminiums in unprece-dented azide- and transition-metal-free transformation to N-sulfonyl amidines in the presence of N-fluorobenzenesulfonimide. This novel C(sp2)-N bond-forming reaction proceeds without excess of any reagent under mild conditions and provides good to high yields of N-sulfonyl amidines by a simple isolation procedure. Density functional theory mechanistic studies into this novel transformation support that the use of a base is required to activate either the trifluoroborate-iminium or the NFSI and promote the C(sp2)-N bond formation via nucleophilic attack of the nitrogen. The utility of the developed methodology is showcased with the synthesis of two bioactive compounds.
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Damijan Knez; Andrej Sterman; Izidor Sosic; Franc Perdih; Gonzalo Darío Nuñez; Tilen Knaflic; Denis Arcon; Maria Besora; Jorge Juan Carbó; Elena Fernández; Zdenko Casar
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Crystallography – Organic
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67311c9e7be152b1d0a55de2/original/azide-and-transition-metal-free-access-to-sulfonyl-amidines-via-c-sp2-n-coupling-of-trifluoroborate-iminiums-with-n-fluorobenzenesulfonimide.pdf
|
62092041bd05a04af3056d41
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10.26434/chemrxiv-2022-3wz8q
|
Automated Search For The Low-lying Energy Isomers of Rhamnolipids and Related Organometallic Complexes
|
Rhamnolipids (RMLs) are a widely studied biosurfactant due to its high biodegradability, low toxicity, and environmentally friendly production, which has the bacterium Pseudomonas aeruginosa as producer and renewable source of feedstock. However, the knowledge of the structure-property relationship of several RMLs congeners is imperative for the design of a high efficient application. Aiming to a better understanding of RMLs at a molecular level, we performed a automated search for
low energy structures of the most abundant congeners, namely, Rha-C10, Rha-C10-C10, Rha-Rha-C10 and Rha-Rha-C10-C10 and their respective congener with two carbon atoms (C2) at the side chain. Besides that, selected neutral metal complexes were also considered. We thus performed a metadynamics search followed by DFT optimizations of selected geometries. In addition, molecular dynamics simulations were also applied. Our results show a plethora of low energy structures for each congener. Although several of them have internal hydrogen bonds, this interaction alone cannot explain the stability. Moreover, geometries in closed conformation were always more stable than ”open” ones and the effect of chain length on the geometry was found to be more prominent between Rha-Rha-C2-C2 and Rha-Rha-C10-C10 . Finally, the energy differences between open and closed conformations for K+ , Ni2+ , Cu2+ and Zn2+ complexes were found to be 23.5 kcal mol−1, 62.8 kcal mol−1 , 24.3 kcal mol−1 and 41.6 kcal mol−1 , respectively, indicating a huge structural reorganization after the complex formation.
|
Leticia Dobler; Ricardo Oliveira
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62092041bd05a04af3056d41/original/automated-search-for-the-low-lying-energy-isomers-of-rhamnolipids-and-related-organometallic-complexes.pdf
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65a3e1f666c13817296b585a
|
10.26434/chemrxiv-2023-drhmj-v2
|
DeepSPInN - Deep reinforcement learning for molecular Structure Prediction from Infrared and 13C NMR spectra
|
Molecular spectroscopy studies the interaction of molecules with electromagnetic radiation, and interpreting the resultant spectra is invaluable for deducing the molecular structures. However, predicting the molecular structure from spectroscopic data is a strenuous task that requires highly specific domain knowledge. DeepSPInN is a deep reinforcement learning method that predicts the molecular structure when given Infrared and 13C Nuclear magnetic resonance spectra by formulating the molecular structure prediction problem as a Markov decision process (MDP) and employs Monte-Carlo tree search to explore and choose the actions in the formulated MDP. On the QM9 dataset, DeepSPInN is able to predict the correct molecular structure for 91.5% of the input spectra in an average time of 77 seconds for molecules with less than 10 heavy atoms. This study is the first of its kind that uses only infrared and 13C nuclear magnetic resonance spectra for molecular structure prediction without referring to any pre-existing spectral databases or molecular fragment knowledge bases, and is a leap forward in automated molecular spectral analysis.
|
Sriram Devata; Bhuvanesh Sridharan; Sarvesh Mehta; Yashaswi Pathak; Siddhartha Laghuvarapu; Girish Varma; Deva Priyakumar
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a3e1f666c13817296b585a/original/deep-sp-in-n-deep-reinforcement-learning-for-molecular-structure-prediction-from-infrared-and-13c-nmr-spectra.pdf
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667ac7d4c9c6a5c07a5b418c
|
10.26434/chemrxiv-2024-j4nzb
|
Bent Naphthodithiophenes: Synthesis and Characterisation of Isomeric Fluorophores
|
Thiophene-containing heteroarenes are one of the most well-known classes of π-conjugated building blocks for photoactive molecules. Isomeric naphthodithiophenes (NDTs) are at the forefront of this research area due to their straightforward synthesis and derivatization. Notably, NDT geometries that are bent – such as naphtho[2,1-b:3,4-b’]dithiophene (α-NDT) and naphtho[1,2-b:4,3-b’]dithiophene (β -NDT) – are seldom employed as photoactive small molecules. This report investigates how remote substituents impact the photophysical properties of isomeric α- and β-NDTs. The orientation of the thiophene units plays a critical role in the emission: in the α(OHex)R2 series conjugation from the end-caps to the NDT core is apparent, while in the β(Oi-Pent)R2 series minimal change is observed unless strong electron acceptors, such as β(Oi-Pent)(PhCF3)2, are employed. This push-pull Acceptor–Donor–Acceptor (A–D–A) fluorophore exhibits positive fluorosolvatochromism that correlates with increasing solvent polarity parameter, ET(30). In total, these results highlight how remote substituents are able to modulate the emission of isomeric bent NDTs.
|
Emmanuel Adusei; Vincent Casetti; Calvin Goldsmith; Madison Caswell; Drecila Alinj; Jimin Park; Matthias Zeller; Alexander Rusakov; Zacharias Kinney
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667ac7d4c9c6a5c07a5b418c/original/bent-naphthodithiophenes-synthesis-and-characterisation-of-isomeric-fluorophores.pdf
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66f5254651558a15ef2a6b67
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10.26434/chemrxiv-2024-vld8w
|
Structural requirements of synthetic anionophores for inorganic phosphate and phosphate esters
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The transmembrane transport of anions is a promising application of synthetic anion receptors. Numerous anionophores have been developed for chloride over the past decades. Despite the biological relevance of phosphate and phosphate esters, very few reports on their transport by synthetic systems exist. Here we report a systematic study on the transport of diphenyl phosphate, phenyl phosphate, and inorganic phosphate by five different anionophores. The transport of these phosphates into liposomes was monitored by fluorescence spectroscopy, 31P NMR spectroscopy, and an ion selective electrode. The results of these experiments showed that diphenyl phosphate is readily transported by most chloride ionophores. The transport of phenyl phosphate is more challenging, but can be enhanced by better shielding of the phosphate group. Inorganic phosphate is the most challenging to transport and was achieved using a macrocyclic anionophore with eight preorganised H-bond donors. These results pave the way for the development of anionophores for inorganic phosphate as well as phosphate esters.
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Aaron Torres-Huerta; Karolis Norvaisa; Alessio Cataldo; Pierre-Olivier Tits; Priyanka Rani Panda; Christopher M. Dias; Anthony P. Davis; Samantha E. Bodman; Stephen J. Butler; Hennie Valkenier
|
Organic Chemistry; Supramolecular Chemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f5254651558a15ef2a6b67/original/structural-requirements-of-synthetic-anionophores-for-inorganic-phosphate-and-phosphate-esters.pdf
|
6525a4f48bab5d20550f4e00
|
10.26434/chemrxiv-2023-68575
|
A General Strategy for N–(Hetero)aryl Piperidine Synthesis Using Zincke Imine Intermediates
|
Methods to synthesize diverse collections of substituted piperidines are valuable due to the prevalence of this heterocycle in pharmaceutical compounds. Here, we present a general strategy to access N-(hetero)arylpiperidines using a pyridine ring-opening, ring-closing approach via Zincke imine intermediates. This process generates pyridinium salts from a wide variety of substituted pyridines and (heteroaryl)anilines; hydrogenation reactions and nucleophilic additions then access the N-(hetero)arylpiperidine derivatives. We successfully applied high-throughput experimentation (HTE) using pharmaceutically relevant pyridines and (heteroaryl)anilines as inputs and developed a one-pot process using anilines as nucleophiles in the pyridinium salt-forming processes. This strategy is viable for generating piperidine libraries and applications such as convergent coupling of complex fragments.
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Jake D. Selingo; Jacob W. Greenwood; Mary Katherine Andrews; Chirag Patel; Andrew J. Neel; Barbara Pio; Michael Shevlin; Eric M. Phillips; Matthew L. Maddess; Andrew McNally
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Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6525a4f48bab5d20550f4e00/original/a-general-strategy-for-n-hetero-aryl-piperidine-synthesis-using-zincke-imine-intermediates.pdf
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6744e0ee5a82cea2fadaa02c
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10.26434/chemrxiv-2024-0jjf6
|
imzML Writer: An Easy-to-Use Python Pipeline for Conversion of Continuously Acquired Raw Mass Spectrometry Imaging Files to imzML Format
|
Mass spectrometry imaging (MSI) is a powerful tool which reveals the contextual distribution of biomolecules in tissues. Acquiring these images involves collecting an information-rich mass spectrum for each pixel of the ion image, which results in large datasets typically exceeding 1 GB. To streamline data processing and interpretation, various toolboxes have been developed for image pre-processing, segmentation, statistical analysis, and visualization. These generally require imaging data to be input in ‘imzML’ format, an Extensible Markup Language file with controlled vocabulary for mass spectrometry and MSI-specific parameters. While major/commercial MSI modalities (e.g. MALDI) come with proprietary file converters, to our knowledge, no open-access user-friendly converters exist for continuously acquired MSI data (e.g. nano-DESI, DESI). Here, we present imzML Writer, an open-access python application which is easy to install and easy to use. imzML Writer has a simple graphical user interface to convert data from MS vendor format into pixel-aligned imzML files suitable for further analysis. We package this application with imzML Scout, a tool to quickly visualize the resulting file(s) and batch export ion images across a range of image/data formats (PNG, TIF, CSV). To demonstrate the utility of files generated by imzML Writer, we processed a nano-DESI image using previously inaccessible toolboxes/data repositories such as Cardinal MSI and METASPACE. Overall, this work provides a simple tool for emerging MSI modality users to access the wealth of advanced MSI processing tools reliant on imzML format.
|
Joseph Monaghan; Kiera Nguyen; Nicholas Woytowich; Alora Keyowski; Kyle Duncan
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Analytical Chemistry; Imaging; Mass Spectrometry
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CC BY NC 4.0
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CHEMRXIV
|
2024-11-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6744e0ee5a82cea2fadaa02c/original/imz-ml-writer-an-easy-to-use-python-pipeline-for-conversion-of-continuously-acquired-raw-mass-spectrometry-imaging-files-to-imz-ml-format.pdf
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6612c17a21291e5d1d4fd45f
|
10.26434/chemrxiv-2023-p4fhz-v2
|
Capturing Carbon Dioxide from Air with Charged-Sorbents
|
Emissions reduction and greenhouse gas removal from the atmosphere are both necessary to achieve net-zero emissions and limit climate change.1 There is thus a need for improved sorbents for the capture of carbon dioxide from the atmosphere, a process known as direct air capture. In particular, low-cost materials that can be regenerated at low temperatures would overcome the limitations of current technologies. In this work, we introduce a new class of designer sorbent materials known as “charged-sorbents”. These materials are prepared through a battery-like charging process which accumulates ions in the pores of low-cost activated carbons, with the inserted ions then serving as adsorption sites for carbon dioxide adsorption. We use our charging process to accumulate reactive hydroxide ions in the pores of a carbon electrode, and find that the resulting sorbent material can rapidly capture carbon dioxide from ambient air via (bi)carbonate formation. Unlike traditional bulk carbonates, charged-sorbent regeneration can be achieved at low temperatures (90-100 ºC), and the sorbent's conductive nature permits direct Joule heating regeneration2,3 using renewable electricity. Given their highly tailorable pore environments and low cost, we anticipate that charged-sorbents will find numerous potential applications in chemical separations, catalysis, and beyond.
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Huaiguang Li; Mary E. Zick; Teedhat Trisukhon; Matteo Signorile; Xinyu Liu; Helen Eastmond; Shivani Sharma; Tristan Spreng; Jack Taylor; Jamie W. Gittins; Cavan Farrow; S. Alexandra Lim; Valentina Crocellà; Phillip J. Milner; Alexander C. Forse
|
Materials Science; Carbon-based Materials; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-08
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6612c17a21291e5d1d4fd45f/original/capturing-carbon-dioxide-from-air-with-charged-sorbents.pdf
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60c740a2f96a00a2be2862f1
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10.26434/chemrxiv.7777085.v1
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(Z)-N'-(1H-Benzo[d]imidazol-2-Yl)-Arylimidamide Adducts of 2-Aminobenzimidazole and Aromatic Nitriles: Structural and Spectroscopic Proof of Regiochemical and Stereochemical Outcomes
|
The selection of a core scaffold or template is of enormous importance in medicinal chemistry. Benzimidazoles are a recurring fragment in medicinal chemistry, and the 2-amino derivative is a versatile example in lead generation. Alkylated and acylated examples abound, however, alternative linkage chemistries leading do more diverse structures are needed. <br />Here we discuss the regiochemistry of nucleophilic addition of 2-aminobenzimidazole to nitriles, leading to imidamide (amidine) adducts. Additionally, we use extensive NMR analysis and ultimately X-ray crystallography to demonstrate both the regiochemistry and stereochemistry of the addition products, arising from derivatisation of the exocylic 2-amino group.
|
Martin Stoermer; Simon Egan; Craig M. Forsyth; Gerard Moloney
|
Bioorganic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a2f96a00a2be2862f1/original/z-n-1h-benzo-d-imidazol-2-yl-arylimidamide-adducts-of-2-aminobenzimidazole-and-aromatic-nitriles-structural-and-spectroscopic-proof-of-regiochemical-and-stereochemical-outcomes.pdf
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6242536f658bc0faa5bc4efe
|
10.26434/chemrxiv-2022-qhs3m
|
Evaluating new blends of HFE-7100 iodine
α-naphthoflavone sprays for fingermark development
|
A global phase-out of the hydrochlorofluorocarbon solvent AK-225 (HCFC-225), a carrier solvent used in certain all-in-one iodine solutions, has mandated a reassessment of HFE-7100 as an alternate carrier solvent. Direct substitution of AK-225 for HFE-7100 failed owing to incompatible solubility, prompting evaluation of blends containing both heptane and dichloromethane. This evaluation of heterogenous formulations of HFE-7100 has yielded a new iodine solution, a modified α-naphthoflavone fixing solution, and an all-in-one iodine developer solution with stability of ~4 hours. The all-in-one blended HFE-7100 spray reagent delivers approximately equivalent fingermark development to the AK-225 all-in-one developer on gyprock, tile, and plastic surfaces in preliminary trials. Sequentially applying HFE-7100 iodine solution, followed by α-naphthoflavone solution, allowed for clear development of fingermarks on paper surfaces. This work outlines alternate HFE-based developers as a stopgap measure in light of the current phase-down of HFC solvents in Australia, and elsewhere, and also provides an updated assignment of the chromophore produced by the iodine-naphthoflavone reaction that is supported by mass spectrometry evidence.
|
Kristen Clarke; Matthew Krosch; Antonio Martinez; William Gee
|
Analytical Chemistry; Analytical Chemistry - General
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6242536f658bc0faa5bc4efe/original/evaluating-new-blends-of-hfe-7100-iodine-naphthoflavone-sprays-for-fingermark-development.pdf
|
63e3bdf71f23f0032d4c5f94
|
10.26434/chemrxiv-2023-pj2fq-v3
|
Dancing Silanols: Stereospecific Rearrangements of Silanol Epoxides into Silanoxy-Tetrahydrofurans and Silanoxy-Tetrahydropyrans
|
We have developed highly stereospecific rearrangements of silanol epoxides into 1’-silanoxy-tetrahydrofurans and
1’-silanoxy-tetrahydropyrans. Upon treatment with Ph3CBF4 and NaHCO3 in CH2Cl2, di-substituted trans-epoxide silanols rearrange into products with an erythro configuration; di-substituted cis-epoxide silanols give products with a threo configuration. To our knowledge, this transformation has little literature precedent. Control experiments show that the rearrangement reaction likely
proceeds by nucleophilic attack of the proximal silanol oxygen onto the epoxide followed by an intramolecular silyl transfer. We have used these reactions as key steps in the syntheses of (±)-solerone and (±)-muricatacin.
|
Shyam Sathyamoorthi; Harshit Joshi; Annu Thomas; Joel Mague
|
Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e3bdf71f23f0032d4c5f94/original/dancing-silanols-stereospecific-rearrangements-of-silanol-epoxides-into-silanoxy-tetrahydrofurans-and-silanoxy-tetrahydropyrans.pdf
|
60e39dd195d7fff26ebd1ddb
|
10.26434/chemrxiv-2021-db566-v2
|
Machine Learning to Accelerate Screening for Marcus Reorganization Energies
|
Understanding and predicting the charge transport properties of π-conjugated materials is an important challenge for designing new organic electronic applications, including solar cells, plastic transistors, light-emitting devices, and chemical sensors. A key component of the hopping mechanism of charge transfer in these materials is the Marcus reorganization energy, which serves as an activation barrier to hole or electron transfer. While modern density functional methods have proven to accurately predict trends in intramolecular reorganization energy, such calculations are computationally expensive. In this work, we outline active machine learning methods to predict computed intramolecular reorganization energies of a wide range of polythiophenes and their use towards screening new compounds with low internal reorganization energies. Our models have an overall root mean square error of ±0.113 eV, but a much smaller RMSE of only ±0.036 eV on the new screening set. Since the larger error derives from high-reorganization energy compounds, the new method is highly effective to screen for compounds with potentially efficient charge transport parameters.
|
Omri Abarbanel; Geoffrey Hutchison
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-07-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e39dd195d7fff26ebd1ddb/original/machine-learning-to-accelerate-screening-for-marcus-reorganization-energies.pdf
|
62d6fdf24e76bf3e7c969b54
|
10.26434/chemrxiv-2022-llt2q-v2
|
Synthesis and Kinetic Stabilization of a Theoretically Predicted Sn(II)-Perovskite Oxide as a Nanoshell
|
Kinetically-stabilized, i.e., metastable, semiconductor dielectrics represent a major new frontier within many key technological fields as compared to thermodynamically-stable solids that have received considerably more attention. Of longstanding interest are Sn(II) perovskites (e.g., Sn(Zr1/2Ti1/2)O3, SZT), which are theoretically predicted Pb-free analogues of (Pb(Zr1/2Ti1/2)O3, PZT), a commercial piezoelectric compound that is dominant in the electronics industry. Herein, we describe the synthesis of this metastable SZT dielectric through a low-temperature flux reaction technique. The SZT has been found, for the first time, to grow and to be stabilized as a nanoshell at the surfaces of Ba(Zr1/2Ti1/2)O3 (BZT) particles, i.e., forming as BZT-SZT core-shell particles, as a result of Sn(II) cation exchange. In situ powder X-ray diffraction (XRD) and transmission electron microscopy data show that the SZT nanoshells result from the controlled cation diffusion of Sn(II) cations into the BZT particles, with tunable thicknesses of ~25 nm to 100 nm. The SZT nanoshell is calculated to possess a metastability of about 0.5 eV atom–1 with respect to decomposition to SnO, ZrO2, and TiO2, and thus cannot currently be prepared as stand-alone particles. Rietveld refinements of XRD data are consistent with a two-phase BZT-SZT model, with each phase possessing a generally cubic perovskite-type structure and nearly identical lattice parameters. Mössbauer spectroscopic data (119Sn) are consistent with Sn(II) cations within the SZT nanoshells and an outer ~5 to 10 nm surface region comprised of oxidized Sn(IV) cations after exposure to air and water. The optical band gap of the SZT shell was found to be ~2.2 eV, which is redshifted by ~1.2 eV as compared to BZT. This closing of the band gap was probed by X-ray photoelectron spectroscopy and found to stem from a shift of the valence band edge to higher energies (~1.07 eV) as a result of the addition of the Sn 5s2 orbitals forming a new higher-energy valence band. In summary, a novel synthetic tactic is demonstrated to be effective in preparing highly metastable SZT and representing a generally useful strategy for the kinetic stabilization of other predicted, metastable dielectrics.
|
Shaun O'Donnell; DJ Osborne; Gowri Krishnan; Theresa Block; Aylin Koldemir; Thomas Small; Rachel Broughton; Jacob Jones; Rainer Pöttgen; Gunther Andersson; Gregory Metha; Paul Maggard
|
Materials Science; Inorganic Chemistry; Nanoscience; Core-Shell Materials; Solid State Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d6fdf24e76bf3e7c969b54/original/synthesis-and-kinetic-stabilization-of-a-theoretically-predicted-sn-ii-perovskite-oxide-as-a-nanoshell.pdf
|
60c755c80f50db2aff397f97
|
10.26434/chemrxiv.12671027.v2
|
Understanding Conformational Entropy in Small Molecules
|
The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.
|
Lucian Chan; Garrett Morris; Geoffrey Hutchison
|
Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755c80f50db2aff397f97/original/understanding-conformational-entropy-in-small-molecules.pdf
|
62fe4c64f9e99c04c480974c
|
10.26434/chemrxiv-2022-731c3-v3
|
Edge-to-Center Propagation of Photochemical Reaction during Single-Crystal-to-Single-Crystal Photomechanical Transformation of 2,5-Distyrylpyrazine Crystals
|
Photomechanical molecular crystals are promising materials as photon-powered artificial actuators. To design and control the photomechanical responses, the spatiotemporal distribution of photoproducts in crystals could be a key factor in addition to molecular structures, molecular packings, illumination conditions, crystal morphology, crystal size, and so on. In this study, we have found that single crystals of 2,5-distyrylpyrazine show a smooth single-crystal-to-single-crystal photomechanical expansion, and the photochemical reaction propagates from the edge to the center of the single crystal. Moreover, we have performed a numerical simulation to reproduce the experimental results and revealed that both the cooperativity effect and the surface effect in the crystal are essential for the edge-to-center propagation of the photochemical reaction. Our results would provide a framework for analyzing the photochemical reaction dynamics in photoresponsive single crystals and a benchmark for future studies of photomechanical molecular crystals.
|
Kohei Morimoto; Daichi Kitagawa; Hikaru Sotome; Syoji Ito; Hiroshi Miyasaka; Seiya Kobatake
|
Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Chemical Kinetics; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fe4c64f9e99c04c480974c/original/edge-to-center-propagation-of-photochemical-reaction-during-single-crystal-to-single-crystal-photomechanical-transformation-of-2-5-distyrylpyrazine-crystals.pdf
|
60c7478a9abda24c98f8c926
|
10.26434/chemrxiv.11574099.v2
|
RNA Phosphorothioate Modification in Prokaryotes and Eukaryotes
|
We report the first RNA phosphorothioate modification in both prokaryotes and eukaryotes. The GpsG modification exists in the Rp configuration and was quantified with liquid chromatography coupled with tandem mass spectrometry. Furthermore, we show the Dnd clusters that regulate DNA PT modification also play roles in RNA PT modification.
|
Ying Wu; Yaning Tang; xiaolong dong; Ya Ying Zheng; Phensinee Haruehanroengra; song mao; Qishan Lin; Jia Sheng
|
Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7478a9abda24c98f8c926/original/rna-phosphorothioate-modification-in-prokaryotes-and-eukaryotes.pdf
|
66269b0321291e5d1d64c3c9
|
10.26434/chemrxiv-2024-ck8c5-v2
|
Auto-VTNA: An Automatic VTNA platform for Determination of Global Rate Equations
|
The ability and desire to generate kinetic data has greatly increased in recent years, requiring more automated and quantitative methods for analysis. In this work, an automated program (Auto-VTNA) is developed, to simplify the kinetic analysis workflow. The Auto-VTNA solver allows all the reaction orders to be determined concurrently, expediting the process of kinetic analysis. Auto-VTNA performs well on noisy or sparse data sets and can handle complex reactions involving changing reaction orders. Quantitative error analysis and facile visualisation allows users to numerically justify and robustly present their findings. Auto-VTNA can be used through a free graphical user interface (GUI), requiring no coding or kinetic knowledge from the user, or can be customised and built on if required. The code and executable application ("Auto-VTNA Calculator") can be found at https://github.com/ddalland/Auto-VTNA.
|
Daniel Dalland; Linden Schrecker; King Kuok (Mimi) Hii
|
Physical Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Chemical Kinetics
|
CC BY 4.0
|
CHEMRXIV
|
2024-04-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66269b0321291e5d1d64c3c9/original/auto-vtna-an-automatic-vtna-platform-for-determination-of-global-rate-equations.pdf
|
60c7408a567dfe4f9eec3bc7
|
10.26434/chemrxiv.7763657.v1
|
Electron Donation by Low-Crystalline Ba-La-Ce Oxygen-Deficient Composite Oxide Accumulating on Ru Nanoparticles for Ammonia Synthesis under Mild Conditions
|
<p>To mitigate global
problems related to energy and global warming, it is helpful to develop an
ammonia synthesis process using catalysts that are highly active under mild
conditions. Here we show that the ammonia synthesis activity of Ru/Ba/LaCeO<i><sub>x</sub></i> pre-reduced at 700 °C is the highest reported among oxide-supported Ru
catalysts. Our results indicate that low crystalline oxygen-deficient composite
oxides, which include Ba<sup>2+</sup>, Ce<sup>3+</sup> and La<sup>3+</sup>,
with strong electron-donating ability, accumulate on Ru particles and thus
promote N≡N bond cleavage, which is the rate determining step for ammonia
synthesis.</p>
|
Katsutoshi Sato; Shin-ichiro Miyahara; Yuta Ogura; Kotoko Tsujimaru; Yuichiro Wada; Takaaki Toriyama; Tomokazu Yamamoto; Syo Matsumura; Katsutoshi Nagaoka
|
Heterogeneous Catalysis; Energy Storage; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7408a567dfe4f9eec3bc7/original/electron-donation-by-low-crystalline-ba-la-ce-oxygen-deficient-composite-oxide-accumulating-on-ru-nanoparticles-for-ammonia-synthesis-under-mild-conditions.pdf
|
60c750e1842e655879db3acb
|
10.26434/chemrxiv.13087769.v1
|
Multi-Label Classification Models for the Prediction of Cross-Coupling Reaction Conditions
|
<div><div><div><p>Machine-learned ranking models have been developed for the prediction of substrate-specific cross-coupling reaction conditions. Datasets of published reactions were curated for Suzuki, Negishi, and C–N couplings, as well as Pauson–Khand reactions. String, descriptor, and graph encodings were tested as input representations, and models were trained to predict the set of conditions used in a reaction as a binary vector. Unique reagent dictionaries categorized by expert-crafted reaction roles were constructed for each dataset, leading to context-aware predictions. We find that relational graph convolutional networks and gradient-boosting machines are very effective for this learning task, and we disclose a novel reaction-level graph-attention operation in the top-performing model.</p></div></div></div>
|
Michael Maser; Alexander Cui; Serim Ryou; Travis DeLano; Yisong Yue; Sarah Reisman
|
Organic Synthesis and Reactions; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750e1842e655879db3acb/original/multi-label-classification-models-for-the-prediction-of-cross-coupling-reaction-conditions.pdf
|
671fa0371fb27ce124d8c4a2
|
10.26434/chemrxiv-2024-jjxd1
|
3D Printing of Strong and Room-temperature Reprocessable Silicone Vitrimers
|
Silicones find use in a myriad of applications from sealants and adhesives to cooking utensils and medical implants. However, state-of-the-art silicone parts fall short in terms of shape complexity and reprocessability. Advances in three-dimensional printing and the discovery of vitrimers have recently led to new opportunities for the shaping and recycling of silicone objects. Here, we report the 3D printing via Direct Ink Writing of silicone vitrimers into complex-shaped parts with high strength and room- temperature reprocessability. The reprocessing properties of the printed objects result from the adaptive nature of the silicone vitrimer, which can deform under stress without losing its network connectivity. Rheological and mechanical experiments reveal that printable inks can be tuned to generate strong parts with high creep resistance and room-temperature reprocessability, two properties that are usually challenging to reconcile in vitrimers. By combining printability, high strength and room-temperature reprocessability, the reported silicone vitrimers represent an attractive sustainable alternative to currently available elastomers in a broad range of established and prospective applications.
|
Stefano Menasce; Rafael Libanori; Fergal Brian Coulter; André R. Studart
|
Materials Science; Polymer Science; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-10-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671fa0371fb27ce124d8c4a2/original/3d-printing-of-strong-and-room-temperature-reprocessable-silicone-vitrimers.pdf
|
60c755bd4c89194089ad4735
|
10.26434/chemrxiv.14153798.v1
|
Mimicking the Microbial Oxidation of Elemental Sulfur with a Biphasic Electrochemical Cell
|
<p>The
lack of an artificial system that mimics elemental sulfur (S<sub>8</sub>)
oxidation by microorganisms inhibits a deep mechanistic understanding of the
sulfur cycle in the biosphere and the metabolism of sulfur-oxidizing
microorganisms. In this article, we present a biphasic system that mimics
biochemical sulfur oxidation under ambient conditions using a liquid|liquid
(L|L) electrochemical cell and gold nanoparticles (AuNPs) as an interfacial
catalyst. The interface between two solvents of very different polarity is an
ideal environment to oxidise S<sub>8</sub>, overcoming the <a>incompatible solubilities </a>of the hydrophobic reactants
(O<sub>2</sub> and S<sub>8</sub>) and hydrophilic products (H<sup>+</sup>, SO<sub>3</sub><sup>2–</sup>,
SO<sub>4</sub><sup>2–</sup>, <i>etc.</i>). The interfacial AuNPs provide a
catalytic surface onto which O<sub>2</sub> and S<sub>8</sub> can adsorb.
Control over the driving force for the reaction is provided by polarizing the
L|L interface externally and tuning the Fermi level of the interfacial AuNPs by
the adsorption of aqueous anions.</p>
|
Marco F. Suárez-Herrera; Jose Solla-Gullon; Micheal D. Scanlon
|
Electrochemistry - Mechanisms, Theory & Study; Interfaces; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755bd4c89194089ad4735/original/mimicking-the-microbial-oxidation-of-elemental-sulfur-with-a-biphasic-electrochemical-cell.pdf
|
627a16d1708767d5ed4d2f81
|
10.26434/chemrxiv-2022-llgw3
|
Templating Effect of Diammonium Cations on Structural and Optical Properties of Lead Bromide Perovskites
|
The role of templating the formation of 2D metal halide perovskites has been investigated by considering the 1,3-phenylenediammonium (1,3-PDA), 1,3-xylylenediamimonium (1,3-XDA), 1,4-phenylenediammonium (1,4-PDA), and 1,4-xylylenediamimonium (1,4-XDA) cations in lead bromide systems. Single-crystal x-ray diffraction confirms the formation 2D Dion-Jacobons (DJ) perovskites for all the cations except for the 1,3-XDA cation leading to a so-called 0D perovskitoid. Analysis of the structural data showed a higher distortion degree for the systems containing the shorter cation, namely 1,4-PDA. A detailed spectroscopic investigation, with both static and time resolved photoluminescence spectroscopy, revealed a broadband emissive component at room temperature with hundreds of nanometers of bandwidth when 1,3-PDA and 1,4-PDA cations are present, while a narrow peak is found for the longer cation, i.e. 1,4-XDA. A broadband emission arises in this last sample as well by decreasing temperature. Such broad emission, as indicated by the analysis of the power and temperature dependence of the PL, can be attributed to trap-mediated excitonic recombination or STEs, and the trend in emissive properties can be correlated to the different level of octahedral distortions. The novel systems reported in this work enlarge the family of broadband emitters and add further clues to develop efficient perovskite-based broadband and white light emitters.
|
Lorenzo Malavasi; Rossella Chiara; Marta Morana; Benedetta Albini; Pietro Galinetto; Annamaria Petrozza; Giulia Folpini; Andrea Olivati; Laura Chelazzi; Samuele Ciattini; Elvira Fantechi
|
Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Materials Chemistry; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627a16d1708767d5ed4d2f81/original/templating-effect-of-diammonium-cations-on-structural-and-optical-properties-of-lead-bromide-perovskites.pdf
|
60c7420f0f50db148b395c25
|
10.26434/chemrxiv.8208407.v1
|
NADH in Solution: A Single State
|
<div>Spectroscopic evidence is presented to show that NADH in aqueous solution does not exist as a folded/unfolded equilibrium but as a single state. The molecule is folded but without base stacking between dihydronicotinamide and adenine.<br /></div>
|
Joachim Hönes; Julia Wack; Katja Schmitz
|
Spectroscopy (Anal. Chem.); Biochemistry; Solution Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-05-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7420f0f50db148b395c25/original/nadh-in-solution-a-single-state.pdf
|
672c64f2f9980725cf6aa750
|
10.26434/chemrxiv-2024-sgrqh
|
Cells Respond to ECM Contexts via Integrin-Ligand Lifetimes: Rediscovery of Loading Rate Enhancement through Bayesian Refinement of Force Spectrum Analysis
|
The phenomenon of loading rate enhancement, where the bond lifetime between protein molecules significantly increases beyond a certain loading rate threshold, has been well-documented across various molecules. However, reports of this phenomenon as a mechanosensing mechanism in cells are scarce, primarily because most reported thresholds exceed physiological norms. In this study, we reevaluate the kinetic properties of integrin-ligand bonds using Single-Molecule Force Spectroscopy and Single-Cell Force Spectroscopy. Our analysis revealed a nonlinear relationship between loading rate and rupture force, with thresholds significantly below the commonly reported 10,000 pN/s. Using a Bayesian-inference-based Micro-interval analysis method, we determined specific loading rate thresholds for integrin α5β1 and α2β1 ligand-binding bonds at 1018.49 pN/s and 2398.23 pN/s, respectively. Given that substrate rigidity correlates with loading rates upon integrins under actomyosin-generated forces, our findings suggest that integrin α5 mediates stronger adhesions on softer substrates compared to integrin α2. These findings demonstrate that integrin-mediated cell adhesion strengthens within physiological loading rate ranges and suggest a mechanism for the subtle regulation of extracellular matrix protein composition in cellular elasticity sensing.
|
Xueyi Yang; Xu Zhang; Yue Xu; Chuanwen Guo; Shenghan Gao; Huitong Jin; Chun Yang
|
Biological and Medicinal Chemistry; Nanoscience; Biophysics; Cell and Molecular Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c64f2f9980725cf6aa750/original/cells-respond-to-ecm-contexts-via-integrin-ligand-lifetimes-rediscovery-of-loading-rate-enhancement-through-bayesian-refinement-of-force-spectrum-analysis.pdf
|
6370e716deff975271e381bb
|
10.26434/chemrxiv-2022-z0f7j
|
Monovalent Germanium Radical Stabilized by a Phenalenyl Scaffold
|
A monovalent (Non-Gomberg type) germanium radical 1 stabilized by phenalenyl-based bidentate ligand was synthe-sized. Because of the high thermal stability originating from spin delocalization over the phenalenyl moiety, it was possi-ble to isolate compound 1 in crystalline form by sublimation at ca. 300 °C. ESR spectra, crystallographic analysis, theo-retical calculations, and reactivities with carbon radicals suggest that the spin of 1 is distributed on the phenalenyl moie-ty, while 1 behaves as a germanium-centered radical in its reactions with C2Cl6, PhSSPh, and p-benzoquinone to form Ge−E (E = Cl, S, O) bonds.
|
Takuya Kodama; Kenta Uchida; Chihiro Nakasuji; Ryohei Kishi; Yasutaka Kitagawa; Mamoru Tobisu
|
Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Main Group Chemistry (Organomet.); Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6370e716deff975271e381bb/original/monovalent-germanium-radical-stabilized-by-a-phenalenyl-scaffold.pdf
|
60c74459469df459a3f432fc
|
10.26434/chemrxiv.7940810.v2
|
Development of the ChIMES Force Field for Reactive Molecular Systems: Carbon Monoxide at Extreme Conditions
|
<p>We have developed a transferable reactive force field for C/O systems under extreme temperature and pressure conditions based on the many-body Chebyshev Interaction Model for Efficient Simulation (ChIMES). The resulting model is shown to recover much of the accuracy of DFT for prediction of structure, dynamics and chemistry when applied to dissociative systems at 1:1 and 1:2 C:O ratios, as well as molten carbon. Our C/O modeling approach exhibits a 10<sup>4</sup> increase in efficiency and linear system size scalability over standard quantum molecular dynamics methods, allowing simulation of significantly larger systems than previously possible. Furthermore, we show that system sizes of at least 500 atoms are required to observe the formation of experimentally predicted molten carbon condensates under oxygen-deficient conditions, indicative of possible system size effects in quantum simulations of these types of systems. Overall, we find the present ChIMES model to be well suited for modeling chemical processes and cluster formation at pressures and temperatures typical of shock waves. We expect that the present C/O modeling paradigm can serve as a template for the development of a high pressure --high temperature organic chemistry force-field. </p>
|
Rebecca Lindsey; Nir Goldman; Laurence E. Fried; Sorin Bastea
|
Computational Chemistry and Modeling; Machine Learning
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74459469df459a3f432fc/original/development-of-the-ch-imes-force-field-for-reactive-molecular-systems-carbon-monoxide-at-extreme-conditions.pdf
|
667ed925c9c6a5c07aaf617c
|
10.26434/chemrxiv-2024-vlvqf-v2
|
Ab initio electronic absorption spectra of para-nitroaniline in different solvents: intramolecular charge transfer effects
|
IIntramolecular charge transfer (ICT) effects of para–nitroaniline (pNA) in eight solvents (cyclohexane, toluene, acetic acid, dichloroethane, acetone, acetonitrile, dimethylsulfoxide, and water) are investigated extensively. The second-order algebraic diagrammatic construction, ADC(2), ab initio wave function is employed with the COSMO implicit and discrete multiscale solvation methods. We found a decreasing amine group torsion angle with increased solvent polarity and a linear correlation between the polarity and ADC(2) transition energies. The first absorption band involves π→π* transitions with ICT from the amine and the benzene ring to the nitro group, increased by 4 -11% for different solvation models of water compared to the vacuum. A second band of pNA is characterized for the first time. This band is primarily a local excitation (LE) on the nitro group, including some ICT from the amine group to the benzene ring that decreases with the solvent polarity. For cyclohexane, the COSMO implicit solvent model shows the best agreement with the experiment, while the explicit model has the best agreement for water.
|
Matheus Maximo-Canadas; Lucas Modesto-Costa; Itamar Borges Jr.
|
Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667ed925c9c6a5c07aaf617c/original/ab-initio-electronic-absorption-spectra-of-para-nitroaniline-in-different-solvents-intramolecular-charge-transfer-effects.pdf
|
60c7528b702a9b833518c184
|
10.26434/chemrxiv.13318151.v1
|
Molecular Frame Dipole Moment of Diatomic Molecules within Relativistic Coupled-Cluster Framework: A Comparative Study of Expectation Value vs. Energy Derivative Approach
|
The ground state molecular frame permanent dipole moment of alkaline earth metal monofluorides and the group-IIB monohydrides have been calculated using two analytic methods: Z-vector method and the linear expectation value method. Results obtained from this methods have been compared with the experimental values and different contributing terms to the total permanent dipole moment have been discussed thoroughly.<br />
|
Soumi Haldar; Kaushik Talukdar; Malaya K Nayak; Sourav Pal
|
Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7528b702a9b833518c184/original/molecular-frame-dipole-moment-of-diatomic-molecules-within-relativistic-coupled-cluster-framework-a-comparative-study-of-expectation-value-vs-energy-derivative-approach.pdf
|
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