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62eccb05d131b709f10d2b67
|
10.26434/chemrxiv-2022-pm30k
|
Cellulose dissolution and gelation in NaOH(aq) under controlled CO2 atmosphere: supramolecular structure and flow properties
|
We investigate the interplay between cellulose crystallization and aggregation with interfibrillar interactions, shear forces, and the local changes in the medium's acidity. The latter is affected by the CO2 chemisorbed from the surrounding atmosphere, which, combined with shear forces, explain cellulose gelation. Herein, rheology, nuclear magnetic resonance (NMR), small and wide-angle X-ray scattering (SAXS/WAXS), and focused ion beam scanning electron microscopy (FIB-SEM) are combined to unveil the fundamental factors that limit cellulose gelation and maximize its dissolution in NaOH(aq). The obtained solutions are then proposed for developing green and environmentally friendly cellulose-based materials.
|
Guillermo Reyes; Alistair W. T. King; Tetyana V. Koso; Paavo A. Penttilä; Harri Kosonen; Orlando J. Rojas
|
Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Cellulosic materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eccb05d131b709f10d2b67/original/cellulose-dissolution-and-gelation-in-na-oh-aq-under-controlled-co2-atmosphere-supramolecular-structure-and-flow-properties.pdf
|
60c73fe2702a9b0eb0189fdf
|
10.26434/chemrxiv.7553054.v1
|
Correlation Between Saturated Fatty Acid Chain-Length and Intermolecular Forces Determined with Terahertz Spectroscopy
|
<p>We measured crystalline (C-form)
saturated fatty acids with even carbon numbers ranging from 12 to 20 using
temperature dependent terahertz time-domain spectroscopy (THz-TDS). Absorption
features between 0.5 to 2.75 THz were identified at temperatures from 96 K to
293 K, and a systematic red-shift was obvserved with the increasing carbon
chain length. The origins of these absorption bands were uncovered using
state-of-the-art <i>ab initio</i> density
functional theory (DFT) calculations. Similar vibrational motions in the
absorption bands of the different materials highlight the unique role that
THz-TDS has for probing weak non-covalent interactions in these materials. Our
results showcase the utility of the terahertz region, which is beyond the scope
of related vibrational techniques, providing direct evidence of the effect of
chain length on the intermolecular interactions of these molecules. </p>
|
Shuting Fan; Michael Ruggiero; Zhengfang Qian; Vincent P. Wallace
|
Computational Chemistry and Modeling; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe2702a9b0eb0189fdf/original/correlation-between-saturated-fatty-acid-chain-length-and-intermolecular-forces-determined-with-terahertz-spectroscopy.pdf
|
6179fc62ff3ba95dc7a5ff35
|
10.26434/chemrxiv-2021-1bk8t
|
Synthesis of the Macrolactone Cores of Maltepolides via a Diene–Ene Ring-Closing Metathesis Strategy
|
Synthesis of the C19-truncated maltepolide E has been accomplished via a diene–ene RCM strategy without damage to the C11–C14 alkenyl epoxy unit. Upon release of the C17-OH group, it attacked at the C14 position with double bond migration and epoxide ring-opening to furnish the C19-truncated maltepolide A and B as proposed for the biosynthesis of maltepolides. Preliminary cytotoxicity data of the synthesized C19-truncated maltepolides against L929 mouse fibroblast cell line suggest irrelevance of the vinyl epoxide and importance of the conjugated dienyl keto unit for the observed anticancer activity.
|
Man Ki Sit; Hui Hui Cao; Yan-Dong Wu; Tsz Chun Yip; Lars Eric Bendel; Wen Zhang; Wei-Min Dai
|
Organic Chemistry; Natural Products
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6179fc62ff3ba95dc7a5ff35/original/synthesis-of-the-macrolactone-cores-of-maltepolides-via-a-diene-ene-ring-closing-metathesis-strategy.pdf
|
6728d53b5a82cea2fa0025a8
|
10.26434/chemrxiv-2024-0nxcv
|
Predicting C-H activation through hydride affinity and homolytic bond dissociation energies
|
Predicted bond dissociation energies (BDEs) can be used to identify C-H bonds that are most likely to react in H-abstraction reactions. However, in many cases, it is not clear whether the reaction oc- curs through a radical or carbocation intermediate. Thus, the C-H hydride affinity (hydricity) may be more predictive of reactive sites than BDEs. In this paper, we introduce HAlator, a quantum chemistry (QM)-based workflow for automatic computations of C–H hydricities, that we bench- mark against 35 experimentally determined C-H hydricities in DMSO. We train the ML model on a diverse dataset of 3278 C-H sites from 740 molecules with C–H hydricities obtained using the QM-based workflow. Our ML model predicts C–H hydricities with a mean absolute error (MAE) and a root mean squared error (RMSE) of 2.30 and 3.74 kcal/mol, respectively. Furthermore, we apply our QM-based workflow and ML model to 250 hydride transfer-like reactions (H abstrac- tions: C-N, C-C, C-X, carbene insertions, oxidations, and oxidative degradation). We further ex- plore the use of ALFABET, an ML model based on BDEs, and achieve a Matthew’s correlation coefficient (MCC) between 0.20 and 0.80 across the models.
|
Rasmus M. Borup; Nicolai Ree; Jan H. Jensen
|
Theoretical and Computational Chemistry; Organic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6728d53b5a82cea2fa0025a8/original/predicting-c-h-activation-through-hydride-affinity-and-homolytic-bond-dissociation-energies.pdf
|
64f96a533fdae147faaa081e
|
10.26434/chemrxiv-2023-plbdr
|
Selective Arylation of Selenocysteine of Thioredoxin Reductase 1 by an Organogold Compound: Expanding the Tool-Box of Metal-Templated Reactions in Cancer Cells
|
Cyclometalated gold(III) complexes have been reported to template C-S cross-coupling reactions in a biological environment and acting as modifiers of cysteine residues. To broaden the scope of organogold complexes for covalent protein post-translational modification in cancer cells, an oxime-containing C^N-cyclometalated gold(III) compound was synthesised featuring a carboxylic acid group for either immobilisation on amine-bearing solid support (Au), or functionalisation with a fluorescent tag (Au-Fluo). Live-cell imaging revealed that Au-Fluo distributed evenly into SW480 colon carcinoma cells, with a slight preference for the nuclear and nucleolar compartments. Thioredoxin reductase 1 (TXNRD1) was observed as the major interactor of Au from SW480 cell lysates in chemoproteomic approaches and a 2 : 1 binding stoichiometry resulted from titration-dependent pull-downs. Direct interactions confirmed a high reactivity of Au towards the catalytic CysSec-dyad at the C-terminus of TXNRD1 and revealed double arylation events at this motif. Therefore, the observed Au-templated arylation of selenocysteine likely contributes to the compound’s biological effects. Proteome profiling of SW480 cancer cells treated with sub-cytotoxic concentrations of Au revealed an apparent reduction of the available selenium pool by down-regulating the detected selenoproteins, except TXNRD1. Additionally, Au treatment induced the NRF2-KEAP1 stress response, pointing towards a disturbance of the intracellular redox balance by Au-mediated covalent targeting of TXNRD1. Inhibition of heme oxygenase-1 (HMOX1), the most strongly induced NRF2-target, showed pronounced synergism with Au treatment. Overall, organogold compounds, templating the formation of C–S(Se) bonds in cells as a novel mode of action, hold promise for the targeted modification of (onco)proteins.
|
Lukas Skos; Claudia Schmidt; Sophie Thomas; Mihyun Park; Riccardo Bonsignore; Giorgia Del Favero; Thomas Mohr; Andrea Bileck; Christopher Gerner; Angela Casini; Samuel M. Meier-Menches
|
Biological and Medicinal Chemistry; Analytical Chemistry; Organometallic Chemistry; Mass Spectrometry; Bioorganometallic Chemistry; Small Molecule Activation (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f96a533fdae147faaa081e/original/selective-arylation-of-selenocysteine-of-thioredoxin-reductase-1-by-an-organogold-compound-expanding-the-tool-box-of-metal-templated-reactions-in-cancer-cells.pdf
|
60c758ebf96a00a2c0288f03
|
10.26434/chemrxiv.14614032.v1
|
A Chemical Approach to 2D-2D Heterostructures Beyond Van Der Waals: High-Throughput On-Device Covalent Connection of MoS2 and Graphene
|
<p>The most widespread method for the synthesis of 2D-2D heterostructures is the direct growth of one material on top of the other. Alternatively, one can manually stack flakes of different materials. Both methods are limited to one crystal/device at a time and involve interfacing the 2D materials through van der Waals forces, to the point that all these materials are known as van der Waals heterostructures. Synthetic chemistry is the paradigm of atomic-scale control, yet its toolbox remains unexplored for the construction of 2D-2D heterostructures. Here, we describe how to covalently connect 2H-MoS<sub>2</sub> flakes to several single-layer graphene field-effect transistors simultaneously, and show that the final electronic properties of the MoS<sub>2</sub>-graphene heterostructure are dominated by the molecular interface. We use a bifunctional molecule with two chemically orthogonal anchor points, selective for sulphides and carbon-based materials. Our experiments highlight the potential of the chemical approach to build 2D-2D heterostructures beyond van der Waals. </p>
|
Manuel Vázquez Sulleiro; Aysegul Develioglu; Ramiro Quirós-Ovies; Natalia Martín Sabanés; I. Jénnifer Gómez; Mariano Vera-Hidalgo; Víctor Sebastián; Jesús Santamaría; Enrique Burzurí; Emilio Pérez
|
Nanodevices; Nanostructured Materials - Nanoscience; Surface; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ebf96a00a2c0288f03/original/a-chemical-approach-to-2d-2d-heterostructures-beyond-van-der-waals-high-throughput-on-device-covalent-connection-of-mo-s2-and-graphene.pdf
|
60c73f18ee301cfd54c7882d
|
10.26434/chemrxiv.7212836.v1
|
An Activity-based Probe Targeting Non-catalytic, Highly Conserved Amino Acid Residues Within Bromodomains
|
<b>Bromodomain-containing proteins are epigenetic modulators involved in a wide range of cellular processes, from physiological recruitment of transcription factors to pathological disruption of gene regulation and cancer development. Since the druggability of these acetyl-lysine reader domains was established, efforts were made to develop potent and selective inhibitors across the entire family. Here we report the development of a small molecule based approach to covalently modify recombinant and endogenous bromodomain-containing proteins by targeting a conserved lysine and a tyrosine residue in the variable ZA or BC loops. Moreover, the addition of a reporter tag, via copper-catalyzed alkyne azide coupling, to an alkyne handle on the probe allowed in-gel visualization and selective pull-down of the desired bromodomains using both recombinant and endogenous proteins.</b>
|
Melissa D’Ascenzio; Kathryn Pugh; Rebecca Konietzny; Georgina Berridge; Cynthia Tallant; Shaima Hashem; Octovia P. Monteiro; Jason R. Thomas; Markus Schirle; Stefan Knapp; Brian D. Marsden; Oleg Fedorov; Chas Bountra; Benedikt M. Kessler; Paul E. Brennan
|
Bioorganic Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-10-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f18ee301cfd54c7882d/original/an-activity-based-probe-targeting-non-catalytic-highly-conserved-amino-acid-residues-within-bromodomains.pdf
|
67d1defbfa469535b900b19a
|
10.26434/chemrxiv-2025-fq66p-v4
|
Reactive Quantum-Mechanical Molecular Dynamics Simulations to Reveal Mechanisms of Enzyme Catalysis
|
A complete understanding of enzyme mechanisms requires atomistic details of chemical reactions. Quantum-based molecular dynamics simulations (QMD) are a potential source of this information, but tradeoffs between accuracy and computational cost have limited their use. Here, we develop a reactive QMD approach to investigate mechanisms of isocyanide hydratase (ICH) catalysis. In QMD simulations, molecular analogs of ICH active site residues reacted with para-nitrophenol isocyanide, forming a thioimidate intermediate. Analysis of simulated atomic configurational and charge dynamics revealed a pathway where protonation of the isocyanide carbon occurs prior to thioimidate formation. X-ray crystallography and functional assays of ICH mutants suggest this order of events might occur during enzyme catalysis. Mobile protons play essential roles in many enzymes, yet they are difficult to observe experimentally, making the ordering of proton-dependent steps ambiguous in many enzyme mechanisms. The ability to directly simulate reactions relevant to enzyme catalysis involving mobile protons demonstrates the significance of our reactive QMD approach and motivates further biological applications.
|
Rae Ann Corrigan Grove; Michael A. Moxley; Christian F. A. Negre; Marc J. Cawkwell; Anders M. N. Niklasson; Susan M. Mniszewski; Nathan Smith; Kevin Prososki; Mark A. Wilson; Michael E. Wall
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1defbfa469535b900b19a/original/reactive-quantum-mechanical-molecular-dynamics-simulations-to-reveal-mechanisms-of-enzyme-catalysis.pdf
|
60c74060f96a006646286291
|
10.26434/chemrxiv.7430216.v2
|
A Generally Applicable Atomic-Charge Dependent London Dispersion Correction Scheme
|
The D4 model is presented for the accurate computation of London dispersion interactions in density functional theory approximations (DFT-D4) and generally for atomistic modeling methods. In this successor to the DFT-D3 model, the atomic coordination-dependent dipole polarizabilities are scaled based on atomic partial charges which can be taken from various sources. For this purpose, a new charge-dependent parameter-economic scaling function is designed. Classical charges are obtained from an atomic electronegativity equilibration procedure for which efficient analytical derivatives are developed. A numerical Casimir-Polder integration of the atom-in-molecule dynamic polarizabilities yields charge- and geometry-dependent dipole-dipole dispersion coefficients. Similar to the D3 model, the dynamic polarizabilities are pre-computed by time-dependent DFT and elements up to radon are covered. For a benchmark set of 1225 dispersion coefficients, the D4 model achieves an unprecedented accuracy with a mean relative deviation of 3.8% compared to 4.7% for D3. In addition to the two-body part, three-body effects are described by an Axilrod-Teller-Muto term. A common many-body dispersion expansion was extensively tested and an energy correction based on D4 polarizabilities is found to be advantageous for some larger systems. Becke-Johnson-type damping parameters for DFT-D4 are determined for more than 60 common functionals. For various energy benchmark sets DFT-D4 slightly outperforms DFT-D3. Especially for metal containing systems, the introduced charge dependence improves thermochemical properties. We suggest (DFT-)D4 as a physically improved and more sophisticated dispersion model in place of DFT-D3 for DFT calculations as well as for other low-cost approaches like semi-empirical models.<br /><br />
|
Eike Caldeweyher; Sebastian Ehlert; Andreas Hansen; Hagen Neugebauer; Sebastian Spicher; Christoph Bannwarth; Stefan Grimme
|
Bonding; Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74060f96a006646286291/original/a-generally-applicable-atomic-charge-dependent-london-dispersion-correction-scheme.pdf
|
633c012dcf38292bb5bc9d0f
|
10.26434/chemrxiv-2022-d3m6p-v2
|
Ensemble Simulations of
2-Hydroxypropyl-β-cyclodextrin Complexes with
All-Atom Molecular Dynamics Simulations
|
2-Hydroxypropyl-β-cyclodextrins (HP-β-CDs) ability to form inclusion complexes with lipophilic compounds is important both to treat Niemann Pick Type C disease
and as part of a more general drug-formulation as a drug carrier. Theoretical studies of inclusion complexes with classical molecular dynamics simulations of HP-β-CDs are
hampered by the fact that there are more than 2 million possible isomers to consider. We construct a general GLYCAM06 (Kirschner, K. N. et. al., J. Comput. Chem.
2007, 29, 622–655) compatible force field to treat all possible isomers of HP-β-CDs and investigate the effect on free energies of binding obtained from the MM/GBSA approach when increasing the degree of substitution. We find improved binding proportional to the added side chains. To show the applicability of the HP-β-CD force field, we generate an ensemble of simulations guided by experimentally determined distributions of isomers from mass spectrometry. Our results for ibuprofen and ketoprofen shows that acceptable accuracy in free energies of binding can be obtained with ensembles generated from around 40 isomers, but this is dependent on the guest molecule. We also investigate a simple linear relation between molecular log(P ) and free energy of binding for inclusion complexes of HP-β-CD. The linear model is promising but we find that the accuracy is too dependent on a single simulation. The presented force field and computational approach should provide for more realistic simulations.
|
Jeppe Tværmose Munk; Simon Nygaard-Thomsen; Thorleif Riis Bay Stokholm; Mads Rosander Langhorn; Casper Steinmann
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2022-10-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c012dcf38292bb5bc9d0f/original/ensemble-simulations-of-2-hydroxypropyl-cyclodextrin-complexes-with-all-atom-molecular-dynamics-simulations.pdf
|
6375253e21b45c37161e1853
|
10.26434/chemrxiv-2022-wrl2l
|
Biomimetic cell structures: Probing Induced pH-Feedback Loops and pH Self-Monitoring in Cytosol Using Binary Enzyme-loaded Polymersomes in Proteinosome
|
Structures and functions of eukaryotic cells with an outer permeable membrane, motility, a cytoskeleton, biomolecules diffusion, and functional organelles can be imitated by a multi-compartmentalized and large-sized protocell containing various synthetic organelles. Herein, two kinds of artificial organelles with stimuli-trigged regulation ability, glucose oxidase-(GOx)-loaded pH-responsive polymersomes A (GOx-Psomes A) and urease-loaded pH-responsive polymersomes B (Urease-Psomes B) for probing biomimetic pH homeostasis, and a pH-sensor (Dextran-FITC) are encapsulated into proteinosomes by Pickering emulsion method. Thus, the polymersomes-in-proteinosome system is realized. Alternating input-regulation of fuels (glucose or urea) outside the protocell penetrates the membrane of proteinosomes and enters into GOx-Psomes A and Urease-Psomes B to produce chemical\biological signals (gluconic acid or ammonia) resulting in pH-feedback loops (pH jump and pH drop). This will counteract the catalytic “switch on” or “switch off” of enzyme-loaded Psomes A and B owing to their different pH-responsive membranes. Thus, the Dextran-FITC promotes a controlled cytosolic spatial organization and the detection of slight pH fluctuations in the lumen of protocells. Overall, this approach shows heterogeneous polymersome-in-proteinosome architectures with sophisticated features such as induced input-regulated pH changes mediated by negative/positive feedback in loops and cytosolic pH self-monitoring, requirements strictly needed in an advanced protocell design.
|
Kehu Zhang; Silvia Moreno; Xueyi Wang; Yang Zhou; Susanne Boye; Dagmar Voigt; Brigitte Voit; Dietmar Appelhans
|
Biological and Medicinal Chemistry; Polymer Science; Bioengineering and Biotechnology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-11-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6375253e21b45c37161e1853/original/biomimetic-cell-structures-probing-induced-p-h-feedback-loops-and-p-h-self-monitoring-in-cytosol-using-binary-enzyme-loaded-polymersomes-in-proteinosome.pdf
|
6231c1ed2c501057a27d082e
|
10.26434/chemrxiv-2022-r6qc2
|
Optical Spectra of Plasmon--Exciton Core--Shell Nanoparticles: A Heuristic Quantum Approach
|
Light--matter coupling in plasmonic nanocavities has been widely studied in the past years. Yet, for core--shell particles, popular electromagnetic models that use the classical Lorentz oscillator to describe the shell predict extinction spectra with three maxima, if the plasmon and the shell absorption are in resonance. In contrast, experiments exhibit only two peaks as also expected from simple quantum models of hybrid states. In order to reconcile the convenient and widely used classical electromagnetic description with experimental data, we connect it to the quantum world by conceiving a heuristic quantum model. Our model is based on the permittivity of a two-level system in a classical electric field derived from the optical Bloch equations. The light--matter coupling is included via the collective vacuum Rabi frequency $\Omega_0$. Using our model, we obtain excellent agreement with a series of experimental extinction spectra of particles with various coupling strengths due to a systematic size variation. The suppression of the third maximum, which mainly stems from the absorption in the shell, can be interpreted as a vacuum induced power broadening, which may occur in lossy (plasmonic) cavities below the strong-coupling regime.
|
Felix Stete; Wouter Koopman; Carsten Henkel; Oliver Benson; Günther Kewes; Matias Bargheer
|
Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Quasiparticles and Excitations; Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6231c1ed2c501057a27d082e/original/optical-spectra-of-plasmon-exciton-core-shell-nanoparticles-a-heuristic-quantum-approach.pdf
|
628e423d87d01f0585f1dc92
|
10.26434/chemrxiv-2022-xtzxz
|
Zirconium-Catalysed Hydrosilylation of Esters and Depolymerisation of Polyester Plastic Waste
|
Schwartz’s reagent, Cp2Zr(H)Cl, has traditionally been used as a stoichiometric reagent for the reduction of unsaturated organic molecules. Recently, methods to use Cp2Zr(H)Cl as a catalyst have been developed through turnover of the Zr–X intermediates, formed upon reaction with an organic substrate, with hydride reagents. Herein, we report the development of a new catalytic pathway for the reduction of esters that uses the bench-stable silane Me(OMe)2SiH (DMMS) as a mild stoichiometric reductant and Cp2Zr(H)Cl as the catalyst. This system exploits the regeneration of Zr–H through the sigma bond metathesis of Zr–O and Si–H to achieve catalyst turnover. These reaction conditions tolerate a range of reducible functional groups (e.g. alkyne, alkene, and nitro) and give high yields of the corresponding alcohol (up to 91% isolated yield). We have also applied this methodology to the reductive depolymerisation of polyesters found in household plastic waste.
|
Liam Donnelly; Marie Kobylarski; Jean-Claude Berthet; Thibault Cantat
|
Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Organocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e423d87d01f0585f1dc92/original/zirconium-catalysed-hydrosilylation-of-esters-and-depolymerisation-of-polyester-plastic-waste.pdf
|
657a11befd283d7904ee54ee
|
10.26434/chemrxiv-2023-bq4fv
|
Investigation of the Electrocatalytic Reduction of Peroxydisulfate Using Scanning Electrochemical Microscopy
|
The elementary steps of the electrocatalytic reduction of S2O82– using the Ru(NH3)63+/2+ redox couple were investigated using scanning electrochemical microscopy (SECM) and steady-state voltammetry (SSV). SECM investigations were carried out in a 0.1 M KCl solution using a 3.5-µm radius carbon ultramicroelectrode (UME) as the SECM tip and a 25-µm radius platinum UME as the substrate electrode. Approach curves were recorded in the positive feedback mode of SECM by reducing Ru(NH3)63+ at the tip electrode and oxidizing Ru(NH3)62+ at the substrate electrode, as a function of the tip-substrate separation and S2O82– concentration. The one-electron reaction between electrogenerated Ru(NH3)62+ and S2O82– yields the unstable S2O83•-, which rapidly dissociates to produce highly oxidizing SO4•–. Because SO4•– is such a strongly oxidizing species, it can be further reduced at both the tip or the substrate, or it can react with Ru(NH3)62+ to regenerate Ru(NH3)63+. SECM approach curves display a complex dependence on the tip-substrate distance, d, due to redox mediation reactions at both the tip and the substrate. Finite element method (FEM) simulations of both SECM approach curves and SSV confirm a previously proposed mechanism for the mediated reduction of S2O82– using Ru(NH3)63+/2+ redox couple. Our results provide a lower limit for dissociation rate constant of S2O83•– (~ 1 × 106 s–1), as well as the rate constants for electron transfer between SO4•– and Ru(NH3)62+ (~ 1 × 109 M–1s–1) and between S2O82– and Ru(NH3)62+ (~7 × 105 M–1s–1).
|
Seyyedamirhossein Hosseini; Gergely Solymosi; Henry White
|
Analytical Chemistry; Electrochemical Analysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657a11befd283d7904ee54ee/original/investigation-of-the-electrocatalytic-reduction-of-peroxydisulfate-using-scanning-electrochemical-microscopy.pdf
|
657b2838e9ebbb4db9e0f0c7
|
10.26434/chemrxiv-2023-wsj63
|
Formation and Stability of μ2-Peroxo on Titanosilicates, Anatase and Rutile: Implications for Zeotype Catalysts
|
Extra-framework TiO2 in titanosilicate oxidation catalysts has generally been linked with low selectivity and great emphasis has been put on developing synthetic protocols that yield anatase-free materials. Here, using 17O solid-state NMR spectroscopy, we investigate the formation and stability of μ2-peroxo groups on both titanosilicates containing or not containing extra-framework TiO2 as well as TiO2 polymorphs. By comparison with TiO2 nanoparticle references, H2O2 activation (e.g. peroxo formation) and decomposition is proposed to be related to the presence of rutile-like extra-framework TiO2. In fact, μ2-peroxo species can form and remain stable on anatase, whereas they decompose quickly on rutile. According to DFT calculations, the high stability of μ2-peroxo surface species on anatase is due to the specific arrangement of μ2-oxo groups on the 101 surface that allows for stabilization of key-intermediates through H-bonding. Notably, the μ2-peroxo species formed on titanosilicates and anatase display distinct 17O NMR spectroscopic signatures, that relates directly to the Ti coordination environments, and can thus be distinguished.
|
Lukas Lätsch; Imke B. Müller; Christoph J. Kaul; Trees De Baerdemaeker; Andrei-Nicolae Parvulescu; Karsten Seidel; Natalia Trukhan; J. Henrique Teles; Christophe Copéret
|
Catalysis
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657b2838e9ebbb4db9e0f0c7/original/formation-and-stability-of-2-peroxo-on-titanosilicates-anatase-and-rutile-implications-for-zeotype-catalysts.pdf
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6422d30391074bccd06d43bc
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10.26434/chemrxiv-2023-dwwdt
|
Density functional theory investigation of green stabilizer reactions: curcumin in nitrocellulose-based propellants
|
Stabilizers are molecules used in the composition of nitrocellulose-based propellants for inhibiting the autocatalytic degradation process that produces nitrous gases and free nitric acids. Curcumin – (1E,6E)-1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione – is a promising green stabilizer in new formulations of environmental and health-friendly single-base propellants. This work investigates reactions between curcumin and nitrogen dioxide NO2 using density functional theory to unveil their mechanisms. For this purpose, we obtained optimized geometries of equilibrium and transition states, minimum energy paths, and thermochemical data for aromatic ring nitration and hydrogen release reactions. The results indicate that nitration of the aromatic ring of curcumin and the formation of a curcumin-based free radical are viable. The computed Gibbs free activation energy (∆‡G°) and activation enthalpy (∆‡H°) for two different temperatures, 298.15 K (room temperature) and 363.15 K (a typical temperature used in aging tests), are respectively 43.64 kcal/mol and 44.78 kcal/mol for the first reaction, and 31.54 kcal/mol and 35.31 kcal/mol for the second. Therefore, the radical-based mechanism is kinetically favored.
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João Luis Nascimento Mossri; Rodrigo Leonardo Barboza Rodrigues; Jakler Nichele; Itamar Borges Jr
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Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Processes
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CC BY NC ND 4.0
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CHEMRXIV
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2023-03-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6422d30391074bccd06d43bc/original/density-functional-theory-investigation-of-green-stabilizer-reactions-curcumin-in-nitrocellulose-based-propellants.pdf
|
60c743f6bb8c1a57f23da414
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10.26434/chemrxiv.9722603.v1
|
Selective Halogenation of Pyridines Using Designed Phosphine Reagents
|
Halopyridines are key building blocks for synthesizing pharmaceuticals, agrochemicals, and ligands for metal complexes, but strategies to selectively halogenate pyridine C–H precursors are lacking. We designed a set of heterocyclic phosphines that are selectively installed at the 4-position of pyridines as phosphonium salts and then displaced with halide nucleophiles. A broad range of unactivated pyridines can be halogenated, and the method is viable for late-stage halogenation of complex pharmaceuticals. The study concludes that both tuning the phosphonium electrophilicity and pyridine substitution patterns influence the efficiency of the carbon-halogen bond-forming step.<br />
|
Jeffrey N. Levy; Ren-Rong Liu; Andrew McNally
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions
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CC BY NC ND 4.0
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CHEMRXIV
|
2019-08-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f6bb8c1a57f23da414/original/selective-halogenation-of-pyridines-using-designed-phosphine-reagents.pdf
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66e7e310cec5d6c14233bf60
|
10.26434/chemrxiv-2024-v4ffr
|
Construction of N−E bonds via Lewis acid-promoted functionalization of chromium-dinitrogen complexes
|
Direct conversion of dinitrogen (N2) into N-containing compounds beyond ammonia under ambient conditions remains a longstanding challenge. Herein, we present a Lewis acid-promoted strategy for diverse nitrogen-element bonds formation from N2 using chromium dinitrogen complex [Cp*(IiPr2Me2)Cr(N2)2]K (1). With the help of Lewis acids AlMe3 and BF3, we successfully trapped a series of fleeting diazenido intermediates and synthesized value-added compounds containing N−B, N−Ge, and N−P bonds with 3d metals for the first time, offering a new method for isolating unstable intermediates. Furthermore, the formation of N−C bonds was realized under more accessible conditions that avoided undesired side reactions. DFT calculations revealed that Lewis acids enhanced the participation of dinitrogen units in the frontier orbitals, thereby promoting electrophilic functionalization.
|
Zhubao Yin; Gao-Xiang Wang; Xuechao Yan; Junnian Wei; Zhenfeng Xi
|
Organometallic Chemistry; Bond Activation; Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2024-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e7e310cec5d6c14233bf60/original/construction-of-n-e-bonds-via-lewis-acid-promoted-functionalization-of-chromium-dinitrogen-complexes.pdf
|
626cd33a5b900931f621cc49
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10.26434/chemrxiv-2022-cnpr2
|
Heptagon-embedded π-Expanded Thieno- and N-Methylpyrrolo-pyridazines with Substantial Out-of-plane Dipole Moment
|
Herein we describe the synthesis and characterization of fully-fused tetraphenyl-thieno[3,4-d]pyridazine 1 and N-methylpyrrolo[3,4-d]pyridazine 2 with two embedded seven-membered rings. Owing to the incorporated heptagon, both of 1 and 2 exhibited Cs-symmetric saddle conformations in the solid state with mean plane deviation around 0.38 Å. π-Expanded thienopyridazine 1 showed a 1-D columnar packing along the b axis with net dipole moment aligning perpendicular to the b axis in the polar crystal system Pc. On the other hand, 2 formed a partially π-stacked brick-work structure in the crystal. In addition to the Cs-symmetric saddle conformations found in the crystals, DFT calculation found C2-symmetric twisted conformations of both 1 and 2 close in energy to the saddle conformations. The barrier of conformational interconversion was calculated to be 32 (1) and 31 kJ·mol−1 (2), and the interconversion occur fast even at −60 °C as evidenced by VT-NMR studies. While 1 and 2 have moderately curved structures, optical and electrochemical studies revealed effective π-conjugation over the fused diphenylene units, which is also supported by DFT calculation. As the result of the intrinsic large dipole moment of thieno- and pyrrolo-pyridazines and the notably curved structure, 1 (2) has a substantial out-of-plane dipole moment of 2.0 (3.3) D in the saddle conformations.
|
Masato Hisada; Daiki Shimizu; Kenji Matsuda
|
Organic Chemistry; Physical Organic Chemistry
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-05-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626cd33a5b900931f621cc49/original/heptagon-embedded-expanded-thieno-and-n-methylpyrrolo-pyridazines-with-substantial-out-of-plane-dipole-moment.pdf
|
61a4eba6dff1cc4266368684
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10.26434/chemrxiv-2021-gq6hr-v2
|
Confronting the Challenging Asymmetric Addition of Vinyl Arene Pronucleophiles into Ketones: Ligand-Controlled Regiodivergent Processes Through a Dearomatized Allyl-Cu Species
|
The selective reductive coupling of vinyl arenes and ketones represents a versatile approach for the rapid construction of enantiomerically enriched tertiary alcohols. Herein, we demonstrate a CuH-catalyzed regiodivergent coupling of vinyl arenes and ketones, in which the selectivity is controlled by the ancillary ligand. This approach leverages an in situ generated benzyl- or dearomatized allyl-Cu intermediate, yielding either the dearomatized or exocyclic addition products, respectively. The method exhibits excellent regio-, diastereo- and enantioselectivity, and tolerates a range of common functional groups and heterocycles. Computational studies suggest that the regio- and enantioselectivity are controlled by the ancillary ligand, while the diastereoselectivity is enforced by steric interactions between the alkyl-Cu intermediate and ketone substrates in a six-membered cyclic transition state.
|
Yuyang Dong; Alexander Schuppe; Binh Khanh Mai; Peng Liu; Stephen Buchwald
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Catalysis; Transition Metal Complexes (Organomet.)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2021-11-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a4eba6dff1cc4266368684/original/confronting-the-challenging-asymmetric-addition-of-vinyl-arene-pronucleophiles-into-ketones-ligand-controlled-regiodivergent-processes-through-a-dearomatized-allyl-cu-species.pdf
|
64fd6e3799918fe537af4c76
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10.26434/chemrxiv-2023-g7h7t
|
Creating Glassy States of Dicarboxylate-bridged Coordination Polymers
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We report the direct formation of dicarboxylate-based coordination polymer glasses through thermal dehydration. The rearrangement of the coordination networks caused by dehydration was monitored by in-situ powder X-ray diffraction, infrared spectroscopy, and synchrotron X-ray characterizations. The microporosity and mechanical properties of these glasses were investigated.
|
Zeyu FAN; Yong-Sheng Wei; Chinmoy Das; Kazuyoshi Kanamori; Hiroki Yamada; Koji ohara; Satoshi Horike
|
Physical Chemistry; Inorganic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fd6e3799918fe537af4c76/original/creating-glassy-states-of-dicarboxylate-bridged-coordination-polymers.pdf
|
677d57226dde43c908a1883c
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10.26434/chemrxiv-2025-3r9qt
|
P1 center network in high-pressure high-temperature diamonds is a readily accessible source of nuclear hyperpolarization at 14 T
|
We investigate nitrogen substitution defects, also known as P1 centers, in type 1b diamonds as a source of electron spin polarization that is readily transferred to 13C nuclear spins within the diamond matrix at 14 Tesla by dynamic nuclear polarization (DNP) at room temperature down to 35 K. The goal was to obtain a quantitative model for clustered P1 centers in diamonds generated under high pressure and high temperature (HPHT). The study relied on frequency-stepped measurements of DNP profiles under magic angle spinning (MAS) using the mm-wave output of a frequency-tunable gyrotron and a regular superconducting NMR magnet set at a single field. The gyrotron output frequency was controlled via the temperature of the gyrotron cavity over 260 MHz centered around 395.3 GHz and had an output power of ~1 W across this range. We observe 13C on/off signal enhancements of up to 700-fold at room temperature under MAS and in static mode, and 130-fold between 35K and 100 K. Modeling of the experimental results revealed the dominant role of P1 clusters harboring inter-P1 dipolar and exchange couplings exceeding 100 MHz in achieving effective 13C DNP at 14.1 T. Clustered P1 centers may be of great utility in generating highly enhanced 13C NMR signal in high-pressure high-temperature diamond as a source of contrast for NMR and MRI applications, or a major decoherence source in quantum sensing applications.
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Quentin Stern; Jinlei Cui; Raj Chaklashiya; Celeste Tobar; Martyna Judd; Orit Nir-Arad; Daphna Shimon; Ilia Kaminker; Hiroki Takahashi; Jagadishwar R. Sirigiri; Songi Han
|
Physical Chemistry; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d57226dde43c908a1883c/original/p1-center-network-in-high-pressure-high-temperature-diamonds-is-a-readily-accessible-source-of-nuclear-hyperpolarization-at-14-t.pdf
|
64206d37647e3dca998945bd
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10.26434/chemrxiv-2023-2260m
|
Synthesis of polydiacetylene (PDA) particles for detection of histamine
|
Histamine poisoning as a problem of public health and safety attracted attention worldwide. There is a significant need for devices that are capable of measuring histamine levels rapidly with high sensitivity. In this study, a colorimetric sensor based on polydiacetylene (PDA) was developed for histamine detection. Under optimal conditions, the biosensor showed a linear response to different concentrations of histamine within the range of 21 ppm to 210 ppm with a low detection limit of 10.1 ppm. Moreover, the biosensor was successfully employed to detect the histamine level in the spiked canned fish sample. With high sensitivity and recovery values, this assay can be used to monitor the quality of canned fish, suggesting that it holds great potential for on-site detection and real-time monitoring.
|
Maryam Naseri; Christian Code; Yi Sun
|
Analytical Chemistry; Polymer Science; Nanoscience; Biopolymers; Nanodevices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64206d37647e3dca998945bd/original/synthesis-of-polydiacetylene-pda-particles-for-detection-of-histamine.pdf
|
6308f9c2f07ee1887af2da16
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10.26434/chemrxiv-2022-hqrbp-v2
|
A Strained Intramolecular P/Al-FLP and its Reactivity toward Allene
|
FLPs featuring aluminum-phosphane interactions, spring-loaded by a rigid biphenylene linker, have been accessed through a route where trimethyltin units at phosphane-functionalized organic backbones are exchanged by an AlCl2 moiety. The latter is saturated through the interaction with the phosphane donors sufficiently to allow for the isolation of the compounds in monomeric form but upon contact with substrates like CO2 these are readily bound by the Al/P site with release of strain. The system could also be utilized for a unique reactivity, namely the activation of allene, which has not been described in FLP chemistry so far.
|
Christian Limberg; Patrick Federmann; Tamino Bosse; Siad Wolff; Beatrice Braun; Christian Herwig
|
Inorganic Chemistry; Organometallic Chemistry; Frustrated Lewis Pairs; Main Group Chemistry (Organomet.); Small Molecule Activation (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6308f9c2f07ee1887af2da16/original/a-strained-intramolecular-p-al-flp-and-its-reactivity-toward-allene.pdf
|
60c74d0aee301c3d39c7a1b0
|
10.26434/chemrxiv.12581819.v1
|
Computational Studies Towards Identification of Lead Herbal Compounds of Medicinal Importance for Development of Nutraceutical Against COVID-19
|
In the present study, we have performed the in-silico study of SARS-CoV-2
structure with different herbal compounds of medicinal importance. We selected
four <a>viral key proteins of SARS-CoV-2 </a>structure i.e ACE-2
Receptor, Main Protease (Mpro), APO Form, Cryo- electron microscopy structure
for the Molecular docking followed by the molecular dynamic simulation. Using
this simple in silico approach based on the molecular docking and <a>MD simulation </a>of protein and phytochemicals, we have
identified potential lead candidates for the development of low cost nutraceuticals,
which can be used against SARS-CoV-2 virus. Our analysis suggested that
phytochemicals obtained from <i>Phyllanthus emblica</i> and <i>Azadirachta
indica</i> have the highest potential to bind with ACE2 receptor or main protease
of SARS-CoV-2, inhibiting the protease enzymatic activity. The lead compounds
of herbal origin were docked and simulated on viral key proteins of SARS-CoV-2 structure
to evaluate the binding affinity of these phytochemicals along with the type of
interaction and its stability in terms of <a>RMSD</a> and <a>Ramachandran plot</a>. Further, these results were also
verified by drug likeness properties by using SwissADME software. Overall, our
results suggest that out of 14 herbal compounds, Nimbolide and Withaferin-A has
great potential to be developed as low-cost nutraceuticals against SARS-CoV-2 virus,
which is the need of hour.
|
Amit Kumar Srivastav; Sanjeev Kumar Gupta; Umesh Kumar
|
Computational Chemistry and Modeling
|
CC BY NC 4.0
|
CHEMRXIV
|
2021-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d0aee301c3d39c7a1b0/original/computational-studies-towards-identification-of-lead-herbal-compounds-of-medicinal-importance-for-development-of-nutraceutical-against-covid-19.pdf
|
67ced7c6fa469535b9b73bff
|
10.26434/chemrxiv-2025-rcztm
|
A Butterfly-like Fluorescent Tracker for Dynamic Polymers
|
Optically tracking constitutional dynamics provides a time-resolved, non-invasive, and visually interpretable approach to unravel-ing microscopic complexity in system chemistry. Here we report a butterfly-like fluorescent tracker, featuring excited-state conformational adaptivity, capable of sensing the subtle microscopic dynamics of polymers as a ratiometric fluorescent probe. The key design is coupling the fluorophore’s conformational relaxation dynamics to microenvironmental constraints imposed by polymer structural features—such as chain length, conformation, and inter-/intramolecular interactions. By employing the fluorophore as a bifunctional initiator, we grafted two dynamic polymer chains onto its phenyl "wings", creating a single-fluorophore tracker that dynamically interacts with its environment. This system functions as a highly sensitive ratiometric probe, optically reporting microscopic polymer dynamics in real time, including polymerization kinetics, chain folding/unfolding transitions, and depolymerization processes. Systematic studies demonstrate the broad applicability of this concept across diverse polymeric systems, with distinct emission signatures enabling differentiation between systems. The probe’s ability to correlate fluorescence output with microenvironmental changes reveals its utility in both fundamental and applied contexts. We anticipate this conformationally adaptive fluo-rescent platform will advance research in dynamic chemistry, particularly for real-time monitoring of polymeric systems and the development of responsive materials.
|
Shudong Zheng; Da-Hui Qu; He Tian; Qi Zhang
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ced7c6fa469535b9b73bff/original/a-butterfly-like-fluorescent-tracker-for-dynamic-polymers.pdf
|
611144d8e540bba328748c64
|
10.26434/chemrxiv-2021-pk3k7-v5
|
Radiative Contributions Dominate Plasmon Broadening for Post-Transition Metals in the Ultraviolet
|
We use classical electrodynamics calculations to investigate the plasmonic properties of the post-transition metals Al, Bi, Ga, In, and Sn, which are active in the ultraviolet, focusing in particular on the material- and resonance-dependent origins of plasmon broadening. Analytic Mie theory, the modified-long wavelength approximation, and the quasistatic dipole approximation together show that radiative processes dominate plasmon dephasing and damping in small (5–25 nm radius) Al, Bi, Ga, In, and Sn spheres. For Al, Ga, In, and Sn, the radiative contribution (~1–2 eV) to the plasmon linewidth is more than 100-fold greater than the non-radiative contribution (0.001–0.02 eV) derived from the bulk dielectric function. This is significantly different than what is observed for Ag spheres, where non-radiative contributions (~0.1 eV) are the primary source of broadening up to a radius of 25 nm. Overall, these data suggest that the plasmonic properties, dephasing, and lifetimes for Al, Ga, In, and Sn —and to a lesser extent Bi— spheres are qualitatively similar. To develop a more general understanding of the relationship between plasmon energy and linewidth, we use a model for ideal free-electron Drude metals. It is seen that the linewidth increases at higher energies even for lossless Drude metals, suggesting that the increased broadening observed in UV-active metals is a generalizable observation. These data have important implications for the use of these metals for ultraviolet plasmonics. The increased importance of radiative damping for post-transition metals could influence the ability to harvest photons, generate hot carriers, and enhance spectroscopy in the ultraviolet while providing new opportunities for manipulating high-energy photons.
|
Maria Fonseca Guzman; Michael Ross
|
Nanoscience; Plasmonic and Photonic Structures and Devices
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611144d8e540bba328748c64/original/radiative-contributions-dominate-plasmon-broadening-for-post-transition-metals-in-the-ultraviolet.pdf
|
6128b58327d906e71a76c40a
|
10.26434/chemrxiv-2021-8wsbs-v2
|
Potential Energy Curves of Molecular Nitrogen for Singly and Doubly Ionized States with Core and Valence Holes
|
<p>Our manuscript, presents the computation of potential energy curves of all possible singly and doubly ionized states of molecular nitrogen. Accurate representation of the potential energy curves of ionized states of N<sub>2</sub> is essential to explicitly treat coupled electron-nuclear dynamics. In this work, we compute the potential energy curves of the valence as well as the core and inner valence singly and doubly ionized states of N<sub>2</sub>. These curves pave way to study the interplay between photoionization and Auger spectra when molecular nitrogen interacts with free electron lasers.</p><p>Computation of inner valence or core ionized potential energy curve is not trivial due to the well-known problem of variational collapse of the wavefunction to the lowest energy state. We circumvent this problem by implementing a two-step optimization scheme within the multi-configurational self-consistent field approach. Such a two-step optimization scheme has been previously implemented to compute potential energy curves of core ionized states of di-atomic molecules with one hole. Herein, we show the general applicability of this two-step optimization method by computing potential energy curves of both singly and doubly ionized states of N<sub>2 </sub>with valence and core holes. Calculation of potential energy curves for core ionized polyatomic systems are scarce. Moreover, our approach is system independent and can be easily extended to calculate multiple-core ionized states. To the best of our knowledge, this is the first calculation of potential energy curves for doubly ionized states of a diatomic molecule<sub> </sub>with two core (or inner valence) holes.</p>
|
Debarati Bhattacharya; K. R. Shamasundar; Agapi Emmanouilidou
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6128b58327d906e71a76c40a/original/potential-energy-curves-of-molecular-nitrogen-for-singly-and-doubly-ionized-states-with-core-and-valence-holes.pdf
|
60c73d35702a9ba9dc189af4
|
10.26434/chemrxiv.5496916.v1
|
pH-Dependent Cooperativity and Existence of a Dry Molten Globule in the Folding of a Miniprotein BBL
|
<p>Solution pH plays an important role in protein dynamics, stability, and folding; however, detailed mechanisms remain poorly understood. Here we use continuous constant pH molecular dynamics in explicit solvent with pH replica exchange to explore the pH-dependent stability and folding mechanism of a miniprotein BBL, which has drawn intense debate in the past. Consistent with the two-state model, simulations showed native and denatured states with pH-dependent populations. However, at pH 7, the folding barrier is marginal and it vanishes as pH is decreased to 5, in agreement with the downhill folding hypothesis. As pH continues to decrease, the unfolding barrier lowers and denaturation is triggered by the protonation of Asp162, consistent with experimental evidence. Interestingly, unfolding proceeded via a sparsely populated intermediate, with intact secondary structure and a compact, unlocked hydrophobic core shielded from solvent, lending support to the recent hypothesis of a universal dry molten globule in protein folding. Our work demonstrates that constant pH molecular dynamics is a unique tool for testing this and other hypotheses to advance the knowledge in protein dynamics, stability, and folding.</p>
|
Jana Shen; Zhi Yue
|
Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-10-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d35702a9ba9dc189af4/original/p-h-dependent-cooperativity-and-existence-of-a-dry-molten-globule-in-the-folding-of-a-miniprotein-bbl.pdf
|
66955dd801103d79c518229f
|
10.26434/chemrxiv-2023-s2zwg-v2
|
In situ Visualization of Cluster-mediated Oxidation Dynamics and Kinetics on Cu(111)
|
The structural evolution of Cu(111) surfaces in O₂ was studied using in situ scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. The
spontaneous formation of Cu₃O clusters was observed on Cu(111) and resolved at an atomic scale. These Cu₃O clusters formed preferentially at step edges, serve as
building blocks, which diffuse across neighboring terraces, coalesce into larger clusters, and eventually transform into "5-7" Cu₂O overlayers at room temperature and above.
DFT calculations elucidated the selective formation of Cu₃O clusters, originating from Cu detachment near steps and facilitating oxide growth front expansion. A comparison
between cluster diffusion and attachment demonstrated the growth dynamics of compact Cu₂O morphologies on terraces. Simulations predicted preferential oxide
growth from {100}-oriented steps and favored O diffusion along adjacent {111} facets, explaining the observed triangular fractal morphologies of Cu2O at steps. Our
combined STM and DFT approach provides insights into cluster-mediated oxidation dynamics on Cu(111) and could be adapted to understand larger-scale oxidation
processes.
|
Hao Chen; Matthew T. Curnan; qingfei Liu; Yunjian Ling; Jiayu Lv; Yangsheng Li; Wugen Huang; Changbao Zhao; Rui Wang; Zhongmiao Gong; Yi Cui; Jeong Woo Han; Judith C. Yang; Wissam A. Saidi; Miquel Salmeron; Fan Yang
|
Physical Chemistry; Materials Science; Catalysis; Heterogeneous Catalysis; Clusters; Spectroscopy (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66955dd801103d79c518229f/original/in-situ-visualization-of-cluster-mediated-oxidation-dynamics-and-kinetics-on-cu-111.pdf
|
64217798647e3dca9994e401
|
10.26434/chemrxiv-2023-8v4gb
|
Recent developments in design of novel water-soluble BODIPYs and their applications: an updated review
|
Boron-dipyrromethene (BODIPY) and their derivatives play an important role in the area of organic fluorophore chemistry. The water-soluble boron-dipyrromethene dyes have increasingly received interest, recently. The structural modification of BODIPY core by incorporating different neutral and ionic hydrophilic groups makes it water soluble. The important hydrophilic groups such as quaternary ammonium, sulfonate, oligo-ethylene glycol, dicarboxylic acid, and sugar moieties significantly increased the solubility of these dyes in the water while preserving their photophysical properties. As a result, these fluorescent dyes are utilized in aqueous systems, for applications such as chemosensors, cell imaging, anti-cancer, bio-labelling, biomedicine, metal ion detection, and photodynamic treatment. This review covers most current developments in design and synthesis of water-soluble BODIPY derivatives and their wide applications since 2014.
|
Chandra Sekhara Mahanta; V. Ravichandiran; Sharada Prasanna Swain
|
Materials Science; Biological Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64217798647e3dca9994e401/original/recent-developments-in-design-of-novel-water-soluble-bodip-ys-and-their-applications-an-updated-review.pdf
|
67863dcbfa469535b9ed8c2b
|
10.26434/chemrxiv-2025-wv370
|
Evans-Polanyi-like models for rapidly predicting barriers of hemicellulose motifs under pyrolysis conditions based on the reactant reactivity parameters
|
This work elucidates Evans-Polanyi-like (EPL) relations to rapidly estimate the standard activation enthalpy of three ubiquitous reaction classes playing a central role in hemicellulose pyrolysis: ring-opening, ring contraction, and elimination. These models leverage computationally cheap local and global electron-density-based chemical reactivity descriptors, such as Fukui’s functions (f), electron population of CO bonds (N), and the gross intrinsic strength bond index (Δgpair), evaluated for reactants solely. More than 270 reactions observed in twenty-eight functionalized β-D-xylopyranoses, the hemicellulose building block, are used under the 20-80 % partition scheme for validating-deriving purposes. By using the relatively simple multilinear regression analysis, four EPL are proposed for informing barriers at the M06-2X/6-311++G(d,p), CBS-QB3, G4, and DLPNO-CCSD(T)-F12/cc-pVTZ-F12//M06-2X/6-311++G(d,p), namely, ΔHDFT = –168.82f ̅– 66.28N ̅ + 328.10Δ ̅gpair – 18.80, ΔHCBS = –189.01(f ) ̅– 65.11N ̅ + 266.44Δ ̅gpair + 13.96, ΔHG4 = –184.99f ̅ – 64.85N ̅ + 275.10Δ ̅gpair + 8.52, and ΔHDLPNO = –187.82f ̅ – 72.45N ̅ + 296.14Δ ̅gpair + 7.72, respectively. An adjusted coefficient of determination of 0.80 characterizes all these parametric polynomials. Moreover, MAE and RMSE equal to ≈3.3 and ≈4.1 kcal mol-1 describe the performance of the best-fitting models at DFT and G4. Conversely, the highest values, MAE = 3.6 and RMSE = 4.7 kcal mol-1, are associated with the CBS-QB3 level. The benchmarking of the computed activation enthalpies at 298 K yields simple functions for high-level estimations from low levels of theory: ΔHCBS = 0.96ΔHDFT + 1.67, ΔHG4 = 0.96ΔHDFT + 1.72, ΔHDLPNO = 1.02ΔHDFT – 1.57, ΔHG4 = 0.96ΔHCBS + 2.86, ΔHDLPNO = 1.01ΔHCBS – 0.14, and ΔHDLPNO = 1.05ΔHG4 – 2.77. R2 ranges from 0.94 to 0.98 across these polynomials. Extrapolating the DPLNO barriers to the complete basis set limit tends to lower them by 0.63 kcal mol-1. EPL expressions are tailored to facilitate the development of chemical kinetic models for hemicellulose pyrolysis, as the reactant structure is the only input required, thereby contributing to the faster deployment of bioproducts at a commercial level.
|
Leandro Ayarde-Henríquez; Jacopo Lupi; Bernardo Ballotta; Stephen Dooley
|
Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67863dcbfa469535b9ed8c2b/original/evans-polanyi-like-models-for-rapidly-predicting-barriers-of-hemicellulose-motifs-under-pyrolysis-conditions-based-on-the-reactant-reactivity-parameters.pdf
|
60c75432f96a0055c82885f6
|
10.26434/chemrxiv.13605998.v1
|
Amphiphilic Distyrylbenzene Derivatives as Potential Therapeutic and Imaging Agents for the Soluble Amyloid-β Oligomers in Alzheimer’s Disease
|
Alzheimer’s
Diseases (AD) is the most common neurodegenerative disease, but efficient
therapeutic and early diagnosis agents for this neurological disorder are still
lacking. <a>Herein, we report the development of a novel
amphiphilic compound, LS-4, generated linking a hydrophobic amyloid fibril-binding
fragment with a hydrophilic azamacrocycle that can dramatically increase the
binding affinity towards various amyloid β (Aβ) peptide aggregates. The
developed compound exhibits uncommon fluorescence turn-on and high binding
affinity for Aβ aggregates, especially for soluble Aβ oligomers. Moreover, upon
the administration of LS-4 to 5xFAD mice, fluorescence imaging of the LS-4-treated
brain sections reveals that LS-4 can readily penetrate the blood-brain-barrier
(BBB) and bind to the Aβ oligomers <i>in vivo</i>, as confirmed by
immunostaining with an Aβ oligomer-specific antibody. In addition, the
treatment of 5xFAD mice with LS-4 significantly reduces the amount of both
amyloid plaques and associated phosphorylated tau (p-tau) aggregates vs. the
vehicle-treated 5xFAD mice, while microglia activation is also reduced. Furthermore,
molecular dynamics simulations corroborate the observation that introducing a hydrophilic
moiety into the molecular structure can significantly enhance the electrostatic
interactions with the polar residues of the Aβ peptide species. Finally, taking
advantage of the strong Cu-chelating property of the azamacrocycle, we
performed a series of radioimaging and biodistribution studies that show the <sup>64</sup>Cu-LS-4
complex binds to the amyloid plaques and can accumulate a significantly larger
extent in the 5xFAD mice brains vs. the WT controls. Overall, these <i>in vitro</i>
and <i>in vivo</i> studies illustrate that the novel strategy to employ an amphiphilic
molecule containing a hydrophilic fragment attached to a hydrophobic amyloid
fibril-binding fragment </a><a>can increase the binding affinity of these compounds for the
soluble Aβ oligomers and can thus be used </a>to detect and regulate the soluble Aβ species in AD.
|
Liang Sun; Hong-Jun Cho; Soumyo Sen; Andres S. Arango; Truc T. Huynh; Yiran Huang; Nilantha Bandara; Buck E. Rogers; Emad Tajkhorshid; Liviu M. Mirica
|
Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75432f96a0055c82885f6/original/amphiphilic-distyrylbenzene-derivatives-as-potential-therapeutic-and-imaging-agents-for-the-soluble-amyloid-oligomers-in-alzheimer-s-disease.pdf
|
6574c5b05bc9fcb5c97548b9
|
10.26434/chemrxiv-2023-g5mz4
|
Mathematical Derivation of Transporting Behaviors of Polymers in Micro-Screw Extrusion Molding
|
This study derived the transporting behavior of polymers in micro-screw extrusion molding. First, the transporting of polymer solids (performed in the first zone of screw) was derived and discussed, then the transporting of polymeric melts (performed in the third zone of screw) was derived with a novel helix-cylinder model, the velocity, flow rate, shear rate and shear stress were investigated and discussed.
|
Ruogu Tang
|
Materials Science; Polymer Science; Materials Processing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6574c5b05bc9fcb5c97548b9/original/mathematical-derivation-of-transporting-behaviors-of-polymers-in-micro-screw-extrusion-molding.pdf
|
60c750ac702a9b6adf18be1f
|
10.26434/chemrxiv.13066964.v1
|
Mechanisms for Flavin Mediated Oxidation: Hydride or Hydrogen-Atom Transfer?
|
Flavins are versatile biological cofactors which catalyze proton-coupled electron transfers (PCET) with varying number and coupling of electrons. Flavin mediated oxidation of nicotinamide adenine dinucleotide (NADH) and of succinate, initial redox reactions in cellular respiration, were examined here with multiconfigurational quantum chemical calculations and a simple analysis of the wave-function proposed to quantify electron transfer along the proton reaction coordinate. The mechanism of NADH oxidation is a prototypical hydride transfer, with two electrons moving concerted with the proton to the same acceptor group. However, succinate oxidation depends on the elimination step and can proceed through the transfer of hydride or hydrogen-atom, with proton and electrons moving to different groups in both cases. These results help to determine the mechanism of fundamental but still debated biochemical reactions, and illustrate a new diagnostic tool for electron transfer that can be useful to characterize a broad class of PCET processes. <br />
|
Felipe Curtolo; Guilherme M. Arantes
|
Biochemistry; Biophysics; Computational Chemistry and Modeling; Theory - Computational; Redox Catalysis; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-10-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750ac702a9b6adf18be1f/original/mechanisms-for-flavin-mediated-oxidation-hydride-or-hydrogen-atom-transfer.pdf
|
66cf24e6f3f4b052906147bc
|
10.26434/chemrxiv-2024-n0l8q-v3
|
Large Language Models as Molecular Design Engines
|
The design of small molecules is crucial for technological applications ranging from drug discovery to energy storage. Due to the vast design space available to modern synthetic chemistry, the community has increasingly sought to use data-driven and machine learning approaches to navigate this space. Although generative machine learning methods have recently shown potential for computational molecular design, their use is hindered by complex training procedures, and they often fail to generate valid and unique molecules. In this context, pre-trained Large Language Models (LLMs) have emerged as potential tools for molecular design, as they appear to be capable of creating and modifying molecules based on simple instructions provided through natural language prompts. In this work, we show that the Claude 3 Opus LLM can read, write, and modify molecules according to prompts, with an impressive 97% valid and unique molecules. By quantifying these modifications in a low-dimensional latent space, we systematically evaluate the model's behavior under different prompting conditions. Notably, the model is able to perform guided molecular generation when asked to manipulate the electronic structure of molecules using simple, natural-language prompts. Our findings highlight the potential of LLMs as powerful and versatile molecular design engines.
|
Debjyoti Bhattacharya; Harrison Cassady; Michael Hickner; Wesley Reinhart
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cf24e6f3f4b052906147bc/original/large-language-models-as-molecular-design-engines.pdf
|
60c746ccee301c0c5bc7959e
|
10.26434/chemrxiv.11413191.v1
|
Visualization of Streams of Small Organic Molecules in Continuous-Flow Electrophoresis
|
Continuous-flow electrophoresis (CFE) separates a stream of a multi-component mixture into multiple streams of individual components inside a thin rectangular chamber. CFE will be able to benefit flow chemistry when it is capable of generically detecting streams of small organic molecules. Here we propose a general approach for molecular stream visualization via analyte-caused obstruction of excitation of a fluorescent layer underneath the separation chamber – fluorescent sublayer-based visualization (FSV). We designed and fabricated a CFE device with one side made of quartz and another side made of UV-absorbing visibly-fluorescent, chemically-inert, machinable plastic. This device was demonstrated to support non-aqueous CFE of small organic molecules and quantitative detection of their streams in real-time with a limit of detection below 100 µM. Thus, CFE may satisfy conditions required for its seamless integration with continuous flow organic synthesis in flow chemistry.<br />
|
Nikita A. Ivanov; Sven Kochmann; Sergey N. Krylov
|
Analytical Chemistry - General; Imaging; Separation Science; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746ccee301c0c5bc7959e/original/visualization-of-streams-of-small-organic-molecules-in-continuous-flow-electrophoresis.pdf
|
60c74d414c891948d5ad37a5
|
10.26434/chemrxiv.12605333.v1
|
Ligand-Mediated Spin State Changes in a Cobalt-Dipyrrin-Bisphenol Complex
|
ABSTRACT: The influence of a redox-active ligand on spin changing events induced by coordination of exogenous donors is investigated within the cobalt complex <b>[Co<sup>II</sup>(DPP<sup>•2‒</sup>)]</b>, bearing a redox-active <b>DPP<sup>2‒</sup></b> ligand (DPP = dipyrrin-bis-(<i>o,p</i>-di-tert-butylphenolato) with a pentafluorophenyl moiety on the meso-position. This square planar complex was subjected to coordination of THF, pyridine, tBuNH<sub>2</sub> and AdNH<sub>2</sub> (Ad = 1‑adamantyl), and the resulting complexes were analyzed with a variety of experimental (XRD, NMR, UV-Vis, HRMS, SQUID, Evans’ method) and computational (DFT, NEVPT2-CASSCF) techniques to elucidate the respective structures, spin states and orbital compositions of the corresponding octahedral bis-donor adducts, relative to <b>[Co<sup>II</sup>(DPP<sup>•2‒</sup>)]</b>. This starting species is best described as an open-shell singlet complex containing a <b>DPP<sup>•2‒</sup></b> ligand radical that is antiferromagnetically coupled to a low-spin (S = ½) cobalt(II) center. The redox-active <b>DPP<sup>n‒</sup></b> ligand plays a crucial role in stabilizing this complex, and in its facile conversion to the triplet THF-adduct <b>[Co<sup>II</sup>(DPP<sup>•2‒</sup>)(THF)<sub>2</sub>]</b> and closed-shell singlet pyridine and amine adducts <b>[Co<sup>III</sup>(DPP<sup>3‒</sup>)(L)<sub>2</sub>]</b> (L = py, tBuNH<sub>2</sub> or AdNH<sub>2</sub>). Coordination of the weak donor THF to <b>[Co<sup>II</sup>(DPP<sup>•2-</sup>)]</b> changes the orbital overlap between the <b>DPP<sup>•2‒</sup></b> ligand radical π-orbitals and the cobalt(II) metalloradical d-orbitals, which results in a spin-flip to the triplet ground state without changing the oxidation states of the metal or <b>DPP<sup>•2‒</sup></b> ligand. In contrast, coordination of the stronger donors pyridine, tBuNH<sub>2</sub> or AdNH<sub>2</sub> induces metal-to-ligand single-electron transfer, resulting in formation of low-spin (S = 0) cobalt(III)-complexes <b>[Co<sup>III</sup>(DPP<sup>3‒</sup>)(L)<sub>2</sub>]</b> containing a fully reduced <b>DPP<sup>3‒</sup></b> ligand, thus explaining their closed-shell singlet electronic ground states.
|
Nicolaas P. van Leest; Wowa Stroek; Maxime A. Siegler; Jarl Ivar van der Vlugt; Bas de Bruin
|
Bonding; Ligands (Inorg.); Magnetism; Spectroscopy (Inorg.); Theory - Inorganic; Transition Metal Complexes (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d414c891948d5ad37a5/original/ligand-mediated-spin-state-changes-in-a-cobalt-dipyrrin-bisphenol-complex.pdf
|
670887c912ff75c3a1195a7f
|
10.26434/chemrxiv-2024-k3v1v
|
Uncovering the Origins of Selectivity in Non-Heme Iron Dioxygenase-Catalyzed Tropolone Biosynthesis
|
Non-heme iron (NHI) enzymes perform diverse oxidative transformations with precise control that is not easily available to small molecule catalysis, such as the biosynthesis of tropolone. Among them, Anc3, a reconstructed ancestral α-ketoglutarate (α-KG) dependent NHI dioxygenase, catalyzes a ring-expansion in the tropolone biosynthesis from cyclohexadienone to afford tropolone natural product stipitaldehyde (ring-expansion product) alongside 3-hydroxyorcinaldehyde (shunt product). This study reveals how the enzyme environment guides the reaction to ring-expansion product preferably over shunt product, where the precise selectivity ratio depends on just a handful of residues. In particular, molecular dynamics (MD) and quantum mechanical/molecular mechanical
(QM/MM) simulations describe how the substrate binds within the NHI active site and can proceed through two distinct mechanisms, ring-expansion or rebound hydroxylation, to yield the two experimentally observed products. Discovery of a linear relationship of different Ea values and hydrogen bond distances between Arg191 and the Fe(III)–OH group reveals that inhibition of the rebound
hydroxylation step increases selectivity towards ring-expansion. Our findings suggest that the rebound hydroxylation rate is further tuned through the Fe(III)–OH bond strength, as influenced by specific secondary sphere coordination effects around the active site. These influences are largely orthogonal to the ring-expansion mechanism, which is shown to prefer to proceed
through a radical pathway. In addition, a cationic pathway initiated by electron transfer from substrate to iron is ruled out based upon thermodynamic infeasibility. Altogether, the atomistic details and reaction mechanisms delineated in this work have the potential to guide the tuning of reaction
pathway in related NHI enzymes for selective oxidation reactions.
|
Taveechai Wititsuwannakul; Kevin Skinner; Joshua Kammeraad; Di Yang; Alison Narayan; Paul Zimmerman
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670887c912ff75c3a1195a7f/original/uncovering-the-origins-of-selectivity-in-non-heme-iron-dioxygenase-catalyzed-tropolone-biosynthesis.pdf
|
63d134df6bc5ca30b61a9d64
|
10.26434/chemrxiv-2021-dtpv3-v12
|
COVID-19: Attacks the 1-Beta Chain of Hemoglobin to Disrupt Respiratory Function and Escape Immunity by Capsid-Like System
|
The genetic recombination of the SARs-CoV-2 virus in bats may result in behaviors comparable to those of certain RNA viruses. This cross-activity helps explain SARs-CoV-2's strange respiratory symptoms and immune evasion abilities. In this present study, the biological roles of SARs-CoV-2 proteins were investigated utilizing bioinformatic techniques involving the search for conserved domains. According to the study, the S and ORF3a proteins of SARs-CoV-2 possess picornavirus/calicivirus capsid domains, can bind hemoglobin, heme, and porphyrin. Both Arg134 of ORF3a and Cys44 of E are iron-binding sites for heme. The ORF3a protein has a region that converts heme into iron and porphyrin. In addition to chitin and polyphenol binding domains, the S protein also contains hemocyanin and phenoloxidase-like domains. The S protein constructs Fe-polyphenol complexes to link the red blood cell membrane, allowing SARs-CoV-2 to hitch a ride on red blood cells for fast delivery to target organs. This type of capsid-like vector delays the immune system but does not significantly alter the function of red blood cells to transport oxygen. Due to the distortion of the cell membrane, red blood cells with an excess of viral particles release hemoglobin to harm the virus. The wbl domains of the S protein respond to nitration, and then phenoloxidase domains oxidize polyphenols, allowing the virus to shed from the red blood cell membrane. ORF3a also attack 1-beta chain of hemoglobin; however, the majority of hemoglobin may retain its native structure. Patients will have variable degrees of respiratory distress and coagulation symptoms, but the hemocyanin domains of the S protein can improve a patient's respiratory status by transporting oxygen.
|
wenzhong liu; hualan li
|
Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d134df6bc5ca30b61a9d64/original/covid-19-attacks-the-1-beta-chain-of-hemoglobin-to-disrupt-respiratory-function-and-escape-immunity-by-capsid-like-system.pdf
|
66afda5d01103d79c5be222d
|
10.26434/chemrxiv-2024-24brz
|
How should we teach medicinal chemistry in higher education to prepare students for a future career as medicinal chemists and drug designers?
- A teacher´s perspective.
|
In the recent two decades, the multidisciplinary field of medicinal chemistry has undergone several conceptual and technology-driven paradigm changes with significant impact on the skill set medicinal chemists need to acquire during their education. Considering the need for academic medicinal chemistry teaching, this article aims at identifying important skills, competences, and basic knowledge as general learning outcomes based on an analysis of the relevant stakeholders and concludes effective teaching strategies preparing students for a future career as medicinal chemists and drug designers.
|
Philipp Klahn
|
Biological and Medicinal Chemistry; Chemical Education; Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66afda5d01103d79c5be222d/original/how-should-we-teach-medicinal-chemistry-in-higher-education-to-prepare-students-for-a-future-career-as-medicinal-chemists-and-drug-designers-a-teacher-s-perspective.pdf
|
60c9b9d7dd81075425a85ae6
|
10.26434/chemrxiv.9775910.v4
|
Getting Students Back on Track: Persistent Effects of Flipping Accelerated Organic Chemistry on Student Achievement, Study Strategies, and Perceptions of Instruction
|
<p>
</p><p>
</p><p>Converting
a first-term, accelerated summer organic chemistry course to a flipped format
reduced the achievement gap in the flipped course and in the second-term
traditional lecture course between Non-Repeaters taking an accelerated course
to “get ahead” and Repeaters taking the course to “get back on track.” The
difference in final exam performance in the second-term course was nearly
halved, the GPA gap in both courses was reduced, and the gap in passing rate
for the second-term course was eliminated. First-generation students who took
the first-term course in the flipped format experienced a final exam score
boost in the second-term course regardless of repeater status. While most
students responded positively to the flipped course structure, repeating
students held a stronger preference for the flipped format. These findings
provide guidance on how to create courses that promote equity, access and
retention of diverse students in STEM.</p>
|
Lynn C. Reimer; Kameryn Denaro; Wenliang He; Renee Link
|
Chemical Education - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9b9d7dd81075425a85ae6/original/getting-students-back-on-track-persistent-effects-of-flipping-accelerated-organic-chemistry-on-student-achievement-study-strategies-and-perceptions-of-instruction.pdf
|
6441a36583fa35f8f6f98326
|
10.26434/chemrxiv-2022-j8nwb-v2
|
Covalent adduct formation as strategy for efficient CO2 fixation in crotonyl-CoA carboxylases/reductases
|
Increasing levels of CO2 in the atmosphere have led to a growing interest into the various ways nature transforms this greenhouse gas into valuable organic compounds. Crotonyl-CoA carboxylases/reductases (Ccr's) are the most efficient biocatalysts for CO2 fixation because of their oxygen tolerance, their high catalytic rate constants and their high fidelity. The reaction mechanism involving hydride transfer from the NADPH cofactor and addition of CO2 to the reactive enolate, however, is not completely understood. In this study, we use computer simulations in combination with high-level ab initio calculations to trace the free energy landscape along two possible reaction paths: In the direct mechanism hydride transfer is immediately followed by CO2 addition whereas in the C2 mechanism a thermodynamically stable covalent adduct between the substrate and the NADPH cofactor is formed. This C2 adduct, which has been previously characterized experimentally, serves as a stable intermediate avoiding the reduction side reaction of the reactive enolate species and it is able to react with CO2 with similar kinetics as the direct reaction mechanism as confirmed by measured kinetic isotope effects. Thus, our results show that nature's most efficient CO2-fixing enzyme uses the formation of a covalent adduct as a strategy to store the reactive enolate species. The emerging microscopic picture of the CO2-fixing mechanism confirms previous experimental observations and provides new insights into how nature handles highly reactive intermediates to fix this inert greenhouse gas.
|
Rodrigo Recabarren; Matthias Tinzl; David Saez; Aharon Gomez; Tobias Erb; Esteban Vöhringer-Martinez
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6441a36583fa35f8f6f98326/original/covalent-adduct-formation-as-strategy-for-efficient-co2-fixation-in-crotonyl-co-a-carboxylases-reductases.pdf
|
60c74eba842e65b173db36d7
|
10.26434/chemrxiv.12665336.v2
|
Room Temperature Alkali Metal Reduction of Carbon Dioxide
|
The reduction of the relatively inert carbon–oxygen bonds of CO<sub>2</sub> to access useful CO<sub>2</sub>-derived organic products is one of the most important fundamental challenges in synthetic chemistry. Facilitating this bond-cleavage using earth-abundant, non-toxic main group elements (MGEs) is especially arduous because of the difficulty in achieving strong inner-sphere interactions between CO<sub>2</sub> and the MGE. Herein we report the first successful chemical reduction of CO<sub>2</sub> at room temperature by alkali metals, promoted by a cyclic(alkyl)(amino) carbene (CAAC). One-electron reduction of CAAC-CO<sub>2</sub> adduct (<b>1</b>) with lithium, sodium or potassium metal yields stable monoanionic radicals clusters [M(CAAC–CO<sub>2</sub>)]<sub>n</sub>(M = Li, Na, K, <b> 2</b>-<b>4</b>) and two-electron alkali metal reduction affords open-shell, dianionic clusters of the general formula [M<sub>2</sub>(CAAC–CO<sub>2</sub>)]<sub>n </sub>(<b>5</b>-<b>8</b>). It is notable that these crystalline clusters of reduced CO<sub>2</sub> may also be isolated via the “one-pot” reaction of free CO<sub>2</sub> with free CAAC followed by the addition of alkali metals – a reductive process which does not occur in the absence of carbene. Each of the products <b>2</b>-<b>8</b> were investigated using a combination of experimental and theoretical methods.<br />
|
Lucas A. Freeman; Akachukwu D. Obi; Haleigh R. Machost; Andrew Molino; Asa W. Nichols; Diane A. Dickie; David
J. D. Wilson; Charles Machan; Robert Gilliard
|
Coordination Chemistry (Inorg.); Ligands (Inorg.); Main Group Chemistry (Inorg.); Organometallic Compounds; Small Molecule Activation (Inorg.); Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eba842e65b173db36d7/original/room-temperature-alkali-metal-reduction-of-carbon-dioxide.pdf
|
63b865de055be7a4eac41867
|
10.26434/chemrxiv-2023-cs6vh
|
High Temperature Transformation, O2 Etching, and Passivation of Single SiOx Nanoparticles: Kinetics and Optical Properties as Structure Probes
|
The surface chemistry and optical properties of silica nanoparticles (NPs) were studied using a single nanoparticle mass spectrometer. Initially, silica NPs were transparent to 532 nm excitation, but after brief exposure to a CO2 laser (10.6 μm) their 532 nm absorptivity increased, and when heated they emitted blackbody-like emissivity in the visible/near IR, signaling that their compositions had become more Si-rich. The transformation was also probed by sublimation rate measurements from 1600 K to 2350 K, and the chemistry of the transformed surface was probed by measuring the O2 etching kinetics of pre-heated silica NPs at 1200 and 1300 K. Sublimation was significant for NP temperatures at TNP ≥ 1900 K, and the NP optical properties showed further slow changes as the NPs sublimed. The O2 etching kinetics for pre-heated silica NPs were similar to those previously reported for single Si NPs under the same conditions, with etching efficiency (EEO2) initially increasing with etching time, then dropping by three orders of magnitude as the NP surface passivated by growth of a thermally stable SiO2 layer. NPs lost up to 50% of their initial masses before passivating. The etching and passivation kinetics at different temperatures and O2 pressures are compared, and comparisons are also made to the temperature and time dependence of EEO2 for pre-heated silica, Si, SiC, and carbon NPs. The comparison between pre-heated Si and silica NPs suggests that the latter retain an O-rich core, and that the core oxygen hastens the passivation process.
|
Daniel Rodriguez; Chris Lau; Abigail Friese; Scott Anderson
|
Physical Chemistry; Nanoscience; Chemical Kinetics; Interfaces; Surface; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b865de055be7a4eac41867/original/high-temperature-transformation-o2-etching-and-passivation-of-single-si-ox-nanoparticles-kinetics-and-optical-properties-as-structure-probes.pdf
|
6408425dcc600523a3d7b27f
|
10.26434/chemrxiv-2023-70vpw
|
Realizing efficient blue and deep-blue delayed fluorescence materials with record-beating electroluminescence efficiencies of 43.4%
|
As promising luminescent materials for organic light-emitting diodes (OLEDs), thermally activated delayed fluorescence materials are booming vigorously in recent years, but robust blue ones still remain challenging. Herein, we report three highly efficient blue and deep-blue delayed fluorescence materials comprised of a weak electron acceptor chromeno[3,2-c]carbazol-8(5H)-one with a rigid polycyclic structure and a weak electron donor spiro[acridine-9,9'-xanthene]. They hold distinguished merits of excellent photoluminescence quantum yields (99%), ultrahigh horizontal transition dipole ratios (93.6%), and fast radiative transition and reverse intersystem crossing, which furnish superb blue and deep-blue electroluminescence with Commission Internationale de IEclairage coordinates (CIEx,y) of (0.14, 0.18) and (0.14, 0.15) and record-beating external quantum efficiencies (exts) of 43.4% and 41.3%, respectively. Their efficiency roll-offs are successfully reduced by suppressing triplet-triplet and singlet-singlet annihilations. Moreover, high-performance deep-blue and green hyperfluorescence OLEDs are achieved by utilizing these materials as sensitizers for multi-resonance delayed fluorescence dopants, providing state-of-the-art exts of 32.5% (CIEx,y = 0.14, 0.10) and 37.6% (CIEx,y = 0.32, 0.64), respectively, as well as greatly advanced operational lifetimes. These splendid results can surely inspire the development of blue and deep-blue luminescent materials and devices.
|
Yan Fu; Hao Liu; Ben Zhong Tang; Zujin Zhao
|
Materials Science; Optical Materials
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6408425dcc600523a3d7b27f/original/realizing-efficient-blue-and-deep-blue-delayed-fluorescence-materials-with-record-beating-electroluminescence-efficiencies-of-43-4.pdf
|
60c73f19567dfe6712ec390b
|
10.26434/chemrxiv.7222028.v1
|
The Perfluorinated Trityl Cation Accessible as a Triflate Derivative
|
While ultimately not isolable for X-ray structural characterization, the free perfluorinated trityl
cation is shown to be observable in neat triflic acid, which represents milder conditions than
previous reports of this cation in “magic acid” or oleum. A triflate-bound species can be generated
in organic solvents using stoichiometric amounts of triflic acid and is shown to be synthetically
viable for hydride abstraction from Et3SiH. It is demonstrated that the para position on the –C6F5
rings is the primary point of attack for decomposition of the cation.<br />
|
Eoghan Delany; Satnam Kaur; Steven Cummings; Kristoffer Basse; David
J. D. Wilson; Jason Dutton
|
Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f19567dfe6712ec390b/original/the-perfluorinated-trityl-cation-accessible-as-a-triflate-derivative.pdf
|
61b4d6ac535d63f573994679
|
10.26434/chemrxiv-2021-wlz9b
|
Polyyne [3]rotaxanes: Synthesis via dicobalt carbonyl complexes and enhanced stability
|
New strategies for synthesizing polyyne polyrotaxanes are being developed as an approach to stable carbyne ‘insulated molecular wires’. Here we report an active metal template route to polyyne [3]rotaxanes, using dicobalt carbonyl masked alkyne equivalents. We synthesized two [3]rotaxanes, both with the same C28 polyyne dumbbell component, one with a phenanthroline-based macrocycle and one using a 2,6-pyridyl cycloparaphenylene nanohoop. The thermal stabilities of the two rotaxanes were compared with that of the naked polyyne dumbbell in decalin at 80 °C, and the nanohoop rotaxane was found to be 4.5 times more stable.
|
Connor Patrick; Joseph Woods; Przemyslaw Gawel; Claire Otteson; Amber Thompson; Tim Claridge; Ramesh Jasti; Harry Anderson
|
Organic Chemistry; Supramolecular Chemistry (Org.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b4d6ac535d63f573994679/original/polyyne-3-rotaxanes-synthesis-via-dicobalt-carbonyl-complexes-and-enhanced-stability.pdf
|
6667406612188379d8ca2573
|
10.26434/chemrxiv-2024-4d95k
|
The current economics and throughput of single cell proteomics by liquid chromatography mass spectrometry
|
Single cell proteomics by mass spectrometry (SCP) is an emerging field of study that has captured the interest and imagination of biologists in a wide array of disciplines. In the pursuit of this new field a dizzying array of technologies and techniques have demonstrated the ability to quantify hundreds to a few thousand proteins in single mammalian cells of typical size. One striking characteristic of these methods is the wide range of relative costs associated with the analysis of each single cell. We have attempted to estimate the cost per cell across 17 different studies based on quotes we have obtained for hardware, reagents and instrument support plans in relation to number of cells that can be analyzed per day. Before including labor or facilities, we find that the cost to analyze a single mammalian cell of typical size can range from less than <$2 per cell to over $50 per cell. The increase in cost appears directly related to the decrease in relative throughput as measured in theoretical maximum number of cells analyzed per day. Perhaps the most surprising observation is that the average number of single cells analyzed across these studies appears to decrease each year. This is striking when compared to the emergence of single cell RNA sequencing where throughput increased, and cost/cell decreased exponentially over the first 7 years of the field’s emergence. While we have made many assumptions to obtain these estimates, we hope that these will be informative for scientists interested in obtaining SCP data and for mass spectrometrists who are considering entering this new field. We have provided a spreadsheet with a simple calculator in the supplemental data to allow others to adjust our calculations based on other variables and new methods which will inevitably be described in the future.
|
Amanda Smythers; Benjamin Orsburn
|
Biological and Medicinal Chemistry; Biochemistry; Cell and Molecular Biology
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6667406612188379d8ca2573/original/the-current-economics-and-throughput-of-single-cell-proteomics-by-liquid-chromatography-mass-spectrometry.pdf
|
60c7575cee301c6165c7b514
|
10.26434/chemrxiv.14397191.v1
|
Photoinduced Deaminative Borylation of Unactivated Aromatic Amines Enhanced by CO2
|
Herein, direct unactivated
C-N borylation of aromatic amines by a photocatalyst was achieved under mild
and metal-free conditions. The C-N borylation of aromatic amines with
bis(pinacolato)diboron (B<sub>2</sub>pin<sub>2</sub>) proceeded in the presence
of a pyrene catalyst under light irradiation (λ = 365 nm) <a>to afford desired borylated
products</a> and aminoborane as a byproduct. The yield of borylated product improved under a
CO<sub>2</sub> atmosphere. Reactions conducted in the presence of a
stoichiometric amount of aminoborane under N<sub>2</sub> or CO<sub>2</sub>
indicated that CO<sub>2</sub> reduced
the inhibitory effect of aminoborane. Optimal reaction conditions were applied to a variety of aromatic amines. Mechanistic studies suggested
that the C-N bond cleavage
and C-B bond formation proceeded via a concerted pathway.
|
Akira Shiozuka; Kohei Sekine; Yoichiro Kuninobu
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7575cee301c6165c7b514/original/photoinduced-deaminative-borylation-of-unactivated-aromatic-amines-enhanced-by-co2.pdf
|
60c7525b842e651060db3d3a
|
10.26434/chemrxiv.13292216.v1
|
Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as Well as of Purple Bacteria
|
Hinge-type molecular models for electron donors in reaction centers of Photosystem I, II, and purple bacteria were investigated using a two-state computational approach based on Frozen-Density Embedding. This methodology, dubbed FDE-diab, is known to avoid consequences of the self-interaction error as far as intermolecular phenomena are concerned, which allows to predict qualitatively correct spin densities for large bio-molecular systems. The calculated spin density distributions are in a good agreement with available experimental results and demonstrated a very high sensitivity to changes in relative orientiation of co-factors and amino-acid protonation states. This allows to validate the previously proposed hinge-type models and make predictions on protonation states of axial histidine molecules. Contrary to the reaction centers in Photosystem I and purple bacteria, the axial histidines from Photosystem II were found to be deprotonated. This fact might shed some light on remarkable properties of Photosystem II reaction centers.
|
Denis Artiukhin; Patrick Eschenbach; Jörg Matysik; Johannes Neugebauer
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY 4.0
|
CHEMRXIV
|
2020-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7525b842e651060db3d3a/original/theoretical-assessment-of-hinge-type-models-for-electron-donors-in-reaction-centers-of-photosystems-i-and-ii-as-well-as-of-purple-bacteria.pdf
|
63a69b6de8047a9c04f3f972
|
10.26434/chemrxiv-2022-52sxb
|
Sandwiched Epitaxy Growth of Single-Crystalline Hexagonal Bismuthene Nanoflakes for Highly Selective Electrocatalytic CO2-to-formate Conversion
|
Two-dimensional (2D) bismuthene material was predicted to possess intriguing physical and electrical properties, such as high-temperature quantum-spin Hall effect, topological edge state, high carrier mobility, and tunable band gap. However, epitaxial growth of single-crystalline 2D bismuthene nanoflakes inevitably requires a high vacuum environment, primarily due to the high surface energy constraints of Bi. Herein, we report the growth of 2D single-crystalline hexagonal bismuthene nanoflakes on Cu foil substrate at atmospheric pressure by chemical vapor deposition. Based on first-principles calculations, the structural transformation of Bi on Cu foil can be suppressed by introducing the top h-BN layer, which potentially compensates for the charge transfer from Bi to the Cu (1 1 1) surface. The sandwich structure is identified by cross-sectional SEM and EDS characterization, demonstrating that bismuthene nanoflakes are sandwiched between the h-BN film and Cu foil. Benefiting from the encapsulation of the top h-BN layer, bismuthene nanoflakes also exhibit excellent thermal stability in ambient air even after annealing at 500 °C for 10 min. For further practical application, bismuthene nanoflakes are utilized for electrochemical CO2 reduction reactions (CO2RR). These bismuthene nanoflakes demonstrate remarkable ability in converting CO2 to formic acid with a Faradaic efficiency of 96.3% at ‒1.0 V (vs. RHE) and exhibit great catalytic stability with a Faradaic efficiency of over 90% in 15 h CO2RR tests. The ultrathin 2D feature of as-prepared bismuthene nanoflakes may result in abundant CO2 adsorption sites and stabilize the intermediate *OCHO, finally favoring the formation of HCOOH. We provide an effective strategy to simultaneously synthesize and passivate 2D single-crystalline bismuthene nanoflakes towards CO2RR, which is expected to be applied to other 2D materials with strong metallic growth behavior.
|
Yi Hu; junchuan liang; Yu-ming Gu; Songyuan Yang; zuoxiu Tie; Jing Ma; Zhong Jin
|
Materials Science; Catalysis; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a69b6de8047a9c04f3f972/original/sandwiched-epitaxy-growth-of-single-crystalline-hexagonal-bismuthene-nanoflakes-for-highly-selective-electrocatalytic-co2-to-formate-conversion.pdf
|
6477ac22be16ad5c573f31d3
|
10.26434/chemrxiv-2023-bkr8c
|
Stereospecific Cu(I)-catalyzed C-O cross-coupling synthesis of acyclic 1,2-di- and trisubstituted vinylic ethers from alcohols and vinylic halides.
|
We report a robust method catalyzed by CuI and trans-N,N'-dimethylcyclohexyldiamine, enabling single-step C-O bond cross-coupling between 1,2-di- and trisubstituted vinylic halides with a variety of functionalized alcohols, pro-ducing acyclic vinylic ethers. In contrast with previous reports, this stereospecific transformation selectively gives each of the (E)- and (Z)-vinylic ether products from the corresponding vinylic halide precursors. This method is compatible with carbohydrate-derived primary and secondary alcohols, and several other functional groups. The conditions are mild enough to reliably generate vinylic allylic ethers without promoting Claisen rearrangements.
|
San Pham; Taehee Kim; Frank McDonald
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6477ac22be16ad5c573f31d3/original/stereospecific-cu-i-catalyzed-c-o-cross-coupling-synthesis-of-acyclic-1-2-di-and-trisubstituted-vinylic-ethers-from-alcohols-and-vinylic-halides.pdf
|
60c74625702a9b4af518ab49
|
10.26434/chemrxiv.10080638.v2
|
Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface
|
DNA lesion such as
metholcytosine(<sup>m</sup>C), 8-OXO-guanine(<sup>O</sup>G), inosine(I) <i>etc</i>
could cause the genetic diseases. Identification of the varieties of lesion
bases are usually beyond the capability of conventional DNA sequencing which is
mainly designed to discriminate four bases only. Therefore, lesion detection
remain challenge due to the massive varieties and less distinguishable readouts
for minor structural variations. Moreover, standard amplification and labelling
hardly works in DNA lesions detection. Herein, we designed a single molecule
interface from the mutant K238Q Aerolysin, whose confined sensing region shows
the high compatible to capture and then directly convert each base lesion into
distinguishable current readouts. Compared with previous single molecule
sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced
by 2-order. The novel K238Q could direct discriminate at least 3 types (<sup>m</sup>C,
<sup>O</sup>G, I) lesions without lableing and quantify modification sites
under mixed hetero-composition condition of oligonucleotide. Such nanopore
could be further applied to diagnose genetic diseases at high sensitivity.
|
Jiajun Wang; Meng-Yin Li; Jie Yang; Ya-Qian Wang; Xue-Yuan Wu; Jin Huang; Yi-Lun Ying; Yi-Tao Long
|
Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74625702a9b4af518ab49/original/direct-read-and-quantify-damage-nucleotide-from-an-oligonucleotide-using-a-single-molecule-interface.pdf
|
67c8a90bfa469535b9148866
|
10.26434/chemrxiv-2025-g1vjf-v2
|
Evaluating Machine Learning Models for Molecular Property Prediction: Performance and Robustness on Out-of-Distribution Data
|
Today, machine learning models are employed extensively to predict the physicochemical and biological properties of molecules. Their performance is typically evaluated on in-distribution (ID) data, i.e., data originating from the same distribution as the training data. However, the real-world applications of such models often involve molecules that are more distant from the training data, which necessitates assessing their performance on out-of-distribution (OOD) data. In this work, we investigate and evaluate the performance of twelve machine learning models, including classical approaches like random forests, as well as graph neural network (GNN) methods, such as message-passing graph neural networks, across eight data sets using seven splitting strategies for OOD data generation. First, we investigate what constitutes OOD data in the molecular domain for bioactivity and ADMET prediction tasks. In contrast to the common point of view, we show that both classical machine learning and GNN models work well (not substantially different from random splitting) on data split based on Bemis-Murcko scaffolds. Splitting based on chemical similarity clustering (K-means clustering using ECFP4 fingerprints) poses the hardest challenge for both types of models. Second, we investigate the extent to which ID and OOD performance have a positive linear relationship. If a positive correlation holds, models with the best performance on the ID data can be selected with the promise of having the best performance on OOD data. We show that the strength of this linear relationship is strongly related to how the OOD data is generated, i.e., which splitting strategies are used for generating OOD data. While the correlation between ID and OOD performance for scaffold splitting is strong (Pearson r ∼ 0.9), this correlation decreases significantly for cluster-based splitting (Pearson r ∼ 0.4). Therefore, the relationship can be more nuanced, and a strong positive correlation is not guaranteed for all OOD scenarios. These findings suggest that OOD performance evaluation and model selection should be carefully aligned with the intended application domain.
|
Hosein Fooladi; Thi Ngoc Lan Vu; Johannes Kirchmair
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8a90bfa469535b9148866/original/evaluating-machine-learning-models-for-molecular-property-prediction-performance-and-robustness-on-out-of-distribution-data.pdf
|
64ec856879853bbd789ad906
|
10.26434/chemrxiv-2023-7p1s5
|
Triplet-triplet annihilation upconversion for calcium sensing
|
Triplet-triplet annihilation upconversion is a bimolecular process converting low-energy light into high-energy one. All available calcium probes, despite their qualities, are downconverting, which leads to the autofluorescence caused by background emission of the intra- and intercellular molecules. Here we report a calcium-sensing system working via upconverted emission. The probe itself was obtained by covalent conjugation of a perylene blue emitter with a calcium-chelating moiety; it was sensitized by a red-light absorbing palladium porphyrin. Sensing was selective towards Ca2+ and occurred in the micromolar domain in aqueous solutions and methanol. The upconverted luminescence only appeared in the presence of calcium ions, with a quantum yield of up to 0.0018.
|
Valeriia D. Andreeva; Tingxiang Yang; Irene Regeni; Benjamin Dietzek-Ivanšić; Sylvestre A. Bonnet
|
Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-08-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ec856879853bbd789ad906/original/triplet-triplet-annihilation-upconversion-for-calcium-sensing.pdf
|
66ad1741c9c6a5c07adad61f
|
10.26434/chemrxiv-2024-6jf2b
|
Exploration of cryptic pockets using enhanced sampling along normal modes: A case study of KRAS G12D
|
Identification of cryptic pockets has the potential to open new therapeutic opportunities by discovering ligand binding sites that remain hidden in static apo structures of a target protein. Moreover, allosteric cryptic pockets can become valuable for designing target-selective ligands when the natural ligand binding sites are conserved in variants of a protein. For example, before an allosteric cryptic pocket was discovered, KRAS was considered undruggable due to its smooth surface and conservation of the GDP/GTP binding pocket across the wild type and oncogenic isoforms. Recent identification of the Switch-II cryptic pocket in the KRASG12C mutant and FDA approval of anti-cancer drugs targeting this site underscores the importance of cryptic pockets in solving pharmaceutical challenges. Here, we present a newly developed approach for the exploration of cryptic pockets using weighted ensemble molecular dynamics simulations with inherent normal modes as progress coordinates applied to the wild type KRAS and the G12D mutant. We performed extensive all-atomic simulations (> 400 microseconds) with and without several co-solvents (xenon, ethanol, benzene), and analyzed trajectories using three distinct methods to search for potential binding pockets. These methods have been applied as a proof-of-concept to KRAS and have shown they can predict known cryptic binding sites. Furthermore, we performed ligand-binding simulations of a known inhibitor (MRTX1133) to shed light on the nature of cryptic pockets in KRASG12D and the role of conformational selection vs induced-fit mechanism in the formation of these cryptic pockets.
|
Neha Vithani; She Zhang; Jeffrey P. Thompson; Lara A. Patel; Alex Demidov; Junchao Xia; Alexander Balaeff; Ahmet Mentes; Yelena A. Arnautova; Anna Kohlmann; J. David Lawson; Anthony Nicholls; A Geoffrey Skillman; David N. LeBard
|
Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ad1741c9c6a5c07adad61f/original/exploration-of-cryptic-pockets-using-enhanced-sampling-along-normal-modes-a-case-study-of-kras-g12d.pdf
|
67b62b886dde43c9089b4180
|
10.26434/chemrxiv-2025-6245x
|
Learning from failures: anatomy and post-mortem analysis of an unsuccessful search for inhibitors of SARS-CoV2 papain-like protease
|
Details of failed computer-aided molecular design campaigns are lacking in the published literature due to the prevalent preference for the publication of positive results and successful research narratives. The lessons learned from failed endeavors therefore remain circumscribed to the gray literature and to the institutional memories of research groups, which may prevent the identification of common pitfalls or the sharing of lessons learned from these failures. In this report we describe a promising inhibitor- design campaign which unexpectedly failed in the experimental test phase, and the likely source for that failure. The target protein for this research was the papain-like protease (PLPro) from SARS-CoV2, which cleaves the host's interferon-stimulated gene 15 protein and leads to the weakening of type 1 interferon response. In this work, we have performed a QSAR-based search of the PubChem database to find molecules with higher affinity to PLPro and, consequently, better inhibitory effect than previously-confirmed inhibitor GRL-0167. The 50 detected candidates were docked to the structure of PLPro, and the complexes of the three molecules bound to the experimentally-confirmed S3-S4 pocket were subjected to triplicate molecular dynamics simulations to ascertain the stability of the binding mode. The simulations showed that one of the candidates remained stably bound to the inhibitory pocket. Analysis of binding energies showed that this molecule was at least as good a binder as previously-confirmed inhibitors. Despite such promising results, these candidates failed experimental validation, and a simple, newly-developed, computational protocol identified self-aggregation as the likely reason for this lack of success. Widespread adoption of this simple protocol will highlight ligands prone to this unhelpful behavior, and hopefully increase the success rate of future molecular design campaigns.
|
Pedro Silva
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b62b886dde43c9089b4180/original/learning-from-failures-anatomy-and-post-mortem-analysis-of-an-unsuccessful-search-for-inhibitors-of-sars-co-v2-papain-like-protease.pdf
|
65f3f07366c138172908270e
|
10.26434/chemrxiv-2024-8t70s
|
PaStEL: Generator of Pathways with Structural Change on Pseudo Free-Energy Landscape from CryoEM Images
|
Noisy cryoEM particle images reflect the conformational heterogeneity of biomolecules and have high potential for the study of biological process. As numerous simulation studies have shown, the study of biological process is attributed to the description of the free energy landscapes on the conformational pathways along with collective variable, which is usually difficult to define. In this study, we propose a methodology to automatically generate plausible conformational pathways via the theoretically isometric latent space trained by deep Auto-Encoder model using cryoEM experimental dataset directly. The proposed method of the PaStEL can speedily show structural change on the plausible conformational pathways along with free energy landscape. Solid theoretical guarantees and tests using synthetic cryoEM data have succeeded in obtaining qualitatively correct energy landscapes on the generated plausible pathways. Furthermore, benchmarking with real cryoEM experimental data of 50S Ribosome has successfully demonstrated that the conformational changes with energy landscapes consistent with existing studies without any manual labor. Finally, the PaStEL was applied to spike proteins of SARS-CoV-2 and successfully characterized the difference in the conformational changes between the wild type and the mutant (D614G) focusing on the Receptor Binding Domain regions.
|
Atsushi Tokuhisa; Kimihiro Yamazaki; Yuichiro Wada; Mutsuyo Wada; Takashi Katoh; Akira Nakagawa; Yoshinobu Akinaga; Yoko Sasakura; Yasushi Okuno
|
Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-03-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f3f07366c138172908270e/original/pa-st-el-generator-of-pathways-with-structural-change-on-pseudo-free-energy-landscape-from-cryo-em-images.pdf
|
618d487e98309bc25859d1d3
|
10.26434/chemrxiv-2021-8xqp2-v2
|
Highly Functional Group Tolerant, (E)-Selective Transfer Semihydrogenation of Alkynes Catalysed by Iridium Complex Bearing Unsymmetrical Ferrocene-Based Phosphine Ligand
|
Herein, we present (E)-selective transfer semihydrogenation of alkynes based on in situ generated iridium complex from [Ir(COD)Cl]2 and unsymmetrical ferrocene-based phosphine ligand in the presence of formic acid as a hydrogen donor. The catalytic system is distinguished by unprecedented chemoselectivity and exceptional stereoselectivity substantiated by the broad scope of test-ed substrates, including natural products derivatives. The uniform reaction conditions may be applied to various alkynes, owing to a lack of over-reduction. The intriguing difference in catalytic activity between unsymmetrical and symmetrical ferrocene-based ligands was attributed to diver-gent coordination and steric hindrance. The presented methodology constitutes a solution to the common limitations of the published catalytic systems.
|
Rafał Kusy; Marcin Lindner; Jakub Wagner; Karol Grela
|
Organic Chemistry; Catalysis; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618d487e98309bc25859d1d3/original/highly-functional-group-tolerant-e-selective-transfer-semihydrogenation-of-alkynes-catalysed-by-iridium-complex-bearing-unsymmetrical-ferrocene-based-phosphine-ligand.pdf
|
6403ca6d9789de3dd9ed107a
|
10.26434/chemrxiv-2023-gh1mw
|
1,6-Addition of Indolizines to para-Quinone Methides with Indium(III) Chloride as Catalyst
|
A 1,6-addition of a wide variety of indolizines to para-quinone methides was developed using only 2 mol% indium chloride as a catalyst. The method successfully allows the regioselective addition of indolizines at positions 1 and 3 to p-quinone methides, leading to the formation of the desired products in excellent yields in most cases (up to 99%) under mild conitions and in short reaction time.
|
Manoel Rodrigues Jr; Ana Senna; Hugo Santos; Lucas Zeoly; Ralph Gomes; Fernando Coelho
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6403ca6d9789de3dd9ed107a/original/1-6-addition-of-indolizines-to-para-quinone-methides-with-indium-iii-chloride-as-catalyst.pdf
|
6466d172a32ceeff2ddee872
|
10.26434/chemrxiv-2023-2rh9j
|
Phase identification and discovery of hidden crystal forms in a polycrystalline pharmaceutical sample using high-throughput 3D electron diffraction
|
3D electron diffraction (3D ED), also known as MicroED, has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, a high-throughput 3D ED method has been implemented to identify six phases in an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using the widely available commercial software EPU-D (Thermo Fisher Scientific) was combined with semi-automated data processing and clustering to collect and process over 100 datasets over three days. Accurate unit cell parameters obtained from 3D ED data allowed identification of GSF Forms III, I, GSF-and PEG IC-I, as well as three additional phases undetected in powder X-ray diffraction data, namely GSF II, GSF-V and a new phase GSF-PEG IC-II. Their structures were directly determined by 3D ED. Through structure analysis, we discovered polymorphism within inclusion complexes built from the same clinical drug-polymer combination. These results demonstrate the ability of the high-throughput method to accurately reveal the phase information of complex, beam-sensitive crystallisation products, which is significant for drug design where crystal form screening is crucial for the overall efficacy of the drug product.
|
Molly Lightowler; Shuting Li; Xiao Ou; Jungyoun Cho; Ao Li; Gerhard Hofer; Jiaoyan Xu; Taimin Yang; Xiaodong Zou; Ming Lu; Hongyi Xu
|
Analytical Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6466d172a32ceeff2ddee872/original/phase-identification-and-discovery-of-hidden-crystal-forms-in-a-polycrystalline-pharmaceutical-sample-using-high-throughput-3d-electron-diffraction.pdf
|
61f030134b950008ec09d285
|
10.26434/chemrxiv-2022-clc3z
|
A spatiotemporal route to understanding metal halide perovskite crystallization
|
A spatiotemporal experimental route is reported for the antisolvent vapor diffusion crystal growth of metal halide perovskites. A computational analysis combining automated image capture and diffusion modeling enables the determination of the critical concentrations required for nucleation and crystal growth from a single experiment. Five different solvent systems and ten distinct organic ammonium iodide salts were investigated with lead iodide, from which nine previously unreported compounds were discovered. Automated image capture of the mother liquor and antisolvent vials were used to determine changes in solution meniscus positions and detect nucleation event location. Matching the observations to a numerical solution of Fick’s second law diffusion model enables the calculation of reactant, solvent and antisolvent concentrations at both the time and position of the first stable nucleation and crystal growth. A machine learning model was trained on the resulting data reveals solvent- and amine-specific crystallization tendencies. Solvent systems that interact more weakly with dissolved lead species promote crystallization, while those with stronger interaction can prevent crystallization through increased solubilities. Organic amines that interact more strongly with inorganic components and exhibit greater rigidity are more likely to be incorporated into crystalline products.
|
Mansoor Ani Najeeb; Rodolfo Keesey; Margaret Zeile; Venkateswaran Shekar; Zhi Li; Nicholas Leiby; Matthias Zeller; Emory Chan; Joshua Schrier; Alexander Norquist
|
Inorganic Chemistry; Solid State Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-01-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f030134b950008ec09d285/original/a-spatiotemporal-route-to-understanding-metal-halide-perovskite-crystallization.pdf
|
65a73ae866c13817299dbb7d
|
10.26434/chemrxiv-2024-17wtz
|
Collective synthesis of highly oxygenated (furano)germacranolides from Elephantopus mollis and Elephantopus tomentosus
|
Germacranolides, secondary metabolites produced by plants, have garnered academic and industrial interest due to their diverse and complex topology as well as a wide array of pharmacological activities. Molephantin, a highly oxygenated germacranolide isolated from medicinal plants, Elephantopus mollis and Elephantopus tomentosus, has exhibited anti-tumor, inflammatory, and leishmanicidal activities. Its chemical structure is based on a highly strained ten-membered macrocyclic backbone with an (E,Z)-dienone moiety, which is fused with an a-methylene-g-butyrolactone and adorned with four successive stereogenic centers. Herein, we report the first synthesis of molephantin via 12 steps starting from readily available building blocks. The synthesis is featured by the highly diastereoselective intermolecular Barbier allylation of the b,g-unsaturated aldehyde with optically active 3-bromomethyl-5H-furan-2-one intermediate and ensuing intramolecular Nozaki-Hiyama-Kishi (NHK) macrocyclization for the construction of the highly oxygenated ten-membered macrocyclic framework. This synthetic route enabled to craft another germacranolide congener, tomenphantopin F. Furthermore, cycloisomerization of molephantin into 2-deethoxy-2b-hydroxyphantomolin could be facilitated by irradiation with ultraviolet A light (lmax = 370 nm), which opened a versatile and concise access to the related furanogermacranolides such as EM-2, phantomolin, 2-O-demethyltomephantopin C, and tomenphantopin C.
|
Rémi Patouret; Ning Cham; Shunsuke Chiba
|
Organic Chemistry; Natural Products
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a73ae866c13817299dbb7d/original/collective-synthesis-of-highly-oxygenated-furano-germacranolides-from-elephantopus-mollis-and-elephantopus-tomentosus.pdf
|
61114eaa711750300ae5d063
|
10.26434/chemrxiv-2021-zsf8s
|
Molecular Dynamics Simulations of the Breathing Phase Transition of MOF Nanocrystallites II: Explicitly Modeling the Pressure Medium
|
One of the most investigated properties of porous crystalline metal-organic frameworks (MOFs) is their potential flexibility to undergo large changes in unit cell size upon guest adsorption or other stimuli, referred to as ”breathing”. Computationally, such phase transitions are usually investigated using periodic boundary conditions, where the system’s volume can be controlled directly. However, we have recently shown that important aspects like the formation of a moving interface between the open and the closed pore form or the free energy barrier of
the first-order phase transition and its size effects can best be investigated using non-periodic nanocrystallite (NC) models [Keupp and Schmid (2019) Adv. Theory Simul. 2, 1900117]. In this case, the application of pressure is not straightforward, and a distance constraint was used
to mimic a mechanical strain enforcing the reaction coordinate. In contrast to this prior work, a mediating particle bath is used here to exert an isotropic hydrostatic pressure on the MOF nanocrystallites. The approach is inspired by the mercury nanoporosimetry used to compress
flexible MOF powders. For such a mediating medium, parameters are presented that require a reasonable additional numerical effort and avoid unwanted diffusion of bath particles into the MOF pores. As a proof-of-concept, NCs of pillared-layer MOFs with different linkers and sizes
are studied concerning their response to external pressure exerted by the bath. By this approach, an isotropic pressure on the NC can be applied in analogy to corresponding periodic simulations, without any bias for a specific mechanism. This allows a more realistic investigation of the
breathing phase transformation of a MOF NC and further bridges the gap between experiment and simulation.
|
Larissa Schaper; Julian Keupp; Rochus Schmid
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-08-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61114eaa711750300ae5d063/original/molecular-dynamics-simulations-of-the-breathing-phase-transition-of-mof-nanocrystallites-ii-explicitly-modeling-the-pressure-medium.pdf
|
635727272e0c63c60f3aa820
|
10.26434/chemrxiv-2022-n306b-v2
|
Merging Electrocatalytic Alcohol Oxidation with C-N Bond Formation by Electrifying Metal-Ligand Cooperative Catalysts
|
The development of energy and atom efficiency processes is thought to play an important role for a sustainable chemical industry of the future. One opportunity could be the electrification of thermal processes to benefit from the inherent advantages of electrochemistry, such as safety, scalability, a cheap and traceless redox agent (electrons), and the possibility to directly control the energy input of a given reaction via the applied potential. Molecular electrocatalytic alcohol oxidation emerged as a powerful tool for energy efficient redox transformations with possible applications in both green synthesis and energy-relevant domains. Using transfer hydrogenation catalysts under electrochemical conditions was shown to be promising avenue in this respect, but is today limited in terms of substrate scope. Here, we reported the electrification of acceptor-less dehydrogenation catalysts for the coupling of alcohol oxidation with C-N bond formation. Imines are thus obtained with excellent selectivity and faradaic efficiency, showing a possibility route towards added-value products from simple building blocks. We hope that the successful electrification of such atom-efficient systems can contribute to a more energy efficient organic redox chemistry.
|
Sitthichok Kasemthaveechok; Niklas von Wolff
|
Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-10-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635727272e0c63c60f3aa820/original/merging-electrocatalytic-alcohol-oxidation-with-c-n-bond-formation-by-electrifying-metal-ligand-cooperative-catalysts.pdf
|
649d146f6e1c4c986b85bd0e
|
10.26434/chemrxiv-2022-6dt28-v3
|
Advances in Honeycomb Layered Oxides: Part I - Syntheses and Characterisations of Pnictogen- and Chalcogen-Based Honeycomb Layered Oxides
|
Advancements in nanotechnology continue to unearth material vistas that presage a new age of revolutionary functionalities replete with unparalleled physical properties and avant-garde chemical capabilities that promise sweeping paradigm shifts in energy, environment, telecommunications and potentially healthcare. At the upper echelons of this realm, the pnictogen and chalcogen class of honeycomb layered oxides have emerged with fascinating crystal chemistry and exotic electromagnetic and topological phenomena that muster multifaceted concepts spanning from materials science to condensed matter physics and potential applications in electrochemistry, quantum mechanics and electronics. In a bid to shed light on the mechanisms governing these biomimetic nanostructures, this review highlights the significant milestones and breakthroughs that have augmented their current knowledgebase of theory, properties and utilities. Herein, we elucidate the vast promising crystal chemistry space against the backdrop of known synthesis and characterisation techniques employed in the development and optimisation of this class of materials. Further, we highlight key theoretical models that have reinvigorated the exploration and characterisation of honeycomb layered oxides within this class and are poised to redefine the frontiers of material research and their applications. We conclude by envisaging future research directions where fascinating physicochemical, topological and electromagnetic properties could be lurking and where valiant efforts ought to be inclined, particularly in the prospective realisation of exotic material compositional space as well as their utility as testing grounds for emergent two-dimensional (2D) topological quantum gravity and conformal field theories.
|
Godwill Kanyolo; Titus Masese; Abbas Alshehabi; Zhen-Dong Huang
|
Materials Science; Nanoscience; Energy; Materials Processing; Nanostructured Materials - Nanoscience; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649d146f6e1c4c986b85bd0e/original/advances-in-honeycomb-layered-oxides-part-i-syntheses-and-characterisations-of-pnictogen-and-chalcogen-based-honeycomb-layered-oxides.pdf
|
63035749f9e99c12a1858533
|
10.26434/chemrxiv-2022-r76xj-v2
|
Dissecting Conjugation and Electronic Effects in the Linear and Non-Linear Optical Properties of Rhenium(I) Carbonyl Complexes
|
Herein, we report a theoretical and experimental analysis of the conjugation and electronic effects on the one-photon (1PA) and two-photon absorption (2PA) properties of a series of Re(I) carbonyl complexes with terpyridine-based ligands. An excellent agreement was obtained between the calculated and experimental 2PA spectra of the k2N-terpyridine tricarbonyl complexes (1a-b), with 2PA cross sections reaching up to ca. 40 GM in DMF. By stepwise lowering the conjugation length in the terpy ligand and changing the local symmetry around the metal centre, we show that conjugation and delocalisation play a major role in increasing 2PA cross sections, and that the character of the excited states does not directly enhance the non-linear properties of these complexes---contrary to the results observed in 1PA. Altogether, these results give valuable guidelines towards more efficient two-photon-absorbing coordination complexes of Re(I), with potential applications in photodynamic therapy and two-photon imaging.
|
Ricardo Fernández-Terán; Estefanía Sucre-Rosales; Lorenzo Echevarria; Florencio Hernández
|
Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Photochemistry (Physical Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63035749f9e99c12a1858533/original/dissecting-conjugation-and-electronic-effects-in-the-linear-and-non-linear-optical-properties-of-rhenium-i-carbonyl-complexes.pdf
|
677b6766fa469535b9e772cd
|
10.26434/chemrxiv-2024-nvmzm-v2
|
Structural diversity in 1D hydrogen-bonded chains assembled through bis(triazole) self–association
|
We show that simple phenyl-1,3-bis(triazole) groups dimerise in solution. Dimerisation of these compounds in CDCl3 is too strong to measure by 1H NMR spectroscopy, and dimerisation in 9:1 CDCl3:d6-acetone is relatively strong (Kdimerisation = 1360 or 4460 M–1, depending on whether preorganising methyl groups are absent or present, respectively). A ditopic compound 1 containing two bis(triazole) groups crystallises to give hydrogen-bonded chains. Four different crystal structures were obtained, all of which are 1D chains, and all of which contain small solvent-filled channels. While the overall structure and packing are similar, diversity in the hydrogen bonding arrangements is observed due to the possibility of the triazole groups adopting either syn or anti conformations.
|
Jordan Smith; Nicholas White
|
Organic Chemistry; Supramolecular Chemistry (Org.); Crystallography – Organic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677b6766fa469535b9e772cd/original/structural-diversity-in-1d-hydrogen-bonded-chains-assembled-through-bis-triazole-self-association.pdf
|
6793aee0fa469535b9aaad4f
|
10.26434/chemrxiv-2025-xqvks-v2
|
Molecular orientation in amorphous calcium phosphate-pyrophosphate
|
Solids in nature typically exist in amorphous or crystalline states depending on the order of their constituent atoms. Generally, the multi-atom molecules (including ions) are highly ordered and oriented in crystals, but their orientation in amorphous solids is disordered except in certain organic materials formed by external regulations. This study finds that the amorphous calcium phosphate-pyrophosphate nanowire (ACPPN), which is prepared without external regulations, displays a molecular orientation of pyrophosphate ions. This discovery broadens our knowledge of the unique structural characteristics of amorphous materials, which would pave a way for further development of advanced solid materials.
|
Chaobo Feng; Hua Zeng; Longxiang Yao; Feng Chen; Bing-Qiang Lu
|
Inorganic Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793aee0fa469535b9aaad4f/original/molecular-orientation-in-amorphous-calcium-phosphate-pyrophosphate.pdf
|
67222717f9980725cf9353c1
|
10.26434/chemrxiv-2024-6vjkz
|
Unlocking the flexibility of multi-material 3D extrusion printing for soft iontronics
|
Iontronics can improve wearable devices, implantable devices, and environmental sensors by replacing traditional rigid electronics with viscoelastic materials that mimic biological tissue. Circuit components, including diodes, transistors, and power sources, have been fabricated with soft materials that utilize ionic current instead of metals and electronic current. However, the fabrication of these iontronic components can be tedious, and widely applicable manufacturing methods are lacking, thus hindering the development of complex iontronic circuits for real-world applications. While 3D printing has recently gained popularity due to its versatility, we suggest that it has been underutilized for iontronics. By combining multi-material 3D printing and iontronics, we show the ability to rapidly iterate ionic diode design and integrate these diodes within a complex structure with advanced mechanical behavior. With an updated 3D model design, we create a new stretchable diode that is insensitive to strain, a feature that can be crucial for applications requiring soft electronics. To further emphasize the adaptability of printing soft materials, we demonstrate that three components of the based ink (conductive polymers, a thickening agent, and a crosslinker) can be used to optimize print quality and the resulting material properties. In doing so, we thoroughly characterize a mixed ionic-electronic conducing ink using poly(3,4-ethylenedioxythiophene): polystyrene sulfonate (PEDOT:PSS) that can provide a foundation for the further development of extrusion printed iontronics. Compared to previously established methods, multi-material printing reduces cost, wasted material, and time required to develop complex devices in a manner that can be personized as well as highly reproducible.
|
Trevor Kalkus; Tamara V. Unterreiner; Målin Schmidt; Laura D. Wächter; Christina R. Schmitt; Ankit Mishra; Christine Selhuber-Unkel
|
Materials Science; Elastic Materials; Polyelectrolytes - Materials
|
CC BY 4.0
|
CHEMRXIV
|
2024-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67222717f9980725cf9353c1/original/unlocking-the-flexibility-of-multi-material-3d-extrusion-printing-for-soft-iontronics.pdf
|
60c73dc9f96a0089fd285e0a
|
10.26434/chemrxiv.6076175.v1
|
Rapid Catalyst Capture Enables Metal-Free Parahydrogen-Based Hyperpolarized Contrast Agents
|
<p>Hyperpolarization techniques based on the use of parahydrogen provide orders of magnitude signal enhancement for magnetic resonance spectroscopy and imaging. The main drawback limiting widespread applicability of parahydrogen-based techniques in biomedicine is the presence of organometallic compounds (the polarization transfer catalysts) in solution with hyperpolarized contrast agents. These catalysts are typically complexes of platinum-group metals and their administration in vivo should be avoided.</p>
<p><br /></p><p>Herein, we show how extraction of a hyperpolarized compound from an organic phase to an aqueous phase combined with a rapid (less than 10 seconds) Ir-based catalyst capture by metal scavenging agents can produce pure parahydrogen-based hyperpolarized contrast agents as demonstrated by high-resolution nuclear magnetic resonance (NMR) spectroscopy and inductively coupled plasma atomic emission spectroscopy (ICP-AES). The presented methodology enables fast and efficient means of producing pure hyperpolarized aqueous solutions for biomedical and other uses.</p>
|
Danila Barskiy; Lucia Ke; Xingyang Li; Vincent Stevenson; Nevin Widarman; Hao Zhang; Ashley Truxal; Alexander Pines
|
Separation Science; Spectroscopy (Anal. Chem.); Transition Metal Complexes (Inorg.); Water Purification; Homogeneous Catalysis; Chemical Kinetics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-04-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dc9f96a0089fd285e0a/original/rapid-catalyst-capture-enables-metal-free-parahydrogen-based-hyperpolarized-contrast-agents.pdf
|
60c74ccf842e657f43db3365
|
10.26434/chemrxiv.12547850.v1
|
A Ligand-Directed Approach to Activity-Based Sensing: Developing Palladacycle Fluorescent Probes that Enable Endogenous Carbon Monoxide Detection
|
Carbon monoxide (CO) is an emerging gasotransmitter and reactive carbon species with broad anti-inflammatory,
cytoprotective, and neurotransmitter functions along with therapeutic potential for the treatment of cardiovascular diseases.
The study of CO chemistry in biology and medicine relative to other prominent gasotransmitters such as NO and H2S
remains challenging, in large part due to limitations in available tools for the direct visualization of this transient and freely
diffusing small molecule in complex living systems. Here we report a ligand-directed activity-based sensing (ABS) approach
to CO detection through palladium-mediated carbonylation chemistry. Specifically, the design and synthesis of a series of
ABS probes with systematic alterations in the palladium-ligand environment (e.g., sp3-S, sp3-N, sp2-N) establish structureactivity relationships for palladacycles to confer selective reactivity with CO under physiological conditions. These
fundamental studies led to the development of an optimized probe, termed Carbon Monoxide Probe-3 Ester Pyridine (COP3E-Py), which enables imaging of CO release in live cell and brain settings, including monitoring of endogenous CO
production that triggers presynaptic dopamine release in fly brains. This work provides a unique tool for studying CO in
living systems and establishes the utility of a synthetic methods approach to activity-based sensing using principles of
organometallic chemistry
|
Johannes Morstein; Denis Höfler; Kohei Ueno; Jonah Jurss; Ryan Walvoord; Kevin Bruemmer; Samir Rezgui; Thomas Brewer; Minoru Saitoe; Brian Michel; Christopher Chang
|
Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-06-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ccf842e657f43db3365/original/a-ligand-directed-approach-to-activity-based-sensing-developing-palladacycle-fluorescent-probes-that-enable-endogenous-carbon-monoxide-detection.pdf
|
66be6fac20ac769e5fb5c72d
|
10.26434/chemrxiv-2024-x80pr
|
Perturbative analysis of the coherent state transformation in ab initio cavity quantum electrodynamics
|
Experimental demonstrations of modified chemical structure and reactivity under strong light-matter coupling have spurred theoretical and computational efforts to uncover underlying mechanisms. Ab initio cavity quantum electrodynamics (QED) combines quantum chemistry with cavity QED to investigate these phenomena in detail. Unitary transformations of ab initio cavity QED Hamiltonians have been used to make them more computationally tractable. We analyze one such transformation, the coherent state transformation, using perturbation theory. Applying perturbation theory up to third order for ground state energies and potential energy surfaces under electronic strong coupling, we show that the coherent state transformation yields better agreement with exact ground state energies. Additionally, we apply perturbation theory up to second order for cavity mode states under bilinear coupling, elucidating how the coherent state transformation accelerates the convergence of the photonic subspace towards the complete basis limit and renders molecular ion energies origin invariant. These findings contribute valuable insights into computational advantages of the coherent state transformation in the context of ab initio cavity quantum electrodynamics methods.
|
Peyton Roden; Jonathan Foley
|
Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Optics
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66be6fac20ac769e5fb5c72d/original/perturbative-analysis-of-the-coherent-state-transformation-in-ab-initio-cavity-quantum-electrodynamics.pdf
|
6787a417fa469535b91f38e7
|
10.26434/chemrxiv-2025-g4kjr
|
Sigmatropic rearrangement enables access to a highly stable spirocyclic nitroxide for protein spin labelling
|
Spin labelling enables the study of biomolecules using electron paramagnetic resonance (EPR) spectroscopy. Here, we describe the synthesis of a cysteine-reactive spin label based on a spirocyclic pyrrolidinyl nitroxide containing an iodoacetamide moiety. The spin label was shown to be highly persistent under reducing conditions while maintaining excellent EPR relaxation parameters up to a temperature of 180 K. After successful double spin labelling of a calmodulin variant, interspin distances were measured by the electron paramagnetic resonance (EPR) spectroscopy experiment double electron-electron resonance (DEER) at 120 K.
|
Mateusz P. Sowiński; Elena M. Mocanu; Hannah Ruskin-Dodd; Aidan P. McKay; David B. Cordes; Janet E. Lovett; Marius Haugland-Grange
|
Physical Chemistry; Organic Chemistry; Analytical Chemistry; Organic Compounds and Functional Groups; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.)
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6787a417fa469535b91f38e7/original/sigmatropic-rearrangement-enables-access-to-a-highly-stable-spirocyclic-nitroxide-for-protein-spin-labelling.pdf
|
60c748cc567dfed51cec4a75
|
10.26434/chemrxiv.11974512.v1
|
Gold Catalyzed Decarboxylative Cross-Coupling of Iodoarenes
|
This report details a decarboxylative cross-coupling of (hetero)aryl carboxylates with iodoarenes in the presence of a gold catalyst (>25 examples, up to 96% yield). Generating an aryl nucleophile via decarboxylation obviates problems associated with transmetalation at a putative gold(III) complex. This reaction is site specific, which overcomes prior limitations associated with gold catalyzed oxidative coupling reactions. The reactivity of the (hetero)aryl carboxylate correlates qualitatively to the field effect parameter (Fortho). Furthermore, each step in a proposed mechanism was observed from isolated gold complexes, supporting a gold catalyzed mechanism.
|
Ryan A. Daley; Joseph Topczewski
|
Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748cc567dfed51cec4a75/original/gold-catalyzed-decarboxylative-cross-coupling-of-iodoarenes.pdf
|
60c752ee567dfed37eec5d90
|
10.26434/chemrxiv.13366379.v1
|
Detection of a SARS-CoV-2 Sequence with Genosensors Using Data Analysis Based on Information Visualization and Machine Learning Techniques
|
<p>We report on genosensors to detect an
ssDNA sequence from the SARS-CoV-2 genome, which mimics the GU280 gp10 gene
(coding the viral nucleocapsid phosphoprotein), using four distinct principles
of detection and treating the data with information visualization and machine
learning techniques. Genosensors were fabricated on either gold (Au)
interdigitated electrodes for electrical and electrochemical measurements or on
Au nanoparticles on a glass slide for optical measurements. They contained a
matrix of 11-mercaptoundecanoic acid (11-MUA) self-assembled monolayer (SAM)
onto which a layer of capture probe (cpDNA) sequence was immobilized. Detection
was performed using electrical and electrochemical impedance spectroscopies and
localized surface plasmon resonance (LSPR). The highest sensitivity was reached
with impedance spectroscopy, including using a low-cost (US$ 100) homemade
impedance analyzer. Complementary ssDNA sequences were detected with a
detection limit of 0.5 aM (0.3 copy/μL).
This performance may be attributed to the high sensitivity of the electrical
impedance technique combined with an appropriate arrangement of the sequences
on the electrodes and hybridization between the complementary sequences, as
inferred from polarization-modulated infrared reflection absorption
spectroscopy (PM-IRRAS). The selectivity of the genosensor was confirmed by
plotting the impedance spectroscopy data with a multidimensional projection
technique (Interactive Document Mapping, IDMAP), where a clear separation was
observed among the samples of the complementary DNA sequence at various
concentrations and from buffer samples containing a non-complementary sequence
and other DNA biomarkers. The diagnosis of SARS-CoV-2 mimicking sequences was
also achieved with machine learning techniques applied to scanning electron
microscope images taken from genosensors exposed to distinct concentrations of
the complementary ssDNA sequences. In summary, the genosensors proposed here
are promising for detecting SARS-CoV-2 genetic material (RNA) in biological
fluids in point-of-care settings. </p>
|
Juliana Coatrini Soares; Andrey Coatrini Soares; Valquiria Cruz Rodrigues; Pedro Ramon Almeida Oiticica; Paulo Augusto Raymundo-Pereira; José L. Bott-Neto; Lorenzo Antonio Buscaglia; Lucas Daniel Chiba Castro; Lucas Correia Ribas; Leonardo Scabini; Laís Canniatti Brazaca; Daniel Souza Correa; Luiz Henrique Capparelli Mattoso; Maria Cristina Ferreira de Oliveira; André Ponce Leon Ferreira Carvalho; Emanuel Carrilho; Odemir Matinez Bruno; Matias Melendez; Osvaldo N. Oliveira Jr
|
Analytical Chemistry - General; Electrochemical Analysis; Microscopy; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752ee567dfed37eec5d90/original/detection-of-a-sars-co-v-2-sequence-with-genosensors-using-data-analysis-based-on-information-visualization-and-machine-learning-techniques.pdf
|
64a997dc9ea64cc167a9e671
|
10.26434/chemrxiv-2023-f0z8n
|
Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining
|
Genomics-guided methodologies have been widely adopted and proven beneficial for the discovery of natural products. However, a major challenge in the field of genome mining is determining how to selectively extract biosynthetic gene clusters (BGCs) for untapped natural products from a substantial number of available genome sequences. In this study, we developed a fungal genome mining pipeline that extracts BGCs encoding enzymes that lack a detectable protein domain and are not recognized as biosynthetic proteins by existing bioinformatic tools. We searched for BGCs encoding a homologue of Pyr4-family terpene cyclases, which are representative examples of domainless enzymes, in approximately 2,000 fungal genomes and discovered several BGCs with unique features. The subsequent characterization of these BGCs led to the discovery of the first fungal onoceroid triterpenoids and unprecedented onoceroid synthases. Our genome mining pipeline has broad applicability in fungal genome mining and can serve as a beneficial tool for accessing diverse, unexploited natural products.
|
Jia Tang; Yudai Matsuda
|
Organic Chemistry; Natural Products
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a997dc9ea64cc167a9e671/original/discovery-of-fungal-onoceroid-triterpenoids-through-domainless-enzyme-targeted-global-genome-mining.pdf
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647a4c224f8b1884b7bba5b4
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10.26434/chemrxiv-2023-1t1tw
|
5,6-Fused Heterocycle Cholate Derivatives as Spore Germination Inhibitors of Clostridioides difficile
|
Clostridioides difficile infection (CDI) is an anaerobic bacterium that is responsible for most antibiotic-associated cases of diarrhea. CDI begins with the ingestion of an environmentally stable spore that germinates within the GI tract under specific conditions. We have shown that the bile salt analog N-phenyl-cholan-24-amide (1) can inhibit spore germination and prevent CDI in animal models of infection. Unfortunately, 1, was stable in the gut of antibiotic-treated animals but was rapidly degraded by gastrointestinal micoflora in the normal gut preventing its use to prevent CDI. We hypothesized that the source of the instability was the amide group. To explore this hypothesis, we removed the amide by either converting it to an amine or to 5,6-fused heterocycles. We found that reduction of the amide to an amine resulted in a significant loss of activity, but conversion to benzimidazole (6a), benzothiazole (6b), or benzoxazole (6c) gave compounds with good antigermination activity. Exploration of other sterane groups such as chenodeoxycholate and deoxycholate gave active compounds only for the benzimidazole series. Examination of 6b showed that it was stable for 24 hours in the presence of feces taken from healthy mice validating the hypothesis that an amide bioisostere would increase the stability of the compound. Mice treated with 6a and 6b also showed no signs of toxicity up to 300 mg/kg daily for 7 days. Each compound was tested for its ability to prevent CDI in a murine model. Compound 6b but not 6a was able to prevent CDI when given at a dose of 50 mg/kg.
|
Shiv Sharma; Jacqueline Phan; Ernesto Abel-Santos; Steven Firestine
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647a4c224f8b1884b7bba5b4/original/5-6-fused-heterocycle-cholate-derivatives-as-spore-germination-inhibitors-of-clostridioides-difficile.pdf
|
612e58d46563697a1d1ec12d
|
10.26434/chemrxiv-2021-bz00c
|
Enhancing Electrochemical Carbon Dioxide Reduction by Polymer-Encapsulated Cobalt Phthalocyanine through Incorporation of Graphite Powder
|
Cobalt phthalocyanine (CoPc) has been extensively studied as a catalyst for the electrochemical reduction of CO2 to value-added products. Previous studies have shown that CoPc is a competent and efficient catalyst when immobilized onto carbon-based electrodes using a polymer binder, especially when immobilized with a graphitic carbon powder support to increase charge transport. In this study, we systematically explore the influence of incorporating graphite powder (GP) into a polymer-encapsulated CoPc on the system’s activity for the electrochemical reduction of CO2. We report a protocol for incorporating GP into CoPc/polymer/GP catalyst films that facilitates physisorption of CoPc to GP, leading to increased activity for CO2 reduction. We show that the activity for CO2 reduction increases with GP loading at low GP loadings, but at sufficiently high GP loadings the activity plateaus as charge transfer is sufficiently fast to no longer be rate limiting. We also demonstrate that axial coordination is still important even in the presence of GP, suggesting that CoPc does not fully coordinate to heteroatoms on the GP surface. We develop a set of optimized conditions under which the CoPc/polymer/GP catalyst systems reduce CO2 with higher activity and similar selectivity to previously reported CoPc/polymer films on edge-plane graphite electrodes. The procedures outlined in this study will be used in future studies to optimize catalyst, polymer, and carbon support loadings for other polymer-catalyst composite systems for electrocatalytic transformations.
|
Taylor Soucy; Yingshuo Liu; Jonah Eisenberg; Charles McCrory
|
Inorganic Chemistry; Catalysis; Electrochemistry; Electrocatalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-09-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612e58d46563697a1d1ec12d/original/enhancing-electrochemical-carbon-dioxide-reduction-by-polymer-encapsulated-cobalt-phthalocyanine-through-incorporation-of-graphite-powder.pdf
|
60c74dfeee301cf721c7a3f5
|
10.26434/chemrxiv.12639215.v2
|
Merging Shuttle Reactions and Paired Electrolysis: E-Shuttle Unlocks Reversible Halogenations
|
<p>Polyhalogenated
molecules have found widespread applications as flame retardants, pest-control
agents, polymers and pharmaceuticals. They also serve as versatile
synthetic intermediates in organic chemistry due to the inherent reactivity of
carbon-halogen bonds. Despite these attractive features, the
preparation of polyhalogenated molecules still mainly relies on the use of
highly toxic and corrosive halogenating reagents, such as Cl<sub>2</sub> and Br<sub>2</sub>,
which are hazardous compounds to transport, store, and handle. Moreover, the use of such
highly reactive reagents inherently makes the development of the reverse
reactions, <i>retro</i>-dihalogenations, highly challenging, despite their
potential for the recycling of persistent halogenated pollutants. Here, we introduce
an electrochemically-assisted shuttle<i> (e-shuttle)</i> paradigm for the
facile and scalable interconversion of alkenes and vicinal dihalides, a class
of reactions which can be used both to synthesize useful polyhalogenated
molecules from simple alkenes and to recycle waste material through <i>retro</i>-dihalogenation.
The power of this reaction is best highlighted by an example, in which different
soils contaminated with a persistent environmental pollutant (Lindane), could
be directly used as Cl<sub>2</sub>-donors for the transfer dichlorination of
simple feedstock alkenes, merging a recycling process with a synthetically
relevant dichlorination reaction. We further demonstrate that this paired electrolysis-enabled
shuttle protocol, which uses a simple setup and inexpensive electrodes, is
applicable to four different, synthetically useful transfer halogenation
reactions, and can be readily scaled-up to a decagram scale. In a broader
context, the symbiotic merging of shuttle reactions and electrochemistry
introduced in this work opens new horizons for safer transfer functionalization
reactions that will address important challenges across the molecular sciences.</p>
<div><br /><div>
</div>
</div>
|
Xichang Dong; Johannes L. Röckl; Siegfried R. Waldvogel; Bill Morandi
|
Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dfeee301cf721c7a3f5/original/merging-shuttle-reactions-and-paired-electrolysis-e-shuttle-unlocks-reversible-halogenations.pdf
|
64e2ddb201042bc1cc681e1b
|
10.26434/chemrxiv-2023-xgsdn
|
Coarse Grained MD Simulation of Bulk and Interfacial Behavior of Mixture of CTAB/SDS Surfactants
|
This is simulation study on corrosion inhibition by surfactants via micelle formation and deposition on Iron (Fe) surfaces. Mainly focused on CTAB/SDS mixtures in aqueous solution at varying concentrations. Micelle properties, including size, shape, aggregation number, cluster size, and surfactant diffusion, were calculated and validated with experimental data. The coarse-grained Fe surface was modeled and validated against experimental water contact-angle data. Subsequently, the deposition of CTAB/SDS mixtures on the Fe surface and air-water interface was studied systematically. We found that the relative ratio of CTAB/SDS in the solution directly influences surfactant deposition behavior, which might impact the corrosion inhibition efficiency.
|
Yogesh Badhe; Dharmendr Kumar; Rakesh Gupta; Vinay Jain; Beena Rai
|
Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e2ddb201042bc1cc681e1b/original/coarse-grained-md-simulation-of-bulk-and-interfacial-behavior-of-mixture-of-ctab-sds-surfactants.pdf
|
673c72f05a82cea2faa6d9eb
|
10.26434/chemrxiv-2024-5vb65
|
Synthesis of Macrocycles via Orthogonal Bond Cleavage of the Pores in Covalent Organic Frameworks
|
Control of selectivity in organic synthesis is essential for guiding chemical reactions towards a desired product when multiple outcomes are possible. Since organic reactions can often yield a range of products, selectivity control ensures that the target product is favoured over others. Herein, we present a new synthetic approach, Clip-off Chemistry, which provides precise selectivity control in the synthesis of organic (macro)molecules through selective orthogonal cleavage within extended structures containing such (macro)molecules, which, in turn, spontaneously form when these extended structures are assembled. We have applied this concept to the synthesis of seven novel macrocycles by selectively cleaving double or triple bonds via ozonolysis within covalent-organic frameworks (COFs). With this demonstration, we believe that Clip-off Chemistry will soon provide generalized access to previously inaccessible (macro)molecules and polymers for diverse applications.
|
Roberto Sánchez-Naya; Juan Pablo Cavalieri; Jorge Albalad; Kaiyu Wang; Carles Fuentes-Espinosa; Teodor Parella; Xavi Ribas; Omar M. Yaghi; Inhar Imaz; Daniel Maspoch
|
Organic Chemistry; Organic Synthesis and Reactions; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673c72f05a82cea2faa6d9eb/original/synthesis-of-macrocycles-via-orthogonal-bond-cleavage-of-the-pores-in-covalent-organic-frameworks.pdf
|
65934ba5e9ebbb4db9369ba0
|
10.26434/chemrxiv-2024-v49vb
|
Selective (a)-L-Rhamnosylation and Neuroprotective Activity Exploration of Cardiotonic Steroids
|
This work describes the studies on the direct C3-glycosylation of the C19-hydroxylated cardiotonic steroids strophanthidol, anhydro-ouabagenin and ouabagenin using a strategy based on in situ protection of the C5 and C19 hydroxyl groups with boronic acids. While this strategy resulted in a successful one-pot C3-selective glycosylation of strophanthidol and anhydro-ouabegenin, it failed to provide ouabain from ouabagenin. The neuroprotective activity of the synthetic and natural glyco-sides against LPS-induced neuroinflammation was explored in neonatal mice primary glia cells. Co-administration of natural and synthetic C3-glycosides at 200 nM concentrations resulted in the significant reduction of the LPS-induced neuroinflam-matory markers IL-6, IL-1, TNFα, and IKBKE, with the anhydro-ouabagenin-3-(a)-L-rhamnoside (anhydro-ouabain) show-ing the most significant effect. At the same time, unglycosylated anhydro-ouabagenin enhanced rather than suppressed LPS-induced neuroinflammation.
|
Ryan Rutkoski; Lucas Kniess Debarba; Lukas Stilgenbauer; Tay Rosenthal; Marianna Sadagurski; Pavel Nagorny
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65934ba5e9ebbb4db9369ba0/original/selective-a-l-rhamnosylation-and-neuroprotective-activity-exploration-of-cardiotonic-steroids.pdf
|
624051fcd09df04d65fccc68
|
10.26434/chemrxiv-2022-tt8v7
|
Antimicrobial Polymers of Linear and Bottlebrush Architecture: Probing the Membrane Interaction and Physicochemical Properties
|
Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focused on random linear copolymers, the development of APs with advanced architectures proved to be more potent in the mimicry of antimicrobial peptides. We recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using diverse spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking E. coli-membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.
|
Alain Murhimalika Bapolisi; Patrycja Kielb; Marek Bekir; Anne-Catherine Lehnen; Christin Radon; Sophie Laroque; Petra Wendler; Henrike M. Müller-Werkmeister; Matthias Hartlieb
|
Physical Chemistry; Polymer Science; Polyelectrolytes - Polymers; Interfaces; Physical and Chemical Properties
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624051fcd09df04d65fccc68/original/antimicrobial-polymers-of-linear-and-bottlebrush-architecture-probing-the-membrane-interaction-and-physicochemical-properties.pdf
|
644c141d6ee8e6b5ed44109b
|
10.26434/chemrxiv-2023-d2wxz-v3
|
Computation of Finite Temperature Mechanical Properties of Zeolitic Imidazolate Framework Glasses by Molecular Dynamics
|
Mechanical properties of amorphous phases of metal-organic frameworks (MOF), such as MOF glasses, are difficult to determine experimentally. Moreover, computational characterization is limited by the level of theory chosen for the description of interatomic interactions and is often computationally expensive. In this work, we have extensively investigated the computation of finite temperature mechanical properties of ZIF-4 in the crystal and glass phases. We critically assessed computational methodologies including ab initio molecular dynamics, reactive force fields, and classical force fields, based on a variety of glass models. We find that ZIF-4 glasses have a larger bulk modulus than the crystal and confirm previous studies that the density is larger for the glass phases. Moreover, we confirm in the case of zeolitic imidazolate framework (ZIF) glasses the relationship between density and bulk modulus, showing that obtaining models of correct density is key to the prediction of physical properties for these systems.
|
Nicolas Castel; François-Xavier Coudert
|
Theoretical and Computational Chemistry; Materials Science
|
CC BY 4.0
|
CHEMRXIV
|
2023-05-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644c141d6ee8e6b5ed44109b/original/computation-of-finite-temperature-mechanical-properties-of-zeolitic-imidazolate-framework-glasses-by-molecular-dynamics.pdf
|
656f52065bc9fcb5c91ade9d
|
10.26434/chemrxiv-2023-25lkq
|
Mechanochemical-Assisted Decarboxylative Sulfonylation of α,β-Unsaturated Carboxylic Acids with Sodium Sulfinate Salts
|
Developing a green and efficient method for synthesizing vinyl sulfones is challenging and highly desirable. We hereby report a green, sustainable, and unprecedented mechanochemical-assisted approach for the decarboxylative sulfonylation of α,β-unsaturated carboxylic acids with sodium sulfinates using only potassium iodide (50 mol%) as an activator under water-assisted grinding conditions. A library of alkyl and aryl vinyl sulfone derivatives was synthesized successfully up to 92% yield with excellent functional group compatibility under a short reaction time. This sulfonylation strategy is well tolerated by aryl α,β-unsaturated carboxylic acids, and alkyl and aryl sodium sulfinate salts. The advantages of this strategy are (i) metal catalyst-, base-, oxidant-, and solvent-free, (ii) operationally simple with a short reaction time, (iii) excellent effective mass yield, atom economy, E-factor, and EcoScale score. The practicality of this method is also demonstrated in the gram-scale synthesis of vinyl sulfones.
|
Anuj Sharma; Barakha Saxena; Roshan Patel; Shruti Sharma
|
Organic Chemistry; Organic Compounds and Functional Groups
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656f52065bc9fcb5c91ade9d/original/mechanochemical-assisted-decarboxylative-sulfonylation-of-unsaturated-carboxylic-acids-with-sodium-sulfinate-salts.pdf
|
60c74a7c4c8919789aad3225
|
10.26434/chemrxiv.11662335.v3
|
In Situ Visualizing the Recognition Between Proteins and Platinum-Damaged DNA in Single-Cells by Correlated Optical and Secondary Ion Mass Spectrometric Imaging
|
<p><b><i>In situ</i> visualization of the recognition and interaction between proteins and drug damaged DNA at single cell level is highly important for understanding the molecular mechanism of action of DNA targeting drugs, yet a great challenge. We herein report a novel approach, termed as correlated optical and secondary ion mass spectrometric imaging (COSIMSi), for exploring the recognition between proteins and cisplatin-damaged DNA in single cells. Genetically encoded EYFP-fused HMGB1, an <i>in vitro</i> well-known specific binder of cisplatin-damaged DNA, and dye-stained DNA, and cisplatin were mapped by LSCM and ToF-SIMS imaging, respectively. The LSCM and SIMS images were aligned with aiding of an addressable silicon wafer to generate fused images, in which the co-localization of the fluorescence and MS signals indicated the formation of HMGB1-Pt-DNA ternary complexes in a dose- and time-dependent manner. In contrast, COSIMSi showed that little HMGB1(F37A)-Pt-DNA complex was produced under the same conditions. Moreover, we demonstrated for the first time that cisplatin lesion on DNA prevented a DNA-binding protein Smad3 from interacting with DNA. These results verify that the COSIMSi is an effective and straightforward tool for <i>in situ</i> visualization of recognition and interaction between proteins and specific damaged DNA in single cells. </b><br /></p>
|
Yu Lin; Kui Wu; Feifei Jia; Ling Chen; Zhaoying Wang; Yanyan Zhang; Qun Luo; Suyan Liu; Luyu Qi; Nan Li; Xiaohong Fang; Pu Dong; Fei Gao; Yao Zhao; Fuyi Wang
|
Biochemical Analysis; Imaging; Mass Spectrometry; Microscopy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a7c4c8919789aad3225/original/in-situ-visualizing-the-recognition-between-proteins-and-platinum-damaged-dna-in-single-cells-by-correlated-optical-and-secondary-ion-mass-spectrometric-imaging.pdf
|
65f682199138d23161a0bd8e
|
10.26434/chemrxiv-2024-h4bsz
|
Photochemical PFAS Degradation in Ion Exchange Resin Regeneration Brine: Effects of Water Matrix Components and Technical Solutions
|
Ion-exchange (IX) is an effective method for PFAS removal from water and wastewater, but the treatment of concentrated PFAS from IX resin regeneration remains a major technical barrier. This study investigates the challenges and solutions associated with photochemical treatment of waste brines from resin regeneration. We first tested the defluorination of perfluorooctanoic acid (PFOA) by UV/sulfite/iodide in synthetic solutions containing individual inorganic and organic species. We identified NO3−, NO2−, and natural organic matter (NOM) as the major inhibitors. NO3− and NO2− quenched hydrated electron (eaq−), but they could be readily removed by increasing the sulfite dose. We used humic acid as a representative NOM. It significantly slowed down defluorination but can be readily removed by ferric flocculation without removing PFOA. The integration of flocculation and UV/S/I treatment successfully treated two waste brines, which primarily contained short-chain PFAS. PFAS removal achieved >99% within 20 hours. The maximum defluorination reached 85% and 70% for the two waste brines, respectively. This study advances UV technologies for PFAS destruction and enhances the sustainability of ion-exchange resin for PFAS removal.
|
Dandan Rao; Jinyong Liu
|
Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry; Wastes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f682199138d23161a0bd8e/original/photochemical-pfas-degradation-in-ion-exchange-resin-regeneration-brine-effects-of-water-matrix-components-and-technical-solutions.pdf
|
60c74f42469df4172bf44650
|
10.26434/chemrxiv.12871430.v1
|
Inducing Open-shell Character in Porphyrins through Surface-assisted Phenalenyl π−Extension
|
Herein, we present a simple and straightforward method for the synthesis of phenalenyl-fused Pors (Por A0, PorA2 and PorA4) through readily available molecular precursors. While PorA0 was prepared by “wet” synthesis, the two- and four-fold phenalenyl-fused Por derivatives PorA2 and PorA4 were fabricated through a surface-assisted cyclodehydrogenation reaction from meso-2,6-dimethylphenyl(dmp) substituted precursors Por(dmp)2 and Por(dmp)4, respectively. In a systemat-ic way, we examined the structural and electronic properties of three surface-supported Pors.<br />
|
Qiang Sun; Roberto Robles; Nicolas Lorente; Giovanni Bottari; Tomás Torres; Roman Fasel; Pascal Ruffieux; Luis M. Mateos
|
Magnetic Materials; Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-08-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f42469df4172bf44650/original/inducing-open-shell-character-in-porphyrins-through-surface-assisted-phenalenyl-extension.pdf
|
60c7442e842e656b6bdb23d1
|
10.26434/chemrxiv.9751682.v1
|
Acoustic Immunosensing of Exosomes Using a Quartz Crystal Microbalance with Dissipation Monitoring
|
Exosomes are endocytic lipid-membrane bound bodies with potential to be used as biomarkers in cancer and neurodegenerative disease. The limitations and scarcity of current exosome characterisation approaches has led to a growing demand for translational techniques, capable of determining their molecular composition and physical properties in physiological fluids. Here, we investigate label-free immunosensing, using a quartz crystal microbalance with dissipation (QCM-D), to detect exosomes by exploiting their surface protein profile. Exosomes expressing the transmembrane protein CD63 were isolated by size-exclusion chromatography from cell culture media. QCM-D sensors functionalised with anti-CD63 antibodies formed a direct immunoassay towards CD63-positive exosomes, exhibiting a limit-of-detection of 1.7x10^8 and 1.1x10^8 exosome sized particles (ESPs) ml^-1 for frequency and dissipation response respectively, i.e., clinically relevant concentrations. Our proof-of-concept findings support the adoption of dual-mode acoustic analysis of exosomes, leveraging both frequency and dissipation monitoring for use in diagnostic assays.
|
Jugal Suthar; Edward Parsons; Bart Hoogenboom; Gareth Williams; Stefan Guldin
|
Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7442e842e656b6bdb23d1/original/acoustic-immunosensing-of-exosomes-using-a-quartz-crystal-microbalance-with-dissipation-monitoring.pdf
|
667d5a94c9c6a5c07a876a8a
|
10.26434/chemrxiv-2024-1zxff
|
Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents
|
Macrocycles are a promising class of compounds as therapeutics for difficult drug targets due to a favourable combination of properties: They often exhibit improved binding affinity compared to their linear counterparts due to their reduced conformational flexibility, while still being able to adapt to environments of different polarity. To assist in the rational design of macrocyclic drugs, there is need for computational methods that can accurately predict conformational ensembles of macrocycles in different environments. Molecular dynamics (MD) simulations remain one of the most accurate methods to predict ensembles quantitatively, although the accuracy is governed by the underlying force field. In this work, we benchmark four different force fields for their application to macrocycles by performing replica exchange with solute tempering (REST2) simulations of eleven macrocyclic compounds and comparing the obtained conformational ensembles to nuclear Overhauser effect (NOE) upper distance bounds from NMR experiments. Especially, the modern force fields OpenFF 2.0 and XFF yield good results, outperforming force fields like GAFF2 and OPLS/AA. We conclude that REST2 in combination with modern force fields can often produce accurate ensembles of macrocyclic compounds. However, we also highlight examples for which all examined force fields fail to produce ensembles that fulfill the experimental constraints.
|
Franz Waibl; Fabio Casagrande; Fabian Dey; Sereina Riniker
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2024-07-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667d5a94c9c6a5c07a876a8a/original/validating-small-molecule-force-fields-for-macrocyclic-compounds-using-nmr-data-in-different-solvents.pdf
|
66d1bdb3a4e53c4876239a56
|
10.26434/chemrxiv-2024-xs327
|
Polarizable AMOEBA force field predicts thin and dense hydration layer around monosaccharides for accurate simulations of carbohydrates in solution
|
Polarizable force fields crucially enhance the modeling of macromolecules in polar media. Here, we present new parameters to model six common monosaccharides with the polarizable AMOEBA force field. These parameters yield a thinner, but denser, hydration layer than that previously reported. This denser hydration layer results in eliminating non- physical aggregation of glucose in water – an issue that has plagued molecular dynamics simulations of carbohydrates for decades.
|
Luke Newman; Mackenzie Patton; Breyanna Rodriguez; Ethan Sumner; Valerie Vaissier Welborn
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY 4.0
|
CHEMRXIV
|
2024-09-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d1bdb3a4e53c4876239a56/original/polarizable-amoeba-force-field-predicts-thin-and-dense-hydration-layer-around-monosaccharides-for-accurate-simulations-of-carbohydrates-in-solution.pdf
|
62e248dfcf66121a7ab88f07
|
10.26434/chemrxiv-2022-6z5sd
|
Why Ortho- and Para-Hydroxy Metabolites Can Scavenge Free Radicals That the Parent Atorvastatin Cannot? Important Pharmacologic Insight from Quantum Chemistry
|
The pharmaceutical success of atorvastatin (ATV),
a widely employed drug against the ``bad'' cholesterol (LDL) and cardiovascular diseases, traces back to its ability to scavenge free radicals. Unfortunately, information on its antioxidant properties is missing or unreliable. Here, we report detailed quantum chemical results for ATV and its
ortho- and para-hydroxy metabolites (o-ATV, p-ATV) in methanolic phase. They comprise global reactivity indices,
bond order indices and spin densities as well as all relevant enthalpies of reaction (bond dissociation BDE, ionization IP and electron attachment EA, proton detachment PDE and proton affinity PA, and electron transfer ETE). With these properties in hand, we can provide the first theoretical explanation of the experimental finding that, due to their free radical scavenging activity, ATV hydroxy metabolites rather than the parent ATV have substantial inhibitory effect on LDL and the like. Surprisingly (because it is contrary to the most cases currently known), we unambiguously found that HAT (direct hydrogen atom transfer) rather than SPLET (sequential proton loss electron transfer) or SET-PT (stepwise electron transfer proton transfer) is the thermodynamically preferred pathway by which o-ATV and p-ATV in methanolic phase can scavenge DPPH$^\bullet$ (1,1-diphenyl-2-picrylhydrazyl) radicals.
|
Ioan Baldea
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-07-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e248dfcf66121a7ab88f07/original/why-ortho-and-para-hydroxy-metabolites-can-scavenge-free-radicals-that-the-parent-atorvastatin-cannot-important-pharmacologic-insight-from-quantum-chemistry.pdf
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65a3fe9366c13817296c7885
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10.26434/chemrxiv-2024-mdqtl
|
The interplay between calcite crystal nucleation on polydiacetylene template and its amorphization by phosphoserine
|
Organisms use a diverse range of organic-inorganic hybrid materials for a variety of purposes, including mechanical support, navigation and protection. These materials are mostly crystalline and are characterized by unique composition, polymorph, crystallite size, shape and crystallographic orientation. The crystalline biominerals are generally formed through amorphous, hydrated transient minerals, but in some, the amorphous phases are stable and persist. Using a biomimetic approach, we address aspects of biological mineralization in vitro and gain insight into the processes and interactions that play roles in the natural systems, in-vivo. In this work, we demonstrate two essential but conflicting methods that are likely to act simultaneously in many mineralizing systems. These are directed crystal nucleation on organic templates, and on the other hand, crystal inhibition to produce the transient amorphous phase. The experimental method in this project mimics aspects of biomineralization processes of calcium carbonate (CaCO3) nucleation. Polydiacetylene (PDA) – a robust, linear conjugated polymer, made from amphiphilic long-chain diacetylene monomers, which upon surface compression, followed by UV polymerization form an ultrathin, stable monolayer structure. PDA simulates the organic template for the CaCO3 crystallization in our experimental system in that it exposed a dense array of acidic groups in well-defined orientation and being a semi-rigid template surface. On PDA templates, calcite crystals nucleate from a (01.2) face and in every single domain of the PDA film they are all coaligned with the crystals' a-axes oriented parallel to the polymer backbone. Supersaturated solutions for CaCO3were prepared either by mixing CaCl2 and Na2CO3, or by bubbling CO2 into CaCO3 suspension, or by slow diffusion of ammonium carbonate into CaCl2 solution in a desiccator. Phosphoserine (P-ser) was added to CaCO3 deposition systems as a crystallization inhibitor, which results in amorphous calcium carbonate (ACC) deposition. The phosphate groups substitute a part of the carbonate groups during the deposition and this way, inhibit the crystallization process. Various concentrations of P-ser in deposition system on PDA templates result in different morphologies and degrees of crystallinity of CaCO3. In this biomimetic system, we demonstrate the conflicting, yet simultaneous influences on biological crystal formation, namely the ordered template and crystal nucleation and crystal inhibition.
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Bidisha Tah ; Amir Berman; Saja Nasser; Jürgen Jopp; Gil Goobes; Anna Stepansky; Yehonatan Glick
|
Physical Chemistry; Materials Science; Biophysical Chemistry; Materials Chemistry; Crystallography
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-01-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a3fe9366c13817296c7885/original/the-interplay-between-calcite-crystal-nucleation-on-polydiacetylene-template-and-its-amorphization-by-phosphoserine.pdf
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67b1e6006dde43c90822dffb
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10.26434/chemrxiv-2024-vx4tb-v3
|
A Deep Learning-Augmented Density Functional
Framework for Reaction Modeling with Chemical
Accuracy
|
Accurate prediction of reaction energetics remains a fundamental challenge in computational chemistry, as conventional density functional theory (DFT) often fails to reconcile high accuracy with computational effi ciency. Here, we introduce Deep post-Hartree-Fock (DeePHF), a machine learning framework that synergistically integrates neural networks with quantum mechanical descriptors to achieve CCSD(T)-level precision while retaining the efficiency of DFT. By establishing a direct mapping between the eigenvalues of local density matrices and high-level correlation energies, DeePHF circumvents the traditional accuracy-scalability trade-off . Trained on a limited dataset of small-molecule reactions, our method demonstrates unprecedented performance across multiple benchmark
datasets, exhibiting exceptional transferability. In fact, its accuracy even surpasses that of advanced double-hybrid functionals, all while maintaining O(N^3) scaling. DeePHF offers a promising pathway to bridge the gap between high-level quantum chemistry methods and the practical demands for scalable, accurate models in computational chemistry, and with further refi nement, it is poised to make signifi cant contributions to the advancement of chemical reaction modeling.
|
Jin Xiao; Yingfeng Zhang; Bowen Li; Shuwen Zhang; Ya Gao; Han Wang ; John Z.H. Zhang; Tong Zhu
|
Theoretical and Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-02-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b1e6006dde43c90822dffb/original/a-deep-learning-augmented-density-functional-framework-for-reaction-modeling-with-chemical-accuracy.pdf
|
66be406620ac769e5fb32424
|
10.26434/chemrxiv-2024-nttnv-v2
|
Introducing Column Chromatography through Colorful Reactions of Guaiazulene
|
We report two related experiments to introduce column chromatography in the context of a second-year organic chemistry lab course or an upper-division advanced organic chemistry lab course. Both experiments involve functionalization of guaiazulene via electrophilic aromatic substitution, and the highly colored starting material and products serve as clear visual indicators of reaction progress and of the purification. The longer version of the experiment scaffolds the chromatography process by guiding students to develop conditions to purify their own unique compound. The products are amenable to a wide variety of characterization techniques, including UV-visible absorbance spectroscopy and 2D NMR spectroscopy. These experiments are highly flexible and have been implemented in a second-year course as an activity taking a single lab period and in an upper-division course as an activity taking three full lab periods. As judged by the results and discussion from their lab reports, students in both classes were largely successful at meeting the learning objectives for these experiments, including monitoring reaction progress using thin-layer chromatography, separating compound mixtures using column chromatography, and assessing the success of a reaction based on experimental data.
|
Paul M. Morgan; Anne M. Wilson; J. Patrick Lutz
|
Organic Chemistry; Chemical Education
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66be406620ac769e5fb32424/original/introducing-column-chromatography-through-colorful-reactions-of-guaiazulene.pdf
|
650a4bb3b927619fe774cecd
|
10.26434/chemrxiv-2023-4h71w
|
Accurate compositional analysis of unknown polymer systems within ±1 wt% errors via thermogravimetry-synchronized reference-free quantitative mass spectrometry.
|
Compositional analysis (CA)—identification and quantification of the system constituents—is the most fundamental and decisive approach to investigate the system of interest. Pyrolysis mass spectrometry (MS) with millidalton resolution is very effective for chemical identification and directly applicable to polymer materials regardless of their solubilities; however, it is less helpful for quantification especially when the references, i.e., pure constituents, are unknown, non-isolable and thus unpreparable. To compensate this weakness, herein we propose reference-free quantitative mass spectrometry (RQMS) with enhanced quantification accuracy assisted by synchronized thermogravimetry (TG). The key to success is the conversion of MS signal intensities of pyrolyzed fragments into weight abundances via mathematically incorporated TG data. In a benchmark test using ternary polymer systems, this new framework named TG-RQMS demonstrates accurate CA within ±1 wt% errors without using any knowledge nor spectra of the references. This simple yet accurate and versatile CA method would be an invaluable tool to investigate polymer materials whose composition is hardly accessible via other analytic methods.
|
Yusuke Hibi; Shiho Uesaka; Masanobu Naito
|
Analytical Chemistry; Polymer Science; Polymer blends; Mass Spectrometry; Spectroscopy (Anal. Chem.)
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650a4bb3b927619fe774cecd/original/accurate-compositional-analysis-of-unknown-polymer-systems-within-1-wt-errors-via-thermogravimetry-synchronized-reference-free-quantitative-mass-spectrometry.pdf
|
60c7405f469df455ecf42c09
|
10.26434/chemrxiv.7701695.v1
|
Click, Zoom, Explore: Interactive 3D (i-3D) Figures in Standard Manuscript PDFs
|
While chemistry exists in three-dimensions, it is published in two. This down-conversion results in a significant loss in information and often necessitates multiple images/figures to convey the complexity, intricacy, and beauty of a given structure. Outlined herein is a concise, straightforward method for incorporating interactive three-dimensional (i-3D) figures into manuscript pdfs. These figures can be generated from a variety of sources and allow for structures, molecular orbitals, unit cells and crystal lattices, as well as biopolymers to be published in the same information rich format as they are created and studied on our computers. These images can be seen and interacted with by anyone reading the manuscript in the standard pdf software (Adobe Reader) – and to fully appreciate this article, please read it using Adobe Reader. It is time for chemistry publications to take advantage of the digital age.
|
Sourav Chatterjee; Sooyeon Moon; Amanda Rowlands; Fred Chin; Peter H. Seeberger; Nabyl Merbouh; Kerry Gilmore
|
Physical Organic Chemistry; Chemical Education - General; Supramolecular Chemistry (Inorg.); Biochemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-02-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7405f469df455ecf42c09/original/click-zoom-explore-interactive-3d-i-3d-figures-in-standard-manuscript-pd-fs.pdf
|
63c0722f1f1258828a9bb2aa
|
10.26434/chemrxiv-2022-l26b9-v2
|
Biological filtration is resilient to wildfire ash-associated organic carbon threats to drinking water treatment
|
Elevated/altered levels of dissolved organic matter (DOM) in water can be challenging to treat after wildfire. Biologically-mediated treatment removes some DOM; its ability to remove elevated/altered post-fire dissolved organic carbon (DOC) resulting from wildfire ash was investigated for the first time. Treatment of wildfire ash-amended (low, moderate, high) source waters by bench-scale biofilters was evaluated in duplicate. Turbidity and DOC were typically well-removed (effluent turbidity ≤ 0.3 NTU; average DOC removal ~20%) in all biofilters during periods of stable source water quality. Daily DOC removal across all biofilters (ash-amended and controls) was generally consistent, suggesting that (i) the biofilter DOC biodegradation capacity was not deleteriously impacted by the ash and (ii) the biofilters buffered the ash-associated increases in water extractable organic matter. DOM fractionation indicates this was because the biodegradable low molecular weight neutral fractions of DOM which increased with ash addition were reduced by biofiltration, while humic substances were largely recalcitrant. Thus, biological filtration was resilient to wildfire ash-associated DOM threats to drinking water treatment, but operational resilience may be compromised if the balance between readily removed and recalcitrant fractions of DOM change, as was observed during brief periods herein.
|
Emma Anne Jackson Blackburn; Sarah E. Dickson-Anderson; William B. Anderson; Monica B. Emelko
|
Organic Chemistry; Earth, Space, and Environmental Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c0722f1f1258828a9bb2aa/original/biological-filtration-is-resilient-to-wildfire-ash-associated-organic-carbon-threats-to-drinking-water-treatment.pdf
|
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