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675bbaee085116a1333e9e3e
|
10.26434/chemrxiv-2024-hd20d
|
Modeling Structural Flexibility in 3D Carbon Models:
A Hybrid MC/MD Approach to Adsorption-Induced Deformation
|
Predicting adsorption-induced deformation in nanoporous carbons is crucial for applications ranging from gas separations and energy storage to carbon capture and enhanced natural gas recovery, where structural changes can significantly impact material performance and process efficiency. The interplay between adsorption and material deformation presents both challenges and opportunities, particularly for CO₂-CH₄ displacement processes in geological structures where matrix swelling can alter reservoir permeability. We investigate adsorption-induced deformation of nanoporous carbons using an original hybrid Monte Carlo/Molecular Dynamics (MC/MD) simulation approach that couples adsorption sampling with structural relaxation. By studying CH4 and CO₂ adsorption on 3D carbon structures of varying densities (0.5-1.0 g/cm³), we demonstrate characteristic non-monotonic deformation behavior, with initial contraction at low pressures followed by expansion at higher pressures. A key contribution is the direct calculation of isothermal compressibility of adsorbate saturated porous structures from the volume fluctuations during NPT-MD simulations, which reveals dramatic mechanical property changes during adsorption. In the process of adsorption, carbon structures exhibit initial softening followed by substantial hardening, with a dramatic increase of the volumetric modulus in denser carbons. Using elastic theory relationships, we estimate the adsorption stresses reaching 175 MPa, that provides crucial insights into potential material degradation mechanisms. For binary CH₄/CO₂ mixtures, increasing CO₂ content amplifies both contraction and expansion effects due to stronger fluid-wall interactions. The iterative MC/MD methodology enables direct observation of the structural evolution and quantitative estimates of the mechanical properties, which are difficult to measure experimentally, advancing our understanding of coupled adsorption-deformation processes in nanoporous materials.
|
Nicholas Corrente; Shivam Parashar; Raleigh Gough; Elizabeth Hinks; Peter Ravikovitch; Alexander Neimark
|
Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675bbaee085116a1333e9e3e/original/modeling-structural-flexibility-in-3d-carbon-models-a-hybrid-mc-md-approach-to-adsorption-induced-deformation.pdf
|
67ab3e2081d2151a02f6045e
|
10.26434/chemrxiv-2025-n2sxg
|
Deconvolute the Impact of Microenvironment on Proton-Coupled Electron Transfers at Electrochemical Interfaces
|
Microenvironment at electrochemical interfaces has a critical impact on the elec-trode-mediated proton-coupled electron transfer (PCET) processes. However, understanding the convoluted effects by microenivornment remains challenging, and deploying the electron tranfer theory of the Marcus-Hush-Chidsey (MHC) framework is limited by its elusive link to experimentally accessible variables other than reaction rates. Herein, we report a general mech-anistic framework based on the MHC theory to deconvolute the effects of microenvironment on the interfacial PCET processes in terms of experimentally accessible variables, as illustrated by the model system of the cation effect on Au-catalyzed CO2 reduction reaction, for which we rationalize the trends by both inorganic and organic cations in a unified picture formulated by hydration free energy of cation and surface charge density.
|
Yifei Xu; Yunze Qiu; Hai Xiao; Bingjun Xu
|
Catalysis; Electrocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2025-02-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab3e2081d2151a02f6045e/original/deconvolute-the-impact-of-microenvironment-on-proton-coupled-electron-transfers-at-electrochemical-interfaces.pdf
|
60c75368bdbb89ec87a3a462
|
10.26434/chemrxiv.13489158.v1
|
High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology
|
Urine is a non-invasive biofluid that is rich in polar metabolites and well-suited for metabolomic epidemiology. However, due to individual variability in health and hydration status, the physiological concentration of urine can differ >15-fold, which can pose major challenges in untargeted LC-MS metabolomics. Although numerous urine normalization methods have been implemented (e.g., creatinine, specific gravity – SG), most are manual and therefore not practical for population-based studies. To address this issue, we developed a method to measure SG in 96-well-plates using a refractive index detector (RID), which exhibited accuracy within 85-115% and <3.4% precision. Bland-Altman statistics showed a mean deviation of -0.0001 SG units (limits of agreement: -0.0014-0.0011) relative to a hand held refractometer. Using this RID-based SG normalization, we developed an automated LC MS workflow for untargeted urinary metabolomics in 96-well-plate format. The workflow uses positive and negative ionization HILIC chromatography and acquires mass spectra in data independent acquisition (DIA) mode at 3 collision energies. Five technical internal standards (tISs) were used to monitor data quality in each method, all of which demonstrated raw coefficients of variation (CVs) <10% in the quality controls (QCs) and <20% in the samples for a small cohort (n=87 samples, n=22 QCs). Application in a large cohort (n=842 urine samples, n=248 QCs), demonstrated CVQC<5% and CVsamples<16% for 4/5 tISs after signal drift correction by cubic spline regression. The workflow identified >540 urinary metabolites including endogenous and exogenous compounds. This platform is suitable for performing urinary untargeted metabolomic epidemiology and will be useful for applications in population-based molecular phenotyping.
|
Isabel Meister; Pei Zhang; Anirban Sinha; C. Magnus Sköld; Åsa M. Wheelock; Takashi Izumi; Romanas Chaleckis; Craig E. Wheelock
|
Analytical Chemistry - General; Biochemical Analysis; Mass Spectrometry; High-throughput Screening
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-12-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75368bdbb89ec87a3a462/original/high-precision-automated-workflow-for-urinary-untargeted-metabolomic-epidemiology.pdf
|
66be7080a4e53c48767e739f
|
10.26434/chemrxiv-2024-5zxw2
|
High pressure microreactor for minute amounts of catalyst on planar supports: a case study of CO2 hydrogenation over Pd0.25Zn0.75Ox nanoclusters
|
High-pressure studies of catalyst quantities down to a few hundred nanograms, particularly well-defined catalysts prepared using physical methods in ultra-high vacuum on planar supports can potentially bridge the surface science and applied catalysis approaches to catalyst development. However, the chemical reactors required for such investigations are lacking.
We present the novel design and evaluation of a 50 µL rectangular microchannel reactor capable of testing small quantities of catalyst at pressures up to 40 bar and temperatures up to 250°C. To evaluate the microreactor's performance, Pd0.25Zn0.75Ox nanoclusters soft-landed on SiO2-coated mica sheets using the cluster beam deposition technique, were tested for the reverse water-gas shift reaction through a series of kinetic experiments.
Experimental results, combined with computational fluid dynamics and mass transport analysis, demonstrate that the proposed microreactor setup allows for testing minute quantities of catalysts with high sensitivity at industrially relevant temperatures and pressures. Although not restricted to a particular catalyst preparation method, the setup is an excellent platform for conducting catalytic tests on composition-controlled, mass-selected, gas-phase nanoparticles deposited on planar substrates, facilitating the development of reliable structure-activity relationships and enabling a more rational design of catalysts.
|
Imran Abbas; Filippo Romeggio; Kacper Pilarczyk ; Simon Kuhn; Christian Danvad Damsgaard ; Jakob Kibsgaard; Peter Lievens; Didier Grandjean; Ewald Janssens
|
Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Alloys; Reaction Engineering; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66be7080a4e53c48767e739f/original/high-pressure-microreactor-for-minute-amounts-of-catalyst-on-planar-supports-a-case-study-of-co2-hydrogenation-over-pd0-25zn0-75ox-nanoclusters.pdf
|
63a2c21aa53ea640a052bcf8
|
10.26434/chemrxiv-2022-v0f54-v2
|
Multimodal Image Registration and Fusion Offer Better Spatial Resolution for Mass Spectrometry Imaging
|
Super-resolution reconstruction has attracted increasing research interest in mass spectrometry imaging (MSI), but it remains a challenging ill-posed problem. In the present study, we proposed a Deep learning based SUper-REsolution model called DeepSURE, where the hematoxylin and eosin (H&E) stain microscopy image is used to pose constrains in the process of super-resolution reconstruction to alleviate the ill-poseness. A novel model architecture is designed to achieve multi-task optimization by incorporating multi-modal image registration and fusion in a mutual reinforced framework. The present results demonstrated that the DeepSURE method is able to produce super-resolution reconstruction image with rich chemical information and detailed structure both on visual inspection and quantitative evaluation. In addition, the method was found able to improve the delimitation of boundary between cancerous and para-cancerous regions in MSI image. Furthermore, the reconstruction of low-resolution spatial transcriptomics data demonstrates that the developed DeepSURE method may find wider applications in biomedical fields.
|
Lei Guo; Jinyu Zhu; Keqi Wang; Kian-Kai Cheng; Jingjing Xu; Liheng Dong; Xiangnan Xu; Can Chen ; Mudassir Shah; Zhangxiao Peng; Jianing Wang ; Zongwei Cai ; Jiyang Dong
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence
|
CC BY NC 4.0
|
CHEMRXIV
|
2022-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a2c21aa53ea640a052bcf8/original/multimodal-image-registration-and-fusion-offer-better-spatial-resolution-for-mass-spectrometry-imaging.pdf
|
618b984bda1506e90d9ce178
|
10.26434/chemrxiv-2021-m0brp
|
Can aluminum, a non-redox metal, alter the thermodynamics of key biological redox processes? The DPPH-QH 2 radical scavenging reaction as a test case.
|
The increased bioavailability of aluminum has led to a concern about its toxicity on living systems. Among the most important toxic effects, it has been proven that aluminum increases oxidative stress in biological systems, a controversial fact, however, due to its non-redox nature. In the present work, we characterize in detail how aluminum can alter redox equilibriums by analyzing its effects on the thermodynamics of the redox scavenging reaction
between DPPH . , a radical compound often used as a reactive oxygen species model, and hydroquinones, a potent natural antioxidant. For the first time, theoretical and experimental redox potentials within aluminum biochemistry are directly compared. Our results fully agree
with experimental reduction and oxidation potentials, unequivocally revealing how aluminum alters the spontaneity of the reaction by stabilizing the reduction of DPPH· to DPPH − and promoting a proton transfer to the diazine moiety, leading to the production of a DPPH-H
species. The capability of aluminum to modify redox potentials shown here confirms previous experimental findings on the role of aluminum to interfere with free radical scavenging reactions, affecting the natural redox processes of living organisms.
|
Jose Lanuza; Veronica Postils; Xabier Lopez
|
Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Physical and Chemical Properties
|
CC BY 4.0
|
CHEMRXIV
|
2021-11-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618b984bda1506e90d9ce178/original/can-aluminum-a-non-redox-metal-alter-the-thermodynamics-of-key-biological-redox-processes-the-dpph-qh-2-radical-scavenging-reaction-as-a-test-case.pdf
|
6488eb034f8b1884b740a6ab
|
10.26434/chemrxiv-2023-g3rlm
|
Reversible CO2 Capture and On-Demand Release by an Acidity-Matched Organic Photoswitch
|
Separation of carbon dioxide (CO2) from point sources or directly from the atmosphere can contribute crucially to climate-change mitigation plans for the coming decades. A fundamental practical limitation for current strategies is the considerable energy cost required to regenerate the sorbent and release the captured CO2 for storage or utilization. The feasibility of these approaches, including thermal stripping, pressure swing desorption, and electrochemical switching, can only be justified by the availability of affordable, storable, and widely distributable renewable energy. A photochemically driven system that demonstrates efficient passive capture and on-demand CO2 release triggered by sunlight as the sole external stimulus would provide an attractive alternative. However, little is known about the thermodynamic requirements for such a process, nor mechanisms for modulating changes in CO2 affinity with photoinduced metastable states. Here, we show that an organic photoswitchable molecule of precisely matched effective acidity can repeatedly capture and release a near-stoichiometric quantity of CO2 according to dark–light cycles. We show that the CO2-derived species rests as a solvent-separated ion pair, and key aspects of its excited-state dynamics that regulate photorelease efficiency are characterized by transient absorption spectroscopy. The thermodynamic and kinetic concepts established herein will serve as guiding principles for the development of viable solar-powered negative emissions technologies.
|
Abdulrahman Alfaraidi; Bryan Kudisch; Nina Ni; Jayden Thomas; Thomas George; Khashayar Rajabimoghadam; Haihui Joy Jiang; Daniel Nocera; Michael Aziz; Richard Liu
|
Physical Chemistry; Organic Chemistry; Energy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6488eb034f8b1884b740a6ab/original/reversible-co2-capture-and-on-demand-release-by-an-acidity-matched-organic-photoswitch.pdf
|
67803b2a6dde43c908ed7bc7
|
10.26434/chemrxiv-2025-wzm1c
|
Construction of an organic cage-based porous ionic liquid using an aminal tying strategy
|
An aminal tying method was applied to post-synthetically
modify a flexible organic cage, RCC1, to construct a porous ionic liquid (PIL). The resulting PIL, [RCC1-IM][NTf2]6, displayed melting behaviour below 100 °C, a transition to a glass phase on melt-quenching, CO2 uptake, and its permanent porosity was confirmed using molecular dynamic simulations.
|
Aiting Kai; Austin Mroz; Kim Jelfs; Andrew Cooper; Marc Little; Rebecca Greenaway
|
Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67803b2a6dde43c908ed7bc7/original/construction-of-an-organic-cage-based-porous-ionic-liquid-using-an-aminal-tying-strategy.pdf
|
62833f2f7087675cfb554c87
|
10.26434/chemrxiv-2022-m1brm
|
Hexagonal Structure Enhancing Damping Efficiency Inspired by Tree Frogs
|
Magnetic fluid shock absorbers (MFSAs) have been successfully applied in eliminating the micro-vibration of the spacecraft’s flexible structures. The method of enhancing the damping of MFSAs has always been the key issue. The tree frog’s toe pads exhibit the strong adhesion, which inspired us to learn from their surface structure. We got hundreds of scanning electron microscope images of the tree frog’s toe pads surface and used the edge extraction algorithm to obtain the result that the geometric shape with the largest proportion in these images is hexagon. According to this result, hexagonal surface textures were added to the inner surface of the MFSA and a small part of the MFSA was taken for further simulation analysis. The flow distribution of the magnetic fluid (MF) acquired from the simulation clearly illustrates that the surface textures cause vortexes formation in the MF layer. These vortexes increase the shear rate between the MF layers, thereby augmenting the flow resistance. The vibration reduction experiments were carried out and MFSAs employed in these experiments were fabricated by 3D printing technology. Consequently, the bionic textures mimicking the tree frog’s toe pads surface can significantly improve the damping performance of MFSAs.
|
Yanwen Li; Decai Li
|
Materials Science; Magnetic Materials
|
CC BY 4.0
|
CHEMRXIV
|
2022-05-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62833f2f7087675cfb554c87/original/hexagonal-structure-enhancing-damping-efficiency-inspired-by-tree-frogs.pdf
|
60c745aeee301c48ecc7937d
|
10.26434/chemrxiv.10101419.v1
|
Biradical Formation by Deprotonation in Thiazole-Derivatives: The Hidden Nature of Dasatinib
|
The formation of stable organic biradicals by a deprotonation process is
reported for a series of conjugated heterocycles that share a
Ph-N(H)-2-thiazole structural motif. We characterise the
paramagnetic electronic ground state by means of continuous-wave and pulse EPR.
We propose a simple
valence bond mechanism for a deprotonation-induced formation of paramagnetic
organic molecules, based on the interplay between the electronegativity of
heteroatomic groups and the recovery of aromaticity to stabilise the biradical species. The Ph-N(H)-2-thiazole motif is found in a
variety of biologically active molecules, exemplified here with the anticancer
drug Dasatinib, and our results suggest a radical-based mechanism for the
protein kinase inhibition activity of the drug. The existence of this structure-property
relationship for an elementary chemical motif suggests that biradical species may be more prevalent than previously thought and have
an important role in bioorganic chemistry.
|
Carlos Heras; Daniel Reta; Rosendo Valero; Guillermo Albareda; Nicholas Chilton; Alistair Fielding; Iberio de P. R Moreira; Josep Maria Bofill; Francisco Lopez Calahorra
|
Physical Organic Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745aeee301c48ecc7937d/original/biradical-formation-by-deprotonation-in-thiazole-derivatives-the-hidden-nature-of-dasatinib.pdf
|
66aa79105101a2ffa8b6a3df
|
10.26434/chemrxiv-2024-qnr9n
|
CO2 Conversion to Butene via a Tandem Photovoltaic-Electrochemical/Photothermocatalytic Process: A Co-Design Approach to Coupled Microenvironments
|
We developed a tandem, unassisted, solar-driven electrochemical and photothermocatalytic process for the single-pass conversion of CO2 to butene using only simulated solar irradiation as the energetic input. The two-step process involves electrochemical CO2 reduction (CO2R) to ethylene followed by ethylene dimerization to butene. We assessed two unassisted electrochemical setups to concentrate ethylene in the CO2R reactor, achieving concentrations up to 5.4 vol.% with 1.8% average solar-to-ethylene conversion and 5.6% average CO2-to-ethylene single-pass conversion under 1-sun illumination. When passed through the photothermocatalytic ethylene oligomerization reactor, we generated 600 ppm of butene under 3-sun illumination. Through analysis of this process, we identified that the presence of H2, CO, and H2O leads to rapid deactivation of the Ni-based ethylene oligomerization catalyst.
|
Kyra M. K. Yap; Aisulu Aitbekova; Matthew Salazar; Tobias A. Kistler; Melanie Rodríguez Pabón; Magel P. Su; Nicholas B. Watkins; Sang-Won Lee; Peter Agbo; Adam Z. Weber; Jonas C. Peters; Theodor Agapie; Adam C. Nielander; Harry A. Atwater; Thomas F. Jaramillo; Alexis T. Bell
|
Materials Science; Catalysis; Energy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aa79105101a2ffa8b6a3df/original/co2-conversion-to-butene-via-a-tandem-photovoltaic-electrochemical-photothermocatalytic-process-a-co-design-approach-to-coupled-microenvironments.pdf
|
6315b3c1be03b2c370eabdae
|
10.26434/chemrxiv-2022-2wnzw
|
Molecular-scale exploration of mechanical properties and interactions of poly(lactic acid) with cellulose and chitin
|
Poly(lactic acid) (PLA), one of the pillars of the current overarching displacement trend switching from oil- to natural-based polymers is often associated with polysaccharides, to benefit from their increased mechanical properties. This association is, however, greatly hampered by the poor PLA/polysaccharide miscibility, whose underlying nature is still vastly unexplored. This work aims at shedding light into the PLA-polysaccharide interactions and reveal structure-property relationships from a fundamental perspective using atomistic molecular dynamics with amorphous cellulose and chitin as representative polysaccharide molecules. Our computational strategy was able to reproduce targeted mechanical properties of pure and/or composite materials, reveal a lesser degree of immiscibility in PLA/chitin compared to PLA/cellulose associations, assert PLA-oriented polysaccharide reorientations and explore how less effective PLA-polysaccharide hydrogen bonds are related to the poor PLA/polysaccharide miscibility.
|
Paulo Mileo; Caroline Krauter; Jeffrey Sanders; Andrea Browning; Mathew Halls
|
Polymer Science; Biopolymers; Cellulosic materials; Polymer blends
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6315b3c1be03b2c370eabdae/original/molecular-scale-exploration-of-mechanical-properties-and-interactions-of-poly-lactic-acid-with-cellulose-and-chitin.pdf
|
6655e55c91aefa6ce13159a5
|
10.26434/chemrxiv-2024-x99z8-v2
|
Hydrogen Economy vs. Hydrogen Embrittlement: Indirect Electrochemical Determination of Hydrogen Diffusion in Steel
|
Hydrogen has reemerged in recent years as a promising environment−friendly energy carrier that can help reduce the world's dependence on fossil fuels. Despite its unique advantages, there are still challenges regarding the storage, packaging, and transportation of hydrogen. Specifically, the phenomenon of hydrogen embrittlement (HE) in metals can hinder the widespread use of hydrogen. This study focuses on the analysis of hydrogen embrittlement and hydrogen permeation through metals, with an emphasis on high−strength and duplex steels. Various steel types were evaluated for their hydrogen permeation properties using a simplified version of the Devanathan−Stachurski permeation cell to measure the diffusion constants und breakthrough times in different steel grades. In combination with Extended X−ray Absorption Fine Structure (EXAFS) analysis, the results indicate that hydrogen embrittlement is dependent on the steel grade and that the manufacturing method plays a key role. Our methodology using indirect electrochemical determination offers rapid and reproducible hydrogen diffusion, providing insights for the development of efficient hydrogen storage systems utilizing steel.
|
Andreas Drichel; Madlin Spiewak; Arne Röttger; Dirk Lützenkirchen−Hecht; Bruno Rodrigues; Adam Slabon
|
Materials Science; Chemical Engineering and Industrial Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-05-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6655e55c91aefa6ce13159a5/original/hydrogen-economy-vs-hydrogen-embrittlement-indirect-electrochemical-determination-of-hydrogen-diffusion-in-steel.pdf
|
63cff99a1fb2a88201df2b54
|
10.26434/chemrxiv-2023-7mq66
|
Phenyl-Substituted Cibalackrot Derivatives: Synthesis, Structure, and Solution Photophysics
|
Three symmetrically and three unsymmetrically substituted cibalackrot (7,14-diphenyldiindolo[3,2,1-de:3',2',1'-ij][1,5]naphthyridine-6,13-dione, 1) dyes carrying two derivatized phenyl rings have been synthesized as candidates for molecular electronics and especially for singlet fission, a process of interest for solar energy conversion. Solution measurements provided singlet and triplet excitation energies and fluorescence yields and lifetimes; conformational properties were analyzed computationally. The molecular properties are close to ideal for singlet fission. However, crystal structures, obtained by single-crystal X-ray diffraction, are rather similar to those of the polymorphs of solid 1, in which formation of a charge-separated state followed by intersystem crossing, complemented with excimer formation, outcompetes singlet fission. Results of calculations by the approximate SIMPLE method suggest which ones among the solid derivatives are the best candidates for singlet fission, but it appears difficult to change the crystal packing in a desirable direction. We also describe the preparation of three specifically deuteriated versions of 1, expected to help sort out the mechanism of fast intersystem crossing in its charge-separated state.
|
Jiří Kaleta; Miroslav Dudič; Lucie Ludvíková; Alan Liška; Alexandr Zaykov; Igor Rončevič; Milan Mašát; Lucie Bednárová; Paul Dron; Simon Teat; JOSEF MICHL
|
Physical Chemistry; Organic Chemistry; Energy
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-01-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cff99a1fb2a88201df2b54/original/phenyl-substituted-cibalackrot-derivatives-synthesis-structure-and-solution-photophysics.pdf
|
632366bafee74e6fe53db775
|
10.26434/chemrxiv-2022-whlz5
|
In Tandem Enantioselective Intramolecular Heck-Matsuda Reactions directly from anilines
|
A new enantioselective intramolecular strategy for the synthesis of enantioenriched bridged benzoxacines, unsaturated spirobenzofurans, methyl-2,3-dihydrobenzofuran acetates, and methyl-2,3-indoline acetate scaffolds in a tandem-like diazotization/Heck Matsuda process directly from anilines has been developed. The process combines the in situ diazotization of the aniline, followed by the intramolecular Heck-Matsuda reaction, thus skipping the isolation and purification of unstable or hard-to-synthesize aryldiazonium salts. The practicality and robustness of the sequence were demonstrated by the synthesis of 26 examples of complex structural motifs with yields up to 91% and enantiomeric ratio (er) up to 97:3, including quaternary stereocenters. The in-tandem processes from anilines were compared to conventional Heck Matsuda reactions using pre-synthesized aryldiazonium salts. With few exceptions, the reactions starting directly from the anilines afforded better overall yields and er, demonstrating the efficiency of this method.
|
Carlos Roque Duarte Correia; Tomaz Chorro; Edson Leonardo Scarpa de Souza; Otto Koster; Ellen Polo; Vitor Hugo da Silva; João Marcos Batista Junior
|
Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-09-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632366bafee74e6fe53db775/original/in-tandem-enantioselective-intramolecular-heck-matsuda-reactions-directly-from-anilines.pdf
|
60c74ba5567dfe80c2ec4f86
|
10.26434/chemrxiv.12367376.v1
|
Peptide Identification and Quantification by Gas Phase Fractionation Enables Proteomics Without Liquid Chromatography
|
<p>Liquid chromatography
mass spectrometry (LC-MS) delivers sensitive peptide analysis for proteomics,
but the methodology requires extensive analysis time, hampering throughput.
Here, we demonstrate that flow injection analysis data-independent acquisition
(FIA-DIA), using gas-phase peptide separation instead of LC, offers extremely
fast proteome analysis. Incorporating ion mobility with FIA-DIA, we demonstrate
the targeted quantification of over 500 proteins within minutes of MS data
collection (~3.5 proteins/second). We show the utility of this technology to
perform a complex multifactorial proteome study of interactions between
nutrients, genotype, and mitochondrial toxins in a collection of cultured human
cells. More than 45,000 quantitative protein measurements from 132 samples were
achieved in only 4.4 hours of MS data collection. Enabling fast, unbiased
proteome quantification without LC, FIA-DIA offers a new approach to boosting
throughput critical to drug and biomarker discovery studies that require
analysis of thousands of proteomes.</p>
|
Jesse Meyer; Natalie M. Niemi; David J. Pagliarini; Joshua J. Coon
|
Mass Spectrometry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba5567dfe80c2ec4f86/original/peptide-identification-and-quantification-by-gas-phase-fractionation-enables-proteomics-without-liquid-chromatography.pdf
|
63adb27fa53ea60d0c5ba55f
|
10.26434/chemrxiv-2022-djr5h
|
Self-healable, Regenerable, and Degradable Dynamic Covalent Nitroalcohol Organogels
|
Dynamic covalent gels have been synthesized from an aromatic trialdehyde and α,ω-dinitroalkanes via the nitroaldol reaction in organic solvents. The gelation process could be finetuned by changing the starting nitroalkanes, solvents, feed concentration, catalyst loading, or reaction temperature. The resulting organogels demonstrated good structural integrity and excellent self-healing ability. Intact xerogels were produced upon drying, without damaging the network, and the solvent-free network could recover its gel form in the presence of an organic solvent. Furthermore, the crosslinked dynameric gel depolymerized to small molecules in response to excess nitromethane.
|
Yunchuan Qi; Mubarak Ayinla; Margaret J. Sobkowicz; Olof Ramström
|
Organic Chemistry; Materials Science; Polymer Science; Supramolecular Chemistry (Org.); Organic Polymers; Polymerization (Polymers)
|
CC BY NC ND 4.0
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CHEMRXIV
|
2022-12-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63adb27fa53ea60d0c5ba55f/original/self-healable-regenerable-and-degradable-dynamic-covalent-nitroalcohol-organogels.pdf
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6577567a7acf130c32020cce
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10.26434/chemrxiv-2023-rqqqb
|
Unveiling Encrypted Antimicrobial Peptides from Cephalopods' Salivary Glands: A Proteolysis-Driven Virtual Approach
|
Antimicrobial peptides (AMPs), with their versatile actions, offer promise against antimicrobial resistance and as templates for novel therapeutic agents. While existing AMP databases primarily feature AMPs from terrestrial eukaryotes, marine sources are gaining attention, with cephalopods emerging as a promising but still underexplored source. This study unveils the potential reservoir of AMPs encrypted within the proteome of cephalopods’ salivary glands using in silico proteolysis. A composite protein database comprising canonical and non-canonical proteins from cephalopods' salivary apparatus was used as the substrate for five proteases involved in three digestion protocols. The resulting millions of peptides were screened using machine learning, deep learning, multi-query similarity-based models, and complex networks. The screening prioritizes antimicrobial activity, the absence of haemolytic and toxic attributes, and structural distinctiveness compared to characterized AMPs. Diverse publicly accessible AMP datasets are produced, catering to various research needs, ranging from those focused solely on antimicrobial activity to refined datasets of non-haemolytic and non-toxic AMPs. Comparative analyses and network science principles were applied to identify singular and representative subsets from non-haemolytic and non-toxic AMPs. All these sets of AMPs and the proposed mining tools serve as valuable assets for peptide drug developers.
|
Guillermin Agüero-Chapin; Dany Domínguez-Pérez; Yovani Marrero-Ponce; Kevin Castillo-Mendieta; Agostinho Antunes
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Artificial Intelligence
|
CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6577567a7acf130c32020cce/original/unveiling-encrypted-antimicrobial-peptides-from-cephalopods-salivary-glands-a-proteolysis-driven-virtual-approach.pdf
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64da732edfabaf06ff474bf2
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10.26434/chemrxiv-2023-w81js
|
Silver-Based Supramolecular Hydrogel for the Development of Smartphone-Enabled Alkaline Phosphatase Sensor
|
Alkaline phosphatase (ALP) is an important protein responsible for various conditions related to hepatobiliary, osteopenia, pregnancy, and certain cancers. Developing an easy-to-use paper-based sensor for ALP would provide a point-of-care diagnostic device. A silver-coordinated cytidine hydrogel is a potential candidate to show responses under different concentrations of ALP. Herein, we prepared and characterized a three-component hydrogel system comprising cytidine, boric acid, and silver nitrate. The gelation occurs rapidly within a minute at room temperature and atmospheric pressure, which makes the system more convenient to use. Reduction of Ag+ by the in situ generated ascorbic acid by ALP allows the development of colorimetric sensor based on the gel-coated paper, enabling quantification of ALP concentration. This portable sensor works efficiently on a smartphone color-scanning app, making point-of-care detection easier. RGB values obtained from scanning indicate the ALP concentration in the range of 1-100 nM, which is independent of mobile cameras. The hydrogel exhibits excellent solvo-reversibility and enables naked-eye colorimetric detection of ALP with a detection limit of 0.23 nM (0.016 U/L). The sensing strategy works well in spiked human serum with a detection limit of 0.34 nM (0.023 U/L) in solution and paper-based sensors. Overall, the cytidine-based gel system presents an effective point-of-care diagnostic system for detecting ALP with high sensitivity.
|
Smarak Islam Chaudhury; Sourav Das; Preeti Bhatt; Bhaskar Sen; Subinoy Rana
|
Analytical Chemistry; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da732edfabaf06ff474bf2/original/silver-based-supramolecular-hydrogel-for-the-development-of-smartphone-enabled-alkaline-phosphatase-sensor.pdf
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63a9a085ff46512cce37e516
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10.26434/chemrxiv-2022-dq5m4
|
Wood for Thermal Energy Storage
|
For thousands of years wood had been used for many fundamental purposes, as a fuel or as a material for building houses and creating tools and furniture. Today, many researches aim to improve the properties of this traditional material for further innovative applications. Here we will consider the enhancement of the wood thermal features by means of its impregnation with phase change materials (PCMs). A PCM is a substance absorbing and releasing thermal energy at a phase transition. Therefore, wood and PCMs can be composed to be useful for the thermal energy storage, that is for heating and cooling applications. Here we propose a discussion of recent literature about development and applications of wood-based composite PCMs.
|
Amelia Carolina Sparavigna
|
Materials Science
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CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a9a085ff46512cce37e516/original/wood-for-thermal-energy-storage.pdf
|
62861e93809e32146f952811
|
10.26434/chemrxiv-2022-dd0l4
|
Carbon Nanodots with Solvatochromic Photoluminescence for the Electrochemical Determination of Estrogenic Steroids in Tap, Nat-ural and Municipal Waste Waters
|
Herein, we utilized carbon nanodots (R-CNDs) for the electrochemical detection of estrogens in tap, natural water samples and simulated effluents from Swedish Waste Water Treatment Plants (WWTPs). R-CNDs were prepared from 2-aminophenol by solvothermal synthesis and used as a modifier for chitosan-based selective membranes. The data obtained from atomic force microscopy and transmission electron microscopy suggest a spherical morphology of the R-CNDs with lateral size in the range of 3–8 nm and the height of 1–8 nm. In contrast to most other known carbon nanodots, R-CNDs are soluble in various organic solvents, including apolar, and less soluble in water. Small nanodots (3 nm) are more hydrophilic than large ones (6–8 nm) and can be separated from the bulk suspension of R-CNDs in heptane by their extraction into water/ethanol mixture. Suspensions of large R-CNDs in apolar solvents exhibit green photoluminescence, while small R-CNDs in polar solvents have orange. This phenomenon was attributed to a solvatochromic rather than to a quantum effect. The R-CNDs were embedded on a chitosan-modified pencil electrode and the electrode was applied for voltammetric determination of four abandoned estrogens: Estrone, Estradiol, Estriol, and Ethynyl Estradiol. The sensor demonstrates a group-selective response to the estrogens with a detection limit of 17.0 nmol·L-1. It can be applied to determine the estrogens in the range of 0.05–4.6 μmol·L−1 in the presence of typical interfering bioactive compounds, such as paracetamol, uric acid, progesterone, sulfamethoxazole, trimethoprim, ibuprofen, caffeine. The developed sensors show repeatability and reproducibility values of 1.8–3.4% and 4.3%, respectively. The efficiency of the was proved by application for tap and lake water samples, where the recovery range was found to be 93–100%. The low cost, stability and high sensitivity and selectivity of fabricated sensors, make R-CNDs a perspective modifier for electrochemical sensors for the detection of estrogen microquantities in variable water samples.
|
Albina Mikhraliieva; Oleg Tkachenko; Raphael Freire; Volodymyr Zaitsev; Yutao Xing; Anton Panteleimonov; Maria Strømme; Tetyana Budnyak
|
Materials Science; Nanoscience; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62861e93809e32146f952811/original/carbon-nanodots-with-solvatochromic-photoluminescence-for-the-electrochemical-determination-of-estrogenic-steroids-in-tap-nat-ural-and-municipal-waste-waters.pdf
|
60c73d0fbb8c1a54e83d96b1
|
10.26434/chemrxiv.5459653.v1
|
Atomic Layer Deposition of LiF and Lithium Ion Conducting (AlF3)(LiF)x Alloys Using Trimethylaluminum, Lithium Hexamethyldisilazide and Hydrogen Fluoride
|
<div>Atomic layer deposition (ALD) of LiF and lithium ion conducting (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloys was developed using trimethylaluminum, lithium hexamethyldisilazide (LiHMDS) and hydrogen fluoride derived from HF-pyridine solution. ALD of LiF was studied using in situ quartz crystal microbalance (QCM) and in situ quadrupole mass spectrometer (QMS) at reaction temperatures between 125°C and 250°C. A mass gain per cycle of 12 ng/(cm<sup>2</sup> cycle) was obtained from QCM measurements at 150°C and decreased at higher temperatures. QMS detected FSi(CH<sub>3</sub>)<sub>3</sub> as a reaction byproduct instead of HMDS at 150°C. LiF ALD showed self-limiting behavior. Ex situ measurements using X-ray reflectivity (XRR) and spectroscopic ellipsometry (SE) showed a growth rate of 0.5-0.6 Å/cycle, in good agreement with the in situ QCM measurements.</div><div>ALD of lithium ion conducting (AlF3)(LiF)x alloys was also demonstrated using in situ QCM and in situ QMS at reaction temperatures at 150°C A mass gain per sequence of 22 ng/(cm<sup>2</sup> cycle) was obtained from QCM measurements at 150°C. Ex situ measurements using XRR and SE showed a linear growth rate of 0.9 Å/sequence, in good agreement with the in situ QCM measurements. Stoichiometry between AlF<sub>3</sub> and LiF by QCM experiment was calculated to 1:2.8. XPS showed LiF film consist of lithium and fluorine. XPS also showed (AlF<sub>3</sub>)(LiF)x alloy consists of aluminum, lithium and fluorine. Carbon, oxygen, and nitrogen impurities were both below the detection limit of XPS. Grazing incidence X-ray diffraction (GIXRD) observed that LiF and (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film have crystalline structures. Inductively coupled plasma mass spectrometry (ICP-MS) and ionic chromatography revealed atomic ratio of Li:F=1:1.1 and Al:Li:F=1:2.7: 5.4 for (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film. These atomic ratios were consistent with the calculation from QCM experiments. Finally, lithium ion conductivity (AlF<sub>3</sub>)(LiF)<sub>x</sub> alloy film was measured as σ = 7.5 × 10<sup>-6</sup> S/cm.</div>
|
Younghee Lee; Daniela M. Piper; Andrew S. Cavanagh; Matthias J. Young; Se-Hee Lee; Steven M. George
|
Thin Films
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2017-10-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0fbb8c1a54e83d96b1/original/atomic-layer-deposition-of-li-f-and-lithium-ion-conducting-al-f3-li-f-x-alloys-using-trimethylaluminum-lithium-hexamethyldisilazide-and-hydrogen-fluoride.pdf
|
666b21905101a2ffa883d62c
|
10.26434/chemrxiv-2024-nxrg6-v2
|
AutoDesigner - Core Design, a De Novo Design Algorithm for Chemical Scaffolds: Application to the Design and Synthesis of Novel Selective Wee1 Inhibitors
|
The hit identification stage of a drug discovery program generally involves the design of novel chemical scaffolds with desired biological activity against the target(s) of interest. One common approach is scaffold hopping, which is the manual design of novel scaffolds based on known chemical matter. One major limitation of this approach is narrow chemical space exploration, which can lead to difficulties in maintaining or improving biological activity, selectivity, and favorable property space. Another limitation is the lack of preliminary structure-activity relationship (SAR) data around these designs, which could lead to selecting suboptimal scaffolds to advance lead optimization. To address these limitations, we propose AutoDesigner - Core Design (CoreDesign), a de novo scaffold design algorithm. Our approach is a cloud-integrated, de novo design algorithm for systematically exploring and refining chemical scaffolds against biological targets of interest. The algorithm designs, evaluates, and optimizes a vast range - from millions to billions - of molecules in silico, following defined project parameters encompassing structural novelty, physicochemical attributes, potency, and selectivity. In this manner, CoreDesign can generate novel scaffolds and also explore preliminary SAR around each scaffold using FEP+ potency predictions. CoreDesign requires only a single ligand with quantifiable binding affinity and an initial binding hypothesis, making it especially suited for the hit-identification stage where experimental data is often limited. To validate CoreDesign in a real-world drug discovery setting, we applied it to the design of novel, potent Wee1 inhibitors with improved selectivity over PLK1. Starting from a single known ligand, CoreDesign rapidly explored over 23 billion molecules to identify 1,342 novel chemical series with a mean of 4 compounds per scaffold. Importantly, all chemical series met the predefined property space requirements. To rapidly analyze this large amount of data and prioritize chemical scaffolds for synthesis, we utilize t-Distributed Stochastic Neighbor Embedding (t-SNE) plots of in silico properties. The chemical space projections allowed us to rapidly identify a structurally novel 5-5 fused core meeting all the hit-identification requirements. Several compounds were synthesized and assayed from the scaffold, displaying good potency against Wee1 and excellent PLK1 selectivity. Our results suggest that CoreDesign can significantly speed up the hit-identification process and increase the probability of success of drug discovery campaigns by allowing teams to bring forward high-quality chemical scaffolds de-risked by the availability of preliminary SAR.
|
Pieter Bos; Fabio Ranalli; Emelie Flood; Shawn Watts; Daigo Inoyama; Jennifer Knight; Anthony Clark; Andrew Placzeck; Jiashi Wang; Aleksey Gerasyuto; Sarah Silvergleid; Wu Yin; Shaoxian Sun; Robert Abel; Sathesh Bhat
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666b21905101a2ffa883d62c/original/auto-designer-core-design-a-de-novo-design-algorithm-for-chemical-scaffolds-application-to-the-design-and-synthesis-of-novel-selective-wee1-inhibitors.pdf
|
60c757c6842e658cf7db4764
|
10.26434/chemrxiv.14459313.v1
|
Thermodynamic Modelling of Hydrogen-Multicomponent Alloy Systems: Calculating Pressure-Composition-Temperature Diagrams
|
<p>The applicability of an alloy as a hydrogen storage media
mostly relies on its pressure-composition-temperature (PCT) diagram. Since the
PCT diagram is composition-dependent, the vast compositional filed of high
entropy alloys, complex concentrated alloys or multicomponent alloys can be
explored to design alloys with optimized properties for each application. In
this work, we present a thermodynamic model to calculate PCT diagrams of body-centered
(BCC) multicomponent alloys. The entropy of the phases is described using the
ideal configurational entropy for interstitial solid solutions with site
blocking effect. As a first approximation, it is assumed that the H partial
molar enthalpy of a phase is constant, so the enthalpy of H mixing varies
linearly with the H concentration. Moreover, the H partial enthalpy of a phase
for a multicomponent alloy was approximated by a simple ideal mixture law of
this quantity for the alloy’s components with the same structure. Experimental
data and DFT calculations were used for parametrization of the enthalpy terms
of eight elements (Ti, V, Cr, Ni, Zr, Nb, Hf, and Ta), which are the components
of the alloys tested in this work. Experimental PCTs of six BCC multicomponent
alloys of four different systems were compared against the calculated ones and
the agreement was remarkable. The model and parameters presented here can be
regarded as a basis for developing powerful alloy design tools for different
hydrogen storage applications.</p>
|
Guilherme Zepon; Bruno Silva; Claudia Zlotea; Walter José Botta; Yannick Champion
|
Alloys; Hydrogen Storage Materials
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757c6842e658cf7db4764/original/thermodynamic-modelling-of-hydrogen-multicomponent-alloy-systems-calculating-pressure-composition-temperature-diagrams.pdf
|
60c74a1f469df4a040f43cb6
|
10.26434/chemrxiv.12148764.v1
|
Repurposing FDA-Approved Drugs for COVID-19 Using a Data-Driven Approach
|
<p>There have been more than 116,000 recorded deaths
worldwide to-date caused by the severe acute respiratory syndrome coronavirus
type 2 (SARS-CoV-2), the etiological agent of the Coronavirus Disease 2019
(COVID-19), and over 1.8 million individuals are currently infected. Although
there are now hundreds of clinical trials for COVID-19, there are currently no
effective licensed treatments, while the numbers of infected individuals continue
to rise at an exponential rate in many parts of the world. Here, we used a
data-driven approach utilizing connectivity mapping and the transcriptional
signature of lung carcinoma cells infected with SARS-CoV-2, to search for drugs
across the spectrum of medicine that have repurposing potential for treating COVID-19.
We also performed chemoinformatic analyses to test whether the identified compounds
were predicted to physically interact with the SARS-CoV-2 RNA-dependent RNA
polymerase or main protease enzymes. Our study identified commonly prescribed FDA-approved
molecules as important candidates for drug repositioning against COVID-19,
including flupentixol, reserpine, fluoxetine, trifluoperazine, sunitinib, atorvastatin,
raloxifene, butoconazole, and metformin. These drugs should not be taken for
treating or preventing COVID-19 without a doctor’s advice, as further research
and clinical trials are now needed to elucidate their efficacy for this purpose.</p>
|
Rodrigo R. R. Duarte; Dennis C. Copertino Jr.; Luis P. Iñiguez; Jez L. Marston; Douglas F. Nixon; Timothy R. Powell
|
Biochemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems; Microbiology
|
CC BY NC 4.0
|
CHEMRXIV
|
2020-04-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1f469df4a040f43cb6/original/repurposing-fda-approved-drugs-for-covid-19-using-a-data-driven-approach.pdf
|
647dd19f4f8b1884b7e0d62d
|
10.26434/chemrxiv-2023-cg5dg
|
Scattering correction for samples with cylindrical domains measured with polarized infrared spectroscopy
|
Scattering artifacts are one of the most common effects distorting transmission spectra in Fourier-Transform Infrared spectroscopy. Their increased impact, strongly diminishing the quantitative and qualitative power of IR spectroscopy, is especially observed for structures with a size comparable to the radiation wavelength. To tackle this problem, a range of preprocessing techniques based on the Extended Multiplicative Scattering Correction method was developed, using physical properties to remove scattering presence in the spectra. However, until recently those algorithms were mostly focused on spherically shaped samples, for example, cells. Here, an algorithm for samples with cylindrical domains is described, with additional implementation of a linearly polarized light case, which is crucial for the growing field of polarized IR imaging and spectroscopy. The approach is tested on a polymer fiber and on human tissue collagen fiber. An open-source code with GPU based implementation is provided, with a calculation time of several seconds per spectrum. Optimizations done to improve the throughput of this algorithm allow the application of this method into the standard preprocessing pipeline of small datasets.
|
Paulina Koziol; Pawel Korecki; Tomasz Wrobel; Karolina Kosowska
|
Analytical Chemistry; Imaging; Microscopy; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-06-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647dd19f4f8b1884b7e0d62d/original/scattering-correction-for-samples-with-cylindrical-domains-measured-with-polarized-infrared-spectroscopy.pdf
|
617529f45c433d65328880cb
|
10.26434/chemrxiv-2021-fvvwb-v3
|
Small but effective: potent light-weight additives modulate prenucleation clusters by specific interactions on the molecular level
|
Small-molecular-weight (MW) additives can strongly impact amorphous calcium carbonate (ACC), playing an elusive role in biogenic, geologic, and industrial calcification. Here, we present molecular mechanisms by which additives regulate stability and composition of both CaCO3 solutions and solid ACC. Potent antiscalants inhibit ACC precipitation by interacting with prenucleation clusters (PNC); they specifically trigger and integrate into PNCs or feed PNC growth. Only PNC-interacting additives are traceable in ACC, considerably stabilizing it against crystallization. The selective incorporation of potent additives in PNCs is a reliable chemical label that provides conclusive chemical evidence that ACC is a molecular precipitate derived PNCs. Our results reveal additive-cluster interactions beyond established mechanistic conceptions. They reassess the role of small-MW molecules in crystallization and biomineralization, while breaking grounds for new sustainable antiscalants.
|
Patrick Duchstein; Philipp I. Schodder; Simon Leupold; Thi Quynh Nhi Dao; Shifi Kababya; Maria R. Cicconi; Dominique de Ligny; Vitaliy Pipich; David Eike; Asher Schmidt; Dirk Zahn; Stephan E. Wolf
|
Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Clusters; Physical and Chemical Processes
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-10-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617529f45c433d65328880cb/original/small-but-effective-potent-light-weight-additives-modulate-prenucleation-clusters-by-specific-interactions-on-the-molecular-level.pdf
|
66768613c9c6a5c07a17c025
|
10.26434/chemrxiv-2024-p1wng
|
Azepination-Induced Frontier Molecular Orbital Delocalization of Multiple Resonance Emitters: Constructing Highly Efficient Narrowband Electroluminescent Materials
|
Developing diversified construction strategies for high-color-purity and efficient multiple resonance thermally activated delayed fluorescence (MR-TADF) materials is a major strategic demand to meet the requirements of ultra-high-definition organic light-emitting diode (OLED) displays, posing a significant challenge to the design and synthesis of emitters at the molecular level. Herein, we propose a strategy for azepination-induced frontier molecular orbital (FMO) delocalization of MR emitters, that is, embedding azepine into the prototype molecule BNCz can effectively improve the π-conjugation degree and extend the FMO delocalization, thereby constructing a series of long-wavelength MR-TADF materials with narrowband emission. Through an intramolecular Scholl reaction, these target molecules with an azepine-embedded core are afforded by one-fold heptagonal cyclization of BNCz core and the phenyl ring attached to (aromatic amine-substituted) aryl precursor. They all exhibit efficient green emission around 520 nm and narrow full-widths at half-maximum (FWHMs) of ≤ 38 nm in toluene. OLEDs employing these emitters show excellent electroluminescence (EL) performances, among which m-PAz-BNCz-based OLED exhibits the optimal EL performances with a peak of 528 nm, a FWHM of 37 nm, Commission Internationale de L’Eclairage (CIE) coordinates of (0.26, 0.70), and a maximum external quantum efficiency (EQE) of 36.2%.
|
Tingting Huang; Yincai Xu; Yupei Qu; Xueying Lu; Kaiqi Ye; Yue Wang
|
Organic Chemistry; Materials Science; Organic Synthesis and Reactions
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-06-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66768613c9c6a5c07a17c025/original/azepination-induced-frontier-molecular-orbital-delocalization-of-multiple-resonance-emitters-constructing-highly-efficient-narrowband-electroluminescent-materials.pdf
|
667dc8ba5101a2ffa8bcfab4
|
10.26434/chemrxiv-2024-j0vp9
|
Organic aerosol formation from 222 nm germicidal light: ozone-initiated vs. non-ozone pathways
|
Germicidal ultraviolet lamps outputting 222 nm light (GUV222) have the potential to reduce the airborne spread of disease through effective inactivation of pathogens, while remaining safe for direct human exposure. However, recent studies have identified these lamps as a source of ozone and other secondary pollutants such as secondary organic aerosol (SOA), and the health effects of these pollutants must be balanced against the benefits of pathogen inactivation. While ozone reactions are likely to account for much of this secondary indoor air pollution, 222 nm light may initiate additional non-ozone chemical processes, including the formation of other oxidants and direct photolytic reactions, which are not as well understood. This work examines the impacts of GUV222 light on SOA formation and composition by comparing limonene oxidation under GUV222 and O3-only control conditions in a laboratory chamber. Differences between these experiments enable us to distinguish patterns in aerosol formation driven by ozone chemistry from those driven by other photolytic processes. These experiments also examine the influence of the addition of NO2 and nitrous acid (HONO), and investigate SOA formation in sampled outdoor air. SOA composition and yield vary only slightly with respect to GUV222 vs ozone-only conditions; NO2 and HONO photolysis do not appreciably affect the observed chemistry. In contrast, we observe consistent new particle formation under high-fluence 222 nm light (45 µW cm-2) that differs dramatically from ozone-only experiments. This observed new particle formation represents an additional reason to keep GUV222 fluence rates to the lowest effective levels.
|
Matthew Goss; Jesse Kroll
|
Earth, Space, and Environmental Chemistry; Atmospheric Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667dc8ba5101a2ffa8bcfab4/original/organic-aerosol-formation-from-222-nm-germicidal-light-ozone-initiated-vs-non-ozone-pathways.pdf
|
62270d8450b621ffb9ed5cba
|
10.26434/chemrxiv-2022-mwj1g-v2
|
In Silico Characterization of Essential Hypothetical Proteins from Francisella tularensis Schu S4 Strain.
|
Francisella tularensis Schu S4 is the causal agent of a sporadic zoonotic disease known as Tularemia, which has shown epidemic outbreaks recently in certain parts of the world. This pathogen is a potential agent of biowarfare or bioterrorism and is classified as a category A pathogen by the National Institute of Allergy and Infectious Diseases. In this virulent strain, 453 genes have been identified as essential genes, indispensable for growth and survival of the pathogen. The functions of 44 proteins encoded by those essential genes were found to be hypothetical and thus defined as essential hypothetical proteins (EHPs). The current study used a wide range of in silico tools and servers to annotate the physicochemical, structural, and functional properties of these EHPs. Of all the EHPs, 24 were functionally annotated with a high degree of confidence and validated by Receiver Operating Characteristic curve analysis. Non-homology assessment revealed 20 pathogen-specific EHPs, which were further analyzed for protein-protein interactions and predicted for secondary and tertiary structure. All the 3D structures were checked on multiple quality assessment servers, and the best models were visualized. The outcome of the study could aid in enhancing current understanding of bacterial pathogenesis with novel drug and vaccine investigations.
|
Sheikh Sunzid Ahmed
|
Biological and Medicinal Chemistry; Bioinformatics and Computational Biology
|
CC BY 4.0
|
CHEMRXIV
|
2022-03-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62270d8450b621ffb9ed5cba/original/in-silico-characterization-of-essential-hypothetical-proteins-from-francisella-tularensis-schu-s4-strain.pdf
|
60c7473c567dfe835cec479b
|
10.26434/chemrxiv.11559660.v1
|
A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase
|
<div><p>Electrostatic interactions play a pivotal role in
enzymatic catalysis and are increasingly modeled explicitly in computational
enzyme design; nevertheless, they are challenging to measure experimentally.
Using vibrational Stark effect (VSE) spectroscopy, we have measured electric
fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have
shown that these fields can be unusually large, but it has been unclear to what
extent they specifically stabilize the transition state (TS) relative to a
ground state (GS). In the following, we use crystallography and computational
modeling to show that KSI’s intrinsic electric field is nearly perfectly
oriented to stabilize the geometry of its reaction’s TS. Moreover, we find that this electric field
adjusts the orientation of its substrate in the ground state so that the
substrate needs to only undergo minimal structural changes upon activation to
its TS. This work provides evidence that
the active site electric field in KSI is preorganized to facilitate catalysis
and provides a template for how electrostatic preorganization can be measured
in enzymatic systems. <br /></p></div>
|
Yufan Wu; Stephen Fried; Steven Boxer
|
Computational Chemistry and Modeling; Biophysical Chemistry; Crystallography
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7473c567dfe835cec479b/original/a-preorganized-electric-field-leads-to-minimal-geometrical-reorientation-in-the-catalytic-reaction-of-ketosteroid-isomerase.pdf
|
66ffe600cec5d6c14222e01a
|
10.26434/chemrxiv-2024-nsv3r
|
A lanthanide MOF with nanostructured node disorder
|
The synthesis and structural characterization of a new metal organic framework, UoB-100(Dy), is reported. Average structure refinements indicate that the node is disordered between two orientations of the nonanuculear secondary building unit (SBU). By performing 3D diffuse scattering (DS) analysis and Monte Carlo (MC) simulations, we confirm the presence of strong correlations between the metal clusters of UoB-100(Dy). These nodes assemble into a complex and novel nanodomain structure. Quantum mechanical calculations identify linker strain as the driving force behind the nanodomain structure. The implications of such a nanodomain structure for the magnetic, gas storage, and mechanical properties of lanthanide MOFs are discussed.
|
Sarah Griffin; Emily Meekel; Johnathan Bulled; Stefano Canossa; Alexander Wahrhaftig-Lewis; Ella Schmidt; Neil Champness
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Materials Chemistry; Crystallography – Inorganic
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ffe600cec5d6c14222e01a/original/a-lanthanide-mof-with-nanostructured-node-disorder.pdf
|
64f21e8ddd1a73847ff905f0
|
10.26434/chemrxiv-2023-3g9g6-v2
|
On the utility of the extracted ion chromatograms for assigning the conjugation sites in bioconjugates synthesized by the maleimide-thiol chemistry
|
Maleimide-thiol chemistry is widely used to synthesize antibody-drug conjugates and conjugate vaccines. The set of MS/MS spectra automatically assigned to proteolytic type 2 peptides with a thiosuccinimide linker and its stabilized products (thiazine and hydrolyzed species), contains valuable information on the conjugation sites. Sample processing before LC-MS/MS analysis transforms the thiosuccinimide linker into its stabilized products. The MS/MS spectra of type 2 peptides must be validated based on objective criteria. The extracted ion chromatogram (XIC) has not been considered previously for this purpose. In the LC-MS/MS analysis, linear peptides eluted in a one-fraction XIC as expected. On the contrary, depending on the analyzed proteolytic digestion, the type 2 peptides with a thiazine linker were detected in 77-100 % of the cases with a two-fraction XIC pattern, probably composed by a mixture of diastereomers. Type 2 peptides with the hydrolyzed thiosuccinimide linker were detected with a mixed-pattern XIC in two, three and four elution fractions in 77 %, 15 % and 8 % of the cases, respectively. The four-fraction XIC pattern is probably composed by the full-chromatographic separation of type 2 peptides cross-linked by two positional isomers of the thiosuccinamic acid linker containing a chiral carbon. Tandem digestions increased the number of type 2 peptides detected with a multiple-fractions XIC pattern. XIC of proteolytic peptides is a relevant source of information considered for data validation. Transcyclization and hydrolysis not only stabilize the thiosuccinimide linker but also permit, together with XIC, a more reliable identification of the conjugation sites by LC-MS/MS analysis.
|
Luis Javier González; Satomy Pousa; Pablo E. Ramos; Vladimir Besada; Paulo Carvalho; Louise Kurt; Michel Batista; Rodrigo Soares; Alejandro Leyva; Rosario Durán; Dhayme Murillo; Abel Fajardo; Hilda Elisa Garay; Alina Rodríguez-Mallón; Toshifumi Takao
|
Analytical Chemistry; Mass Spectrometry
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-09-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f21e8ddd1a73847ff905f0/original/on-the-utility-of-the-extracted-ion-chromatograms-for-assigning-the-conjugation-sites-in-bioconjugates-synthesized-by-the-maleimide-thiol-chemistry.pdf
|
65af7b199138d231618a2a79
|
10.26434/chemrxiv-2023-gprl2-v2
|
Combining Extrapolated Electron Localization Functions and Berlin’s Binding Functions for the Prediction of Dissociative Electron Attachment
|
Computational study of electronic resonances is still a very challenging topic, with the phenomenon of dissociative electron attachment (DEA) being one of the multiple features worth investigating. Recently, we extended the charge stabilization method from energies to properties of conceptual density functional theory and applied this to metastable anionic states of ethene and chlorinated ethene derivatives, to study the DEA mechanism present in these compounds. We now present an extension to spatial functions, namely the electronic Fukui function and the electron localization function. The results of our analysis show that extrapolated spatial functions are relevant and useful for more precise localization of the unbound electron. Furthermore, we report for the first time the combination of the electron localization function with Berlin’s binding function for these challenging electronic states. This promising methodology allows for accurate predictions of when and where DEA will happen in the molecules studied and provides more insight into the process.
|
Charlotte Titeca; Thomas-Christian Jagau; Frank De Proft
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-01-24
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65af7b199138d231618a2a79/original/combining-extrapolated-electron-localization-functions-and-berlin-s-binding-functions-for-the-prediction-of-dissociative-electron-attachment.pdf
|
60c756c60f50dbb7f939813f
|
10.26434/chemrxiv.14312612.v1
|
Multi-fidelity Sequential Learning for Accelerated Materials Discovery
|
We introduce a new agent-based framework for materials discovery that combines multi-fidelity modeling and sequential learning to lower the number of expensive data acquisitions while maximizing discovery. We demonstrate the framework's capability by simulating a materials discovery campaign using experimental and DFT band gap data. Using these simulations, we determine how different machine learning models and acquisition strategies influence the overall rate of discovery of materials per experiment. The framework demonstrates that including lower fidelity (DFT) data, whether as a-priori knowledge or using in-tandem acquisition, increases the discovery rate of materials suitable for solar photoabsorption. We also show that the performance of a given agent depends on data size, model selection, and acquisition strategy. As such, our framework provides a tool that enables materials scientists to test various acquisition and model hyperparameters to maximize the discovery rate of their own multi-fidelity sequential learning campaigns for materials discovery.
|
Aini Palizhati; Muratahan Aykol; Santosh Suram; Jens Strabo Hummelshøj; Joseph H. Montoya
|
Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756c60f50dbb7f939813f/original/multi-fidelity-sequential-learning-for-accelerated-materials-discovery.pdf
|
65e0e6d366c1381729e01436
|
10.26434/chemrxiv-2024-v0gw7
|
Frataxin Traps Low Abundance Quaternary Structure to Stimulate Human Fe-S Cluster Biosynthesis
|
Iron-sulfur clusters are essential protein cofactors synthesized in human mitochondria by an NFS1-ISD11-ACP-ISCU2-FXN assembly complex. Surprisingly, researchers have discovered three distinct quaternary structures for cysteine desulfurase subcomplexes, which display similar interactions between NFS1-ISD11-ACP protomeric units but distinct dimeric interfaces between the protomers. Although the role of these different architectures is unclear, possible functions include regulating activity and promoting the biosynthesis of distinct sulfur-containing biomolecules. Here, crystallography, native ion-mobility mass spectrometry, and chromatography methods reveal the Fe-S assembly subcomplex exists as an equilibrium mixture of these different quaternary structures. Our results suggest Friedreich's ataxia (FRDA) protein frataxin (FXN) functions as a "molecular lock" and shifts the equilibrium towards one of the architectures to stimulate the cysteine desulfurase activity and promote iron-sulfur cluster biosynthesis. An NFS1-designed variant similarly shifts the equilibrium and partially replaces FXN in activating the complex. These results suggest that eukaryotic cysteine desulfurases are unusual members of the morpheein class of enzymes that control their activity through their oligomeric state. Overall, the findings support architectural switching as a regulatory mechanism linked to FXN activation of the human Fe-S cluster biosynthetic complex and provide new opportunities for therapeutic interventions of the fatal neurodegenerative disease FRDA.
|
Seth Cory; Cheng-Wei Lin; Steven Havens; Shachin Patra; Christopher Putnam; Mehdi Shirzadeh; David Russell; David Barondeau
|
Biological and Medicinal Chemistry; Biochemistry; Biophysics; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0e6d366c1381729e01436/original/frataxin-traps-low-abundance-quaternary-structure-to-stimulate-human-fe-s-cluster-biosynthesis.pdf
|
60c74930337d6c3443e276ae
|
10.26434/chemrxiv.12038682.v1
|
Solubilization of Itraconazole by Surfactants and Phospholipid-Surfactant Mixtures: Interplay of Amphiphile Structure, pH and Electrostatic Interactions
|
Although surfactants are frequently used in enabling formulations of poorly water-soluble drugs, the link between their structure and drug solubilization capacity is still unclear. We studied the solubilization of the “brick-dust” molecule itraconazole by 16 surfactants and 3 phospholipid:surfactant mixtures. NMR spectroscopy was used to study in more details the drug-surfactant interactions. Very high solubility of itraconazole (up to 3.6 g/L) was measured in anionic surfactant micelles at pH = 3, due to electrostatic attraction between the oppositely charged (at this pH) drug and surfactant molecules. <sup>1</sup>H NMR spectroscopy showed that itraconazole is ionized at two sites (2+ charge) at these conditions: in the phenoxy-linked piperazine nitrogen and in the dioxolane-linked triazole ring. The increase of amphiphile hydrophobic chain length had a markedly different effect, depending on the amphiphile type: the solubilization capacity of single-chain surfactants increased, whereas a decrease was observed for double-chained surfactants (phosphatidylglycerols). The excellent correlation between the chain melting temperatures of phosphatidylglycerols and itraconazole solubilization illustrated the importance of hydrophobic chain mobility. This study provides rules for selection of itraconazole solubilizers among classical single-chain surfactants and phospholipids. The basic physics underpinning the described effects suggests that these rules should be transferrable to other “brick-dust” molecules.
|
Zahari Vinarov; Gabriela Gancheva; Nikola Burdzhiev; Slavka S. Tcholakova
|
Biophysical Chemistry; Physical and Chemical Processes; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74930337d6c3443e276ae/original/solubilization-of-itraconazole-by-surfactants-and-phospholipid-surfactant-mixtures-interplay-of-amphiphile-structure-p-h-and-electrostatic-interactions.pdf
|
60cb3b65926ad0778401a757
|
10.26434/chemrxiv-2021-vhp3n-v3
|
SBMOpenMM: A Builder of Structure-Based Models for OpenMM
|
Molecular dynamics (MD) simulations have become a standard tool to correlate the structure and function of biomolecules, and significant advances have been made in the study of proteins and their complexes. A major drawback of conventional MD simulations is the difficulty and cost of obtaining converged results, especially when
exploring potential energy surfaces containing considerable energy barriers. This limits the wide use of MD calculations to determine the thermodynamic properties of biomolecular processes. Alternatively, a wide range of Structure-Based Models (SBMs) has been used in the literature to unravel the basic mechanisms of biomolecular dynamics.
Here we introduce SBMOpenMM, a Python library to build force fields for SBMs, that
uses the OpenMM framework to create and run SBM simulations. The code is
flexible, user-friendly, and profits from the high customizability and performance
provided by the OpenMM platform.
|
Martin Floor
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics
|
CC BY 4.0
|
CHEMRXIV
|
2021-06-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cb3b65926ad0778401a757/original/sbm-open-mm-a-builder-of-structure-based-models-for-open-mm.pdf
|
6474ce37be16ad5c571ec659
|
10.26434/chemrxiv-2023-7mclf
|
Quantification of Solution-Free Blood Cell Staining by Sorption Kinetics of Romanowsky Stains to Agarose Gels
|
Imaging and quantification of stained blood cells are important for identifying the cells in hematology and for diagnosing diseased cells or parasites in cytopathology. Romanowsky staining have been used traditionally to produce hues in blood cells using anionic eosin Y and cationic methylene blue. While Romanowsky stains have been widely used in cytopathology, end-users have experienced problems with varying results in staining due to premature precipitation or evaporation of methanol, leading to the inherent inconsistency of solution-based Romanowsky staining. Here, we demonstrate that staining and destaining of blood smear are controllable by the contact time of agarose gel stamps. While the extent of staining and destaining are discernable by hue values of stamped red blood cells in micrographs, quantification of adsorbed and desorbed Romanowsky dye molecules (in particular, eosin Y, methylene blue, and azure B) from and to the agarose gel stamps needs a model that can explain the sorption process. We find predictable sorption of the Romanowsky dye molecules from the pseudo-second-order kinetics models for adsorption and the one phase decay model for desorption. Thus, the method of agarose gel stamping demonstrated here could be an alternative to solution-based Romanowsky staining with predictable quantity of sorption and timing of contact.
|
Chae Yun Bae; Hamid Esmaeili; Syed Zamin; Min Jeong Seol; Eunmi Hwang; Suk Kyung Beak; Younghoon Song; Bhuvnesh Bharti; Jangwook Jung
|
Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6474ce37be16ad5c571ec659/original/quantification-of-solution-free-blood-cell-staining-by-sorption-kinetics-of-romanowsky-stains-to-agarose-gels.pdf
|
60c73d59f96a001e7e285d81
|
10.26434/chemrxiv.5786853.v1
|
Poly(2-ethyl-2-oxazoline-co-N-propylethylene imine)s by controlled partial reduction of poly(2-ethyl-2-oxazoline)
|
The partial reduction of poly(2-ethyl-2-oxazoline) was investigated. A series of poly(2-ethyl-2-oxazoline-co-N-propylethylene imine)s were synthesized by direct reduction using lithium aluminum hydride or borane/dimethylsulfide (BH<sub>3</sub>/DMS), respectively. It is shown that the degree of reduction can be readily controlled either by the reaction time when using an excess of LiAlH<sub>4</sub> or by the stoichiometry of BH<sub>3</sub>/DMS as was demonstrated by 1H-NMR spectroscopy. Differential scanning calorimetry revealed that the glass transition temperature of the products decreased with increasing degree of reduction up to 25% of reduction, above which no glass transition could be detected. This control over the reduction allows the tailor synthesis of partially cationic polymers, which, in combination over the hydrophilic/lipophilic balance through the side chain length allows a tight control over materials properties. Such materials may be interesting, <i>inter alia</i>, for biomaterials or organic electronics.
|
Maria Pfister; Annemarie Ringhand; Corinna Fetsch; Robert Luxenhofer
|
Drug delivery systems; Polyelectrolytes - Polymers
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-01-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d59f96a001e7e285d81/original/poly-2-ethyl-2-oxazoline-co-n-propylethylene-imine-s-by-controlled-partial-reduction-of-poly-2-ethyl-2-oxazoline.pdf
|
64d9a1054a3f7d0c0d214af1
|
10.26434/chemrxiv-2023-8mj8n
|
Carbofluorination of Alkenes with gem-Difluorinated Cyclopropanes as Bifunctional Reagents Enabled by Well-Define Rhodium Catalysts
|
Herein, we report a Rh-catalyzed carbofluorination of alkenes using gem-difluorinated cyclopropanes as bifunctional reagents. The developed method tolerates a wide range of alkenes, providing access to secondary, tertiary fluorides and gem-difluorides with 100% atom-economy under mild conditions. The resulting fluorides can be further transformed to yield C−C, C−N, and C−O bifunctionalization products. Cationic dicarbonyl rhodium tetrafluoroborate has been identified to be the only highly efficient catalyst in this reaction. Preliminary mechanistic studies reveal that the addition of fluorine atom to alkenes is mediated by tetrafluoroborate ion, which acts as a fluorine anion shuttle.
|
Yaxin Zeng; Zhong-Tao Jiang; Yulei Zhu; Jinqi Chen; Han Zhang; Ying Xia
|
Organic Chemistry; Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d9a1054a3f7d0c0d214af1/original/carbofluorination-of-alkenes-with-gem-difluorinated-cyclopropanes-as-bifunctional-reagents-enabled-by-well-define-rhodium-catalysts.pdf
|
65e63e529138d23161aa14da
|
10.26434/chemrxiv-2024-7dw8z
|
High Throughput Methodology for Investigating Green Hydrogen Generating Processes using Colorimetric Detection Films and Machine Vision
|
The generation of hydrogen from abundant and renewable precursors driven by sunlight will be a cornerstone of a future, sustainable hydrogen infrastructure. Current methods to monitor the evolution of hydrogen in such photocatalytic systems such as gas chromatography, mass spectrometry, manometry or Raman spectroscopy are either expensive and low throughput or lack sensitivity and selectivity over other gasses. This impediment hinders the generation of photo-driven hydrogen evolution data necessary for machine learning and artificial intelligence-based protocols. This work presents an open-source approach for studying solar-driven hydrogen evolution reactions (HERs) in parallel that uses colorimetric hydrogen detection films in tandem with an image analysis software capable of providing metrics such as hydrogen amount, hydrogen evolution rates, incubation times, and plateau times, and more. The sensing medium is composed of 0.05 % (w/w) Pt impregnated molybdenum (VI) oxide or tungsten (VI) oxide which was incorporated into poly(vinyl alcohol) films placed under clear, gas impermeable septa. To conduct experiments, users require only blue reaction-driving high intensity LEDs, a camera, and uniform lighting to take pictures as the septa darken. This work introduces a sample configuration in which nine samples in hydrogen sensitive septa-capped vials were illuminated and the gas evolution is monitored using a RaspberryPi for image capture and storage. Two calibration methods are presented, one uses a gravimetric hydrogen evolution with Zn/HCl that is compared to a direct hydrogen injection. Both methods allow the accurate correlation of normalized intensity values of film photographs to mole fractions of H2 ranging from 0 to 50%. Four light-driven HERs are described that highlight the capabilities of the detection method, two of which were conducted using the novel septa-based instrumentation while the other two experiments used the films on a 108 multiwell plate using a previously discussed photoreactor.
|
Savannah Talledo; Andrew Kubaney; Mitchell A. Baumer; Keegan Pietrak; Stefan Bernhard
|
Catalysis; Energy; Homogeneous Catalysis; Energy Storage; Fuels - Energy Science; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e63e529138d23161aa14da/original/high-throughput-methodology-for-investigating-green-hydrogen-generating-processes-using-colorimetric-detection-films-and-machine-vision.pdf
|
60c741a8ee301ca429c78ce9
|
10.26434/chemrxiv.7806089.v2
|
Towards Density Functional Approximations from Coupled Cluster Correlation Energy Densities
|
<div>
<div>
<div>
<p>(Semi-)local density functional approximations (DFAs) are the workhorse electronic structure methods in
condensed matter theory and surface science. The correlation energy density εc(r) (a spatial function that
yields the correlation energy Ec upon integration) is central to defining such DFAs. Unlike Ec, εc(r) is not
uniquely defined, however. Indeed, there are infinitely many functions that integrate to the correct Ec for
a given electron density ρ. The challenge for constructing useful DFAs is thus to find a suitable connection
between εc(r) and ρ. Herein, we present a new such approach by deriving εc(r) directly from the coupled-
cluster (CC) energy expression. The corresponding energy densities are analyzed for prototypical two-electron
systems. To explore their usefulness for designing DFAs, we construct a semilocal functional to approximate
the numerical CC correlation energy densities. Importantly, the energy densities are not simply used as
reference data, but guide the choice of the functional form, leading to a remarkably simple and accurate
correlation functional for the Helium isoelectronic series.
</p>
</div>
</div>
</div>
|
Johannes T. Margraf; Christian Kunkel; Karsten Reuter
|
Theory - Computational; Quantum Computing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-04-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a8ee301ca429c78ce9/original/towards-density-functional-approximations-from-coupled-cluster-correlation-energy-densities.pdf
|
621ffe8f91a2e66c5ae2b69d
|
10.26434/chemrxiv-2022-l8z6j
|
Enhanced methanol production over non-promoted Cu-MgO-Al2O3 materials with ex-solved 2 nm Cu particles:
Insights from an Operando spectroscopic study
|
Enhanced methanol production is obtained over a non-promoted Cu-MgO-Al2O3 mixed oxide catalyst derived from a Cu-Mg-Al hydrotalcite precursor (HT) containing narrowly distributed small Cu NPs (2 nm). Conversions close to the equilibrium (20%) with a methanol selectivity of 67% are achieved at 230 °C, 20 bar and space velocity of 571 mL.gcat-1.h-1. Based on operando spectroscopic studies, the striking activity of this Cu based catalyst is ascribed to the stabilization of Cu+ ions favored under reaction conditions due to lattice reorganization associated with the “HT-memory effect”, promoted by water. Temperature resolved IR-MS experiments have enabled the discernment of monodentate formate species, stabilized on Cu+ as the intermediate in methanol synthesis, in line with the results of DFT calculations. These monodentate formate species are much more reactive than bridge formate species, behaving the last ones as intermediates in methane and CO formation. Moreover, poisoning of the Cu0 surface by strongly adsorbed species behaving as spectators is observed under reaction conditions. This work represents a detailed spectroscopic study highlighting the influence of the reaction pressure on the stabilization of active surface sites, and the possibility of enhancing methanol production on usually less active non-promoted nano-sized copper catalysts, providing that the proper support is selected, allowing the stabilization of doped Cu+. Thus, methanol formation rate of 2.6·10-3molMeOH·gcat-1·h-1 at 230 °C, 20 bar and WHSV = 28500 mL·gcat-1·h-1, is obtained on the Cu-MgO-Al2O3 HT-derived catalyst with 71% methanol selectivity, compared to 2.2·10-4 molMeOH·gcat-1·h-1 with 54% methanol selectivity obtained on a reference Cu/(Al2O3-MgO) catalyst not derived from a HT structure.
|
Jorge Cored; Jaime Mazarío; Cristina Cerdá-Moreno; Pablo G. Lustemberg; M. Verónica Ganduglia-Pirovano; Marcelo Domine; Patricia Concepción
|
Catalysis; Heterogeneous Catalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621ffe8f91a2e66c5ae2b69d/original/enhanced-methanol-production-over-non-promoted-cu-mg-o-al2o3-materials-with-ex-solved-2-nm-cu-particles-insights-from-an-operando-spectroscopic-study.pdf
|
64ba514fae3d1a7b0d17f796
|
10.26434/chemrxiv-2023-sf90v
|
Making Photocatalysts Screenable -
A Milli Scale Multi-Batch Screening Photoreactor as Extension for the Modular Photoreactor
|
Development and evaluation of new photocatalytic systems requires screening of large parameter spaces. For such investigations, a photonically characterized, simple, and low-cost multi-batch screening photoreactor is presented that enables the screening of up to 49 sealed 4 mL milli batch reactors. The reactor concept is based on theoretical contemplation of the geometrical and optical properties of suited reflector concepts and utilizes basic components of the modular photoreactor introduced recently. Raytracing, radiometry and chemical actinometry were used for the photonic characterization. Applicability of the screening setup under catalytic conditions was evaluated using a benchmark system for photoinduced hydrogen evolution consisting of [Ru(bpy)3](PF6)2 as photosensitizer, ascorbic acid as sacrificial agent and Mo3S132- as catalyst. Extending screening to metal-free organic photosensitizers, bimane compounds are reported as photosensitizers for photoinduced hydrogen evolution in various catalytic systems.
|
Daniel Kowalczyk; Gergely Knorr; Kalina Peneva; Dirk Ziegenbalg
|
Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Photocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ba514fae3d1a7b0d17f796/original/making-photocatalysts-screenable-a-milli-scale-multi-batch-screening-photoreactor-as-extension-for-the-modular-photoreactor.pdf
|
60c743b20f50db8d6f395fa0
|
10.26434/chemrxiv.9524219.v1
|
Discovery of Highly Polymorphic Organic Materials: A New Machine Learning Approach
|
<div><div><p>Polymorphism is the capacity of a molecule to adopt different conformations or molecular packing arrangements in the solid state. This is a key property to control during pharmaceutical manufacturing because it can impact a range of properties including stability and solubility. In this study, a novel approach based on machine learning classification methods is used to predict the likelihood for an organic compound to crystallise in multiple forms. A training dataset of drug-like molecules was curated from the Cambridge Structural Database (CSD) and filtered according to entries in the Drug Bank database. The number of separate forms in the CSD for each molecule was recorded. A metaclassifier was trained using this dataset to predict the expected number of crystalline forms from the compound descriptors. This approach was used to estimate the number of crystallographic forms for an external validation dataset. These results suggest this novel methodology can be used to predict the extent of polymorphism of new drugs or not-yet experimentally screened molecules. This promising method complements expensive ab initio methods for crystal structure prediction and as integral to experimental physical form screening, may identify systems that with unexplored potential.</p>
</div>
</div>
|
Zied Hosni; Annalisa Riccardi; Stephanie Yerdelen; Alan R. G. Martin; Deborah Bowering; Alastair Florence
|
Solid State Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-08-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b20f50db8d6f395fa0/original/discovery-of-highly-polymorphic-organic-materials-a-new-machine-learning-approach.pdf
|
66876833c9c6a5c07a554f1e
|
10.26434/chemrxiv-2024-p9ntc
|
How Ir-Rh Alloys Improve Electrochemical Ammonia Oxidation Activity Studied by Density Functional Theory
|
The electrochemical ammonia oxidation reaction (AOR) has applications in hydrogen storage and ammonia waste remediation. Using density functional theory, we investigate the mechanism of AOR on Ir, Rh, and their alloys at varied atomic ratios Ir75Rh25, Ir50Rh50, and Ir25Rh75 towards N2(g), NO2–(aq) and NO3–(aq) formation. This work introduces a method for computational alloy design by considering both electronic energy and configurational entropy. The structures considered are selective to N2(g) formation and all favoured *N-N coupling. An Ir50Rh50 alloy was found to reduce the theoretical onset potential for N2(g) formation relative to pure Ir while not exhibiting a downhill coupling step corresponding to catalyst poisoning by *N as shown for pure Rh, consistent with previous experimental work. The formation of NO2–(aq) and NO3–(aq) demand significantly higher potentials, typically limited by the final hydroxylation step before desorption.
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Brendan Laframboise; Shayne Johnston; Leanne Chen
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Theoretical and Computational Chemistry; Catalysis; Energy; Theory - Computational; Electrocatalysis; Energy Storage
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CC BY NC 4.0
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CHEMRXIV
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2024-07-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66876833c9c6a5c07a554f1e/original/how-ir-rh-alloys-improve-electrochemical-ammonia-oxidation-activity-studied-by-density-functional-theory.pdf
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60c73cc9702a9be9c6189aa5
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10.26434/chemrxiv.14731695.v1
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Improved pH-Controlled Release of Phenformin from Low-Defect Graphene Compared to Graphene Oxide
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Graphene-based drug carriers provide a promising addition to current cancer drug 8 delivery options. Increased accessibility of high-quality graphene made by plasma- enhanced chemical vapor deposition (PE-CVD) makes it an attractive material to re-visit in comparison to the widely studied graphene oxide (GO) in drug delivery. Here we show the potential of re-purposing the metabolic drug phenformin for cancer treatment in terms of stability, binding, and pH-controlled release. Using covalent attachment of polyethylene glycol (PEG) onto pristine (PE-CVD) graphene, we show that the PEG stabilized graphene nanosheets (PGNS) drug carrier is stable in aqueous solutions, exhibit a higher binding affinity towards phenformin than conventional GO. Moreover, we experimentally demonstrate an improved drug release in PGNS than GO in pH levels lower than physiological conditions comparable to an acidic tumor microenvironment.
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Abdelnour Alhourani; Jan-Lukas Førde; Lutz Eichacker; Lars Herfindal; Hanne Hagland
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Nanostructured Materials - Materials
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CC BY NC ND 4.0
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CHEMRXIV
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2021-06-07
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9702a9be9c6189aa5/original/improved-p-h-controlled-release-of-phenformin-from-low-defect-graphene-compared-to-graphene-oxide.pdf
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6357bbbdaa2784114c4ba1a2
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10.26434/chemrxiv-2022-z3419
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Identification of drug metabolites with infrared ion spectroscopy – application to midazolam in vitro metabolism
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The identification of biotransformation products of drug compounds is a crucial step in drug development. Over the last decades, liquid chromatography-mass spectrometry (LC-MS) has become the method of choice for metabolite profiling because of its high sensitivity and selectivity. However, determining the full molecular structure of the detected metabolites, including the exact biotransformation site, remains challenging on the basis of MS alone. Here we explore infrared ion spectroscopy (IRIS) as a novel MS-based method for the elucidation of metabolic pathways in drug metabolism research. Using the drug midazolam as an example, we identify several biotransformation products directly from an in vitro drug incubation sample. We show that IR spectra of the aglycone MS/MS fragment ions of glucuronide metabolites establish a direct link between detected phase I and phase II metabolites. Moreover, using quantum-chemically computed IR spectra of candidate structures, we are able to assign the exact sites of biotransformation in absence of reference standards. Additionally, we demonstrate the utility of IRIS for structural elucidation by identifying several ring-opened midazolam derivatives formed in an acidic environment.
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Rianne van Outersterp; Jonathan Martens; Giel berden; Arnaud Lubin; Filip Cuyckens; Jos Oomens
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Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Spectroscopy (Anal. Chem.)
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CC BY 4.0
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CHEMRXIV
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2022-10-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6357bbbdaa2784114c4ba1a2/original/identification-of-drug-metabolites-with-infrared-ion-spectroscopy-application-to-midazolam-in-vitro-metabolism.pdf
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661b08f491aefa6ce18223c3
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10.26434/chemrxiv-2024-gmmql
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Introductory Information about Quantum Dots and their Applications
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Quantum dots (QDs), a type of nanoparticles, have displayed promising applications within many scientific fields. A QD is a nanoscale semiconductor particle with unique quantum mechanical properties. These tiny structures, typically ranging from 1 to 10 nanometers in diameter, exhibit distinct electronic and optical behaviors due to their size-dependent quantum confinement effects. Their applications improve upon quality, energy consumption, and efficiency in LEDs, batteries, catalysts, solar energy, and more. This review article goes over the fundamentals of nanochemistry as a whole, before proceeding into more in-depth procedures on synthesizing quantum dots and delving into various applications today. The key points of this article are to introduce scholars who are new to the field of quantum dots in the fundamentals of quantum chemistry before elaborating on the improvements quantum dots have brought to many fields. This article covers in-depth enough to grasp most concepts behind these applications, but as a whole, this field is still relatively new, in which case new applications and improvements of quantum dots can be found. In the future, quantum dots may become a key to advancing society, with possible applications in medicinal processes, more efficient energy storage, better energy generation, and quantum computing, in addition to what QDs already improved within those fields.
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Brady Yang; Jesus Valdiviezo
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Materials Science; Nanoscience; Energy; Optical Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience
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CC BY NC 4.0
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CHEMRXIV
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2024-04-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661b08f491aefa6ce18223c3/original/introductory-information-about-quantum-dots-and-their-applications.pdf
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60c749ce4c8919b836ad3126
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10.26434/chemrxiv.12108612.v1
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Synthesis and Dual-Mode Electrochromism of Anisotropic Monoclinic Nb12O29 Colloidal Nanoplatelets
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<div>Transition metal oxide nanocrystals with dual-mode electrochromism hold promise for smart windows enabling spectrally selective solar modulation. We have developed the colloidal synthesis of anisotropic monoclinic Nb12O29 nanoplatelets (NPLs) to investigate the dual-mode electrochromism of niobium oxide nanocrystals. The precursor for synthesizing NPLs was prepared by mixing NbCl5 and oleic acid to form a complex that was subsequently heated to form an oxide-like structure capped by oleic acid, denoted as niobium oxo cluster. By initiating the synthesis using niobium oxo clusters, preferred growth of NPLs over other polymorphs was observed. The structure of the synthesized NPLs was examined by X-ray diffraction in conjunction with simulations, revealing that the NPLs are monolayer monoclinic Nb12O29, thin in the [100] direction and extended along the b and c directions. Besides having monolayer thickness, NPLs show decreased intensity of Raman signal from Nb-O bonds with higher bond order when compared to bulk monoclinic Nb12O29, as interpreted by calculations. Progressive electrochemical reduction of NPL films led to absorbance in the near-infrared region (stage 1) followed by absorbance in both the visible and near-infrared regions (stage 2), thus exhibiting dual-mode electrochromism. The mechanisms underlying these two processes were distinguished electrochemically by cyclic voltammetry to determine the extent to which ion intercalation limits the kinetics, and by verifying the presence of localized electrons following ion intercalation using X-ray photoelectron spectroscopy. Both results support that the near-infrared absorption results from capacitive charging and the onset of visible absorption in the second stage is caused by ion intercalation.</div>
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Hsin-Che Lu; Sandeep Ghosh; Naman Katyal; Graeme Henkelman; Vikram S. Lankanpal; Delia Milliron
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Nanostructured Materials - Materials
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CC BY NC ND 4.0
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CHEMRXIV
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2020-04-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749ce4c8919b836ad3126/original/synthesis-and-dual-mode-electrochromism-of-anisotropic-monoclinic-nb12o29-colloidal-nanoplatelets.pdf
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64f0e04979853bbd78d0c089
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10.26434/chemrxiv-2023-fr8zf
|
Virtual Choose-Your-Own-Adventure Prelabs Improve Student Understanding of Analytical Chemistry Concepts and Instrumentation
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The COVID-19 pandemic forced instructors of chemistry lab classes to develop a variety of alternative materials for remote delivery of traditionally hands-on content. One solution to this challenge was virtual choose-your-own-adventure (CYOA) laboratories that allowed students to practice realistic decision-making and collect authentic data. With the return to in-person instruction, these CYOA labs can be modified into prelab exercises to support and supplement in-person experiments. Four virtual CYOA labs were adapted into prelab exercises for an upper-division instrumental analysis course to prepare students for experiments in chromatography method development and electronic circuit design. Students were surveyed to gauge their opinions on the prelabs and their comfort in the laboratory overall. Survey results indicated that students enjoyed the CYOA prelab activities and found them helpful in feeling prepared for experiments and understanding the source and quality of their experimental data. Virtual CYOA prelabs may be a good way for instructors to expand the depth of their lab curriculum and reduce the anxiety their students feel before complex experiments.
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Madison Flesch; Nicholas Humphrey; Stephen Mang
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Chemical Education; Chemical Education - General
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CC BY NC 4.0
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CHEMRXIV
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2023-09-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0e04979853bbd78d0c089/original/virtual-choose-your-own-adventure-prelabs-improve-student-understanding-of-analytical-chemistry-concepts-and-instrumentation.pdf
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65ac3f8966c1381729e71ddd
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10.26434/chemrxiv-2024-jz473
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In Defense of (Certain) Pople-Type Basis Sets
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A recent study suggests that Gaussian basis sets in the 6-311G family are inappropriate for thermochemical calculations based on density functional theory, emphasizing the need for polarization functions but omitting tests of Pople basis sets containing a full complement thereof. Here, we point out that certain basis sets in the 6-311G category yield error statistics with respect to benchmark calculations that are comparable to def2-TZVP, at about half the cost. More elaborate Pople basis sets can rival the accuracy of def2-QZVPD at 5-10% of the cost. We also clarify the role of integral thresholds in achieving robust convergence in the presence of diffuse basis functions.
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Montgomery Gray; Paige Bowling; John Herbert
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Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational
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CC BY 4.0
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CHEMRXIV
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2024-01-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ac3f8966c1381729e71ddd/original/in-defense-of-certain-pople-type-basis-sets.pdf
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61d77344f51b22805b0b670a
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10.26434/chemrxiv-2022-3g59b
|
A Potentially Limitless Chiral Pool via Conglomerate Crystallisation: Unidentified Spontaneous Resolution in the CSD.
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Conglomerate crystallisation is the behaviour responsible for spontaneous resolution and the discovery of molecular chirality by Pasteur. The phenomenon of conglomerate crystallisation of chiral organic molecules has been left largely undocumented and offers synthetic chemists a potential new chiral pool not reliant on biological systems to supply stereochemical information. While other crystallographic behaviours can be interrogated by automated searching, conglomerate crystallisations are not identified within the Cambridge Structural Database (CSD) and are therefore not accessible by conventional means. By conducting a manual search of the CSD, a list of over 1,700 chiral species capable of conglomerate crystallisation was curated by inspection of the synthetic routes described in each publication. The majority of these are produced by synthetic chemists who seldom note and rarely exploit the implications this phenomenon can have on the enantioenrichment of their crystalline materials. We propose that this list represents a limitless chiral pool which will continually grow in size as more conglomerate crystals are synthesised and recorded.
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Mark Walsh; James Barclay; Callum Begg; Jinyi Xuan; Matthew Kitching
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Organic Chemistry; Natural Products; Stereochemistry; Crystallography – Organic
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CC BY NC ND 4.0
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CHEMRXIV
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2022-01-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d77344f51b22805b0b670a/original/a-potentially-limitless-chiral-pool-via-conglomerate-crystallisation-unidentified-spontaneous-resolution-in-the-csd.pdf
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60c754ecee301c861ac7b075
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10.26434/chemrxiv.12195372.v3
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The N-Terminal Helix-Turn-Helix Motif of Transcription Factors MarA and Rob Drives DNA Recognition
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<div>
<div>
<p>DNA-binding proteins play an important role in gene regulation and cellular function. The transcription factors MarA and Rob are two homologous members of the AraC/XylS family that regulate multidrug resistance. They share a common DNA-binding domain, and Rob possesses an additional C-terminal domain that permits binding of low-molecular weight effectors. Both proteins possess two helix-turn-helix (HTH) motifs capable of binding DNA; however, while MarA interacts with its promoter through both HTH-motifs, prior studies indicate that Rob binding to DNA via a single HTH-motif is sufficient for tight binding. In the present work, we perform microsecond time scale all-atom simulations of the binding of both transcription factors to different DNA sequences to understand the determinants of DNA recognition and binding. Our simulations characterize sequence-specific changes in dynamical behavior upon DNA binding, showcasing the role of Arg40 of the N-terminal HTH-motif in allowing for specific tight binding. Finally, our simulations demonstrate that an acidic C-terminal loop of Rob can control the DNA binding mode, facilitating interconversion between the distinct DNA binding modes observed in MarA and Rob. In doing so, we provide detailed molecular insight into DNA binding and recognition by these proteins, which in turn is an important step towards the efficient design of anti-virulence agents that target these proteins.</p>
</div>
</div>
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Marina Corbella; Qinghua Liao; Catia Moreira; Peter M. Kasson; Shina Caroline Lynn Kamerlin
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Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2021-01-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754ecee301c861ac7b075/original/the-n-terminal-helix-turn-helix-motif-of-transcription-factors-mar-a-and-rob-drives-dna-recognition.pdf
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60f8a8e80b093e26e8e2b751
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10.26434/chemrxiv-2021-kl74l
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High-throughput Screening of Vanadium (IV) Oxide via Continuous Hydrothermal Flow Synthesis Reactor
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The synthesis of inorganic nanoparticles using continuous hydrothermal flow synthesis (CHFS) reactor systems is an up-and-coming process to manufacture high-quality nanomaterials with singular control of the experimental parameters on the scale of seconds as opposed to hours. VO2-based systems manufactured using an autoclave reactor lack scalability, and current commercial products feature particle sizes too large for feasible application. In this paper, the detailed implementation of a CHFS system that can operate at and above supercritical water conditions (22.06 MPa at 374˚C) is described. Control over the CHFS system’s temperature, flow rate, and precursor concentration parameters allowed the tunability of size, crystallinity, and shape of VO2 nanoparticles to be investigated across seven studies. The resulting VO2 nanoparticles were characterized for size, shape, morphology, and crystallinity using dynamic light scattering (DLS), scanning electron microscopy (SEM), and x-ray diffraction (XRD). This investigation resulted in new operating procedures that enable the synthesis of high-quality, uniform, spherical, and pure M-phase VO2 nanoparticles under 50 nm in diameter in the residence time of a few seconds. Additionally, the procedure described in this paper is performed in a single step, thus eliminating the tedious post-annealing process.
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Mai Tran; Elizabeth Rasmussen; Elena Shevchenko; Jie Li
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Materials Science; Nanoscience; Materials Processing; Optical Materials; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2021-07-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f8a8e80b093e26e8e2b751/original/high-throughput-screening-of-vanadium-iv-oxide-via-continuous-hydrothermal-flow-synthesis-reactor.pdf
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62f641685bdc6855a7f34cf1
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10.26434/chemrxiv-2022-9w59c
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One-dimensional fragments of fullerene C60 that exhibit robustness toward multi-electron reduction and pronounced light absorption
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Fullerenes are compelling molecular materials owing to their exceptional robustness toward multi-electron reduction. Although scientists have attempted to address this feature by synthesizing various fragment molecules, the origin of this electron affinity remains unclear. Several structural factors have been suggested, including high symmetry, curved structures, and five-membered ring substructures. To elucidate the role of the five-membered ring substructures without the influence of high symmetry and curved structure, we herein report the synthesis and electron-accepting properties of oligo(biindenylidene)s, a one-dimensional fragment of fullerene C60. Electrochemical studies corroborated that oligo(biindenylidene)s accept electrons equal to the number of five-membered rings in their main chains. Moreover, ultraviolet/visible/near-infrared absorption spectroscopy revealed that oligo(biindenylidene)s exhibit significantly enhanced absorption covering the entire visible region in relation to C60. These results highlight the significance of the pentagonal substructure for attaining stability toward multi-electron reduction and provide a new strategy for the molecular design of electron-accepting -conjugated hydrocarbons.
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Masahiro Hayakawa; Naoyuki Sunayama; Shu I. Takagi; Asuka Tamaki; Shigehiro Yamaguchi; Aiko Fukazawa
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Organic Chemistry; Physical Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-08-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f641685bdc6855a7f34cf1/original/one-dimensional-fragments-of-fullerene-c60-that-exhibit-robustness-toward-multi-electron-reduction-and-pronounced-light-absorption.pdf
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65a5aab566c1381729870ab2
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10.26434/chemrxiv-2023-wn28g-v2
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Catalytic Water Electrolysis by Co-Cu-W Mixed Metal Oxides: In-sights from Operando X-ray Absorption Spectroscopy
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Mixed Metal oxides (MMOs) are a promising class of electrocatalysts for the oxygen evolution reaction (OER) and hydrogen evolu-tion reaction (HER). Despite their importance for sustainable energy schemes, our understanding of relevant reaction pathways, catalytically active sites and synergistic effects is rather limited. Here, we applied synchrotron-based X-ray absorption spectrosco-py (XAS) to explore the evolution of an amorphous Co-Cu-W MMO electrocatalyst, shown previously to be an efficient bifunc-tional OER and HER catalyst for water splitting. Ex-situ K- and L-edge XAS measurements provided structural environments and the oxidation state of the metals involved, revealing Co2+ (octahedral), Cu+/2+ (tetrahedral / square-planar) and W6+ (octahedral) cen-ters. Operando XAS investigations, including X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS), elucidated the dynamic structural transformations of Co, Cu, and W metal centers during OER or HER. The ex-perimental results indicate that Co3+ and Cu0 are the active catalytic sites involved in OER and HER, respectively, while Cu2+ and W6+ play crucial roles as structure stabilizers, suggesting strong synergistic interactions within the Co-Cu-W MMO system. These results, combined with the Tafel slope analysis, revealed that the bottleneck intermediate during OER is Co3+ hydroperoxide, whose formation is accompanied by changes in the Cu-O bond lengths, pointing to a possible synergistic effect between Co and Cu ions. Our study reveals important structural effects taking place during MMO-driven OER/HER electrocatalysis and provides es-sential experimental insights into the complex catalytic mechanism of emerging noble metal-free MMO electrocatalysts for full water splitting.
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Nikita Gupta; Carlo Segre; Carsten Streb; Dandan Gao; Ksenija Glusac
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Physical Chemistry; Inorganic Chemistry; Catalysis; Electrocatalysis; Heterogeneous Catalysis; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-01-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a5aab566c1381729870ab2/original/catalytic-water-electrolysis-by-co-cu-w-mixed-metal-oxides-in-sights-from-operando-x-ray-absorption-spectroscopy.pdf
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66cbb4baa4e53c48769f3dfd
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10.26434/chemrxiv-2024-6p4pr
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Inspired Nanomaterials from meteorite [tetrataenite(NiFe)] for advanced materials engineering for catalysis technologies and Beyond
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To innovate new performance nanomaterials for several engineering fields in order to meet the mankind needs. Researchers from worldwide are focusing on the search of those materials and to create easy ways of designing and synthesizing those expected materials. So, due to the important features of materials coming from the class of rare-earth transition materials, it is known that they possess several applications including catalysis, optoelectronic, X-ray scanning technologies, and so fourth. Furthermore, from an inspiration of a material coming from natural mineral (meteorite), it is demonstrated that tetrataenite (NiFe) is a new technological materials for many applications with a properties similar close to the rare-earth materials. So, in this review article it is shown that many composite catalysts might be designed and synthesized from this row materials with a satisfactory properties. It can be applied for both oxidation and reduction reaction as oxygen evolution reaction (OER), (nitrite, nitrate, nitrogen) transformation to ammonia, and as well as carbon dioxide (CO2) conversion to high value-added products. Therefore, the exploration of tetrataenite would be advantages for considerable engineering technologies and it may solve many issues in fields like catalysis and biomedical engineering areas.
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Mamadou Kalan DIALLO
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Physical Chemistry; Materials Science; Catalysis; Alloys; Geological Materials; Heterogeneous Catalysis
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CC BY 4.0
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CHEMRXIV
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2024-08-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cbb4baa4e53c48769f3dfd/original/inspired-nanomaterials-from-meteorite-tetrataenite-ni-fe-for-advanced-materials-engineering-for-catalysis-technologies-and-beyond.pdf
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6305ac3cf9e99c7af087a82a
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10.26434/chemrxiv-2022-z139w
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Study of FTIR spectroscopy combined with Chemometrics in the characterization of vegetable tannin from Ceriops decandra
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The functionality and widespread application of tannins mainly depend upon their chemical structure. Successful characterization of tannin mainly results in whether it is hydrolysable or condensed. In this study, a tannin-enriched plant Ceriops decandra bark hot water extract was conducted UV-Visible spectroscopy and FTIR spectroscopy along with Chemometrics to characterize its tannin class. However, the λmax value at 264.5 nm in UV-Visible spectroscopy and the FTIR peaks at 1616 cm-1, 1516 cm-1, 1450 cm-1, 1215 cm-1, and 1026 cm-1 revealed the presence of tannin. Again, considering this λmax value with two FTIR peaks at 1709 cm-1 and 1315 cm-1 gave an estimation of the existence of hydrolysable tannin. The study of two Chemometrics tools, principal component analysis (PCA) and hierarchical cluster analysis (HCA) of FTIR spectral data combined with four standard tannins such as Mimosa, Quebracho, Chestnut, and Tara, showed a significant dissimilarity of C. decandra tannin to two condensed tannins (Mimosa and Quebracho) along with meaningful concord to two hydrolysable tannins (Chestnut and Tara). Thus, the rapid characterization using multiple analytical methods and multivariate analysis suggests a harmonious outcome for C. decandra bark, containing hydrolysable tannin.
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Md. Mokarom Hossain; Fatema- Tuj-Zohra; Sobur Ahmed
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Analytical Chemistry; Spectroscopy (Anal. Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2022-08-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6305ac3cf9e99c7af087a82a/original/study-of-ftir-spectroscopy-combined-with-chemometrics-in-the-characterization-of-vegetable-tannin-from-ceriops-decandra.pdf
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65e6e50be9ebbb4db9ef6021
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10.26434/chemrxiv-2024-t785c
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Synthesis of amorphic and hexagonal boron nitride via high temperature treatment of NH3BH3 and Li(BH3NH2BH2NH2BH3)
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Thermal decomposition of NH3BH3 and Li(BH3NH2BH2NH2BH3) was investigated at temperatures up to 1000°C at various conditions under inert atmosphere. It was found that complete dehydrogenation of ammonia borane towards amorphous boron nitride (a-BN) occurs already at 850°C when using monel reactors or at 1000°C by hot isostatic pressing method (HIP), which is significantly lower than it was earlier reported. Li(BH3NH2BH2NH2BH3) was found to decompose towards hexagonal boron nitride (h-BN) at 1000°C by HIP method while at 850°C in monel reactors towards a mixture of a-BN and h-BN. The findings are confirmed by Fourier-transform infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD) and scanning electron microscopy (SEM).
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Agnieszka Prus; Rafal Owarzany; Daniel Jezierski; Krzysztof Perkowski; Karol J. Fijalkowski
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Physical Chemistry; Inorganic Chemistry; Solid State Chemistry; Physical and Chemical Properties; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2024-03-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e6e50be9ebbb4db9ef6021/original/synthesis-of-amorphic-and-hexagonal-boron-nitride-via-high-temperature-treatment-of-nh3bh3-and-li-bh3nh2bh2nh2bh3.pdf
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6697610a5101a2ffa89b4b57
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10.26434/chemrxiv-2024-2wg0k-v2
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Gravitationally-induced Wave-function Collapse Time for Molecules
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The Diósi-Penrose model states that the wave-function collapse ending a quantum superposition occurs due to the instability of coexisting gravitational potentials created by distinct geometric conformations of the system in different states. The Heisenberg time-energy principle can be invoked to estimate the collapse time for the energy associated with this instability, the gravitational self-energy. This paper develops atomistic models to calculate the Diósi-Penrose collapse time. It applies them to a range of systems, from small molecules to large biological structures and macroscopic systems. An experiment is suggested to test the Diósi-Penrose hypothesis, and we critically examine the model, highlighting challenges from an atomistic perspective, such as gravitational self-energy saturation and limited extensivity.
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Anderson Alves Tomaz; Rafael Souza Mattos; Mario Barbatti
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Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics
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CC BY 4.0
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CHEMRXIV
|
2024-07-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6697610a5101a2ffa89b4b57/original/gravitationally-induced-wave-function-collapse-time-for-molecules.pdf
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60c74c6d9abda2a294f8d29f
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10.26434/chemrxiv.12479195.v1
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Sustainable Harvesting of Microalgae by Coupling Chitosan Flocculation and Electro-Floatation
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<p><a></a>In this study, we proposed a new method for edible microalgae harvesting by coupling chitosan flocculation and electro-floatation using carbon electrodes, and tested it at different operation conditions. The surface charge of microalgae cells was measured to explore the underlying mechanisms. The responses of growth medium to microalgae harvesting were also investigated to evaluate the feasibility of sustainable utilization of culture medium. </p><p>(1) Microalgae harvesting efficiency</p><p>The microalgae harvesting efficiency of the proposed method were tested using <i>Chlorella vulgaris </i>(<i>C. vulgaris</i>). <i>C. vulgaris</i>cells (FACHB-24) were purchased from the Institute of Hydrobiology, Chinese Academy of Sciences, and cultured in the BG11 medium, which consists of 500 mg L<sup>-1</sup> Bicin, 100 mg L<sup>-1</sup> KNO<sub>3</sub>, 100 mg L<sup>-1</sup> b-C<sub>3</sub>H<sub>7</sub>O<sub>6</sub>PNa<sub>2</sub>, 50 mg L<sup>-1</sup> NaNO<sub>3</sub>, 50 mg L<sup>-1</sup>Ca(NO<sub>3</sub>)<sub>2</sub>•4H<sub>2</sub>O, 50 mg L<sup>-1</sup> MgCl<sub>2</sub>•6H<sub>2</sub>O, 40 mg L<sup>-1</sup> Na<sub>2</sub>SO<sub>4</sub>, 20 mg L<sup>-1</sup> H<sub>3</sub>BO<sub>3</sub>, 5 mg L<sup>-1</sup> Na<sub>2</sub>EDTA, 5 mg L<sup>-1</sup> MnCl<sub>2</sub>•4H<sub>2</sub>O, 5 mg L<sup>-1</sup> CoCl<sub>2</sub>•6H<sub>2</sub>O and 0.8 mg L<sup>-1</sup> Na<sub>2</sub>MoO<sub>4</sub>•2H<sub>2</sub>O, 0.5 mg L<sup>-1</sup> FeCl<sub>3</sub>•6H<sub>2</sub>O and 0.5 mg L<sup>-1</sup> ZnCl<sub>2</sub>. The batch cultures were conducted in an illuminating incubator (LRH-250-G, Guangdong Medical Apparatus Co., Ltd., China) with continuous cool white fluorescent light of 2500 ± 500 lux on a 12 h light and 12 h darkness regime at the temperature of 30 ± 1°C.</p><p>The microalgae harvesting efficiency system consists of a flat stir paddle <a></a><a></a>(Zhongrun Water Industry Technology Development Co., Ltd., China) for mixing during chitosan flocculation and two round carbon electrode plates (Jinjia Metal Co., Ltd., China) for electro-floatation. The carbon electrode plate has a surface area of 55.4 cm<sup>2</sup> and a thickness of 0.2 cm, which was horizontally installed at the bottom with a gap of 2 cm between the two plates. There are 85 small round holes on each carbon electrode plate to allow gas bubbles freely pass it during electrolysis, such that the effective surface area was 38.7 cm<sup>2</sup>. The electric current was supplied by a direct current power supply (DF1730SL5A, Ningbo Zhongce Dftek Electronics Co., Ltd., China). </p><p><i>C. vulgaris</i> culture at the exponential growth phase was used in the microalgae harvesting test. The initial cell concentration was set to 3.63 × 10<sup>10</sup> cells L<sup>-1</sup>. 0.5 L of readily prepared <i>C. vulgaris</i> solution was transferred to the harvesting cell. Water-soluble chitosan was purchased from Qingdao Yunzhou Bioengineering Co. Ltd., China. Prior to the test, a chitosan stock solution (2 g L<sup>-1</sup>) was prepared as follows: 1 g chitosan was added to 0.5 L distilled water and completely diluted by stirring. After chitosan was added, the microalgae solution was stirred at 200 rpm for 2 min and 40 rpm for another 10 min; electro-floatation was started in the last 5 min during chitosan flocculation. The microalgae solution was allowed to stand for 10 min, and then water samples were carefully collected from an outlet 2 cm above the carbon electrode plate to enumerate the cell number using an Axioskop 2 mot plus microscope (Carl ZEISS, Germany). The microalgae harvesting efficiency was calculated as (initial cell concentration-sample cell concentration)/initial cell concentration × 100%. In the test, the chitosan dosage was set to 0, 2, 4, 6, 8, 10, 12 and 15 mg L<sup>-1</sup>, and the current density was set to 0, 0.2, 0.4 and 0.6 A. All the tests were conducted in triplicate at the raw microalgae solution pH of 8.6.</p><p>(2) Surface charges of chitosan, microalgae cells and microalgae flocs</p><p>The surface charges of chitosan, microalgae cells and microalgae flocs were characterized using a Zetasizer 2000 (Malvern Co. United Kingdom). </p><p>(3) Sustainable utilization of microalgae culture medium</p><p>Before and after microalgae harvesting, medium nutrients (phosphate, ammonium and nitrate) were measured according to Chinese Monitoring Analysis Method of Water and Wastewater; medium pH and temperature were measured using a Yellow Springs Instruments (Yellow Springs, Ohio, USA)</p><p>(4) Cost evaluation</p><p>The cost of microalgae harvesting was estimated by summing flocculants and energy costs per unit of harvested microalgae biomass. The chitosan and electric power are 0.03 USD g<sup>-1</sup> and 0.08 USD (kWh)<sup>-1</sup>, respectively.</p>
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Lin Zhu; Hui Xu; Weijie Guo; Jianghua Yu; Wenqing Shi
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Bioengineering and Biotechnology
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CC BY NC 4.0
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CHEMRXIV
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2020-06-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c6d9abda2a294f8d29f/original/sustainable-harvesting-of-microalgae-by-coupling-chitosan-flocculation-and-electro-floatation.pdf
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60c74e4cbb8c1a283d3db716
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10.26434/chemrxiv.12675428.v1
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Accelerated Computation of Free Energy Profile at Ab Initio QM/MM Accuracy via a Semi-Empirical Reference-Potential. III. Gaussian Smoothing on Density-of-States
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Calculations of free energy profile, aka potential of mean force (PMF), along a chosen collective variable (CV) are now routinely applied to the studies of chemical processes, such as enzymatic reactions and chemical reactions in condensed phases. However, if the ab initio QM/MM level of accuracy is required for the PMF, it can be formidably expensive even with the most advanced enhanced sampling methods, such as umbrella sampling. To ameliorate this difficulty, we developed a novel method for the computation of free energy profile based on the reference-potential method recently, in which a low-level reference Hamiltonian is employed for phase space sampling and the free energy profile can be corrected to the level of interest (the target Hamiltonian) by energy reweighting in a nonparametric way. However, when the reference Hamiltonian is very different from the target Hamiltonian, the calculated ensemble averages, including the PMF, often suffer from numerical instability, which mainly comes from the overestimation of the density-of-states (DoS) in the low-energy region. Stochastic samplings of these low-energy configurations are rare events. If a low-energy configuration has been sampled with a small sample size N, the probability of visiting this energy region is ~ 1/N (shall be exactly 1/N for a single ensemble), which can be orders-of-magnitude larger than the actual DoS. In this work, an assumption of Gaussian distribution is applied to the DoS in each CV bin, and the weight of each configuration is rescaled according to the accumulated DoS. The results show that this smoothing process can remarkably reduce the ruggedness of the PMF and increase the reliability of the reference-potential method.
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Wenxin Hu; Pengfei Li; Jia-Ning Wang; Yuanfei Xue; Yan Mo; Jun Zheng; Xiaoliang Pan; Yihan Shao; Ye Mei
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Quantum Mechanics; Statistical Mechanics; Thermodynamics (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2020-07-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e4cbb8c1a283d3db716/original/accelerated-computation-of-free-energy-profile-at-ab-initio-qm-mm-accuracy-via-a-semi-empirical-reference-potential-iii-gaussian-smoothing-on-density-of-states.pdf
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62309601d7562724e8190c3f
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10.26434/chemrxiv-2021-v89w1-v3
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Dynamic Au–C σ-Bonds Leading to an Efficient Synthesis of [n]Cycloparaphenylenes (n = 9 – 15) by a Self-Assembly
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The transmetalation of the digold(I) complex [Au2Cl2(dcpm)] (1) (dcpm = bis(dicyclohexylphosphino)methane) with oligophenylene diboronic acids gave the triangular macrocyclic complexes [Au2(C6H4)x(dcpm)]3 (x = 3, 4, 5) with yields of over 70%. On the other hand, when the other digold(I) complex [Au2Cl2(dppm)] (1') (dcpm = bis(diphenylphosphino)methane) was used, only a negligible amount the triangular complex was obtained. The control experiments revealed that the dcpm ligand accelerated an intermolecular Au(I)–C σ-bond-exchange reaction, and that this high reversibility is the origin of the selective formation of the triangular complexes. Structural analyses and theoretical calculations indicate that dcpm ligand increases the electrophilicity of the Au atom in the complex, thus facilitating the exchange reaction, though cyclohexyl group is an electron-donating group. Furthermore, the oxidative chlorination of the macrocyclic gold complexes afforded a series of [n]cycloparaphenylenes (n = 9, 12, 15) in 78–88% isolated yields. The reaction of two different macrocyclic Au complexes gave a mixture of macrocyclic complexes incorporating different oligophenylene linkers, from which a mixture of [n]cycloparaphenylenes with various numbers of phenylene units was obtained in good yields.
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Yohei Tanji; Yusuke Yoshigoe; Shinichi Saito; Kohtaro Osakada; Eiichi Kayahara; Shigeru Yamago; Yoshitaka Tsuchido; Hidetoshi Kawai
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Organic Chemistry; Organometallic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Transition Metal Complexes (Organomet.)
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CC BY NC ND 4.0
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CHEMRXIV
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2022-03-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62309601d7562724e8190c3f/original/dynamic-au-c-bonds-leading-to-an-efficient-synthesis-of-n-cycloparaphenylenes-n-9-15-by-a-self-assembly.pdf
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65bcfd7d66c1381729d04f6b
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10.26434/chemrxiv-2024-nj0p6-v2
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Combined Network and High Resolution Mass Spectrometry Analysis of the Formose Reaction Reveals Mechanisms for Emergent Behaviors
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The formose reaction (FR) autocatalytically converts simple plausibly prebiotic feedstocks into molecules of biological interest, including ribose. Autocatalysis is a hallmark of life, thus various studies have explored the formose reaction with respect to the origins of life. The FR is robust under appropriate conditions, occurring readily at low temperatures from various substrates, and has been implicated in the generation of meteoritic organic compounds. We explored the FR here using a combination of in silico modeling techniques and high resolution mass spectrometry. The models match experimental results well, and point to the FR being much more complex than previously modeled or measured, and help explain the FR’s potential to generate homochirality and primitive compartments, both of which are also hallmarks of life, before the emergence of the complex directed molecular encoding suggested by the RNA World model. These results suggest the FR requires further study with regard to the origins of life, and its importance may lie in the way it enables and coordinates emergent chemistries, rather than the particular products it generates, such as ribose.
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Romulo Cruz-Simbron; Siddhant Sharma; Aayush Arya; Jessica Ray; Alejandro Lozano; Jakob Lykke Andersen; Huan Chen; Henderson James Cleaves II
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Theoretical and Computational Chemistry; Analytical Chemistry; Mass Spectrometry; Chemoinformatics - Computational Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-02-05
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bcfd7d66c1381729d04f6b/original/combined-network-and-high-resolution-mass-spectrometry-analysis-of-the-formose-reaction-reveals-mechanisms-for-emergent-behaviors.pdf
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618ed6dbe0ea84511a951909
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10.26434/chemrxiv-2021-1x2zl
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Implicit solvent models fail to reproduce secondary structures of de novo designed peptides
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We test a range of standard implicit solvent models and protein forcefields for a set of 5 experimentally characterized, designed α-helical peptides. 65 combinations of forcefield and implicit solvent models are evaluated in >800 µs of molecular dynamics simulations. The data show that implicit solvent models generally fail to reproduce the experimentally observed secondary structure content, and none performs well for all 5 peptides. The results show that these models are not usefully predictive.
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Eric Lang; Emily Baker; Derek Woolfson; Adrian Mulholland
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
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2021-11-15
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618ed6dbe0ea84511a951909/original/implicit-solvent-models-fail-to-reproduce-secondary-structures-of-de-novo-designed-peptides.pdf
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668500915101a2ffa841838b
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10.26434/chemrxiv-2024-xfssk
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Overriding Cage Effect in Electron Donor-Acceptor Photoactivation of Diaryliodonium Reagents: Synthesis of Chalcogenides
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In recent times, diaryliodonium reagents (DAIRs) have witnessed a resurgence as an arylating agent, especially under photoinduced conditions. However, reactions proceeding through electron donor-acceptor (EDA) complex formation with DAIRs are restricted to electron-rich reacting partners serving as donors due to the well-known cage effect. We discovered a visible-light-induced convenient and practical EDA platform to activate DAIRs for generating and concomitant utilization of resulting aryl radicals for synthesizing organic chalcogenides that are prevalent in natural products and biologically active compounds. In this process, an array of DAIRs and dichalcogenides react in the presence of 1,4 diazabicyclo[2.2.2]octane (DABCO) as a cheap and readily available donor, furnishing a diverse variety of di(hetero)aryl and aryl/alkyl chalcogenides in good yields. The method is scalable, features a broad scope with good yields, and operates under open-to-air conditions. The photoinduced chalcogenation technology is suitable for late-stage functionalizations and disulfide bioconjugations and facilitates access to biologically relevant thioesters, dithiocarbamates, sulfoximines, and sulfones. Moreover, the discovered method applies to synthesizing diverse pharmaceuticals, such as vortioxetine, promazine, mequitazine, and dapsone, under amenable conditions.
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Prahallad Meher; Sushanta Kumar Parida; Sanat Kumar Mahapatra; Lisa Roy; Sandip Murarka
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Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
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2024-07-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668500915101a2ffa841838b/original/overriding-cage-effect-in-electron-donor-acceptor-photoactivation-of-diaryliodonium-reagents-synthesis-of-chalcogenides.pdf
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60c7516b337d6cffc4e28524
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10.26434/chemrxiv.12117483.v2
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Guest Encapsulation Within Surface-Adsorbed Self-Assembled Cages
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Coordination cages encapsulate a wide variety of guests in the solution state. This ability renders them useful for applications such as catalysis and the sequestration of precious materials. Here we report a simple and general method for the immobilisation of coordination cages on alumina. Cage loadings were quantified via adsorption isotherms and guest displacement assays demonstrated that the adsorbed cages retained the ability to encapsulate and separate guest and non-guest molecules. Finally, we used a system of two cages adsorbed on to different regions of alumina to stabilise and separate a pair of Diels-Alder reagents. The addition of a single competitive guest resulted in the controlled release of the reagents, thus triggering their reaction. We envisage this method of coordination cage immobilisation on solid phases to be applicable to the extensive library of reported cages, enabling new applications based upon selective solid-phase molecular encapsulation.
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Hugh Ryan; Cally Haynes; Alyssa Smith; Angela Grommet; Jonathan Nitschke
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Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Self-Assembly; Surface
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CC BY NC ND 4.0
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CHEMRXIV
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2020-10-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7516b337d6cffc4e28524/original/guest-encapsulation-within-surface-adsorbed-self-assembled-cages.pdf
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63bc39773af973835b618192
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10.26434/chemrxiv-2023-nlx1z
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FEFOS: A method to derive oxide formation energies from oxidation states
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Herein we report a method to extract formation energies from oxidation states, which we call FEFOS. This new scheme predicts the formation energies of binary oxides through analysing unary oxide formation energies as a function of their oxidation states. Taking averages of fitted quadratic equations that represent how elements respond to oxidation and reduction, the weights of these averages are determined by constraing the compound to be neutral. The performance of FEFOS results in mean absolute errors of ca. 0.10 eV/atom when tested against Materials Project data for oxides with general formulas A1–zBzO, A1–zBzO1.5, and A1–zBzO2 with specific coordinations. Our FEFOS method not only allows for the prediction of binary oxide formation energies with low variance and high interpretability, but also compares well with state-of-the-art deep learning methods without being biased by training data and the need for large resources to compute it. Finally, we discuss the potential applications of the FEFOS method in tackling the problem of inverse design for catalysis.
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Michael Craig; Felix Kleuker; Michal Bajdich; Max Garcia-Melchor
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Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Thermodynamics (Physical Chem.)
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CC BY NC 4.0
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CHEMRXIV
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2023-01-11
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bc39773af973835b618192/original/fefos-a-method-to-derive-oxide-formation-energies-from-oxidation-states.pdf
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626bc89fd048ed357f5578f3
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10.26434/chemrxiv-2021-stf76-v2
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In Situ Assembly of Platinum (II)-Metallopeptide Nanostructures Inhibits Energy Homeostasis and Cellular Metabolism
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Nanostructure-based functions are omnipresent in nature and essential for the diversity of life. Unlike small molecules, which are often inhibitors of enzymes or biomimetics with established methods of elucidation, we show that functions of nanoscale structures in cells are complex and can implicate system-level effects such as the regulation of energy and redox homeostasis. Herein, we
design a platinum (II) containing tripeptide that assembles into intracellular fibrillar nanostructures upon molecular rearrangement in the presence of endogenous H2O2. The formed nanostructures blocked metabolic functions, including aerobic glycolysis and oxidative phosphorylation, thereby shutting down ATP production. As a consequence, ATP-dependent actin formation and glucose metabolite-
dependent histone deacetylase activity are downregulated. We demonstrate that assembly-driven nanomaterials offer a rich avenue to achieve broad-spectrum bioactivities that could provide new opportunities in drug discovery.
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Zhixuan Zhou; Konrad Maxeiner; Pierpaolo Moscariello; Siyuan Xiang; Yingke Wu; Colette J. Whitfield; Lujuan Xu; Anke Kaltbeitzel; Shen Han; David Mücke; Haoyuan Qi; Manfred Wagner; Ute Kaiser; Katharina Landfester; Ingo Lieberwirth; David Y.W. Ng; Tanja Weil
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Nanoscience; Nanostructured Materials - Nanoscience
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CC BY NC ND 4.0
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CHEMRXIV
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2022-05-02
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626bc89fd048ed357f5578f3/original/in-situ-assembly-of-platinum-ii-metallopeptide-nanostructures-inhibits-energy-homeostasis-and-cellular-metabolism.pdf
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65606ec3cf8b3c3cd7028401
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10.26434/chemrxiv-2023-5v7tx-v2
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Non-covalent Functionalized Schottky Interface at Ti3C2Tx/n-Si Van der Waals Heterojunction
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Low dimensional 2D materials such as graphene and carbon nano tubes have attracted significant attention from the solid-state device community and are considered as a potential candidate electrode to make functional contact with the Silicon (Si) and other industry compatible semiconductors. In this work we envisioned to utilize one such interesting 2D material Ti3C2Tx belonging to a rapidly emerging family of transition metal carbides/nitrides also known as MXene´s to fabricate the classical yet interesting Schottky junctions by simple drop casting of aqueous conducting colloidal solution of Ti3C2Tx on c-Si. Precisely, we anticipate to tune the work function of the Ti3C2Tx as well as the built-in potential of these Ti3C2Tx/c-Si Van der Waals heterojunction through inserting ultrathin interlayer of cationic polyelectrolytes/organic dipoles with a defined dipole moment value. In order to accomplish the interface engineering inclusion poly(ethylene)amine (PEI 0.1%), third generation poly(amido-)amine (PAMAM G3)), were tested between the Ti3C2TX and c-Si substrates. Charge transport properties of the fabricated Schottky devices with the structure of Ti3C2TX/organic dipole (O.D.) /c-Si were evaluated through systematic analysis of the current-voltage (I-V) and capacitance-voltage (C-V) results. I-V measurements under dark conditions revealed that Schottky diodes fabricated with the (PEI 0.1%) and PAMAM G3 interlayers exhibited lowest reverse saturation current density (J0) value and improved built in potential (Vbi) value as compared to the devices with only 2D-Ti3C2Tx as contact. We report reduction in the work function value of Ti3C2Tx from 5.8 eV to 4.2 eV for Ti3C2Tx/PEI (0.1%) and 3.3 eV for Ti3C2Tx/PAMAM G3 heterostructures. On the basis of the inferences drawn from the surface analysis we ascribe this reduction in work function value to the formation of interfacial dipoles at the Ti3C2Tx/O.D. interface. Importantly this study highlights an innovative method to tune the work function of the Ti3C2Tx MXene inclusion of organic dipoles as interlayers.
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Eloi Ros Costals; Xavier Francesc Cappela; Thomas Tom; Sergio Giraldo; Marcel Placidi; Cristobal Voz; Joaquim Puigdollers; Edgardo Saucedo; Zacharie Jehl Li Kao; Kunal Jogendra Tiwari
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Materials Science; Nanoscience; Energy; Carbon-based Materials; Hybrid Organic-Inorganic Materials; Thin Films
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CC BY NC ND 4.0
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CHEMRXIV
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2023-11-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65606ec3cf8b3c3cd7028401/original/non-covalent-functionalized-schottky-interface-at-ti3c2tx-n-si-van-der-waals-heterojunction.pdf
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6655ef1121291e5d1d797642
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10.26434/chemrxiv-2024-xpn8c
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Do we really need ligands in Ir-catalyzed C–H borylation?
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Direct borylation of C–H bonds is a privileged strategy to access versatile building blocks and valuable derivatives of complex molecules (late-stage functionalization, metabolite synthesis). This perspective aims to provide an overview and classification of the catalytic systems developed in this fast-growing area of research. Unexpected selectivity differences between two established directed-borylation systems have been discovered using high-throughput experimentation highlighting the importance of classical control experiments in catalysis research.
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Janis M. Zakis; Simone L. Kuhn; Joanna Wencel-Delord; Tomas Smejkal
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Catalysis; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2024-05-29
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6655ef1121291e5d1d797642/original/do-we-really-need-ligands-in-ir-catalyzed-c-h-borylation.pdf
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6335ad6dba8a6d8a79616f8c
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10.26434/chemrxiv-2022-59f05
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Analysis of small molecule mixtures by super-resolved 1H NMR spectroscopy
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Analysis of small molecules is essential to metabolomics, natural products, drug discovery, food technology and many other areas of interest. Current barriers preclude from identifying the constituent molecules in a mixture as overlapping clusters of NMR lines pose a major challenge in resolving signature frequencies for individual molecules. While homonuclear decoupling techniques produce much simplified pure shift spectra, they often affect sensitivity. Conversion of typical NMR spectra to pure shift spectra by signal processing without a priori knowledge about the coupling patterns is essential for accurate analysis. We developed a super-resolved wavelet packet transform based 1H NMR spectroscopy that can be used in high-throughput studies to reliably decouple individual constituents of small molecule mixtures. We demonstrate the efficacy of the method on the model mixtures of saccharides and amino acids in the presence of significant noise.
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Aritro Sinha Roy; Madhur Srivastava
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Physical Chemistry; Analytical Chemistry; Spectroscopy (Physical Chem.); Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2022-09-30
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6335ad6dba8a6d8a79616f8c/original/analysis-of-small-molecule-mixtures-by-super-resolved-1h-nmr-spectroscopy.pdf
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60c755bcbdbb89f7b7a3a8b3
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10.26434/chemrxiv.14077220.v2
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Transmembrane Anion Transport Promoted by Thioamides
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Thioamide groups represent useful hydrogen-bonding motifs for
the development of active transmembrane anion transporters.
Using a 1,8-dithioamidocarbazole scaffold the superior
performance of thioamides compared with the parent amides has
been demonstrated.<br />
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Robert Pomorski; María García-Valverde; roberto quesada; Michał J. Chmielewski
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Supramolecular Chemistry (Org.)
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CC BY NC ND 4.0
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CHEMRXIV
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2021-03-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755bcbdbb89f7b7a3a8b3/original/transmembrane-anion-transport-promoted-by-thioamides.pdf
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633d6bbfea6a225b1809e24e
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10.26434/chemrxiv-2022-0hl5p-v3
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SolvBERT for solvation free energy and solubility prediction: a demonstration of an NLP model for predicting the properties of molecular complexes
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Deep learning models based on NLP, mainly the Transformer family, have been successfully applied to solve many chemistry-related problems, but their applications are mostly limited to chemical reactions. Meanwhile, solvation is an important concept in physical and organic chemistry, describing the interaction of solutes and solvents. This interaction leads to a solvation complex, a molecular complex similar to a reactant-reagent complex. In this study, we introduced the SolvBERT model, which reads the solute and solvents through the SMILES representation of the solvation complex. SolvBERT is pretrained in an unsupervised learning fashion using a large database of computational solvation free energies. The pretrained model can be used to predict the experimental solvation free energy or solubility, depending on the fine-tuning database. To the best of our knowledge, this multi-task prediction capability has not been observed in previously developed graph-based models for predicting the properties of molecular complexes. Furthermore, the performance of our SolvBERT in predicting solvation free energy is comparable to the state-of-the-art graph-based model DMPNN, mainly due to the clustering feature of the pretraining phase of the model, as demonstrated by the TMAP visualization algorithm.
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Jiahui Yu; Chengwei Zhang; Yingying Cheng; Yun-Fang Yang; Yuan-Bin She; Fengfan Liu; Weike Su; An Su
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Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties
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CC BY NC ND 4.0
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CHEMRXIV
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2022-10-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633d6bbfea6a225b1809e24e/original/solv-bert-for-solvation-free-energy-and-solubility-prediction-a-demonstration-of-an-nlp-model-for-predicting-the-properties-of-molecular-complexes.pdf
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60c7497d4c891999e4ad30b7
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10.26434/chemrxiv.12061734.v1
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Computational design of ACE2-based short peptide inhibitors of SARS-CoV-2
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<div>Peptide inhibitors against the SARS-CoV-2 coronavirus, currently causing a worldwide pandemic, are designed and simulated. The inhibitors are formed by two sequential self-supporting alpha-helices (bundle) extracted from the protease domain (PD) of angiotensin-converting enzyme 2 (ACE2), which binds to the SARS-CoV-2 receptor binding domains. Molecular dynamics simulations revealed that the peptides maintain their secondary structure and provide a highly specific and stable binding (blocking) to SARS-CoV-2, determined by their sequences and conformations. The proposed peptide inhibitors could provide simple therapeutics against the COVID-19 disease.</div>
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Yanxiao Han; Petr Kral
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Computational Chemistry and Modeling
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-04-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7497d4c891999e4ad30b7/original/computational-design-of-ace2-based-short-peptide-inhibitors-of-sars-co-v-2.pdf
|
658b0cf7e9ebbb4db9cf0190
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10.26434/chemrxiv-2023-mrt47
|
Molecular Beam Scattering of Ammonia from a Dodecane Flat Liquid Jet
|
The evaporation and scattering of ND3 from a dodecane flat liquid jet are investigated and compared to previous molecular beam scattering studies from liquid surfaces. Evaporation is well-described by a Maxwell–Boltzmann flux distribution with a cosθ angular distribution at the liquid temperature. Scattering experiments at Ei = 28.8 kJ mol−1 over a range of deflection angles show evidence for impulsive scattering and thermal desorption. At a deflection angle of 90°, the thermal desorption fraction is 0.54, which is ~4 % higher than other molecules previously scattered from dodecane and consistent with work performed on NH3 scattering from a squalane wetted wheel. ND3 scattering from dodecane results in super-specular scattering, as seen in previous experiments on dodecane. The impulsive scattering channel is fitted to a “soft-sphere” model, yielding an effective surface mass of 55 amu and an internal excitation of 5.08 kJ mol−1. Overall, impulsively scattered ND3 behaves similarly to other small molecules scattered from dodecane.
|
Steven Saric; Walt Yang; Daniel M. Neumark
|
Physical Chemistry; Physical and Chemical Processes; Surface
|
CC BY NC 4.0
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CHEMRXIV
|
2023-12-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658b0cf7e9ebbb4db9cf0190/original/molecular-beam-scattering-of-ammonia-from-a-dodecane-flat-liquid-jet.pdf
|
65405101a8b423585a9ceb26
|
10.26434/chemrxiv-2023-8vj0g
|
Real-Time NMR-Based Drug Discovery to Identify Inhibitors against Fatty Acid Synthesis in Living Cancer Cells
|
The aberrant metabolism of fatty acids is recognized as a key driver in the development and progression of tumors. Although numerous inhibitors have been developed to target this pathway, finding drugs with high specificity that do not disrupt normal cellular metabolism remains a formidable challenge. In this manuscript, we introduced a novel real-time NMR-based drug screening technique that operates within living cells. This technique provides a direct way to putatively identify molecular targets involved in specific metabolic processes, making it a powerful tool for cell-based drug screening. Using 2-13C acetate as a tracer, combined with 3D cell clusters and a bioreactor system, our approach enables real-time detection of inhibitors that target fatty acids metabolism within living cells. As a result, we successfully demonstrate the initial application of this method in discovering traditional Chinese medicines that specifically target fatty acid metabolism. Elucidating the mechanisms behind herbal medicines remains challenging due to the complex nature of their compounds and the presence of multiple targets. Remarkably, our findings demonstrate the significant inhibitory effect of Poria cocos on fatty acid synthesis within cells, thereby illustrating the potential of this approach in analyzing fatty acid metabolism events and identifying candidate drugs that selectively inhibit fatty acid synthesis at the cellular level. Moreover, this systematic approach represents a valuable strategy for discovering the intricate effects of herbal medicine.
|
Biao Liu; Caixiang Liu; Xin Chai; Xinyu Fan; Tao Huang; Jianhua Zhan; Qinjun Zhu; Danyun Zeng; Zhou Gong; Yunhuang Yang; Zhou Xin; Bin Jiang; Xu Zhang; Maili Liu
|
Biological and Medicinal Chemistry; Analytical Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65405101a8b423585a9ceb26/original/real-time-nmr-based-drug-discovery-to-identify-inhibitors-against-fatty-acid-synthesis-in-living-cancer-cells.pdf
|
65aa23cb9138d2316143b912
|
10.26434/chemrxiv-2024-96nz6
|
Integration of Wnt-inhibitory Activity and Structural Novelty Scoring Results to Uncover Novel Bioactive Natural Products: New Bicyclo[3.3.1]non-3-ene-2,9-diones from the Leaves of Hymenocardia punctata.
|
In natural products (NP) research, methods for the efficient prioritization of natural extracts (NEs) are key for discovering novel bioactive NPs. In this study a biodiverse collection of 1600 NEs, previously analyzed by UHPLC-HRMS2 metabolite profiling was screened for Wnt pathway regulation. The results of the biological screening drove the selection of a subset of 30 non-toxic NEs with an inhibitory IC50 ≤ 5 μg/mL. To increase the chance of finding structurally novel bioactive NPs, Inventa, a computational tool for automated scoring of NEs based on structural novelty was used to mine the HRMS2 analysis and dereplication results. After this, 4 out of the 30 bioactive NEs were shortlisted by this approach. The most promising sample was the ethyl acetate extract of the leaves of Hymenocardia punctata (Phyllanthaceae). Further phytochemical investigations of this species resulted in the isolation of three known prenylated flavones (3, 5, 7) and ten novel bicyclo[3.3.1]non-3-ene-2,9-diones (1, 2, 4, 6, 8-13), named Hymenotamayonins. Assessment of the Wnt inhibitory activity of these compounds revealed that two prenylated flavones and three novel bicyclic compounds showed interesting activity without apparent cytotoxicity. This study highlights the potential of combining Inventa's structural novelty scores with biological screening results to effectively discover novel bioactive NPs in large NE collections.
|
Luis Quiros-Guerrero; Laurence Marcourt; Nathareen Chaiwangrach; Alexey Koval; Emerson Ferreira-Queiroz; Bruno David; Antonio Grondin; Vladimir Katanaev; Jean-Luc Wolfender
|
Organic Chemistry; Analytical Chemistry; Natural Products; Mass Spectrometry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-01-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aa23cb9138d2316143b912/original/integration-of-wnt-inhibitory-activity-and-structural-novelty-scoring-results-to-uncover-novel-bioactive-natural-products-new-bicyclo-3-3-1-non-3-ene-2-9-diones-from-the-leaves-of-hymenocardia-punctata.pdf
|
66678ee812188379d8ce0cb4
|
10.26434/chemrxiv-2024-073ld-v2
|
A General Nucleation Model For Semiconductor Nanocrystals
|
We introduce a non-classical model for nanocrystal nucleation in solution which centers on the dynamic interplay of chemical bond breakage and formation, coupled with the desolvation of precursor molecules, which we term the molecular chemistry (MC) model. Departing from classical theory, our model employs the bond count as the key variable rather than particle size, thereby redefining the role of supersaturation and its role in determining the so-called critical nucleus size. We apply the model to CdSe nanocrystal formation in non-polar solvents and showcase its efficacy in predicting solvent dynamics, precursor characteristics, crystal phase, stoichiometry, "magic number" behavior, and transition states. While the coupled-cluster method is used to determine the bond energy, we show that it is possible to derive reaction pathways by reducing the calculations to algebraic approximations for the nucleation energy. This singular set of bond energy parameters allows nanocrystal nucleation and growth to be conceptualized as a straightforward chemical reaction.
|
Zifei Chen; Salvy Russo; Paul Mulvaney
|
Physical Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Theory - Inorganic; Clusters; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-06-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66678ee812188379d8ce0cb4/original/a-general-nucleation-model-for-semiconductor-nanocrystals.pdf
|
677d11836dde43c9089a9181
|
10.26434/chemrxiv-2025-s87p9
|
A Nanoscale view of Solid-State Batteries
|
The demand for safe energy storage with high energy density is growing and as lithium-ion batteries are nearing their performance limits, solid-state batteries have emerged as promising successors. Solid-state batteries offer higher energy density, enhanced safety, and faster charge rates. However, their commercialization remains constrained by solid/solid interface processes, including metal filament formation, chemically or mechanically unstable electrolyte/electrode interfaces, and inhomogeneous cathodic reactions. Advanced nanoscale characterization techniques are essential for unveiling the mechanistic origins of solid-state battery degradation and performing real-time monitoring of nanoscale changes within battery materials, which reveal critical insights into dynamic interfacial processes under operational conditions. Such knowledge may unlock the full potential of solid-state batteries by guiding the development of new materials, battery architectures, and microstructures for improved performance and durability. This review surveys research on solid-state battery materials and components and examines how various nanoscale characterization techniques can diagnose and mitigate degradational phenomena in these electrochemical devices. We review recent studies examining different solid-state processes in solid-state batteries with a particular focus on the growth of filaments, metal deposition and secondary phase formation at the electrolyte/anode interface, interdiffusion and parasitic reactions at electrolyte/cathode interface, uneven cathodic reactions, mechanical failure of the electrodes, unwanted electronic leakage, and grain boundary heterogeneities within the electrolyte. Lastly, we describe future method developments enabling a deeper insight into the operation and degradation of solid-state batteries.
|
Mohamad Khoshkalam; Fardin Ghaffari-Tabrizi ; Dennis Christensen
|
Materials Science; Nanoscience; Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2025-01-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d11836dde43c9089a9181/original/a-nanoscale-view-of-solid-state-batteries.pdf
|
60ffcaaa0321140c7cb81be1
|
10.26434/chemrxiv-2021-xmjt1
|
Enhancement of DNA Droplet Formation Ability in Liquid–Liquid Phase Separation by Introduction of Artificial Nucleobase
|
Controlling liquid–liquid phase separation (LLPS) of biomolecules is a challenge for understanding its biological phenomena and developing drugs for LLPS associated diseases. We found that substitution of DNA bases with 5-nitroindoles, known as universal bases, considerably improves the droplet formation ability of DNA. Our findings show the feasibility of introducing an artificial DNA nucleobase with a superior droplet formation ability, paving the way for the development of novel control systems for LLPS.
|
Ryu Tashiro; Tomohiro Kitagawa; Yuta Ito
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ffcaaa0321140c7cb81be1/original/enhancement-of-dna-droplet-formation-ability-in-liquid-liquid-phase-separation-by-introduction-of-artificial-nucleobase.pdf
|
64e398ca01042bc1cc7114f6
|
10.26434/chemrxiv-2023-10202-v2
|
Free and Internal Energies for the Adsorption of Short Alkanes into the Zeolite SSZ-13 from Ab Initio Molecular Dynamics Simulations
|
Electronic structure calculations have become a valuable tool in understanding chemical reactions of hydrocarbons in zeolite pores. However, commonly applied approaches to calculate free energies based on static electronic structure calculations significantly overestimate the entropic penalty for molecular adsorption into zeolite pores. Here, we use ab initio molecular dynamics (AIMD) simulations to model the adsorption of methane, ethane, and propane to purely siliceous and protonated SSZ-13. In our analyses we focus on the internal and Helmholtz free energies of adsorption of each molecule and compare our results to various approaches for the calculation of free energies based on static calculations. We find that only an approach that retains two thirds of the translational entropy of the adsorbate upon adsorption compares favorably with AIMD simulations. However, comparison to experimental measurements of Gibbs free energies of adsorption reported in the literature implies that we might not have captured the full complexity of alkane adsorption in our model. We expect that results in this work will help to develop a better understanding of alkane adsorption in zeolites, and that the provided data will serve as a benchmark for free energy calculations of alkane adsorption in zeolites in the future.
|
Daniel J. Hutton; Florian Göltl
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis; Thermodynamics (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-08-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e398ca01042bc1cc7114f6/original/free-and-internal-energies-for-the-adsorption-of-short-alkanes-into-the-zeolite-ssz-13-from-ab-initio-molecular-dynamics-simulations.pdf
|
60c73e57ee301c4297c7870b
|
10.26434/chemrxiv.6890807.v1
|
Bimolecular Reaction Dynamics in the Phenyl - Silane System: Exploring the Prototype of a Radical Substitution Mechanism
|
<p>We
present a combined experimental and theoretical investigation of the
bimolecular gas phase reaction of the phenyl radical (C<sub>6</sub>H<sub>5</sub>)
with silane (SiH<sub>4</sub>) under single collision conditions to investigate
the chemical dynamics of forming phenylsilane (C<sub>6</sub>H<sub>5</sub>SiH<sub>3</sub>)
via a bimolecular radical substitution mechanism at a tetra-coordinated
silicon atom. Verified by electronic structure and quasiclassical trajectory
calculations, the replacement of a single carbon atom in methane by silicon
lowers the barrier to substitution thus defying conventional wisdom that
tetra-coordinated hydrides undergo preferentially hydrogen abstraction. This
reaction mechanism provides fundamental insights into the hitherto unexplored
gas phase chemical dynamics of radical substitution reactions of mononuclear
main group hydrides under single collision conditions and highlights the distinct
reactivity of silicon compared to its isovalent carbon. This mechanism might be
also involved in the synthesis of cyanosilane
(SiH<sub>3</sub>CN) and methylsilane (CH<sub>3</sub>SiH<sub>3</sub>) probed in
the circumstellar envelope of the carbon star IRC+10216. </p>
|
Michael Lucas; Aaron M. Thomas; Tao Yang; Ralf I. Kaiser; Alexander M. Mebel; Diptarka Hait; Martin Head-Gordon
|
Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics; Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-08-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e57ee301c4297c7870b/original/bimolecular-reaction-dynamics-in-the-phenyl-silane-system-exploring-the-prototype-of-a-radical-substitution-mechanism.pdf
|
60c74a6a337d6c90d2e278c6
|
10.26434/chemrxiv.12200324.v1
|
A Deep Neural Network for the Rapid Prediction of X-ray Absorption Spectra
|
<p>X-ray spectroscopy delivers strong impact across the physical and biological sciences by providing end-users with highly-detailed information about the electronic and geometric structure of matter. To decode this information in challenging cases, e.g. <i>in operando</i> catalysts, batteries, and temporally-evolving systems, advanced theoretical calculations are necessary. The complexity and resource requirements often render these out of reach for end-users, and therefore data are often not interpreted exhaustively, leaving a wealth of valuable information unexploited. In this paper, we introduce supervised machine learning of X-ray absorption spectra, by developing a deep neural network (DNN) that is able to estimate Fe K-edge X-ray absorption near-edge structure spectra in less </p><p>than a second with no input beyond geometric information about the local environment of the absorption site. We predict peak positions with sub-eV accuracy and peak intensities with errors over an order of magnitude smaller than the spectral variations that the model is engineered to capture. The performance of the DNN is promising, as illustrated by its application to the structural refinement of iron(II)tris(bipyridine) and nitrosylmyoglobin, but also highlights areas for which future developments should focus.</p>
|
Conor Rankine; Marwah Madkhali; Thomas Penfold
|
Theory - Computational; Machine Learning; Artificial Intelligence
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-04-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a6a337d6c90d2e278c6/original/a-deep-neural-network-for-the-rapid-prediction-of-x-ray-absorption-spectra.pdf
|
64a27b1fba3e99daef6ec92a
|
10.26434/chemrxiv-2023-c9rv3
|
Rapid, solvent-minimized and sustainable access to various types of ferroelectric-fluid molecules by harnessing mechano-chemical technology
|
Recently, ferroelectric fluid, such as ferroelectric nematic liquid crystals (NFLCs) and ferroelectric smectic A LCs (SmAFLCs), has been of great fundamental and practical interest owing to its excellent polarization properties (e.g., dielectric permittivity, polarization, and nonlinear optical coefficient). To deeply understand the physical underpinning of such emergent ferroelectric phases and develop state-of-the-art device applications, effective preparation of various NF molecules is essential. Herein, to expand the NFLC molecular library, we implemented a mechanochemical (MC) technique for the production of LCs, demonstrating its high synthetic compatibility with NF/SmAFLCs. Chemical building blocks with high polarity can be bonded one by one through various ball-milling MC reactions, resulting in rapid access to NFLC molecules, a series of DIO, RM734, UUZU, and BIOTN, with high yield within 2.7–7 h for 4–8 steps. For a new DIO variant, in which a terminal alkyl chain was completely removed, for the first time, we discovered the direct phase transition from the isotropic liquid from the SmAF phase. Furthermore, the highly bistable polarization memory (~5.2 μC cm−2) in the SmAF phases was evaluated using the positive–up–negative–down (PUND) method.
|
Hiroya Nishikawa; Motonobu Kuwayama; Atsuko Nihonyanagi; Barun Dhara; Fumito Araoka
|
Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Liquid Crystals; Materials Processing; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a27b1fba3e99daef6ec92a/original/rapid-solvent-minimized-and-sustainable-access-to-various-types-of-ferroelectric-fluid-molecules-by-harnessing-mechano-chemical-technology.pdf
|
60c747294c8919715dad2c48
|
10.26434/chemrxiv.10062515.v2
|
Gasification Pathways and Reaction Mechanisms of Primary Alcohols in Supercritical Water
|
<div>
<p></p><p>Supercritical water gasification
is a promising waste-to-energy technology with the ability to convert aqueous
and/or heterogeneous organic feedstocks to high-value gaseous products.
Reaction behavior of complex molecules in supercritical water can be inferred
through knowledge of the reaction pathways of model compounds in supercritical
water. In this study methanol, ethanol, and isopropyl alcohol are gasified in a
continuous supercritical water reactor at temperatures between 500 and 560 °C,
and for residence times between 3 and 8 s. <i>In situ</i> Raman spectroscopy is
used to rapidly identify and quantify reaction products. The results suggest
the dominance of chain-branching, free radical reaction mechanisms that are
responsible for decomposing primary alcohols in the supercritical water
environment. The presence of a catalytic surface is proposed to be highly
significant for initiating radical reactions. Global reaction pathways are
proposed, and mechanisms for free radical reaction initiation, propagation, and
termination are discussed in light of these and previously published
experimental results.</p><br /><p></p></div>
|
Brian Pinkard; John Kramlich; Igor V. Novosselov
|
Analytical Chemistry - General
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-12-23
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747294c8919715dad2c48/original/gasification-pathways-and-reaction-mechanisms-of-primary-alcohols-in-supercritical-water.pdf
|
62ea148dd131b75e770ac068
|
10.26434/chemrxiv-2022-3dl97-v2
|
Precision synthesis and atomistic analysis of deep blue cubic quantum dots made via self-organization
|
As a crystal approaches a few nm in size, atoms become nonequivalent, bonds vibrate, and quantum effects emerge. To study quantum dots (QDs) with structural control common in molecular science, we need atomic precision synthesis and analysis. We describe here the synthesis of QDs of lead bromide perovskite via self-organization of a lead malate chelate complex and PbBr3– under ambient conditions. Millisecond and angstrom resolution electron microscopic analysis revealed the structure and the dynamic behavior of individual QDs—structurally uniform cubes made of 64 lead atoms, where eight malate molecules are located on the eight corners of the cubes, and oleylamonium cations lipophilize and stabilize the edges and faces. Lacking translational symmetry, the cube is to be viewed as a molecule rather than a nanocrystal. The QD exhibits quantitative photoluminescence and stable electroluminescence at 460 nm with a narrow half-maximum linewidth of 15 nm, reflecting minimum structural defects. This controlled synthesis and precise analysis demonstrate the potential of cinematic chemistry for the characterization of nanomaterials beyond the conventional limit.
|
Olivier J. G. L. Chevalier; Takayuki Nakamuro; Wataru Sato; Satoru Miyashita; Takayuki Chiba; Junji Kido; Rui Shang; Eiichi Nakamura
|
Materials Science; Nanoscience; Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2022-08-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ea148dd131b75e770ac068/original/precision-synthesis-and-atomistic-analysis-of-deep-blue-cubic-quantum-dots-made-via-self-organization.pdf
|
67728650fa469535b93e01e5
|
10.26434/chemrxiv-2024-265qk-v2
|
Insights into the Self-Assembly and Interaction of SARS-CoV-2 Fusion Peptides with Biomimetic Plasma Membrane Models
|
The COVID-19 pandemic, which was caused by SARS-CoV-2, initiated a global health crisis in 2019. SARS-CoV-2 is a single-stranded RNA virus encased in a lipid envelope that houses key structural proteins, including the Spike glycoprotein, which mediates viral entry into host cells. Within the Spike protein, the S2 subunit, and particularly its fusion domain, plays a critical role in merging viral and host membranes. Understanding the fusion domain interactions at the molecular level is important for advancing applications such as the development of novel antiviral therapies. This study investigates the self-assembly of SARS-CoV-2 S2 subunit fusion peptides (FPs) and their interaction with biomimetic plasma membrane (PM) models composed of physiological mixes of phospholipids, sphingomyelin, and cholesterol. Complementary techniques, including atomic force microscopy, neutron reflectometry and grazing incidence X-ray diffraction, provided detailed insights into lipid nano-mechanics and in-plane molecular structure. Our findings reveal several types of FP assemblies at the PM interface, including the formation of rigid fibres, spiral structures, and segregated domains. These behaviours are influenced by FP intrinsic features such as hydrophobicity and molecular structure, and the resultant interactions with lipid headgroups and tail regions. This work enhances our molecular-level understanding of FP-lipid interactions, shedding light on viral entry mechanisms. Furthermore, the ability of these peptides to self-assemble, modulated by the surrounding lipid environment, positions them as promising building blocks for innovative functional biomaterials.
|
Nisha Pawar; Andreas Santamaria ; Brigida Romano; Krishna C. Batchu; Valerie Laux; Eduardo Guzman; Nathan R. Zaccai; Alberto Alvarez-Fernandez; Armando Maestro
|
Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biochemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67728650fa469535b93e01e5/original/insights-into-the-self-assembly-and-interaction-of-sars-co-v-2-fusion-peptides-with-biomimetic-plasma-membrane-models.pdf
|
60c7576eee301c5f4ec7b533
|
10.26434/chemrxiv.14401301.v1
|
Revealing Internal Heavy Chalcogen Atom Effect on the Photophysics of Dibenzo[a,j]phenazine-Cored Donor–Acceptor–Donor Triad
|
<div><div><div><p>A new twisted donor–acceptor–donor (D–A–D) multi-photofunctional organic molecule comprising of phenoselenazine as the electron-donors (Ds) and dibenzo[a,j]phenazine (DBPHZ) as the electron-acceptor (A) has been developed. The developed selenium-incorporated D–A–D compound is featured with multi-color polymorphism, distinct mechanochromic luminescence, chemically-stimulated luminochromism, thermally-activated delayed fluorescence, and room- temperature phosphorescence. The internal heavy atom effect on the photophysical properties of the D–A–D system has been investigated through the comparison with the physicochemical properties of a previously developed sulfur analogue and a tellurium analogue.</p></div></div></div>
|
Shimpei Goto; Yuya Nitta; Nicolas Decarli; Leonardo Evaristo de Sousa; Patrycja Stachelek; Norimitsu Tohnai; Satoshi Minakata; Piotr de Silva; Przemyslaw Data; Youhei Takeda
|
Dyes and Chromophores; Optical Materials; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-04-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7576eee301c5f4ec7b533/original/revealing-internal-heavy-chalcogen-atom-effect-on-the-photophysics-of-dibenzo-a-j-phenazine-cored-donor-acceptor-donor-triad.pdf
|
60c745bd567dfe0616ec44ef
|
10.26434/chemrxiv.10247522.v1
|
Understanding the Influence of Manufacturing and Material Parameters on the Mechanical Properties of Polymer-Clay Composites: An Exploratory Statistical Analysis
|
<div>This paper analyses a set of previously obtained experimental results on various clay fillers added to high density polyethylene (HDPE). The composite material was compounded using an extrusion process and manufactured into tensile test samples by means of hot pressing. Various manufacturing parameters (number of extrusions, press time, sample cooling method), material (polymer grade, clay type, clay weight loading) and testing parameters (strain rate) were investigated to determine their influence on the mechanical properties of the composite system. <br /></div><div>Exploratory data analysis was first employed by graphically representing the data using scatter plots to identify any main characteristics, patterns or anomalies. The statistical analysis was used to quantify the effects of the ultimate tensile strength by first conducting a one way ANOVA analysis before developing a linear model for the response variable analysis. For the percentage elongation to failure, the observations was first grouped into three groups, Brittle, Intermediate or Ductile. A linear discriminant analysis was performed to classify the groups considering a training set of 80% randomly selected observations and testing on the remaining 20%. <br /></div><br />
|
Natasha Botha; Roelof Coetzer; helen inglis; johan labuschagne
|
Composites; Materials Processing
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-11-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745bd567dfe0616ec44ef/original/understanding-the-influence-of-manufacturing-and-material-parameters-on-the-mechanical-properties-of-polymer-clay-composites-an-exploratory-statistical-analysis.pdf
|
60c755640f50db4cd3397ed6
|
10.26434/chemrxiv.14083196.v1
|
TMtopo Dataset — Quantum Geometries and Density Topology for 1.1k Transition Metal Complexes
|
In this work, we report the TMtopo data set containing optimized geometries, quantum calculated properties, and quantum topological descriptors for 1110 first row TM complexes. Properties were computed at the TPSSh/Def2-TZVP level of theory and the quantum topological descriptors were collected under the framework of the Quantum Theory of Atoms in Molecules (QTAIM), including a systematic topological survey of the Laplacian of the electron density, ∇<sup>2</sup>ρ(r). This survey yielded novel insights on the proliferation of inner Valence Shell Charge Concentrations (iVSCCs, local minima of ∇<sup>2</sup>ρ(r)) in the metal center, suggesting that their number is determinant for the stabilization of the metal center in a more intense manner than their arrangement opposing each of the metal’s ligands (<i>Inorg. Chem.</i> 2016, <b>55</b>, 3653). Pairwise representation of the collected properties revealed overall low correlation, although some structure could be perceived in the data (specially when considering the topological features of ∇ 2 ρ(r)). This suggests that the TMtopo data set could be usefully exploited in the data-driven discovery of new TM complexes with interesting properties for applications in as catalysis, opto-electronics and sustainable energy production and storage.
|
Filipe Teixeira; Edgar Silva-Santos; M. Natália D. S. Cordeiro
|
Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-25
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755640f50db4cd3397ed6/original/t-mtopo-dataset-quantum-geometries-and-density-topology-for-1-1k-transition-metal-complexes.pdf
|
62de2e203787f10c46c5458c
|
10.26434/chemrxiv-2022-p7c9r
|
Spin Hyperpolarization in Modern Magnetic Resonance
|
Magnetic resonance techniques are successfully utilized in a broad range of scientific disciplines and in a number of practical applications, with medical MRI being the most widely-known example. Currently, both fundamental and applied magnetic resonance are enjoying a major boost owing to the dramatic signal enhancement provided by the rapidly-developing field of spin hyperpolarization. Such techniques are able to enhance signal intensities in magnetic resonance by several orders of magnitude, and thus to largely overcome its major disadvantage of relatively low sensitivity compared to other analytical techniques. This provides new impetus for existing applications, and, even more importantly, this opens the gates to numerous novel and exciting possibilities in the broad fields of fundamental and applied magnetic resonance. There are many different techniques that fall under the umbrella term “hyperpolarization”. Existing reviews cover the various subfields, but they are mostly addressed separately, and are seldom perceived as integral parts of the same field. In this review we attempt to unify the many methods that are used to hyperpolarize nuclear spins into one picture. Specifically, before delving into the individual techniques, we provide a detailed analysis of the underlying principles of spin hyperpolarization. We attempt to uncover and classify the origins of hyperpolarization; to establish its sources and the specific mechanisms that enable the flow of polarization from a source to the target nuclear spins. After outlining the inner workings of hyperpolarization, we give a more detailed analysis of individual hyperpolarization techniques: the mechanisms by which they work, fundamental and technical requirements, characteristic applications, unresolved issues and possible future directions. While a substantial progress has been achieved in the field of spin hyperpolarization in recent years, the continuing growth of activity indicates that this is just the beginning. It is unlikely that fundamentally new sources of hyperpolarization will be uncovered in the near future, but we expect the field to flourish as new ways to improve and utilize current hyperpolarization techniques are identified and implemented. There is great scope for cross-fertilization between known methods, and developments in one area (e.g., prolonging polarization lifetimes, or creating more efficient excitation-detection schemes) can have a very broad impact across the entire field of hyperpolarization. We hope this review will facilitate this process, since advances in hyperpolarization will help to overcome existing challenges in magnetic resonance and enable novel applications.
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James Eills ; Dmitry Budker; Silvia Cavagnero; Eduard Y. Chekmenev; Stuart J. Elliott; Sami Jannin; Anne Lesage; Jörg Matysik; Thomas Meersmann; Thomas Prisner; Jeffrey A. Reimer; Hanming Yang; Igor V. Koptyug
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Analytical Chemistry; Spectroscopy (Anal. Chem.)
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CC BY NC 4.0
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CHEMRXIV
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2022-08-02
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62de2e203787f10c46c5458c/original/spin-hyperpolarization-in-modern-magnetic-resonance.pdf
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60c7552a567dfe7a78ec61f8
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10.26434/chemrxiv.13580942.v2
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Silica-supported PdGa Nanoparticles: Metal Synergy for Highly Active and Selective CO2-to-CH3OH Hydrogenation
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A precise synthesis of small (<2 nm) supported palladium-gallium alloyed nanoparticles on Ga<sup>III </sup>sites dispersed on silica (PdGa@SiO<sub>2</sub>) is reported. This material, prepared via a Surface Organometallic Chemistry (SOMC) approach, is highly active and selective in hydrogenation of CO<sub>2</sub> to methanol.
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Scott Docherty; Nat Phongprueksathat; Erwin Lam; Gina Noh; Olga V. Safonova; Atsushi Urakawa; Christophe Copéret
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Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2021-02-11
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7552a567dfe7a78ec61f8/original/silica-supported-pd-ga-nanoparticles-metal-synergy-for-highly-active-and-selective-co2-to-ch3oh-hydrogenation.pdf
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60c741234c89197869ad223f
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10.26434/chemrxiv.7228940.v4
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Bayesian Optimization for Conformer Generation
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<p>Generating low-energy molecular conformers is a key task for many areas of computational chemistry, molecular modeling and cheminformatics. Most current conformer generation methods primarily focus on generating geometrically diverse conformers rather than finding the most probable or energetically lowest minima. Here, we present a new stochastic search method called the Bayesian</p><p>Optimization Algorithm (BOA) for finding the lowest energy conformation of a given molecule. We compare BOA with uniform random search, and systematic search as implemented in Confab, to determine which method finds the lowest energy. Energetic difference, root-mean-square deviation (RMSD), and torsion fingerprint deviation (TFD) are used to quantify the performance of the conformer search algorithms. In general, we find BOA requires far fewer evaluations than systematic or uniform random search to find low-energy minima. For molecules with four or more rotatable bonds, Confab typically evaluates 10<sup>4</sup> (median) conformers in its search, while BOA only requires 10<sup>2</sup> energy evaluations to find top candidates. Despite using evaluating fewer conformers, 20 − 40% of the time BOA finds lower-energy conformations than a systematic Confab search for molecules with four or more rotatable bonds.</p>
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Lucian Chan; Geoffrey Hutchison; Garrett Morris
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Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
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CC BY 4.0
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CHEMRXIV
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2019-02-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741234c89197869ad223f/original/bayesian-optimization-for-conformer-generation.pdf
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60c73eed702a9bd3f9189e68
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10.26434/chemrxiv.7184945.v1
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Ab Initio Thermodynamics of Iridium Surface Oxidation and Oxygen Evolution Reaction
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<p>Iridium-based materials
are considered as state-of-the-art electrocatalysts for oxygen evolution
reaction (OER), however, their stability and catalytic activity greatly depend on
surface-state changes induced by electrochemical cycling. To better understand
the behavior of the low-index Ir surfaces in an electrochemical environment, we
perform a systematic thermodynamic analysis by means of the density functional
theory (DFT) calculations. Based on computed surface energies of the Ir(111),
(110) and (100) facets as a function of applied electrode potential and
coverage of adsorbed water species we determine stability maps and predict
equilibrium shapes of Ir nanoparticles. Our calculations also show that
metastable oxide precursors formed at the initial stages of Ir surface
oxidation are responsible for enhanced catalytic activity towards OER as compared
to metal surfaces covered by oxygen adsorbates and thick-oxide films. Such enhancement
occurs not only due to the modified thermodynamic stability of OER intermediates,
but also because thin-oxide layers may display the more energetically favorable
I2M (interaction of two M-O units) rather than WNA (water nucleophilic
attack) OER mechanism.</p><br />
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Konstantin Klyukin; Alexandra Zagalskaya; Vitaly Alexandrov
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Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis; Electrochemistry - Mechanisms, Theory & Study; Surface
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CC BY NC ND 4.0
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CHEMRXIV
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2018-10-10
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73eed702a9bd3f9189e68/original/ab-initio-thermodynamics-of-iridium-surface-oxidation-and-oxygen-evolution-reaction.pdf
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65e3052a66c138172906c76a
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10.26434/chemrxiv-2024-05g0b
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Cluster Analysis as a Tool for Quantifying Structure-Transport Properties in Simulations of Superconcentrated Electrolyte
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Using molecular dynamics simulations and graph-theory-based cluster analysis, we investigate the structure-transport properties of typical water-in-salt electrolytes. We demonstrate that ions exhibit distinct dynamics across different ionic clusters—namely, solvent-separated ion pairs (SSIPs), contact ion pairs (CIPs), and aggregates (AGGs). We assess the average proportions of various ionic species and their lifetimes. Our method reveals a dynamic decoupling of ion kinetics, with each species independently contributing to the overall molecular motion. This is evidenced by the fact that the total velocity autocorrelation function (VACF) and power spectrum can be expressed as a weighted sum of independent functions for each species. The experimental data on the ionic conductivity of the studied LiTFSI electrolytes align well with our theoretical predictions at various concentrations, based on the proportions and diffusion coefficients of free ions derived from our analysis. The insights gained into the solvation structures and dynamics of different ionic species enable us to elucidate the physical mechanisms driving ion transport in such superconcentrated electrolytes, providing a comprehensive framework for the future design and optimization of electrolytes.
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Sheng Bi; Mathieu Salanne
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Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties
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CC BY NC ND 4.0
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CHEMRXIV
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2024-03-04
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e3052a66c138172906c76a/original/cluster-analysis-as-a-tool-for-quantifying-structure-transport-properties-in-simulations-of-superconcentrated-electrolyte.pdf
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60c74ab3337d6c5b8de27960
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10.26434/chemrxiv.12249755.v1
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On the Accurate Description of Photoionization Dynamical Parameters
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Calculation of dynamical parameters for photoionization requires an accurate description<br />of both initial and final states of the system, as well as of the outgoing electron.<br />We here show, that using a linear combination of atomic orbitals (LCAO) B-spline density<br />functional (DFT) method to describe the outgoing electron, in combination with<br />correlated equation-of-motion coupled cluster singles and double (EOM-CCSD) Dyson<br />orbitals, gives good agreement with experiment and outperforms other simpler approaches,<br />like plane and Coulomb waves, used to describe the photoelectron. Results<br />are presented for cross sections, angular distributions and dichroic parameters in chiral<br />molecules, as well as for photoionization from excited states. We also present a comparison<br />with the results obtained using Hartree-Fock (HF) and density-functional theory<br />molecular orbitals selected according to Koopmans’ theorem for the bound states.
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Torsha Moitra; Aurora Ponzi; Henrik Koch; Sonia Coriani; Piero Decleva
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Theory - Computational
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CC BY NC ND 4.0
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CHEMRXIV
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2020-05-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ab3337d6c5b8de27960/original/on-the-accurate-description-of-photoionization-dynamical-parameters.pdf
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61c19ee67f367e034f5adb11
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10.26434/chemrxiv-2021-jkhzw-v2
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Integrating Synthetic Accessibility with AI-based Generative Drug Design
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Generative models are frequently used for de novo design in drug discovery projects to propose new molecules. However, the question of whether or not the generated molecules can be synthesized is not systematically taken into account during generation, even though being able to synthesize the generated molecules is a fundamental requirement for such methods to be useful in practice. Methods have been developed to estimate molecule synthesizability, but, so far, there is no consensus on whether or not a molecule is synthesizable. In this paper we introduce the Retro-Score (RScore), which computes a synthetic feasibility score of molecules by performing a full retrosynthetic analysis through our data-driven synthetic planning software Spaya, and its dedicated API: Spaya-API (https://spaya.ai). After a comparison of RScore with other synthetic scores from the literature, we describe a pipeline to generate molecules that validate a list of targets while still being easy to synthesize. We further this idea by performing experiments comparing molecular generator outputs across a range of constraints and conditions. We show that the RScore can be learned by a Neural Network, which leads to a new score: RSPred. We demonstrate that using the RScore or RSPred as a constraint during molecular generation enables to obtain more synthesizable solutions, with higher diversity. The open-source Python code containing all the scores and the experiments can be found on https://github.com/iktos/generation-under-synthetic- constraint.
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Maud Parrot; Hamza Tajmouati; Vinicius Barros Ribeiro da Silva; Brian Ross Atwood; Robin Fourcade; Yann Gasthon-Mathé; Nicolas Do Huu; Quentin Perron
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Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Machine Learning; Artificial Intelligence
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CC BY NC ND 4.0
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CHEMRXIV
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2021-12-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c19ee67f367e034f5adb11/original/integrating-synthetic-accessibility-with-ai-based-generative-drug-design.pdf
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