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60c73e95702a9b0d05189d94
|
10.26434/chemrxiv.6462002.v2
|
A Priori Bond-Valence and Bond-Length Calculations in Rock-Forming Minerals
|
<i>A priori </i>bond-valences and bond-lengths are calculated for a series of rock-forming minerals. Comparison of <i>a priori </i>and observed bond-lengths allows structural strain to be assessed for those minerals.
|
Olivier Charles Gagné; Patrick H.J. Mercier; Frank Christopher Hawthorne
|
Bonding; Minerals; Solid State Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-07-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e95702a9b0d05189d94/original/a-priori-bond-valence-and-bond-length-calculations-in-rock-forming-minerals.pdf
|
63a1e12aa53ea66f0851f0fa
|
10.26434/chemrxiv-2022-q1hf6-v2
|
Minimizing Product Inhibition in DNA Self-Replication: Insights for Prebiotic Replication from the Role of the Enzyme in Lesion-Induced DNA Amplification
|
Self-replication of nucleic acids in the absence of enzymes such as polymerases or ligases represents an important and poorly understood step in the origin of life. In fact, the self-replication of nucleic acids remains strongly hindered by product inhibition, even when enzymes are present. Studying one of the few successful examples of enzymatic DNA self-replication based on a simple ligation chain reaction can shed light on how this fundamental process may have originally evolved. Previously, our group reported lesion-induced DNA amplification (LIDA), which is an isothermal ligase chain reaction. It was proposed that the lesion, a destabilizing abasic group, played an important role in reducing product inhibition. However, using abasic groups in non-enzymatic ligation cycles did not yield appreciable amplification. In order to identify the unknown factors that overcome product inhibition in LIDA, we have performed a detailed kinetic and thermodynamic analysis of the process, employing isothermal titration calorimetry (ITC) and global fitting of PAGE fluorescence data to characterize the individual steps of the amplification process. We found that in the absence of an enzyme, the ligated product binds four to five orders of magnitude more tightly to the template than to the shorter unligated strands of the intermediate complex. In the presence of T4 DNA ligase, this stability gap was reduced by two orders of magnitude, such that the intermediate and product complexes were roughly equal in stability. Thus, the ligase helps overcome product inhibition by reducing the affinity difference between the DNA product duplex and the intermediate complex. Furthermore, kinetic simulations showed that the stability of the intermediate complex, as well as the rate constant of ligation, significantly impacts the rate of self-replication, suggesting that catalysts that stabilize the intermediate complex might be a route to efficient nonenzymatic replication.
|
Hansol Park; Shyam Parshotam; Sarah Hales; Anthony Mittermaier; Julianne Gibbs
|
Biological and Medicinal Chemistry; Biochemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a1e12aa53ea66f0851f0fa/original/minimizing-product-inhibition-in-dna-self-replication-insights-for-prebiotic-replication-from-the-role-of-the-enzyme-in-lesion-induced-dna-amplification.pdf
|
6671ac1201103d79c580a465
|
10.26434/chemrxiv-2024-lp9rw
|
Carbon-Resource Recovery from Vinyl Polymers of Cyclic Ketene Acetal Esters Using High-Temperature Water
|
Vinyl polymer prepared from 2-methylene-4H-benzo[d][1,3]dioxin-4-one (MBDO), a cyclic ketene acetal ester, is a chemically recyclable polymer that is hydrolyzed to salicylic acid (SA) and acetic acid (AA). Despite this potential, the polymer, poly-MBDO required a strong acid or base in organic solvent for the hydrolysis. In this study, we report the quantitative conversion of poly-MBDO to phenol by treatment in high-temperature water. Hydrolysis of poly-MBDO afforded SA, which underwent rapid decarboxylation to phenol. For example, poly-MBDO quantitatively afforded phenol upon heating in water at 300 °C for 5 min and freeze-drying. Although the hydrolysis of the main chain was incomplete, the products were volatile and removed by drying the reaction mixture, leaving the residue of pure phenol. Since SA is industrially synthesized from phenol and CO2, the synthesis of poly-MBDO from phenol is in principle possible. The quantitative conversion of poly-MBDO to phenol can also be considered as upcycling, since phenol is a raw material for various fine chemicals.
|
Yasuhiro Kohsaka; Akane Kazama; Keigo Matsuo; Shigeru Deguchi; Mitsumasa Osada
|
Polymer Science; Chemical Engineering and Industrial Chemistry; Organic Polymers; Reaction Engineering
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-06-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6671ac1201103d79c580a465/original/carbon-resource-recovery-from-vinyl-polymers-of-cyclic-ketene-acetal-esters-using-high-temperature-water.pdf
|
65d39e0f9138d2316178d158
|
10.26434/chemrxiv-2024-d21q1
|
Biomass Electrocatalysts: Exploiting Haemoglobin-derived Fe Sites Coordinated with S, N-enriched Carbon for Efficient Oxygen Electro-reduction
|
Biomass resources offer a diverse array of low-cost feedstocks for the manufacture electrocatalysts for the energy sector. In this study, haemoglobin (Hb), lignin, tannic acid and urea were used to develop FeSN/C electrocatalysts comprising iron highly dispersed on S,N-codoped carbon for the oxygen reduction reaction (ORR). By pyrolyzing precursor mixtures containing Hb, lignin, tannic acid and urea in appropriate mass ratios, S,N-codoped carbons with highly dispersed Fe sites were obtained with ORR performance superior to Pt/C. The developed FeSN/C electrocatalyst exhibited an ORR onset potential of 0.98 V vs. RHE in 0.1 M KOH, a half-wave potential (E1/2) of 0.87 V and a low Tafel slope of 54 mV/dec. Notably, the electrocatalyst selectively catalysed the 4-electron ORR pathway and exhibited a high methanol tolerance. This work encourages the design of biomass-derived electrocatalysts for oxygen reduction reaction, in particular showing that haemoglobin in bovine blood is a suitable for use an iron source when making Fe-N-C electrocatalysts.
|
Nagaraju Shilpa; Jun-Xi Wu; Geoffrey Waterhouse; Bicheng Zhu; Jadranka Travas-Sejdic; David Williams
|
Catalysis; Nanoscience; Electrocatalysis; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-02-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d39e0f9138d2316178d158/original/biomass-electrocatalysts-exploiting-haemoglobin-derived-fe-sites-coordinated-with-s-n-enriched-carbon-for-efficient-oxygen-electro-reduction.pdf
|
60c73ef6567dfe37ffec38f0
|
10.26434/chemrxiv.7195370.v1
|
On the Role of Valence and Semi-Core Electron Correlation on Spin-Gaps in Fe(II)-Porphyrins
|
The role of valence and semi-core correlation in differentially stabilizing the intermediate spin-state of Fe(II)-porphyrins is analyzed. CASSCF treatment of the valence correlation, with a (32,34) active space containing metal 3d, 4d orbitals<br />and the entire π system of the porphyrin, is necessary to stabilize the intermediate spin-state for this system. Semi-core correlation provides a quantitatively significant (~1.5 kcal/mol) but less important correction. Accounting for both types of correlation enlarges the (<sup>3</sup>E<sub>g</sub>−<sup>5</sup>A<sub>1g</sub>) spin-gap to −5kcal/mol.<br />
|
Giovanni Li Manni; Daniel Kats; David Tew; Ali Alavi
|
Computational Chemistry and Modeling; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-10-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ef6567dfe37ffec38f0/original/on-the-role-of-valence-and-semi-core-electron-correlation-on-spin-gaps-in-fe-ii-porphyrins.pdf
|
65755338cf8b3c3cd739cf04
|
10.26434/chemrxiv-2023-85ww5
|
Enumeration, Nomenclature and Stability Rules of Carbon Nanobelts
|
With the recent breakthroughs and advances in synthetic chemistry, carbon nanobelts (CNBs) have become an emerging hot spot in chemistry and materials science. Owing to their unique molecular structures, CNBs have intriguing properties with applications in synthetic materials, host–guest chemistry, optoelectronics, and so on. Although a considerable number of CNBs with diverse forms have been synthesized to date, no systematic nomenclature is available yet for this important family of macrocycles. Moreover, little is known about the detailed isomerism of CNBs, which, in fact, exhibits greater complexity than that of carbon nanotubes. The copious variety of CNB isomers, along with the underlying structure–property relationships, bears fundamental relevance to the ongoing design and synthesis of novel nanobelts. In this paper, we propose an elegant approach to systematically enumerate, classify, and name all possible isomers of CNBs. Besides the simplest, standard CNBs defined by chiral indices (n, m), the nonstandard CNBs (n, m, l) involves an additional winding index l. Based on extensive quantum chemical calculations, we present a comprehensive study of the relative isomer stability of CNBs containing up to 30 rings. A simple Hückel-based model with a high predictive power reveals that the relative stability of standard CNBs is governed by the π stabilization and the strain destabilization induced by cylindrical carbon framework, and the former effect prevails the latter. For nonstandard CNBs, a third stability factor, the H...H repulsion in the benzo[c]phenanthrene-like motifs, is shown to be also important and can be incorporated into the simple quantitative model. In general, lower-energy CNB isomers have a larger HOMO–LUMO gap, suggesting that their thermodynamic stability coincides with kinetic stability. The determined most stable CNB isomers can be considered as the optimal targets for future synthesis. These results lay an initial foundation and provide a useful theoretical tool for further research on CNBs and related analogs.
|
Yang Wang; Yi Zhou; Ke Du
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65755338cf8b3c3cd739cf04/original/enumeration-nomenclature-and-stability-rules-of-carbon-nanobelts.pdf
|
60c742b2337d6c779ae26ad1
|
10.26434/chemrxiv.8490149.v1
|
Identifying Physico-Chemical Laws from the Robotically Collected Data
|
<p>A mixed-integer nonlinear programming (MINLP) formulation for symbolic regression was proposed to identify physical models from noisy experimental data. The formulation was tested using numerical models and was found to be more efficient than the previous literature example with respect to the number of predictor variables and training data points. The globally optimal search was extended to identify physical models and to cope with noise in the experimental data predictor variable. The methodology was coupled with the collection of experimental data in an automated fashion, and was proven to be successful in identifying the correct physical models describing the relationship between the shear stress and shear rate for both Newtonian and non-Newtonian fluids, and simple kinetic laws of reactions. Future work will focus on addressing the limitations of the formulation presented in this work, by extending it to be able to address larger complex physical models.</p><p><br /></p>
|
Liwei Cao; Danilo Russo; Vassilios S. Vassiliadis; Alexei Lapkin
|
Computational Chemistry and Modeling; Machine Learning; Robotics
|
CC BY 4.0
|
CHEMRXIV
|
2019-07-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b2337d6c779ae26ad1/original/identifying-physico-chemical-laws-from-the-robotically-collected-data.pdf
|
60c755feee301c3fddc7b27d
|
10.26434/chemrxiv.14170508.v1
|
Hydroxychloroquine Immediate Release Tablets: Formulation and Evaluation of a Solid Dosage Form
|
Hydroxychloroquine (HCQ) is a quinoline derivate used for the treatment of malaria and rheumatoid disorders. During early phases of the SARS-CoV2 (COVID-19) pandemic, preliminary and later not substantiated reports suggested that HCQ might benefit COVID-19 patients. This had sparked a worldwide and rapidly rising demand for HCQ drug products. Consequently, patients with pre-existing rheumatic diseases in Switzerland were confronted with an acute drug shortage.<br /><br />We have therefore designed, produced and characterized a generic HCQ drug formulation. The proposed HCQ formulation can be manufactured by using a minimal number of operation steps (mixing, wet granulation, sieving, blending, compression) and readily available pharmaceutical excipients.<br /><br />HCQ tablets were manufactured by granulation of the active pharmaceutical ingredient (API), blending with the external phase and compaction using a non instrumented single punch tablet press. Analytics and identification of the API was performed by a combination of NMR, ESI-MS, FTIR and HPLC. HCQ tablets met the quality criteria for an immediate release HCQ dosage form.<br /><br /><div>We hope that free access to non-proprietary protocols covering analytical procedures, formulation design, and manufacturing instructions for HCQ tablets will help to bridge existing and future supply chain gaps.</div><div><br /></div><div><br /></div>
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Tomaz Einfalt; Pascal Detampel; Daniel Häussinger; Jens Casper; Christoph R. Meier; Maxim Puchkov; Jörg Huwyler
|
Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755feee301c3fddc7b27d/original/hydroxychloroquine-immediate-release-tablets-formulation-and-evaluation-of-a-solid-dosage-form.pdf
|
61c0c93cf52bc4db7fc7ad73
|
10.26434/chemrxiv-2021-796ql
|
HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multi-Scale Simulations of Soft Matter
|
We present HylleraasMD (HyMD), a comprehensive implementation of the recently proposed Hamiltonian formulation of hybrid particle-field molecular dynamics (hPF). The methodology is based on tunable, grid-independent length-scale of coarse graining, obtained by filtering particle densities in reciprocal space. This enables systematic convergence of energies and forces by grid refinement, also eliminating non-physical force aliasing. Separating the time integration of fast modes associated with internal molecular motion, from slow modes associated with their density fields, we implement the first time-reversible hPF simulations. HyMD comprises the optional use of explicit electrostatics, which, in this formalism, corresponds to the long-range potential in Particle-Mesh Ewald. We demonstrate the ability of HhPF to perform simulations in the microcanonical and canonical ensembles with a series of test cases, comprising lipid bilayers and vesicles, surfactant micelles, and polypeptide
chains, comparing our results to established literature. An on-the-fly increase of the characteristic coarse graining length significantly speeds up dynamics, accelerating self-diffusion and leading to expedited aggregation. Exploiting this acceleration, we find that the time scales involved in the self-assembly of polymeric structures can lie in the tens to hundreds of picoseconds instead of the multi microsecond regime observed with comparable coarse-grained models.
|
Morten Ledum; Samiran Sen; Xinmeng Li; Manuel Carrer; Yu Feng; Michele Cascella; Sigbjørn Løland Bore
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Self-Assembly
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c0c93cf52bc4db7fc7ad73/original/hylleraas-md-a-domain-decomposition-based-hybrid-particle-field-software-for-multi-scale-simulations-of-soft-matter.pdf
|
60c7572e567dfe70f9ec661e
|
10.26434/chemrxiv.14315474.v2
|
Melt Electrowriting of Poly(vinylidene Fluoride-Co-Trifluoroethylene)
|
Poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-co-TrFE)) is an electroactive polymer with growing interest for applications in biomedical materials and flexible electronics. In this study, a solvent-free additive manufacturing technique called melt electrowriting (MEW) has been utilized to fabricate well-defined microperiodic structures of P(VDF-co-TrFE). Melt electrowriting of the highly viscous polymer melts was initiated using a heated collector at temperatures above 120 °C and required remarkably slow collector speeds below 100 mm/min. This contribution shows electrohydrodynamic processing of fibers with micrometer resolution into defined structures with an important electroactive polymer.<br />
|
Juliane Kade; Biranche Tandon; Jan Weichhold; Dario Pisignano; Luana Persano; Robert Luxenhofer; Paul D Dalton
|
Fibers; Materials Processing; Multilayers; Fluoropolymers; Polymer scaffolds; Fluid Mechanics; Process Control
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7572e567dfe70f9ec661e/original/melt-electrowriting-of-poly-vinylidene-fluoride-co-trifluoroethylene.pdf
|
63bc39023af973d11a61811b
|
10.26434/chemrxiv-2022-4lc1p-v2
|
Low dimensional metal-organic magnets as a route towards the S=2 Haldane phase
|
Metal-organic magnets (MOMs), modular magnetic materials where metal atoms are connected by organic linkers, are promising candidates for next-generation quantum technologies. MOMs readily form low-dimensional structures, and so are ideal systems to realise physical examples of key quantum models, including the Haldane phase, where a topological excitation gap occurs in integer-spin antiferromagnetic (AFM) chains. Thus far the Haldane phase has only been identified for S = 1, with S ≥ 2 still unrealised because the larger spin imposes more stringent requirements on the magnetic interactions. Here, we report the structure and magnetic properties of CrCl2(pym) (pym=pyrimidine), a new quasi-1D S = 2 AFM MOM. We show, using X-ray and neutron diffraction, bulk property measurements, density-functional theory calculations and inelastic neutron spectroscopy (INS) that CrCl2(pym) consists of AFM CrCl2 spin chains (J1 = −1.13(4) meV) which are weakly ferromagnetically coupled through bridging pym (J2 = 0.10(2) meV), with easy-axis anisotropy (D = −0.11(1) meV). We find that although small compared to J1, these additional interactions are sufficient to pre- vent observation of the Haldane phase in this material. Nevertheless, the proximity to the Haldane phase together with the modularity of MOMs suggests that layered Cr(II) MOMs are a promising family to search for the elusive S = 2 Haldane phase.
|
Jem Pitcairn; Andrea Iliceto ; Laura Cañadillas-Delgado ; Oscar Fabelo; Cheng Liu; Christian Balz; Andreas Weilhard; Stephen Argent; Andrew Morris; Matthew Cliffe
|
Inorganic Chemistry; Coordination Chemistry (Inorg.); Magnetism; Solid State Chemistry; Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-01-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63bc39023af973d11a61811b/original/low-dimensional-metal-organic-magnets-as-a-route-towards-the-s-2-haldane-phase.pdf
|
6423420791074bccd07210bb
|
10.26434/chemrxiv-2023-2q6df
|
Direct Alkylative Reductive Amination using 1-Allylsilatrane
|
Homoallylic amines prepared via addition of allylsilanes often require preformed imine substrates, metal catalysts, fluoride activators, or use of protected amines. In this metal-free, air- and water-tolerant procedure, aromatic aldehyde and aniline substrates undergo direct alkylative reductive amination using easily accessible 1-allylsilatrane.
|
David Raveenthrarajan; Thershan Satkunarajah; Brooklyn Kostiuk; Marc Adler
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY 4.0
|
CHEMRXIV
|
2023-03-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6423420791074bccd07210bb/original/direct-alkylative-reductive-amination-using-1-allylsilatrane.pdf
|
64259d6591074bccd088fe2e
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10.26434/chemrxiv-2022-3tfg6-v5
|
Reaching selective fluorescence phosphate detection over pyrophosphate with a cerium-based chemosensor in aqueous media
|
Phosphate ions are important molecules used in critical activities, such as those in agriculture or medicine. However, because of their chemical makeup, sensing them using a chemosensor is difficult. In the past, chemists attempted to solve this issue by creating sophisticated chemical structures as receptors, but with mixed results. Here, using just chemicals that are readily accessible on the market, we establish a straightforward metal extrusion-based fluorescence indicator displacement assay (MEFID) for phosphate detection. Using a fluorophore and cerium ammonium nitrate (CAN), phosphate ions in aqueous solutions are probed. With an average concentration higher than copper and being the most prevalent rare earth on the planet (48 p.p.m.), cerium is an intriguing metal for the identification of analytes. We demonstrate, that the inorganic complex detects phosphate ions in low micromolar concentrations, either spectrophotometrically, by 31P NMR, or with the naked- eye, with high selectivity over common competing anions, including halides, acetate, carbonate, and, remarkably, pyrophosphate. In addition, perturbation of the sensor with phosphorylated molecules such as ATP is minimal. The development of receptors that endures a precipitation offers systems for the purification of surface waters as presented by the probing of environmental samples.
|
Thibaud Rossel; Bruno Therrien; Kyrian Engel; Maya Mischler; Gabriel Di Lullo; Valentin Piccard
|
Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Environmental Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64259d6591074bccd088fe2e/original/reaching-selective-fluorescence-phosphate-detection-over-pyrophosphate-with-a-cerium-based-chemosensor-in-aqueous-media.pdf
|
670fd42b51558a15ef42e50f
|
10.26434/chemrxiv-2024-5bjnw
|
Unraveling the Meaning of Effective Uptake Coefficients in Multiphase and Aerosol Chemistry
|
Reactions of gas phase molecules with surfaces play key roles in atmospheric and environmental chemistry. Reactive uptake coefficients (γ), the fraction of gas-surface collisions that yield a reaction, are used to quantify the kinetics in these heterogeneous and multiphase systems. Unlike rate coefficients for homogeneous gas or liquid phase reactions, uptake coefficients are emergent quantities that depend upon a multitude of underlying elementary steps. As such, uptake coefficients adopt complex scaling behavior with reactant concentrations and other physicochemical properties of the interface, making predictions of γ particularly challenging.
Typically, γgas is obtained by measuring the loss rate of a gas phase molecule above a liquid or solid surface relative to its collision frequency. By definition, γgas ≤ 1. Highly efficient reactions proceed at or near the gas-surface collision frequency and exhibit values of γgas near unity. Alternatively, heterogeneous kinetics are often measured using the consumption rate of a condensed phase reactant normalized to the gas-surface collision frequency, yielding instead an effective uptake coefficient (γeff). In many cases, γeff and γgas are not equal, yielding additional insights into the nature of the reaction. For example, substantial diffusive limitations in the condensed phase may inhibit reactivity, yielding γeff << γgas. In contrast, γeff > γgas in the presence of condensed phase secondary reactions, with values of γeff often exceeding 1 for the case of radical chain reactions.
In this account, we will discuss how measurements of γeff in aerosol reveal the origins of complex physical and chemical behavior in multiphase reactions that can be uniquely observed and understood through the lens of effective uptake coefficients. For example, the scaling of γeff with water vapor in aqueous systems, or shell thickness in core-shell aerosol, yields insight into relative transport and reaction timescales of gaseous oxidants, while the scaling of γeff with oxidant and trace gas concentrations provides a distinctive signature of the underlying competition between free radical propagation and termination mechanisms. Further, changes in γeff induced by careful selection of the molecular structure of the condensed-phase reactants help identify new reaction pathways and indirectly report on the reaction kinetics of short-lived species, including Criegee Intermediates. Through these examples we will show how proper experimental design and accurate measurements of an effective uptake coefficient can be used to interrogate complex multiphase reaction mechanisms.
|
Ryan Reynolds; Kevin Wilson
|
Physical Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Chemical Kinetics; Interfaces
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CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670fd42b51558a15ef42e50f/original/unraveling-the-meaning-of-effective-uptake-coefficients-in-multiphase-and-aerosol-chemistry.pdf
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60c74be9bb8c1a65ed3db305
|
10.26434/chemrxiv.12385967.v1
|
Transition Structures Between Unbound and Bound SARS-CoV-2 Spike Protein to Human ACE2: Potential Targets for Drug Design
|
The recent outbreak of COVID-19 caused by SARS-CoV-2 led to a race in finding a cure. Different drug targets were recognized, but in most cases the main target has been identified in the virus spike protein because it is crucial for the virus to gain entry into human cells. The virus spike protein undergoes large dynamic changes in order to bind to the entry point in human cells, which is a surface protein known as Angiotensin-Converting Enzyme 2 (ACE2). The spike – ACE2 interaction represents the major target for vaccines and antiviral drugs. Incidentally, all intermediate structures in the folding pathways could become potential drug targets. This study reports the simulation of the transition pathway of the spike protein and includes its animation that can help also non-experts to visually understand how the infection starts. The simulation of the spike protein's transition pathway has been done by using the NMSim software, which makes use of a three-step protocol including Coarse Grain, Normal Mode Analysis, and Elastic Network Model methods, providing realistic intermediates at a reasonable simulation time.
|
Nicola Zanna
|
Bioinformatics and Computational Biology
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CC BY NC 4.0
|
CHEMRXIV
|
2020-06-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74be9bb8c1a65ed3db305/original/transition-structures-between-unbound-and-bound-sars-co-v-2-spike-protein-to-human-ace2-potential-targets-for-drug-design.pdf
|
6238d4a8658bc0dd34b33eae
|
10.26434/chemrxiv-2022-x85xg
|
Effect of refinement and production technology on the molecular composition of edible cottonseed oils from a large industrial scale production
|
Unrefined, refined and refined-deodorized cottonseed oils from pressing or extraction technologies were screened using NMR and GC-MS. GC-MS of intact and derivatized oils allowed tentative annotation of ~100 compounds. These included fatty acids (FA), linoleic (51-57%), oleic (18-23%), palmitic (21-23%) and stearic acids (2-2.2%) in hydrolysed oils, and β-sitosterol (31-43%), free FA (7-34%), γ- and α-tocopherol (11-22%), and squalene (2-4%) in intact oils. NMR spectra of intact oils contained 90 resonances and were dominated by methylene (41%), methyl (14%), and methine (6.8%) protons of FA and triglycerides. Analysis of the molecular profiles revealed a dominating effect of the processing followed by the production technology. Oil refinement reduced undesirable free FA, diglycerides and gossypol, but increased hydrocarbons and aldehydes. The refined press oil contained higher levels of steroids and less free FA compared to refined extract oil. Thus, the study showed potentials of foodomics to evaluate the quality of edible oils.
|
Bekzod Khakimov; Yongxin Ye; Jaloliddin Khushvakov ; Akmal Boboev; Rano Akramova; Obidjon Yunusov; Dilbar Dalimova; Shahlo Turdikulova; Sharafitdin Mirzaakhmedov; Søren Engelsen
|
Agriculture and Food Chemistry; Food
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-03-22
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6238d4a8658bc0dd34b33eae/original/effect-of-refinement-and-production-technology-on-the-molecular-composition-of-edible-cottonseed-oils-from-a-large-industrial-scale-production.pdf
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6780f86881d2151a0292f1d2
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10.26434/chemrxiv-2025-d65jx
|
A portable and versatile rGO-Co₃O₄-Pt Nanocomposite-based Electrochemical Sensor for In Vitro and In Vivo Cardiac Stress Monitoring
|
Excessive reactive oxygen species (ROS) under pathophysiological conditions primarily initiate oxidative stress, which contributes to the development of atherosclerosis and other cardiovascular diseases. Hydrogen peroxide (H2O2) is a crucial oxidative stress biomarker due to its stability and significant role in signaling pathways linked to cellular damage. Hence, H₂O₂ detection is crucial for early disease diagnosis, understanding oxidative stress mechanisms, and therapeutic intervention, especially in cardiac health, where oxidative damage is significant. However, efficient, highly selective & sensitive, quick, and accurate H₂O₂ detection remains a challenge in the protracted battle against oxidative stress-related diseases. The study presents a fast, portable, low-cost, and versatile oxidative stress detection platform using a rGO-Co₃O₄-Pt nanocomposites electrochemical sensor platform, which can be remotely controlled. The sensors offer ultrasensitive, versatile cardiac stress monitoring, with H2O2 detection up to 2.50 µM, low LOD (0.16 µM) and LOQ (0.50 µM), with anti-interference capability and biocompatibility, indicating the possibility of real-sample analysis. Furthermore, we conducted studies on doxorubicin (DOX)-induced cardiotoxicity in vitro (HL-1 cell lines) and in vivo (adult C57BL/6J mice model). The study indicates that the rGO-Co₃O₄-Pt nanocomposite electrochemical sensor platform can efficiently and accurately detect diseases. This work provides direct experimental evidence of ROS detection and offers an efficient electronic platform that is significantly lighter, cheaper, and smaller than alternatives.
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Sima Singh; Stefania Melini; Ada Raucci; Arshid Numan; Mohammad Khalid; Rosaria Meli; Claudio Pirozzi; Stefano Cinti
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Analytical Chemistry; Electrochemical Analysis
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CC BY 4.0
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CHEMRXIV
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2025-01-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6780f86881d2151a0292f1d2/original/a-portable-and-versatile-r-go-co3o4-pt-nanocomposite-based-electrochemical-sensor-for-in-vitro-and-in-vivo-cardiac-stress-monitoring.pdf
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65c8d1af66c138172966ca30
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10.26434/chemrxiv-2024-7z779
|
pH Stimuli Responsive Dextran Gated Mesoporous Silica as a Viable Delivery Vehicle
|
Mesoporous materials hold immense potential due to their diverse applications (catalysis, separation, drug delivery, etc.) viability. To unlock this potential, controlling the transport of molecules within their nanochannels is crucial. This study explores a novel technique to manipulate pore properties by hetero-functionalizing mesoporous silica with carboxylic acid and propylamine groups, creating pH-responsive surfaces. The negatively charged surface at basic pH attracts and loads a cationic dye through electrostatic interactions. This cargo can be efficiently released by switching to acidic pH, reversing the surface charge. Furthermore, the system incorporates dextran as a "gatekeeper" for controlled release. The study demonstrates significant differences in release profiles between functionalized materials, highlighting the effectiveness of this approach. Notably, the functionalization method strategy using 1,4-dioxane and appropriate reaction timing enables the desired properties for the first time. This work paves the way for designing advanced mesoporous materials with tailored functionalities for various applications.
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Yusuf Olatunji WAIDI
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Materials Science; Nanoscience; Controlled-Release Systems; Nanofabrication; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
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2024-02-13
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c8d1af66c138172966ca30/original/p-h-stimuli-responsive-dextran-gated-mesoporous-silica-as-a-viable-delivery-vehicle.pdf
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669c6b1fc9c6a5c07a05b369
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10.26434/chemrxiv-2024-xbhb9
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Taming Tethered Nitreniums for Alkene Functionalization Reactions
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Here, we present the first examples of amino-trifluoroacetoxylations of alkenes using N-alkoxy carbamate tethers. The trifluoroacetate group can be conveniently removed from the product by treatment with a solution of NH3 in MeOH. Hypervalent iodine oxidants mediate this transformation, providing a “green” alternative to existing intramolecular aminohydroxylation protocols which use toxic metals such as osmium. In all cases examined, the reaction is regioselective and stereospecific, with the geometry of the starting alkene controlling the diastereomeric outcome. By analogy to prior art and
from our own observations, we posit that a transient nitrenium species serves as a key intermediate in this transformation.
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Shyam Sathyamoorthi; Raju Silver; Appasaheb Nirpal
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Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2024-07-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669c6b1fc9c6a5c07a05b369/original/taming-tethered-nitreniums-for-alkene-functionalization-reactions.pdf
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67640e19fa469535b915189e
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10.26434/chemrxiv-2024-4w3qp
|
Indoor Surface Emissions of Volatile Organic Compounds induced by Germicidal UV (222 & 254 nm) Illumination.
|
The application of germicidal ultraviolet (GUV) lamps has recently attracted increased attention as a measure to mitigate indoor disease transmission. Among the most commonly employed are traditional mercury lamps and krypton-chloride excimer lamps, which emit UV-C light with peak wavelengths of 254 nm (GUV254) and 222 nm (GUV222) respectively. This study investigates volatile organic compound (VOC) surface emissions induced by GUV254 and GUV222 lamps across various surface materials. Near surface proton-transfer-reaction time-of-flight mass spectrometer (PTR-TOF-MS) measurements revealed significantly increased surface emissions during GUV illumination, enhancing emissions with up to >300% for a single compound. In addition to compounds intrinsic to the illuminated surface, GUV light also increased surface off-gassing of externally applied compounds including limonene and 4-oxopentanal (4-OPA). The magnitude of the enhanced surface emissions was found to decrease with the GUV light pathlength resembling the expected decrease of the irradiance. Overall, greater surface emissions were observed for the GUV222 lamp compared to the GUV254 lamp. Conclusively, this study identifies UV-induced surface emissions as a significant contributor to indoor VOCs during GUV lamp application.
|
Sara Bjerre Sørensen; Kasper Kristensen
|
Earth, Space, and Environmental Chemistry; Environmental Science
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CC BY NC ND 4.0
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CHEMRXIV
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2024-12-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67640e19fa469535b915189e/original/indoor-surface-emissions-of-volatile-organic-compounds-induced-by-germicidal-uv-222-254-nm-illumination.pdf
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63b732671699ca39dae4ef75
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10.26434/chemrxiv-2023-9p1d9
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Alkylation of amines with allylic alcohols and deep eutectic solvents as metal-free and green catalyst
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A novel approach for the allylic alkylation of anilines, hydrazides and indole derivatives by the direct use of allylic alcohols is described under very mild conditions, such as room temperature and using sustainable deep eutectic solvents (DESs). The search of the optimum DES to be used in the reaction reveals that a simple mixture of choline chloride (ChCl) and lactic acid provides excellent results for a wide substrate scope and with high isolated yields. This methodology represents a great improvement compared to other procedures described in literature, for which high temperatures, stronger reaction conditions or metal catalysts are usually required. In some cases, this protocol affords to the first examples of trapping allylic carbocations with indole derivatives. All these features make this procedure an appealing and green alternative in comparison with other examples reported in literature on alkylation of amines by allylic alcohols. Preliminary mechanistic studies using unsymmetrically substituted alcohols support that the reaction should proceed by an SN1 pathway.Introduction.
|
Stephany Zárate-Roldán; M. Concepción Gimeno; Raquel P. Herrera
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Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-01-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b732671699ca39dae4ef75/original/alkylation-of-amines-with-allylic-alcohols-and-deep-eutectic-solvents-as-metal-free-and-green-catalyst.pdf
|
6793f5dc81d2151a02d59494
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10.26434/chemrxiv-2025-fvct3
|
Harnessing a Ketone-Accepting Pictet-Spenglerase for the Asymmetric Construction of 1,1-Disubstituted Tetrahydro-ß-Carboline Alkaloids
|
In light of the ubiquity of 1,1’-disubstituted tetrahydro-ß-carboline (THBC) motif in alkaloid natural products, developing asymmetric methodology for its preparation is highly valuable. Despite the immense progress towards achieving stereoselective Pictet-Spengler reaction with aldehydes, the analogous reaction with ketones is still underdeveloped. Exploiting KslB, a Pictet-Spenglerase from the biosynthesis of kitasetaline, we develop a general, diastereoselective, and protecting-group free method for the construction of densely functionalized THBCs with α-quaternary center by coupling tryptophan derivatives and α-keto acids. We determine the stereochemistry of kitasetalic acid, KslB’s physiological product and a key biosynthetic intermediate towards kitasetaline, and established that KslB’s selectivity is opposite to what is achieved chemically. Our investigations of KslB show its high activity (TTN>438,000), substrate promiscuity, and tolerance for high substrate concentrations (0.1M). Additionally, a TrpB-KslB cascade enables the construction of complex tricyclic products from simple indoles in one-pot. X-ray structural characterization of KslB sheds light on potential active site interactions to account for its stereoselectivity and ability to accept ketone substrates.
|
Ruiying Jiang; Nour Wasfy; Takahiro Mori; Megan Hoang; Ikuro Abe; Hans Renata
|
Organic Chemistry; Catalysis; Biocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-01-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793f5dc81d2151a02d59494/original/harnessing-a-ketone-accepting-pictet-spenglerase-for-the-asymmetric-construction-of-1-1-disubstituted-tetrahydro-carboline-alkaloids.pdf
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65115f5260c37f4f7669c560
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10.26434/chemrxiv-2023-dlkgl
|
Multi-objective Bayesian optimisation using q-Noisy Expected Hypervolume Improvement (qNEHVI) for Schotten-Baumann reaction
|
Amide bond formation is one of the most prevalent reactions in pharmaceutical industry, among which the Schotten-Baumann reaction has attracted attention as a potential green amide formation approach. However, the use of water in the reaction system often causes undesired hydrolysis and can generate a multiphase system. This makes the reaction space complex and challenging to find the optimal conditions. In this study, a Schotten-Baumann reaction was studied in continuous flow and was optimised with two objectives using a Bayesian optimisation algorithm based on the q-Noisy Expected Hypervolume Improvement (qNEHVI) acquisition function. The algorithm guided the experiment design over a range of electrophiles, equivalents, solvents and flow rates, and was able to identify the Pareto front of optimal solutions efficiently. Based on the optimisation results, reaction under flow and batch conditions were compared; undesired hydrolysis was suppressed successfully using the flow conditions. Finally, the relationship between solvent and flow rate was discussed to gain more insights into this reaction.
|
Jiyizhe Zhang; Naoto Sugisawa; Kobi Felton; Shinichiro Fuse; Alexei Lapkin
|
Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions
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CC BY 4.0
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CHEMRXIV
|
2023-09-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65115f5260c37f4f7669c560/original/multi-objective-bayesian-optimisation-using-q-noisy-expected-hypervolume-improvement-q-nehvi-for-schotten-baumann-reaction.pdf
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60c7544a0f50db9e3a397cf2
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10.26434/chemrxiv.13643417.v1
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Eightfold Electrophilic Methylation of Octacyanotungstate [W(CN)8]4−/3−: Preparation of Homoleptic, Eight-coordinate Methylisocyanide Complexes [W(CNMe)8]4+/5+
|
Homoleptic eight-fold coordinated methylisocyanide complexes of W(IV) and
W(V) have been prepared for the first time. The reaction of [NBu4]4[W(CN)8] with methyl triflate
MeOTf gives [W(CNMe)8][OTf]4. The even stronger methylating mixture of methyl fluoride MeF
and arsenic pentafluoride AsF5 in liquid sulfur dioxide SO2 is able to fully alkylate both
[NBu4]4[W(CN)8] and [NBu4]3[W(CN)8]. The paramagnetic octakis(methylisocyanide)-
tungsten(V) [W(CNMe)8][AsF6]5 is thermally highly unstable above −30 °C. All compounds have been characterized via single-crystal X-ray diffraction, IR and Raman, as well as NMR or EPR
spectroscopy<br />
|
Malte Sellin; Susanne Margot Rupf; Ulrich Abram; Moritz Malischewski
|
Coordination Chemistry (Inorg.); Ligands (Inorg.); Organometallic Compounds; Transition Metal Complexes (Inorg.); Crystallography – Inorganic
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CC BY 4.0
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CHEMRXIV
|
2021-01-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7544a0f50db9e3a397cf2/original/eightfold-electrophilic-methylation-of-octacyanotungstate-w-cn-8-4-3-preparation-of-homoleptic-eight-coordinate-methylisocyanide-complexes-w-cn-me-8-4-5.pdf
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643aa00b1d262d40ea873186
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10.26434/chemrxiv-2023-l4jb4
|
Improving efficiency and sustainability of chitin bioconversion through a combination of Streptomyces secretomes and mechanical-milling
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Chitin, particularly α-chitin, is the most abundant and highly recalcitrant form, fortified by an intricate network of hydrogen bonds. Efficient valorization of α-chitin requires a mild pre-treatment and enzymatic hydrolysis. Streptomyces spp. secrete chitin-active CAZymes that can efficiently tackle the recalcitrant problem of chitin biomass. To better understand the potential of Streptomyces spp., a comparative analysis was performed between the novel isolate, Streptomyces sp. UH6 and the well-known chitin degraders, S. coelicolor and S. griseus. Growth studies and FE-SEM analysis revealed that all three Streptomyces spp. could utilize and degrade both α- and β-chitin. Zymogram analysis showed expression of 5-7 chitinases in the secretomes of Streptomyces strains. The chitin-active-secretomes produced by Streptomyces sp. UH6 and S. griseus were optimally active at acidic pH (pH 4.0 and 5.0) and 50°C. Time-course degradation of α- and β-chitin with the secretomes generated N-acetyl-D-glucosamine (GlcNAc) and N,N-diacetylchitobiose [(GlcNAc)2] as the predominant products. Further, the highly crystalline α-chitin was subjected to pre-treatment by ball-milling, which reduced the crystallinity from 88% to 56.6% and increased the BET surface area by 3-folds. Of note, the activity of all three Streptomyces secretomes was improved by a mild pre-treatment, while Streptomyces sp. UH6 secretome displayed improved GlcNAc and (GlcNAc)2 yields by 14.4 and 9.6-folds, respectively. Overall, our results suggest that the Streptomyces chitin-active-secretomes, particularly Streptomyces sp. UH6, can be deployed for efficient valorization of chitin biomass and to establish an economically feasible and eco-friendly process for valorizing highly recalcitrant α-chitin.
|
Lal Duhsaki; Saumashish Mukherjee ; Jogi Madhuprakash
|
Catalysis; Biocatalysis
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CC BY NC ND 4.0
|
CHEMRXIV
|
2023-04-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643aa00b1d262d40ea873186/original/improving-efficiency-and-sustainability-of-chitin-bioconversion-through-a-combination-of-streptomyces-secretomes-and-mechanical-milling.pdf
|
60c73f79842e653fe5db1abc
|
10.26434/chemrxiv.7381943.v1
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Assessment of Density Functional Theory in Predicting Interaction Energies Between Water and Polycyclic Aromatic Hydrocarbons: From Water on Benzene to Water on Graphene
|
<div>
<div>
<div>
<p>The interaction of water with polycyclic aromatic hydrocarbons, from benzene to
graphene, is investigated using various exchange-correlation functionals selected across
generalized gradient approximation (GGA), meta-GGA, and hybrid families within the
density functional theory (DFT) hierarchy. The accuracy of the different functionals
is assessed through comparisons with high-level electronic structure methods, including random phase approximation (RPA), diffusion Monte Carlo (DMC), and coupled-cluster with single, double, and perturbative triple excitations (CCSD(T)). Relatively
large variations are found in the interaction energies predicted by different DFT models, with GGA functionals underestimating the interaction strength for configurations
with the water oxygen pointing toward the aromatic molecules, and the meta-GGA
B97M-rV and hybrid ωB97M-V functionals providing nearly quantitative agreement
with CCSD(T) values available for the water-benzene, water-coronene, and water-circumcoronene dimers, which, in turn, are within ∼1 kcal/mol of the corresponding
RPA and DMC results. Similar trends among GGA, meta-GGA, and hybrid functionals are observed for the larger polycyclic aromatic hydrocarbon molecules considered
in this analysis (up to C216H36). By performing absolutely localized molecular orbital
energy decomposition analyses (ALMO-EDA) of the DFT results, it is found that,
independently of the number of carbon atoms and exchange-correlation functional,
the dominant contributions to the interaction energies between water and polycyclic
aromatic hydrocarbon molecules are the electrostatic and dispersion terms while polarization and charge transfer effects are negligibly small. Calculations carried out
with GGA and meta-GGA functionals indicate that, as the number of carbon atoms
increases, the interaction energies slowly converge to the corresponding values obtained
for an infinite graphene sheet. Importantly, water-graphene interaction energies calculated with the B97M-rV functional appear to deviate by more than 1 kcal/mol from
the available RPA and DMC values.
</p>
</div>
</div>
</div>
|
Adeayo Ajala; Vamsee K. Voora; Narbe Mardirossian; Filipp Furche; Paesani Lab
|
Computational Chemistry and Modeling; Theory - Computational; Interfaces; Quantum Mechanics
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f79842e653fe5db1abc/original/assessment-of-density-functional-theory-in-predicting-interaction-energies-between-water-and-polycyclic-aromatic-hydrocarbons-from-water-on-benzene-to-water-on-graphene.pdf
|
6377c75977ffe76e59f38a39
|
10.26434/chemrxiv-2022-4bd1p-v3
|
Elementary Decomposition Mechanisms of Lithium Hexafluorophosphate in Battery Electrolytes and Interphases
|
Electrolyte decomposition constitutes an outstanding challenge to long-life Li-ion batteries (LIBs) as well as emergent energy storage technologies, contributing to protection via solid electrolyte interphase (SEI) formation and irreversible capacity loss over a battery's life. Major strides have been made to understand the breakdown of common LIB solvents; however, salt decomposition mechanisms remain elusive. In this work, we use density functional theory to explain the decomposition of lithium hexafluorophosphate (LiPF6) salt under SEI formation conditions. Our results suggest that LiPF6 forms POF3 primarily through rapid chemical reactions with Li2CO3, while hydrolysis should be kinetically limited at moderate temperatures. We further identify selectivity in the proposed autocatalysis of POF3, finding that POF3 preferentially reacts with highly anionic oxygens. These results provide a means of interphase design in LIBs, indicating that LiPF6 reactivity may be controlled by varying the abundance or distribution of inorganic carbonate species or by limiting the transport of PF6- through the SEI.
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Evan Spotte-Smith; Thea Petrocelli; Hetal Patel; Samuel Blau; Kristin Persson
|
Theoretical and Computational Chemistry; Catalysis; Energy; Computational Chemistry and Modeling; Homogeneous Catalysis; Energy Storage
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CC BY NC 4.0
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CHEMRXIV
|
2022-11-21
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377c75977ffe76e59f38a39/original/elementary-decomposition-mechanisms-of-lithium-hexafluorophosphate-in-battery-electrolytes-and-interphases.pdf
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666884a6409abc03452af949
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10.26434/chemrxiv-2024-hr692
|
Interpretable deep-learning pKa prediction for small molecule drugs via atomic sensitivity analysis
|
Machine learning (ML) models play a crucial role in predicting properties essential to drug development, such as a drug’s logscale acid-dissociation constant (pKa). Despite recent architectural advances, these models often generalize poorly to novel compounds due to a scarcity of ground-truth data. Further, these models lack interpretability, in part due to a dependence on explicit encodings of input molecules’ molecular substructures. To this end, atomic-resolution information is accessible in chemical structures by observing model response to atomic perturbations of an input molecule; however, no methods exist that systematically utilize this information for model and molecular analysis. Here, we present BCL-XpKa, a substructure-independent, deep neural network (DNN)-based pKa predictor that generalizes well to novel small molecules. BCL-XpKa discretizes pKa prediction from a regression problem into a multitask-classification problem, which accumulates data for prediction at biologically relevant pH values and records the model’s uncertainty in its prediction as a discrete distribution for each pKa prediction. BCL-XpKa outperforms modern ML pKa predictors and accurately models the effects of common molecular modifications on a molecule’s ionizability. We then leverage BCL-XpKa’s substructure independence to introduce atomic sensitivity analysis (ASA), which quickly decomposes a molecule’s predicted pKa value into its respective atomic contributions without model retraining. When paired with BCL-XpKa, ASA informs that BCL-XpKa has implicitly learned high-resolution information about molecular substructures. We further demonstrate ASA’s utility in structure preparation for protein-ligand docking by identifying ionization sites in 97.8% and 83.4% of complex small molecule acids and bases. We then apply ASA with BCL-XpKa to understand the physicochemical liabilities and guide optimization of a recently published KRAS-degrading PROTAC.
|
Joseph DeCorte; Benjamin Brown; Jens Meiler
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry
|
CC BY NC 4.0
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CHEMRXIV
|
2024-06-12
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666884a6409abc03452af949/original/interpretable-deep-learning-p-ka-prediction-for-small-molecule-drugs-via-atomic-sensitivity-analysis.pdf
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658c5fc99138d23161a24042
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10.26434/chemrxiv-2023-r7whl
|
RNase H-sensitive multifunctional ASO-based nanostructures as promising tools for the treatment of multifactorial complex pathologies
|
Combined therapies play a key role in the fight against complex pathologies, such as cancer and related drug-resistance issues. This is particularly relevant in targeted therapies where inhibition of the drug target can be overcome by cross-activating complementary pathways. Unfortunately, the drug combinations approved to date –mostly based on small molecules– face several problems such as toxicity effects, which limit their clinical use. To address these issues, we have designed a new class of RNase H-sensitive nanostructure (3ASO) that can be disassembled intracellularly upon cell entry, leading to the simultaneous release of three different therapeutic oligonucleotides (ONs), tackling each of them the mRNA of a different protein. Here, we used Escherichia coli RNase H1 as a model to study an unprecedent mode of recognition and cleavage, that is mainly dictated by the topology of our RNA·DNA-based hybrid construct. As a model system for our technology we have created 3ASO nanostructures designed to specifically inhibit the expression of HER2, Akt and Hsp27 in HER2+ breast cancer cells. These trifunctional ON tools displayed very low toxicity and good levels of antiproliferative activity in HER2+ breast cancer cells. The present study will be of great potential in the fight against complex pathologies involving multiple mRNA targets, as the proposed cleavable designs will allow the efficient single-dose administration of different ON drugs simultaneously.
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Aida Mata-Ventosa; Ariadna Vila-Planas; Aina Solsona-Pujol; Jordi de la Dueña; Maria Torrents; Eduardo Izquierdo-García; Marçal Pastor-Anglada; Sandra Pérez-Torras; Montserrat Terrazas
|
Biological and Medicinal Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-12-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658c5fc99138d23161a24042/original/r-nase-h-sensitive-multifunctional-aso-based-nanostructures-as-promising-tools-for-the-treatment-of-multifactorial-complex-pathologies.pdf
|
66f9667412ff75c3a1dac244
|
10.26434/chemrxiv-2024-lcmhl
|
An Ultra-Deep Quantitative Plasma Proteomics Strategy
|
Blood is considered as the most valuable biofluid for protein biomarker screening as it contains a comprehensive human proteome, including cytokines and tissue leakage proteins that reflect ongoing disease states. Though widely used in large-scale protein quantification, mass spectrometry (MS)-based proteomic strategies still face great challenges in protein biomarker discovery in the blood, due to the particularly large dynamic range of proteins and the strong suppression effect by high-abundant proteins in the blood. As a promising alternative, nanomaterials enrichment-based protein corona strategy is highly efficient in increasing proteome coverage, but with the drawback of potentially disrupting the original protein concentration in the blood. Therefore, we proposed an ultrasensitive strategy that capable of enhancing mass spectrometry signals of the low abundant proteins/peptide to promote quantification of more than 2000 proteins at 288 SPD or 5000 plasma proteins at 36 SPD throughput from neat plasma without enrichment. Our strategy leverages the unique multiplexing properties of TMT labeling to sum the “total” MS1 signal of the same peptide from a boosting channel using nanomaterials enriched protein digests and the study channels using digests of neat plasma to trigger MS/MS fragmentation more efficiently and sensitively for low abundant protein identification, while the reporter ions provide quantitative information. In this way, in depth coverage of low abundant protein in neat plasma can be achieved without the risk of disrupting their original quantification. Accurate and reproducible quantification of plasma proteins with concentration down to low ng/L range was achieved, which is still rate in the field. Sensitive differentiation of plasma proteome characteristics among healthy individuals by this method indicated its potential in disease biomarker screening.
|
Jialin Li; Chuanping Zhao; Yuanyuan Liu; Wanjun Zhang; Weijie Qin
|
Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-09-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f9667412ff75c3a1dac244/original/an-ultra-deep-quantitative-plasma-proteomics-strategy.pdf
|
65c539cf9138d23161b4eb2f
|
10.26434/chemrxiv-2024-lxtq2
|
Chiral π-Conjugated Double Helical Aminyl Diradical with Triplet Ground State
|
We report a neutral high-spin diradical of chiral C2-symmetric bis[5]diazahelicene with ΔEST ≈ 0.4 kcal mol-1, as determined by EPR spectroscopy/SQUID magnetometry. The diradical is the most persistent among all high-spin aminyl radicals reported to date by a factor of 20, with a half-life up to 6 days in 2-MeTHF at room temperature. Its triplet ground state and excellent persistence may be associated with the unique spin density distribution within the dihydrophenazine moiety, characterizing two effective 3-electron C-N bonds analogous to the N-O bond of nitroxide radical. The enantiomerically enriched (ee ≥ 94%) (MM)- and (PP)-enantiomers of the precursors to the diradicals are obtained by either preparative chiral supercritical flow chromatography (SFC) or resolution via functionalization with chiral auxiliary of the C2-symmetric racemic tetraamine. The barrier for racemization of the solid tetraamine is ΔG‡ = 43 ± 0.01 kcal mol-1 in the 483 – 523 K range. The experimentally estimated lower limit of the barrier for racemization of diradical, ΔG‡ ≥ 26 kcal mol-1 in 2-MeTHF at 293 K, is comparable to the DFT-determined barrier of ΔG‡ = 31 kcal mol-1 in the gas phase at 298 K. While the enantiomerically pure tetraamine displays strong chiroptical properties, with anisotropy factor |g| = |Δε|/ε = 0.036 at 376 nm, |g| ≈ 0.005 at 548 nm of the high-spin diradical is comparable to that recently reported triplet ground state diradical dication. Notably, the radical anion intermediate in the generation of diradical exhibits large SOMO-HOMO inversion, SHI = 35 kcal mol-1.
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Haoxin Guo; Joshua B. Lovell; Chan Shu; Maren Pink; Martha Morton; Suchada Rajca; Andrzej Rajca
|
Organic Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-02-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c539cf9138d23161b4eb2f/original/chiral-conjugated-double-helical-aminyl-diradical-with-triplet-ground-state.pdf
|
60d77238261611d7608c6815
|
10.26434/chemrxiv-2021-hxb4r
|
Determining the Acetic Acid Concentration in White Vinegar: An At-Home Undergraduate Chemistry Experiment During the COVID-19 Pandemic
|
Due to the COVID-19 pandemic, many university-level chemistry laboratory experiments transitioned online. This created an educational challenge because students are unable to access reagents and instruments typical in a university lab setting. It is also difficult for students to connect theory to practice since real-lab experimentation is not possible in a virtual online for-mat. In our online Introductory Quantitative Analysis Laboratory course (GW Chem 2123W) in spring 2021, students were required to design and perform an experiment that could be safely conducted at home which can also demonstrate key princi-ples of quantitative analysis. Herein, we conducted a reliable at-home experiment that utilizes university-level acid/base titra-tion techniques to determine the acetic acid concentration in white vinegar. The experiment used sodium bicarbonate in the form of baking soda to titrate the Whole Foods white vinegar which is advertised to contain 6% of acetic acid. We reliably obtained an equivalence point for the titration from which the actual concentration of acetic acid in the vinegar was calculated with error analysis to be 19% higher than the advertised value. The analytical techniques demonstrated in this experiment supplement practical knowledge of acid/base techniques learned in the online classroom and prompt adoption of this meth-odology in online laboratory curriculum. This experiment can also be readily applied to measure other acidic solutions such as vinegar and juice for at-home experiment
|
Philip Parel; Lydia Burnett; Morgan Geoffroy; John Parel; Ling Hao
|
Analytical Chemistry; Chemical Education; Chemical Education - General; Analytical Chemistry - General
|
CC BY 4.0
|
CHEMRXIV
|
2021-06-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d77238261611d7608c6815/original/determining-the-acetic-acid-concentration-in-white-vinegar-an-at-home-undergraduate-chemistry-experiment-during-the-covid-19-pandemic.pdf
|
65ba24cb66c1381729a39f5e
|
10.26434/chemrxiv-2024-trv94
|
Supercritical CO2 technology for the treatment of End-of-Life Lithium ion batteries
|
The Li-ion batteries (LIBs) penetration in the automotive market makes more urgent the boosting of zero-waste battery recycling. This can play a crucial role in developing a circular economy through the recovery of critical raw materials (CRMs), as well as non-metallic components back to use. In recent years, the recycling technologies for LIBs entered in a new stage focused on the development of i) advanced pre-treatment processes to separate all the valuable battery components, and ii) more sustainable metallurgical approaches. Compared to the common recycling processes, Supercritical Fluid (SCF) technology is environmentally benign, chiefly if CO2 is used as the SCF (scCO2).
This review aims at providing an overview on the current progresses and the open challenges of SCF technology for the treatment of End-of-Life LIBs. The fundamentals of SCF technology process are discussed, providing the reader a brief overview of principles, operation procedures and instrumentation. Thereafter, the main applications in the field of batteries recycling are reviewed, including electrolyte recovery and high-rate extraction of critical metals from the cathode. Finally, a focus is given on the huge innovation potential of scCO2 to separate and reuse the fluorinated binder from the electrode. At present, the binder is burnt in the common recycling processes, leading to hazardous fluorinated gas emissions.
|
Pietro Cattaneo; Fiorenza D'Aprile; Valeriy Kapelyushko; Piercarlo Mustarelli; Eliana Quartarone
|
Polymer Science; Energy; Materials Chemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba24cb66c1381729a39f5e/original/supercritical-co2-technology-for-the-treatment-of-end-of-life-lithium-ion-batteries.pdf
|
6455244f27fccdb3ea8aa9d0
|
10.26434/chemrxiv-2023-cxzcz
|
Weakly Coordinating Organic Cations are Intrinsically Capable of Supporting CO2 Reduction Catalysis
|
The rates and selectivity of electrochemical CO2 reduction are known to be strongly influenced by the identity of alkali cations in the medium. However, experimentally, it remains unclear whether cation effects arise predominantly from coordinative stabilization of surface intermediates or from changes in the mean-field electrostatic environment at the interface. Herein, we show that Au- and Ag-catalyzed CO2 reduction can occur in the presence of weakly coordinating (poly)tetraalkylammonium cations. Through competition experiments in which the catalytic activity of Au was monitored as a function of the ratio of the organic to metal cation, we identify regimes in which the organic cation exclusively controls CO2 reduction selectivity and activity. We observe substantial CO production in this regime, suggesting that CO2 reduction catalysis can occur in the absence of Lewis acidic cations and thus, coordinative interactions between the electrolyte cations and surface-bound intermediates are not required for CO2 activation. For both Au and Ag, we find that tetraalkylammonium cations support catalytic activity for CO2 reduction on par with alkali metal cations, but with distinct cation activity trends between Au and Ag. These findings support a revision in electrolyte design rules to include water-soluble organic cation salts as potential supporting electrolytes for CO2 electrolysis.
|
Sophia Weng; Wei Lun Toh; Yogesh Surendranath
|
Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Small Molecule Activation (Inorg.); Electrocatalysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-05-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6455244f27fccdb3ea8aa9d0/original/weakly-coordinating-organic-cations-are-intrinsically-capable-of-supporting-co2-reduction-catalysis.pdf
|
67dad5616dde43c9086d27f7
|
10.26434/chemrxiv-2024-zj7sn-v2
|
Quantifying acetylation-induced changes in the plant secondary cell wall structure and dynamics
|
Lignin and carbohydrate rich secondary plant cell walls are abundantly available in the biosphere, and is a notable renewable feedstock for biofuels and biomaterials. Particularly for construction applications, wood that is resistant to fungal degradation is highly desirable. Chemical modifications, such as acetylation, have been successfully demonstrated to inhibit wood decay by microorganisms. It is well known that acetylation reduces wood moisture content, which slows down motions within the cell wall when measured by X-ray fluorescence microscopy experiments and molecular simulations. The open question is whether acetylation inhibits decay strictly by reducing moisture content, or if specific interactions with the acetyl group hinder motion within the cell wall and further inhibit decay. We investigate these hypotheses directly through molecular simulation, acetylating exposed hemicellulose and lignin hydroxyl groups in existing models for secondary plant cell wall structure to 5-18% weight-percent gain. By comparing diffusive behavior for cell wall polymers, water, and select ions (Na+ and Fe3+ ), we can track the dynamics within the cell wall and identify the causal mechanisms for reduced transport and uptake of these metal ions by acetylated cell walls. We find that the change from hydroxyl to acetyl group alone does not account for reduced transport, with only modest changes in diffusion when acetylated cell walls are expanded to provide constant moisture level. The most substantial changes in diffusion occur where the additional acetylation displaces water, reducing the moisture content for the cell wall. Utilizing these simulations, we further analyze the interactions between ions and cell wall polymers and the evolution of dynamic water pockets within the structure. Ions interact more frequently with the acetyl group than the hydroxyl groups they replace, yielding to increased ion interactions on aggregate upon acetylation. Collectively, these findings elucidate the molecular mechanism through which acetylation affects secondary plant cell walls at atomic resolution.
|
Murtaza Barkarar; Daipayan Sarkar; Christopher Hunt; Josh Vermaas
|
Theoretical and Computational Chemistry; Materials Science; Biological Materials
|
CC BY 4.0
|
CHEMRXIV
|
2025-03-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dad5616dde43c9086d27f7/original/quantifying-acetylation-induced-changes-in-the-plant-secondary-cell-wall-structure-and-dynamics.pdf
|
60c74ba1bb8c1ab7f73db260
|
10.26434/chemrxiv.12365282.v1
|
Screening of Chloroquine, Hydroxychloroquine and Its Derivatives for Their Binding Affinity to Multiple SARS-CoV-2 Protein Drug Targets
|
Recently Chloroquine and its derivative Hydroxychloroquine have garnered enormous interest amongst the clinicians and health authorities’ world over as a potential treatment to contain COVID-19 pandemic. The present research aims at investigating the therapeutic potential of Chloroquine and its potent derivative Hydroxychloroquine against SARS-CoV-2 viral proteins. At the same time we have screened some chemically synthesized derivatives of Chloroquine and compared their binding efficacy with chemically synthesized Chloroquine derivatives through <i>in silico</i>approaches. For the purpose of the study, we have selected some essential viral proteins and enzymes implicated in SARS-CoV-2 replication and multiplication as putative drug targets.<br />
|
Mallikarjuna Nimgampalle; Vasudharani Devanthan; Ambrish Saxena
|
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/60c74ba1bb8c1ab7f73db260/original/screening-of-chloroquine-hydroxychloroquine-and-its-derivatives-for-their-binding-affinity-to-multiple-sars-co-v-2-protein-drug-targets.pdf
|
60c73fe2bb8c1a66f03d9c6a
|
10.26434/chemrxiv.7552139.v1
|
A Peptoid with Extended Shape in Water
|
<div>
<div>
<div>
<p>“Peptoids” was proposed, over decades ago, as a term describing analogs of peptides that exhibit
better physicochemical and pharmacokinetic properties than peptides. Oligo-(N-substituted glycines)
(oligo-NSG) was previously proposed as a peptoid due to its high proteolytic resistance and membrane permeability. However, oligo-NSG is conformationally flexible and is difficult to achieve a
defined shape in water. This conformational flexibility is severely limiting biological application of
oligo-NSG. Here, we propose oligo-(N-substituted alanines) (oligo-NSA) as a new peptoid that
forms a defined shape in water. A synthetic method established in this study enabled the first isolation and conformational study of optically pure oligo-NSA. Computational simulations, crystallographic studies and spectroscopic analysis demonstrated the well-defined extended shape of oligo-NSA realized by backbone steric effects. The new class of peptoid achieves the constrained conformation without any assistance of N-substituents and serves as an ideal scaffold for displaying
functional groups in well-defined three-dimensional space, which leads to effective biomolecular
recognition.
</p>
</div>
</div>
</div>
|
Jumpei Morimoto; Yasuhiro Fukuda; Takumu Watanabe; Daisuke Kuroda; Kouhei Tsumoto; Shinsuke Sando
|
Bioorganic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Chemical Biology; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2019-01-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe2bb8c1a66f03d9c6a/original/a-peptoid-with-extended-shape-in-water.pdf
|
641d7e5b647e3dca996eb1b0
|
10.26434/chemrxiv-2023-pf268-v2
|
RT-Tranformer: Retention Time Prediction
for Metabolite Annotation to Assist in
Metabolite Identification
|
Liquid chromatography retention times (RTs) prediction can assist in metabolite identification, which is a critical task and challenge in non-targeted metabolomics.However, different chromatographic methods (CM) may result in different RTs for the same metabolite. Current RT prediction methods lack sufficient scalability to transfer from one specific chromatographic method to another. Therefore, we present RT-Transformer, a novel deep neural network model coupled with graph attention network (GAT) and 1D-Transformer, which can predict RTs under any chromatographic methods. First, we obtain a pre-trained model by training RT-Transformer on the large small molecule retention time (SMRT) dataset containing 80038 molecules, and then project the resulting model onto different chromatographic methods based on transfer learning. When tested on the METLIN dataset, as other authors did, the average absolute error reached 27.30 after removing samples with retention times fewer than five minutes. Still, it reached 33.41 when no samples were removed. The pre-trained RT-Transformer was further transferred to 5 datasets corresponding to different chromatographic conditions and fine-tuned. According to the experimental results, RT-Transformer achieves competitive performance compared to state-of-the-art methods.In addition, RT-Transformer was applied to 41 external molecular RT datasets. Extensive evaluations indicate that RT-Transformer has excellent scalability in predicting RTs for liquid chromatography and improves the accuracy of metabolite identification.
|
jun xue; Bingyi Wang; Weihua li
|
Analytical Chemistry; Mass Spectrometry; Separation Science
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-03-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641d7e5b647e3dca996eb1b0/original/rt-tranformer-retention-time-prediction-for-metabolite-annotation-to-assist-in-metabolite-identification.pdf
|
60c7545c337d6c3c3ee28a26
|
10.26434/chemrxiv.13587035.v1
|
Scalable nanoprecipitation of niclosamide and in vivo demonstration of long-acting delivery after intramuscular injection
|
<p>The spread of SARS-CoV-2 across the world requires
the formation of a range of interventions that include immunomodulatory or
antiviral therapeutics and repurposing of existing drug compounds is an
important strategy to rapidly identify possible options. Niclosamide is a cheap
and generic drug compound with a proven <i>in vitro</i> ability to inhibit
viral replication of SARS-CoV-2; this drug also has known poor oral bioavailability
due to very low water solubility. Here,
we demonstrate the nanoparticle formulation of niclosamide using a new, cheap
and scalable process to enable long-acting injectable administration and show
extended circulating drug exposure <i>in vivo</i> over 28 days using a rodent
model after depot injection.</p>
|
James Hobson; Alison Savage; Andrew Dwyer; Catherine Unsworth; Usman Arshad; Henry Pertinez; helen box; Lee Tatham; Rajith K. R. Rajoli; Megan Neary; Joanne Sharp; Anthony Valentijn; Christopher David; Paul Curley; Neill Liptrott; Tom Mcdonald; Andrew Owen; Steve Rannard
|
Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7545c337d6c3c3ee28a26/original/scalable-nanoprecipitation-of-niclosamide-and-in-vivo-demonstration-of-long-acting-delivery-after-intramuscular-injection.pdf
|
654e2c842c3c11ed712393a3
|
10.26434/chemrxiv-2023-1tb6m
|
Solvent-free NMC electrodes for Li-ion batteries: unravelling the microstructure and formation of the PTFE nano-fibril network
|
The microstructure and electrochemical performance of solvent-free processed and slurry cast Li(Ni0.6Co0.2Mn0.2)O2 (NMC622) based electrodes for Li ion batteries has been investigated. In contrast to a moss-like PVDF-based carbon binder domain in slurry cast electrodes, the PTFE binder in solvent-free electrodes had a hierarchical morphology composed of primary fibrils of a few μm in diameter and 100's μm in length that branched into secondary and then ever finer fibrils, down to diameters of 10's nm or below. A mechanism for the formation of the branch-like morphology observed in PTFE-based solvent-free electrodes is also presented. Even the finest fibrils were confirmed to survive typical cathode cycling conditions. The solvent-free electrodes had progressively higher discharge capacities with increasing discharge rate, increasing to 150% at 2C compared with slurry cast equivalents, and capacity faded 40% slower over 200 cycles at C/3. Impedance analysis showed the solvent-free microstructure enabled reduced charge transfer resistance and ionic resistance, arising from minimal obscuration of the active material surface and no pore blockage.
|
Guillaume Matthews; Sam Wheeler; Julia Ramírez-González; Patrick Grant
|
Energy; Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-11-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e2c842c3c11ed712393a3/original/solvent-free-nmc-electrodes-for-li-ion-batteries-unravelling-the-microstructure-and-formation-of-the-ptfe-nano-fibril-network.pdf
|
6582a1fd9138d23161181406
|
10.26434/chemrxiv-2023-0m355-v2
|
Effectiveness of molecular fingerprints for exploring the chemical space of natural products
|
Natural products are a diverse class of compounds with promising biological properties, such as high potency and excellent selectivity. However, they have different structural motifs than typical drug-like compounds, e.g., a wider range of molecular weight, multiple stereocenters and higher fraction of sp3-hybridized carbons. This makes the encoding of natural products via molecular fingerprints difficult, thus restricting their use in cheminformatics studies. To tackle this issue, we explored over 30 years of research to systematically evaluate which molecular fingerprint provides the best performance on the natural product chemical space. We considered 20 molecular fingerprints from four different sources, which we then benchmarked on over 100,000 unique natural products from the COCONUT (COlleCtion of Open Natural prodUcTs) and CMNPD (Comprehensive Marine Natural Products Database) databases. Our analysis focused on the correlation between different fingerprints and their classification performance on 13 bioactivity prediction datasets. Our results show that different encodings can provide fundamentally different views of the natural product chemical space, leading to substantial differences in pairwise similarity and performance. While Extended Connectivity Fingerprints are the de-facto option to encoding drug-like compounds, other fingerprints resulted to match or outperform them for bioactivity prediction of natural products. These results highlight the need to evaluate multiple fingerprinting algorithms for optimal performance and suggest new areas of research. Finally, we provide an open-source Python package for computing all molecular fingerprints considered in the study, as well as data and scripts necessary to reproduce the results, at https://github.com/dahvida/NP_Fingerprints.
|
Davide Boldini; Davide Ballabio; Viviana Consonni; Roberto Todeschini; Francesca Grisoni; Stephan Sieber
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-12-21
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6582a1fd9138d23161181406/original/effectiveness-of-molecular-fingerprints-for-exploring-the-chemical-space-of-natural-products.pdf
|
679b8f68fa469535b970b65a
|
10.26434/chemrxiv-2025-5461s-v2
|
Design, Synthesis and Preclinical Evaluation of a brain-permeable PET Tracer for P2Y12R Imaging in the Brain
|
Microglia, the innate immune cells of the central nervous system (CNS), act as first responders in the context of brain injury or neurodegeneration. Their ability to switch between different neuroprotective and neurotoxic phenotypes, plays a central role in maintaining brain homeostasis. Recently, the P2Y12 receptor (P2Y12R) has been identified as a promising molecular biomarker for microglia, as its expression level is directly dependent on microglia phenotype and function. A decline in P2Y12R expression is indicative of damage, microglial malfunction or chronic neuroinflammation, as observed in neurodegenerative diseases such as Alzheimer's disease (AD). Novel therapeutic strategies aiming to modulate microglia phenotypes directly depend on matching diagnostic tools for success control. Accordingly, a suitable P2Y12R positron emission tomography (PET) tracer is hypothesised to provide valuable in vivo information regarding microglia activation within the CNS. However, P2Y12R PET tracers with sufficient brain retention for neuroimaging have not been reported so far. Herein, we report the first brain-permeable P2Y12R PET tracer for in vivo imaging of P2Y12R-positive microglia. Nicotinate [18F]12 exhibited nanomolar affinity for the target receptor and favourable in silico parameters. Tracer specificity was proven by in vitro autoradiography (ARG) and brain uptake was confirmed by PET imaging in wild-type (WT) mice and ex vivo biodistribution. Ex vivo metabolite analysis indicated the exclusive presence of intact tracer in the mouse brain, with no evidence of any radio-metabolites. The tracer showed a reduced uptake in microglia-depleted mice after PLX-5622 diet, in comparison to WT and Trem2 knock-out (Trem2-/-) mice. Ex vivo immunohistochemistry (IHC) results and PET data revealed a strong correlation between microglia, P2Y12R expression levels and tracer uptake giving strong evidence that P2Y12 PET signal reflects P2Y12R binding. This novel tracer represents an important step forward in P2Y12 PET imaging in the context of neuroinflammation.
|
Emanuel Joseph; Lea H. Kunze; Rebecca Schaefer; Giovanna Palumbo; Benjamin Kugelmann; Stephan Wagner; Sven Lammich; Regina Feederle; Michael Willem; Rudolf A. Werner; Matthias Brendel; Simon Lindner
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
|
CHEMRXIV
|
2025-01-31
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679b8f68fa469535b970b65a/original/design-synthesis-and-preclinical-evaluation-of-a-brain-permeable-pet-tracer-for-p2y12r-imaging-in-the-brain.pdf
|
62c743ca638326c3ed445d91
|
10.26434/chemrxiv-2022-mmpps
|
Identification and Characterization of Designer Phencyclidines (PCPs) in Forensic Casework
|
With the sustained prevalence and introduction of new emerging drugs throughout the world there is a need for continued development and maintenance of platforms that enable rapid identification and characterization of unknown compounds. To complement existing efforts, a collaborative platform between the National Institute of Standards and Technology (NIST) and practicing forensic agencies is being deployed which enables laboratories to leverage techniques and expertise that may not exist at their facilities. Using this approach, unknown compounds are identified and characterized using a suite of analytical tools to obtain (1) a rapid preliminary identification followed by (2) a more complete characterization and confirmation of the preliminary identification. To demonstrate this platform, the characterization of three previously unreported analogs of phencyclidine (PCP) are described. A preliminary identification of the three substances was obtained using direct analysis in real time mass spectrometry (DART-MS) with confirmation by nuclear magnetic resonance (NMR) spectroscopy, gas chromatography mass spectrometry (GC-MS) and gas chromatography flame ionization detection (GC-FID).
|
Edward Sisco; Aaron Urbas
|
Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c743ca638326c3ed445d91/original/identification-and-characterization-of-designer-phencyclidines-pc-ps-in-forensic-casework.pdf
|
660433ed66c1381729f950d5
|
10.26434/chemrxiv-2024-z3dw6
|
Native cryo-correlative light and synchrotron X-ray fluorescence imaging of proteins and essential metals in developing neurons
|
Essential metals such as iron, copper and zinc are required for a wide variety of biological processes. For example, they act as cofactors in many proteins, conferring enzymatic activity or structural stability. Interactions between metals and proteins are often difficult to characterize due to the low concentration of metals in biological tissues and the sometimes labile nature of the chemical bonds involved. To better understand the cellular functions of essential metals, we correlate protein localization, using fluorescence light microscopy (FLM), and metal distribution with synchrotron X-ray fluorescence (SXRF), a high-sensitivity and high-spatial-resolution technique for metal imaging. Both chemical imaging modalities are implemented under cryogenic conditions to preserve native cell structure and chemical element distribution. As a proof of concept, we applied cryo-FLM and cryo-SXRF correlative imaging to cultured primary hippocampal neurons. Neurons were labeled under live conditions with fluorescent F-actin and tubulin dyes, then samples were flash-frozen and observed in a frozen hydrated state. This methodology, cryo-FLM combined to cryo-SXRF, revealed the distribution of iron, copper and zinc relative to F-actin and tubulin in the growth cones, dendrites, axons, and axonal en passant boutons of developing neurons.
|
Richard Ortega; Monica Fernandez Monreal; Noemie Pied; Stephane Roudeau; Peter Cloetens; Asuncion Carmona
|
Analytical Chemistry; Imaging; Microscopy; Spectroscopy (Anal. Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-28
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660433ed66c1381729f950d5/original/native-cryo-correlative-light-and-synchrotron-x-ray-fluorescence-imaging-of-proteins-and-essential-metals-in-developing-neurons.pdf
|
61c857f7d6dcc22df045b15a
|
10.26434/chemrxiv-2021-r2d6j
|
Dynamics of methyl radical formation by 266 nm photolysis of xylenes and mesitylene
|
The 266 nm photodissociation of three xylene isomers and mesitylene leading to the formation of methyl radical was examined. The kinetic energy release profiles for the methyl radical were almost identical for all the three isomers of xylene and mesitylene, while substantial differences were observed for the corresponding profiles of the co-fragment produced by loss of one methyl group. This observation be attributed to the formation of the methyl radical from alternate channels. The total kinetic energy distribution profiles were rationalized based on the dissociation of {sp2}C–C{sp3} bond in the cationic state, wherein the {sp2}C–C{sp3} bond dissociation energy is lowered relative to the ground state. The dissocaiton in the cationic state follows a resonant three-photon absorption process, resulting in maximum total kinetic energy of about 1.6 – 1.8 eV for the photofragments. A results in. Fitting of the TKER distribution profiles to empirical function reveals that the dynamics of {sp2}C–C{sp3} bond dissociation is insensitive to the position of substitution but marginally dependent on the number of methyl groups.
|
Namitha Brijit Bejoy; Monali Kawade; Sumitra Singh; G Naresh Patwari
|
Physical Chemistry; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-12-27
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c857f7d6dcc22df045b15a/original/dynamics-of-methyl-radical-formation-by-266-nm-photolysis-of-xylenes-and-mesitylene.pdf
|
6735f629f9980725cf2cc066
|
10.26434/chemrxiv-2024-7mf2j
|
Design, Synthesis, and Unprecedented Interactions of Covalent Dipeptide-Based Inhibitors of SARS-CoV-2 Main Protease and its Variants Displaying Potent Antiviral Activity
|
The main protease (Mpro) of SARS-CoV-2 is a key drug target for the development of antiviral therapeutics. Here, we designed and synthesized a series of small-molecule peptidomimetics with various cysteine-reactive electrophiles. Several compounds were identified as potent SARS-CoV-2 Mpro inhibitors, including compounds 8n (IC50 = 0.0752 µM), 8p (IC50 = 0.0887 µM), 8r (IC50 = 0.0199 µM), 10a (IC50 = 0.0376 µM), 10c (IC50 = 0.0177 µM), and 10f (IC50 = 0.0130 µM). Most of them additionally inhibited cathepsin L and were also active against SARS-CoV-1 and MERS-CoV Mpro. In Calu-3 cells, several inhibitors, including 8r, 10a, and 10c, displayed high antiviral activity in the nanomolar range without showing cellular toxicity. The co-crystal structure of SARS-CoV-2 Mpro in complex with 8p revealed covalent binding to the enzyme’s catalytic residue Cys145 and showed specific, unprecedented interactions within the substrate binding pocket. Compounds 8n and 10c, especially 8n, were effective against a panel of naturally occurring nirmatrelvir-resistant mutants, particularly E166V, and showed metabolic stability and additional favorable pharmacokinetic properties, making it a suitable candidate for further preclinical development.
|
Thanigaimalai Pillaiyar; Philipp Flury; Nadine Krüger; Katharina Sylvester; Julian Breidenbach; Ghazl Al Hamwi; Jingxin Qiao; Yan Chen; Cheila Rocha; Mateus Serafim ; Elany Barbosa da Silva; Stefan Pohlmann; Antti Poso; Thales Kronenberger; Katharina Rox; Anthony O’Donoghue; Shengyong Yang; Sträter Norbert; Michael Gütschow; Stefan A. Laufer; Christa E. Müller
|
Biological and Medicinal Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-11-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6735f629f9980725cf2cc066/original/design-synthesis-and-unprecedented-interactions-of-covalent-dipeptide-based-inhibitors-of-sars-co-v-2-main-protease-and-its-variants-displaying-potent-antiviral-activity.pdf
|
60c753a0f96a00a4662884ce
|
10.26434/chemrxiv.13518050.v1
|
ClipsMS: An Algorithm for Analyzing Internal Fragments Resulting from Top-Down Mass Spectrometry
|
<p>Here we describe ClipsMS, an algorithm that can assign both terminal and internal fragments generated by top-down MS fragmentation. Further, ClipsMS can be used to locate various modifications on the protein sequence. Using ClipsMS to assign TD-MS generated product ions, we demonstrate that for apo-myoglobin, the inclusion of internal fragments increases the sequence coverage up to 78%. Interestingly, many internal fragments cover complimentary regions to the terminal fragments that enhance the information that is extracted from a single top-down mass spectrum. Analysis of oxidized apo-myoglobin using terminal and internal fragment matching by ClipsMS confirmed the locations of oxidation sites on the two methionine residues. Internal fragments can be beneficial for top-down protein fragmentation analysis, and ClipsMS can be a valuable tool for assigning both terminal and internal fragments present in a top-down mass spectrum.</p>
|
Carter Lantz; Muhammad A. Zenaidee; Benqian Wei; Zachary Hemminger; Rachel R. Ogorzalek Loo; Joseph Loo
|
Mass Spectrometry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-01-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753a0f96a00a4662884ce/original/clips-ms-an-algorithm-for-analyzing-internal-fragments-resulting-from-top-down-mass-spectrometry.pdf
|
67076b5bcec5d6c142c0a0dd
|
10.26434/chemrxiv-2024-10047
|
Supercritical Hydrothermal Synthesis of Quasi-1D Chain Fluorocarbonate NaDy(CO3)F2 with Giant Rotating Magnetocaloric Effect
|
Strong quantum fluctuations and weak magnetic interactions in quasi-1D chain rare-earth (RE) magnets prevent long-range magnetic ordering, preserving magnetic entropy for ultra-low temperature refrigeration. Here, a Dy-based 1D chain carbonate, NaDy(CO3)F2, has been successfully grown into millimeter-level single crystals in supercritical hydrothermal conditions. Its crystal structures can be indexed by an orthorhombic unit cell (space group #62 Pnma) consisting of Dy-based zigzag chains, with the distribution of interchain Dy∙∙∙Dy distance (4.46 Å) larger than that of the intrachain Dy∙∙∙Dy distance (3.78 Å). The temperature-dependent magnetic susceptibility and specific heat measurements mark the onset of long-range magnetic ordering (TN ~ 2.4 K) for NaDy(CO3)F2. Moreover, its isothermal magnetic entropy change (ΔSmag) was examined based on millimetre-size single crystals. Our results unveil the direction-dependent magnetocaloric effect (MCE) of NaDy(CO3)F2, providing an excellent example of achieving a giant MCE via rotating the crystallographic direction of well-oriented single crystals.
|
Ruixin Guo; Jingfang Tong; Lun Jin; Weijie Lin; Zhengzhong Deng; Changzhao Pan; Haitao Zhou; Shu Guo
|
Inorganic Chemistry; Magnetism; Materials Chemistry; Crystallography – Inorganic
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-10-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67076b5bcec5d6c142c0a0dd/original/supercritical-hydrothermal-synthesis-of-quasi-1d-chain-fluorocarbonate-na-dy-co3-f2-with-giant-rotating-magnetocaloric-effect.pdf
|
619038762bf8a9563adb5642
|
10.26434/chemrxiv-2021-1bs1t
|
Directed Palladium Catalyzed Acetoxylation of Indolines. Total Synthesis of N-Benzoylcylindrocarine
|
We describe a palladium catalyzed C7-acetoxylation of indolines with a range of amide directing groups. While a variety of substituents are tolerated on the indoline-core and the N1-acyl group, the acetoxylation is most sensitive to the C2- and C6-indoline substituents. The practicality of this indoline C7-acetoxylation is demonstrated using a cinnamamide substrate on mmol-scale. Several N1-acyl groups, including those present in natural alkaloids, guide C7-acetoxylation of indoline substrates over a competitive C5-oxidation. The application of this chemistry allowed for the first synthesis of N-benzoylcylindrocarine by late-stage C17-acetoxylation of N-benzoylfendleridine.
|
Kristen Flynn; Kolby White; Mohammad Movassaghi
|
Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-11-16
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619038762bf8a9563adb5642/original/directed-palladium-catalyzed-acetoxylation-of-indolines-total-synthesis-of-n-benzoylcylindrocarine.pdf
|
60c75872bb8c1ac96a3dca1b
|
10.26434/chemrxiv.14497959.v2
|
MAYGEN - an Open-Source Chemical Structure Generator for Constitutional Isomers Based on the Orderly Generation Principle
|
<p>The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering.</p><p>Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN’s architecture and algorithm are outlined and the software is benchmarked against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution OMG. MAYGEN outperforms OMG by an order of magnitude and gets close to and occasionally outperforms MOLGEN in performance.</p>
|
Mehmet Aziz Yirik; Maria Sorokina; Christoph Steinbeck
|
Chemoinformatics
|
CC BY 4.0
|
CHEMRXIV
|
2021-05-03
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75872bb8c1ac96a3dca1b/original/maygen-an-open-source-chemical-structure-generator-for-constitutional-isomers-based-on-the-orderly-generation-principle.pdf
|
60ccc95ac6229574a919dc2f
|
10.26434/chemrxiv-2021-cbjd2
|
Huzinaga Projection Embedding for Efficient and Accurate Energies of Systems with Localized Spin-densities
|
We demonstrate the accuracy and efficiency of the restricted open-shell and unrestricted formulation of the absolutely localized Huzinaga projection operator embedding method. Restricted open-shell and unrestricted Huzinaga projection embedding in the full system basis is formally exact to restricted open-shell and unrestricted Kohn-Sham density functional theory, respectively. By utilizing the absolutely localized basis, we significantly improve the efficiency of the method, while maintaining high accuracy. The open-shell embedding method is shown to calculate electronic energies of a variety of systems to within 1 kcal/mol accuracy of the full system wave function result. For certain highly localized reactions, such as spin transition energies on transition metals, we find that very few atoms are necessary to include in the wave function region, in order to achieve desired accuracy. Here we apply our method to several representative examples such as spin splitting energies, catalysis on transition metals, and radical reactions.
|
Daniel Graham; Xuelan Wen; Dhabih V. Chulhai; Jason Goodpaster
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-07-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ccc95ac6229574a919dc2f/original/huzinaga-projection-embedding-for-efficient-and-accurate-energies-of-systems-with-localized-spin-densities.pdf
|
6537d4afc3693ca9930449b2
|
10.26434/chemrxiv-2023-pldr0-v3
|
Molecular insights into the formation of drug-polymer inclusion complex
|
Drug-polymer inclusion complex (IC) has been viewed as a novel solid form of drugs for property modification. Nonetheless, our understanding of the formation mechanism remains limited. This work aims to provide insight into the molecular processes governing the structural construction of carbamazepine (CBZ) and griseofulvin (GSF) channel-type ICs in the presence of guest polymers. Leveraging microdroplet melt crystallization, we successfully unveiled the single-crystal structures of these ICs, enabling theoretical analysis. Our investigation, which encompasses structural analysis, density functional theory calculations, and molecular dynamics (MD) simulations, elucidates the disparity between CBZ and GSF channels in terms of their autonomy in the absence of guest polymers. CBZ molecules can spontaneously assemble into stable channel structures independently, capitalizing on their unique mortise-tenon architecture and robust π...π interactions. In contrast, GSF channels lack sufficient support from weak Cl...O and C-H...π intermolecular interactions and necessitate the insertion of guest molecules to stabilize their structures. Regardless of the structural reliance on guest polymers, channel size is determined by the size, shape, and conformation of the host molecules, as well as intermolecular interactions. Interestingly, while the eleven structurally determined drug-polymer ICs adopt diverse approaches to construct channel structures, their channel sizes consistently fall within a narrow range of 3.86-5.18 Å, slightly larger than the radial diameter of the guest polymers (2.83-3.50 Å). Consequently, we propose that a crucial prerequisite for the formation of drug-polymer ICs is that the host molecules have the capacity to self-assemble into a porous structure with accommodating channels for guest polymers. Additionally, our results confirm the efficacy of microdroplet melt crystallization in rapidly synthesizing drug-polymer ICs and cultivating their single crystals of high quality and sufficient size. This achievement overcomes the challenges associated with structure elucidation and promises to promote further research into the formation mechanism of drug-polymer ICs. We anticipate that these findings will inspire continued exploration of this novel solid form, facilitating theoretical predictions and practical applications in pharmaceutical development.
|
Ming Lu; Binbin Liu; Changrui Li; Ziqiao Chen; Xiao Ou; Shuting Li; Ao Li; Pin Chen
|
Physical Chemistry; Crystallography
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-10-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6537d4afc3693ca9930449b2/original/molecular-insights-into-the-formation-of-drug-polymer-inclusion-complex.pdf
|
64abdca59ea64cc167c178c9
|
10.26434/chemrxiv-2023-n7j7d
|
Fast determination of weak protein-ligand affinities by STD NMR: The Reduced Dataset STD NMR approach (rd-STD NMR)
|
STD NMR is a powerful ligand-based tool for screening small molecules and low molecular weight fragments for their interaction with a given macromolecule, and it has become the spectroscopic technique of choice for the study of medium/weak affinity protein-ligand interactions. In the pharmaceutical industry, there is a great interest in the accurate and fast determination of protein-fragment binding affinities, typically low. STD NMR is a uniquely suited technique to accurately determine weak proteinligand affinities. However, a drawback of the technique is that, in order to gain quantitative structural or affinity information from STD NMR experiments, long series of experiments at increasing values of the saturation time of the protein must be carried out, to get the full analysis of the so-called STD NMR build-up curve (“initial slopes approach”). To resolve this limitation, we have developed a protocol that allows to get accurate initial slopes using STD NMR data acquired at only 2 saturation times. We demonstrate that our protocol, called the Reduced Dataset STD NMR approach (rd-STD NMR), allows the very fast determination of dissociation constants of low affinity protein-ligand interactions.
|
Gabriel Rocha; Jonathan Ramírez-Cárdenas; Samuel Walpole; Ridvan Nepravishta; Carmen Ortiz; Jesús Angulo; Juan C. Muñoz-García
|
Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Supramolecular Chemistry (Org.); Biochemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-07-11
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64abdca59ea64cc167c178c9/original/fast-determination-of-weak-protein-ligand-affinities-by-std-nmr-the-reduced-dataset-std-nmr-approach-rd-std-nmr.pdf
|
60c74b44bb8c1a806e3db18c
|
10.26434/chemrxiv.12312263.v1
|
Plant-Derived Natural Polyphenols as Potential Antiviral Drugs Against SARS-CoV-2 via RNA‐dependent RNA Polymerase (RdRp) Inhibition: An In-Silico Analysis
|
<p>The
sudden outburst of Coronavirus disease (COVID-19) has left the entire world to
a standstill. COVID-19 is caused by Severe Acute Respiratory Syndrome
Coronavirus 2 (SARS-CoV-2). As per the report from the WHO, more than 4.5
million people have been infected by SARS-CoV-2 with more than 3,00,000 deaths across
the globe. As of now, there is no therapeutic drug or vaccine approved for the
treatment of SARS-CoV-2 infection. Hence, the outbreak of COVID-19 poses a
massive threat to humans. Due to the time taking process of new drug design and
development, drug repurposing might be the only viable solution to tackle
COVID-19. RNA‐dependent RNA polymerase (RdRp) catalyzes SARS-CoV-2 RNA
replication, <i>i.e.</i> the synthesis of
single-stranded RNA genomes, an absolutely necessary step for the survival and
growth of the virus. Thus, RdRp is an obvious target for antiviral drug design.
Interestingly, several plant-derived polyphenols have been shown to inhibit
enzymatic activities of RdRp of various RNA viruses including polio-virus type
1, parainfluenza virus type 3, and respiratory syncytial virus etc. More
importantly, natural polyphenols have been used as a dietary supplementation
for humans for a long time and played a beneficial role in immune homeostasis.
Therefore, we were curious to study the binding of dietary polyphenols with
RdRp of SARS-CoV-2 and assess their potential as an effective therapy for
COVID-19. In this present work, we made a library of twenty potent polyphenols that
have shown substantial therapeutic effects against various diseases. The
polyphenols were successfully docked in the catalytic pocket of RdRp of SARS-CoV
and SARS-CoV-2, and detailed studies on ADME prediction, toxicity prediction
and target analysis were performed. The study reveals that EGCG, quercetagetin,
and myricetin strongly bind to the active site of SARS-CoV-2 RdRp. Our studies
suggest that EGCG, quercetagetin, and myricetin can inhibit RdRp and represent
an effective therapy for COVID-19. </p>
|
Satyam Singh; Avinash Sonawane; Sushabhan Sadhukhan
|
Natural Products; Computational Chemistry and Modeling
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2020-05-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b44bb8c1a806e3db18c/original/plant-derived-natural-polyphenols-as-potential-antiviral-drugs-against-sars-co-v-2-via-rna-dependent-rna-polymerase-rd-rp-inhibition-an-in-silico-analysis.pdf
|
60c73f9e842e655830db1b28
|
10.26434/chemrxiv.6894605.v2
|
Illuminating the Secrets of Crystals - Microcrystal Electron Diffraction in Structural Biology
|
An exploration of the crystallographic theory of the relatively novel method of Microcrystal Electron Diffraction (MicroED), via comparison to X-ray crystallography at the theoretical and practical level as it applies to biological macromolecules. We then attempt to outline the limitations and challenges that the technique currently faces in structural biology, and suggest future areas of study that may improve and optimize the technique.
|
Rob Barringer; Thomas Meier
|
Biochemistry; Biophysics; Cell and Molecular Biology; Chemical Biology; Structure
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2018-11-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9e842e655830db1b28/original/illuminating-the-secrets-of-crystals-microcrystal-electron-diffraction-in-structural-biology.pdf
|
60ee8a3eb95bdd06d062074b
|
10.26434/chemrxiv-2021-v2pnn
|
Chemformer: A Pre-Trained Transformer
for Computational Chemistry
|
Transformer models coupled with Simplified Molecular Line Entry System (SMILES) have
recently proven to be a powerful combination for solving challenges in cheminformatics. These
models, however, are often developed specifically for a single application and can be very
resource-intensive to train. In this work we present Chemformer model – a Transformerbased
model which can be quickly applied to both sequence-to-sequence and discriminative
cheminformatics tasks. Additionally, we show that self-supervised pre-training can improve
performance and significantly speed up convergence on downstream tasks. On direct synthesis
and retrosynthesis prediction benchmark datasets we publish state-of-the-art results for top-
1 accuracy. We also improve on existing approaches for a molecular optimisation task and
show that Chemformer can optimise on multiple discriminative tasks simultaneously. Models,
datasets and code will be made available after publication.
|
Ross Irwin; Spyridon Dimitriadis; Jiazhen He; Esben Bjerrum
|
Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2021-07-15
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ee8a3eb95bdd06d062074b/original/chemformer-a-pre-trained-transformer-for-computational-chemistry.pdf
|
67575a3d7be152b1d071f2e5
|
10.26434/chemrxiv-2024-9rvkg
|
Development of a scalable synthetic route to (1R,5R)-2,2-dimethoxybicyclo[3.1.0]hexan-3-one: an important intermediate in the synthesis of lenacapavir
|
(1R,5R)-2,2-Dimethoxybicyclo[3.1.0]hexan-3-one is used in the asymmetric synthesis of lenacapavir. Herein, we report an enantioselective synthesis of this important chiral intermediate from the inexpensive commodity (R)-epichlorohydrin. This synthetic method comprises 6 steps, including a 4-step telescoped bicyclic ketone synthesis, I2-promoted hydroxylation, and an Albright-Goldman oxidation. This sequence affords (1R,5R)-2,2-dimethoxybicyclo[3.1.0]hexan-3-one in an overall 25% isolated yield as an enantiomerically pure compound. The entire process has been successfully demonstrated on a hundred-gram scale.
|
Aline Nunes De Souza; Nagaraju Sakkani; Daryl Guthrie; Rajkumar Sahani; John Saathoff; Sam Hochstetler; Justina Burns; Saeed Ahmad; George Laidlaw; B. Frank Gupton; Douglas Klumpp; limei jin
|
Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry; Stereochemistry
|
CC BY NC 4.0
|
CHEMRXIV
|
2024-12-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67575a3d7be152b1d071f2e5/original/development-of-a-scalable-synthetic-route-to-1r-5r-2-2-dimethoxybicyclo-3-1-0-hexan-3-one-an-important-intermediate-in-the-synthesis-of-lenacapavir.pdf
|
60c75481469df4bd16f44f66
|
10.26434/chemrxiv.13669235.v1
|
Origin of Protonation Side Products in Pd-Catalyzed Decarboxylative Allylation Reactions: Evidence for In Situ Modification of Triphenylphosphine Ligand
|
Palladium-catalyzed decarboxylative allylation (DcA) is a well-established method of
carbon-carbon bond formation. This type of coupling is quite attractive, as the only byproduct is
CO2. While a wide variety of ligands have been employed with Pd(0) or Pd(II) precatalysts in DcA
reactions, the ligand structure is most often based on a triarylphosphine core. Despite their
demonstrated utility, DcA processes have been hindered by the formation of protonation side
products. While this phenomenon has been widely acknowledged, little has been reported on
the origin of the proton. Herein, we address this and provide multiple lines of experimental
evidence for the proton originating from the triarylphosphine ligand. <br />
|
Monica A. Gill; Samuel
W. J. Shields; Jeff Manthorpe
|
Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation; Catalysis; Ligands (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75481469df4bd16f44f66/original/origin-of-protonation-side-products-in-pd-catalyzed-decarboxylative-allylation-reactions-evidence-for-in-situ-modification-of-triphenylphosphine-ligand.pdf
|
674b9ec07be152b1d0861525
|
10.26434/chemrxiv-2024-jcvhx
|
Exo-Linker: Positional Reconfiguration Driving Significant Advances in ADC Stability and Efficacy
|
Antibody-drug conjugates (ADCs) have transformed targeted cancer therapy by combining the specificity of monoclonal antibodies with the cytotoxic potency of small-molecule drugs. However, payload instability, hydrophobicity, and premature cleavage limit their efficacy and safety. This study presents Exo-Linker technology as a novel solution to these issues. By repositioning cleavable peptide linkers like Glu-Val-Cit and Glu-Glu-Val-Cit at the exo-position of the p-aminobenzyl carbamate moiety, Exo-Linkers improve stability, hydrophilicity, and resistance to enzymatic degradation.
Key findings highlight the superior pharmacokinetics, tumor-suppressive efficacy, and enzymatic stability of Exo-Linker ADCs in preclinical models, significantly outperforming traditional Val-Cit-based linkers. Integration with the second-generation AJICAP platform broadens therapeutic windows, ensures precise drug-to-antibody ratio control, and minimizes aggregation. Exo-Linkers establish a new standard for ADC development, overcoming critical limitations of traditional linkers while enabling safer and more effective cancer treatments. This innovative approach redefines the therapeutic landscape, enhances patient outcomes, and broadens the scope of ADC applications.
|
Tomohiro Watanabe; Tomohiro Fujii; Yutaka Matsuda
|
Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-12-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674b9ec07be152b1d0861525/original/exo-linker-positional-reconfiguration-driving-significant-advances-in-adc-stability-and-efficacy.pdf
|
6527281545aaa5fdbbcd7258
|
10.26434/chemrxiv-2023-1xz7b-v3
|
Ground State Orbital Analysis Predicts S1 Charge Transfer in Donor–Acceptor Materials
|
Donor-acceptor (D-A) materials, such as D-A co- crystals and D-A copolymers, can exhibit a wide range of unique photophysical properties with applications in next-generation optoelectronics. The properties of D-A dimer models, computed with electronic structure calculations, are often employed to predict properties of D-A materials. One of the most important D-A dimer quantities is the degree of charge transfer (DCT) in the S1 state, which correlates with properties such as fluorescence lifetimes and intersystem crossing rates. Predictive metrics of the S1 DCT generally require an excited state quantum chemistry calculation. Presented here is a novel metric for predicting the degree of charge transfer (DCT) in the S1 electronic state of D-A materials, computed solely with ground state orbital analysis. This metric computes the average of two quantities: (1) the degree of similarity between the highest occupied molecular orbital (HOMO) in the donor molecule and the D-A complex and (2) the degree of similarity between the lowest occupied molecular orbital (LUMO) in the acceptor molecule and the D-A complex. A linear relationship between this similarity metric and the DCT in the S1 state (HOMO → LUMO transition) is demonstrated for a data set of 31 D-A dimers. The integration of this novel orbital structure- function relationship into high-throughput screening methods is discussed alongside best practices for choosing molecular geometries and quantifying the DCT.
|
Ali Abou Taka; John M. Herbert; Laura M. McCaslin
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Materials Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2023-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6527281545aaa5fdbbcd7258/original/ground-state-orbital-analysis-predicts-s1-charge-transfer-in-donor-acceptor-materials.pdf
|
64382c5b1d262d40ea65d444
|
10.26434/chemrxiv-2023-tf3r8
|
Correlation evaluation of ion adsorption-based rare earth leaching performance based on zeta potential drop leaching
|
Rare earth elements are indispensable raw materials for advanced aero-engines, special optical materials, and high-performance electronic products. With the development of social economy, the global demand for rare earth resources is increasing, and rare earths have become a key metal for the development of new industries and frontier technologies that are highly valued both at home and abroad. ion-adsorbed rare earth ores are an important source of rare earths, so the efficient green leaching of ion-adsorbed rare earths is important. Researchers found that the selection of efficient green leaching agent for ion-adsorbed rare earths is based on the zeta potential of tailing clay minerals in addition to leaching efficiency, and both zeta potential and leaching ion concentration are related to mineral acidity and alkalinity, and the pH of tailing water suspension is a direct indicator of environmental water quality requirements. Therefore, the efficiency of the leaching process is closely integrated with the environmental evaluation, and the characteristics and correlation of the changes in zeta potential, pH, conductivity and pollutant concentration of the pulp of clay mineral content during the leaching process of ore leaching and tailings aqueous electrolyte solution leaching are studied by evaluating the leaching system, and a set of correlation leaching efficiency and environmental impact evaluation method is established based on the results of the above analysis, which is of scientific development of ion adsorption rare earth resources It has important theoretical significance and practical application value.
|
Xunhe Li; Yongxiu Li; Xuezhen Zhou; Huajiao Zhou; Kang Wang
|
Chemical Engineering and Industrial Chemistry; Natural Resource Recovery
|
CC BY 4.0
|
CHEMRXIV
|
2023-04-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64382c5b1d262d40ea65d444/original/correlation-evaluation-of-ion-adsorption-based-rare-earth-leaching-performance-based-on-zeta-potential-drop-leaching.pdf
|
6272a2f5a42e9ca3e333a80f
|
10.26434/chemrxiv-2022-w7tlg
|
Two-Dimensional Confinement for Generating Thin
Single Crystals for Time-Resolved Electron
Diffraction and Spectroscopy: An Intramolecular
Proton Transfer Study
|
Thin single organic crystals (≤1 μm) with large area (≥100 × 100 μm2) are desirable to explore their
photoinduced processes using transmission-based ultrafast spectroscopy and electron-diffraction
techniques. Here we present a method to grow thin large area single crystals of a prototypical proton
transfer system, 1,5-dihydroxyanthraquinone. As a proof of concept, we perform optical
measurements on as-grown samples and recorded the data in transmission mode.
|
Hyein Hwang; Vandana Tiwari; Hong-Guang Duan; Simon F. Bittmann; Friedjof Tellkamp; Ajay Jha; R. J. Dwayne Miller
|
Physical Chemistry; Optics; Photochemistry (Physical Chem.); Crystallography
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6272a2f5a42e9ca3e333a80f/original/two-dimensional-confinement-for-generating-thin-single-crystals-for-time-resolved-electron-diffraction-and-spectroscopy-an-intramolecular-proton-transfer-study.pdf
|
652efcb78bab5d20559012ee
|
10.26434/chemrxiv-2023-3vtfc
|
Theoretical basis for interpreting heterodyne chirality-selective sum frequency generation spectra of water
|
Chirality-selective vibrational sum frequency generation spectroscopy (chiral SFG) has emerged as a powerful technique for the study of biomolecular hydration water due to its sensitivity to the induced chirality of the first hydration shell. Thus far, water O-H vibrational bands in phase-resolved heterodyne chiral SFG spectra have been fit using one Lorentzian function per vibrational band, and the resulting fit has been used to infer the underlying frequency distribution. Here, we show that this approach may not correctly reveal the structure and dynamics of hydration water. Our analysis illustrates that the chiral SFG responses of symmetric and asymmetric O-H stretch modes of water have opposite phase and equal magnitude and are separated in energy by intramolecular vibrational coupling and a heterogeneous environment. The sum of the symmetric and asymmetric responses implies that an O-H stretch in a heterodyne chiral SFG spectrum should appear as two peaks with opposite phase and equal amplitude. Using pairs of Lorentzian functions to fit water O-H stretch vibrational bands, we improve spectral fitting of previously acquired experimental spectra of model beta-sheet proteins and reduce the number of free parameters. The fitting allows us to estimate the vibrational frequency distribution and thus reveals the molecular interactions of water in hydration shells of biomolecules directly from chiral SFG spectra.
|
Daniel Konstantinovsky; Ty Santiago; Matthew Tremblay; Garth Simpson; Sharon Hammes-Schiffer; Elsa Chui-Ying Yan
|
Physical Chemistry; Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.)
|
CC BY 4.0
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CHEMRXIV
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2023-10-18
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652efcb78bab5d20559012ee/original/theoretical-basis-for-interpreting-heterodyne-chirality-selective-sum-frequency-generation-spectra-of-water.pdf
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6792b0fefa469535b991b8fd
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10.26434/chemrxiv-2024-36w9w-v2
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Resolving the Coverage Dependence of Surface Reaction Kinetics with Machine Learning and Automated Quantum Chemistry Workflows
|
Microkinetic models for catalytic systems require estimation of many thermodynamic and kinetic parameters that can be calculated for isolated species and transition states using ab initio methods. However, the presence of nearby co-adsorbates on the surface can dramatically alter these thermodynamic and kinetic parameters causing them to be dependent on species coverage fractions. As there are combinatorially many co-adsorbed configurations on the surface, computing the coverage dependence of these parameters is far less straightforward. We present a framework for generating and applying machine learning models to predict coverage-dependent parameters for microkinetic models. Our toolkit enables automatic calculation and evaluation of co-adsorbed configurations allowing us to sample 2,000 co-adsorbed adsorbates and transition states (TSs) for a diverse set of 9 reactions on Cu(111), a challenging surface, with four possible co-adsorbates. This dataset was then used to train subgraph isomorphic decision trees (SIDTs) to predict the stability and association energy of configurations. We were able to achieve mean absolute errors (MAEs) of 0.106 eV on adsorbates, 0.172 eV on TSs, and due to natural error cancellation in SIDTs for relative properties, 0.130 eV on reaction energies and 0.180 eV on activation barriers. We describe how to use these models to predict coverage- dependent corrections for adsorbates and TSs, and demonstrate on H∗, HO∗ and O∗ comparing the generated SIDT model with an iteratively refined version.
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Matthew S. Johnson; David H. Bross; Judit Zador
|
Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis
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CC BY NC ND 4.0
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CHEMRXIV
|
2025-01-27
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6792b0fefa469535b991b8fd/original/resolving-the-coverage-dependence-of-surface-reaction-kinetics-with-machine-learning-and-automated-quantum-chemistry-workflows.pdf
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60c74e33337d6c1fcfe27f43
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10.26434/chemrxiv.12722483.v1
|
COVID19 Approved Drug Repurposing: Pocket Similarity Approach
|
<p>SARS CoV 2 has spread worldwide and caused a major outbreak of coronavirus disease 2019 (COVID-19). To date, no licensed drug or a vaccine is available against COVID19.</p><p>Starting from all of the resolved SARS CoV2 crystal structures, this study aims to find inhibitors for all of the SARS CoV2 proteins. To achieve this, I used PocketMatch to test the similarity of approved drugs binding sites against all of the binding sites found on SARS CoV 2 proteins. After that docking was used to confirm the results.</p><p>I found drugs that inhibit the main protease, Nsp12 and Nsp3. The discovered drugs are either in clinical trials (Sildenafil, Lopinavir, Ritonavir) or have in vitro antiviral activity (Nelfinavir, Indinavir, Amprenavir, depiqulinum , Gemcitabine, Raltitrexed, Aprepitant, montelukast, Ouabain, Raloxifene) whether against SARS CoV 2 or other viruses. In addition to this, further analysis of pockets revealed a steroidal pocket that might open the door to hypotheses on why the mortality of men is higher than women.</p><p>Many of the in silico repurposing studies test binding of the compound to the target using docking. The significance of this study adds to the similarity between the drug binding site and the target binding site. This takes into consideration the dynamic behaviour of the pocket after ligand binding.</p><div><br /></div>
|
Mohamed Fadlalla
|
Drug Discovery and Drug Delivery Systems
|
CC BY 4.0
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CHEMRXIV
|
2020-07-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e33337d6c1fcfe27f43/original/covid19-approved-drug-repurposing-pocket-similarity-approach.pdf
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60c74e740f50db0e6d39721a
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10.26434/chemrxiv.12752408.v1
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Amphiphilic Ionic Liquid Induced Fusion of Phospholipid Liposomes
|
Membrane fusion is a key biological phenomenon with potential applications in biotechnology. In this work, we provide biophysical and structural evidence that liposomes composed of POPC/POPG phospholipids undergo fusion in the presence of ionic liquids containing 1-alkyl-3-methyl-imidazolium cations. The fusion phenomenon is confirmed using dynamic light scattering based size measurements, and Fluorescence based dye leakage and lipid mixing assays. <sup>1</sup>H-<sup>1</sup>H NOESY measurements using solid-state NMR spectroscopy were performed to obtain insights into fusion mechanism. It is found that ionic liquid induced splaying of phospholipid chains is crucial for overcoming the hydration barrier between the merging bilayers. Also, transiently lived fusion-holes are formed at the initial stages of bilayer mixing resulting in a leaky fusion phenomenon. <br /><br />Although considered as “green” alternatives to conventional solvents, ionic liquids can exhibit cytotoxicity by altering the structural integrity of cellular membrane. Our study provides mechanistic details of the evolution of phospholipid membrane structure resulting in membrane fusion when subjected to increasing ionic liquid concentrations. We believe that findings of this study will further our understanding of ionic liquids induced cytotoxicity and non-protein assisted membrane fusion. <br /><br />
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Sandeep Kumar; Navleen Kaur; Venus Singh Mithu
|
Biophysics; Biophysical Chemistry; Self-Assembly
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CC BY NC ND 4.0
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CHEMRXIV
|
2020-08-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e740f50db0e6d39721a/original/amphiphilic-ionic-liquid-induced-fusion-of-phospholipid-liposomes.pdf
|
60c75380f96a001d41288475
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10.26434/chemrxiv.13499439.v1
|
Mechanistic Analysis of Light-Driven Overcrowded Alkene-Based Molecular Motors by Multiscale Molecular Simulations
|
We analyze light-driven overcrowded alkene-based molecular motors, an intriguing class of small molecules that have the potential to generate MHz-scale rotation rates. The full rotation process is simulated at multiple scales by combining quantum surface-hopping molecular dynamics (MD) simulations for the photoisomerization step with classical MD simulations for the thermal helix inversion step. A Markov state analysis resolves conformational substates, their interconversion kinetics, and their roles in the motor’s rotation process. Furthermore, motor performance metrics, including rotation rate and maximal power output, are computed to validate computations against experimental measurements and to inform future designs. Lastly, we find that to correctly model these motors, the force field must be optimized by fitting selected parameters to reference quantum mechanical energy surfaces. Overall, our simulations yield encouraging agreement with experimental observables such as rotation rates, and provide mechanistic insights that may help future designs.
|
Mudong Feng; Michael K. Gilson
|
Computational Chemistry and Modeling
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CC BY 4.0
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CHEMRXIV
|
2020-12-30
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75380f96a001d41288475/original/mechanistic-analysis-of-light-driven-overcrowded-alkene-based-molecular-motors-by-multiscale-molecular-simulations.pdf
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6453908f27fccdb3ea7a4b59
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10.26434/chemrxiv-2023-d5d3r
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Stronger together: Polymeric sulfur ylides with minimal charge separation open a new generation of antifouling and biofilm preventing materials
|
Zwitterionic polymers are widely employed hydrophilic building blocks for antifouling coatings with numerous applications across a wide range of fields, including but not limited to biomedical science, drug delivery and nanotechnology. Zwitterionic polymers are considered as an attractive alternative to polyethylene glycol because of their enhanced biocompatibility and effectiveness to prevent non-specific protein adsorption and formation of biofilms. To this end, zwitterionic polymers are classified in two categories, namely polybetaines and polyampholytes. Yet, despite a fundamental interest to drive the development of new antifouling materials, the chemical composition of zwitterionic polymer remains severely limited. Here, we propose an entirely new class of antifouling polymers, namely poly(sulfur ylides) belonging to the largely overlooked class of poly(ylides). We show that poly(sulfur ylides) effectively prevent the adhesion of biomolecules and formation of biofilms from pathogenic bacteria. While surface energy analysis reveals strong hydrogen-bond acceptor capabilities of poly(sulfur ylide) and suggests a repellent hydration barrier, membrane damage of pathogenic bacteria induced by poly(sulfur ylides) indicates a killing-by-contact mechanism. Such synergistic effect of poly(sulfur ylides) offers distinct advantages over polyethylene glycol when designing antifouling materials in the future. We expect that our findings will pave the way for the development of a range of ylide-based materials with antifouling properties that have yet to be explored, opening up new innovative directions at the interface of chemistry, biology, and material science.
|
Bela B. Berking; Georgia Poulladofonou; Dimitrios Karagrigoriou; Daniela A. Wilson; Kevin Neumann
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Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Organic Polymers; Microbiology; Materials Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
|
2023-05-05
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6453908f27fccdb3ea7a4b59/original/stronger-together-polymeric-sulfur-ylides-with-minimal-charge-separation-open-a-new-generation-of-antifouling-and-biofilm-preventing-materials.pdf
|
67cade0f81d2151a027e50d0
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10.26434/chemrxiv-2025-lw0rp
|
Design of 2-aminobenzothiazole derivatives targeting trypanosomatid PTR1 by a multidisciplinary fragment-based approach
|
Pteridine reductase 1 (PTR1) is a key folate pathway enzyme of pathogenic trypanosomatids that reduces biopterin to dihydro- and tetrahydrobiopterin. It is a promising target for drug design against diseases such as sleeping sickness or leishmaniases. Amongst known PTR1 inhibitors, 2-aminobenzothiazole derivatives that target the PTR1 biopterin pocket were previously found to show good overall toxicity profiles and some of them display promising anti-parasite activity. On the other hand, compounds containing a 3,4-dichlorophenyl moiety, such as 1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine (I), interact in a different region of the T. brucei PTR1 (TbPTR1) binding pocket. In this work, we develop two compound series in which a 2-aminobenzothiazole moiety is connected to a 3,4-dichlorophenyl moiety via different linkers. A bespoke in-house compound library was virtually screened by computational docking against TbPTR1 and L. major PTR1 (LmPTR1). Five selected compounds were synthesized, three of which display low-micromolar activity against TbPTR1, and two of these were also found to be low-micromolar inhibitors of T. brucei. In addition, one of the latter compounds shows inhibitory activity against LmPTR1 and L. infantum, demonstrating dual-inhibition potential. Quantum chemical calculations and crystallography guided the design of further compounds whose structure-activity relationship (SAR) showed that the halogen at the meta position of the phenyl ring is energetically more favorable for anti-PTR1 activity than at the para position, but that single halogen substitutions resulted in lower anti-parasite activities. Overall, our multidisciplinary fragment-based approach resulted in compounds with experimentally validated designed binding modes, that were less toxic and more active against the T. brucei parasite than the parent compound I.
|
Joanna Panecka-Hofman; Pasquale Linciano; Ina Pöhner; Edyta Dyguda-Kazimierowicz; Wiktoria Jedwabny; Giacomo Landi; Nuno Santarem; Gesa Witt; Bernhard Ellinger; Maria Kuzikov; Rosaria Luciani; Stefania Ferrari; Stefano Mangani; Cecilia Pozzi; Anabela Cordeiro-da-Silva; Sheraz Gul; Maria Paola Costi; Rebecca Wade
|
Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling
|
CC BY 4.0
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CHEMRXIV
|
2025-03-19
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cade0f81d2151a027e50d0/original/design-of-2-aminobenzothiazole-derivatives-targeting-trypanosomatid-ptr1-by-a-multidisciplinary-fragment-based-approach.pdf
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61643d400ad1ff4a0291a99e
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10.26434/chemrxiv-2021-3mktf
|
Making molecules vibrate: Interactive web environment for the teaching of infrared spectroscopy
|
Infrared spectroscopy (IR) is a staple structural elucidation and characterization technique due to its ability to identify functional groups and its ease of use. Interestingly, it allows capturing electronic effects via their influence on the bond strength of "probes" such as the carbonyl group and also offers a wealth of examples for discussion on the theory of electronic transitions.
For this reason, IR spectroscopy is typically taught both in theoretical classes and in applied structural analysis courses. In practice, there is rarely a link between those courses, and both suffer from the lack of exploratory learning, i.e., tools with which students can explore the interplay between symmetry and selection rules, as well as electronic effects and vibrational frequencies — with almost immediate feedback. In practice, this might lead to students that are well skilled in looking up vibrational frequencies in lookup tables but do not understand the links to electronic effects and reactivity.
Here, we introduce a web app that leverages semi-empirical quantum mechanical (or force-field based) calculations, performed on a web service, in an interactive interface to provide an environment in which students can explore how slight changes to the structure manifest in changes of the spectrum.
This approach avoids the time-consuming handling of potentially hazardous materials that might not be readily available and invites students to play with spectroscopy — to "see" and "test" electronic effects that are so commonplace in organic chemistry education.
As a "side effect" our web app also provides a powerful aid for research scientists to investigate how different structural modifications, such as substitution, isomerism, or steric strain, would manifest in the infrared spectrum.
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Kevin Maik Jablonka; Luc Patiny; Berend Smit
|
Theoretical and Computational Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry
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CC BY NC 4.0
|
CHEMRXIV
|
2021-10-12
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61643d400ad1ff4a0291a99e/original/making-molecules-vibrate-interactive-web-environment-for-the-teaching-of-infrared-spectroscopy.pdf
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62cdd313724581d057925dc1
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10.26434/chemrxiv-2022-lfnw1
|
Electric-Field-Induced Coupling of Aryl Iodides with a Nickel(0) Complex
|
The influence of electric fields has been postulated as a major factor for rapid catalysis in enzymatic systems. Here, we show that external electric fields can modulate the reactivity of an otherwise kinetically inert transition metal complex to affect a coupling reaction. An air-stable nickel(0) complex is demonstrated to exhibit no reactivity towards the oxidative addition of aryl iodides at room temperature. However, when an external electric field was applied to this reaction solution with a scanning tunneling microscope, the biaryl coupling product was detected in-situ through single-molecule conductance measurements and ex-situ through high-resolution mass spectrometry. These results highlight the importance of electric field effects in reaction chemistry, and demonstrate the application of STM studies towards electric field induced organometallic transformations.
|
Nicholas Orchanian; Sophia Guizzo; Michael Steigerwald; Colin Nuckolls; Latha Venkataraman
|
Physical Chemistry; Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Bond Activation; Coordination Chemistry (Organomet.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-14
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cdd313724581d057925dc1/original/electric-field-induced-coupling-of-aryl-iodides-with-a-nickel-0-complex.pdf
|
64f260d379853bbd78e55897
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10.26434/chemrxiv-2023-4n8v1
|
Hematocrit-independent sampling enables white blood cell counts from patterned dried blood spot cards
|
The accurate and efficient measurement of white blood cell (WBC) counts is vital for monitoring general patient health and can aid in diagnosing a range of possible infections or diseases. Even with their importance universally acknowledged, access to WBC counts is largely limited to those with access to phlebotomists and centralized clinical laboratories, which house the instrumentation that perform the tests. As a result, large populations of people (e.g., those that are home-bound or live in remote locations) lack facile access to testing. Dried blood spot (DBS) cards are often used to bridge these gaps in access to testing by offering the ability to collect blood at home for ambient shipping to laboratories. However, it is well understood that these cards, which are prepared from cellulose cardstocks without further modification, suffer from variabilities in accuracy and precision due to uncontrolled sample spreading and hematocrit effects, which has hindered their use to determine WBC counts. In this manuscript, we present a method to obtain an accurate WBC count using a patterned dried blood spot (pDBS) card, which comprises collection zones that meter volumes of dried blood. We demonstrate that, unlike the gold standard DBS card (Whatman 903), our pDBS design allows for the collection of a reproducible, average volume of blood volume over the range of hematocrits from 25–55%. We then used qPCR to quantify the 18S rRNA gene to determine WBC counts from the volumes of blood that are metered in pDBS zones. We observe that WBC counts generated from our method are comparable to those measured by a HemoCue point-of-care WBC analyzer. Our approach to using pDBS cards as a blood collection device has the potential to support at-home sampling and other patient populations that need WBC counts but lack access to clinical facilities.
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Allison J. Tierney; Kim C. Williamson; V. Ann Stewart; Charles R. Mace
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Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-09-04
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f260d379853bbd78e55897/original/hematocrit-independent-sampling-enables-white-blood-cell-counts-from-patterned-dried-blood-spot-cards.pdf
|
60c758b7f96a00cadc288e9c
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10.26434/chemrxiv.14535966.v2
|
Chemical Tuning of NaSICON Surfaces for Fast-Charging Na Metal Solid-State Batteries
|
<p>Solid-state
batteries (SSBs) with alkali metal anodes hold great promise as energetically
dense and safe alternatives to conventional Li-ion cells. Whilst, in principle,
SSBs have the additional advantage of offering virtually unlimited plating
current densities, fast charges have so far only been achieved through sophisticated
interface engineering strategies. Here, we reveal that such interface
engineering can be easily achieved by tuning the chemistry of NaSICON solid
electrolytes (Na<sub>3.4</sub>Zr<sub>2</sub>Si<sub>2.4</sub>P<sub>0.6</sub>O<sub>12</sub>)
and taking advantage of the thermodynamic
stabilization of a Na<sub>3</sub>PO<sub>4</sub> layer on their surface upon
thermal activation. The optimized planar Na|NZSP interfaces are characterized
by their exceptionally low interface resistances (down to 0.1 Ω cm<sup>2 </sup>at room temperature) and, more
importantly, by their tolerance to large plating current densities (up to 10 mA
cm<sup>-2</sup>) even for extended cycling periods of 30 minutes (corresponding
to an areal capacity 5 mAh cm<sup>-2</sup>).</p>
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Edouard Querel; Ieuan Seymour; Andrea Cavallaro; Qianli Ma; Frank Tietz; Ainara Aguadero
|
Energy Storage
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2021-05-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758b7f96a00cadc288e9c/original/chemical-tuning-of-na-sicon-surfaces-for-fast-charging-na-metal-solid-state-batteries.pdf
|
65e75071e9ebbb4db9f60c30
|
10.26434/chemrxiv-2024-lnbct
|
Enhancing photothermal energy transduction through inter- and intramolecular interactions of multiple two-photon dyes appended onto Calix[4]arene
|
Organic dyes-based photothermal agents (OPTAs) has received increasing attention as alternative to inorganic materials due to their higher biocompatibility and extensive diversification. Maximizing non-radiative deexcitation channels is crucial to improve the photothermal conversion efficiency (PCE) of OPTAs. This is typically achieved through individual molecular design or collective enhancement using supramolecular strategies. Furthermore, photothermal therapy (PTT) generally relies on linear one-photon absorption of the light source by the OPTA, with less consideration given to non-linear two-photon absorption (2PA) strategies, despite their potential benefits. Here, a synergistic strategy, which combines intramolecular and intermolecular quenching, is employed to maximize the photothermal efficiency of diphenylamino substituted distyryl dicyanobenzene (DSB), an outstanding two-photon absorbing chromophore. One to three DSB units have been introduced on the conic p-tert-butyl-calix[4]arene (CX), serving as a preorganizing platform to allow aggregates formation and promote intramolecular quenching within the multichromophoric systems. Importantly, the multichromophoric molecules had very high two photon absorption capabilities with cross sections (2PA) reaching maximal values of 3290 GM at 810 nm. Experimental data accompanied by large scale Molecular Dynamics (MD) simulations and Time-Dependent Density Functional Theory (TD-DFT) calculations shed light onto the interaction mechanism in those multiple DSB-appended CX compound to rationalize their optical properties. Then, the formulation with Pluronic F127 amphiphile yields water-dispersible nanoprecipitates (Nps) in which the PCE is further maximized and the photobleaching reduced due to the combination of intra and intermolecular quenching. The high two-photon absorption in the near-infrared (NIR) window associated to high PCE of these nanosized OPTAs could serve as basis to future in vivo 2P-PTT applications.
|
Isabelle Toubia; Yann Bernhard; Valentin Diez Cabanes; Stephania Abdallah; Rana Mhanna; Tioga Gulon; Stéphane Parant; Jean-Pierre Malval; Jean-Bernard Regnouf-de-Vains; Antonio Monari; Mariachiara Pastore; Andreea Pasc
|
Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-03-07
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e75071e9ebbb4db9f60c30/original/enhancing-photothermal-energy-transduction-through-inter-and-intramolecular-interactions-of-multiple-two-photon-dyes-appended-onto-calix-4-arene.pdf
|
67631f99fa469535b901d213
|
10.26434/chemrxiv-2024-28g0t
|
Untangling Sources of Error in the Density-Functional Many-Body Expansion
|
Development of meta-generalized gradient approximations (meta-GGAs) has generally led to more accurate density-functional approximations, albeit ones that have more stringent requirements for the quadrature grids that are used to evaluate the exchange-correlation energy. Here, we demonstrate that grid-induced errors are amplified when meta-GGAs are used in conjunction with a many-body expansion, which is a popular means to parameterize classical force fields using electronic structure calculations. At the same time, delocalization errors are exacerbated by the many-body expansion, leading to exaggerated estimates of nonadditive n-body interactions, as illustrated here for anion–water clusters using the meta-GGA functionals SCAN and wB97X-V. Standard grids that are typically accurate for noncovalent interactions with meta-GGA functionals result in runaway error accumulation when used with the many-body expansion. Denser grids eliminate this problem and expose the inherent self-interaction error, which must be mitigated using other strategies that are discussed herein.
|
Dustin Broderick; John Herbert
|
Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning
|
CC BY 4.0
|
CHEMRXIV
|
2024-12-20
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67631f99fa469535b901d213/original/untangling-sources-of-error-in-the-density-functional-many-body-expansion.pdf
|
63da8b6f01ecc690f91be0e3
|
10.26434/chemrxiv-2023-r344r
|
I(III)-Mediated Arene C-H Amination using (Hetero)Aryl Nucleophiles
|
Herein, we report the metal-free oxidative C-H amination of arenes via a heterocyclic group transfer reaction from an I(III) N-HVI reagent. N-heterocycles serve as an oxidatively masked amine nucleophile and the resulting N-aryl pyridinium salts are inert to further oxidation. The products provide a versatile handle to access valuable aryl amine derivatives. The reaction proceeds under mild conditions and has good scope of both arene and N-heterocycle.
|
Bill Motsch; Jasjit Kaur; Sarah Wengryniuk
|
Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2023-02-02
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da8b6f01ecc690f91be0e3/original/i-iii-mediated-arene-c-h-amination-using-hetero-aryl-nucleophiles.pdf
|
620ceeeca6fb4d4a2957c43d
|
10.26434/chemrxiv-2022-g64d8
|
Fluorogenic and Genetically-Targeted Red-Emitting Molecular Calcium indicator
|
We introduce a strategy for the fluorogenic and genetic targeting of a calcium sensor by combining a protein fluorogen with the BAPTA sensing group. The resulting dual-input probe acts like a fluorescent AND logic gate with a Ca2+-sensitive red emission that is activated only upon reaction with the protein self-labeling tag HaloTag with a 18-fold intensity enhancement. The fluorogenic targeting of the calcium probe was evidenced by the selective wash-free imaging of calcium in the nucleus of Hela cells expressing a nuclear HaloTag protein.
|
Sylvestre P. J. T. Bachollet; Nicolas Pietrancosta; Jean-Maurice Mallet; Blaise Dumat
|
Biological and Medicinal Chemistry; Chemical Biology
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-02-18
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620ceeeca6fb4d4a2957c43d/original/fluorogenic-and-genetically-targeted-red-emitting-molecular-calcium-indicator.pdf
|
66b5067901103d79c53f511b
|
10.26434/chemrxiv-2024-36wg8
|
Unifying Geochemical Scenario for the Origin of a High Cellular Potassium to Sodium Ratio in Living Cells
|
Potassium ion is the most common compound in all living organisms, with intercellular [K+]:[Na+] ratios greater than 1 across all domains of life. While most natural aquifers are rich in sodium, it is believed that localized potassium-rich environments were crucial for initiating prebiotic reaction networks leading to the origin of life. Several current hypotheses, based on modern geochemical observations, suggest that hydrothermal fields and their associated clays could have provided such environments. My work expands on current prebiotic theories regarding the origins of high potassium concentrations by providing a geochemical basis for the empirical observations proposed by other authors. Here, I show how abiotic enrichment in potassium can occur during the acidic alteration of a wide range of aluminum silicate rocks through the formation of alum salts (KAl(SO4)2•12H2O). I further propose how simple and well-known alum chemistry can lead to the accumulation of important biological molecules, such as phosphates, ammonia, and carboxylic acids. I provide a general thermodynamic model, proof-of-concept experiments, and a chemical rationale for the plausibility and importance of potassium-rich environments in the origin of life. This work suggests that potassium enrichment could have been one of the earliest steps in the origins of life, defining the reaction conditions where most prebiotic reactions took place. Since potassium is both the most common and simplest component in all living organisms on Earth, understanding the geochemical conditions that lead to potassium enrichment is valuable for comprehending the origins of life on Earth and the search for life elsewhere in the universe, including on our closest neighbor, Mars.
|
Olga Taran
|
Physical Chemistry; Earth, Space, and Environmental Chemistry; Geochemistry; Hydrology and Water Chemistry; Solution Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-08-09
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5067901103d79c53f511b/original/unifying-geochemical-scenario-for-the-origin-of-a-high-cellular-potassium-to-sodium-ratio-in-living-cells.pdf
|
64c3a985ce23211b20b29fc6
|
10.26434/chemrxiv-2023-s0xl4
|
Towards a Stochastic Complete Active Space Second Order Perturbation Theory
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In this work an internally contracted Stochastic Complete Active Space Second Order Perturbation Theory, Stochastic–CASPT2, is reported. The method relies on stochastically sampled reduced density matrices (RDMs) up to rank four and con- tractions thereof with the generalized Fock matrix. A new protocol for calculating higher–order RDMs in FCIQMC has been designed based on: (1) restricting sampling of the corresponding excitations to a deterministic subspace, (2) averaging the RDMs from independent dynamics and (3) projecting the resulting RDMs onto the closest positive semi-definite matrix. Our protocol avoids previously encountered numerical conditioning problems stemming from numerical noise in the orthogonalisation of the perturber overlap matrix. The Chromium dimer CASSCF(12,12)/CASPT2 binding curve is computed as a proof of concept.
|
Arta A. Safari; Giovanni Li Manni; Robert J. Anderson
|
Theoretical and Computational Chemistry; Theory - Computational
|
CC BY NC ND 4.0
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CHEMRXIV
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2023-07-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c3a985ce23211b20b29fc6/original/towards-a-stochastic-complete-active-space-second-order-perturbation-theory.pdf
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650e351b60c37f4f7646d33b
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10.26434/chemrxiv-2023-3scq4
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Development and Application of Hybrid AIMD/cDFT Simulations for Atomic-to-Mesoscale Chemistry
|
Many important geochemical and biogeochemical processes involve reactivity and dynamics in complex solutions. Gaining a fundamental understanding of these reaction mechanisms is a challenging goal that requires advanced computational and experimental approaches. However, important techniques such as molecular simulation have limitations in terms of scales of time, length and system complexity. Furthermore, among currently available solvation models, there are very few designed to describe the interaction between the molecular scale and mesoscale. To help address this challenge, here we establish a novel hybrid approach that couples first principle plane-wave density functional theory (DFT) with classical density functional theory (cDFT). In this approach, a region of interest described by ab initio molecular dynamics (AIMD) interacts with the surrounding medium described using cDFT to arrive at a self-consistent ground state. cDFT is a robust but efficient mesoscopic approach to accurate thermodynamics of bulk electrolyte solutions over a wide concentration range (up to 2 molar concentrations). Benchmarking against commonly used continuum models of solvation such as SMD, as well as experiment, demonstrates that our hybrid AIMD/cDFT method is able to produce reasonable solvation energies for a variety of molecules and ions. With this model, we also examined solvent effects on a prototype S$_N$2 reaction of the nucleophilic attack of a chloride ion on methyl chloride in solution. The resulting reaction pathway profile and the solution phase barrier agree well with the experiment, showing that our AIMD/cDFT hybrid approach can provide insight into the specific role of solvent on the reaction coordinate.
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Duo Song; Eric Bylaska; Maria Sushko; Kevin Rosso
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Theoretical and Computational Chemistry
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CC BY 4.0
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CHEMRXIV
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2023-09-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650e351b60c37f4f7646d33b/original/development-and-application-of-hybrid-aimd-c-dft-simulations-for-atomic-to-mesoscale-chemistry.pdf
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658524299138d231613d512d
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10.26434/chemrxiv-2023-vmrtq
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Non-Degenerate Two-Photon Absorption of Fluorescent Protein Chromophores
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Two-photon absorption (2PA), where a pair of photons are absorbed simultaneously, is recognized as a potent bioimaging technique, which depends on the quantified 2PA probability, defined as cross-section (σ2PA). The absorbed photons either have equivalent (ω1 = ω2) or different frequencies (ω1 ≠ ω2), where the former is degenerate 2PA (D-2PA) and the latter is non-degenerate 2PA (ND-2PA). ND-2PA is of particular interest since it is a promising imaging technology with flexibility of photon frequencies and enhanced cross-sections, however, it remains a relatively unexplored area compared to D-2PA. This work utilizes time-dependent density functional theory (TD-DFT) and second-order approximate coupled-cluster with the resolution-of identity approximation (RI-CC2), for the excitation from S0 to S1, to investigate σD-2PA and σND-2PA of fluorescent protein chromophore models. Interestingly, comparison of the CAMB3LYP and RI-CC2 computations show a qualitative trend in the computed σND-2PA improvements and vertical excitation energy, ΔE. As expected, the computed values of σND-2PA are quantitatively larger than σD-2PA, where chromophores with the largest values of σD-2PA show greater potential for σND-2PA improvement. Anionic chromophores demonstrated improvements up to 14%, while substantial enhancements were observed in neutral chromophores with some achieving a 30% increase.
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Ismael A. Elayan; Alex Brown
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Theoretical and Computational Chemistry; Physical Chemistry; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
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2023-12-26
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658524299138d231613d512d/original/non-degenerate-two-photon-absorption-of-fluorescent-protein-chromophores.pdf
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61449cffaeaa6e6296ef3f01
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10.26434/chemrxiv-2021-7w0dt
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Role of Terminal Groups in Aromatic Molecules on the Growth of Al2O3-Based Hybrid Materials
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Hybrid materials composed of organic and inorganic components offer the opportunity to develop interesting materials with well-controlled properties. Molecular Layer Deposition (MLD) is a suitable thin film deposition technique for the controlled growth of thin, conformal hybrid films. Despite the great interest in these materials, a detailed understanding of the atomistic mechanism of MLD film growth is still lacking. This paper presents a first principles investigation of the detailed mechanism of the growth of hybrid organic-inorganic thin films of aluminium oxide and aromatic molecules with different terminal groups deposited by MLD. We investigate the chemistry of the MLD process between the post-TMA pulse methyl-terminated Al2O3 surface and the homo- or hetero- bifunctional aromatic compounds with hydroxy (OH) and/or amino (NH2) terminal groups: hydroquinone (HQ), p-phenylenediamine (PD) and 4-aminophenol (AP). Double reactions of aromatic molecules with the alumina surface are also explored. We show that all aromatic precursor molecules bind favourably to the methyl terminated Al2O3, via formation of Al-O and Al-N bonds and CH4 elimination. While reaction energetics suggest a higher reactivity of the OH group with TMA in comparison to the NH2 group, which could enable the double reaction phenomenon for HQ we propose that the upright configuration will be present so that the organic molecules are self-assembled in an upright configuration, which leads to thicker hybrid films. Interactions between the methyl-terminated Al2O3 with substituted phenyls are investigated to examine the influence of phenyl functionalisation on the chemistry of the terminal groups. Reaction energetics show that phenyl functionalization actually promotes an upright configuration of the molecule, which leads to thicker and more flexible films, as well as tuning the properties of the aromatic components of the hybrid films. We also investigate the interactions between methyl-terminated Al2O3 with new possible MLD organic precursors, hydroquinone bis(2-hydroxyethyl)ether and 1,1'-biphenyl-4,4'-diamine. DFT shows that both aromatic molecules react favourably with TMA and are worthy of further experimental investigation.
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Arbresha Muriqi; Maarit Karppinen; Michael Nolan
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Theoretical and Computational Chemistry; Inorganic Chemistry; Reaction (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry
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CC BY NC 4.0
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CHEMRXIV
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2021-09-20
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61449cffaeaa6e6296ef3f01/original/role-of-terminal-groups-in-aromatic-molecules-on-the-growth-of-al2o3-based-hybrid-materials.pdf
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6421ac04647e3dca9996f9b4
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10.26434/chemrxiv-2023-whtfd
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Hydride-free Hydrogenation: Unraveling the Mechanism of Electrocatalytic Alkyne Semihydrogenation by Nickel-Bipyridine Complexes
|
Hydrogenation reactions of carbon-carbon unsaturated bonds are central in synthetic chemistry. Efficient catalysis of these reactions classically recourses to heterogeneous or homogeneous transition-metal species. Whether thermal or electrochemical, C–C multiple bond catalytic hydrogenation commonly involves metal hydrides as key intermediates. Here, we report that the electrocatalytic semihydrogenation of alkynes by molecular Ni complexes proceeds without the mediation of a hydride intermediate. Through a combined experimental and theoretical investigation, we disclose a mechanism that primarily involves a nickelacyclopropene resting state upon alkyne binding to a low-valent Ni(0) species. A following sequence of protonation and electron transfer steps via Ni(II) and Ni(I)-vinyl intermediates then leads to olefin release in an overall ECEC pattern as the most favored pathway. Our results also evidence that pathways involving hydride intermediates are strongly disfavored, which in turns promotes high semihydrogenation selectivity by avoiding competing hydrogen evolution. While bypassing catalytically competent hydrides, this type of mechanism still retains inner-metal-sphere characteristics with the formation of organometallic intermediates, often essential to control regio- or stereo-selectivity. We think that this approach to electrocatalytic reductions of unsaturated organic groups can open new paradigms for hydrogenation or hydroelementation reactions.
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Gabriel Durin; Mi-Young Lee; Thomas Weyhermueller; Nicolas KAEFFER; Walter Leitner
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Catalysis; Organometallic Chemistry; Energy; Electrocatalysis; Coordination Chemistry (Organomet.); Kinetics and Mechanism - Organometallic Reactions
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CC BY NC ND 4.0
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CHEMRXIV
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2023-03-28
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421ac04647e3dca9996f9b4/original/hydride-free-hydrogenation-unraveling-the-mechanism-of-electrocatalytic-alkyne-semihydrogenation-by-nickel-bipyridine-complexes.pdf
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65a827ff9138d23161277c4c
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10.26434/chemrxiv-2024-r8d5m
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Visible Light-Induced EDA-Mediated C-3 Coupling of Quinoxalin-2(1H)-ones with Unactivated Aryl Iodides
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Visible light-induced C-3 arylation of quinoxalin-2(1H)-ones with abundantly available aryl iodides with good yields via an EDA-complex formation has been accomplished. Both aryl/heteroaryl iodides and quinoxalin-2(1H)-ones possessing electron-donating as well as electron-withdrawing groups were coupled well to access the desired products in good yields. The radical scavenging, EPR, UV-visible experiments, and quantum yield revealed that the reaction went through a radical pathway via a SET process. Furthermore, the protocol could also be applied for late-stage functionalization, illustrated the practicability of the present protocol.
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Anuj Sharma; Nihal Singh; Anoop Sharma; Jitender Singh
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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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2024-01-23
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a827ff9138d23161277c4c/original/visible-light-induced-eda-mediated-c-3-coupling-of-quinoxalin-2-1h-ones-with-unactivated-aryl-iodides.pdf
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65e0c01d66c1381729dd4ea3
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10.26434/chemrxiv-2024-szsq8
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Oxide Encapsulated Ruthenium Oxide Catalysts for Selective Oxygen Evolution in Unbuffered pH Neutral Seawater
|
Direct seawater electrolysis is a promising approach to producing green hydrogen in water-scarce environments using renewable energy. However, the undesirable chlorine evolution reaction (CER) and hypochlorite evolution reaction (HCER) compete with the desired oxygen evolution reaction (OER) at the anode electrocatalyst. This issue is most pronounced in unbuffered pH neutral solutions due to local acidification resulting from the OER. To overcome this challenge, this study explores the use of silicon oxide (SiOx) and titanium oxide (TiOx) nanoscale overlayers coated on metallic ruthenium (Ru) and ruthenium oxide (RuOx) thin film electrodes to block chloride ions from reaching active sites during operation in unbuffered 0.6 M NaCl electrolyte. Using a combination of (electro)analytical techniques, encapsulated RuOx anodes are shown to effectively suppress Cl- transport to buried catalyst active sites while allowing for the desired OER to occur, leading to increases in OER faradaic efficiency at moderate overpotentials. Evidence for the ability of SiOx overlayers to block Cl- ions from reaching the active buried interface was obtained by monitoring the OH stretching mode of OH adsorbates using in situ Raman spectroscopy. This study also reports trade-offs between the activity, selectivity, and stability of bare and encapsulated Ru and RuOx electrocatalysts, finding that the magnitude of these trade-offs strongly depends on the nature of both the catalyst and overlayer material. The most promising anode electrocatalyst is RuOx encapsulated by 4 nm of SiOx, which gives the largest improvement in OER faradaic efficiency while demonstrating a relatively stable operating current and minimal increases in overpotential.
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Daniela Bushiri; Amanda Baxter; Onaolapo Odunjo; Daniela Fraga Alvarez; Yong Yuan; Jingguang Chen; Daniel Esposito
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Catalysis; Energy; Electrocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2024-03-01
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0c01d66c1381729dd4ea3/original/oxide-encapsulated-ruthenium-oxide-catalysts-for-selective-oxygen-evolution-in-unbuffered-p-h-neutral-seawater.pdf
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652e1b4345aaa5fdbb2adc0e
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10.26434/chemrxiv-2023-8dg41
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The utility of supercritical fluid chromatography for the separation and potential purification of organic light-emitting diode (OLED) materials
|
Screen technology for “smart” devices continues to advance as researches seek to enhance display performance by reducing energy consumption and improving color characteristics. To that end, researchers are turning to organic light-emitting diodes (OLEDs) as the display materials due to higher energy saving and richer color compared to liquid crystal displays (LCDs). However, one major setback of the OLED technology is that the devices are very sensitive to the impurities present in the OLED materials, impacting device lifetime, stability, and overall performance. The isolation of large quantities of the main OLED components from the synthetic impurities is challenging using the traditional purification process (i.e., train sublimation), which has poor reproducibility, and high capital and operating cost. Supercritical fluid chromatography (SFC) could lend itself as an alternative technique for the profiling of impurities and their purification. In this study, we investigated the use of SFC to analyze a mixture of amorphous monomeric molecular glasses with charge-transporting property typical of OLED materials. The separation behavior of four different chromatographic columns containing the stationary phases 1-aminoanthracene (1-AA), naphthyl, 2-ethylpyridine, and C-18 were examined to perform the SFC separations. The effect of using three different co-solvents (i.e., isopropyl alcohol, acetonitrile, and tetrahydrofuran) to the CO2 mobile phase on the separation selectivity and resolution was also investigated. For the probe mixture used, the naphthyl column in combination with the addition of acetonitrile as co-solvent provided the best separation in terms of resolution. The SFC method was farther optimized for co-solvent composition, temperature, pressure, and flow rate. The SFC analysis showed high resolution and short analysis time compared to HPLC, and also provided for the separation of small components that have been attributed to impurities in the sample.
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Tanvir Amit; Luis Colon
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Analytical Chemistry; Separation Science
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CC BY NC ND 4.0
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CHEMRXIV
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2023-10-17
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e1b4345aaa5fdbb2adc0e/original/the-utility-of-supercritical-fluid-chromatography-for-the-separation-and-potential-purification-of-organic-light-emitting-diode-oled-materials.pdf
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64677d85a32ceeff2de8207a
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10.26434/chemrxiv-2023-0zq5v
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Establishing Physical and Chemical Mechanisms of Polymerization and Pyrolysis of Phenolic Resins for Carbon-Carbon Composites
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The complex structural and chemical changes that occur during polymerization and pyrolysis critically affect material properties but are difficult to characterize in situ. This work presents a novel, experimentally validated methodology for modeling the complete polymerization and pyrolysis processes for phenolic resin using reactive molecular dynamics. The polymerization simulations produced polymerized structures with mass densities of 1.24 ± 0.01 g/cm3 and Young’s moduli of 3.50 ± 0.64 GPa, which are in good agreement with experimental values. The structural properties of the subsequently pyrolyzed structures were also found to be in good agreement with experimental X-ray data for the phenolic-derived carbon matrices, with interplanar spacings of 3.81 ± 0.06 Å and crystallite heights of 10.94 ± 0.37 Å. The mass densities of the pyrolyzed models, 2.01 ± 0.03 g/cm3, correspond to skeletal density values, where the volume of pores is excluded in density calculations for the phenolic resin-based pyrolyzed samples. Young’s moduli are underpredicted at 122.36 ± 16.48 GPa relative to experimental values of 146 – 256 GPa for nanoscale amorphous carbon samples.
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Ivan Gallegos; Josh Kemppainen; Jacob Gissinger; Malgorzata Kowalik; Adri van Duin; Kristopher Wise; S. Gowtham; Gregory Odegard
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Theoretical and Computational Chemistry; Materials Science; Polymer Science; Carbon-based Materials; Composites; Computational Chemistry and Modeling
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CC BY NC 4.0
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CHEMRXIV
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2023-05-22
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64677d85a32ceeff2de8207a/original/establishing-physical-and-chemical-mechanisms-of-polymerization-and-pyrolysis-of-phenolic-resins-for-carbon-carbon-composites.pdf
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638e40fc0fd9928430396a31
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10.26434/chemrxiv-2022-s9dvr
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On the limitations of thermal atomic layer deposition of InN using ammonia
|
Chemical vapor deposition (CVD) of indium nitride (InN) is severely limited by the low thermal stability of the material, and thus low temperature deposition processes, such as atomic layer deposition (ALD), are needed to deposit InN films. The two chemically and structurally closely related materials aluminum nitride (AlN) and gallium nitride (GaN) has been deposited by both plasma and thermal ALD, with ammonia (NH3) as nitrogen precursor in thermal processes. InN, however, has only been deposited using plasma ALD, indicating that there might be a limitation to thermal ALD with NH3 for InN. We use quantum-chemical density functional theory (DFT) calculations to compare the adsorption process of NH3 on GaN and InN to investigate if differences in the process could account for the lack of thermal ALD of InN. Our findings show a similar adsorption mechanism on both materials, in which NH3 could adsorb onto a vacant site left by a desorbing methyl group from the surfaces. The difference in energy barrier for this adsorption indicates that the process is many magnitudes slower on InN compared to GaN. The slow adsorption kinetics would hinder NH3 from adsorption onto InN in the timeframe of the ALD growth process and thus limit the availability of a thermal ALD process.
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Karl Rönnby; Henrik Pedersen; Lars Ojamäe
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Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Materials Processing; Thin Films; Surface
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CC BY 4.0
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CHEMRXIV
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2022-12-06
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638e40fc0fd9928430396a31/original/on-the-limitations-of-thermal-atomic-layer-deposition-of-in-n-using-ammonia.pdf
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637fbea00146eff5a4049304
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10.26434/chemrxiv-2022-xc9md
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Stereoselective N-Heterocyclic Carbene Catalyzed Formal [4+2] Cycloaddition: Access to Chiral Heterocyclic Cyclohexenones
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The present study reports an asymmetric NHC-catalyzed formal [4+2] cycloaddition of heterocyclic alkenes containing polarized double bond with azolium-dienolate intermediate generated from α-bromo-α,β-unsaturated aldehydes without external oxidation of Breslow intermediate. Heterocyclic cyclohexenones were produced in good isolated yields (typically about 90%) with good stereochemical outcomes (typically dr > 20/1, and 70-99% ee). The synthetic utility of the protocol was exemplified by the scope of heterocyclic alkenes.
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Ladislav Lóška; Vojtěch Dočekal; Ivana Císařová; Jan Veselý
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Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis
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CC BY NC ND 4.0
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CHEMRXIV
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2022-11-25
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637fbea00146eff5a4049304/original/stereoselective-n-heterocyclic-carbene-catalyzed-formal-4-2-cycloaddition-access-to-chiral-heterocyclic-cyclohexenones.pdf
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60c75620469df46c0df4527e
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10.26434/chemrxiv.14214014.v1
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Proton Transfer and Kinetic Isotope Effect in Morita-Baylis-Hillman Reaction Under Solvent Effects. a Detailed Computational Study
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Solvent effects of CH<sub>2</sub>Cl<sub>2</sub>, CH<sub>3</sub>CN,
THF and DMSO on the profile of the Morita-Baylis-Hillman (MBH) reaction were
discovered to lower the activation energy of aldol step. Proton-transfer through
seven-membered TS state structure enroute Hofmann elimination and also the four-membered
TS structure are sufficiently low energy processes in comparison to aldol
reaction and, hence, unlikely to contribute to the overall kinetics of the
reaction. As an exception, proton-transfer through seven-membered TS structure
constitutes the rate-controlling event for the DABCO-catalyzed reaction of
methyl acrylate with <i>p</i>-nitrobenzaldehyde
under the solvent effects of DMSO. The acetal route
was not found to contribute to kinetic isotope effect, which has otherwise been
measured to be as high as 5.2 ± 0.6. The simultaneous proton-transfer to the aldol-derived
alkoxide and abstraction of proton from the a-carbon
of activated alkene by hydroxylic solvents was found to be barrier-less. The reported catalysis
by hydroxylic solvents is therefore likely by lowering
the activation energy of the aldol step due to activation of aldehyde possibly by
protonation or hydrogen-bonding. The present computational results are in excellent agreement with the more
than three decade old experimental findings of Hill and Isaacs.<sup> </sup>These
authors have reported the aldol step as rate-limiting and absolutely no kinetic
isotope effect.
|
Veejendra Yadav
|
Physical Organic Chemistry
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CC BY NC ND 4.0
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CHEMRXIV
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2021-03-16
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https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75620469df46c0df4527e/original/proton-transfer-and-kinetic-isotope-effect-in-morita-baylis-hillman-reaction-under-solvent-effects-a-detailed-computational-study.pdf
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66e91b6051558a15ef36c20e
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10.26434/chemrxiv-2024-r007f
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How nitro group position determines the emission properties of diketopyrrolopyrroles
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Two complex π-expanded diketopyrrolopyrroles (EDPPs) have been prepared following multistep but straightforward strategy. We discovered that the fate of these molecules in the excited state can be controlled by subtle differences in their structure. When NO2 groups are located at a distant position, the quadrupolar, centrosymmetric dye possesses strong red emission across the solvents’ polarity scale. However, when NO2 groups are adjacent to the lactam moiety, the EDPP has negligible emission even in non-polar solvents. Density Functional Theory (DFT) calculations indicate that the primary distinction between the two molecules lies in the structural planarity. The molecule with NO 2 groups adjacent to the lactam moiety exhibits a loss of planarity due to the Coulombic repulsion between these groups. The calculations also suggest that the nitro group does not participate in the S0→S1 excitation. Furthermore, for both compounds, the first two excited states (one bright and one dark) are found to be very close in energy. The change in molecular geometry affects the non-radiative deactivation of excited states, leading to the two distinct emission behaviors. Experiments in glassy solvent at low temperatures reveal that at 77 K, the photophysics of both dyes becomes the same, which proves that thermal activation is the key mechanism for non-radiative decay of the excited state for non-emissive EDPP.
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Kamil Skonieczny; Francesco Di Maiolo; Sara Venturi; Alessandro Iagatti; Alessandro Ricci; Francesco Bertocchi; Daniel T. Gryko; Andrea Lapini
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Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.)
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CC BY 4.0
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CHEMRXIV
|
2024-09-17
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e91b6051558a15ef36c20e/original/how-nitro-group-position-determines-the-emission-properties-of-diketopyrrolopyrroles.pdf
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63d3f56a1a1ead39e3b9f37b
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10.26434/chemrxiv-2023-fcgcx
|
Stabilizing an all-aqueous two-phase system using oil-in-water droplets to mimic double emulsions
|
The production of water-in-water emulsion droplets, the coalescence of which is prevented by adding oil-in-water micrometric droplets is reported. Hexadecane (O) and cetyl trimethyl ammonium bromide (CTAB) were added to a W/W emulsion made of dextran (Dex)-enriched droplets in a Polyethyleglycol (PEG)-enriched continuous phase and the mixture was further sonicated. Using Nile red to label the oil droplets afforded to observe their presence at the surface of Dex droplets (5 µm) allowing stabilizing them, preventing coalescence of the W/W emulsion, and mimicking W/O/W double emulsions. Addition of sulfate derivative of Dextran (DexSulf) allowed stable droplets of slightly larger diameter. By contrast, addition of carboxymethyl Dextran (CMDex) destabilized the initial aqueous double-like emulsion, yielding sequestration of the oil droplets within the Dex-rich phase. Interestingly, addition of DexSulf to that unstable emulsion re-yielded stable droplets. Similar findings (destabilization) were obtained when adding sodium dodecyl sulfate (SDS) to the initial double-like emulsion, which reformed stable droplets when adding positively charged Dextran (DEAEDex) derivative. The use of fluorescently (FITC) labelled derivatives of Dextran (Dex, CMDex, DEAEDex and DexSulf) allowed to follow their position within, out or at the interface of droplets in the above-mentioned mixtures. These findings are expected to be of interest in the field of materials chemistry.
|
J-Paul Douliez
|
Physical Chemistry; Polymer Science; Materials Chemistry
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CC BY 4.0
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CHEMRXIV
|
2023-02-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3f56a1a1ead39e3b9f37b/original/stabilizing-an-all-aqueous-two-phase-system-using-oil-in-water-droplets-to-mimic-double-emulsions.pdf
|
6397ab8392f08400d5330cbc
|
10.26434/chemrxiv-2022-d1qzf
|
Theoretical studies of the interaction between silver and lipids present in HepG2 cells
|
We performed DFT and TDDFT calculations to determine interactions between silver atom and model cell membrane of human hepatocellular carcinoma (HepG2) cells or human liver cells. Specifically, we chose the two major lipid constituents of HepG2 cells which are 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1-palmitoyl-2-oleoyI-sn-glycero-3-phosphoethanolamine (POPE) to represent HepG2 cell membrane. Silver atom (Ag0) and silver ion (Ag+) are used as silver models to represent possible point-to-point interaction and the effect of silver ion (Ag+) leakage. The results show that exposure of POPC to silver ion (Ag+) at a high concentration can cause structural conformational changes from being originally bent to straight conformation. In addition, the interaction between silver ion (Ag+) and the lipids can cause significant amount of charge transfer that ranges from 0.14 to 0.16 for POPC and 0.12 to 0.14 for POPE. Moreover, though silver ion (Ag+) binds three to five times stronger to the lipids than silver atom (Ag0), both interactions are Van der Waals interaction. Finally, the presence of silver atom (Ag0) in the lipids can be detected using UV-Vis spectrophotometer by occurrence of a red shift which is seen at 376 nm and 372 nm for POPC and POPE respectively. However, detecting silver ion (Ag+) using this method is not feasible as no apparent shifts are shown.
|
Pamela Ubaldo; Lichang Wang
|
Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Physical and Chemical Properties; Spectroscopy (Physical Chem.)
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CC BY NC ND 4.0
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CHEMRXIV
|
2022-12-13
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6397ab8392f08400d5330cbc/original/theoretical-studies-of-the-interaction-between-silver-and-lipids-present-in-hep-g2-cells.pdf
|
6706eab8cec5d6c142b83e10
|
10.26434/chemrxiv-2024-vx1df-v2
|
High-Pressure Electrides: A Quantum Chemical Perspective
|
It has long been assumed that all matter will assume simple closed-packed lattices and become metallic under pressure, in accordance with the Thomas-Fermi-Dirac (TFD) model. However, this model struggles to explain pressure driven complex structural transitions that have been observed in elements, including sodium, challenging our conventional understanding of compressed matter. Moreover, in stark contrast to the TFD picture, first-principles calculations suggest that various elements and compounds become electrides under pressure. Electrides, characterized by concentrations of charge density at interstitial regions, can be thought of as ionic compounds where electrons behave as the anions. Though ambient-pressure molecular electrides have been extensively studied via experiments and computations, high-pressure electrides (HPEs) are not well understood. The identification and characterization of HPEs has been, to date, purely based on theory including topological analysis of the electron density and the electron localization function. Here, we review these theoretical analyses tools and suggest guidelines that can be used to classify systems as electrides. Moreover, we describe models used to rationalize the electronic structure of HPEs, drawing parallels with ambient pressure molecular systems, and urge for the development of experimental techniques that provide evidence for the theoretically calculated charge localization.
|
Stefano Racioppi; Eva Zurek
|
Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry
|
CC BY 4.0
|
CHEMRXIV
|
2024-10-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706eab8cec5d6c142b83e10/original/high-pressure-electrides-a-quantum-chemical-perspective.pdf
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62e3a5b6e7fc8f5d718dcf92
|
10.26434/chemrxiv-2022-nw4fb
|
Trajectory Surface Hopping for a Polarizable
Embedding QM/MM
|
We present the implementation of trajectory surface hopping nonadiabatic dynamics for a
polarizable embedding QM/MM formulation. The time-dependent density functional theory
has been used as the quantum mechanical level of theory, whereas the molecular mechanics
description has involved the polarizable AMOEBA force field. This implementation has been
obtained by integrating the surface-hopping program Newton-X NS with an interface between
the Gaussian 16 and Tinker suites of codes to calculate QM/AMOEBA energies and forces.
The implementation has been tested on a photoinduced electron-driven proton-transfer reaction
involving pyrimidine and a hydrogen-bonded water surrounded by a small cluster of water
molecules and within a large water droplet.
|
Mattia Bondanza; Baptiste Demoulin; Filippo Lipparini; Mario Barbatti; Benedetta Mennucci
|
Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.)
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2022-07-29
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e3a5b6e7fc8f5d718dcf92/original/trajectory-surface-hopping-for-a-polarizable-embedding-qm-mm.pdf
|
66156d1321291e5d1d789515
|
10.26434/chemrxiv-2023-9b6w2-v2
|
Transcending Lifshitz Theory: Reliable Prediction of Adhesion Forces between Hydrocarbon Surfaces in Condensed Phases using Molecular Contact Thermodynamics
|
Works of adhesion W(Lifshitz) between hydrocarbon surfaces in 260 liquids were calculated using Lifshitz theory and compared with interaction free energies ∆∆G determined using a model in which the interactions between a molecule and a liquid are described by a set of surface site interaction points (SSIP). The predictions of these models diverge in significant ways. Interaction free energies calculated using the SSIP approach are typically small and vary little, but in contrast, Lifshitz theory yields works of adhesion that span a broad range. Moreover, the SSIP model also yields significantly different ∆∆G values in some liquids for which, in contrast, Lifshitz theory predicts similar values of W. These divergent predictions were tested using atomic force microscopy. The experimentally determined work of adhesion was found to be closer to the value predicted using the SSIP model than to W(Lifshitz). Still greater differences were found in the interaction energies calculated using the two models when liquid mixtures were considered. For mixtures of methanol and benzyl alcohol, ∆∆G declines smoothly as the benzyl alcohol concentration increases, but W(Lifshitz) decreases to a minimum and then increases, reaching a larger value for benzyl alcohol than for methanol. The experimental adhesion data were correlated closely with the predictions of the SSIP model. We conclude that the molecular-scale treatment intrinsic to the SSIP approach enables adhesive interactions to be modelled more accurately than is possible using Lifshitz theory, which instead uses the bulk properties of the medium to predict work of adhesion values.
|
Oscar Siles-Brugge; Christopher Hunter; Graham Leggett
|
Physical Chemistry; Nanoscience; Interfaces; Surface; Thermodynamics (Physical Chem.); Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-10
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66156d1321291e5d1d789515/original/transcending-lifshitz-theory-reliable-prediction-of-adhesion-forces-between-hydrocarbon-surfaces-in-condensed-phases-using-molecular-contact-thermodynamics.pdf
|
60c7470abb8c1a74093da9c1
|
10.26434/chemrxiv.11501376.v1
|
Do We Really Understand Graphene Nanoribbons? A New Understanding of the 3n, 3n±1 Rule, Edge “Magnetism” and Much More
|
Using the inherent shell structure of graphene and geometrical/topological constrains, we verify that there are only three families of armchair graphene nanoribbons (AGNR) with Z zigzag edge-rings, categorized by Z=3n, 3n±1, n=1,2,… each with unique aromatic, electronic and topological properties. The Z=3n+1, 3n AGNR-families are aromatic with large bandgaps,characteristic aromaticity-patterns, and unique “active” frontier orbitals, in contrast to the ordinary ones. Such AGNRs due to sublattice/molecular-group symmetry-conflict develop 2n zigzag-edge-localized “gapless” frontier-states, which are “pseudospin-polarized” (not real-spin-polarized) with total pseudospin S=n, effectively optimizing sublattice “balance” and total energy. The “active” frontier orbitals, obtained after neglecting such gapless non-bonding states, have large “active” bandgaps, which are in very good agreement with experiment. The Z=3n-1 AGNRs have mixt aromatic, electronic and topological character, with vanishingly small bandgaps. Zigzag GNRs, contrary to opposite reports, have no magnetic zigzag edges, unless magnetization due to polarization of atomic pz orbital angular momentum is operative<br />
|
Aristides Zdetsis
|
Nanostructured Materials - Nanoscience
|
CC BY NC ND 4.0
|
CHEMRXIV
|
1970-01-01
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7470abb8c1a74093da9c1/original/do-we-really-understand-graphene-nanoribbons-a-new-understanding-of-the-3n-3n-1-rule-edge-magnetism-and-much-more.pdf
|
65461f2ba8b423585aed278d
|
10.26434/chemrxiv-2023-7l062
|
PolyBorylated Alkenes as Energy-Transfer Reactive Groups for the Generation of polyBorylated Biradicals: Access to Multi-Borylated Cyclobutanes Combined with 1,5-HAT Event
|
While polyborylated alkenes are being recognized for their elevated status as highly valuable reagents in modern organic synthesis, allowing efficient access to a diverse array of transformations, including the formation of C–C and C–heteroatom bonds, their potential as energy-transfer reactive groups has remained unexplored. Yet, this potential holds the key to generating elusive polyborylated biradical species, which can be captured by radophile olefins, thereby leading to the construction of new highly-borylated scaffolds. Herein, we report a designed energy-transfer strategy for photosensitized [2+2]-cycloadditions of poly-borylated alkenes with various olefins enabling the regioselective synthesis of diverse poly-borylated cyclobutane motifs, including the 1,1-di-, 1,1,2-tri-, and 1,1,2,2-tetra-borylated cyclobutanes. In fact, these compounds belong to a family that presently lacks efficient synthetic pathways. Interestingly, when α-methylstyrene was used, the reaction involves an interesting 1,5-hydrogen atom transfer. Mechanistic deuterium-labeling studies have provided insight into the outcome of 1,5-hydrogen atom transfer process. In addition, the polyborylated cyclobutanes are then demonstrated to be useful in selective oxidation processes resulting in the formation of cyclobutanones and γ-lactones.
|
Nicole Hanania; Nadim Eghbarieh; Ahmad Masarwa
|
Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photocatalysis
|
CC BY 4.0
|
CHEMRXIV
|
2023-11-06
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65461f2ba8b423585aed278d/original/poly-borylated-alkenes-as-energy-transfer-reactive-groups-for-the-generation-of-poly-borylated-biradicals-access-to-multi-borylated-cyclobutanes-combined-with-1-5-hat-event.pdf
|
660e8da321291e5d1d0a5150
|
10.26434/chemrxiv-2024-p3wcl
|
Catalyst Supraparticles: Tuning the Structure of Spray-dried Pt/SiO2 Supraparticles via Salt-based Colloidal Manipulation to Control their Catalytic Performance
|
The structure of supraparticles (SP) is a key parameter for achieving advanced functionalities arising from the combination of different nanoparticle (NP) types in one hierarchical entity. However, whenever a droplet-assisted forced assembly approach is used, e.g., spray-drying, the achievable structure is limited by the inherent drying phenomena of the method. Especially, mixed NP dispersions of differently-sized colloids are heavily affected by segregation during the assembly. Herein, the influence of the colloidal arrangement of Pt and SiO2 NPs within a single supraparticulate entity is investigated. A salt-based electrostatic manipulation approach of the utilized NPs is proposed to customize the structure of spray-dried Pt/SiO2 SPs. By this, size-dependent separation phenomena of NPs during solvent evaporation, that limit the catalytic performance in the reduction of 4-nitrophenol, are overcome by achieving even Pt NP distribution. Additionally, the textural properties (pore size and distribution) of the SiO2 pore framework are altered to improve the mass transfer within the material leading to increased catalytic activity. The suggested strategy demonstrates a powerful, material-independent, and universally applicable approach to deliberately customize the structure and functionality of multi-component SP systems. This opens up new ways of colloidal material combinations and structural designs in droplet-assisted forced assembly approaches like spray-drying.
|
Philipp Groppe; Jakob Reichstein; Simon Carl; Carlos Cuadrado Collados; Bart-Jan Niebuur; Kailun Zhang; Benjamin Apeleo Zubiri; Jörg Libuda; Tobias Kraus; Tanja Retzer; Matthias Thommes; Erdmann Spiecker; Susanne Wintzheimer; Karl Mandel
|
Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Heterogeneous Catalysis; Materials Chemistry
|
CC BY NC ND 4.0
|
CHEMRXIV
|
2024-04-08
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e8da321291e5d1d0a5150/original/catalyst-supraparticles-tuning-the-structure-of-spray-dried-pt-si-o2-supraparticles-via-salt-based-colloidal-manipulation-to-control-their-catalytic-performance.pdf
|
643e581a1d262d40eaaf9d22
|
10.26434/chemrxiv-2023-brx8k
|
Novel Patterns for Polymerization of Interlocked Molecular Cages
|
Polymerization of conventional polymers has been widely studied since the last century by forming covalent or mechanical bonds, where the latter leads to intrinsic topological properties of knots and links. However, the conventional perspective of discrete functional groups may suffer from limitation in polymerization of molecular cages by mechanical bonds of links. With a standpoint of combinatorics and statistical mechanics, we develop a practical, both graph based and kinetic model for this distinctive polymerization, indicating their diverse topological isomers and unique termination of polymerization, revealing their novel patterns from conventional linear polymers. This novel pattern and derived model may provide further strategies towards design and modification of molecular cages and their polymerization.
|
Zhenghong Chen; Weihao Wang; Shaodong Zhang
|
Physical Chemistry; Polymer Science; Polymerization kinetics; Statistical Mechanics
|
CC BY NC 4.0
|
CHEMRXIV
|
2023-04-26
|
https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643e581a1d262d40eaaf9d22/original/novel-patterns-for-polymerization-of-interlocked-molecular-cages.pdf
|
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