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60c753e30f50db705f397c2c | 10.26434/chemrxiv.13568267.v1 | Rapid Interfacial Exchange of Li Ions Dictates High Coulombic Efficiency in Li Metal Anodes | <p>Although Li metal batteries offer the highest possible
specific energy density, practical application is plagued by Li filament growth
with adverse effects on both Coulombic efficiency and battery safety. The structure
and resulting properties of the solid electrolyte interphase (SEI) on Li metal is
critical to controlling Li deposition morphologies and achieving high
efficiency batteries. In this report, we use a combination of nuclear magnetic
resonance (NMR) spectroscopy and X-ray photoelectron spectroscopy (XPS) to show
that fast Li transport and low solubility at the electrode/SEI interface in 0.5
M LiNO<sub>3</sub> + 0.5 M LiTFSI electrolyte bi-salt in 1,3-dioxolane:dimethoxyethane
(DOL:DME, 1:1, v/v) are responsible for the formation of low surface area Li
deposits and high Coulombic efficiency, despite the fact that the SEI is
thicker and chemically more heterogeneous than LiTFSI alone. These data suggest
that SEI design strategies that increase SEI stability and Li interfacial exchange
rate will lead to more even current distribution, ultimately providing a new
framework to generate smooth Li morphologies during plating/stripping.</p> | Richard May; Keith Fritzsching; Dimitri Livitz; Steven R. Denny; Lauren Marbella | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e30f50db705f397c2c/original/rapid-interfacial-exchange-of-li-ions-dictates-high-coulombic-efficiency-in-li-metal-anodes.pdf |
60efc6a09ab06e00f74ec20c | 10.26434/chemrxiv-2021-2tbjp | Hidden Hemibonding in the Aqueous Hydroxl Radical | The existence of a two-center, three-electron hemibond in the first solvation shell of OH(aq) has long been a matter of debate. The hemibond manifests in ab initio molecular dynamics simulations as a small-r feature in the oxygen radial distribution function (RDF) for H2O...OH, but that feature disappears when semilocal density functionals are replaced with hybrids, suggesting a self-interaction artifact. Using periodic simulations at the PBE0+D3 level, we demonstrate that the hemibond is actually still present (as evidenced by delocalization of the spin density onto nearby water molecules) but is obscured by the hydrogen-bonded feature in the RDF, due to a slight elongation of the hemibond. Computed electronic spectra for OH(aq) are in excellent agreement with experiment and confirm that hemibond-like configurations play an outsized role in the spectroscopy due to an intense charge-transfer transition that is strongly attenuated in hydrogen-bonded configurations. Apparently, 25% exact exchange does not eliminate delocalization of unpaired spins. | Bhaskar Rana; John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60efc6a09ab06e00f74ec20c/original/hidden-hemibonding-in-the-aqueous-hydroxl-radical.pdf |
60c7436f0f50db4602395efa | 10.26434/chemrxiv.8120654.v3 | Sulfamides Direct Radical-Mediated Chlorination of Aliphatic C–H Bonds | Sulfamides guide intermolecular chlorine transfer to gamma-C(sp<sup>3</sup>) centers. This unusual position-selectivity arises because accessed sulfamidyl radical intermediates engage in otherwise rare 1,6-hydrogen-atom transfer processes. The disclosed chlorine-transfer reaction relies on a light-initiated radical chain-propagation mechanism to oxidize C(sp<sup>3</sup>)-H bonds. | Melanie Short; Mina Shehata; Matthew Sanders; Jennifer Roizen | Organic Synthesis and Reactions; Photochemistry (Org.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7436f0f50db4602395efa/original/sulfamides-direct-radical-mediated-chlorination-of-aliphatic-c-h-bonds.pdf |
60c73f5d842e65d313db1aa3 | 10.26434/chemrxiv.7342943.v1 | Giant Star-Shaped Nitrogen-Doped Nanographenes | <div><div><div><p>Star-shaped nanographenes are large monodisperse polycyclic aromatic hydrocarbons that extend in size beyond the nanometer and have shown a lot of promise in a wide range of applications including electronics, energy conversion and sensing. Herein we report a new family of giant star-shaped N-doped nanographenes with diameters up to 6.5 nm. Furthermore, the high solubility of this SNG family in neutral organic solvents at room temperature allowed a complete structural, optoelectronic and electrochemical characterisation, which together with charge transport studies illustrate their n-type semiconducting character.</p></div></div></div> | Juan P. Mora-Fuentes; Alberto Riaño-Carnerero; Diego Cortizo-Lacalle; Akinori Saeki; Manuel Melle-Franco; Aurelio Mateo-Alonso | Organic Synthesis and Reactions; Physical Organic Chemistry; Carbon-based Materials; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5d842e65d313db1aa3/original/giant-star-shaped-nitrogen-doped-nanographenes.pdf |
61b9c4cca53f1bb3ff9c6238 | 10.26434/chemrxiv-2021-k4rwx | Preparation of Ultrathin and Degradable Polymeric Films by Electropolymerization of 3-Amino-L-Tyrosine | The resource intensive and environmentally unfriendly synthesis, recycling and disposal of today’s plastics has sparked interest in greener polymer processing. Bioderived polymers are one of many current areas of research that show promise for a sustainable future. One bioderived polymer that has been in the spotlight for the past decade due to its unique properties is polydopamine (PDA). Its ability to adhere to virtually any surface showing high stability in a wide pH range from 2-10 and in several organic solvents makes it a suitable candidate for several applications ranging from medical devices, coatings to biosensing applications. However, its strong and broad light absorption limits many applications that rely on transparent material, moreover fluorescence applications are limited by the high quenching efficiency of PDA. Therefore, new bioderived polymers that share similar features as PDA without fluorescent quenching are highly desirable. In this study, the electropolymerization of a bioderived analogue of dopamine, 3-amino-L-tyrosine (ALT) is demonstrated. The properties of the resultant polymer, poly-amino-L-tyrosine (p-ALT), exhibit several characteristics complementary to or even exceeding those of PDA and of its analog, poly-norepinephrine (p-NorEp), rendering p-ALT attractive for the development of sensors and photoactive devices. Cyclic voltammetry, spectroelectrochemistry and electrochemical quartz crystal microbalance have been applied to study the electrodeposition of this material and the resulting polymeric films have been compared to PDA and p-NorEp. Impedance spectroscopy revealed increased ions permeability of p-ALT with respect PDA and p-NorEp. Moreover reduced fluorescence quenching of p-ALT film was achieved supporting its application as coating for biosensors, organic semiconductors and new nanocomposite materials. | Tommaso Marchesi D’Alvise ; Sruthi Sunder ; Roger Hasler ; Julia Moser; Wolfgang Knoll ; Christopher V. Synatschke; Sean Harvey ; Tanja Weil | Materials Science; Analytical Chemistry; Biodegradable Materials; Coating Materials; Electrochemical Analysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b9c4cca53f1bb3ff9c6238/original/preparation-of-ultrathin-and-degradable-polymeric-films-by-electropolymerization-of-3-amino-l-tyrosine.pdf |
60c745fe702a9bc17318ab1f | 10.26434/chemrxiv.9626492.v2 | Fast and Quantitative Phospholipidomic Analysis of SH-SY5Y Neuroblastoma Cell Cultures Using LC-MS/MS and 31P NMR | Phospholipid quantification by <sup>31</sup>P NMR and lipid separation and
detection by LC-MS/MS. Fatty acid quantification using scripted
reconstruction of elution profile for each fatty acid associated with
each lipid species. The combination of NMR and and MS data is
complementary and allows better quantification and more complete
description than each approach would allow by itself. Datasets exists
for both whole-cell and plasma membrane fraction, and we also describe
and document the extraction techniques. | Martin Jakubec; Espen Bariås; Fedor Kryuchkov; Linda Veka Hjørnevik; Øyvind Halskau | Biochemical Analysis; Mass Spectrometry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745fe702a9bc17318ab1f/original/fast-and-quantitative-phospholipidomic-analysis-of-sh-sy5y-neuroblastoma-cell-cultures-using-lc-ms-ms-and-31p-nmr.pdf |
657e77c49138d23161d5f18e | 10.26434/chemrxiv-2023-ml3wd | Probing the 13C nuclear spin relaxation of diamond nanoparticles with solid-state NMR | Diamond nanoparticles represent an elegant class of nanoscale materials with many promising applications in nanotechnology. Solid-state NMR is a powerful technique to investigate the atomic-level structure and dynamics of nanomaterials in their natural state. The present study illustrates the application of high-resolution 13C NMR to nanomaterials characterization, and the fundamental 13C spin-lattice relaxation times highlight the spatial arrangement of surface-associated paramagnetic centers around the core sp3 carbon assembly of diamond nanoparticles, delineating the unique size-dependent physicochemical characteristics of diamond nanoparticles. | Subhasish Chatterjee | Physical Chemistry; Materials Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657e77c49138d23161d5f18e/original/probing-the-13c-nuclear-spin-relaxation-of-diamond-nanoparticles-with-solid-state-nmr.pdf |
60c73f1bbdbb8950f7a37f14 | 10.26434/chemrxiv.7221953.v1 | Adiabatic Electronic Motion in Forming Covalent Bond | <div>In studying a dynamical process of the chemical reaction, it is decisive to get appropriate information from an electronic current density. To this end, we divide one-body electronic density into a couple of densities, that is, an electronic sharing density and an electronic contraction density. Since the one-body electronic current density defi ned directly through the microscopic electronic wave function gives null value under the Born-Oppenheimer molecular dynamics, we propose to employ the Maxwell's displacement current density de fined by means of the one-body electronic density obtained under the same approximation. Applying the electronic sharing and the electronic contraction current densities to a hydrogen molecule, we show these densities give important physical quantities for analyzing a dynamical process of the covalent bond.</div> | Michihiro Okuyama; Fumihiko Sakata | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1bbdbb8950f7a37f14/original/adiabatic-electronic-motion-in-forming-covalent-bond.pdf |
60c742ad337d6c08dbe26aad | 10.26434/chemrxiv.8362103.v1 | Tuning the Photoluminescence of DNA-Wrapped Carbon Nanotubes by pH | These findings contribute in several ways to our
understanding of DNA wrapping structure on the encased SWCNT and provide a
basis for design of nanotube-based sensors for detecting local pH gradients in
restricted environments, such as in living cells and microfluidic channels. | Niyousha Mohammadshafie | Bioorganic Chemistry; Carbon-based Materials; Nanostructured Materials - Nanoscience; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ad337d6c08dbe26aad/original/tuning-the-photoluminescence-of-dna-wrapped-carbon-nanotubes-by-p-h.pdf |
66fbbe3fcec5d6c142c59349 | 10.26434/chemrxiv-2024-pgldf | The helix-turn-helix motif in Pseudomonas aeruginosa ExsA monomer can recognize DNA and stabilize the putative ligand-binding domain | Pseudomonas aeruginosa is an opportunistic human pathogen. One of the most potent virulence factors in its arsenal is the Type III Secretion System (T3SS). This secretion apparatus transports effector toxins directly into host cells, thereby causing cell damage or death. Expression of the T3SS is regulated by a master transcriptional regulator, ExsA. To date, no drugs targeting ExsA are available and only static structural models of the protein have been generated, focusing on the C-terminal regulatory domain (CTD). Here, we used µsec atomistic molecular dynamics (MD) simulations to investigate the conformational dynamics in the full-length ExsA (bound to DNA) and in the N-terminal DNA-binding domain (NTD). These data show how the CTD and NTD likely interact with one other. We also subjected the MD trajectories to binding pocket prediction and geometry analyses. This revealed a lipid-binding pocket in the β-sheet bundle and also identified two novel potential druggable pockets at the NTD/CTD interface, which could be used in future structure-based drug discovery campaigns. Overall, a single helix-turn-helix motif seems to drive ExsA monomer DNA recognition and stabilize the putative ligand-binding domain. | Jack Greenhalgh; Prasanthi Medarametla; Antti Poso; Martin Welch; Thales Kronenberger; Taufiq Rahman | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fbbe3fcec5d6c142c59349/original/the-helix-turn-helix-motif-in-pseudomonas-aeruginosa-exs-a-monomer-can-recognize-dna-and-stabilize-the-putative-ligand-binding-domain.pdf |
6630c98d21291e5d1d14607f | 10.26434/chemrxiv-2024-mn36l | Glutamate “flick” enables proton tunneling during fast redox biocatalysis | Redox enzymes capable of carrying out multi-electron reactions serve as blueprints for the rational design of bio-inspired catalysts for future green technologies. During catalysis, enzymes transition through multiple ‘active’ intermediate states. Movement of both electrons and substrate to/from the active site is precisely controlled to achieve the equivalent of high Faradaic efficiencies, with minimal electrons wasted in detrimental side reactions. High turnover frequencies in metalloenzymes such as the nickel-iron (NiFe) hydrogenases require mechanisms for highly-choreographed movement of two quantum particles, protons and electrons. According to Marcus theory, structural rigidity is key to a low reorganisation energy barrier for rapid, outer-sphere electron transfer. However, this is at odds with the requirement for a degree of conformational flexibility to enable rapid proton tunnelling between residues separated by distances greater than ~2.7 Å. Here we exploit the specific redox poising possible with electrochemical control of protein crystals and characterise, structurally and spectroscopically, [NiFe]-hydrogenase in each of the key states of the catalytic cycle as well as its CO-bound and oxidised states. These structures confirm extraordinarily fixed metal coordination at the active site, conducive to fast multi-electron catalysis, and reveal a subtle carboxylate ‘flick’ that provides molecular detail of how glutamate acts as a proton shuttle. | Stephen B. Carr; Wangzhe Li; Kin Long Wong; Rhiannon M. Evans; Sophie E. T. Kendall-Price; Kylie A. Vincent; Philip A. Ash | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630c98d21291e5d1d14607f/original/glutamate-flick-enables-proton-tunneling-during-fast-redox-biocatalysis.pdf |
616a748df718dfc6b0e05c1f | 10.26434/chemrxiv-2021-850lc | Design and synthesis of novel orexin 2 receptor agonists based on naphthalene skeleton | A novel series of naphthalene derivatives were designed and synthesized based on the strategy focusing on the restriction of the flexible bond rotation of OX2R selective agonist YNT-185 (1) and their agonist activities against orexin receptors were evaluated. The 1,7-naphthalene derivatives showed superior agonist activity than 2,7-naphthalene derivatives, suggesting that the bent form of 1 would be favorable for the agonist activity. The conformational analysis of 1,7-naphthalene derivatives indicated that the twisting of the amide unit out from the naphthalene plane is important for the enhancement of activity. The introduction of a methyl group on the 2-position of 1,7-naphthalene ring effectively increased the activity, which led to the discovery of the potent OX2R agonist 28c (EC50 = 9.21 nM for OX2R, 148 nM for OX1R). The structure-activity relationship results were well supported by a comparison of the docking simulation results of the most potent derivative 28c with an active state of agonist-bound OX2R cryo-EM SPA structure. These results suggested important information for understanding the active conformation and orientation of pharmacophores in the orexin receptor agonists, which is expected as a chemotherapeutic agent for the treatment of narcolepsy. | Tsubasa Hino; Tsuyoshi Saitoh; Yasuyuki Nagumo; Naoshi Yamamoto; Noriki Kutsumura; Yoko Irukayama-Tomobe; Yukiko Ishikawa; Ryuji Tanimura; Masashi Yanagisawa; Hiroshi Nagase | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616a748df718dfc6b0e05c1f/original/design-and-synthesis-of-novel-orexin-2-receptor-agonists-based-on-naphthalene-skeleton.pdf |
6732e6445a82cea2fad980a7 | 10.26434/chemrxiv-2024-j366f | Controlled Gel Toughening with Tetrafunctional Cyclobutane Mechanophores | Customizing the toughness of single-network polymer gels independently of their composition and topology remains an unsolved challenge. Traditionally, polymer network toughening is achieved by using specialized monomers or solvents, or by adding secondary networks or fillers that substantially alter composition and may limit applications. Here, we report a new class of force-responsive molecules—tetrafunctional cyclobutanes (TCBs)—that enables the simple synthesis of end-linked gels with nearly identical compositions yet substantially decreased or increased toughness. This behavior is shown to arise from force-coupled chemo- and regio-selective TCB reaction pathways that are dependent on subtle changes in TCB substituents and that dictate bulk gel toughness through a topological descriptor we refer to as network strand continuity. This work introduces tetrafunctional mechanophores and the corresponding concepts of regio- and chemoselective force-coupled reactivity to the field of polymer network mechanochemistry, providing a new design concept for tuning the toughness of simple, commonly used single network gels. | Abraham Herzog-Arbeitman; Ilia Kevlishvili; Devosmita Sen; Julianna Lian; Joshika Chakraverty; Shu Wang; Bradley Olsen; Heather Kulik; Stephen Craig; Jeremiah Johnson | Organic Chemistry; Polymer Science; Physical Organic Chemistry; Hydrogels; Organic Polymers; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6732e6445a82cea2fad980a7/original/controlled-gel-toughening-with-tetrafunctional-cyclobutane-mechanophores.pdf |
658055009138d23161f52aa0 | 10.26434/chemrxiv-2023-2s07m-v2 | The Effect of Particle Size on the Optical and Electronic Properties of Hydrogenated Silicon Nanoparticles | We use a combination of GW-BSE and time-dependent DFT to study the optical and electronic properties of hydrogen terminated silicon nanoparticles. We predict that the lowest excited states of these silicon nanoparticles are excitonic in character and that the corresponding excitons are completely delocalised over the volume of the particle. The size of the excitons is precited to increase proportionally with the particle size. Conversely, we predict that the fundamental gap, the optical gap, and the exciton binding energy increase with decreasing particle size. The exciton binding energy is predicted to counter-act the variation in the fundamental gap and hence to reduce the variation of the optical gap with particle size. The variation in the exciton binding energy itself is probably caused by a reduction in the dielectric screening with decreasing particle size. The intensity of the excited state corresponding to the optical gap and other low energy excitations are predicted to increase with decreasing particle size. We explain this increase in terms of the ‘band structure’ becoming smeared out in reciprocal space with decreasing particle size, increasing the ‘overlap’ between the occupied and unoccupied quasiparticle states and thus, the oscillator strength. Fourier transforms of the lowest excitons show that they inherit the periodicity of the frontier quasiparticle states. This combined with the delocalisation of the exciton and the large exciton binding energy means that the excitons in silicon nanoparticles combine aspects of Wannier-Mott, delocalisation and effect of periodicity of the underlying structure, and Frenkel, large exciton binding energy, excitons. | Eimear Madden; Martinus Antonius Zwijnenburg | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658055009138d23161f52aa0/original/the-effect-of-particle-size-on-the-optical-and-electronic-properties-of-hydrogenated-silicon-nanoparticles.pdf |
621e2e5bc45c0b1fb2215555 | 10.26434/chemrxiv-2022-kw6tp | Tension-Induced Phase Transformation and Anomalous Poisson Effect in Violet Phosphorene | Two-dimensional violet phosphorene (VP) nanosheets are promising semiconductor materials with unique cross structures distinct from those of their allotropes such as black phosphorene and blue phosphorene, but their mechanical behaviors remain almost unexplored. By using the first-principles calculations, in this paper we investigate the mechanical behaviors of monolayer, bilayer, and bulk VP under uniaxial tension. A phase transformation from the open-pore phase to closed-pore phase is observed in VP structures when under a specific tensile strain. It is revealed that the phase transformation is attributed to the competition between the rotation and elongation of sub-nano rods in VP structures during the loading process. Due to the phase transformation, the in-plane Poissons ratio of monolayer VP can become greater than 1.2, while the bulk VP possesses a negative out-of-plane Poissons ratio with a magnitude up to -0.3 at a certain strain. These results indicate that Poisson effects in VP are superior to those in any other existing two-dimensional materials. In addition, based on the tensor analysis of elastic constants, a strong mechanical anisotropy is observed in VP structures both before and after the phase transformation. Besides the mechanical properties, the band gap of all VP structures decreases as the applied tensile strain increases, which can eventually transform into the metallic state prior to their fracture. The combination of unique phase transformation, anomalous Poisson effect, strong mechanical anisotropy and tunable electronic properties render VP be a novel nanoscale metamaterial with multifunctional applications. | Penghua Ying; Xiaowen Li; Xiaobin Qiang; Yao Du; Jin Zhang; Lang Chen; Zheng Zhong | Physical Chemistry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621e2e5bc45c0b1fb2215555/original/tension-induced-phase-transformation-and-anomalous-poisson-effect-in-violet-phosphorene.pdf |
679757f581d2151a02247d1d | 10.26434/chemrxiv-2025-vk3rl | Novel earth-abundant Cu and Fe-based chalcogenide cocatalysts for photocatalytic hydrogen evolution | While photocatalysis offers an attractive route towards the sustainable production of hydrogen (H2) and other green fuels or commodity chemicals, significant improvements in efficiency and reductions in production costs are still needed. Traditionally, noble metal cocatalysts are used to increase the activity and selectivity of a photocatalyst. In this work, we systematically investigate different nanomaterials based on the abundant and inexpensive elements Cu and Fe as cocatalysts on TiO2 (P25) for the photocatalytic hydrogen evolution reaction (HER) under simulated sunlight as well as under UV irradiation. All the investigated Cu and Fe sulfides/oxides can be obtained via simple and fast microwave-assisted synthesis. In addition, we show how further modifications, such as partial oxidation of the sulfides or doping of CuFe2O4 with Ni, can have a tremendous effect on the performance as a cocatalyst, increasing the activity by a factor of more than 15 compared to pristine TiO2 and by a factor of almost 6 compared to TiO2 equipped with undoped CuFe2O4 under AM 1.5G simulated sunlight. Under UV irradiation, an H2 evolution rate of more than 2.3 mmol h-1 was achieved. Thus, this work opens a new design platform for the synthesis of earth-abundant cocatalysts for noble metal substitution in photocatalysis. | Judith Zander; Roland Marschall | Catalysis; Energy; Electrocatalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679757f581d2151a02247d1d/original/novel-earth-abundant-cu-and-fe-based-chalcogenide-cocatalysts-for-photocatalytic-hydrogen-evolution.pdf |
668567ee5101a2ffa8490412 | 10.26434/chemrxiv-2024-jsfbr | pH-mediated Manipulation of the Histidine Brace in LPMOs and Generation of a Tri-anionic Variant, Investigated by EPR, ENDOR, ESEEM and HYSCORE Spectroscopy | Lytic polysaccharide monooxygenases (LPMOs) are enzymes that catalyze the oxidative depolymerization of polysaccharides through activation of strong C-H bonds. Their active site is composed of a copper ion that is coordinated by the so-called histidine brace, consisting of two histidine residues that coordinate the metal ion in a T-shaped arrangement. The unique structure of this motif and its suggested ability to generate and stabilize highly oxidizing intermediates has sparked considerable interest, leading to various hypotheses on its role for LPMOs and LPMO-inspired biomimetic complexes. To gain detailed insights into the electronic and geometric structure of the histidine brace and test its chemical variability, we have used advanced electron paramagnetic resonance (EPR) techniques, in combination with isotopic labelling (15N, 2H) of the AA10 LPMO SmAA10A over a wide pH range (pH 4.0 - pH 12.5), in which the monocopper site remains intact and the protein does not exhibit permanent damage. Between pH 4 and 11.5, Electron Nuclear Double Resonance (ENDOR) spectroscopy identifies and discriminates between coordinating waters and hydroxo ions (pKa1 = 9.65) at an open-site of the histidine brace. Above pH 11.5, deprotonation of the two remote nitrogen nuclei of the coordinating imidazole moieties and of the coordinating N-terminal amine function was observed via ENDOR, Electron Spin Echo Envelope Modulation (ESEEM) and Hyperfine Sublevel Correlation (HYSCORE) spectroscopies. This is associated with major electronic changes in the histidine brace, including increased σ-donor capabilities of the imidazolates and an overall reduced interaction of the deprotonated amine function with the copper center. This observation highlights the possible larger role of the imidazole moieties, potentially stabilizing potent oxidants during turnover. The associated spectroscopic and electronic changes of the LPMO are discussed in reference with functional biomimetic complexes. The presented study demonstrates the application of advanced EPR techniques for a thorough characterization of the active site in LPMOs, which ultimately sets a foundation for and affords an outlook on future applications characterizing reaction intermediates. | Julia Haak; Ole Golten; Morten Sørlie; Vincent Eijsink; George Cutsail III | Inorganic Chemistry; Bioinorganic Chemistry; Bonding; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668567ee5101a2ffa8490412/original/p-h-mediated-manipulation-of-the-histidine-brace-in-lpm-os-and-generation-of-a-tri-anionic-variant-investigated-by-epr-endor-eseem-and-hyscore-spectroscopy.pdf |
60c748ed0f50db174739683e | 10.26434/chemrxiv.11996589.v1 | Monitoring Polymer-Assisted Mechanochemical Cocrystallisation Through in Situ X-Ray Powder Diffraction | Time-resolved mechanochemical cocrystallisation studies have so-far focused solely on neat and liquid-assisted grinding. Here, we report the monitoring of polymer-assisted grinding reactions using <i>in situ</i> X-ray powder diffraction, revealing that reaction rate is almost double compared to neat grinding and independent of the molecular weight and amount of used polymer additives.<br /> | Luzia S. Germann; Sebastian T. Emmerling; Manuel Wilke; Robert E. Dinnebier; Mariarosa Moneghini; Dritan Hasa | Organic Polymers; Polymers; Solid State Chemistry; Chemical Kinetics; Self-Assembly; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748ed0f50db174739683e/original/monitoring-polymer-assisted-mechanochemical-cocrystallisation-through-in-situ-x-ray-powder-diffraction.pdf |
64b9214cae3d1a7b0d0b4ec8 | 10.26434/chemrxiv-2023-hmhrj | X-ray induced ultrafast charge transfer in thiophene-based conjugated polymers controlled by core-hole clock spectroscopy | We explore ultrafast charge transfer (CT) resonantly induced by hard x-ray radiation in organic thiophene-based polymers at the sulfur K-edge. A combination of core-hole clock spectroscopy with real-time propagation time-dependent density functional theory simulations gives an insight into the electron dynamics underlying the CT process. Our method provides control over CT by a selective excitation of a specific resonance in the sulfur atom with monochromatic x-ray radiation. Our combined experimental and theoretical investigation establishes that the dominant mechanism of CT in polymer powders and films consists of electron delocalization along the polymer chain occurring on the low-femtosecond time scale. | Nicolas Velasquez; Fernanda Brandalise Nunes; Oksana Travnikova; Iyas Ismail; Renaud Guillemin; Jessica B. Martins; Denis Céolin; Loïc Journel; Laure Fillaud; Dimitris Koulentianos; Chinnathambi Kamal; Ralph Püttner; Maria Novella Piancastelli; Marc Simon; Michael Odelius; Marcella Iannuzzi; Tatiana Marchenko | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b9214cae3d1a7b0d0b4ec8/original/x-ray-induced-ultrafast-charge-transfer-in-thiophene-based-conjugated-polymers-controlled-by-core-hole-clock-spectroscopy.pdf |
66c0ad2b20ac769e5fea8d9f | 10.26434/chemrxiv-2024-jfdmw | Sulfate radical anion-based degradation of metazachlor herbicide in the water and gas: A theoretical study | Metazachlor (MTZ) herbicide oxidation initiated by sulfate radical anion (SO4●-) in water and gas was investigated using the density functional theory (DFT) at the M06-2X/6-311++G(3df,3pd)//M06-2X/6-31+G(d,p) level of theory. Mechanisms and kinetics of MTZ oxidation via three oxidation mechanisms were investigated, including abstraction (Abs), addition (Add), and single electron transfer (SET). Results show that most oxidation reactions are favorable and spontaneous in both phases. The overall rate constants at 298.15K in water is 5.06 × 1010 M-1 s-1 whereas the one in gas is many times higher, 1.51 × 1013 M-1 s-1. Notably, the degradation in water is non-selected with the fastest reaction being SET with 5.76 × 109 M-1 s-1 and 11.39% of the kapp and Г, respectively. On the contrary, the one in gas almost occurs via Abs reaction with the fastest one being Abs-H24 with kapp and Г values being 1.08 × 1013 M-1 s-1 and 71.76%. In addition, the influence of temperature on the degradation kinetics is evaluated. Results show that the degradation in water increases as a function of temperature (283 to 323 K), while the drawback trend is found in the gas phase from 253 to 323 K. Diving into the chemical nature of the hydrogen abstraction processes, it is noteworthy that the most predominant Abs reactions at the methyl and methylene groups occur via the proton-coupled electron transfer (PCET) mechanism. Overall, the SO4●--based degradation is an effective and potential method for removing MTZ herbicide. | Dinh Hieu Truong; Thi Ai Nhung Nguyen; Sonia Taamalli; Abderrahman El Bakali; Florent Louis; Duy Quang Dao | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c0ad2b20ac769e5fea8d9f/original/sulfate-radical-anion-based-degradation-of-metazachlor-herbicide-in-the-water-and-gas-a-theoretical-study.pdf |
630c4d5511986cd6a549f8b4 | 10.26434/chemrxiv-2022-6q7d0 | Improving reactivity of naphthalimide-based GST probe by imparting TPP cation: Development and application for live cell imaging | Glutathione S-transferases (GSTs) are a superfamily of multifunctional enzymes comprising multiple classes and subtypes. This paper describes the synthesis and characterization of TPPBN-1, a naphthalimide derivative conjugated with a triphenylphosphonium (TPP) cation. When 4-bromonaphthalimide (BrNaph), a previously characterized GST substrate, was conjugated to a TPP cation, the conjugate showed increased reactivity towards most alpha- and mu-class GSTs, particularly the GSTA2 subtype, compared to the parent compound, but hardly towards Pi-class GSTs. Using this probe with enhanced reactivity, the enzymatic activity of endogenous GSTA1/2 in HepG2 cells was visualized by confocal fluorescence microscopy. The results demonstrated that modification with TPP cations, which are often used as tags for targeting mitochondria, can be used to enhance the reactivity of probes for specific GST subtypes. | Yuuta Fujikawa; Kenta Terakado; Sayaka Nezu; Kota Noritsugu; Yuki Maemoto; Akihiro Ito; Hideshi Inoue | Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630c4d5511986cd6a549f8b4/original/improving-reactivity-of-naphthalimide-based-gst-probe-by-imparting-tpp-cation-development-and-application-for-live-cell-imaging.pdf |
60c74338bb8c1a55a83da2b8 | 10.26434/chemrxiv.7854980.v2 | The Role of Molecular Modeling & Simulation in the Discovery and Deployment of Metal-Organic Frameworks for Gas Storage and Separation | Metal-organic frameworks (MOFs) are highly tunable, extended-network, crystalline, nanoporous materials with applications in gas storage, separations, and sensing. We review how molecular models and simulations of gas adsorption in MOFs have informed the discovery of performant MOFs for methane, hydrogen, and oxygen storage, xenon, carbon dioxide, and chemical warfare agent capture, and xylene enrichment. Particularly, we highlight how large, open databases of MOF crystal structures, post-processed to enable molecular simulations, are a platform for computational materials discovery. We discuss how to orient research efforts to routinize the computational discovery of MOFs for adsorption-based engineering applications. | Arni Sturluson; Melanie T. Huynh; Alec Kaija; Caleb Laird; Sunghyun Yoon; Feier Hou; Zhenxing Feng; Christopher E. Wilmer; Yamil J. Colon; Yongchul Chung; Daniel Siderius; Cory Simon | Nanostructured Materials - Materials; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74338bb8c1a55a83da2b8/original/the-role-of-molecular-modeling-simulation-in-the-discovery-and-deployment-of-metal-organic-frameworks-for-gas-storage-and-separation.pdf |
62fa71b3bde086d49a625920 | 10.26434/chemrxiv-2022-05mz4 | Modeling ionic conductivity and activation energy in garnet-structured solid electrolytes: the role of composition, grain boundaries and processing | All-solid-state batteries (ASSBs) are one of the most forthcoming elements of the electrochemical energy systems of new generation. One of the most attractive perspectives of using all-solid- state batteries as the platform for energy storage is the increased safety, energy density and possible device miniaturization. During the last decades the intensive research of the solid state electrolyte materials has been observed. Among the most investigated and attractive candidates for Li-ion batteries one can distinguish the garnet-structured solid electrolytes, NASICONs, LGPS electrolytes and argyrodites. Despite the ever-growing interest to ASSB technologies there is a room in their chemistry to be explored especially concerning the aspects of the defects, vibrational characteristics, strain- and facet-engineering effects. The aim of this study is to investigate the possible role of composition, disorder and the synthesis details on the Li-ion conductivity and activation energies in garnet-structured solid electrolytes. | Natalia Kireeva; Aslan Yu. Tsivadze; Vladislav S. Pervov | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fa71b3bde086d49a625920/original/modeling-ionic-conductivity-and-activation-energy-in-garnet-structured-solid-electrolytes-the-role-of-composition-grain-boundaries-and-processing.pdf |
60c757c90f50db789d39831a | 10.26434/chemrxiv.14459826.v1 | Tunability of Interactions Between the Core and Shell in Rattle-Type Particles Studied with Liquid-Cell Electron Microscopy | <div>Yolk-shell or rattle-type particles consist of a core particle that is free to move inside a thin shell. A stable core with a fully accessible surface is of interest in fields such as catalysis and sensing. However, the stability of a charged nanoparticle core within the cavity of a charged thin shell remains largely unexplored. Liquid-cell (scanning) transmission electron microscopy (LC(S)TEM) is an ideal technique to probe the core-shell interactions at nanometer spatial resolution. Here we show by means of calculations and experiments that these interactions are highly tunable. We found that in dilute solutions adding a monovalent salt led to stronger confinement of the core to the middle of the geometry. In deionized water the Debye length becomes comparable to the shell radius R<sub>shell</sub>, leading to a less steep electric potential gradient and a reduced core-shell interaction, which can be detrimental to the stability of nanorattles. For a salt concentration range of 0.5-250mM the repulsion was relatively long-ranged due to the concave geometry of the shell. At salt concentrations of 100 and 250mM the core was found to move almost exclusively near the shell wall, which can be due to hydrodynamics, a secondary minimum in the interaction potential or a combination of both. The possibility of imaging nanoparticles inside shells at high spatial resolution with liquid-cell electron microscopy makes rattle particles a powerful experimental model system to learn about nanoparticle interactions. Additionally, our results highlight the possibilities for manipulating the interactions between core and shell that could be used in future applications.</div> | Tom Welling; Kanako Watanabe; Albert Grau-Carbonell; Joost de Graaf; Daisuke Nagao; Arnout Imhof; Marijn A. van Huis; Alfons Van Blaaderen | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757c90f50db789d39831a/original/tunability-of-interactions-between-the-core-and-shell-in-rattle-type-particles-studied-with-liquid-cell-electron-microscopy.pdf |
611d36b530688d3fee943db8 | 10.26434/chemrxiv-2021-cpxh9 | UV-adVISor: Attention-Based Recurrent Neural Networks to Predict UV-Vis Spectra | Ultraviolet-visible (UV-Vis) absorption spectra are routinely collected as part of high-performance liquid chromatography (HPLC) analysis systems and can be used to identify chemical reaction products by comparison to reference spectra. Here, we present UV-adVISor as a new computational tool for predicting UV-Vis spectra from a molecule’s structure alone. UV-Vis prediction was approached as a sequence-to-sequence problem. We utilized Long-Short Term Memory and attention-based neural networks with Extended Connectivity Fingerprint diameter 6 or molecule SMILES to generate predictive models for UV-spectra. We have produced two spectrum datasets (Dataset I, N = 949 and Dataset II, N = 2222) using different compound collections and spectrum acquisition methods to train, validate, and test our models. We evaluated the prediction accuracy of the complete spectra by the correspondence of wavelengths of absorbance maxima and with a series of statistical measures (the best test set median model parameters are in parentheses for Model II), including RMSE (0.064), R2 (0.71), and dynamic time warping (DTW, 0.194) of the entire spectrum curve. Scrambling molecule structures with experimental spectra during training resulted in a degraded R2, confirming the utility of the approaches for prediction. UV-adVISor is able to provide fast and accurate predictions for libraries of compounds. | Fabio Urbina; Kushal Batra; Kevin Luebke; Jason White; Daniel Matsiev; Lori Olson; Jeremiah Malerich; Maggie Hupcey; Peter Madrid; Sean Ekins | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611d36b530688d3fee943db8/original/uv-ad-vi-sor-attention-based-recurrent-neural-networks-to-predict-uv-vis-spectra.pdf |
664472d391aefa6ce10e01c5 | 10.26434/chemrxiv-2024-js244-v3 | Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics | We develop ∂-HylleraasMD (∂-HyMD), a fully end-to-end differentiable molecular dynamics software based on the Hamiltonian hybrid particle-field formalism, and use it to establish a protocol for automated optimization of force field parameters. ∂-HyMD is templated on the recently established HylleraaasMD software, while using the JAX autodiff framework as the main engine for the differentiable dynamics. ∂-HyMD exploits an embarrassingly parallel optimization algorithm by spawning independent simulations, whose trajectories are simultaneously processed by reverse mode automatic differentiation to calculate the gradient of the loss function, which is in turn used for iterative optimization of the force-field parameters. We show that parallel organization facilitates the convergence of the minimization procedure, avoiding the known memory and numerical stability issues of differentiable molecular dynamics approaches. We showcase the effectiveness of our implementation by producing a library of force field parameters for standard phospholipids, with either zwitterionic or anionic heads, and with saturated or unsaturated tails. Compared to the all-atom reference, the force field obtained by ∂-HyMD yields better density profiles than the parameters derived from previously utilized gradient-free optimization procedures. Moreover, ∂-HyMD models can predict with good accuracy properties not included in the learning objective, such as lateral pressure profiles, and are transferable to other systems, including triglycerides. | Manuel Carrer; Henrique Musseli Cezar; Sigbjørn Løland Bore; Morten Ledum; Michele Cascella | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Machine Learning; Biophysical Chemistry; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664472d391aefa6ce10e01c5/original/learning-force-field-parameters-from-differentiable-particle-field-molecular-dynamics.pdf |
651342a7ade1178b242c1828 | 10.26434/chemrxiv-2023-gxbps | Examining the Electronic Structures of Monouranium Endohedral Metallofullerenes: Solution Versus Solid-State Effects in U@C82 | In uranium endohedral metallofullerenes, cage isomer dependent oxidation states have been theoretically deter-mined for U3+@C2v(9)-C823- and U4+@C2(5)-C824+. Solution phase EPR supports this assessment; however, in the solid-state, EPR, SQUID magnetometry, and XANES suggest both isomers adopt a common metal-oxidation state. This inves-tigation shows the redox active uranium center may be sensitive to changes at the carbon cage, demonstrating that solution versus solid-state factors is a possible consideration when determining the electronic structure and reactivity of these unique systems. | Jesse Murillo; Alejandra Gomez-Torres; Yang-Rong Yao; Yuzki Oey; Joshua Wright; Ram Seshadri; Luis Echegoyen; Ning Chen; Skye Fortier | Organometallic Chemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651342a7ade1178b242c1828/original/examining-the-electronic-structures-of-monouranium-endohedral-metallofullerenes-solution-versus-solid-state-effects-in-u-c82.pdf |
65b6040a9138d23161e64390 | 10.26434/chemrxiv-2024-9257k | Optimizing telescoped heterogeneous catalysis with noise-resilient multi-objective Bayesian optimization | This study evaluates the noise resilience of multi-objective Bayesian optimization (MOBO) algorithms in chemical synthesis, an aspect critical for processes like telescoped reactions and heterogeneous catalysis but seldom systematically assessed. Through simulation experiments on amidation, acylation, and SNAr reactions under varying noise levels, we identify the qNEHVI acquisition function as notably proficient in handling noise. Subsequently, qNEHVI is employed to optimize a two-step heterogeneous catalysis for the continuous-flow synthesis of hexafluoroisopropanol. Achieving considerable optimization within just 20 experimental runs, we report an E-factor of 0.3744 and a conversion rate of 76.20%, with optimal conditions set at 5.00 sccm and 35.00℃ for the first step, and 80.00 sccm and 170℃ for the second. This research highlights qNEHVI's potential in noisy multi-objective optimization and its practical utility in refining complex synthesis processes. | Guihua Luo; Xilin Yang; Weike Su; Tingting Qi; Qilin Xu; An Su | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Machine Learning; Reaction Engineering; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b6040a9138d23161e64390/original/optimizing-telescoped-heterogeneous-catalysis-with-noise-resilient-multi-objective-bayesian-optimization.pdf |
60c747cbf96a006f16286fbe | 10.26434/chemrxiv.11796150.v1 | Speeding Up Discovery of Auxetic Zeolite Frameworks by Machine Learning | <div>
<div>
<div>
<p>The characterization of the mechanical properties of crystalline materials is nowadays considered a routine computational task in DFT calculations. However, its high
computational cost still prevents it from being used in high-throughput screening
methodologies, where a cheaper estimate of the elastic properties of a material is required. In this work, we have investigated the accuracy of force field calculations for
the prediction of mechanical properties, and in particular for the characterization of
the directional Poisson’s ratio. We analyze the behavior of about 600,000 hypothetical zeolitic structures at the classical level (a scale three orders of magnitude larger
than previous studies), to highlight generic trends between mechanical properties and
energetic stability. By comparing these results with DFT calculations on 991 zeolitic
frameworks, we highlight the limitations of force field predictions, in particular for
predicting auxeticity. We then used this reference DFT data as a training set for a
machine learning algorithm, showing that it offers a way to build fast and reliable predictive models for anisotropic properties. The accuracies obtained are, in particular,
much better than the current “cheap” approach for screening, which is the use of force fields. These results are a significant improvement over the previous work, due to the
more difficult nature of the properties studied, namely the anisotropic elastic response.
It is also the first time such a large training data set is used for zeolitic materials.
</p></div></div></div><div><div><div>
</div>
</div>
</div> | Romain Gaillac; Siwar Chibani; François-Xavier Coudert | Metamaterials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747cbf96a006f16286fbe/original/speeding-up-discovery-of-auxetic-zeolite-frameworks-by-machine-learning.pdf |
613f16d090051e69dbf17fc3 | 10.26434/chemrxiv-2021-lj2bz | High-Performance, Single-Crystal Gold Bowtie Nano-Antennas via Epitaxial Electroless Deposition | Material quality can play a critical role in the performance of nanometer-scale plasmonic structures. Here, we highlight a novel deposition strategy for single-crystal noble metal deposition and provide a direct and quantitative comparison between the fabrication yield, durability, and efficiency of bowtie nano-antennas fabricated from monocrystalline and polycrystalline gold films using subtractive nanofabrication. Focused ion beam milling of monocrystalline Au(100) films deposited through epitaxial electroless deposition to form bowtie nano-antennas produces devices that demonstrate key performance enhancements over devices patterned identically from polycrystalline Au films deposited via physical vapor deposition. Single-crystal bowties reveal significant improvements in pattern transfer fidelity and device yield, the ability to tailor and model local plasmonic field enhancements and marked improvement in their thermal and mechanical stability over those fabricated from polycrystalline Au films. This work underscores the performance advantages of single-crystal nanoscale plasmonic materials and describes a straightforward, solution-phase deposition pathway to achieve them. We anticipate that this approach will be broadly useful in applications where local near-fields can enhance light−matter interactions, including for the fabrication of optical sensors, photocatalytic structures, hot carrier-based devices, and nanostructured noble metal architectures targeting nano-attophysics. | Sasan V. Grayli; Saeid Kamal; Gary Leach | Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f16d090051e69dbf17fc3/original/high-performance-single-crystal-gold-bowtie-nano-antennas-via-epitaxial-electroless-deposition.pdf |
62b8a3a958b3d67c3a603834 | 10.26434/chemrxiv-2022-l8p90 | Photochemical Aerobic Upcycling of Polystyrene Plastics to Commodity Chemicals | Since United Nations has set goals dealing with climate change, the chemical industry has focused on recycling the already-used polymers, targeting the reinsertion of plastic waste to market via new products through reforming. Upcycling of polystyrene plastic waste is becoming one of the hottest field of research in plastic upconversion. Herein, we introduce a novel, green, organocatalytic and photochemical aerobic upcycling process of polystyrene to benzoic acid, utilizing anthraquinone as the photocatalyst, LED 390 nm as the irradiation source and air as the sole oxidant. The developed protocol was applied successfully to the upcycling of daily-life used polystyrene products, leading to yields varying from 25-58%. Moreover, the obtained upcycled product from the polystyrene materials was employed to the successful synthesis of bioactive molecules, such as acetylsalicylic acid. | Nikolaos F. Nikitas; Christoforos Kokotos | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b8a3a958b3d67c3a603834/original/photochemical-aerobic-upcycling-of-polystyrene-plastics-to-commodity-chemicals.pdf |
659694339138d231612c89dd | 10.26434/chemrxiv-2023-8lv3v-v2 | Manganese Catalysed Synthesis of Polyketones Using Hydrogen Borrowing Approach | We report here a new method to make polyketones from the coupling of diketones and diols using a manganese pincer complex. The methodology allows us to access a new type of polyketone (polyarylalkylketone) containing aryl, alkyl, and ether functionalities bridging the gap between the two classes of commercially available polyketones – aliphatic polyketones and polyaryletherketones. Using this methodology, twelve new polyketones have been synthesized and characterised using various analytical techniques to understand their chemical, physical, morphological, and mechanical properties. Based on previous reports and our studies, we suggest that the polymerization occurs via a hydrogen-borrowing mechanism that involves the dehydrogenation of diols to dialdehyde followed by aldol condensation of dialdehyde with diketones to form chalcone derivatives and their subsequent hydrogenation to form polyarylalkylketones. | Pavel Kulyabin; Oxana Magdysyuk; Aaron B Naden; Daniel M Dawson; Ketan Pancholi; Matthew Walker; Massimo Vassalli; Amit Kumar | Catalysis; Polymer Science; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659694339138d231612c89dd/original/manganese-catalysed-synthesis-of-polyketones-using-hydrogen-borrowing-approach.pdf |
61f444ea1fd2740ad21e6a04 | 10.26434/chemrxiv-2022-z1r95 | Imaging Orientation of a Single Molecular Hierarchical Self-Assembled Sheet: The Combined Power of a Vibrational Sum Frequency Generation Microscopy and Neural Network | In this work, we determined the tilt angles of molecular units in hierarchical self-assembled materials on a single-sheet level, which were not available previously. This was achieved by developing a fast linescanning vibrational sum frequency generation (VSFG) hyperspectral imaging technique in combination with neural network analysis. Rapid VSFG imaging enables polarization resolved images on a single sheet level to be measured within a short time period, circumventing technical challenges due to long term optical setup instability. The polarization resolved hyperspectral images were then used to extract the supramolecular tilt angle of a self-assembly through a set of spectra-tilt angle relationships which were solved through neural network techniques. This unique combination of both novel techniques offers a new pathway to resolve molecular level structural knowledge of self-assembled materials. Understanding these properties can further drive self-assembly design from a bottom-up approach for applications in biomimetic and drug delivery researches. | Jackson Wagner; Zishan Wu; Wei Xiong | Biological and Medicinal Chemistry; Analytical Chemistry; Microscopy; Spectroscopy (Anal. Chem.); Drug Discovery and Drug Delivery Systems; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f444ea1fd2740ad21e6a04/original/imaging-orientation-of-a-single-molecular-hierarchical-self-assembled-sheet-the-combined-power-of-a-vibrational-sum-frequency-generation-microscopy-and-neural-network.pdf |
66c2db4620ac769e5f0a6464 | 10.26434/chemrxiv-2024-6fz5j | Neutron Imaging for Automotive Polymer Electrolyte Fuel Cells During Rapid Cold Starts | The phase transition from supercooled water to ice is closely related to the electrochemical performance and lifetime of an energy device at sub-zero temperatures. In particular, fuel cells for passenger cars face this issue because they are frequently started and stopped under sub-zero conditions during the winter season. However, there is a lack of visual information regarding the processes that occur within the fuel cell stack, and insight into how to improve the safety and performance during cold starts is lacking. In this study, we developed an operando neuron imaging system to visualize the water distribution inside an automotive single cell simulating a fuel cell stack during cold starts. This was achieved using a rapid-temperature heating unit. In addition, we showcase cold-start tests at three different sub-zero temperatures, and the obtained results suggest that pre-conditioning residual water and post-cold-start meltwater have an impact on the rapid cold-start performance. | Wataru Yoshimune; Yuki Higuchi; Fangzhou Song; Shogo Hibi; Yoshihiro Matsumoto; Hirotoshi Hayashida; Hiroshi Nozaki; Takenao Shinohara; Satoru Kato | Energy; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c2db4620ac769e5f0a6464/original/neutron-imaging-for-automotive-polymer-electrolyte-fuel-cells-during-rapid-cold-starts.pdf |
60c73edb567dfef06fec38ca | 10.26434/chemrxiv.7157258.v1 | A Designed Protein Binding-Pocket to Control Photochemical Isomerization | <p>ESIPT involves a photochemical isomerization and creates the opportunity for the emission of two distinct wavelengths of light from a single fluorophore. The selectivity between these two wavelengths of emission is dependent on the environment around the fluorophore and suggests the possibility for ratiometric monitoring of protein microenvironments. Unfortunately, nonspecific binding of ESIPT fluorophores does not often lead to dramatic changes in the ratio between the two wavelengths of emission. A protein binding pocket was designed to selectively discriminate between the two channels of emission available to an ESIPT fluorophore. More broadly, this work demonstrates that specific interactions between the protein and the fluorophore are essential to realize strong ratiometric differences between the two possible wavelengths of emission. The design strategies proposed here lead to an ESIPT fluorophore that can discern subtle differences in the interface between two proteins.</p> | Bryan J. Lampkin; Cecilia Monteiro; Evan T. Powers; Paige M. Bouc; Jeffery W. Kelly; Brett VanVeller | Bioorganic Chemistry; Photochemistry (Org.); Biophysics | CC BY 4.0 | CHEMRXIV | 2018-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edb567dfef06fec38ca/original/a-designed-protein-binding-pocket-to-control-photochemical-isomerization.pdf |
60c74eb6bdbb89dacba39bfb | 10.26434/chemrxiv.12271655.v2 | Protein-Bound Calcium Phosphate in Uremic Rat Serum: A Quantitative Study | Protein-bound calcium (prCa) constitutes about
40% of serum total calcium, in which albumin is the most dominant protein. Given the chemical interaction between calcium and phosphate (Pi), the
increased serum Pi in chronic kidney disease may cause changes in the
composition and structure of the prCa fraction. Here, we report <a>the phosphate binding on the protein-bound calcium in
uremic rat serum.</a> Using adenine-fed rats as a uremic model, we determined
the levels of calcium and phosphate fractions in rat serum by ultrafiltration,
and found that the level of protein-bound phosphate (prPi) in the uremic serum
was markedly higher than in control. The elevated prPi level was comparable to
the prCa level, consistent with the presence of <a>protein-bound
calcium phosphate</a> pr(Ca)<sub>j-m</sub>(CaPi)<sub>m</sub>. We then confirmed
its presence by ex vivo X-ray absorption near-edge
structure spectroscopy, revealing the discrete state of the calcium phosphate
clusters associated with protein. Finally, in a quantitative investigation
using Ca- and Pi-boosted serum, we discovered the threshold concentration for
the Pi binding on prCa, and determined the binding constant. The threshold,
while preventing Pi from binding to prCa in normal condition, allows excess Pi
to do so. The protein-bound calcium phosphate could act as a link between the
metabolism of serum proteins and the homeostasis of phosphate and calcium, and
it deserves further investigation
whether the molar ratio of (prPi/prCa)×100% may serve as a serum index of the vascular
calcification status in chronic kidney disease. | Hong-Xing Fan; Bao-Di Gou; Yu-Xi Gao; Gang Wu; Shu-Hu Liu; Fan Li; Tian-Lan Zhang | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eb6bdbb89dacba39bfb/original/protein-bound-calcium-phosphate-in-uremic-rat-serum-a-quantitative-study.pdf |
65aa42a266c1381729ccaaa4 | 10.26434/chemrxiv-2024-hff6n | Comparison of Classical and Fractional Viscoelastic Models for Describing Entangled Polymer Solutions | Fractional viscoelastic models provide an excellent description of rheological data for polymer systems with power-law behavior. However, the physical interpretation of their model parameters, which carry fractional units of time, remains elusive. We show that for poly(ethylene oxide) (PEO) solutions, the fractional Maxwell model (FMM) requires fewer model elements than classical spring-dashpot models for a reasonable description of the data and that it can be applied consistently to solutions with varying degrees of viscoelasticity. The fractional parameters exhibit scaling laws similar to classical parameters as a function of polymer concentration. To attach physical meaning to the fractional parameters, we derive an analytical expression for the relaxation time spectrum associated with the FMM and find it to be equivalent to the empirical dual asymptote model. | Robert Franz Schmidt; Horst Henning Winter; Michael Gradzielski | Polymer Science; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65aa42a266c1381729ccaaa4/original/comparison-of-classical-and-fractional-viscoelastic-models-for-describing-entangled-polymer-solutions.pdf |
66d7ee29cec5d6c14212660d | 10.26434/chemrxiv-2024-d33w4 | Localization of CuO, NiO, and Co3O4 sintering additives in dense proton-conducting perovskite ceramics based on BaSnO3 | Sintering additives have been widely employed to achieve good sinterability of barium-based proton-conducting perovskites (based on BaZrO3, BaCeO3, BaTiO3, BaHfO3, BaThO3, and BaSnO3). This is of particular importance for the fabrication of multilayered ceramic cells, in which the thin-film electrolyte layer can be primarily densified at relatively low sintering temperatures (1350–1500 °C). The introduction of sintering additives facilitates the fabrication of gas-tight ceramics; however, the precise nature of their localization and their effects on the functional properties remain uncertain and even questionable. In this study, we present a comprehensive characterization of ceramic materials based on Y-doped BaSnO3 prepared with the addition of three sintering additives (copper, cobalt, and nickel oxides) at 1 wt%. Although these introduced oxides belong to a group of compounds with similar physicochemical properties, each additive exerts a distinct influence on the microstructural and electrochemical properties of the ceramics owing to their own chemical localization features. These features are discussed in detail in the present work, providing useful information in the field of using sintering additives for the preparation of oxide ceramics for high-temperature applications. | George Starostin; Mariam Akopian; Gennady Vdovin; Inna Starostina; Dmitry Medvedev | Materials Science; Ceramics | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d7ee29cec5d6c14212660d/original/localization-of-cu-o-ni-o-and-co3o4-sintering-additives-in-dense-proton-conducting-perovskite-ceramics-based-on-ba-sn-o3.pdf |
60c749ce469df4533af43c35 | 10.26434/chemrxiv.12052869.v2 | Probing the 14-3-3 Isoform-Specificity Profile of Interactions Stabilized by Fusicoccin A | Fusicoccin A (FC) is a fungal phytotoxin that stabilizes protein–protein interactions (PPIs) between 14-3-3 adapter proteins and their phosphoprotein interaction partners. In recent years, FC has emerged as an important chemical probe of human 14-3-3 PPIs implicated in cancer and neurological diseases. These previous studies have established the structural requirements for FC-induced stabilization of 14-3-3·client phosphoprotein complexes; however, the effect of different 14-3-3 isoforms on FC activity has not been systematically explored. This is a relevant question for the continued development of FC variants because there are seven distinct isoforms of 14-3-3 in humans. Despite their remarkable sequence and structural similarities, a growing body of experimental evidence supports both tissue-specific expression of 14-3-3 isoforms and isoform-specific functions <i>in vivo</i>. Herein, we report the isoform-specificity profile of FC <i>in vitro</i>using recombinant human 14-3-3 isoforms and a focused library of fluorescein-labeled hexaphosphopeptides mimicking the C-terminal 14-3-3 recognition domains of client phosphoproteins targeted by FC in cell culture. Our results reveal modest isoform preferences for individual client phospholigands and demonstrate that FC differentially stabilizes PPIs involving 14-3-3s. Together, these data provide strong motivation for the development of non-natural FC variants with enhanced selectivity for individual 14-3-3 isoforms. | James Frederich; Ananya Sengupta; Josue Liriano; Ewa A. Bienkiewicz; Brian G. Miller | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749ce469df4533af43c35/original/probing-the-14-3-3-isoform-specificity-profile-of-interactions-stabilized-by-fusicoccin-a.pdf |
64ec26603fdae147fafc2edf | 10.26434/chemrxiv-2023-1b5tb | Integrating Multiscale and Machine Learning Approaches towards the SAMPL9 LogP Challenge | Three techniques intertwining and integrating quantum mechanics (QM), molecular mechanics (MM), and unsupervised machine learning were utilized in the prediction of the toluene-water partition coefficient (logP tol/w) for sixteen drug molecules as part of the ninth iteration of the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) series of blind prediction challenges. The three blind submissions yielded mean unsigned errors (MUE) ranging from 1.53-2.93 logPtol/w units. Out of all submissions (ranked and unranked), one of these methods yielded the third lowest MUE of 1.53 indicating an overall increase in errors with respect to predicting octanol-water partition coefficients (logPo/w¬) for similar drug-like molecules. After applying numerous QM and MM approaches into multiscale and data-driven approaches to supplement the initial analysis, MUEs were reduced to 1.00 logPtol/w units when using density functional theory (DFT) on a single conformation, while generating an ensemble of rotamer structures elucidates subtle electronic and structural effects that are not considered in the analysis of a single conformation. Computational approaches developed for these SAMPL challenges will continue to serve as standard predictive tools for rational drug design. | Michael Draper; Asa Waterman; Jonathan Dannatt; Prajay Patel | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ec26603fdae147fafc2edf/original/integrating-multiscale-and-machine-learning-approaches-towards-the-sampl9-log-p-challenge.pdf |
60c746c1469df4f06ff436d7 | 10.26434/chemrxiv.7929038.v2 | Electrolyte Competition Controls Surface Binding of CO Intermediates to CO2 Reduction Catalysts | Adsorbed CO is a critical intermediate in the electrocatalytic reduction of CO<sub>2</sub> to fuels. Directed design of CO<sub>2</sub>RR electrocatalysts have centered on strategies to understand and optimize the differences in CO adsorption enthalpy across surfaces. Yet, this approach has largely ignored the role of competitive electrolyte adsorption in defining the CO surface population relevant for catalysis. Using in situ infrared spectroelectrochemistry, we disclose the contrasting influence of electrolyte competition on reversible CO binding to Au and Cu catalysts. Whereas reversible CO binding to Au surfaces is driven by substitution and reorientation of adsorbed water, CO binding to Cu surfaces requires the reductive displacement of adsorbed carbonate anions. The divergent role of electrolyte competition for CO adsorption on Au vs. Cu leads to a ~600 mV difference in the potential region where CO accumulates on the two surfaces. The contrasting CO adsorption stoichiometry on Au and Cu also explains their disparate reactivity: water adsorption drives CO liberation from Au surfaces, impeding further reduction, whereas carbonate desorption drives CO accumulation on Cu surfaces, allowing for further reduction to hydrocarbons. These studies provide direct insight into how electrolyte constituents can serve as powerful design parameters for fine-tuning of CO surface populations and, thereby, CO<sub>2</sub>-to-fuels reactivity.<br /> | Anna Wuttig; Jaeyune Ryu; Yogesh Surendranath | Electrocatalysis; Heterogeneous Catalysis; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c1469df4f06ff436d7/original/electrolyte-competition-controls-surface-binding-of-co-intermediates-to-co2-reduction-catalysts.pdf |
60c74124bb8c1aca533d9ecd | 10.26434/chemrxiv.7959182.v1 | Photocatalytic TiO2 Micromotors for Removal of Microplastics and Suspended Matter | <p></p><p> Environmental contamination is a
major global challenge and the effects of contamination are found in most habitats.
In recent times, the pollution by microplastics has come to the global
attention and their removal displays an extraordinary challenge with no
reasonable solutions presented so far. One of the new technologies holding many
promises for environmental remediation on the microscale are self-propelled
micromotors. They present several properties that are of academic and technical
interest, such as the ability to overcome the diffusion limitation in catalytic
processes and their phoretic interaction with their environment. Here, we
present two novel strategies for the elimination of microplastics using
photocatalytic Au@Ni@TiO<sub>2</sub> -based micromotors. We show that
individual catalytic particles as well as assembled chains show excellent
collection and removal of suspended matter and microplastics from natural water
samples.</p><p></p> | Linlin Wang; Andrea Kaeppler; Dieter Fischer; Juliane Simmchen | Magnetic Materials; Nanostructured Materials - Materials; Thin Films; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2019-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74124bb8c1aca533d9ecd/original/photocatalytic-ti-o2-micromotors-for-removal-of-microplastics-and-suspended-matter.pdf |
64e48388dd1a73847f4a29d3 | 10.26434/chemrxiv-2023-3mwbk | In silico analysis of correlation between physicochemical properties of ligands and binding affinity to protein targets | In silico analysis is a powerful technique to identify better therapeutic interventions. Molecular docking is widely used to screen ligands through analysing binding affinities for target receptors. In this study we screened ligands for two proteins which are potential drug targets: deoxyuridine triphosphate nucleotidohydrolase (dUTPase) and 6- phosphoglucolactonase (6PGL). The enzyme dUTPase plays crucial roles in DNA replication and repair and has been implicated in a number of cancers in humans and the protein 6PGL is involved in the pentose phosphate pathway. We used 500 compounds from the dictionary of marine natural products to make the ligand library. The MarvinSketch was used for generating ligand structures. For virtual screening we used the PyRx software which utilizes Autodock vina for molecular docking. Ligand- receptor interactions were visualized using the BIOVIA Discovery Studio Visualizer software. From 500 compounds, 355 ligands followed the Lipinski rule of five. For dUTpase, ligand243 showed the highest binding affinity (-18.2 Kcal/mole). Interestingly, the same ligand exhibited the highest binding affinity (-17.5 Kcal/mole) for 6-PGL. We couldn’t find any significant correlation between binding affinities and physicochemical properties of the ligands. The dUTpase protein has been implicated in cancer pathophysiologies and the 6PGL has been identified as targets for treating sleeping sickness and malarial infections. We found that the ligand243 can bind to both of these drug targets with high affinities. Thus, this ligand can further be developed as a candidate drug for cancer, sleeping sickness and malarial infections. | Md. Aktar Hossain; Saima Sultana | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e48388dd1a73847f4a29d3/original/in-silico-analysis-of-correlation-between-physicochemical-properties-of-ligands-and-binding-affinity-to-protein-targets.pdf |
60c747854c89193833ad2d16 | 10.26434/chemrxiv.11623509.v1 | Using the Chemistry of Pharmaceuticals to Introduce Sustainable Chemistry and Systems Thinking in General Chemistry | Introductory college chemistry courses are required by a wide range of science curricula. This fact has tended to frame the courses as places where core, fundamental ideas are taught, so that a foundation of knowledge might be called upon by students when they are in subsequent courses. Unfortunately, the preponderance of compartmentalized fundamental topics bolsters learning that has challenges in terms of transfer of knowledge to other science settings. One method that has been proposed to help alleviate this concern is to incorporate systems thinking and rich contexts that directly connect foundational chemistry ideas to larger systems. One area that shows strong potential for such efforts is the science of pharmaceuticals. Adding examples related to the chemistry of drugs, both within the large lecture setting of general chemistry and within smaller discussion groups. The role of example problems, student writing projects and group construction of systems thinking related visualizations of the context of pharmaceutical chemistry are reported. | Tom Holme | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747854c89193833ad2d16/original/using-the-chemistry-of-pharmaceuticals-to-introduce-sustainable-chemistry-and-systems-thinking-in-general-chemistry.pdf |
60c73fdfee301c0ab8c789b7 | 10.26434/chemrxiv.7531544.v1 | Cavity Catalysis by Co-operative Vibrational Strong Coupling of Reactant and Solvent Molecules | <i>para</i>-nitrophenyl acetate hydrolysis is studied under vibrational strong coupling in a Fabry-Perot cavity. By tuning the cavity resonance to the C=O vibrational stretching mode of both the reactant and solvent molecules, it is found that the reaction is accelerated by an order of magnitude. It is shown that this cavity catalysis involves a co-operative strong coupling effect between the solvent and reactant molecules. The reaction rate follows an exponential relation with respect to the solvent coupling strength. The combination of co-operative effects and cavity catalysis confirms the potential of VSC as a new frontier in chemistry. <br /> | Jyoti Lather; Pooja Bhatt; Anoop Thomas; Thomas W. Ebbesen; Jino George | Chemical Kinetics; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdfee301c0ab8c789b7/original/cavity-catalysis-by-co-operative-vibrational-strong-coupling-of-reactant-and-solvent-molecules.pdf |
63ea73c5fcfb27a31fb9ac4b | 10.26434/chemrxiv-2022-tsrr6-v2 | Investigating Daptomycin-Membrane Interactions Using Native MS and Fast Photochemical Oxidation of Peptides in Nanodiscs | Daptomycin is a cyclic lipopeptide antibiotic that targets the lipid membrane of Gram-positive bacteria. Membrane fluidity and charge can affect daptomycin activity, but its mechanisms are poorly understood because it is challenging to study daptomycin interactions within lipid bilayers. Here, we combined native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) to study daptomycin-membrane interactions with different lipid bilayer nanodiscs. Native MS suggests that daptomycin incorporates randomly and does not prefer any specific oligomeric states when integrated into bilayers. FPOP reveals significant protection in most bilayer environments. Combining the native MS and FPOP results, we observed that stronger membrane interactions are formed with more rigid membranes, and pore formation may occur in more fluid membranes to expose daptomycin to FPOP oxidation. Electrophysiology measurements further sup-ported the observation of polydisperse pore complexes from the mass spectrometry data. Together, these results demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments to shed light on how antibiotic peptides interact with and within lipid membranes. | Deseree Reid; Tapasyatanu Dash; Zhihan Wang; Craig Aspinwall; Michael Marty | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ea73c5fcfb27a31fb9ac4b/original/investigating-daptomycin-membrane-interactions-using-native-ms-and-fast-photochemical-oxidation-of-peptides-in-nanodiscs.pdf |
619bcbe158bc4b62329ed3c3 | 10.26434/chemrxiv-2021-r591n | Anion-π Catalysis Enabled by the Mechanical Bond | We report a series of rotaxane-based anion-π catalysts in which the mechanical bond between a bipyridine macrocycle and an axle containing an NDI unit is intrinsic to the activity observed, including a [3]rotaxane that catalyses an otherwise disfavoured Michael addition in >60 fold selectivity over a competing decarboxylation pathway that dominates under Brønsted base conditions. The results are rationalized by detailed experimental investigations, electrochemical and computational analysis. | John Maynard; Bartomeu Galmés; Athanasios Stergiou; Mark Symes; Antonio Frontera; Steve Goldup | Organic Chemistry; Catalysis; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2021-11-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619bcbe158bc4b62329ed3c3/original/anion-catalysis-enabled-by-the-mechanical-bond.pdf |
65dfbc3ce9ebbb4db98286c2 | 10.26434/chemrxiv-2023-7wx16-v2 | Multimodal Acridine Photocatalysis Enables Direct Access to Thiols from Carboxylic Acids and Elemental Sulfur | Development of photocatalytic systems that facilitate mechanistically different steps in complex catalytic manifolds by distinct activation modes can enable previously inaccessible synthetic transformations. However, multimodal photocatalytic systems remain understudied, impeding their implementation in catalytic methodology. We report herein a photocatalytic access to thiols that directly merges the structural diversity of carboxylic acids with the ready availability of elemental sulfur without substrate preactivation. The photocatalytic transformation provides a direct radical-mediated segue to one of the most biologically important and synthetically versatile organosulfur functionalities, whose synthetic accessibility remains largely dominated by two-electron-mediated processes based on toxic and uneconomical reagents and precursors. The two-phase radical process is facilitated by a multimodal catalytic reactivity of acridine photocatalysis that enables both the singlet excited state PCET-mediated decarboxylative carbon–sulfur bond formation and the previously unknown radical reductive disulfur bond cleavage by a photoinduced HAT process in the silane–triplet acridine system. The study points to a significant potential of multimodal photocatalytic systems in providing new directions to previously inaccessible transformations. | Arka Porey; Seth Fremin; Sachchida Nand; Ramon Trevino; William Hughes; Shree Krishna Dhakal; Viet Nguyen; Samuel Greco; Hadi Arman; Oleg Larionov | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dfbc3ce9ebbb4db98286c2/original/multimodal-acridine-photocatalysis-enables-direct-access-to-thiols-from-carboxylic-acids-and-elemental-sulfur.pdf |
60c743950f50db0c34395f59 | 10.26434/chemrxiv.9255209.v1 | Influence of the Para-Substituent in Lanthanoid Complexes of Bistetrazole Substituted Calix[4]arenes | 5,11,17,23-Tetra-tert-butyl-25,27-dihydroxy-26,28-bis(tetrazole-5-ylmethoxy)calix[4]arene has been reported to form remarkable Ln19 and Ln12 elongated clusters, upon addition of aqueous ammonium carboxylates. The impact of the <i>para</i> substituent on lanthanoid cluster formation has been studied by synthesising two new bis-tetrazole calixarenes, with <i>p</i>-H, and <i>p</i>-allyl substituents. Solution phase dynamic light scattering measurements of the reaction mixtures indicated that clusters are not formed with the <i>p</i>-H and <i>p</i>-allyl derivatives, in contrast with the behaviour of the <i>t-</i>butyl analogue. Lanthanoid complexes of the <i>p</i>-H and <i>p</i>-allyl calixarenes were characterised by single crystal X-ray diffraction, and were found to form mononuclear complexes, linked to form a one-dimensional coordination polymer for the <i>p</i>-allyl system. All of the complexes were isolated as ammonium salts, with ammonium cation included in the calixarene cavity in most cases. It is concluded that the nature of the <i>para</i> substituent has a profound impact on the lanthanoid cluster formation process, and derivatives with more subtle structural changes will be required to determine if additional lanthanoid “bottlebrush” clusters can be isolated.<br /><br /> | Rene Z.H. Phe; Brian Skelton; Massimiliano Massi; Mark Ogden | Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743950f50db0c34395f59/original/influence-of-the-para-substituent-in-lanthanoid-complexes-of-bistetrazole-substituted-calix-4-arenes.pdf |
6554cf6adbd7c8b54b514d16 | 10.26434/chemrxiv-2023-hdj6t-v2 | A Unified Approach to (E)- and (Z)-Olefins Enabled by
Low-Valent Tungsten Catalysis | Achieving regio- and stereoselective formation of products from simple chemical building blocks is one the most important roles of catalysis in organic synthesis. Repositioning an alkene functional group through catalytic alkene isomerization represents a powerful synthetic strategy for preparing valuable alkene products from comparatively simple chemical feedstocks. The utility of this approach, however, hinges on the ability to control the positional and stereoisomerism to access a single product among numerous potential isomeric byproducts. Here, a positionally selective alkene isomerization in which modulation of the ligand environment of the homogeneous tungsten catalyst grants access to either the (E)- or (Z)-stereoisomer is described. Compared to previously reported alkene isomerization methods, this reaction offers exquisite chemo- and regioselectivity from a simple, commercially available precatalyst and ligand. Preliminary mechanistic studies suggest that tungsten’s ability to adopt 7-coordinate geometry is crucial for stereoselectivity and that substrate directivity prevents over-isomerization to the conjugated alkene, as is commonly observed with other catalysts. These features allows for exclusive formation of β,γ-unsaturated carbonyl compounds that are otherwise difficult to prepare. | Tanner Jankins; Camille Rubel; Hang Chi Ho; Raul Martin-Montero; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Stereochemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6554cf6adbd7c8b54b514d16/original/a-unified-approach-to-e-and-z-olefins-enabled-by-low-valent-tungsten-catalysis.pdf |
60c75485702a9b3f5b18c53c | 10.26434/chemrxiv.13670212.v1 | Active Coacervate Droplets Are Protocells That Grow and Resist Ostwald Ripening | Active coacervate droplets are liquid condensates coupled to a chemical reaction that turns over their components, keeping the droplets out of equilibrium. This turnover can be used to drive active processes such as growth, and provide an insight into the chemical requirements underlying (proto)cellular behaviour. Moreover, controlled growth is a key requirement to achieve population fitness and survival. Here we present a minimal, nucleotide-based coacervate model for active droplets, and report three key findings that make these droplets into evolvable protocells. First, we show that coacervate droplets form and grow by the fuel-driven synthesis of new coacervate material. Second, we find that these droplets do not undergo Ostwald ripening, which we attribute to the attractive electrostatic interactions within complex coacervates, active or passive. Finally, we show that the droplet growth rate reflects experimental conditions such as substrate, enzyme and protein concentration, and that a different droplet composition (addition of RNA) leads to altered growth rates and droplet fitness. These findings together make active coacervate droplets a powerful platform to mimic cellular growth at a single-droplet level, and to study fitness at a population level.<br /> | Karina K. Nakashima; Merlijn H. I. van Haren; Alain A. M. André; Irina Robu; Evan Spruijt | Chemical Kinetics; Interfaces; Self-Assembly; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75485702a9b3f5b18c53c/original/active-coacervate-droplets-are-protocells-that-grow-and-resist-ostwald-ripening.pdf |
67655d1b6dde43c908c4abd3 | 10.26434/chemrxiv-2024-wcb80 | Room-temperature barocaloric effect in [Fe(pap 5NO2)2] spin-crossover material | We examine the pressure dependence of the spin-crossover transition in [Fe(pap-5NO2)2] that occurs near room temperature. We employ a combination of high-pressure calorimetry and powder X-ray diffraction measurements, conducted both under variable-pressure and variable temperature conditions. Both methods indicate that the spin-crossover transition shifts linearly to higher temperatures with increasing pressure, while simultaneously exhibiting an increase in the width of the thermal hysteresis. We report a giant barocaloric effect, revealing isothermal entropy changes in the 70.2-79.1 J kg-1 K-1 range and adiabatic temperature changes between 19.6 and 25.9 K for a pressure change of 2 kbar. Although the effect diminishes under reversible conditions, it remains substantial, with values of 70.2 J kg-1 K-1 and 13.5 K, respectively. | David Gracia; Vera Cuartero; Catalin Popescu; Adelais Trapali; Talal Mallah; Marie-Laure Boillot; Javier Blasco; Gloria Subias; Marco Evangelisti | Materials Science; Inorganic Chemistry; Energy; Magnetic Materials; Coordination Chemistry (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67655d1b6dde43c908c4abd3/original/room-temperature-barocaloric-effect-in-fe-pap-5no2-2-spin-crossover-material.pdf |
65d8e28d66c13817295beed6 | 10.26434/chemrxiv-2024-02bp6 | Chemocatalytic Conversion of Dinitrogen to Ammonia Mediated by a Tungsten Complex | Whereas molybdenum dinitrogen complexes have played a major role as catalytic model systems of nitrogenase, corresponding tungsten complexes have in most cases found to be catalytically inactive. Herein we present a modified pentadentate tetrapodal (pentaPod) phosphine ligand in which two dimethylphosphine groups of the original PMe2PPh2 ligand have been replaced with phospholanes (Pln). The derived molybdenum complex [Mo(N2)(PPln2PPPh2)] generates 22 and the analogous tungsten complex [W(N2)(PPln2PPPh2)] 7 equivalents of NH3 from N2 in the presence of 180 equiv.s of SmI2/H2O, rendering the latter the first tungsten complex chemocatalytically converting N2 to NH3. In contrast, the parent tungsten complex [W(N2)(PMe2PPh2)] generates ammonia from N2 only in a slightly overstoichiometric fashion. The reasons for these reactivity differences are investigated with the help of spectroscopic and electrochemical methods. | Felix Tuczek; Anna-Marlene Vogt; Tobias Adrian Engesser; Jan Krahmer; Niels Michaelis; Mareike Pfeil; Jannik Junge; Christian Näther; Nicolas Le Poul | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d8e28d66c13817295beed6/original/chemocatalytic-conversion-of-dinitrogen-to-ammonia-mediated-by-a-tungsten-complex.pdf |
60c74adbf96a002d9c287507 | 10.26434/chemrxiv.12264503.v1 | COVID-19 Repurposed Therapeutics Targeting the Viral Protease and Spike-protein:ACE2 Interface using MD-based Pharmacophore and Consensus Virtual Screening | <p>Molecular dynamics (MD) and enhanced sampling MD was performed for 100 ns on the biological assembly of the COVID-19 protease (<a href="https://www.rcsb.org/structure/6lu7">6LU7</a>), and a template of the COVID-19 S-protein:ACE2 receptor interface (99.88% coverage of 6M0J; model03, <a href="https://swissmodel.expasy.org/interactive/HLkhkP/models/">swissmodel</a>). Apo-site pharmacophores of the resulting structural clusters were used to mine the FDA database (8700 compounds), and a multi-target library was developed from MD-based hits in high affinity sites across 100 ns. Consensus hits from high throughput docking in crystal structures 5R82, 6LU7 and 6Y2F (protease), and 6VW1 (S-protein:ACE2) were also added, and the resulting libraries were re-docked into MD sites to collect potential COVID-19 re-purposed therapeutics by estimated binding energies. </p> | Brady Garabato; Federico Falchi; Andrea Cavalli | Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74adbf96a002d9c287507/original/covid-19-repurposed-therapeutics-targeting-the-viral-protease-and-spike-protein-ace2-interface-using-md-based-pharmacophore-and-consensus-virtual-screening.pdf |
60c74ff74c891985bdad3cd3 | 10.26434/chemrxiv.12973844.v1 | Fast Oxygen Ion Migration in Cu–In–oxide Bulk and Its Utilization for Effective CO2 Conversion at Lower Temperature | Efficient activation of CO<sub>2</sub> at low
temperature was achieved by reverse water–gas shift <i>via</i> chemical looping
(RWGS‑CL) by virtue of fast oxygen ion migration in Cu–In–structured oxide,
even at lower temperatures. Results show that novel Cu–In<sub>2</sub>O<sub>3</sub>
structured oxide can show a remarkably higher CO<sub>2</sub> splitting rate
than ever reported. Various analyses revealed that RWGS‑CL on Cu–In<sub>2</sub>O<sub>3</sub>
is derived from redox between Cu–In<sub>2</sub>O<sub>3</sub> and Cu<i><sub>x</sub></i>In<i><sub>y</sub></i>
alloy. Key factors for high CO<sub>2</sub> splitting were fast migration of
oxide ions in alloy and the preferential oxidation of the interface of alloy–In<sub>2</sub>O<sub>3</sub>
in the bulk of the particles. The findings reported herein can open up new
avenues to achieve effective CO<sub>2</sub> conversion at lower temperatures. | Takuma Higo; Jun-Ichiro Makiura; Yutaro Kurosawa; Kota Murakami; Shuhei Ogo; Hideaki Tsuneki; Yasushi Hashimoto; Yasushi Sato; Yasushi Sekine | Solid State Chemistry; Redox Catalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff74c891985bdad3cd3/original/fast-oxygen-ion-migration-in-cu-in-oxide-bulk-and-its-utilization-for-effective-co2-conversion-at-lower-temperature.pdf |
60c7579fbb8c1afbef3dc893 | 10.26434/chemrxiv.14439080.v1 | Magnetically Induced Ring-Current Strengths of Planar and Nonplanar Molecules: New Insights from the Pseudo-π Model | <p>The
π-contribution to the
magnetically induced current densities, ring-current strengths, and induced
magnetic fields of large
planar molecules (as kekulene) and three-dimensional molecules (as
[10]cyclophenacene and chiral toroidal nanotubes C<sub>2016 </sub>and C<sub>2196</sub>)
have been computed using the
pseudo-π model with the
gauge-including magnetically induced currents method. The magnetic response
analysis shows that π-electrons are the main actors of the electron
delocalization in carbon systems regardless of their size, suggesting that the
π- component of the ring-current strengths can be used for assessing the
aromatic character of this kind of molecules. Computations using the pseudo-π
model yield current densities and induced magnetic fields that are not
contaminated by contributions from core and σ-electrons allowing investigations
of large molecular structures as polycyclic aromatic hydrocarbons and
cylindrical or toroidal carbon nanotubes.</p> | Mesías Orozco-Ic; Maria Dimitrova; jorge barroso; Dage Sundholm; Gabriel Merino | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7579fbb8c1afbef3dc893/original/magnetically-induced-ring-current-strengths-of-planar-and-nonplanar-molecules-new-insights-from-the-pseudo-model.pdf |
679c66496dde43c9080fe507 | 10.26434/chemrxiv-2025-6ngh9 | Structure–Property Relationship between Copper Ions and Hot Electron Relaxation in Colloidal Quantum Dots | The structure and physical properties of materials, such as elementary exciton processes, are closely interconnected. Doping heteroatoms into a host crystal enables modulation of the physical properties without altering the intrinsic electronic structure. Doping copper ions in colloidal semiconductor quantum dots (QDs) has been shown to suppress hot electron relaxation. However, the relationship between the local environment of the heteroatoms in the host crystal and the physical properties has been insufficiently explored. In this study, CdSe and InP QDs were synthesized in the presence of copper ions (Cu:CdSe and Cu:InP QDs, respectively). Femtosecond transient absorption spectroscopy was performed to investigate the hot electron relaxation dynamics, and X-ray absorption fine structure (XAFS) measurements were performed to elucidate the local environment of the copper ions. Hot electron relaxation was slower in the Cu:CdSe QDs than in the CdSe QDs, whereas no such trend was observed for the Cu:InP QDs. XAFS analyses indicated that the copper ions substituted for cadmium ions in the CdSe QDs, whereas the copper ions segregated on the surface of the InP QDs. This behavior can be explained by the solid solubility of the respective materials: CdSe and Cu2Se are miscible, facilitating substitution, whereas InP and Cu3P are immiscible, resulting in the formation of a heterostructure. The combination of time-resolved spectroscopy and XAFS measurements is an effective method for elucidating structure–property relationships, and it will aid in comprehensively understanding the effect of heteroatoms in the host crystal on the physical properties. | Ayari Yamada; Daichi Eguchi; Tokuhisa Kawawaki; Yuichi Negishi; Naoto Tamai | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679c66496dde43c9080fe507/original/structure-property-relationship-between-copper-ions-and-hot-electron-relaxation-in-colloidal-quantum-dots.pdf |
60c749d9337d6c22bfe27795 | 10.26434/chemrxiv.12116163.v1 | Accelerated Reactivity Mechanism and Interpretable Machine Learning Model of N-Sulfonylimines Towards Fast Multicomponent Reactions | Predicting the outcome of chemical reactions using machine learning models has emerged as a promising research area in chemical science. However, the use of such models to prospectively test new reactions by interpreting chemical reactivity is limited. We have developed a new fast and one-pot multicomponent reaction of <i>N</i>-sulfonylimines with heterogenous reactivity. Fast reaction times (<5 min) for both acyclic and cyclic sulfonylimine encouraged us to investigate plausible reaction mechanisms using quantum mechanics to identify intermediates and transition states. The heterogeneous reactivity of <i>N</i>-sulfonylimine lead us to develop a human-interpretable machine learning model using positive and negative reaction profiles. We introduce chemical reactivity flowcharts to help chemists interpret the decisions made by the machine learning model for understanding heterogeneous reactivity of <i>N-</i>sulfonylimines. The model learns chemical patterns to accurately predict the reactivity of <i>N</i>-sulfonylimine with different carboxylic acids and can be used to suggest new reactions to elucidate the substrate scope of the reaction. We believe our human-interpretable machine learning approach is a general strategy that is useful to understand chemical reactivity of components for any multicomponent reaction to enhance synthesis of drug-like libraries. | Krupal P. Jethava; Jonathan A Fine; Yingqi Chen; Ahad Hossain; Gaurav Chopra | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Process Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d9337d6c22bfe27795/original/accelerated-reactivity-mechanism-and-interpretable-machine-learning-model-of-n-sulfonylimines-towards-fast-multicomponent-reactions.pdf |
635986e318a8cc0f6652ba4c | 10.26434/chemrxiv-2022-g2c00 | Assessments of Variational Autoencoder in Protein Conformation Exploration | Molecular dynamics (MD) simulations have been extensively used to study protein dynamics and subsequently functions. However, they are unable to sufficiently explore the conformational space within equilibrium timescales. The purpose of this study is to evaluate the feasibility of using variational autoencoders to assist the exploration of protein conformational landscapes. Using three modeling systems, we show that variational autoencoders are capable of capturing high-level hidden information which distinguishes alternate protein conformations, which can be readily used for generating unseen and physically plausible protein conformations to direct sampling to favored conformational spaces. Based on our investigations, we also find that VAE prefers interpolation than extrapolation and increasing latent space dimension can lead to a trade-off between performances and difficulties, thus we propose that the initial data preparation is important for building VAE models to explore protein conformational landscapes. | Sian Xiao; Zilin Song; Hao Tian; Peng Tao | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635986e318a8cc0f6652ba4c/original/assessments-of-variational-autoencoder-in-protein-conformation-exploration.pdf |
67d641c881d2151a028c65f3 | 10.26434/chemrxiv-2025-bkl88 | The origin of the unequal catalytic acceleration of ligand exchange at Pd(II) center by ReO4– | An in-depth understanding of the kinetic aspects of ligand exchange is valuable for designing and controlling metal-catalyzed reactions and coordination self-assembly under kinetic control. Based on our recent finding that the self-assembly of cis-protected mononuclear Pd(II) complex (M) and tritopic ligand (L) was largely improved by ReO4–, affording an M6L4 square-based pyramid almost quantitatively, which is much higher than under thermodynamic control, we investigated the origin of the unusual catalytic effect of ReO4– by quantitative analysis of a mononuclear model system. The acceleration of ligand exchange by ReO4– was largely affected by the coordination ability of the leaving ligand, whereas NO3– similarly accelerated ligand exchange regardless of the coordination ability of the leaving ligands. DFT calculations of the transition state (TS) of ligand exchanges indicate that unequal acceleration by ReO4– is due to its late TS, in which the stability of TS is affected by the nature of the leaving ligand, whereas the ligand exchange with NO3– proceeds via an early TS. | Tsukasa Abe; Satoshi Takahashi; Shuichi Hiraoka | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d641c881d2151a028c65f3/original/the-origin-of-the-unequal-catalytic-acceleration-of-ligand-exchange-at-pd-ii-center-by-re-o4.pdf |
66e40c3651558a15efdb2b0d | 10.26434/chemrxiv-2024-9l6jc-v3 | Exploring Inhomogeneous Surfaces: Evolutionary Exploration of Ti-rich SrTiO3(110) Surface Reconstructions via Active Learning | The investigation of inhomogeneous surfaces, where various local structures co-exist, is crucial for understanding interfaces of technological interest, yet it presents significant challenges. Here, we study the atomic configurations of the (2 × m) Ti-rich surfaces at (110)-oriented SrTiO3 by bringing together scanning tunneling microscopy and transferable neural-network force fields combined with evolutionary exploration. We leverage an active learning methodology to iteratively extend the training data as needed for different configurations. Training on only small well-known reconstructions, we are able to extrapolate to the complicated and diverse overlayers encountered in different regions of the heterogeneous SrTiO3(110)-(2×m) surface. Our machine-learning-backed approach generates several new candidate structures, in good agreement with experiment and verified using density functional theory. The approach could be extended to other complex metal oxides featuring large coexisting surface reconstructions. | Ralf Wanzenböck; Esther Heid; Michele Riva; Giada Franceschi; Alexander M. Imre; Jesús Carrete; Ulrike Diebold; Georg K. H. Madsen | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e40c3651558a15efdb2b0d/original/exploring-inhomogeneous-surfaces-evolutionary-exploration-of-ti-rich-sr-ti-o3-110-surface-reconstructions-via-active-learning.pdf |
60c757bf702a9b687418cb71 | 10.26434/chemrxiv.14456394.v1 | Electrostatic Regulation of Blue Copper Sites | <div>
<p>In the
last 50 years, the blue copper proteins became central targets of
investigation. Extensive experiments focused on the first- and
second-coordination spheres of Cu to probe the effect of local perturbations on
its properties. We found that local electric fields, generated by charged
residues evolutionarily placed throughout the protein edifice, constitute an
additional significant factor regulating blue copper proteins. These fields are
not random, but exhibit a highly specific directionality, negative with respect
to Cu-S<sub>Cys</sub> and Cu-S<sub>Met</sub> in the Cu
first shell. The field magnitude contributes to fine-tuning of the geometric
and electronic properties of Cu sites in individual blue copper proteins.
Specifically, the local electric fields evidently control the Cu-S<sub>Met</sub>
bond distance, Cu(II)-S<sub>Cys</sub> bond covalency, and the energies of the
frontier molecular orbitals, which, in turn, govern the Cu(II/I) reduction
potential and the relative absorption intensities at 450 nm and 600 nm.</p>
</div>
<br /> | Daniel Bím; Anastassia N. Alexandrova | Bioinorganic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757bf702a9b687418cb71/original/electrostatic-regulation-of-blue-copper-sites.pdf |
60c74f7abb8c1a2f553db937 | 10.26434/chemrxiv.12907316.v1 | Regio-Selectivity Prediction with a Machine-Learned Reaction Representation and On-the-Fly Quantum Mechanical Descriptors | <div>
<div>
<div>
<p>We introduce a new method that combines machine-learned reaction representation with selected quantum mechanical descriptors to predict regio-selectivity in general substitution reactions. We construct a reactivity descriptor database based on ab initio calculations of 130k organic molecules, and train
a multi-task constrained model to calculate demanded descriptors on-the-fly.
</p>
</div>
</div>
</div> | Yanfei Guan; Connor Coley; Haoyang wu; Duminda Ranasinghe; esther heid; Thomas J. Struble; Lagnajit Pattanaik; William H. Green; Klavs F. Jensen | Organic Synthesis and Reactions; Process Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f7abb8c1a2f553db937/original/regio-selectivity-prediction-with-a-machine-learned-reaction-representation-and-on-the-fly-quantum-mechanical-descriptors.pdf |
63dd24969da0bc6b33846489 | 10.26434/chemrxiv-2023-f13jf | Metal clusters supported on transition metal carbides for efficient CH4 and CO2 conversion | Small particles of transition metals (TM) supported on transition metal carbides (TMC) -TMn@TMC- provide a plethora of design opportunities for catalytic applications due to their highly exposed active centres, efficient atom utilisation and the physicochemical properties of the TMC support, which polarises the electron density of the supported particle enhancing its catalytic properties. To date, however, only a very small subset of TMn@TMC catalysts have been tested experimentally and it is unclear which combinations may best catalyse which chemical reactions. Herein, we address this question by performing a high-throughput screening study using periodic Density Functional Theory calculations to elucidate the stability and catalytic performance of all possible combinations between 7 metals (Rh, Pd, Pt, Au, Co, Ni and Cu) supported on 11 stable surfaces of TMCs with 1:1 stoichiometry (TiC, ZrC, HfC, VC, NbC, TaC, MoC and WC) towards CH4 and CO2 conversion technologies. We analyse the generated database to unravel trends or simple descriptors in their resistance towards metal aggregate formation and sintering, oxidation, stability in the presence of adsorbate species, and study their adsorptive and catalytic properties, to facilitate the discovery of novel materials in the future. In addition, we identify Pdn@ZrC, Ptn@ZrC, Pdn@HfC, Ptn@HfC, Nin@VC, Pdn@VC, Nin@NbC and Pdn@NbC as promising catalysts, all of them being new for experimental validation, thus expanding the chemical space for efficient conversion of CH4 and CO2. | Hector Prats; Michail Stamatakis | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dd24969da0bc6b33846489/original/metal-clusters-supported-on-transition-metal-carbides-for-efficient-ch4-and-co2-conversion.pdf |
6286929c44bdd527f8693c0b | 10.26434/chemrxiv-2022-t3g9m | Cobalt-Catalyzed Hydrogenation Reactions Enabled by Ligand-Based Storage of Dihydrogen | The use of supporting ligands which can store either protons or electrons has emerged as a powerful strategy in catalysis. While these strategies are potent individually, natural systems mediate remarkable transformations by combining storage of both protons and electrons in the secondary coordination sphere. As such, there has been recent interest in using this strategy to enable fundamentally new transformations. Furthermore, outsourcing H-atom or hydrogen storage to ancillary ligands can also enable new mechanistic pathways and thereby selectivity. Here we describe the application of this strategy to facilitate radical reactivity in Co-based hydrogenation catalysis. Metalation of previously reported dihydrazonopyrrole ligands with Co results in paramagnetic complexes which are best described as having Co(II) oxidation states. These complexes catalytically hydrogenate olefins with low catalyst loadings under mild conditions (1 atm H2, 23 °C). Mechanistic, spectroscopic, and computational investigations indicate that this system goes through a radical hydrogen-atom transfer (HAT) type pathway that is distinct from classic organometallic mechanisms and is supported by the ability of the ligand to store H2. These results show how ancillary ligands can facilitate efficient catalysis and furthermore how classic organometallic mechanisms for catalysis can be altered by the secondary coordination sphere. | Sophie Anferov; Alexander Filatov; John Anderson | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bioinorganic Chemistry; Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6286929c44bdd527f8693c0b/original/cobalt-catalyzed-hydrogenation-reactions-enabled-by-ligand-based-storage-of-dihydrogen.pdf |
624f95993ec361a3f3f49f8a | 10.26434/chemrxiv-2022-c9n92 | Markovnikov Alcohols via Epoxide Hydroboration
by Molecular Rock-Forming Metal Catalysts | Synthesis of branched “Markovnikov” alcohols is crucial to various chemical industries. The catalytic reduction of substituted epoxides under mild conditions is a highly attractive method for preparing such alcohols. Classical methods based on heterogeneous or homogeneous transition metal-catalyzed hydrogenation, hydroboration or hydrosilylation usually suffer from poor selectivity, reverse regioselectivity, limited functional group compatibility, high cost and/or low availability of the catalysts. Here we report the discovery of a highly regioselective (up to 99%) hydroboration of nonsymmetrical epoxides catalyzed by ligated alkali metal triethylborohydride, an old archetypal reductant in organic chemistry. The chemoselectivity and turnover efficiencies of the present catalytic approach are excellent. Thus, terminal and internal epoxides with ene, yne, aryl, and halo groups were selectively and quantitatively reduced under a substrate-to-catalyst ratio (S/C) of up to 1000. | Guoqi Zhang; Haisu Zeng; Shengping Zheng; Michelle Neary; Pavel Dub | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624f95993ec361a3f3f49f8a/original/markovnikov-alcohols-via-epoxide-hydroboration-by-molecular-rock-forming-metal-catalysts.pdf |
653a3a1848dad2312064808b | 10.26434/chemrxiv-2023-h2867 | CuOx – enriched Co3O4 surfaces enable selective formaldehyde sensing at low temperature | Designing highly reactive surface clusters at the nanoscale on metal-oxide supports enables selective molecular interactions in low-temperature catalysis and chemical sensing. Yet, finding effective material combinations and identifying the reactive site remains challenging and a key obstacle for rational catalyst/sensor design. Here, we demonstrate the low-temperature oxidation of formaldehyde with CuOx clusters on Co3O4 nanoparticles yielding an excellent sensor for this critical air pollutant. When fabricated by flame-aerosol technology, such CuOx clusters are finely dispersed onto the surface, while some Cu ions are incorporated into the Co3O4 lattice enhancing thermal stability. Most importantly, infrared spectroscopy of adsorbed CO and temperature-programmed reduction in H2 identified Cuδ+ species in these clusters as active sites. In fact, its surface concentration correlated with the apparent activation energy of formaldehyde oxidation (Spearman’s coefficient ρ = 0.89) and sensor response (0.96). At optimal composition, such sensors detected even the lowest formaldehyde levels of 3 parts-per-billion at 75 °C, superior to the state-of-the-art sensors. Also, selectivity to other aldehydes, ketones, alcohols, and inorganic compounds, robustness to relevant humidity levels and stable performance over 4 weeks were achieved, rendering such sensors promising as low-power gas detectors in air and food quality control as well as in health monitoring. | Matteo D'Andria; Frank Krumeich; Ryan Wang; Andreas Güntner | Analytical Chemistry; Nanoscience; Analytical Apparatus; Nanofabrication; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a3a1848dad2312064808b/original/cu-ox-enriched-co3o4-surfaces-enable-selective-formaldehyde-sensing-at-low-temperature.pdf |
60c746bdbdbb892028a38c5d | 10.26434/chemrxiv.11374338.v1 | Gibberellin JRA-003: A Selective Inhibitor of Nuclear Translocation of IKKalpha | <div>The small molecule gibberellin JRA-003 (1) was identified as an inhibitor of the NF-kB (nuclear kappa-light-chain enhancer of activated B cells) pathway. Here we find that JRA-003 binds to and significantly inhibits the nuclear translocation of pathway-activating kinases IKKalpha (IkB kinase alpha) and IKKbeta (IkB kinase beta). Analogs were synthesized and NF-kB-inhibiting gibberellins were found to be cytotoxic in cancer-derived cell lines (HS 578T, HCC 1599, RC-K8, Sud-HL4, CA 46, and NCIH 4466). Not only was JRA-003 (1) identified as the most potent synthetic gibberellin against cancer-derived cell lines, it displayed no cytotoxicity in cells derived from non-cancerous sources (HEK 293T, HS 578BST, HS 888Lu, HS 895Sk, HUVEC). This selectivity suggests a promising approach for the development of new therapeutics.</div> | James Annand; Andrew Henderson; Kyle Cole; Aaron Maurais; Jorge Becerra; Yejun Liu; Eranthie Weerapana; Angela Koehler; Anna Mapp; Corinna Schindler | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746bdbdbb892028a38c5d/original/gibberellin-jra-003-a-selective-inhibitor-of-nuclear-translocation-of-ik-kalpha.pdf |
64df9f4800bbebf0e667afcd | 10.26434/chemrxiv-2023-2ndlx-v2 | Analysis of Metabolites in Human Gut: Illuminating the Design of Gut-Targeted Drugs | Gut-targeted drugs provide a new drug modality besides that of oral, systemic molecules, that could tap from the growing knowledge of gut metabolites of bacterial or host origin and their involvement in biological processes and health through their interaction with gut targets (bacterial or host, too). Understanding the properties of gut metabolites can provide hints for the design of gut-targeted drugs. In the present work we analyze a large set of gut metabolites, both shared with serum or present only in gut, and compare them with oral systemic drugs. We find patterns specific for these two subsets of metabolites that could be used to design drugs targeting the gut. In addition, we develop and openly share a Super Learner model to predict gut permanence, in order to aid in the design of molecules with appropriate profiles to remain in the gut, resulting in molecules with putatively reduced secondary effects and distribution issues. | Alberto Gil-Pichardo; Andrés Sánchez-Ruiz; Gonzalo Colmenarejo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64df9f4800bbebf0e667afcd/original/analysis-of-metabolites-in-human-gut-illuminating-the-design-of-gut-targeted-drugs.pdf |
643cee681d262d40ea9ed631 | 10.26434/chemrxiv-2023-qkmpc | Solvent Mediated Excited State Hydrogen Transfer in 6-Azaindole - S3,4 and 2,6-Diazaindole - S3,4 Clusters (S= H2O, NH3) | Excited state hydrogen (ESHT) and proton (ESPT) transfer pathways in the solvent clusters of 6-azaindole 6AI-S3,4 and 2,6-diazaindole 26DAI-S3,4 (S=H2O, NH3) were computationally explored to understand the fate of photo-excited biomolecules. The ESHT energy barriers in (H2O)3 complexes (39.6-41.3 kJmol-1) were decreased in (H2O)4 complexes (23.1-20.2 kJmol-1). Lengthening the solvent chain reduced the barrier because of the relaxed transition states geometries with reduced angular strains. Replacing the water molecule with ammonia drastically decreased the energy barriers to 21.4-21.3 kJmol-1 in (NH3)3 complexes and 8.1-9.5 kJ mol-1 in (NH3)4 complexes. The transition state was identified as Ha atom attached to the first solvent molecule. The formation of stronger hydrogen bonds in (NH3)3,4 complexes resulted in facile ESHT reaction than that in the (H2O)3,4 complexes. The ESPT energy barriers, in 6AI-S3,4 and 26DAI-S3,4 are found to range between 40-73 kJmol-1. The above values were significantly higher than that of the ESHT processes and hence are considered a minor channel in the process. The energetics of ESHT and ESPT explored in this study would be of great importance to study the photochemistry of N-rich biomolecules in the presence of various protic environments. | Simran Baweja; Bhavika Kalal; Prajoy Kumar Mitra; surajit Maity | Theoretical and Computational Chemistry; Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643cee681d262d40ea9ed631/original/solvent-mediated-excited-state-hydrogen-transfer-in-6-azaindole-s3-4-and-2-6-diazaindole-s3-4-clusters-s-h2o-nh3.pdf |
60c74c284c89198cc3ad35bb | 10.26434/chemrxiv.12440015.v1 | Microstructural Control of Polymers Achieved Using Controlled Phase Separation During 3D Printing with Oligomer Libraries: Dictating Drug Release for Personalized Subdermal Implants | <p>Controlling the
microstructure of materials by means of phase separation is a versatile tool for
optimizing material properties. In this study, we show that ink jet 3D printing
of polymer blends gives rise to controllable phase separation that can be used to
tailor the release of drugs. We predicted phase separation using high
throughput screening combined with a model based on the Flory-Huggins
interaction parameter, and were able to show that drug release from 3D printed
structures can be predicted from observations based on single drops of mixtures.
This new understanding gives us hierarchical compositional control, from
droplet to device, allowing release to be ‘dialed up’ without any manipulation
of geometry. This is an important advance for implants that need to be
delivered by cannula, where the shape is highly constrained and thus the usual geometrical
freedoms associated with 3D printing cannot be exploited, bringing a hitherto
unseen level of understanding to emergent material properties of 3D printing.</p> | Laura Ruiz-Cantu; Gustavo Trindade; Vincenzo Taresco; Zuoxin Zhou; Laurence Burroughs; Elizabeth Clark; Felicity R. A. J. Rose; Morgan Alexander; Christopher Tuck; Richard Hague; Clive Roberts; Derek Irvine; Ricky Wildman | Biocompatible Materials; Biodegradable Materials; Controlled-Release Systems; Core-Shell Materials; Oligomers; Biopolymers; Drug delivery systems; Polymer blends; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c284c89198cc3ad35bb/original/microstructural-control-of-polymers-achieved-using-controlled-phase-separation-during-3d-printing-with-oligomer-libraries-dictating-drug-release-for-personalized-subdermal-implants.pdf |
62e09dc7dc4c7848fa4105b3 | 10.26434/chemrxiv-2022-9r7nl | Engineering chiral induction in centrally functionalized ortho-phenylenes | Work on foldamers, non-biological oligomers that mimic the hierarchical structure of biomacromolecules, continues to yield new architectures of ever increasing complexity. o-Phenylenes, a class of helical aromatic foldamers, are well-suited to this area because of their structural simplicity and the straightforward characterization of their folding in solution. However, control of structure requires, by definition, control over folding handedness. Control over o-phenylene twist sense is currently lacking. While chiral induction from groups at o-phenylene termini has been demonstrated, it would be useful to instead direct twisting from internal positions in order to leave the ends free. Here, we explore chiral induction in a series of o-phenylenes with chiral imides at their centers. Conformational behavior has been studied by NMR and CD spectroscopies and DFT calculations. Chiral induction in otherwise unfunctionalized o-phenylenes is generally poor. However, strategic functionalization of the helix surface with trifluoromethyl and methyl groups allows it to better interact with the imide groups, greatly increasing diastereomeric excesses. The sense of chiral induction is consistent with computational models that suggest that it primarily arises from a steric effect. | Sumalatha Peddi; Juliana M. Livieri; Gopi Nath Vemuri; C. Scott Hartley | Organic Chemistry; Physical Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e09dc7dc4c7848fa4105b3/original/engineering-chiral-induction-in-centrally-functionalized-ortho-phenylenes.pdf |
6502da0999918fe537eea2bd | 10.26434/chemrxiv-2023-gwh9j | Discussion on designing three chemical instruments | This paper talks about how to use our soft ionization mass spectrometry theory to design three instruments. Including ion source, mass spectrometer, Instrument for measuring single bond forces between atoms | Jiehong Luo | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6502da0999918fe537eea2bd/original/discussion-on-designing-three-chemical-instruments.pdf |
67547555085116a133adacff | 10.26434/chemrxiv-2023-r6t15-v4 |
The invisible footprint of climbing shoes: high exposure to rubber additives in indoor facilities
| There is growing concern about rubber-derived compounds (RDCs), predominantly originating from tire and road wear particles. Other consumer products, including sports equipment, also contain RDCs and human exposure to these compounds is of particular interest due to demonstrated toxicity to animal species. In this study, we investigated RDCs intentionally incorporated into climbing shoes for enhanced performance. We found high concentrations of 15 rubber derived-compounds (RDCs) in shoe sole samples (Σ15 RDCs: 25 – 3405 µg/g), aerosol particulate matter (Σ15 RDCs: 2.6 - 37 µg/g), and settled dust (Σ15 RDCs: 1.5 - 55 µg/g) in indoor climbing halls. The estimated daily intake via inhalation/ingestion of Σ15 RDCs for climbers and employees in some of these facilities ranged from 1.7 to 48 ng/kg/day, exceeding known intake levels of RDCs from other sources. Abrasion powder resulting from friction between climbing shoes and footholds is the likeliest source of high concentrations of RDCs observed in aerosol particulate matter and settled dust, since other emission sources could be excluded. These findings reveal a previously unknown human exposure route of RDCs. | Anya Sherman; Thibault Masset; Lukas Wimmer; Leah K. Leah Maruschka; Lea Ann Dailey; Thorsten Hüffer; Florian Breider; Thilo Hofmann | Analytical Chemistry; Polymer Science; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67547555085116a133adacff/original/the-invisible-footprint-of-climbing-shoes-high-exposure-to-rubber-additives-in-indoor-facilities.pdf |
60c740404c891940a0ad20c7 | 10.26434/chemrxiv.7675928.v1 | Kinetics of Formic Acid Decomposition in Subcritical and Supercritical Water - A Raman Spectroscopic Study | The decomposition of formic acid is studied in a
continuous sub- or supercritical water reactor at temperatures between 300 and
430°C, a pressure of 25 MPa, residence times between 4 and 65 s, and a
feedstock concentration of 3.6 wt%. <i>In-situ
</i>Raman spectroscopy is used to produce real-time data and accurately
quantify decomposition product yields of H<sub>2</sub>, CO<sub>2</sub>, and CO.
Collected spectra are used to determine global decomposition rates and kinetic
rates for individual reaction pathways. First-order global Arrhenius parameters
are determined as log <i>A</i> (s<sup>-1</sup>)
= 1.6 ± 0.20 and <i>E<sub>A </sub></i>= 9.5
± 0.55 kcal/mol for subcritical decomposition, and log <i>A</i> (s<sup>-1</sup>) = 12.56 ± 1.96 and <i>E<sub>A </sub></i>= 41.90 ± 6.08 kcal/mol for supercritical
decomposition. Subcritical and supercritical Arrhenius parameters for
individual pathways are proposed. The variance in rate parameters is likely due
to changing thermophysical properties of water across the critical point. There
is strong evidence for a surface catalyzed free-radical mechanism responsible
for rapid decomposition above the critical point, facilitated by low density at
supercritical conditions. | Brian Pinkard; David Gorman; Elizabeth Rasmussen; John Kramlich; Per G. Reinhall; Igor V. Novosselov | Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740404c891940a0ad20c7/original/kinetics-of-formic-acid-decomposition-in-subcritical-and-supercritical-water-a-raman-spectroscopic-study.pdf |
6654a47721291e5d1d65fc70 | 10.26434/chemrxiv-2024-phrrl | De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics | The binding affinity of antibodies to specific antigens stems from a remarkably broad repertoire of hypervariable loops known as complementarity-determining regions (CDRs). While recognizing the pivotal role of the heavy-chain 3 CDRs (CDR-H3s) in maximizing antibody-antigen affinity and specificity, the key structural determinants responsible for their adaptability to diverse loop sequences, lengths, and non-canonical structures are hitherto unknown. To address this question, we achieved a de novo synthesis of bulged CDR-H3 mimics excised from their full antibody context. CD and NMR data revealed that these stable standalone -hairpin scaffolds are well-folded and retain many of the native bulge CDR-H3 features in water. In particular, the tryptophan residue highly conserved across CDR-H3 sequences was found to extend the kinked base of these -bulges through a combination of stabilizing intramolecular hydrogen bond and CH/ interaction. The structural ensemble consistent with our NMR observations exposed the dynamic nature of residues at the base of the loop, suggesting that -bulges act as molecular hinges connecting the rigid stem to the more flexible loops of CDR-H3s. We anticipate that this deeper structural understanding of CDR-H3s will lay the foundation to inform the design of antibody drugs broadly and engineer novel CDR-H3 peptide scaffolds as therapeutics. | Stephane Roche; Guangkuan Zhao; Alexis Richaud; Thomas Williamson; Michael Feig | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654a47721291e5d1d65fc70/original/de-novo-synthesis-and-structural-elucidation-of-cdr-h3-loop-mimics.pdf |
60e9e154551cb0a2a7ae49e7 | 10.26434/chemrxiv-2021-n6mn7 | Deep Convolutional Neural Network Algorithm for Prediction of the Mechanical Properties of Friction Stir Welded Copper Joints from its Microstructures | Convolutional Neural Network (CNN) is a special type of Artificial Neural Network which takes input in the form of an image. Like Artificial Neural Network they consist of weights that are estimated during training, neurons (activation functions), and an objective (loss function). CNN is finding various applications in image recognition, semantic segmentation, object detection, and localization. The present work deals with the prediction of the welding efficiency of the Friction Stir Welded joints on the basis of microstructure images by carrying out training on 3000 microstructure images and further testing on 300 microstructure images. The obtained results showed an accuracy of 80 % on the validation dataset. | Akshansh Mishra; Asmita Suman | Materials Science; Alloys | CC BY NC 4.0 | CHEMRXIV | 2022-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e9e154551cb0a2a7ae49e7/original/deep-convolutional-neural-network-algorithm-for-prediction-of-the-mechanical-properties-of-friction-stir-welded-copper-joints-from-its-microstructures.pdf |
670d603f51558a15ef0fee31 | 10.26434/chemrxiv-2024-tlxf2 | Anion-exchange Mediated Synthesis of Hollow 2D Layered Materials and Heterostructures: Mechanism and Room-Temperature Gas Sensing Properties | The designing of nanostructures with unique morphologies and enhanced functionalities is a cornerstone of modern materials science. Ion exchange reactions in inorganic crystals offer a versatile approach for precisely controlling the composition, morphology and properties of the materials through stepwise transformations. In this study, we report the anion exchange-mediated conversion of 2D layered material SnS2 into SnSe2, with SnS2-SnSe2 lateral heterostructures as intermediates. This transformation, driven by the disparate diffusion rates of S²⁻ and Se²⁻ ions, leads to the generation of hexagonal nanorings of SnSe2 (inaccessible by direct synthetic routes) via the Kirkendall effect. By carefully balancing the diffusion kinetics through concentration control, we also successfully synthesized continuous SnSe2 nanosheets. To elucidate the anion exchange mechanism, we conducted a comprehensive investigation using electron microscopy techniques, varying parameters such as time, precursor concentration, and reagents. Our findings revealed that the exchange process initiates at the edges of the template SnS2 nanosheets and progresses inward. Cross-sectional atomic-resolution electron microscopy of the interfaces and layer stacking in the SnS2-SnSe2 heterostructure uncovered numerous defects, attributed to ion migration and lattice mismatch, which were not detectable in planar views. Furthermore, as-synthesized materials are explored for gas-sensing applications. Our anion-exchange-derived SnS2-SnSe2 heterostructure and SnSe2 exhibited exceptional selectivity and sensitivity towards NO2 gas (response > 700%) at room temperature comparable to state-of-art sensors, significantly outperforming the pristine SnS2 material, which required elevated temperatures (150°C) for optimal response. This study underscores the potential of anion exchange as a powerful tool for designing novel nanomaterials with tailored properties and applications, particularly in the realm of gas sensing. | Rajeev Kumar Rai; Naveen Goyal; Deepak Sharma; Ranit Ram; Koushik Jagadish; Navakanta Bhat; N. Ravishankar | Materials Science; Nanoscience; Core-Shell Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d603f51558a15ef0fee31/original/anion-exchange-mediated-synthesis-of-hollow-2d-layered-materials-and-heterostructures-mechanism-and-room-temperature-gas-sensing-properties.pdf |
62286d83ce899bfd5cb19910 | 10.26434/chemrxiv-2022-qxprq | New Steroidal Saponins from Rhizomes of Trillium govanianum: Gram Scale Isolation and Acetylcholinesterase Inhibitory Activity Evaluation | Three previously unknown steroidal saponins named as govanoside C-E (1-3) along with four known compounds, govanoside B (4), protodioscin (5), 20β-hydroxyecdysone (6), and polypodine B (7) have been isolated from the rhizomes of Trillium govanianum Wall. ex D.Don. The structures of isolated compounds were elucidated by detailed analysis of 1D and 2D NMR, mass and IR spectroscopic data. Compounds 1 and 2 contained a rare sugar moiety i.e. 6-deoxy allose, while compound 3 has acetylated rhamnose moiety in its glycone part. Acid hydrolysis of new compounds followed by derivatization for GC analysis of glycone moieties was carried out for the confirmation of monomer saccharides present in each molecule. In addition, we have developed a protocol for the isolation of major steroidal saponin present in the rhizomes of Trillium govanianum i.e. borassoside E in gram scale. Parent extract, fractions and all pure molecules were screened to evaluate their antagonistic effects on acetylcholinesterase activity. Among extract and fractions, water fraction (IC50 value: 90.2 μg/ mL) was found most active whereas among pure molecules govanoside E (3) (IC50 value: 8.62 μM) was found most active against acetylcholinesterase. The molecular docking analysis was also carried out to further study the molecular interactions and binding free energy of the pure molecules with acetylcholinesterase. | Prithvi Pal Singh; Patil Shivprasad Suresh; Anmol -; Upendra Sharma | Organic Chemistry; Natural Products; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62286d83ce899bfd5cb19910/original/new-steroidal-saponins-from-rhizomes-of-trillium-govanianum-gram-scale-isolation-and-acetylcholinesterase-inhibitory-activity-evaluation.pdf |
60c74e41bdbb896204a39b5c | 10.26434/chemrxiv.12683831.v2 | Combining Indolizines and Isatins via Brønsted-Acid Catalyzed Friedel-Crafts Alkylation in Water | <p>The controlled mono-addition of indolizines to isatins under very mild conditions is described. The reaction occurs in water using diphenylphosphate (DPP) as catalyst and is dramatically accelerated by adding a surfactant (sodium dodecyl sulfate – SDS). Using this methodology, 19 new 3-hydroxy-3-indolizinyl-2-oxindoles scaffolds were synthesized (up to >99% yield). Notably, in organic solvents only bis-addition products were observed, in poor yields and in prolonged times. The very low solubility of the mono-addition product in water was determinant for the observed selectivity .<br /></p> | Bruno Boni Guidotti; Thiago Sabino da Silva; José Tiago Menezes Correia; Fernando Coelho | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e41bdbb896204a39b5c/original/combining-indolizines-and-isatins-via-br-nsted-acid-catalyzed-friedel-crafts-alkylation-in-water.pdf |
63da935f5391e5d2ea724d34 | 10.26434/chemrxiv-2023-5l9m7 | Surfactant co-formulants in glyphosate-based herbicides: Detection and quantification in human urine | Polyethoxylated tallow amine (POEA) surfactants in glyphosate formulations are understudied. They may constitute greater health risks than glyphosate itself. Lack of validated biomarkers of exposure and metabolism, as well as analytical methods for measuring POEA, limit study of a formulations toxicity and associated risk. We report an exploratory analytical workflow using liquid chromatography coupled with a triple quadrupole mass spectrometer (LC-MS) in conjunction with neutral loss (NL) and product ion (PI) screening tools as an effective data acquisition tool to screen for POEA homologues in human urine. These features made it possible to find POEA at lower levels, which would not have been possible without screening tools and chemical standards. | Ravikumar Jagani; Jia Chen; Shirisha Yelamanchili; Mary Wolff; Syam Andra | Analytical Chemistry; Analytical Chemistry - General | CC BY 4.0 | CHEMRXIV | 2023-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63da935f5391e5d2ea724d34/original/surfactant-co-formulants-in-glyphosate-based-herbicides-detection-and-quantification-in-human-urine.pdf |
67bd70b9fa469535b9d30cc9 | 10.26434/chemrxiv-2025-j7zl0 | Chemiluminescent 2-Coumaranones: Synthesis, Luminescence Mechanism, and Emerging Applications | 2-Coumaranones have emerged as a highly promising class of chemiluminescent compounds, distinguished by their unique structural properties that facilitate efficient light emission. This review provides a comprehensive analysis of their synthesis, structural characteristics, and chemiluminescence mechanisms, integrating historical perspectives with the latest advancements in the field. Beyond their intrinsic photophysical and chemical properties, 2-coumaranones have demonstrated broad utility across bioanalytical and material sciences. Notable applications include enzyme-catalyzed chemiluminescence in aqueous systems, glucose and urease-triggered detection assays, and mechano-base-responsive luminescence for stress sensing. Additionally, recent developments in chemiluminescent protective groups and their incorporation into advanced functional materials underscore the versatility of these compounds. Despite significant progress, key challenges remain, particularly in optimizing quantum yield, emission properties, and solvent compatibility for practical applications. Future research should prioritize the development of highly tunable 2-coumaranone derivatives with enhanced spectral and kinetic properties, further expanding their potential in diagnostics, bioimaging, and mechanoluminescent sensing. By addressing these challenges, 2-coumaranones could pave the way for next-generation chemiluminescent technologies with unprecedented sensitivity and adaptability. | Stefan Schramm; Tim Lippold; Isabelle Navizet | Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd70b9fa469535b9d30cc9/original/chemiluminescent-2-coumaranones-synthesis-luminescence-mechanism-and-emerging-applications.pdf |
646498eafb40f6b3eeb9cb2e | 10.26434/chemrxiv-2023-bls76 | Direct Laser Synthesis and Patterning of High Entropy Oxides from Liquid Precursors | High entropy oxides are a class of materials distinguished by the use of configurational entropy to drive material synthesis. These materials are being examined for their exciting physiochemical properties and hold promise in numerous fields, such as chemical sensing, electronics, and catalysis. Patterning and integration of high entropy materials into devices and platforms can be difficult due to their thermal sensitivity and incompatibility with many conventional thermally-based processing techniques. In this work, we present a laser-based technique, laser-induced thermal voxels, that combines the synthesis and patterning of high entropy oxides into a single process step, thereby allowing patterning of high entropy materials directly onto substrates. As a proof-of-concept, we target the synthesis and patterning of a well-characterized rock salt-phase high entropy oxide, (Mg0.2Co0.2Ni0.2Cu0.2Zn0.2)O, as well as a spinel-phase high entropy oxide, (Mg0.2Ni0.2Co0.2Cu0.2Zn0.2)Cr2O4. We show through electron microscopy and X-ray analysis that the materials created are atomically homogenous and are primarily of the rock salt or spinel phase. These findings show the efficacy of laser induced thermal voxel processing for the synthesis and patterning of high entropy materials and enable new routes for integration of high entropy materials within microscale platform and devices. | Alexander Castonguay; Nabila Nova; Lauren Dueñas; Shannon McGee; M. Lodhi; Yang Yang; Lauren Zarzar | Materials Science; Inorganic Chemistry; Ceramics; Materials Processing; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646498eafb40f6b3eeb9cb2e/original/direct-laser-synthesis-and-patterning-of-high-entropy-oxides-from-liquid-precursors.pdf |
60c742ea469df4c457f4307e | 10.26434/chemrxiv.8321156.v2 | How [FeFe]-Hydrogenase Facilitates Bidirectional Proton Transfer | Hydrogenases are metalloenzymes that catalyse the interconversion of protons and molecular hydrogen, H2. [FeFe]-hydrogenases show particularly high rates of hydrogen turnover and have inspired numerous compounds for biomimetic H2 production. Two decades of research on the active site cofactor of [FeFe]-hydrogenases have put forward multiple models of the catalytic proceedings. In comparison, understanding of the catalytic proton transfer is poor. We were able to identify the amino acid residues forming a proton transfer pathway between active site cofactor and bulk solvent; however, the exact mechanism of catalytic proton transfer remained inconclusive. Here, we employ in situ IR difference spectroscopy on the [FeFe]-hydrogenase from Chlamydomonas reinhardtii evaluating dynamic changes in the hydrogen-bonding network upon catalytic proton transfer. Our analysis allows for a direct, molecular unique assignment to individual amino acid residues. We found that transient protonation changes of arginine and glutamic acid residues facilitate bidirectional proton transfer in [FeFe]-hydrogenases.<br /> | Moritz Senger; Viktor Eichmann; Konstantin Laun; Jifu Duan; Florian Wittkamp; Günther Knör; Ulf-Peter Apfel; Thomas Happe; Martin Winkler; Joachim Heberle; Sven T. Stripp | Biochemistry; Biophysics; Chemical Biology; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ea469df4c457f4307e/original/how-fe-fe-hydrogenase-facilitates-bidirectional-proton-transfer.pdf |
60c755cc469df46b0ef451d1 | 10.26434/chemrxiv.14165066.v1 | Standard Underpotential Deposition Shift. A New Parameter to Characterize the UPD Phenomenon. | <p>Underpotential deposition (UPD) is a phenomenon where atoms of an element M are deposited from ions M<sup>n+</sup> on a substrate S at potentials more positive than for the deposition of M<sup>n+ </sup>on M. These systems have been studied for more than a century and are interesting from both the applied and the fundamental point of view. Despite the vast literature on the subject, there is no thermodynamic parameter so far able to characterize an UPD system. Even if the so-called “UPD shift” has been used for decades, the limitations of this parameter has been fully recognized in the field. Herein, using a simple Nernstian treatment and straightforward measurements, we show how to measure and calculate a new proposed fundamental thermodynamic parameter namely, the “Standard UPD potential”. We showed results for the deposition of Cu+2 on Au in acidic media, in solutions containing ClO4- or SO4-2 anions. We obtained Standard UPD potential= 0.65 ± 0.02 V, independently of the concentration of the acid and the nature of the anion.</p><p> </p> | Rafael Alcides Vicente; Heloísa Vampré Nascimento Gomes; Pablo Fernández | Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755cc469df46b0ef451d1/original/standard-underpotential-deposition-shift-a-new-parameter-to-characterize-the-upd-phenomenon.pdf |
65e57f4ce9ebbb4db9dc1c8b | 10.26434/chemrxiv-2024-qggc0 | Pd-Catalyzed Picolinamide-Directed C(sp2)-H Sulfonylation of Amino Acids/Peptides with Sodium Sulfinates | This report describes a Pd-catalyzed picolinamide-directed site-selective C(sp2)-H sulfonylation of amino acids and peptides with sodium sulfinate in moderate to good yields. Sulfonylation of levodopa and dopamine drug molecules and late-stage di-rected peptide sulfonylation are studied for the first time. Broad substrate scope having various functionalities, late-stage drug modifications, various post synthetic utilities such as chalcogenation, bromination, olefination, and arylation are potential ad-vantages. | Nagendra Sharma; Raghunath Bag | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioorganic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e57f4ce9ebbb4db9dc1c8b/original/pd-catalyzed-picolinamide-directed-c-sp2-h-sulfonylation-of-amino-acids-peptides-with-sodium-sulfinates.pdf |
62b98d037da6cec35d222ffc | 10.26434/chemrxiv-2022-7tkt5 | Four distinct network patterns of supramolecular/polymer composite hydrogels controlled by formation kinetics and interfiber interactions | Synthetic composite hydrogels comprising supramolecular fibers and covalent polymers have attracted considerable attention because their properties are similar to biological connective tissues. However, an in-depth analysis of the network structures has not been performed. In this study, we discovered the composite network can be categorized into four distinct patterns regarding morphology and colocalization of the components using in situ, real-time confocal imaging. Time-lapse imaging of the network formation process reveals that the patterns are governed by two factors, the order of the network formation and the interactions between the two different fibers. Additionally, the imaging studies revealed a unique composite hydrogel undergoing dynamic network remodeling on the scale of a hundred micrometers to more than one millimeter. Such dynamic properties allow for fracture-induced artificial patterning of a network three dimensionally. This study introduces a valuable guideline to the design of hierarchical composite soft materials. | Keisuke Nakamura; Ryou Kubota ; Itaru Hamachi | Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.); Hydrogels; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b98d037da6cec35d222ffc/original/four-distinct-network-patterns-of-supramolecular-polymer-composite-hydrogels-controlled-by-formation-kinetics-and-interfiber-interactions.pdf |
60c741eabb8c1a41513da037 | 10.26434/chemrxiv.8179274.v1 | The Rattling and Rotation Behaviours of the Hydrated Excess Proton in Water | <p><b>The rattling and rotation behaviours of the hydrated
excess proton (H<sup>+</sup>) in water are investigated using the density
functional theory–quantum chemical cluster model (DFT-CM) method. The rattling
pathways for the target proton <sup>*</sup>H<sup>+</sup> between two adjacent O
atoms in the form of Zundel configurations with symmetrical solvation
environments are obtained. The zero-point contribution reduces the reaction
energy barrier and enables the rattling to occur spontaneously at room
temperature. The rotational behaviour of <sup>*</sup>H<sup>+</sup> in the form
of <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup> is found. Upon <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*
</sup>rotation, <sup>*</sup>H<sup>+</sup> changes its position accompanied by concerted
displacement of surrounding solvent water molecules and the breaking and formation
of hydrogen bonds. The “<sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup>
rotating migration mechanism” is proposed for the proton transfer mechanism in
water — the same <sup>*</sup>H<sup>+</sup> migrates via <sup>*</sup>H<sup>+</sup>·H<sub>2</sub>O<sup>*</sup>
rotation through void in solvent water, rather than different protons hopping
along water hydrogen bond chains as known as the Grotthuss mechanism.</b></p><p><b> </b></p> | Shuping Bi | Hydrology and Water Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741eabb8c1a41513da037/original/the-rattling-and-rotation-behaviours-of-the-hydrated-excess-proton-in-water.pdf |
668e7674c9c6a5c07ade84b5 | 10.26434/chemrxiv-2024-b76v4-v2 | Re-engineering lysozyme solubility and activity through surfactant complexation | Hydrophobic ion-pairing is an established solubility engineering technique that uses amphiphilic surfactants to modulate drug lipophilicity and facilitate encapsulation in polymeric and lipid-based drug delivery systems. For proteins, surfactant complexation can also lead to unfolding processes and loss in bioactivity. In this study, we investigated the impact of two surfactants, sodium dodecyl sulphate (SDS) and dioctyl sulfosuccinate (DOSS) on lysozyme’s solubility, activity, and structure. SDS and DOSS were combined with lysozyme at increasing charge ratios (4:1, 2:1, 1:1, 1:2 and 1:4) via hydrophobic ion pairing at pH 4.5. Maximum complexation efficiency at the 1:1 charge ratio was confirmed by protein quantitation assays and zeta potential measurements, showing a near neutral surface charge. Lysozyme lipophilicity was successfully increased, with log D n-octanol/PBS values up to 2.5 with SDS and 1.8 with DOSS. Bioactivity assays assessing lysis of M. lysodeikticus cell walls showed up to a 2-fold increase in lysozyme’s catalytic ability upon complexation with SDS at ratios less than stoichiometric, suggesting favourable mechanisms of stabilisation. Secondary structural analysis using Fourier-transform infrared spectroscopy indicated that lysozyme underwent a partial unfolding process upon complexation with low SDS concentrations. Molecular dynamic simulations further confirmed that at these low concentrations, a positive conformation was obtained with the active site residue Glu 35 more solvent-exposed. Combined, this suggested that sub-stoichiometric SDS altered the active site’s secondary structure through increased backbone flexibility, leading to higher substrate accessibility. For DOSS, low surfactant concentrations retained lysozyme’s native function and structure while still increasing the protein’s lipophilic character. Our research findings demonstrate that modulation of protein activity can be related to surfactant chemistry and that controlled ion-pairing can lead to re-engineering of lysozyme solubility, activity, and structure. This has significant implications for advanced protein applications in healthcare, particularly towards the development of formulation strategies for oral biotherapeutics. | Jiaming Mu; Leran Mao; Gavin Andrews; Sheiliza Carmali | Biological and Medicinal Chemistry; Nanoscience; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668e7674c9c6a5c07ade84b5/original/re-engineering-lysozyme-solubility-and-activity-through-surfactant-complexation.pdf |
6495bd352e632767b0ab56be | 10.26434/chemrxiv-2023-kwwv3 | MoFlowGAN: Combining adversarial and likelihood learning for targeted molecular generation | Deep generative models for molecular graphs offer a new avenue for property optimization in drug discovery. Optimizing differentiable models that generate molecular graphs is certainly faster, cheaper, and much more accessible than traditional methods of chemical synthesis. Recent advances in generative modeling have managed to address many of the challenges surrounding generation of chemically-valid molecular graphs from latent representations, however the question of generating high-quality molecules remains. Herein we introduce MoFlowGAN a tandem normalizing flow model that can also be trained on both adversarial and reward objectives. We train our model on QM9 to generate high-quality and drug-like compounds. Our experiments show that MoFlowGAN is competitive with current state-of-the-art generative models while requiring far fewer training resources. | Nathan Mancheun Lui; Max D Li; Matthew Ford | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6495bd352e632767b0ab56be/original/mo-flow-gan-combining-adversarial-and-likelihood-learning-for-targeted-molecular-generation.pdf |
60d17af0461f563777482998 | 10.26434/chemrxiv-2021-4ws60-v5 | Synthesis, Characterization, and Effects of Molecular Structure on Phase Behavior of 4-Chloro-1,3-Diazobenzene Bent-Core Liquid Crystals with High Photosensitivity | In this study, a series of novel compounds were synthesized by adding azo functional groups and chlorine substituent to the central bent-cores to form a 4-chloro-1,3-dizaophenylene bent-core. The structure, mesogenic properties, and photosensitivity of these synthesized compounds were evaluated experimentally. The results show that these compounds exhibit a broad temperature window up to 63.8 °C for nematic phase and fast <i>trans – cis</i> photoisomerization in seconds with 80% conversion. Quantum mechanics modeling confirms that using azos as the central linkages can effectively reduce the molecular dipole moment, which appears to promote favorable mesogenic behaviors and photonic characteristics. Moreover, varying the carbon number in the terminal alkyl chains can alter molecular dipole, especially the polarizability anisotropy, of which the variation is strongly correlated with the phase transition temperature and temperature range of nematic phase. These findings suggest that reducing molecular dipole can promote favorable mesogenic and photonic properties. | Jinying Lu; Daoren Yan; Zhiyong Zhang; Zelong Zhang | Organic Chemistry; Materials Science; Liquid Crystals; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d17af0461f563777482998/original/synthesis-characterization-and-effects-of-molecular-structure-on-phase-behavior-of-4-chloro-1-3-diazobenzene-bent-core-liquid-crystals-with-high-photosensitivity.pdf |
65414f95c573f893f18730ba | 10.26434/chemrxiv-2023-r4jt6 | Bis(N-xylyl-imino)phenyl “NCN” Iridium Pincer Complexes.
Thermodynamics of Ligand Binding and C-C Bond Cleavage | Iridium dibromide complexes of the phenyldiimine ligand 2,6-bis(1-((2,6-dimethylphenyl)imino)ethyl)phenyl, trans-(XyPhDI)IrBr2L, have been synthesized, and relative Ir-L BDFEs have been experimentally determined for a wide range of corresponding adducts of ligands L. An estimate of the absolute enthalpy of Ir-L binding has been obtained from dynamic NMR measurements. The results of DFT calculations are in very good agreement with the relative and absolute experimental values. Computational studies were extended to the formation of adducts of (XyPhDI)IrH2 and (XyPhDI)Ir(I), as well as other (pincer)Ir(I) fragments, (Phebox)Ir(I) and (PCP)Ir(I), to enable a comparison of electronic and steric effects with these archetypal pincer ligands. Attempts to reduce (XyPhDI)IrBr2(MeCN) to a hydride or an Ir(I) complex yielded a dinuclear CN-bridged complex with a methyl ligand on the cyanide-C-bound Ir center (characterized by scXRD), indicating that C-CN bond cleavage took place at that Ir center. DFT calculations indicate that the C-CN bond cleavage occurs at one Ir center with strong assistance by coordination of the CN nitrogen to the other Ir center. | Soumyadipa Das; Souvik Mandal; Santanu Malakar; Thomas J. Emge; Alan S. Goldman | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65414f95c573f893f18730ba/original/bis-n-xylyl-imino-phenyl-ncn-iridium-pincer-complexes-thermodynamics-of-ligand-binding-and-c-c-bond-cleavage.pdf |
66412da221291e5d1d1721b8 | 10.26434/chemrxiv-2024-f7t09 | α-Bromoacetate as a Mild and Safe Brominating Agent in the Light-Driven Vicinal Dibromination of Unactivated Alkene and Alkynes | Light-induced vicinal dibromination of unactivated alkenes and alkyne has been demonstrated by using methyl alpha-bromoacetate as a mild brominating agent. Near-visible light (370 nm) light-emitting diode (LED) mediates this simple dibromination reaction under mild conditions with the inexpensive and non-toxic -bromoacetate. The reaction proceeds well with both terminal and internal alkenes and alkynes, and those contained in natural products and N/O-heterocycles, indicating its versatility in synthesizing dibrominated organic compounds. | Harshvardhan Singh; Supuni I. N. Hewa Inaththappulige; Raj K. Tak; Ramesh Giri | Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66412da221291e5d1d1721b8/original/bromoacetate-as-a-mild-and-safe-brominating-agent-in-the-light-driven-vicinal-dibromination-of-unactivated-alkene-and-alkynes.pdf |
60c74646702a9b8ac618ab96 | 10.26434/chemrxiv.10059860.v2 | Demystifying and Unravelling the Factual Molecular Structure of the Biopolymer Sporopollenin | <p></p><p>Sporopollenin
is a natural, highly cross-linked biopolymer composed of carbon, hydrogen, and oxygen, which forms the outer wall of pollen grains. Sporopollenin is resilient
to chemical degradation.<sup> </sup>Because
of this stability, its exact chemical structure and the biochemical pathways
involved in its biosynthesis remains a mystery and
unresolved.<sup> </sup></p>
<p>We have identified and characterized the molecular structure of
the clean, intact sporopollenin using soft ionization mass spectrometric and
nuclear magnetic resonance techniques. These analyses showed that sporopollenin
contained a poly(hydroxyacid) dendrimer-like network, which accounted for the
sporopollenin empirical formula. In addition, the identified hydroxy acid
monomers contained a beta diketone moiety, which most probably accounts for the
known antioxidant activity of sporopollenin. Moreover, our elucidation studies allowed
us to identify a unique circular polyhydroxylated tetraketide polymer. This polymer acted as the rigid backbone on
which the poly(hydroxyacid) network can be built, forming the scaffold of the spherical sporopollenin exine.</p><br /><p></p> | Abanoub Mikhael; Kristina Jurcic; Celine Schneider; David carr; Gregory L. Fisher; Travis D. Fridgen; Alberto Diego-Taboada; Grahame Mackenzie; JOSEPH BANOUB | Chemical Biology; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74646702a9b8ac618ab96/original/demystifying-and-unravelling-the-factual-molecular-structure-of-the-biopolymer-sporopollenin.pdf |
60c753209abda2d953f8df27 | 10.26434/chemrxiv.13404611.v1 | Assessing the Sequence Dependence of Pyrimidine-Pyrimidone (6-4) Photoproduct in a Duplex Double-Stranded DNA: A Challenge for Microsecond Range Simulation | Sequence dependence of the (6-4)photoproduct dynamics when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing a different upstream and downstream flexibilities. Moreover, REST2 simulations allow to probe structures possibly important for damaged DNA recognition. <br /> | Natacha Gillet; Alessio Bartocci; Elise Dumont | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753209abda2d953f8df27/original/assessing-the-sequence-dependence-of-pyrimidine-pyrimidone-6-4-photoproduct-in-a-duplex-double-stranded-dna-a-challenge-for-microsecond-range-simulation.pdf |
63a57050a2da4b2a090e12e1 | 10.26434/chemrxiv-2022-26428 | Double Deprotonation of CH3CN by an Iron–Aluminium Complex | Herein we present the first double deprotonation of acetonitrile (CH3CN) using a bimetallic iron-aluminium complex. The products of this reaction contain an exceeding simple yet rare [CHCN]2– dianion moiety that bridges two metal fragments. DFT calculations suggest that the bonding to the metal centres is primarily ionic in nature. Mechanistic studies reveal the intermediacy of a monomeric [CH2CN]– complex, which has been characterised in-situ. Our findings provide an important example in which a bimetallic metal complex achieves a new type of reactivity not previously encountered with monometallic counterparts. The isolation of a [CHCN]2– dianion through simple deprotonation of CH3CN also offers the possibility of a establishing a broader chemistry of this motif. | Benedek Stadler; Nikolaus Gorgas; Andrew White; Mark Crimmin | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bond Activation; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a57050a2da4b2a090e12e1/original/double-deprotonation-of-ch3cn-by-an-iron-aluminium-complex.pdf |
60c752ec9abda24460f8dec2 | 10.26434/chemrxiv.13277870.v2 | Advances in Automated Transition State Theory Calculations: Improvements on the AutoTST Framework | <div>Kinetic modeling of combustion chemistry has made substantial progress in recent years with the development of increasingly detailed models. However, many of the chemical kinetic parameters utilized in detailed models are estimated, often inaccurately. To help replace rate estimates with more accurate calculations, we have developed AutoTST, an automated Transition State Theory rate calculator. This work describes improvements to AutoTST, including: a systematic conformer search to find an ensemble of low energy conformers, vibrational analysis to validate transition state geometries, more accurate symmetry number calculations, and a hindered rotor treatment when deriving kinetics. These improvements resulted in location of transition state geometry for 93% of cases and generation of kinetic parameters for 74% of cases. Newly calculated parameters agree well with benchmark calculations and perform well when used to replace estimated parameters in a detailed kinetic model of methanol combustion.</div> | Nathan Harms; Carl Underkoffler; Richard West | Computational Chemistry and Modeling; Theory - Computational; Reaction Engineering; Chemical Kinetics | CC BY NC 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752ec9abda24460f8dec2/original/advances-in-automated-transition-state-theory-calculations-improvements-on-the-auto-tst-framework.pdf |
66fc06bccec5d6c142cae9d3 | 10.26434/chemrxiv-2024-b9hh5 | On-Demand Nitric Oxide Generation via Thermal Decomposition of N-Trityl Dihydro-1,2-Oxazines | Inhaled nitric oxide (iNO) is a promising therapy for a wide variety of pulmonary conditions but is limited by the cost, portability, and safety limitations of the compressed gas cylinders used in conventional iNO delivery systems. On-demand generation of iNO via thermally controlled decomposition of an NO-genic precursor is an attractive alternative to systems based on compressed gas cylinders. However, most NO-releasing materials, which would form the basis of such a system, are designed for in-vivo applications, not gas flow release at elevated temperatures. Novel NO donors with tunable kinetics suited for simple thermal generation are needed to realize such iNO delivery systems. Here we report the development of a patently new class of NO donors based on N-trityl 3,6-dihydro-1,2-oxazines. We show that these molecules release nitric oxide when heated above 90 °C and that their release kinetics can be modified through variation of the substitution pattern on the oxazine ring. Amorphous solid dispersions of these molecules in porous polymers exhibit consistent, thermoresponsive gas flow nitric oxide release. Collectively, this work adds a new class of NO donor to the basis set of known NO-genic molecules and establishes a potential technological basis for a low-power, small-footprint iNO delivery system. | Shuxiao Li; Nathan Blackburn; Cassandra Ward; James Bour | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fc06bccec5d6c142cae9d3/original/on-demand-nitric-oxide-generation-via-thermal-decomposition-of-n-trityl-dihydro-1-2-oxazines.pdf |
65efd9f266c1381729cc67a8 | 10.26434/chemrxiv-2024-j1kqg | A Quest for Parsimonious Topology of Polyhedral Cavities in Metal–Organic Frameworks | A new topology previously unknown in metal–organic frameworks (MOFs) provides an important clue to uncovering a new series of polyhedral MOFs. We report a novel MOF crystallized in a parsimonious mep topology based on Frank–Kasper (FK) polyhedra. The distribution of angles in a tetrahedral arrangement (T-O-T) is crucial for the formation of FK polyhedra in mep topology. This finding led us to investigate the T-O-T angle distribution in related zeolites and zeolitic imidazolate frameworks (ZIFs). Unlike zeolites, it is extremely difficult to achieve high T-O-T angles in ZIFs, which prevents the formation of some FK topologies. Density functional theory (DFT) total energy calculations support a correlation between T-O-T angles and the feasibility of new tetrahedron-based FK frameworks. This result may lead to innovative ways of accessing new cellular topologies by simple chemical tweaking of T-O-T angles. | Soochan Lee; Sungmin Lee; Yuna Kwak; Masood Yousaf; Hoi Ri Moon; Sung June Cho; Noejung Park; Wonyoung Choe | Inorganic Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65efd9f266c1381729cc67a8/original/a-quest-for-parsimonious-topology-of-polyhedral-cavities-in-metal-organic-frameworks.pdf |
60c753ca842e65a027db4013 | 10.26434/chemrxiv.13553030.v1 | Cysteine Borylation in Unprotected Peptides | Synthetic bioconjugation at cysteine (Cys) residues in peptides and proteins has emerged as a
powerful tool in chemistry. Soft nucleophilicity of the sulfur in Cys renders an exquisite
chemoselectivity with which various functional groups can be placed onto this residue under
benign conditions. While a variety of reactions have been successful at producing Cys-based
bioconjugates, the majority of these feature sulfur-carbon bonds. We report Cys-borylation,
wherein a benchtop stable Pt(II)-based organometallic reagent can be used to transfer a boron-rich
cluster onto a sulfur moiety in unprotected peptides forging a boron-sulfur bond. Discovered Cysborylation proceeds at room temperature and is tolerant to a variety of functional groups present
in complex polypeptides. The resultant bioconjugates show no additional toxicity compared to
their Cys aryl-based congeners. Finally, we demonstrate how the developed Cys-borylation can
enhance the proteolytic stability of the produced peptide bioconjugates while maintaining the
binding affinity to a protein target. | Mary A. Waddington; Alice Zheng; Julia M. Stauber; Elamar
Hakim Moully; Liban M. A. Saleh; Petr Kral; Alexander Spokoyny | Bioorganometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753ca842e65a027db4013/original/cysteine-borylation-in-unprotected-peptides.pdf |
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