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63d972e5d8f55fd0aa988b97 | 10.26434/chemrxiv-2022-t92nd-v5 | A “short blanket” dilemma for a state-of-the-art neural network potential for water: Reproducing experimental properties or the physics of the underlying many-body interactions? | Deep neural network (DNN) potentials have recently gained popularity in computer simulations of a wide range of molecular systems, from liquids to materials. In this study, we explore the possibility of combining the computational efficiency of the DeePMD framework and the demonstrated accuracy of the MB-pol data-driven many-body potential to train a DNN potential for large-scale simulations of water across its phase diagram. We find that the DNN potential is able to reliably reproduce the MB-pol results for liquid water but provides a less accurate description of the vapor-liquid equilibrium properties. This shortcoming is traced back to the inability of the DNN potential to correctly represent many-body interactions. An attempt to explicitly include information about many-body effects results in a new DNN potential that exhibits opposite performance, being able to correctly reproduce the MB-pol vapor-liquid equilibrium properties but losing accuracy in the description of the liquid properties. These results suggest that DeePMD-based DNN potentials are not able to correctly "learn" and, consequently, represent many-body interactions, which implies that DNN potentials may have limited ability to predict properties for state points that are not explicitly included in the training process. The computational efficiency of the DeePMD framework can still be exploited to train DNN potentials on data-driven many-body potentials, which can thus enable large-scale, "chemically accurate" simulations of various molecular systems, with the caveat that the target state points must have been adequately sampled by the reference data-driven many-body potential in order to guarantee a faithful representation of the associated properties. | Yaoguang Zhai; Alessandro Caruso; Sigbjørn L. Bore; Zhishang Luo; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Machine Learning; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d972e5d8f55fd0aa988b97/original/a-short-blanket-dilemma-for-a-state-of-the-art-neural-network-potential-for-water-reproducing-experimental-properties-or-the-physics-of-the-underlying-many-body-interactions.pdf |
60c746cdbb8c1a34af3da97a | 10.26434/chemrxiv.11413866.v1 | Single Molecular Catalysis Identifying Activation Energy of Intermediate Product and Rate-Limiting Step in Plasmonic Photocatalysis | Plasmon mediated photocatalysis provides a novel strategy for harvesting solar energy. Identification of rate determining step and its activation energy in plasmon mediated photocatalysis plays critical roles for understanding the contribution of hot carriers that facilitates rational designing catalysts with integrated high photo-chemical conversion efficiency and catalytic performance. However, it remains a challenge due to a lack of research tools with spatiotemporal resolution that capable of capturing intermediates. In this work, we used a single molecular fluorescence approach to investigate a localized surface plasmon resonance (LSPR) enhanced photocatalytic reaction with sub-turnover resolution. By introducing variable temperature as an independent parameter in plasmonic photocatalysis, the activation energies of tandem reaction steps, including intermediate generation, product generation and product dissociation, were clearly differentiated, and intermediates generation was found to be the rate-limiting step. Remarkably, the cause of plasmon enhanced catalysis performance was found to be its ability of lowering the activation energy of intermediates generation. This study gives new insight into the photo-chemical energy conversion pathways in plasmon enhanced photocatalysis and sheds light on designing high performance plasmonic catalysts. | Di Li | Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746cdbb8c1a34af3da97a/original/single-molecular-catalysis-identifying-activation-energy-of-intermediate-product-and-rate-limiting-step-in-plasmonic-photocatalysis.pdf |
63a0354aa53ea6785d504e28 | 10.26434/chemrxiv-2022-v2sm6 | On the key role of electrolyte-electrode van der Waals interactions in the simulation of ionic liquids-based supercapacitors | The performance of supercapacitors is governed by the structure and dynamics of ions at the solid/liquid interface. At the molecular scale, these properties result from a subtle combination of electrolyte--electrolyte and electrolyte--electrode interactions. Although the former are well captured by conventional force fields, validated against experiments, the latter are much more difficult to parameterize accurately. In this work, by using constant potential classical molecular dynamics, we investigate the effect of the strength of the electrode-electrolyte van der Waals interactions on the interfacial properties for a system composed of the 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic liquid and a graphite electrode. We show that stronger van der Waals interactions lead to a decrease in the exchange of co-ions by counter-ions with the increase of potential difference and, thus, to a lower capacitance of the devices. The ion exchange dynamics is strongly affected, but the charging rate remains constant over the whole range of studied parameters. This study emphasizes the need for a careful parameterization of force fields for electrode materials in future classical molecular dynamics studies. | Camille Bacon; Alessandra Serva; Celine Merlet; Patrice Simon; Mathieu Salanne | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Energy Storage; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a0354aa53ea6785d504e28/original/on-the-key-role-of-electrolyte-electrode-van-der-waals-interactions-in-the-simulation-of-ionic-liquids-based-supercapacitors.pdf |
661ed4ba21291e5d1df9d6ef | 10.26434/chemrxiv-2024-pz45l | Machine Learning in Complex Organic Mixtures: Applying Domain Knowledge Allows for Meaningful Performance with Small Datasets. | The ability to quantify individual components of complex mixtures is a challenge found throughout the life and physical sciences. An improved capacity to generate large datasets along with the uptake of machine-learning (ML) based analysis tools has allowed for various ‘omics’ disciplines to realize exceptional advances. Other areas of chemistry that deal with complex mixtures often cannot leverage these advances. Environmental samples, for example, can be more difficult to access and the resulting small datasets are less appropriate for unconstrained ML approaches. Herein, we present an approach to address this latter issue. Using a very small environmental dataset—35 high-resolution mass spectra gathered from various solvent extractions of Canadian petroleum fractions—we show that the application of specific domain knowledge can lead to ML models with notable performance. | Katelyn Le; Jagoš R. Radović; Justin L. MacCallum; Stephen R. Larter; Jeffrey F. Van Humbeck | Theoretical and Computational Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Mass Spectrometry; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661ed4ba21291e5d1df9d6ef/original/machine-learning-in-complex-organic-mixtures-applying-domain-knowledge-allows-for-meaningful-performance-with-small-datasets.pdf |
63b34aaddadddc750ca36b93 | 10.26434/chemrxiv-2023-m0r2f | Thermodynamics of Li+–Crown Ether Interactions in Aqueous Solvent | Lithium ion-based batteries are ubiquitous in modern technology due to applications in personal electronics and high-capacity storage for electric vehicles. Concerns about lithium supply and battery waste have prompted interest in lithium recycling methods. The crown ether, 12-crown-4, has been studied for its abilities to form stable complexes with lithium ions (\ce{Li+}). In this paper, molecular dynamics simulations are applied to examine the binding properties of a 12-crown-4—\ce{Li+} system in aqueous solution. It was found that 12-crown-4 did not form stable complexes with \ce{Li+} in aqueous solution due to the binding geometry which was prone to interference by surrounding water molecules. In addition, the binding properties of sodium ions (\ce{Na+}) to 12-crown-4 are examined for comparison. Subsequently, calculations were performed with the crown ethers 15-crown-5 and 18-crown-6 to study their complexation with \ce{Li+} as well. It was determined that binding was unfavorable for both types of ions for all three crown ethers tested, though 15-crown-5 and 18-crown-6 showed a marginally greater affinity for \ce{Li+} than 12-crown-4. Metastable minima present in the potential of mean force for \ce{Na+} render binding marginally more likely there. We discuss these results in the context of membrane based applications of crown ethers for \ce{Li+} separations. | Ramón González-Pérez; Stephen Adams; Alexander W. Dowling; William A. Phillip; Jonathan Whitmer | Theoretical and Computational Chemistry; Physical Chemistry; Statistical Mechanics; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b34aaddadddc750ca36b93/original/thermodynamics-of-li-crown-ether-interactions-in-aqueous-solvent.pdf |
629555d7d504183954c96de4 | 10.26434/chemrxiv-2022-jp6hz | Catalytic production of ammonia from dinitrogen employing molybdenum complexes bearing N-heterocyclic carbene-based PCP-type pincer ligands | Here, we established a mechanistic insight into the catalytic production of ammonia from dinitrogen via the combination of samarium diiodide (SmI2) and water in the presence of molybdenum complexes bearing PCP-type pincer ligands as the catalysts. The experimental and theoretical studies revealed that the rate-determining step was the proton-coupled electron transfer (PCET) during the formation of the N–H bond on the molybdenum imide complex at high catalyst concentrations. Additionally, we confirmed that the concentration of the catalyst affected the rate-determining step and the dimerisation step of the catalyst became the rate-determining step at a low catalyst concentration. Thus, we designed PCP-type pincer ligands in which various substituents were introduced at the positions 5 and/or 6, to accelerate the rate-determining PCET reaction and observed that the introduction of electron-withdrawing groups promoted the reaction rate, as predicted by density-functional theory calculations. Finally, the molybdenum trichloride complex bearing a trifluoromethyl group containing PCP-type pincer ligand functioned as the most effective catalyst for producing up to 60,000 equivalents of ammonia based on the molybdenum atom of the catalyst, with a turnover frequency of up to 800 equivalents/Mo·min−1. The amount of ammonia produced via this reaction, as well as its production rate, were approximately one order of magnitude larger than those obtained under the previous reaction conditions. The findings reported herein can contribute to the development of an environmentally friendly next-generation nitrogen fixation system. | Yoshiaki Nishibayashi; Yuya Ashida; Takuro Mizushima; Kazuya Arashiba; Akihito Egi; Hiromasa Tanaka; Kazunari Yoshizawa | Organometallic Chemistry; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629555d7d504183954c96de4/original/catalytic-production-of-ammonia-from-dinitrogen-employing-molybdenum-complexes-bearing-n-heterocyclic-carbene-based-pcp-type-pincer-ligands.pdf |
60c747c2702a9b61cb18ae4d | 10.26434/chemrxiv.11771388.v1 | NMR in Analysis of the Nutritional Value of Lipids from Muscles and Livers of Wild Amazonian Fishes with Different Eating Habits over Seasonal Variation | <div>Lipid composition of the Amazonian fishes remains unexplored although fishes in general show very high nutritional potential. Endogenous and environmental factors can influence the lipid contents of fishes among which, in the Amazon River, seasonal dynamics influences stand out. Herein, nine most consumed fish species were analyzed and their lipid composition evaluated in terms of effects of tissue from where were extracted, season of the Amazon River and the fish eating habits. Higher amounts of lipids were obtained from livers than dorsal muscles in all studied species. Statistical analysis has shown that Amazonian fishes present different lipid profiles according to their eating habits, which mainly comprises saturated fatty acids to distinguish detritivorous livers, and linolenic acid, cholesterol, polar lipids for carnivorous and piscivorous fish muscles. Furthermore, in Amazonian fish, some very important lipids for human nutrition are present, such as omega 3 and 6 fatty acids whose availability depended on the tissue metabolism and fishes’ eating habit along the seasonal periods. For example, our findings indicate that the piscivorous fish C. monoculus presented higher levels of linoleic acid for liver than linolenic acid and the opposite occurred for muscles. The omega 6 and 3 fatty acids ratio was influenced by the season dynamic of the Amazon River and availability of food according with each specific eating habit, poiting mainly to the piscivorous fishes as the healthiest fish for human consumption. </div><div><br /></div> | Banny Correia; Gilberto Gaspar Duarte Ortin; Maiara da Silva Santos; Raquel Susana Torrinhas; Natalia Cristina Mor; Adalberto Luis Val; Ljubica Tasic | Food | CC BY NC 4.0 | CHEMRXIV | 2020-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747c2702a9b61cb18ae4d/original/nmr-in-analysis-of-the-nutritional-value-of-lipids-from-muscles-and-livers-of-wild-amazonian-fishes-with-different-eating-habits-over-seasonal-variation.pdf |
60e27ac3f7373f797a45149c | 10.26434/chemrxiv-2021-sxlwm-v2 | Mesoporous Silica with Covalently Immobilized Anthracene as Adsorbent for SPE Recovery of PAHs Pollutants from Highly Lipidic Solutions | Two samples of functionalized mesoporous silica
containing anchored anthrylmethylamine groups (SiO<sub>2</sub>-Ant) have been
prepared by surface assembling (1) and one step silane immobilization (2). Both
adsorbents can be attributed to bimodal balanced hydrophobic-hydrophilic
adsorbents with loading of anthracene groups about 15-33%. The adsorbents have
been used for SPE of anthracene from organic solvents (acetonitrile, acetone
and heptane) and model solutions of lipids (myristic acid and vegetable oil).
The obtained results were compared with commercial C18 SPE cartridge. While C18
cartridge recovers anthracene from water-containing media (acetonitrile/water,
1/1), SiO<sub>2</sub>-Ant cartridges much more efficient in extraction of
anthracene from non-polar solvent (heptane). Lipids macrocomponents such as
myristic acid and vegetable oil do not decrease the dynamic adsorption capacity
and recovery of the model PAH on SiO<sub>2</sub>-Ant. It was demonstrated that
π-π stacking interaction with the analyte determine the selectivity of SiO<sub>2</sub>-Ant
towards of anthracene. This makes SiO<sub>2</sub>-Ant attractive for selective
pre-concentration of PAHs from high lipid content objects, such as vegetable
oils. | Albina Mikhraliieva; Rodrigo Araújo Gonçalves; Volodymyr Zaitsev | Analytical Chemistry; Environmental Analysis; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e27ac3f7373f797a45149c/original/mesoporous-silica-with-covalently-immobilized-anthracene-as-adsorbent-for-spe-recovery-of-pa-hs-pollutants-from-highly-lipidic-solutions.pdf |
674dc5277be152b1d0af2339 | 10.26434/chemrxiv-2024-p6q7p | Going nuclear: Improved antisense oligonucleotide activity through conjugation with a nuclear importer | Antisense oligonucleotides (ASOs) are a promising class of therapeutics designed to modulate gene expression. Both key mechanisms of action for ASOs operate in the nucleus: splice-switching ASOs modify pre-mRNA, processed in the nucleus, and mRNA-degrading ASOs require RNase H, an enzyme predominantly active in the nucleus. Therefore, to achieve maximal efficacy, ASOs require efficient nuclear delivery. Current ASO therapeutics shuttle in and out of the nucleus inefficiently. In this work, we have synthesised ASO conjugates for active nuclear import, by covalent conjugation with a potent small-molecule nuclear importer, (+)-JQ1. (+)-JQ1 is a well-characterised high-affinity binder for members of the BET bromodomain family of proteins and was recently shown to transport cytoplasmic proteins into the nucleus. Our (+)-JQ1-ASO conjugates outperformed their unmodified counterparts for both splice-switching and mRNA knockdown in the nucleus, at all concentrations tested. In particular, we improved the performance of Oblimersen, a BCL-2 ASO drug that failed phase-III clinical trials, showing that this therapeutic may merit re-evaluation. This work shows that the covalent modification of ASOs with a small-molecule nuclear importer can significantly improve target engagement and pave the way for more effective therapeutics. | Disha Kashyap; Thomas Milne; Michael Booth | Biological and Medicinal Chemistry; Organic Chemistry; Bioengineering and Biotechnology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-12-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674dc5277be152b1d0af2339/original/going-nuclear-improved-antisense-oligonucleotide-activity-through-conjugation-with-a-nuclear-importer.pdf |
60ddebafe924192bd7e181fd | 10.26434/chemrxiv-2021-n18xc | Phage-Assisted Continuous Evolution and Selection of Enzymes for Chemical Synthesis | Ligand-dependent biosensors are valuable tools for coupling the intracellular concentrations of small molecules to easily detectable readouts such as absorbance, fluorescence, or cell growth. While ligand-dependent biosensors are widely used for monitoring the production of small molecules in engineered cells and for controlling or optimizing biosynthetic pathways, their application to directed evolution for biocatalysts remains underexplored. As a consequence, emerging continuous evolution technologies are rarely applied to biocatalyst evolution. Here, we develop a panel of ligand-dependent biosensors that can detect a range of small molecules. We demonstrate that these biosensors can link enzymatic activity to the production of an essential phage protein to enable biocatalyst-dependent phage assisted continuous evolution (PACE) and phage-assisted continuous selection (PACS). By combining these phage-based evolution and library selection technologies, we demonstrate we can evolve enzyme variants with improved and expanded catalytic properties. Finally, we show that the genetic diversity resulting from a highly mutated PACS library is enriched for active enzyme variants with altered substrate scope. These results lay the foundation for using phage-based continuous evolution and selection technologies to engineer biocatalysts with novel substrate scope and reactivity. | Krysten A. Jones; Harrison M. Snodgrass; Ketaki Belsare; Bryan C. Dickinson; Jared C. Lewis | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Chemical Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ddebafe924192bd7e181fd/original/phage-assisted-continuous-evolution-and-selection-of-enzymes-for-chemical-synthesis.pdf |
6486cabf4f8b1884b72d4ce4 | 10.26434/chemrxiv-2023-qlzj4 | Synthetic and analytical routes to the L-amino acid conjugates of cis-OPDA and their identification and quantification in plants | Cis-(+)-12-oxophytodienoic acid (cis-(+)-OPDA) is a bioactive jasmonate, a precursor of jasmonic acid, which also displays signaling activity on its own. Modulation of cis-(+)-OPDA actions may be carried out via biotransformation leading to metabolites of various functions, similar to other phytohormones. This work introduces a methodology for the synthesis of racemic cis-OPDA conjugates with amino acids (OPDA-aa) and their deuterium-labeled analogs, which enables the identification and accurate quantification of these compounds in plants. We have developed a highly sensitive liquid chromatography-tandem mass spectrometry-based method for the reliable determination of seven OPDA-aa (OPDA-Alanine, OPDA-Aspartate, OPDA-Glutamate, OPDA-Glycine, OPDA-Isoleucine, OPDA-Phenylalanine, and OPDA-Valine) from minute amount of plant material. The extraction from 10 mg of fresh plant tissue by 10% aqueous methanol followed by single-step sample clean-up on hydrophilic–lipophilic balanced columns prior to final analysis was optimized. The method was validated in terms of accuracy and precision, and the method parameters such as process efficiency, recovery and matrix effects were evaluated. In mechanically wounded 30-day-old Arabidopsis thaliana leaves, five endogenous (+)-OPDA-aa were identified and their endogenous levels reached a maximum of pmol/g. The time-course accumulation revealed a peak 60 min after the wounding, roughly corresponding to the accumulation of cis-(+)-OPDA. Current synthetic and analytical methodologies support studies on cis-(+)-OPDA conjugation with amino acids and research into the biological significance of these metabolites in plants. | Václav Mik; Tomáš Poslíšil; Federica Brunoni; Jiří Grúz; Vladimíra Nožková; Claus Wasternack; Otto Miersch; Miroslav Strnad; Kristýna Floková; Ondřej Novák; Jitka Široká | Organic Chemistry; Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6486cabf4f8b1884b72d4ce4/original/synthetic-and-analytical-routes-to-the-l-amino-acid-conjugates-of-cis-opda-and-their-identification-and-quantification-in-plants.pdf |
62f7753ea01447e65bb5dce0 | 10.26434/chemrxiv-2022-ll9p1 | Polyureas as SEI-forming Additives for Li Metal Anodes | We report here the first example of the use of an organic “polyurea” polymer as a SEI-forming additive for the lithium metal anode for lithium oxygen batteries. The presence of a suitable polyurea can significantly increase the coulombic efficiency and cycling of the anode in the presence of oxygen in the liquid electrolyte. The findings demonstrate proof of concept for the application of polyureas and other organic polymers for next-generation type batteries with metal anode. | Ronja Haas; Luca Kaufer; Chang Gao; Angus McLuskie; Gavin Peters; Amit Kumar; Daniel Schröder | Materials Science; Polymer Science; Energy; Catalysts; Organic Polymers; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f7753ea01447e65bb5dce0/original/polyureas-as-sei-forming-additives-for-li-metal-anodes.pdf |
60c74437bb8c1a3e823da46e | 10.26434/chemrxiv.9761477.v1 | Escaping Scaling Relationships for Water Dissociation at Interfacial Sites of Zirconia-Supported Rh and Pt Clusters | <p>Water dissociation is an important reaction involved in many industrial processes and a good model reaction for probing the activity of catalytic sites. In this computational study, the dissociation of water at interfacial sites of globally optimized ZrO2 sup- ported Pt and Rh clusters is investigated under the framework of density functional theory. Our findings demonstrate that the perimeter sites of these small clusters can activate water, but the dissociation behavior varies considerably between sites. It is shown that the studied clusters break scaling relationships for water dissociation, suggesting these catalysts may achieve activities beyond the maximum imposed by such relations. Furthermore, we observed large differences in the thermodynamics of the water dissociation reaction between global minimum and near-global minimum isomers of the clusters. Overall, our results highlight the uniqueness of interfacial sites in catalytic reactions, and the need for developing new concepts and tools to deal with the associated complexity.</p> | Minttu
M. Kauppinen; Ville Korpelin; Anand Mohan Verma; Marko Melander; Karoliina Honkala | Catalysts; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74437bb8c1a3e823da46e/original/escaping-scaling-relationships-for-water-dissociation-at-interfacial-sites-of-zirconia-supported-rh-and-pt-clusters.pdf |
61fe26a8216867b9b96c200f | 10.26434/chemrxiv-2022-mhj41-v2 | Arsenic(V) Immobilization in Fly Ash and Lead-Zinc Mine Tailing-based Geopolymer: Performance and Mechanism Insight | Global mining activities produce thousands of millions of toxic-bearing mine tailing (MT) wastes each year. Storage of the mine tailings not only encroaches upon large areas of cropland but also arouses additional ecological and environmental risks especially when the toxics (e.g., arsenic) are leached out during the stormy weather. Herein we demonstrate that geopolymerization of a mixture of the toxic-bearing mine tailings and the coal fly ash (FA) with a blending of sodium hydroxide (NaOH) and sodium silicate solution can effectively immobilize extra arsenic (As) species derived from arsenic-bearing wastes in the geopolymer specimens, which also possess high compressive strengths (e.g., > 25 MPa for specimens with 54 wt.% FA and activated with 10 M NaOH), allowing them to be further used as low-carbon, cement-free building materials. The geopolymer strength was found to depend clearly upon the NaOH concentration, the fly ash content, the arsenic content, and the curing time, with the maximum being 37.07 MPa for a specimen with 54 wt.% FA, 0.03 wt.% As activated with 10 M NaOH and cured for 28 days. Leaching tests showed that all specimens can achieve an immobilization efficiency as high as 95.4% toward As, and that the leachabilities of both As and other toxic heavy metals are far below the limits of the Chinese leaching standard for hazardous wastes (GB 5085.3 − 2007). Microstructural analyses using X-ray diffractometer (XRD), scanning electron microscopic (SEM), Fourier transform infrared (FTIR) indicate that the As species was physically encapsulated along with the formation of geopolymer gels at first, and then chemically incorporated into the crystalline phases (e.g., calcium silicate, and calcium silicate hydroxide) derived from the geopolymer gels as a result of prolonging the curing time. The developed FA/MT-based geopolymers represent a promising green material for both the remediation of As-bearing lands and the construction industry. | Alseny Bah; Jie Jin; Andrea Ramos; Feihu Li | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fe26a8216867b9b96c200f/original/arsenic-v-immobilization-in-fly-ash-and-lead-zinc-mine-tailing-based-geopolymer-performance-and-mechanism-insight.pdf |
60c75008842e657804db394b | 10.26434/chemrxiv.12982019.v1 | A Three-Dimensional Tetraphenylethylene-Based Fluorescence Covalent Organic Framework for Molecular Recognition | <p><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a>The development of
highly-sensitive recognition of </a><a></a><a></a><a></a><a></a><a>hazardous </a>chemicals, such as volatile organic compounds (VOCs) and polycyclic aromatic hydrocarbons (PAHs), is of
significant importance because of their widespread social concerns related to
environment and human health. Here, we
report a three-dimensional (3D) covalent organic framework (COF, termed
JUC-555) bearing tetraphenylethylene (TPE) side chains as an
aggregation-induced emission (AIE) fluorescence probe for sensitive
molecular recognition.<a></a><a> </a>Due to the rotational restriction of TPE rotors in highly
interpenetrated framework after inclusion of dimethylformamide (DMF), JUC-555 shows impressive AIE-based strong fluorescence. Meanwhile, owing to the large pore size (11.4 Å) and suitable intermolecular distance of aligned TPE
(7.2 Å) in JUC-555, the obtained
material demonstrates an
excellent performance in the molecular recognition of
hazardous chemicals, e.g., nitroaromatic explosives, PAHs, and even thiophene
compounds, via a fluorescent quenching mechanism. The quenching constant (<i>K</i><sub>SV</sub>) is two orders of magnitude better than
those of other fluorescence-based porous materials reported to date. This
research thus opens 3D functionalized COFs as a promising identification tool
for environmentally hazardous substances.</p> | Junxia Ren; Yaozu Liu; Xin Zhu; Yangyang Pan; Yujie Wang; Hui Li; Yue Tian; Qinghai Zhou; Taifeng Liu; Shilun Qiu; Qianrong Fang; Shengxiong Xiao | Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75008842e657804db394b/original/a-three-dimensional-tetraphenylethylene-based-fluorescence-covalent-organic-framework-for-molecular-recognition.pdf |
6290f924d504181fa9c5524e | 10.26434/chemrxiv-2022-5pl5p | Activity of metal-fluorine states upon delithiation of disordered rocksalt oxyfluorides. | The capacity of transition metal oxides as Li-ion battery cathodes is limited by instabilities that arise when high states of charge are achieved. Oxyfluorides with a disordered rock-salt structure have emerged as attractive alternatives, but the role of F in their electrochemical function, particularly when metals reach high formal oxidation states through cationic redox, remains to be ascertained. Using XAS measurements of Mn, O and F, we reveal the existence of Mn-F covalent interactions in Li2MnO2F and Li2Mn2/3Nb1/3O2F. New unoccupied states evolve from both Mn-F and Mn-O interactions when the phases are delithiated. The results challenge the assumption of F as largely a spectator ion, providing instead a nuanced picture of redox compensation in oxyfluorides. They suggest the existence of unique knobs of design of battery cathodes in these chemical spaces, by manipulating the covalent interactions between transition metals and two different anions. | Indrani Roy; Khagesh Kumar; Haifeng Li; John william Freeland; Fanny rodolakis; Jordi Cabana | Inorganic Chemistry; Analytical Chemistry; Energy; Spectroscopy (Anal. Chem.); Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6290f924d504181fa9c5524e/original/activity-of-metal-fluorine-states-upon-delithiation-of-disordered-rocksalt-oxyfluorides.pdf |
65a12b3e9138d23161c2a092 | 10.26434/chemrxiv-2024-h8ddb-v2 | Electrochemical detection of glutamate and histamine using redox-labeled stimuli-responsive polymer as a synthetic target receptor | Glutamate (Glu) and histamine (His) are two major neurotransmitters that play many critical roles in brain physiological functions and neurological disorders. Therefore, specific and sensitive monitoring of Glu and His is essential in the diagnosis and treatment of various mental health and neurodegenerative disorders. Both being non-electroactive species, direct electrochemical detection of Glu and His has been challenging. Herein, we report a stimuli-responsive polymer-based biosensor for the electrochemical detection of Glu and His. The polymer-based target receptors consist of a linear chain stimuli-responsive templated polymer hybrid that is labeled with an osmium-based redox-active reporter molecules to elicit conformation-dependent electrochemical responses. The polymers are then attached to a gold electrode to implement an electrochemical sensor. The cyclic voltammetry (CV) and square-wave voltammetry (SWV) results confirmed the polymers’ conformational changes due to the specific target (i.e., Glu and His) recognition and the corresponding electrochemical detection capabilities. The voltammetry results indicate that this biosensor can be used as a ‘signal-on’ and ‘signal-off’ sensors for the detection of Glu and His concentrations, respectively. The developed biosensor also showed excellent regeneration capability by fully recovering the initial current signal after rinsing with deionized water. To further validate the polymer’s utility as a target bioreceptor, the surface plasmon resonance (SPR) technique was used to characterize the binding affinity between the designed polymers and the target chemical. The SPR results exhibited the equilibrium dissociation constants (KD) of 2.40 µM and 1.54 µM for the polymer-Glu and polymer-His interactions, respectively. The results obtained this work strongly suggest that the proposed sensing technology could potentially be used as a platform for monitoring non-electroactive neurochemicals from animal models. | Leila Ahmadian Alam; Arturo Andrade; Edward Song | Analytical Chemistry; Polymer Science; Polymerization (Polymers); Biochemical Analysis; Electrochemical Analysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a12b3e9138d23161c2a092/original/electrochemical-detection-of-glutamate-and-histamine-using-redox-labeled-stimuli-responsive-polymer-as-a-synthetic-target-receptor.pdf |
6481dbd4be16ad5c57a61524 | 10.26434/chemrxiv-2023-6q06z-v2 | Accurate and efficient spin-phonon coupling and spin dynamics calculations for molecular solids | Molecular materials are poised to play a significant role in the development future opto-electronic and quantum technologies. A crucial aspect of these areas is the role of spin-phonon coupling and how it facilitates energy-transfer processes such as intersystem crossing, quantum decoherence, and magnetic relaxation. Thus, it is of significant interest to be able to accurately calculate molecular spin-phonon coupling and spin dynamics in the condensed phase. Here we examine the various approximations inherent in spin-phonon coupling and spin dynamics calculations on molecular solids by performing a case study on a single-molecule magnet. Three key results are: i) finite crystalline slab calculations should be avoided; ii) the phonon spectrum in reciprocal space should be sampled as densely as possible; and iii) phonon linewidths, as calculated by periodic density-functional theory, are likely overestimated at low temperature, but are not essential to obtain accurate magnetic relaxation rates provided point ii is adhered to. Calculations using this approach are facilitated by the open-source packages we have developed, which enable cost-effective and accurate spin-phonon coupling calculations on molecular solids with quantitative accuracy. | Rizwan Nabi; Jakob Staab; Andrea Mattioni; Jon Kragskow; Daniel Reta; Jonathan Skelton; Nicholas Chilton | Theoretical and Computational Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Magnetism; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6481dbd4be16ad5c57a61524/original/accurate-and-efficient-spin-phonon-coupling-and-spin-dynamics-calculations-for-molecular-solids.pdf |
64359975736114c9635346e6 | 10.26434/chemrxiv-2023-5sw1f | Process Development for the Manufacture of the Antimalarial Amodiaquine Dihydrochloride Dihydrate | A robust process technology for the manufacture of the active pharmaceutical ingredient (API) amodiaquine dihydrochloride dihydrate (ADQ, 3), an important antimalarial, is reported. The process consists of a three-step synthetic route that involves a Mannich reaction, condensation with 4,7-dichloroquinoline (DCQ, 5) and rehydration. Additionally, a cost-competitive process for the production of DCQ (5) is also reported wherein DCQ (5) was prepared in four steps from meta-chloroaniline (7). 4-Amido-2-(diethylaminomethyl)phenol (14), DCQ (5), and ADQ (3) were obtained in yields of 92, 89 and 90% respectively. | Mukut Gohain; Modibo S Malefo; Phaladi Kunyane; Chantal Scholtz; Sangeeta Baruah; Andile Zitha; Gerrit van der Klashorst; Hannes Malan | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Process Chemistry; Industrial Manufacturing | CC BY 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64359975736114c9635346e6/original/process-development-for-the-manufacture-of-the-antimalarial-amodiaquine-dihydrochloride-dihydrate.pdf |
6698a081c9c6a5c07a934f35 | 10.26434/chemrxiv-2024-kq19w | A double-walled noncovalent carbon nanotube by columnar packing of nanotube fragments | Double-walled nanotubes are promising materials in various scientific fields because of their high stability and large surface area. Herein, we report the synthesis of double-walled noncovalent carbon nanotubes (CNTs) through host-guest complexation of nanotube fragments and tube-forming crystal engineering. As the smallest fragment of double-walled CNTs, a host-guest complex of perfluorocycloparaphenylene (PFCPP) and carbon nanobelt (CNB) was synthesized by mixing them in solvents. The immediate complexation of the PF[12]CPP⊃(6,6)CNB complex with a remarkably high association constant (Ka) of 2×105 L/mol was observed. Time-dependent 1H NMR and thermogravimetry measurements revealed that the stability of (6,6)CNB was significantly improved by encapsulation. X-ray crystallography confirmed the robust belt-in-ring structure of this complex. As indicated by the short distance between PF[12]CPP and (6,6)CNB (2.8 Å), intermolecular orbital interactions exist between the belt and the ring, which were further supported by theoretical calculation and phosphorescence quenching experiments. While the PF[12]CPP⊃(6,6)CNB complex adopts various crystal packing structures, chloroform was discovered to be a magic “glue” solvent inducing one-dimensional alignment of the PF[12]CPP⊃(6,6)CNB complex to build an unprecedented double-walled noncovalent CNT structure. | Daiki Imoto; Hiroki Shudo; Akiko Yagi; Kenichiro Itami | Organic Chemistry; Supramolecular Chemistry (Org.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6698a081c9c6a5c07a934f35/original/a-double-walled-noncovalent-carbon-nanotube-by-columnar-packing-of-nanotube-fragments.pdf |
60c73d29842e6519a9db1732 | 10.26434/chemrxiv.5469241.v1 | Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics | <p>Determining
the conformations accessible to carbohydrate ligands in aqueous solution is
important for understanding their biological action. In this work, we evaluate
the conformational free energy surfaces of Lewis oligosaccharides in explicit
aqueous solvent using a multidimensional variant of the swarm-enhanced sampling
molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased
MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl
Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer
landscapes in general agreement with the other biased methods and with triplicate
unbiased 10 ms trajectories;
these simulations find a predominance of closed conformer and a range of low
occupancy open forms. The msesMD simulations also suggest closed-to-open
transitions in the tetrasaccharide are facilitated by changes in ring puckering
of its GlcNAc residue away from the <sup>4</sup>C<sub>1</sub> form, in line
with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations
predict a minor population of an open form in solution, corresponding to a rare
lectin-bound pose observed crystallographically. Overall, from comparison with
biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough
to fully sample glycan conformations in aqueous solution. However, the
computational efficiency and intuitive approach of the msesMD method suggest
potential for its application in glycomics as a tool for analysis of
oligosaccharide conformation.</p> | Irfan Alibay; Kepa K. Burusco; Neil J. Bruce; Richard A. Bryce | Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2017-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d29842e6519a9db1732/original/identification-of-rare-lewis-oligosaccharide-conformers-in-aqueous-solution-using-enhanced-sampling-molecular-dynamics.pdf |
60c7574af96a0021b9288c2e | 10.26434/chemrxiv.14390414.v1 | Molecular Packing of Non-Fullerene Acceptors for Organic Solar Cells: Distinctive Local Morphology in Y6 Versus ITIC Derivatives | Since a couple of years ago, Y6 has emerged as one of the main non-fullerene acceptors for organic solar cells as its use leads to superior power conversion efficiencies. It is thus of major interest to investigate the multi-scale phenomena that are responsible for Y6’s efficacy. Here, we modeled neat films of Y6 and earlier non-fullerene acceptors, IT-4F and ITIC, using a combination of density functional theory calculations and molecular dynamics simulations, to investigate the various factors that control their charge and exciton transport rates. We find that the molecular packing in Y6 is drastically different from that in IT-4F and ITIC. At the nano-scale, the local morphology of Y6 consists of a large number of directional face-on stackings and well-connected transport networks. Y6 also consistently shows higher electronic couplings for LUMOs, HOMOs, and local excitations than ITIC-type acceptors, which results in fast transport rates for electron, holes, and excitons. Importantly, when considering dimers, their configurations in Y6 are more diverse than in ITIC-type acceptors, with many of those similar to the configurations observed in the Y6 crystal structure reported recently. Most Y6 dimer configurations exhibit strong binding interactions, large electronic couplings, and high transport rates, which when taken together rationalize the better performance of OSCs based on Y6. | Grit Kupgan; XianKai Chen; Jean-Luc Bredas | Computational Chemistry and Modeling; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7574af96a0021b9288c2e/original/molecular-packing-of-non-fullerene-acceptors-for-organic-solar-cells-distinctive-local-morphology-in-y6-versus-itic-derivatives.pdf |
646f52d3e64f843f41c0996f | 10.26434/chemrxiv-2023-gx3fk | Electrophilic Activation of Molecular Bromine Mediated by I(III) | In pursuit of a genuine Bromo-λ3-iodane, it has been found that the combination of Br2 and electron deficient λ3-iodanes can result in delivery of both bromine atoms from Br2 to a range of aryl substrates, some highly deactivated. These brominations occur rapidly in common chlorinated solvents at room temperature and can be obtained with the catalytic activation of commercially available PhI(OAc)2 and PhI(OTFA)2. para-NO2 substituted derivatives are employed to direct bromination towards more deactivated substrates. The mechanism of Br2 activation is discussed with insights being made, however remains unclear. | Jason Dutton; Tania _; Lachlan Sharp-Bucknall; Lachlan Barwise | Organic Chemistry; Inorganic Chemistry; Organic Synthesis and Reactions; Main Group Chemistry (Inorg.) | CC BY NC 4.0 | CHEMRXIV | 2023-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646f52d3e64f843f41c0996f/original/electrophilic-activation-of-molecular-bromine-mediated-by-i-iii.pdf |
6362171caca198211beefbc9 | 10.26434/chemrxiv-2022-6pv54-v2 | Screening Unknown Novel Psychoactive Substances Using GC-MS Based Machine Learning | In recent years, there is a large increase in structural diversity of novel psychoactive substances (NPS), exacerbating drug abuse issues as these variants evade classical detection methods such as spectral library matching. Gas chromatography mass spectrometry (GC-MS) is commonly used to identify these NPS. To tackle this issue, machine learning models are developed to address the analytical challenge of identifying unknown NPS, using only GC-MS data. 891 GC-MS spectra are used to train and evaluate multiple supervised machine learning classifiers, namely artificial neural network (ANN), convolutional neural network (CNN) and balanced random forest (BRF). 7 classes, comprising 6 NPS classes (cathinone, cannabinoids, phenethylamine, piperazine, tryptamines and fentanyl) and other unrelated compounds can be effectively classified with a macro-F1 score ~ 0.9, averaged across all cross-validation folds. These results indicate that machine learning models are a promising complement as an effective NPS detection tool. | Swee Liang Wong; Justin Tan; Li Teng Ng; Jonathan Pan | Analytical Chemistry; Chemoinformatics; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6362171caca198211beefbc9/original/screening-unknown-novel-psychoactive-substances-using-gc-ms-based-machine-learning.pdf |
60c744a4bdbb895645a38865 | 10.26434/chemrxiv.9867776.v1 | Homopolymer Self-Assembly via Poly(propylene Sulfone) Networks | <p>Natural molecules such as peptides and DNA organize dynamically into hierarchical structures with diverse morphologies and sizes. The ability to mimic this self-assembly behavior in synthetic materials has remained an elusive goal. We report on poly(propylene sulfone), a synthetic homopolymer that self-assembles into nanoscale hydrogels of various morphologies including spherical, vesicular, and cylindrical in aqueous solution. Experiments and simulations demonstrate that while the polymer chains are roughly extended and minimally aggregated in DMSO, the addition of water overcomes the steric limitations imposed by the sulfones and induces formation of molecular networks through sulfone-sulfone bonding. Networks collapse and reorganize into distinct morphologies upon hydration, endowing an exceptional capability for capturing organic molecules. This simple system presents a robust platform for controlling nanofabrication.<br /></p> | Fanfan Du; Baofu Qiao; Sharan Bobbala; sijia yi; Monica Olvera de la Cruz; Evan Scott | Nanofabrication | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744a4bdbb895645a38865/original/homopolymer-self-assembly-via-poly-propylene-sulfone-networks.pdf |
64fbde1899918fe5379dfe07 | 10.26434/chemrxiv-2023-sbl1f | Nonlinear Dielectric Response of Dilute Protein Solutions | A theory for the nonlinear dielectric response of dilute protein solutions is presented. The field-dependent dielectric function of the protein solution changes linearly with the electric field squared in the lowest order. The slope of this dependence is expressed in terms of the protein dipole moment $M_0$, its volume fraction in solution $\eta_0$, and the second osmotic virial coefficient. For practical conditions, the nonlinear dielectric response scales as $\eta_0^3 M_0^8$. This strong dependence on the protein dipole moment and concentration establishes a sharp contrast between the nonlinear response of solvated proteins relative to the surrounding polar solvent. Nonlinear dielectric response can serve as a sensitive tool for monitoring protein conformations and physiological activity. | Dmitry Matyushov | Physical Chemistry; Biophysical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64fbde1899918fe5379dfe07/original/nonlinear-dielectric-response-of-dilute-protein-solutions.pdf |
60c757b0469df4f367f45500 | 10.26434/chemrxiv.14450580.v1 | Catalytic Radical-Polar Crossover Ritter Reaction | A catalytic radical-polar crossover Ritter reaction is described. The transformation proceeds under acid-free conditions and tolerates a variety of functional groups. The catalyst design overcomes limitations in the substitution pattern of starting materials and enables hydroamidation of a diverse range of alkenes. Formation of hydrogen contributes to the background consumption of reductant and oxidant and competes with the desired pathway, pointing to a mechanistic link between hydrogen atom transfer-initiated organic reactions and hydrogen evolution catalysis. | Eric Touney; Riley Cooper; Sarah Bredenkamp; David George; Sergey Pronin | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757b0469df4f367f45500/original/catalytic-radical-polar-crossover-ritter-reaction.pdf |
63c24a057410255988eefa69 | 10.26434/chemrxiv-2023-8xsbj | Photo-redox Catalyzed C-S and C-C Bond Forming Cascade Cy-clization/Dearomatization of Biaryls: Sustainable Route to Func-tionalized Spirocyclohexa[5.5] and [4.5]trienones | An efficient approach towards photo-oxidative cascade cyclization reaction between biaryls and AgSCF3 or ArSSAr or Ar-SO2H or ArCOCO2H is reported to obtain structurally diverse SCF3 or SAr or SO2Ar or COAr containing spirotrienone using 0.1 mol% RFTA as a photocatalyst under visible light irradiation. Single-crystal X-ray diffraction analysis was performed to confirm the final product. A series of control experiments, UV and fluorescence quenching study, radical inhibition experi-ments were performed to establish the reaction mechanism. | Barnali Roy; Debayan Sarkar | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c24a057410255988eefa69/original/photo-redox-catalyzed-c-s-and-c-c-bond-forming-cascade-cy-clization-dearomatization-of-biaryls-sustainable-route-to-func-tionalized-spirocyclohexa-5-5-and-4-5-trienones.pdf |
67371f585a82cea2fa33848f | 10.26434/chemrxiv-2024-n3zvr | Pseudo-Lithium Vacancies in Hydrogen Rich Li3OCl | The antiperovskite Li3OCl is a Li-ion solid electrolyte that has shown a wide variety of properties over a large range of temperatures. Previous reports align Li3OCl as a superionic conductor, however reproducibility has been poor due to its hygroscopic nature suggesting that reports are in fact, Li3 – xOHxCl. Most studies in the literature focus on pure Li3OCl however, and do not take into account the role of hydrogen in the material. Here, we develop a full defect model of H-doped Li3OCl, showing that the nominal Schottky disorder diminishes with hydrogen incorporation. Additionally, H helps to facilitate Li-ion mobility in Li3OCl by firstly introducing rotatable OH species as well as forming HLi which relaxes off site to form what we define as a “pseudo-VLi” enhancing the ionic conductivity in line with experimentally observed values. Intentional hydrogen doping of hygroscopic materials constitute an underexplored strategy for enhancing ionic transport properties. | Benjamin Williamson; Kristoffer Eggestad; Sverre Selbach | Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67371f585a82cea2fa33848f/original/pseudo-lithium-vacancies-in-hydrogen-rich-li3o-cl.pdf |
6580a28d66c13817298481a4 | 10.26434/chemrxiv-2023-gft5p | Balancing Group I Monoatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field | Molecular dynamics (MD) simulations are a commonly used method for investigating molecular behavior at the atomic level. Achieving reliable MD simulation results necessitates the use of an accurate force field. In the present work, we present a new protocol to enhance the quality of group 1 monoatomic ions (specifically Li+, Na+, K+, Rb+, and Cs+) with respect to their interactions with common polar model compounds in biomolecules in condensed phases in the context of the Drude polarizable force field. Instead of adjusting pre-existing individual parameters for ions, model compounds, and water, we employ atom-pair specific LJ (known as NBFIX in CHARMM) and through-space Thole dipole screening (NBTHOLE) terms to fine-tune the balance of ion-model compound, ion-water, and model compound-water interactions. This involved establishing a protocol for the optimization of NBFIX and NBTHOLE parameters targeting the difference between molecular mechanical (MM) and quantum mechanical (QM) potential energy scans (PES). It is shown that targeting PES involving complexes that include multiple model compounds and/or ions as trimers and tetramers yields parameters that produce condensed phase properties in agreement with experimental data. Validation of this protocol involved the reproduction of experimental thermodynamic benchmarks, including solvation free energies of ions in methanol and N-methyl acetamide, osmotic pressures, ionic conductivities, and diffusion coefficients within the condensed phase. These results show the importance of including more complex ion-model compound complexes beyond dimers in the QM target data to account for many-body effects during parameter fitting. The presented parameters represent a significant refinement of the Drude polarizable force field, which will lead to improved accuracy for modeling ion-biomolecular interactions. | Yiling Nan; Alex MacKerell | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6580a28d66c13817298481a4/original/balancing-group-i-monoatomic-ion-polar-compound-interactions-for-condensed-phase-simulation-in-the-polarizable-drude-force-field.pdf |
63a03fa0e8047a5117ee50d5 | 10.26434/chemrxiv-2022-9vvst | Mechanistic Studies of the Palladium-Catalyzed S,O-Ligand promoted C-H Olefination of Aromatic Compounds | Pd-catalyzed C-H functionalization reactions of non-directed substrates have recently emerged as an attractive alternative to the use of directing groups. Key to the success of these transformations has been the discovery of new ligands capable of increasing both the reactivity of the inert C-H bond and the selectivity of the process. Among them, a new type of S,O-ligand has shown to be highly efficient in promoting a variety of Pd-catalyzed C-H olefination reactions of non-directed arenes. Despite the success of this type of S,O-ligand, its role in the C-H functionalization processes is unknown. Herein, we describe a detailed mechanistic study focused on elucidating the role of the S,O-ligand in the Pd-catalyzed C-H olefination of non-directed arenes. For this purpose, several mechanistic tools, including isolation and characterization of reactive intermediates, NMR and kinetic studies, isotope effects and DFT calculations have been employed. The data from these experiments suggest that the C-H activation is the rate-determining step in both cases with and without the S,O-ligand. Furthermore, the results indicate that the S,O-ligand triggers the formation of more reactive Pd cationic species, which explains the observed acceleration of the reaction. Together, these studies shed light on the role of the S,O-ligand in promoting Pd-catalyzed C-H functionalization reactions | Kananat Naksomboon; Enrique Gómez-Bengoa; Jaya Mehara; Jana Roithová; Edwin Otten; María Ángeles Fernández-Ibáñez | Organic Chemistry; Catalysis; Physical Organic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a03fa0e8047a5117ee50d5/original/mechanistic-studies-of-the-palladium-catalyzed-s-o-ligand-promoted-c-h-olefination-of-aromatic-compounds.pdf |
60c74164f96a006d12286419 | 10.26434/chemrxiv.8028134.v1 | A New Interpretation of the Structure and Solvent Dependence of the Far UV Circular Dichroism Spectrum of Short Oligopeptides | In this work, we carry out new time-dependent density functional theory calculations on the cationic tripeptide GAG in implicit and explicit water to determine the transitions that give rise to the observed CD signals of polyproline II and β-strand conformations. Our results reveal a plethora of electronic transitions that are governed by configurational interactions between multiple molecular orbital transitions of comparable energy. We also show that reproducing the CD spectra of polyproline II and β-strand conformations requires the explicit consideration of water molecules. The structure dependence of delocalized occupied orbitals contributes to the experimentally-observed invalidation of Flory’s isolated pair hypothesis. | Anshuman Kumar; Reinhard Schweitzer-Stenner; Bryan Wong | Biochemistry; Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74164f96a006d12286419/original/a-new-interpretation-of-the-structure-and-solvent-dependence-of-the-far-uv-circular-dichroism-spectrum-of-short-oligopeptides.pdf |
60c748d0ee301c1d5cc7997e | 10.26434/chemrxiv.11981622.v1 | Meta-Learning Initializations for Low-Resource Drug Discovery | Building in silico models to predict chemical properties and activities is a crucial step in drug discovery. However, drug discovery projects are often characterized by limited labeled data, hindering the applications of deep learning in
this setting. Meanwhile advances in meta-learning have enabled state-of-the-art
performances in few-shot learning benchmarks, naturally prompting the question: Can meta-learning improve deep learning performance in low-resource
drug discovery projects? In this work, we assess the efficiency of the Model-Agnostic Meta-Learning (MAML) algorithm – along with its variants FO-MAML
and ANIL – at learning to predict chemical properties and activities. Using the
ChEMBL20 dataset to emulate low-resource settings, our benchmark shows that
meta-initializations perform comparably to or outperform multi-task pre-training
baselines on 16 out of 20 in-distribution tasks and on all out-of-distribution tasks,
providing an average improvement in AUPRC of 7.2% and 14.9% respectively.
Finally, we observe that meta-initializations consistently result in the best performing models across fine-tuning sets with k ∈ {16, 32, 64, 128, 256} instances.<br /> | Cuong Q. Nguyen; Constantine Kreatsoulas; Kim M. Branson | Chemoinformatics; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748d0ee301c1d5cc7997e/original/meta-learning-initializations-for-low-resource-drug-discovery.pdf |
67c60f51fa469535b9c9764d | 10.26434/chemrxiv-2025-qh8p1 | Deciphering self-assembly mechanisms of IRMOF-n-inspired three-dimensional cubic-symmetry nanoporous crystals from multiscale simulations | The formation mechanisms of metal-organic frameworks (MOFs) are not fully understood. Therefore, experimental realization of potential “breakthrough” MOFs is hindered by uncertainty on the synthesis conditions that would allow the constituent nodes and linkers to self-assemble into the targeted MOF structure. Here, a multiscale endeavor using density functional theory (DFT) calculations, followed by metadynamics with DFT-informed classical atomistic potentials, followed by standard molecular dynamics (MD) and Hamiltonian replica exchange (HREX) simulations with a metadynamics-informed, coarse-grained (CG) model, was used to study the self-assembly mechanism of cubic-symmetry porous crystals inspired by the IRMOF-n family of MOFs. Mechanistic differences were examined for different values of node-linker coordination strength—understood as the free energy penalty for breaking a coordination bond in a solvated environment. Our integrated analyses of HREX-derived free energy surfaces and standard MD trajectories indicate that at coordination strengths typical of the IRMOF-n family in dimethylformamide (DMF) (i.e., 52 kJ/mol), disassembled nodes and linkers are favored to overcome a small 1.3 kJ/mol free energy barrier to first form solid amorphous clusters, which then overcome a series of barriers (the largest of which is 3.7 kJ/mol) to heal and form ordered, more stable, cubic-symmetry crystals. This healing seems to occur through the splintering/reattaching of small clusters from/to large clusters. Our analyses also suggest that if coordination strength is moderately weakened (e.g., to 40 kJ/mol), crystals form without the preliminary formation of amorphous clusters. However, further coordination strength weakening (e.g., to 36 kJ/mol) makes the formation of sizable crystals unfavorable thermodynamically. On the other hand, strengthening the coordination would increase the free energy barrier to heal the amorphous clusters into crystals. Accordingly, if coordination becomes too strong (e.g., 65+ kJ/mol), healing may become unlikely. In practical terms, our study suggests that MOF formation is favored only when the free energy of coordination, accounting for solvent effects, falls within a relatively narrow range (approximately 40 to 65 kJ/mol), at least at 300 K, for MOFs with cubic symmetries. | Katherine Ardila; Tsung-Wei Liu; Diego Gomez-Gualdron; Alexander Pak | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c60f51fa469535b9c9764d/original/deciphering-self-assembly-mechanisms-of-irmof-n-inspired-three-dimensional-cubic-symmetry-nanoporous-crystals-from-multiscale-simulations.pdf |
67988dcc6dde43c908af2f28 | 10.26434/chemrxiv-2025-gwdd6 | Uncovering the Individual Hydrogen Bond Strengths and Cooperativity in Pure (H2S)n and Mixed (H2O)m(H2S)n (m + n = 2 to 8) Clusters | The present investigation deals with the estimation individual hydrogen bond (HB) energ¬¬y in pure (H2S)n (n = 3 to 8) and mixed (H2O)m(H2S)n (m + n = 2 to 8) clusters. A deeper understanding of individual interactions in these clusters are brought out in terms of energetics. Such a knowledge from the experimental studies is difficult. Therefore, the present investigation is important. The calculated results show that the hydrogen bonding strengths in these clusters range from 0.10 to 11.06 kcal mol-1 at the MP2(full)/aug-cc-pVTZ level. The O-H…O HB being the strongest (0.10 to 11.06 kcal mol-1), followed by O-H…S HB (1.36 to 6.89 kcal/mol), S-H…O HB (1.08 to 6.39 kcal mol-1), and S-H…S HB (1.35 to 4.23 kcal mol-1) being the weakest. The hydrogen bonding energies in dimers follow the same rank ordering, with lower energies due to the loss of cooperativity. Thus, cooperativity contributions in the hydrogen bonding range from 0.83 to 5.96 kcal mol-1. The HB energies in pure (H2S)n clusters are similar but slightly smaller compared to those in mixed (H2O)m(H2S)n (m + n = 2 to 8) clusters. These results provide important insights into the structure and energetics of hydrogen bonding in pure and mixed clusters, and sheds light on the various interactions in chemical and biological systems. Such a profound knowledge of individual energetics is missing from the literature. | Deepak Patkar | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Chemical Education - General; Computational Chemistry and Modeling; Clusters | CC BY 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67988dcc6dde43c908af2f28/original/uncovering-the-individual-hydrogen-bond-strengths-and-cooperativity-in-pure-h2s-n-and-mixed-h2o-m-h2s-n-m-n-2-to-8-clusters.pdf |
6372559d56c6f4150e6ceef0 | 10.26434/chemrxiv-2022-dm96r | Total Synthesis of Pargamicin A | We report the total synthesis and configurational assignment of pargamicin A, a highly oxidized non-ribosomal peptide that potently inhibits the growth of drug-resistant bacteria. Our synthetic approach relies on late-stage piperazine ring formation and careful selection of condensation reagents to assemble the densely substituted hexapeptide backbone. This work enables the synthesis of pargamicin congeners for the development of structure-activity relationships and informs strategies to access other sterically congested piperazic acid-containing natural products. | Yassin Elbatrawi; Taylor Gerrein; Avraz Anwar; Kamlesh Makwana; David Degen; Richard Ebright; Juan Del Valle | Organic Chemistry; Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6372559d56c6f4150e6ceef0/original/total-synthesis-of-pargamicin-a.pdf |
60c752efbdbb89a240a3a3ab | 10.26434/chemrxiv.13359437.v1 | Ionic Strength of the Liquid Phase of Different Sludge Streams in a Wastewater Treatment Plant | Data from literature were gathered to evaluate the composition of the liquid phase of the different streams in a wastewater treatment plant. Ionic strength were calculated from these data, and then discussed compared to existing literature. | Thomas Prot; Leon Korving; Mark van Loosdrecht | Water Purification | CC BY 4.0 | CHEMRXIV | 2020-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752efbdbb89a240a3a3ab/original/ionic-strength-of-the-liquid-phase-of-different-sludge-streams-in-a-wastewater-treatment-plant.pdf |
67ab41626dde43c90863e00a | 10.26434/chemrxiv-2025-pvztk | Multi-objective evolutionary strategy for improving semiempirical Hamiltonians in the study of enzymatic reactions at the QM/MM level of theory | Quantum mechanics/molecular mechanics (QM/MM) simulations are crucial for understanding enzymatic reactions, but their accuracy depends heavily on the quantum-mechanical method used. Semiempirical methods offer computational efficiency but often struggle with accuracy in complex systems. This work presents a novel multi-objective evolutionary strategy for optimizing semiempirical Hamiltonians, specifically designed to enhance their performance in enzymatic QM/MM simulations while remaining broadly applicable to condensed-phase systems. Our methodology combines automated parameter optimization, targeting \textit{ab initio} or density functional theory (DFT)-reference potential energy surfaces, atomic charges, and gradients, with comprehensive validation through minimum free energy path (MFEP) calculations. To demonstrate its effectiveness, we applied our approach to improve the GFN2-xTB Hamiltonian using two enzymatic systems that involve hydride transfer reactions where the activation energy barrier is severely underestimated: Crotonyl-CoA carboxylase/reductase (CCR) and dihydrofolate reductase (DHFR). The optimized parameters showed significant improvements in reproducing potential and free energy surfaces, closely matching higher-level DFT calculations. Through an efficient two-stage optimization process, we first developed parameters for CCR using reaction path data, then refined these parameters for DHFR by incorporating a targeted set of additional training geometries. This strategic approach minimized the computational cost while achieving accurate descriptions of both systems, as validated through QM/MM simulations using the Adaptive String Method (ASM). Our method represents an efficient approach for optimizing semiempirical methods to study larger systems and longer timescales, with potential applications in enzymatic reaction mechanisms studies, drug design, and enzyme engineering. | José Luís Velázquez-Libera; Rodrigo Recabarren; Esteban Vöhringer-Martinez; Yamisleydi Salgueiro; J. Javier Ruiz-Pernía; Julio Caballero; Iñaki Tuñón | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2025-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ab41626dde43c90863e00a/original/multi-objective-evolutionary-strategy-for-improving-semiempirical-hamiltonians-in-the-study-of-enzymatic-reactions-at-the-qm-mm-level-of-theory.pdf |
67c1ffff81d2151a027880b4 | 10.26434/chemrxiv-2025-qkmp5 | Plasmon-Induced Resonant Energy Transfer and Flat Band Formation in Fe and Co Doped Ni(II) Hydroxide for Efficient Photocatalytic Oxygen Evolution | Enhancing photocatalytic oxygen evolution is vital for renewable energy. In this work, we demonstrate how plasmon-induced resonant energy transfer (PIRET) from gold nanoparticles (AuNPs) to Fe and Co doped nickel hydroxide (Ni(OH)₂) can improve this process. PIRET involves the transfer of energy from excited AuNPs to nearby molecules, boosting their reactivity. We show that doping Ni(OH)₂ with Fe or Fe/Co reduces the band gap and forms flat bands, enabling efficient energy transfer and enhancing electronic properties. Our results show that NiFe layered double hydroxide (NiFeLDH) achieves superior oxygen evolution reaction (OER) activity than Ni(OH)₂ due to PIRET. This study demonstrates the crucial role of PIRET in enhancing plasmonic energy transfer and the synergistic effects of doping and AuNP coupling. These findings highlight the broader potential of material engineering in advancing efficient and sustainable energy technologies. | Benjamin Kaufold; Parisa Nematollahi ; Bernardo Barbiellini; Dirk Lamoen; Arun Bansil; Hana Cheng; Sijia Dong; Sanjeev Mukerjee | Physical Chemistry; Materials Science; Catalysis; Heterogeneous Catalysis; Photocatalysis; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c1ffff81d2151a027880b4/original/plasmon-induced-resonant-energy-transfer-and-flat-band-formation-in-fe-and-co-doped-ni-ii-hydroxide-for-efficient-photocatalytic-oxygen-evolution.pdf |
64b7cad9b605c6803bffc11c | 10.26434/chemrxiv-2023-vxpk5 | ChatGPT Generated Content and Similarity Index in Chemistry & Allied Sciences | The main objective of this study is to verify similarity index of ChatGPT generated content in the field of chemistry and its allied subjects. To complete this study twenty sub subjects of chemistry based on controlled vocabulary tools such as Dewey Decimal Classification (DDC) system, Sears List of Subject Headings and Library of Congress Subject Headings (LCSH) have considered for sample, followed by content generation and similarity check using iThenticate, Urkund and Turnitin. The percentage of matching paragraphs is relatively low as the three plagiarism software shows 12%, 1% and 5% respectively. | Deep Kumar Kirtania | Chemical Education | CC BY 4.0 | CHEMRXIV | 2023-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b7cad9b605c6803bffc11c/original/chat-gpt-generated-content-and-similarity-index-in-chemistry-allied-sciences.pdf |
65418516c573f893f18965dd | 10.26434/chemrxiv-2023-jj5jl | Exploring Alternate Methods to High-Level Vibrational Correction Calculations of NMR Spin-Spin Coupling Constants | Traditional nuclear magnetic resonance (NMR) calculations typically treat systems with a Born-Op penheimer-derived electronic wavefunction that is solved for a fixed nuclear geometry. One can numerically account for this neglected nuclear motion by averaging over property values for all nuclear geometries with a vibrational wavefunction and
adding this expectation value as a correction to an equilibrium property value. Presented are benchmark coupled-cluster singles and doubles (CCSD) vibrational corrections to spin-spin coupling constants (SSCCs) computed at the level of vibrational second-order perturbation theory (VPT2) using the vibrational averaging driver of the CFOUR program. As CCSD calculations of vibrational corrections are very costly, cheaper electronic structure methods are explored via a newly developed Python vibrational averaging program within the Dalton Project. Namely, the second-order polarisation propagator approximation (SOPPA) and density functional theory (DFT) with the B3LYP and PBE0 exchange-correlation functionals are compared to the benchmark CCSD//CCSD(T) and experimental values. CCSD//CCSD(T) corrections are also combined with literature CC3 equilibrium values to form the highest-order vibrationally corrected values available i.e. CC3//CCSD(T) + CCSD//CCSD(T). CCSD//CCSD(T) statistics showed favourable statistics in comparison to experimental values, albeit at an unfavourably high computational cost. A cheaper CCSD//CCSD(T) + B3LYP method showed quite similar mean absolute deviation (MAD) values as CCSD//CCSD(T), concluding that CCSD//CCSD(T) + B3LYP is optimal in terms of cost and accuracy. With reference to experimental values, a vibrational correction was not worth the cost for all other methods tested. Finally, deviation statistics showed that CC3//CCSD(T) + CCSD//CCSD(T) vibrational corrected equilibrium values deteriorated in comparison to CCSD//CCSD(T) attributed to the use of a smaller basis and/or lack of solvation effects for the CC3 equilibrium calculations. | Ronan Gleeson; Patrick A. Aggelund; Frederik C. Østergaard; Kasper F. Schaltz; Stephan P. A. Sauer | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65418516c573f893f18965dd/original/exploring-alternate-methods-to-high-level-vibrational-correction-calculations-of-nmr-spin-spin-coupling-constants.pdf |
647fca3ebe16ad5c5793798e | 10.26434/chemrxiv-2023-frrq8 | Rapid Electron Transfer Self-Exchange in Conformationally Dynamic Copper Coordination Complexes | We report the electron transfer (ET) self-exchange rate constants (k11) for a pair of CuII/I complexes utilizing dpaR (dpa = dipicolylaniline, R = OMe, SMe) ligands assessed by NMR line-broadening experiments. These ligands afford copper complexes that are conformationally dynamic in one oxidation state. With R = OMe, the CuI complex is dynamic, while with R= SMe, the CuII complex is dynamic. Both complexes exhibit unexpectedly large k11 of 2.48(6) x 105 and 2.21(9) × 106 M‒1 s‒1 for [CuCl(dpaOMe)]+/0 and [CuCl(dpaSMe)]+/0, respectively. Among the fastest reported for molecular copper coordination complexes to date, that of [CuCl(dpaSMe)]+/0 exceeds all others by an order of magnitude and compares only to those observed in type 1 blue copper proteins. The dynamicity of these complexes establish pre-steady-state con-formational equilibria that minimize the inner sphere reorganization energies to 0.71 and 0.62 eV for R = OMe and SMe, respectively. In contrast to the emphasis on rigidity in the formulation of entatic states applied to blue copper proteins, the success of these two systems highlight the relevance of conformational dynamicity in mediating rapid ET. | Paul J. Griffin; Lisa Olshansky | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647fca3ebe16ad5c5793798e/original/rapid-electron-transfer-self-exchange-in-conformationally-dynamic-copper-coordination-complexes.pdf |
60c74d67702a9b9da518b84a | 10.26434/chemrxiv.12613823.v1 | Semisynthetic Analogs of the Antibiotic Fidaxomicin – Design, Synthesis, and Biological Evaluation | <p>The glycoslated macrocyclic antibiotic fidaxomicin (1, tiacumicin B, lipiarmycin A3) displays good
to excellent activity against Gram-positive bacteria and was approved for the treatment of Clostridium difficile
infections (CDI). Main limitations of the compound include low water solubility, which impacts further clinical
use. We report on the synthesis of new fidaxomicin derivatives based on structural design and utilizing an
operationally simple one-step protecting group-free preparative approach from the natural product. An increase
in solubility of up to 25-fold with largely retained activity was observed. Furthermore, hybrid antibiotics were
prepared that show improved antibiotic activities</p> | Andrea Dorst; Regina Berg; Christoph Gertzen; Daniel Schäfle; katja zerbe; myriam gwerder; Simon Schnell; Peter Sander; Holger Gohlke; Karl Gademann | Natural Products; Drug Discovery and Drug Delivery Systems; Microbiology; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d67702a9b9da518b84a/original/semisynthetic-analogs-of-the-antibiotic-fidaxomicin-design-synthesis-and-biological-evaluation.pdf |
650d6d25ed7d0eccc302ab62 | 10.26434/chemrxiv-2023-6tt1w | Carbon footprint and mitigation strategies of three chemistry laboratories | As the global imperative for decarbonization gains momentum, the need for action in chemistry laboratories becomes increasingly apparent. This study examines the 2019 carbon footprint of three French chemistry laboratories encompassing energy, purchases, travels, and commutes. The average per capita carbon footprint stands at 5.6 teqCO2/year, positioning chemistry laboratories slightly above the median calculated across all disciplines. Key contributors are purchases (31–42%) and heating (23–33%), driven by fume hoods, heavy equipment and consumables. Attainable mitigations strategies suggest a 40-50% reduction by 2030. Pivotal efforts involve transitioning heating sources to renewables, extending equipment lifespan, collaborative resource management, as well as a limitation in the use of planes and thermic cars. Such changes imply actions at the level of the government, the university and the individual. We suggest fostering a sustainable research environment in chemistry laboratories by rationalizing experimental practices and dedicating time to consider the socio-environmental implications of research. | Andre Estevez-Torres; Fabienne Gauffre; Guillaume Gouget; Chloé Grazon; Philippe Loubet | Earth, Space, and Environmental Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650d6d25ed7d0eccc302ab62/original/carbon-footprint-and-mitigation-strategies-of-three-chemistry-laboratories.pdf |
6542737948dad23120db4b51 | 10.26434/chemrxiv-2023-gv3j7 | Highly Efficient Bulk-Crystal-Sized Exfoliation of 2D Materials under Ultra-High Vacuum | Two-dimensional (2D) materials represent the ultimate limit of miniaturization along the vertical direction, where several fascinating quantum mechanical effects—that are otherwise inaccessible—appear, generating widespread interest in fundamental and applied research. However, the preparation of scalable monolayers is a requirement that is hindered because of the lack of suitable synthesis and manipulation techniques. Here, we report a facile approach for obtaining bulk-crystal-sized 2D monolayers with a yield of almost 100% under ultra-high vacuum (UHV) conditions. We have exfoliated MoS2 on Au and Ag substrates to demonstrate the exfoliation process, where the spectroscopic measurements suggest a very strong dispersive interaction between the metal substrate and MoS2, resulting in a high strain field on the topmost layer of the bulk crystal, which is substantially relaxed in the subsequent layer. This vertically inhomogeneous distribution of the strain field reduced the magnitude of interlayer van der Waals interactions, resulting in the high selectivity of monolayer exfoliation. Along with the scalable exfoliation of monolayers, our method also paves a route to obtain 2D monolayers of materials that are unstable under ambient conditions. | Golam Haider; Bazlul Karim; Jan Plšek ; Michele Gastaldo; Martin Kalbac | Physical Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6542737948dad23120db4b51/original/highly-efficient-bulk-crystal-sized-exfoliation-of-2d-materials-under-ultra-high-vacuum.pdf |
6512c22fa69febde9eb5f493 | 10.26434/chemrxiv-2023-fm8zb-v2 | A Guanidium Salt as a Chaotropic Agent for Aqueous Battery Electrolytes | This study investigates a salt design principle for aqueous battery electrolytes by combining chaotropic ions, guanidium cations (Gdm) and bis(trifluoromethanesulfonyl)imide anions (TFSI), forming GdmTFSI. This salt's crystal structure was solved via single-crystal X-ray diffraction and characterized using Fourier-transform infrared spectroscopy. Study reveals that GdmTFSI salt disrupts the hydrogen bonding network of aqueous solutions, impacting water reactivity at electrochemical interfaces. | John Brown; Juan Forero-Saboya; Benoît Baptise; Martin Karlsmo; Gwenaëlle Rousse ; Alexis Grimaud | Organic Chemistry; Energy; Energy Storage; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6512c22fa69febde9eb5f493/original/a-guanidium-salt-as-a-chaotropic-agent-for-aqueous-battery-electrolytes.pdf |
65e5ed7866c13817292d123f | 10.26434/chemrxiv-2024-l0q8c | Non-volatile resistive switching in nanoscaled elemental tellurium by vapor transport deposition on gold | Two-dimensional (2D) materials are highly promising as resistive switching materials for neuromorphic and in-memory computing owing to their fascinating properties derived from their low thickness. However, most of the reported 2D resistive switching materials struggle with complex growth methods or limited growth area. Tellurium, a novel member of single-element 2D materials, is showing pioneering characteristics such as simplicity in chemistry, structure, and synthesis which make it highly suitable for various applications. This study presents the first memristor design based on nanoscaled elemental tellurium synthesized by vapor transport deposition (VTD) method at a temperature as low as 100 °C in full compliance with a back-end-of-line (BEOL) processing. We demonstrate that the memristive behavior of nanoscaled tellurium can be enhanced by selecting gold as the substrate material which results in a lower set voltage and reduced energy consumption. In addition, the formation of conductive paths which in turn lead to resistive switching behavior on the gold substrate is proven to be driven by the gold-tellurium interface reconfiguration during the VTD process as revealed by energy electron loss spectroscopy analysis of the interface. Our findings reveal the potential of nanoscaled tellurium as a versatile and scalable material for neuromorphic computing systems as well as the influential role of gold as electrode material in enhancing tellurium’s memristive performance. | Sara Ghomi; Christian Martella; Yoonseok Lee; Paolo Targa; Andrea Serafini; Davide Codegoni; Chiara Massetti; Sepideh Gharedaghi; Alessio Lamperti; Carlo Grazianetti; Deji Akinwande; Alessandro Molle | Materials Science; Nanoscience; Nanostructured Materials - Materials; Thin Films; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e5ed7866c13817292d123f/original/non-volatile-resistive-switching-in-nanoscaled-elemental-tellurium-by-vapor-transport-deposition-on-gold.pdf |
60c743b4f96a004993286862 | 10.26434/chemrxiv.9582527.v1 | A Ruthenium(II) Complex Containing a Redox-Active Semiquinonate Ligand as Potential Chemotherapeutic Agent: From Synthesis to In Vivo Studies | Chemotherapy remains one of the dominant treatments to cure cancer. However, due to the many inherent drawbacks, there is a surge for new chemotherapeutic drugs. More specifically, the discovery of new drug candidates able to overcome severe side effects, the occurrence of resistance and the inefficacy toward metastatic tumours is highly desirable. In this work, we designed a new chemotherapeutic drug candidate against cancer, namely [Ru(DIP)2(sq)]PF6 (Ru-sq) (DIP = 4,7-diphenyl-1,10-phenanthroline; sq = semiquinonate ligand). The aim was to combine the great potential expressed by Ru(II) polypyridyl complexes and the singular redox and biological properties associated to the catecholate moiety. Several pieces of experimental evidence (e.g., X-ray crystallography, electron paramagnetic resonance, electrochemistry) demonstrate that the semiquinonate is the preferred oxidation state of the dioxo ligand in this complex. The biological activity of Ru-sq was then scrutinised in vitro and in vivo, and the results highlight the tremendous potential of this complex as a chemotherapeutic agent against cancer. Ru-sq was notably found have a much higher cytotoxic activity than cisplatin on several cell lines (i.e. in the nanomolar range), and, contrary to cisplatin, to have mitochondrial disfunction as one of its modes of action. The multicellular targets of Ru-sq could potentially be the key to overcome one of the main drawbacks of cisplatin i.e. the occurrence of resistance. Moreover, Ru-sq exhibited impressing activity on Multi Cellular Tumour Spheroids (MCTS) model, leading to a growth inhibition of the tumour even 13 days after treatment (20 μM). Very importantly, using two different in vivo models, it could be demonstrated that this compound is extremely well-tolerated by mice and has a very promising activity, curing, in some cases, tumour-bearing mice.<br /> | Anna Notaro; Angelo Frei; Riccardo Rubbiani; Marta Jakubaszek; Uttara Basu; Severin Koch; Cristina Mari; Mazzarine Dotou; Olivier Blacque; Jérémie Gouyon; Fethi Bedioui; Nils Rotthowe; Rainer
F. Winter; Bruno Goud; Stefano Ferrari; Mickaël Tharaud; Martina Řezáčová; Jana Humajová; Pavel Tomšík; Gilles Gasser | Bioinorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b4f96a004993286862/original/a-ruthenium-ii-complex-containing-a-redox-active-semiquinonate-ligand-as-potential-chemotherapeutic-agent-from-synthesis-to-in-vivo-studies.pdf |
60c741254c89195e0cad2263 | 10.26434/chemrxiv.7965128.v1 | The Concept of Essential Use for Determining When Uses of PFASs Can Be Phased Out | Because of the extreme persistence of per- and polyfluoroalkyl substances (PFASs) and their
associated risks, the Madrid Statement argues for stopping their use where they are deemed
not essential or when safer alternatives exist. To determine when uses of PFASs have an
essential function in modern society, and when they do not, is not an easy task. Here, we: 1)
develop the concept of “essential use” based on an existing approach described in the Montreal
Protocol, 2) apply the concept to various uses of PFASs to determine the feasibility of
elimination or substitution of PFASs in each use category, and 3) outline the challenges for
phasing out uses of PFASs in society. In brief, we developed three distinct categories to
describe the different levels of essentiality of individual uses. A phase-out of many uses of
PFASs can be implemented because they are not necessary for the betterment of society in
terms of health and safety, or because functional alternatives are currently available that can
be substituted into these products or applications. Some specific uses of PFASs would be
considered essential because they provide for vital functions and are currently without
established alternatives. However, this essentiality should not be considered as permanent;
rather, constant efforts are needed to search for alternatives. We provide a detailed description
of several ongoing uses of PFASs and discuss whether these uses are essential or nonessential according to the three essentiality categories. We suggest applying this concept of
essential uses to all uses of PFASs, and considering its use also for other chemicals of concern. | Ian Cousins; Gretta Goldenman; Dorte Herzke; Rainer Lohmann; Mark Miller; Carla A. Ng; Sharyle Patton; Martin Scheringer; Xenia Trier; Lena Vierke; Zhanyun Wang; Jamie DeWitt | Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741254c89195e0cad2263/original/the-concept-of-essential-use-for-determining-when-uses-of-pfa-ss-can-be-phased-out.pdf |
66d8528f12ff75c3a15efe60 | 10.26434/chemrxiv-2024-s0mmw | A combined experimental and computational exploration of heteroleptic cis-Pd2L2L’2 coordination cages through geometric complementarity | Heteroleptic (mixed-ligand) coordination cages are of interest as host systems with more structurally and functionally complex cavities than homoleptic architectures. The design of heteroleptic cages, however, is far from trivial. In this work, we experimentally probed the self-assembly of Pd(II) ions with binary ligand combinations in a combinatorial fashion to search for new cis-Pd2L2L’2 heteroleptic cages. A hierarchy of computational analyses was then applied to these systems with the aim of elucidating key factors for rationalising self-assembly outcomes. Simple and inexpensive geometric analyses were shown to be effective in identifying complementary ligand pairs. Preliminary results demonstrated the viability of relatively rapid semi-empirical calculations for predicting the topology of thermodynamically favoured assemblies with rigid ligands, whilst more flexible systems proved challenging. Stemming from this, key challenges were identified for future work developing effective computational forecasting tools for self-assembled metallo-supramolecular systems. | Andrew Tarzia; Wentao Shan; Victor Posligua; Cameron Cox; Louise Male; Benjamin Egleston; Rebecca Greenaway; Kim Jelfs; James Lewis | Theoretical and Computational Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d8528f12ff75c3a15efe60/original/a-combined-experimental-and-computational-exploration-of-heteroleptic-cis-pd2l2l-2-coordination-cages-through-geometric-complementarity.pdf |
60c73d0fbb8c1a36933d96a8 | 10.26434/chemrxiv.5439880.v1 | First-Principles Evaluation of the Potential of Borophene as a Monolayer Transparent Conductor | Two-dimensional
boron is promising as a tunable monolayer metal for nano-optoelectronics. We study
the optoelectronic properties of two likely allotropes of two-dimensional boron using
first-principles density functional theory and many-body perturbation theory. We
find that both systems are anisotropic metals, with strong energy- and thickness-dependent
optical transparency and a weak (<1%) absorbance in the visible range.
Additionally, using state-of-the-art methods for the description of the
electron-phonon and electron-electron interactions, we show that the electrical
conductivity is limited by electron-phonon interactions. Our results indicate
that both structures are suitable as a transparent electrode. | Lyudmyla Adamska; Sridhar Sadasivam; Jonathan J. Foley; Pierre Darancet; Sahar Sharifzadeh | Optics; Quantum Mechanics; Quasiparticles and Excitations; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2017-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d0fbb8c1a36933d96a8/original/first-principles-evaluation-of-the-potential-of-borophene-as-a-monolayer-transparent-conductor.pdf |
62839aa56cae1ce1f00d0b8e | 10.26434/chemrxiv-2022-skbjz | UV Light is no Longer Required for the Activation of 1,3,4-Oxadiazolines | Carbenes play a key role in a plethora of organic transformations. Although stabilized diazo carbonyl compounds predominate as a source of electrophilic carbenes, the hazardous nature of non-stabilized analogues calls for their in situ generation from stable precursors. Among these, 1,3,4-oxadiazolines serve as diazoalkane surrogates under UV light irradiation. In view of their diverse reactivities and straightforward synthesis, milder methodologies for the activation of these compounds, that permit the use of UV light-sensitive substrates, are of high significance. Herein, we report the visible-light-induced activation of oxadiazolines by triplet energy transfer catalysis that, in contrast to UV-induced processes, enables generation of carbenes. The formed reactive species react with electron-poor olefins, giving valuable spirocyclopropanes. Mechanistic investigations, both theoretical and experimental, uncover plausible pathways and highlight the importance of the triplet energy-transfer steps. | Katarzyna Orłowska; Joao Victor Santiago; Piotr Krajewski; Irena Deperasińska; Katarzyna Zawada; Wojciech Chaładaj; Dorota Gryko | Organic Chemistry; Catalysis; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62839aa56cae1ce1f00d0b8e/original/uv-light-is-no-longer-required-for-the-activation-of-1-3-4-oxadiazolines.pdf |
64f4f087dd1a73847f1da191 | 10.26434/chemrxiv-2023-l2jq2 | A Palladium Cluster-Organic Framework | Acquiring spatial control of nanoscopic metal clusters is central to their function as efficient multi-electron catalysts. However, dispersing metal clusters on surfaces or in porous hosts is accompanied by an intrinsic heterogeneity that hampers detailed understanding of the chemical structure and its relation to reactivities. Tethering pre-assembled molecular metal clusters into polymeric, crystalline 2D or 3D networks constitutes an unproven approach to realizing ordered arrays of chemically well-defined metal clusters. Herein, we report the facile synthesis of a {Pd3} cluster-based organometallic framework from a molecular triangulo-Pd3(CNXyl)6 (Xyl = xylyl; Pd3) cluster under chemically mild conditions. The formally zero-valent Pd3 cluster readily engages in a complete ligand exchange when exposed to a chemically similar, ditopic isocyanide ligand, resulting in the spontaneous polymerization into a 2D coordination network (Pd3-MOF). The structure of Pd3-MOF could be unambiguously determined by continuous rotation 3D electron diffraction (3D-ED) experiments to an overall resolution of ~1.0 Å (>99% completeness), showcasing the applicability of 3D-ED to nanocrystalline, organometallic polymers. Importantly, the realization of Pd3-MOF paves the way for the exploitation of metal clusters as building blocks for rigidly interlocked metal nanoparticles at the molecular limit. | Xiyue Liu; James N. McPherson; Carl Emil Andersen; Mike S. B. Jørgensen; René Wugt Larsen; Fabrice Wilhelm; Andrei Rogalev; Christian Göb; Kasper Steen Pedersen | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Coordination Chemistry (Organomet.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f4f087dd1a73847f1da191/original/a-palladium-cluster-organic-framework.pdf |
615c1d4fcada1f7446cbe0b8 | 10.26434/chemrxiv-2021-00rj4 | Electrochemical Ozone Generation Using Compacted High Pressure High Temperature Boron Doped Diamond Microparticle Electrodes | Electrochemical ozone production (EOP) from water is an attractive, green technology for disinfection. Boron doped diamond (BDD) electrodes, grown by chemical vapor deposition (CVD), have been widely adopted for EOP due to their wide anodic window in water and excellent chemical and electrochemical stability. High pressure high temperature (HPHT) synthesis, an alternative growth technique used predominantly for the high-volume synthesis of nitrogen doped diamond microparticles, has been seldom employed for the production of conductive BDD electrodes. In this letter, we demonstrate, for the first time, the use of BDD electrodes fabricated from HPHT conductive BDD microparticles for EOP. The BDD microparticles are first compacted to produce freestanding solid electrodes and then laser micromachined to produce a perforated electrode. The HPHT BDD electrodes are shown to exhibit high EOP, producing 2.23 ± 0.07 mg L-1 of ozone per ampere of current, at consistent levels for a continuous 20 hr period with no drop off in performance. | Georgia Wood; Irina Terrero Rodriguez; Josh Tully; Shayantan Chaudhuri ; Julie Macpherson | Materials Science; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Materials Processing; Water Purification | CC BY NC 4.0 | CHEMRXIV | 2021-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615c1d4fcada1f7446cbe0b8/original/electrochemical-ozone-generation-using-compacted-high-pressure-high-temperature-boron-doped-diamond-microparticle-electrodes.pdf |
66ac73ff01103d79c588de38 | 10.26434/chemrxiv-2024-gqgm3 | Stable Monometallic Ir(I) complexes of Porphycene through β,β'-Bipyrrole Fusion | Iridium complexation was investigated for β-tetraisopropyldinaphthoporphycene. Use of 1,5-cyclooctadiene and dimethylformamide separately as solvents led to the formation of Ir(I) complex with COD as a secondary ligand, and an additional complex where COD is oxidized. These are the first examples of complexes of porphycene or its isomers, where in-core iridium is stabilized in +1 oxidation state without any carbonyl ligands. The latter complex found to be stable under aerobic conditions at elevated temperature. Details of synthesis, characterization and photophysical properties of the Ir(I) complexes are presented here. | Sameeta Sahoo; Pradeepta Panda | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ac73ff01103d79c588de38/original/stable-monometallic-ir-i-complexes-of-porphycene-through-bipyrrole-fusion.pdf |
61e5458577a416290cd42881 | 10.26434/chemrxiv-2022-x731g-v2 | DNA-Liposome Hybrid Carriers for Triggered
Cargo Release | The encapsulation of chemotherapeutics by biocompatible carrier structures holds great promise to preserve their therapeutic activity and favor their delivery to tumor sites. To enhance the bioavailability of a drug at the targeted tissue, triggered release mechanisms have received increasing research interest. Many approaches rely on exogeneous triggers such as the irradiation of ultrasound, visible or even ionizing electromagnetic waves. However, such exogenous triggers can be challenging to implement in a specific manner. Therefore, designing carriers responsive to endogenous moieties, such as nucleic acid biomarkers, is a desirable step in the search of personalized drug delivery nanoplatforms. This study presents an approach to building a biocompatible DNA-liposome hybrid nanocarrier for potential triggered release purposes. We form a DNA mesh on large unilamellar liposomes incorporating a trigger-responsive DNA building block. Upon incubation with a single-stranded DNA trigger sequence a hairpin closes and the building block is allowed to self-contract. By this process, we demonstrate elevated release of the dye calcein and the drug doxorubicin. The incubation of the doxorubicin-laden active hybrid carrier with HEK293T cells suggests increased cytotoxicity relative to a control carrier without the triggered release mechanism. In the future, the trigger could be provided by peritumoral nucleic acid sequences and lead to site-selective release of encapsulated chemotherapeutics. | Kevin N. Baumann; Tim Schröder; Prashanth S. Ciryam; Diana Morzy; Philip Tinnefeld; Tuomas P. J. Knowles; Silvia Hernández-Ainsa | Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e5458577a416290cd42881/original/dna-liposome-hybrid-carriers-for-triggered-cargo-release.pdf |
60c74db9469df47d33f44340 | 10.26434/chemrxiv.12650009.v1 | Ligand-Controlled Regiodivergence in Nickel-Catalyzed Hydroarylation and Hydroalkenylation of Alkenyl Carboxylic Acids | <div>A nickel-catalyzed regiodivergent hydroarylation and hydroalkenylation of unactivated alkenyl carboxylic acids is reported, whereby the ligand environment around the metal center dictates the regiochemical outcome. Markovnikov hydrofunctionalization products are obtained under mild ligand-free conditions, with up to 99% yield and >20:1 selectivity. Alternatively, anti-Markovnikov products can be accessed with a novel 4,4-disubstituted Pyrox ligand in excellent yield and >20:1 selectivity. Both electronic and steric effects on the ligand contribute to the high yield and selectivity. Mechanistic studies suggest a change in the turnover-limiting and selectivity-determining step induced by the optimal ligand. DFT calculations reveal that in the anti-Markovnikov pathway, repulsion between the ligand and the alkyl group is minimized (by virtue of it being 1° versus 2°) in the rate- and regioselectivity-determining transmetalation transition state. <br /></div> | Zi-Qi Li; Yue Fu; Ruohan Deng; Van Tran; Yang Gao; Peng Liu; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Theory - Computational; Homogeneous Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db9469df47d33f44340/original/ligand-controlled-regiodivergence-in-nickel-catalyzed-hydroarylation-and-hydroalkenylation-of-alkenyl-carboxylic-acids.pdf |
60c74377ee301c062fc78ff2 | 10.26434/chemrxiv.9209450.v1 | Structural Evidence of Photoisomerization Pathways in Fluorescent Proteins | <p>Double-bond photoisomerization in
molecules such as the green fluorescent protein (GFP) chromophore can occur
either via a volume-demanding one-bond-flip pathway or via a volume-conserving
hula-twist pathway. Understanding the factors that determine the pathway of photoisomerization
would inform the rational design of photoswitchable GFPs as improved tools for
super-resolution microscopy. In this communication, we reveal the
photoisomerization pathway of a photoswitchable GFP, rsEGFP2, by solving
crystal structures of <i>cis</i> and <i>trans</i> rsEGFP2 containing a
monochlorinated chromophore. The position of the chlorine substituent in the <i>trans</i> state breaks the symmetry of the
phenolate ring of the chromophore and allows us to distinguish the two
pathways. Surprisingly, we find that the pathway depends on the arrangement of
protein monomers within the crystal lattice: in a looser packing, the
one-bond-flip occurs, whereas in a tighter packing (7% smaller unit cell size),
the hula-twist occurs.</p><p>
</p><p> </p><p>
</p><p> </p><p>
</p><p> </p>
<p> </p> | Jeffrey Chang; Matthew Romei; Steven Boxer | Dyes and Chromophores; Biophysical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74377ee301c062fc78ff2/original/structural-evidence-of-photoisomerization-pathways-in-fluorescent-proteins.pdf |
60c75080567dfe2a1dec5880 | 10.26434/chemrxiv.12629903.v3 | The Importance of Solid-state Molecular Motion to Room Temperature Phosphorescence | <div>Molecular motion is often considered detrimental to luminescence because it favors
nonradiative decay. However, nothing is absolute, and molecular motion can also do useful work if
utilized properly. For example, photothermal therapy makes use of the heat generated in light
irradiation for cancer treatment. To further explore the merits of molecular motion, ortho-substituted
benzoic acids were used as model compounds to evaluate the importance of molecular motion to
luminescence in the solid state. It is verified that the twisting of the carboxylic acid group can activate
spin vibronic coupling to facilitate intersystem crossing to result in more efficient room temperature
phosphorescence (RTP). A five-state model is established to understand the ISC process and an
effective pre-twisted molecular design strategy is put forward for the development of efficient RTP
materials.</div> | Yujie Tu; Junkai Liu; Xuepeng Zhang; Tsz Shing Cheung; Xuewen He; Jing Guo; Jacky W. Y. Lam; Sijie Chen; Ben Zhong Tang | Aggregates and Assemblies; Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75080567dfe2a1dec5880/original/the-importance-of-solid-state-molecular-motion-to-room-temperature-phosphorescence.pdf |
63dfceaea8f79476ca6ad0f6 | 10.26434/chemrxiv-2023-gkwln | Supramolecular Self-assembly of Engineered Polyproline Helices | The ability to rationally design biomaterials to form desired supramolecular constructs presents an ever-growing research field, with many burgeoning works within recent years providing exciting results, however, there exists a broad expanse of promising avenues of research yet to be investigated. As such we have set out to make use of the polyproline helix as a rigid, tuneable, and chiral ligand for the design and synthesis of supramolecular constructs. In this investigation we show how an oligoproline tetramer can be specifically designed and functionalised, allowing predictable tuning of supramolecular interactions to engineer the formation of supramolecular peptide frameworks with varying properties. Consequently, laying the groundwork for further studies utilising the polyproline helix, with the ability to design desired supramolecular structures, having tuneable structural features and functionalities. | Dominic F Brightwell; Giada Truccolo; Kushal Samanta; Helena J Shepherd; Aniello Palma | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dfceaea8f79476ca6ad0f6/original/supramolecular-self-assembly-of-engineered-polyproline-helices.pdf |
60c75953337d6cf7ece29395 | 10.26434/chemrxiv.14685381.v1 | Photocatalytic Cycloaddition Reaction of Triarylphosphines with Alkynes Forming Cyclic Phosphonium Salts | Herein reported is a photocatalytic cycloaddition reaction of triarylphosphines with alkynes. Phosphonium salts of unique bicyclic structures are synthesized through a radical pathway under mild reaction conditions. The phosphonium salts are subjected to the Wittig olefination reaction to afford structurally interesting phosphine oxides. | Yusuke Masuda; Daichi Ikeshita; Masahiro Murakami | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75953337d6cf7ece29395/original/photocatalytic-cycloaddition-reaction-of-triarylphosphines-with-alkynes-forming-cyclic-phosphonium-salts.pdf |
6718d3f3d433919392f1adf2 | 10.26434/chemrxiv-2024-b9kjg | Machine Learning-Assisted Design of Metal–Organic Frameworks for Hydrogen Storage: A High-Throughput Screening and Experimental Approach | Various theoretical approaches, including big data and high-throughput screening techniques, have been explored in developing new materials due to their significant potential time-saving advantages. However, it remains a significant challenge to experimentally realize new materials that are predicted. In this study, we propose a novel materials design strategy that utilizes machine-learning (ML) techniques to predict new porous materials that show promise for hydrogen storage and are likely to be feasible to synthesize. By leveraging ML techniques and metal−organic framework (MOF) databases, we are able to predict the synthesizability of MOF structures. This is evidenced by the successful synthesis of a new vanadium-based MOF that exhibits excellent performance for cryogenic H2 storage. Notably, the total gravimetric and volumetric H2 uptakes are as high as 9.0 wt % and 50.0 g/L at 77 K and 150 bar. This ML-assisted materials design offers an efficient and promising approach for developing hydrogen storage materials. | Wan-Tae Kim; Weon-Gyu Lee; Hong-Eun An; Hiroyasu Furukawa; WooSeok Jeong; Sung-Chul Kim; Jeffrey Long; Sohee Jeong; Jung-Hoon Lee | Theoretical and Computational Chemistry; Materials Science; Hydrogen Storage Materials; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6718d3f3d433919392f1adf2/original/machine-learning-assisted-design-of-metal-organic-frameworks-for-hydrogen-storage-a-high-throughput-screening-and-experimental-approach.pdf |
65c43c6e9138d23161a7099f | 10.26434/chemrxiv-2024-jx761 | Interdiffusion-Enhanced Cation Exchange for HgSe and HgCdSe Nanocrystals with Infrared Bandgaps | Colloidal semiconductor nanocrystals based on CdSe have been precisely optimized for photonic applications in the visible spectrum, with modern products exhibiting structural uniformity, near 100% quantum yield, and linewidths narrower than 100 meV. Here we report homogeneous nanocrystals with tunable bandgaps in the infrared based on HgSe and Hg(x)Cd(1–x)Se alloys deriving from CdSe precursors. We find that Ag+ catalyzes cation interdiffusion to reduce the CdSe-HgSe alloying temperature from 250 °C to 80 °C. Together with ligands that modulate surface cation exchange rates, interdiffusion-enhanced Hg2+ exchange of diverse CdSe nanocrystals proceeds homogeneously and completely. The products retain sizes, shapes, and uniformity of the parent nanocrystals but exhibit enhanced absorption. After passivation with heteroepitaxial CdZnS shells, photoluminescence wavelength is tunable in the shortwave infrared by composition without changing size, with 80–91% quantum yield and linewidths near 100 meV. These materials may find applications in infrared photonic devices and infrared bioimaging. | Wonseok Lee; Andrew Smith | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Optics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c43c6e9138d23161a7099f/original/interdiffusion-enhanced-cation-exchange-for-hg-se-and-hg-cd-se-nanocrystals-with-infrared-bandgaps.pdf |
62c6b4c7fb63816c63cfa510 | 10.26434/chemrxiv-2022-4zzq4 | Biocatalytic cascades towards iminosugar scaffolds reveals promiscuous activity of shikimate dehydrogenases | Protecting group-free chemoenzymatic and biocatalytic cascade synthesis of iminosugars from sugar aminopolyols has been achieved using Galactose oxidase F2 and chemical or enzymatic imine reduction. Putative iminosugar oxidoreductases were identified through genome mining, with several shikimate dehydrogenases (SDH) found to effect iminosugar formation. The SDH catalysed transformation is the first example of such activity on an iminosugar scaffold, and provides support for the reduction of iminosugar intermediates by endogenous enzymes in iminosugar biosynthesis. | Christopher Swanson; Grayson Ford; Ashley Mattey; Lea Gourbeyre; Sabine Flitsch | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c6b4c7fb63816c63cfa510/original/biocatalytic-cascades-towards-iminosugar-scaffolds-reveals-promiscuous-activity-of-shikimate-dehydrogenases.pdf |
611191a77117505ba2e5f651 | 10.26434/chemrxiv-2021-590p0 | Impact of warhead modulations on the covalent inhibition of SARS-CoV-2 Mpro explored by QM/MM simulations | The COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus-2, SARS-CoV-2, shows the need for effective antiviral treatments. Here, we present a simulation study of the inhibition of the SARS-CoV-2 main protease (Mpro), a cysteine hydrolase essential for the life cycle of the virus. The free energy landscape for the mechanism of the inhibition process is explored by QM/MM umbrella sampling and free energy perturbation simulations at the M06-2X/MM level of theory for two proposed peptidyl covalent inhibitors sharing the same recognition motif while featuring distinct cysteine-targeting warheads. Regardless of intrinsic reactivity of the modelled inhibitors, namely a Michael acceptor and a hydroxymethylketone activated carbonyl, our results confirm that the inhibitory process takes place by means of a two-step mechanism, in which the formation of an ion pair C145/H41 dyad precedes the protein-inhibitor covalent bond formation, in both cases. The nature of this second step appears to be strongly dependent on the functional groups introduced in the warhead: in the present study, while the nucleophilic attack of the C145 sulfur atom on the C of the double bond of the Michael acceptor takes place concertedly to the proton transfer from H41 to C, in the compound with an activated carbonyl the sulfur attacks the carbonyl carbon concomitant to the proton transfer from H41 to the carbonyl oxygen through the hydroxyl group. Analysis of the free energy profiles, structures along the reaction path, and interactions between the inhibitors and the different pockets of the active site on the protein shows a measurable impact of the warhead on the kinetics and thermodynamics of the process. The present results can be used as a guide to select warheads to design efficient irreversible and reversible inhibitors of SARS-CoV-2 Mpro. | Sergio Marti; Kemel Arafet; Alessio Lodola; Adrian Mulholland; Katarzyna Swiderek; Vicent Moliner | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2021-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611191a77117505ba2e5f651/original/impact-of-warhead-modulations-on-the-covalent-inhibition-of-sars-co-v-2-mpro-explored-by-qm-mm-simulations.pdf |
613f6e908e38a37dd551b458 | 10.26434/chemrxiv-2021-kmxgd | 3D Printed Reactors and Kessil Lamp Holders for Flow Photochemistry: Design and System Standardization | A low-cost 3D printed standardized flow-photochemistry setup has been designed and developed for use with a pressure-driven flow system using photochemistry lamps available in most laboratories. In this research, photochemical reactors were 3D printed from polypropylene which facilitated rapid optimization of both reactor geometry and experimental setup of the lamp housing system. To exemplify the rapidity of this approach to optimization, a Kessil LED lamp was used in the bromination of a range of toluenes in the 3D printed reactors in good yields with residence times as low as 27 seconds. The reaction compared favorably with the batch photochemical procedure and was able to be scaled up to a productivity of 75 mmol h-1. | Matthew Penny; Stephen Hilton | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613f6e908e38a37dd551b458/original/3d-printed-reactors-and-kessil-lamp-holders-for-flow-photochemistry-design-and-system-standardization.pdf |
61b09c9c0e35eb0f63992a40 | 10.26434/chemrxiv-2021-g0k1t | Ratiometric Flapping Force Probe That Works in Polymer Gels | A ratiometric flapping force probe that can evaluate the nanoscale stress concentration in the polymer chain network of common organogels has been developed. Stress-dependent dual-fluorescence properties of the chemically doped flapping force probe has been demonstrated even when the probe is solvated in the wet materials (Figure 1). The fluorescence ratiometric analysis is robust against the local concentration change induced by the macroscopic polymer deformation. While the force-responsive FRET dyads, widely used in mechanobiology, are sensitive to the distance and orientation of the two chromophores, the flapping fluorophore works as a single-component flexible force probe regardless of the FRET efficiency. Realtime and reversible spectral response to the mechanical stress is observed with a low threshold on the order of sub-MPa compression due to its conformational flexibility. The previously reported flapping probe only shows a negligible response in the solvated environments because the undesired spontaneous planarization occurs in the S1 excited state, even without mechanical force. The excited-state engineering by changing the flapping wings from the anthraceneimide units to the pyreneimide units endows this molecule with the force probe function in the wet conditions. The structurally modified force probe also has an advantage in terms of a wide dynamic range of the fluorescence response in solvent-free elastomers, which enabled the ratiometric fluorescence imaging of the molecular-level stress concentration during the crack growth in a stretched polyurethane film. The percentage of the stressed force probes has been experimentally estimated to be approximately 30–40% before the fracture of the elastomers. The flapping force probe is useful for elucidating the toughening mechanism of recently focused unique topological gels and elastomers at molecular level. | Takuya Yamakado; Shohei Saito | Organic Chemistry; Materials Science; Polymer Science; Photochemistry (Org.); Elastic Materials; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b09c9c0e35eb0f63992a40/original/ratiometric-flapping-force-probe-that-works-in-polymer-gels.pdf |
62ffb1881945ad64c1df1dfe | 10.26434/chemrxiv-2022-vqbxg | Automated relative binding free energy calculations: from SMILES to ΔΔG | In drug discovery, computational methods are a key part of making informed design decisions and prioritising compounds. In particular, optimizing compound affinity is a central concern during the early stages of development. In the last 10 years, alchemical free energy (FE) calculations have transformed our ability to incorporate accurate in silico potency predictions in design decisions, and represent the 'gold standard' for augmenting experiment-driven drug discovery. However, relative FE calculations are complex to set up and require significant expert intervention to prepare the calculation and analyse the results. Additionally, some of the commonly employed simulation engines for FE calculation are provided as closed-source software, and do not allow for fine-grained control over the underlying settings.
In this work, we introduce an end-to-end relative FE workflow based on the non-equilibrium switching approach that facilitates calculation of binding free energies starting from SMILES strings. The workflow is implemented using fully modular steps, allowing various components to be exchanged depending on licence availability. Open-source options for ligand parameterization, embedding, docking, perturbation map generation and FE calculation steps are available to make the workflow fully open-source. We further investigate the dependence of the calculated free energy accuracy on the initial ligand pose generated by various docking algorithms. We show that both commercial and open-source docking engines can be used to generate poses that lead to good correlation of free energies with experimental reference data. Incorporating experimental information about binding pose generally leads to a more accurate set of predictions, particularly in more challenging cases.
The code is freely available at https://github.com/MolecularAI/Icolos, where several example relative FE workflows can be found in both commercial and open-source flavours. | Harry Moore; Christian Margreitter; Jon Paul Janet; Ola Engkvist; Bert de Groot; Vytautas Gapsys | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ffb1881945ad64c1df1dfe/original/automated-relative-binding-free-energy-calculations-from-smiles-to-g.pdf |
60c74690702a9b6b5618ac1a | 10.26434/chemrxiv.11354216.v1 | Direct 17O-Isotopic Labeling of Oxides Using Mechanochemistry | While oxygen-17 NMR is increasingly being used for elucidating the structure and reactivity of complex molecular and materials systems, much effort is still required for it to become a routine analytical technique. One of the main difficulties for its development comes from the very low natural abundance of oxygen-17, which implies that isotopic labeling is generally needed prior to NMR analyses. However, 17O-enrichment protocols are often unattractive in terms of cost, safety, and/or practicality, even for compounds as simple as metal oxides. Here, we demonstrate how mechanochemistry can be used in a highly efficient way for the direct 17O-isotopic labeling of a variety of s-, p- and d-block oxides which are of major interest for the preparation of functional ceramics and glasses: Li2O, CaO, Al2O3, SiO2, TiO2, and ZrO2. For each oxide, the enrichment step was performed under ambient conditions in less than 1 hour and at low cost, which makes these synthetic approaches highly appealing in comparison to the existing literature. Using high-resolution 17O solid state NMR and Dynamic Nuclear Polarization, atomic-level insight into the enrichment process is achieved, especially for titania and alumina. Indeed, it was possible to demonstrate that enriched oxygen sites are present not only at the surface, but also within the oxide particles. Moreover, information on the actual reactions occurring during the milling step could be obtained by 17O NMR, both in terms of their kinetics and the nature of the reactive species. Finally, it was demonstrated how high resolution 17O NMR can be used for studying the reactivity at the interfaces between different oxide particles during ball-milling, especially in cases when X-ray diffraction techniques are uninformative. More generally, such investigations will be useful not only for producing 17O-enriched precursors efficiently, but also for understanding better mechanisms of mechanochemical processes themselves. <br /> | Chia-Hsin Chen; Emeline Gaillard; Frédéric Mentink-Vigier; Kuizhi Chen; Zhehong Gan; Philippe Gaveau; Bertrand Rebière; Romain Berthelot; Pierre Florian; Christian Bonhomme; Mark E. Smith; Thomas-Xavier Métro; Bruno Alonso; Danielle Laurencin | Materials Processing; Interfaces; Spectroscopy (Physical Chem.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74690702a9b6b5618ac1a/original/direct-17o-isotopic-labeling-of-oxides-using-mechanochemistry.pdf |
66c83c72a4e53c4876545e7c | 10.26434/chemrxiv-2024-btm9c | A Refined Set of Universal Force Field Parameters for Some Metal Nodes in Metal-Organic Frameworks | Metal-organic frameworks (MOFs) exhibit promise as porous materials for carbon capture due to their design versatility and large pore sizes. The generic force field (e.g. UFF and Dreiding) uses one set of Lennard-Jones parameters for each element, while MOFs have a much richer local chemical environment than those used to fit the UFF. When MOFs contain hard-Lewis acid metals, UFF systematically overestimates $CO2$ uptakes within MOFs. To address this, we developed a workflow to affordably and efficiently generate reliable force fields to predict \ce{CO2} adoption isotherms of MOFs containing metals from groups IIA (e.g. Mg, Ca, Sr, Ba) and IIIA (e.g., Al, Ga, In), connected to various carboxylate ligands. This method uses experimental isotherms as input. The optimal parameters are obtained by minimizing the loss function of the experimental and simulated isotherms, in which we use the Multistate Bennett Acceptance Ratio (MBAR) theory can be used to derive the functionality relationship of loss functions in terms of force field parameters. | Yutao Li; Xin Jin; Elias Moubarak; Berend Smit | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c83c72a4e53c4876545e7c/original/a-refined-set-of-universal-force-field-parameters-for-some-metal-nodes-in-metal-organic-frameworks.pdf |
60c757309abda22f93f8e662 | 10.26434/chemrxiv.14377046.v1 | Boosting Dissolution-Dynamic Nuclear Polarization by Multiple-Step Dipolar Order Mediated 1H->13C Cross-Polarization | <p>Dissolution-dynamic nuclear polarization can be boosted by employing multiplecontact cross-polarization techniques to transfer polarization from 1H to 13C spins. The method is efficient and significantly reduces polarization build-up times, however, it involves high-power radiofrequency pulses in a superfluid helium environment which limit its implementation and applicability and prevent a significant scaling-up of the sample size.</p>
<p>We propose to overcome this limitation by a stepwise transfer of polarization using a lowenergy and low-peak power radiofrequency pulse sequence where the 1H®13C polarization transfer is mediated by a dipolar spin order reservoir. An experimental demonstration is presented for [1-13C]sodium acetate. A solid-state 13C polarization of ~43.5% was achieved using this method with a build-up time constant of ~5.1 minutes, leading to a ~28.5% 13C polarization in the liquidstate after sample dissolution. The low-power multiple-step polarization transfer efficiency with respect to the most advanced and highest-power multiple-contact cross-polarization approach was found to be ~0.69.</p> | Stuart J. Elliott; Olivier Cala; Quentin Chappuis; Samuel Cousin; Morgan Ceillier; Venita Decker; Sami Jannin | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757309abda22f93f8e662/original/boosting-dissolution-dynamic-nuclear-polarization-by-multiple-step-dipolar-order-mediated-1h-13c-cross-polarization.pdf |
65265848bda59ceb9a544908 | 10.26434/chemrxiv-2023-xtqq8 | High entropy hexagonal manganites for fast oxygen absorption and release | Hexagonal manganites (RMnO3) display large capacity for oxygen storage and release at temperatures below 400 °C. A challenging trade-off is that larger R3+ cations improve both the absorption capacity and the exchange kinetics, but also destabilize the layered hexagonal structure with respect to competing orthorhombic perovskite phase. Here, high-entropy RMnO3 materials with 5 or 6 rare earth elements are prepared as both bulk and nanocrystalline materials, and the resulting configurational entropy stabilizes the hexagonal phase for compositions RMn1-xTixO3 where R = Y, Gd-Er and x = 0, 0.15. These high-entropy hexagonal manganites show similar oxygen storage capacity as the best known single or double R3+ compositions, and greatly enhanced oxidation kinetics. Importantly, both the oxygen capacity and oxidation kinetics are insensitive to the exact R3+ composition. This improves the commercial application potential of hexagonal manganites for oxygen storage and separation from air. | Frida Hemstad Danmo; Aamund Westermoen; Kenneth Marshall; Dragos Stoian; Tor Grande; Julia Glaum; Sverre M. Selbach | Materials Science; Ceramics; Nanostructured Materials - Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65265848bda59ceb9a544908/original/high-entropy-hexagonal-manganites-for-fast-oxygen-absorption-and-release.pdf |
66044afce9ebbb4db9b22a8c | 10.26434/chemrxiv-2024-m92kq | Harnessing strain-release driven reactivity of a chiral SuFEx reagent: Stereocontrolled access to sulfinamides, sulfonimidamides, and sulfoximines | Efforts aimed at enriching the chemical and structural diversity of small molecules have invigorated synthetic exploration in the last two decades. Spatially defined molecular functionality serves as the foundation to construct unique chemical space to further advance discovery science. The chiral SuFEx reagent t-BuSF provides a modular platform for the stereocontrolled bifunctionalization of sulfur. Here we report a third functional feature of t-BuSF enabled by carbamoyl torsional strain-release that further expands the S(IV) and S(VI) chemical space accessible as showcased in over seventy examples, multiple applications in medicinal chemistry, organocatalysis, and diversity-oriented synthesis. The methods presented herein allow for rapid asymmetric diversification around a stereodefined sulfur center with readily available building blocks, improving upon the current state-of-the-art for sulfinyl and sulfonimidoyl synthesis. | Paresh Athawale; Zachary Shultz; Alexandra Saputo; Yvonne Hall; Justin Lopchuk | Biological and Medicinal Chemistry; Organic Chemistry; Combinatorial Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66044afce9ebbb4db9b22a8c/original/harnessing-strain-release-driven-reactivity-of-a-chiral-su-f-ex-reagent-stereocontrolled-access-to-sulfinamides-sulfonimidamides-and-sulfoximines.pdf |
63d3bb62ae221a70d33f33fb | 10.26434/chemrxiv-2023-bcqzh | Solvent induced 1H NMR chemical shifts of annulenes | We investigate the effect of solvent polarity on the 1H NMR chemical shifts of [n]annulenes (n = 12, 18, and 30) using density functional theory and corroborate the computational results with Onsager’s reaction field theory. We observe that there is a complete deshielding of the proton NMR chemical shifts for the outer protons and these shifts depend linearly on the dielectric function of the solvents reaction field for certain annulenes (n = 12 and 30). For the asymmetric C2 structure of [18]annulene, the inner protons are observed to vary nonlinearly with the function of solvent dielectrics due to the influence of the asymmetry parameter “C”, which generates an anisotropic environment inside the annulene ring cavity.
| Swrangsi Goyary; Manash Jyoti Sarmah; Himangshu Prabal Goswami; Nilamoni Nath | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3bb62ae221a70d33f33fb/original/solvent-induced-1h-nmr-chemical-shifts-of-annulenes.pdf |
60c73f9e9abda256ddf8bb38 | 10.26434/chemrxiv.7454420.v1 | Variable-Temperature Multinuclear Solid-State NMR Study of Oxide Ion Dynamics in Fluorite-Type Bismuth Vanadate and Phosphate Solid Electrolytes | <p>In this study, we employ a multinuclear, variable-temperature NMR spectroscopy approach to characterise and measure oxide ionic motion in the V- and P-substituted bismuth oxide materials Bi0.913V0.087O1.587, Bi0.852V0.148O1.648 and Bi0.852P0.148O1.648, previously shown to have excellent ionic conduction properties. Two main <sup>17</sup>O NMR resonances are distinguished for each material, corresponding to O in the Bi–O and V–O/P–O sublattices. Using variable-temperature (VT) measurements ranging from room temperature to 923 K, the ionic motion experienced by these different sites has then been characterised, with coalescence of the two environments in the V-substituted materials clearly indicating a conduction mechanism facilitated by exchange between the two sublattices. The lack of this coalescence in the P-substituted material indicates a different mechanism, confirmed by <sup>17</sup>O T1 (spin-lattice relaxation) NMR experiments to be driven purely by vacancy motion in the Bi–O sublattice. <sup>51</sup>V and <sup>31</sup>P VT-NMR experiments show high rates of tetrahedral rotation even at room temperature, increasing with heating. An additional VO4 environment appears in <sup>17</sup>O and <sup>51</sup>V NMR spectra of the more highly V-substituted Bi0.852V0.148O1.648, which we ascribe to differently distorted VO4 tetrahedral units that disrupt the overall ionic motion, consistent both with linewidth analysis of the 17O VT-NMR spectra and experimental results of Kuang <i>et al.</i> showing a lower oxide ionic conductivity in this material compared to Bi0.913V0.087O1.587 (<i>Chem. Mater. </i>2012, 24, 2162). This study shows solid-state NMR is particularly well suited to understanding connections between local structural features and ionic mobility, and can quantify the evolution of oxide-ion dynamics with increasing temperature.</p> | Matthew Dunstan; David M. Halat; Matthew Tate; Ivana Radosavljevic Evans; Clare P. Grey | Thermal Conductors and Insulators; Solid State Chemistry; Structure | CC BY 4.0 | CHEMRXIV | 2018-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9e9abda256ddf8bb38/original/variable-temperature-multinuclear-solid-state-nmr-study-of-oxide-ion-dynamics-in-fluorite-type-bismuth-vanadate-and-phosphate-solid-electrolytes.pdf |
6495a4761dcbb92a5e7430d1 | 10.26434/chemrxiv-2023-10vvw-v3 | Unnatural endo type-B PPAPs as novel compounds with activity against Mycobacterium tuberculosis. | Before the emergence of SARS-CoV-2, tuberculosis (TB) was the leading cause of infectious disease mortality worldwide. Like all antibiotic-exposed bacteria Mycobacterium tuberculosis (Mtb) developed multidrug-resistant (MDR) and exten-sively drug-resistant (XDR) strains which require new antibiotics with novel mechanism of actions. Hyperforin, a natural type-A polyprenylated polycyclic acylphloroglucinol (PPAP) isolated from St. John’s wort, is known for its antibacterial, antidepressant and antimycobacterial activity. However, hyperforin is not stable and easily degradable in light, heat it and oxidizes. Here we report photo- and benchstable type-B PPAPs with structural similarity to hyperforin and enhanced an-timycobacterial activity. We tested a panel of PPAPs and identified our previously reported molecule PPAP22 as lead compound. Converting PPAP22 into the corresponding sodium salt, PPAP53, enhanced the solubility dramatically. We show that PPAP53 inhibits the growth of virulent, extracellular Mtb. Strikingly, the activity is more pronounced intracel-lular Mtb residing in human primary macrophages without damaging the host cell or lung cells. Importantly PPAP53 was also highly active against drug-resistant Mtb. Additionally, we analysed the in vitro properties of PPAP53 in terms of CYP-induction and PXR interaction. Taken together we introduce type-B PPAPs are a new class of antimycobacterial com-pounds, with remarkable activity and favorouble physical properties. | Philipp Peslalz; Mark Grieshober; Frank Kraus; Anton Bleisch; Flavia Izzo; Dajana Lichtenstein ; Helen Hammer; Andreas Vorbach; Kyoko Momoi; Ulrich Zanger; Heike Brötz-Oesterhelt; Albert Braeuning; Bernd Plietker; Steffen Stenger | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6495a4761dcbb92a5e7430d1/original/unnatural-endo-type-b-ppa-ps-as-novel-compounds-with-activity-against-mycobacterium-tuberculosis.pdf |
62a0bc99804dbe403e3ebcaf | 10.26434/chemrxiv-2022-1xsq2 | Infrared Diffusion-Ordered Spectroscopy Reveals
Molecular Size and Structure | Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size.
We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity. | Giulia Giubertoni; Gijs Rombouts; Federico Caporaletti; Antoine Deblais; Rianne van Diest; Joost Reek; Daniel Bonn; Sander Woutersen | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a0bc99804dbe403e3ebcaf/original/infrared-diffusion-ordered-spectroscopy-reveals-molecular-size-and-structure.pdf |
646612c7a32ceeff2dd7d288 | 10.26434/chemrxiv-2023-wgdm0 | The Liverpool Materials Discovery Server: A suite of computational tools for the collaborative discovery of materials | The discovery of new materials often requires collaboration between experimental and computational chemists. Web based platforms allow more flexibility in this collaboration by giving access to computational tools without the need for access to computational researchers. We present Liverpool Materials Discovery Server (lmds.liverpool.ac.uk), one such platform which currently hosts six state of the art computational tools in an easy to use format. We describe the development of this platform, highlighting the advantages and disadvantages the methods used. In addition, we provide source code, and setup scripts to enable other research groups to create similar platforms, to promote collaboration both within and between research groups. | Samantha Durdy; Cameron J. Hargreaves; Mark Dennison; Benjamin Wagg; Michael Moran; Jon A. Newnham; Michael W. Gaultois; Matthew J. Rosseinsky; Matthew Dyer | Theoretical and Computational Chemistry; Materials Science; Materials Processing; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646612c7a32ceeff2dd7d288/original/the-liverpool-materials-discovery-server-a-suite-of-computational-tools-for-the-collaborative-discovery-of-materials.pdf |
60c7478cbb8c1a177c3daac3 | 10.26434/chemrxiv.11720679.v1 | Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation | The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br />wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br />transition by a “wine-rack” type motion of the square lattice. We studied this not<br />yet fully understood behavior using an accurate first principles parameterized force<br />field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br />benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br />cations for an interface between a closed and an open pore phase traveling through<br />the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br />conventional simulations in small supercells this mechanism is prevented by periodic<br />boundary conditions (PBC), enforcing a synchronous transformation of the entire<br />crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br />side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br />tally known to have different properties with the side-chains acting as fixed guest<br />molecules. First, in order to extend the parameterization for such flexible groups,<br />1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br />structure force based fit method. The resulting parametrization for a library of<br />fu-MOFs is then validated with respect to a set of reference systems and shows very<br />good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br />length is studied with respect to the influence of the side-chains on the breathing<br />behavior. For small supercells in PBC a systematic trend of the closed pore volume<br />with the chain length is observed. However, for a nanocrystallite model a distinct<br />interface between a closed and an open pore phase is visible only for the short chain<br />length, whereas for longer chains the interface broadens and a nearly concerted trans-<br />formation is observed. Only by molecular dynamics simulations using accurate force<br />fields such complex phenomena can be studied on a molecular level. | Julian Keupp; Johannes P. Dürholt; Rochus Schmid | Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2020-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7478cbb8c1a177c3daac3/original/influence-of-flexible-side-chains-on-the-breathing-phase-transition-of-pillared-layer-mo-fs-a-force-field-investigation.pdf |
60c74b75bb8c1a23393db23a | 10.26434/chemrxiv.12127818.v2 | Selective Oxidation of Pharmaceuticals and Suppression of Perchlorate Formation during Electrolysis of Fresh Human Urine | <p>Many pharmaceutical compounds are excreted unchanged or as active metabolites via urine. They pass through conventional wastewater treatment processes and present a risk to aquatic ecosystems and humans. Point-source remediation of source-separated urine provides a promising alternative to destroy pharmaceuticals before dilution with wastewater. Electrochemical advanced oxidation processes are one possible option for degrading pharmaceuticals in urine, but they often lead to the formation of oxidation byproducts (OBPs) including chlorate, perchlorate, and halogenated organics at hazardous concentrations due to high background chloride concentrations. Here, we show that the high urea content of fresh human urine suppresses the formation of oxychlorides by inhibiting formation of HOCl/OCl‒ during electrolysis, while still enabling the oxidation of pharmaceuticals by •OH due to the slow rate of urea oxidation by •OH. This results in improved performance when compared to equivalent treatment of hydrolyzed aged urine. This (primarily indirect) electrochemical oxidation scheme is shown to degrade the model pharmaceuticals cyclophosphamide and sulfamethoxazole with surface-area-to-volume-normalized pseudo-first-order observed rate constants greater than 0.08 cm/min in authentic fresh human urine matrixes. It results in two orders-of-magnitude decrease in pharmaceutical concentrations in 2 hours while generating three orders-of-magnitude lower oxychloride byproduct concentrations in synthetic fresh urine as compared to synthetic hydrolyzed aged urine matrixes. Importantly, this proof-of-principle shows that simple and safe electrochemical methods can be used for point-source-remediation of pharmaceuticals in fresh human urine (before storage and hydrolysis), without formation of significant oxychloride byproducts. <br /></p> | James
A. Clark; Yuhang Yang; Nathanael C. Ramos; Michael C. Dodd; Hugh W. Hillhouse | Environmental Science; Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b75bb8c1a23393db23a/original/selective-oxidation-of-pharmaceuticals-and-suppression-of-perchlorate-formation-during-electrolysis-of-fresh-human-urine.pdf |
629848ec23bf1fffb5b1f7f5 | 10.26434/chemrxiv-2022-cpg6j-v2 | Programmed ripening of nanoparticles using a DNA template | Nanoparticle (NP) ripening is a process where energetically favored larger particles grow at the expense of smaller ones: while important in NP synthesis, it is often difficult to control during NP applications. Here, we unveil a new Contact-dependent, Localized Galvanic Ripening (CLGR) mechanism that enables precise control of NP ripening in solution. As neighboring silver NPs on a DNA origami template grow homogeneously to the point of making contact, the subtle size-dependent electrochemical potential differences of the NPs promote one silver shell to erode and redeposit locally onto the adjacent NP, leading to asymmetric structures. The unique on/off control through NP contact in CLGR presents a strategy to program the erosion and growth of specific NPs in a construct, which we exploit to synthesize customized heterogeneous core-shell NP structures with pre-designed plasmonic properties. CLGR is an essential phenomenon to consider for future nanodevice and nanophotonics designs. | Xin Luo; Jun Zhu; Felix Rizzuto; R. Bruce Lennox; Hanadi Sleiman | Inorganic Chemistry; Nanoscience; Nanofabrication; Kinetics and Mechanism - Inorganic Reactions; Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629848ec23bf1fffb5b1f7f5/original/programmed-ripening-of-nanoparticles-using-a-dna-template.pdf |
60c73fcff96a00bca228615f | 10.26434/chemrxiv.7495808.v1 | A Thermochemical Computational Study on Hydroxyquinolines and their Azulene Analogues | Ab initio CBS-QB3 method has been used to determine
gas-phase enthalpies of formation for 34 compounds including a number of hydroxyquinoline
isomers, the corresponding azulene analogues and their parent systems. The mean
absolute deviation of 4.43 kJ/mol reveals good agreement between our results
and the available experimental data. Relative thermodynamic stabilities of
hydroxyquinoline isomers and related analogues were discussed and several
isomerization reactions enthalpies were derived. The same level of theory has
also been utilized to calculate adiabatic ionization energies and electron
affinities for the molecules with known experimental values and the agreement
between theory and experiment was found to be within 8 kJ/mol. | Moyassar Meshhal; Safinaz El-Demerdash; Ahmed El-Nahas | Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fcff96a00bca228615f/original/a-thermochemical-computational-study-on-hydroxyquinolines-and-their-azulene-analogues.pdf |
67ddc9cd6dde43c908c39d8e | 10.26434/chemrxiv-2025-lqqv4-v2 | Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma
| DNA polymerases are essential enzymes responsible for accurate genome replication and repair, with divalent metal cofactors playing a crucial role in their catalytic function. Polymerase gamma (Pol γ) is the primary DNA polymerase in mitochondria, ensuring the faithful replication of mitochondrial DNA. The choice of metal cofactor, typically magnesium (Mg²⁺) or manganese (Mn²⁺), influences its structural stability, enzymatic activity, and fidelity. In this study, we employed molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how Mg²⁺ and Mn²⁺ affect the flexibility, active site stabilization, and catalytic efficiency of Pol γ. It is seen that Mn²⁺ increases overall protein flexibility, whereas Mg²⁺ provides greater active site stabilization. Intermolecular interaction analysis of individual residues are consistent with experimental mutagesis reports, and highlight the importance of specific residues, many of which are evolutionarily conserved, and some are involved in pathogenic mutations. Despite this, Mn²⁺ enhances catalytic efficiency, exhibiting higher exoergicity (-3.65 kcal/mol vs. -1.61 kcal/mol for Mg²⁺) and a lower activation barrier. Inter-molecular interaction analysis reveals that Mn²⁺ provides a larger stabilization of the transition state and product complex, favoring reaction progression. Investigation of the effects of electric field in the active site suggest that the O3’ atom on the DNA primer base experiences a larger polarization in the system with Mn2+ ions when compared to Mg2+, with dipole directions consistent with the catalytic reaction progress. Our findings highlight a trade-off between structural stability and catalytic efficiency, providing insights into the role of metal ions in mitochondrial polymerase function and their implications for mutagenesis and mitochondrial disorders. | Arkanil Roy; G. Andrés Cisneros | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ddc9cd6dde43c908c39d8e/original/comparison-of-magnesium-and-manganese-ions-on-the-structural-and-catalytic-properties-of-human-dna-polymerase-gamma.pdf |
657335f65bc9fcb5c9609e31 | 10.26434/chemrxiv-2023-jjx9l | Recovery of Europium from E-Waste Using Redox Active Tetrathiotungstate Ligands | Rare-earth elements, indispensable to our modern economy, are challenging to purify due to their chemical similarities. Here we introduce a strategy to recycle europium from e-waste, leveraging the redox non-innocence of tetrathiotungstate ligands, achieving its selective separation from energy-saving lamps under ambient conditions with separation factors uover 1000 and recovery efficiency as high as 99%, without pre-treatment of the waste. | Marie Perrin; Paul Dutheil; Victor Mougel | Inorganic Chemistry; Lanthanides and Actinides; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657335f65bc9fcb5c9609e31/original/recovery-of-europium-from-e-waste-using-redox-active-tetrathiotungstate-ligands.pdf |
638faa3cb103af94f10d8c94 | 10.26434/chemrxiv-2022-nssm2 | A 5V-class Cobalt-free Battery Cathode with High Loading Enabled by Dry Coating | Transitioning toward more sustainable materials and manufacturing methods will be critical to continue supporting the rapidly expanding market for lithium-ion batteries. Meanwhile, energy storage applications are demanding higher power and energy densities than ever before, with aggressive performance targets like fast charging and greatly extended operating ranges and durations. Due to its high operating voltage and cobalt-free chemistry, the spinel-type LiNi0.5Mn1.5O4 (LNMO) cathode material has attracted great interest as one of the few next-generation candidates capable of addressing this combination of challenges. However, severe capacity degradation and poor interphase stability have thus far impeded the practical application of LNMO. In this study, by leveraging a dry electrode coating process, we demonstrate LNMO electrodes with stable full cell operation (up to 68% after 1000 cycles) and ultra-high loading (up to 9.5 mAh/cm2 in half cells). This excellent cycling stability is ascribed to a stable cathode-electrolyte interphase, a highly distributed and interconnected electronic percolation network, and robust mechanical properties. High-quality images collected using plasma focused ion beam scanning electron microscopy (PFIB-SEM) provide additional insight into this behavior, with a complementary 2-D model illustrating how the electronic percolation network in the dry-coated electrodes more efficiently supports homogeneous electrochemical reaction pathways. These results strongly motivate that LNMO as a high voltage cobalt-free cathode chemistry combined with an energy-efficient dry electrode coating process opens the possibility for sustainable electrode manufacturing of cost-effective and high-energy-density cathode materials. | Weiliang Yao; Mehdi Chouchane; Weikang Li; Shuang Bai; Zhao Liu; Letian Li; Alexander X. Chen; Baharak Sayahpour; Ryosuke Shimizu; Ganesh Raghavendran; Yu-Ting Chen; Darren H.S. Tan; Bhagath Sreenarayanan; Crystal K. Waters; Allison Sichler; Benjamin Gould; Dennis J. Kountz; Darren J. Lipomi; Minghao Zhang; Ying Shirley Meng | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638faa3cb103af94f10d8c94/original/a-5v-class-cobalt-free-battery-cathode-with-high-loading-enabled-by-dry-coating.pdf |
673334835a82cea2fadfe6a8 | 10.26434/chemrxiv-2024-q9j9k-v2 | Indoloindolizines: A New Class of Polycyclic Aromatic Materials from Design to Organic Field-Effect Transistor Applications | The development of stable and tunable polycyclic aromatic compounds (PACs) is crucial for advancing organic optoelectronics. Conventional polycyclic aromatic hydrocarbons (PAHs), such as acenes, often suffer from poor stability due to photooxidation and oligomerization, which are linked to their frontier molecular orbital energy levels. To address these limitations, we have designed and synthesized a new class of π-expanded indoloindolizines by merging indole and indolizine moieties into a single polycyclic framework. Guided by the Glidewell-Lloyd rule—which predicts that in fused polycyclic systems, larger rings lose aromaticity in favor of smaller ones—we achieved precise modulation of the electronic structure by controlling the aromaticity of specific rings. Benzannulation at targeted positions allowed fine-tuning of the HOMO-LUMO gap, leading to distinct shifts in optoelectronic properties. We developed a scalable synthetic protocol to produce a wide range of π-expanded derivatives. The structural, electronic, and optical properties of these compounds were extensively characterized. Single-crystal X-ray diffraction confirmed their molecular structure, while theoretical calculations provided insights into the observed experimental trends. These indoloindolizines exhibit vivid colors and fluorescence across the visible spectrum, and enhanced stability against photooxidation. Reactivity studies demonstrated high regioselectivity in electrophilic substitutions, highlighting the indole-like behavior of these compounds and opening avenues for further functionalization. To showcase the practical utility of these materials, we fabricated organic field-effect transistors (OFETs) using the newly developed indoloindolizines, which revealed competitive performance with ambipolar charge transport properties. Overall, our work establishes indoloindolizines as a promising platform for the development of stable, tunable organic materials for optoelectronic applications. By leveraging rational molecular design guided by the Glidewell-Lloyd rule, we offer a new pathway for molecular innovation in organic electronics. | Abhishek Pareek; Muhammad Yasir Mehboob; Maciej Cieplak; Maciej Majdecki; Hubert Szabat; Krzysztof Noworyta; Piotr Połczyński; Maja Morawiak; Piyush Sharma; Cina Foroutan-Nejad; Przemysław Gaweł | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673334835a82cea2fadfe6a8/original/indoloindolizines-a-new-class-of-polycyclic-aromatic-materials-from-design-to-organic-field-effect-transistor-applications.pdf |
62b1b0c97da6ce535c19d40c | 10.26434/chemrxiv-2022-59qc9 | Reaction dynamics of Diels-Alder reactions from machine learned potentials | Recent advances in the development of reactive machine-learned potentials (MLPs) promise to transform reaction modelling. However, such methods have remained computationally expensive and limited to experts. Here, we employ different MLP methods (ACE, NequIP, GAP), combined with automated fitting and active learning, to study the reaction dynamics of representative Diels-Alder reactions. We demonstrate that the ACE and NequIP MLPs can consistently achieve chemical accuracy (± 1 kcal mol−1) to the ground-truth surface with only a few hundred reference calculations. These strategies are shown to enable routine ab initio-quality classical and quantum dynamics and obtain dynamical quantities such as product ratios and free energies from non-static methods. For ambimodal reactions, product distributions were found to be strongly dependent on the QM method and less so on the type of dynamics propagated. | Tom Young; Tristan Johnston-Wood; Hanwen Zhang; Fernanda Duarte | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b1b0c97da6ce535c19d40c/original/reaction-dynamics-of-diels-alder-reactions-from-machine-learned-potentials.pdf |
60c7442d702a9b65b618a752 | 10.26434/chemrxiv.9750716.v1 | Quantifying Triplet State Formation in Zinc Dipyrrin Complexes | Photocatalysis is a promising method to harness solar energy and use it to form fuels and other high value chemicals, but most sensitizers used in photocatalytic reactions are complexes of rare and expensive metals such as ruthenium and iridium. Zinc dipyrromethene complexes have potential to be a more earth-abundant alternative, but their photophysical properties are largely unexplored. In this study, triplet state formation was quantified in two zinc dipyrromethene complexes, with a and without heavy atoms, by transient absorption spectroscopy. Without heavy atoms the triplet quantum yield was 16% in toluene and 27% in THF. With the addition of heavy I atoms the triplet quantum yield is increased to 62-63% and is insensitive to solvent polarity. These triplet yields meet or exceed those of successful organic photosensitizers, illustrating the potential for zinc dipyrromethene complexes as photosensitizers | Norah Z. Alqahtani; Toni G. Blevins; Catherine McCusker | Photosensitizers; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7442d702a9b65b618a752/original/quantifying-triplet-state-formation-in-zinc-dipyrrin-complexes.pdf |
60c74d1ef96a0037a92878b0 | 10.26434/chemrxiv.12579137.v1 | A Network Medicine Approach to Investigation and Population-based Validation of Disease Manifestations and Drug Repurposing for COVID-19 | The global Coronavirus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to unprecedented social and economic consequences. The risk of morbidity and mortality due to COVID-19 increases dramatically in the presence of co-existing medical conditions while the underlying mechanisms remain unclear. Furthermore, there are no proven effective therapies for COVID-19. This study aims to identify SARS-CoV-2 pathogenesis, diseases manifestations, and COVID-19 therapies using network medicine methodologies along with clinical and multi-omics observations. We incorporate SARS-CoV-2 virus-host protein-protein interactions, transcriptomics, and proteomics into the human interactome. Network proximity measure revealed underlying pathogenesis for broad COVID-19-associated manifestations. Multi-modal analyses of single-cell RNA-sequencing data showed that co-expression of <i>ACE2 </i>and <i>TMPRSS2 </i>was elevated in absorptive enterocytes from the inflamed ileal tissues of Crohn's disease patients compared to uninflamed tissues, revealing shared pathobiology by COVID-19 and inflammatory bowel disease. Integrative analyses of metabolomics and transcriptomics (bulk and single-cell) data from asthma patients indicated that COVID-19 shared intermediate inflammatory endophenotypes with asthma (including<i>IRAK3</i> and <i>ADRB2</i>). To prioritize potential treatment, we combined network-based prediction and propensity score (PS) matching observational study of 18,118 patients from a COVID-19 registry. We identified that melatonin (odds ratio (OR) = 0.36, 95% confidence interval (CI) 0.22-0.59) was associated with 64% reduced likelihood of a positive laboratory test result for SARS-CoV-2. Using PS-matching user active comparator design, melatonin was associated with 54% reduced likelihood of SARS-CoV-2 positive test result compared to angiotensin II receptor blockers or angiotensin-converting enzyme inhibitors (OR = 0.46, 95% CI 0.24-0.86). | Yadi Zhou; Yuan Hou; Jiayu Shen; Asha Kalianpur; Joe Zein; Daniel A. Culver; Samar Farha; Suzy Comhair; Claudio Fiocchi; Michaela U. Gack; Reena Mehra; Thaddeus S Stappenbeck; Timothy Chan; Charis Eng; Jae U. Jung; Lara Jehi; Serpil Erzurum; Feixiong Cheng | Biochemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d1ef96a0037a92878b0/original/a-network-medicine-approach-to-investigation-and-population-based-validation-of-disease-manifestations-and-drug-repurposing-for-covid-19.pdf |
62a98d561fdc3450d63a8077 | 10.26434/chemrxiv-2022-jcqcr | Three-Component Synthesis of Pyridylacetic Acid Derivatives by Arylation/Decarboxylative Substitution of Meldrum’s Acids | A convenient and simple three-component synthesis of substituted pyridylacetic acid derivatives is reported. The approach centres on the dual reactivity of Meldrum’s acid derivatives, initially as nucleophiles to perform substitution on activated pyridine-N-oxides, then as electrophiles with a range of nucleophiles to trigger ring-opening and decarboxylation. | Tarn Johnson; Stephen Marsden | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a98d561fdc3450d63a8077/original/three-component-synthesis-of-pyridylacetic-acid-derivatives-by-arylation-decarboxylative-substitution-of-meldrum-s-acids.pdf |
67bcb6496dde43c9084abb65 | 10.26434/chemrxiv-2024-977zk-v2 | Conductive Polymer Coatings Control Reaction Selectivity in All-Iron Redox Flow Batteries | Aqueous all-iron redox flow batteries are an attractive and economic technology for grid-scale energy storage owing to their use of abundant and environmentally benign iron as redox active material and water as solvent. However, the battery operation is challenged by the plating/stripping reactions of iron and the competing hydrogen evolution reaction at the negative electrode, which hinder performance and durability. Here we tailor the reaction selectivity of the negative electrode by introducing conductive polymer coatings onto porous carbonaceous electrodes. We conformally coated two conductive polymers, poly(3,4-ethylenedioxythiophene) (PEDOT) and poly(pyrrole) (PPy) with the dopant poly(4-styrenesulfonate) (PSS), and studied the resulting electrochemistry on model electroanalytical platforms and redox flow batteries. Both polymers decrease the hydrogen evolution current on rotating disc electrodes, with PPy/PSS strongly inhibiting the reaction at high overpotentials. In full all-iron redox flow cells, we find that PPy/PSS coating extends cyclability and significantly reduces hydrogen evolution, while PEDOT/PSS coating improves the round-trip efficiency, possibly acting as a redox shuttle for iron stripping reactions. These findings motivate the broader investigation and implementation of conductive polymers to engineer reaction selectivity for flow batteries and other electrochemical technologies. | Emre B. Boz; Ameya Bondre; Ronald de Bruijne; Antoni Forner-Cuenca | Materials Science; Polymer Science; Energy; Conducting polymers; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bcb6496dde43c9084abb65/original/conductive-polymer-coatings-control-reaction-selectivity-in-all-iron-redox-flow-batteries.pdf |
676191f3fa469535b9e78189 | 10.26434/chemrxiv-2024-19bp3 | Borohydride Oxidation as Counter Reaction in Reductive Electrosynthesis | An efficient reaction at the counter electrode is of key importance for the success of net oxidative and net reductive electrochemical transformations. For electrooxidative processes, cathodic proton reduction to H2 serves as the benchmark counter reaction. In contrast, net reductive electrochemical transformations have less attractive oxidative counter reactions to choose from and commonly rely on dissolution of a sacrificial anode that effectively results in stoichiometric metal consumption for the processes. In this study, we demonstrate that anodic borohydride oxidation has great potential to successfully replace the use of such sacrificial anodes for a variety of electroreductive organic transformations. This anodic transformation effectively serves as the inverse of cathodic proton reduction, producing H2 using inert carbon-based electrode materials. | Julius Kuzmin; Malin Lill; Guillermo Ahumada; Ellymay Goossens; Astrid Kjaer Steffensen; Anders Riisager; Helena Lundberg | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676191f3fa469535b9e78189/original/borohydride-oxidation-as-counter-reaction-in-reductive-electrosynthesis.pdf |
60c75566ee301cef3cc7b192 | 10.26434/chemrxiv.14101535.v1 | Unraveling the Effect of Defects, Domain Size, and Chemical Doping on Photophysics and Charge Transport in Covalent Organic Frameworks | We present a novel theoretical
approach to understanding the effect of electronic defects, domain size, and chemical
dopants on the infrared spectral line shape and three-dimensional charge
transport of positively charged polarons (“holes”) in doped (and undoped) Covalent
Organic Frameworks (COFs). The simulated spectra are in excellent agreement
with very recent measurements conducted on Iodine doped COF films. Through a
detailed systematic analysis, we can also determine the polaron coherence
lengths both along the 2D COF plane (intraframework) and through the molecular
columns (interframework). The coherence lengths are important quantities in
determining the anisotropic charge mobilities and conductivities in such films
and are therefore of major interest in understanding the operation of organic
electronic devices such as transistors and solar cells. By obtaining the first
quantitative agreement with iodine doped TANG-COF, we identify well defined
spectral signatures that provides conclusive evidence on why doped COFS have so
far shown lower bulk conductivity compared to doped polythiophenes. | Raja Ghosh; Francesco Paesani | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75566ee301cef3cc7b192/original/unraveling-the-effect-of-defects-domain-size-and-chemical-doping-on-photophysics-and-charge-transport-in-covalent-organic-frameworks.pdf |
60c750cf567dfe47d9ec5921 | 10.26434/chemrxiv.13031183.v2 | A Convenient Way for the Synthesis of Mono N-Alkylated Ethanolamine | <p><i>N-</i>alkylated ethanol amines,
especially the <i>N-</i>monoalkylated
ethanol amines, feature widely applications in industries. This manuscript
would introduce a new methodology to prepare <i>N-</i>monoalkylated ethanol amine derivatives that could avoid potential
side reactions forming <i>N,N-</i>dialkylated
by-products.</p> | ZHE LI; Changren Yan | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750cf567dfe47d9ec5921/original/a-convenient-way-for-the-synthesis-of-mono-n-alkylated-ethanolamine.pdf |
628e895ed5555085bda798d2 | 10.26434/chemrxiv-2022-0gj08 | Qualitative Analysis of Real Drug Evidence using DART-MS and the Inverted Library Search Algorithm | Chromatographic-less mass spectrometry techniques like direct analysis in real time mass spectrometry (DART-MS) are steadily being employed as seized drug screening tools. However, these newer analytical platforms require new computational methods to best make-use of the collected data. The inverted library search algorithm (ILSA) is a recently developed method designed specifically for working with mass spectra of mixtures collected with DART-MS, and has been implemented as a function in the NIST/NIJ DART-MS Data Interpretation Tool (DIT). This paper demonstrates how DART-MS and the ILSA/DIT can be used to analyze seized drug evidence, while discussing insights gathered during the evaluation of several adjudicated case samples. The evaluation verified that the combination of DART-MS and the ILSA/DIT can be used as an informative tool to help analysts screen seized drug evidence, but also revealed several factors an analyst must consider while employing these methods—all of these considerations are summarized in this paper. | Edward Sisco; Meghan G. Appley; Stephen S. Tennyson; Arun S. Moorthy | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e895ed5555085bda798d2/original/qualitative-analysis-of-real-drug-evidence-using-dart-ms-and-the-inverted-library-search-algorithm.pdf |
60c743f5469df4625bf43288 | 10.26434/chemrxiv.9729338.v1 | Biofunctional Catheter Coatings Based on Chitosan-Fatty Acids Derivatives | Multifunctional and biofunctional coatings for medical devices are an attractive strategy towards tailoring the interactions of the device with the body, thereby influencing the host response, and the susceptibility to microbial colonization. Here we describe the development of a coating process to yield amphiphilic, lubricious coatings, resistant to bacterial colonization, based on chitosan. Chitosan-fatty acid derivatives were obtained by simultaneous O,N-acylation of chitosan with either linoleic, alpha-linolenic, or dilinoleic acid. Chemical characterization of new materials was carried out using <sup>1</sup>H NMR, FTIR, and XPS. Surface properties of coated polyester samples were studied using SEM and contact angle measurements, which indicated that the incorporation of hydrophobic constituents into chitosan macromolecules led to a decrease of both surface roughness and water contact angle. Importantly, tribological testing demonstrated that these new coatings decrease the coefficient of friction due to the self-organization of fatty acid (from 0.53 for the neat chitosan to 0.35 for chitosan-fatty acid derivative). Meanwhile, preliminary bacterial colonization tests indicated significant—over 80%—reduction in <i>E. coli</i> colonization following coating with chitosan-linoleic and chitosan-alpha-linolenic derivatives. Finally, cytotoxicity and hemocompatibility studies confirmed that all amphiphilic chitosan-fatty acid derivatives were non-toxic and non-hemolytic. Collectively, our results demonstrate the potential of the developed coating strategy, particularly the chitosan-linoleic and chitosan-alpha-linolenic acid derivatives, for applications as biofunctional catheter coatings. | Agata Niemczyk; Agata Goszczynska; Monika Gołda-Cępa; Andrzej Kotarba; Peter Sobolewski; Miroslawa El Fray | Biocompatible Materials; Coating Materials; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f5469df4625bf43288/original/biofunctional-catheter-coatings-based-on-chitosan-fatty-acids-derivatives.pdf |
63043bc7d147b2210bb5009e | 10.26434/chemrxiv-2022-jkzp3 | Bioinspired gradient stretchable aerogels for ultrabroad-response-range wearable pressure sensors | With the increasing demand for electronic skin, health management, and extreme pressure monitoring, development of broad-response-range flexible pressure sensors is in urgent need. However, the reported flexible pressure sensors usually show a narrow detection range. It’s a great challenge to achieve a broad detection range of 1 Pa-10 MPa for a flexible pressure sensor. Herein, unprecedented bioinspired wearable pressure sensors based on highly stretchable reduced graphene oxide/polyurethane foam composite aerogels with modulus-gradient porous structures have been reported. A hot pressing method is applied to increase the modulus and compressive strength of the high-modulus layer of the aerogel, which ensures their compressibility at high pressures and significantly enhances the upper detection limit. Benefiting from their unique superelastic (90-99% reversible strain) and gradient structures with the gradient modulus spanning from 5.4 kPa to 430 kPa and gradient compressive stress (at 90% strain) spanning from 25 kPa to 37 MPa, the resulting pressure sensors exhibit a record-breaking detection range of 1 Pa-12.6 MPa. In addition, the pressure sensors can withstand 10000 cycles at a high pressure of 1 MPa, which can’t be achieved by traditional flexible pressure sensors. This work provides a versatile and powerful strategy towards next-generation high-performance broad-response-range flexible electronics. | Xiaoyu Zhang; Zhenyu Hu; Xing Liang; Qi Sun; Jia Huang; Guoqing Zu | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63043bc7d147b2210bb5009e/original/bioinspired-gradient-stretchable-aerogels-for-ultrabroad-response-range-wearable-pressure-sensors.pdf |
64d0db394a3f7d0c0dc103df | 10.26434/chemrxiv-2023-j88dg | Sample Efficient Reinforcement Learning with Active Learning for Molecular Design | Reinforcement learning (RL) is a powerful and flexible paradigm for searching for solutions in high-dimensional action spaces. However, bridging the gap between playing computer games with thousands of simulated episodes and solving real scientific problems with complex and involved environments (up to actual laboratory experiments) requires improvements in terms of sample efficiency to make the most of expensive information. The discovery of new drugs is a major commercial application of RL, motivated by the very large nature of the chemical space and the need to perform multiparameter optimization (MPO) across different properties. In silico methods, such as virtual library screening (VS) and de-novo molecular generation with RL, show great promise in accelerating this search. However, incorporation of increasingly complex computational models in these workflows requires increasing sample efficiency. Here, we introduce an active learning system linked with an RL model (RL-AL) for molecular design, which aims to improve the sample-efficiency of the optimization process. We identity and characterize unique challenges combining RL and AL, investigate the interplay between the systems, and develop a novel AL approach to solve the MPO problem. Our approach greatly expedites the search for novel solutions relative to baseline-RL for simple ligand- and structure-based oracle functions, with a 1000-75 000%-increase in hits generated for a fixed oracle budget and a 14-65-fold reduction in computational time to find a specific number of hits. Furthermore, compounds discovered through RL-AL display substantial enrichment of a multi-parameter scoring objective, indicating superior efficacy in curating high-scoring compounds, without a reduction in output diversity. This significant acceleration improves the feasibility of oracle functions that have largely been overlooked in RL due to high computational costs, for example free energy perturbation methods, and in principle is applicable to any RL domain. | Michael Dodds; Jeff Guo; Thomas Löhr; Alessandro Tibo; Ola Engkvist; Jon Paul Janet | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d0db394a3f7d0c0dc103df/original/sample-efficient-reinforcement-learning-with-active-learning-for-molecular-design.pdf |
60c740e04c891902a9ad21e0 | 10.26434/chemrxiv.7841555.v1 | Tradeoffs and Compatibilities of Chemical Properties in CpHqFrOs System | <p>To comply with the Kigali amendment to the Montreal Protocol in
2016, it becomes an urgent matter to develop new refrigerants with low global
warming potential with simultaneously meeting conventional requirements of
cooling performance, safety, and non-destructive to the ozone layer. Because
each requirement links to different chemical property, proper control of
various chemical properties is necessary to achieve the requirements. However,
it seems to be extremely difficult to satisfy all the requirements simultaneously
due to the tradeoffs among the properties. For this reason, we need to
correctly recognize how these chemical properties behave when the composition
of molecule is changed. Here we have done in silico screening that combines
quantum chemical calculation, machine learning, and database search, where
10,163 molecules were exhaustively investigated within the properly imposed
constraints, then we have found several candidates for new refrigerants. It should
be noted that the synthesis of refrigerants is more difficult than that of
ordinary organic molecules because glassware cannot be used for the synthesis
of fluorine-containing molecules that most refrigerants apply. This makes in
silico screening a more useful approach in the design of refrigerants. </p> | Yasuharu Okamoto | Theory - Computational; Quantum Computing; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e04c891902a9ad21e0/original/tradeoffs-and-compatibilities-of-chemical-properties-in-cp-hq-fr-os-system.pdf |
64e3a2fd01042bc1cc71a1e1 | 10.26434/chemrxiv-2023-9b6v1 | The Utility of Thiocarbohydrazide for Generating Novel Triazole and Pyrazole Derivatives Containing a Sulfur Moiety as Anti-microbial Agents | A crucial class of chemicals with uses in numerous fields is the thiocarbohydrazide class. This study aims to investigate the efficiency of thiocarbohydrazide (1) for creating innovative triazole and pyrazole derivatives that include a sulfur moiety with prospective biological activity, as the chemistry of thiocarbohydrazides has drawn increased interest in both synthetic organic chemistry and biological domains. When thiocarbohydrazide (1) intereacts with carboxylic acids 2a-c (stearic acid, gallic acid and 4-hydrobenzoic acid) afforded the corresponding 4H-1,2,4-triazole deivatives 3a-c, which ultimately underwent a reaction with salicylic acid 4, chloroacetic acid 6, 2-bromo-1,3-diphenylpropane-1,3-dione (9), ethyl cyanoacetate, furan-2-carbaldehyde (15) and acetylacetone 17 to afford the respective triazolo[3,4-b][1,3,4]thiadiazole derivative 5b, 7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazine derivatives 8a-c, 11a-c, 13, 5-(furan-2-yl)-4H-1,2,4-triazole-3-thiol (16) and 3,5-dimethyl-1H-pyrazole-1-carbothiohydrazide (18). Each constructed product's molecular structure was reinforced by executing IR, 1H NMR, and mass spectrometry techniques. Some of the constructed chemicals' anti-bacterial and anti-fungal effectiveness was also evaluated against Staphylococcus aureus ATCC 25923 (Gram Positive Bacteria), Proteus vulgaris RCMB 004 (1) ATCC 13315 (Gram Negative Bacteria), Aspergillus fumigatus (RCMB 002008) and Candida albicans RCMB 005003 (1) ATCC 10231 (Fungi). According to these research findings, some of the examined compounds have promising antimicrobial properties. | Marwa Fouad | Organic Chemistry; Bioorganic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2023-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e3a2fd01042bc1cc71a1e1/original/the-utility-of-thiocarbohydrazide-for-generating-novel-triazole-and-pyrazole-derivatives-containing-a-sulfur-moiety-as-anti-microbial-agents.pdf |
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