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637543a853ab80468028250c | 10.26434/chemrxiv-2022-844vc | Acetylcholinesterase (AchE) receptor-based In-Silico drug discovery for Alzheimer’s Disease | In Alzheimer’s disease acetylcholine esterase is a lead enzyme for increasing the patient
health. The current most effective drug donepezil in this paper the donepezil core which
is not participating in receptor-ligand binding was substituted with another core and the
the library was prepared. Computer-aided drug design (CADD), especially in the field of structure-based plays a significant role in the design and optimization of drug-like molecules, in CADD
virtual screening remains at the top, the virtual screening is used to screen the library
generated against the receptor. Molecular docking analysis was used for the analysis of the
analyzing the ligand and receptor docking. The docked compounds were then further
analyzed to check their drug-likeness properties and the parameters like receptor-ligand
binding energy and their modes of interaction distance from the active site of the receptor
were done further synthetic and biological assays can be performed for a details analysis of
drug activity and study of the pharmacokinetics and pharmacodynamic properties of the
drug. | Rajesh Kumar Sahoo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637543a853ab80468028250c/original/acetylcholinesterase-ach-e-receptor-based-in-silico-drug-discovery-for-alzheimer-s-disease.pdf |
60c73f1f0f50dbe6f9395744 | 10.26434/chemrxiv.5917330.v2 | A Toolkit to Quantify Target Compounds in Thin Layer Chromatography Experiments | Thin layer chromatography (TLC) is one of the basic experimental procedures in chemistry and allows the demonstration of various chemical principles in an educational setting. An often-overlooked aspect of TLC is the capability to quantify isolated target compounds in an unknown sample. Here, we present a suitable route to implement quantitative analysis in a lesson plan. We provide a free, stand-alone software that allows students to obtain quantitative information and present two suitable experiments, namely the absorbance-based quantification of the colorant Sudan IV and the fluorescence-based quantification of Rhodamine 6G, a fluorophore widely used in biotechnology. Students conduct TLC experiments following established routes, then take pictures of their TLC plates with their mobile phones and finally quantify the amount of different compounds in the separate bands they observe. | Stuart Ibsen; Niamh Mac Fhionnlaoich; Luis Serrano; Alaric Taylor; Runzhang Qi; Stefan Guldin | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1f0f50dbe6f9395744/original/a-toolkit-to-quantify-target-compounds-in-thin-layer-chromatography-experiments.pdf |
62fdff841045f0b800fd82dc | 10.26434/chemrxiv-2022-4jd98 | Cu-Mediated Thianthrenation and Phenoxathiination of Arylborons | Great success in synthetic chemistry is motivated by the development of novel and reactive linchpins for carbon-carbon and carbon-heteroatom bond formation reactions, that has dramatically altered chemists’ approach to building molecules. Herein, we report the readily synthesis of aryl sulfonium salts, a novel versatile electrophilic linchpin, via an unprecedented Cu-mediated thianthrenation and phenoxathiination of commercially available arylborons with thianthrene and phenoxathiine, providing a series of aryl sulfonium salts in high efficiency. More importantly, by leveraging the sequential Ir-catalyzed C–H borylation and Cu-mediated thianthrenation of arylborons, the formal thianthrenation of arenes are also achieved. As the Ir-catalyzed C–H borylation with undirected arenes normally occurred at the less steric hindrance position, thus providing a complementary method for thianthrenation of arenes in comparison with the electrophilic thianthrenation. This process is capable of late-stage functionalization of a series of pharmaceuticals, which might find wide synthetic applications in both industry and academic sectors. | Xiao-Yue Chen; Yichen Wu; Jia-Hui Bai; Yin-Long Guo; Peng Wang | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fdff841045f0b800fd82dc/original/cu-mediated-thianthrenation-and-phenoxathiination-of-arylborons.pdf |
60c755f6567dfe81d3ec63a3 | 10.26434/chemrxiv.14175383.v1 | Towards an Understanding of Ligand Induced Functional Conformational Changes of MexB Efflux Transporter | <p>MexB, an RND-superfamily efflux pump, plays a vital role in
conferring resistance to cytotoxic molecules, including antibiotics, upon Gram-negative
bacteria. Although the principal mechanistic elements of switching between the
access, binding and extrusion conformers of the protomers of tripartite efflux
transporters have been described previously, details surrounding the further
mechanism that ends in either substrate extrusion or pump inhibition are
limited to observations based on the type of ligand bound to the transporter. A
central but missing link in the structure/mechanism relationship is a
description of how ligand-induced conformational changes in the presence of a
membrane and changing transporter protonation state lead to either substrate
extrusion or inhibition of the pump. Here, we report that differences in
conformational changes are governed by ligand binding to the transporter. The
current study describes important new information about ligand-induced
structural rearrangements and conformational changes of MexB in relation to the
protonation state of critical acidic residues. We used tetracycline (TET) as a
model substrate of MexB and phenylalanine-arginine beta-naphthylamide (PAβN) as a
model inhibitor of MexB to study the aforementioned conformational changes. This new information will contribute
to the design of new, effective and selective efflux pump inhibitors that could
play key roles in reversing antimicrobial resistance.</p> | Khondaker Miraz Rahman; Shirin Jamshidi; J Mark Sutton; Sara Jambarsang | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755f6567dfe81d3ec63a3/original/towards-an-understanding-of-ligand-induced-functional-conformational-changes-of-mex-b-efflux-transporter.pdf |
64c88fe6ce23211b20e9ffb7 | 10.26434/chemrxiv-2023-wbm3p | Diastereoselective congested β-amido ketone synthesis via
NHC-catalyzed radical–radical coupling
| N-Heterocyclic carbene catalysis merging with photoredox PCET enabled amidoacylation of alkenes to construct sterically congested cyclic β-amido ketone skeleton bearing α-tertiary or quaternary carbon centers with high diastereoselectivity. The reaction involves generating amidyl radicals via oxidative PCET under photoredox catalysis, followed by rapid intramolecular cyclization to form the carbon-centered radical. The precise control of electron transfer in the two radical generation mechanisms is required to achieve this diastereoselective radical–radical coupling. The photocatalyst 3CzClIPN greatly facilitates this reaction based on its high oxidation potential and moderate reduction potential. The correlation between the redox potential of the photocatalyst and the yield provides an analogy for the reaction mechanism. Further transformation of the product afforded acyclic 3-amino butane-1,4-diol as a single diastereomer. This protocol allows the mild synthesis of structurally crowded bioactive molecules. | Yukiya Sato; Yusuke Miyamoto; Takanori Matsui; Yuto Sumida; Hirohisa Ohmiya | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c88fe6ce23211b20e9ffb7/original/diastereoselective-congested-amido-ketone-synthesis-via-nhc-catalyzed-radical-radical-coupling.pdf |
62a844d9804dbe0853454e66 | 10.26434/chemrxiv-2022-wcnn3-v2 | Diffusion of Water Confined between Graphene Oxide Layers: Implications for Membrane Filtration | Among the carbon-based two-dimensional materials, graphene oxide (GO) has been attracting a growing interest due to its capability to be utilized in the field of water remediation. Therefore, an atomistic understanding of the transport properties of water in layered GO is pivotal for the development of novel GO membranes. Surprisingly, the very issue of the two-dimensional self-diffusion of water confined between two GO sheets appears to be controversial and simulations showing either a slow-down or no effect have been reported. In any case the formation of Hydrogen bonds, i.e. among the confined water and between water and the GO functional groups, was identified to control diffusion. However, results of molecular dynamics simulations heavily depend on the used forces. Density functional theory and empirical force fields are on opposite when it comes to accuracy and numerical costs.
As a compromise in the present study we performed molecular dynamics simulations using a density functional theory-based tight method (xTB) to investigate the diffusion of water confined between GO sheets. Specifically, we considered six GO/water models, differing in the ordering of epoxide and hydroxyl groups as well as in the thickness of the water layer. For these models, having GO inter-layer distances between 8 and 12 \AA{} we find a reduction of the diffusion coefficient by a factor in between two and three as compared with bulk water.
One possible origin of this effect is the temporary trapping of water within Hydrogen-bonded water bridges between the GO sheets. The proposed mechanism should be taken into account when developing, for instance, GO membranes for water remediation or applications in the field of selective transport in separation membranes. | Moyassar Meshhal; Oliver Kuehn | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a844d9804dbe0853454e66/original/diffusion-of-water-confined-between-graphene-oxide-layers-implications-for-membrane-filtration.pdf |
624d4c8d3affe485d340f116 | 10.26434/chemrxiv-2022-wfhc5 | Palladium-Catalyzed Tandem Ester Dance/Decarbonylative Cou-pling Reactions | “Dance reaction” on the aromatic ring is a powerful method in organic chemistry to translocate functional groups on arene scaffolds. Notably, dance reactions of halides and pseudo-halides offer a unique platform for the divergent synthesis of substituted (het-ero)aromatic compounds when combined with transition-metal-catalyzed coupling reactions. Herein, we report a tandem reaction of ester dance and decarbonylative coupling enabled by palladium catalysis. In this reaction, 1,2-translocation of the ester moiety on the aromatic ring is followed by decarbonylative coupling with nucleophiles to enable the installation of a variety of nucleophiles at the posi-tion adjacent to the ester in the starting material. The key to this reaction is to use dcypt, an electron-rich, bulky diphosphine ligand. Vari-ous decarbonylative couplings such as C–H arylation, amination, intramolecular etherification, and intermolecular arylation are success-fully executed following the ester dance. | Masayuki Kubo; Naomi Inayama; Eisuke Ota; Junichiro Yamaguchi | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624d4c8d3affe485d340f116/original/palladium-catalyzed-tandem-ester-dance-decarbonylative-cou-pling-reactions.pdf |
60c743f6ee301c3437c790aa | 10.26434/chemrxiv.9124730.v2 | Macroporous Poly(norbornadiene) is a Fast Oxygen Scavenger Material at Room Temperature | Emulsion templated norbornadiene is cured via ROMP yielding macroporous poly(norbornadiene)foams of 76% porosity exhibiting appealing stiffness combined with considerable ductility. The foams are readily oxidized in the presence of air at room temperature exhibiting an oxygen uptake capacity of more than 300 mg O<sub>2</sub>/g foam. In closed volumes of air a final oxygen level of a maximum of 5 ppm can be achieved after several hours at room temperature. The synergism of the porous morphology and the chemical nature of the polymer allows for the first example of a purely organic oxygen scavenger material with properties distinctly surpassing the state-of-the art in the field.<br /> | Efthymia Vakalopoulou; Sergey M. Borisov; Christian Slugovc | Organic Polymers; Food | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f6ee301c3437c790aa/original/macroporous-poly-norbornadiene-is-a-fast-oxygen-scavenger-material-at-room-temperature.pdf |
65ef2638e9ebbb4db97490fd | 10.26434/chemrxiv-2024-kz9t8 | Exploring the Reactivity of Rigid 1-Azadienes Derived from Methylene γ-Lactams. Applications to the Stereoselective Synthesis of γ-Spirolactams. | A study on the reactivity of rigid 1-azadienes derived from methylene γ-lactams is reported. Through the functionalization of 1-amino α,β-unsaturated γ-lactam derivatives, easily available from a multicomponent reaction of amines, aldehydes and pyruvates it is possible to in situ generate rigid 1-azadienes locked by a γ-lactam core. The 4π-system of those rigid 1-azadienes can behave as both diene and dienophile species, through a spontaneous cyclodimerization reaction, or exclusively as dienes or dienophiles if they are trapped with imines or cyclopentadiene, respectively. The use of chiral rigid 1-azadienes as dienophiles in the cycloaddition reaction with cyclopentadiene leads to the formation of γ-spirolactams bearing four stereogenic centers in a highly stereospecific manner, reporting the first example of the use of methylene-γ-lactams in the synthesis of spirocycles. | Adrián López-Francés; Zuriñe Serna-Burgos; Xabier del Corte; Jesús M. de los Santos; Abel de Cózar; Javier Vicario | Theoretical and Computational Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef2638e9ebbb4db97490fd/original/exploring-the-reactivity-of-rigid-1-azadienes-derived-from-methylene-lactams-applications-to-the-stereoselective-synthesis-of-spirolactams.pdf |
631120d849042ad153c8c4d8 | 10.26434/chemrxiv-2021-vr21g-v3 | Identification of single Ru(II) ions on ceria as a highly active catalyst for abatement of NOx pollutants | Atom trapping allows to prepare catalysts with atomically dispersed Ru ions Ru1O5 on (100) facets of ceria, as identified by EXAFS, infra-red spectroscopy and DFT calculations. This is a new class of ceria-based materials with Ru properties drastically different from the known M/ceria materials. They show excellent activity in industrially important catalytic NO oxidation reaction, a critical step that requires use of large loadings of expensive noble metals in diesel aftertreatment systems. Ru1/CeO2 catalysts are stable during continuous cycling, ramping and cooling as well as presence of moisture. Furthermore, Ru1/CeO2 shows unprecedentedly high NOx storage properties during cold start due to formation of stable Ru-NO complexes as well as high spill-over rate of NOx to the support. Only ~0.05 wt% of Ru is required to have excellent NOx storage. Single Ru ions forming Ru1O5 sites exhibit remarkably higher stability during calcination in air/steam up to 750 ºC in contrast to RuO2 nanoparticles that become volatile at temperature slightly above ambient. We clarify the location of Ru(II) ions on the ceria surface and experimentally identify mechanism of NO oxidation (as well as reactive storage) using DFT calculations and in-situ DRIFTS/Mass-spectroscopy measurements. Furthermore, we show the high reactivity of Ru1/CeO2 for NO reduction by CO: only 0.1-0.5 wt% of atomically dispersed Ru is sufficient to achieve high activity at low temperatures. With the aid of excitation-modulation in-situ infra-red measurements and XPS measurement, we uncover the individual elementary steps of NO reduction by CO on an atomically dispersed ceria-supported catalyst, highlighting the unique properties of Ru1/CeO2 catalyst and its propensity to form oxygen vacancies/Ce+3 sites that are critical for NO reduction even at low Ru loadings. Our study highlights the applicability of novel ceria-based single-atom catalysts to industrially relevant NO and CO abatement. | Konstantin Khivantsev; Nicholas R. Jaegers; Hristiyan A. Aleksandrov; Libor Kovarik; Mark Engelhard; Inhak Song; Jinshu Tian; Linxiao Chen; Debora Meira; Xavier Isidro Pereira Hernandez; Georgi N. Vayssilov; Yong Wang; János Szanyi | Physical Chemistry; Catalysis; Nanoscience; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631120d849042ad153c8c4d8/original/identification-of-single-ru-ii-ions-on-ceria-as-a-highly-active-catalyst-for-abatement-of-n-ox-pollutants.pdf |
6116610103182f06801f3b48 | 10.26434/chemrxiv-2021-c3zxp | ‘Cookies on a tray’: Superselective Hierarchical Microstructured Poly(L-lactide) Surface As a Decoy For Cells | In this research we developed a micro-sized hierarchical structures on a poly(L-lactide) (PLLA) surface. The obtained structures consist of round-shaped protrusions with a diameter of ~20 µm, a height of ~3 µm, and the distance between them ~ 30 µm. We explored the effect of structuring PLLA to design a non-cytotoxic material with increased roughness to encourage cells to settle on the surface. The PLLA foils were prepared using the casting melt extrusion technique and were modified using ultra-short pulse irradiation – a femtosecond laser operating at λ=1030 nm. A hierarchical microstructure was obtained resembling 'cookies on a tray'. The cellular response of fibro- and osteoblasts cell lines was investigated. The conducted research has shown that the laser-modified surface is more conducive to cell adhesion and growth (compared to unmodified surface) to such an extent that allows the formation of highly-selectively patterns consisting of living cells. In contrast to eukaryotic cells, the pathogenic bacteria Staphylococcus aureus covered modified and unmodified structures in an even, non-preferential manner. In turn, adhesion pattern of eukaryotic fungus Saccharomyces boulardii resembled that of fibro- and osteoblast cells rather than that of Staphylococcus. The discovered effect can be used for fabrication of personalized and smart implants in regenerative medicine. | Bartłomiej Kryszak; Konrad Szustakiewicz; Paulina Dzienny; Adam Junka; Justyna Paleczny; Patrycja Szymczyk-Ziółkowska; Viktoria Hoppe; Michał Grzymajło; Arkadiusz Antończak | Materials Science; Polymer Science; Biocompatible Materials; Biodegradable Materials; Materials Processing; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6116610103182f06801f3b48/original/cookies-on-a-tray-superselective-hierarchical-microstructured-poly-l-lactide-surface-as-a-decoy-for-cells.pdf |
67dc1456fa469535b9f337e6 | 10.26434/chemrxiv-2025-c04n1 | Anti-inflammatory effects of polyglycerol sulfates and natural polyanions in type 2 inflammation | Type 2 inflammation is an essential defense mechanism of the innate and adaptive immune systems, but when dysregulated, it can cause chronic atopic diseases like allergic asthma and atopic dermatitis. Thymic stromal lymphoprotein (TSLP) helps drive type 2 inflammation by guiding T cells toward a type 2 helper cell (TH2) subtype and stimulating B cells’ antibody production. Fibronectin (FN) has recently been found at elevated levels in the plasma of children with atopic dermatitis and shown a potential proinflammatory role in bronchial epithelium tissue models. Both proteins’ surface charges suggest potential interaction with charged molecules. Seeking new strategies against type 2 inflammation, we found that negatively charged polyglycerol sulfates strongly bind to TSLP and FN. We confirmed that these molecules inhibit inflammation by reducing the TSLP-mediated type 2 polarization of CD4+ T cells. We found that adding polyglycerol sulfate to FN-triggered inflamed bronchial epithelium models reduced TSLP expression and interleukin 6 secretion. | Clemens Krage; Peyman Malek Mohammadi Nouri; Jens Dernedde; Jayachandran N. Kizhakkedathu; Sarah Hedtrich; Rainer Haag; Katharina Achazi | Biological and Medicinal Chemistry; Biochemistry | CC BY 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dc1456fa469535b9f337e6/original/anti-inflammatory-effects-of-polyglycerol-sulfates-and-natural-polyanions-in-type-2-inflammation.pdf |
60c74a9dee301ce9bec79c90 | 10.26434/chemrxiv.12234665.v1 | One-Pot Synthesis and Conformational Analysis of 6-Membered Cyclic Iodonium Salts | In this article we describe an efficient approach for the synthesis of cyclic diaryliodonium salts. The method is based on benzyl alcohols as starting materials and consists of an Friedel-Crafts-arylation/oxidation sequence. Besides a deep optimization, particluar focusing on the choice and ratios of the utilized Bronsted-acids and oxidants, we explore the substrate scope of this transformation. We also discuss an interesting isomerism of cyclic iodonium salts substituted with aliphatic substituents at the bridge head carbon. <br /> | Lucien Caspers; Julian Spils; Mattis Damrath; Enno Lork; Boris Nachtsheim | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a9dee301ce9bec79c90/original/one-pot-synthesis-and-conformational-analysis-of-6-membered-cyclic-iodonium-salts.pdf |
678a839681d2151a0289bd1b | 10.26434/chemrxiv-2025-2931g | Synthesis of the spirotetracyclic core of the ginkgolides via a malonyl radical cascade | The ginkgolides are a family of terpene trilactone natural products exclusive to the Ginkgo biloba tree. Here, we present a concise synthesis of their spirotetracyclic core via a manganese(III)-mediated oxidative radical cascade. Beginning from six simple starting materials, this route enables the diastereoselective synthesis of rings A, B, D and E of the natural product in nine steps, laying the foundations for their total synthesis. | Jonathan Burton; Pol Hernández-Lladó; Kirsten Christensen | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a839681d2151a0289bd1b/original/synthesis-of-the-spirotetracyclic-core-of-the-ginkgolides-via-a-malonyl-radical-cascade.pdf |
60c75361842e653c42db3f59 | 10.26434/chemrxiv.13484763.v1 | Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes | <div>CAMKK2 is a serine/threonine kinase and an activator of AMPK whose dysregulation is linked
with multiple diseases. Unfortunately, STO-609, the tool inhibitor commonly used to probe
CAMKK2 signaling, has limitations. To identify promising scaffolds as starting points for the
development of high-quality CAMKK2 chemical probes, we utilized a hinge-binding scaffold hopping strategy to design new CAMKK2 inhibitors. Starting from the potent but promiscuous
disubstituted 7-azaindole GSK650934 (CAMKK2 IC50 = 3 nM), a total of 32 compounds,
composed of single ring, 5,6-, and 6,6-fused heteroaromatic cores were synthesized. The
compound set was specifically designed to probe interactions with the kinase hinge-binding
residues. These compounds were evaluated in vitro in biochemical and cellular assays for
CAMKK2 inhibition. Compared to GSK650394 and STO-609, thirteen of our compounds
displayed similar or better CAMKK2 inhibitory potency in vitro, while compounds 13g and 45
had greatly improved selectivity for CAMKK2 across the kinome. Our systematic survey of hinge
binding chemotypes identified several potent and selective inhibitors of CAMKK2 to serve as
starting points for medicinal chemistry programs aimed at the identification of CAMKK2 chemical
probes and clinical candidates<br /></div> | benjamin eduful; Sean O'Byrne; Louisa Temme; Christopher R. M. Asquith; Yi Liang; Alfredo Picado; Joseph Pilotte; Carrow Wells; William Zuercher; Carolina Catta-Preta; Priscila Zonzini Ramos; André Santiago; rafael Counago; Christopher G Langendorf; Kevin Nay; Jonathan S Oakhill; Thomas L Pulliam; Chenchu Lin; Dominik Awad; Timothy M. Willson; Daniel E Frigo; John W. Scott; David Drewry | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75361842e653c42db3f59/original/hinge-binder-scaffold-hopping-identifies-potent-calcium-calmodulin-dependent-protein-kinase-kinase-2-camkk2-inhibitor-chemotypes.pdf |
65205c2bbda59ceb9a03715a | 10.26434/chemrxiv-2023-dq6hn-v2 | Continuous Real-Time Detection of Serotonin using Aptamer-Based Electrochemical Biosensor | Serotonin (5-HT) is a critical neurotransmitter involved in many neuronal functions, and 5-HT depletion has been linked to several mental diseases. The fast release and clearance of serotonin in the extracellular space, low analyte concentrations and a multitude of interfering species make detection of serotonin challenging. This work presents an electrochemical aptamer-based biosensing platform that can monitor 5-HT continuously with high sensitivity and selectivity. Our electrochemical sensor showed a response time of approximately 1 minute to a step change in the serotonin concentration (from 0 to 25 nM) in continuous monitoring using single frequency EIS (electrochemical impedance spectroscopy) technique. The developed sensing platform was able to detect 5-HT in the range 25 nM – 100 nM in the continuous sample fluid flow. The electrochemical sensor showed promising selectivity against other species with similar chemical structures and redox potentials including dopamine (DA), norepinephrine (NE), L-tryptophan (L-TP), 5-hydroxyindoleacetic acid (5-HIAA), and 5-hydroxytryptophan (5-HTP). The proposed sensing platform is able to achieve time resolution on the order of a minute with high selectivity in the nanomolar range demonstrating a potential for monitoring serotonin from neurons in organ-on-a-chip or brain-on-a-chip-based platforms. | Habib M. N. Ahmad; Arturo Andrade; Edward Song | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Electrochemical Analysis; Bioengineering and Biotechnology | CC BY NC 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65205c2bbda59ceb9a03715a/original/continuous-real-time-detection-of-serotonin-using-aptamer-based-electrochemical-biosensor.pdf |
61a8dda9a02d164816e13cbb | 10.26434/chemrxiv-2021-q62pm | Facile synthesis of biomass-based carbon materials nano-Ni-based catalysts and its application in selective hydrogenation of alkynes | The development of high efficiency, excellent selectivity, and super activity metal catalyst for chemical selective hydrogenation of alkynes to olefin is of great significance in the field of the chemical industry. At the same time, the development of a large number of available base metal catalysts for organic conversion remains an important objective of chemical research. Herein, we report a facile preparation of a simple, high catalytic activity, environmentally friendly, and inexpensive biomass carbon material supported nano-nickel catalyst from lignin residue. The entire preparation process of the catalyst is simple, reliable, economical, and environmentally friendly, which provides a potential utilization prospect for large-scale industrial applications of biomass-based carbon material catalysts. Biomass-based lignin residues can not only reduce the high oxidation state of nickel ions into nickel nanoparticles by the in-situ reducing gas generated during the calcination process, but the mesoporous structure of lignin residue also promotes the adsorption of nickel metal, which greatly improved the catalytic activity of biomass-based Ni-based catalysts. The simple synthetic green, cost-effective and sustainable biomass-based Ni-based catalyst shows good performance in the selective hydrogenation of phenylacetylene, reaching 97.2% conversion and 84.3% styrene selectivity, respectively. | Jianguo liu; Jiangmin Sun; Longlong Ma | Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a8dda9a02d164816e13cbb/original/facile-synthesis-of-biomass-based-carbon-materials-nano-ni-based-catalysts-and-its-application-in-selective-hydrogenation-of-alkynes.pdf |
638f7f600a812737ebd5dd93 | 10.26434/chemrxiv-2022-575bs | Implementation of Real-Time TDDFT for Periodic Systems in the Open-Source PySCF Software Package | We present a new implementation of real-time time-dependent density functional theory (RT-TDDFT) for calculating excited-state dynamics of periodic systems in the open-source Python-based PySCF software package.
Our implementation uses Gaussian basis functions in a velocity gauge formalism and can be applied to periodic surfaces, condensed-phase, and molecular systems. As representative benchmark applications, we present optical absorption calculations of various molecular and bulk systems, and a real-time simulation of field-induced dynamics of a (ZnO)4 molecular cluster on a periodic graphene sheet. We present representative calculations on optical response of solids to infinitesimal external fields as well as real-time charge-transfer dynamics induced by strong pulsed laser fields. Due to the widespread use of the Python language, our RT-TDDFT implementation can be easily modified and provides a new capability in the PySCF code for real-time excited-state calculations of chemical and material systems. | Kota Hanasaki; Zulfikhar Ali; Min Choi; Mauro Del Ben; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Theory - Computational; Quantum Mechanics; Quasiparticles and Excitations | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638f7f600a812737ebd5dd93/original/implementation-of-real-time-tddft-for-periodic-systems-in-the-open-source-py-scf-software-package.pdf |
617c02497a002178c63ec690 | 10.26434/chemrxiv-2021-s599c | Probing a Local Viscosity Change at the Nematic-Isotropic Liquid Crystal Phase Transition by a Ratiometric Flapping Fluorophore | Local viscosity change in the thermal phase transition of a nematic liquid crystal, 5CB, has been analyzed by doping fluorescent viscosity probes, flapping fluorophores (FLAP) as well as a molecular rotor BODIPY-C12. As a result, only flapping anthraceneimide has successfully monitored a small viscosity change (corresponding to a few cP (centipoise) change in shear viscosity around 25 cP) in the nematic-to-isotropic phase transition by ratiometric spectroscopy. In addition, analysis of fluorescence anisotropy indicates that the emissive species (planarized flapping anthraceneimides) are aligned parallel to the director of 5CB in the nematic phase. | Ryo Kimura; Hidetsugu Kitakado; Takuya Yamakado; Hiroyuki Yoshida; Shohei Saito | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Optics; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617c02497a002178c63ec690/original/probing-a-local-viscosity-change-at-the-nematic-isotropic-liquid-crystal-phase-transition-by-a-ratiometric-flapping-fluorophore.pdf |
65d898779138d23161ce552c | 10.26434/chemrxiv-2024-p12qz | Modeling the initiation phase of the catalytic cycle in the glycyl-radical enzyme benzylsuccinate synthase | The reaction of benzylsuccinate synthase, the radical-based addition of toluene to a fumarate cosubstrate, is initiated by hydrogen-transfer from a conserved cysteine to the nearby glycyl radical in the active center of the enzyme. In this study we analyze this step by comprehensive computer modeling, predicting (i) the influence of bound substrates or products, (ii) the energy profiles of forward- and backward hydrogen-transfer reactions, (iii) their kinetic constants and potential mechanisms, (iv) enantiospecificity differences and (v) kinetic isotope effects. Moreover, we support several of the computational predictions experimentally, providing evidence for the predicted H/D-exchange reactions into the product and at the glycyl radical site. Our data indicate that the hydrogen transfer reactions between the active site glycyl and cysteine are principally reversible, but their rates differ strongly dependent on their stereochemical orientation, transfer of protium or deuterium, and the presence or absence of substrates or products in the active site. This is particularly evident for the isotope exchange of the remaining protium atom of the glycyl radical to deuterium, which appears dependent on substrate or product binding, explaining why it is observed in some, but not all glycyl-radical enzymes. | Maciej Szaleniec; Gabriela Oleksy; Anna Sekuła; Ivana Aleksić; Rafał Pietras; Marcin Sarewicz; Kai Krӓmer; Antonio J. Pierik; Johann Heider | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biophysics; Computational Chemistry and Modeling; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d898779138d23161ce552c/original/modeling-the-initiation-phase-of-the-catalytic-cycle-in-the-glycyl-radical-enzyme-benzylsuccinate-synthase.pdf |
60c743cdbb8c1aa6b93da3ca | 10.26434/chemrxiv.9639227.v1 | Halide Anion Activated Reactions of Michael Acceptors with Tropylium Ion | Tropylium bromide undergoes non-catalyzed,
regioselective additions to a large variety of Michael acceptors. In this way,
acrylic esters are converted into ß-bromo-α-cycloheptatrienyl-propionic esters.
The reactions are interpreted by nucleophilic attack of bromide ions at the
electron-deficient olefins and trapping of the incipient carbanion by the
tropylium ion. Quantum chemical calculations were performed to elucidate the
analogy to the amine or phosphine-catalyzed Rauhut-Currier reactions.
Subsequent synthetic transformations of the bromo-cycloheptatrienylated adducts
are reported. | Mohanad A. Hussein; Uyen P. N. Tran; Vien T. Huynh; Junming Ho; Mohan Bhadbhade; Herbert Mayr; Thanh Vinh Nguyen | Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743cdbb8c1aa6b93da3ca/original/halide-anion-activated-reactions-of-michael-acceptors-with-tropylium-ion.pdf |
622cb3b7bbeaf3005d065387 | 10.26434/chemrxiv-2022-480fn | Pendent trifluoroethanol reveals solvation dependent mechanisms of electrocatalytic CO2 reduction by rhenium(I) bipyridine fac-tricarbonyl | Local proton sources capable of interacting with catalytic intermediates have been shown to affect proton-dependent reactions. Herein we report the synthesis of a Re(diimine)(CO)3Cl catalyst analog containing a trifluoroethanol-appended bipyridine ligand (bpy-CF3OH), and the corresponding methyl-ether (bpy-CF3OMe) to study the role of the pendent proton donor in electrocatalytic CO2 reduction. Compared to the parent catalyst, Re(bpy)(CO)3Cl, and Re(bpy-CF3OMe)(CO)3Cl, the alcohol analog revealed additional electrocatalytic features and a 200 mV anodic shift in catalytic onset potential. We also show evidence of proton-coupled electron transfer or hydrogen bond-assisted catalysis in all analogs, detailed by a progressive anodic shift in the main catalytic wave with increasing [H2O] which displays slopes of ~120 mV log[H2O]–1. Multiple catalytic mechanisms appeared to occur simultaneously in all the analogs, and attempts were made to differentiate their dependence on [H2O] and [CO2]. The effect of a local proton source is significant under conditions where [H2O] < 1 M but becomes negligible at high [H2O]. These results suggest that the appended alcohol affects the solvation of the molecule, and may act directly as a proton source or as part of a proton shuttle. | Bradley Brennon; Danh Ngo; Wesley Kramer | Inorganic Chemistry; Catalysis; Electrochemistry; Small Molecule Activation (Inorg.); Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622cb3b7bbeaf3005d065387/original/pendent-trifluoroethanol-reveals-solvation-dependent-mechanisms-of-electrocatalytic-co2-reduction-by-rhenium-i-bipyridine-fac-tricarbonyl.pdf |
64532e2b27fccdb3ea74e373 | 10.26434/chemrxiv-2023-b1nr2 | Effect of Quantum Delocalization on Temperature Dependent Double Proton Transfer in Molecular Crystals of Terephthalic Acid | Double proton transfers (DPT) are important for several physical processes, both in molecules and in the condensed phase. While these have been widely studied in biological systems, their study in crystalline environments is rare. In this work, using Path Integral Molecular Dynamics simulations we have studied temperature dependent DPT in molecular crystals of terephthalic acid (TPA). In accordance with experimental reports, we find evidence for a double proton transfer induced order-to-disorder transition that is sensitive to the inclusion of nuclear quantum effects. Our simulations show that in addition to the presence of L and R tautomers of terepthalic acid, there are a small but non negligible concentration of positive and negatively charged pairs of TPA molecules. At the onset of the transition at low temperatures, DPT likely occurs through a tunnelling mechanism while at room temperature, likely involves the dominance of activated hopping. Through an analysis of the electronic structure of the system using Wannier functions, we show that the H atom shuttling between the donor and acceptor O atoms involves a proton. | Unmesh Mondal; Ivan Girotto; Ali Hassanali; Prasenjit Ghosh | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64532e2b27fccdb3ea74e373/original/effect-of-quantum-delocalization-on-temperature-dependent-double-proton-transfer-in-molecular-crystals-of-terephthalic-acid.pdf |
60c74de4ee301ca613c7a3b8 | 10.26434/chemrxiv.12671612.v1 | Does Tyrosine Protect S. Coelicolor Laccase from Oxidative Degradation? | We have investigated the roles of tyrosine (Tyr) and
tryptophan (Trp) residues in the four-electron reduction of oxygen catalyzed by
<i>Streptomyces coelicolor</i> laccase
(SLAC). During normal enzymatic turnover in laccases, reducing equivalents are
delivered to a type 1 Cu center (Cu<sub>T1</sub>) and then are transferred over
13 Å to a trinuclear Cu site (TNC: (Cu<sub>T3</sub>)<sub>2</sub>Cu<sub>T2</sub>)
where O<sub>2</sub> reduction occurs. The TNC in SLAC is surrounded by a large
cluster of Tyr and Trp residues that can provide reducing equivalents when the
normal flow of electrons is disrupted. Canters and coworkers have shown that
when O<sub>2</sub> reacts with a reduced SLAC variant lacking the Cu<sub>T1</sub>
center, a Tyr108<sup>·</sup>
radical near the TNC forms rapidly. We have found that ascorbate reduces the
Tyr108<sup>·</sup><sup> </sup>radical
in wild-type SLAC about 10 times faster than it reacts with the Cu<sub>T1</sub><sup>2+</sup>
center, possibly owing to radical transfer along a Tyr/Trp chain. Aerobic
oxidation of two reduced SLAC mutants (Y108F and W132F) leads to the formation
of a long-lived (~15 min) Tyr<sup>·</sup><sup> </sup>radical with distinct
absorption at 408 nm. The diffusion of redox equivalents away from the primary
enzymatic pathway in SLAC may indicate a poorly optimized enzyme or a mechanism
to protect against protein damage. | Patrycja Kielb; Harry B. Gray; Jay R. Winkler | Biocatalysis; Redox Catalysis; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de4ee301ca613c7a3b8/original/does-tyrosine-protect-s-coelicolor-laccase-from-oxidative-degradation.pdf |
678a7f056dde43c908f3ba14 | 10.26434/chemrxiv-2025-6mvmv | 2H Quadrupolar Coupling Constant: A Spectroscopic Ruler for Transition Metal–Hydride Bond Distances in Molecular and Surface Sites | Transition-metal hydrides (TMHs) find numerous applications across fields, from catalysis to H2 storage. Yet, determining the structure of TMHs can remain a challenge, as hydrogen is difficult to detect by X-ray based or classical spectroscopic techniques. Considering that deuterium isotope (D) is a quadrupolar nucleus (I = 1) and that a quadrupolar coupling constant (CQ) depends on the distance between D and its bonding partner E (dED), we evaluate this trend across molecularly-defined transition-metal deuterides (TMDs) through a systematic investigation across TM block elements using both computations and experiments. We show that the M–D bond distance (dMD) in [Å] correlates with the CQ values in [kHz] as dMD = 7.83(CQ + 28.7)-1/3 - independently from the nature of the TM - with an accuracy > 0.04-0.08 Å. Based on experimental CQ values measured by 2H solid-state NMR, this simple correlation is then used to obtain the M-D bond distances in two silica-supported TMDs (M = Zr and Ir), notable heterogeneous catalysts, representing early and late TMDs, where evaluating M-D bond distances by other means is very challenging. Considering the ease of measurement, this method is readily applicable to a large range of diamagnetic terminal M–Ds, from molecular to surface sites, making 2H NMR a method of choice to measure TMDs bond distances. | Domenico Gioffrè; Christophe Copéret; Cäcilie Müller; Scott R. Docherty; Alexander Yakimov | Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a7f056dde43c908f3ba14/original/2h-quadrupolar-coupling-constant-a-spectroscopic-ruler-for-transition-metal-hydride-bond-distances-in-molecular-and-surface-sites.pdf |
61de3399636cc9ac2947ec5f | 10.26434/chemrxiv-2022-kk0ww | Asymmetric Defluoroallylation of 4-Trifluoromethylpyridines Enabled by Umpolung C-F Bond Activation | Carbon-fluorine bond activation reaction of the trifluoromethyl group represent an important approach to fluorine-containing molecules. While selective defluorofunctionalization reactions of CF3-containing substrates have been achieved by invoking difluorocarbocation, difluorocarboradical, or difluoroorganometallic species as the key intermedi-ate, the transformations via fluorocarbanion mechanism remained a limited success. Furthermore, the enantioselective defluorotransformation of CF3 group has not yet been realized. Herein, we report a defluorofunctionalization reaction of 4-trifluoromethylpyridines involving pyridyldifluoromethyl anion as the key intermediate, which was developed based upon our previous studies on the N-boryl pyridyl anion chemistry. When combined with Ir-catalysis, asymmetric defluoroallylation of 4-trifluoromethylpyridines could be achieved to forge a difluoroalkyl-substituted chiral center. The present work opens up a new opportunity for the defluorofunctionalization of CF3 group, and provides new insights into the N-boryl pyridyl anion chemistry. | Fei-Yu Zhou; Lei Jiao | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61de3399636cc9ac2947ec5f/original/asymmetric-defluoroallylation-of-4-trifluoromethylpyridines-enabled-by-umpolung-c-f-bond-activation.pdf |
60c757170f50db53033981d8 | 10.26434/chemrxiv.14370308.v1 | Barrier-Free Microfluidic Paper Analytical Devices for Multiplex Colorimetric Detection of Analytes | <p>In recent years, microfluidic paper analytical devices (μPADs) have been extensively utilized to conduct multiplex colorimetric assays. Despite their simple and user-friendly operation, the need for patterning paper with wax or other physical barriers to create flow channels makes large scale manufacturing cumbersome. Moreover, convection of rehydrated reagents in the test zones leads to non-uniform colorimetric signals, which makes quantification challenging. To overcome these challenges, we present a new device design called barrier-free μPAD (BF-μPAD) that consists of a stack of two paper membranes having different wicking rates – the top layer acting as a fluid distributing layer and the bottom layer containing reagents for colorimetric detection. Multiple analytes can be detected using this assembly without the need to pattern either layer with wax or other barriers. In one embodiment, a device is capable of delivering the sample fluid to 20 distinct dried reagent spots stored on an 8cm x 2cm membrane in as few as 30 seconds. The multiplexing feature of BF-μPAD is demonstrated for colorimetric detection of salivary thiocyanate, protein, glucose, and nitrite. Most importantly, the device improves the limit of detection of colorimetric assays performed on conventional μPADs by more than 3.5x. To understand fluid imbibition in the paper assembly, the device geometry is modelled in COMSOL Multiphysics using Richards equation; the results obtained provide insights into the non-intuitive flow pattern producing perfectly uniform signals in the barrier-free assembly.<b></b></p> | Ayushi Chauhan; Bhushan Toley | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757170f50db53033981d8/original/barrier-free-microfluidic-paper-analytical-devices-for-multiplex-colorimetric-detection-of-analytes.pdf |
619f5d1b784805839a9a5940 | 10.26434/chemrxiv-2021-1j0cd-v3 | Environmentally friendly and roll-processed flexible organic solar cells based on PM6:Y6. | Organic Solar Cells (OSCs) have reached the highest efficiencies using lab-scale on active areas far below 0.1 cm^2. This tends to widen the so-called “lab-to-fab gap”, which is one of the most important challenges to make OSCs competitive. The most commonly used fabrication technique is spin-coating, which has poor compatibility with large-scale techniques and substantial material waste. Moreover, other techniques such as blade or slot-die coating are much more suitable for roll-to-roll manufacturing processes, which is one of the advantages the technology has compared, for example, to silicon solar cells. However, only a few studies report solar cells using these fabrication techniques. Additionally, for the environmentally friendly OSC scale-up, inks based on non-hazardous solvent systems are needed. In this work, slot-die coating has been chosen to coat the PM6:Y6 active layer, using o-xylene, a green solvent, without additives. The optimal coating parameters are defined through fine-tuning of the coating parameters, such as the drying temperature and solution concentration. Moreover, ternary devices with PCBM, and fully printed devices are also fabricated. Power conversion efficiencies of 6.26% and 7.16% are achieved for binary PM6:Y6 and ternary PM6:Y6:PCBM devices, respectively. | Marcial Fernández Castro; Jean Truer; Moises Espindola-Rodriguez; Jens Wenzel Andreasen | Organic Chemistry; Polymer Science; Energy; Conducting polymers; Organic Polymers; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619f5d1b784805839a9a5940/original/environmentally-friendly-and-roll-processed-flexible-organic-solar-cells-based-on-pm6-y6.pdf |
66dc164b12ff75c3a1a9eb85 | 10.26434/chemrxiv-2024-dnf75 | Facile Generation of ortho-Quinodimethanes Toward Polycy-clic Compounds | The Diels–Alder reaction is a cornerstone of organic synthesis, enabling the construction of complex molecular archi-tectures through the cycloaddition of a diene and a dienophile. Among the various dienes employed in this reaction, ortho-quinodimethane stands out as an exceptionally powerful intermediate due to its high reactivity, making it par-ticularly effective for constructing benzo-fused polycyclic skeletons found in biologically important molecules such as natural products and pharmaceuticals. [1–3] Although this method has been widely applied in total synthesis,[4–7] the requirement for the laborious preparation of its precursors remains a significant challenge. This study presents a so-lution through a conceptually distinct palladium-catalyzed generation of ortho-quinodimethane via a multicompo-nent assembly reaction of readily available chemicals, specifically 2-vinylbromoarenes, diazo species, and carbon nucleophiles bearing a dienophile moiety. This approach leads to the synthesis of a diverse range of polycyclic com-pounds. The key to the present methodology is the unlocking of unprecedented reactivity in a benzyl–palladium in-termediate,[8,9] which facilitates distal C–C bond formation on the vinyl group. The synthetic applications of this ortho-quinodimethane generation method are demonstrated through the synthesis of a range of polycyclic compounds, in-cluding a natural product, highlighting the convergent and diversity-generating nature of this reaction. | Kazuya Inagaki; Yuna Onozawa; Yuki Fukuhara; Daisuke Yokogawa; Kei Muto; Junichiro Yamaguchi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66dc164b12ff75c3a1a9eb85/original/facile-generation-of-ortho-quinodimethanes-toward-polycy-clic-compounds.pdf |
60c7426a469df496b9f42fa1 | 10.26434/chemrxiv.7877846.v2 | The chemfp Project | <div>This paper describes the 10 years of work and research results of the chemfp project, available from http://chemfp.com/ . The project started as a way to promote the FPS format for cheminformatics fingerprint exchange. This is a line-oriented text format meant to be easy to read and write. It supports metadata such as the fingerprint type and data provenance.The chemfp package for Python was developed to provide the basic command-line tools and Python API for working with fingerprint data, because a format without useful tools will not be used. <br /></div><div><br /></div><div>The similarity search performance improved by an order of magnitude over the decade, due to careful implementation and effective use of CPU hardware, including AVX2 support for faster popcount calculations than the built-in POPCNT instruction. The implementation details for high-performance search have rarely been discussed in the literature. As a result, many tools and published papers use implementations which are not close to the machine's capabilities.</div><div><br /></div><div>This paper describes those details to help with future optimization efforts.</div><div><br /></div><div>The most advanced version of chemfp evaluates about 130 million
1024-bit fingerprint Tanimotos per second on a single core of a
standard x86-64 server machine. When combined with the BitBound
algorithm, a k=1000 nearest-neighbor search of the 1.8
million 2048-bit Morgan fingerprints of ChEMBL 24 averages 27
ms/query and the same search of the 970 million PubChem fingerprints
averages 220 ms/query, making chemfp one of the fastest similarity
search tools available for CPUs. This appears to be several times faster than previously published work in the field, including in papers which use much more sophisticated data structures.</div><div><br /></div><div>A close analysis shows that nearly all earlier work assumes that the intersection popcount was the limiting performance factor, while on modern hardware uncompressed search is effectively memory bandwidth limited. For example, AVX2 search is 10% faster when memory prefetching, and the popcount evaluation time is far faster than fetching a random location in main memory. It proved difficult to evaluate existing tool performance because in the few cases where the tools were available, each used its own format, data sets, and search tasks.</div><div><br /></div><div>This paper introduces the chemfp benchmark data set to help make head-to-head comparisons easier in the future, and to help promote the FPS format. The FPS format is slow for tasks like web server reloads and command-line scripting. This paper also describes the FPB format, which is a binary application format for fast loads. </div> | Andrew Dalke | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426a469df496b9f42fa1/original/the-chemfp-project.pdf |
60c73e10ee301c1da2c7867e | 10.26434/chemrxiv.6086294.v2 | Hunting for Organic Molecules with Artificial Intelligence: Molecules Optimized for Desired Excitation Energies | <p><a></a>This work presents a proof-of-concept study in artificial-intelligence-assisted (AI-assisted) chemistry where a machine-learning-based molecule generator is coupled with density functional theory (DFT) calculations, synthesis, and measurement. Although deep-learning-based molecule generators have shown promise, it is unclear to what extent they can be useful in real-world materials development. To assess the reliability of AI-assisted chemistry, we prepared a platform using the ChemTS molecule generator and a DFT simulator, and attempted to generate novel photo-functional molecules whose lowest excited states lie at desired energetic levels. A ten-day run on 12 cores discovered 86potential photo-functional molecules around target lowest excitation levels, designated as 200, 300, 400, 500, and 600 nm. Among the molecules discovered, six were synthesized and five were confirmed to reproduce DFT predictions in ultraviolet visible absorption measurements. This result shows the potential of AI-assisted chemistry to discover ready-to-synthesize novel molecules with modest computational resources.<br /></p><p><br /></p><div>The Android robot is reproduced or modified from work created and shared by Google and used </div><div>according to terms described in the Creative Commons 3.0 Attribution License.</div> | Masato Sumita; Xiufeng Yang; Shinsuke Ishihara; Ryo Tamura; Koji Tsuda | Chemoinformatics; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e10ee301c1da2c7867e/original/hunting-for-organic-molecules-with-artificial-intelligence-molecules-optimized-for-desired-excitation-energies.pdf |
60c7567b4c89194a43ad485f | 10.26434/chemrxiv.14249057.v1 | On-Chip Glucose Detection Based on Glucose Oxidase Encapsulated on a Platinum Modified Gold Microband Electrode | We report a two-step
electrodeposition process incorporating glucose oxidase onto a platinum-
modified gold microband electrode with an o-phenylenediamine and ß-cyclodextrin
mixture. The bare microband electrodes were fabricated on silicon using
standard microfabrication methods i.e. lithography and etching techniques. The
two-step electrode modification process was characterized using cyclic
voltammetry, electrochemical impedance spectroscopy and scanning electron
microscopy. The enzymatic based microband biosensor exhibited a linear response
to glucose from 2.5-15 mM using both linear sweep voltammetry and
chronoamperometric measurements in buffer based solutions. The resulting
miniaturized glucose sensor presented a number of advantages such as ease of
use, fast response time, measuring within physiologically relevant glucose concentrations
in addition to sensing in small sample volumes without the need for an external
counter and reference electrode. The biosensor performance was tested in 30 µl
volumes of undiluted fetal bovine serum. Whilst a reduction in signal was
evident within 100 % serum samples, the sensor achieved linear glucose
detection with increasing glucose concentrations (2-12 mM). | Julia Madden; Colm Barrett; Fathima Laffir; Michael Thompson; Paul Galvin; Alan O'Riordan | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7567b4c89194a43ad485f/original/on-chip-glucose-detection-based-on-glucose-oxidase-encapsulated-on-a-platinum-modified-gold-microband-electrode.pdf |
66d18b6620ac769e5f575002 | 10.26434/chemrxiv-2024-hqfmj | Electrostatic Control of Electronic Structure in Modular Inorganic Crystals | The rules that govern structure and bonding, established for elemental solids and simple compounds, are challenging to apply to more complex crystals formed of polyatomic building blocks such as layered or framework materials. Whether these modular building blocks are electrically neutral or charged influences the physical properties of the resulting crystal. Despite the prevalence of alternating charged units, their effects on the electronic structure remains unclear. We demonstrate how the distribution of charged building blocks, driven by differences in electrostatic potential, governs the electronic band energies formed in layered crystals. This coarse-grained model predicts the spatially separated valence and conduction band edges observed in the metal-oxyhalide Ba2Bi3Nb2O11Cl and explains observed property trends in the Sillén–Aurivillius crystal system. Moreover, the general nature of the model allows for extension to other modular structure types, illustrated for Sillén and Ruddesden-Popper compounds, and can support the rational design of electronic properties in diverse materials. | Kanta Ogawa; Aron Walsh | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d18b6620ac769e5f575002/original/electrostatic-control-of-electronic-structure-in-modular-inorganic-crystals.pdf |
60c74cc7bdbb89c37aa3987e | 10.26434/chemrxiv.12530468.v1 | Creating Gaussian Process Regression Models for Molecular Simulations Using Adaptive Sampling | <div>FFLUX is a new force field that combines the accuracy of quantum mechanics with the speed of force </div><div>fields, without any link to the architecture of classical force fields. This force field is atom‐focused and </div><div>adopts the parameter‐free topological atom from Quantum Chemical Topology (QCT). FFLUX uses </div><div>Gaussian Process Regression (GPR) (aka kriging) models to make predicƟons of atomic properties, which </div><div>in this work are atomic energies according to QCT’s InteracƟng Quantum Atom (IQA) approach. Here </div><div>we report the adaptive sampling technique Maximum Expected Prediction Error (MEPE) to create data‐</div><div>compact, efficient and accurate kriging models (sub kJ mol‐1 for water, ammonia, methane and </div><div>methanol, and sub kcal mol‐1 for N‐methylacetamide (NMA)). The models cope with large molecular </div><div>distortions and are ready for use in molecular simulation. A brand new press‐one‐buƩon Python </div><div>pipeline, called ICHOR, carries out the training. </div> | Matthew J. Burn; Paul Popelier | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cc7bdbb89c37aa3987e/original/creating-gaussian-process-regression-models-for-molecular-simulations-using-adaptive-sampling.pdf |
65d867239138d23161cbb910 | 10.26434/chemrxiv-2024-zk9qv | Event Tracking: A systematic method for analyzing nucleation and growth in hierarchical self-assembly | Molecular self-assembly has garnered significant attention in the field of biomaterials and nanotechnology due its potential for creating novel materials with diverse applications. The entire process is guided by either classical nucleation and growth or formation of multiple nucleus and their growth and finally the fusion of the self- assembled states. Systematic way to track this nucleation, growth and fusion process is still unknown. We have developed an algorithm to systematically identify all the possible molecular events. The events provide immediate information when a cluster or individual molecule combines with another cluster or molecule, or when a cluster or molecule detaches from another, during each stage of the mechanism. By comprehensively examining the entire process, we can gain a clearer understanding of the molecular mechanisms involved in the assembly process. We applied this algorithm to self-assembly of some ultrashort peptides. Through a systematic analysis, we identify commonalities and differences in the self-assembly mechanism of various ultrashort peptides. This comparative analysis contributes to a deeper understanding of the mechanisms governing ultrashort peptide self-assembly, offering valuable guidance for the rational design of biomaterials which can serve various technological and biomedical purposes. | Argha Chakraborty; Rumela Adhikary; Sangeeta Das; Avisek Das | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Aggregates and Assemblies; Computational Chemistry and Modeling; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d867239138d23161cbb910/original/event-tracking-a-systematic-method-for-analyzing-nucleation-and-growth-in-hierarchical-self-assembly.pdf |
60c743f6702a9b733118a70e | 10.26434/chemrxiv.9718382.v1 | In Situ Monitoring of Mechanochemical Synthesis of Calcium Urea Phosphate Fertilizer Cocrystal Reveals Water-Based Autocatalysis | Using the mechanosynthesis of the calcium phosphate and urea fertilizer cocrystal as a model, we provide the first in situ investigation of autocatalysis in a mechanochemical reaction. The application of in situ Raman spectroscopy and synchrotron X-ray diffraction provided the first direct evidence of a mechanochemical system in which a reaction product (water) mediates the rate of transformation and underpins positive feedback kinetics. | Patrick Julien; Luzia S. Germann; Hatem M. Titi; Martin Etter; Robert E. Dinnebier; Lohit Sharma; Jonas Baltrusaitis; Tomislav Friscic | Hybrid Organic-Inorganic Materials; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743f6702a9b733118a70e/original/in-situ-monitoring-of-mechanochemical-synthesis-of-calcium-urea-phosphate-fertilizer-cocrystal-reveals-water-based-autocatalysis.pdf |
60c7534bf96a002de328840f | 10.26434/chemrxiv.13093454.v2 | Wrapping up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus. | <p>
Simulating
huge biomolecular complexes of million atoms at relevant biological
timescales is becoming accessible to the broad scientific community.
That proves to be crucial for urgent responses against emergent
diseases in
real
time. Yet, there are still issues to sort
regarding the system setup so that Molecular Dynamics (MD)
simulations can be run in a simple and standard way. Here, we
introduce an optimized pipeline for building and simulating enveloped
virus-like particles (VLP). First, the membrane packing problem is
tackled with new features and optimized options in PACKMOL. This
allows preparing
accurate membrane models of thousands of lipids in the context of a
VLP within
a few
hours using a single CPU. Then, the assembly of the VLP system is
done within the multiscale framework of the coarse-grained SIRAH
force field. Finally, the equilibration protocol provides a system
ready for production MD simulations within
a few
days on broadly accessible GPU resources. The pipeline is applied to
study the Zika Virus as a test case for large biomolecular systems.
The VLP stabilizes at approximately 0.5 microseconds
of
MD simulation, reproducing correlations greater than 0.90 against
experimental density maps from cryo-electron microscopy. Detailed
structural analysis of the protein
envelope also shows very good agreement in root mean square
deviations and B-factors with the experimental data. The
level of details attained shows for the first time
a possible role of anionic phospholipids in stabilizing the envelope.
Combining
an efficient and reliable setup procedure with an accurate
coarse-grained
force
field provides a valuable pipeline for simulating arbitrary viral
systems or sub-cellular compartments, paving the way towards
whole-cell simulations.</p> | Martín Soñora; Leandro Martinez; Sergio Pantano; Matías R. Machado | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7534bf96a002de328840f/original/wrapping-up-viruses-at-multiscale-resolution-optimizing-packmol-and-sirah-execution-for-simulating-the-zika-virus.pdf |
64d212414a3f7d0c0dced297 | 10.26434/chemrxiv-2023-r9n12 | Not as simple as we thought: a rigorous examination of data aggregation in materials informatics | Recent Machine Learning (ML) developments have opened new perspectives on accelerating the discovery of new materials. However, in the field of materials informatics, the performance of ML estimators is heavily limited by the nature of the available training datasets, which are often severely restricted and unbalanced. Among practitioners, it is usually taken for granted that more data corresponds to better performance. Here, we investigate whether different ML models for property predictions benefit from the aggregation of large databases into smaller repositories. To do this, we probe three different aggregation strategies prioritizing training size, element diversity, and composition diversity. For classic ML models, our results consistently show a reduction in performance under all the considered strategies. Deep Learning models show more robustness, but most changes are not significant. Furthermore, to assess whether this is a consequence of a distribution mismatch between datasets, we simulate the data acquisition process of a single dataset and compare a random selection with prioritizing chemical diversity. We observe that prioritizing composition diversity generally leads to a slower convergence toward better accuracy. Overall, our results suggest caution when merging different data sources and discourage a biased acquisition of novel chemistries when building a training dataset. | Federico Ottomano; Giovanni De Felice; Vladimir Gusev; Taylor Sparks | Materials Science | CC BY 4.0 | CHEMRXIV | 2023-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d212414a3f7d0c0dced297/original/not-as-simple-as-we-thought-a-rigorous-examination-of-data-aggregation-in-materials-informatics.pdf |
64f0fbf479853bbd78d1e3f0 | 10.26434/chemrxiv-2023-x72qv-v3 | Atomic layer deposition of zinc oxide on mesoporous zirconia using zinc(II) acetylacetonate and air | The self-terminating chemistry of atomic layer deposition (ALD) ideally enables the growth of homogeneously distributed materials on an atomic scale. This study investigates the ALD of zinc oxide (ZnO) on mesoporous zirconium oxide (ZrO2) using zinc acetylacetonate [Zn(acac)2] and synthetic air in a fixed-bed powder ALD reactor. A broad variety of methods, including thermogravimetry analysis, scanning electron microscopy with energy dispersive X-ray spectroscopy, low energy ion scattering, X-ray absorption near edge structure, X-ray photoelectron spectroscopy, in situ diffuse reflectance infrared Fourier transform spectroscopy-mass spectrometry, and density functional theory calculations were used to analyze the reactant and the resulting samples. The factors affecting the zinc loading (wt%) on ZrO2 were investigated by varying the ALD reaction temperature (160 °C–240 °C), the calcination temperature of zirconium oxide (400 °C–1000 °C) and the ALD cycle number (up to three). The studied process showed self-terminating behavior, with the areal number density of zinc of approximately two atoms per square nanometer per cycle. Zinc was distributed throughout ZrO2. After the Zn(acac)2 reaction, acac ligands were removed using synthetic air at 500 °C. In the following cycles, the already-deposited ZnO acted as nuclei for further ZnO growth. This study demonstrates the potential of Zn(acac)2 as an ALD reactant and provides an initial understanding of ZnO growth via ALD on high surface area porous particles as an example for catalytic applications. | Jihong Yim; Eero Haimi; Miia Mäntymäki; Vile Kärkäs; René Bes; Aitor Arandia Gutierrez; Kristoffer Meinander; Philipp Brüner; Thomas Grehl; Lars Gell; Tiia Viinikainen; Karoliina Honkala; Simo Huotari; Reetta Karinen; Matti Putkonen; Riikka L. Puurunen | Inorganic Chemistry; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanocatalysis - Catalysts & Materials; Nanofabrication; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f0fbf479853bbd78d1e3f0/original/atomic-layer-deposition-of-zinc-oxide-on-mesoporous-zirconia-using-zinc-ii-acetylacetonate-and-air.pdf |
634f0be6e79b3f52b8ee5d16 | 10.26434/chemrxiv-2022-dmqq3 | Positively bound: Remapping of Increased Positive Charge Drives SARS-CoV-2 Spike Evolution to Optimize its Binding to Cell Surface Receptors | The SARS-CoV-2 Omicron sub-lineage contains a significant number of mutations in the spike protein relative to earlier SARS-CoV-2 variants. Most notably, these mutations significantly increased the positive charge of the spike protein that is postulated to confer increased infectivity, potentially through enhanced interactions with cell surface receptors, and an altered host-cell entry mechanism. While heparan sulfate (HS) was shown to be a key co-receptor in the host-cell entry of SARS-CoV-2, the effect of spike charge on its interactions with heparan sulfate has not been clearly elucidated. Here, we investigate the role of evolving spike positive charge in accelerating long-range interactions to heparan sulfate and ACE2 in the glycocalyx. We show that the positively charged Omicron evolved enhanced binding rates to the negatively charged glycocalyx. Moreover, we discovered that while the Omicron spike-ACE2 affinity is comparable to Delta, the Omicron spike interactions with heparan sulfate are significantly enhanced, giving rise to a ternary complex of spike-HS-ACE2 with a larger proportion of double-bound and triple-bound ACE2. Our findings suggest that SARS-CoV-2 variants evolve to be more dependent on heparan sulfate in viral attachment and infection. We leveraged this understanding for the successful and sensitive detection of the Omicron variant. The evolving enhanced binding of SARS-Cov-2 to heparan sulfate presents new therapeutic and diagnostic opportunities. | Sang Hoon Kim; Fiona L. Kearns; Mia A. Rosenfeld; Lane Votapka; Lorenzo Casalino; Micah Papanikolas; Rommie E. Amaro; Ronit Freeman | Theoretical and Computational Chemistry; Materials Science; Analytical Chemistry; Analytical Chemistry - General; Environmental Analysis; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634f0be6e79b3f52b8ee5d16/original/positively-bound-remapping-of-increased-positive-charge-drives-sars-co-v-2-spike-evolution-to-optimize-its-binding-to-cell-surface-receptors.pdf |
60c741e8f96a0014ca2864fc | 10.26434/chemrxiv.8159645.v1 | Copper-Catalyzed Benzylic C–H Coupling with Alcohols via Radical Relay | Cross coupling reactions enable rapid convergent synthesis of diverse molecules and provide the foundation for modern chemical synthesis. The most widely used methods employ sp2-hybridized coupling partners, such as aryl halides or related pre-functionalized substrates. Here, we demonstrate copper-catalyzed oxidative cross-coupling of benzylic C–H bonds with alcohols to afford benzyl ethers, enabled by mechanistic insights that led to a novel reductant-based strategy for in situ regeneration of the active copper catalyst. The reactions employ the C–H substrate as the limiting reagent and exhibit broad scope with respect to both substrate partners. This approach to direct site-selective functionalization of sp3 C–H bonds provides the basis for efficient three-dimensional diversification of organic molecules and should find widespread utility in organic synthesis, particularly for medicinal chemistry applications. | Huayou Hu; Si-Jie Chen; Shane Krska; Shannon Stahl | Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e8f96a0014ca2864fc/original/copper-catalyzed-benzylic-c-h-coupling-with-alcohols-via-radical-relay.pdf |
60c75305469df4acc9f44ca0 | 10.26434/chemrxiv.13371413.v1 | Photocatalytic Rejuvenation Enabled Self-Sanitizing, Reusable, and Biodegradable Masks Against COVID-19 | Personal protective equipment (PPE) has been highly recommended by the U.S.
Centers for Disease Control and Prevention (CDC) for self-protection under the disastrous
SARS-CoV-2 (COVID-19) pandemic. Nevertheless, the massive utilization of PPE,
especially the N95 respirators and sing-use masks, encounters significant challenges
in recycling and sterilizing the used masks. To tackle the environmental
pollution of currently used masks made of synthetic plastic, in this work, we designed
a reusable, biodegradable, and antibacterial mask. The mask was prepared by
electrospinning of polyvinyl alcohol (PVA), poly(ethylene oxide) (PEO), and cellulose
nanofiber (CNF), and with subsequent esterification and then deposition of nitrogen-doped
TiO<sub>2 </sub>(N-TiO<sub>2</sub>). The fabricated mask containing photocatalytic
N-TiO<sub>2</sub> can reach ~100% sterilization under light source (200-2500 nm, 106 Wm<sup>-2</sup>)
as 0.1 sun simulation for only 10 min. Thus, the used mask can be rejuvenated through
light irradiation and reused, which represents one of the handiest technologies
for handling used masks. Furthermore, the intermolecular interactions between
PVA, PEO and CNF enhanced electrospinnability and the mechanical
performance of the resultant mask. The obtained masks possess superior mechanical
strength (10-fold elastic modulus and 2-fold tensile strength higher than a commercial single
use mask). The comprised electrospun nanofibers with porous structures in
between as well as strong electrostatic attraction enabled breathability (83.4 L
min<sup>-1</sup> of air flow rate) and superior particle filterability (98.7 %).
Therefore, this novel mask could be a great alternative to current masks to
addressing the urgent need for sustainable, reusable, environmentally friendly,
and efficient personal protection designs under the ongoing COVID-19 contagion. | Qiang Li; Yongchao Yin; Daxian Cao; Pengcheng Luan; Ying Wang; Xiao Sun; hongli zhu | Biodegradable Materials; Fibers; Materials Processing; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75305469df4acc9f44ca0/original/photocatalytic-rejuvenation-enabled-self-sanitizing-reusable-and-biodegradable-masks-against-covid-19.pdf |
60c75031702a9b9f9618bd06 | 10.26434/chemrxiv.13003952.v1 | Ionic Conduction Through Reaction Products at the Electrolyte/electrode Interface in All-Solid-State Li⁺ Batteries | The development of all-solid-state lithium ion batteries has been hindered by the formation of a poorly conductive interphase at the interface between electrode and electrolyte materials. In the manuscript, we shed light on this problem by computationally evaluating potential lithium ion diffusion pathways through metastable arrangements of product phases that can form at 56 interfaces between common electrode and electrolyte materials. The evaluation of lithium-ion conductivities in the product phases is made possible by the use of machine-learned interatomic potentials trained on the fly. We identify likely reasons for the degradation of solid-state battery performance and discuss how these problems could be mitigated. These results provide enhanced understanding of how interface impedance growth limits the performance of all-solid-state lithium-ion batteries. | Chuhong Wang; Koutarou Aoyagi; Muratahan Aykol; Tim Mueller | Computational Chemistry and Modeling; Machine Learning; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75031702a9b9f9618bd06/original/ionic-conduction-through-reaction-products-at-the-electrolyte-electrode-interface-in-all-solid-state-li-batteries.pdf |
678051316dde43c908ef76e8 | 10.26434/chemrxiv-2025-clgct | Proteome-wide Covalent Targeting of Acidic Residues with Tunable N-Aryl Aziridines | Carboxylate side chains in aspartic and glutamic acids play critical roles in protein structure and function due to their polarity and negative charge. These acidic residues, which are abundant in high-value drug targets, represent attractive yet underexplored hotspots for covalent inhibitor discovery. In this study, we introduce N-aryl aziridines as a systematically tunable, chemoselective scaffold for covalent targeting of carboxylates across the proteome. Using a library of N-pyridinium aziridine-based fragments combined with chemoproteomics-enabled target deconvolution, we identified lead hits for aspartates and glutamates in proteins such as mitochondrial carrier homolog 2 (MTCH2), RUN and FYVE domain-containing protein 1 (RUFY1), and delta(24)-sterol reductase (DHCR24). Modular build-and-couple synthetic logic enabled fragment evolution via Ni-catalyzed cross-coupling to access N-aryl aziridines with enhanced affinities for MTCH2 and RUFY1. Notably, N-aryl aziridine 5b selectively modified RUFY1 at E502, disrupting its interactions within the endosomal trafficking network and impairing receptor recycling. This work establishes N-aryl aziridines as versatile carboxylate-targeting covalent inhibitor scaffolds, broadening the scope of covalent ligand discovery.
| Nan Qiu; Hao Tan; Dany Pechalrieu; Daniel Abegg; Deepanshu Fnu; Poulami Mukherjee; Angel Renteria Gomez; Osvaldo Gutierrez; David C. Powers; Alexander Adibekian | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678051316dde43c908ef76e8/original/proteome-wide-covalent-targeting-of-acidic-residues-with-tunable-n-aryl-aziridines.pdf |
664d635e21291e5d1de8c96a | 10.26434/chemrxiv-2024-b3m60 | Chemical etching of silicon assisted by graphene oxide under negative electric bias | Chemical etching of silicon assisted by graphene oxide (GO) is attracting attention as a new method to fabricate micro- or nano- structures. GO promotes the reduction of an oxidant, and holes are injected into silicon, resulting in the preferential dissolution of the silicon under GO. We developed a new etching method that applies a negative bias to the silicon substrate. The silicon under GO was more selectively etched in an etchant consisting of hydrofluoric acid and nitric acid. We assume that this is attributed to the difference in hole concentration in the silicon under GO and in the bare silicon. In addition, the in-plane diffusion of holes in silicon is suppressed by this method, resulting in forming highly anisotropic pores. We combined this etching method with microcontact printing (μCP) of GO, showing its potential for silicon microfabrication. | Yuta Goto; Shuta Sakamoto; Toru Utsunomiya; Takashi Ichii; Sugimura Hiroyuki | Physical Chemistry; Materials Science; Materials Processing; Surface | CC BY NC 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664d635e21291e5d1de8c96a/original/chemical-etching-of-silicon-assisted-by-graphene-oxide-under-negative-electric-bias.pdf |
65bd33079138d231614c0771 | 10.26434/chemrxiv-2024-mtk6s | Erastin-like anti-Warburg compounds X1 and X4 are GLS2-selective covalent glutaminase inhibitors | The Warburg effect is a metabolic alteration in cancer cells characterized by aerobic glycolysis and lactate production. A recent phenotypic screen for compounds that reverse Warburg metabolism identified two compounds, X1 and X4, that restore the mitochondrial membrane potential, decrease lactate production, and increase the level of reactive oxygen species in cancer cells. Here we show that X1 and X4 are GLS2-selective covalent glutaminase inhibitors. Glutaminase enzymes hydrolyze glutamine to glutamate, which supports cancer cell metabolism through TCA cycle anaplerosis and glutathione biosynthesis. The GLS1 glutaminase isozyme has well-established roles in cancer cell metabolism. Conversely, GLS2 is an enigmatic enzyme with reported roles in both tumor promotion and tumor suppression and remains an underdeveloped drug target. This finding suggests roles for GLS2 in supporting Warburg metabolism and managing oxidative stress in cancer cells. X1 and X4 may accelerate the development of high-quality inhibitors of GLS2 to clarify its unique roles in cancer cell metabolism. | Clea Crane; Morgan Miele; Ranjini Iyengar; Noah Strathmann; Sainabou Jallow; Scott Ulrich | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd33079138d231614c0771/original/erastin-like-anti-warburg-compounds-x1-and-x4-are-gls2-selective-covalent-glutaminase-inhibitors.pdf |
66354621418a5379b06184fe | 10.26434/chemrxiv-2024-0hww3 | Harnessing Medicinal Chemical Intuition from Collective Intelligence | Over the last decade, the combination of collective intelligence with computational methods has transformed complex problem-solving. Here, we investigate if and how collective intelligence can be applied to drug discovery, focusing on the lead optimization stage of the discovery process. For this study, 92 Sanofi researchers with diverse scientific expertise participated anonymously in a lead optimization exercise. Their feedback was used to build a collective intelligence agent that was compared to an artificial intelligence model developed in parallel. This work has led to three major conclusions. First, a significant improvement of collective versus individual decisions in optimizing ADMET endpoints is observed. Second, for all endpoints apart from hERG inhibition, the collective intelligence performance exceeds the artificial intelligence model. Third, we observe a complementarity between collective intelligence and AI for complex tasks, demonstrating the potential of hybrid predictions. Overall, this research highlights the potential of collective intelligence in drug discovery. The entire dataset, including questionnaire responses, and developed models are available for access on GitHub. | Pierre Llompart ; Kwame Amaning; Marc Bianciotto; Bruno Filoche-Rommé; Yann Foricher; Pablo Mas; David Papin; Jean-Philippe Rameau; Laurent Schio; Gilles Marcou; Alexandre Varnek; Mehdi Moussaid; Claire Minoletti; Paraskevi Gkeka | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66354621418a5379b06184fe/original/harnessing-medicinal-chemical-intuition-from-collective-intelligence.pdf |
669fb12c01103d79c55bec24 | 10.26434/chemrxiv-2024-kkjwj | Finding non-fluorinated alternatives to fluorinated gases used as refrigerants | Hydrofluorocarbons (HFCs) and so-called hydrofluoroolefins (HFOs) are used as refrigerants in air conditioning, refrigeration, chillers, heat pumps and devices for dehumidification and drying. However, many HFCs, including R-134a and R-125, have a high global warming potential and some of the HFCs and HFOs degrade atmospherically and form persistent degradation products. Thus, there is an urgent need to replace fluorinated refrigerants with non-fluorinated working fluids to avoid direct emissions due to leakage, incorrect loading or removal. It is important, however, also to select refrigerants with high efficiencies to avoid indirect CO2 emissions due to a (too) high energy consumption during the use phase. The present study investigates the available non-fluorinated alternatives to fluorinated refrigerants and shows that a transition to non-fluorinated refrigerants, in general, is possible and has happened in many sectors already. Technically, there are only slight barriers to overcome to replace fluorinated refrigerants in almost all newly developed systems conforming to existing standards. Additionally, we show that alternatives are available even for some use cases for which derogations have been proposed in the PFAS restriction proposal and suggest making these derogations more specific to support bringing the use of non-fluorinated refrigerants into practice. | Juliane Glüge; Katharina Breuer; Armin Hafner; Christian Vering; Dirk Müller; Ian T. Cousins; Rainer Lohmann; Gretta Goldenman; Martin Scheringer | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669fb12c01103d79c55bec24/original/finding-non-fluorinated-alternatives-to-fluorinated-gases-used-as-refrigerants.pdf |
673cd2c0f9980725cfcade23 | 10.26434/chemrxiv-2024-pn13j | Influence of coverage dependence on the thermophysical properties of adsorbates and its impact on microkinetic models | This work focuses on the impact of lateral interactions on the thermophysical properties of adsorbates. We present different parameterizations for coverage-dependent enthalpy, entropy, and heat capacity in a mean-field microkinetic model. These models are tested against two systems, CO/Pt(111) and CO/Co(0001), using two different funtionals. A detailed investigation into how coverage influences the thermophysical properties of \co{} is presented. Our analysis of the repulsive interaction in adsorption energy suggests that coverage effects are mainly indirect (adsorbate--metal and surface relaxation) for lower coverages, but are both indirect and direct (adsorbate--adsorbate) for higher coverages. We place a particular emphasis of studying the impact of coverage on the vibrational partition function and how this affects the entropy of adsorbates. Higher coverages typically lead to increased repulsive interactions, which should further constrain the large-amplitude modes that contribute the most to the vibrational entropy. In some cases, however, the opposite effect occurred; the vibrational entropy actually increased, because surface crowding forced adsorbates to different binding locations that had lower frequencies. However, our result highlighted cases where coverage-dependent entropy should be included, such as for adsorbates with lateral vibrational modes and for systems at high temperatures. These methods for including coverage-dependent properties into mean-field microkinetics in a thermodynamically consistent way are now available in the open-source software Cantera. | Jongyoon Bae; Bjarne Kreitz; Andrew Peterson; Claude Franklin Goldsmith | Physical Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673cd2c0f9980725cfcade23/original/influence-of-coverage-dependence-on-the-thermophysical-properties-of-adsorbates-and-its-impact-on-microkinetic-models.pdf |
64920cd9853d501c00389da8 | 10.26434/chemrxiv-2023-2c5j3 | Spatiotemporally Controlled Emergence of Nanoparticle Microvortices under Electric Field | Controlled assembly of nanoparticles (NPs) has garnered much interest over the past two decades. Beyond established techniques, new methods utilizing local short-range or large-scale long-range interactions remain to be explored to achieve diverse micro- and nanoscale structures. Here, we report the controlled emergence of vortex-pair arrays within monodispersed gold nanorods (AuNRs) by applying a direct current (dc) electric field across a pair of sawtooth electrodes. By employing in situ darkfield microscopy and particle collective analysis, we elucidate the mechanism behind the formation and stabilization of the NP vortices, attributing it to the combined effects of the electrode shape, high NP density, and high solution viscosity. We further explored the controllability of the vortex-pair arrays and obtained multiple complex vortices patterns. Our findings will facilitate the investigation of efficient and controlled dynamic assembly of NPs under external fields and help manufacture next-generation optoelectronic functional materials. | QI PAN; Xijian Lin; Shiyuan Wei; Jinghong Su; Hansen Zhao; Xiaojie Duan; Guoqing Hu; Yan He | Analytical Chemistry; Nanoscience; Imaging; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64920cd9853d501c00389da8/original/spatiotemporally-controlled-emergence-of-nanoparticle-microvortices-under-electric-field.pdf |
6126bb40abeb63033dc06b3c | 10.26434/chemrxiv-2021-q22x8 | Tert-Butoxide-Mediated Protodeformylation of Tertiary Homobenzaldehydes | Tert-butoxide mediates the protodeformylation of tertiary homobenzaldehydes and related compounds at ambient temperature. Both geminal dialkyl and geminal diaryl substituents are tolerated. Monocyclic aromatic homobenzaldehydes require cyclic gem-dialkyls or gem-diaryls for efficient protodeformylation, whereas gem-dimethyls are sufficient for protodeformylation of polycyclic arenyl substrates. Our data suggest a stabilized radical is generated upon attack of the aldehyde by tert-butoxide. | Xiao Cai; Benjamin J. Stokes | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6126bb40abeb63033dc06b3c/original/tert-butoxide-mediated-protodeformylation-of-tertiary-homobenzaldehydes.pdf |
649abe2a6e1c4c986b6a78c4 | 10.26434/chemrxiv-2023-lxghm | A multiplexing activity-based protein profiling platform for dissection of a native bacterial xyloglucan-degrading system | Bacteria and yeasts grow on biomass polysaccharides by expressing and excreting a complex array of glycoside hydrolase (GH) enzymes. Identification and annotation of such GH pools, which are valuable commodities for sustainable energy and chemistries, by conventional means (genomics, proteomics) is complicated, as primary sequence or secondary structure alignment with known active enzymes is not always predictive for new ones. Here we report a “low-tech”, easy-to-use and sensitive, multiplexing activity-based protein profiling platform to characterize the xyloglucan-degrading GH system excreted by the soil saprophyte, Cellvibrio japonicus when grown on xyloglucan. A suite of activity-based probes bearing orthogonal fluorophores allows for the visualization of accessory exo-acting glycosidases, which are then identified using biotin-bearing probes. Substrate specificity of xyloglucanases is directly revealed by imbuing xyloglucan structural elements into bespoke activity-based probes. Our ABPP platform provides a highly useful tool to dissect xyloglucan-degrading systems from various sources and to rapidly select potentially useful ones. The observed specificity of the probes moreover bodes well for the study of other biomass polysaccharide degrading systems, by modelling probe structures to those of desired substrates. | Nicholas McGregor; Casper de Boer; Quentin Foucart; Thomas Beenakker; Wendy Offen; Jeroen Codee; Lianne Willems; Herman Overkleeft; Gideon Davies | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Microbiology | CC BY NC 4.0 | CHEMRXIV | 2023-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649abe2a6e1c4c986b6a78c4/original/a-multiplexing-activity-based-protein-profiling-platform-for-dissection-of-a-native-bacterial-xyloglucan-degrading-system.pdf |
67d2fbdd81d2151a023e1f52 | 10.26434/chemrxiv-2025-m2xh9 | Modulating the Electronic Structure of Biphenyl Metalloporphyrins | Metalloporphyrins and Porphyrins (MPs) have garnered increasing attention as potential candidates for molecular-based electronic devices and single atom catalysis. Recent studies have found that electronic structure calculations are important factors in controlling the performance of MPs as building blocks for single-molecule devices. Our study includes central 3d-metals from Sc to Cu and anchoring groups such as -SH, -SeH, and -TeH substituted at the meso-position of the porphyrin rings. We conducted Quantum chemistry calculations, primarily Density Function Theory (DFT), for geometry optimizations, calculated bond lengths, and analyzed the molecular orbitals, and electronic structure descriptors to gain insights into the reactivity trends and electronic structure of these systems. In addition to these analyses, we explored the spin multiplicity and the distribution of spin-up and spin-down electrons, which are critical factors influencing electron transport properties and the rectification behavior of metalloporphyrins in molecular junctions. The results suggest that the central metal and spin multiplicity significantly shape the electronic properties and potential reactivity of MP molecules. This study provides insights into how the selection of the central metal and control of spin channels influence the electronic structure and reactivity of metalloporphyrin molecules. This knowledge is essential for designing MP-based materials with tailored properties for diverse applications in molecular junctions, catalysis, photovoltaics, and sensing. | Beenish Bashir; Andre Clayborne | Physical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d2fbdd81d2151a023e1f52/original/modulating-the-electronic-structure-of-biphenyl-metalloporphyrins.pdf |
6224b89150b621ce05eb5c73 | 10.26434/chemrxiv-2022-t180g | Confinement of Luminescent Guests in Metal-Organic Frameworks: Understanding Pathways from Synthesis and Multimodal Characterization to Potential Applications of LG@MOF Systems | This review gives an authoritative, critical, and accessible overview of an emergent class of fluorescent materials termed “LG@MOF” — engineered from the nanoscale confinement of luminescent guests (LG) in a metal-organic framework (MOF) host, realizing a myriad of unconventional materials with fascinating photophysical and photochemical properties. We begin by summarizing the synthetic methodologies and design guidelines for representative LG@MOF systems, where the major types of fluorescent guest encompass organic dyes, metal ions, metal complexes, metal nanoclusters, quantum dots, and hybrid perovskites. Subsequently, we discuss the methods for characterizing the resultant guest-host structures, guest loading, photophysical properties, and review local-scale techniques recently employed to elucidate guest positions. A special emphasis is paid to the pros & cons of the various methods in the context of LG@MOF. In the following section, we provide a brief tutorial on the basic guest-host phenomena, focusing on the excited state events and nanoscale confinement effects underpinning the exceptional behavior of LG@MOF systems. The review finally culminates in the most striking applications of LG@MOF materials, particularly the “turn-on” type fluorochromic chemo- and mechano-sensors, non-invasive thermometry and optical pH sensors, electroluminescence and innovative security devices. This review offers a comprehensive coverage of general interest to the multidisciplinary materials community to stimulate frontier research in the vibrant sector of light-emitting MOF composite systems. | Mario Gutiérrez; Yang Zhang; Jin-Chong Tan | Materials Science; Nanoscience; Dyes and Chromophores; Hybrid Organic-Inorganic Materials; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6224b89150b621ce05eb5c73/original/confinement-of-luminescent-guests-in-metal-organic-frameworks-understanding-pathways-from-synthesis-and-multimodal-characterization-to-potential-applications-of-lg-mof-systems.pdf |
60c753e6842e6549e0db4036 | 10.26434/chemrxiv.13570790.v1 | Thermal and Structural Characterization of Two Commercially Available Technical Lignins for High-value Applications | <p>Lignin is a complex polyaromatic macromolecule and a potential source of various sustainable materials and feedstock chemicals. To this end, researchers have made some considerable efforts in the high-value applications of lignin, even though there is a limited success so far. This is mainly because the exact structure of native lignin is still virtually unknown due to its highly heterogeneous nature. Besides, technical lignin undergoes unintended structural modifications during the chemical pulping and extraction processes making its final structure even more complicated. Therefore, understanding the lignin structure and its macromolecular characteristics is essential for its proper utilization. In this study, two technical lignins, such as indulin AT and alkali-treated lignin, were investigated for thermal and structural characterization. Various thermal behaviors were studied using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). Indulin AT was found to be thermally more stable compared to alkali lignin. Structural characterization was performed using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and proton nuclear magnetic resonance spectroscopy (<sup>1</sup>H NMR). Cupric oxide oxidation was utilized to selectively degrade the lignin into its monomers (H/G/S-moieties), which were identified with GC-MS. The results suggested that the selected lignins are mainly composed of G-type monomers. The detailed characterization studies also revealed some minor structural differences between the two lignins due to their respective delignification process. Indulin AT underwent higher structural modifications due to the harsher delignification process and hinted to show more recalcitrance toward depolymerization than alkali lignin.</p> | Tanvir Amit; Ranen Roy; Douglas E. Raynie | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753e6842e6549e0db4036/original/thermal-and-structural-characterization-of-two-commercially-available-technical-lignins-for-high-value-applications.pdf |
61ef7b191fd27410b61a4494 | 10.26434/chemrxiv-2022-632cr | Hybrid Field Theory and Particle Simulation
Model of Polyelectrolyte-Surfactant
Coacervation | Solutions of oppositely-charged polyelectrolytes and surfactants have been widely studied for a variety of applications; they play an important role in the formulation of personal care products, can be used as an effective strategy for drug encapsulation, and serve as analogues to biological systems such as biomolecular condensates. Surfactant molecules self-assemble into micellar macroions that are known to form complexes with oppositely-charged polyelectrolytes, and can undergo a bulk liquid-liquid phase separation known as complex coacervation. This process results in a `coacervate' phase that is rich in macroions, and a `supernatant' phase that is dilute in macroions. It is challenging to model this phase separation process, due to the disparate length scales and strong Coulombic interactions in these mixed macroion systems. In this work, we present a hybrid simulation and field theory model to describe polyelectrolytes/surfactants solutions, where the surfactant species has self-assembled into worm-like micelle structures. We use self-consistent field theory (SCFT) to model the polyelectrolytes in the solution which interact with the surfactant micelles. The surfactant micelle structures are determined by performing Monte Carlo (MC) simulations, which are used to determine applied external fields in the SCFT portion of the model. We use these calculations to determine the system free energy and map the phase diagrams for polyelectrolyte-surfactant coacervates, and subsequently consider the effect of a number of molecular parameters such as polyelectrolyte chain length, the volume of the interacting micelle surface-sites, and the electrostatic binding energy between the polyelectrolyte and micelle surface. Our model shows that local charge-charge correlations are critical for phase separation to occur. Additionally, we evaluate the statistics of micelle bridging by the polyelectrolyte, and the relationship between bridging and the densities of the macroions and salt ions. This hybrid SCFT/MC model can be generalized to study a variety of mixed macroion systems, and make predictions for phase behavior and molecular structure. | Jason Madinya; Charles Sing | Polymer Science; Polyelectrolytes - Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ef7b191fd27410b61a4494/original/hybrid-field-theory-and-particle-simulation-model-of-polyelectrolyte-surfactant-coacervation.pdf |
6133e30527d90682e67dd29d | 10.26434/chemrxiv-2021-gmv5j | Structural and Data Science-Driven Analysis to Assess Substrate Specificity of Diketopiperazine Reverse Prenyltransferase NotF: Cascade Biocatalytic Synthesis of (–)-Eurotiumin A | Prenyltransfer is an early-stage carbon–hydrogen bond (C–H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Towards the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). In the biosynthesis of cytotoxic notoamide metabolites, PT NotF is responsible for catalyzing the first tailoring event of C2 reverse prenyltransfer of brevianamide F (cyclo(L-Trp-L-Pro)). Obtaining a high-resolution crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent exposed substrate binding site, intimating NotF may possess significant substrate promiscuity. To assess the full potential of NotF’s broad substrate selectivity, we synthesized a panel of 30 tryptophanyl DKPs with a suite of sterically and electronically differentiated amino acids, which were selectively prenylated by NotF in often synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library enabled the development of a descriptive statistical model that provided insight into the origins of NotF’s substrate promiscuity. Through this unique approach for understanding enzyme scope, we identified key substrate descriptors such as electrophilicity, size, and flexibility, that govern enzymatic turnover by NotF. Additionally, we demonstrated the ability to couple NotF-catalyzed prenyltransfer with oxidative cyclization using recently characterized flavin monooxygenase, BvnB, from the brevianamide biosynthetic pathway. This one-pot, in vitro biocatalytic cascade proceeds with exceptional substrate recognition, and enabled the first chemoenzymatic synthesis of the marine fungal natural product, (–)-eurotiumin A, in three steps and 60% overall yield. | Samantha P. Kelly; Vikram V. Shende; Autumn R. Flynn; Qingyun Dan; Ying Ye; Janet L. Smith; Sachiko Tsukamoto; Matthew S. Sigman; David H. Sherman | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Natural Products; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6133e30527d90682e67dd29d/original/structural-and-data-science-driven-analysis-to-assess-substrate-specificity-of-diketopiperazine-reverse-prenyltransferase-not-f-cascade-biocatalytic-synthesis-of-eurotiumin-a.pdf |
61d94503636cc9252d4294d6 | 10.26434/chemrxiv-2021-tcn0f-v2 | Prediction of Protein pKa with Representation Learning | The behavior of proteins is closely related to the protonation states of the residues. Therefore, prediction and measurement of pKa are essential to understand the basic functions of proteins. In this work, we develop a new empirical scheme for protein pKa prediction that is based on deep representation learning. It combines machine learning with atomic environment vector (AEV) and learned quantum mechanical representation from ANI-2x neural network potential (J. Chem. Theory Comput. 2020, 16, 4192). The scheme requires only the coordinate information of a protein as the input and separately estimates the pKa for all five titratable amino acid types. The accuracy of the approach was analyzed with both cross-validation and an external test set of proteins. Obtained results were compared with the widely used empirical approach PROPKA. The new empirical model provides accuracy with MAEs below 0.5 for all amino acid types. It surpasses the accuracy of PROPKA and performs significantly better than the null model. Our model is also sensitive to the local conformational changes and molecular interactions. | Hatice Gokcan; Olexandr Isayev | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2022-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d94503636cc9252d4294d6/original/prediction-of-protein-p-ka-with-representation-learning.pdf |
642b8b05db1a20696e7ac883 | 10.26434/chemrxiv-2023-rjv6c | Combining SILCS and Artificial Intelligence for High-Throughput Prediction of Drug Molecule Passive Permeability | The membrane permeability of drug molecules imparts a significant role in the development of new therapeutic agents. Accordingly, methods to predict the passive permeability of drug candidates during a medicinal chemistry campaign offer the potential to accelerate the drug design process. In this work, we combine the physics-based Site identification by ligand competitive saturation (SILCS) method with data-driven artificial intelligence (AI) to create a high-throughput predictive model for passive permeability of drug-like molecules. In the study we present a comparative analysis of four regression models to predict membrane permeabilities of small drug-like molecules. The input feature vector used to train the developed prediction model includes absolute free energies profiles of ligands through a POPC-cholesterol bilayer based on ligand grid free energy (LGFE) profiles obtained from the SILCS approach. Use of the membrane free energy profiles from SILCS offers information on the physical forces contributing to ligand permeability while the use of AI yields a more predictive model trained on experimental PAMPA permeability data for a collection of 229 molecules. This combination allows for rapid estimations of ligand permeability at a level of accuracy beyond currently available predictive models while offering insights into the contributions of the functional groups in the ligands to the permeability barrier, thereby offering quantitative information to facilitate rational ligand design. | Alexander MacKerell; Poonam Pandey | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b8b05db1a20696e7ac883/original/combining-silcs-and-artificial-intelligence-for-high-throughput-prediction-of-drug-molecule-passive-permeability.pdf |
6616868221291e5d1d8804b6 | 10.26434/chemrxiv-2024-8293t | Core-electron contributions to the magnetic response of molecules with heavy elements and their significance in aromaticity assessments | This study delves into the magnetic response of core electrons and their influence on the global magnetic response of systems planar and three-dimensional containing heavy elements, employing the removing valence electron (RVE) approximation. We also explore electronic aromaticity indices to understand the potential role of core electrons on electron delocalization in absence of an external perturbation. The study reveals that core electrons significantly contribute to the overall magnetic response, especially to the magnetic shielding, affecting the interpretation of aromaticity. In contrast, the calculation of the electronic aromaticity indices suggests a negligible participation of the core electrons to the electron delocalization. Despite its widespread use, the study emphasizes caution in labeling systems as strongly aromatic based solely on shielding function computations. It is noteworthy to emphasize the limitations associated with each aromaticity criterion, particularly in the context of magnetic shielding function calculations, the core-electron effect contamination is undeniable. Hence, the integration of various criteria becomes imperative for attaining a comprehensive understanding of magnetic responses within complex systems. | Mesías Orozco Ic; Luis Soriano-Agueda; Dage Sundholm; Eduard Matito; Gabriel Merino | Theoretical and Computational Chemistry; Physical Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Theory - Computational; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6616868221291e5d1d8804b6/original/core-electron-contributions-to-the-magnetic-response-of-molecules-with-heavy-elements-and-their-significance-in-aromaticity-assessments.pdf |
6622a9b3418a5379b034fed1 | 10.26434/chemrxiv-2024-jb1v4 | Si6Tip6: the Largest and Most Complicated Ever Experimental Gas Phase Molecular Structure | The largest (ra = 19.9 A) and by far the most complicated (234 atoms, C1 symmetry, 696 independent geometrical parameters, 27261 interatomic terms) experimental molecular structure of a cage-type Si6Tip6 (Tip = 2,4,6-iPr3C6H2) isomer has been investigated in the gas phase by the electron diffraction method supplemented with theoretical simulations. A detailed analysis of the current possibilities for experimentally investigating of large molecular structures is performed. A series of density functional theory (DFT) approximations and the role of dispersion interactions have been benchmarked using the obtained data. Based on the refined geometry of Si6Tip6 various quantum-chemical methods have been applied for investigation of the electronic structure of its Si6 core. In particular, natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), interacting quantum atoms (IQA), fractional occupation number weighted density (FOD) and complete active space self-consistent field (CASSCF) methods were utilized. Diradical character of the molecule has been assessed by the UHF and CASSCF approximations. The problem of bonding between the hemispheroidal silicon atoms has been investigated. | Yury Vishnevskiy; Yannic Heider; David Scheschkewitz | Physical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6622a9b3418a5379b034fed1/original/si6tip6-the-largest-and-most-complicated-ever-experimental-gas-phase-molecular-structure.pdf |
60c757089abda23076f8e61a | 10.26434/chemrxiv.14362238.v1 | Low-Valent Tungsten Redox Catalysis Enables Controlled Isomerization and Carbonylative Functionalization of Alkenes | Tungsten catalysis has played an instrumental role in the history of organometallic chemistry, with electrophilic, fully oxidized W(VI) catalysts featuring prominently in olefin polymerization and metathesis reactions. Here, we report that the simple W(0) precatalyst, W(CO)<sub>6</sub>, catalyzes the isomerization and hydrocarbonylation of alkenes via a W(0)/W(II) redox couple. The 6- to 7-coordinate geometry changes associated with this redox process are key in allowing isomerization to take place over multiple positions and stop at a defined unactivated internal site that is primed for <i>in situ</i> functionalization. DFT studies and crystallographic characterization of multiple directing-group-bound W(II) model complexes illuminate potential intermediates of this redox cycle and showcase the capabilities of the 7-coordinate W(II) geometry to facilitate challenging alkene functionalizations. | Tanner Jankins; William Bell; Yu Zhang; Zi-Yang Qin; Milan Gembicky; Peng Liu; Keary Engle | Organic Synthesis and Reactions; Homogeneous Catalysis; Theory - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757089abda23076f8e61a/original/low-valent-tungsten-redox-catalysis-enables-controlled-isomerization-and-carbonylative-functionalization-of-alkenes.pdf |
6562b515cf8b3c3cd7212a60 | 10.26434/chemrxiv-2023-kvsvl | Tutorials on How to Build Non-Markovian Dynamic Models from Molecular Dynamics Simulations for Studying Protein Dynamics | Protein conformational changes play crucial roles in their biological functions. In recent years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) simulations has emerged as a powerful tool for modeling complex protein conformational changes. In MSMs, dynamics are modeled as a sequence of Markovian transitions among metastable conformational states at discrete time intervals (called lag time). A major challenge for MSM is that the lag time must be long enough to allow transitions among states to become memoryless (or Markovian). However, this lag time is constrained by the length of individual MD simulations available to track these transitions. To address this challenge, we have recently developed Generalized Master Equation (GME)-based approaches, encoding non-Markovian dynamics using a time-dependent memory kernel. In this tutorial, we introduce the theory behind two recently developed GME-based non-Markovian dynamic models: the Quasi Markov State Model (qMSM) and the Integrative Generalized Master Equation (IGME). We subsequently outline the procedures for constructing these models and provide a step-by-step tutorial on applying qMSM and IGME to study two peptide systems: the alanine dipeptide and villin headpiece. This tutorial is available at https://github.com/xuhuihuang/GME_tutorials. The protocols detailed in this tutorial aim to be accessible for non-experts interested in studying the biomolecular dynamics using these non-Markovian dynamic models. | Yue Wu; Siqin Cao; Yunrui Qiu; Xuhui Huang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6562b515cf8b3c3cd7212a60/original/tutorials-on-how-to-build-non-markovian-dynamic-models-from-molecular-dynamics-simulations-for-studying-protein-dynamics.pdf |
678129936dde43c9080215a1 | 10.26434/chemrxiv-2025-bdrzc | Chemical-Intuition-Based Machine-Learning (ML) yield prediction for Mizoroki-Heck C-glycosylation | Machine-learning (ML) algorithms have emerged as a powerful tool in the field of organic chemistry. While these algorithms have proven to be highly efficient, they are often constrained by the availability of data. In addressing this limitation, we propose a ML-based yield prediction algorithm that operates in a low data regime, leveraging knowledge-based chemical descriptors without requiring extensive computational resources. This model has been utilized to predict Mizoroki-Heck C-glycosylation outcomes. | Thibaud Mabit | Theoretical and Computational Chemistry; Organic Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678129936dde43c9080215a1/original/chemical-intuition-based-machine-learning-ml-yield-prediction-for-mizoroki-heck-c-glycosylation.pdf |
63d1537410cb6a379ae66df6 | 10.26434/chemrxiv-2022-zdmf1-v3 | Base-free synthesis of benchtop stable Ru(III)-NHC complexes from RuCl3·3H2O and their use as precursors for Ru(II)-NHC complexes | A series of Ru(III)-NHC complexes, identified as [RuIII(PyNHCR)(Cl)3(H2O)] (1a-c), have been prepared, starting from RuCl3·3H2O following a base-free route. The Lewis acidic Ru(III) centre operates via a halide-assisted, electrophilic C-H activation for carbene generation. Best results were obtained with azolium salts having I- anion while ligand precursors with Cl-, BF4-, and PF6- gave no complex formation and those with Br- gave a product with mixed halides. The structurally simple, air and moisture-stable complexes represent rare examples of paramagnetic Ru(III)-NHC complexes. Further, these benchtop stable Ru(III)-NHC complexes were shown to be excellent metal precursors for the synthesis of new [RuII(PyNHCR)(Cl)2(PPh3)2] (2a-c) and [RuII(PyNHCR)(CNCMe)I]PF6 (3a-c) complexes. All the complexes have been characterised using spectroscopic methods, and structures of 1a, 1b, 2c and 3a have been determined using the single-crystal X-ray diffraction technique. This work allows easy access to new Ru-NHC complexes for the study of new properties and novel applications. | Nida Shahid; Rahul Kumar Singh; Navdeep Srivastava; Amrendra K. Singh | Organometallic Chemistry; Coordination Chemistry (Organomet.); Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d1537410cb6a379ae66df6/original/base-free-synthesis-of-benchtop-stable-ru-iii-nhc-complexes-from-ru-cl3-3h2o-and-their-use-as-precursors-for-ru-ii-nhc-complexes.pdf |
60c750b4567dfe3ec9ec58ef | 10.26434/chemrxiv.12931670.v2 | A Many-Body, Fully Polarizable Approach to QM/MM Simulations | <div>
<div>
<div>
<p>We present a new development in quantum mechanics/molecular mechanics (QM/MM) methods by replacing conventional MM models with data-driven many-body (MB) representations
rigorously derived from high-level QM calculations. The new QM/MM approach builds on top
of mutually polarizable QM/MM schemes developed for polarizable force fields with inducible dipoles and uses permutationally invariant polynomials to effectively account for quantum-
mechanical contributions (e.g., exchange-repulsion, and charge transfer and penetration) that
are difficult to describe by classical expressions adopted by conventional MM models. Us-
ing the many-body MB-pol and MB-DFT potential energy functions for water, which include
explicit 2-body and 3-body terms fitted to reproduce the corresponding CCSD(T) and PBE0 2-
body and 3-body energies for water, we demonstrate a smooth energetic transition as molecules
are transferred between QM and MM regions, without the need of a transition layer. By effectively elevating the accuracy of both the MM region and the QM/MM interface to that of the
QM region, the new QM/MB-MM approach achieves an accuracy comparable to that obtained
with a fully QM treatment of the entire system. </p>
</div>
</div>
</div> | Eleftherios Lambros; Filippo Lipparini; G. Andres Cisneros; Paesani Lab | Computational Chemistry and Modeling; Theory - Computational; Clusters; Physical and Chemical Processes; Physical and Chemical Properties; Quantum Mechanics; Solution Chemistry; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b4567dfe3ec9ec58ef/original/a-many-body-fully-polarizable-approach-to-qm-mm-simulations.pdf |
64092310cc600523a3e16ad4 | 10.26434/chemrxiv-2023-1zx8l | Analyzing and Predicting the Viscosity of Polymer Nanocomposites in the Conditions of Temperature, Shear Rate, and Nanoparticles Loading with Molecular Dynamics Simulations and Machine Learning | Predicting the viscosity of polymer nanocomposites (PNCs) is of critical importance as it governs a dominant role in PNCs processing and application. Machine learning (ML) algorithms, enabled by pre-existing experimental and computational data, have emerged as robust tools for the prediction of quantitative relationships between feature parameters and various physical properties of materials. In this work, we employed nonequilibrium molecular dynamics (NEMD) simulation with ML models to systematically investigate the viscosity of PNCs over a wide range of NPs loading, shear rates and temperature.With the increase in shear rates, shear thinning takes place as the value of viscosity decreases on the orders of magnitude. In addition, the NPs loading -dependence and T-dependence reduce to the extent that it is not visible at high shear rates. The value of viscosity for PNCs is proportional to NPs loading and inversely proportional to T below the intermediate shear rates. Using the obtained NEMD results, four machine learning models were trained to provides eective predictions for the viscosity. The extreme gradient boosting (XGBoost) model yields the best accuracy in viscosity prediction under complex conditions and is further used to evaluate feature importance. This quantitative structure-property relationship (QSPR) model used physical views to investigate the effect of process parameters, such as temperature, NPs loading and shear rates, on the viscosity of PNCs and paves the path for theoretically proposing reasonable parameters for successful processing. | Haoxiang Li; Hao Tian; Yewei Chen; Sian Xiao; Yangyang Gao; Xiuying Zhao; Liqun Zhang | Polymer Science | CC BY 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64092310cc600523a3e16ad4/original/analyzing-and-predicting-the-viscosity-of-polymer-nanocomposites-in-the-conditions-of-temperature-shear-rate-and-nanoparticles-loading-with-molecular-dynamics-simulations-and-machine-learning.pdf |
6421a441647e3dca9996a4c2 | 10.26434/chemrxiv-2023-0cbr9 | Degree of Carbon Nitride Photocharging Controls Energetics of Hydrogen Transfer in Photochemical Cascade Processes | Photocharging of graphitic carbon nitrides (g-CN) is a process of electrons and charge-compensating cations accumulation in the material that is triggered by irradiating a mixture of the semiconductor and an electron donor with light. Although this process has been applied in sensing, energy storage and organic synthesis, the energetics of g-CN discharging has not been studied in details. Herein, we investigate transfer of e‒/H+ from g-CN photocharged with electrons and either protons (H+) or ammonium cations (NH4+) to an oxidant, such as O2 and imine. NH4+ exerts a strong stabilizing effect, which makes e‒/H+ transfer uphill. Especially in aqueous environment, NH4+ yields air-stable photocharged sodium poly(heptazine imide). In mildly-reduced g-CN, H+ do not stabilize electrons, which results in spontaneous transfer of e‒/H+ to oxidants. Facile transfer of e‒/H+ is a key step in a photocatalytic oxidative-reductive cascade – tetramerization of benzylic amines, which involves two photocatalytic events: i) oxidation of two benzylic amine molecules to the imine with a concomitant storage of 2e‒/2H+ in g-CN and ii) reduction of the imine to α-aminoalkyl radical that involves 1e‒/1H+ transfer. | Oleksandr Savateev; Karlo Nolkemper; Thomas Kühne; Yevheniia Markushyna; Markus Antonietti | Theoretical and Computational Chemistry; Materials Science; Energy; Carbon-based Materials; Photosensitizers; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6421a441647e3dca9996a4c2/original/degree-of-carbon-nitride-photocharging-controls-energetics-of-hydrogen-transfer-in-photochemical-cascade-processes.pdf |
61e2fd304a603d7d99314784 | 10.26434/chemrxiv-2022-d2q4n | Thermal-electrochemical parameters of a high energy lithium-ion cylindrical battery | To accurately predict the lifetime of commercial cells, multi-physics models can be used, however the accuracy of the model is heavily reliant upon the quality of the input thermodynamics and kinetic parameters. The thermal properties and the variability of the transport and thermodynamic properties with temperature and state-of-charge (SoC) in a high energy 21700 cylindrical cell were measured. The parameters are used in a DFN and 0D thermal model, and the model was tested against experimental data from the commercial cell. The results demonstrate an improved model fit by 27% when including the parameter dependency upon SoC and temperature, compared to without. The maximum power is limited by the negative electrode, which has lower diffusion coefficients and current exchange density over the full SOC window compared to the positive electrode, particularly at 50% and 80% SoC (x=0.45 and 0.85), reflected in high activation energies of up to 60 kJ K-1 and low diffusion coefficients of 5 x 10-13 cm-2 s-1 at 25 °C. At 45 °C, the reaction rate increases to greater than that of the positive, diffusion also increases, 2 x10-12 cm-2 s-1, but is still limiting. This work provides for the first time an electrochemical and thermal experimental dataset for a high energy cell, and provides insights into the rate limitations and prediction errors. | Kieran O'Regan; Ferran Brosa Planella; W. Dhammika Widanage; Emma Kendrick | Physical Chemistry; Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e2fd304a603d7d99314784/original/thermal-electrochemical-parameters-of-a-high-energy-lithium-ion-cylindrical-battery.pdf |
67bc7bc581d2151a02d94302 | 10.26434/chemrxiv-2025-bqzl2 | Material Characterization of NMC Black Mass from End-of-Life Lithium-Ion Batteries for Enhanced Recycling Strategies | Recycling black mass (BM) obtained from NMC-based end-of-life lithium-ion batteries (LIBs) is hindered by metallic impurities (Al and Cu), residual electrolytes, and PVDF (polyvinylidene fluoride) binder. Pre-treatment of BM, such as milling and pyrolysis, to remove these impurities necessitates characterizing its physicochemical properties that affect such pre-treatment methods. More importantly, a judicious combination of characterization techniques can provide an integrated framework for efficiently planning pre-treatment and recycling processes. In this study, industrial BM samples from end-of-life NMC622, NMC111, and NMC901 LIBs are characterized. The comparative characterization of BM using FBRM (focused beam reflectance measurement) and laser diffraction techniques showed that applying square weighting to the chord length distribution measured by FBRM yields values close to the actual particle size, while also providing a method that can be used for real-time analysis of recycling processes. XRD (x-ray diffraction), complemented by SEM (scanning electron microscopy) and metal composition data confirmed that crystalline NMC phases remain intact in untreated BM and graphite exists as a mixture of 2H and 3R phases. Additionally, Raman spectroscopy with SEM elemental analysis provided insights into the carbonaceous deposits and metal particles on graphite surfaces. Qualitative TGA/MS (thermogravimetry with mass spectrometry) of BM under pyrolytic conditions allowed the identification of residual electrolytes and PVDF through the evolution of carbonaceous and fluorinated gases. Quantitative TGA/MS under oxidative conditions allowed quantification of total carbon in BM and estimation of PVDF. Explored characterization techniques highlight the impact of pre-treatment processes and provide a decision framework for selecting and optimizing recycling strategies. | Hammad Farooq; Sulalit Bandyopadhyay | Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc7bc581d2151a02d94302/original/material-characterization-of-nmc-black-mass-from-end-of-life-lithium-ion-batteries-for-enhanced-recycling-strategies.pdf |
621be851c6bb55474a76fda5 | 10.26434/chemrxiv-2022-kdd5s | Spatial variation in cost of electricity-driven continuous ammonia production in the United States | Cost-effective, low-carbon ammonia production is necessary for decarbonizing its existing uses, but could also enable decarbonization of other difficult-to-electrify end uses like shipping where energy density is a key criterion. Here, we assess the levelized cost of ammonia production (95% availability) at industrial-scale quantities (250 tonnes/day) in 2030 from integrating commercial technologies for renewable electricity generation, electrolysis, ammonia synthesis and energy storage. Our analysis accounts for the spatial and temporal variability in cost and emissions attributes of electricity supply from variable renewable energy (VRE) sources and the grid, and its implications on plant design, operations, cost and emissions. Based on 2030 technology cost and grid projections, we find that grid-connected ammonia in the midcontinental U.S. costs 0.54-0.64 $/kg, as compared to 0.3-0.4 $/kg for natural gas-based ammonia and
depending on the generation mix of the grid, may have higher or lower CO2 emissions. Fully VRE-based ammonia production, even with simultaneous wind and PV utilization,
is more expensive than grid connected outcomes, due to the need for storage to manage VRE intermittency and continuous ammonia production. Instead, using VRE
and grid electricity for ammonia production under moderate carbon policy (50$/tonne CO2 price) in the midcontinental U.S. can achieve 55-100% CO2 emissions reduction
per tonne of ammonia compared to natural gas routes and corresponds to levelized cost range of 0.54-0.63 $/kg NH3). Further cost reductions are shown to be possible if the
ammonia synthesis loop can be made more flexible, which reduces the need for round- the-clock electricity supply and the substitute use of battery storage with ammonia
storage. | Abhishek Bose; Nikifar Lazouski; Michal Gala; Karthish Manthiram; Dharik Mallapragada | Energy; Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Petrochemicals; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621be851c6bb55474a76fda5/original/spatial-variation-in-cost-of-electricity-driven-continuous-ammonia-production-in-the-united-states.pdf |
67470dac7be152b1d00d8ac9 | 10.26434/chemrxiv-2024-vgvhk-v3 | Deep Supramolecular Language Processing for Co-crystal Prediction | Approximately 40% of marketed drugs exhibit suboptimal pharmacokinetic profiles. Co-crystallization, where pairs of molecules form a multicomponent crystal, constitutes a promising strategy to enhance physicochemical properties without compromising the pharmacological activity. However, finding promising co-crystal pairs is resource-intensive, due to the vast number of possible combinations. We present DeepCocrystal, a novel deep learning approach designed to predict co-crystal formation by processing the 'chemical language' from a supramolecular vantage point. Rigorous validation of DeepCocrystal showed a balanced accuracy of 78% in realistic scenarios, outperforming existing models. By leveraging properties of molecular string representations, DeepCocrystal can also estimate the uncertainty of its predictions. We harness this capability in a challenging prospective study, and successfully discovered two novel co-crystal of diflunisal, an anti-inflammatory drug. This study underscores the potential of deep learning - and in particular of chemical language processing - to accelerate co-crystallization, and ultimately drug development, in both academic and industrial contexts. | Rebecca Birolo; Rıza Özçelik; Andrea Aramini; Roberto Gobetto; Michele Remo Chierotti; Francesca Grisoni | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67470dac7be152b1d00d8ac9/original/deep-supramolecular-language-processing-for-co-crystal-prediction.pdf |
653ff55ec573f893f1745816 | 10.26434/chemrxiv-2023-86njv | Nonadiabatic dynamics with classical trajectories: The problem of an initial coherent superposition of electronic states. | Advances in coherent light sources and development of pump-probe techniques in recent decades have opened the way to study electronic motion in its natural time-scale. When an ultrashort laser pulse interacts with a molecular target a coherent superposition of electronic states is created and the triggered electron dynamics is coupled to the nuclear motion. A natural and computationally efficient choice to simulate this correlated dynamics are trajectory-based methods where the quantum-mechanical electronic evolution is coupled to a classical-like nuclear dynamics. These methods must approximate the initial correlated electron-nuclear state by associating an initial electronic wavefunction to each classical trajectory in the ensemble. Different possibilities exist that reproduce the initial populations of the exact molecular wavefunction when represented in a basis. We show that different choices yield different dynamics, and explore the effect of this choice in Ehrenfest, surface-hopping, and exact-factorization-based coupled-trajectory schemes in a model system. | Evaristo Villaseco Arribas; Neepa Maitra; Federica Agostini | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653ff55ec573f893f1745816/original/nonadiabatic-dynamics-with-classical-trajectories-the-problem-of-an-initial-coherent-superposition-of-electronic-states.pdf |
6671a14801103d79c57fec93 | 10.26434/chemrxiv-2024-6mjmb | Chemoselective silver-catalyzed nitrene transfer: Tunable syntheses of azepines and cyclic carbamimidates | Azepines and their saturated azepane counterparts are important moieties in bioactive molecules but are underrepresented in current drug screening libraries. Herein, we report a mild and efficient azepine formation via silver-catalyzed dearomative nitrene transfer. A 2,2,2-trichloroethoxysulfonyl (Tces)-protected carbamimidate nitrene precursor, coupled with the appropriate ligand for silver, is essential for achieving the unexpected chemoselectivity between arene dearomatization and benzylic C(sp3)–H amination. Potential applications in the late-stage diversification of azepines to complex molecular scaffolds and diastereoselective hydrogenations to high Fsp3 azepanes are also highlighted. | Emily Schroeder; Chenxi Lin; Zhenyao Dai; Amory Griffin; Thomas Hotvedt; Ilia Guzei; Jennifer Schomaker | Organic Chemistry; Catalysis; Organometallic Chemistry; Bond Activation; Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6671a14801103d79c57fec93/original/chemoselective-silver-catalyzed-nitrene-transfer-tunable-syntheses-of-azepines-and-cyclic-carbamimidates.pdf |
60c74770337d6c7bf6e27347 | 10.26434/chemrxiv.11597133.v1 | Synthesis and Pharmacokinetic Study of a 11C-Labeled Cholesterol 24-Hydroxylase Inhibitor Using ‘In-Loop’ [11C]CO2 Fixation Method | <div>
<table>
<tr>
<td>
<p><a>Cholesterol
24-hydroxylase is</a> a monooxygenase encoded by
CYP46A1, which is specifically expressed in the brain where it controls
cholesterol elimination by producing 24<i>S</i>-hydroxylcholesterol
(24-HC) as the major metabolite. Selective blockade of CYP46A1 activity may
suppress neuronal cell death, Aβ deposition and p-tau accumulation by
decreasing 24-HC formation, which thereafter serves as potential therapeutic
pathway for Alzheimer’s disease. In this work, we showcase the efficient
synthesis and preliminary pharmacokinetic evaluation of a novel cholesterol 24-hydroxylase inhibitor <b>1</b> by positron emission tomography study. </p>
</td>
</tr>
</table>
</div> | Zhen Chen; Jiahui Chen; Natalia Mast; Jian Rong; Xiaoyun Deng; Tuo Shao; Hualong Fu; Qingzhen Yu; Jiyun Sun; Yihan Shao; Lee Josephson; Thomas Lee Collier; Irina Pikuleva; Steven Liang | Bioorganic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74770337d6c7bf6e27347/original/synthesis-and-pharmacokinetic-study-of-a-11c-labeled-cholesterol-24-hydroxylase-inhibitor-using-in-loop-11c-co2-fixation-method.pdf |
66fa63aa51558a15ef9211e3 | 10.26434/chemrxiv-2024-3qpvm | Merging Hydrogen-Atom-Transfer and the Truce-Smiles Rearrangement for Synthesis of beta-Arylethylamines from Unactivated Allylsulfonamides | Arylethylamines are crucial elements in pharmaceutical molecules, making methods for their synthesis highly significant. The Truce-Smiles rearrangement is a well-developed strategy to synthesize arylethylamine motifs via aryl migration. However, most examples require amide substrates to activate the alkene to attack by a radical precursor. This strategy both limits the product scope to amide containing compounds as well as necessitating the incorporation of specific functional groups arising from the initial radical addition. In this work, we overcome these limitations, delivering a hydrogen-atom-transfer from a cobalt catalyst to unactivated alkenes to yield -arylethylamines with simple alkyl chains. DFT studies reveal that increasing the steric hindrance in at least one of the ortho positions on the migrating aromatic group promotes ipso over ortho addition, selectivity that contrasts with previous methods. | Hanqi Zhou; Danijela Lunic; Nil Sanosa; Diego Sampedro; Ignacio Funes-Ardoiz; Christopher Teskey | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa63aa51558a15ef9211e3/original/merging-hydrogen-atom-transfer-and-the-truce-smiles-rearrangement-for-synthesis-of-beta-arylethylamines-from-unactivated-allylsulfonamides.pdf |
66d805e6cec5d6c142153a81 | 10.26434/chemrxiv-2025-tmb5b | Heteronuclear Spin Decoupling under Cryogenic
Magic-Angle-Spinning Dynamic Nuclear
Polarization Conditions | Heteronuclear decoupling is an essential element in the solid-state magic-angle spinning (MAS) Dynamic nuclear polarization (DNP) experiments involving low gamma
(γ) nuclei like 13C and 15N coupled to protons. Under the constraints of limited (< 100 kHz) maximum radio frequency (RF) amplitude and intermediate (30-45 kHz) spinning frequencies, imposed by the cryogenic DNP setup, the typically utilized heteronuclear decoupling schemes like TPPM and SPINAL-64 suffer from near rotary-resonance recoupling (R3). Here, we demonstrate the effectiveness of the refocused continuous-wave (rCW) decoupling sequence for heteronuclear 1H decoupling near the R3 regime under
DNP conditions. We compare the performance of rCWApA decoupling with the widely used SPINAL-64 scheme and show a significant improvement in the heteronuclear
decoupling efficiency, confirmed through T2' evaluations. The superior decoupling efficiency of rCWApA stems from its half-wave symmetry in the RF interaction frame,
which enables effective decoupling of first and second-order effective heteronuclear coupling Hamiltonian, even at low RF amplitude levels and hence minimizing R3 effects
better than any other decoupling scheme. | Ribal Jabbour; Zeba Qadri; P K Madhu; Asif Equbal | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d805e6cec5d6c142153a81/original/heteronuclear-spin-decoupling-under-cryogenic-magic-angle-spinning-dynamic-nuclear-polarization-conditions.pdf |
627ecc7ea42e9c06ec3ff7f4 | 10.26434/chemrxiv-2022-59f1v | Multireference Study of Optically Addressable Vanadium-based Molecular Qubit Candidates | Molecular electron spin qubits with optical manipulation schemes are some of the most promising candidates for modern quantum technologies. Key values that determine a compound’s viability for optical-spin initialization and readout include its singlet-triplet gap and zero-field splitting (ZFS) parameters. Generally, these values are very small in magnitude and are thus difficult to reproduce with theoretical methods. Here we study a previously identified optically addressable molecular qubit, (C6F5)3trenVCNtBu (tren = tris(2-aminoethyl)amine), using the complete active space self-consistent field (CASSCF) and post-CASSCF methods (CASPT2, MC-PDFT, and HMC-PDFT). Of those methods, we successfully reproduce the singlet-triplet gap and ZFS parameters with reasonable accuracy using 0.5 HMC-PDFT and CASPT2. Four additional V3+ complexes with differing ligands were also investigated. We found that the ligands have minimal effect on the spin properties of the molecule and propose them to be optically addressable qubit candidates. These potential qubits are further analyzed in terms of ab initio ligand field theory (AILFT) to understand the influence of the ligands on the singlet-triplet gap and ZFS parameters. | Teffanie Goh; Riddhish Pandharkar; Laura Gagliardi | Theoretical and Computational Chemistry; Inorganic Chemistry; Magnetism; Theory - Inorganic; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627ecc7ea42e9c06ec3ff7f4/original/multireference-study-of-optically-addressable-vanadium-based-molecular-qubit-candidates.pdf |
66806a1201103d79c5817710 | 10.26434/chemrxiv-2024-9cqk6 | The amenability of different solvents to electrospray ionization mass spectrometry
| Electrospray ionization mass spectrometry is capable of transferring ions from solution to the gas phase across a broad range of solvents. A systematic investigation of the relative performance of different solvents has not been previously conducted, and we sought to remedy this situation. Fourteen solvents across a wide range of polarities were investigated for their ability to provide strong signals for four permanently charged ions. We found the best solvents to be acetone, acetonitrile, dichloromethane, tetrahydrofuran, and the previously unused (in an ESI-MS context) trifluorotoluene. | Charles Killeen; Antonia Kropp; Ian Chagunda; Emily Jackson; J. Scott McIndoe | Analytical Chemistry; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66806a1201103d79c5817710/original/the-amenability-of-different-solvents-to-electrospray-ionization-mass-spectrometry.pdf |
60c759089abda22042f8ea0d | 10.26434/chemrxiv.14635665.v1 | Machine Learning 3D-Resolved Prediction of Electrolyte Infiltration in Battery Porous Electrodes | Electrolyte infilitration is one of the critical steps of the manufacturing process of lithium ion batteries. Along with being the most time-consuming step in manufacturing, electrolyte wetting directly impacts the battery cell energy density, power density and cycle life. We present here an innovative machine learning model to fast and
accurately predict electrolyte infiltration in three dimensions in
lithium ion battery electrodes. Our machine learning model is able to speed up the infiltration predictions by several orders of magnitude compared to a physics-based model based on Lattice Boltzmann Method, paving the way towards massive computational screening of electrode mesostructures/electrolyte pairs to unravel their impact on the cell wetting and optimize electrolyte infiltration conditions.<br /> | Abbos Shodiev; Marc Duquesnoy; Oier Arcelus; Mehdi Chouchane; Jianlin Li; Alejandro A. Franco | Materials Processing; Machine Learning; Artificial Intelligence; Industrial Manufacturing; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759089abda22042f8ea0d/original/machine-learning-3d-resolved-prediction-of-electrolyte-infiltration-in-battery-porous-electrodes.pdf |
654f4a0fdbd7c8b54b10b7e0 | 10.26434/chemrxiv-2023-pmkhn | Long-range solvent templating and counterion behavior at a charged, nanoscale surfaces | The ordering of solvent molecules around nanostructures is of broad scientific importance from understanding biological processes to the manipulation of nanomaterials in liquids, to optimiz-ing the performance of electrochemical devices. However, experimental measurements of this solvent ordering are scarce. Herein, the structures of concentrated solutions of anionic carbon nanotubes in two amidic solvents are measured via total neutron scattering leading to a previ-ously unattainable picture of nanoparticle solvation, revealing a far richer structure than hitherto assumed. The solvent molecules form densely-packed, concentric shells around the charged carbon nanotubes, ordered according to two distinct orientations due to competing effects. Firstly, a surface monolayer that maximizes attractive interactions between anionic surface and solvent molecular dipole moment. The second orientation extends ~40 Å into the bulk solvent, with molecules preferentially oriented perpendicularly to the first layer due to dipole interac-tions with the charged nanoparticle. This complex, long-ranged order drastically differs from the simplistic treatment of the solvent in classical models commonly employed to understand these systems. Moreover, our analysis indicates that a fraction of counterions condense on the sur-face as a Stern layer which are desolvated due to the solvent preferentially interacting with the charged surface. Ions at further distances are fully solvated, and their distribution is strongly in-fluenced by the dense solvation shells around the nanotube. Our results thus underscore the critical importance of multi-body interactions in solvated nanoscale systems, highlighting new competing ion/surface solvation effects crucial for understanding electrolyte-surface interfaces in supercapacitors, batteries, and electrolytically-gated devices. | Camilla Di Mino; Thomas Headen; Nadir Basma; David Buckley; Patrick Cullen; Martin Wilding; Milo Shaffer; Neal Skipper; Adam Clancy; Christopher Howard | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Solution Chemistry; Structure; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654f4a0fdbd7c8b54b10b7e0/original/long-range-solvent-templating-and-counterion-behavior-at-a-charged-nanoscale-surfaces.pdf |
644bc42d0d87b493e36fe0ca | 10.26434/chemrxiv-2023-9l4mp-v2 | A comparison among bio-derived acids as selective eco-friendly leaching agents for cobalt: the case study of hard metals waste enhancement | Peculiar chemical, mechanical and magnetic properties make cobalt a key metal for a variety of “hot” applications like cathode production of Li-ion batteries. Cobalt is also the preferred metallic binder for tungsten carbide tools manufacturing. The recent increasing criticality of cobalt and tungsten is driving the interest of manufacturers and researchers towards high-rate recycling of Hard Metals (HMs) waste for limiting the demand of raw materials. A simple and environmentally friendly hydrometallurgical route for Co selective dissolution from HM wastes was developed by using weak, bio-derived and biodegradable organic acids (OAs). In this study OAs, namely acetic (HAc), citric (H3Cit), maleic (H2Mal), lactic (HLac), succinic (H2Suc), lactobionic (HLB), and itaconic (H2It) acids, were selected for their pKa1 values spanning from 1.8 to 4.7 and systematically tested as selective cobalt leaching agents from WC-Co-based wastes in water, isolating the formed complexes at the solid state. Thereby, all of them seemed to be efficient in selective Co-leaching, achieving almost quantitative Co dissolution from HM by-products still at low concentration level and room conditions in a short time, leaving the residual WC unreacted and ready to be re-employed for industrial purposes. Nevertheless, two main categories of organic acids were distinguished depending on their oxidizing/complexing behavior: Class 1 OAs, where the metal oxidation is carried out by H+; Class 2 OAs where oxidation is played by an external oxidant like O2. A combined experimental/theoretical investigation is here described to show the reasons behind this peculiar behavior and laid the foundation for a wider discussion on the leaching capabilities of OAs towards elemental metals. Due to the demonstrated effectiveness, low cost, eco-friendliness and large availability through biotechnological fermentative processes, particular attention is here devoted to the use of HLac in hydrometallurgy as an example of Class 2 OA. WC-Co materials recovered by HLac mild hydrometallurgy demonstrated a metallurgical quality suitable for re-employment in the HM manufacturing process. | Amadou Oumarou Amadou; Martina Cera; Stefano Trudu; Martina Piredda; Stefano Cara; Gian Pietro De Gaudenzi; Avtar Singh Matharu; Luciano Marchiò; Matteo Tegoni; Aldo Muntoni; Giorgia De Gioannis; ANGELA SERPE | Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644bc42d0d87b493e36fe0ca/original/a-comparison-among-bio-derived-acids-as-selective-eco-friendly-leaching-agents-for-cobalt-the-case-study-of-hard-metals-waste-enhancement.pdf |
61f45f0ae4d9b81fcefb682c | 10.26434/chemrxiv-2022-mbtxb | Rhodium Disulfur and Dioxygen Complexes: Examination of Boron Secondary Coordination Sphere Effects | A series of diphosphine-ligated rhodium(III) h2-peroxo and -persulfido compounds are targeted with one subset containing a boron-rich secondary coordination sphere (SCS). A systematic investigation using both experimental and theoretical methods has been performed to assess whether peripheral boranes can be used to engage with rhodium(III)-bound chalcogenides. For the model compound, [RhI(dnppe)2]BPh4 (dnppe = 1,2-bis(di-n-propylphosphino)ethane), adducts of the form [RhI(dnppe)2(h2-Ch2)]BPh4 (Ch = O or S) were characterized. For the octaboranyl compound, [RhI(P2BCy4)2]BPh4 (P2BCy4 = 1,2-bis(di(3-dicyclohexylboranyl)propylphosphino)ethane), however, treatment with O2 resulted in SCS decomposition via B—O bond formation, while reaction with 0.25 equivs. S8 provided [RhI(P2BCy4)2(2-S2)]BPh4, which based on variable-temperature 31P NMR spectroscopic measurements, does not exhibit a B—S interaction. Using a compound with a single pendant borane as a model, potential energy surface (PES) scans were found to suggest kinetic and thermodynamic feasibility of a B—O interaction with DG(B—O) = —2.5 kcal mol-1; a stationary point for the related B—S system was not located. | Devon Facchinato; Joseph Zurakowski; Marcus Drover | Inorganic Chemistry; Organometallic Chemistry; Bonding; Coordination Chemistry (Inorg.); Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f45f0ae4d9b81fcefb682c/original/rhodium-disulfur-and-dioxygen-complexes-examination-of-boron-secondary-coordination-sphere-effects.pdf |
668352455101a2ffa817b5a3 | 10.26434/chemrxiv-2024-8hvs7 | Divergent Synthesis of Cyclobutyl and Biscyclobutenyl Amines via Lewis Acid-Catalyzed Reaction of Bicyclo[1.1.0]butanes with Triazinanes | In this study, we describe a Lewis acid-catalyzed divergent synthesis of cyclobutyl and biscyclobutenyl amines by exploiting the distinct reactivity exhibited by bicyclo[1.1.0]butane (BCB) ketones and esters with triazinanes. The cycloaddition of BCB ketones with triazinanes yields 2,4-diazabicyclo[4.1.1]octanes (aza-BCOs) under B(C6F5)3 catalysis. A direct acidic treatment of the resulting aza-BCOs efficiently cleaves the aminal moiety, leading to a series of medicinally intriguing cis-cyclobutyl diamines. This "cycloaddition/ring-opening" process can be conducted in either a stepwise or one-pot manner. In contrast, the reaction of BCB esters with triazinanes produces a range of beautiful butterfly-shaped biscyclobutenyl amines under In(OTf)3 catalysis. Both reactions feature simple operation, mild reaction conditions, and a broad substrate scope. Mechanistic studies reveal that the distinct reaction pathways originate from the different activation modes of BCBs by Lewis acid, the reaction of BCB ketones with triazinanes follows a stepwise (2+2+3) rather than (4+3) cycloaddition, and the reaction of BCB esters with triazinanes involves a Leitch’s carbocation intermediate. We believe that our findings will promote the exploration of BCB chemistry to access more synthetically challenging cyclobutane frameworks. | Shiyong Peng; Yijun Duan; Feng Chen; Ye Guo; Yuncheng Liu; Ming Lang; Jinbao Peng; Jian Wang | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668352455101a2ffa817b5a3/original/divergent-synthesis-of-cyclobutyl-and-biscyclobutenyl-amines-via-lewis-acid-catalyzed-reaction-of-bicyclo-1-1-0-butanes-with-triazinanes.pdf |
60c75414842e6554eadb40a8 | 10.26434/chemrxiv.13606715.v1 | Incorporating Fluorescent Nanomaterials in Organically Modified Sol-Gel Materials – Creating Single Composite Optical pH Sensors | <br /><br />Optical sensors hold the promise of providing the coupling between the tangible and the digital world that we are currently experiencing with physical sensors. The core of optical sensor development lies in materials development, where specific requirements of opposing physicochemical properties create a significant obstacle. The sensor material must provide dye retention, while ensuring porosity for analyte transport. The sensor material must provide hydrophobic pockets for dyes to ensure high signal intensity, while remaining fully hydrophobic to measure in water. We have previously reported optical sensors, where we compromised on sensor manufacturing by using a double-layer composite. Here, we report a composite organically modified sol-gel (ORMOSIL) polymer, where polystyrene (PS) nanoparticles (NPs) have been incorporated. This allows all the opposing requirements on optical sensor materials to be fulfilled, and by introducing a hydrophobic reference dye in the fully hydrophobic compartments of the sensor material we show that we can incorporate any hydrophobic fluorophore in this material, even those which are suffering from quenching in water. In this work, PS NPs with 1,13-dimethoxyquinacridinium (DMQA) were immobilized in a composite sol-gel material with pH responsive diazaoxatriangulenium (DAOTA) dyes prior to curing. The multicomponent sensor composite was cured on a polycarbonate hemiwicking substrate, and the resulting fluorescence intensity ratiometric optical pH sensor was shown to have excellent performance. We expect that this type of composite sensor materials will allow the creation of next generation industrial chemosensors.<br /><br /> | David Bartos; Morten Rewers; Lu Wang; Thomas Just Sørensen | Dyes and Chromophores; Nanostructured Materials - Materials; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75414842e6554eadb40a8/original/incorporating-fluorescent-nanomaterials-in-organically-modified-sol-gel-materials-creating-single-composite-optical-p-h-sensors.pdf |
662239a621291e5d1d293cbf | 10.26434/chemrxiv-2024-2n4xd | Electrochemical nitrogen reduction reaction to ammonia using perovskite-type oxynitrides BaMO2N (M = Nb, Ta) and enhancement of the activity by acid treatment | The electrochemical nitrogen reduction reaction (ENRR) to NH3 is one of the potential alternatives to the Harber-Bosch (HB) process. Metal nitrides and oxynitrides have been proposed as suitable catalysts. However, an ENRR catalyst that is stable during the ENRR and demonstrates a high Faradaic efficiency (FE) has never been reported. Perovskite-type oxynitrides, BaMO2N (M = Nb, Ta) are promising catalysts for the ENRR because of the coexisting of N vacancies that function as N2 mole-cule adsorption sites and a robust crystal lattice resulting from the metal-oxygen bonds. Herein, we demonstrate electro-chemical NH3 production using the perovskite oxynitride catalysts with high FE values over 60%. The Ta and Nb oxynitrides showed NH3 production rates of 6.8 and 9.2 μgNH3/h·mgcat, with the FE values of 73% and 39%, respectively. Acid treatment using 6 M nitric acid enhanced their activity to 8.0 and 15 μgNH3/h·mgcat with 63% and 67% of FE values for the Ta and Nb oxynitrides, respectively. The amount of NH3 produced was approximately ten times larger than the nitrogen content of the oxynitride catalysts, indicating that the NH3 was dominantly produced from N2, not from decomposition of the catalysts. | Haruka Kusano; Akira Miura; Mikio Higuchi; Yuji Masubuchi | Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662239a621291e5d1d293cbf/original/electrochemical-nitrogen-reduction-reaction-to-ammonia-using-perovskite-type-oxynitrides-ba-mo2n-m-nb-ta-and-enhancement-of-the-activity-by-acid-treatment.pdf |
67405efc7be152b1d0534b91 | 10.26434/chemrxiv-2024-wmn17 | A carbon cathode for lithium mediated electrochemical ammonia
synthesis | To introduce the potential for tuneability of the cathode in lithium mediated ammonia synthesis,
we report a carbon cathode which produces ammonia at a Faradaic efficiency of 37 %. This
provides a basis to optimise properties of carbon electrodes to achieve high current densities
and Faradaic efficiencies.
| Craig Burdis; Romain Tort; Anna Winiwarter; Jesús Barrio; Magda Titirici; Ifan Stephens | Materials Science; Catalysis; Energy; Carbon-based Materials; Fuels - Materials; Electrocatalysis | CC BY 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67405efc7be152b1d0534b91/original/a-carbon-cathode-for-lithium-mediated-electrochemical-ammonia-synthesis.pdf |
60c741084c8919aebfad222d | 10.26434/chemrxiv.7905344.v1 | Plasmon-Induced Hot-Carrier Generation differences in Gold and Silver Nanoclusters | In the last thirty years, the study of plasmonic properties of noble metal nanostructures has become a very dynamic research area. The design and manipulation of matter in the nanometric scale demand a deep understanding of the underlying physico-chemical processes that operate in this size regimen. Here, a fully atomistic study of the spectroscopic and photodynamic properties of different icosahedral silver and gold nanoclusters have been carried out by using Time-Dependent Density Functional Tight-Binding (TD-DFTB) model. Optical absorption spectra of different icosahedral silver and gold nanoclusters of diameters between 1 and 4 nanometers has been simulated. Furthermore, the energy absorption process have been quantified by means of calculating a fully quantum absorption cross-section using the information contained in the reduced single-electron density matrix. This approach allows us take into account for the quantum confinement effects dominating in this size regime. Likewise, the plasmon-induced hot-carrier generation process under laser illuminations have been explored from a fully dynamical perspective. We have found noticeable differences in the energy absorption mechanisms and the plasmon-induced hot-carrier generation process in both metals which can be explained by their respective electronic structures. These difference can be attributed to the existence of ultra-fast electronic dissipation channels in gold nanoclusters that are absented in silver nanoclusters. To the best of our knowledge, this is the first report that addresses this topic from a real time fully atomistic time-dependent approach. <br /> | Oscar A. Douglas-Gallardo; Matias Berdakin; Thomas Frauenheim; Cristián G Sánchez | Plasmonic and Photonic Structures and Devices; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741084c8919aebfad222d/original/plasmon-induced-hot-carrier-generation-differences-in-gold-and-silver-nanoclusters.pdf |
62311da3a4ed95494621c2f6 | 10.26434/chemrxiv-2022-jgpqv | Single polymer sorbent fibers for high performance and rapid direct air capture | Polymers of intrinsic microporosity (PIM) fibers based on amidoxime and amine functionalities were formulated into high- performance CO2 adsorbents. Fiber sorbents were composed of a single porous polymer component as well as molecular amines to increase the CO2 capture kinetics. The highest CO2 uptake capacity (3.3 wt% CO2 at 400 ppm) among all PIM-based sorbents to date was reported. Moreover, sorbents exhibited rapid CO2 adsorption rates (5 min adsorption cycle) and cost efficient regeneration (70oC, no vacuum) which are imperative to reducing the cost of direct air capture. | Ali Sekizkardes; Victor Kusuma; Jeffrey Culp; Patrick Muldoon; James Hoffman; David Hopkinson | Materials Science; Energy; Fibers; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62311da3a4ed95494621c2f6/original/single-polymer-sorbent-fibers-for-high-performance-and-rapid-direct-air-capture.pdf |
66ccc41df3f4b052902dd824 | 10.26434/chemrxiv-2024-b2n7q | Direct Synthesis of Ethers from Alcohols & Aldehydes Enabled by an Oxocarbenium Ion Interception Strategy | A new method has been established for formation of ethers from aldehydes and alcohols – a net reductive etherification. Reactions of these entities with phosphines in the presence of acid enable formation of α-(alkoxyalkyl)phosphonium salts, which, upon hydrolysis, result in formation of ether products in isolated yields of 63–92%. Formation and hydrolysis of the α-(alkoxyalkyl)phosphonium salts were done in an efficient telescoped two-step, one-pot process. Formation of the key phosphonium salt intermediates was found to occur in preference to acetal formation, and is proposed to involve interception of oxocarbenium ions formed by reaction of the aldehyde, alcohol and acid by phosphine. This method represents the first instance in which net reductive etherifications have been achieved without the requirement for use of hydrides or hydrogen as reductants, and exhibits excellent functional group tolerance, thus enabling facile hydride-free synthesis of ethers. These are amongst the most important functional groups in organic synthesis and the most frequently encountered functional groups in the structures of pharmaceutical agents. | Dara Curran; Helge Müller-Bunz; Kirill Nikitin; Peter Byrne | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ccc41df3f4b052902dd824/original/direct-synthesis-of-ethers-from-alcohols-aldehydes-enabled-by-an-oxocarbenium-ion-interception-strategy.pdf |
61e570737110e669a467474f | 10.26434/chemrxiv-2021-t61fx-v2 | Divergent Synthesis of Indolenine and Indoline Ring Systems by Palladium-Catalyzed Asymmetric Dearomatization of Indoles | Dearomatized indole derivatives bearing a C3- or C2-stereocenter exist ubiquitously in natural products and biologically active molecules. Despite remarkable advances in their chemical synthesis, stereoselective and regio-divergent methods are still in a high demand. Herein, a Pd-catalyzed intermolecular asymmetric spiroannulation of 2,3-disubstituted indoles with internal alkynes has been developed for the efficient construction of indoline structures with a C2-quaternary stereocenter. Stereospecific aza-semipinacol rearrangement of these indoline derivatives under acidic conditions afforded indolenine products bearing a C3-quaternary stereocenter, where the selectivity for the rearranging group could be controlled by the reaction sequence. The asymmetric spiroannulation together with the subsequent aza-semipinacol rearrangement enabled a divergent access to dearomatized indole derivatives with either a C3- or a C2-quaternary stereocenter. | Dong Gao; Lei Jiao | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e570737110e669a467474f/original/divergent-synthesis-of-indolenine-and-indoline-ring-systems-by-palladium-catalyzed-asymmetric-dearomatization-of-indoles.pdf |
60c73fdaf96a00e04128616e | 10.26434/chemrxiv.7496627.v1 | Pyramidal Heteroanion-Directed and Reduced MoV-Driven Assembly of Multi-Layered Polyoxometalate Cages | The fabrication of redox-active polyoxometalates (POMs)
that can switch between multiple states is critical for their application
in electronic devices, yet, a sophisticated synthetic methodology is
not well developed for such cluster types. Here we describe the
heteroanion-directed and reduction-driven assembly of a series of
multi-layered POM cages 1-10 templated by 1-3 redox-active
pyramidal heteroanions. The heteroanions greatly affect the selfassembly of the resultant POM cages, leading to the generation of
unprecedented three-layered peanut-shaped - 4, 7 and 8 - or bulletshaped - 5 and 6 - structures. The introduction of reduced
molybdate is essential for the self-assembly of the compounds and
results in mixed-metal (W/Mo), and mixed-valence (WVI/MoV) 1-10,
as confirmed by redox titration, UV-Vis-NIR, NMR spectroscopy and
mass spectrometry. 11, the tetrabutyl ammonium (TBA) salt
derivative of the fully oxidized 3, is produced as a model structure for
measurements to confirm that 1-10 are a statistical mixture of
isostructural clusters with different ratios of W/Mo. Finally, multilayered POM cages exhibit dipole relaxations due to the presence of
mixed valence WVI/MoV metal centers, demonstrating their potential
uses for electronic materials. | Qi Zheng,; Manuel Kupper; Weimin Xuan; Hirofumi Oki; Ryo Tsunashima; De-Liang Long; Leroy Cronin | Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdaf96a00e04128616e/original/pyramidal-heteroanion-directed-and-reduced-mo-v-driven-assembly-of-multi-layered-polyoxometalate-cages.pdf |
65fd5179e9ebbb4db940d941 | 10.26434/chemrxiv-2024-twzr2 | Diversification of pharmaceutical manufacturing processes: Taking the plunge into the non-PGM catalyst pool | Recent global events have led to the cost of platinum group metals (PGMs) reaching unprecedented heights. Many chemical companies are therefore starting to seriously consider and evaluate if, and where, they can substitute PGMs for non-PGMs in their catalytic processes. This review covers recent large-scale applications of non-PGM catalysts in the modern pharmaceutical industry. By highlighting these selected successful examples of non-PGM-catalyzed processes from the literature, we hope to emphasize the enormous potential of non-PGM catalysis and inspire further development within this field to enable this technology to progress towards manufacturing processes. We also present some historical context and review the perceived advantages and challenges of implementing non-PGM catalysts in the pharmaceutical manufacturing environment. | Hui Zhao; Anne Ravn; Michael Haibach; Keary Engle; Carin Johansson Seechurn | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fd5179e9ebbb4db940d941/original/diversification-of-pharmaceutical-manufacturing-processes-taking-the-plunge-into-the-non-pgm-catalyst-pool.pdf |
60c753d1bdbb895b1fa3a50d | 10.26434/chemrxiv.13553534.v1 | Comparative Molecular Dynamics Study of the Roles of Anion– Cation and Cation–Cation Correlation in Cation Diffusion in Li2B12H12 and LiCB11H12 | Complex hydrides are potential candidates for the solid electrolyte of all-solid-state batteries owing to their high ionic conductivities, in which icosahedral anion reorientational motion plays an essential role in high cation diffusion. Herein, we report molecular dynamics (MD) simulations based on a refined force field and first-principles calculations of the two complex hydride systems Li<sub>2</sub>B<sub>12</sub>H<sub>12</sub> and LiCB<sub>11</sub>H<sub>12</sub> to investigate their structures, order–disorder phase-transition behavior, anion reorientational motion, and cation conductivities. For both systems, force-field-based MD successfully reproduced the structural and dynamical behavior reported in experiments. Remarkably, it showed an entropy-driven order–disorder phase transition associated with high anion reorientational motion. Furthermore, we obtained comparative insights into the cation around the anion, cation site occupancy in the interstitial space provided by anions, cation diffusion route, role of cation vacancies, anion reorientation, and effect of cation–cation correlation on cation diffusion. We also determined the factors that activate anion reorientational motion leading to a low to high conductivity phase transition. These findings are of fundamental importance in fast ion-conducting solids to diminish the transition temperature for practical applications.<b></b> | Kartik Sau; Tamio Ikeshoji; Sangryun Kim; Shigeyuki Takagi; Shin-ichi Orimo | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753d1bdbb895b1fa3a50d/original/comparative-molecular-dynamics-study-of-the-roles-of-anion-cation-and-cation-cation-correlation-in-cation-diffusion-in-li2b12h12-and-li-cb11h12.pdf |
65709964cf8b3c3cd7eac790 | 10.26434/chemrxiv-2023-9g3fn | Migration of Zeolite-Encapsulated Subnanometre Platinum Clusters via Reactive Neural Network Potentials | The migration of atoms and small clusters is an important process in sub-nanometre scale heterogeneous catalysis, affecting activity, accessibility and deactivation through sintering. Control of migration can be partially achieved via encapsulation of sub-nanometre metal particles into porous media such as zeolites. However, a general understanding of the migration mechanisms and their sensitivity to particle size and framework environment is lacking. Here, we extend the time-scale and sampling of atomistic simulations of platinum cluster diffusion in siliceous zeolite frameworks, by introducing a reactive neural network potential of density functional quality. We observe that Pt atoms migrate in a qualitatively different manner from clusters, occupying the dense region of the framework and avoiding the free pore space. We also find that for cage-like zeolite CHA there exists a maximum in self diffusivity for the Pt dimer beyond which, confinement effects hinder intercage migration. By extending the quality of sampling, NNP-based methods allow for the discovery of novel dynamical processes at the atomistic scale, bringing modelling closer to operando experimental characterization of catalytic materials. | Christopher Heard; Lukáš Grajciar; Andreas Erlebach | Theoretical and Computational Chemistry; Catalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65709964cf8b3c3cd7eac790/original/migration-of-zeolite-encapsulated-subnanometre-platinum-clusters-via-reactive-neural-network-potentials.pdf |
66b09b40c9c6a5c07a0c5396 | 10.26434/chemrxiv-2024-rwq71 | The Catalytic Mechanism of the Plastic-Degrading Enzyme Urethanase UMG-SP2 | The recently discovered metagenomic urethanases UMG-SP1, UMG-SP2, and UMG-SP3 have emerged as promising tools to improve existing chemical processes for polyurethane (PU) waste recycling. These enzymes are capable of breaking down urethane bonds in low molecular weight dicarbamates using the Ser-Sercis-Lys triad for catalysis, similar to other members of the amidase signature protein superfamily. Understanding the catalytic mechanism of these urethanases is crucial for enhancing their enzymatic activity and improving PU bio-recycling processes. In this study, we employed hybrid quantum mechanics/molecular mechanics methods to delve into the catalytic machinery of the UMG-SP2 urethanase in breaking down a model PU substrate. Our results indicate that the reaction proceeds in two stages: STAGE 1 acylation, in which the enzyme becomes covalently bound to the PU substrate, releasing an alcohol-leaving group; STAGE 2 - deacylation, in which a catalytic water hydrolyzes the enzyme:ligand covalent adduct, releasing the product in the form of a highly unstable carbamic acid, expected to rapidly decompose into an amine and carbon dioxide. We found that STAGE 1 comprises the rate-limiting step of the overall reaction, consisting of the cleavage of the substrate’s urethane bond by its ester moiety and the release of the alcohol-leaving group (overall Gibbs activation energy of 20.8 kcal·mol-1). Lastly, we identified point mutations that are expected to enhance the enzyme's turnover for the hydrolysis of urethane bonds by stabilizing the macrodipole of the rate-limiting transition state. These findings expand our current knowledge of urethanases and homolog enzymes from the amidase signature superfamily, paving the way for future research on the enzymatic depolymerization of PU plastic materials. | Pedro Paiva; Luís M. C. Teixeira; Ren Wei; Weidong Liu; Jens P. Morth; Peter Westh; Allan R. Petersen; Martin B. Johansen; Andreas Sommerfeldt; Alexander Sandahl; Daniel E. Otzen; Pedro A. Fernandes; Maria J. Ramos | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Biocatalysis; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b09b40c9c6a5c07a0c5396/original/the-catalytic-mechanism-of-the-plastic-degrading-enzyme-urethanase-umg-sp2.pdf |
60c73d51702a9b7a04189b65 | 10.26434/chemrxiv.5678872.v1 | Ion-Ion interactions affect (re)folding dynamics of ubiquitin ions in the gas phase. Distinct folding intermediates formed via charge-reduction pathways | <p>Using Ubiquitin as an exemplar protein we examine
the effect of net charge reduction post electrospray ionisation by exposure to
the electron transfer reagent, 1,3-dicyanobenzene. We monitor the change in gas
phase conformation of both precursor and products with ion mobility mass
spectrometry (IM-MS). Dramatic conformational rearrangement is seen for low
charge state ions upon exposure to the electron transfer reagent. Ions with low
charge states sprayed from both native-like and denaturing solvent conditions undergo
structural transitions to conformers with cross sections in the range measured
for the native structure (<sup>TW</sup>CCS<sub>N2</sub><sub>®</sub><sub>He</sub>, 950-1000 Å<sup>2</sup>). Thus, we infer that some memory of the
solution phase structure is retained in the gas phase. Intermediate structures
are seen in the reduction of the [M+6H]<sup>6+</sup> ion sprayed from both
native-like and denaturing solvents. Further, the reduction pathway of this ion
shows compaction to structures with a <sup>TW</sup>CCS<sub>N2</sub><sub>®</sub><sub>He</sub> centred at 1069 Å<sup>2</sup> (5+) and 949 Å<sup>2</sup> (4+) for ions
originating from native-like and denaturing solvents respectively. We propose
that charge reduction sites for radical anion localisation (to effect electron
transfer) are not easily accessible in the case of ubiquitin molecules
originating from native-like solution conditions. This highlights the
importance of salt bridge interactions in maintaining the structural integrity
of a protein in the gas phase. Most interestingly, two distinct conformer
populations are seen for the 6+ charge-reduced product originating from the 7+
and, the 6+ exposed to radical anions (post ESI); we infer that these
populations are intermediate in the refolding of ubiquitin in the gas phase,
sometimes transient. Overall, we are able to monitor the refolding pathway of
ubiquitin in the gas phase as its charge is reduced and show that charge-charge
interactions play a significant role in the gas phase conformation adopted;
whereby specific conformations are formed. </p> | Jacquelyn R. Jhingree; Perdita E. Barran | Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51702a9b7a04189b65/original/ion-ion-interactions-affect-re-folding-dynamics-of-ubiquitin-ions-in-the-gas-phase-distinct-folding-intermediates-formed-via-charge-reduction-pathways.pdf |
67325863f9980725cfe146e9 | 10.26434/chemrxiv-2024-r1wz8 | A Hexametallic Copper Aluminylene Aluminyl | Heterobimetallic compounds with aluminyl ligands have hitherto gained a significant interest due to promising small molecule activation pathways including challenging substrates. While recently some trimetallic derivatives have been introduced, the steric demands required by these known systems has precluded the access of higher nuclearity systems. We herein report on a first hexametallic copper aluminylene aluminyl namely [(AlCp*)Cu{Al(HMDS)2}]2 ([5]2). The synthesis and characterization are enabled via designed Al(I) transfer using (AlCp*)4 and precursor complex [(PtBu3)Cu(HMDS)] (1). The associated pathway for aluminum transfer via different intermediates is discussed. This includes single crystal X-ray crystallography (SC-XRD), multinuclear NMR spectroscopy, control experiments and state-of-the art quantum chemical calculations. Preliminary reactivity studies showed that [5]2 can not only be constructed stepwise but also deconstructed to a bimetallic species with an N-heterocyclic carbene | Fabian Dankert; Arbias Kadriu; Eva Hevia | Inorganic Chemistry; Bonding; Organometallic Compounds; Reaction (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67325863f9980725cfe146e9/original/a-hexametallic-copper-aluminylene-aluminyl.pdf |
679b892181d2151a028d5195 | 10.26434/chemrxiv-2025-kc0ns | Photocatalytic Degradation of Ampicillin Under Sunlight Using a Boron Cerium and Silver Ternary Doped Titanium Dioxide Catalyst Synthesized via the EDTA-Citrate Method | Nowadays, we can see that in river water, traces of antibiotics can be found, which is an emerging problem. Also, pharmaceutical companies' wastewater contains antibiotic traces present in it in a significant amount which makes it an excellent experimental domain to work upon. Which is very harmful if taken by humans without its treatment, so to treat it as early as possible is very necessary, else the bacteria emerging in that water will be converted to superbugs and then curing the disease from that bacteria will be exceedingly difficult as they have resistive power to that antibiotic. For that, we have prepared a tri-doped photocatalyst by doping boron cerium and silver in a titanium dioxide structure. It can work under sunlight light because the presence of silver in this boron amount is increased so that it can satisfactorily degrade antibiotics. Cerium is for water disinfection in the further catalyst. Its amount was also increased. Then the characterization analysis was performed with the help of DLS analysis with the help of a nanoparticle size analyzer, and we got particle size in the range of 115 to 600 nanometer XRD analysis. We got a band gap Of 2.3 to 2.4 electron Volt.BET surface area analysis showed us a surface area of about 25 m2/g.So instead of the UVA lights now, it was performed under the sunlight and the degradation percent was increased significantly to approx 70 percent. | Yash Mishra; Hari Mahalingam | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679b892181d2151a028d5195/original/photocatalytic-degradation-of-ampicillin-under-sunlight-using-a-boron-cerium-and-silver-ternary-doped-titanium-dioxide-catalyst-synthesized-via-the-edta-citrate-method.pdf |
61ef7f42e4d9b86b35f72920 | 10.26434/chemrxiv-2022-qwglr | Porous lanthanide metal-organic frameworks with metallic conductivity | Metallic charge transport and porosity appear almost mutually exclusive. Whereas metals demand large numbers of free carriers and must have minimal impurities and lattice vibrations to avoid charge scattering, the voids in porous materials limit the carrier concentration, provide ample space for impurities, and create more charge-scattering vibrations due to the size and flexibility of the lattice. No microporous material has been conclusively shown to behave as a metal. Here, we demonstrate that single crystals of the porous metal-organic framework Ln1.5HOTP (Ln = La, Nd; HOTP = 2,3,6,7,10,11-hexaoxytriphenylene) show the highest room-temperature conductivities of all porous materials, along with clear temperature-deactivated transport. A structural transition consistent with charge density wave ordering, present only in metals and rare in any materials, provides additional conclusive proof of the metallic nature of the materials. | Grigorii Skorupskii; Khoa N. Le; Dmitri Leo M. Cordova; Luming Yang; Tianyang Chen; Christopher H. Hendon; Maxx Q. Arguilla; Mircea Dincă | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ef7f42e4d9b86b35f72920/original/porous-lanthanide-metal-organic-frameworks-with-metallic-conductivity.pdf |
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