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64956e9124989702c2d5640a | 10.26434/chemrxiv-2023-84qzw | Direct in situ measurement of polymorphic transition temperatures in thermo-mechanochemical reactions | For the first time, we directly measured the onset and completion temperatures of polymorphic transitions in thermo-mechanochemical reactions by simultaneous in situ synchrotron powder X-ray diffraction and temperature monitoring. We determined the thermo-mechanochemical polymorphic transition temperature in 1-adamantyl-1-diamantyl ether to be 31 °C lower than the transition temperature determined by DSC. | Jasna Alić; Martin Etter; Mirta Rubčić; Zoran Štefanić; Marina Šekutor; Krunoslav Užarević; Tomislav Stolar | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2023-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64956e9124989702c2d5640a/original/direct-in-situ-measurement-of-polymorphic-transition-temperatures-in-thermo-mechanochemical-reactions.pdf |
61fbf310216867a78a69fe24 | 10.26434/chemrxiv-2022-wvkrz | Construction of Seven-Membered Cycles through Base Promoted [4+3] Domino Annulation of Crotonate-derived Sulfur Ylides with Diene | A sequential [4+3] domino annulation of crotonate-derived Sulfur Ylides with Diene has been reported. With base promoted, this general method can realize the synthesis of highly functional none-fused cycles including nitrogen heterocycles and carbocycles which are widely and important in pharmaceutical molecules with excellent yield respectively, showing a great application potential. Meanwhile, this is also a supplementary to sulfur ylide chemistry as the C3 synthesizer. | Yang Liu; Joost Berkhong | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fbf310216867a78a69fe24/original/construction-of-seven-membered-cycles-through-base-promoted-4-3-domino-annulation-of-crotonate-derived-sulfur-ylides-with-diene.pdf |
61723bd96c5aa0f5361d9fbf | 10.26434/chemrxiv-2021-jth2r | Combining Generative Adversarial Network and First-Principles Based Microkinetics for Heterogeneous Catalyst Design | Microkinetic analysis based on density functional theory (DFT) was combined with a generative adversarial network (GAN) to enable artificial proposal of heterogeneous catalysts based on the DFT-calculated dataset. The approach was applied to the NH3 formation reaction on Ru-Rh alloy surfaces as an example. The NH3 formation turnover frequency (TOF) was calculated by DFT-based microkinetics. Specifically, six elementary reactions (N2 dissociation, H2 dissociation, NHx (x = 1–3) formation, and NH3 desorption) were explicitly considered, and their reaction energies were evaluated by DFT. On the basis of TOF values and atomic compositions, new alloy surfaces were generated using the GAN. This approach successfully generated the surfaces not included in the initial dataset but have higher TOF values. The N2 dissociation reaction was more exothermic for the generated surfaces, leading to higher TOF. The present study shows that automatic improvement of catalyst materials is possible by using the iterative steps of DFT calculation and sample generation by GAN. | Atsushi Ishikawa | Theoretical and Computational Chemistry; Catalysis; Theory - Computational; Machine Learning; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2021-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61723bd96c5aa0f5361d9fbf/original/combining-generative-adversarial-network-and-first-principles-based-microkinetics-for-heterogeneous-catalyst-design.pdf |
63908a7c44ccbcc2ab11752a | 10.26434/chemrxiv-2022-ghmvg | Aromaticity-driven singlet-triplet inversions | Molecules with inversion of the singlet and triplet excited state energies are highly promising for the development of a new generation of OLED emitters. Currently, only one class of molecules with these inversions have been identified, in the form of azaphenalenes. Here, we screen a curated database of reported organic crystal structures to identify existing compounds for violations of Hund’s rule in the lowest excited states and identify two new classes of molecules with this behavior. The first is a class of zwitterions where the singlet-triplet inversions occur in the third excited singlet state, which limits their relevance to molecular emitters. The second class consists of two high-symmetry odd-membered polycyclic aromatic hydrocarbons, a fused azulene dimer and a bicalicene, where the lowest excited singlet states violate Hund’s rule. The high D2h symmetry of the two molecules is stabilized by the connectivity of the polycyclic structure, which we rationalize by studying the aromaticity of the ring components. This class of aromaticity-stabilized high-symmetry hydrocarbons shows promise as the next generation of building blocks for organic light-emitting diode emitters. | J. Terence Blaskovits; Marc H. Garner; Clemence Corminboeuf | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Photochemistry (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63908a7c44ccbcc2ab11752a/original/aromaticity-driven-singlet-triplet-inversions.pdf |
671a2f2d98c8527d9e32d5dd | 10.26434/chemrxiv-2024-jz9tb | An optimized sol-gel process for dyeing cotton fabrics with organic dyes | An optimized sol-gel process was developed to dye cotton fabric with organic dyes. Several model dyes were synthesized and characterized, and then used to prepare the corresponding sol-gel solutions on basis of the n-propyltriethoxysilane (nPTES) precursor. These solutions were applied to the fabric via the pad-dry-cure method. The affinity of the dyes toward the fabric was evaluated by measuring their uptake from the dye bath, which was found to vary between 3% and 16% depending on the molecular structure of the dye. Furthermore, four dyeing parameters were studied with respect to their effect on (i) the exhaustion of the dye bath using UV-visible spectroscopy, and (ii) on the obtained nuance of the textile employing colorimetric (Datacolor) and diffuse-reflectance spectroscopy. The process parameters are dyeing temperature, dye concentration, impregnation time, and the number of dyeing cycles. Our results showed the transfer of dye from bath to textile depends only weakly on temperature, and below 40°C the transfer reaches an optimum. Also, the dye transfer is rapid, where already after 1 minute, the color strength on the textile is close to the plateau value. However, residual dye uptake from the bath continues for up to 2 hours. Further intensification of the textile coloration requires the deposition of additional sol-gel layers or an increase in the dye bath concentration. On basis of these results, the optimal conditions of dyeing by this process were proposed. | Tarik AABOUB; Martinus H.V. WERTS | Materials Science; Coating Materials; Dyes and Chromophores; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a2f2d98c8527d9e32d5dd/original/an-optimized-sol-gel-process-for-dyeing-cotton-fabrics-with-organic-dyes.pdf |
65c4c1db66c1381729361a4f | 10.26434/chemrxiv-2024-r2dwh | Monitoring cancer treatment in live melanoma cells using FLIM | Anticancer therapies with cisplatin and volasertib (BI 6727) were monitored by fluorescence lifetime imaging microscopy (FLIM) in live SK-Mel-2 melanoma cells. A CdSe/ZnS quantum dot functionalized with a peptide containing D-penicillamine and histidine (CdSe/ZnS-PH) was used as intracellular pH fluorescent probe. A faster cytosol acidification was observed for cells treated with cisplatin when compared to volasertib. The first changes in the intracellular pH were found after 2 h of treatment with cisplatin and 8 h with volasertib. Additionally, the apoptosis of SK-Mel-2 cells was also monitored by FLIM for both cancer treatments. Similar low percentages of apoptotic cells were observed after short incubation periods (2–8 h) with both drugs. In contrast, late apoptosis and death were found for a large fraction of cells during 24-hour incubation with cisplatin but not volasertib. There is not a clear correlation between the onset of apoptosis and the cytosol acidification, but the early acidification observed in cisplatin treatment could accelerate apoptosis and cell death. For longer periods, MMT assays showed a similar inhibitory effect for treatments after 72 hours of incubation, but with a significantly lower IC50 for volasertib. This study proves the potential of FLIM technique in the study of the mechanism of action of antitumor drugs. | Diego Herrera-Ochoa; Iván Bravo; Andrés Garzón Ruiz | Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c4c1db66c1381729361a4f/original/monitoring-cancer-treatment-in-live-melanoma-cells-using-flim.pdf |
6254fa2e103388fac2e9c4c0 | 10.26434/chemrxiv-2022-dlxrh | Versatile biogenesis of Silver-Copper nanoparticles over arylated pulp sugarcane bagasse- derived biochar: high catalytic performance | Agrowaste-derived materials for the supporting of nanocatalysts is attracting a great attention due to the abundance and the physicochemical features they provide as bio-sourced underlying materials. The main idea is built around the conversion of junk material into functional material, a journey of waste from "trash to treasure". Herein, we suggest a versatile method to elaborate phytochemically reduced Ag/Cu nanoparticles supported on aryl-sulfonated sugarcane bagasse pulp-derived biochar. Biochar was first prepared by a slow pyrolysis of the biomass at 500°C under N2:H2 95%:5% inert atmosphere. Thereafter, in-situ arylation of the biochar surface has been performed to obtain SO3H-biochar. Silver and copper ions loading in SO3H-biochar has been established via a wet impregnation in a hydroalcoholic medium. Finally, the natural liquid extract of sugarcane bagasse has been employed to reduce the metallic ions instead of the toxic NaBH4 very commonly used, the obtained SO3H-biochar@Ag/Cu has been characterized by XRD, XPS, SEM and RAMAN spectroscopy. The catalytic activity of the nanocomposite has been investigated in the oxidative degradation of malachite green oxalate. A total mineralization of the dye has been registered and the experimental data was found to give a relatively good fitting to the pseudo-first-order model with a mineralization apparent constant rate equals to 65 10-3 min-1. | Youssef Snoussi; Mohamed M. Chehimi; Souad Ammar; Mohamed El Garah; Ahmed M. Khalil | Catalysis; Chemical Engineering and Industrial Chemistry; Water Purification; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6254fa2e103388fac2e9c4c0/original/versatile-biogenesis-of-silver-copper-nanoparticles-over-arylated-pulp-sugarcane-bagasse-derived-biochar-high-catalytic-performance.pdf |
678722edfa469535b90fe695 | 10.26434/chemrxiv-2025-tm8ch | CIAA: Integrated Proteomics and Structural Modeling for Understanding Cysteine Reactivity with Iodoacetamide Alkyne | Cysteine residues play key roles in protein structure and function and can serve as targets for chemical probes and even drugs. Chemoproteomic studies have revealed that heightened cysteine reactivity towards electrophilic probes, such as iodoacetamide alkyne (IAA), is indicative of likely residue functionality. However, while the cysteine coverage of chemoproteomic studies has increased substantially, these methods still only provide a partial assessment of proteome-wide cysteine reactivity, with cysteines from low abundance proteins and tough-to-detect peptides still largely refractory to chemoproteomic analysis. Here we integrate cysteine chemoproteomic reactivity datasets with structure-guided computational analysis to delineate key structural features of proteins that favor elevated cysteine reactivity towards IAA. We first generated and aggregated multiple descriptors of cysteine microenvironment, including amino acid content, solvent accessibility, residue proximity, secondary structure, and predicted pKa. We find that no single feature is sufficient to accurately predict reactivity. Therefore, we developed the CIAA (Cysteine reactivity towards IodoAcetamide Alkyne) method, which utilizes a Random Forest model to assess cysteine reactivity by incorporating descriptors that characterize the 3D structural properties of thiol microenvironments. We trained the CIAA model on existing and newly generated cysteine chemoproteomic reactivity data paired with high-resolution crystal structures from the Protein Data Bank (PDB), with cross validation against an external dataset. CIAA analysis reveals key features driving cysteine reactivity, such as backbone hydrogen bond donor atoms, and reveals still underserved needs in the area of computational predictions of cysteine reactivity, including challenges surrounding protein structure selection dataset curation. Thus our work provides a strong foundation for deploying artificial intelligence (AI) on cysteine chemoproteomic datasets. | Lisa Boatner; Jerome Eberhardt; Flowreen Shikwana; Matthew Holcomb; Peiyuan Lee; Kendall Houk; Stefano Forli; Keriann Backus | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678722edfa469535b90fe695/original/ciaa-integrated-proteomics-and-structural-modeling-for-understanding-cysteine-reactivity-with-iodoacetamide-alkyne.pdf |
64273c4016782ec9e62597fc | 10.26434/chemrxiv-2023-7vgfx | Direct measurements of size-independent lithium diffusion and reaction times in individual polycrystalline battery particles | Polycrystalline Li(Ni,Mn,Co)O2 (NMC) secondary particles are the most common cathode materials for Li-ion batteries. During electrochemical (dis)charge, lithium is believed to diffuse through the bulk and enter (leave) the secondary particle at the surface. Based on this model, smaller particles would cycle faster due to shorter diffusion lengths and larger surface-area-to-volume ratios. In this work, we evaluate this widespread assumption by developing a new high-throughput single-particle electrochemistry platform using the multi-electrode array from neuroscience. By measuring the reaction and diffusion times for 21 individual particles in liquid electrolytes, we find no correlation between the particle size and either the reaction or diffusion times, which is in stark contrast to the prevailing lithium transport model. We propose that electrochemical reactions occur inside secondary particles, possibly due to electrolyte penetration into cracks. Our high-throughput, single-particle electrochemical platform further opens new frontiers for robust, statistical quantification of individual particles in electrochemical systems. | Jinhong Min; Lindsay Gubow; Riley Hargrave; Jason Siegel; Yiyang Li | Materials Science; Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2023-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64273c4016782ec9e62597fc/original/direct-measurements-of-size-independent-lithium-diffusion-and-reaction-times-in-individual-polycrystalline-battery-particles.pdf |
67de138bfa469535b92a6e5e | 10.26434/chemrxiv-2025-87n46 | Probing the Atomic Arrangement of Honeycomb Layered Oxides via Optimum Bright-Field Scanning Transmission Electron Microscopy (OBF–STEM) | Honeycomb-layered oxides are gaining considerable interest across diverse fields, including electrochemistry, materials science, and condensed matter physics. Transmission electron microscopy (TEM) has significantly advanced our atomistic understanding of these materials; however, certain honeycomb-layered oxides, particularly solid-state electrolytes, are highly beam-sensitive, making conventional TEM techniques challenging to apply. Here, we employ low-dose atomic resolution optimum bright-field (OBF) scanning TEM (STEM) to maximise the signal-to-noise ratio, enabling the probing of the arrangement of atoms in honeycomb-layered Na2Zn2TeO6. This successful application of OBF–STEM facilitates the characterisation of local atomic structures in electron-beam-sensitive honeycomb-layered materials, thereby pushing the frontier of such observation techniques towards effectively investigating emergent phenomena occurring upon topotactic ion exchange reaction with molten Ag salt. | Titus Masese; Godwill Kanyolo; Yoshinobu Miyazaki; Kimiya Sukegawa; Tomohiro Saito | Materials Science; Nanoscience; Energy; Multilayers; Nanostructured Materials - Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67de138bfa469535b92a6e5e/original/probing-the-atomic-arrangement-of-honeycomb-layered-oxides-via-optimum-bright-field-scanning-transmission-electron-microscopy-obf-stem.pdf |
628bad6187d01f80b9ef4394 | 10.26434/chemrxiv-2022-4skxb | Towards Metal-free Photocatalysis: Photochemical Regeneration of Organic Hydride Donors Using Phenazine-based Photosensitizers | Earth-abundant chromophores and catalysts are important molecular building blocks for artificial photosynthesis applications. Our team previously reported that metal-free hydride donors, such as biomimetic benzoimidazole-based motifs, can reduce CO2 selectively to the formate ion and that they can be electrochemically regenerated using the proton-coupled mechanism. To enable direct utilization of solar energy, we report here the photochemical regeneration of a benzoimidazole-based hydride donor using a phenazine-based metal-free chromophore. The photochemical regeneration was investigated under different experimental conditions involving varying sacrificial donors, proton donors, solvents and component concentrations. The best hydride regeneration yield of 50% was obtained with phenol as a proton source and thiophenolate as a sacrificial electron donor. The mechanism of photochemical regeneration was studied using steady-state and time-resolved UV/Vis spectroscopies. Based on the results of these studies, we hypothesize that the initial photoinduced electron transfer from photoexcited phenazine chromophores involves the benzoimidazole cation and that this process is likely coupled with proton transfer to generate protonated benzoimidazole-based radical cation. The second photoinduced electron transfer is hypothesized to generate the hydride form. Our findings provide the requisite information for the future development of reductive photocatalysts for solar energy and light-harvesting applications utilizing earth-abundant metal-free materials. | Ravindra Weerasooriya; Matthew Drummer Drummer; Brian Thomas Phelan,; Jonathan Gesiorski; Emily Ann Sprague; Lin Chen; Ksenija Glusac | Physical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628bad6187d01f80b9ef4394/original/towards-metal-free-photocatalysis-photochemical-regeneration-of-organic-hydride-donors-using-phenazine-based-photosensitizers.pdf |
60c74d72bb8c1a47e13db5d5 | 10.26434/chemrxiv.12619697.v1 | High Pressure High Temperature Synthesis of Highly Boron Doped Diamond Microparticles and Porous Electrodes for Electrochemical Applications | <p>High
pressure high temperature (HPHT) synthesis of crystallographically well-defined
boron doped diamond (BDD) microparticles, suitable for electrochemical
applications and using the lowest P and T (5.5 GPa and 1200°C) growth conditions to date, is reported. This is aided through the use
of a metal (Fe-Ni) carbide forming catalyst and an aluminum
dibromide (AlB<sub>2</sub>) boron source. The latter also acts as a nitrogen sequester, to reduce
boron-nitrogen charge compensation effects. Raman microscopy and electrochemical
measurements on individual microparticles reveal they are suitably doped to be
considered metallic-like and contain negligible sp<sup>2</sup> bonded carbon. A
compaction process is used to create macroscopic porous electrodes from the
BDD microparticles. Voltammetric analysis of the one-electron reduction of
Ru(NH<sub>3</sub>)<sub>6</sub><sup>3+</sup> reveals large capacitive and
resistive components to the current-voltage curves, originating from solution
trapped within the porous material. Scanning electrochemical cell microscopy
(SECCM) is employed to map the local electrochemical activity and porosity at
the micron scale. These electrodes retain the advantageous properties of polycrystalline
BDD grown by chemical vapor deposition, such as large aqueous solvent window
and resistance to corrosion, but with the additional benefits of a high, electrochemically
accessible, surface area. </p> | Georgia Wood; Mark Newton; Viacheslav Shkirskiy; Patrick R. Unwin; Julie Macpherson; Mark Munday; Carmen Walters | Carbon-based Materials; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d72bb8c1a47e13db5d5/original/high-pressure-high-temperature-synthesis-of-highly-boron-doped-diamond-microparticles-and-porous-electrodes-for-electrochemical-applications.pdf |
67a9e458fa469535b9bb2721 | 10.26434/chemrxiv-2025-gsw8x | Single molecule peptide synthesis without any side-chain protection using a nanopore and a sub-nanometer positioning system | Peptide synthesis without side-chain protection is proposed at the single molecule level. A peptide is synthesized C-to-N or N-to-C as an extension to a homopeptide header with one end bound to a fixed surface and the other free and enclosed by a nanopore. The surface is mounted on a platform that can be moved with 0.1-0.15 nm precision; the pore acts like a ribosome tunnel to protect amino acid (AA) side-chains from unwanted couplings and also prevents aggregation and cyclization. Synthesis occurs in cycles with the following steps: a coupling agent attaches an end-protected AA to the terminal residue of the growing header at the end of the pore; completion of coupling is detected optically; coupling agent, protector, and excess AAs are washed out; the platform is retracted by 3.5 Å; the newly added AA is deprotected and the protector washed out. On completion of synthesis the platform is moved toward the pore by the added peptide’s length, the peptide is separated from the header. A combination of electrical potential and hydraulic pressure keeps the peptide fully stretched at all times. The nanopore plays a secondary role, no measurements are made on it. Parallel synthesis can be done with an array of headers and an array of nanopores, capacities of up to a femtomole may be possible. In principle there is no limit to the length of the peptide that can be synthesized. With no side-chain protection, minimal reagent amounts, reduced washing, and almost no post-synthesis cleanup, the method has a potentially high level of greenness. | G Sampath | Theoretical and Computational Chemistry; Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a9e458fa469535b9bb2721/original/single-molecule-peptide-synthesis-without-any-side-chain-protection-using-a-nanopore-and-a-sub-nanometer-positioning-system.pdf |
66420b68418a5379b0251f87 | 10.26434/chemrxiv-2024-c29k4 | A Self-Assembled Multiphasic Thin Film as an Oxygen Electrode for Enhanced Durability in Reversible Solid Oxide Cells | The implementation of nanocomposite materials as electrode layers represents a potential turning point for next-generation of solid oxide cells in order to reduce the use of critical raw materials. However, the substitution of bulk electrode materials by thin films is still under debate especially due to the uncertainty about their performance and stability under operando conditions, which restricts their use in real applications. In this work, we propose a multiphase nanocomposite characterized by a highly disordered microstructure and high cationic intermixing as a result from thin-film self-assembly of a perovskite-based mixed ionic-electronic conductor (lanthanum strontium cobaltite) and a fluorite-based pure ionic conductor (samarium-doped ceria) as an oxygen electrode for reversible solid oxide cells. Electrochemical characterization shows remarkable oxygen reduction reaction (fuel cell mode) and oxygen evolution activity (electrolysis mode) in comparison with state-of-the-art bulk electrodes, combined with outstanding long-term stability at operational temperatures of 700 ºC. The disordered nanostructure was implemented as a standalone oxygen electrode on commercial anode-supported cells, resulting in high electrical output in fuel cell and electrolysis mode for active layer thicknesses of only 200 nm (>95% decrease in critical raw materials with respect to conventional cathodes). The cell was operated for over 300 hours displaying excellent stability. Our findings unlock the hidden potential of advanced thin-film technologies for obtaining high-performance disordered electrodes based on nanocomposite self-assembly combining long durability and minimized use of critical raw materials.
| Fjorelo Buzi; Kosova Kreka ; Jose Santiso ; Laetitia Rapenne ; Zijie Sha; James Douglas; Francesco Chiabrera; Alex Morata; Monica Burriel ; Stephen Skinner ; Lucile Bernadet; Federico Baiutti; Albert Tarancón | Materials Science; Energy; Ceramics; Thin Films; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66420b68418a5379b0251f87/original/a-self-assembled-multiphasic-thin-film-as-an-oxygen-electrode-for-enhanced-durability-in-reversible-solid-oxide-cells.pdf |
60c74172702a9b429918a279 | 10.26434/chemrxiv.8048738.v1 | Chemical Bonding in Excited States: Electron Localization, Delocalization and Statistics in Real Space | <p>In this contribution, we continue with our
enterprise regarding the systematization of chemical bonding in excited states.
We show how real space electron localization and delocalization measures,
coupled to the statistical analysis of electron number distribution functions,
may be used to discover <i>uncharted territories in chemical bonding </i>that
are not easily accessible by other theoretical or computational means. The
possibility of exotic bonding landscapes in excited states was already
predicted years ago (<i>PCCP</i> 9, 1087, 2007). Here we demonstrate how
easily these situations can be met.</p> | José Luis Casals-Sainz; Jesús Jara-Cortés; Jesús Hernández-Trujillo; José Manuel Guevara-Vela; Evelio Francisco; Angel Martín Pendás | Computational Chemistry and Modeling; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74172702a9b429918a279/original/chemical-bonding-in-excited-states-electron-localization-delocalization-and-statistics-in-real-space.pdf |
6130da9090051e2b1be76a81 | 10.26434/chemrxiv-2021-lh9q1-v2 | Utilizing selective chlorination to synthesize new triangulenium dyes | Access to functionalization of new sites on the triangulenium core structure has been achieved at an early stage by chlorination with N-chlorosuccinimide (NCS), giving rise to two new triangulenium dyes (1 and 2). By introducing the chlorine functionalities in the acridinium precursor, positions complementary to those previously accessed by electrophilic aromatic substitution of the final dyes can be accesed. The chlorination is selective, giving only one regioisomer for both mono- and dichlorination products. For the monochlorinated acridinium compound a highly selective ring-closing reaction was discovered to generate only a single regioisomer of the cationic [4]helicene product. This discovery aspired further investigations into the mechanism of [4]helicene formation and to the first isolation of the previously proposed intermediate of the two-step SNAr reaction, key to all aza-bridged triangulenium and helicenium systems. A late stage functionalization of DAOTA+ with NCS gave rise to a different dichlorinated compound (2). The fully ring closed chlorinated triangulenium dyes 1, 2 and 3 show a redshift in absorption and emission relative to the non-chlorinated analogues, while still maintaining relatively high fluorescence quantum yields of 36%, 26%, and 41%, and long fluorescence lifetimes of 15 ns, 12.5 ns and 16 ns, respectively. Cyclic voltammetry shows that chlorination of the triangulenium dyes significantly lowers reduction potentials and thus allows for efficient tuning of redox and photo-redox properties. | Jesper Dahl Jensen; Niels Bisballe; Laura Kacenauskaite; Maria Storm Thomsen; Junsheng Chen; Ole Hammerich; Bo W. Laursen | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6130da9090051e2b1be76a81/original/utilizing-selective-chlorination-to-synthesize-new-triangulenium-dyes.pdf |
614204c3b817b471451e2be8 | 10.26434/chemrxiv-2021-5nn16 | A selenium-based cysteine surrogate for protein chemical synthesis | We provide in this protocol detailed procedures for the synthesis of SetCys cysteine surrogate and its use for chemical synthesis of proteins through the redox-controlled assembly of three peptide segments in one-pot. | Olga Firstova; Vangelis Agouridas; Vincent Diemer; Oleg Melnyk | Biological and Medicinal Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614204c3b817b471451e2be8/original/a-selenium-based-cysteine-surrogate-for-protein-chemical-synthesis.pdf |
60c74ff0702a9b7d2b18bc83 | 10.26434/chemrxiv.12958226.v1 | Computational Screening of Doped Graphene Electrodes for Alkaline CO2 Reduction | The electrocatalytic CO<sub>2</sub> reduction reaction (CO<sub>2</sub>RR) is considered as one of the most promising approaches to synthesizing carbonaceous fuels and chemicals without utilizing fossil resources. However, current technologies are still in the early phase focusing primarily on identifying optimal electrode materials and reaction conditions. Doped graphene-based materials are among the best CO<sub>2</sub>RR electrocatalysts and in the present work we have performed a computational screening study to identify suitable graphene catalysts for CO<sub>2</sub>RR to CO under alkaline conditions. Several types of modified-graphene frameworks doped with metallic and non-metallic elements were considered. After establishing thermodynamically stable electrodes, the electrochemical CO<sub>2</sub>RR to CO is studied in the alkaline media. Both concerted proton-coupled electron transfer (PCET) and decoupled proton and electron transfer (ETPT) mechanisms were considered by developing and using a generalization of the computational hydrogen electrode approach. It is established that the CO<sub>2</sub> electrosorption and associated charge transfer along the ETPT pathway are of utmost importance and significantly impact the electrochemical thermodynamics of CO<sub>2</sub>RR. Our study suggests an exceptional performance of metal-doped nitrogen-coordinated graphene electrodes, especially 3N-coordinated graphene electrodes. | Anand Mohan Verma; Karoliina Honkala; Marko Melander | Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ff0702a9b7d2b18bc83/original/computational-screening-of-doped-graphene-electrodes-for-alkaline-co2-reduction.pdf |
6246035d3affe4aa143c3848 | 10.26434/chemrxiv-2022-mc4gb | How Robust are Modern Graph Neural Network Potentials in Long and Hot Molecular Dynamics Simulations? | Graph neural networks (GNNs) have emerged as a powerful machine learning approach for the prediction of molecular properties. In particular, recently proposed advanced GNN models promise quantum chemical accuracy at a fraction of the computational cost. While the capabilities of such advanced GNNs have been extensively demonstrated on benchmark datasets, there have been few applications in real atomistic simulations. Here, we therefore put the robustness of GNN interatomic potentials to the test, using the recently proposed GemNet architecture as a testbed. Models are trained on the QM7-x database of organic molecules and used to perform extensive MD simulations. We find that low test set errors are not sufficient for obtaining stable dynamics and that severe pathologies sometimes only become apparent after hundreds of ps of dynamics. Nonetheless, highly stable and transferable
GemNet potentials can be obtained with sufficiently large training sets. | Sina Stocker; Johannes Gasteiger; Florian Becker; Stephan Günnemann; Johannes T. Margraf | Theoretical and Computational Chemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6246035d3affe4aa143c3848/original/how-robust-are-modern-graph-neural-network-potentials-in-long-and-hot-molecular-dynamics-simulations.pdf |
60c75149bb8c1a81993dbc68 | 10.26434/chemrxiv.12278318.v2 | Impact of Wet-Dry Cycling on the Phase Behavior and Compartmentalization Properties of Complex Coacervates | <div>Wet-dry cycling on the early Earth is thought to have facilitated production of molecular building blocks of life, but thus far its impact on self-assembly and compartmentalization of resulting (macro)molecules has been limited. We investigated dehydration/rehydration of complex coacervates, which are membraneless compartments formed by phase separation of polyelectrolyte solutions, and suggested as protocell models. Depending on initial composition of a poly(diallyldimethylammonium)/poly(acrylic acid) system, drying enabled formation or disassembly of coacervate droplets. In compartments surviving tenfold dehydration, partitioning of a fluorescent RNA oligonucleotide decreased, while its local concentration inside the coacervates remained nearly constant, despite increasing tenfold globally. RNA mobility was also enhanced as the system dehydrated. These changes can be understood as resulting from drying induced compositional movements on the phase diagram, with increased ionic strength being particularly important in determining coacervate properties. These results showed that wet-dry cycling can alter the phase behavior and protocell-relevant functions of complex coacervates.</div> | Hadi Fares; Alexander Marras; Jeffrey Ting; Matthew Tirrell; Christine Keating | Polyelectrolytes - Polymers; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75149bb8c1a81993dbc68/original/impact-of-wet-dry-cycling-on-the-phase-behavior-and-compartmentalization-properties-of-complex-coacervates.pdf |
670d721e51558a15ef1128e7 | 10.26434/chemrxiv-2024-lthtv | Modelling the Impact of Alloying State Dynamics on-the Reactivity of Group-10-Metal-Gallium Nanoparticles. | Bimetallic nanoparticles are catalysts for reactions, such as COx hydrogenation or propane dehydrogenation. Recently, gallium has been identified as a promoter which enables dispersion of group-X-metal sites, raising activity and selectivity. However, quantitative information on alloying dynamics under reaction conditions are not readily available and a gen-eral computational method to access such information is missing. Here, an ab initio molecular dynamics workflow with enhanced sampling methods is used to probe the alloying behavior of Ni-, Pd-, and Pt-Ga nanoparticles under operating conditions (T = 600°C) in presence of H2 or CO. The three metals display different alloying behaviors with Ga: Ni forms a core surrounded by gallium, while Pd and Pt form different alloyed structures. Both H2 and CO shift the alloying state to different extents. A set of three descriptors is proposed to compare and quantify the alloying behavior of these catalyst models: (i) the position αmin of the most stable alloying state; (ii) the curvature ηα of the free energy at αmin, referred to as the alloying hardness; (iii) the skew κα of the free energy at αmin, which relates to its propensity to alloy or segregate. The influence of the alloying behavior on the propane dehydrogenation activity of NiGa and PtGa is assessed: the energetic cost of alloy reorganization in the activation energy has been quantified. Extracting quantitative alloying descriptors from ab initio molecular dynamics is a promising tool to take alloy reorganization into account, both for mechanistic studies and for rational catalyst design. | Quentin Pessemesse; Alexandre Perochon; Christophe Copéret; Marie-Eve L. Perrin; Pierre-Adrien Payard | Theoretical and Computational Chemistry; Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d721e51558a15ef1128e7/original/modelling-the-impact-of-alloying-state-dynamics-on-the-reactivity-of-group-10-metal-gallium-nanoparticles.pdf |
65c60dfce9ebbb4db9fcd947 | 10.26434/chemrxiv-2023-b8wmh-v2 | Deconvoluting Low Yield from Weak Potency in Direct-to-Biology Workflows with Machine Learning | High throughput and rapid biological evaluation of small molecules is an essential factor in drug discovery and development. Direct-to-Biology (D2B), whereby compound purification is foregone, has emerged as a viable technique in time efficient screening, specifically for PROTAC design and biological evaluation. However, one notable limitation is the prerequisite of high yielding reactions to ensure the desired compound is indeed the compound responsible for biological activity. Herein, we report a machine learning based yield-assay deconfounder capable of deconvoluting low yield from low potency to identify false negatives. We validated this approach by identifying promising SARS-CoV-2 main protease inhibitors with nanomolar activity that rivaled potency observed from the standard D2B workflow. Furthermore, we show how our framework can be utilized in a broad, in silico screen with to produce compounds of similar potency as a D2B assay. | William McCorkindale; Mihajlo Filep; Nir London; Alpha A. Lee; Emma King-Smith | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c60dfce9ebbb4db9fcd947/original/deconvoluting-low-yield-from-weak-potency-in-direct-to-biology-workflows-with-machine-learning.pdf |
647899d14f8b1884b7a7e824 | 10.26434/chemrxiv-2023-n8prz-v2 | Enhancing Inhibition of Both α-Synuclein Aggregation and Neuroinflammation: New Insights into the C-9 Modification of Doxycycline | Doxycycline, a semi-synthetic tetracycline, is a widely used antibiotic for mild-to-moderate infections. However, its pleiotropic effects, such as anti-inflammatory and antioxidant properties, combined with its ability to interfere with α-synuclein inhibiting its aggregation, make it an attractive candidate for repositioning in Parkinson's disease treatment. Nevertheless, the antibiotic activity of doxycycline restricts its potential for long-term treatment of Parkinsonian patients. Eighteen novel doxycycline derivatives were designed with substitution at C9. Specifically, the dimethyl-amino group at C4 was reduced to significantly diminish the antibiotic activity, and several coupling reactions were performed at position C9 of the D ring. Using biophysical models, we found that seven compounds were more effective than the parent compound in inhibiting α-synuclein aggregation. Furthermore, two of these derivatives exhibited better anti-inflammatory effects at non-cytotoxic concentrations on microglial cell culture. Thus, we identified two design-based tetracyclines as the most promising candidates for further preclinical investigations. In addition, our study provides new insights into the structure-activity relationship of tetracyclines as neuroprotective molecules. | Clémence Rose; Rodrigo Hernán Tomas-Grau; Brenda Zabala; Jean-Michel Brunel; Patrick P. Michel; Rosana Chehin; Rita Raisman-Vozari; Laurent Ferrié; Bruno Figadère | Biological and Medicinal Chemistry; Organic Chemistry; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647899d14f8b1884b7a7e824/original/enhancing-inhibition-of-both-synuclein-aggregation-and-neuroinflammation-new-insights-into-the-c-9-modification-of-doxycycline.pdf |
642f03000784a63aeea74ee1 | 10.26434/chemrxiv-2023-8lnlk | High throughput proteomics enabled by a fully automated dual-column liquid chromatography system coupled with mass spectrometry | This technical note presents a dual-column liquid chromatography system coupled with mass spectrometry (LC-MS), designed for high-throughput bottom-up proteomic analysis. Utilizing two 2-position 10-port valves, a binary nanoflow pump, and an integrated loading pump, the system enables the simultaneous operation of two parallel subsystems. Each subsystem comprises a trap column and an analytical column. A T-junction union is employed to divide the mobile phase from the loading pump into two parts, which permits one set of columns to undergo washing and equilibration while the subsequent sample is injected. Meanwhile, the previous sample elutes and undergoes analysis on the alternate set of columns, significantly increasing the analysis throughput. The approach demonstrates high reproducibility when analyzing HeLa tryptic digests, with average relative standard deviations (RSD) of 1.64% for protein identification across nine consecutive runs. This system exhibits comparable capacity for protein identification and proteome depth to that of traditional single-column systems. Owing to its straightforward equipment requirements and set up process, this method is highly accessible and easily adopted by other laboratories. | Liang Chen; Ziwei Zhang; Yu Gao | Analytical Chemistry; Mass Spectrometry; Separation Science | CC BY NC 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642f03000784a63aeea74ee1/original/high-throughput-proteomics-enabled-by-a-fully-automated-dual-column-liquid-chromatography-system-coupled-with-mass-spectrometry.pdf |
65a621e79138d2316105fa32 | 10.26434/chemrxiv-2024-vtztv | Evaporative drying of sessile droplets as a means of monitoring UiO-66 MOF synthesis and quality | We demonstrate a simple droplet drying based diagnostic approach to monitor the UiO-66 MOF (metal organic framework) synthesis and it’s quality using the sessile drop drying phenomenon. Drying a sessile droplet involves evaporation-driven hydrodynamic flow and particle nature-dependent self-assembled deposition. In general, the MOF synthesis process involves different sizes and physicochemical natures of particles in every stage of the synthesis. Equivalent quantities of each of purifed pore-activated UiO-66 MOF, yet to be purifed pore-inactivated UiO-66 MOF, and reaction precursors of UiO-66 MOF give different deposition patterns when a well-dispersed aqueous droplet of these materials undergo drying over substrates of varying stiffness and wettability. Yet to be purifed pore-inactivated UiO-66 MOF nanoparticles undergo transport towards the droplet periphery leading to a thick ring-like deposition at the dried droplet edge. Under appropriate condition of drying, such deposit leads to desiccationtype mud-like reticular cracking. We study the origin of such ring-like deposits and cracks to understand how it get influenced by the presence of thermal Marangoni flow feld and the addition of salts contributing to surface charge density of UiO-66 particles controlling their stability. We clearly demonstrate ZrOCl2 salt trapped in non-purifed pore-inactivated UiO-66 MOF moiety is the principal reason for ring-like deposit formation and subsequent cracking in its drying aqueous droplet edge. In general, Lewis acid salts (like FeCl3, SnCl2, ZrOCl2), those also act as Brønsted-acid upon hydrolysis, influence surface charge density and colloidal stability of dispersed UiO-66 MOF particles. As a result immediate particle coagulation gets avoided, so those travel to the droplet edge leading to the formation of ring-like deposition and subsequent cracking upon drying. Further we show crack patterns on such deposit are highly dependent on the stiffness and temperature of depositing substrates via a competition between axial and lateral strain at the deposit-substrate interface. | Salini Kar; Nandita Basu; Mostakim Sk; Mithun Chowdhury | Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a621e79138d2316105fa32/original/evaporative-drying-of-sessile-droplets-as-a-means-of-monitoring-ui-o-66-mof-synthesis-and-quality.pdf |
60c7477d842e653e74db298f | 10.26434/chemrxiv.11678400.v1 | Active Learning of Many-Body Configuration Space: Application to the Cs+–water MB-nrg Potential Energy Function as a Case Study | <div>
<div>
<div>
<p>The efficient selection of representative configurations that are used in high-level electronic structure calculations needed for the development of many-body molecular models
poses a challenge to current data-driven approaches to molecular simulations. Here, we
introduce an active learning (AL) framework for generating training sets corresponding to
individual many-body contributions to the energy of a N-body system, which are required
for the development of MB-nrg potential energy functions (PEFs). Our AL framework is
based on uncertainty and error estimation, and uses Gaussian process regression (GPR)
to identify the most relevant configurations that are needed for an accurate representation
of the energy landscape of the molecular system under exam. Taking the Cs<sup>+</sup>–water system as a case study, we demonstrate that the application of our AL framework results in
significantly smaller training sets than previously used in the development of the original
MB-nrg PEF, without loss of accuracy. Considering the computational cost associated with
high-level electronic structure calculations for training set configurations, our AL framework is particularly well-suited to the development of many-body PEFs, with chemical and
spectroscopic accuracy, for molecular simulations from the gas to condensed phase.
</p>
</div>
</div>
</div> | Yaoguang Zhai; Alessandro Caruso; Sicun Gao; Paesani Lab | Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7477d842e653e74db298f/original/active-learning-of-many-body-configuration-space-application-to-the-cs-water-mb-nrg-potential-energy-function-as-a-case-study.pdf |
641337a6dab08ad68f36ff14 | 10.26434/chemrxiv-2022-q6s7p-v2 | Polymorphism mediated by electric fields: A first principles study on organic/inorganic interfaces | Organic/inorganic interfaces are known to exhibit rich polymorphism, where different polymorphs often possess significantly different properties. Which polymorph forms during an experiment depends strongly on environmental parameters such as deposition temperature and partial pressure of the molecule to be adsorbed. To prepare desired polymorphs these parameters are varied. However, many polymorphs are difficult to access with the experimentally available temperature- pressure ranges. In this contribution, we investigate how electric fields can be used as an additional lever to make certain structures more readily accessible. On the example of tetracyanoethylene (TCNE) on Cu(111), we analyze how electric fields change the energy landscape of interface systems. TCNE on Cu(111) can form either lying or standing polymorphs, which exhibit significantly different work functions. We combine first-principles calculations with a machine-learning based structure search algorithm and ab-initio thermodynamics to demonstrate that electric fields can be exploited to shift the temperature of the phase transition between standing and lying polymorphs by up to 100 K.
| Johannes J. Cartus; Andreas Jeindl; Anna Werkovits; Lukas Hörmann; Oliver T. Hofmann | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanofabrication; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641337a6dab08ad68f36ff14/original/polymorphism-mediated-by-electric-fields-a-first-principles-study-on-organic-inorganic-interfaces.pdf |
60c755b00f50db275b397f80 | 10.26434/chemrxiv.14150225.v1 | Temperature Sensitive and Reversible Halide Ion Exchange in Inorganic-Organic Hybrid CH3NH3Pbl3-xBrx Mixed-halide Perovskite | Ion exchange of
organic-inorganic hybrid perovskite plays an important role in controlling the
performance of materials ant its devices. In this study, we found an
interesting phenomenon that the precipitate in the in suspension (CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3-x</sub>Br<sub>x</sub>
in γ – butyrolactone) presented different colors at high and room temperature.
The mechanism study shows that the phenomenon is controlled by temperature
sensitive and reversible halide ion exchange in organic-inorganic hybrid CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3-x</sub>Br<sub>x</sub>
mixed-halide perovskite. The results of structure phase, element composition
morphology and band gap indicate that high temperature 55 °C is beneficial to
the increasing of I content in MAPbI<sub>3-x</sub>Br<sub>x </sub>and room
temperature or lower is beneficial to increasing of Br content in MAPbI<sub>3-x</sub>Br<sub>x</sub>.measurement
were carried out. Compared with MAPbI<sub>0.76</sub>Br<sub>2.24</sub>
precipitate obtained at room temperature, MAPbI<sub>1.17</sub>Br<sub>1.83 </sub>precipitate
obtained at high temperature exhibit wider lattice spacing, better
crystallinity, better morphology and narrower band gap.<sub> </sub>The results
and findings in this study will arouse the interest of readers or experts in
the field of organic-inorganic hybrid perovskite materials and related
optoelectronic applications. | Shuting Cui; Xun Sun; SiWen Tao; Huawei Zhou; Jie Yin; Xianxi Zhang | Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755b00f50db275b397f80/original/temperature-sensitive-and-reversible-halide-ion-exchange-in-inorganic-organic-hybrid-ch3nh3pbl3-x-brx-mixed-halide-perovskite.pdf |
6217b49f5f1d9a711ca62fe2 | 10.26434/chemrxiv-2022-ctz02 | Synthesis and styrene copolymerization of novel oxy ring-disubstituted isobutyl phenylcyanoacrylates | Novel oxy ring-disubstituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH(CH3)2 (where R is 4-methoxy-2-methyl, 4-methoxy-3-methyl, 3-ethoxy-4-methoxy, 4-ethoxy-3-methoxy, 3,4-dibenzyloxy, 2-benzyloxy-3-methoxy, 3-benzyloxy-4-methoxy, 2,3-methylenedioxy) were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, 1H and 13C NMR. The acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis and the structures were analyzed by FTIR, 1H and 13C NMR. | Megan Bailey; Margaret A. Barcinski; Adrian L. Galloway; Alyssa M. Guzman; Syed Hussaini; Naimah A. Khatib; Elli D.R. Parisi; Tripp Tuff; Brockton D. Williams; Sara Rocus; William Schjerven; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6217b49f5f1d9a711ca62fe2/original/synthesis-and-styrene-copolymerization-of-novel-oxy-ring-disubstituted-isobutyl-phenylcyanoacrylates.pdf |
60c74fd5469df472c2f4476d | 10.26434/chemrxiv.12949430.v1 | Stability of Zeolitic-imidazolate Frameworks in Humid Environments: Disentangling the Roles of Confined vs. Surface Water | <div>Most of the chemistry in nanoporous materials with small pore sizes and windows are known to occur on the surface of the material which is in immediate contact with substrate/solvent, rather than inside the pores and channels. Experimentally, it is not straightforward to distinguish the chemistry of confinement from the surface. Comprehensive molecular dynamics simulations coupled with quantum mechanical calculations are employed to decipher stability of zeolitic-imidazolate frameworks in aqueous solutions. Water adsorption properties are compared and contrasted in crystalline bulk vs. nanopoarticles of ZIF-8 as a representative of the ZIF family in order to fully disentangle how water interacts with the surface of the material which contains coordinatively unsaturated metal sites compared to the pristine bulk. </div><div>Our following detailed mechanistic study reveals the significantly higher propensity of the surface with coordinatively unsaturated Zn$^{2+}$ sites toward water attack and hydrolysis. Our results presented in this work are general and are applicable to other nanoporous materials with small particle sizes, pores and windows and are useful in devising plans for synthesis of more robust water stable materials for applications that involve atmospheric and/or bulk water.</div> | Mohammad R. Momeni; Farnaz A. Shakib | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Theory - Computational; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fd5469df472c2f4476d/original/stability-of-zeolitic-imidazolate-frameworks-in-humid-environments-disentangling-the-roles-of-confined-vs-surface-water.pdf |
60c74ee29abda24c74f8d746 | 10.26434/chemrxiv.12818180.v1 | One-Step Synthesis of Acylboron Compounds via Cu-Catalyzed Carbonylative Borylation of Alkyl Halides | A Cu-catalyzed carbonylative borylation of
unactivated alkyl halides has been developed, enabling
efficient synthesis of aliphatic potassium acyltrifluoroborates (KATs) in high yields by treating the in-situ formed
tetracoordinated acylboron intermediates with aqueous
KHF2. A variety of functional groups are tolerated under
the mild reaction conditions, and primary, secondary and
tertiary alkyl halides are all applicable. In addition, this
method also provides facile access to N-methyliminodiacetyl (MIDA) acylboronates as well as α-methylated
potassium acyltrifluoroborates in a one-pot manner.
Mechanistic studies indicate a radical atom transfer carbonylation (ATC) mechanism to form acyl halide intermediates that are subsequently borylated by
(NHC)CuBpin.<br /> | Cheng Li-Jie; Zhao Siling; Neal Mankad | Organic Synthesis and Reactions; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ee29abda24c74f8d746/original/one-step-synthesis-of-acylboron-compounds-via-cu-catalyzed-carbonylative-borylation-of-alkyl-halides.pdf |
670cf2b3cec5d6c1421928ce | 10.26434/chemrxiv-2024-np6gc | Investigation of FeNi alloy foams at high oxygen evolution reaction rates using a dry anode setup in alkaline environment | We investigated the composition-activity relationship of porous FeNi alloy foams for the alkaline oxygen evolution reaction (OER). We compared conventional transient behavior using cyclic voltammetry with the performance at high geometric current densities up to 3.0 A cm-2 achieved at quasi steady-state conditions employing pulsed electrolysis. The experiments were performed under setup parameters, we introduce as dry anode conditions for anion exchange membrane (AEM) water electrolyzers. In this context, a dry anode refers to an electrode setup in which the catalyst is not directly submerged in a liquid medium, unlike conventional electrodes fed with an alkaline electrolyte. Instead, the anode is purged with humidified gas. Eleven different compositions in the FeNi alloy space (93 – 2 at. % Fe) were synthesized using the hydrogen bubble template method, resulting in porous foams with similar structures. A rigorous statistical analysis of all measured data was conducted to ensure reproducibility. The influence of bubble formation on the solution resistance is elucidated and, consequently, the apparent performance is assessed. The most efficient alloy composition required an averaged mean potential of 1.82 VRHE for 3 A cm-2 under quasi steady-state conditions. | Etienne Berner; Gustav K.H. Wiberg; Matthias Arenz | Materials Science; Catalysis; Alloys; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670cf2b3cec5d6c1421928ce/original/investigation-of-fe-ni-alloy-foams-at-high-oxygen-evolution-reaction-rates-using-a-dry-anode-setup-in-alkaline-environment.pdf |
65e633cae9ebbb4db9e5e607 | 10.26434/chemrxiv-2024-nhrn8 | Leptochelins A-C, Cytotoxic Metallophores Produced by Geographically Dispersed Leptothoe Strains of Marine Cyanobacteria | Metals are important co-factors in the metabolic processes of cyanobacteria including photosynthesis, cellular respiration, DNA replication, and the biosynthesis of primary and secondary metabolites. In adaptation to the marine environment, cyanobacteria use metallophores to acquire trace metals when necessary as well as reduce potential toxicity from excessive metal concentrations. Leptochelins A-C were identified as structurally novel metallophores from three geographically dispersed cyanobacteria of the genus Leptothoe. The leptochelins are halogenated linear NRPS-PKS hybrid products with multiple heterocycles that have potential for hexadentate and tetradentate coordination with metal ions. The genomes of the three leptochelin producers were sequenced, and retrobiosynthetic analysis revealed one candidate biosynthetic gene cluster (BGC) consistent with the structure of leptochelin. The putative BGC is highly homologous in all three Leptothoe strains, and all possess genetic signatures associated with metallophores. Post-column infusion of metals using an LC-MS metabolomics workflow performed with leptochelin A and B revealed promiscuous binding of iron, copper, cobalt, and zinc, but with greatest preference for copper. Iron depletion and copper toxicity experiments support the hypothesis that leptochelin metallophores may play a key ecological role in iron acquisition and in copper detoxification. In addition, the leptochelins possess significant cytotoxicity against several cancer cell lines. | Nicole E. Avalon; Mariana A. Reis; Christopher C. Thornburg; R. Thomas Williamson; Daniel Petras; Allegra T. Aron; George F. Neuhaus; Momen Al-Hindy; Jana Mitrevska; Leonor Ferreira; João Morais; Yasin El Abiead; Evgenia Glukhov; Kelsey L. Alexander; F. Alexandra Vulpanovici; Matthew J. Bertin; Syrena Whitner; Hyukjae Choi; Gabriella Spengler; Kirill Blinov; Ameen M. Almohammadi; Lamiaa A. Shaala; William R. Kew; Ljiljana Paša-Tolić; Diaa T. A. Youssef; Pieter C. Dorrestein; Vitor Vasconcelos; Lena Gerwick; Kerry L. McPhail; William H. Gerwick | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Drug Discovery and Drug Delivery Systems; Environmental biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e633cae9ebbb4db9e5e607/original/leptochelins-a-c-cytotoxic-metallophores-produced-by-geographically-dispersed-leptothoe-strains-of-marine-cyanobacteria.pdf |
645a52aff2112b41e9439c0a | 10.26434/chemrxiv-2023-lc7d9-v2 | A Molecular-Level Mechanistic Framework for Interfacial Proton Coupled Electron Transfer Kinetics | Electrochemical proton coupled electron transfer (PCET) reactions are critical to energy conversion and catalysis. These reactions can be driven by outer-sphere electron transfer to a soluble molecule (OS-PCET) or through an inner-sphere mechanism by interfacial polarization of a surface-bound active site (I-PCET). The pH-dependent kinetics of OS-PCET have been extensively studied at the molecular level, but the inherent heterogeneity of most surfaces has impeded molecular-level understanding of I-PCET. Herein, we employ graphite conjugated carboxylic acids (GC COOH) as molecularly well-defined hosts of I-PCET to isolate the intrinsic pH dependent kinetics of this reaction. Using variable scan rate voltammetry, we measure the rates of I-PCET across the entire pH range and find a pronounced “V”-shaped dependence on pH with a rate minimum at pH 10 that rises log-linearly to pH 0 and pH 14. This kinetic profile spans three orders of magnitude in rate and lacks the pH-independent regions characteristic of electrochemical OS-PCET reactions. To explain these trends, we develop a mechanistic model for I PCET that invokes CPET involving hydronium/water or water/hydroxide donor-acceptor pairs. This relatively simple model captures the entire data set with only four adjustable parameters corresponding to the standard rate constants and charge transfer coefficients of the two donor/acceptor couples. From this analysis, we find that I PCET with water/hydroxide is four-fold more sluggish than with hydronium/water, but both reactions display similar charge transfer coefficients near 0.7, indicating a late transition state. These studies highlight the key mechanistic and kinetic distinctions between OS PCET and I-PCET and provide a baseline framework for understanding and modeling more complex I PCET reactions critical to energy conversion and catalysis. | Noah Lewis; Ryan Bisbey; Karl Westendorff; Alexander Soudackov; Yogesh Surendranath | Inorganic Chemistry; Energy; Electrochemistry; Inorganic Acid/Base Chemistry; Kinetics and Mechanism - Inorganic Reactions; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645a52aff2112b41e9439c0a/original/a-molecular-level-mechanistic-framework-for-interfacial-proton-coupled-electron-transfer-kinetics.pdf |
61701df54c04e89c62885031 | 10.26434/chemrxiv-2021-b8ncl | CrabNet for explainable deep learning in materials science: bridging the gap between academia and industry | Despite recent breakthroughs in deep learning for materials informatics, there exists a disparity between their popularity in academic research and their limited adoption in the industry. A significant contributor to this “interpretability-adoption gap” is the prevalence of black-box models and the lack of built-in methods for model interpretation. While established methods for evaluating model performance exist, an intuitive understanding of the modeling and decision-making processes in models is nonetheless desired in many cases.
In this work, we demonstrate several ways of incorporating model interpretability to the structure-agnostic Compositionally Restricted Attention-Based network, CrabNet. We show that CrabNet learns meaningful, material property-specific element representations based solely on the data with no additional supervision. These element representations can then be used to explore element identity, similarity, behavior, and interactions within different chemical environments. Chemical compounds can also be uniquely represented and examined to reveal clear structures and trends within the chemical space. Additionally, visualizations of the attention mechanism can be used in conjunction to further understand the modeling process, identify potential modeling or dataset errors, and hint at further chemical insights leading to a better understanding of the phenomena governing material properties.
We feel confident that the interpretability methods introduced in this work for CrabNet will be of keen interest to materials informatics researchers as well as industrial practitioners alike.
| Anthony Wang; Mahamad Salah Mahmoud; Mathias Czasny; Aleksander Gurlo | Theoretical and Computational Chemistry; Materials Science; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61701df54c04e89c62885031/original/crab-net-for-explainable-deep-learning-in-materials-science-bridging-the-gap-between-academia-and-industry.pdf |
630fba2e521cb700d8addd40 | 10.26434/chemrxiv-2022-gk2cs | Synthesis, Structure, and Hydroboration Reactivity of Anionic Nickel(0) Complexes Supported by Bidentate NHC-Pyridone Ligands | A family of anionic, formally nickel(0) complexes supported by bidentate NHC–pyridone ligands is described. The unsymmetric chelating environment and capping [K(18-crown-6)]+ countercation allow isolation of single-component, monometallic complexes in high yield. The steric and electronic properties are assessed through a battery of experimental (NMR, IR, UV/vis, X-ray diffraction) and computational tools. Catalytic activity for highly branched-selective hydroboration of styrene with HBpin is demonstrated. Control experiments implicate an important role of the pyridone in establishing reactivity and regioselectivity, suggesting the potential to leverage secondary coordina-tion sphere effects with these single-component precatalysts for reagent activation and delivery. | C. Rose Kennedy; Medina Afandiyeva; Xijue Wu; Abhishek Kadam; William Brennessel | Organic Chemistry; Catalysis; Organometallic Chemistry; Catalysis; Ligand Design; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630fba2e521cb700d8addd40/original/synthesis-structure-and-hydroboration-reactivity-of-anionic-nickel-0-complexes-supported-by-bidentate-nhc-pyridone-ligands.pdf |
61916db79960f3c21fac5304 | 10.26434/chemrxiv-2021-v0pjv | Chiral control of spin-crossover dynamics in Fe(II) complexes | Iron-based spin-crossover (SCO) complexes hold tremendous promise as multifunctional switches in molecular devices. However, real-world technological applications require the excited high-spin (HS) state to be kinetically stable – a feature that has only been achieved at cryogenic temperatures in the light-induced excited spin-state trapping effect. Here we demonstrate HS state trapping by controlling the chiral configuration of FeII(4,4’-dimethyl-2,2’-bipyridine)3 in solution, associated for stereocontrol with enantiopure ∆- or Λ-TRISPHAT anions. We characterize the HS state relaxation using a newly developed ultrafast circular dichroism technique in combination with transient absorption and anisotropy measurements. We find that the decay of the HS state is accompanied by ultrafast changes of its optical activity, reflecting the coupling to a symmetry-breaking torsional twisting mode, contrary to the commonly assumed picture. Furthermore, we show that the diastereoselective ion-pairing with the enantiopure anions suppresses the vibrational population of the identified twisting mode, thereby achieving a four-fold extension of the HS lifetime. Transferred to the solid state, this novel strategy may thus significantly improve the kinetic stability of iron(II)-based magnetic switches at room temperature. | Malte Oppermann; Francesco Zinna; Jérôme Lacour; Majed Chergui | Physical Chemistry; Organometallic Chemistry; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61916db79960f3c21fac5304/original/chiral-control-of-spin-crossover-dynamics-in-fe-ii-complexes.pdf |
622aecefc91cf2f53e4a6ca6 | 10.26434/chemrxiv-2022-mld88-v2 | Telltale Diamagnetism at 50 K of a Coordination Polymer System | The synthesis of coordination polymers (e.g., Prussian blue) is as old as modern chemistry itself, but never stops surprising people. We here report superconductivity observed of a designer coordination polymer system sporting the chemically soft mercaptan and hard carboxyl groups. The mercapto-carboxyl (dubbed Mercarb, or QiuSuo in Mandarin Pinyin) synergy hints at Daoism and here carries over from the molecular to the solid state: the soft sulfur donors bond with Co2+/Ni2+ (or other transition metal ions) to afford 2D sheets for charge transport, while the interlayer metal-carboxylate domain is more ionic and mediates the transition into the superconductive state. Besides the flexible QiuSuo design, this CP system is suited for doping (e.g., with μ2-OH2 units to effect charge balance by transforming into μ2-OH-), in order to fine-tune the electron-hole balance, and to achieve high-temperature superconductivity. | Jun He; Xinhe Ye; Zhiqing Liu; Liangming Tang; Jieying Hu; Zhengtao XU | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Polymers; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622aecefc91cf2f53e4a6ca6/original/telltale-diamagnetism-at-50-k-of-a-coordination-polymer-system.pdf |
60c74d46ee301c4da8c7a25f | 10.26434/chemrxiv.12570551.v2 | In Silico Identification of Potential Allosteric Inhibitors of the SARS-CoV-2 Helicase | <p>The COVID-19 pandemic ravages the globe
causing unprecedented health and economic challenges. As the world prospects
for a cure, scientists are looking critically at strategic protein targets
within the SARS-CoV-2 that have therapeutic significance. One of such targets
is the Helicase which is an enzyme that affects all aspects of SARS-CoV-2 RNA
metabolism. The aim of this study is to identify small molecules from natural
products that have strong binding affinity with and inhibitory activity against
an allosteric site (Pocket 26) of SARS-CoV-2 Helicase. Pyrx was used for the <i>in silico</i> molecular docking simulations
of SARS-CoV-2 Helicase (QHD43415-12.pdb) against a library of small molecules
obtained from edible African plants. Triphenylmethane which had a docking score
of -7.4 kcal/mol was chosen as a reference molecule. Virtual screening for oral
bioavailability was done based on the molecular descriptors of the compounds as
provided by Pubchem. SwissADME, pkCSM, and Molinspiration were used for further
screening for molar refractivity, saturation, promiscuity, pharmacokinetic
properties, and bioactivity respectively. The Galaxy webserver which uses the
GROMACS software was used for the molecular dynamic simulation and analyses.
The lead compounds are Gibberellin A12, A20 and A51 obtained from Green peas
and the Okra plant. <a>Gibberellin A20 and A51 </a>performed
better than the standard. Gibberellin A51 is predicted to show the greatest
inhibitory activity against SARS-CoV-2 Helicase. It is recommended that the
inhibitory activities of the lead compounds be further investigated.</p> | Adekunle Rowaiye; Olukemi Onuh; Titilayo Asala; Amoge Ogu; Doofan Bur; Ezinne Nwankwo; Uchenna Orji; Zainab Ibrahim; Jamila Hamza; Adaku Ugorji | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d46ee301c4da8c7a25f/original/in-silico-identification-of-potential-allosteric-inhibitors-of-the-sars-co-v-2-helicase.pdf |
60c74392469df41ef5f431f8 | 10.26434/chemrxiv.9252971.v1 | Oxidative Coupling of Aryl Boronic Acids with Aryl- and Alkylamines via Cooperative Photoredox and Copper Catalysis | <p>Copper(II)-catalyzed
oxidative cross-couplings of aryl boronic acids with aryl- and alkylamines have
been accomplished across a range of substrates in the presence of a ruthenium(II)-photoredox
cocatalyst under mild aerobic conditions. This modified C−N cross-coupling
reaction allows the incorporation of alkylamines to both electron poor− and
electron-rich aryl boronic acids with low photocatalyst loadings and under
ambient atmosphere. The coupling protocol provides secondary amines in yields
of 63-90% during the safe, procedurally improved process. </p> | Jennifer Marshall; Juliana O'Brien; Andrew Wommack | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74392469df41ef5f431f8/original/oxidative-coupling-of-aryl-boronic-acids-with-aryl-and-alkylamines-via-cooperative-photoredox-and-copper-catalysis.pdf |
65c83cf466c1381729611d58 | 10.26434/chemrxiv-2024-t0h0z | Plasma-activated tight and uniform grown of metal-organic frame-work on carbon cloth for stable Li metal anode | The significant expansion in volume and the formation of dendrites on lithium metal anodes lead to poor electrochemical reversi-bility. In this study, ZnO, N-dually doped carbon (p-ZNCC) was synthesized using oxygen plasma assistance and zeolitic imidazo-late framework-8 (ZIF-8). The use of plasma ensures tight and uniform growth of ZIF-8 particles on carbon fiber, promoting the formation of lithiophilic pyrrolic N after sintering. This enables uniform lithium deposition and rapid lithium-ion diffusion during the operation. The resulting lithium electrode with the p-ZNCC host (p-ZNCC-Li) exhibits stable lithium stripping/plating for up to 3000 h and a voltage hysteresis of 36 mV when cycled at 10 mA cm-2-10 mAh cm-2. Electrochemical impedance spectroscopy (EIS) reveals low charge transfer resistance and a high diffusion coefficient for p-ZNCC-Li. Moreover, the LNMO||p-ZNCC-Li cell demonstrates improved capacity retention at 1 C after 250 cycles. This study introduces a novel approach to growing metal-organic frameworks (MOFs) with dual lithiophilic spots on carbon cloth, promising advancements in lithium metal anode design. | Zilong Zhuang; Xinqiang Rao; Fuming Zhang; Vijaykumar Jadhav; Daniel Tan | Energy; Energy Storage | CC BY 4.0 | CHEMRXIV | 2024-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c83cf466c1381729611d58/original/plasma-activated-tight-and-uniform-grown-of-metal-organic-frame-work-on-carbon-cloth-for-stable-li-metal-anode.pdf |
60c750b9f96a003887287ebb | 10.26434/chemrxiv.12675368.v2 | Alkyl Halides as Both Hydride and Alkyl Sources in Catalytic Regioselective Reductive Olefin Hydroalkylation | Among the plethora of catalytic methods developed for hydrocarbofunctionalization of olefins to date, reactions that regioselectively install a functionalized alkyl unit at the 2-position of a terminal unactivated C=C bond to afford branched products are scarce. Here, we show that a Ni-based catalyst in conjunction with a stoichiometric reducing agent promote Markovnikov-selective hydroalkylation of unactivated alkenes tethered to a recyclable 8-aminoquinaldine directing auxiliary. These mild reductive processes employ readily available primary and secondary haloalkanes as both the hydride and alkyl donor, obviating the need for additional hydrosilane, acidic or basic additives. Reactions of alkenyl amides with ≥five-carbon chain length regioselectively afforded β-alkylated products through remote hydroalkylation, underscoring the fidelity of the catalytic process and the directing group's capability in stabilizing five-membered nickelacycle intermediates. The operationally simple protocol exhibits exceptional functional group tolerance and is amenable to the synthesis of bioactive molecules as well as regioconvergent transformations. | Xianxiao Chen; Weidong Rao; Tao Yang; Ming Joo Koh | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750b9f96a003887287ebb/original/alkyl-halides-as-both-hydride-and-alkyl-sources-in-catalytic-regioselective-reductive-olefin-hydroalkylation.pdf |
60c747fdee301c46ecc797e5 | 10.26434/chemrxiv.11828673.v1 | Green Reconstruction of MIL-100 (Fe) in Water for High Crystallinity and Enhanced Guest Encapsulation | <p><a></a><a>MIL‑100 (Fe) is a highly porous and environmentally friendly metal‑organic framework (MOF) considered as a promising carrier for drug delivery, and for gas separation and capture applications. However, this functional material suffers from elaborated and toxic synthesis that may hinder its biomedical use and large‑scale production to afford commercial applications. Herein, we report a ‘green’ mechanochemical water immersion approach to yield highly crystalline MIL‑100 (Fe) material. Subsequently, we have harnessed this strategy for facile fabrication of guest@MOF composite systems, comprising (guests) 5‑fluorouracil, caffeine, or aspirin encapsulated in the pores of (host) MIL‑100 (Fe). Inelastic neutron scattering was uniquely used to probe the guest‑host interactions arising from pore confinement of the drug molecules, giving additional insights into the reconstruction mechanism</a>. Our results pave the way to the green production of MIL‑type materials and bespoke guest-encapsulated composites for biotechnological applications.</p> | Barbara Souza; Annika Moslein; Kirill Titov; James D. Taylor; Svemir Rudic; Jin-Chong Tan | Biocompatible Materials; Composites; Core-Shell Materials; Hybrid Organic-Inorganic Materials; Materials Processing; Nanofabrication; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747fdee301c46ecc797e5/original/green-reconstruction-of-mil-100-fe-in-water-for-high-crystallinity-and-enhanced-guest-encapsulation.pdf |
64250065647e3dca99ba918d | 10.26434/chemrxiv-2023-6z4fp | Is HF really necessary? Revisiting silica etching protocols in particle brushes | Particle brushes are an emerging type of hybrid polymer material at present, among which the polymer brush with silica as the core is a the most common type. Normally, hydrofluoric acid is used to etch these particles prior to chromatographic analysis, but hydrofluoric acid is particularly hazardous to humans and the environment. Herein we reports the use of NH4HF2 instead of hydrofluoric acid for the etching process and is extended to particle brushes with other inorganic cores such as barium titanate. | Feichen Cui; Yang Sui; Yipeng Zhang; Zhikun Xie; Jiajun Yan | Polymer Science; Nanoscience; Organic Polymers; Polymer brushes; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64250065647e3dca99ba918d/original/is-hf-really-necessary-revisiting-silica-etching-protocols-in-particle-brushes.pdf |
60f1ce691053170509410d7e | 10.26434/chemrxiv-2021-kqntm-v2 | Bagasse derived C@Fe3C/Fe3O4 composite: An Approach towards low cost electrocatalyst for oxygen reduction reaction | As the world is heading towards sustainable future, it is highly important to develop low-cost electrocatalysts for energy generation devices. Herein, we report synthesis of iron-carbon hybrid (C@Fe3C/Fe3O4) nanocomposite for oxygen reduction reaction (ORR), synthesized using bagasse as a carbon source material and Fe(III) precursor at 900 ˚C. The synthesized C@Fe3C/Fe3O4 composite exhibits a high surface area of ~930 m2/g. The electrode material has a 0.86 V overpotential vs RHE. Moreover, the electrocatalyst shows catalytic stability upto 44,000 s at the static potential of 0.25 V vs RHE at the rotation speed of 1600 rpm. Herein, the electron transfer number is calculated to be 3.76-3.94 which suggest that the electrocatalyst could catalyze ORR nearly through a 4 electron transfer process in alkaline solution. | Rashmi Manippady; Ziyauddin Khan; Akshaya Samal; Manav Saxena | Inorganic Chemistry; Energy; Electrochemistry; Fuels - Energy Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f1ce691053170509410d7e/original/bagasse-derived-c-fe3c-fe3o4-composite-an-approach-towards-low-cost-electrocatalyst-for-oxygen-reduction-reaction.pdf |
641455442bfb3dc251ebc815 | 10.26434/chemrxiv-2023-spz0g-v2 | DrugEx: Deep Learning Models and Tools for Exploration of Drug-like Chemical Space | The discovery of novel molecules with desirable properties is a classic challenge in medicinal chemistry. With the recent advancements of machine learning, there has been a surge of de novo drug design tools. However, few resources exist that are both user-friendly as well as easily customisable. In this application note, we present the new versatile open-source software package DrugEx for multi-objective reinforcement learning. This package contains the consolidated and redesigned scripts from the prior DrugEx papers including multiple generator architectures and a variety of scoring tools and multi-objective optimisation methods. It has a flexible application programming interface and can readily be used via the command line interface or the graphical user interface GenUI. The DrugEx package is publicly available at https://github.com/CDDLeiden/DrugEx | Martin Sicho; Sohvi Luukkonen; Helle W. van den Maagdenberg; Linde Schoenmaker; Olivier J.M. Béquignon; Gerard J.P. van Westen | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641455442bfb3dc251ebc815/original/drug-ex-deep-learning-models-and-tools-for-exploration-of-drug-like-chemical-space.pdf |
60c74b219abda2a409f8cfd7 | 10.26434/chemrxiv.12287786.v1 | Should We Think Positive or Negative About Dihydrobenzofuran Neolignans? an ESI-MS/MS Study | <p>This study elucidates
the gas-phase fragmentation pathways of a series of biologically active
benzofuran neolignans (BNs) and dihydrobenzofuran neolignans (DBNs) by means of
electrospray ionization accurate-mass tandem and sequential mass spectrometry (ESI-MS/MS
and ESI-MS<sup>n</sup>) and thermochemical data estimated by using Computational
Chemistry and the B3LYP/6-31+G(d,p) model. In their deprotonated forms, these compounds
produced more diagnostic product ions as compared to the corresponding
protonated molecules. Moreover, a series of odd-electron product ions (radical
anions) were detected, which has not been reported for protonated DBNs. Direct C<sub>2</sub>H<sub>3</sub>O<sub>2</sub>•
elimination from the precursor ion (deprotonated molecule) only occurred for
the BNs and can help to distinguish these compounds from the DBNs. Although the
product ion [M‒CH<sub>3</sub>OH]<sup>‒</sup> emerged in the spectrum of all the DBNs analyzed here,
the mechanism through which this ion originates strongly depends on specific structural
features, so that further [M‒CH<sub>3</sub>OH]<sup>‒</sup> fragmentation generates important diagnostic product
ions. Comparison between the ESI-MS/MS data of these compounds in the negative
ion mode (deprotonated molecule) and in the positive ion mode (protonated
molecule) revealed that the negative ion mode provides much more information (at
least one diagnostic product ion emerged for all the analyzed compounds) and
does not require the use of additives to produce the precursor ions
(deprotonated molecules). </p> | Herbert Dias; Eduardo Crevelin; Vinicius Palaretti; Ricardo Vessecchi; Antônio Eduardo Crotti | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b219abda2a409f8cfd7/original/should-we-think-positive-or-negative-about-dihydrobenzofuran-neolignans-an-esi-ms-ms-study.pdf |
62051097cbb4f49f5dbc0e63 | 10.26434/chemrxiv-2022-gsl9b-v2 | Cathodoluminescence of zinc oxide crystals grown from melt under high pressure in the presence of ytterbium oxide | A mixture of poly- and single crystals of zinc and ytterbium (2 at.%) oxides have been grown from the melt at high temperature (1430°C) and high pressure (3.8 GPa). The crystals were transparent under examination with naked eye. The diameter of crystals was in the range from 0.005 to 2 mm. X-ray diffraction confirmed presence of individual zinc and ytterbium oxides in the recovered samples. No change of zinc oxide lattice parameters was observed compared to pristine zinc oxide. Cathodoluminescence spectra of the mixture were recorded at 77 and 293 K. The collected spectra exhibit UV, green and near-infrared bands due to exciton recombination, presence of oxygen vacancies and ytterbium ions in ZnO crystals, respectively. | Andrei N. Baranov; Mikhail V. Shestakov; Mikhail V. Chukichev; Victor A. Tafeenko; Vladimir A. Mukhanov; Vladimir L. Solozhenko | Materials Science; Materials Processing; Optical Materials | CC BY 4.0 | CHEMRXIV | 2022-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62051097cbb4f49f5dbc0e63/original/cathodoluminescence-of-zinc-oxide-crystals-grown-from-melt-under-high-pressure-in-the-presence-of-ytterbium-oxide.pdf |
628b927d6cae1c6058141f6f | 10.26434/chemrxiv-2022-gm12z | Mechanosynthesis and Photophysics of Colour-tunable Photoluminescent Group 13 Metal Complexes with Sterically Demanding 3,5-di-tert-butyl Substituted Salen and Salophen Ligands | A series of four photoluminescent Al and In complexes were synthesised using an environmentally-benign mechanosynthetic strategy. Both the sterically crowded 3,5-di-tert-butyl functionalised salophen, salen ligands and the complexes are synthesised in the solid-state and fully characterised. The photophysics and electrochemistry of these complexes were studied, the results suggested that these novel group 13 complexes can be alternatives of traditional photoluminescent complexes and to avoid the use of organic solvents, helps to reduce the environmental impact of the process and also improves its energy efficiency. | Felix Leon; Chenfei Li; Javier F. Reynes; Varun K. Sigh; Lian Xiao; How Chee Ong; Gavin Hum; Handong Sun; Felipe Garcia | Inorganic Chemistry; Main Group Chemistry (Inorg.); Organometallic Compounds; Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b927d6cae1c6058141f6f/original/mechanosynthesis-and-photophysics-of-colour-tunable-photoluminescent-group-13-metal-complexes-with-sterically-demanding-3-5-di-tert-butyl-substituted-salen-and-salophen-ligands.pdf |
63997d9fb103af9e0a18a8ef | 10.26434/chemrxiv-2022-rb0xk-v2 | Crystallographic Study of Solvates and Solvate Hydrates of an Antibacterial Furazidin | In this study we present a detailed crystallographic analysis of multiple solvates of an antibacterial furazidin. Solvate formation of furazidin was investigated by crystallizing it from pure solvents and solvent-water mixtures. Crystal structure analysis of the obtained solvates and computational calculations were used to identify the main factors leading to the intermolecular interactions present in the solvate crystal structures and resulting in formation of the observed solvates and solvate hydrates. Furazidin forms pure solvates and solvate hydrates with solvents having large hydrogen bond acceptor propensity and with a hydrogen bond donor and acceptor formic acid. In solvate hydrates the incorporation of water allows formation of additional hydrogen bonds and results in more efficient hydrogen bond network in which water is “hooking” the organic solvent molecule, and this slightly reduces the cut-off of solvent hydrogen bond acceptor propensity required for obtaining a solvate. The crystal structures of all pure solvates are formed from molecule layers and in almost all structures solvent is hydrogen bonded to the furazidin, but the packing in each solvate is unique. In contrast, the hydrogen bonding and packing in most solvate hydrates are nearly identical. | Liāna Orola; Anatoly Mishnev; Dmitrijs Stepanovs; Agris Bērziņš | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Pharmaceutical Industry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63997d9fb103af9e0a18a8ef/original/crystallographic-study-of-solvates-and-solvate-hydrates-of-an-antibacterial-furazidin.pdf |
60c744fb0f50db508c3961cf | 10.26434/chemrxiv.9941723.v1 | Diastereo- and Enantioselective CuH-Catalyzed Hydroamination of Strained Trisubstituted Alkenes | Amine-substituted cyclobutanes and cyclopropanes are important substructures in biologically active compounds. Moreover, many of the cycloalkane units bear multiple substituents and stereocenters. Therefore, synthetic methods that produce polysubstituted aminocyclobutanes and aminocyclopropanes in a highly diastereo- and enantioselective manner are of importance. Herein, we describe the diastereo- and enantioselective synthesis of various types of polysubstituted aminocyclobutanes and aminocyclopropanes through CuH-catalyzed hydroamination of 1-substituted cyclobutenes and cyclopropenes. These strained trisubstituted alkenes exhibit much higher reactivity compared to their unstrained analogues in the initial hydrocupration step of the reaction. Moreover, an interesting reversal of regioselectivity was observed in the hydroamination of 1-aryl-substituted cyclobutenes compared to the cyclopropene analogues. The origins of the enhanced reactivity of strained trisubstituted alkenes as well as the differences in the regio- and enantioselectivity between reactions with cyclobutenes and cyclopropenes were investigated computationally. | Sheng Feng; Hua Hao; Peng Liu; Stephen L. Buchwald | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fb0f50db508c3961cf/original/diastereo-and-enantioselective-cu-h-catalyzed-hydroamination-of-strained-trisubstituted-alkenes.pdf |
6710c9e5cec5d6c142669e5b | 10.26434/chemrxiv-2024-587vq | Nanoflow Size Exclusion Chromatography – Native Mass Spectrometry of Intact Proteoforms and Protein Complexes | Native size-exclusion chromatography (SEC) coupled with native mass spectrometry (nMS) enables the characterization of proteins and protein complexes by combining liquid-phase separation (SEC) and mass measurement of the complexes (nMS). This approach allows for an increase in the throughput of native MS experiments, reduces the bias that may be present due to the co-ionization of oligomers, and facilitates online sample buffer exchange. SEC-nMS uses volatile buffers and relatively wide-diameter columns (e.g., ≥ 1 mm), with flow rates in the tens of µL/minute. To ionize sample components under this flow regime, relatively harsh electrospray ionization (ESI) desolvation conditions are needed, which may result in protein dissociation/denaturation. Also, relatively large amounts of samples are required (several µgs). Herein, we describe the development of a nanoflow SEC-nMS method using 200 µm I.D. columns, operated at 500 nL•min-1. This approach allows buffer exchange, oligomer separation, and mild ionization conditions (e.g., without the assistance of heated gas flow or temperature). Compared to microflow (1 mm I.D. column), the nanoflow method achieved a 4-fold increase in MS peak intensity, despite using a sample 20 times less concentrated (0.05 mg mL-1 for nanoflow vs. 1 mg mL-1 for microflow). Furthermore, we evaluated the impact in terms of sensitivity and separation efficiency of three injection approaches: large-volume injection (1μL), nano-volume injection (50nL), and an online mix-bed ion-exchange capillary trap column. The final method, using nano-volume injection, was applied to several model protein and protein complexes to showcase performance and applicability to the study of sample-limited analysis.
| Ziran Zhai; Andrea F.G. Gargano | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710c9e5cec5d6c142669e5b/original/nanoflow-size-exclusion-chromatography-native-mass-spectrometry-of-intact-proteoforms-and-protein-complexes.pdf |
64cfd75bdfabaf06ffd2ff13 | 10.26434/chemrxiv-2023-g34tx-v2 | Machine Learning-Boosted Docking Enables the Efficient Structure-Based Virtual Screening of Giga-Scale Enumerated Chemical Libraries | The emergence of ultra-large screening libraries, filled to the brim with billions of readily available compounds, poses a growing challenge for docking-based virtual screening. Machine Learning (ML)-boosted strategies like the tool HASTEN combine rapid ML prediction with the brute-force docking of small fractions of such libraries to increase screening throughput and take on giga-scale libraries. In our case study of an anti-bacterial chaperone and an anti-viral kinase, we first generated a brute-force docking baseline for 1.56 billion compounds in the Enamine REAL lead-like library with the fast Glide HTVS protocol. With HASTEN, we observed robust recall of 90% of the true 1000 top-scoring virtual hits in both targets when docking only 1% of the entire library. This reduction of the required docking experiments by 99% significantly shortens the screening time.In the kinase target, the employment of a hydrogen bonding constraint resulted in a major proportion of unsuccessful docking attempts and hampered ML predictions. We demonstrate the optimization potential in the treatment of failed compounds when performing ML-boosted screening and benchmark and showcase HASTEN as a fast and robust tool in a growing arsenal of approaches to unlock the chemical space covered by giga-scale screening libraries for everyday drug discovery campaigns. | Toni Sivula; Laxman Yetukuri; Tuomo Kalliokoski; Heikki Käsnänen; Antti Poso; Ina Pöhner | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cfd75bdfabaf06ffd2ff13/original/machine-learning-boosted-docking-enables-the-efficient-structure-based-virtual-screening-of-giga-scale-enumerated-chemical-libraries.pdf |
65781bdbfd283d7904d16b3b | 10.26434/chemrxiv-2023-t7v1b | CoPolDB: A Copolymerization Database for Radical Polymerization | Although a large amount of knowledge on copolymers and coplymerization has been already accumulated in literature, there are no freely available databases with a proper graphical user interface (GUI) on copolymerization. Focusing on copolymerization with only two types of monomers (due to the focus on fundamentals) and copolymerization in radical polymerization, i.e. the most major polymerization, we present CoPolDB, a database of copolymerization with numerous helpful GUI functions, including two: 1) graphically showing multiple connections (with different reactivity ratios) between two monomers and the corresponding copolymer, assisting users' intuitive understanding, and 2) providing a list of alternative monomers for each monomer pair, according to the similarity to the original monomer. We believe that CoPolDB is a useful resource to understand the current copolymerization status entirely and comprehensively as well as an inspiring tool to promote polymer chemistry research. CoPolDB is available via https://www.copoldb.jp/. | Kei-ichiro Takahashi; Hiroshi Mamitsuka; Masatoshi Tosaka; Nanyi Zhu; Shigeru Yamago | Theoretical and Computational Chemistry; Analytical Chemistry; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65781bdbfd283d7904d16b3b/original/co-pol-db-a-copolymerization-database-for-radical-polymerization.pdf |
60c74de7567dfee731ec5417 | 10.26434/chemrxiv.12671144.v1 | A Rapid and Sensitive Method for Chiroptical Sensing of a-Amino Acids via Click-like Labeling with o-Phthaladehyde and p-Toluenethiol | A highly practical method for comprehensive chiroptical sensing of free a amino acids with streamlined operation and high sensitivity via dual CD/UV measurements is developed. The assay takes advantage of an efficient and selective three-component labeling reaction of primary amines with <i>o</i>-phthalaldehyde and <i>p</i>-toluenethiol reagents, to derivatize the NH<sub>2</sub> group of analytes into an isoindole chromophore. The covalent labeling generates sensitive UV and CD readouts, both of which show excellent linear relationship with the concentration of analyte. The high reactivity and the novel chromogenic reporting mechanism allow fast and accurate measurement without background interference. The sensing assay works well for a remarkably broad range of analyte concentrations, with an unprecedented lower limit at 10 micromolar. We expect this method can be readily adapted for high throughput experimentation analysis using CD instrument equipped with a multiwell plate reader. | Bo Li; Jie Zhang; Li Li; Gong Chen | Physical Organic Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de7567dfee731ec5417/original/a-rapid-and-sensitive-method-for-chiroptical-sensing-of-a-amino-acids-via-click-like-labeling-with-o-phthaladehyde-and-p-toluenethiol.pdf |
65035b0b99918fe537f4c544 | 10.26434/chemrxiv-2023-fx8j3 | Kinetic Fractionation of Antimony Isotopes during Reduction by Sulfide | Stable isotope ratios of antimony (Sb) in the environment can provide valuable information on sources and processes such as redox transformations. To investigate the fractionation when Sb(V) is chemically reduced by sulfide to Sb(III), experiments with 0.008 to 0.01 mM Sb(V) and 0.009 to 6 mM sulfide at a pH of 1 to 8 were performed. Experiments at pH 1 to 6 precipitated Sb2S3, while at pH 7 to 8 Sb(III) remained in solution. The Sb(III) product was enriched in the lighter isotope. The isotopic fractionation (ε ≈ δinstantaneous product – δreactant) for the pH 1 experiment was -1.42 ± 0.04‰ while the pH 5 to 8 experiments ranged from -0.46 ± 0.04‰ to -0.62 ± 0.04‰. The small magnitude of fractionation observed in experiments at circumneutral pH may decrease the utility of Sb isotope measurement as reduction indicators in natural systems, as adsorption of Sb has been shown to fractionate isotopes in the same direction and similar magnitude (up to 1.14‰) (Wasserman, 2020; Zhou et al., 2023). | Hannah J. Veldhuizen; Joel S. MacKinney; Thomas M. Johnson | Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry; Hydrology and Water Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65035b0b99918fe537f4c544/original/kinetic-fractionation-of-antimony-isotopes-during-reduction-by-sulfide.pdf |
643529c70784a63aeeed3403 | 10.26434/chemrxiv-2023-69wcr | Electrochemical Dearomatizing Spirolactonization and Spiroetherification of Free Arenols | An electrochemical oxidative ortho-dearomatization of naphthols and phenols with an intramolecular C–O bond formation has been developed. A careful optimization of the reaction parameters allowed for the application of free arenols as the starting materials, in contrast to the existing alternative procedures necessitating aryl methyl ethers substrates. The reaction delivers an array of spirolactones and spiroethers in yields up to 97%, under simple experimental conditions: in a constant current mode, using an undivided cell, and without an inert atmosphere. The method avoids using catalysts or stoichiometric oxidants (e.g., hypervalent iodine reagents), generating hydrogen as the sole side-product. | Somayyeh Sarvi Beigbaghlou; Robert S. Yafele; Marcin Kalek | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643529c70784a63aeeed3403/original/electrochemical-dearomatizing-spirolactonization-and-spiroetherification-of-free-arenols.pdf |
632317f866db9d5d82d7485a | 10.26434/chemrxiv-2022-4r7vm-v2 | Using metal-organic frameworks to confine liquid samples for nanoscale NV-NMR | Atomic-scale magnetic field sensors based on nitrogen vacancy (NV) defects in diamonds are an exciting platform for nanoscale nuclear magnetic resonance (NMR) spectroscopy. The detection of NMR signals from a few zeptoliters to single molecules or even single nuclear spins has been demonstrated using NV-centers close to the diamond surface. However, fast molecular diffusion of sample molecules in and out of nanoscale detection volumes impedes their detection and limits current experiments to solid-state or highly viscous samples. Here, we show that restricting diffusion by confinement enables nanoscale NMR spectroscopy of liquid samples. Our approach uses metal-organic frameworks (MOF) with angstrom-sized pores on a diamond chip to trap sample molecules near the NV-centers. This enables the detection of NMR signals from a liquid sample, which would not be detectable without confinement. These results set the route for nanoscale liquid-phase NMR with high spectral resolution. | Kristina Liu; Xiaoxin Ma; Roberto Rizzato; Anna-Lisa Semrau; Alex Henning; Ian Sharp; Roland Fischer; Dominik Bucher | Physical Chemistry; Materials Science; Thin Films; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632317f866db9d5d82d7485a/original/using-metal-organic-frameworks-to-confine-liquid-samples-for-nanoscale-nv-nmr.pdf |
65dd4348e9ebbb4db9590d3a | 10.26434/chemrxiv-2024-xprjf | Chemically Recyclable, High Molar Mass Polyoxazolidinones via Ring Opening Metathesis Polymerization | The development of robust methods for the synthesis of chemically recyclable polymers with tunable properties is necessary for the design of next-generation materials. Polyoxazolidinones (POxa) – polymers with five-membered urethanes in their backbones – are an attractive target because they are strongly polar and have high thermal stability, but existing step-growth syntheses limit molar masses and chemical recyclability to monomer is rare. Herein, we report the synthesis of high molar mass POxa via ring opening metathesis polymerization of oxazolidinone-fused cyclooctenes. These novel polymers show <5% mass loss up to 382–411 °C and have tunable glass transition temperatures (14–56 °C) controlled by side chain structure. We demonstrate facile chemical recycling to monomer and re-polymerization despite moderately high monomer ring strain energies, which we hypothesize is facilitated by the conformational restriction introduced by the fused oxazoli-dinone ring. This method represents the first chain growth synthesis of POxa and provides a versatile platform for the study and application of this emerging subclass of polyurethanes. | Arpan Pal; Allison Wong; Jessica Lamb | Organic Chemistry; Polymer Science; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dd4348e9ebbb4db9590d3a/original/chemically-recyclable-high-molar-mass-polyoxazolidinones-via-ring-opening-metathesis-polymerization.pdf |
67b3e1bdfa469535b9c934b3 | 10.26434/chemrxiv-2025-pp3xl | Graphically-Defined Model Reactions are Extensible, Accurate, and Systematically Improvable | Achieving fast and accurate reaction prediction is central to a suite of chemical applications. Nevertheless, classic approaches based on templates or simple models are typically fast but with limited scope or accuracy, while the emerging machine learning-based models are limited in their transferability due to the lack of large reaction databases. Here, we address these limitations by formalizing the model reaction concept based on fixed-depth condensed reaction graphs that are shown to achieve a cost and accuracy balance that is applicable to many problems. The model reaction concept can be utilized to provide reliable predictions of activation energies and transition state geometries for a large range of organic reactions. In addition, using an alkane pyrolysis system as a benchmarking example, we show that the accuracy of the activation energy prediction can be further improved by adding correction terms based on the empirical Br{\o}nsted-Evans-Pokanyi (BEP) relationship. These successful applications demonstrate that the model reaction can serve as a general tool to reduce the cost associated with ab initio transition state searches. | Qiyuan Zhao; Veerupaksh Singla; Hsuan-Hao Hsu; Brett Savoie | Theoretical and Computational Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b3e1bdfa469535b9c934b3/original/graphically-defined-model-reactions-are-extensible-accurate-and-systematically-improvable.pdf |
650868b1b6ab98a41cabdc2d | 10.26434/chemrxiv-2023-6pjq4 | Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method | Umbrella sampling molecular dynamics simulations are widely used to enhance sampling along the reaction coordinate of chemical reactions. The effect of the artificial bias can be removed using methods such as the Dynamic Weighted Histogram Analysis Method (DHAM), which in addition to the global free energy profile also provides kinetic information on barrier-crossing rates directly from the Markov matrix. Here we present a binless formulation of DHAM, which extends DHAM to high-dimensional and Hamiltonian-based biasing, allowing the study of electron transfer (ET) processes, where enhanced sampling is usually not possible based on simple geometric grounds. We show the capabilities of binless DHAM on examples such as aqueous ferrous-ferric ET and intramolecular ET in the radical anion of benzoquinone–tetrathiafulvalene–benzoquinone (Q-TTF-Q)–. From classical Hamiltonian-based umbrella sampling simulations and electronic coupling values from quantum chemistry calculations, binless DHAM provides ET rates for adiabatic and nonadiabatic ET reactions alike, in excellent agreement with experiment. | Zsuzsanna Koczor-Benda; Teodora Mateeva; Edina Rosta | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650868b1b6ab98a41cabdc2d/original/direct-calculation-of-electron-transfer-rates-with-the-binless-dynamic-histogram-analysis-method.pdf |
673d8524f9980725cfe53116 | 10.26434/chemrxiv-2024-1hl8v-v2 | Beta-Thioamide Sulfone enabled Copper-Catalyzed Ring-Opening/Sulfonylation of Cyclopropenes: Access to Alkyl Aryl Sulfones | Sulfone motifs play important roles in bioactive compounds and functional materials. The development of efficient methodologies for constructing sulfonyl-containing compounds has thus attracted considerable attention. Here, we introduce a protocol for the preparation of alkyl aryl sulfones under mild conditions. This protocol employs -thioamide sulfone as a novel sulfone motif donor. It forms sulfinates in situ under basic conditions, which then undergo cross-coupling with the intermediates that were generated from ligand-free copper-catalyzed cyclopropenes (CPEs) ring-opening. | Arshad Ali; Cherry Chung; Jingru Wang; Lang Liu; Chongyuan Wang ; Yidong Liu; Qin Yin; Shaoquan Lin | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673d8524f9980725cfe53116/original/beta-thioamide-sulfone-enabled-copper-catalyzed-ring-opening-sulfonylation-of-cyclopropenes-access-to-alkyl-aryl-sulfones.pdf |
6537a0972431cc1dac6e280d | 10.26434/chemrxiv-2023-j0bv8-v2 | Electronic Structure of Metalloporphenes, Antiaromatic Analogs of Graphene | Zinc porphene is a two-dimensional material made of fully fused zinc porphyrins in a tetragonal lattice. It has a fully conju-gated π-system, making it similar to graphene. Zinc porphene has recently been synthesized and shown to be a semiconduc-tor (Nat. Comm., 2023, 14, 6308.). This is in contrast with all previous predictions of its electronic structure, which indi-cated metallic conductivity. We show that the gap-opening in zinc porphene is caused by a Peierls distortion of its unit cell from square to rectangular, thus giving the first account of its electronic structure in agreement with experiment. Accounting for this distortion requires a proper treatment of electron delocalization, which can be done using hybrid functionals with a substantial amount of exact exchange. Such a functional, PBE38, is then applied to predict the properties of many first tran-sition row metalloporphenes, some of which have already been prepared. We find that changing the metal strongly affects the electronic structure of metalloporphenes, resulting in a rich variety of both metallic conductors and semiconductors, which may be of great of interest to molecular electronics and spintronics. Properties of these materials are mostly governed by the extent of the Peierls distortion and the number of electrons in their π system, analogous to changes in aromaticity observed in cyclic conjugated molecules upon oxidation or reduction. These results give an account of how the concept of antiaromaticity can be extended to periodic systems. | Ivan Pavlak; Lujo Matasović; Eric Buchanan; Josef Michl; Igor Rončević | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6537a0972431cc1dac6e280d/original/electronic-structure-of-metalloporphenes-antiaromatic-analogs-of-graphene.pdf |
6166e7b98b620d86644e0aac | 10.26434/chemrxiv-2021-z3xm8-v2 | Commercial-Scale Visible-light Trifluoromethylation of 2-Chlorothiophenol using CF3I gas. | Despite the growth of photoredox methods in academia, application of photoredox at scale in the pharmaceutical and fine chemical industries has been slow. In this report, a photoredox trifluoromethylation of a thiophenol was modified from the original literature report and the mechanism was investigated to define key scale-up parameters. The mechanistic insight was leveraged in the design and execution of two different reactor designs: an LED-based plug flow photoreactor as well as a laser-based continuous stirred tank photoreactor. In one of the first examples of commercial scale photoredox chemistry, the process was scaled to provide over 500 kilograms of the desired intermediate and amended to fully continuous manufacturing. | Kaid Harper; Timothy Grieme; Timothy Towne; Daniel Mack; Moiz Diwan; Yi-Yin Ku; Jeremy Griffin; Robert Miller; En-xuan Zhang; Zhi-qing Liu; Song-yuan Zheng; Ning-ning Zhang; Srinivas Grangula; Jia-long Yuan; Ping-zhong Huang; James Gage | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Photochemistry (Org.); Physical Organic Chemistry; Process Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6166e7b98b620d86644e0aac/original/commercial-scale-visible-light-trifluoromethylation-of-2-chlorothiophenol-using-cf3i-gas.pdf |
60c75448842e652133db4112 | 10.26434/chemrxiv.13637819.v1 | NMR Refinement and Peptide Folding Using the GROMACS Software | <div><div><div><p>Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and performing restrained molecular simulations. Here we report on the implementation of a script to extract NMR restraints from a NMR-STAR file and export it to the GROMACS software. With this package it is possible to model distance restraints, dihedral restraints and orientation restraints. The output from the script is validated by performing simulations with and without restraints, including the ab initio refinement of one peptide.</p></div></div></div> | Anna Sinelnikova; David van der Spoel | Biophysical Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75448842e652133db4112/original/nmr-refinement-and-peptide-folding-using-the-gromacs-software.pdf |
677ccda56dde43c908950576 | 10.26434/chemrxiv-2024-62546-v3 | Supersaturation, Nucleation, and Phase Separation
of Mesoscopic Materials | Supersaturation, nucleation, and phase separation are ubiquitous phenomena of great interest in both science and industry. However, a unified, quantitative understanding of these phenomena has yet to be achieved for mesoscopic materials. Here, we present a set of general equations that determine the monomer saturation degree, the size distribution and free energy of mesoscopic materials, as well as their phase transition conditions. These equations reveal that, under supersaturation, the largest cluster size (LCS) is an important state-variable; the supersaturation degree decreases with the LCS, approaching unity in the macroscopic limit. We identify the critical supersaturation condition, above which the nuclei undergo the phase transition to form large crystals. Below this critical supersaturation, the nucleus size distribution is either a unimodal function or a monotonically decreasing function of size, depending on system and temperature. We also predict the most probable nucleus size and the direction of spontaneous changes of the LCS. Our theory provides a unified, quantitative explanation of the nucleus-size-distribution across six different systems, including nanoparticles and biological condensates. This work will serve as a general theoretical framework for understanding, predicting, and designing nucleation and phase transitions in mesoscopic material systems. | Jingyu Kang; Donghee Kim; Sanggeun Song; Jonghwa Han; Yongwon Jung; Sangwoon Yoon; Youngjae Ryu; Sungjee Kim; Byung Hyo Kim; Jeong-Mo Choi; Mino Yang; Joonkyung Jang; Taeghwan Hyeon; Jungwon Park; Ji-Hyun Kim; Jaeyoung Sung | Physical Chemistry; Statistical Mechanics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ccda56dde43c908950576/original/supersaturation-nucleation-and-phase-separation-of-mesoscopic-materials.pdf |
62b94c777da6ce8eb421e9bf | 10.26434/chemrxiv-2022-4dxs2-v2 | N2O selectivity in industrial NH3 oxidation on Pt-gauze is determined by interaction of local flow and surface chemistry:
A simulation study using mechanistic kinetics
| Despite significant effort spent on the investigation of catalytic ammonia oxidation at
the molecular scale, there is surprisingly little work that investigates the behavior of the
established reaction mechanisms under industrial conditions in the presence of mass
transfer limitations.
This paper presents reactive flow simulations of ammonia oxidation on platinum
gauzes under industrial operating conditions, combining a mechanistic description of
the surface chemistry with the computation of the flow-, temperature and concentration
fields around the platinum wires.
Overall, the simulations yield temperature- and concentration fields, as well as integral
N2O selectivity in line with industrial experience and (limited available) experimental
data. In particular, the simulations predict the experimentally observed increase of the
integral N2O selectivity with increasing flow velocity, decreasing wire diameter and
wire-to-wire distance, and increased surface area due to surface reconstruction.
The main result of the paper is that the local interaction of flow and surface chemistry
leads to a variation in the local N2O selectivity across the gauze:The N2O and N2
selectivity is higher on the front side of a wire than on the rear side.
A reduced N2O selectivity is observed where one wire is shadowed by another wire.
Increased N2O selectivity is observed at stagnation points where upstream wires direct
the flow so that it hits a downstream wire with higher velocity.
These examples show that - through the flow directing effect of the upstream wires- the
selectivity on an individual wire is influenced by the presence of other wires. This
observation provides a mechanistic explanation for the industrial observation that
optimized gauze geometries can lead to reduced N2O formation. | Michael Haas; Teng-Wang Nien; Anton Fadic; Joe P. Mmbaga; Markus Klingenberger; Dirk Born; Bastian J. M. Etzold; Robert Hayes; Martin Votsmeier | Catalysis; Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Reaction Engineering; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b94c777da6ce8eb421e9bf/original/n2o-selectivity-in-industrial-nh3-oxidation-on-pt-gauze-is-determined-by-interaction-of-local-flow-and-surface-chemistry-a-simulation-study-using-mechanistic-kinetics.pdf |
6652101e91aefa6ce1fad94b | 10.26434/chemrxiv-2024-vkg59 | Contextual Analysis of Scientific Publications for Advancing writing Skills (CASPArS): Self-Learning for Science Writing Using Top Scientists’ Literature | Writing is an essential component of scientific activity. As such, it is necessary to develop strategies to provide equitable training opportunities for science writing. In order to provide learners with ways to improve their writing regardless of their language background and/or institutional and departmental environments, this article describes a self-learning strategy, Contextual Analysis of Scientific Publications for Advancing writing Skills (CASPArS), that employs contextual analysis of top scientists’ publications. By using full-text search software to analyze several hundred selected publications, the CASPArS method affords a visual representation of proper usage of words/phrases of interest, facilitating learners to understand writing patterns and rules in leading scientific papers. In order to increase the accessibility of the method for diverse communities around the world, a free-search software sin3rou and 500 open-access chemistry papers by 150 US researchers have been included in the Supporting Information. Using this CASPARS strategy, learners/students are able to develop appropriate writing through “professors’ eyes” by taking advantage of established scientific writers’ experience and knowledge of language usage. | Jun Ohata; James D. Martin; Ana Ison | Chemical Education | CC BY NC 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6652101e91aefa6ce1fad94b/original/contextual-analysis-of-scientific-publications-for-advancing-writing-skills-casp-ar-s-self-learning-for-science-writing-using-top-scientists-literature.pdf |
60c74846ee301c7d00c79822 | 10.26434/chemrxiv.11875446.v1 | Fast Identification of Possible Drug Treatment of Coronavirus Disease -19 (COVID-19) Through Computational Drug Repurposing Study | <p>The recent outbreak of novel coronavirus disease -19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very efficient to apply computer-aided drug design techniques to quickly identify promising drug repurposing candidates, especially after the detailed 3D-structures of key virous proteins are resolved. Taking the advantage of a recently released crystal structure of COVID-19 protease in complex with a covalently-bonded inhibitor, N3,<sup>1</sup> I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an endpoint method called MM-PBSA-WSAS.<sup>2-4</sup> Several promising known drugs stand out as potential inhibitors of COVID-19 protease, including Carfilzomib, Eravacycline, Valrubicin, Lopinavir and Elbasvir. Carfilzomib, an approved anti-cancer drug acting as a proteasome inhibitor, has the best MM-PBSA-WSAS binding free energy, -13.82 kcal/mol. Streptomycin, an antibiotic and a charged molecule, also demonstrates some inhibitory effect, even though the predicted binding free energy of the charged form (-3.82 kcal/mol) is not nearly as low as that of the neutral form (-7.92 kcal/mol). One bioactive, PubChem 23727975, has a binding free energy of -12.86 kcal/mol. Detailed receptor-ligand interactions were analyzed and hot spots for the receptor-ligand binding were identified. I found that one hotspot residue HIS41, is a conserved residue across many viruses including COVID-19, SARS, MERS, and HCV. The findings of this study can facilitate rational drug design targeting the COVID-19 protease.</p><p>
</p> | Junmei Wang | Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74846ee301c7d00c79822/original/fast-identification-of-possible-drug-treatment-of-coronavirus-disease-19-covid-19-through-computational-drug-repurposing-study.pdf |
60c74600567dfeb186ec454f | 10.26434/chemrxiv.10316162.v1 | Quantum Mechanical/Molecular Mechanical investigation of the reduction mechanism of Cysteine Sulfinic acid of Peroxiredoxin via Sulfiredoxin | <div><div><div><p>The formation of the overoxidized cysteine sulfinic acid in proteins has been connected to be associated with various diseases including cancer and age-related diseases. This post-transitional modification of proteins under oxi- dative stress has been known to be irreversible. However, in eukaryotic, the overoxidation of typical 2-Cys perxoiredoxins (Prxs) to sulfinic acid is reversible via a repair enzyme known as sulfiredoxin (Srx) leading to the regulation of both per- oxide signaling and Prxs chaperon activity. In this study, the molecular modeling techniques including molecular dynam- ics simulations (MD) and the hybrid quantum mechanical/molecular mechanical (QM/MM) approach were used to eluci- date the atomistic details of this unique reaction in sulfur chemistry. Our results support the previous experimentally pro- posed mechanism in which the sulfinic acid oxygen perform an in line direct nucleophilic attack on the γ-phosphate of ATP forming sulfinic acid phosphoryl ester intermediate and ADP, via a low barrier of 16.3 kJ mol-1. Subsequently, the formed intermediate is directly reduced via an SN2 mechanism by the Srx-Cys99 forming thiosulfinate. Our results suggest that the rate-limiting step of the reduction mechanism is associated with the reduction step of the thiosulfinate intermedi- ate. This work significantly improves the current knowledge of this unique reaction, which could contribute to the discov- ery of new groups of antioxidants capable of reducing this irreversible overoxidized state in other proteins.</p></div></div></div> | Hisham Dokainish; James Gauld | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74600567dfeb186ec454f/original/quantum-mechanical-molecular-mechanical-investigation-of-the-reduction-mechanism-of-cysteine-sulfinic-acid-of-peroxiredoxin-via-sulfiredoxin.pdf |
65f0768566c1381729d9a0b6 | 10.26434/chemrxiv-2024-z8l9r | Engineering Central Substitutions in Heptamethine Dyes via Aryl-lithium Addition for Improved Fluorophore Performance | As a major family of red-shifted fluorophores that operate beyond the visible light, polymethine dyes are pivotal in light-based biological techniques. However, the methods for tuning this kind of fluorophores by structural modification remain restricted to bottom-up synthesis and modification using coupling or nucleophilic substitutions. In this study, we introduce a two-step, late-stage functionalization process for heptamethine dyes. This process enables the substitution of the central chloride atom in the commonly used 4'-chloro heptamethine scaffold with various aryl groups using aryllithium reagents. This method borrows the building block and designs from the xanthene dye community, and offers a mild and convenient way for the diversification of heptamethine fluorophores. Notably, this efficient conversion allows for the synthesis of heptamethine-X, the heptamethine scaffold with two ortho-substituents on the 4’-aryl modification, which brings enhanced stability and reduced aggregation to the fluorophore. We showcase the utility of this synthesis by a facile synthesis of a fluorogenic, membrane-localizing fluorophore that outperforms the commercial counterparts with higher brightness and contrast. Overall, this method establishes the synthetic similarities between polymethine and xanthene fluorophores, and provides reference for future optimizing heptamethine fluorophores for their biological applications. | Lei Guo; Meek Yang; Bin Dong; Seth Lewman; Alex Van Horn; Shang Jia | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Imaging | CC BY NC 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f0768566c1381729d9a0b6/original/engineering-central-substitutions-in-heptamethine-dyes-via-aryl-lithium-addition-for-improved-fluorophore-performance.pdf |
60c7457bee301c13aec79304 | 10.26434/chemrxiv.10029068.v1 | Adhesion and Surface Layers on Silicon Anodes Suppress Formation of c-Li3.75Si and Solid Electrolyte Interphase | <div>The formation of c-Li3.75Si is known to be detrimental to silicon anodes in lithium-ion batteries. To suppress the formation of this crystalline phase and improve the electrochemical performance of Sibased anodes, three approaches were amalgamated: addition of a nickel adhesion sublayer, alloying of the silicon with titanium, and the addition of either carbon or TiO2 as a capping layer. The silicon-based films were analyzed by a suite of methods, including scanning electron microscopy (SEM) and a variety of electrochemical methods, as well as X-ray photoelectron spectroscopy (XPS) to provide insights into the composition of the resulting solid electrolyte interphase (SEI). A nickel adhesion layer decreased the extent of delamination of the silicon from the underlying copper substrate, compared to Si deposited directly on Cu, which resulted in less capacity loss. Alloying of silicon with titanium (85% silicon, 15% titanium) further increased the stability. Finally, capping these multilayer electrodes with either a thin 10 nm layer of carbon or TiO2 resulted in the best electrode behavior, and lowest cumulative relative irreversible capacity. TiO2 is slightly more effective in enhancing the capacity retention, most likely due to differences in the resulting solid electrolyte interphase (SEI). The combination of an adhesion layer, alloying, and surface coatings shows a cumulative suppression of the formation of c-Li3.75Si and SEI, resulting in the greatest improvement of capacity retention when all three are incorporated together. However, these strategies appear to only delay the onset of the c-Li3.75Si phase; eventually, the c-Li3.75Si phase will form, and at that point, the rate of capacity degradation of all the electrodes becomes similar.</div> | Hezhen Xie; Sayed Youssef Sayed; W. Peter Kalisvaart; Simon Jakob Schaper; Peter Müller-Buschbaum; Erik Luber; Brian Olsen; Martin Haese; Jillian Buriak | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457bee301c13aec79304/original/adhesion-and-surface-layers-on-silicon-anodes-suppress-formation-of-c-li3-75si-and-solid-electrolyte-interphase.pdf |
60c7432e4c891981e5ad25c4 | 10.26434/chemrxiv.8965475.v1 | High-Performance Group Transfer Catalysis by Copper Complex with Redox-Active Ligand in an Entatic State | <div>Metalloenzymes use earth-abundant non-noble metals to perform</div><div>high‐fidelity transformations in the biological world. To ensure chemical efficiency, metalloenzymes have acquired evolutionary reactivity‐enhancing tools. Among these, the entatic state model states that a strong steric entatic state, strongly improving the reactivity. However, while the original definition refers both to the transfer of electrons or chemical groups, the chemical application of this concept in synthetic systems has mostly focused on electron transfer, therefore eluding chemical transformations. Here we report that a highly‐strained redox-active ligand enables a cooper complex to perform catalytic nitrogen- and carbon-‐group transfer in as fast as two minutes, thus exhibiting a strong increase in reactivity compared to its unstrained analogue. This is the first report combining two reactivity-‐enhancing features from metalloenzymes, entasis and redox cofactors, applied to group-transfer catalysis.<br /></div> | Yufeng Ren; Jeremy Forte; Khaled Cheaib; Nicolas Vanthuyne; Louis Fensterbank; Hervé Vezin; Maylis Orio; Sébastien Blanchard; Marine DESAGE-EL MURR | Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7432e4c891981e5ad25c4/original/high-performance-group-transfer-catalysis-by-copper-complex-with-redox-active-ligand-in-an-entatic-state.pdf |
60c73ee2842e659dcadb19db | 10.26434/chemrxiv.7182095.v1 | Dual Ligand-Enabled Nondirected C–H Cyanation of Arenes | Aromatic nitriles are key structural units in organic chemistry and thus highly attractive targets for C–H activation. Herein the development of an arene-limited, nondirected C–H cyanation based on the use of two complementary ligands is reported. The reaction enables the cyanation of arenes by C–H activation in the absence of directing groups and is thus complementary to established approaches.<br /> | Hao Chen; Arup Mondal; Manuel van Gemmeren | Organic Compounds and Functional Groups; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ee2842e659dcadb19db/original/dual-ligand-enabled-nondirected-c-h-cyanation-of-arenes.pdf |
67af08696dde43c908d20229 | 10.26434/chemrxiv-2025-17w5j | Improved Solubility Predictions in scCO2 Using Thermodynamics-Informed Machine Learning Models | Accurate solubility prediction in supercritical carbon dioxide (scCO2) is crucial for optimizing experimental design by eliminating unnecessary and costly trials at an early stage, thereby streamlining the workflow. A comprehensive solubility database containing 31975 records has been compiled, providing a foundation for developing predictive models applicable to a diverse class of chemical compounds, with a particular focus on drug-like substances. In this study, we propose a Domain-Aware Machine Learning approach that incorporates thermodynamic properties governing phase transitions to solubility predictions in scCO2. Predictive models were developed using the CatBoost algorithm and a graph-based architecture employing directed message passing to identify the most effective approach. Furthermore, auxiliary properties of the solute, including melting point, critical parameters, enthalpy of vaporization, and Gibbs free energy of solvation, were predicted as part of this work. The findings underscore the efficacy of incorporating domain-specific thermodynamic features to enhance the predictive accuracy of scCO2 solubility modeling. The interpretation and the applicability domain assessment have confirmed the qualitative selection of the employed descriptors, demonstrating their ability to generalize to unique compounds that fall outside the defined domain. | Dmitriy Makarov; Nikolai Kalikin; Yury Budkov; Pavel Gurikov; Sergey Kruchinin; Abolghasem Jouyban; Michael Kiselev | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af08696dde43c908d20229/original/improved-solubility-predictions-in-sc-co2-using-thermodynamics-informed-machine-learning-models.pdf |
64c3e60b9ed5166e93a08736 | 10.26434/chemrxiv-2023-jqhg1-v2 | Maximizing single-pass conversion does not result in practical readiness for CO2 reduction electrolyzers | To integrate electrochemical CO2 reduction into the chemicals industry at scale, the outlet streams from CO2 electrolyzers must be product rich. Single-pass conversion is becoming increasingly common as a performance benchmark for CO2 electrolyzers because it suggests concentrated products and reduced separation energy for many catalytic processes. However, our analysis shows that CO2R reactor configurations that maximize single-pass conversion currently suffer from low product concentration in the outlet stream. This is because they restrict CO2 flow or operate in acidic cathode environments, which promote considerable hydrogen evolution as a side reaction. For any gas products besides syngas, high single-pass conversion does not signify that separation energy losses have been eliminated, or that product streams are directly suitable as feedstocks for downstream processes. We therefore recommend that researchers targeting CO2R scaleup report product concentrations rather than relying on single-pass conversion as an indicator of overall performance. Maximizing product concentration is a more meaningful target than maximizing single-pass conversion. | Shashwati da Cunha; Joaquin Resasco | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c3e60b9ed5166e93a08736/original/maximizing-single-pass-conversion-does-not-result-in-practical-readiness-for-co2-reduction-electrolyzers.pdf |
60fc07bd171fc7a0adb87039 | 10.26434/chemrxiv-2021-9w3tc | De novo drug design using reinforcement learning with graph-based deep generative models | Machine learning methods have proven to be effective tools for molecular design, allowing for efficient exploration of the vast chemical space via deep molecular generative models. Here, we propose a graph-based deep generative model for de novo molecular design using reinforcement learning. We demonstrate how the reinforcement learning framework can successfully fine-tune the generative model towards molecules with various desired sets of properties, even when few molecules have the goal attributes initially. We explored the following tasks: decreasing/increasing the size of generated molecules, increasing their drug-likeness, and increasing protein-binding activity. Using our model, we are able to generate 95% predicted active compounds for a common benchmarking task, outperforming previously reported methods on this metric. | Sara Romeo Atance; Juan Viguera Diez; Ola Engkvist; Simon Olsson; Rocío Mercado | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fc07bd171fc7a0adb87039/original/de-novo-drug-design-using-reinforcement-learning-with-graph-based-deep-generative-models.pdf |
60d6a968e21133e145e0d70c | 10.26434/chemrxiv-2021-320dd | Modulating the Conductance in Graphene Nanoribbons with Multi-Barriers Under an Applied Voltage | The electronic transmission and conductance produced by Dirac electrons in an armchair graphene nanoribbon under an external voltage are investigated with the transfer matrix method. We investigate the velocity and voltage of nanoribbons in the presence of single and multiple barriers and show that the transmission coefficients can be controlled by varying the order of the mode, the number of carbon atoms, and the barrier velocities. In particular, we find that the nanoribbon appears to be fully transparent when the barrier and Fermi velocities are equal. Our numerical results show that the electronic conductance is sensitive to the applied external voltage and number of carbon atoms, which can be used to tailor the electronic properties of graphene-based devices. | Hassen Dakhlaoui; Shaffa Almansour; Walid Belhadj; Bryan Wong | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Carbon-based Materials; Nanodevices; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d6a968e21133e145e0d70c/original/modulating-the-conductance-in-graphene-nanoribbons-with-multi-barriers-under-an-applied-voltage.pdf |
60c740a49abda2fdc5f8bd3a | 10.26434/chemrxiv.7798973.v1 | Site-Specific Protein Covalent Attachment to Nanotubes and Its Electronic Impact on Single Molecule Function | <p>Functional
integration of proteins with carbon-based nanomaterials such as nanotubes holds
great promise in emerging electronic and optoelectronic applications. Control over protein attachment
poses a major challenge for consistent and useful device fabrication,
especially when utilizing single/few molecule properties. Here, we exploit
genetically encoded phenyl azide photochemistry to define the direct covalent
attachment of three different proteins, including the fluorescent protein GFP, to
carbon nanotube side walls. Single molecule fluorescence revealed that on
attachment to SWCNTs GFP’s fluorescence changed in terms of intensity and
improved resistance to photobleaching; essentially GFP is fluorescent for much
longer on attachment. The site of attachment proved important in terms of
electronic impact on GFP function, with the attachment site furthest from the
functional center having the larger effect on fluorescence. Our approach
provides a versatile and general method for generating intimate protein-CNT
hybrid bioconjugates. It can be potentially applied easily to any protein of
choice; attachment position and thus interface characteristics with the CNT can
easily be changed by simply placing the phenyl azide chemistry at different
residues by gene mutagenesis. Thus, our approach will allow consistent
construction and modulate functional coupling through changing the protein attachment
position.</p> | Adam Beachey; Harley Worthy; William David Jamieson; Suzanne Thomas; Benjamin Bowen; J. Emyr Macdonald; Martin Elliott; Oliver K. Castell; Dafydd Jones | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740a49abda2fdc5f8bd3a/original/site-specific-protein-covalent-attachment-to-nanotubes-and-its-electronic-impact-on-single-molecule-function.pdf |
65004eceb338ec988a5918e1 | 10.26434/chemrxiv-2023-c13md-v2 | The Chemical Bond in the Di-Atomics, HX, where X = F,O,N,C,B,Be: Orbital Exchange Calculations | This paper extends orbital exchange method calculations to include the series of di-atomic molecules, HX, where X = F,O,N,C,B and Be. In these molecules the hydrogen (H) can bond as both spin up and spin down with the two sigma electrons on X, thereby increasing the extent of bonding versus the normal single bond. The F,O,N and C of the HX molecules exhibit an [HX,H+X-] sigma resonance with the species in (0.75,0.25) proportion. The impact of this sigma resonance, in conjunction with the H spin up/down character, on the orbital overlaps and the bond energy is quantified. The molecules HB and HBe, while not showing resonance, do exhibit dual bonding resulting from the H spin up/down characteristic. The bond length results are within 0.006 Angstrom units of experiment. Dipole moments, that have been measured for the F,O,N and C molecules, are within 0.03 Debye of experiment. Bond energies are accurate to 0.1 electron volt. Precise bond energies are not obtained because of the difficulty in precisely defining the H orthogonalization parameters. | Paul Merrithew | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65004eceb338ec988a5918e1/original/the-chemical-bond-in-the-di-atomics-hx-where-x-f-o-n-c-b-be-orbital-exchange-calculations.pdf |
67707c6e81d2151a023a4837 | 10.26434/chemrxiv-2024-m9xgc-v2 | Advancing Multiscale Molecular Modeling with Machine Learning-Derived Electrostatics | We introduce an innovative machine learning (ML)-based framework for multiscale molecular modeling, in which the ML subsystem is treated as an electrostatic entity interacting with its molecular mechanics (MM) environment through classical electrostatics. The integration of ML accuracy with multiscale modeling is accomplished by leveraging the capabilities of the ANI neural networks to predict geometry-dependent atomic partial charges at the Minimal Basis Iterative Stockholder (MBIS) level, going beyond static mechanical embedding. This ML/MM approach can closely approximate state-of-the-art multi-scale quantum-classical (QM/MM) methods while significantly lowering computational requirements, thereby facilitating more efficient and precise simulations in computational chemistry. The method requires no additional training beyond the initial model setup and is integrated into Amber, one of the most widely used software suites for molecular modeling, ensuring accessibility to the broader community. We validate its performance across a variety of challenging applications, including solvation structure, vibrational spectra, torsion free energy profiles, and protein-ligand interactions, achieving excellent agreement with QM/MM benchmarks. This framework not only advances the frontiers of multiscale modeling but also showcases the potential of machine learning to achieve quantum-level accuracy with exceptional efficiency for complex chemical systems. | Jonathan A. Semelak; Pickering Ignacio; Kate K. Huddleston; Justo Olmos; Juan S Grassano; Camila Clemente; Salvador I. Drusin; Marcelo Marti; Mariano C. Gonzalez Lebrero; Adrian E. Roitberg; Dario A. Estrin | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67707c6e81d2151a023a4837/original/advancing-multiscale-molecular-modeling-with-machine-learning-derived-electrostatics.pdf |
622f3edb2d837410cf8159d1 | 10.26434/chemrxiv-2022-73wjn | Investigating the Nanostructure of the Stratum Corneum Lipid Matrix: A Combined Neutron Diffraction & Molecular Dynamics Simulations Approach | The human skin provides a physiochemical and biological protective barrier to the body due to the unique structure of its outermost layer the stratum corneum. This layer consists of corneocytes and a multi-lamellar lipid matrix forming a composite, which mainly determines the barrier function of the stratum corneum. A substantiated understanding of this barrier is necessary, as controlled breaching or modulation of the same is also essential for many topical drug delivery and personal care applications.
In this study, we have discussed the state-of-the-art of neutron diffraction techniques (using specifically deuterated lipids) for stratum corneum lipid analysis and combined it with the information obtained from molecular dynamics simulations, to understand the structure and barrier function of the stratum corneum.
As an example, the effect of ceramide concentration on a lipid lamella system consisting of CER[NP]/CER[AP]/Cholesterol/free fatty acid is studied. This study demonstrates the usefulness of the combined approach of neutron diffraction and molecular dynamics simulation for effective analysis of the skin lipid systems. The optimization of force fields by comparison with experimental data is furthermore an important step in the direction of providing a predictive quality. | Yogesh Badhe; Thomas Schmitt; Rakesh Gupta; Beena Rai; Reinhard H H Neubert | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622f3edb2d837410cf8159d1/original/investigating-the-nanostructure-of-the-stratum-corneum-lipid-matrix-a-combined-neutron-diffraction-molecular-dynamics-simulations-approach.pdf |
60c7475eee301ce216c796a6 | 10.26434/chemrxiv.11637759.v1 | Continuous Flow Synthesis of ZIF-8 Biocomposites with Tuneable Particle Size | Zeolitic Imidazolate Framework (ZIF) biocomposites show the capacity to protect and deliver bio-therapeutics. To date, the progress in this research area is based on laboratory batch methods. To further explore the potential of ZIF-biocomposites for application to biomedicine and biotechnology, the continuous production of ZIF-biocomposites of specific particle size is desirable. We report the first continuous flow synthetic method for the encapsulation of a model protein (BSA) and a clinical therapeutic (α1-antitrypsin, AAT) in ZIF-8. We studied the in situ kinetics of nucleation, growth and crystallization of BSA-ZIF-8 by SAXS. By controlling the injection time of ethanol, we could quench the particle growth via ethanol-induced crystallization. The particle size of the biocomposite was tuned in the 40-100 nm range by varying residence time prior to introduction of ethanol.<br /> | Francesco Carraro; Jason D. Williams; Mercedes Linares-Moreau; chiara parise; Weibin Liang; Heinz Amenitsch; Christian Doonan; C. Oliver Kappe; paolo falcaro | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7475eee301ce216c796a6/original/continuous-flow-synthesis-of-zif-8-biocomposites-with-tuneable-particle-size.pdf |
60c754b8bdbb897172a3a6e0 | 10.26434/chemrxiv.13719649.v1 | Multifunctional Inhibitor Mixture for Reducing Bacteria Growth and Corrosion on Marine Grade Steel | <p><a></a>High strength steel in marine
environments suffers from severe corrosion susceptibility and the presence of
bacteria can exacerbate the effect, accelerating degradation via
microbiologically influenced corrosion (MIC). Here we propose a novel approach
to MIC inhibition by designing a system capable of limiting the effects of both
bacteria growth and corrosion. The combination of a newly synthesised compound,
cetrimonium 4-hydroxycinnamate, with lanthanum 4-hydroxycinnamate was the only
system tested to date that could both inhibit abiotic corrosion in artificial
seawater and minimise bacteria consortium densities over an exposure period of
24 hours. </p>
<p>The electrochemical data for the La+Cet mixture demonstrated
the significant inhibition of both abiotic corrosion to a level similar to
La(4OHCin)<sub>3</sub>, as well as the ability to reduce bacteria densities of
single strains and a consortium. This is unlike the La+CetNal mixture which
accelerated abiotic corrosion and the La+IMI which had an insignificant effect
on microbial densities (Catubig et al. 2020). </p>
<p>A compatible mixture of ionic inhibitors was achieved by
using the same cinnamate anion. </p>
<p>This mixture of Cet-4OHCin and La(4OHCin)<sub>3</sub>
demonstrated significant abiotic corrosion inhibition and bacteria density
reductions, making it a strong candidate as an MIC inhibitor system for 80HLES.
</p>
<p>The Cet-4OHCin compound and its mixture with La(4OHCin)<sub>3</sub>
retained relatively low sensitivity towards skin and intestinal cells, making
it a safer and more attractive alternative than other more hazardous corrosion
inhibitor materials. </p> | Rainier Catubig; Agnes Michalczyk; Wayne Neil; Grant McAdam; John Forsyth; Mahdi Ghorbani; Ruhamah Yunis; Leigh Ackland; Maria Forsyth; Anthony Somers | Biochemistry; Environmental biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754b8bdbb897172a3a6e0/original/multifunctional-inhibitor-mixture-for-reducing-bacteria-growth-and-corrosion-on-marine-grade-steel.pdf |
6157059cd1fc336090fad4bb | 10.26434/chemrxiv-2021-7pz5m | High-entropy intermetallics serve an ultrastable single-atom Pt for propane dehydrogenation | Propane dehydrogenation (PDH) has been a promising propylene production process that can compensate for the increasing global demand for propylene. However, Pt-based catalysts with high stability at ≥600°C have barely been reported because the catalysts typically result in short catalyst life owing to side reactions and coke formation. Herein, we report a new class of heterogeneous catalysts using high-entropy intermetallics (HEIs). Pt–Pt ensembles, which cause side reactions, are entirely diluted by the component inert metals in PtGe-type HEI; thereby, unfavorable side reactions are drastically inhibited. The resultant HEI: (PtCoCu)(GeGeSn)/Ca–SiO2 exhibited an outstandingly high catalytic stability, even at 600°C (kd−1 = τ = 4146 h = 173 d), and almost no deactivation of the catalyst was observed two months for the first time. | Yuki Nakaya; Eigo Hayashida; Hiroyuki Asakura; Ken-ichi Shimizu; Shinya Furukawa | Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6157059cd1fc336090fad4bb/original/high-entropy-intermetallics-serve-an-ultrastable-single-atom-pt-for-propane-dehydrogenation.pdf |
62bc7adf52acb7793b77cd1d | 10.26434/chemrxiv-2022-wjsd9 | A Stereoselective Photoinduced Cycloisomerization Inspired by Ophiobolin A | A concise, modular, and stereoselective synthetic entry point to the 5-8-5 carbocyclic core of the ophiobolins is described. This strategy exploits the chiral tertiary alcohol of ophiobolin A to guide assmebly of the 5-8-5 scaffold in a single step via photoinitiated isomerization. Mechanistic insights into the origin of stereocontrol in this reaction are described, as are efforts to elaborate the resultant 5-8-5 polycycle to the pharmacophore of ophiobolin A. | James Law; Daniel Callen; Elena Paola; Gabe Gomes; James Frederich | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62bc7adf52acb7793b77cd1d/original/a-stereoselective-photoinduced-cycloisomerization-inspired-by-ophiobolin-a.pdf |
621c382d011b586c35b7aea9 | 10.26434/chemrxiv-2022-5mcgj | Defluorinative Carboimination of Trifluoromethyl Ketones | The monofunctionalized carbodefluorination of readily accessible CF3 groups is acknowledged as an attractive approach to the preparation of partially fluorinated molecules. However, their defluorinative difunctionalization remains a challenging and unmet goal. Herein, we report an
unprecedented defluorinative carboimination of trifluoromethyl ketones via a strategy of silver
carbene-initiated rearrangement, in which both C–F bond and carbonyl group of the trifluoromethyl ketones were functionalized simultaneously, thus providing a straightforward synthetic method for medicinally relevant α,α-difluoroimines. The current approach involves a
silver carbene-initiated intramolecular cascade process by integrating successive cleavage of C–F bond and formation of C–C and C=N bonds on a single molecule entity, which differs relevantly from the stepwise mechanism of reported carbodefluorination of CF3 groups. Mechanistic studies
disclose that silver catalysis plays a critical role, particularly in the stages of C–F bond cleavage
and aza-Claisen rearrangement. | Xiaolong Zhang; Yongquan Ning; Zhaohong Liu; Shuang Li; Giuseppe Zanoni; Xihe Bi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621c382d011b586c35b7aea9/original/defluorinative-carboimination-of-trifluoromethyl-ketones.pdf |
6534c6f5c3693ca993d92d94 | 10.26434/chemrxiv-2023-33vmf | Simultaneous Extraction of Intra- and Inter-Cycle Features for Predicting Lithium-Ion
Battery's Knees Using Convolutional and Recurrent Neural Networks | Early and accurate prediction of their degradation behavior helps investigate the lifespan of lithium-ion batteries (LIBs). Charge-discharge cycling data can be used for this purpose, but simultaneous feature extraction regarding LIB’s intra- and inter-cycle behavior, despite its importance, has not been thoroughly investigated. In this study, machine learning methods are proposed to facilitate the simultaneous extraction of intra- and inter-cycle features from VIT cycling datasets for the knees prediction of LIBs. The length of each cycling data is made the same by realigning the data in terms of voltage or using zero-padding, depending on the type of dataset used. The cycling dataset is arranged as an array along the time and cycle axes before applying convolutional neural networks (CNNs) and/or recurrent neural networks (RNNs) for feature extraction. Three ways to use these nonlinear regression tools are explored, which are 2-dimensional CNN (2D CNN), RNN + 1-dimensional CNN (1D CNN), and RNN + 2D CNN. The performances of the resulting knees prediction models are evaluated using the benchmark dataset. Our results confirm the benefit of explicitly considering cycle-to-cycle behavior in conjunction with intra-cycle temporal behavior in building the data-driven prediction model. The possibility of reducing the input data requirement is examined to facilitate the early prediction of knees. It is shown that the input size can be reduced down to the first 60 cycles from 100 cycles with comparable prediction performance. | Jaewook Lee; Jay H. Lee | Energy; Chemical Engineering and Industrial Chemistry; Process Control; Quality Control; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6534c6f5c3693ca993d92d94/original/simultaneous-extraction-of-intra-and-inter-cycle-features-for-predicting-lithium-ion-battery-s-knees-using-convolutional-and-recurrent-neural-networks.pdf |
60c74648842e65c002db27b1 | 10.26434/chemrxiv.11299097.v1 | Rapid Quantification of Prion Proteins | <p>Prion
diseases are a group of fatal transmissible neurological conditions caused by
the change in conformation of the normal intrinsic cellular prion protein (PrP<sup>C</sup>)
in to the highly ordered insoluble amyloid state conformer (PrP<sup>SC</sup>). We present a rapid assay using Aptamers and Resistive Pulse
Sensing, RPS, to extract and quantify proteins from complex sample matrices, demonstrate
with the quantification of PrP<sup>c</sup>. We functionalise the surface
of superparamagnetic beads, SPBs, with a DNA aptamer. First SPB’s termed
P-Beads, are used to pre-concentrate the analyte from a large sample volume.
The PrP<sup>c</sup> protein is then eluted from the P-Beads before aptamer
modified sensing beads, S-Beads, are added. The velocity of the S-Beads
through the nanopore reveals the concentration of the PrP<sup>c</sup> protein. The
process is done in under an hour and allows the detection of picomol’s of
protein. The technique could be easily adopted to the mutated version of the
protein and integrated into clinical workflows for the screening of blood
donations and transfusions. </p> | Matthew Healey; Muttuswamy Sivakumaran; Mark Platt | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74648842e65c002db27b1/original/rapid-quantification-of-prion-proteins.pdf |
670535a151558a15ef80eec6 | 10.26434/chemrxiv-2024-dd245 | Novel Analytical Toolkit Concept for the Characterization and Development of Halogen Free Flame Retardants (HFFR): A case study with P and P-N based Flame Retardants. | This study presents a novel toolkit concept for the characterization and development of halogen-free flame-retardant (HFFR) specially based on P and P-N flame retardant systems, aimed at understanding and predicting the influence of flame-retardant additives in polymers especially polyolefins. The development of this toolkit concept is based on the existing research on flame-retardant mechanisms. From a comprehensive literature survey, we identified several key parameters that control the flammability of materials. This toolkit concept includes several analytical techniques to quantitatively measure these parameters.
The primary parameters influencing the flammability of polymer materials are found to be the surface ignition temperature, thermal degradation kinetics, total amount of volatiles produced during combustion, chemical composition of the volatiles, and the presence of flame retardants, particularly phosphorus and phosphorus-nitrogen-based derivatives (PFR), in the gas phase, condensed phase, or in both.
This paper presents our findings on surface ignition temperature (Tign) and kinetic degradation parameters such as Arrhenius activation energy (Ea) and frequency factor (A) from Thermo-Gravimetric Analysis (TGA)/SDTA) measurements. Additionally, we report the Total Volatile Organic Compounds (TVOC) produced during combustion, determined using Thermal Desorption (TD)/Gas Chromatography (GC)/Mass Spectrometry (MS) techniques, and the chemical composition of the volatiles identified through MS analysis of GC chromatograms for several model HFFR polypropylene (PP) formulations containing phosphorus (P) or phosphorus-nitrogen (P-N) based derivatives (PFR). The presence of flame retardants in the gas or condensed phase, and their activity in either phase or both, was determined using Inductively Coupled Plasma (ICP) and Surface Focussed Mass Spectrometer (SFMS).
In this report, the validity of the analytical results from this toolkit concept is also presented for several model formulations by comparing the analytical results with fire retarding properties of these model formulations with standard UL-94V fire tests. Applicability of this toolkit was demonstrated by investigating the influence for a proprietary additive, Paxymer® in these HFFR systems.
| Swaraj Paul | Analytical Chemistry; Chemical Engineering and Industrial Chemistry; Analytical Chemistry - General; Analytical Apparatus; Quality Control | CC BY 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670535a151558a15ef80eec6/original/novel-analytical-toolkit-concept-for-the-characterization-and-development-of-halogen-free-flame-retardants-hffr-a-case-study-with-p-and-p-n-based-flame-retardants.pdf |
65410eb548dad23120c6f203 | 10.26434/chemrxiv-2023-rdkn3 | Manipulating the electronic properties and structure of MoO3 nanosheets with light via an excited-state proton transfer mechanism | Light is an attractive source of energy to regulate stimuli-responsive chemical systems, enabling control over chemical and physical processes. Here, we use light as a gating source to control the redox state, the formation of a localized surface plasmonic resonance (LSPR), and the structure of molybdenum oxide (MoO3) nanosheets, which are important for a wide array of applications. However, the light excitation is not of the MoO3 nanosheets but rather of a pyranine (HPTS) photoacid, which in turn undergoes an excited state proton transfer (ESPT) process. We show that the ESPT process from HPTS to the nanosheets and the intercalation of protons within the MoO3 nanosheets triggers the reduction of the nanosheets and the formation of an LSPR peak, a process that is reversible, meaning that in the absence of light, the LSPR peak disappears and the nanosheets return to their oxidized form. We further show that this reversible process is accompanied by a change in the nanosheet size and morphology. | Yuval Gilad Barzilay; Anna Yucknovsky; Nadav Amdursky | Physical Chemistry; Nanoscience; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65410eb548dad23120c6f203/original/manipulating-the-electronic-properties-and-structure-of-mo-o3-nanosheets-with-light-via-an-excited-state-proton-transfer-mechanism.pdf |
664b4faa91aefa6ce182dc37 | 10.26434/chemrxiv-2023-nbplp-v2 | Modelling interactions between rubidium atom and magnetometer cell wall molecules | Magnetometer cell wall coat molecules play an important role in preserving the life-time of pumped alkali metal atoms for use in magnetometers that are capable of measuring very small magnetic fields. The goal of this study is to help rationalise the design of the cell coat molecules. Rubidium-87 is studied in terms of its interaction with three template cell coat molecules; ethane, ethene and methyltrichlorosilane (MeTS). Ab initio electronic structure methods are applied to investigate the effect that the coat molecules have on the 2S ground state and 2P excited state of 87Rb. We find that, from the ab initio results, the three template molecules have differing effects with MeTS having the largest effect on the ground state and ethane or ethene having the largest effect on the non-degenerate excited states. | Gregoire David; Andrew M. Teale; David M. Rogers | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Coating Materials; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664b4faa91aefa6ce182dc37/original/modelling-interactions-between-rubidium-atom-and-magnetometer-cell-wall-molecules.pdf |
67bd1094fa469535b9c9edda | 10.26434/chemrxiv-2024-cm32m-v2 | From C-F Activation to Catalytic Regioselective Hydrodefluorination of Pyridines with a Bench-Stable Nickel Complex | The nickel(0) complex [Ni(iPrPN)(COD)] (iPrPN = 2-[(N-diisopropylphosphino)methylamino]pyridine, COD = 1,5-cyclooctadiene) was an efficient precatalyst for the hydrodefluorination of pyridines employing pinacolborane (HBPin). 2-fluoro and 2,6-difluoropyridines were hydrodefluorinated at the 2- and 6-positions under mild condi-tions. Mechanistic experiments allowed to identify COD decoordination followed by C-F activation as the catalyst en-try pathway to the cycle and the [Ni(iPrPN)(COD)] complex as the catalyst resting-state. The Ni(II) fluoride complex, [NiF(iPrPN)(6-Fpy)] (6-Fpy = 6-fluoropyrid-2-yl), was identified as an intermediate in the cycle and a bench-stable precatalyst for the process. | Victor Duran Arroyo; Roger Nunez; Rebeca Arevalo | Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Bond Activation; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bd1094fa469535b9c9edda/original/from-c-f-activation-to-catalytic-regioselective-hydrodefluorination-of-pyridines-with-a-bench-stable-nickel-complex.pdf |
67bc1a166dde43c90834a429 | 10.26434/chemrxiv-2025-9fk9f | Total synthesis of 1’-epi-septosones B and C and the originally assigned structures of spiroetherones A and B | Septosones B and C and spiroetherones A and B are two pairs of polycyclic avavane-type meroterpenoids which possess the same distinctive spiro[4.5]decane backbone but opposite orientations and exhibit promising biological activity. We report here the total synthesis of 1’-epi-septosones B and C and the originally assigned structures of spiroetherones A and B through an unusual stereospecific 1,2-alkyl migration of a 6/6 fused dienone tertiary alcohol to a spiro[4.5] enedione scaffold, which also led to the structural revision of spiroetherones A and B. More importantly, two new compounds were found to exhibit significant anticancer activity against Hep G2, MV-4-11, and MOLT-4 cell lines with IC50 value as low as 2.1 µM through bioactivity profiling of the synthetic advanced intermediates. | Qunlong Zhang; Jingyi Kang; Tiancheng Tan; Guanjun Dong; Jianwei Chen; Zhaoyong Lu | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc1a166dde43c90834a429/original/total-synthesis-of-1-epi-septosones-b-and-c-and-the-originally-assigned-structures-of-spiroetherones-a-and-b.pdf |
669814f95101a2ffa8a6c92f | 10.26434/chemrxiv-2024-phhx1 | Mastering the Use of Nanoprobes Beamlines for Electrochemistry: The Importance of Tracking Radiation Damage and Exploring Material Heterogeneity | Electrochemistry plays a crucial role in addressing energy transition challenges, with synchrotron radiation (SR) significantly enhancing the understanding of electrochemical systems. SR's importance has grown with the advent of fourth-generation synchrotron facilities, which offer specialized beamlines for spatially-resolved studies of nanomaterials. These facilities enable novel techniques, but also introduce challenges, especially with the need for high brilliance and potential radiation damage to samples. In addition, nanoscale spatial resolution allows detailed examination of material heterogeneity linking properties like morphology and electronic state to overall activity and, in some cases, an increase in sensitivity. However, this also raises issues of representativeness in data analysis and presentation. In this work, we discuss these two topics. First, we illustrate the importance of tracking radiation damage via control experiments in electrochemistry using fourth-generation beamlines. Then, we show the advantages/disadvantages of nanoscale analysis in enhancing XAS sensitivity, emphasizing the importance of careful data interpretation and communication to avoid misleading information. | Pablo Fernandez; Rafael Vicente; Itamar Neckel | Physical Chemistry; Catalysis; Electrocatalysis; Physical and Chemical Properties; Radiation; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669814f95101a2ffa8a6c92f/original/mastering-the-use-of-nanoprobes-beamlines-for-electrochemistry-the-importance-of-tracking-radiation-damage-and-exploring-material-heterogeneity.pdf |
60c74351567dfe5183ec40a8 | 10.26434/chemrxiv.9037475.v1 | Enhanced Sol-Gel Production and Robocasting for Artificial Photosynthesis | In this study, a titanium based Sol-Gel solution was derived using a rotary evaporator. By rapidly removing solvents, this tool significantly decreased the time needed to polymerize the solution and drastically accelerated the Sol-Gel process. The original intent of this experiment was to investigate the Sol-Gel's properties as a photocatalyst, however improvements to the materials synthesis took precedence. The properties of this Sol-Gel were also observed in a simple desktop 3D printer. The printers traditional thermoplastic nozzle was modified with a syringe to extrude the highly viscous Sol-Gel into basic shapes and lines. | Frank Parsons; Ben Caroway | Catalysts; Polymerization (Polymers); Inorganic Acid/Base Chemistry; Polymers; Photocatalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74351567dfe5183ec40a8/original/enhanced-sol-gel-production-and-robocasting-for-artificial-photosynthesis.pdf |
66e47536cec5d6c142f8d45e | 10.26434/chemrxiv-2024-2npx7 | Scalable electrocatalyzed formation of C–O bonds using flow reactor technology | The development of modular and robust synthetic routes that can serve both in medicinal and process chemistry setting is rare. Generally, highly modular medicinal chemistry routes are too hazardous and expensive to be translated into a process chemistry environment. Taking the case study of delamanid, a pharmaceutical compound used for multidrug-resistant tuberculosis treatment, the development of a sustainable and modular but scalable synthesis of C–O bonds via electrocatalytic method is presented. In this work, the electrochemical batch reaction was studied, addressing critical reproducibility issues related with the process. Furthermore, the reaction was successfully translated to a flow elec-trochemical reactor design, which allowed the use of carbon felt electrodes. The high modularity of the protocol was demonstrated by the synthesis of 11 different examples, while the scalability of the reaction was proven by a gram scale preparation of a key intermediate for the synthesis of delamanid. | Michael Prieschl; David Cantillo; C. Oliver Kappe; Gabriele Laudadio | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e47536cec5d6c142f8d45e/original/scalable-electrocatalyzed-formation-of-c-o-bonds-using-flow-reactor-technology.pdf |
65773b457acf130c3200dbce | 10.26434/chemrxiv-2023-zbtlg-v2 | Following structural changes in iridium nanoparticles during oxygen evolution electrocatalysis with operando X-ray total scattering | Understanding the structure of nanoparticles under (electro)catalytic operating conditions is crucial for uncovering structure-property relationships. By combining operando X-ray total scattering and PDF analysis with operando small angle X-ray scattering, we obtain comprehensive structural information on ultra-small (< 3 nm) iridium nanoparticles and track their changes during the acidic oxygen evolution reaction. When subjected to electrochemical conditions at reducing potentials, the metallic Ir nanoparticles are found to be decahedral clusters. Upon electrochemical oxidation, iridium oxide forms, containing small rutile-like clusters composed of edge- and corner-connected [IrO6] octahedra of very confined range. These rutile domains are less than 1 nm. Combined with SAXS analysis of the particle size, we find that the iridium oxide phase active in the oxygen evolution reaction (OER) lacks crystalline order. | Rebecca Pittkowski; Stefanie Punke; Andy S. Anker; Aline Bornet; Nicolas Magnard; Nicolas Schlegel; Marta Mirolo; Jakub Drnec; Jacob J. K. Kirkensgaard; Matthias Arenz; Kirsten M. Ø. Jensen | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Electrocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65773b457acf130c3200dbce/original/following-structural-changes-in-iridium-nanoparticles-during-oxygen-evolution-electrocatalysis-with-operando-x-ray-total-scattering.pdf |
60c7581c469df4922cf4559c | 10.26434/chemrxiv.14501436.v1 | Iron-Catalyzed Cross-Coupling of Thioesters and Organomanganese Reagents | We report a Fukuyama-type coupling of thioesters
with aliphatic organomanganese reagents utilizing a cheap and easily available
iron(III) catalyst. The reactions exhibit a wide tolerance of solvents and
functional groups (e.g. ketones, esters, aryl(pseudo)halides) allowing for the conversion
of thioesters derived from natural products and pharmaceutical compounds. Investigations
showed a strong steric influence from each reaction component (carboxylic
moiety, thiol substituent and manganese reagent), which enabled regioselective
transformation of dithioesters. Tandem transformations combining the coupling
with an additional step were observed. Our experiments provide insights into
the potential of the employed aliphatic manganese reagents, such as the interaction
between iron, manganese and oxygen, which allows for a smooth conversion. | Valentin Jacob Geiger; Ivana Fleischer | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7581c469df4922cf4559c/original/iron-catalyzed-cross-coupling-of-thioesters-and-organomanganese-reagents.pdf |
6789436e81d2151a026cdc3d | 10.26434/chemrxiv-2025-2htdh | Data Efficient Molecular Image Representation Learning using Foundation Models | Deep learning (DL) in chemistry has made significant progress, yet its applicability is limited by the scarcity of large, labeled datasets and the difficulty of extracting meaningful molecular features. Recently, molecular representation learning (MRL) has emerged as a powerful approach to these challenges by decoupling feature extraction and property prediction. In MRL, a deep network is first trained to learn molecular features from large, unlabeled datasets and then finetuned for property prediction in smaller, specialized domains. The advent of foundation models, which are large models trained on diverse datasets capable of addressing various downstream tasks, has also transformed the field of DL. For example, large language models (LLMs) like OpenAI’s GPT-4 can be finetuned with minimal additional data for tasks considerably different from their training. While MRL methods have been widely applied across chemical applications, these models are typically trained from scratch on molecular data. This study proposes that foundation models can serve as an advantageous starting point for developing MRL models. We explore this idea by leveraging OpenAI's CLIP vision foundation model as the backbone for MoleCLIP, a molecular image representation learning framework. On standard benchmarks, MoleCLIP requires significantly less molecular pretraining data to match the performance of state-of-the-art models. Furthermore, MoleCLIP outperformed existing models on homogeneous catalysis datasets, emphasizing its robustness to distribution shifts, which allows it to adapt effectively to varied tasks and datasets. This successful application of a general foundation model to chemical tasks highlights the potential of innovations in DL research to advance synthetic chemistry and, more broadly, any field where molecular property description is central to discovery. | Yonatan Harnik; Hadas Shalit Peleg; Amit Bermano; Anat Milo | Theoretical and Computational Chemistry; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6789436e81d2151a026cdc3d/original/data-efficient-molecular-image-representation-learning-using-foundation-models.pdf |
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