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65bb448166c1381729b7ad9f | 10.26434/chemrxiv-2024-gqb5j | Terpolymerization of Elemental Sulfur Waste with Propylene Oxide and Carbon Disulfide as a
Strategy where Copolymerization fails | Elemental sulfur, a waste product of the oil
refinement process, represents a promising raw material for
the synthesis of degradable polymers. We show that simple
lithium alkoxides facilitate the polymerisation of elemental
sulfur S8 with industrially relevant propylene oxide (PO) and
CS2 (a base chemical sourced from waste S8 itself) to give
poly(monothiocarbonate-alt-Sx) in which x can be controlled
by the amount of supplied sulfur. The in-situ generation of
thiolate intermediates obtained by a rearrangement, which
follows CS2 and PO incorporation, allows to combine S8 and
epoxides into one polymer sequence that would otherwise
not be possible. Mechanistic investigations reveal that alkyl
oligosulfide intermediates from S8 ring opening and sulfur
chain length equilibration represent the better nucleophiles
for inserting the next PO if compared to the trithiocarbonates
obtained from the competing CS2 addition, which causes
the sequence selectivity. The polymers can be crosslinked
in-situ with multifunctional thiols to yield reprocessable and
degradable networks. Our report demonstrates how
mechanistic understanding allows to combine intrinsically
incompatible building blocks for sulfur waste utilisation. | Cesare Gallizioli; David Battke; Helmut Schlaad; Peter Deglmann; Alex Plajer | Polymer Science | CC BY 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bb448166c1381729b7ad9f/original/terpolymerization-of-elemental-sulfur-waste-with-propylene-oxide-and-carbon-disulfide-as-a-strategy-where-copolymerization-fails.pdf |
634a258b339972a2e58b67cc | 10.26434/chemrxiv-2022-6bjc9 | Epitaxial thin film of high entropy oxide as electrocatalyst for oxygen evolution reaction | High entropy oxides (HEOs), which contain multiple elements in the same crystallographic site, are a promising platform for electrocatalysis in oxygen evolution reaction (OER). However, to date, all OER studies involving HEOs have used it in polycrystalline bulk form. In this study, the OER activity of a set of single crystalline thin films of (La0:2Pr0:2Nd0:2Sm0:2Eu0:2)NiO3, grown on NdGaO3
substrates have been investigated. The OER activity increases with the thickness of the film. X-ray absorption
spectroscopy measurements find an increase in Ni d-O p covalency and a decrease in charge transfer energy with the increase in film thickness. These facilitate higher charge transfer between Ni and surface absorbates, resulting in higher OER activity. However, the epitaxial stabilization of
thicker film becomes difficult due to the requirement of +3 oxidation state of Ni and the OER activity of a 75 unit cell thick film is found to be the optimal in the present study. This work demonstrates that the thickness of perovskite oxides can be used as a parameter to enhance OER activity. | Ranjan Kumar Patel; Ramesh Naidu Jenjeti; Rajat Kumar; Nandana Bhattacharya; Christoph Klewe; Padraic Shafer; S. Sampath; Srimanta Middey | Materials Science; Catalysis; Thin Films; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634a258b339972a2e58b67cc/original/epitaxial-thin-film-of-high-entropy-oxide-as-electrocatalyst-for-oxygen-evolution-reaction.pdf |
63134e58faf4a41831054e98 | 10.26434/chemrxiv-2022-snxxm | Engineering enzyme substrate scope complementarity for promiscuous cascade synthesis | Biocatalytic cascades are uniquely powerful for the efficient, asymmetric synthesis of bioactive compounds. The high specificity of enzymes can enable one-pot reactions where the substrates, intermediates, and products react only with the intended enzyme. However, this same specificity can hinder the substrate scope of biocatalytic cascades because each constituent enzyme requires complementary activity. Here, we implement a substrate multiplexed screening (SUMS) approach to improve the substrate scope overlap of a two-enzyme cascade via directed evolution. This cascade leverages an L-threonine transaldolase, ObiH, to produce a range of β-OH amino acids that are subsequently decarboxylated to produce chiral 1,2-amino alcohols. Crucially, for the success of this cascade, we engineered a tryptophan decarboxylase to act efficiently on β-OH amino acids while avoiding activity on L-threonine, which is needed for ObiH activity. We leverage this exquisite selectivity with matched substrate scopes to produce a variety of chiral 1,2-amino alcohols in a one-pot cascade from aldehydes or styrene oxides. This route constitutes a new disconnection for the synthesis of β-adrenergic receptor agonists and shows how SUMS can be used to guide the development of promiscuous, C-C bond forming cascades. | Allwin D. McDonald; Samantha K. Bruffy; Aadhishre T. Kasat; Andrew R. Buller | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63134e58faf4a41831054e98/original/engineering-enzyme-substrate-scope-complementarity-for-promiscuous-cascade-synthesis.pdf |
670d0ac312ff75c3a1621aad | 10.26434/chemrxiv-2024-7blcg | EnDiTrap: Pull-down-based pipeline for detection of endocrine-disrupting chemicals | Most environmental matrices contain a diverse range of synthetic and natural compounds, some of which exhibit toxic effects. Nevertheless, current methods often do not provide sufficient resolution and power to specifically identify compounds responsible for the biological effects of the complex environmental mixtures. Here, we present the development of the EnDiTrap pipeline that facilitates the identification of compounds that specifically interact with targets involved in the regulation of the endocrine system. We used heterologously expressed ligand binding domain (LBD) of retinoic acid receptor alpha (RARα) as a model system for pull-down-based pipeline development, consequent optimization, and standardization. The applicability of the EnDiTrap pipeline was validated using standard ligand and tested through a case study with environmental samples of freshwater blooms. Results showed that the EnDiTrap pipeline significantly helps to reduce the number of putative features and facilitates the identification of suspect compounds responsible for observed biological effects. We also compared the performance of the software tools Compound Discoverer and MSDial commonly used for processing and analysis of mass spectrometry data. This comparison provided insight into the impact of different software processing on the outcome that brought interestingly contrasting results. This study enhances our ability to specifically identify effect drivers in environmental mixtures of chemicals. Moreover, the developed EnDiTrap pipeline can be applied to various protein targets thus presenting broad applicability. | Ludek Sehnal; Garry Codling; Marie Smutná; Roman Grabic; Klára Hilscherová | Biological and Medicinal Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Analysis; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670d0ac312ff75c3a1621aad/original/en-di-trap-pull-down-based-pipeline-for-detection-of-endocrine-disrupting-chemicals.pdf |
6750f7f35a82cea2fa061f22 | 10.26434/chemrxiv-2024-143h3 | Assessing the magnitude of multi-site flaring events attributed to supply chain disruptions in oil and gas production basins | Flaring in oil and gas production is used to combust flammable hydrocarbons that otherwise would be vented to the atmosphere. One potential cause of flaring is intermittent disruptions in gas supply chains between oil and gas production sites and gathering and boosting operations. Since gathering and boosting facilities serve multiple production facilities, these types of supply chain disruptions would be expected to cause simultaneous flaring at multiple upstream sites in the regions served by a gathering and boosting facility experiencing a disruption, unless production sites are able to use other gathering and boosting facilities or the production sites immediately shut-in production. To assess the potential magnitude of this type of event, the overall frequency of multiple flares being detected in a localized area (<5 km radius from another flare) was assessed using spatiotemporal patterns in satellite based daily flare detections using the VIIRS Nightfire (VNF) product. Multiple detections in a localized area are unlikely if flaring is caused by independent conditions at individual sites. In contrast, multi-site detections in a localized area may be indicative of potential supply chain disruptions. Hundreds of flares in the Eagle Ford production region in south central Texas that are detected infrequently (<18% observations) were evaluated. For these infrequently detected flares, which account for approximately half of flared gases in the region, 87% had 80-100% of their detections classified as multi-site events. This suggests that efforts to reduce flaring should consider impacts of supply chain disruptions. | Colette Schissel; Erin Tullos; David Allen | Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6750f7f35a82cea2fa061f22/original/assessing-the-magnitude-of-multi-site-flaring-events-attributed-to-supply-chain-disruptions-in-oil-and-gas-production-basins.pdf |
628e09ab809e32f7969c495b | 10.26434/chemrxiv-2022-f2gf6 | Diagonal free processing of conventional phase sensitive COSY using Filter Diagonalization Method |
Diagonal peak suppression of homonuclear multi-dimensional correlation NMR spectra is an area of research that has seen a constant influx of new methods designed to remove the intense but mostly redundant diagonal auto-correlation peaks. These methods, while at their job, aim to retain the intensity, position, lineshape, and sensitivity of the information-rich cross peaks as faithfully as possible. Most of these methods offer some alternative data acquisition scheme that delivers the same correlation information as the original spectrum but with suppressed diagonal peaks. Here we present not an alternative pulse sequence, but a new processing tool based on the Filter Diagonalization Method (FDM) which produces a diagonal free phase-sensitive COSY spectrum from the conventionally acquired data. The method revisits difference spectroscopy but with an unconventional pair of one experimental and one FDM generated synthetic spectrum instead of two experimental ones and thus is economical in terms of spectrometer time. To demonstrate, the processing tool was applied first on a simple coupled two-spin system of 2-Bromo-5-chlorothiophene and then to a more complex system of several coupled spins in sucrose.
| Indranil Ghosh; Subhayan Chakraborty; Shalini Pandey; Arindam Ghosh | Physical Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628e09ab809e32f7969c495b/original/diagonal-free-processing-of-conventional-phase-sensitive-cosy-using-filter-diagonalization-method.pdf |
60c74972bdbb896aeaa39196 | 10.26434/chemrxiv.12061377.v1 | Thermoelasticity in Organic Semiconductors Determined with Terahertz Spectroscopy and Quantum Quasi-Harmonic Simulations | The thermomechanical response of organic semiconducting solids is an essential aspect to consider in the design of materials for advanced applications, and in particular, flexible electronics. The non-covalent intermolecular forces that exist in organic solids not only result in a diverse set of mechanical properties, but also a critical dependence of those same properties on temperature. However, studying the thermoelastic response of solids is experimentally challenging, often requiring large single-crystals and sensitive experimental apparatus. An alternative contactless approach involves using low-frequency vibrational spectroscopy to characterize the underlying intermolecular forces, and then combining this information with solid-state density functional theory simulations to retrieve the mechanical response of materials. This methodology leverages recent advances in the quasi-harmonic approximation to predict the temperature evolution of crystalline structures, dynamics, and associated forces, and then utilizes this information to determine the elastic tensor as a function of temperature. Here, this methodology is illustrated for two prototypical organic semiconducting crystals, rubrene and BTBT, and suggests a new alternative means to characterizing the thermoelastic response of organic materials. | Peter A. Banks; Jefferson Maul; Mark T. Mancini; Adam C. Whalley; Alessandro Erba; Michael Ruggiero | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74972bdbb896aeaa39196/original/thermoelasticity-in-organic-semiconductors-determined-with-terahertz-spectroscopy-and-quantum-quasi-harmonic-simulations.pdf |
67297546f9980725cf1cb4e7 | 10.26434/chemrxiv-2024-h9z3q | Block-copolymer directed in-situ synthesis of Mesoporous SiCN and Supported Au & Ag nanoparticles for Catalysis | Novel concerted copolymerization, microphase separation, and crosslinking strategy for the synthesis of mesoporous SiCN with high surface area has been developed. Influence of pore size and surface area by changing length and ratio of porogen organic block is demonstrated. Longer the chain length and higher the porogen ratio trends the SiCN under mesoporous region with high surface area. Whereas shorter chain length porogen trends the SiCN under microporous region. The de Boer method, Brunauer–Emmett–Teller (BET), and statistical thickness plot (t-plot) are utilised to confirm mesoporous and microporous textural properties of the SiCN. The same synthetic strategy is also extended to the synthesis of mesoporous SiCN supported metal nanoparticles. Well distributed in situ formation of gold and silver nanoparticles during the synthesis of mesoporous SiCN is emerged followed by successful prevention of sintering at 1000°C. Synthesized materials are mainly characterized by transmission electron microscopy, scanning electron microscopy, atomic force microscopy, powder X-ray diffrectometer and nitrogen physisorption techniques. | Saravana K T Pillai; Gunter Motz; Winfried Kretschmer | Materials Science; Catalysis; Catalysts; Ceramics; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67297546f9980725cf1cb4e7/original/block-copolymer-directed-in-situ-synthesis-of-mesoporous-si-cn-and-supported-au-ag-nanoparticles-for-catalysis.pdf |
618078c892abe0c26731be6d | 10.26434/chemrxiv-2021-hm34v | How Globally Aromatic Are Six-Porphyrin Nanorings? | A recent Research Article published in this journal by Matito and coworkers claimed that none of the oxidation states of a butadiyne-linked six-porphyrin nanoring exhibit global aromaticity or antiaromaticity. Here we show that this conclusion is incorrect. A combination of density functional theory (DFT) calculations and experimental NMR data provides compelling evidence for global (anti)aromaticity in a variety of six-porphyrin nanorings in their 2+, 4+ and 6+ oxidation states. The strength of the predicted ring current depends on the choice of DFT functional, so it is crucial to use a functional that reproduces the experimental 1H NMR chemical shifts in these cations. | Jie-Ren Deng; David Bradley; Michael Jirásek; Harry Anderson; Martin Peeks | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Physical Organic Chemistry; Spectroscopy (Anal. Chem.); Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618078c892abe0c26731be6d/original/how-globally-aromatic-are-six-porphyrin-nanorings.pdf |
649cff359ea64cc167269293 | 10.26434/chemrxiv-2023-wrzhc | Structural Determinants of the Binding and Activation of Estrogen Receptor alpha by Phenolic Thieno[2,3-d]pyrimidines | Synthetic, structural, and computational approaches were used to solve the puzzle as to how a phenolic nonsteroidal estrogen 1 with only a single H-bond to its receptor was more potent than an isomer 2 which formed an intricate network of H-bonds. Synthesis of a series of substituted phenols revealed that pKa was not a determinant of estrogenic activity. First-principles calculation also failed to explain the difference in activity of 1 and 2. Molecular dynamics revealed that 1 formed a more stable receptor complex compared to 2, which may explain its increased activity despite forming fewer apparent H-bonds with the protein. | Vamshi Sammeta; Brian Anderson; John Norris; Chad Torrice; Carstyn Joiner; Shubin Liu; Haoxi Li; Konstantin Popov; Sean Fanning; Donald McDonnell; Timothy Willson | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649cff359ea64cc167269293/original/structural-determinants-of-the-binding-and-activation-of-estrogen-receptor-alpha-by-phenolic-thieno-2-3-d-pyrimidines.pdf |
615d6482aa918d06bc2194d8 | 10.26434/chemrxiv-2021-snnr7 | Photoconductivity of Intrinsic Semiconductor Phthalocyanine-Based Covalent Organic Polymer with Benzimidazole Linkage | Novel phthalocyanine-based benzimidazole linked conjugated covalent organic polymer (NiPc-COP1) have been synthesized with multiple randomly ordered crystalline morphology. This unique alignment leads to significantly enhanced panchromatic light-absorption capability, thus high photoconductivity with high photoresponce speed. | Ercan Duygulu; Onur Alev; Yurii Chumakov; Zafer Ziya Öztürk; MEHMET MENAF AYHAN; Fatma Yüksel | Organic Chemistry; Polymer Science; Photochemistry (Org.); Conducting polymers; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615d6482aa918d06bc2194d8/original/photoconductivity-of-intrinsic-semiconductor-phthalocyanine-based-covalent-organic-polymer-with-benzimidazole-linkage.pdf |
6366e4fcecdad5c2c0fc08f0 | 10.26434/chemrxiv-2022-j15lg | "N2O2" Metal-azaDIPY complexes: a new class of NIR-fluorophores | Aza-BODIPYs are an increasingly studied class of fluorophores. They can be seen as an "aza-DIPY" ligand rigidified by a metalloid, a boron atom. Based on this idea, a series of complexes of group 13 metals (aluminum and gallium) have been synthesized and characterized. Impact of the metal and of the nature of the substituents of aza-DIPY core were investigated. The photophysical and electrochemical properties were determined and an X-ray structure of an azaGaDIPY was obtained. These data reveal that azaGaDIPY and azaAlDIPY exhibit significant red-shifted fluorescence compared to their analogue aza-BODIPY. Their emission can go up to 800 nm for the maximum emission length and up to NIR-II for the emission tail. This, associated with their electrochemical stability (no metal release whether oxidized or reduced) make them a promising class of fluorophores for optical medical imaging. Moreover, X-ray structure and molecular modeling studies have shown that this red shift seems to be more due to the geometry around the boron/metal than to the nature of the metal. | Amélie Godard; Laura Abad Galan; Jean Rouillon; Shaymaa Al Shehimy; Wassima Tajani; Charlotte Cave; Raluca Malacea-Kabbara; Yoann Rousselin; Pierre Le Gendre; Arnaud Fihey; Mohamed Bendellaa; Benoit Busser; Lucie Sancey; Boris Le Guennic; Christophe Bucher; Olivier Maury; Christine Goze; Ewen Bodio | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Photochemistry (Org.); Coordination Chemistry (Inorg.); Electrochemistry - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6366e4fcecdad5c2c0fc08f0/original/n2o2-metal-aza-dipy-complexes-a-new-class-of-nir-fluorophores.pdf |
664352f8418a5379b03cb230 | 10.26434/chemrxiv-2024-32j2t | Evaluating the generalizability of graph neural networks for predicting collision cross section | Ion Mobility coupled with Mass Spectrometry (IM-MS) is a promising analytical technique that enhances molecular characterization by measuring collision cross-section (CCS) values, which are indicative of the molecular size and shape. However, the effective application of CCS values in structural analysis is still constrained by the limited availability of experimental data, necessitating the development of accurate machine learning (ML) models for in silico predictions. In this study, we evaluated state-of-the-art Graph Neural Networks (GNNs), trained to predict CCS values using the largest publicly available dataset to date. Although our results confirm the high accuracy of these models within chemical spaces similar to their training environments, their performance significantly declines when applied to structurally novel regions. This discrepancy raises concerns about the reliability of in silico CCS predictions and underscores the need for releasing further publicly available CCS datasets. To mitigate this, we demonstrate how generalization can be partially improved by extending models to account for additional features such as molecular fingerprints, descriptors, and the molecule types. Lastly, we also show how confidence models can support by enhancing the reliability of the CCS estimates. | Chloe Engler Hart; António José Preto; Shaurya Chanana; David Healey; Tobias Kind; Daniel Domingo-Fernández | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664352f8418a5379b03cb230/original/evaluating-the-generalizability-of-graph-neural-networks-for-predicting-collision-cross-section.pdf |
678ea074fa469535b9da619b | 10.26434/chemrxiv-2025-qhx69 | Water molecules in the cannabinoid receptor 2 binding site crucially impact the discovery of novel ligands | The cannabinoid receptor 2 (CB2R) is of considerable therapeutic and scientific interest. Hence, the discovery of novel molecules that target and modulate this receptor, ideally selectively over its closest relative, the cannabinoid receptor 1, is of great importance. In this study, we aimed to discover novel ligands targeting the CB2R using large library in silico docking screens. However, since the CB2R binding site is difficult to target with in silico methods due to its hydrophobic nature, we used a variety of screening approaches, including the placement of water molecules in predicted water sites of the receptor binding site, and screening against multiple docking setups and receptor conformations. We systematically evaluated these different approaches to support future screens to the CB2R and other receptors. In the present work, each setup contributed different ligands of varying intrinsic activities, leading to an overall improved hit rate compared to that of a single screen. Of the novel ligands of the CB2R discovered and experimentally confirmed in this study, one series features high-affinity ligands with a previously undescribed scaffold. | Magdalena M. Scharf; Morgan Scott-Dennis; Leire Borrega-Roman; Franziska N. Z. Giese; Darya Plevako; David A. Sykes; Dmitry B. Veprintsev; Peter Kolb | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ea074fa469535b9da619b/original/water-molecules-in-the-cannabinoid-receptor-2-binding-site-crucially-impact-the-discovery-of-novel-ligands.pdf |
65673334cf8b3c3cd7652610 | 10.26434/chemrxiv-2023-tbck9 | Accessing Rare α-Heterocyclic Aziridines via Brønsted Acid-catalyzed Michael Addition/Annulation: Scope, Limitations, and Mechanism | We report an approach to the diastereoselective synthesis of 1,2-disubstituted heterocyclic aziridines. A Brønsted acid-catalyzed conjugate addition of anilines to trisubstituted heterocyclic chloroalkenes provides an intermediate 1,2-chloroamine. Diastereocontrol was found to vary significantly with solvent selection, with computational modelling confirming selective, spontaneous fragmentation in the presence of trace acids, proceeding through a pseudo-cyclic, protonated intermediate and transition state. These chloroamines can then be converted to the aziridine by treatment with LiHMDS with high stereochemical fidelity. This solvent-induced stereochemical enrichment thereby enables an efficient route to rare cis-aziridines with high dr. The scope, limitations, and mechanistic origins of selectivity are also presented. | Timothy Hilton; Andrew Leach; Aidan McKay; Allan Watson | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Theory - Computational; Acid Catalysis | CC BY 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65673334cf8b3c3cd7652610/original/accessing-rare-heterocyclic-aziridines-via-br-nsted-acid-catalyzed-michael-addition-annulation-scope-limitations-and-mechanism.pdf |
6509bfd2ed7d0eccc3d3b286 | 10.26434/chemrxiv-2023-9csh2 | A Membrane-Electrolyte System Approach to
Understanding Ionic Conductivity and Crossover
in Alkaline Flow Cells | Membrane transport properties are crucial for electrochemical devices, and these properties
are influenced by the composition and concentration of the electrolyte in contact with the membrane. We apply this general membrane-electrolyte system approach to alkaline flow batteries, studying conductivity and ferricyanide crossover of Nafion and E-620. We report
undetectable crossover for as-received Nafion and E-620 after both sodium and potassium exchange, but high ferricyanide permeability of 10^−7 to 10^−8 cm^2 s^−1 for Nafion subjected to pre-treatment prevalent in the flow battery literature. We show how the electrolyte mass fraction in hydrated membranes regulates the influence of ion concentration on membrane conductivity, identifying that increasing electrolyte concentration may not increase membrane conductivity even when it increases electrolyte conductivity. To illustrate this behavior we introduce a new metric, the membrane penalty, as the ratio of the conductivity of the electrolyte to that of the membrane equilibrated with the electrolyte. We discuss the tradeoff between flow battery volumetric capacity and areal power density that arises from these findings. Finally, we apply insights from this approach to provide recommendations for use of membranes in alkaline flow cells, and electrochemical reactors in general. | Thomas George; Isabelle Thomas; Naphtal Haya; John Deneen; Cliffton Wang; Michael Aziz | Polymer Science; Energy; Fluoropolymers; Polyelectrolytes - Polymers; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6509bfd2ed7d0eccc3d3b286/original/a-membrane-electrolyte-system-approach-to-understanding-ionic-conductivity-and-crossover-in-alkaline-flow-cells.pdf |
60c74eed842e654e2edb3738 | 10.26434/chemrxiv.12820652.v1 | Mukaiyama Aldol Reaction Catalyzed by (Benz)imidazolium-Based Halogen Bond Donors | A series of cationic monodentate and bidentate
iodo(benz)imidazolium-based halogen bond (XB) donors were employed as
catalysts in a Mukaiyama aldol reaction. While 5 mol% of a monodentate variant
showed noticeable activity, a <i>syn</i>-preorganized
bidentate XB donor provided a strong performance even with 0.5 mol% loading. In
contrast to the very active BAr<sup>F</sup><sub>4</sub> salts, PF<sub>6</sub>
or OTf salts were either inactive or showed background reaction. Repetition
experiments clearly ruled out a potential hidden catalysis by elemental iodine
and demonstrated the stability of our catalyst over three consecutive cycles. | Revannath L. Sutar; Nikita Erochok; Stefan Huber | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eed842e654e2edb3738/original/mukaiyama-aldol-reaction-catalyzed-by-benz-imidazolium-based-halogen-bond-donors.pdf |
60ef1555af9cdb6ab3dbeb44 | 10.26434/chemrxiv-2021-b0rpt | Patterned Dried Blood Spot Cards for Improved Sampling of Whole Blood | Dried blood spot (DBS) cards perform many functions for sampling blood that is intended for subsequent laboratory analysis, which include: (i) obviating the need for a phlebotomist by using fingersticks, (ii) enhancing the stability of analytes at ambient or elevated environmental conditions, and (iii) simplifying transportation of samples without a cold chain. However, a significant drawback of standard DBS cards is the potential for sampling bias due to unrestricted filling caused by the hematocrit of blood, which often limits quantitative or reproducible measurements. Alternative microsampling technologies have minimized or eliminated this bias by restricting blood distribution, but these approaches deviate from clinical protocols and present a barrier to broad adoption. Herein, we describe a patterned dried blood spot (pDBS) card that uses wax barriers to control the flow and distribution of blood and provide enhanced sampling by minimizing the hematocrit effect. Patterned cards reproducibly fill four replicate extraction zones independent of the hematocrit. We demonstrate a 3-fold improvement in accuracy for the quantitation of hemoglobin using pDBS cards compared to unpatterned cards. Patterned cards also facilitate the near quantitative recovery (ca. 95%) of sodium with no evidence of a statistically significant difference between dried and liquid blood samples. Similarly, recovery of select amino acids was conserved in comparison to a recent report with improved inter-card precision. We anticipate that this approach presents a viable method for preparing and storing samples of blood in limited resource settings while maintaining current clinical protocols for processing and analyzing dried blood spots. | Keith R. Baillargeon; Jessica C. Brooks; Philip R. Miljanic; Charles R. Mace | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ef1555af9cdb6ab3dbeb44/original/patterned-dried-blood-spot-cards-for-improved-sampling-of-whole-blood.pdf |
617748c8d7e1ee6a1a34aad4 | 10.26434/chemrxiv-2021-lw8sm | Illuminating mechanochemical reactions by combining real-time fluorescence emission monitoring and periodic time-dependent density-functional calculations | We provide a proof-of-principle demonstration of the first dual-spectroscopic method for direct and real-time observation of mechanochemical reactions by ball milling, supported by high-level molecular and periodic density-functional theory (DFT) calculations, including periodic time-dependent (TD-DFT) calculations to model solid-state fluorescence spectra. By combining standard Raman and fluorescence benchtop spectrometers in a single readily accessible tandem monitoring technique, we simultaneously observe changes to the supramolecular structure during mechanochemical polymorph transformation and cocrystallization of the model pharmaceutical system indometacin. The observed time-resolved in situ spectroscopic data is supported by ex situ X-ray diffraction and solid-state nuclear magnetic resonance spectroscopy measurements. First principles calculations facilitate the interpretation of both real-time spectroscopic and ex situ data by demonstrating how changes in crystalline environment affect vibrational and electronic excited states. | Patrick A. Julien; Mihails Arhangelskis; Luzia S. Germann; Martin Etter; Robert E. Dinnebier; Andrew J. Morris; Tomislav Friscic | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemical Kinetics; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617748c8d7e1ee6a1a34aad4/original/illuminating-mechanochemical-reactions-by-combining-real-time-fluorescence-emission-monitoring-and-periodic-time-dependent-density-functional-calculations.pdf |
634667e2fb0fd88c15357865 | 10.26434/chemrxiv-2021-g7hmw-v2 | Spectrally-selective Time-resolved Emission through Fourier-filtering (STEF) | In this manuscript we demonstrate that directing the emitted photon stream from a fluorescent
sample through a fixed path-length imbalanced Mach-Zehnder interferometer allows us to separate and
resolve the dynamics of different emitters without the use of filtering optics. Our method, Spectrallyselective Time-resolved Emission through Fourier-filtering (STEF) takes advantage of a careful selection
of interferometer position where one signal can be canceled (or enhanced) due to its unique spectral
characteristics. STEF is straightforward to implement and provides a complementary approach to separate
spectrally overlapped signals based on their coherence length and carrier frequency. We also discuss how
one can implement STEF with an imperfect Mach-Zehnder interferometer, increasing the utility of this
method, and demonstrate how Mach-Zehnder filtering can be used to image fluorophores in biologically
relevant samples. | Anthony Sica; Timothy Atallah; Justin Caram | Physical Chemistry; Optics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634667e2fb0fd88c15357865/original/spectrally-selective-time-resolved-emission-through-fourier-filtering-stef.pdf |
60e88721338e926e6d096601 | 10.26434/chemrxiv-2021-96vd4 | Catch the next designer drug: A comparison of methods for predicting in vitro pharmacological profiles using molecular fingerprints | Facing the growing trend of emerging new psychoactive substances (NPS) and their threat to public health, more effective methods of NPS prediction and identification are of critical importance. In this study, we aimed to compare methods for predicting the pharmacological profile of unknown compounds based on the chemical structures described by molecular fingerprints. We built predictive models based on the high-throughput screening (HTS) data sets using four different machine learning algorithms for a total of 10 targets and validated the performance of the models using in vitro bioassay data collected from the literature for an external NPS compound set. Clustering analysis revealed that the MACCS fingerprint may be more suitable for describing the similarity of pharmacological profiles of NPS, indicated by the highest adjusted Rand index (0.46) between the two clustering trees. The SVM classifiers validated by the external NPS set achieved ROC AUC above 0.80 and MCC above 0.45, therefore were used to generate the multi-target pharmacological profiles. The hit rate for retrieving pharmacologically similar compound pairs using MACCS calculated Tanimoto coefficient was below 1.85%, in contrast, the models were more successful in identifying similar compound pairs (MCC = 0.72), which were otherwise considered dissimilar by molecular fingerprints.
| kedan he | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e88721338e926e6d096601/original/catch-the-next-designer-drug-a-comparison-of-methods-for-predicting-in-vitro-pharmacological-profiles-using-molecular-fingerprints.pdf |
66c0ba3e20ac769e5feb4153 | 10.26434/chemrxiv-2024-0n1df | Impact of binder content on particle fracture and microstructure of solvent-free electrodes for Li-ion batteries | The fraction of polytetrafluoroethylene (PTFE) binder in solvent-free Li-ion battery electrodes is shown to have a dramatic impact on their processability, microstructural evolution and elec- trochemical performance. We show experimentally that increasing binder fraction from 0.5 to 4 wt.% transformed the electrode microstructure from an efficient, open structure containing PTFE nano-fibrils to a cemented morphology with blocked porosity. The solvent-free electrodes showed a classical visco-elastic response during compression, comprising three distinct regions of deformation. The electrode stiffness and yield/flow strength increased non-linearly with binder fraction such that for higher binder contents (>2wt.%), there was extensive LiNi0.6Co0.2Mn0.2O2 (NMC) particle fracture during the calendering process, with cracks propagating along the grains of polycrystalline NMC particles. Conversely at lower binder fraction (<2wt.%), the PTFE readily fibrillated into highly textured (100) crystalline nano-fibrils and NMC particles remained largely intact. These electrodes showed superior electrochemical performance due to higher ionic mobility through the open nano-fibrillar microstructure and intact NMC particles. | Guillaume Matthews; Benjamin Meyer; Christopher Doerrer; Julia Ramirez-Gonzalez; Ed Darnbrough; Noel Hallemans; David Armstrong; Patrick Grant | Materials Science; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c0ba3e20ac769e5feb4153/original/impact-of-binder-content-on-particle-fracture-and-microstructure-of-solvent-free-electrodes-for-li-ion-batteries.pdf |
673f5c747be152b1d037505a | 10.26434/chemrxiv-2024-4tmq3 | Revitamize LFP! Ascorbic Acid-Assisted Direct Regeneration of Spent LiFePO4 for Li-ion Batteries | The increasing demand for lithium-ion batteries (LIBs), primarily driven by the expanding electric vehicle market and the growing need for efficient energy storage, presents both significant opportunities and challenges. The efficient and cost-effective regeneration of spent LIBs is crucial to minimizing environmental impact and fostering a true circular economy for battery materials. In this study, we introduce an innovative one-step lithiation process for spent LiFePO4 cathodes, conducted in aqueous solution under ambient conditions. This method utilizes readily available and low-cost reagents, including a lithium source and ascorbic acid (vitamin C) as a green reducing agent, offering a substantial advantage over traditional techniques that require harsh conditions and complex setups. The lithiation reaction proceeds rapidly, producing pure and fully regenerated LFP. This environmentally friendly process has been successfully demonstrated at the scale of 18650 cells with electrodes composed entirely of recycled LFP. These cells exhibit excellent electrochemical performance, even after 1000 cycles at 1C rate, comparable to those made with pristine LFP. By providing a sustainable, cost-effective, and easily scalable solution for LFP cathode regeneration, our approach supports the closure of the materials loop, contributing to the sustainable management of LIBs and advancing the shift toward a circular economy. | Tassadit Ouaneche; Lorenzo Stievano; Francois Rabuel; Arash Jamali; Claude Guéry; Laure Monconduit; Moulay Tahar Sougrati; Nadir Recham | Inorganic Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Electrochemistry; Natural Resource Recovery; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673f5c747be152b1d037505a/original/revitamize-lfp-ascorbic-acid-assisted-direct-regeneration-of-spent-li-fe-po4-for-li-ion-batteries.pdf |
6133c1096563696d9d222bbd | 10.26434/chemrxiv-2021-xb6sx-v2 | Star-shaped Triazine-derivatives: would they crossbind SARS-CoV-2 spike helices? | This work describes synthesizable water-soluble Triazine-derivatives computationally crossbinding the S spike helices of Severe Acute Respiratory Syndrome coronavirus (SARS)-CoV-2. The "spring-loaded switch-folding” (S-SLSF) α-helices included in the S homotrimer top-to-bottom cavity and implicated in viral-host membrane fusion were targeted by star-shaped Trihydroxyl-Triphenyl-Triazines (TTT) leads at subnanomolar binding-scores. Exploration of in silico leads among millions of molecular candidates, included several similar searches, core-replacement, fragment extensions, or convolutional neural network deep-screening combined with hundreds of water-soluble lead-derivatives identified by manual iterations and commercially available building-blocks for chemical synthesis. The lead-derivatives are briefly discussed for in vitro validation and possibilities of fusion inhibition substituting mutations. | julio coll | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6133c1096563696d9d222bbd/original/star-shaped-triazine-derivatives-would-they-crossbind-sars-co-v-2-spike-helices.pdf |
66d7924e12ff75c3a14f5258 | 10.26434/chemrxiv-2024-6ggsq | Ontology-conformal recognition of materials entities using language models | Retrieving structured materials information from unstructured textual data is essential for data mining and automatically developing comprehensive ontologies. Information extraction is a complex task composed of multiple subtasks and thus often relies on systems of task-specialized language models. A foundation language model can in principle address not only a variety of those subtasks but also a range of domains without the need of generating costly large-scale annotated datasets for each downstream task. While the materials science domain, which is adversely affected by data scarcity, would strongly benefit from this, foundation language models struggle with information extraction subtasks in domain-specific settings. This applies also to the so-called named entity recognition (NER) subtask which aims to detect relevant entity types in natural language.
This work aims to assess whether foundation large language models (LLMs) can successfully perform NER in the materials mechanics and fatigue domain to alleviate the data annotation burden. Specifically, we compare the few-shot prompting of foundation LLMs with the current state-of-the-art, fine-tuned task-specific NER models. The study is performed on two materials fatigue datasets which contain annotations at a comparatively fine-grained level. Both datasets cover adjacent domains to assess how well both NER methodologies generalize when presented with typical domain shifts. Task-specific models are shown to significantly outperform general foundation models. However, the GPT-4 foundation model attains promising F1-scores with the proposed two-stage prompting strategy despite being provided with only ten demonstrations. Under those circumstances, it outperformed task-specific models for some rather general entity types. Different ways onwards to improve foundation LLM-based NER are discussed. Our findings reveal a strong dependence on the quality of few-shot demonstrations in ICL to handle domain-shift. The study also highlights the significance of domain-specific pre-training by comparing task-specific models that differ primarily in their pre-training corpus. | Rachana Niranjan Murthy; Sai Teja Potu; Akhil Thomas; Lokesh Mishra; Natalie Prange; Ali Riza Durmaz | Materials Science; Alloys; Materials Processing | CC BY 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d7924e12ff75c3a14f5258/original/ontology-conformal-recognition-of-materials-entities-using-language-models.pdf |
63a1bf2916e9a8eea82f101f | 10.26434/chemrxiv-2022-6skf7 | Thermodynamic formulation on Ostwald’s law of dilution and the acid dissociation constant Ka | The thermodynamic background of Ostwald’s law of dilution, which gives the acid dissociation constant (Ka), is revealed. The feature of Ka as a constant is understandable in the same context as the equilibrium shift of the gas reaction by pressure. The Ka quantity becomes constant under dilution as far as the solution is an ideal mixture. Because the character depends only on the number of solute particles present, the constant Ka is one of the colligative properties of a dilute solution. | Yukiteru Katsumoto | Physical Chemistry; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a1bf2916e9a8eea82f101f/original/thermodynamic-formulation-on-ostwald-s-law-of-dilution-and-the-acid-dissociation-constant-ka.pdf |
6320c9d73e2e36b25d354da6 | 10.26434/chemrxiv-2022-xz3tv | A 1-pot synthesis of the SARS-CoV-2 Mpro Inhibitor Nirmatrelvir, the key ingredient in Paxlovid
| A newly devised route to the Pfizer drug nirmatrelvir is reported that reduces the overall sequence to a 1-pot process and relies on a commercially available, green coupling reagent, T3P. The overall yield of the targeted material, isolated as its MTBE solvate, is 53%. | Juan Caravez; Karthik Iyer; Rahul Kavthe; Joseph Kincaid; Bruce Lipshutz | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6320c9d73e2e36b25d354da6/original/a-1-pot-synthesis-of-the-sars-co-v-2-mpro-inhibitor-nirmatrelvir-the-key-ingredient-in-paxlovid.pdf |
60c74b0a842e657139db3060 | 10.26434/chemrxiv.12279911.v1 | The Calcite (104) Surface - Electrolyte Structure: A 3D Comparison of Surface X-Ray Diffraction and Simulations | <div>Adsorption and incorporation of ions is known to influence the morphology and growth of calcite. Using surface X-ray diffraction, the interfacial structure of calcite in contact with CaCO3, MgCl2, CaCl2</div><div>and BaCl2 solutions was determined. All of these conditions yield a comparable interfacial structure,</div><div>meaning that there is no significant ion adsorption. This allows for the first time a thorough comparison in all three dimensions with state-of-the-art computer simulations, involving molecular dynamics</div><div>based on both DFT and two different force field models. Additionally, the simulated structures are</div><div>used to calculate the corresponding structure factors, which in turn are compared to those obtained</div><div>from experiment, thereby avoiding the need for fitting or subjective interpretation. In general, there</div><div>is a good agreement between experiment and the simulations, though there are some small discrepancies in the atomic positions, which lead to an inadequate fit of certain features characteristic of the</div><div>structure of water at the interface. Of the three simulation methods examined, the DFT results were</div><div>found to agree best with the experimental structure.</div> | Sander Brugman; Paolo Raiteri; Paolo Accordini; Frank Megens; Julian Gale; Elias Vlieg | Interfaces; Structure; Surface; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b0a842e657139db3060/original/the-calcite-104-surface-electrolyte-structure-a-3d-comparison-of-surface-x-ray-diffraction-and-simulations.pdf |
64c9ce93ce23211b20f77131 | 10.26434/chemrxiv-2023-brjnz | Breaking Kinetic Record for Cysteine Bioconjugation with Organometallic Reagents | Through mechanistic work and rational design, we have developed the fastest abiotic Cys bioconjugation. As a result, the developed organometallic Au(III) bioconjugation reagents enable selective labelling of Cys moieties down to pM concentrations and allow for the rapid construction of complex heterostructures from peptides, proteins, and oligonucleotides. This work showcases how organometallic chemistry can be interfaced with biomolecules and lead to the range of reactivities that are unmatched by classical organic chemistry tools. | Evan Doud; James Tilden; Joseph Treacy; Elaine Chao; Hayden Montgomery; Grace Kunkel; Nima Adhami; Tyler Kerr; Arnold Rheingold; Christopher Frost; Kendall Houk; Heather Maynard; Alexander Spokoyny | Biological and Medicinal Chemistry; Inorganic Chemistry; Organometallic Chemistry; Bioinorganic Chemistry; Bioorganometallic Chemistry; Coordination Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c9ce93ce23211b20f77131/original/breaking-kinetic-record-for-cysteine-bioconjugation-with-organometallic-reagents.pdf |
622e3b6e0350dd7a00d71782 | 10.26434/chemrxiv-2022-hwsl7-v2 | Photoreactivity of donor-acceptor stilbene complexes in a macrocyclic host | Host-guest 2:1 complexation of photoreactive alkene guests improves the selectivity of [2+2] photodimerizations by templating alkene orientation prior to irradiation. Host-guest chemistry can also provide 1:1:1 complexes through the inclusion of electronically complementary donor and acceptor guests, but the photoreactivity of such complexes has not been investigated. In this work, we investigated a series of donor and acceptor stilbenes and found 1:1:1 complexes with cucurbit[8]uril that exhibited charge-transfer (CT) absorption bands in the visible and near-IR regions. Irradiation of the CT band of an azastilbene, 4,4’-stilbenedicarboxylate, and cucurbit[8]uril ternary complex led to a selective cross-[2+2] photocycloaddition, while other substrate pairs exhibited no productive chemistry upon CT excitation. Using transient absorption (TA) spectroscopy, we were able to understand the variable photoreactivity of different stilbene donor-acceptor complexes. We found that the back electron transfer (BET) following CT excitation of the photoreactive complex is positioned deep in the Marcus inverted region due to electrostatic stabilization of the ground state, allowing [2+2] to effectively compete with this relaxation pathway. Control reactions revealed that the cucurbit[8]uril host not only serves to template the reaction from the ground state, but also protects the long-lived radical ions formed by CT from side reactions. This protective role of the host suggests that donor-acceptor host-guest ternary complexes could be used to improve existing CT-initiated photochemistry or access new reactivity. | Christopher Eckdahl; Carrie Ou; Suyog Padgaonkar; Mark Hersam; Emily Weiss; Julia Kalow | Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622e3b6e0350dd7a00d71782/original/photoreactivity-of-donor-acceptor-stilbene-complexes-in-a-macrocyclic-host.pdf |
625980b4d048edbc4143f880 | 10.26434/chemrxiv-2022-wwsw7 | Hybrid, Interpretable Machine Learning for Thermodynamic Property Estimation using Grammar2vec for Molecular Representation | Property prediction models have been developed for several decades with varying degrees of performance and complexity, from the group contribution-based methods to molecular simulations-based methods. An interesting issue in this area is finding an appropriate representation of molecules inherently suited for the property modeling problem. Here, we propose Grammar2vec, a SMILES grammar-based framework for generating dense, numeric molecular representations. Grammar2vec embeds molecular structural information contained in the grammar rules underlying SMILES string representations of molecules. We use Grammar2vec representations to build machine learning-based models for estimating normal boiling point (Tb) and critical temperature (Tc) and benchmark their performance against the popularly used group contribution (GC)-based methods. To ensure interpretability of the developed ML model, we perform a Shapley values-based analysis to estimate feature importance and simplify (or prune) the trained model. | Vipul Mann; Karoline Brito; Rafiqul Gani; Venkat Venkatasubramanian | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625980b4d048edbc4143f880/original/hybrid-interpretable-machine-learning-for-thermodynamic-property-estimation-using-grammar2vec-for-molecular-representation.pdf |
6439db0108c86922ffffb149 | 10.26434/chemrxiv-2023-t422x | Advanced microflow manipulation strategy in paper-based microfluidics towards smart analytical chemistry: A concise review | Microfluidics has emerged as a rapidly growing field in recent years, offering numerous advantages over traditional methods for various applications such as biomedical analysis, environmental monitoring, and chemical synthesis. Among the many areas of microfluidics research, the manipulation of fluids plays a crucial role. In this review, the focus will be on recent advances in fluid manipulation techniques such as mixing, dilution, separation, accumulation, flow delay, and flow accelerations. Looking to the future, microfluidics research will continue to explore new ways to manipulate fluids in microscale environments. Challenges include the need for better integration of different manipulation techniques, such as combining mixing and separation techniques, and the development of more complex microfluidic systems. Additionally, advancements in material science will continue to play a critical role in improving the functionality of microfluidic devices. Despite these challenges, the potential for microfluidics to revolutionize various fields remains high, and ongoing research in this area is likely to continue to yield exciting new discoveries and innovations. | Siting Liu; Gong Chen; An Mei; Xunjie Lu; Fuyao Zhao; Zihan Li; Jiayi Wang | Chemical Engineering and Industrial Chemistry; Fluid Mechanics | CC BY 4.0 | CHEMRXIV | 2023-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6439db0108c86922ffffb149/original/advanced-microflow-manipulation-strategy-in-paper-based-microfluidics-towards-smart-analytical-chemistry-a-concise-review.pdf |
6707e13951558a15efb37066 | 10.26434/chemrxiv-2024-0xbvl | Assessment of Electron-Proton Correlation Functionals for Vibrational Spectra of Shared-Proton Systems by Constrained Nuclear-Electronic Orbital Density Functional
Theory | Proton transfer plays a crucial role in various chemical and biological processes. A major theoretical challenge in simulating proton transfer arises from the quantum nature of the proton. Recently, the constrained nuclear-electronic orbital (CNEO) framework has been developed to efficiently and accurately account for nuclear quantum effects, particularly quantum nuclear delocalization effects, in quantum chemistry calculations and molecular dynamics simulations. In this paper, we systematically investigate challenging proton transfer modes in a series of shared-proton systems with the CNEO framework, focusing on evaluating existing electron-proton correlation functionals. Our results show that CNEO accurately describes proton transfer vibrational modes and significantly outperforms conventional DFT. The inclusion of the epc17-2 electron-proton correlation functional in CNEO produces similar performance to CNEO without electron-proton correlations, while the epc17-1 functional yields less accurate results, comparable to conventional DFT. These findings hold true for both asymmetrical and symmetrical shared-proton systems. Therefore, until a more accurate electron-proton correlation functional is developed, we recommend performing CNEO vibrational spectrum calculations without using electron-proton correlation functionals. | Yuzhuo Yang; Yuzhe Zhang; Yang Yang; Xi Xu | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6707e13951558a15efb37066/original/assessment-of-electron-proton-correlation-functionals-for-vibrational-spectra-of-shared-proton-systems-by-constrained-nuclear-electronic-orbital-density-functional-theory.pdf |
60c7489cf96a00078c2870bd | 10.26434/chemrxiv.11949390.v1 | Organocatalytic Control over a Fuel-Driven Transient Esterification Network | <p>Signal transduction in living systems is the conversion of information into a chemical change and the principal process by which cells communicate. This process enables phenomena such as time-keeping and signal amplification. In nature, these functions are encoded in non-equilibrium (bio)chemical reaction networks (CRNs) controlled by enzymes. While these catalytically controlled processes are an integral part of biocatalytic pathways, man-made analogs are rare. Here, we incorporate catalysis in an artificial fuel driven out-of-equilibrium CRN. The study entails the design of an organocatalytically controlled fuel driven esterification CRN, where the forward (ester formation) and backward reaction (ester hydrolysis) are controlled by varying the ratio of two different organocatalysts: pyridine and imidazole. This catalytic regulation enables full control over ester yield and lifetime. The fuel-driven strategy is subsequently used in the design of a responsive polymer system, where transient polymer conformation and aggregation can be controlled through variation of fuel and catalysts levels. Altogether, we show how organocatalysis is an important tool to exert control over a man-made fuel driven system and induce a change in a macromolecular superstructure, as ubiquitously found in natural non-equilibrium systems. </p> | Michelle van der Helm; Chang-Lin Wang; Mariano Macchione; Eduardo Mendes; Rienk Eelkema | Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7489cf96a00078c2870bd/original/organocatalytic-control-over-a-fuel-driven-transient-esterification-network.pdf |
630b215ed147b2252cbbaa1f | 10.26434/chemrxiv-2022-2mb2s | Bioinspired Gradient Poly(ionic liquid) Ionogels for Ionic Skins with an Ultrawide Pressure Detection Range | Recently, with the increasing demand for artificial skins and human bodily motion/physical signals monitoring, flexible pressure sensors with a wide detection range are urgently needed. Transparent and stretchable gels with ionic conductivities are considered to be ideal candidates for flexible pressure sensors. However, the gel-based pressure sensors usually show a relatively narrow detection range, which significantly limits their practical applications. Herein, we report an unprecedented bioinspired highly flexible modulus/conductivity-dual-gradient poly(ionic liquid) (PIL) ionogel, which is achieved by constructing three layers of PIL ionogels with different monomer concentrations via a layer-by-layer gelation method. The flexible pressure sensor based on the gradient PIL ionogel exhibits an ultrabroad detection range of 10 Pa-1 MPa. This wearable pressure sensor is highly stable in environments and able to monitor both the tiny pressures as low as 10-100 Pa and the high pressures up to 0.1-1 MPa during human body movements. This work provides a powerful strategy for the preparation of flexible gradient materials that are promising for wearable electronics with a wide pressure detection range. | Xiaoyu Zhang; Sheng Zeng; Zhenyu Hu; Xing Liang; Qi Sun; Jia Huang; Guoqing Zu | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2022-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630b215ed147b2252cbbaa1f/original/bioinspired-gradient-poly-ionic-liquid-ionogels-for-ionic-skins-with-an-ultrawide-pressure-detection-range.pdf |
645930f01ca6101a45ff8fd1 | 10.26434/chemrxiv-2023-r3f3x-v2 | Design rules for obtaining narrow luminescence from semiconductors made in solution | Solution processed semiconductors are in demand for present and next-generation optoelectronic technologies ranging from displays to quantum light sources because of their scalability and ease of integration into devices with diverse form factors. One of the central requirements for semiconductors used in these applications is a narrow photoluminescence (PL) linewidth. Narrow emission linewidths are needed to ensure both color and single-photon purity, raising the question of what design rules are needed to obtain narrow emission from semiconductors made in solution. In this review we first examine the requirements for colloidal emitters for a variety of applications including light-emitting diodes, photodetectors, lasers, and quantum information science. Next, we will delve into the sources of spectral broadening, including “homogeneous” broadening from dynamical broadening mechanisms in single-particle spectra, heterogeneous broadening from static structural differences in ensemble spectra, and spectral diffusion. Then, we compare the current state of the art in terms of emission linewidth for a variety of colloidal materials including II-VI quantum dots (QDs) and nanoplatelets, III-V QDs, alloyed QDs, metal-halide perovskites including nanocrystals and 2D structures, doped nanocrystals, and, finally, as a point of comparison, organic molecules. We end with some conclusions and connections, including an outline of promising paths forward. | Hao Nguyen; Grant Dixon; Florence Dou; Shaun Gallagher; Stephen Gibbs; Dylan Ladd; Emanuele Marino; Justin Ondry; James Shanahan; Eugenia Vasileiadou; Stephen Barlow; Daniel Gamelin; David Ginger; David Jonas; Mercouri Kanatzidis; Seth Marder; Daniel Morton; Christopher Murray; Jonathan Owen; Dmitri Talapin; Michael Toney; Brandi Cossairt | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Solution Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645930f01ca6101a45ff8fd1/original/design-rules-for-obtaining-narrow-luminescence-from-semiconductors-made-in-solution.pdf |
6251c4965b9009d8750991ad | 10.26434/chemrxiv-2022-5pt38-v2 | Rapid Online Oxidation of Proteins and Peptides via Electrospray-Accelerated Ozonation | When combined with mass spectrometry, solution-phase labeling such as oxidative foot printing, hydrogen/deuterium exchange, and covalent labeling are powerful tools for the analysis of protein conformation. The throughput of these work-flows, however, is frequently limited due to their reliance on slow labeling reactions, proteolysis, and chromatographic separations to be fully realized. Here, we present an ozone-driven oxidation reaction that occurs on the microsecond time-scale during the electrospray ionization (ESI) process. Selective oxidation of methionine and tryptophan residues in pep-tides and proteins occurs spontaneously upon the introduction of ozone into the ESI chamber. Trp and Met residues are frequently buried in folded proteins and thus, when applied to natively folded cytochrome C and carbonic anhydrase, little oxidation is observed. When these proteins are denatured and ozonated, a dramatic increase in the number of oxidation events and yield is measured. This methodology’s applicability to any instrument equipped with an ESI source, facile interpretation of results, limited sample handling, high-throughput nature, and rapid labeling reaction makes this technique a promising new tool for the analysis of protein folding. | Nicholas Borotto; Talitha Richards | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6251c4965b9009d8750991ad/original/rapid-online-oxidation-of-proteins-and-peptides-via-electrospray-accelerated-ozonation.pdf |
620e2883cbb4f42247c40e43 | 10.26434/chemrxiv-2022-zg04g | Passive control of temperature fluctuations through a sunlight-induced spin transition in a molecule-based material | The increasing environmental protection demand has prompted the development of passive thermal regulation systems that reduce temperature fluctuations in buildings. Here, we demonstrate that the heat generated by the sun can trigger a spin transition in a spin-crossover (SCO) material, resulting in a color change. This leads to a cooling effect in respect to other similar materials, due to an increase in light reflection. In addition, when the material is cooled, a dampening of the temperature decrease is produced. Therefore, these materials could potentially be implemented for passive temperature control in buildings. Furthermore, SCO materials are remarkably stable upon cycling and highly versatile, which allows for the design of compounds with properties tailored for the desired climatic conditions and comfort temperature. | Esther Resines-Urien; Miguel Angel Garcia Garcia-Tuñon; Mar Garcia-Hernandez; Jose Alberto Rodriguez-Velamazan; Ana Espinosa De los Monteros; Jose Sanchez Costa | Materials Science; Inorganic Chemistry; Magnetic Materials; Optical Materials; Coordination Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e2883cbb4f42247c40e43/original/passive-control-of-temperature-fluctuations-through-a-sunlight-induced-spin-transition-in-a-molecule-based-material.pdf |
60c74dad842e653fdfdb34e1 | 10.26434/chemrxiv.12649145.v1 | Mechanisms of Drug Solubilization by Polar Lipids in Biorelevant Media | Despite the widespread use of lipid excipients in both academic research and oral formulation development, rational selection guidelines are still missing. In the current study, we aimed to establish a link between the molecular structure of commonly used polar lipids and drug solubilization in biorelevant media. We studied the effect of 26 polar lipids of the fatty acid, phospholipid or monoglyceride type on the solubilization of fenofibrate in a two-stage <i>in vitro</i> GI tract model. The main trends were checked also with progesterone and danazol.<br />Based on their fenofibrate solubilization efficiency, the polar lipids can be grouped in 3 main classes. Class 1 substances (n = 5) provide biggest enhancement of drug solubilization (>10-fold) and are composed only by unsaturated compounds. Class 2 materials (n = 10) have an intermediate effect (3-10 fold increase) and are composed primarily (80 %) of saturated compounds. Class 3 materials (n = 11) have very low or no effect on drug solubilization and are entirely composed of saturated compounds.<br />The observed behaviour of the polar lipids was rationalized by using two classical physicochemical parameters: the acyl chain phase transition temperature (<i>T</i><sub>m</sub>) and the critical micellar concentration (CMC). Hence, the superior performance of class 1 polar lipids was explained by the double bonds in their acyl chains, which: (1) significantly decrease <i>T</i><sub>m</sub>, allowing these C18 lipids to form colloidal aggregates and (2) prevent tight packing of the molecules in the aggregates, resulting in bigger volume available for drug solubilization. Long-chain (C18) saturated polar lipids had no significant effect on drug solubilization because their <i>T</i><sub>m</sub> was much higher than the temperature of the experiment (<i>T</i> = 37 C) and, therefore, their association in colloidal aggregates was limited. On the other end of the spectrum, the short chain octanoic acid manifested a high CMC (50 mM), which had to be exceeded in order to enhance drug solubilization. When these two parameters were satisfied (C > CMC, <i>T</i><sub>m</sub> < <i>T</i><sub>exp</sub>), the increase of the polar lipid chain length increased the drug solubilization capacity (similarly to classical surfactants), due to the decreased CMC and bigger volume available for solubilization.<br />The hydrophilic head group also has a dramatic impact on the drug solubilization enhancement, with polar lipids performance decreasing in the order: choline phospholipids > monoglycerides > fatty acids.<br />As both the acyl chain length and the head group type are structural features of the polar lipids, and not of the solubilized drugs, the impact of <i>T</i><sub>m</sub> and CMC on solubilization by polar lipids should hold true for a wide variety of hydrophobic molecules. The obtained mechanistic insights can guide rational drug formulation development and thus support modern drug discovery pipelines.<br /> | Vladimir Katev; Zahari Vinarov; Slavka S. Tcholakova | Drug Discovery and Drug Delivery Systems; Biophysical Chemistry; Self-Assembly; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dad842e653fdfdb34e1/original/mechanisms-of-drug-solubilization-by-polar-lipids-in-biorelevant-media.pdf |
612abdbd27d9065e3b782cfd | 10.26434/chemrxiv-2021-4lgcl | Molecular prosthetics for long-term functional imaging with fluorescent reporters | Voltage-sensitive fluorescent reporters can reveal fast changes in membrane potential in neurons and cardiomyocytes. However, in many cases, illumination in the presence of the fluorescent reporters results in disruptions to action potential shape that limits the length of recording sessions. We show here that a molecular prosthetic approach, previously limited to fluorophores, rather than indicators, can be used to substantially prolong imaging in neurons and cardiomyocytes. | Vincent Grenier; Kayli Martinez; Brittany Benlian; Derek Garcia-Almedina; Benjamin Raliski; Steven Boggess; Johnathan Maza; Samantha Yang; Evan Miller | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Photochemistry (Org.); Imaging; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2021-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612abdbd27d9065e3b782cfd/original/molecular-prosthetics-for-long-term-functional-imaging-with-fluorescent-reporters.pdf |
60c74aabbb8c1ae36b3db055 | 10.26434/chemrxiv.12167916.v2 | Mapping C−H•••M interactions in confined spaces: (α-ICyDᴹᵉ)Au, Ag, Cu complexes reveal “contra-electrostatic H-bonds” masquerading as anagostic interactions | <p>What happens when a C−H bond is forced to interact with unpaired pairs of electrons at a positively charged metal? Such interactions can be considered as “contra-electrostatic” H-bonds, which combine the familiar orbital interaction pattern characteristic for the covalent contribution to the conventional H-bonding with an unusual contra-electrostatic component. While electrostatics is strongly stabilizing component in the conventional C−H<b>•••</b>X bonds where X is an electronegative main group element, it is destabilizing in the C−H<b>•••</b>M contacts when M is Au(I), Ag(I), or Cu(I) of NHC−M−Cl systems. Such remarkable C−H<b>•••</b>M interaction became experimentally accessible within (α-ICyD<sup>Me</sup>)MCl, NHC−Metal complexes embedded into cyclodextrins. Computational analysis of the model systems suggests that the overall interaction energies are relatively insensitive to moderate variations in the directionality of interaction between a C−H bond and the metal center, indicating stereoelectronic promiscuity of fully filled set of <i>d</i>-orbitals. A combination of experimental and computational data demonstrates that metal encapsulation inside the cyclodextrin cavity forces the C−H bond to point toward the metal, and reveals a still attractive “contra-electrostatic” H-bonding interaction.</p> | Gabriel dos Passos Gomes; Guangcan Xu; Xiaolei Zhu; Lise-Marie Chamoreau; Yongmin Zhang; Olivia Bistri Aslanoff; Sylvain Roland; Igor Alabugin; Matthieu Sollogoub | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aabbb8c1ae36b3db055/original/mapping-c-h-m-interactions-in-confined-spaces-i-cy-d-me-au-ag-cu-complexes-reveal-contra-electrostatic-h-bonds-masquerading-as-anagostic-interactions.pdf |
60c73fa2469df49e47f42b18 | 10.26434/chemrxiv.7462067.v1 | Evaluating Large-Scale STEM Outreach Efficacy with a Consistent Theme: Thermodynamics for Elementary School Students | A biannual chemistry demonstration-based show named “Energy and U” was created to extend the general outreach themes of STEM fields and a college education with a specific goal: to teach the First Law of Thermodynamics to elementary school students. Energy is a central concept in chemical education, most STEM disciplines, and it is the concept at the foundation of many of the greatest challenges faced by society today. The effectiveness of the program was analyzed using a clicker survey system. This study provides one of the first examples of incorporating real-time feedback into large- scale chemistry-based outreach events for elementary school students in order to quantify and better understand the broader impact and learning outcomes. | Joseph DeWilde; Esha Rangnekar; Jeffrey Ting; Joseph Franek; Frank S. Bates; Marc A. Hillmyer; David A. Blank | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fa2469df49e47f42b18/original/evaluating-large-scale-stem-outreach-efficacy-with-a-consistent-theme-thermodynamics-for-elementary-school-students.pdf |
610a4c5a40c8bdfa0e9aa692 | 10.26434/chemrxiv-2021-4722v | A sensitive and compact optical detector based on lock-in amplification | We report a sensitive, fixed-wavelength, lock-in-based optical detector built from a light-emitting diode, two colour filters, a photodetector, a small number of discrete analogue components, and a low-cost microcontroller development board. We describe the construction, operating principle, use and performance of the optical detector, which may be used for both absorption- and fluorescence- measurements in either a 10-mm pathlength cuvette or a low-volume (< 100 μl) flow-cell. For illustrative purposes the detector is applied here to a cholesterol assay based on the enzyme-mediated conversion of (non-emissive) Amplex Red into the fluorescent dye resorufin, providing a detection limit of ~200 nM – some four orders of magnitude lower than the typical concentration of cholesterol in human serum. (The resorufin molecule itself is detectable down to concentrations of ~20 nM). The system may be readily adapted to other biomolecules through a simple change of enzyme. | Andrew J Harvie; Surendra K Yadav; John C de Mello | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Apparatus; Biochemical Analysis | CC BY 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610a4c5a40c8bdfa0e9aa692/original/a-sensitive-and-compact-optical-detector-based-on-lock-in-amplification.pdf |
60c74ab9ee301cb2e9c79cc0 | 10.26434/chemrxiv.12245537.v1 | Molecular Doping in Multi-Molecule Polymer-Dopant Complexes Shows Reduced Coulomb Binding | <p>The mechanistic study of molecular doping of organic semiconductors (OSC) requires</p><p>an improved understanding of the role and formation of integer charge transfer complexes</p><p>(ICTC) on a microscopic level. In the present work we go one crucial step beyond</p><p>the simplest scenario of an isolated bi-molecular ICTC and study ICTCs formed of</p><p>up to two (poly[2,6-(4,4-bis(2-ethylhexyl)-4H-cyclopenta[2,1-b,3,4-b”]dithiophene)-alt-4,7-(2,1,3-</p><p>benzothiadiazole)](PCPDT-BT) oligomers and up to two CN6-CP molecules. We find that depending</p><p>on geometric arrangement, complexes containing two conjugated oligomers and two</p><p>dopant molecules can show p-type doping with double integer charge transfer, resulting in either</p><p>two singly doped oligomers or one doubly doped oligomer. Interestingly, compared to an individual</p><p>oligomer-dopant complex, the resulting in-gap states on the doped oligomers are significantly</p><p>lowered in energy. Indicating that, already in the relatively small systems studied here, Coulomb</p><p>binding of the doping-induced positive charge to the counter-ion is reduced which is an elemental</p><p>step towards generating mobile charge carriers through molecular doping.</p> | Chuanding Dong; Stefan Schumacher | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ab9ee301cb2e9c79cc0/original/molecular-doping-in-multi-molecule-polymer-dopant-complexes-shows-reduced-coulomb-binding.pdf |
67ca1536fa469535b94460c7 | 10.26434/chemrxiv-2025-z97l3 | Controlled Formation of DNA Condensates as Artificial Nuclei in Monodisperse Giant Vesicles | Several studies have attempted to replicate the complex hierarchy of eukaryotic cells for the bottom-up construction of artificial cells. Specifically, reconstruction of liquid–liquid phase separation systems as membrane-less organelles is one of the key focuses of this research field, with DNA condensates acting as versatile building blocks whose associative interactions can be precisely controlled via sequence design. However, such control is only possible at the nanoscale as control over the size and morphology of the lipid vesicles and liquid–liquid phase separation systems at the meso-to-microscale is determined by the kinetic aspects of their formation processes. Microfluidics is well-suited for controlling dynamic molecular assemblies at the cellular scale. In this study, we report the controlled condensation of DNA nanostars in monodisperse giant vesicles (GVs) generated using a microfluidic device by manipulating the concentrations of DNA and salt associated with the GV volume changes. Our approach facilitates the precise control of the dynamics of DNA condensate formation, final size of condensates, formation of multiple condensates, and reversible formation/dissociation of condensates in GVs, serving as a chassis for an artificial cell. Furthermore, our approach eliminates the need for thermal annealing during DNA condensation, supporting the coexistence of enzyme-containing biochemical reaction systems, such as gene expression systems. | Ryotaro Yoneyama; Naoya Morikawa; Ryota Ushiyama; Tomoya Maruyama; Reiko Sato; Mamiko Tsugane; Masahiro Takinoue; Hiroaki Suzuki | Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca1536fa469535b94460c7/original/controlled-formation-of-dna-condensates-as-artificial-nuclei-in-monodisperse-giant-vesicles.pdf |
60c75510bdbb892174a3a778 | 10.26434/chemrxiv.14034623.v1 | Changing the Game of Time Resolved X-Ray Diffraction on the Mechanochemistry Playground by Downsizing | <p>Time
resolved in situ (TRIS) monitoring has revolutionised the study of
mechanochemical transformations but has been limited by available data quality.
We report how a combination of new miniaturised grinding jars together
with innovations in X-ray powder diffraction data collection and state-of-the-art
analysis strategies transform the power of TRIS synchrotron mechanochemical
experiments. Accurate phase compositions, comparable to those obtained by <i>ex
situ</i> measurements, can be obtained with small sample loadings. Moreover, microstructural parameters
(crystal size and microstrain) can be also determined with high confidence. This
strategy applies to all chemistries, is readily implemented, and yields high-quality
diffraction data even using a low energy synchrotron source. This offers a
direct avenue towards the mechanochemical investigation of reactions comprising
scarce, expensive, or toxic compounds. Our strategy is applied to model
systems, including inorganic, metal-organic, and organic mechanosyntheses, resolves
previously misinterpreted mechanisms in mechanochemical syntheses, and promises
broad, new directions for mechanochemical research.<b></b></p> | Giulio
I. Lampronti; Adam Michalchuk; Paolo P. Mazzeo; Ana Belenguer; Jeremy K. M. Sanders; Alessia Bacchi; Franziska Emmerling | Materials Processing; Materials Chemistry; Crystallography; Crystallography – Inorganic; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75510bdbb892174a3a778/original/changing-the-game-of-time-resolved-x-ray-diffraction-on-the-mechanochemistry-playground-by-downsizing.pdf |
60c73f9d702a9b62f5189f32 | 10.26434/chemrxiv.7436795.v1 | General Cyclopropane Assembly via Enantioselective Redox-Active Carbene Transfer to Aliphatic Olefins | Asymmetric cyclopropane synthesis currently requires bespoke strategies, methods, substrates and reagents, even when targeting similar compounds. This limits the speed and chemical space available for discovery campaigns. Here we introduce a practical and versatile diazocompound, and we demonstrate its performance in the first unified asymmetric synthesis of functionalized cyclopropanes. We found that the redox-active leaving group in this reagent enhances the reactivity and selectivity of geminal carbene transfer. This effect enabled the asymmetric cyclopropanation of a wide range of olefins including unactivated aliphatic alkenes, enabling the 3-step total synthesis of (–)-dictyopterene A. This unified synthetic approach delivers high enantioselectivities that are independent of the stereoelectronic properties of the functional groups transferred. Our results demonstrate that orthogonally-differentiated diazocompounds are viable and advantageous equivalents of single-carbon chirons<i>.</i> | Marc Montesinos-Magraner; Matteo Costantini; Rodrigo Ramirez-Contreras; Michael E. Muratore; Magnus J. Johansson; Abraham Mendoza | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9d702a9b62f5189f32/original/general-cyclopropane-assembly-via-enantioselective-redox-active-carbene-transfer-to-aliphatic-olefins.pdf |
631d38303940c23643fad9c2 | 10.26434/chemrxiv-2022-4sg1s | Uncertainty Quantification of Michaelis-Menten Kinetic Rates and Its Application to the Analysis of CRISPR-Based Diagnostics | Michaelis-Menten kinetics is an essential model to rationalize enzyme reactions. The quantification of Michaelis-Menten parameters can be very challenging as it is sensitive to even small experimental errors. We here present a quantification of the uncertainty inherent to the experimental determination of kinetic rate parameters for enzymatic reactions. We study the influence of several sources of uncertainty and bias, including the inner filter effect, pipetting errors, number of points in the Michaelis-Menten curve, and flat-field correction. Using Monte Carlo simulations and analyses of experimental data, we compute typical uncertainties of k_cat, K_M, and catalytic efficiency k_cat/K_M. As a salient example, we analyze the extraction of such parameters for CRISPR-Cas systems. CRISPR diagnostics have recently attracted much interest and yet reports of these enzymatic kinetic rates have been highly unreliable and inconsistent. | Alexandre S. Avaro; Juan G. Santiago | Catalysis; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631d38303940c23643fad9c2/original/uncertainty-quantification-of-michaelis-menten-kinetic-rates-and-its-application-to-the-analysis-of-crispr-based-diagnostics.pdf |
671f9c8c98c8527d9ea0e769 | 10.26434/chemrxiv-2024-4tdgm | Molecular Insights into the Adsorption of Deposit Control Additives from Hydrocarbon Fuels | Deposits can reduce engine performance and increase emissions, particularly in modern direct-injection engines. Surfactants known as deposit control additives (DCAs) ad- sorb and self-assemble on the surface of deposit precursors to keep them suspended in the fuel. Here, we show how molecular simulations can be used to virtually screen the ability of surfactants to bind to a major class of carbonaceous deposits, polyaromatic hydrocarbons. We use molecular dynamics with the adaptive biasing force method to generate the potential of mean force as a function of the distance between the surfactants and model deposits in gasoline and diesel fuel surrogates. We find that a zwitterionic surfactant outperforms non-ionic polyisobutylene succinimide for bind- ing to these aromatic species. The amine groups in the succinimide head-group only weakly adsorb on the polyaromatic deposit, while additional functional groups in the zwitterionic surfactant, particularly the ammonium ion, markedly enhance the binding strength. We decompose the adsorption free energies of the surfactants into entropic and enthalpic components, to find that the latter dominates the attraction from these non-aqueous solvents. The adsorption free energy of both surfactants is slightly weaker from n-hexadecane (diesel) than iso-octane (gasoline), which is due to the stronger molecular layering on the deposit of the former. Density functional theory calculations of the adsorption of DCA fragments validate the force field used in the molecular dy- namics simulations and provide further insights into the nature of the intermolecular interactions. The approach introduced here show considerable promise for accelerating the discovery of novel DCAs to facilitate more advanced fuel formulations to reduce emissions. | Carlos Corral-Casas; Carlos Ayestarán-Latorre; Chiara Gattinoni; Mark Brewer; Jörn Karl; Daniele Dini; James P. Ewen | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Interfaces | CC BY 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f9c8c98c8527d9ea0e769/original/molecular-insights-into-the-adsorption-of-deposit-control-additives-from-hydrocarbon-fuels.pdf |
60c73e3a702a9b30d4189cfb | 10.26434/chemrxiv.6723473.v1 | Metal-Organic Framework Glasses with Permanent Accessible Porosity | To date, only several microporous, and even fewer nanoporous, glasses have been produced, always via post synthesis acid treatment of phase separated dense materials, e.g. Vycor glass. In comparison, high internal surface areas are readily achieved in crystalline materials, such as metal-organic frameworks (MOFs). It has recently been discovered that a new family of melt quenched glasses can be produced from MOFs, though they have thus far have lacked the accessible and intrinsic porosity of their crystalline precursors. Here, we report the first glasses that are permanently, and reversibly porous toward incoming gases, without post synthetic treatment. We characterized the structure of these glasses using a range of experimental techniques, and demonstrate pores in the 4-8 angstrom range. The discovery of MOF-glasses with permanent accessible porosity reveals a new category of porous glass materials, that are potentially elevated beyond conventional inorganic and organic porous glasses, by their diversity and tunability. | Chao Zhou; Louis Longley; Andraz Krajnc; Glen J. Smales; Ang Qiao; Ilknur Erucar; Cara M. Doherty; Aaron W. Thornton; Anita
J. Hill; Christopher W. Ashling; Omid T. Qazvini; Seok June Lee; Philip A. Chater; Nicholas J. Terrill; Andrew J. Smith; Yuanzheng Yue; Gregor Mali; David
A. Keen; Shane G. Telfer; Thomas D. Bennett | Hybrid Organic-Inorganic Materials; Liquid Crystals | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e3a702a9b30d4189cfb/original/metal-organic-framework-glasses-with-permanent-accessible-porosity.pdf |
660ed15091aefa6ce1c9b50b | 10.26434/chemrxiv-2024-l7qqv | On the Core Hole Effect to Valence Excitations: Tracking and Visualizing the Same Excitation in XPS Shake-Up and UV-Absorption Spectra | Introducing a core hole significantly alters the electronic structure of a molecule, making various X-ray spectroscopy techniques valuable for investigating the valence electronic structure in the presence of a core hole. In this study, we visually demonstrate the influence of core hole on valence excitations by computing ultraviolet-visible (UV) absorption and the shake-up satellites in X-ray photoelectron spectra (XPS) of pyrrole, furan, and thiophene, This is complemented by the natural transition orbital (NTO) analysis of transitions, both with and without a core hole. Employing equivalent core hole time-dependent density functional theory (ECH-TDDFT) and TDDFT methods, we achieved balanced accuracy for both the two spectra, Our results not only align well with experiments but also facilitate a reliable comparative analysis. We tracked the same involved valence transition in both spectra, offering a vivid illustration of the core hole effect through the alteration in corresponding particle NTOs introduced by a 1s core hole on a C$_\alpha$ or C$_\beta$ atom or the O atom. Our analysis deepens the understanding of the core hole effect on valence transitions which exist in general X-ray spectroscopies. | Jun-Rong Zhang; Sheng-Yu Wang; Weijie Hua | Theoretical and Computational Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660ed15091aefa6ce1c9b50b/original/on-the-core-hole-effect-to-valence-excitations-tracking-and-visualizing-the-same-excitation-in-xps-shake-up-and-uv-absorption-spectra.pdf |
60c74cdb0f50db3a92396f16 | 10.26434/chemrxiv.12551627.v1 | Self-Assembly of N-Heterocyclic Carbenes on Au(111) | The production of ordered arrays of organic molecules on
metallic surfaces by means of self-assembly is one of the
most powerful methods for controlled patterning on the
nanometer scale. Although the self-assembly of sulfurbased ligands has been studied for decades, the thermal
and oxidative instability of these systems introduces
challenges in many potential applications. In recent
years, it has been shown that a new ligand class,
N-heterocyclic carbenes (NHCs), bind to metal surfaces
via a metal–carbon covalent bond, resulting in
monolayers with much greater stability. However,
fundamental questions surrounding self-assembly in this
new ligand class remain unanswered, including the simple
questions of what controls NHC orientation on the
surface and under what conditions they self-assemble.
Herein we describe how NHC structure, surface density,
deposition temperature, and annealing temperature
control mobility, thermal stability, NHC surface
geometry, self-assembly, and the exact chemical nature of
the surface structures. These data provide the first general
set of guidelines to enable the rational design of highly
ordered NHC-based monolayers. Considering that NHCs
may supplant thiols as the functionalization agent of
choice in a wide range of applications, a detailed
understanding of their surface chemistry is crucial for the
success of these next-generation monolayers. | Alex Inayeh; Ryan Groome; Ishwar Singh; Alex Veinot; Felipe Iima; Roberto Miwa; Cathleen Crudden; Alastair McLean | Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cdb0f50db3a92396f16/original/self-assembly-of-n-heterocyclic-carbenes-on-au-111.pdf |
67add7e8fa469535b92930c5 | 10.26434/chemrxiv-2025-w2qd3 | Evaluation of Physicochemical Properties and Metal Electrodeposition from Deep Eutectic Mixtures based on Choline Chloride and Cobalt Chloride Hexahydrate | Deep Eutectic Solvents (DESs) are a novel class of liquid mixtures exhibiting tunable physicochemical properties as a function of the nature and ratio of their components. In this paper, we present the preparation and characterization of mixtures with different molar ratios of choline chloride – cobalt chloride hexahydrate, a system that is reported to form a DES. To define the physicochemical nature of the mixtures, their phase transitions have been studied in detail by Differential Scanning Calorimetry (DSC). Furthermore, the characterization of the systems also included measurements of physicochemical properties such as thermal stability, electrical conductivity, viscosity, density, and electrochemical window. The dependence on temperature of density and electrical conductivity has also been evaluated. Finally, electrodeposition of a uniform layer of cobalt with a very low content of impurities was achieved. The obtained coatings displayed different morphologies depending on the molar ratio of precursors and experimental conditions. | Andrea Volpe; Chiara Pelosi; Celia Duce; Gianluca Ciancaleoni; Luca Bernazzani | Physical Chemistry; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67add7e8fa469535b92930c5/original/evaluation-of-physicochemical-properties-and-metal-electrodeposition-from-deep-eutectic-mixtures-based-on-choline-chloride-and-cobalt-chloride-hexahydrate.pdf |
627d5e2cf053dfb99a19fed9 | 10.26434/chemrxiv-2022-7lcpl | Electron-rich silicon containing phosphinanes for rapid Pd-catalyzed C-X coupling reactions | Palladium-catalyzed cross-coupling reactions are among the most useful and efficient methods for direct access to complex structures in organic synthesis. However, heteroatom-containing compounds can complicate such coupling reactions due to their competitive coordination with the palladium catalyst and electronic effects. As a result, good yields are often only obtained under harsher reaction conditions, such as high temperatures and long reaction times. Here we report the design of a highly active phosphine ligand that provides excellent yields for C-N coupling reactions at ambient temperature. Incorporation of the phosphorus atom into a cyclohexane ring maintains the pyramidal structure of the phosphorus while reducing steric hindrance. This, and a silicon atom in the cyclohexane moiety, results in an electron-rich phosphinane ligand. This novel silicon containing SabPhos ligand can be obtained in excellent yields in a straightforward synthesis. In palladium catalyzed reactions, this ligand facilitates the coupling of a broad range of heteroaryl chlorides via C-C bonds with boronic acids and C-N bonds with secondary amines in excellent yields under mild conditions. | Sabrina Kräh; Iris Kachel; Oliver Trapp | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Ligand Design | CC BY NC 4.0 | CHEMRXIV | 2022-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627d5e2cf053dfb99a19fed9/original/electron-rich-silicon-containing-phosphinanes-for-rapid-pd-catalyzed-c-x-coupling-reactions.pdf |
60c73dd7337d6c6f39e26256 | 10.26434/chemrxiv.5990998.v2 | Who Makes the Call --- and How? | Recently we proposed that mission statements incorporating the concept of reducing uncertainty could provide a framework for learning the bread and depth of information that exists about health and safety. We briefly explained the definition of uncertainty in the context of health and safety, with the unifying principle being that everything you learn about safety is about exerting greater control. Acquiring more knowledge about an experiment, using equipment appropriately, designing experiments well, executing procedures well, and obtaining appropriate training are all mechanisms for increasing control.<div><br /></div><div>Both researchers and their institutions can be the actors exerting control. But who should make the risk-based decisions related to the design of an experiment? Insecurity about the consequences of our own decisions frequently makes us want to have someone else decide a matter about safety, especially when that matter involves a gray area. Here we explain why researchers should be the main decision-makers about the safety of their experiments, with the researchers striving to thoroughly and creatively reduce the uncertainty of the well-being of themselves, their colleagues, and the environment. Even more, after comprehending the unifying principle outlined above for <b>learning</b> information about safety, researchers should make their primary goal in safety to be conceiving mechanisms for exerting greater control over their experiments that <b>go beyond</b> the mechanisms that health and safety practitioners teach. The essay ends by discussing how decision-making by researchers can improve the culture of safety.</div> | Camilla Kao; Che-I Kao | Chemical Education - General | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd7337d6c6f39e26256/original/who-makes-the-call-and-how.pdf |
60c74eeb469df46f23f44591 | 10.26434/chemrxiv.12818891.v1 | A Delocalized Cobaltoviologen with Seven Reversibly Accessible Redox States and Highly Tunable Electrochromic Behaviour | Cobalt(II) mediates electronic coupling between two N-methyl-pyridinium-terpyridine
ligands that are related to redox-active N,N-dialkyl-4,4'-bipyridinium
dications (viologens). Borderline Class II/III electronic delocalization
imparts the cobaltoviologen complex with distinct electronic properties (e.g. 7
accessible redox states) relative to those of viologens, leading to enhanced
electrochromic properties. | Iram F. Mansoor; Derek Wozniak; yilei wu; Mark C. Lipke | Dyes and Chromophores; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Electrochemistry; Ligands (Inorg.); Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eeb469df46f23f44591/original/a-delocalized-cobaltoviologen-with-seven-reversibly-accessible-redox-states-and-highly-tunable-electrochromic-behaviour.pdf |
60c756a6bb8c1a62cf3dc677 | 10.26434/chemrxiv.13671226.v2 | A Post-HF Approach to the Sunscreen Octyl Methoxycinnamate | Octyl methoxycinnamate (OMC) is a commercial sunscreen with excellent UVB filter properties. However, it is known to undergo a series of photodegradation processes that decrease its effectiveness as UVB filter. In particular, the trans (E) form - which is considered so far the most stable isomer - converts to the cis (Z) form under the effect of light.
In this work, by using post-Hartree-Fock approaches (CCSD, CCSD(t) and CCSD+T(CCSD)) on ground state OMC geometries optimized at the MP2 level we show that the cis and trans form of the gas-phase OMC molecule have comparable stability.
Our results suggest that the cis form is stabilized by intra-molecular dispersion interactions, leading to a folded, more compact structure than the trans isomer.<br /> | Ettore Fois; Mario Oriani; gloria tabacchi | Theory - Computational; Physical and Chemical Properties; Quantum Mechanics; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756a6bb8c1a62cf3dc677/original/a-post-hf-approach-to-the-sunscreen-octyl-methoxycinnamate.pdf |
60c752bc469df48667f44c1b | 10.26434/chemrxiv.13340468.v1 | On the Aromaticity and Acidity of 1-Hydroxy-4,5-benzotropylium Derivatives | <p>
The aromaticity of 1-hydroxy-4,5-benzotropylium was assessed
based on experimental and theoretical investigations. An X-ray
crystallographic analysis revealed a decrease of bond alternation in the seven-membered ring of 1-hydroxy-4,5-benzotropylium derivatives compared with that of the parent 4,5-benzotropones,
which is indicative of an increase in aromaticity upon protonation. NICS and AICD calculation also
supported the increased aromaticity of 1-hydroxy-4,5-benzotropylium. The p<i>K</i><sub>a</sub> values for a series of 1-hydroxy-4,5-benzotropylium
derivatives were also determined. </p> | Takuya Kodama; Yuki Kawashima; Zhirong Deng; Mamoru Tobisu | Physical Organic Chemistry; Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752bc469df48667f44c1b/original/on-the-aromaticity-and-acidity-of-1-hydroxy-4-5-benzotropylium-derivatives.pdf |
60c73f5a4c89193c35ad1f58 | 10.26434/chemrxiv.7314746.v1 | Operando EQCM-D with Simultaneous in Situ EIS: New Insights into Interphase Formation in Li-Ion Batteries | Investigation of the SEI formation on Cu current collectors in Li-ion batteries by <i>operando</i> EQCM-D with simultaneous <i>in situ</i> EIS.<br /> | Paul Kitz; Matthew Lacey; Petr Novák; Erik Berg | Electrochemistry; Energy Storage; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5a4c89193c35ad1f58/original/operando-eqcm-d-with-simultaneous-in-situ-eis-new-insights-into-interphase-formation-in-li-ion-batteries.pdf |
60c75912702a9b477418ce30 | 10.26434/chemrxiv.14637741.v1 | Contrasting Effects of Inhibitors Li+ and Be2+ on Catalytic Cycle of Glycogen Synthase Kinase-3β | <div>Ionic lithium shows rare effectiveness for treating bipolar disorder and is a promising drug for treating neurodegenerative diseases. Unfortunately, lithium suffers from significant drawbacks as a drug, mainly a narrow therapeutic window. Among the different targets of lithium, glycogen synthase kinase 3β (GSK-3β) might be the one responsible for its therapeutic effects. Developing alternative, selective inhibitors of this kinase could avoid lithium side effects, but efforts to do so have met little success so far. A detailed, atomistic understanding of Li+ inhibition and a more detailed understanding of the phosphorylation reaction GSK-3β catalyzes would therefore facilitate the development of new drugs. In this study, we use extensive sampling of catalytic states with our mixed quantum-classical dynamics method QM/DMD and binding affinities from a competitive metal affinity (CMA) approach to fill out the atomic scale picture of Li+ GSK-3β inhibition. We compare Li+ action with Be2+, another known inhibitor, and find our results in agreement with in-vitro kinetics studies. Ultimately, our simulations show that Li+ inhibition is driven primarily by directly decreasing the reaction rate of the phosphorylation step, rather than reducing catalytic turnover through tight binding to different GSK-3β states like Be2+ inhibition. The effect of these metals derive from electrostatic differences and especially their smaller atomic radii compared to the native Mg2+ and thus provides insight for the development of GSK-3β inhibitors based on other paradigms.</div> | David Reilley; Zaher Arraf; Anastassia N. Alexandrova | Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75912702a9b477418ce30/original/contrasting-effects-of-inhibitors-li-and-be2-on-catalytic-cycle-of-glycogen-synthase-kinase-3.pdf |
60dbc6f3bc1d6e1cc3cd1df7 | 10.26434/chemrxiv-2021-hm07j-v2 | Synthesis of 1-(1-Arylvinyl)pyridin-2(1H)-ones from Ketones and 2-Fluoropyridine | Pyridone skeletons are found in numerous biologically active molecules and pharmaceuticals. 1-(1-Arylvinyl)pyridin-2(<i>1H</i>)-ones are synthetic intermediates derived from the enamide moiety, and only few examples of the synthesis of 1-(1-arylvinyl)-2-pyridones have been reported. In this work, a simple and efficient procedure for the synthesis of <i>N</i>-vinyl-substituted pyridones from ketones and 2-fluoropyridine in the presence of trifluoromethane sulfonic anhydride, followed by base treatment is described. Various ketones with electron-donating or -withdrawing groups at the benzene rings can be used in this reaction. A preliminary mechanistic study indicates that it is not very likely that both vinyl triflates and vinyl cations play major roles as intermediates in this transformation. The thus obtained pyridones can be subsequently transformed via C–H arylation and radical alkylation reactions. | Takuji Kawamoto; Shunya Ikeda; Akio Kamimura | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60dbc6f3bc1d6e1cc3cd1df7/original/synthesis-of-1-1-arylvinyl-pyridin-2-1h-ones-from-ketones-and-2-fluoropyridine.pdf |
60c744fb4c8919fb44ad28e5 | 10.26434/chemrxiv.9938105.v1 | Transient Supramolecular Assembly by Programmable pH Cycles | <div>Transient self-assembly is a necessary step towards the development of life-like materials. Our approach allows to program pH-driven supramolecular assembly in the time domain with tailorable lag- and life-times, overcoming the limitations of previously described approaches and setting a new standard for active materials design.<br /></div><div><br /></div> | Guido Panzarasa; Alexandre L. Torzynski; Tianqi Sai; Katrina Smith-Mannschott; Eric R. Dufresne | Aggregates and Assemblies; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fb4c8919fb44ad28e5/original/transient-supramolecular-assembly-by-programmable-p-h-cycles.pdf |
60c741cd842e65660edb1f7a | 10.26434/chemrxiv.7965140.v2 | Optimal Designs of Pairwise Calculation: an Application to Free Energy Perturbation in Minimizing Prediction Variability | Predicting binding free energy of ligand-protein complexes has been a grand challenge in the field of computational chemistry since the early days of molecular modeling. Multiple computational methodologies exist to predict ligand binding affinities. Pathway-based Free Energy Perturbation (FEP), Thermodynamic Integration (TI) as well as Linear Interaction Energy (LIE), and Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PBSA/GBSA) have been applied to a variety of biologically relevant problems and achieved different levels of predictive accuracy. Recent advancements in computer hardware and simulation algorithms of molecular dynamics and Monte Carlo sampling, as well as improved general force field parameters, have made FEP a principal approach for calculating the free energy differences, especially when calculating the host-guest binding affinity differences upon chemical modification.<br /><br />Since the FEP-calculated binding free energy difference, denoted ddGFEP only characterizes the difference in free energy between pairs of ligands or complexes, not the absolute binding free energy value of each individual host-guest system, denoted dG, we examine two rarely asked questions in FEP application:<br /><br />1) Which values would be more appropriate as the prediction to assess the ligands prospectively: the calculated pairwise free energy differences, ddGFEP, or the estimated absolute binding energies, d^G, transformed from ddGFEP?<br />2) In the situation where only a limited number of ligand pairs can be calculated in FEP, can the perturbation pairs be optimally selected with respect to the reference ligand(s) to maximize the prediction precision?<br /><br />These two questions underline the viability of an often-neglected assumption in pairwise comparisons: that the pairwise value is sufficient to make a quantitative and reliable characterization of an individual ligand's properties or activities. This implicit assumption would be true if there was no error in each pairwise calculation. Recently pair designs such as multiple pathways or cycle closure analyses provided calculation error estimation but did not address the statistical impact of the two questions above. The error impact is fully minimized by conducting an exhaustive study that obtains all NC2 = N(N-1)/2 pairs for a set N molecules; more if there is directionality (dGi,j != dGj,i). Obviously, that study design is impractical and unnecessary. Thus, we desire to collect the right amount of data that is 1) feasibly attainable, 2) topologically sufficient, and 3) mathematically synthesizable so that we can mitigate inherent calculation errors and have higher confidence in our conclusions.<br /><br />The significance of above questions can be illustrated by a motivating example shown in Figure 1 and Table 1, which considers two different perturbation graph designs for 20 ligands with the same number of FEP perturbation pairs, 19, and the same reference, Ligand 1. These two designs reached different conclusions in rank ordering ligand potencies due to errors inherent in the FEP derived estimates. Based on design A, ligands 5, 7, 14, 15 would be selected as the best four (20%) picks since those d^G estimates are the most favorable. Design B would yield ligands 5, 12, 18, 19 as best for the same reason. Without knowing the true value, dGTrue of the other 19 ligands, we lack a prospective metric to assess which design could be more precise even though, retrospectively, we know that both designs had reasonably good agreement with the true values, as measured through correlation and error metrics. However, the top picks from neither design were consistent with the true top four ligands, which are ligands 7, 10, 12, 18. Yet, if all of the 20C2 =190 pairs could have been calculated as listed in the last column of Table 1, the best four ligands would have been correctly identified. Additionally, the other metrics included in Table 1 were significantly improved. However, as mentioned above, calculating all possible pairs, or even a significant fraction of all possible pairs, is unlikely in practice, especially when number of molecules are large. Given this restriction, is it possible to objectively determine whether design A or B will give more precise predictions?<br /><br />In this report, we investigated the performance of the calculated ddGFEP values compared to the pairwise differences in least squares derived d^G estimates both analytically and through simulations. Based on our findings, we recommend applying weighted least squares to transforming ddGFEP values into d^G estimates. Second, we investigated the factors that contribute to the precision of the d^G estimates, such as the total number of computed pairs, the selection of computed pairs, and the uncertainty in the computed ddGFEP values. The mean squared error, denoted MSE and Spearman's rank correlation, are used as performance metrics.<br /><br />To illustrate, we demonstrated how the structural similarity can be included in design and its potential impact on prediction precision. As in the majority of reported FEP studies on binding affinity prediction, the ddGFEP pairs were selected based on chemical structure similarity. Pairs with small chemical differences are assumed to be more likely to have smaller errors in ddGFEP calculation. Together using the constructed mathematic system and literature examples, we demonstrate that some of pair-selection schemes (designs) are better than the others. To minimize the prediction uncertainty, it is recommended to wisely select design optimality criterion to suit<br />practical applications accordingly.<br /> | Qingyi Yang; Woodrow W. Burchett; Gregory S. Steeno; David L. Mobley; Xinjun Hou | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741cd842e65660edb1f7a/original/optimal-designs-of-pairwise-calculation-an-application-to-free-energy-perturbation-in-minimizing-prediction-variability.pdf |
60c749d44c89190c9aad3133 | 10.26434/chemrxiv.12114987.v1 | Mining the NIST Mass Spectral Library Reveals the Extent of Sodium Assisted Inductive Cleavage in Collision-Induced Fragmentation | Interpretation and annotation of fragmentation mass spectra strongly depends on our knowledge of collision-induced fragmentation mechanisms. Computational methods for interpretation of fragmentation operate in the boundaries of recognized fragmentation rules. The prevalence of non-sodiated fragment ions in sodiated ion fragmentation spectra is not yet fully recognized by the mass spectrometry community. Here, we investigated the extent of “Sodium Assisted Inductive Cleavage” (SAIC), a charge migration fragmentation occurring in the fragmentation spectra of sodiated precursors. The NIST17 fragmentation library was mined for evidence of SAIC. A substantial amount of fragment ions in sodiated precursor spectra can be linked to SAIC. Thus, this fragmentation mechanism must be considered to allow for accurate interpretation of fragmentation spectra. | Marcus Ludwig; Corey D. Broeckling; Pieter Dorrestein; Kai Dührkop; Emma Schymanski; Sebastian Boecker; Louis-Felix Nothias | Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749d44c89190c9aad3133/original/mining-the-nist-mass-spectral-library-reveals-the-extent-of-sodium-assisted-inductive-cleavage-in-collision-induced-fragmentation.pdf |
60c74c270f50db54d2396dc0 | 10.26434/chemrxiv.12424958.v1 | Sequence Analysis and Structure Prediction of SARS-CoV-2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus | <p>This paper
has attempted into the structure prediction and functional analysis of two such
accessory proteins, 9b and ORF14, in the absence of experimental structures.
Sequence analysis, structure prediction, functional characterization, and
evolutionary analysis based on the UniProtKB reviewed the amino acid sequences
of SARS-CoV-2 9b (P0DTD2) and ORF14 (P0DTD3) proteins. Modeling has been presented with the
introduction of hybrid comparative and <i>ab-initio</i>
modeling. The evolutionary analysis of both the proteins of human SARS-CoV-2
indicates close relatedness to the bat coronavirus.</p>
<p> </p> | CHITTARANJAN BARUAH; PAPARI DEVI; DHIRENDRA K SHARMA | Biochemistry; Bioinformatics and Computational Biology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c270f50db54d2396dc0/original/sequence-analysis-and-structure-prediction-of-sars-co-v-2-accessory-proteins-9b-and-orf14-evolutionary-analysis-indicates-close-relatedness-to-bat-coronavirus.pdf |
61b14373dcbea2332a9b4c03 | 10.26434/chemrxiv-2021-x39fb | The Role of Through-Bond Stereoelectronic Effects in the Reactivity of 3-Azabicyclo[3.3.1]nonanes | Hyperconjugation/conjugation through-bond stereoelectronic effects were studied with density functional theory (DFT) in the context of 3-azabicyclo[3.3.1]nonanes to unravel puzzling differences in reactivity between a vinylogous chloride (4) and a vinylogous ester (5). These compounds—whose structures differ only by one substituent—were found to display strikingly different reactivities in hydrochloric acid by Risch and co-workers (J. Am. Chem. Soc. 1991, 113, 9411–9412). Computational analyses of substituent effects, noncovalent interactions, natural bond orbitals, isodesmic reactions, and hydration propensities lead to a model for which the role of remote, through-bond stereoelectronic effects is key to explaining 4 and 5’s diverging reactivity. | Croix Laconsay; Tyler Rho; Dean Tantillo | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b14373dcbea2332a9b4c03/original/the-role-of-through-bond-stereoelectronic-effects-in-the-reactivity-of-3-azabicyclo-3-3-1-nonanes.pdf |
60c74829bdbb8966c8a38f47 | 10.26434/chemrxiv.11860155.v1 | Cellular Uptake and Cytosolic Delivery of a Cyclic Cystine Knot Scaffold | Cyclotides are macrocyclic peptides that have exceptionally stable structures and been reported to penetrate cells, making them promising scaffolds for the delivery of peptide inhibitory sequences to target intracellular proteins. However, their cellular uptake and cytosolic localization have been poorly understood until now, which has limited their therapeutic potential. In this study, the recently developed chloroalkane penetration assay was combined with established assays to characterize the cellular uptake and cytosolic delivery of the prototypic cyclotide, kalata B1. We show that kalata B1 enters the cytosol at low efficiency, but introducing various epitopes, including a single hydrophobic amino acid, into its loop 6 significantly improved its cytosolic delivery. Our results provide a foundation for the further development of a structurally unique class of scaffolds for the delivery of therapeutic cargoes into cells.<br /> | Huawu Yin; Yen-Hua Huang; Kirsten Deprey; Nicholas Condon; Joshua Kritzer; David Craik; Conan Wang | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74829bdbb8966c8a38f47/original/cellular-uptake-and-cytosolic-delivery-of-a-cyclic-cystine-knot-scaffold.pdf |
6114c569424ea35733882a52 | 10.26434/chemrxiv-2021-p8gds | Controlled aggregation properties of modified single amino acids | We report the self-assembled structure formed by Fmoc protected charge single amino acid Fmoc-L-glutamic acid 5-tert-butyl ester (Fmoc-Glu(OtBu)-OH), Fmoc-L-aspartic acid 4-tert-butyl ester (Fmoc-Asp(OtBu)-OH), and Na-Fmoc-Ne-Boc-L-lysine (Fmoc-Lys(Boc)-OH). The self-assembled architecture formed by the charge aliphatic amino acids were assessed under different conditions such as concentration, temperature and pH. Fmoc-Glu(OtBu)-OH assembled to spheres at both lower and higher concentration under room temperature condition. However, it forms a broom stick like morphology at both lower and higher concentration on heating. Fmoc-Asp(OtBu)-OH on the other hand formed rod like at both both low and high concentration and also on hhealing. Fmoc-Lys(Boc)-OH also self-assemble to sphere like morphology in all conditions irrespective of concentration and heating. Since these structure are very intriguing, our future endevorous is to study these structure through different microscopic techniques such as scanning electron microscopy (SEM), Transmission Electron microscopy (TEM). The mechanisms of the structure formation by these amino acids will be characterized by using solution state NMR, FTIR and TGA in future. The self-assembled structures formed by modified amino acids are easy and facile route to design novel nanoarchitectures which may be potentially useful in future for various type of applications in the field of material chemistry, bioscience, biomedical. | Nidhi Gour; Bharti Koshti; Soumick Naskar; Vivekshinh Kshtriya; Hanuman Narode | Biological and Medicinal Chemistry; Nanoscience; Chemical Biology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6114c569424ea35733882a52/original/controlled-aggregation-properties-of-modified-single-amino-acids.pdf |
6736e964f9980725cf4005cd | 10.26434/chemrxiv-2024-db29k-v2 | Electric Vehicle Pattern-based Battery Cycling Dataset and Its Application in Predicting Rapid Degradation | Previous studies aimed at predicting the lifetime of lithium-ion batteries often rely on cycling data characterized by charge and discharge rates that do not reflect the typical usage conditions of electric vehicles (EVs), or they focus on batteries that degrade slowly, limiting their applicability to scenarios where batteries degrade more rapidly. This study introduces a new cycling experiment dataset that mirrors realistic EV charge and discharge profiles and includes conditions that simulate rapid pressure increases due to various side reactions or mechanical impacts.We establish a criterion for identifying cells that experience abrupt capacity fades. Utilizing a two-dimensional convolutional neural network, we accurately classify cells prone to rapid degradation using only the voltage, current and temperature data from the first 3 cycles, achieving over 99% accuracy. Furthermore, we predict the state of health (SOH) of each classified cell at 270 cycles with a root mean square error (RMSE) of less than 2%. | Jaewook Lee; Seonyoung Jegal; Mikyung Chung; Seunghyun Kim; Min Jun Kim; Dong-Wook Koh; Jay H. Lee | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Quality Control | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6736e964f9980725cf4005cd/original/electric-vehicle-pattern-based-battery-cycling-dataset-and-its-application-in-predicting-rapid-degradation.pdf |
61aa1b59bc299cfb7087cccb | 10.26434/chemrxiv-2021-whpsw | Identifying Novel Inhibitors for Hepatic Organic Ani-on Transporting Polypeptides by Machine-learning based Virtual Screening | Integration of statistical learning methods with structure-based modeling approaches is a contemporary strategy to identify novel lead compounds in drug discovery. Hepatic organic anion transporting polypeptides (OATP1B1, OATP1B3, and OATP2B1) are classical off-targets and it is well recognized that their ability to interfere with a wide range of chemically unrelated drugs, environmental chemicals, or food additives can lead to unwanted adverse effects like liver toxicity, drug-drug or drug-food interactions.
Therefore, the identification of novel (tool) compounds for hepatic OATPs by virtual screening approaches and subsequent experimental validation is a major asset for elucidating structure-function relationships of (related) transporters: they enhance our understanding about molecular determinants and structural aspects of hepatic OATPs driving ligand binding and selectivity.
In the present study, we performed a consensus virtual screening approach by using different types of machine learning models (proteochemometric models, conformal prediction models, and XGBoost models for hepatic OATPs), followed by molecular docking of preselected hits using previously established structural models for hepatic OATPs. Screening the diverse REAL drug-like set (Enamine) shows a comparable hit rate for OATP1B1 (36% actives) and OATP1B3 (32% actives), while the hit rate for OATP2B1 was even higher (66% actives). Percentage inhibition values for 44 selected compounds were subsequently determined using dedicated in vitro assays, and guided the priori-tization of several highly potent novel hepatic OATP inhibitors: six (strong) OATP2B1 inhibitors (IC50 values ranging from 0.04 to 6 μM), three OATP1B1 inhibitors (2.69 to 10 μM), and five OATP1B3 inhibitors (1.53 to 10 μM) inhibitors, were identified. Strikingly, two novel OATP2B1 inhibitors were uncovered (C7, H5) which show high affinity (IC50 values: 40 nM and 390 nM) comparable to the recently described estrone-based inhibitor (IC50 = 41 nM).
A molecularly detailed explanation for the observed differences in ligand binding to the three transporters is given by means of structural comparison of the detected binding sites and docking poses.
| Alzbeta Tuerkova; Brandon Bongers; Ulf Norinder; Orsolya Ungvári; Virag Szekely; Andrey Tarnovskiy; Gergely Szakács; Csilla Özvegy-Laczka; Gerard J. P. van Westen; Barbara Zdrazil | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aa1b59bc299cfb7087cccb/original/identifying-novel-inhibitors-for-hepatic-organic-ani-on-transporting-polypeptides-by-machine-learning-based-virtual-screening.pdf |
60c74e5bbdbb895691a39b7d | 10.26434/chemrxiv.12743720.v1 | Elimination of Oxygen Interference in the Electrochemical Detection of Monochloramine, Using In-Situ pH Control at Interdigitated Electrodes | Disinfection
by chloramination of water systems is an alternative to chlorination that is
frequently used in North America. In such a case, monochloramine is used as the
primary source of chlorine for disinfection. Regular monitoring of the residual
concentrations of this species is crucial to ensure adequate disinfection. An
amperometric sensor for monochloramine would provide fast, reagent free
analysis, however the presence of dissolved oxygen in water complicates sensor
development. In this work, we have explored the use of in-situ pH control as a
method of eliminating oxygen as an interferent by conversion of monochloramine
to dichloramine. The electrochemical reduction of dichloramine occurs outside
the oxygen reduction window and is therefore not affected by oxygen
concentration. Potential sweep methods were used to investigate the conversion
of monochloramine to dichloramine at pH 3. The pH control method was used to
calibrate monochloramine concentrations between 1 and 10 ppm, with a detection
limit of 0.03 ppm. Tests were carried out in high alkalinity samples, wherein
it was found that the sensitivity of this method effectively remained
unchanged. Monochloramine was also quantified in the presence of common
interferents (copper, phosphate and iron) which had no significant impact on
the analysis | Ian Seymour; Benjamin O'sullivan; Pierre Lovera; Alan O'Riordan; James Rohan | Electrochemical Analysis; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e5bbdbb895691a39b7d/original/elimination-of-oxygen-interference-in-the-electrochemical-detection-of-monochloramine-using-in-situ-p-h-control-at-interdigitated-electrodes.pdf |
67b8f4fc6dde43c908e9599f | 10.26434/chemrxiv-2025-pk208 | Revealing Anisotropic Growth of Liraglutide Oligomers by Native Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation | Oligomerization is an intriguing problem, particularly at the early stages of precursor formation, where the mechanisms of oligomer growth are difficult to study due to their complexity and heterogeneity. Liraglutide, a widely used drug for diabetes and obesity, has demonstrated various oligomerization outcomes across different studies. In this study, we integrate native ion mobility mass spectrometry (nIM-MS) and molecular dynamics (MD) simulations to unravel the assembly mechanisms of liraglutide oligomers. Our findings reveal that while assembly pathways vary in their steps, they consistently converge into a structure resembling a fuzzy oil drop model. Furthermore, a key residue is identified as a determining factor in oligomerization. The preference for specific shapes varies at different stages of oligomer formation, depending on the oligomer size. A theoretical model is proposed to fit collisional cross-section (CCS) data and is verified through both nIM-MS experiments and MD simulations, ultimately establishing an anisotropic growth mechanism for liraglutide. Additional MD simulations provide deeper insights into monomer conformations, which are closely linked to oligomer formation. A bias toward forming extended conformers is shown to facilitate assembly of larger oligomers in this self-assembling system. | Zhenyu Xi; Syuan-Ting Alex Kuo; Xiao Cong; Xin Yan; David Russell | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b8f4fc6dde43c908e9599f/original/revealing-anisotropic-growth-of-liraglutide-oligomers-by-native-ion-mobility-mass-spectrometry-and-molecular-dynamics-simulation.pdf |
6321bb6c49042a540ad723da | 10.26434/chemrxiv-2022-f71c2 | NMR Signatures and Electronic Structures of Ti-sites in Titanosilicalite-1 from solid-state 47/49Ti NMR Spectroscopy | Although titanosilicalite-1 (TS-1) is among the most successful oxidation catalysts used in industry, its active site structure is still debated. Recent efforts have mostly focused on understanding the role of defect sites and extra-framework Ti. Insights into the positions and distributions of framework tetrahedral Ti sites remain scarce, in part due to the lack of direct characterization techniques with sufficient sensitivity. Here, we report the 47/49Ti solid-state NMR characterization of TS-1 and its molecular models, [Ti(OTBOS)4] and [Ti(OTBOS)3(OiPr)]. Analysis of their spectroscopic signatures, augmented by computational studies, shows pronounced differences that originate from specific arrangements of the second coordination sphere of Ti atoms, yielding information on titanium siting in TS-1. | Lukas Lätsch; Imke B. Müller ; Alia Hassan; Barbara Perrone; Sadig Aghazada; Zachariah J. Berkson ; Alexander V. Yakimov ; Trees De Baerdemaeker; Andrei-Nicolae Parvulescu; Karsten Seidel; J. Henrique Teles ; Christophe Copéret | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6321bb6c49042a540ad723da/original/nmr-signatures-and-electronic-structures-of-ti-sites-in-titanosilicalite-1-from-solid-state-47-49ti-nmr-spectroscopy.pdf |
654d4fd12c3c11ed71197ffd | 10.26434/chemrxiv-2023-965sk | Molecular Tailoring of Phenothiazine Derivatives for High Performance Non-Aqueous Organic Redox Flow Batteries | Non-aqueous organic redox flow batteries (NAORFBs) have gained significant attention as a promising electrochemical energy storage technology, offering numerous advantages such as grid-scale electricity production with variable intermittent delivery, decoupled energy and power density, and simplified manufacturing processes. However, despite their promising attributes, this system faces certain challenges including limited solubility, poor electrochemical stability of radicals, low redox potential, and inadequate ionic conductivity, hampering their widespread commercial utilization. In recent years, molecular engineering has emerged as a transformative tool for designing and synthesizing of high-performance redox-active molecules for NAORFBs. These molecules, such as quinone, nitroxyl radicals, dialkoxybenzenes, phenothiazine, phenazine, pyridiniums, and viologen derivatives, offer precise control over solubility, stability, and redox potential through the strategic introduction or removal of functional groups.
Our team has focused extensively on molecular engineering, with a specific focus on the phenothiazine core. Through a concise synthesis process, we have successfully synthesized a series of finely tuned phenothiazine derivatives with adjustable redox potentials, solubility, and stability. These tailored derivatives have demonstrated remarkable longevity when applied in NAORFBs. The selection of appropriate supporting electrolytes and membranes plays a significant role in achieving high performance RFBs. In this account, we commence by summarizing the results of our comprehensive examination of various supporting electrolytes and commercially available membranes, assessing their effects to stability, electrochemical reversibility, and crossover rates of redox-active molecules such as N-[2-(2-methoxyethoxy)ethyl]phenothiazine (MEEPT). This comprehensive analysis provides a fundamental framework for evaluating the supporting materials for novel catholytes or anolytes. In efforts to fine-tune the solubility and redox potential of phenothiazines, we have employed molecular tailoring techniques. For instance, the introduction of alkyl or alkoxy groups on the nitrogen atom of phenothiazine has significantly improved solubility and electrochemical stability. These modifications have provided neutral molecules miscible with the commonly used organic solvents and allowed their radicals to reach concentrations of up to 0.5 M. However, monosubstituted phenothiazines still exhibit a relatively low usable oxidation potential, at 0.3 V vs. ferrocene/ferrocenium (Fc/Fc+). To address this limitation, we further modified the phenothiazine core by introducing substituents at positions 3 and 7. This alteration resulted in a notable increase in the stable oxidation potential. Notably, N-ethyl-3,7-bis(2-(2-methoxyethoxy)ethoxy)phenothiazine (B(MEEO)EPT) exhibited an oxidation potential of 0.65 V vs. Fc/Fc+. In pursuit of cost-effective NAORFBs, we developed a novel ionic compound named ethylpromethazine bis(trifluoromethanesulfonyl)imide (EPRT-TFSI). Through a concise three-step synthesis, EPRT-TFSI compound displayed a high redox potential of 1.12 V vs Fc/Fc+, a solubility of up to 1.3 M, and an ionic conductivity as high as 25 mS cm-1. The utilization of such ionic compounds eliminates the necessity for additional supporting salts in the electrolytes. Furthermore, we conducted investigations into the stability of radicals at various concentrations, employing different counter anions while maintaining controlled moisture levels in ambient environments. These stability tests provide valuable insights and guidelines for synthesizing other stable redox-active molecules. Our dedicated research efforts have been instrumental in advancing the development of high-performance NAORFBs, bringing us closer to realizing their potential as a prominent energy storage technology.
| Zhiming Liang | Organic Chemistry; Energy; Organic Compounds and Functional Groups; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654d4fd12c3c11ed71197ffd/original/molecular-tailoring-of-phenothiazine-derivatives-for-high-performance-non-aqueous-organic-redox-flow-batteries.pdf |
66fa9c36cec5d6c142acca1b | 10.26434/chemrxiv-2024-rpl60-v2 | Photocatalytic Semi-Hydrogenation of Acetylene to Polymer-Grade Ethylene with Molecular and Metal-Organic Framework Cobaloximes | The semi-hydrogenation of acetylene to ethylene in ethylene-rich gas streams is a high-priority industrial chemical reaction for producing polymer-grade ethylene. Traditional thermocatalytic routes for acetylene reduction to ethylene, despite progress, still require high temperatures and high H2 consumption, possess relatively low selectivity, and use a noble metal catalyst. Light-powered strategies are starting to emerge, given that they have the potential to use directly the abundant and sustainable solar irradiation, but are ineffective. Here we report an efficient, >99.9% selective, visible-light powered, catalytic conversion of acetylene to ethylene. Our catalyst is a homogeneous molecular cobaloxime that operates in tandem with a photosensitizer at room temperature and bypasses the use of non-environmentally friendly and flammable H2 gas feed. The reaction proceeds through a cobalt-hydride intermediate with nearly 100% conversion of acetylene under competitive (ethylene co-feed) conditions after only 50 minutes, and with no evolution of H2 or over-hydrogenation to ethane. We further incorporate the cobaloxime as linker in a metal-organic framework; the result is a heterogeneous catalyst for the conversion of acetylene under competitive (ethylene co-feed) conditions that can be recycled up to six times and remains catalytically active for 48 hours, before significant loss of performance is observed. | Aaron E.B.S. Stone; Anna Fortunato; Xijun Wang; Edoardo Saggioro; Randall Q. Snurr; Joseph T. Hupp; Francesca Arcudi; Luka Dordevic | Catalysis; Heterogeneous Catalysis; Homogeneous Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fa9c36cec5d6c142acca1b/original/photocatalytic-semi-hydrogenation-of-acetylene-to-polymer-grade-ethylene-with-molecular-and-metal-organic-framework-cobaloximes.pdf |
61b0be800e35ebb2d2994dd5 | 10.26434/chemrxiv-2021-zg20r | Non-enzymatic oligonucleotide ligation in photoswitchable coacervate protocells sustains compartment-content coupling | Modern cells are adaptive chemical compartments tightly regulated by an underlying DNA-encoded program. Reproducing such a coupling between information content and chassis in synthetic compartments represents a key step to the assembly of evolvable protocells, but remains challenging. Here, we rationally exploit complexation between end-reactive oligonucleotides able to stack into long physical polymers and a cationic azobenzene photoswitch to produce three different phases – soft solids, liquid crystalline or isotropic coacervates droplets – that promote non-enzymatic oligonucleotide ligation, with a marked phase-dependent reaction efficiency. Changes in the population of polynucleotides during polymerization induce in turn phase transitions that dramatically alter the physical properties of the compartments. Dynamical modulation of coacervate assembly and dissolution via trans-cis azobenzene photoisomerisation is last used to demonstrate cycles of light-actuated oligonucleotide ligation. Overall, by combining a tight reaction-structure coupling and environmental responsiveness, our light-responsive reactive coacervates provide a novel general route to the non-enzymatic synthesis of polynucleotides, and pave the way to the emergence of a primitive genotype-phenotype coupling in membrane-free protocells. | Tommaso Pietro FRACCIA; Nicolas MARTIN | Organic Chemistry; Polymer Science; Supramolecular Chemistry (Org.); Polyelectrolytes - Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b0be800e35ebb2d2994dd5/original/non-enzymatic-oligonucleotide-ligation-in-photoswitchable-coacervate-protocells-sustains-compartment-content-coupling.pdf |
66f50fdb12ff75c3a182f1e6 | 10.26434/chemrxiv-2024-dscn9 | Total Synthesis of Three Classes of Ring C-seco Limonoids | The nimbin-type, salannin-type and nimbolinin-type are
three structurally related classes of ring C-seco limonoids possessing a complicated hexacyclic framework with a broad range of biological activities. Herein, a convergent and divergent route to access these classes was disclosed by the efficient and protecting-group-free syntheses of 52 ring C-seco limonoids. Key transformations include: 1) a catalytic asymmetric intermolecular Diels-Alder reaction to forge the A-ring bearing desired stereochemistry at C4 and C5; 2) a diastereoselective Pd-catalyzed reductive Heck reaction for the formation of the C8-C9 bond; 3) a sulfonyl hydrazone-mediated etherification and a regioselective
5-exo-trig radical cyclization for construction of the central
tetrahydrofuran ring of the natural products; 4) BF3·Et2O-promoted biomimetic skeletal rearrangement reaction of the salannin-type to generate the nimbolinin-type. | Shicheng Jin; Dawei Ma | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f50fdb12ff75c3a182f1e6/original/total-synthesis-of-three-classes-of-ring-c-seco-limonoids.pdf |
63f5af65fcfb27a31f35f8df | 10.26434/chemrxiv-2022-tp1cm-v4 | Detection of fibril nucleation in micrometer-sized protein condensates
and suppression of Sup35NM fibril nucleation by liquid-liquid phase
separation | Elucidating the link between amyloid fibril formation and liquid–liquid phase separation (LLPS) is crucial in understanding the pathologies of various intractable human diseases. However, the effect of condensed protein droplets
generated by LLPS on nucleation (the initial step of amyloid formation) remains unclear because of the lack of available
quantitative analysis techniques. This study aimed to develop a measurement method for the amyloid droplet nucleation rate based on image analysis. We developed a method to fix micrometer-sized droplets in gel for long-term observation of protein droplets with known droplet volumes. By combining this method with image analysis, we determined the nucleation dynamics in droplets of a prion disease model protein, Sup35NM, at the single-event level. We found that the nucleation was
unexpectedly suppressed by LLPS above the critical concentration (C*) and enhanced below C*. We also revealed that the lag time in the Thioflavin T assay, a semi-quantitative parameter of amyloid nucleation rate, does not necessarily reflect nucleation tendencies in droplets. Our results suggest that LLPS can suppress amyloid nucleation, contrary to the conventional hypothesis that LLPS enhances it. We believe that the proposed quantitative analytical method will provide insights into the role of LLPS from a pathological perspective | Mao Fukuyama; Suguru Nishinami; Yoko Maruyama; Taiki Ozawa; Shunsuke Tomita; Yumiko Ohhashi; Motohiro Kasuya; Masao Gen; Eri Chatani; Kentaro Shiraki; Akihide Hibara | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f5af65fcfb27a31f35f8df/original/detection-of-fibril-nucleation-in-micrometer-sized-protein-condensates-and-suppression-of-sup35nm-fibril-nucleation-by-liquid-liquid-phase-separation.pdf |
60c74c1c567dfe2301ec50c1 | 10.26434/chemrxiv.12430067.v1 | A Membrane Transporter Determines the Spectrum of Activity of a Potent DNA-Targeted Hybrid Anticancer Agent | <i>Cytotoxic drugs that are
mechanistically distinct from current chemotherapies are attractive components
of personalized combination regimens for combating aggressive forms of cancer.
To gain insight into the cellular mechanism of a highly potent platinum–acridine hybrid agent, we
performed a correlation analysis of NCI-60 compound screening results and gene
expression profiles. We discovered a plasma membrane transporter, human
multidrug and toxin extrusion protein 1 (hMATE1, SLC47A1), as the dominant
pan-cancer predictor for cancer cell chemosensitivity to the hybrid agent. We
have validated the role of hMATE1 using transporter inhibition, gene knockdown,
and chemical sensitization assays. The results suggest that hMATE1 may have
applications as a molecular marker to identify and target tumors that are likely
to respond to platinum–acridines. Furthermore, enhancement of hMATE1 expression
by epigenetic drugs emerges as a potential co-treatment strategy to sensitize
tumor tissue to platinum–acridines and other anticancer drugs transported by
hMATE1.</i> | Xiyuan Yao; Noah Watkins; Heather Brown-Harding; Ulrich Bierbach | Bioinformatics and Computational Biology; Cell and Molecular Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c1c567dfe2301ec50c1/original/a-membrane-transporter-determines-the-spectrum-of-activity-of-a-potent-dna-targeted-hybrid-anticancer-agent.pdf |
64a3e60e6e1c4c986bc8de2f | 10.26434/chemrxiv-2023-hwwjd | γ-Functional Iminiumthiolactones for Single or Double Modification of Peptides | Thiolactones have been extensively studied as efficient ligation strategy, yet, their reactivity towards bio-based building blocks remains limited. In this manuscript, we present their more reactive successors, iminiumthiolactones (ITL), which show superior reactivity towards amine-containing substrates. Based on the Traut’s reagent we synthesized several ITLs from glycidol precursors and investigated several orthogonal modification reactions. After performing basic calculations on our substrates to substantiate their predicted reactivity, we picked one of our derivatives (γ-allyl functional ITL 3b) to study model reactions and explore the orthogonality of its different reaction pathways. As a more challenging substrate, we further choose Lysozyme C to be modified with our γ-allyl ITL (3b) using low reactant concentrations (1 mM or 50 μM), near-neutral pH (7.4 or 8.0) and stoichiometric reactant ratios. Under the studied conditions, we successfully demonstrate that our ITL derivative exhibits orthogonal and enhanced reactivity in a single or double modification towards biological substrates. As such, we believe that γ-functional ITLs may open up promising opportunities to incorporate biological building blocks into existing functional molecules, polymeric frameworks and materials. | Stefan Mommer; Nina Warner; Caroline Lienert | Biological and Medicinal Chemistry; Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Biochemistry | CC BY 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a3e60e6e1c4c986bc8de2f/original/functional-iminiumthiolactones-for-single-or-double-modification-of-peptides.pdf |
658712cd66c1381729e4d3d2 | 10.26434/chemrxiv-2023-c1c33 | Improving the Conductance Blockage Model of Cylindrical Nanopores – from 2D to Thick Membranes | The ionic current blockage from a nanopore sensor is a fundamental metric for characterizing its dimensions and for sizing and identifying molecules translocating through. Yet, models for precisely predicting the conductance of a nanopore in both an open and a blocked state are lacking, which leads to significant errors in the determination of the expected blockage depth from a given translocating molecule and of the pore diameter and length. Here, using oblate spheroidal coordinates as a framework to study the conductance of a nanopore, we demonstrate that the widely used Kowalczyk et al. model significantly overestimates the contribution from the access region in the presence of a cylindrical obstruction. We present a highly precise analytical model for the blocked conductance of 2D nanopores and extend it to cylindrical pores of varying membrane thicknesses. Using finite element simulations, our results show that errors in the calculation of the conductance blockage are maximal for pores with aspect ratios of d/L≈5, but are minimal for both d/L≫1 and d/L≪1. The model presented is especially precise for ultra-thin membranes, with prediction errors below 3% for all pore sizes tested with a membrane thickness of 0.3 nm. By improving on the conductance model of the nanopore system, more accurate estimates of the expected blockage depth from a translocating molecule and of pore dimensions can be obtained, with great practical value for many biosensing applications. | Martin Charron; Zachary Roelen; Vincent Tabard-Cossa | Nanoscience; Nanofluidics | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658712cd66c1381729e4d3d2/original/improving-the-conductance-blockage-model-of-cylindrical-nanopores-from-2d-to-thick-membranes.pdf |
64e2a54b694bf1540cb20e77 | 10.26434/chemrxiv-2023-znr6r | The Hydrated Structure Factor in Additive Effect on Enantioselective Organocatalytic Transfer Hydrogenation Reactions with Hantzsch Esters | Acid additives were frequently used in amine-catalyzed asymmetric catalysis as a practical strategy for the promotion of reaction activity/selectivity with a reduced amount of chiral catalyst. A fact is that the acid additives were discovered mostly by chance rather than by a logic prediction. Two bioinspired hydrated mechanisms for the organocatalytic transfer hydrogenation reactions were proposed in this work. And the proposed different acid-water-imine hydrated structures involved mechanism could well explain the additive effect supported by the reported experimental data. The new insight shows promise for assisting a logic acid additive screening in cationic imine-mediated asymmetric catalysis. | Liuqun Gu | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e2a54b694bf1540cb20e77/original/the-hydrated-structure-factor-in-additive-effect-on-enantioselective-organocatalytic-transfer-hydrogenation-reactions-with-hantzsch-esters.pdf |
65e603cc9138d23161a79601 | 10.26434/chemrxiv-2023-llpnk-v3 | Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution | Directed evolution (DE) mimics natural selection to improve the functions of a target protein. Machine learning (ML) has significantly streamlined DE by aiding in several steps, which includes identifying starting variants, generating diverse libraries and modeling sequence-fitness relationships. To date, the majority of ML-assisted DE (MLDE) approaches has relied predominantly on sequence information due to the challenges and cost of obtaining protein structure information. Here, we introduce a structure-augmented MLDE (saMLDE) approach for selecting high fitness variants from a library of Protein G B1 domain. We adopted and applied a zero-shot sequence-based prediction method (offering the potential to discover new insights without extensive training data) to select an initial training library of 96 variants for the saMLDE campaign. To leverage protein structure information, we used protein structure prediction with AlphaFold2 and molecular docking simulations performed with Rosetta FlexPepDock, resulting in structure-based features derived with an induced fit model. After three rounds of the saMLDE campaign, we demonstrated that saMLDE incorporating structural information gradually improves the average fitness scores and the precision of predicted binders. In addition, we found that the initial library selection with zero-shot subset selection methods significantly impacted the average fitness scores and precision, consequently influencing the overall directed evolutionary trajectories. | Lane Yutzy; Kenny Nguyen; Peter Vallet; Jianxiong Li; Jielin Yu; Ronggui He; Le Yan; Joohyun Kim; Jangwook Jung | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e603cc9138d23161a79601/original/augmentation-of-structure-information-to-the-sequence-based-machine-learning-assisted-directed-protein-evolution.pdf |
64ab09b0ba3e99daefc9391c | 10.26434/chemrxiv-2023-w0h1p | OpenMSCG: A Software Tool for Bottom-up Coarse-graining | The “bottom-up” approach to coarse-graining – for building accurate and efficient computational models to simulate large-scale and complex phenomena and processes – is an important approach in computational chemistry, biophysics, and materials science. As one example, the multiscale coarse-graining (MS-CG) approach to developing CG models can be rigorously derived using statistical mechanics applied to fine-grained, i.e., all-atom simulation data for a given system. Under a number of circumstances, a systematic procedure such as MS-CG modeling is particularly valuable. Here we present the development of the OpenMSCG software, a modularized open-source software that provides a collection of successful and widely applied bottom-up CG methods, including Boltzmann Inversion (BI), Force-Matching (FM), Ultra-Coarse-Graining (UCG), Relative Entropy Minimization (REM), Essential Dynamics Coarse-Graining (ED-CG), and Heterogeneous Elastic Network Modeling (HeteroENM). OpenMSCG is a high-performance and comprehensive toolset that can be used to derive CG models from large-scale fine-grained simulation data in file formats from common molecular dynamics (MD) software packages, such as GROMACS, LAMMPS and NAMD. OpenMSCG is modulized in the Python programming framework, which allows users to create and customize modeling “recipes” for reproducible results, thus greatly improving the reliability, reproducibility, and sharing of bottom-up CG models and their applications. | Yuxing Peng; Alexander J. Pak; Aleksander E. P. Durumeric; Patrick G. Sahrmann; Sriramvignesh Mani; Jaehyeok Jin; Timothy D. Loose; Jeriann R. Beiter; Gregory A. Voth | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ab09b0ba3e99daefc9391c/original/open-mscg-a-software-tool-for-bottom-up-coarse-graining.pdf |
67a7527d6dde43c9080ebe5d | 10.26434/chemrxiv-2025-t3z9k | Enabling accurate and large-scale explicitly correlated CCSD(T) computations via a reduced-cost and parallel implementation | Parallel algorithms to accelerate explicitly correlated second-order Moller–Plesset (MP2) and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] calculations and benchmarks on extended molecular systems are reported. A hybrid Open Multi-Processing (OpenMP)/Message Passing Interface (MPI) parallel approach is used to distribute the computational load among processor cores and compute nodes. The intermediates at both the MP2 and the CCSD(T) levels are expressed in a density fitting formalism, using only three-index quantities to decrease the amount of data to be stored and communicated. To further reduce compute time, the frozen natural orbital, the natural auxiliary function, and the natural auxiliary basis schemes are implemented in a hybrid parallel manner. The combination of these three approximations and our recent size-consistent explicitly correlated triples correction with the new hybrid parallelization offers a unique accuracy-over-cost performance among explicitly correlated CC methods. Our comprehensive benchmarks demonstrate excellent parallel scaling of the cost-determining operations up to hundreds of processor cores. As demonstrated on the non-covalent interaction energy of the corannulene dimer, highly- accurate explicitly correlated CCSD(T) calculations can be carried out for systems of 60-atoms and 2500 orbitals, which were beyond computational limits without local correlation approximations. This enables various applications, such as benchmarking of or, for certain size ranges, replacing local CCSD(T) or density functional methods as well as the further advancement of robust thermochemistry protocols designed for larger molecules of ca. 20–50-atoms. | Bence Ladóczki; László Gyevi-Nagy; Péter R. Nagy; Mihály Kállay | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a7527d6dde43c9080ebe5d/original/enabling-accurate-and-large-scale-explicitly-correlated-ccsd-t-computations-via-a-reduced-cost-and-parallel-implementation.pdf |
66a5edcd5101a2ffa85a5c56 | 10.26434/chemrxiv-2024-8kzsh | Key Developments in Magnesiothermic Reduction of Silica: Insights into Reactivity and Future Prospects | Porous Si (p-Si) nanomaterials are an exciting class of inexpensive and abundant materials within the field of energy storage. Specifically, porous Si has been explored in battery anodes to improve charge storage capacity, to generate clean fuels through photocatalysis and photoelectrochemical processes, for the stoichiometric conversion of CO2 to value added chemicals, and as a chemical H2 storage material. p-Si can be made from synthetic, natural, and waste SiO2 sources through a facile and inexpensive method called magnesiothermic reduction (MgTR). This yields a material with tunable properties and excellent energy storage capabilities. In order to tune the physical properties that affect performance metrics of p-Si, a deeper understanding of the mechanism of the MgTR and factors affecting it is required. In this perspective, we review the key developments in MgTR and discuss the thermal management strategies used to control the properties of p-Si. Additionally, we explore future research directions and approaches to bridge the gap between laboratory-scale experiments and industrial applications. | Maximilian Yan; Sarah Martell; Siddharth Patwardhan; Mita Dasog | Inorganic Chemistry; Nanoscience; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a5edcd5101a2ffa85a5c56/original/key-developments-in-magnesiothermic-reduction-of-silica-insights-into-reactivity-and-future-prospects.pdf |
679b860f81d2151a028ccb72 | 10.26434/chemrxiv-2025-45zp2 | Deep Learning-based Image Caption Generator for Real-time Monitoring and Predictive Control of Concentration of Polluting gases | The automatic generation of image captions in natural language is a critical and challenging task, particularly in the context of environmental monitoring and control. This paper presents a novel deep learning-driven image captioning system designed for real-time monitoring and predictive control of pollutant gas concentrations. The proposed system leverages advanced machine learning techniques to analyze images captured during gas capture processes, generating semantically rich and grammatically accurate captions that describe the visual content. At the core of the system is a hybrid architecture that integrates a Convolutional Neural Network (CNN) for high-level feature extraction from input images and a Gated Recurrent Unit (GRU) for sequential caption generation. The CNN effectively identifies and extracts relevant features from the images, while the GRU models the temporal dependencies inherent in the data, allowing for the generation of coherent and contextually appropriate captions. This dual approach not only enhances the accuracy of the captions but also facilitates a deeper understanding of the processes being monitored. In addition to caption generation, the system incorporates a predictive control module that utilizes the generated captions to forecast future behaviors of the gas capture processes. This predictive capability enables operators to make informed decisions, optimizing the efficiency and effectiveness of pollutant gas management in industrial applications. The proposed system demonstrates significant potential for real-time applications, providing a robust tool for environmental monitoring and control. By enabling the efficient and sustainable utilization of gases, this innovative approach contributes to the broader goal of reducing environmental impact and promoting cleaner industrial practices. The results indicate that deep learning techniques can significantly enhance the capabilities of image captioning systems, paving the way for their application in various domains beyond environmental monitoring. | Yash Mishra; Kedarnath Senapati | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679b860f81d2151a028ccb72/original/deep-learning-based-image-caption-generator-for-real-time-monitoring-and-predictive-control-of-concentration-of-polluting-gases.pdf |
64c91ad6658ec5f7e58f9496 | 10.26434/chemrxiv-2023-51bpl | Highly porous metal-organic framework liquids and glasses via a solvent-assisted linker exchange strategy of ZIF-8 | By combining the porosity of crystalline metal-organic frameworks (MOFs) with the unique processability of the liquid state, melt-quenched MOF glasses offer exciting opportunities for molecular separation. However, progress in this field is limited by two factors. Firstly, only very few MOFs melt at elevated temperature and transform into stable glasses upon cooling of the corresponding MOF liquid. Secondly, the MOF glasses obtained thus far feature only very small porosities and extremely small pore sizes. Here we demonstrate solvent-assisted linker exchange (SALE) as a versatile method to prepare highly porous melt-quenched MOF glasses from the canonical ZIF-8. Two additional organic linkers are incorporated into the non-meltable ZIF-8, yielding high-entropy, linker-exchanged ZIF-8 derivatives undergoing crystal-to-liquid-to-glass phase transitions by thermal treatment. The ZIF-8 glasses demonstrate unprecedented porosities of about 25%, adsorb large amounts of technologically relevant C3 and C4 hydrocarbons, and feature high kinetic sorption selectivities for the separation of propylene from propane. | Wen-Long Xue; Pascal Kolodzeiski; Hanna Kavaleuskaya; Suresh Vasa; Athanasios Koutsianos; Roman Pallach; Jianbo Song; Louis Frentzel-Beyme; Rasmus Linser; Sebastian Henke | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c91ad6658ec5f7e58f9496/original/highly-porous-metal-organic-framework-liquids-and-glasses-via-a-solvent-assisted-linker-exchange-strategy-of-zif-8.pdf |
66b29f755101a2ffa84caba6 | 10.26434/chemrxiv-2024-ldx87 | Dynamics of amphiphilic poly(ε-caprolactone)
micelles with doxorubicin and transition
temperature predictions using all-atom
molecular dynamics simulation | Despite the advent of novel therapeutics, efficient delivery of antineoplastic drugs
remains a challenge. Biodegradable polymeric micelles represent a promising frontier
by offering enhanced drug solubility, tumor targeting, and controlled release profiles.
However, the underlying dynamics governing the drug encapsulation and solvation
within these micellar structures are still vague and poorly understood. In this
study, we used amphiphilic poly(γ-benzyloxy-ε-caprolactone)-b-poly(γ-2-[2-(2-methoxy
ethoxy)ethoxy]ethoxy-ε-caprolactone) as a model copolymer with doxorubicin as a
model drug and performed all-atom molecular dynamics simulations to understand
the regulating mechanism of the encapsulation process. The results are in good agreement
with the experimental results. In addition, we interpreted the dynamic behavior
of the polymeric micelles and vital intermolecular interactions that play a key role in
drug encapsulation. Our study provides a theoretical approach to obtain insights for
designing and enhancing novel anticancer drug carriers for therapeutics. | Tejas Shah; Mihaela C. Stefan; Hedieh Torabifard | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b29f755101a2ffa84caba6/original/dynamics-of-amphiphilic-poly-caprolactone-micelles-with-doxorubicin-and-transition-temperature-predictions-using-all-atom-molecular-dynamics-simulation.pdf |
65bb2b359138d231612da189 | 10.26434/chemrxiv-2024-9r68l-v2 | Photochemical Dearomative Skeletal Modifications of Heteroaromatics | Dearomatization has emerged as a powerful manifold for rapid construction of 3D molecular architectures
from simple, abundant, and planar (hetero)arenes. The field has evolved beyond the simple
dearomatization driven by new synthetic technology development. With the renaissance of photocatalysis
and expanding the activation mode, the last few years have witnessed impressive developments on
innovative photochemical dearomatization methodologies, enabling skeletal modifications of the
dearomatic structures. They offer truly efficient and useful tools for facile construction of highly complex
structures in synthesis of nature products and drug discovery. In this review, we aim to provide a
mechanistically insightful overview on these innovations based on the degree of skeletal alternation,
categorized into dearomative functionalization and skeletal editing, and highlight their synthetic utilities. | Peng Ji; Kuaikuai Duan; Menglong Li; Zhiyuan Wang; Xiang Meng; Yueteng Zhang; Wei Wang | Physical Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bb2b359138d231612da189/original/photochemical-dearomative-skeletal-modifications-of-heteroaromatics.pdf |
60c75258bdbb892076a3a251 | 10.26434/chemrxiv.13286477.v1 | Zero-field NMR J-Spectroscopy of Organophosphorus Compounds | In this paper, we report the results of theoretical and experimental studies on basic organophosphorus compounds using zero-field NMR, where spin dynamics are investigated in the absence of a magnetic field with the dominant heteronuclear J-coupling. We demonstrate that the zero-field NMR enables distinguishing the chemicals owing to their unique electronic environment even for identical spin systems. Such information can be obtained just in a single measurement, while amplitudes and widths of observed low-field NMR resonances enable to study of processes affecting spin dynamics. An excellent agreement between simulations and measurements of the spectra, particularly in the largest frequency J-couplings range ever reported in zero-field NMR is demonstrated. | Seyma Alcicek; Piotr Put; Vladimir Kontul; Szymon Pustelny | Physical Organic Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75258bdbb892076a3a251/original/zero-field-nmr-j-spectroscopy-of-organophosphorus-compounds.pdf |
67a5177c6dde43c908d60db8 | 10.26434/chemrxiv-2025-n8s5s | Fragmentation of deprotonated plumeran indole alkaloids by electrospray ionization tandem mass spectrometry | The fragmentation of four deprotonated plumeran indole (PIAs), namely alkaloids aspidospermidine (1), demethoxypalosine (2), aspidocarpine (3), and aspidolimine (4) plumeran indole alkaloids (PIA), previously isolated from Aspidosperma spruceanum has been investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS) in the negative ion mode. The fragmentation pathways have been established on the basis of accurate mass data. Our results demonstrated that the main product ions of deprotonated 1-4 result from remote hydrogen rearrangements. The most abundant product ion in the product ion spectrum of 2, 3, and 4 was the result of a ketene elimination (methylketene for 2 and 3, and a ketene for 4) directly from the precursor ion. The product ion of m/z 183 was diagnostic for compound 2, whereas the radical elimination of •CH3 occurred only for 3 and 4, which display an aromatic methoxyl group in their structures. These results indicated that ESI(–)-MS/MS could be also used for the identification of PIAs 1-4 in crude extracts using LC-ESI-MS/MS, especially when the extracts are more complex | Yan Robles; Ricardo Vessecchi; Ivo Vieira; Raimundo Braz-Filho; Antônio Crotti | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Mass Spectrometry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a5177c6dde43c908d60db8/original/fragmentation-of-deprotonated-plumeran-indole-alkaloids-by-electrospray-ionization-tandem-mass-spectrometry.pdf |
60c75387842e65cb18db3f72 | 10.26434/chemrxiv.13503369.v1 | The Use of UiO-Type MOFs in Vapour Phase Soai Reactions | We report a novel vapour phase procedure to perform the Soai reaction in an absolute asymmetric synthesis fashion: the substrate is confined in the pores of the UiO-type MOFs, and vapour phase reactions with Zn(i-Pr)<sub>2</sub> are performed in a sealed environment, Different MOFs lead to different outcomes in terms of enantiomeric excess, handedness of the product and reaction rate. This is one of the first examples of absolute asymmetric synthesis performed inside a MOF. | Giuesppe rotunno; Gurpreet Kaur; Andrea Lazzarini; Carlo Buono; Mohamed Amedjkouh | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75387842e65cb18db3f72/original/the-use-of-ui-o-type-mo-fs-in-vapour-phase-soai-reactions.pdf |
624c5dbe54b5d9e07beb2e75 | 10.26434/chemrxiv-2022-ctcnv | Uncovering the Synchronous Role of Bis-borane with Nucleophilic Solvent as Frustrated Lewis pair in Metal-free Catalytic Dehydrogenation of Ammonia-borane | Metal free catalysis has emerged as a viable alternative for transition metal based catalysts for enabling different chemical processes, particularly for de/hydrogenation reactions. Herein, employing theoretical studies we reveal the unexpected Frustrated Lewis Pair like reactivity of a boron based catalyst, 9,10-dichlorodiboraanthracene and the ethereal solvent to enable dehydrogenation of ammonia-borane (NH3BH3, AB) under mild conditions. The mechanistic channels thus uncovered reveal that the boron catalyst abstracts a hydride from NH3BH3 followed by crucial stabilisation of the NH3BH2+ moiety by the nucleophilic action of the solvent. H2 is released by the combination of hydride and proton from the borohydride moiety and the solvated NH3BH2+ respectively. Catalysis becomes unfeasible if the Lewis base-like action of the ethereal solvent is not taken into consideration. Thus it is suggested that the clandestine partnership of the Lewis Acid, Boron catalyst and the Lewis Base, ethereal solvent, i.e. FLP like action enables dehydrogenation of NH3BH3 in the instant case. | Munia Sultana; Ishita Bhattacharjee; Sourav Bhunya; Ankan Paul | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Frustrated Lewis Pairs; Inorganic Acid/Base Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624c5dbe54b5d9e07beb2e75/original/uncovering-the-synchronous-role-of-bis-borane-with-nucleophilic-solvent-as-frustrated-lewis-pair-in-metal-free-catalytic-dehydrogenation-of-ammonia-borane.pdf |
63ff8cd9897b18336f563e24 | 10.26434/chemrxiv-2023-fh7nz | Morin loaded mesoporous molecular sieves as novel devices to the potential treatment of tumor pathologies | several human pathological conditions. Despite this, the administration of morin represents a challenge due to its low aqueous solubility and high sensitivity. Mesoporous silica materials have emerged as new biocompatible tools for drug delivery, as their pore size can be modulated for maximum surface area to volume ratio. In this contribution, we evaluate the ability of iron-modified mesoporous materials for morin loading and controlled delivery. Methods: The SBA-15 and MCM-41 sieves were synthesized and modified with iron. Characterization by transmission electron microscopy, XRD and UV-Vis revealed adequate pore size and agglomerates of very small metallic nanospecies (nanoclusters), without larger iron oxide nanoparticles. FT-IR spectra confirmed the presence of silanol groups in the solid hosts, which can interact with different groups present in the morin molecules. The incorporation of morin was also corroborated by UV-Vis spectroscopy. Results: SBA-15 materials were more efficient in terms of morin loading capacity due to their larger pore diameter. Finally, biosafety studies using normal epithelial cells revealed that neither the loaded nor the unloaded materials exerted toxicity, even at doses of 1 mg/ml. Conclusions: these findings expand knowledge about mesoporous materials as suitable carriers of flavonoids with the aim of improving therapies for a wide range of pathologies. | María Gabriela Montiel Schneider; María Julia Martin; Natalia Cuello; Florencia Favatela; Claudia Gentili; Verónica Elias; Griselda Eimer; Verónica Lassalle | Materials Science; Biocompatible Materials; Biological Materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ff8cd9897b18336f563e24/original/morin-loaded-mesoporous-molecular-sieves-as-novel-devices-to-the-potential-treatment-of-tumor-pathologies.pdf |
67adbe90fa469535b9274e62 | 10.26434/chemrxiv-2025-n4pfz | Carbene-Supported Triphosphorus Anion | The stabilization of reactive anionic main group species utilizing carbenes constitutes a burgeoning and scarcely explored field. Herein, we report the synthesis of an anionic triphosphorus [P3]ˉ unit, supported by two cyclic (alkyl)(amino)carbenes (CAACs) in the form of potassium salts. This anion features a planar W-shaped conjugated C-P-P-P-C framework, characterized by 5-center-6-electron π delocalization and an additional σ lone pair located on each of the three phosphorus atoms. Remarkably, this anion is not only strongly basic and nucleophilic but also reductive, positioning versatile functionalization of the [P3] unit. This approach has advanced the isolation of unique carbene-supported cores, including [HP3], [P3N3R]ˉ, [P3O]ˉ and [P6], thus expanding the frontiers of phosphorus chemistry. Moreover, the addition of the two phosphorus fragments upon P-P bond cleavage of the [P3] unit to the triple bond of diphenylacetylene for the synthesis of an extended conjugated system was described. | Yanbo Mei; Xue-Yi He; Jiancheng Li; Mo Liu; Qiuming Liang; Chengbo Yang; Liu Leo Liu | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67adbe90fa469535b9274e62/original/carbene-supported-triphosphorus-anion.pdf |
679418d16dde43c908447808 | 10.26434/chemrxiv-2025-qxw48-v2 | V2O5 as Potential Hole Transport Material for Tin-based Non-toxic
Perovskite Solar Cells | Perovskite solar cells (PSCs) have emerged as a promising technology due to their remarkable efficiency and stability improvements over the years. However, commercialization is hindered by challenges such as material toxicity, high costs, and limited stability. To address these issues, this study investigates vanadium pentoxide (V2O5) as a novel, cost-effective hole transport material (HTM) for non-toxic perovskite solar cells. A unique cell structure comprising V2O5 as the HTM, CsSnI3 as the absorber material, and WS2 as the electron transport material (ETM) was proposed and optimized using SCAPS-1D simulations. The optimized device achieved a power conversion efficiency (PCE) of 24.71%, with an open-circuit voltage (Voc) of 0.8489 V, a short-circuit current density (Jsc) of 35.601 mA/cm², and a fill factor (FF) of 81.75%. Additionally, the V2O5-based structure demonstrated the lowest material costs compared to conventional HTMs. By addressing the challenges of lead toxicity and high production costs, this study highlights the potential of V2O5 as an efficient and sustainable alternative for next-generation perovskite solar cells. | Rukon Uddin; Subrata Bhowmik | Energy; Photovoltaics | CC BY 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679418d16dde43c908447808/original/v2o5-as-potential-hole-transport-material-for-tin-based-non-toxic-perovskite-solar-cells.pdf |
624c5bf03b5f99130dcf1664 | 10.26434/chemrxiv-2022-9jcht | Effect of current density on the Li – Li6PS5Cl solid electrolyte interphase | Understanding the nature and evolution of interphasial products at the Li metal – solid electrolyte interface is crucial in solid-state lithium batteries (SSBs). Using operando X-ray photoelectron spectroscopy and electrochemical impedance spectroscopy, we highlight the role of lithium plating current density on the evolution of the Li6PS5Cl–Li solid electrolyte interphase (SEI) composition in a “lithium-free” anode configuration. We conclude that higher current densities facilitate the formation of a more uniform, Li3P-rich SEI thereby decreasing the electrode-electrolyte interfacial impedance. This study improves understanding of the role of plating kinetics in lithium-free SSBs and suggests a new strategy to modulate electrode-electrolyte interphases to achieve more efficient lithium plating. | Sudarshan Narayanan; Ulderico Ulissi; Joshua Gibson; Yvonne Chart; Robert Weatherup; Mauro Pasta | Materials Science; Energy; Ceramics; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624c5bf03b5f99130dcf1664/original/effect-of-current-density-on-the-li-li6ps5cl-solid-electrolyte-interphase.pdf |
60c756069abda2a7e9f8e484 | 10.26434/chemrxiv.14195648.v1 | Limited Accessibility to Surface Area Generated by Thermal Pretreatment of Electrodes Reduces Its Impact on Redox Flow Battery Performance | Thermal oxidation of carbon electrodes is a common approach to improving flow battery performance. Here, we investigate how thermal pretreatment increases electrode surface area and the effect this added surface area has on electrode performance. Specifically, we rigorously analyze the surface area of Freudenberg H23 carbon paper electrodes, a binder-free model material, by systematically varying pretreatment temperature (400, 450, and 500 °C) and time (0 to 24 h) and evaluating changes in the physical, chemical, and electrochemical properties of the electrodes. We compare physical surface area, measured by a combination of gas adsorption techniques, to surface area measured via electrochemical double layer capacitance. We find good agreement between the two at shorter treatment times (0-3 h); however, at longer treatment times (6-24 h), the surface area measured electrochemically is an underestimate of the physical surface area. Further, we use gas adsorption to measure a pore size distribution and find that the majority of pores are in the micropore range (< 2 nm), and ca. 60% of the added surface area are in the sub-nanometer (< 1 nm) pore size range. We postulate that the solvated radii and imperfect wetting of electrochemical species may hinder active species transport into these recessed regions, explaining the discrepancy between electrochemical and physical surface area. These results are supported with in situ flow cell testing, where single-electrolyte polarization measurements show little improvement with increasing surface area. Further, using a simple convection-reaction model to simulate electrode overpotential as a function of surface area, we find that increasing surface area improves the performance to a point, but the mass transport to and the catalytic activity of the reaction sites offer greater comparative impact. Ultimately, this work aims to inform the design of electrodes that offer maximal accessible surface area to redox species. | Katharine Greco; Jude Bonesteel; Nicolas Chanut; Charles Wan; Yet- Ming Chiang; Fikile Brushett | Carbon-based Materials; Electrochemical Analysis; Electrochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756069abda2a7e9f8e484/original/limited-accessibility-to-surface-area-generated-by-thermal-pretreatment-of-electrodes-reduces-its-impact-on-redox-flow-battery-performance.pdf |
60c73f9c469df4fe31f42b04 | 10.26434/chemrxiv.7418429.v1 | Ba3CrN3H: A New Nitride-Hydride with Trigonal Planar Cr4+ | Single crystal synthesis of a new nitride-hydride Ba3CrN3H. X-ray diffraction, nuclear magnetic resonance, and bond-valance sum and density functional theory calculations confirmed the presence and location of the anionic hydrogen in this compound. | Nathaniel W. Falb; Jennifer N. Neu; Tiglet Besara; Jeffrey B. Whalen; David J. Singh; Theo Siegrist | Solid State Chemistry; Transition Metal Complexes (Inorg.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f9c469df4fe31f42b04/original/ba3cr-n3h-a-new-nitride-hydride-with-trigonal-planar-cr4.pdf |
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