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6794dc0c6dde43c90857c7e0 | 10.26434/chemrxiv-2025-1np7n | Structural Order of Mg-Stabilized Amorphous Calcium Carbonate and Its Associated Phase Transformation | Biominerals formed by marine organisms exhibit intricate structures and support a remarkable range of functionalities. Recent advances in our understanding of biomineralization highlight the pivotal role of magnesium-stabilized amorphous calcium carbonate (Mg-ACC) as a transient precursor in the formation of calcareous biominerals. This feature article summarizes recent in vitro studies of Mg-ACC, illustrating the concepts of particle attachment, secondary nucleation, domain segregation, and mesocrystal formation. Some conceptual issues associated with the ongoing debate between classical nucleation theory and non-classical nucleation theory are discussed. We suggest that solid-state NMR measurements of the van Vleck second moment provide a stringent test for any proposed atomic model of Mg-ACC. The coordination environment of Mg2+ ions and the significance of bicarbonate ions in Mg-ACC are discussed. The diffusion of Mg2+ ions within the calcitic lattice of high-Mg calcite offers a mechanistic insight into the 'dolomite problem'. The fusion of neighboring high-Mg calcite spherulites highlights their potential role as versatile building blocks for calcareous biomineral skeletal frameworks. | Shu Li Li; Chieh Tsao; Sheng-Yu Yang; Jerry Chun Chung Chan | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6794dc0c6dde43c90857c7e0/original/structural-order-of-mg-stabilized-amorphous-calcium-carbonate-and-its-associated-phase-transformation.pdf |
6632dbbb91aefa6ce1ea4eb7 | 10.26434/chemrxiv-2024-bhprr | Modeling Intermolecular Interactions With XDM Dispersion Corrections to Neural Network Potentials | Neural network potentials (NNPs) are an innovative approach for calculating the potential energy and forces of a chemical system. In principle, these methods are capable of modeling large systems with an accuracy approaching that of a high-level ab initio calculation but with a much smaller computational cost. Due to their training to density-functional theory (DFT) data and neglect of long-range interactions, some classes of NNPs require an additional term to include London dispersion physics. In this perspective, we discuss the requirements for a dispersion model for use with an NNP, focusing on the MLXDM (Machine Learned eXchange Hole Dipole Moment) model developed by our groups. This model is based on the DFT-based XDM dispersion correction, which calculates interatomic dispersion coefficients in terms of atomic moments and polarizabilities, both of which can be effectively approximated using neural networks. | Nguyen Thien Phuc Tu; Siri Williamson; Erin Johnson; Christopher Rowley | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6632dbbb91aefa6ce1ea4eb7/original/modeling-intermolecular-interactions-with-xdm-dispersion-corrections-to-neural-network-potentials.pdf |
60c757e7702a9b10d118cbc1 | 10.26434/chemrxiv.14447676.v1 | A Thermogelling Organic-Inorganic Hybrid Hydrogel with Excellent Printability, Shape Fidelity and Cytocompatibility for 3D Bioprinting | In this study, an advanced hybrid ink was developed, based on a thermogelling block copolymer, alginate and clay. The reversible thermogelling and shear thinning properties polymer acts at the same time as a fugitive material on the macromolecular level and facilitates the cell-laden extrusion based bioprinting. <br /> | Chen Hu; Taufiq Ahmad; Malik Salman Haider; Lukas Hahn; Philipp Stahlhut; Jürgen Groll; Robert Luxenhofer | Aggregates and Assemblies; Biocompatible Materials; Composites; Hybrid Organic-Inorganic Materials; Materials Processing; Biopolymers; Hydrogels; Organic Polymers; Polymer blends; Polymer scaffolds; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757e7702a9b10d118cbc1/original/a-thermogelling-organic-inorganic-hybrid-hydrogel-with-excellent-printability-shape-fidelity-and-cytocompatibility-for-3d-bioprinting.pdf |
60c74022bb8c1af8833d9d4d | 10.26434/chemrxiv.7315358.v2 | Stereoselective Aminoiodination of Activated Alkynes with Organoiodine(III) Reagents and Amines via Multiple-Site Functionalization: Access to Iodinated Enamines and N-Aryl Indoles | <p>A stereoselective aminoiodination of activated alkynes with
PhI(OAc)<sub>2</sub> and amines <i>via</i> multiple-site
functionalization to afford (<i>Z</i>)diethyl
2-(diphenylamino)-3-iodomaleate derivatives with superior yields has been described.
The key feature of this reaction is the incorporation of iodide
and aryl group concurrently in the same molecule in a stereoselective manner by
employing PhI(OAc)<sub>2</sub>
as electrophilic reagent as well as iodide and aryl group source. The
high stereoselectivity of the reaction can be explained based on the structure
of the possible intermediates, the conformations of which controlled by the
hydrogen bonding, steric hindrance and electrostatic attractions. This
reaction proceeds under mild conditions, providing various dialkyl
2-(diphenylamino)-3-iodomaleates by a single operation starting
from activated alkynes. The robustness of our strategy is revealed by making of
bis (dialkyl 2-(diphenylamino)-3-iodomaleate) derivatives involving formation
of four new C-N bonds and two C-I bonds with a single step. The synthesized
inactive 3° enamines (dialkyl
2-(diphenylamino)-3-iodomaleates) could be further transformed
into highly substituted indoles via Pd
catalyzed C-H and C-I activation under non-acidic conditions. </p><br /> | sagar arepally; Narenderreddy Katta; Ajoy Chamuah; Sharada Duddu. S | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74022bb8c1af8833d9d4d/original/stereoselective-aminoiodination-of-activated-alkynes-with-organoiodine-iii-reagents-and-amines-via-multiple-site-functionalization-access-to-iodinated-enamines-and-n-aryl-indoles.pdf |
60c74e39ee301cd98ac7a472 | 10.26434/chemrxiv.12725666.v1 | A Visible and Near-Infrared Light Activatable Diazo-Coumarin Probe for Fluorogenic Protein Labeling in Living Cells | Chemical modification
of proteins in living cells permits valuable glimpses into the molecular
interactions that underpin dynamic cellular events. While genetic engineering
methods are often preferred, selective labeling of endogenous proteins in a complex
intracellular milieu with chemical approaches represents a significant
challenge. In this study, we report novel diazo-coumarin compounds that can be
photo-activated by visible (430‒490 nm) and near-infrared light (800 nm) irradiation to photo-uncage
reactive carbene intermediates, which could subsequently undergo insertion
reaction with concomitant fluorescence “turned-on”. With these new molecules in
hand, we have developed a new approach for rapid, selective and fluorogenic labeling
of endogenous protein in living cells. By using CA-II and eDHFR as model
proteins, we demonstrated that subcellular localization of proteins can
be precisely visualized by live-cell imaging and protein levels can be reliably
quantified in multiple cell types using flow cytometry. Dynamic
protein regulations such as hypoxia induced CA-IX accumulation can also be
detected. In addition, by
two-photon excitation with an 800 nm laser, cell-selective labeling can also be
achieved with spatially controlled irradiation. Our method circumvents the
cytotoxicity of UV light and obviates the need for introducing external
reporters with “click chemistries”. We believe that this approach of
fluorescence labeling of endogenous protein by bioorthogonal photo-irradiation
opens up exciting opportunities for discoveries and mechanistic interrogation
in chemical biology. | Sheng-Yao Dai; Dan Yang | Bioorganic Chemistry; Photochemistry (Org.); Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e39ee301cd98ac7a472/original/a-visible-and-near-infrared-light-activatable-diazo-coumarin-probe-for-fluorogenic-protein-labeling-in-living-cells.pdf |
659b5e779138d231616b2e04 | 10.26434/chemrxiv-2024-pd20z | Deep learning of multimodal networks with topological regularization for drug repositioning | Motivation: Computational techniques for drug-disease prediction are essential in enhancing drug discovery and repositioning. While many methods utilize multimodal networks from various biolog-ical databases, few integrate comprehensive multi-omics data, including transcriptomes, proteomes, and metabolomes. We introduce STRGNN, a novel graph deep learning approach that predicts drug-disease relationships using extensive multimodal networks comprising proteins, RNAs, metab-olites, and compounds. We have constructed a detailed dataset incorporating multi-omics data and developed a learning algorithm with topological regularization. This algorithm selectively leverages informative modalities while filtering out redundancies.
Results: STRGNN demonstrates superior accuracy compared to existing methods and has identified several novel drug effects, corroborating existing literature. STRGNN emerges as a powerful tool for drug prediction and discovery. The source code for STRGNN, along with the dataset for perfor-mance evaluation, is available at https://github.com/yuto-ohnuki/STRGNN.git.
| Yuto Ohnuki; Manato Akiyama; Yasubumi Sakakibara | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659b5e779138d231616b2e04/original/deep-learning-of-multimodal-networks-with-topological-regularization-for-drug-repositioning.pdf |
64a5706aba3e99daef8f33df | 10.26434/chemrxiv-2023-gcxt4 | New strategies of Designing Nickel-based Multifunctional Materials for Various Catalytic Applications: New advances | The search for new avenue of designing of novel candidate materials is on the cutting edges research and nanotechnology fields. Highly active, selective and as well as stable materials are required for many catalysis and environmental applications. These avenues include, both simulation and physicochemical methods. Indeed, in the past few decades, the utilization of Ni based materials for nickel composite catalysts synthesis have grown exponentially, as they exhibit powerful catalytic performances. Ni-based catalysts anchored on various forms of matrixes like (Carbons, Polymers, metal oxides, metal carbide, metal sulphide, zeolite, and so fourth) revealed themselves to possess high intrinsic catalytic activity, selectivity and fully stable for hydrogen (H2) release from diverse sources as (Ammonia, and Amine) borane, water splitting, hydrogen iodide, and so on. Also, nickel-based catalysts deserve advanced properties for dry reforming of methane (DRM). Furthermore, Ni-based materials have enhanced properties for several catalytic oxidation reactions including oxygen evolution (OER), alcohol oxidation (AOR), hydrogen oxidation reactions (HOR), and so forth. It is explained that, Ni NPs anchored over aluminosilicates seems to be a perfect model catalyst for organic sulfur removal through the catalytic adsorption process, and also might be extended to other catalysis and environment applications. Hence, it is taught that the upcoming research careers can be deeply focused on these aspects: i) making bimetallic catalysts, ii) the use of a promoter, iii) the use of three distinct supports for a catalyst, and the last one is to fully consider the design route of the catalyst as each method has its unique benefits. Therefore, these aspects will affect the performance of the resulting materials, which will lead to raise the Ni active site, low-temperature processability, and excellent resistance to coke, deactivation, and as well as sintering effects over Ni-based catalysts. These will lead to a suitable advantages for catalyst engineering and their related applications, as Ni-based materials are cost-effective as compared to platinum based materials. | Mamadou Kalan DIALLO | Materials Science; Catalysis; Catalysts; Nanostructured Materials - Materials; Electrocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a5706aba3e99daef8f33df/original/new-strategies-of-designing-nickel-based-multifunctional-materials-for-various-catalytic-applications-new-advances.pdf |
627541826b12b6b69c67dd1d | 10.26434/chemrxiv-2022-q841n | Rediscovering N-Methyltetranitropyrrole – A Versatile High Energy Material via Facile Two-step Eco-friendly Synthetic Approach | A highly efficient 2-step method was developed as an environmentally benign process for the synthesis of N-methyltetranitropyrrole (1) employing metal nitrate/conc. sulphuric acid as nitrating reagent. This method resulted 1 in high purity having higher thermal stability along with reduced sensitivity, which makes it a versatile high energy material. An over-oxidized high energy product was also isolated during optimization | Vikranth Thaltiri; Shanmugapriya V; Yadagiri Thigulla; Pradeepta Panda | Organic Chemistry; Organic Compounds and Functional Groups; Process Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627541826b12b6b69c67dd1d/original/rediscovering-n-methyltetranitropyrrole-a-versatile-high-energy-material-via-facile-two-step-eco-friendly-synthetic-approach.pdf |
60c74cd9f96a00810528784e | 10.26434/chemrxiv.12547262.v1 | Harnessing Chalcogen-bonding Interactions To Establish Conformational Control in Dirhodium(II) Paddlewheel Complexes | Novel well-defined <i>D</i><sub>2</sub>-symmetric dirhodium(II) carboxylate complexes that bear axially chiral binaphthothiophene delta-amino acid derivatives have been developed. Conformational control was achieved through chalcogen-bonding interactions between sulfur and oxygen atoms in each ligand, providing well-defined and uniform asymmetric environments around the catalytically active Rh(II) centers. These structural properties render such complexes excellent catalysts for the inside-type asymmetric intramolecular C–H insertion into alpha-aryl-alpha-diazoacetates to yield a variety of <i>cis</i>- alpha, beta-diaryl gamma-lactones, as well as the corresponding <i>trans</i>-isomers through epimerization, in high diastereo- and enantioselectivities. Short total syntheses of the naturally occurring gamma-lactones cinnamomumolide, cinncassin A<sub>7</sub>, and cinnamomulactone were also accomplished using this conformationally controlled catalyst.<br /><br /> | Takuya Murai; Wenjie Lu; Toshifumi Kuribayashi; Kazuhiro Morisaki; Yoshihiro Ueda; Shohei Hamada; Takahiro Sasamori; Norihiro Tokitoh; Takeo Kawabata; Takumi Furuta | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cd9f96a00810528784e/original/harnessing-chalcogen-bonding-interactions-to-establish-conformational-control-in-dirhodium-ii-paddlewheel-complexes.pdf |
60c74c0f469df48041f43fee | 10.26434/chemrxiv.12062685.v2 | Optimal Dissociation Methods Differ for N- and O-glycopeptides | <p><a>Site-specific characterization of glycosylation requires
intact glycopeptide analysis, and recent efforts have focused on how to best interrogate
glycopeptides using tandem mass spectrometry (MS/MS). Beam-type collisional
activation, i.e., higher-energy collisional dissociation (HCD), has been a
valuable approach, but stepped collision energy HCD (sceHCD) and electron
transfer dissociation with HCD supplemental activation (EThcD) have emerged as
potentially more suitable alternatives. Both sceHCD and EThcD have been used
with success in large-scale glycoproteomic experiments, but they each incur
some degree of compromise. Most progress has occurred in the area
N-glycoproteomics. There is growing interest in extending this progress to
O-glycoproteomics, which necessitates comparisons of method performance for the
two classes of glycopeptides. Here, we systematically explore the advantages and
disadvantages of conventional HCD, sceHCD, ETD, and EThcD for intact
glycopeptide analysis and determine their suitability for both N- and
O-glycoproteomic applications. For N-glycopeptides, HCD and sceHCD generate
similar numbers of identifications, although sceHCD generally provides higher
quality spectra. Both significantly outperform EThcD methods, indicating that
ETD-based methods are not required for routine N-glycoproteomics. Conversely,
ETD-based methods, especially EThcD, are indispensable for site-specific
analyses of O-glycopeptides. Our data show that O-glycopeptides cannot be
robustly characterized with HCD-centric methods that are sufficient for
N-glycopeptides, and glycoproteomic methods aiming to characterize
O-glycopeptides must be constructed accordingly.</a></p> | Nicholas Riley; Stacy A. Malaker; Marc D. Driessen; Carolyn Bertozzi | Analytical Chemistry - General; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c0f469df48041f43fee/original/optimal-dissociation-methods-differ-for-n-and-o-glycopeptides.pdf |
6734eebef9980725cf171df2 | 10.26434/chemrxiv-2024-fhn98 | Adaptive Representation of Molecules and Materials in Bayesian Optimization | Bayesian optimization (BO) is increasingly used in molecular optimization and in guiding self-driving laboratories for automated materials discovery. A crucial aspect of BO is how molecules and materials are represented as feature vectors, where both the completeness and compactness of these representations can influence the efficiency of the optimization process. Traditionally, a fixed representation is chosen by expert chemists or applying data-driven feature selection methods on available labelled datasets. However, when dealing with novel optimization tasks, prior knowledge or large datasets are often unavailable, and relying on these even can introduce bias into the search process. In this work, we demonstrate a Feature Adaptive Bayesian Optimization (FABO) framework, which integrates feature selection in the Bayesian optimization process to dynamically adapt material representations throughout the optimization cycles. We demonstrate the effectiveness of this adaptive approach across several molecular optimization tasks, including the discovery of high-performing metal-organic frameworks (MOFs) in three distinct tasks, each involving unique property distributions and requiring a distinct representation. Our results show that the adaptive nature of the representation leads to outperforming random search baseline and scenarios where prior knowledge of the feature space is available. Notably, for known optimization tasks, FABO automatically identifies representations that are aligned with human chemical intuition, validating its utility for optimization tasks where such insights are not available in advance. Lastly, we show how a biased representation can adversely impact BO performance, highlighting the importance of adaptive representation to different tasks. Our findings highlight FABO as a robust approach for navigating large, complex materials search spaces in automated discovery campaigns. | Mahyar Rajabi Kochi; Negareh Mahboubi; Aseem Partap Singh Gill; Seyed Mohamad Moosavi | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734eebef9980725cf171df2/original/adaptive-representation-of-molecules-and-materials-in-bayesian-optimization.pdf |
60c74168bdbb895926a38332 | 10.26434/chemrxiv.7940525.v2 | Characterization of reactive organometallic species via MicroED | Here we apply microcrystal electron diffraction (MicroED) to the structural determination of transition metal complexes. We find that the simultaneous use of 300 keV electrons, very low electron doses, and an ultra-sensitive camera allows for the collection of data without cryogenic cooling of the stage. This technique reveals the first crystal structures of the classic zirconocene hydride, colloquially known as “Schwartz’s reagent”, a novel Pd(II) complex not amenable to solution-state NMR or X-ray crystallography, and five other paramagnetic or diamagnetic transition metal complexes. | Christopher Jones; Matthew Asay; Lee Joon Kim; Jack Kleinsasser; Ambarneil Saha; Tyler J. Fulton; Kevin Berkley; Duilio Cascio; Andrey Malyutin; Matthew Conley; Brian M. Stoltz; Vincent LaVallo; Jose A. Rodriguez; Hosea Nelson | Microscopy; Coordination Chemistry (Inorg.); Organometallic Compounds; Coordination Chemistry (Organomet.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74168bdbb895926a38332/original/characterization-of-reactive-organometallic-species-via-micro-ed.pdf |
619171c92bf8a94e80dc6a7f | 10.26434/chemrxiv-2021-5s5j8 | Ultrafast base rotations mediate a solvent-assisted back-electron transfer in UV-excited DNA single strands | The photochemistry of DNA systems is characterized by the ultraviolet (UV) absorption of π-stacked nucleobases, resulting in exciton states delocalized over several bases. As their relaxation sensitively depends on local stacking conformations, disentangling the ensuing electronic and structural dynamics has remained an experimental challenge, despite their fundamental role in protecting the genome from potentially harmful UV radiation. Here we use transient absorption and transient absorption anisotropy spectroscopy with broadband femtosecond deep-UV pulses (250-360 nm) to resolve the exciton dynamics of UV-excited adenosine single strands under physiological conditions. Due to the exceptional deep-UV bandwidth and polarization sensitivity of our experimental approach, we simultaneously resolve the population dynamics, charge-transfer (CT) character and conformational changes encoded in the UV transition dipoles of the π-stacked nucleotides. Whilst UV excitation forms fully charge-separated CT excitons in less than 0.3 ps, we find that most decay back to the ground state via a solvent-assisted back-electron transfer. This deactivation mechanism is accompanied by a structural relaxation of the photoexcited base-stack, which we identify as an inter-base rotation of the nucleotides. Our results finally complete the exciton relaxation mechanism for adenosine single strands and offer a direct view into the coupling of electronic and structural dynamics in aggregated photochemical systems. | Benjamin Bauer; Rahul Sharma; Majed Chergui; Malte Oppermann | Physical Chemistry; Optics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619171c92bf8a94e80dc6a7f/original/ultrafast-base-rotations-mediate-a-solvent-assisted-back-electron-transfer-in-uv-excited-dna-single-strands.pdf |
637006aa8e0d35785b1951b8 | 10.26434/chemrxiv-2022-dhd35 | Self-Spinning Filaments for Autonomously Linked Microfibers | Filamentous bundles are ubiquitous in Nature, achieving highly adaptive functions and structural integrity from assembly of diverse mesoscale supramolecular elements. Engineering routes to synthetic, topologically integrated analogs demands precisely coordinated control of multiple filaments’ shapes and positions, a major challenge when performed without complex machinery or labor-intensive processing. Here, we demonstrate a photocreasing design that encodes local curvature and twist into mesoscale polymer filaments, enabling their programmed transformation into target 3-dimensional geometries. Importantly, patterned photocreasing of filament arrays drives autonomous spinning to form linked filament bundles that are highly entangled and structurally robust. In individual filaments, photocreases unlock paths to arbitrary, 3-dimensional curves in space. Collectively, photocrease-mediated bundling establishes a transformative paradigm enabling smart, self-assembled mesostructures that mimic performance-differentiating structures in Nature (e.g., tendon and muscle fiber) and the macro-engineered world (e.g., rope). | Dylan Barber; Todd Emrick; Gregory Grason; Alfred Crosby | Materials Science; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637006aa8e0d35785b1951b8/original/self-spinning-filaments-for-autonomously-linked-microfibers.pdf |
673e310c7be152b1d0f13fa4 | 10.26434/chemrxiv-2024-g3wwk-v2 | Neoteric Solvents for Exploratory Catalysis: Hydrophosphination Catalysis with CHEM21 Solvents | The development of catalytic hydrophosphination has placed little emphasis on solvent effects, and most exploratory studies continue to be in toxic or environmentally harmful solvents. A comparative analysis of hydrophosphination catalysis using the three major categories of substrates, styrene, Michael acceptors, and unactivated alkenes, has been undertaken to assess a transition to green solvent alternatives. The compound selected, Cu(acac)2, has been identified as a highly active and perhaps most general precatalyst for hydrophosphination, which is enabled by photochemical conditions. Eight solvents were investigated from categories outlined in the CHEM21 guide, and seven were highly effective for most reactions. These results demonstrate a straightforward path to improving the sustainability of future studies in this and related catalytic reactions through bioavailable solvents, as well as highlighting potential pitfalls in reactions involving phosphine substrates. | Emma Finfer; Rory Waterman | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Main Group Chemistry (Inorg.); Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e310c7be152b1d0f13fa4/original/neoteric-solvents-for-exploratory-catalysis-hydrophosphination-catalysis-with-chem21-solvents.pdf |
662d05ac418a5379b0dfbeaf | 10.26434/chemrxiv-2024-1x3jv | Development of a desorption electrospray ionization –multiple-reaction-monitoring mass spectrometry (DESI-MRM) workflow for spatially mapping oxylipins in pulmonary tissue | Oxylipins are a class of low abundant lipids formed via oxygenation of fatty acids. These compounds include potent signaling molecules (e.g., octadecanoids, eicosanoids) that can exert essential functions in the pathophysiology of inflammatory diseases including asthma. While some oxylipin signaling cascades have been unraveled using LC-MS/MS-based methods, measurements in homogenate samples do not represent the spatial heterogeneity of lipid metabolism. Mass spectrometry imaging (MSI) directly detects analytes from a surface, which enables spatial mapping of oxylipin biosynthesis and migration within tissue. MSI has lacked the sensitivity to routinely detect low abundant oxylipins; however, new multiple-reaction-monitoring (MRM)-based MSI technologies provide increased sensitivity. In this study, we developed a workflow to apply desorption electrospray ionization coupled to a triple quadrupole mass spectrometer (DESI-MRM) to spatially map oxylipins in pulmonary tissue. The targeted MSI workflow screened guinea pig lung extracts using LC-MS/MS to filter oxylipin targets based on their detectability by DESI-MRM. A panel of 6 oxylipins was then selected for DESI-MRM imaging derived from either arachidonic acid (TXB2, 11-HETE, 12-HETE), linoleic acid (12,13-DiHOME) or alpha-linolenic acid (16-HOTrE). To parse this new data type, a custom build R package (quantMSImageR) was developed with functionality to label regions-of-interest as well as quantify and analyze lipid distributions. The spatial distributions quantified by DESI-MRM were supported by LC-MS/MS analysis, with both indicating that 16-HOTrE and 12-HETE were associated with airways, while 12,13-DiHOME and arachidonic acid mapped to parenchyma. This study realizes the potential of targeted-MSI to routinely map low abundant oxylipins with high specificity at scale. | Matthew Smith; Mu Nie; Mikael Adner; Jesper Säfholm; Craig Wheelock | Analytical Chemistry; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662d05ac418a5379b0dfbeaf/original/development-of-a-desorption-electrospray-ionization-multiple-reaction-monitoring-mass-spectrometry-desi-mrm-workflow-for-spatially-mapping-oxylipins-in-pulmonary-tissue.pdf |
653130c2c3693ca9937d31e8 | 10.26434/chemrxiv-2022-n11dq-v2 | Soft drug-inhibitors for the epigenetic targets Lysine-Specific Demethylase 1 (LSD1) and Histone Deacetylases (HDACs) | Epigenetic modulators such as Lysine-specific Demethylase 1 (LSD1) and Histone Deacetylases (HDACs), are drug targets for cancer, neuropsychiatric disease or inflammation but inhibitors of these enzymes exhibit considerable side effects. For a potential local treatment with reduced systemic toxicity, we present here soft drug candidates as new LSD1 and HDAC inhibitors. A soft drug is a compound that is degraded in vivo to less active metabolites, after having achieved its therapeutic function. This has been successfully applied for corticosteroids in the clinic but soft drugs targeting epigenetic enzymes are scarce, with the HDAC inhibitor remetinostat being the only example. We have developed new methyl ester containing inhibitors targeting LSD1 respectively HDACs and compared the biological activity of these to their respective carboxylic acids cleavage products. In vitro activity assays, cellular experiments, and a stability assay identified potent HDAC and LSD1 soft drug candidates that are superior to their corresponding carboxylic acids in cellular models. | Johannes Seitz; Marina Auth; Tony Prinz; Mirjam Hau; Pavlos Tzortzoglou; Johannes Schulz-Fincke; Karin Schmidtkunz; Dominica Willmann; Eric Metzger; Lutz Hein; Sebastian Preissl; Roland Schüle; Manfred Jung | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653130c2c3693ca9937d31e8/original/soft-drug-inhibitors-for-the-epigenetic-targets-lysine-specific-demethylase-1-lsd1-and-histone-deacetylases-hda-cs.pdf |
64dcd03e69bfb8925a06128e | 10.26434/chemrxiv-2023-ggnz0 | Deep Generative Design of Porous Organic Cages via a
Variational Autoencoder | Porous organic cages (POCs) are a class of porous molecular materials characterised by their tunable,
intrinsic porosity; this functional property makes them candidates for applications including guest storage and separation. Typically formed via dynamic covalent chemistry reactions from multifunctionalised molecular precursors, there is an enormous potential chemical space for POCs due to the fact they can be formed by combining two relatively small organic molecules, which themselves have an enormous chemical space. However, identifying suitable molecular precursors for POC formation is challenging, as POCs often lack shape persistence (the cage collapses upon solvent removal with loss of its cavity), thus losing a key functional property (porosity). Generative machine learning models have potential for targeted computational design of large functional molecular systems such as POCs. Here, we present a deep-learning-enabled generative model, Cage-VAE, for the targeted
generation of shape-persistent POCs. We demonstrate the capacity of Cage-VAE to propose novel, shape-persistent POCs, via integration with multiple efficient sampling methods, including bayesian optimization and spherical linear interpolation. | Jiajun Zhou; Austin Mroz; Kim Jelfs | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dcd03e69bfb8925a06128e/original/deep-generative-design-of-porous-organic-cages-via-a-variational-autoencoder.pdf |
60c741c9f96a003c022864bd | 10.26434/chemrxiv.8131235.v1 | A Cobalt-Iron Double-Atom Catalyst for the Oxygen Evolution Reaction | Single atom catalysts exhibit well-defined active sites and potentially maximum atomic efficiency. However, they are unsuitable for reactions that benefit from bimetallic promotion such as the oxygen evolution reaction (OER) in alkaline medium. Here we show that a single atom Co precatalyst can be in-situ transformed into a Co-Fe double atom catalyst for OER. This catalyst exhibits one of the highest turnover frequencies among metal oxides. Electrochemical, microscopic, and spectroscopic data including those from operando X-ray absorption spectroscopy, reveal a dimeric Co-Fe moiety as the active site of the catalyst. This work demonstrates double-atom catalysis as a promising approach for the developed of defined and highly active OER catalysts. | Lichen Bai; Chia-Shuo Hsu; Duncan Alexander; Hao Ming Chen; Xile Hu | Carbon-based Materials; Nanocatalysis - Catalysts & Materials; Electrochemistry; Electrocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2019-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741c9f96a003c022864bd/original/a-cobalt-iron-double-atom-catalyst-for-the-oxygen-evolution-reaction.pdf |
62c178d152acb711177cb198 | 10.26434/chemrxiv-2022-h0pzl | Chemical bonding in representative astrophysically relevant neutral, cation, and anion HCnH chains | Most existing studies assign a polyynic and cumulenic character of chemical bonding in carbonbased
chains relying on values of the bond lengths. Building on our recent work, in this paper we add further evidence on the limitations of such an analysis and demonstrate the signi cant insight gained via natural bond analysis. Presently reported results include atomic charges, natural bond
order and valence indices obtained from ab initio computations for representative members of the
astrophysically relevant neutral and charged HC2k/2k+1H chain family. They unravel a series of counter-intuitive aspects and/or help naive intuition in properly understanding microscopic processes,
e.g., electron removal from or electron attachment to a neutral chain. Demonstrating that the Wiberg indices adequately quantify the chemical bonding structure of the HC2k/2k+1H chains while the often heavily advertised Mayer indices do not | represents an important message
conveyed by the present study. | Ioan Baldea | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c178d152acb711177cb198/original/chemical-bonding-in-representative-astrophysically-relevant-neutral-cation-and-anion-h-cn-h-chains.pdf |
64f9a170b338ec988a0a4c58 | 10.26434/chemrxiv-2023-s7frj | Manipulating Stereoselectivity of Parahydrogen Addition to Acetylene to Unravel Interconversion of Ethylene Nuclear Spin Isomers | Symmetric molecules exist as distinct nuclear spin isomers (NSIMs). A deeper understanding of their properties, including interconversion, requires efficient techniques for NSIMs enrichment. Selective hydrogenation of acetylene with parahydrogen (p-H2) was used to achieve the enrichment of ethylene NSIMs and to study their equilibration processes. The effect of stereoselectivity of H2 addition to acetylene on the imbalance of ethylene NSIMs was experimentally demonstrated by using different heterogeneous catalysts (an immobilized Ir complex and two supported Pd catalysts). The interconversion of NSIMs with time during ethylene storage was studied with NMR spectroscopy by reacting ethylene with bromine water which renders the p-H2-derived protons in the produced 2-bromoethan(2H)ol (BrEtOD) magnetically inequivalent, thereby revealing the non-equilibrium nuclear spin order of ethylene. A thorough analysis of the shape and transformation of the 1H NMR spectra of hyperpolarized BrEtOD allowed us to reveal the initial distribution of produced ethylene NSIMs and their equilibration processes. Comparison of the results obtained with different catalysts was key to properly attributing the derived characteristic time constants to different NSIMs interconversion processes: ~ 3-6 s for interconversion between NSIMs with the same inversion symmetry (i.e., within g or u manifolds) and ~ 1700-2200 s between NSIMs with different inversion symmetries. | Sergey V. Sviyazov; Simon V. Babenko; Ivan V. Skovpin; Larisa M. Kovtunova; Nikita V. Chukanov; Alexander Yu. Stakheev; Dudari B. Burueva; Igor V. Koptyug | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f9a170b338ec988a0a4c58/original/manipulating-stereoselectivity-of-parahydrogen-addition-to-acetylene-to-unravel-interconversion-of-ethylene-nuclear-spin-isomers.pdf |
60c746c0469df42618f436d5 | 10.26434/chemrxiv.11396622.v1 | The Importance of Ligand Selection on the Formation of Bimetallic Phosphide Catalysts Derived from Metal-Organic Frameworks | Coordination polymers (CPs)
and metal-organic frameworks (MOFs) have emerged as versatile precursors for
transition-metal phosphides catalysts. However, the controlled synthesis of
MOF-derived bimetallic phosphides remains a challenge, as mixtures of various
phosphide phases are often formed. Here, it is shown that controlling the
formation of pure CoMoP and CoMoP<sub>2</sub> requires a careful choice of the
ligands used to construct the MOF precursors, based on the chemical properties
of the metals. In particular, the nature and number of the coordination
moieties of the ligand play a key role. CoMoP and CoMoP<sub>2</sub> particles
coated with N-doped carbon were derived from phosphonate-based MOFs and
compared as hydrogen evolution reaction (HER) electrocatalysts in acidic medium.
CoMoP<sub>2</sub> is more active and shows a turnover frequency (TOF) of 0.9 s<sup>-1</sup>
compared to 0.4 s<sup>-1</sup> for CoMoP. The higher intrinsic activity of the
CoMoP<sub>2</sub> catalytic sites correlates with the differences in the
electronic structure of the materials, with a larger charge transfer from the
molybdenum to the phosphorous found for CoMoP<sub>2</sub>. | Sayed M. El-Refaei; Patrícia Russo; Patrick Amsalem; Norbert Koch; Nicola Pinna | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c0469df42618f436d5/original/the-importance-of-ligand-selection-on-the-formation-of-bimetallic-phosphide-catalysts-derived-from-metal-organic-frameworks.pdf |
64a34e6c9ea64cc16763ecc4 | 10.26434/chemrxiv-2023-s1kp3 | Quantum Dynamics Simulations of the 2D Spectroscopy for Exciton Polaritons | We develop an accurate and numerically efficient non-adiabatic path-integral approach to simulate the non- linear spectroscopy of exciton-polariton systems. This approach is based on the partial linearized density matrix (PLDM) approach to model the exciton dynamics with an explicit propagation of the phonon bath environment, combined with a stochastic Lindblad dynamics approach to model the cavity loss dynamics. Through simulating both linear and polariton 2-dimensional electronic spectra (2DES), we systematically investigate how light-matter coupling strength and cavity loss rate influence the optical response signal. Our results confirm the polaron decoupling effect, which is the reduced exciton-phonon coupling among polariton states due to the strong light-matter interactions. We further demonstrate that the polariton coherence time can be significantly prolonged compared to the electronic coherence outside the cavity. | Elious Mondal; Eric Koessler; Justin Provazza; Nickolas Vamivakas; Steven Cundiff; Todd Krauss; Pengfei Huo | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Optics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a34e6c9ea64cc16763ecc4/original/quantum-dynamics-simulations-of-the-2d-spectroscopy-for-exciton-polaritons.pdf |
6210316a7a054a7cba12969e | 10.26434/chemrxiv-2021-tmsdg-v3 | Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions | Transferable high dimensional neural network potentials (HDNNP) have shown great promise as an avenue to increase the accuracy and domain of applicability of existing atomistic force fields for organic systems relevant to life science. We have previously reported such a potential (Schrödinger-ANI) that has broad coverage of druglike molecules. We extend that work here to cover ionic and zwitterionic druglike molecules expected to be relevant to drug discovery research activities. We report a novel HDNNP architechture, which we call QRNN, that predicts atomic charges and uses these charges as descriptors in an energy model which delivers conformational energies within chemical accuracy when measured against the reference theory it is trained to. Further, we find that delta learning based on a semi-empirical level of theory approximately halves the errors. We test the models on torsion energy profiles, relative conformational energies, geometric parameters and relative tautomer errors. | Leif Jacobson; James Stevenson; Farhad Ramezanghorbani; Delaram Ghoreishi; Karl Leswing; Ed Harder; Robert Abel | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6210316a7a054a7cba12969e/original/transferable-neural-network-potential-energy-surfaces-for-closed-shell-organic-molecules-extension-to-ions.pdf |
6307db500187d90434a130ad | 10.26434/chemrxiv-2022-9x79m | Competition between ultralong organic phosphorescence
and thermally activated delayed fluorescence in dichloro
derivatives of 9-benzoylcarbazole | Optoelectronic materials based on metal-free organic molecules represent a promising alternative to traditional inorganic devices. Significant attention has been devoted to the development of the third generation of OLEDs which are based on the temperature-activated delayed fluorescence (TADF) mechanism. In the last few years, several materials displaying ultra-long organic phosphorescence (UOP) have been designed using strategies such as crystal engineering and halogen functionalisation. Both TADF and UOP are controlled by the population of triplet states and the energy gaps between the singlet and triplet manifolds. In this paper, we explore the competition between TADF and UOP
in the molecular crystals of three dichloro derivatives of 9H-carbazol-3-yl(phenyl)methanone. We investigate the excited state mechanisms in solution and the crystalline phase and address the effects of exciton transport and temperature on the rates of direct and reverse intersystem crossing under
the Marcus-Levich-Jortner model. We also analyse how the presence of isomeric impurities and the stabilisation of charge transfer states affect these processes. Our simulations explain the different mechanisms observed for the three derivatives and highlight the role of intramolecular rotation and crystal packing in determining the energy gaps. This work contributes to a better understanding of the connection between chemical and crystalline structures that will enable the design of efficient materials. | Amir Sidat; Federico J. Hernández; Ljiljana Stojanovic; Alston J. Misquitta; Rachel Crespo-Otero | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Physical and Chemical Processes; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6307db500187d90434a130ad/original/competition-between-ultralong-organic-phosphorescence-and-thermally-activated-delayed-fluorescence-in-dichloro-derivatives-of-9-benzoylcarbazole.pdf |
66477295418a5379b08c889b | 10.26434/chemrxiv-2024-q1d47 | Efficient Chemical Equilibria Calculation by Artificial Neural Networks for Ammonia Cracking and Synthesis | The calculation of chemical equilibria in detailed reactor simulations frequently requires elaborate numerical solution of the governing equations in an iterative way, which is often computationally expensive and can significantly increase the overall computation time. In order to reduce these computational costs, we introduce a ready-to-use tool, ANNH3, for calculation of equilibrium composition for synthesis and cracking of ammonia based on a neural network. This tool provides excellent agreement with the conventional approach in the range of 135 – 1000 °C and 1 – 100 bar and is ca. 100 times faster than conventional stoichiometry-based concepts. While speed-up is significant even for the relatively simple case of ammonia synthesis and decomposition, we expect an even higher performance gain for the equilibrium calculation in reaction systems where more components and multiple reactions are involved. | Hannes Stagge; Theresa Kunz; Sina Ramsayer; Robert Güttel | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Thermodynamics (Chem. Eng.); Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66477295418a5379b08c889b/original/efficient-chemical-equilibria-calculation-by-artificial-neural-networks-for-ammonia-cracking-and-synthesis.pdf |
642b6699a029a26b4cde3e3e | 10.26434/chemrxiv-2023-sgnl1 | Electroreductive Synthesis of Nickel(0) Complexes | Over the last fifty years, the use of nickel catalysts for facilitating organic transformations has
skyrocketed. Ni(0) sources act as useful precatalysts because they can enter a catalytic cycle through
ligand exchange, without needing to undergo additional elementary steps. However, most Ni(0)
precatalysts are synthesized with stoichiometric aluminum–hydride reductants, pyrophoric reagents that
are not atom-economical and must be used at cryogenic temperatures. Here, we demonstrate that Ni(II)
salts can be reduced on preparative scale using electrolysis to yield a variety of Ni(0) and Ni(II) complexes
that are widely used as precatalysts in organic synthesis, including bis(1,5-cyclooctadiene)nickel(0)
[Ni(COD)2]. This method overcomes the reproducibility issues of previously reported methods by
standardizing the procedure, such that it can be performed anywhere in a robust manner. It can be easily
transitioned to large scale through an electrochemical recirculating flow process. We anticipate that this
work will accelerate adoption of preparative electrochemistry for the synthesis of low-valent
organometallic complexes in academia and industry. | Camille Rubel; Yilin Cao; Tamara El-Hayek Ewing; Gabriele Laudadio; Gregory Beutner; Steven Wisniewski; Xiangyu Wu; Phil Baran; Julien Vantourout; Keary Engle | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Electrochemistry - Organometallic; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b6699a029a26b4cde3e3e/original/electroreductive-synthesis-of-nickel-0-complexes.pdf |
67cfb827fa469535b9d2f4be | 10.26434/chemrxiv-2025-9h9rm | Graph neural networks to predict atomic transition charges and exciton couplings in organic semiconductors | Exciton couplings between molecules in organic semiconductors are important parameters for simulating exciton diffusion, however they are time-consuming to compute from first-principles. Previous works have developed machine-learned models to predict exciton couplings, however these models have mostly been restricted to specific molecule and cannot generalize over databases of organic materials. In this paper, we present a graph neural network (GNN) that can predict exciton couplings between organic molecules by using atomic transition charges as an intermediary. Our GNN is shown to predict exciton coupling between important fused-ring electron acceptors (FREAs), as well as many other molecules found in the Cambridge Crystallographic Data Centre crystal database. We also show that these predicted couplings can be used for accurate simulations of exciton diffusion. This work therefore overcomes the key limitation of previous machine-learned models for exciton couplings, thereby bringing us closer to the possibility of performing high-throughput virtual screening of organic materials for photovoltaic applications. | Geoffrey Weal; Maryam Nurhuda; Justin Hodgkiss; Paul Hume; Daniel Packwood | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cfb827fa469535b9d2f4be/original/graph-neural-networks-to-predict-atomic-transition-charges-and-exciton-couplings-in-organic-semiconductors.pdf |
6716ced512ff75c3a11dfdd8 | 10.26434/chemrxiv-2024-ww74d | Maximizing Driving Force in the Design of N-oxyl Hydrogen Atom Transfer Catalysts | Increasing the bond dissociation enthalpy (BDE) of potential hydrogen atom transfer (HAT) catalysts has the potential to un-lock a greater substrate scope for radical C-H functionalization reactions. For the archetype N-oxyl catalyst phthalimide-N-oxyl (PINO), tuning the BDEO-H of its precursor N-hydroxyphthalimide (NHPI) by substitution of the the aryl ring has minimal effects, limiting meaningful advances in catalyst development by modifications of PINO. Herein, we demonstrate that inserting a heteroatom between one of the carbonyl groups of PINO and the aryl ring significantly increases the BDEO-H. For example, an N-phenyl moiety, O-atom or S-atom raises the BDEO-H by 6.5, 6.9 and 8.1 kcal/mol, respectively, relative to NHPI – which translates to an increased kHAT of 4, 36.3 and 24.3, respectively. Our studies of these compounds and a panel of analogs thereof highlight three advantages of this strategy: 1) high synthetic accessibility of catalyst candidates; 2) simultaneous optimization across multiple parameters; and 3) effective activity tuning. These new scaffolds are promising for the development of next-generation HAT catalysts and C-H functionalization reactions. | Cheng Yang; Luke Farmer; Olaya Bernardo; Sahil Arora; Subrata Ghosh; Stephen Maldonado; Derek Pratt; Corey Stephenson | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Electrocatalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6716ced512ff75c3a11dfdd8/original/maximizing-driving-force-in-the-design-of-n-oxyl-hydrogen-atom-transfer-catalysts.pdf |
66d8dc62cec5d6c142270ff4 | 10.26434/chemrxiv-2024-rv2tv | DNA nanotechnology in the undergraduate laboratory: Toehold-less strand displacement in switchback DNA | Dynamic DNA nanostructures that reconfigure into different shapes are used in several applications in biosensing, drug delivery and data storage. One of the ways to produce such structural transformations is by a process called strand displacement. This laboratory experiment demonstrates a strand displacement reaction in a two-stranded DNA nanostructure called switchback DNA by the addition of a third strand. In this process, the difference in the affinity between the component DNA strands is used to convert switchback DNA into conventional duplex DNA. Students are introduced to the concept through gel electrophoresis and quantitative analysis of DNA nanostructure reconfiguration. The experiment presented here follows a series of DNA nanotechnology-based exercises in an undergraduate setting and is tailored for adaptation in a chemistry, biology, or biochemistry laboratory with minimal costs. | Bharath Raj Madhanagopal; Arun Richard Chandrasekaran | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d8dc62cec5d6c142270ff4/original/dna-nanotechnology-in-the-undergraduate-laboratory-toehold-less-strand-displacement-in-switchback-dna.pdf |
62874c245d94853701c8182c | 10.26434/chemrxiv-2022-05rf1 | Semi-automatic scheme for early-stage material search: developing solvent-solubility prediction of tetraphenylporphyrin derivatives securing chemical-space coverage | This study developed and implemented a semi-automatic material exploration scheme to modelize the solvent-solubility of tetraphenylporphyrin derivatives. In particular, the scheme involved the following steps: definition of a practical chemical search space, prioritization of molecules in the space using an extended algorithm for submodular function maximization without requiring biased variable selection or pre-existing data, synthesis & automatic measurement, and machine-learning model estimation. The optimal evaluation order selected using the algorithm covered several similar molecules (32% of all targeted molecules, whereas that obtained by random sampling and uncertainty sampling was ~7% and ~4%, respectively) with a small number of evaluations (10 molecules: 0.13% of all targeted molecules). The derived binary classification models predicted ‘good solvents’ with an accuracy > 0.8. Overall, we confirmed the effectivity of the proposed semi-automatic scheme in early-stage material search projects for accelerating a wider range of material research. | Raku Shirasawa; Ichiro Takemura; Shinnosuke Hattori; Yuuya Nagata | Theoretical and Computational Chemistry; Organic Chemistry; Combinatorial Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62874c245d94853701c8182c/original/semi-automatic-scheme-for-early-stage-material-search-developing-solvent-solubility-prediction-of-tetraphenylporphyrin-derivatives-securing-chemical-space-coverage.pdf |
620e61834e899e7f6b5138b8 | 10.26434/chemrxiv-2022-0qg2k | Quantifying Local pH Changes in Carbonate Electrolyte during Copper-Catalysed CO2 Electroreduction Using In Operando 13C NMR | The electrochemical carbon dioxide reduction on copper attracted considerable attention within the last decade, since Cu is the only elemental transition metal that catalyses the formation of short-chain hydrocarbons and alcohols. Research in that field is mainly concentrated on understanding the reaction mechanism in terms of adsorbates and intermediates. Furthermore, dynamic changes in the microenvironment of the catalyst, i.e. local pH and CO2 concentration values, play an equivalently decisive role in the selectivity of product formation. In this study, we present an in operando 13C Nuclear Magnetic Resonance (NMR) technique that enables the simultaneous measurement of pH and CO2 concentration in electrode vicinity during electroreduction. The influence of applied potential and buffer capacity of the electrolyte on the formation of formate is demonstrated. Herewith, theoretical considerations are confirmed experimentally and the importance of the interplay between catalyst and electrolyte is highlighted. | Michael Schatz; Sven Jovanovic; Rüdiger-A. Eichel; Josef Granwehr | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e61834e899e7f6b5138b8/original/quantifying-local-p-h-changes-in-carbonate-electrolyte-during-copper-catalysed-co2-electroreduction-using-in-operando-13c-nmr.pdf |
675080fe5a82cea2faf8c1a5 | 10.26434/chemrxiv-2024-2tt9k-v2 | RADE: A Reduced Approach to Density-Functional Expansion | Density-functional theory (DFT) has become an extensively and successfully used tool in the studies of molecules and materials. However, DFT remains computationally expensive, especially for exploring the conformational space of molecular systems comprising a few hundred atoms. Here, we present a Reduced Approach to Density-functional Expansion (RADE), devised to substantially reduce the computational cost of standard DFT methods. RADE can be implemented fully non-empirically as an efficient first-principles electronic structure method. Preliminary results for molecules containing elements H, C, N, and O indicate that this method can in general reproduce well the results from standard DFT calculations. | Yaoquan Tu; Aatto Laaksonen | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2024-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675080fe5a82cea2faf8c1a5/original/rade-a-reduced-approach-to-density-functional-expansion.pdf |
6706866c51558a15ef9b8eea | 10.26434/chemrxiv-2024-h7tsx | Photoresponsive Helical Foldamers: Conformational Control through Hybridization and Light-Induced Protonation | Helical foldamers constitute particularly relevant targets in the field of host-guest chemistry, be that as hosts or substrates. In this context, the strategies reported so far to control the dimensions and shape of foldamers mainly involve modifications of the skeleton through covalent synthesis. Herein, we prepared an oligopyridine dicarboxamide foldamer substituted by photo-active tetraphenylethylenes (TPE). We demonstrate that it is possible to toggle the length of a helical foldamer by two means. First, the elongation of foldamers can be tuned by adjusting the concentration, as demonstrated by DOSY NMR spectroscopy and X-ray diffraction analyses on both the single and the double helix structures. Secondly, and in a more original manner, a photo-induced protonation process triggered by TPE units promotes a novel pathway to unfold helical foldamers, leading to dramatic conformational and spectroscopic changes. | Louis Hardoin; Rana Kdouh; Youssef Aidibi; Soussana Azar; Benjamin Siegler; Magali Allain; Sébastien Goeb; Eric Levillain; Pierre-Antoine Bouit; Olivier Galangau; Marc Sallé; David Canevet | Physical Chemistry; Organic Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706866c51558a15ef9b8eea/original/photoresponsive-helical-foldamers-conformational-control-through-hybridization-and-light-induced-protonation.pdf |
61dd8c8ef51b227f7911ecc2 | 10.26434/chemrxiv-2022-dh6bh | Heavy-Atom Tunneling in the Covalent/Dative Bond Complexation of Cyclo[18]carbon–piperidine | Recent quantum chemical computations demonstrated the electron-acceptance behavior of this highly reactive cyclo[18]carbon (C18) ring with piperidine (pip). The C18–pip complexation exhibited a double-well potential along the N–C reaction coordinate, forming a van der Waals (vdW) adduct and a more stable, strong covalent/dative bond (DB) complex by overcoming a low activation barrier. By means of direct dynamical computations using canonical variational transition state theory (CVT), including the small-curvature tunneling (SCT), we show the conspicuous role of heavy atom quantum mechanical tunneling (QMT) in the transformation of vdW to DB complex in the solvent phase near absolute zero. Below 50 K, the reaction is entirely driven by QMT, while at 30 K, the QMT rate is too rapid (kT ~ 0.02 s-1), corresponding to a half-life time of 38 s, indicating that the vdW adduct will have a fleeting existence. We also explored the QMT rates of other cyclo[n]carbon–pip systems. This study sheds light on the decisive role of QMT in the covalent/DB formation of the C18–pip complex at cryogenic temperatures. | Ashim Nandi; Gershom (Jan M.L.) Martin | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Chemical Kinetics; Structure | CC BY NC 4.0 | CHEMRXIV | 2022-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61dd8c8ef51b227f7911ecc2/original/heavy-atom-tunneling-in-the-covalent-dative-bond-complexation-of-cyclo-18-carbon-piperidine.pdf |
66548271418a5379b0663965 | 10.26434/chemrxiv-2024-vf8v3 | Electron Beam Induced Modification of N-Heterocyclic Carbenes – Carbon Nanomembrane Formation | Electron irradiation of self-assembled monolayers (SAMs) is a versatile tool for a variety of lithographic methods and formation of new 2D materials such as carbon nanomembranes (CNMs) with potential application in ultrafiltration. While the interaction between the electron beam and standard aromatic or aliphatic thiolate SAMs on gold has been well studied, the behavior of more complex systems such as N-heterocyclic carbenes (NHCs), which are recently attracting growing attention due to their ultra-high chemical and thermal stability, remains completely unknown. In the current work, we analyze the low-energy electron irradiation of SAMs on gold based on the series of NHC molecules featuring different number of benzene moieties (0, 1 and 2), and different size of the nitrogen side groups (methyl, isopropyl) to modify their packing density. The changes in monolayer thickness and composition are carefully analyzed by the X-ray photoelectron spectroscopy (XPS) as a function of electron dose. Our results provide design rules to optimize NHC SAMs structure for their effective modification by the electron irradiation. Such optimization becomes particularly interesting considering that the analyzed NHC monolayers exhibit a much higher stability of their bonding with the metal substrate towards electron irradiation compared to standard thiols or recently applied carboxylic acids. Thus, the NHC SAMs offer an interesting alternative for chemical lithography where structural modification of SAMs by electron or photon beams should be limited mainly to the functional group. Moreover, delamination and transferring of electron irradiated NHC monolayers on holey TEM grid reveals formation of carbon nanomembranes (CNMs). As we show this process is also very sensitive to the structure of NHC SAMs and for properly designed system enables formation of continuous, freestanding CNMs, which are sulfur free and thus much more suitable for some ultrafiltration applications compared to standard CNMs fabricated from thiols and therefore contaminated with reactive sulfur. | Daria Cegiełka; Martha Frey; Krzysztof Kozieł; Christof Neumann; Andrey Turchanin; Piotr Cyganik | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66548271418a5379b0663965/original/electron-beam-induced-modification-of-n-heterocyclic-carbenes-carbon-nanomembrane-formation.pdf |
664dd73c21291e5d1df63cb6 | 10.26434/chemrxiv-2024-1t00j | A molecular strategy for creating functional vesicles with balancing structural stability and stimuli-responsiveness | Vesicles, closed bilayer structures composed of amphiphiles, draw much attention as functional materials for water remediation and biomedical applications. Toward next-generation functional vesicles, both structural stability and stimuli-responsiveness are required. However, there is a dilemma between these properties because the desired membrane structure differs for structural stability and stimuli sensitivity. Here, we have provided a new approach for developing giant vesicles (GVs) through the molecular design and synthesis of amphiphiles having/not having amide linkages in the hydrophobic moiety. From the 1H NMR analysis and fluorescence spectrum of environmental-responsive probes, intermolecular hydrogen bonding between amide linkages in the membrane contributed to enhance structural stability of GVs. Moreover, by adding amphiphiles having photoresponsive azobenzene moiety to GVs composed of amphiphiles having/not having amide linkages, a different manner in photoresponsive deformation was observed: the former exhibited irreversible deformation, but the latter reversible manner due to photoisomerisation of azobenzene under ultraviolet and the subsequent visible light illumination. This was also owing to the stable membrane structure caused by intermolecular hydrogen bonding. | Shoi Sasaki; Hibiki Ueno; Noriyoshi Arai; Kouichi Asakura; Taisuke Banno | Physical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664dd73c21291e5d1df63cb6/original/a-molecular-strategy-for-creating-functional-vesicles-with-balancing-structural-stability-and-stimuli-responsiveness.pdf |
627ea8f5f053dfe15d1b1473 | 10.26434/chemrxiv-2022-sdjdg | Techno-economic analysis of atmospheric water generation by hybrid nanofluids to mitigate global water scarcity | Globally, multiple efforts are made to develop active atmospheric water generation (AWG) or atmospheric water extraction (AWE) systems, particularly using direct-air cooling technology to produce water from ambient air. However, this legacy technique is highly energy-intensive, it can only be operated when the local dew point is above the freezing point of water, allows bacteria to grow within the system, and does not scale to create enough water to offer solutions for most industries, services, or agriculture. Liquid desiccant-based AWG methods show promising performance advantages and offer a versatile approach to help address the thermodynamic, health risks, and geographic constraints currently encountered by conventional active AWG systems. In this study, we performed a techno-economic analysis of a liquid desiccant-based AWG system with a continuous operating style. An energy balance was performed on a single design point of AWG system configuration while using LiCl liquid desiccant loaded with multi-walled carbon nanotubes (MWCNTs). We showed that the MWCNTs can be doped in LiCl for effective heat transfer during water desorption, resulting in a lowering of the sensible heat load by ≈ 49% on the AWG system. We demonstrated that the specific energy consumption (SEC) can currently be obtained as low as 0.67 kWh/gal while changing the inlet desiccant stream concentration of MWCNTs-doped LiCl at given conditions. While the production cost of water (COW) showed a significant dependency over the region, the economic analysis revealed that the cost of water can be produced at a minimum selling price of $0.085 per gallon based on the 2021 annual average wholesale electricity cost of $0.125 per kWh in the U.S., thereby, providing a strong foundation for future research to meet the desirable and competitive water costs by 2026 but before 2031. | Venkateswara Rao Kode; David Stuckenberg; Erick Went; Owen Erickson; Ethan Plumer | Materials Science; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627ea8f5f053dfe15d1b1473/original/techno-economic-analysis-of-atmospheric-water-generation-by-hybrid-nanofluids-to-mitigate-global-water-scarcity.pdf |
677ec9a881d2151a02562b0f | 10.26434/chemrxiv-2025-9tpw3 | Deriving the Isoelectric Point of Amino Acids from Acid-Base Equilibria
| This paper presents a refined method for calculating the isoelectric point (pI) of amino acids, focusing on the dominant zwitterionic form in solution. The approach improves pI calculations and extends to predicting pH values in amphoteric solutions, including titrations of polyprotic acids and bases. | Gayan Senavirathne | Biological and Medicinal Chemistry; Analytical Chemistry; Chemical Education; Analytical Chemistry - General; Biochemical Analysis | CC BY 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677ec9a881d2151a02562b0f/original/deriving-the-isoelectric-point-of-amino-acids-from-acid-base-equilibria.pdf |
66a8dcc75101a2ffa896f32b | 10.26434/chemrxiv-2024-w1g7v | pH-sulfate synergy regulates processing and mechanics of mussel byssus protein condensates | Fluid protein condensates are used as precursor phases for fabricating extracellular protein-based materials including elastin, spider silk, and mussel byssus. The byssus, utilized by mussels for anchoring in marine environments, consists of tough, self-healing adhesive fibers. Byssus formation involves the secretion of protein condensate droplets under acidic conditions that subsequently solidify under basic seawater conditions. We currently have a poor understanding of the physicochemical triggers and molecular-level interactions at play, in particular the role of pH and sulfate anions previously identified during native fabrication. Here, we investigated the pH and sulfate-dependent structural and mechanical response of condensates made from a recombinant byssus protein (mfp-1) using optical tweezers microrheology, FRAP, confocal Raman spectroscopy, NMR, and cryo-EM. We found that the protein concentration in condensates increased, and the viscoelastic response became more rigid under basic conditions in the presence of sulfate ions compared with chloride ions, consistent with spectroscopic analysis indicating different molecular interactions under these different chemical conditions. These studies highlight the crucial interplay between sulfate anions and pH in tuning condensate viscoelasticity via control of intermolecular interactions, providing insights into the natural byssus formation process with relevance for bio-inspired materials processing of sustainable plastics and materials for tissue engineering. | Hamideh R. Alanagh; Magda G. Sánchez-Sánchez; Michael R. Wozny; Yeganeh Habibi; Candace Jarade; Tara Sprules; Mike Strauss; Anthony Mittermaier; Adam G. Hendricks; Matthew J. Harrington | Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Biophysical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a8dcc75101a2ffa896f32b/original/p-h-sulfate-synergy-regulates-processing-and-mechanics-of-mussel-byssus-protein-condensates.pdf |
6798fd3bfa469535b9304049 | 10.26434/chemrxiv-2025-9zrh0 | Evaluating molecular similarity measures: Do similarity measures reflect electronic structure properties?
| The rapid adoption of big data, machine learning (ML), and generative artificial intelligence (AI) in chemical discovery has heightened the importance of quantifying molecular similarity. Molecular similarity, commonly assessed as the distance between molecular fingerprints, is integral to applications such as database curation, diversity analysis, and property prediction. AI tools frequently rely on these similarity measures to cluster molecules under the assumption that structurally similar molecules exhibit similar properties. However, this assumption is not universally valid, particularly for continuous properties like electronic structure properties. Despite the prevalence of fingerprint-based similarity measures, their evaluation has largely depended on biological activity datasets and qualitative metrics, limiting their relevance for non-biological domains. To address this gap, we propose a framework to evaluate the correlation between molecular similarity measures and molecular properties. Our approach builds on the concept of neighborhood behavior and incorporates kernel density estimation (KDE) analysis to quantify how well similarity measures capture property relationships. Using a dataset of over 350 million molecule pairs with electronic structure, redox, and optical properties, we systematically evaluate the correlation between several molecular fingerprint generators, distance functions, and these properties. Both the curated dataset and the evaluation framework are publicly available. | Rebekah Duke; Chih-Hsuan Yang; Baskar Ganapathysubramanian; Chad Risko | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6798fd3bfa469535b9304049/original/evaluating-molecular-similarity-measures-do-similarity-measures-reflect-electronic-structure-properties.pdf |
63c6f7132f7a7a4987c961c4 | 10.26434/chemrxiv-2023-0v38p | Hybrid Catalysts for Enantioselective Photo-Phosphoric Acid Catalysis | The syntheses of two novel, organic and chiral photocatalysts are presented. By combining donoracceptor cyanoarene-based photocatalysts with a chiral phosphoric acid, bifunctional catalysts have been designed. In preliminary proof of concept reactions, their use in both enantioselective energytransfer and photoredox catalysis was demonstrated.
| Alessa Rolka; Burkhard Koenig; Dean Toste | Catalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c6f7132f7a7a4987c961c4/original/hybrid-catalysts-for-enantioselective-photo-phosphoric-acid-catalysis.pdf |
64023de29789de3dd9de4053 | 10.26434/chemrxiv-2023-04x6p | Uncovering the active species in amine-mediated CO2 reduction to CO on Ag | Electrochemical reactive capture of CO2, which integrates CO2 capture with its conversion directly from amine and other capture solutions, is of growing interest but introduces considerable complexity to the electrochemical process due to the wide range of possible reactant participants. In this work, we reveal the governing parameters and basic mechanism behind amine-mediated CO2 conversion as an essential first step towards improving these processes. We first demonstrate the critical influence of CO2 partial pressure of the capture stream on the resulting solution pH, which directly affects amine speciation and the Faradaic efficiency (FE) of CO production on Ag. Moreover, by considering amines of different pKa and with different propensities to form the amine-CO2 adduct carbamate, we show that CO2R FE is governed primarily by dissolved CO2, enabling some amine-containing solutions to have comparable CO2R selectivity and kinetics to amine-free bicarbonate solutions. Finally, descriptors of high selectivity CO production are identified. | Graham Leverick; Elizabeth M. Bernhardt; Aisyah Ilyani Ismail; Jun Hui Law; A. Arifutzzaman; Mohamed Kheireddine Aroua; Betar M. Gallant | Energy; Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64023de29789de3dd9de4053/original/uncovering-the-active-species-in-amine-mediated-co2-reduction-to-co-on-ag.pdf |
65310f3f87198ede079d2ec8 | 10.26434/chemrxiv-2023-dh114 | Accurate prediction of ligand binding for a flexible protein using P-score ranking. | Protein ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining Supervised Molecular Dynamics (SuMD) with Dynamical Averaging Quantum Mechanics Fragment Molecular Orbital (DA-QM-FMO). This is illustrated using a set of five ligands targeting the SARS-CoV-2 Papain-like protease protein. This combination significantly increased the ability to predict the experimental binding structure of protein-ligand complexes independent from the starting position of the ligands or the binding site conformation. We found that the predictive power could be enhanced by combining the residence time (SuMD) and interaction energies (DA-QM-FMO) as descriptors in a novel scoring function named the P-score. | Peter E. G. F. Ibrahim; Fabio Zuccotto; Ulrich Zachariae; Ian Gilbert; Mike Bodkin | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65310f3f87198ede079d2ec8/original/accurate-prediction-of-ligand-binding-for-a-flexible-protein-using-p-score-ranking.pdf |
645d8368fb40f6b3ee6ebbe0 | 10.26434/chemrxiv-2021-s0vqp-v3 | Dielectric metal/metal oxide nanocomposites: modeling
response properties at multiple scales | Nanocomposites with metallic inclusions show great promise as tunable functional materials, particularly for applications where high permittivities are desirable, such as charge-storage. These applications strain quantum mechanical computational approaches, as any representative sample of the material includes hundreds if not thousands of atoms. Many continuum methods offer some predictive power for matrix-inclusion composites, but cannot be directly applied to composites with small inclusions, for which quantum and interfacial effects dominate. Here, we develop an adjustable finite element approach to calculate the permittivities of composites consisting of a metal-oxide matrix with nanometer-scale silver inclusions, by introducing an interfacial layer in the model. The approach involves solving the Laplace equation with Dirichlet and Neumann boundary conditions. We demonstrate that such a continuum model, when appropriately informed using quantum mechanical results, can capture many of the relevant polarization effects in a metal/metal oxide nanocomposite, including those that contain arbitrarily-small inclusions, at a fraction of the computational cost of performing the full quantum mechanics. | Brett Henderson; Archita Adluri; Irina Paci | Theoretical and Computational Chemistry; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanodevices; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645d8368fb40f6b3ee6ebbe0/original/dielectric-metal-metal-oxide-nanocomposites-modeling-response-properties-at-multiple-scales.pdf |
62e79cb73b834eb97ae11e53 | 10.26434/chemrxiv-2022-dnzbk | Catalytic enantioselective 6𝝿 photocyclization of acrylanilides | Controlling absolute stereochemistry in catalytic photochemical reactions is generally challenging owing to high rates of background reactivity. Successful strategies broadly rely on selective excitation of the reaction substrate when associated with a chiral catalyst. Recent stud-ies have demonstrated that chiral Lewis acid complexes can enable selective energy transfer from a photosensitizer to facilitate enantiose-lective triplet state reactions. Here, we apply this approach to the enantioselective catalysis of a 6π photocyclization through the design of an iridium photosensitizer optimized to undergo energy transfer to a reaction substrate only in the presence of a chiral Lewis acid complex. Amongst a group of iridium(III) sensitizers, enantioselectivity and yield closely correlate with photocatalyst triplet energy within a narrow window enabled by a modest reduction in substrate triplet energy upon binding a scandium/ligand complex. These results demonstrate that photocatalyst tuning offers a means to suppress background reactivity and improve enantioselectivity in photochemical reactions. | Benjamin Jones; Pearse Solon; Mihai Popescu; Ji-Yuan Du; Robert Paton; Martin Smith | Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e79cb73b834eb97ae11e53/original/catalytic-enantioselective-6-photocyclization-of-acrylanilides.pdf |
60d9d25c926ad03435038632 | 10.26434/chemrxiv-2021-mm08f | Organocatalytic synthesis of vinylene carbonates | The organocatalytic synthesis of vinylene carbonates from benzoins and acyloins was studied using diphenyl carbonate as a carbonyl source. A range of N-Heterocyclic Carbene (NHC) precursors were screened and it was found that imidazolium salts were the most active for this transformation. The reaction occurs at 90°C under solvent-free conditions. A wide range of vinylene carbonates (symmetrical and unsymmetrical, aromatic or aliphatic), including some derived from natural products, were prepared with 20-99% isolated yields (24 examples). The reaction was also developed using thermomorphic polyethylene-supported organocatalysts as recoverable and recyclable species. The use of such species facilitates the workup and allows the synthesis of vinylene carbonates on the preparative scale (> 30 g after 5 runs). | Killian Onida; Alice J. Haddleton; Sébastien Norsic; Christophe Boisson; Franck D'Agosto; Nicolas Duguet | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d9d25c926ad03435038632/original/organocatalytic-synthesis-of-vinylene-carbonates.pdf |
67089b5c12ff75c3a11a8e12 | 10.26434/chemrxiv-2024-c87hb | Two-Photon Absorption of BODIPY, BIDIPY, GADIPY, and SBDIPY | Substituted boron-dipyrromethene compounds (BODIPYs) have gained significant attention due to their tunable photophysical properties, including two-photon absorption (2PA), a nonlinear optical process where two photons are absorbed simultaneously. The tuning of BODIPY's photophysical properties has recently led to the synthesis of pnictogen-containing derivatives, such as SBDIPY and BIDIPY, where boron is replaced by antimony (Sb) or bismuth (Bi), respectively, as well as other analogues like GADIPY, which contain gallium (Ga). This study presents a computational investigation into their 2PA properties, exploring the impact of various substitutions across these systems. The 2PA cross-sections (σ2PA), electronic excitation energies (ΔE), and dipole moments (µ00, µ11, µ01, Δµ) were computed for 18 DIPY chromophores in the gas-phase with time-dependent density-functional theory (TD-DFT) using several functionals (CAM-B3LYP, ωB97X, M06-2X, M11, and MN15), and then compared to RI-CC2 results. The computed mean absolute errors were small, with the MN15, CAM-B3LYP, and M06-2X functionals being among the best-performing for the properties analyzed. In general, for the parent (unsubstituted) compounds, replacing the core atom in DIPY chromophores results in negligible changes to their σ2PA. However, extending the conjugation through the addition of phenyl substituents significantly increases σ2PA values, and the nature of the core atom impacts the magnitude of this enhancement. | Ismael A. Elayan; Mingmin Zhou; Alex Brown | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67089b5c12ff75c3a11a8e12/original/two-photon-absorption-of-bodipy-bidipy-gadipy-and-sbdipy.pdf |
6556b881dbd7c8b54b6bbf9e | 10.26434/chemrxiv-2023-vtljm | Molecular dynamics simulation study of water structure and dynamics on the gold electrode surface with adsorbed 4-mercaptobenzonitrile | Understanding water dynamics at charged interfaces is of great importance in various fields, such as catalysis, biomedical processes, and solar cell materials. In this study, we implemented molecular dynamics simulations of a system of pure water interfaced with Au electrodes, on one side of which 4-mercaptobenzonitrile (4-MBN) molecules are adsorbed. We calculated time correlation functions of various dynamic quantities such as the hydrogen bond status of the N atom of the adsorbed 4-MBN molecules, the rotational motion of the water OH bond, hydrogen bonds between 4-MBN and water, and hydrogen bonds between water molecules in the interface region. Using the Luzar-Chandler model, we analyzed the hydrogen bond dynamics between a 4-MBN and a water molecule. The dynamic quantities we calculated can be divided into two categories: those related to the collective behavior of interfacial water molecules and the H-bond interaction between a water molecule and the CN group of 4-MBN. We found that these two categories of dynamic quantities exhibit opposite trends in response to applied potentials on the Au electrode. We anticipate the present work will help improve our understanding of the interfacial dynamics of water in various electrolyte systems. | Kijeong Kwac; Nan Yang; Matthew Ryan; Martin Zanni; Minhaeng Cho | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6556b881dbd7c8b54b6bbf9e/original/molecular-dynamics-simulation-study-of-water-structure-and-dynamics-on-the-gold-electrode-surface-with-adsorbed-4-mercaptobenzonitrile.pdf |
60c74e054c8919d6a2ad391a | 10.26434/chemrxiv.12687887.v1 | Multivalency Pattern Recognition to Sort Colloidal Assemblies | <i>Multivalent interactions are an important principle for self-assembly, and have been widely used to assemble colloidal systems. However, binding partners on colloids are typically statistically distributed, which falls short of the possibilities arising from geometrically controlled multivalency patterns as for instance found in viruses. Herein, we use the ultimate precision provided by 3D DNA origamis to introduce colloidal scale multivalency pattern recognition via designing geometrically precise interaction patterns at patches of patchy nanocylinder. This gives rise to self-sorting of colloidal assemblies despite having the same type and number of supramolecular binding motifs – solely based on the pattern located on a 20 x 20 nm cross section. The degree of sorting can be modulated by the geometric overlap of patterns and homo, mixed and alternating supracolloidal polymerizations are demonstrated. We demonstrate that geometric positioning of multivalency patterns provides additional control to organize soft matter, and we believe the concept to be of importance for engineering biological response and to be generalizable for other precision nanoparticles and soft matter objects.</i> | Sebastian Loescher; Andreas Walther | Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e054c8919d6a2ad391a/original/multivalency-pattern-recognition-to-sort-colloidal-assemblies.pdf |
614237f342198e52eb77c452 | 10.26434/chemrxiv-2021-cwhv4 | A Favorable Path to Domain Separation in the Orange Carotenoid Protein | The Orange Carotenoid Protein (OCP) is responsible for nonphotochemical quenching (NPQ) in cyanobacteria, a defense mechanism against potentially damaging effects of excess light conditions. This soluble two-domain protein undergoes profound conformational changes upon photoactivation, involving translocation of the ketocarotenoid inside the cavity followed by domain separation. Domain separation is a critical step in the photocycle of OCP because it exposes the N-terminal domain (NTD) to perform quenching of the phycobilisomes. Many details regarding the mechanism and energetics of OCP domain separation remain unknown. In this work, we apply metadynamics to elucidate the protein rearrangements that lead to the active, domain-separated, form of OCP. We find that translocation of the ketocarotenoid canthaxanthin has a profound effect on the energetic landscape and that domain separation only becomes favorable following translocation. We further explore, characterize, and validate the free energy surface (FES) using equilibrium simulations initiated from different states on the FES. Through pathway optimization methods, we characterize the most probable path to domain separation and reveal the barriers along that pathway. We find that the free energy barriers are relatively small (<5 kcal/mol), but the overall estimated kinetic rate is consistent with experimental measurements (>1 ms). Overall, our results provide detailed information on the requirement for canthaxanthin translocation to precede domain separation and an energetically feasible pathway to dissociation. | Mahmoud Sharawy; Natalia B. Pigni; Eric R. May; José A. Gascón | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614237f342198e52eb77c452/original/a-favorable-path-to-domain-separation-in-the-orange-carotenoid-protein.pdf |
61a8a288a02d16f623e114bc | 10.26434/chemrxiv-2021-2q31m | A Binuclear Cobalt Complex for Molecular CO2 Electrocatalysis | A pyrazole–based ligand substituted with terpyridine groups at the 3 and 5positions has been synthesized to form the dinuclear cobalt complex 1, that electrocatalytically reduces carbon dioxide (CO2) to carbon monoxide (CO) in the presence of Brønsted acids in DMF. Chemical, electrochemical and UV–vis spectro–electrochemical studies under inert atmosphere indicate a single 2 electron reduction process of complex 1 at first, followed by a 1 electron reduction at the ligand. Infrared spectro–electrochemical studies under CO2 and CO atmosphere allowed us to identify a reduced CO–containing dicobalt complex which results from the electroreduction of CO2. In the presence of trifluoroethanol (TFE), electrocatalytic studies revealed single–site mechanism with up to 94 % selectivity towards CO formation when 1.47 M TFE were present, at –1.35 V vs Saturated Calomel Electrode in DMF (0.39 V overpotential). The low faradaic efficiencies obtained (<50%) are attributed to the generation of CO–containing species formed during the electrocatalytic process, which inhibit the reduction of CO2. | Antoine Bohn; Juan José Moreno; Pierre Thuéry; Marc Robert; Orestes Rivada Wheelaghan | Catalysis; Organometallic Chemistry; Energy; Electrocatalysis; Electrochemistry - Organometallic; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a8a288a02d16f623e114bc/original/a-binuclear-cobalt-complex-for-molecular-co2-electrocatalysis.pdf |
673ea6e87be152b1d0079a38 | 10.26434/chemrxiv-2024-d2zh7-v2 | Enantioselective Synthesis of Calix[4]arenes with Axial and Inherent Chiralities via Palladium/Chiral Norbornene Cooperative Catalysis | Inherently chiral calix[4]arenes exhibit broad applications in asymmetric catalysis, chiral recognition, and materials science. However, their synthesis remains a significant challenge. Herein, we report a highly efficient method for the construction of calix[4]arenes with both axial and inherent chiralities through palladium/chiral norbornene (Pd/NBE*) cooperative catalysis. In this cascade reaction, the initial intro-duced axial chirality is dictated by Pd/NBE* cooperative catalysis, while the latter inherent chirality is controlled by the preestablished axial chirality via an unprecedented axial-to-inherent diastereoinduction process. This method employs ortho-calix[4]arene-tethered aryl iodides and β-substituted naphthyl bromides as starting materials, enabling the synthesis of a wide range of five- and six-membered benzo-fused calix[4]arenes with axial and inherent chiralities (30 examples) in one step with excellent enantioselectivities and diastereoselectivities. Preliminary studies of photophysical and chiroptical properties reveal that these axially and inherently chiral calix[4]arenes possess promis-ing glum values, demonstrating their potential in developing new organic optoelectronic materials. | Yiming You; Hongwei Cheng; Xiao Huang; Peng Wang; Hengjiang Cong; Hong-Gang Cheng; Qianghui Zhou | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Stereochemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ea6e87be152b1d0079a38/original/enantioselective-synthesis-of-calix-4-arenes-with-axial-and-inherent-chiralities-via-palladium-chiral-norbornene-cooperative-catalysis.pdf |
6441231b83fa35f8f6f4a20f | 10.26434/chemrxiv-2023-cl4m5 | Scalable all-inorganic halide perovskite photoanodes with >100 h operational stability containing Earth-abundant materials | The application of halide perovskites in photoelectrochemical generation of solar fuels and feedstocks is hindered by the instability of perovskites in aqueous electrolytes and the use of expensive electrode and catalyst materials, particularly in photoanodes driving kinetically slow water oxidation. Here, we incorporate solely Earth-abundant materials to fabricate a CsPbBr3-based photoanode that reaches a low onset potential of +0.4 VRHE and 8 mA cm-2 photocurrent density at +1.23 VRHE for water oxidation, close to the radiative efficiency limit of CsPbBr3. This photoanode retains 100% of its stabilized photocurrent density after >100 h continuous operation, that can be extended to weeks by replacing the inexpensive graphite sheet upon signs of deterioration. The improved performance is due to an efficiently electrodeposited NiFeOOH catalyst on a protective self-adhesive graphite sheet, and enhanced charge transfer achieved by phase engineering of CsPbBr3. Devices with >1cm2 area, and low-temperature processing demonstrate the potential for low capital cost, stable, and scalable perovskite photoanodes. | Matyas Daboczi; Junyi Cui; Filipp Temerov; Salvador Eslava | Physical Chemistry; Materials Science; Energy; Catalysts; Fuels - Energy Science; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6441231b83fa35f8f6f4a20f/original/scalable-all-inorganic-halide-perovskite-photoanodes-with-100-h-operational-stability-containing-earth-abundant-materials.pdf |
64acfc1e9ea64cc167d0512d | 10.26434/chemrxiv-2023-rtm7d | Bioinspired Total Synthesis of Hyperireflexolides A and B | Hyperireflexolides A and B have been synthesized in six steps using a strategy based on the dearomatization and fragmentation of a simple acylphloroglucinol starting material. The dearomatized acylphloroglucinol undergoes a sequence of oxidative radical cyclization, retro-Dieckmann fragmentation, stereodivergent intramolecular carbonyl-ene reactions and final α-hydroxy-β-diketone rearrangements to give the target natural products. This sequence is based on a biosynthetic proposal that claims the hyperireflexolides as highly rearranged polycyclic polyprenylated acylphloroglucinols (PPAPs), which is supported by a biosynthetically anticipated structure revision of hyperireflexolide B. In addition, hyperireflexolides A and B were synthesized using a convergent, non-biomimetic strategy that diastereoselectively constructs five C–C bonds onto a 2-cyclopentenone core. | Andreas zur Bonsen; Christopher Sumby; Jonathan George | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64acfc1e9ea64cc167d0512d/original/bioinspired-total-synthesis-of-hyperireflexolides-a-and-b.pdf |
667b7abd5101a2ffa882a0b5 | 10.26434/chemrxiv-2024-43jt4 | Synthesis of Vanillin from Biomass-Derived Isoeugenol Using Immobilized Cobalt-Porphyrin on Hydroxyl-rich Graphene Oxide Catalyst | Synthesis of vanillin from isoeugenol by oxidation has been investigated using cobalt(II) porphyrin (CoTCPP: meso-tetrakis(4-carboxy)phenyl porphyrinato cobalt(II)) covalently linked to hydroxyl-rich graphene oxide (GOOH) as a heterogeneous catalyst. The catalyst was thoroughly characterized by various spectroscopic techniques, such as FT-IR, XRD, N2 adsorption-desorption, XPS, and SEM-EDS analytical techniques. Catalytic activity of the CoTCPP/GOOH gave an excellent yield of 75.1% in the conversion of isoeugenol to vanillin using molecular oxygen for 20 h reaction at 100 °C in 3.0 MPa oxygen pressure. The catalyst showed exceptional stability upon multiple reuses without significant loses in activity. Accordingly, the present study highlights the promise of CoTCPP/GOOH as a heterogeneous catalyst for the efficient aerobic oxidation of biomass-derived platform chemicals into valuable end-products. | Anjali Kaiprathu; Shun Nishimura | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667b7abd5101a2ffa882a0b5/original/synthesis-of-vanillin-from-biomass-derived-isoeugenol-using-immobilized-cobalt-porphyrin-on-hydroxyl-rich-graphene-oxide-catalyst.pdf |
6162c767a3d2c97449d1e402 | 10.26434/chemrxiv-2021-cn0px | Efficiently transforming from values of a function on a sparse grid to basis coefficients | In many contexts it is necessary to determine coefficients of a basis expansion of a function ${f}\left(x_1, \ldots, x_D\right) $ from values of the function at points on a sparse grid. Knowing the coefficients, one has an interpolant or a surrogate. For example, such coefficients are used in uncertainty quantification. In this chapter, we present an efficient method for computing the coefficients. It uses basis functions that, like the familiar piecewise linear hierarchical functions, are zero at points in previous levels. They are linear combinations of any, e.g. global, nested basis functions $\varphi_{i_k}^{\left(k\right)}\left(x_k\right)$. Most importantly, the transformation from function values to basis coefficients is done, exploiting the nesting, by evaluating sums sequentially. When the number of functions in level $\ell_k$ equals $\ell_k$ (i.e. when the level index is increased by one, only one point (function) is added) and the basis function indices satisfy ${\left\lVert\mathbf{i}-\mathbf{1}\right\lVert_1 \le b}$, the cost of the transformation scales as $\mathcal{O}\left(D \left[\frac{b}{D+1} + 1\right] N_\mathrm{sparse}\right)$, where $N_\mathrm{sparse}$ is the number of points on the sparse grid. We compare the cost of doing the transformation with sequential sums to the cost of other methods in the literature.
| Tucker CARRINGTON; Robert Wodraszka | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6162c767a3d2c97449d1e402/original/efficiently-transforming-from-values-of-a-function-on-a-sparse-grid-to-basis-coefficients.pdf |
66a166edc9c6a5c07ad03944 | 10.26434/chemrxiv-2024-c0vmg | 17O NMR spectroscopy reveals CO2 speciation and dynamics in hydroxide-based carbon capture materials. | Carbon dioxide capture technologies are set to play a vital role in mitigating the current climate crisis. Solid-state 17O NMR spectroscopy can provide key mechanistic insights that are crucial to effective sorbent design and development. In this work, we present the fundamental aspects and complexities for the study of hydroxide-based CO2 capture systems by 17O NMR spectroscopy. We perform static DFT NMR calculations to assign peaks for general hydroxide CO2 capture products, finding that 17O NMR can readily distinguish between bicarbonate, carbonate and water species. However, in application to CO2 binding in two test case hydroxide-functionalised metal-organic frameworks – MFU-4l and KHCO3-CD-MOF, we find that a dynamic treatment is necessary to obtain agreement between computational and experimental spectra. We therefore introduce a workflow that leverages machine-learning force fields to capture dynamic effects across multiple chemical exchange regimes, providing a significant improvement on static DFT predictions. In MFU-4l, we parameterise, in a pre-determined fashion, a two-component dynamic motion of the bicarbonate motif involving a rapid carbonyl seesaw motion and intermediate hydroxyl proton hopping. For KHCO3-CD-MOF, we combined experimental and modelling approaches to propose a new mixed carbonate-bicarbonate binding mechanism and thus, we open new avenues for the study and modelling of hydroxide-based CO2 capture materials by 17O NMR spectroscopy.
| Benjamin Rhodes; Lars Schaaf; Mary Zick; Suzi Pugh; Jordon Hilliard; Shivani Sharma; Casey Wade; Gabor Csanyi; Phillip Milner; Alex Forse | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a166edc9c6a5c07ad03944/original/17o-nmr-spectroscopy-reveals-co2-speciation-and-dynamics-in-hydroxide-based-carbon-capture-materials.pdf |
646b164bf2112b41e9f2a7b0 | 10.26434/chemrxiv-2023-90082 | 3DDPDs: Describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors | Proteochemometric (PCM) modelling is a powerful computational drug discovery tool used in bioactivity prediction of potential drug candidates relying on both chemical and protein information. In PCM features are computed to describe small molecules and proteins, which directly impact the quality of the predictive models. State-of-the-art protein descriptors, however, are calculated from the protein sequence and neglect the dynamic nature of proteins. This dynamic nature can be computationally simulated with molecular dynamics (MD). Here, novel 3D dynamic protein descriptors (3DDPDs) were designed to be applied in bioactivity prediction tasks with PCM models. As a test case publicly available G protein-coupled receptor (GPCR) MD data from GPCRmd was used. GPCRs are membrane-bound proteins, which are activated by hormones and neurotransmitters, and constitute an important target family for drug discovery. GPCRs exist in different conformational states that allow transmission of diverse signals and that can be modified by ligand interactions, among other factors. To translate the MD-encoded protein dynamics two types of 3DDPDs were considered: one-hot encoded residue-specific (rs) and embedding-like protein-specific (ps) 3DDPDs. The descriptors were developed by calculating distributions of trajectory coordinates and partial charges, applying dimensionality reduction, and subsequently condensing them into vectors per residue or protein, respectively. 3DDPDs were benchmarked on a number of PCM tasks against state-of-the-art non-dynamic protein descriptors. Our rs- and ps3DDPDs outperformed non-dynamic descriptors in regression tasks using a temporal split, and showed comparable performance with a random split and in all classification tasks. Combinations of non-dynamic descriptors with 3DDPDs did not result in increased performance. Finally, the power of 3DDPDs to capture dynamic fluctuations in mutant GPCRs was explored. The results presented here show the potential of including protein dynamic information on machine learning tasks, specifically bioactivity prediction, and open opportunities for applications in drug discovery, including oncology. | Marina Gorostiola González; Remco L. van den Broek; Thomas G.M. Braun; Magdalini Chatzopoulou; Willem Jespers; Adriaan P. IJzerman; Laura H. Heitman; Gerard J.P. van Westen | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646b164bf2112b41e9f2a7b0/original/3ddp-ds-describing-protein-dynamics-for-proteochemometric-bioactivity-prediction-a-case-for-mutant-g-protein-coupled-receptors.pdf |
66d0cf3720ac769e5f466a4c | 10.26434/chemrxiv-2024-jzk7n | Drug interaction profiles classification: Sørensen–Dice coefficient based on MM/GBSA energies to explore focal adhesion kinase inhibitors | Quantitative comparison of ligand-target interaction profiles is often challenging due to subjective interpretations in visual inspection or limitation to predefined interactions in analytical methods. Moreover, traditional analyses tend to overlook the dynamic nature of the interactions, focusing instead on mean energy values. By describing ligand-residue interactions as energy distributions, we account for these dynamics. Assuming a Gaussian distribution, the mean and standard deviation are sampled from molecular dynamics simulations. Using the Sørensen-Dice similarity index, we constructed a metric where the overlap between Gaussian interactions quantifies their similarity. For ligand comparison, the average per-residue similarity is employed. This method allows for post-processing techniques like clustering and dimensionality reduction. We applied it to the focal adhesion kinase (FAK) type II inhibitors targeting the ATP binding site, identifying interaction patterns among the inhibitors. | Patricia Quispe; Leandro Martínez Heredia; Ignacio León; Martin Lavecchia | 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 | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d0cf3720ac769e5f466a4c/original/drug-interaction-profiles-classification-s-rensen-dice-coefficient-based-on-mm-gbsa-energies-to-explore-focal-adhesion-kinase-inhibitors.pdf |
60c7416a9abda22a30f8be90 | 10.26434/chemrxiv.8051921.v1 | Spherical-Shape Assumption for Protein–Aptamer Complexes Facilitates Prediction of their Electrophoretic Mobility | The pdf file describes the results of this study, which aims at developing a model to accurately predict electrophoretic mobilities of protein–aptamer complexes. The excel file contains source data for electropherograms (signal vs time) which were obtained in this study and used to determine the migration times and electrophoretic mobilities of proteins, aptamers, ssDNAs, protein–aptamer complexes, and protein–ssDNA complexes. Additional sheets in the excel file contain values of all migration times and mobilities obtained from the electropherograms. | Stanislav Beloborodov; Svetlana Krylova; Sergey Krylov | Biochemical Analysis; Separation Science; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7416a9abda22a30f8be90/original/spherical-shape-assumption-for-protein-aptamer-complexes-facilitates-prediction-of-their-electrophoretic-mobility.pdf |
60c73d4e702a9b3a2b189b2d | 10.26434/chemrxiv.5554159.v1 | Activity enhancement of platinum oxygen-reduction electrocatalysts using ion-beam induced defects | High activity is one of the primary requirements for the
catalysts in proton exchange membrane fuel
cell applications. Platinum (Pt) is the best-known catalyst especially
for oxygen reduction at the cathode; however, further activity improvements are
still required. Previous computational studies suggested that the catalytic activity of Pt
nanoparticles could be enhanced by a Pt−carbon support interaction. We have recently found that an enhanced electronic
interaction occurs at the interface between an argon-ion (Ar<sup>+</sup>)-irradiated
glassy carbon (GC) surface and Pt nanoparticles. Here, we report a more than
two-fold increase in specific activity (SA) for the Pt nanoparticles on the Ar<sup>+</sup>-irradiated
GC substrate compared to that on the non-irradiated GC substrate. The mechanism
of this activity enhancement was investigated by local structure analysis of
the interface. Ar<sup>+</sup> irradiation of the carbon support led to the
formation of the Pt−C bonding, thus protecting the deposited Pt nanoparticles
from oxidation. | Tetsuya Kimata; Kenta Kakitani; Shunya Yamamoto; Iwao Shimoyama; Daiju Matsumura; Akihiro Iwase; Wei Mao; Tomohiro Kobayashi; Tetsuya Yamaki; Takayuki Terai | Electrochemistry - Mechanisms, Theory & Study; Radiation; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2017-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4e702a9b3a2b189b2d/original/activity-enhancement-of-platinum-oxygen-reduction-electrocatalysts-using-ion-beam-induced-defects.pdf |
614e29c818be85545e2f34eb | 10.26434/chemrxiv-2021-5dznt-v2 | Carbon-Negative Cement Manufacturing from Seawater-Derived Magnesium Feedstocks | This study describes and demonstrates a carbon-negative process for manufacturing cement from widely abundant seawater-derived magnesium (Mg) feedstocks. In contrast to conventional Portland cement, which starts with carbon-containing limestone as the source material, the proposed process uses membrane-free electrolyzers to facilitate the conversion of carbon-free magnesium ions (Mg2+) in seawater into magnesium hydroxide (Mg(OH)2) precursors for the production of Mg-based cement. After a low-temperature carbonation curing step converts Mg(OH)2 into magnesium carbonates through reaction with carbon dioxide (CO2), the resulting Mg-based binders can exhibit compressive strength comparable to that achieved by Portland cement after curing for only two days. Although the proposed “cement-from-seawater” process requires similar energy use per ton of cement as existing processes, its potential to achieve a carbon-negative footprint makes it highly attractive to decarbonize one of the most carbon intensive industries. | Palash Badjatya; Abdullah Akca; Daniela Fraga Alvarez; Baoqi Chang; Siwei Ma; Xueqi Pang; Emily Wang; Quinten van Hinsberg; Daniel Esposito; Shiho Kawashima | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Carbon-based Materials; Materials Processing; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614e29c818be85545e2f34eb/original/carbon-negative-cement-manufacturing-from-seawater-derived-magnesium-feedstocks.pdf |
60c752c14c8919839dad4193 | 10.26434/chemrxiv.13340675.v1 | Deciphering Molecular Self-Assembly through Electron Microscopy and Fluorescence Correlation Spectroscopy | Supramolecular self-assembly
of small organic molecules has emerged as a powerful tool to construct
well-defined micro- and nanoarchitecture through fine-tuning a range of
intermolecular interactions. The size, shape, and optical properties of these
nanostructures largely depend on the temperature and polarity of the medium,
along with the specific self-assembled pattern of molecular building units. The
engineering of supramolecular self-assembled nanostructures with morphology-dependent tunable emission is in high demand due to the
promising scope in nanodevices and molecular machines. However, challenges are
probing the evolution of molecular aggregates from a true solution and
directing the self-assembly process in a pre-defined fashion. The structure of molecular
aggregates in the solution can be predicted from fluorescence correlation spectroscopy (FCS) and dynamic light scattering
(DLS) analysis. On the other hand, the morphology of the aggregates can also be
visualized through electron microscopy. Nevertheless, a direct correlation
between emission from molecular aggregates in the aqueous dispersion and their
morphology obtained through a solid-state characterization is missing. In the present
study, we decipher the sequential evolution of molecular nanofibers from
solution to spherical and oblong-shaped nanoparticles through the variation of
solvent polarity, adjusting the <a>hydrophobic-hydrophilic
interactions</a>. The intriguing case of
molecular self-assembly is elucidated employing a newly designed π-conjugated
thiophene derivative (TPAn) through a combination of steady-state absorption, emission measurements, FCS, and electron microscopy. The FCS analysis and microscopy results infer that
small-sized nanofibers in the dispersion are further agglomerated, resulting in
a network of nanofibers upon solvent evaporation. <a>The
evolution of organic nanofibers and subtle control over the self-assembly
process demonstrated in the current investigation provides a general paradigm
to correlate the size, shape, and emission properties of diverse fluorescent
molecular aggregates in complex heterogeneous media, including a human cell. </a> | Subhankar Kundu; Arkaprava Chowdhury,; Somen Nandi; Kankan Bhattacharyya; Abhijit Patra | Aggregates and Assemblies | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752c14c8919839dad4193/original/deciphering-molecular-self-assembly-through-electron-microscopy-and-fluorescence-correlation-spectroscopy.pdf |
6793c5a5fa469535b9b2f631 | 10.26434/chemrxiv-2025-ts81d | Tandem Cu/ZnO/ZrO2-SAPO-34 System for Dimethyl Ether (DME) Synthesis from CO2 and H2: Catalyst Optimization, Techno-Economic and Carbon-Footprint Analyses | To alleviate detrimental effects associated with anthropogenic emissions, the use of CO2 and H2 as feedstocks for their conversion to associated with dimethyl ether (DME) with tandem catalysts is an attractive and sustainable route. First, we investigated, for the first time, the catalytic activity of bifunctional admixtures of Cu-ZnO-ZrO2 (CZZ) and a silicoaluminophosphate, SAPO-34, for CO2 hydrogenation to DME, and optimized their reactivity with an emphasis on identifying optimum synthesis conditions for CZZ including Cu:Zn:Zr molar ratio, and ageing and calcination temperatures. The highest methanol (MeOH) productivity (10.8 mol kgcat-1 h-1) was observed for CZZ-611 aged at 40°C and calcined at 500°C. When coupled with SAPO-34, CZZ/SAPO-34 reached 20% CO2 conversion and 56% DME selectivity at optimized conditions (260°C, 500 psig, and 2000 mL gCZZ-1 h-1) and was stable for 50 h time-on-stream. Next, we performed kinetic modeling to translate lab-scale findings to industrial packed-bed reactors followed by a techno-economic analysis (TEA) with cradle-to-gate environmental footprint evaluation to evaluate its industrial applicability. TEA of a 20,000 tpy DME plant revealed raw material costs as the main operating costs drivers (H2 cost comprises 47% of total cost). Considering green H2 ($4/kg H2) and captured CO2 as feed, the minimum DME selling price (MDSP) was $3.21/kg, ~3.6x higher than market price ($0.88/kg). MDSP drops to $1.99/kg with grey H2 ($1/kg H2) and fluctuates ±$0.14 with changes in CAPEX (±30%) and other economic factors. The plant’s carbon footprint was mainly affected by H2 source. Green and grey H2 resulted in emissions of 0.21 and 4.4 kg CO2 eq/kg DME, respectively. Importantly, negative carbon-footprint can be achieved by using green H2 and CO2 captured directly from air. Overall, our work showed tandem catalysis as a promising approach towards sustainable DME production and identifies the pathway towards making it cost-competitive with fossil-fuels. | Jasan Mangalindan; Fatima Mahnaz; Jenna Vito; Navaporn Suphavilai; Manish Shetty | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Acid Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6793c5a5fa469535b9b2f631/original/tandem-cu-zn-o-zr-o2-sapo-34-system-for-dimethyl-ether-dme-synthesis-from-co2-and-h2-catalyst-optimization-techno-economic-and-carbon-footprint-analyses.pdf |
60c73f20f96a00ee77286063 | 10.26434/chemrxiv.7261016.v1 | Unraveling the Improved ORR Activities in Pt/TiO2/C Hybrids: The Role of Pt Morphology and Reactive Surface Species | Further improvements and mechanistic understanding of the electrocatalytic enhancements towards the oxygen reduction reaction (ORR) are required to meet cost/energy demands and thus enable their practical applications in polymer electrolyte fuel cells. An investigation of the electrocatalytic enhancement mechanisms and stability of controlled electrocatalysts comprised Pt nanoparticles supported on TiO2/C materials was herein performed. The catalysts were prepared by depositing Pt, over the surface of TiO2 colloidal spheres. These materials were then supported onto Vulcan carbon to produce Pt/TiO2/C. The effect of Pt coverage at the TiO2 surface as well as the Pt/TiO2 loading on carbon over their ORR activity and stability were investigated. Results indicate that the control over Pt coverage at the surface played a pivotal role on activity optimization, in which an association between Pt content at the TiO2 surface and ORR activity was established. The ORR activity and stability were superior as compared to commercial Pt/C (E-TEK). Variations in catalytic activity could be correlated with the morphological features and with the concentration of surface reactive groups. Results described herein suggest that the understanding of the electrocatalytic enhancement mechanism together with the controlled synthesis of Pt-based nanomaterials may lead to tailored surface properties and thus ORR activities. | Eduardo C. M. Barbosa; Luanna S. Parreira; Isabel C. de Freitas; Luci R. Aveiro; Daniela C. de Oliveira; Mauro C. dos Santos; Pedro H. C. Camargo | Nanostructured Materials - Materials; Electrochemical Analysis; Nanostructured Materials - Nanoscience; Electrocatalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f20f96a00ee77286063/original/unraveling-the-improved-orr-activities-in-pt-ti-o2-c-hybrids-the-role-of-pt-morphology-and-reactive-surface-species.pdf |
6445858ee4bbbe4bbf246826 | 10.26434/chemrxiv-2023-jg5l5 | Mapping the Frontier Orbital Energies of Imidazolium-based Cations Using Machine Learning | The knowledge of frontier orbital, highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO), energies is vital for studying chemical and electrochemical stability of compounds, their corrosion inhibition potential, reactivity, etc. Density functional theory (DFT) calculations provide a direct route to estimate these energies, either in the gas-phase or condensed phase. However, the application of DFT methods becomes computationally intensive when hundreds of thousands of compounds are to be screened. Such is the case when all the isomers for the 1-alkyl-3-alkyllimidazolium cation [C$_n$C$_m$im]$^+$ (n = 1-10, m=1-10) are considered. Enumerating the isomer space of [C$_n$C$_m$im]$^+$ yields close to 316,000 cation structures. Calculating frontier orbital energies for each would be computationally very expensive and time-consuming using DFT. In this article, we develop a machine learning model based on extreme gradient boosting (XGBoost) method using the a small subset of the isomer space and predict the HOMO and LUMO. Using the model, the HOMO energies are predicted with a mean-absolute error (MAE) of 0.4 eV and the LUMO energies with MAE of 0.2 eV. Inferences are also drawn on type of the descriptors deemed important for the HOMO and LUMO energy estimates. Application of the machine learning model results in a drastic reduction in computational time required for such calculations. | Pratik Dhakal; Wyatt Gassaway; Jindal Shah | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6445858ee4bbbe4bbf246826/original/mapping-the-frontier-orbital-energies-of-imidazolium-based-cations-using-machine-learning.pdf |
60c73e574c89195bf1ad1d8e | 10.26434/chemrxiv.6863864.v1 | Unzipping Natural Products: Improved Natural Product Structure Predictions by Ensemble Modeling and Fingerprint Matching | This pre-print explores ensemble modeling of natural product targets to match chemical structures to precursors found in large open-source gene cluster repository antiSMASH. Commentary on method, effectiveness, and limitations are enclosed. All structures are public domain molecules and have been reviewed for release. | William A. Shirley; Brian
P. Kelley; Yohann Potier; John H. Koschwanez; Robert Bruccoleri; Michael Tarselli | Bioinformatics and Computational Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e574c89195bf1ad1d8e/original/unzipping-natural-products-improved-natural-product-structure-predictions-by-ensemble-modeling-and-fingerprint-matching.pdf |
655cb792dbd7c8b54bb574ca | 10.26434/chemrxiv-2023-d3wrv-v2 | LC-ESI-HRMS - lipidomics of phospholipids – Characterization of extraction, chromatography and detection parameters | Lipids are a diverse class of molecules involved in many biological functions including cell signaling or cell membrane assembly. Owing to this relevance, LC-MS/MS based lipidomics emerged as a major field in modern analytical chemistry. Here, we thoroughly characterized the influence of MS and LC settings – of a Q Exactive HF operated in Full MS/data-dependent MS2 TOP N acquisition mode - in order to optimize the semi-quantification of polar lipids. Optimization of MS-source settings improved the signal intensity by factor 3 compared to default settings. Polar lipids were separated on an ACQUITY Premier CSH C18 reversed-phase column (100 x 2.1 mm, 1.7 µm, 130 Å) during an elution window of 28 min, leading to a sufficient number of both data points across the chromatographic peaks, as well as MS2 spectra. Analysis was carried out in positive and negative ionization mode enabling the detection of a broader spectrum of lipids and to support the structural characterization of lipids. Optimal sample preparation of biological samples was achieved by liquid-liquid extraction using MeOH/MTBE resulting in an excellent extraction recovery >85% with an intra-day and inter-day variability <15%. The optimized method was applied on the investigation of changes in the phospholipid pattern in plasma from human subjects supplemented with n3-PUFA (20:5 and 22:6). The strongest increase was observed for lipids bearing 20:5, while 22:4 bearing lipids were lowered. Specifically, LPC 20:5_0:0 and PC 16:0_20:5 were found to be strongest elevated, while PE 18:0_22:4 and PC 18:2_18:2 were decreased by n3-PUFA supplementation. These results were confirmed by targeted LC-MS/MS using commercially available phospholipids as standards. | Katharina Rund; Laura Carpanedo; Robin Lauterbach; Tim Wermund; Annette West; Luca Wende; Philipp Calder; Nils Helge Schebb | Biological and Medicinal Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655cb792dbd7c8b54bb574ca/original/lc-esi-hrms-lipidomics-of-phospholipids-characterization-of-extraction-chromatography-and-detection-parameters.pdf |
660e1649418a5379b004910f | 10.26434/chemrxiv-2024-b0m7w | PregPred: an In-Silico Alternative to Animal Testing for Predicting Developmental Toxicity Potential | Background: Understanding potential prenatal and development toxicity hazard associated with the use of pharmaceutical and cosmetic products is an important component of women health. This hazard can be estimated from chemical structure of respective agents using Quantitative Structure-Activity Relationship (QSAR) models; however, the development of reliable models is challenging due to the complex nature of this endpoint.
Methods: Aggregating and curating data from the Food and Drug Administration (FDA), Teratogen Information System (TERIS) database, and select independent studies, we have created, to the best of our knowledge, the largest publicly available dataset comprising compounds annotated as developmental toxicants or not toxicants.
Results: We built several binary classification QSAR models exhibiting a correct classification rate of 62-72%, a sensitivity of 66-75%, a specificity of 59-82%, and high coverage of 70-90% assessed using five-fold external validation protocol. We developed a publicly accessible web portal PregPred for developmental toxicity prediction of both overall toxicity and trimester-specific toxicity predictions.
Conclusions: Due to high accuracy and coverage as well as public accessibility of the respective web portal, our models can be employed as a computational tool to support regulatory assessment of pharmaceutical and cosmetic products in alignment with the 3Rs (refining, reducing, and replacing) of animal testing. This in silico model holds the potential to substantially influence the field of developmental toxicology, steering regulatory practices toward safer drug development for pregnant women. The first-of-its-kind curated dataset of developmental toxicants and all developed models implemented as a user-friendly web tool, PregPred, are freely available at https://pregpred.mml.unc.edu/).
| Ricardo Tieghi; Marielle Rath; Jose Moreira-Filho; James Wellnitz; Holli-Joi Martin; Kathleen Gates; Helena Hogberg-Durdock; Nicole Kleinstreuer; Alexander Tropsha; Eugene Muratov | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660e1649418a5379b004910f/original/preg-pred-an-in-silico-alternative-to-animal-testing-for-predicting-developmental-toxicity-potential.pdf |
6540eb2548dad23120c52242 | 10.26434/chemrxiv-2023-wwbt0 | The Hitchhiker’s Guide to Statistical Analysis of Feature-based Molecular Networks from Non-Targeted Metabolomics Data | Feature-Based Molecular Networking (FBMN) is a popular analysis approach for LC-MS/MS-based non-targeted metabolomics data. While processing LC-MS/MS data through FBMN is fairly streamlined, downstream data handling and statistical interrogation is often a key bottleneck. Especially, users new to statistical analysis struggle to effectively handle and analyze complex data matrices. In this protocol, we provide a comprehensive guide for the statistical analysis of FBMN results. We explain the data structure and principles of data clean-up and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/), to lower the barrier of entry for new users. Together, the protocol, code, and web app provide a complete guide and toolbox for FBMN data integration, clean-up, and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking (GNPS and GNPS2) and can be adapted to other MS feature detection, annotation, and networking tools. | Abzer K. Pakkir Shah; Axel Walter; Filip Ottosson; Francesco Russo; Marcelo Navarro-Díaz; Judith Boldt; Jarmo-Charles Kalinski; Eftychia E. Kontou; James Elofson; Alexandros Polyzois; Carolina González-Marín; Shane Farrell; Marie R. Aggerbeck; Thapanee Pruksatrakul; Nathan Chan; Yunshu Wang; Magdalena Pöchhacker; Corinna Brungs; Beatriz Cámara; Andrés M. Caraballo-Rodríguez; Andres Cumsille; Fernanda de Oliveira; Kai Dührkop; Yasin El Abiead; Christian Geibel; Lana G. Graves; Martin Hansen; Steffen Heuckeroth; Simon Knoblauch; Anastasiia Kostenko; Mirte CM. Kuijpers; Kevin Mildau; Stilianos Papadopoulos Lambidis; Paulo Wender Portal Gomes; Tilman Schramm; Karoline Steuer-Lodd; Paolo Stincone; Sibgha Tayyab; Giovanni Andrea Vitale; Berenike C. Wagner; Shipei Xing; Marquis T. Yazzie; Simone Zuffa; Martinus de Kruijff; Christine Beemelmanns; Hannes Link; Christoph Mayer; Justin JJ van der Hooft; Tito Damiani; Tomáš Pluskal; Pieter C. Dorrestein; Jan Stanstrup; Robin Schmid; Mingxun Wang; Allegra T. Aron; Madeleine Ernst; Daniel Petras | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Chemoinformatics; Mass Spectrometry; Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540eb2548dad23120c52242/original/the-hitchhiker-s-guide-to-statistical-analysis-of-feature-based-molecular-networks-from-non-targeted-metabolomics-data.pdf |
60c74e8eee301c2264c7a501 | 10.26434/chemrxiv.12770504.v1 | The Lipid-Chaperon Hypothesis: A Common Molecular Mechanism of Membrane Disruption by Intrinsically Disordered Proteins | <p>Increasing number of human diseases have
been shown to be linked to aggregation and amyloid formation by intrinsically
disordered proteins (IDPs). Amylin, amyloid-β, and α-synuclein are,
indeed, involved in type-II diabetes, Alzheimer’s, and Parkinson’s,
respectively. Despite the correlation of the toxicity of these proteins at
early aggregation stages with membrane damage, the molecular events underlying
the process is quite complex to understand. In this study, we demonstrate the
crucial role of free lipids in the formation of lipid-protein complex, which
enables an easy membrane insertion for amylin,
amyloid-β,
and α-synuclein. Experimental results from a variety of biophysical
methods and molecular dynamics results reveal this common molecular pathway in
membrane poration is shared by amyloidogenic (amylin, amyloid-β, and α-synuclein) and non-amyloidogenic (rat IAPP, β-synuclein) proteins. Based
on these results, we propose a “lipid-chaperone” hypothesis as a unifying
framework for protein-membrane poration.<b></b></p> | Michele
F. M. Sciacca; Fabio Lolicato; Carmelo Tempra; Federica Scollo; Bikash R. Sahoo; Matthew D. Watson; Sara García-Viñuales; Danilo Milardi; Antonio Raudino; Jennifer C. Lee; Ayyalusamy Ramamoorthy; Carmelo La Rosa | Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e8eee301c2264c7a501/original/the-lipid-chaperon-hypothesis-a-common-molecular-mechanism-of-membrane-disruption-by-intrinsically-disordered-proteins.pdf |
64904169853d501c0021cc9e | 10.26434/chemrxiv-2023-34k6l | Exploring the Role of Solvent Polarity in Mechanochemical Knoevenagel Condensation: In-situ Tracking and Isolation of Reaction Intermediates | Mechanochemistry has proven to be a highly effective method for the synthesis of organic compounds. We studied the kinetics of the catalyst-free Knoevenagel reaction between 4-nitrobenzaldehyde and malononitrile, activated and driven by ball milling. The reaction was investigated in the absence of solvents (neat grinding) and in the presence of solvents with different polarities (liquid-assisted grinding). The reaction was monitored using time-resolved in-situ Raman spectroscopy and powder X-ray diffraction (PXRD). Our results indicate a direct relationship between solvent polarity and reaction kinetics, with higher solvent polarity leading to faster product (2-(4-nitrobenzylidone)malononitrile) formation. For the first time, we were able to isolate and determine the structure of an intermediate 2-(hydroxy(4-nitrophenyl)methyl)malononitrile based on PXRD data | Kerstin Scheurell; Ines Martins ; Claire Murray; Franziska Emmerling | Organic Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Materials Chemistry; Crystallography – Organic | CC BY NC 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64904169853d501c0021cc9e/original/exploring-the-role-of-solvent-polarity-in-mechanochemical-knoevenagel-condensation-in-situ-tracking-and-isolation-of-reaction-intermediates.pdf |
60c751cc9abda204a9f8dcb3 | 10.26434/chemrxiv.13210802.v1 | Anchoring Carboxyl Functionalized Gold-Aryl Nanoparticles to Graphene Oxide Platforms for Environmental Nanoremediation | Graphene oxide (GO) was decorated
with gold-aryl (Au-C) nanoparticles AuNPs-COOH by sodium borohydride reduction of
aryldiazonium tetrachloroaurate(III) salt at room temperature in aqueous
solutions. BET (Brunauer-Emmett-Teller) measurements supported the anchoring of GO by AuNPs modified with
carboxyl functional groups; surface area dropped significantly. Morphology of
AuNPs-COOH/GO nanocomposite (NC) was probed using AFM and TEM and images showed
surface roughness and wrinkling. Molecular dynamics (MD) calculations endowed
support of favorable wrinkling at the edges and carboxyl intercalation to GO
surface of types p-p, hydrogen bonding, and
hydrophobic interactions. Solvent accessible surface area calculations (SASA) of
GO showed a decrease in total surface area, in agreement with BET results. Environmental
nanoremediation of the catalytic reduction of nitrophenol and the electrocatalytic
reduction of CO<sub>2 </sub>(model pollutants) were investigated. The apparent rate constants
K<sub>app</sub> of the four catalytic reduction cycles of nitrophenol were measured. The highest value is 1.17 × 10<sup>-1</sup> min<sup>-1 </sup>for
the first cycle which decreased to 4.49 × 10<sup>-2</sup> min<sup>-1</sup> for
the fourth cycle. Electrocatalytic
studies revealed that the NC enhanced the CO<sub>2</sub> reduction. The NC
exhibited higher current densities in the CO<sub>2</sub> solution saturated (48
mA/cm<sup>2</sup>) compared to N<sub>2</sub> (37 mA/cm<sup>2</sup>), indicating
its superior catalytic activity in CO<sub>2</sub>
reduction. | Javad Parambath; Najrul Hussain; Mahreen Arooj; Maria Omastova; Mohamed Chehimi; Changseok Han; Ahmed A. Mohamed | Interfaces; Physical and Chemical Properties; Quantum Mechanics; Spectroscopy (Physical Chem.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751cc9abda204a9f8dcb3/original/anchoring-carboxyl-functionalized-gold-aryl-nanoparticles-to-graphene-oxide-platforms-for-environmental-nanoremediation.pdf |
651cd2318bab5d20559a7044 | 10.26434/chemrxiv-2023-906jv | Accelerated and controlled polymerization of N-carboxyanhydrides catalyzed by acids | It has been widely accepted that acidic species, such as HCl, inhibit the polymerization process of N-carboxyanhydrides (NCAs), which have to be removed to guarantee the successful synthesis of polypeptides. Herein, we showed that the im-pact of organic acids on NCA polymerization was dependent on their pKa values in dichloromethane. While stronger acids like trifluoroacetic acids completely blocked the chain propagation as expected, weaker acids such as acetic acids accel-erated the polymerization rate instead. The addition of acids not only protonated the propagating amino groups but also activated NCA monomers, whose balance determined the catalytic or inhibitory effect. Additionally, the acid-catalyzed polymerization exhibited one-stage kinetics that differed from conventional cooperative covalent polymerizations, result-ing in excellent control over molecular weights even with an accelerated rate. The pKa-dependence inspired us to turn the inhibitory acids into catalysts on demand, promoting the controlled polymerization from non-purified NCA monomers. This work highlights the possibility to change the conventional understanding of a catalyst/inhibitor by altering reaction conditions, which not only sheds light on the design of new catalysts, but also offers a practical strategy to prepare poly-peptide materials in an efficient and controlled manner. | Xingliang Liu; Jing Huang; Jiaqi Wang; Haonan Sheng; Zhen Yuan; Wanying Wang; Wenbin Li; Ziyuan Song; Jianjun Cheng | Polymer Science; Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651cd2318bab5d20559a7044/original/accelerated-and-controlled-polymerization-of-n-carboxyanhydrides-catalyzed-by-acids.pdf |
60c74a549abda22733f8ce20 | 10.26434/chemrxiv.12186531.v1 | Live-Cell Epigenome Manipulation by Synthetic Histone Acylation Catalyst System | <div><div><div><p>Chemical modifications of histones play a pivotal role in the epigenome and regulation of gene expression, and their abnormality is tightly linked to numerous disease states in humans. Therefore, chemical tools to manipulate epigenome hold promise for both therapy and the elucidation of epigenetic mechanisms. We previously developed the chemical catalyst LANA-DSH, which binds to nucleosomes via a LANA peptide ligand, and selectively acylates proximal histone H2BK120 to the catalyst moiety by acti- vating acyl-CoAs. Thus far, however, histone acylation by a chem- ical catalyst system in living cells has not yet been demonstrated. Here, we report a chemical catalyst system, composed of a nucleo- some-binding catalyst (PEG-LANA-DSH) and a cell-permeable thioester acyl donor (NAC-acyl), that can promote regioselective lysine acylation of histones in living cells. Whereas LANA-DSH is rapidly decomposed in cells, attachment of polyethylene glycol (PEG) to the LANA moiety can prevent this undesired degradation. Increasing the size of PEG conferred LANA with greater in-cell stability, but reduced catalytic activity, indicating that there is an optimum PEG length balancing stability and catalytic activity. The optimized PEG-LANA-DSH catalyst 11 efficiently promoted H2BK120 acetylation in living cells, which subsequently sup- pressed ubiquitination of H2BK120, a mark regulating various chromatin functions, such as transcription and DNA damage re- sponse. Thus, our chemical catalyst system will be useful as a unique tool to manipulate the epigenome for therapeutic purposes or further understanding epigenetic mechanisms.</p></div></div></div> | Yusuke Fujiwara; Yuki Yamanashi; Yuko Sato; Tomoya Kujirai; Hitoshi Kurumizaka; Hiroshi Kimura; Kenzo Yamatsugu; Shigehiro Kawashima; Motomu Kanai | Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a549abda22733f8ce20/original/live-cell-epigenome-manipulation-by-synthetic-histone-acylation-catalyst-system.pdf |
60c74440bb8c1a0fc53da499 | 10.26434/chemrxiv.9772499.v1 | Simultaneous Determination of Per- and Polyfluoroalkyl Substances and Bile Acids in Human Serum Using Ultra-High-Performance Liquid Chromatography-Tandem Mass Spectrometry | There is evidence of a positive association between per- and polyfluoroalkyl substances (PFAS) and cholesterol levels in human plasma, which may be due to common reabsorption of PFAS and bile acids (BAs) in the gut. Here we report development and validation of a method that allows simultaneous, quantitative determination of PFAS and BAs in plasma, using 150 uL or 20 uL of sample. The method involves protein precipitation using 96-well plates. The instrumental analysis was performed with ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS), using reverse-phase chromatography, with the ion source operated in negative electrospray mode. The mass spectrometry analysis was carried out using multiple reaction monitoring mode. The method proved to be sensitive, robust and with sufficient linear range to allow reliable determination of both PFAS and BAs. The method detection limits were between 0.01 and 0.06 ng⋅mL-1 for PFAS and between 0.002 and 0.152 ng⋅mL-1 for BAs, with the exception of glycochenodeoxycholic acid (0.56 ng⋅mL-1). The PFAS measured showed excellent agreement with certified plasma PFAS concentrations in NIST SRM 1957 reference plasma. The method was tested on serum samples from 20 healthy individuals. In this proof-of-concept study, we identified significant associations between plasma PFAS and BA levels, which suggests that PFAS may alter the synthesis and/or uptake of BAs. | Samira Salihovic; Alex Dickens; Ida Schoultz; Frida Fart; Lisanna Sinisalu; Tuomas Lindeman; Jonas Halfvarsson; Matej Oresic; Tuulia Hyötyläinen | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74440bb8c1a0fc53da499/original/simultaneous-determination-of-per-and-polyfluoroalkyl-substances-and-bile-acids-in-human-serum-using-ultra-high-performance-liquid-chromatography-tandem-mass-spectrometry.pdf |
60c749cb337d6c63a1e27784 | 10.26434/chemrxiv.12091176.v1 | Targeted Degradation of Oncogenic KRASG12C by VHL-recruiting PROTACs | <p>We report the development of LC-2, the first PROTAC capable of degrading endogenous KRAS<sup>G12C</sup>.<sup> </sup> LC-2 covalently binds KRAS<sup>G12C</sup> with a MRTX849 warhead and recruits the E3 ligase VHL, inducing rapid and sustained KRAS<sup>G12C</sup> degradation leading to suppression of MAPK signaling in both homozygous and heterozygous KRAS<sup>G12C</sup> cell lines. LC-2 demonstrates that PROTAC-mediated degradation is a viable option for attenuating oncogenic KRAS levels and downstream signaling in cancer cells.</p> | Michael J. Bond; Ling Chu; Dhanusha A. Nalawansha; Ke Li; Craig Crews | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749cb337d6c63a1e27784/original/targeted-degradation-of-oncogenic-krasg12c-by-vhl-recruiting-prota-cs.pdf |
60c747790f50dbf7c03965eb | 10.26434/chemrxiv.11542503.v2 | Bismuthanylstibanes | Thermally-robust bismuthanylstibanes are prepared in a one-step, high yield reaction, providing the first examples of neutral Bi–Sb σ-bonds in the solid state. DFT calculations indicate that the bis(silylamino)naphthalene scaffold is well-suited for supporting otherwise labile bonds. The reaction chemistry of the Bi–Sb bond is exploited by showing insertion of a sulfur atom, providing the first documented example of a Bi–S–Sb bonding moiety. <br /> | Katherine Marczenko; Saurabh Chitnis | Bonding; Theory - Inorganic; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747790f50dbf7c03965eb/original/bismuthanylstibanes.pdf |
60c74b81ee301c873ec79e95 | 10.26434/chemrxiv.12343994.v1 | Synthesis of 1,2,3-Triazole-Containing Furanosyl Nucleoside Analogs and Their Phosphate, Phosphoramidate or Phoshonate Derivatives as Potential Sugar Diphosphate or Nucleotide Mimetics | <p>The
synthesis of a variety of novel, rather stable and potentially bioactive
nucleoside analogs and nucleotide mimetics based on xylofuranose scaffolds and
comprising a 1,2,3-triazole moiety
as a surrogate for a nucleobase or a phosphate group is reported. Isonucleosides
embodying a 3-<i>O</i>-(benzyltriazolyl)methyl
moiety at C-3 were accessed by using the Cu(I)-catalyzed “click” 1,3-dipolar
cycloaddition between 3-<i>O</i>-propargyl-1,2-<i>O</i>-isopropylidene-α-D-xylofuranose
and benzyl azide as the key step. Related isonucleotides comprising a phosphate
or a phosphoramidate moiety at C-5 were obtained via 5-<i>O</i>-phosphorylation of acetonide-protected 3-<i>O</i>-propargyl xylofuranose followed by “click” cycloaddition or by Staudinger
reaction of a 5ʹ-azido <i>N</i>-benzyltriazole
isonucleoside with triethyl phosphite, respectively. Hydroxy, amino- or bromomethyl triazole 5ʹ-isonucleosides
were synthesized through thermal cycloaddition between 5-azido 3-<i>O</i>-benzyl/dodecyl-1,2-<i>O</i>-isopropylidene-α-D-xylofuranoses
and propargyl alcohol, propargylamine or propargyl bromide, respectively. The
regiochemical outcome of the cycloaddition reactions was influenced by nature
of the alkyne hetero substituent (alkyne CH<sub>2</sub>X substituent). The 5´-isonucleosides were converted into
their [(xylofuranos-5-yl)triazolyl]methyl
phosphate, phosphoramidate and phosphonate derivatives as prospective sugar
diphosphate mimetics by an appropriate method involving treatment with diethyl
phosphorochloridate or a Michaelis-Arbuzov reaction. 4-Phosphonomethyl-1-xylofuranos-5ʹ-yl triazoles
were converted into 1,2-<i>O</i>-acetyl glycosyl donors and
subsequently subjected to nucleosidation with uracil leading to the
corresponding uracil nucleoside 5ʹ-(triazolyl)methyl phosphonates, whose structure
potentially mimics that of a nucleoside diphosphate. </p>
<p><b> </b></p> | Andreia Fortuna; Paulo J. Costa; Fátima Piedade; M. Conceição Oliveira; Nuno Manuel Xavier | Bioorganic Chemistry; Organic Synthesis and Reactions; Computational Chemistry and Modeling; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b81ee301c873ec79e95/original/synthesis-of-1-2-3-triazole-containing-furanosyl-nucleoside-analogs-and-their-phosphate-phosphoramidate-or-phoshonate-derivatives-as-potential-sugar-diphosphate-or-nucleotide-mimetics.pdf |
66f1bdd351558a15efe86910 | 10.26434/chemrxiv-2024-gk1bp | SMARTpy: A Python Package for the Generation of Cavity-Specific Steric Molecular Descriptors and Applications to Diverse Systems | Steric molecular descriptors designed for machine learning (ML) applications are critical for connecting structure-function relationships to mechanistic insight. However, many of these descriptors are not suitable for application to com-plex systems, such as catalyst reactive site pockets. In this context, we recently disclosed a new set of 3D steric molecular descriptors that were originally designed for dirhodium(II) tetra-carboxylate catalysts. Herein, we expand the Spatial Molding for Rigid Targets (SMART) descriptor toolkit by releasing SMARTpy; an automated, open-source Python API package for computational workflow integration of SMART descriptors. The impact of the structure of the molecular probe for generation of SMART descriptors was analyzed. Resultant SMART descriptors and pocket features were found to be highly dependent upon probe selection, and do not scale linearly. Flexible probes with smaller substituents can explore narrow pocket regions resulting in a higher resolution pocket imprint. Macrocyclic probes with larger substituents are more applicable to larger cavities with smooth boundaries, such as dirhodium paddlewheel complexes. In these cases, SMARTpy provides comparable descriptors to the original calculation method using UCSF Chimera. Finally, we analyzed a series of case studies demonstrating how SMART descriptors can impact other areas of catalysis, such as organocatalysis, biocatalysis, and protein pocket analysis. | Beck Miller; Ryan Cammarota; Matthew Sigman | Theoretical and Computational Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1bdd351558a15efe86910/original/smar-tpy-a-python-package-for-the-generation-of-cavity-specific-steric-molecular-descriptors-and-applications-to-diverse-systems.pdf |
677b03206dde43c9086944cb | 10.26434/chemrxiv-2025-318k4 | A Live Cell BRET Probe to Quantify PRMT5-MTA Uncompetitive Target Engagement | The PRMT5 methyltransferase plays a global role in cell physiology and is an established therapeutic target in cancer. In 10% of human cancers, deletion of the MTAP gene results in accumulation of MTA, exposing a synthetic lethality and opportunity for precision medicine by selective targeting of PRMT5 in this context. Reported small molecule PRMT5 inhibitors engage either cosubstrate (SAM) or peptide-substrate pockets through diverse mechanisms. A subset of chemotypes demonstrate uncompetitive engagement with SAM or its inhibitory metabolic precursor, MTA. Here we describe the development of a cell-permeable BRET probe CBH-002 that acts as a dynamic biosensor of the intracellular SAM/MTA pool. Using this probe, we evaluate a range of diverse PRMT5 inhibitors to mechanistically characterize and quantify uncompetitive target engagement and ternary complex formation at PRMT5-SAM and -MTA complexes in live cells, enabling direct insights into drug mechanism-of-action and metabolite-dependent response to inhibitors. | Elisabeth Rothweiler; Ani Michaud; Jakub Stefaniak; Usha Singh; James Vasta; Michael Beck; Jennifer Ward; Catherine Rogers; Esra Balıkçı; Jeppe Tranberg-Jensen; Jesper Hansen; Peter Loppnau; Paul Brennan; Peter Tonge; Matthew Robers; Kilian Huber | Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2025-01-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677b03206dde43c9086944cb/original/a-live-cell-bret-probe-to-quantify-prmt5-mta-uncompetitive-target-engagement.pdf |
60c7504f4c891922e7ad3d5c | 10.26434/chemrxiv.13019591.v1 | Predi-XY: A Python Program for Automated Generation of NICS-XY-Scans Based on an Additivity Scheme | We detail the development of a new Python-based program for automatic generation of NICS-XY-Scans of cata-condensed polycyclic aromatic systems. <div>The program uses an underlying additivity scheme, which enables generation of the Scans using only smaller building blocks within the larger systems, and circumvents the need for quantum mechanical calculations. </div> | Alexandra Wahab; Felix Fleckenstein; Stefan Feusi; Renana Gershoni-Poranne | Physical Organic Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7504f4c891922e7ad3d5c/original/predi-xy-a-python-program-for-automated-generation-of-nics-xy-scans-based-on-an-additivity-scheme.pdf |
67a2263681d2151a02260ab7 | 10.26434/chemrxiv-2025-3tg1x-v2 | Designing Molecular Qubits: Computational Insights into First-Row and Group 6 Transition Metal Complexes | The discovery of novel molecular systems for quantum information processing remains a major challenge for advancing molecular qubit technology. In the realm of optically addressable systems, a previously synthesized and characterized Cr(IV) pseudo-tetrahedral complex, featuring four strongly donating o-tolyl ligands surrounding the chromium center, has demonstrated potential as a qubit candidate. This study proposes analogs of this complex through a metal substitution strategy, extending the investigation to new complexes. The new metal centers were selected from first-row and Group 6 transition metals. Multiconfigurational methods such as the complete active space followed by second-order perturbation theory and multiconfiguration pair-density functional theory were utilized to calculate energy gaps between electronic states with different spins and zero-field splitting (ZFS). The results corroborate previous experimental findings for the Cr complex. Additionally, this study identifies a previously unsynthesized Ti(II) compound as a promising candidate for molecular qubits. This finding highlights the role of computational multireference methods in the rational design of qubit systems. | Arturo Sauza-de la Vega; Andrea Darù; Stephanie Nofz; Laura Gagliardi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a2263681d2151a02260ab7/original/designing-molecular-qubits-computational-insights-into-first-row-and-group-6-transition-metal-complexes.pdf |
64f91ea779853bbd78406bd3 | 10.26434/chemrxiv-2023-x6xkv-v2 | High-performance and chemically self-charging flexible aqueous zinc-ion batteries based on organic cathodes with Zn2+ and H+ storage | Chemically self-charging aqueous zinc-ion batteries (AZIBs) via air oxidation will provide new opportunities for future wearable electronic devices. Herein, we display two high-performances flexible AZIBs based on trifluorohexaazatrinaphthylene (TFHATN)/trichlorohexaazatrinaphthylene (TCLHATN) cathode, which can be recharged via air without using external power supply. The flexible Zn//TFHATN/Zn//TCLHATN battery presents good mechanical flexibility and high volumetric energy density of 9.2/10.7 mWh cm-3. The air-recharging capability originates from a spontaneous redox reaction between the discharged TFHATN/TCLHATN cathode and O2 from air. After exposed to air for 15 h, the discharged Zn//TFHATN/Zn//TCLHATN battery can be recharged to 1.2 V around, exhibits high discharge capacity, high-rate performance, higher self-charging cycle stability (8 cycles), and works well in chemical or/and galvanostatic charging mixed modes, displaying good reusability. This work provides a strategy for developing high-performance flexible air-rechargeable AZIBs. | Qi Liu; Xiuting Song; Haoqi Su; Xiaojuan Chen; Baozhu Yang; Huimin Zhang; Yiwen Lu; Qingyan Jiang | Organic Chemistry; Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f91ea779853bbd78406bd3/original/high-performance-and-chemically-self-charging-flexible-aqueous-zinc-ion-batteries-based-on-organic-cathodes-with-zn2-and-h-storage.pdf |
648113dcbe16ad5c579edbe6 | 10.26434/chemrxiv-2023-fnj9h | Iridium-Catalyzed Regio- and Enantioselective Propargylic C−H Silylation | ABSTRACT: We report a highly enantioselective intermolecular silylation of the propargylic C(sp3)−H bonds of alkynes for the formation of propargylic silanes. The optimized protocol afforded enantioenriched α-silylated alkynes in good to high yield with excellent levels of stereocontrol under mild conditions. A variety of silyl triflates, either commercial or in situ-generated, were used as the silylation reagents, and a broad range of simple and functionalized alkynes, including aryl alkyl acetylenes, dialkyl acetylenes, and 1,3-enynes, were successfully employed as substrates. In the case of dialkyl acetylene substrates, silylation took place in a highly regi-oselective manner. Preliminary mechanistic experiments suggest a catalytic cycle in which electrophilic addition of the silyl triflate reagent to the Ir center and subsequent deprotonation of a dicationic Ir–alkyne complex are key steps. | Jin Zhu; Hai Chang; Yiming Wang | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Bond Activation | CC BY 4.0 | CHEMRXIV | 2023-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648113dcbe16ad5c579edbe6/original/iridium-catalyzed-regio-and-enantioselective-propargylic-c-h-silylation.pdf |
66b5b89d01103d79c55251a0 | 10.26434/chemrxiv-2024-mq77k | Orthogonal Phase Transfer of Oppositely Charged FeII4L6 Cages | Coordination cages and their encapsulated cargo can be manoeuvred between immiscible liquid layers in a process referred to as phase transfer. Among the stimuli reported to drive phase transfer, counterion exchange is the most widespread. This method exploits the principle that counterions contribute strongly to the solubility preferences of coordination cages, and involves exchanging hydrophilic and hydrophobic counterions. Nevertheless, phase transfer of anionic cages remains relatively unexplored, as does selective phase transfer of individual cages from mixtures. Here we compare the phase transfer behaviour of two FeII4L6 cages with the same size and geometry, but with opposite charges. As such, this study presents a rare example wherein an anionic cage undergoes phase transfer upon countercation exchange. We then combine these two cages, and demonstrate that their quantitative separation can be achieved by inducing selective phase transfer of either cage. These results represent unprecedented control over the movement of coordination cages between different physical compartments, and are anticipated to inform the development of next-generation supramolecular systems. | Ebba S. Matic; Maylis Bernard; Alexandra J. Jernstedt; Angela Grommet | Inorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b5b89d01103d79c55251a0/original/orthogonal-phase-transfer-of-oppositely-charged-fe-ii4l6-cages.pdf |
621b43a27c13f45a2c6037bd | 10.26434/chemrxiv-2022-j702p | Trapping an Oxidized and Protonated Intermediate of the [FeFe]-Hydrogenase Cofactor under Mildly Reducing Conditions | The H-cluster is the catalytic cofactor of [FeFe]-hydrogenase, a metalloenzyme that catalyzes the production of hydrogen gas (H2). The H-cluster carries two cyanide and three carbon monoxide ligands, making it an excellent target for IR spectroscopy. In previous work, we identified an oxidized and protonated H-cluster species, whose IR signature differs from the oxidized resting state (Hox) by a small but distinct shift to higher frequencies. This ‘blue shift’ was explained by a protonation at the [4Fe-4S] sub-complex of the H-cluster. The novel species, denoted HoxH, was preferentially accumulated at low pH and in the presence of the exogenous reductant sodium dithionite (NaDT). When HoxH was reacted with H2, the hydride state (Hhyd) was formed, a key intermediate of [FeFe]-hydrogenase turnover. A recent publication revisited our protocol for the accumulation of HoxH in wild-type [FeFe]-hydrogenase, concluding that inhibition by NaDT decay products rather than cofactor protonation causes the spectroscopic ‘blue shift’. Here, we demonstrate that HoxH formation does not require the presence of NaDT (or its decay products), but accumulates also with the milder reductants tris(2-carboxyethyl)phosphine, dithiothreitol, or ascorbic acid, in particular at low pH. Our data consistently suggest that HoxH is accumulated when deprotonation of the H-cluster is impaired, thereby preventing the regain of the oxidized resting state Hox in the catalytic cycle. | Moritz Senger; Jifu Duan; Mariia V. Pavliuk; Ulf-Peter Apfel; Michael Haumann; Sven Stripp | Physical Chemistry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621b43a27c13f45a2c6037bd/original/trapping-an-oxidized-and-protonated-intermediate-of-the-fe-fe-hydrogenase-cofactor-under-mildly-reducing-conditions.pdf |
64b1af88b605c6803bb6dac7 | 10.26434/chemrxiv-2023-155w8 | Effect of Sterically Protective Groups on the Aromaticity of Fully Unsaturated Oligoquinanes | Oligoquinane derivatives have unique aromatic properties, which dictate the stability of the molecules and their potential applications in various devices. Due to the challenge in their synthesis, systematic studies of these molecules are still lacking. In this work, we perform density function theory and nucleus-independent chemical shift (NICS) calculations on 24 oligoquinane derivatives that are composed of two, four, five, and six five-membered rings. Pentaquinane without any protection groups was predicted to be aromatic and stable. It would be interesting to synthesize the molecule and carry out further electronic and optical measurements.
Among introducing various protection groups to the bare oligoquinanes, single bond protection was found to be the least effective in the change of aromaticity of oligoquinane. In the protection of benzene rings, aromaticity change depends on the configuration of the molecule formed. HOMO-LUMO energy gap and UV-Vis absorption also depends on the molecular shape. The results show the potential application of the oligoquinanes as they can be diversely tuned for specific applications, and therefore is worthy of future studies. | Junpeng Zhuang; Kyle Plunkett; Lichang Wang | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b1af88b605c6803bb6dac7/original/effect-of-sterically-protective-groups-on-the-aromaticity-of-fully-unsaturated-oligoquinanes.pdf |
60c74909337d6ccc66e2764f | 10.26434/chemrxiv.9885167.v3 | Membrane-Binding Peptides for Extracellular Vesicles On-Chip Analysis | Small extracellular vesicles (EVs) present fairly distinctive lipid membrane features in the extracellular environment. These include high curvature, lipid packing defects and a relative abundance in lipids such as phosphatidylserine and ceramide. EVs membrane could be then considered as a "universal" marker, alternative or complementary to traditional characteristic surface-associated proteins. Here we introduce the use of membrane sensing peptides as new, highly efficient ligands for EVs capturing onto bioanalytical chips to directly integrate EVs capturing and analysis on a microarray platform, even using serum without pre-isolation steps. EVs were analyzed by label-free, single particle counting and by fluorescence co-localization immune-staining with labelled anti-CD9/anti-CD63/anti-CD81 antibodies. Peptides performed as selective yet general EVs baits and showed a binding capacity higher than anti-tetraspanins antibodies. Insights into surface chemistry for optimal peptide performance are also discussed, as capturing efficiency is strictly bound to probes surface orientation and multivalency effects. We anticipate that this new class of ligands, also due to the versatility and limited costs of synthetic peptides, may greatly enrich the molecular toolbox for EVs analysis. | Alessandro Gori; Alessandro Romanato; Greta Bergamaschi; Alessandro Strada; Paola Gagni; Roberto Frigerio; Dario Brambilla; Riccardo Vago; Silvia Galbiati; Silvia Picciolini; Marzia Bedoni; George G. Daaboul; Marcella Chiari; Marina Cretich | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74909337d6ccc66e2764f/original/membrane-binding-peptides-for-extracellular-vesicles-on-chip-analysis.pdf |
67b66b99fa469535b916025e | 10.26434/chemrxiv-2025-w5hqm | Hexadehydro Diels–Alder/Alkynyliodanation Cascade: A Highly Regioselective and Expedient Entry to Polycyclic Aromatics | We report here a cascade process that integrates the hexadehydro Diels–Alder (HDDA) reaction with alkynyliodanation of the resulting aryne, enabling the efficient synthesis of highly substituted aryl-λ3-iodanes. By simply heating a mixture of a tetrayne, consisting of tethered 1,3-diynes, and an alkynylbenziodoxole, the tetrayne-derived aryne undergoes highly regioselective insertion into the alkynyl–iodine(III) bond, producing a 1,4-dialkynyl-2-iodanyl-3-arylbenzene derivative in good yield. Notably, the observed regioselectivity contrasts with the typical regioselectivity patterns reported in related HDDA/aryne trapping reactions, likely due to steric factors influencing the four-centered transition states. The unique regiochemical arrangement of the iodanyl, alkynyl, and aryl substituents offers a versatile platform for subsequent π-extension reactions. These downstream transformations enable the divergent construction of polyaromatic frameworks, such as helicenes and cyclopenta[cd]pyrenes, underscoring the utility of aryne carboiodanation in complex aromatic synthesis. | Naohiko Yoshikai; Shunya Morohashi; Liejin Zhou; Kazuya Kanemoto; Eunsang Kwon | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b66b99fa469535b916025e/original/hexadehydro-diels-alder-alkynyliodanation-cascade-a-highly-regioselective-and-expedient-entry-to-polycyclic-aromatics.pdf |
662084a5418a5379b012c08f | 10.26434/chemrxiv-2024-c4wb9 | Positive and negative impacts of interfacial hydrogen bonds on photocatalytic hydrogen evolution | Understanding the behavior of water molecules at solid–liquid interfaces is crucial for various applications such as photocatalytic water splitting, a key technology for sustainable fuel production and chemical transformations. Despite extensive studies conducted in the past, the impact of microscopic structure of interfacial water molecules on photo-catalytic reactivity has not been directly examined. In this study, using real-time mass spectrometry and Fourier-transform infrared spectroscopy, we demonstrated the crucial role of hydrogen bond (H-bond) networks on the photo-catalytic hydrogen evolution in thickness-controlled water adsorption layers on various TiO2 photocatalysts. Under controlled water vapor environments with a relative humidity (RH) below 70%, we observed a monotonic increase in the H2 formation rate with increasing RH, indicating that reactive water molecules were present not only in the first adsorbed layer but also in several overlying layers. In contrast, at RH > 70%, when more than three water layers covered the catalyst surface, the H2 formation rate turned to decrease dramatically because of the structural rearrangement and hardening of the interfacial H-bond network induced during further water adsorption. This unique many-body effect of interfacial water was consistently observed for various TiO2 particles with different crystalline structures, including brookite, anatase, and a mixture of anatase and rutile. Our results demonstrated that depositing several water layers in a water vapor environment with RH ~70% is optimal for photocatalytic hydrogen evolution rather than liquid-phase reaction conditions in aqueous solutions. This study provides molecular-level insights for designing interfacial water conditions to enhance photocatalytic performance. | Zhongqiu Lin; Hikaru Saito; Hiromasa Sato; Toshiki Sugimoto | Physical Chemistry; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662084a5418a5379b012c08f/original/positive-and-negative-impacts-of-interfacial-hydrogen-bonds-on-photocatalytic-hydrogen-evolution.pdf |
619fd3307c89161a5344b5f7 | 10.26434/chemrxiv-2021-pvvfq | Plastic Microbead Accumulation in our Freshwaters:
North American Great Lakes Assessments and Perspective | The authors review recent studies conducted across the Great Lakes of North America to assess the quantity and type of microplastic waste found in these waters, sediments, and beaches. Findings from their own studies are shared, sampling plastic pollution from remote and secluded Nature Reserves in Lake Erie (ON), and the Ottawa River watershed (QC), showing significant accumulation of microbeads. Spherical ‘microbeads’ made of plastics are now ubiquitous in a wide range of personal healthcare and cleansing products, used by the average North American consumer now at upwards of quadrillions per day. Designed to be flushable, these plastic microbeads inevitably end up in municipal wastewater streams, and then to a large extent leak into our freshwater ecosystems. Recent studies throughout the important Great Lakes system of North America have reported microbeads at essentially all locations examined. On the shorelines, in surface waters, throughout water columns, and in sediments of these freshwater systems, microbeads are now ever-present, and are accumulating in significant amounts. Their small and stable shape and composition, and limited pathways to degradation produce a long lifespan, with the capacity to remain in the freshwater environment for potentially hundreds of years. This review collects and compares initial microbead studies between 2013–2021 in the Great Lakes region to provide a snapshot of the current levels and locations, and to serve as a baseline for future tracking to assess progress as the microbead contamination and accumulation problem is addressed. We as well present findings from our own local study of microplastic/bead accumulation downstream of the Great Lakes, in the St. Lawrence and Ottawa rivers near Montreal. Aspects of microbead contamination represent a unique subset of the worldwide microplastic problem, in that much control remains over their life cycle and eventual fate. Consequently, the power to address this microbead problem can rest with polymer chemists and engineers, who, armed with a better understanding of the relevant physical polymer properties of the beads that govern their movement into the aquatic environment, hold the ability to rationally redesign microbead composition and develop removal techniques. | Mary Torrance; Emma Gillies; Tristan Borchers; Avery Shoemaker; Christopher Barrett | Polymer Science; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619fd3307c89161a5344b5f7/original/plastic-microbead-accumulation-in-our-freshwaters-north-american-great-lakes-assessments-and-perspective.pdf |
60c7422f842e65de67db202d | 10.26434/chemrxiv.8244572.v1 | Conformational Entropy as a Means to Control the Behavior of Poly(diketonenamine) Vitrimers In and Out of Equilibrium | Here we show how to control the thermomechanical behavior of vitrimers, both in and out of equilibrium, by incorporating into the dynamic covalent network linear polymer segments varying in both molecular weight (MW = 0–12 kg mol–1) and conformational degrees of freedom. While increasing MW of linear segments predictably yields a lower storage modulus (E’) at the rubbery plateau after softening above the glass transition (Tg), due to the lower network density, we further find that both Tg and the characteristic time (t*) of stress-relaxation when deformed are independently governed by the conformational entropy of the embodied linear segments. We also find that activation energies (Ea) for vitrimer bond exchange in the solid-state are lower, by as much as 19 kJ mol−1, for networks incorporating flexible chains, and that the network’s topology freezing temperature (Tv) decreases with increasing MW of flexible linear segments, but increases with increasing MW of stiff linear segments. Therefore, the dynamics of vitrimer reconfigurability are influenced not only by the energetics of associative bond exchange for a given network density, but also foundationally by the entropy of polymer chains within the network. | Changfei He; Peter Christensen; Trevor Seguin; Brandon Wood; Kristin Persson; Thomas Russell; Brett Helms | Biopolymers; Organic Polymers; Polymer chains; Polymerization (Polymers); Polymer scaffolds | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422f842e65de67db202d/original/conformational-entropy-as-a-means-to-control-the-behavior-of-poly-diketonenamine-vitrimers-in-and-out-of-equilibrium.pdf |
673e5c75f9980725cf1635e7 | 10.26434/chemrxiv-2024-shvp5 | Reactions of a prototypical phenolic antioxidant with radicals in polyethylene: insights from density functional theory | Phenolic antioxidants are widely used to prevent oxidation, which is the main degradation process for many polymers, in particular polyolefins among which polyethylene is the most employed one. Although it is generally understood that one of the main mechanisms by which phenolic antioxidants prevent or slow down oxidation is by deactivating radicals and preventing the formation of alkyl radicals, detailed understanding at the atomic scale of the hierarchy of radical reactions is still lacking. Here, we investigate the interaction of a prototypical phenolic antioxidant, butylated hydroxytoluene (BHT), with radicals in a polyethylene model by means of static and dynamic simulations based on density functional theory. We focus on the H-transfer reactions between BHT and radical species by evaluating the associated energy barriers and analyses the conditions in which these relevant reactions occur by first principles molecular dynamics simulation. Our polyethylene model includes a realistic surface of a crystalline lamella, thus describing the local atomic environment in which the reactions mainly take place. Our results suggest that the H-transfer reaction of the BHT molecule with an alkoxy radical is spontaneous and the energy barrier is small (~0.1 eV) with a peroxy radical. Conversely, direct scavenging of alkyl radicals by BHT seems excluded. Our molecular dynamics simulations highlight the influence of steric hindrance and antioxidant diffusion within amorphous regions on antioxidant efficiency. | Yunho Ahn; Guido Roma; Xavier Colin | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Organic Polymers; Polymerization kinetics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e5c75f9980725cf1635e7/original/reactions-of-a-prototypical-phenolic-antioxidant-with-radicals-in-polyethylene-insights-from-density-functional-theory.pdf |
65292c4a8bab5d20554598dd | 10.26434/chemrxiv-2023-c0741 | Statistically derived proxy potentials accelerate geometry optimisation of crystal structures | Geometry optimisation is a ubiquitous task in computational materials science, but the number of systems for which fast and reliable force field models have been developed is limited. This leaves local energy minimisation using computationally expensive density functional theory (DFT) as the only reliable route to structure optimisation. At the same time, the available crystal structures of known materials contain the information about the interatomic interactions that produced these stable compounds, expressed as the interatomic distances between all the constituent atoms. We use this relationship to statistically learn the effective interatomic interactions in crystalline inorganic solids from their structures. By analysing pairwise interatomic distances in the reported crystallographic data for inorganic materials, we have constructed statistically derived proxy potentials (SPPs) that can be used for structure optimisation. We apply such optimisation step to markedly improve the quality of the input crystal structures for DFT calculations and demonstrate that the SPPs accelerate geometry optimisation for three systems relevant to battery materials. As this approach is chemistry-agnostic and can be used at scale, we produced a database of all possible pair potentials in a tabulated form ready to use. | Dmytro Antypov; Christopher M. Collins; Andrij Vasylenko; Vladimir Gusev; Michael W. Gaultois; George R. Darling; Matthew S. Dyer; Matthew J. Rosseinsky | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65292c4a8bab5d20554598dd/original/statistically-derived-proxy-potentials-accelerate-geometry-optimisation-of-crystal-structures.pdf |
6241ff57bdebbaaa466f9be1 | 10.26434/chemrxiv-2022-9z9g2 | Sustainable and Scalable Synthesis of Noroxymorphone via a Key Electrochemical N-Demethylation Step | Noroxymorphone is a pivotal intermediate in the synthesis of important opioid antagonists such as naloxone and naltrexone. The preparation of noroxymorphone from thebaine, a naturally occurring opioate isolated from poppy extract, is a multistep sequence in which oxycodone is first generated and then N- and O-demethylated. Both demethylations are problematic from the safety and sustainability viewpoint, as they involve harmful reagents such as alkyl chloroformates or boron tribromide. Herein, we present a green, safe an efficient telescoped process for the N- and O-demethylation of oxycodone. The method is based on the anodic oxidative intramolecular cyclization of the N-methyl tertiary amine with the 14-hydroxyl group of the morphinan, followed by hydrolysis with hydrobromic acid, which releases the carbon from both heteroatoms. The electrolysis process has been transferred to a scalable flow electrolysis cell, significantly improving the reaction throughput and increasing the space-time yield over 300-fold with respect to batch. The sustainability of the new methodology has been assessed by means of green metrics and qualitative indicators. The sustainability assessment has demonstrated that the new methodology is far superior to the conventional chloroformate process | Florian Sommer; Roman Gerber Aeschbacher; Urs Thurnheer; C. Oliver Kappe; David Cantillo | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Chemistry; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6241ff57bdebbaaa466f9be1/original/sustainable-and-scalable-synthesis-of-noroxymorphone-via-a-key-electrochemical-n-demethylation-step.pdf |
60c755690f50db64bc397ed7 | 10.26434/chemrxiv.14102675.v1 | Computational Estimation of Potential Inhibitors from the Known Drugs against the Main Protease of SARS-CoV-2 | The coronavirus disease (COVID-19) pandemic caused by a severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide recently, leading to
a global social and economic disruption. Although the emergently approved vaccine
programs against SARS-CoV-2 have been rolled out globally, the number of COVID-19
daily cases and deaths has remained significantly high. Here, we attempted to
computationally screen for possible medications for COVID-19 via rapidly estimate the
highly potential inhibitors from an FDA-approved drug database against the main
protease (Mpro) of SARS-CoV-2. The approach combined molecular docking and fast
pulling of ligand (FPL) simulations that were demonstrated to be accurate and suitable
for quick prediction of SARS-CoV-2 Mpro inhibitors. The results suggested that twentyseven compounds were capable of strongly associating with SARS-CoV-2 Mpro. Among
them, the seven top leads are daclatasvir, teniposide, etoposide, levoleucovorin,
naldemedine, cabozantinib, and irinotecan. The potential application of these drugs in
COVID-19 therapy has thus been discussed. | Nguyen Minh Tam; Pham Minh Quan; Nguyen Xuan Ha; Pham Cam Nam; Huong Thi Thu Phung | Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755690f50db64bc397ed7/original/computational-estimation-of-potential-inhibitors-from-the-known-drugs-against-the-main-protease-of-sars-co-v-2.pdf |
65ce770966c1381729bad575 | 10.26434/chemrxiv-2024-fvxrb | Limestone conversion to cement clinker precursor in a zero-gap electrolyzer | The carbon intensity of industrial cement production could be reduced if the high-temperature kilns used to decompose limestone (CaCO3(s)) were replaced. One possible solution is to use electrochemical reactors to convert CaCO3(s) into Ca(OH)2(s). The challenge is that the continuous-flow electrochemical reactors reported to date all require voltages that are too high (>4 V at 100 mA cm–2) to be put into practice. A key reason for these high voltages is that the reactors contain a chemical chamber, inserted between the anode and cathode chambers, that leads to a high Ohmic resistance. In this study, we present an electrolyzer that decomposes CaCO3(s) into reactive Ca2+ ions using only two chambers. This cell design, with an anode and cathode chamber separated by a membrane instead of a chemical chamber, follows a “zero-gap” design akin to hydrogen-producing electrolyzers and fuel cells. This cement electrolyzer is capable of operating at a full cell voltage (Ecell) of merely 0.38 V at 100 mA cm–2, and with 100% faradaic efficiency (FE). This strikingly low Ecell is 1.4 V lower than any other reported Ecell. We achieved this goal by not only eliminating the chemical chamber, but by also engaging the reversible redox activity of (hydro)anthraquinones to mediate oxidation and reduction within a narrow electrochemical window. This streamlined reactor is capable of operating at a record low voltages of 0.38 V at 100 mA cm–2, and 4.23 V at 1 A cm–2. | Tengxiao Ji; Shaoxuan Ren; Gaopeng Jiang; Yumeng Yang; Siwei Ma; Christopher Waizenegger; Yongwook Kim; Andrew Jewlal; Monika Stolar; Curtis Berlinguette | Inorganic Chemistry; Catalysis; Energy; Electrochemistry; Electrocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ce770966c1381729bad575/original/limestone-conversion-to-cement-clinker-precursor-in-a-zero-gap-electrolyzer.pdf |
618400af81c4fc8962ecb040 | 10.26434/chemrxiv-2021-zz8q0 | Non-natural protein-protein communication mediated by a DNA-based, antibody-responsive device | We report here the rational design and optimization of an antibody responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the “translator,” that regulates the activity of a downstream target protein. As proof of principle, we demonstrate antibody-induced control of the proteins thrombin and Taq DNA polymerase. The resulting strategy is versatile and, in principle, can be easily adapted to control artificial protein-protein communication in artificial regulatory networks. | Simona Ranallo; Daniela Sorrentino; Elisabetta Delibato; Gianfranco Ercolani; Kevin W. Plaxco; Francesco Ricci | Biological and Medicinal Chemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618400af81c4fc8962ecb040/original/non-natural-protein-protein-communication-mediated-by-a-dna-based-antibody-responsive-device.pdf |
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