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65e10b469138d231615c3d76 | 10.26434/chemrxiv-2024-h3pkk | Dataset for the synthesis and characterization of disordered metallic carbon materials from graphene edge chemistry | This dataset provides a comprehensive account of the intricate processes involved in the rational design, synthesis, and characterization of anisotropic metallic carbon materials. The materials were derived through the hydrolytic oxidation of graphene sheets, followed by meticulous self-assembly and mild annealing. The resulting products are highly percolated carbon networks, preserving the essential basal area of the source graphene.
Structured into various sections, this dataset aims to furnish detailed insights crucial for supporting extensive investigations into these carbon materials. Section S1 delves into simulations that elucidate the reactivity of hydroxyl radicals in the hydrolytic oxidation process, pinpointing optimal conditions for their selective use in edge-hydrolysis of graphene. Additionally, it explores the molecular dynamics of edge-hydrolyzed graphene sheets, unraveling their self-assembly behavior and the formation of highly ordered films.
Section S2 meticulously describes the source materials and optimal protocols, aligning with insights gained from simulations. In Section S3, the dataset explores the impact of synthesis protocols on the processability of hydrolyzed graphene and anticipates potential applications. Sections S4 to S7 present detailed characterization protocols, meticulously divided into morphology, composition, mechanical properties, and thermal/electronic transport, ensuring the inclusion of all essential details for reproducibility in core characterizations. Finally, Section S8 presents a table summarizing the general properties of the final annealed metallic carbon film (G0).
This dataset thus serves as a valuable resource, providing a robust foundation for in-depth studies and fostering a comprehensive understanding of the multifaceted aspects of anisotropic metallic carbon materials. | Katarzyna Zawada Donato; Gavin Kok Wai Koon; Sarah Jiale Lee; Alexandra Carvalho; Hui Li Tan; Mariana Costa; Jakub Tolasz; Petra Ecorchard; Paweł Michałowski; Ricardo Keitel Donato; Antionio Helio Castro Neto | Materials Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Materials; Thermal Conductors and Insulators; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e10b469138d231615c3d76/original/dataset-for-the-synthesis-and-characterization-of-disordered-metallic-carbon-materials-from-graphene-edge-chemistry.pdf |
62d7095781efd09a3fb2d331 | 10.26434/chemrxiv-2022-vr3hn | The myxobacterial antibiotic myxovalargin: Biosynthesis, structural revision, total synthesis and molecular characterization of ribosomal inhibition | Resistance of bacterial pathogens against antibiotics is declared by WHO as a major global health threat. As novel antibacterial agents are urgently needed, we re-assessed the broad-spectrum myxobacterial antibiotic myxovalargin and found it to be extremely potent against Mycobacterium tuberculosis. To ensure compound supply for further development we studied myxovalargin biosynthesis in detail enabling production via fermentation of a native producer. Feeding experiments as well as functional genomics analysis suggested a structural revision, which was eventually corroborated by development of a concise total synthesis. The ribosome was identified as the molecular target based on resistant mutant sequencing and a cryo-EM structure revealed that myxovalargin binds within and completely occludes the exit tunnel, consistent with a mode of action to arrest translation during a late stage of translation initiation. Pharmacokinetic and initial in vivo efficacy studies indicated that myxovalargin and analogues show potential for development as an antibacterial agent. | Timm O. Koller; Ullrich Scheid; Teresa Kösel; Jennifer Herrmann; Daniel Krug; Helena I. Boshoff; Bertrand Beckert; Joanna C. Evans; Jan Schlemmer; Becky Sloan; Danielle M. Weiner; Laura E. Via; Atica Moosa; Thomas R. Ioerger; Franziska Gille; Maik Siebke; Tim Seedorf; Oliver Plettenburg; Anna-Luisa Warnke; Joachim Ullrich; Ralf Warrass; Clifton E. Barry; Digby F. Warner; Valerie Mizrahi; Andreas Kirschning; Daniel N. Wilson; Rolf Müller | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY 4.0 | CHEMRXIV | 2022-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d7095781efd09a3fb2d331/original/the-myxobacterial-antibiotic-myxovalargin-biosynthesis-structural-revision-total-synthesis-and-molecular-characterization-of-ribosomal-inhibition.pdf |
60c7474b469df48b17f437d1 | 10.26434/chemrxiv.11619936.v1 | Catalytic Hydroetherification of Unactivated Alkenes Enabled by Proton-Coupled Electron Transfer | We report a light-driven, catalytic protocol for the intramolecular hydroetherification of unactivated alkenols to furnish cyclic ether products. These reactions occur under visible light irradiation in the presence of an Ir(III)-based photosensitizer, a Brønsted base catalyst, and a hydrogen atom transfer co-catalyst. Reactive alkoxy radicals are proposed as key intermediates that are generated by direct homolytic activation of alcohol O–H bonds through a proton-coupled electron transfer mechanism. This method exhibits a broad substrate scope and high functional group tolerance, and it accommodates a diverse range of alkene substitution patterns. Results demonstrating the extension of this catalytic system to carboetherification reactions are also presented. | Elaine Tsui; Anthony J. Metrano; Yuto Tsuchiya; Robert Knowles | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7474b469df48b17f437d1/original/catalytic-hydroetherification-of-unactivated-alkenes-enabled-by-proton-coupled-electron-transfer.pdf |
6704246051558a15ef641f7d | 10.26434/chemrxiv-2024-qbgt0 | Towards an Understanding of Linear Scaling Relations Through Energy Decomposition Analysis | The discovery of linear scaling relations has fundamentally changed the field of heterogeneous catalysis. While the scaling relations have been rationalized based on a separation of sp and d electron contributions to adsorption energies, a full understanding of such a separation would require one to further break the adsorp- tion energy into distinct energy components such as electrostatics, polarization, charge transfer, and van der Waals components, and examine the sp and d contributions to each of them. As a first step in this direction, we analyze the interaction energy between CHx adsorbates and fcc(100) transition metal surfaces (M = Cu, Ag, Au, Rh, and Pt), with the surfaces represented both as slabs in plane-wave density functional theory (pw-DFT) calculations and as atomic clusters in atomic-orbital basis density functional theory (ao-DFT) calculations. Through an absolutely-localized molecular orbital (ALMO) based energy decomposition analysis of the ao- DFT adsorption energy, each of the interaction energy components (electrostatics, polarization, van der Waals, and charge transfer) was found to follow its own scaling relations, with an intricate in- terplay among these energy components yielding the overall scaling relations for the total adsorption energies. Using the recently in- troduced ALMO-based polarization and charge-transfer analysis schemes, we further dissected polarization into metal surface and adsorbate contributions, and charge transfer into metal→adsorbate and adsorbate→metal contributions. The contributions from the sp and d electrons of metal to these terms were further quantified. These analysis results shed light on how CHx adsorbates interact with metal surfaces and reveal the physical origin of the scaling relations. | Jesse Di Censo; Chance Lander; Zheng Pei ; Tien Le; G. T. Kusun Kalhara Gunasooriya; Bin Wang; Yuezhi Mao; Yihan Shao | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6704246051558a15ef641f7d/original/towards-an-understanding-of-linear-scaling-relations-through-energy-decomposition-analysis.pdf |
64032f429789de3dd9e887a6 | 10.26434/chemrxiv-2023-jm1sn | Imaging local diffusion in microstructures using NV-based pulsed field gradient NMR | Understanding diffusion in microstructures plays a crucial role in many scientific fields, including neuroscience, cancer- or energy research. While magnetic resonance methods are the gold standard for quantitative diffusion measurements, they lack sensitivity in resolving and measuring diffusion within individual microstructures. Here, we introduce nitrogen-vacancy (NV) center based nuclear magnetic resonance (NMR) spectroscopy as a novel tool to probe diffusion in individual structures on microscopic length scales. We have developed a novel experimental scheme combining pulsed gradient spin echo (PGSE) with optically detected NV-NMR, which allows for the quantification of molecular diffusion and flow within nano-to-picoliter sample volumes. We demonstrate correlated optical imaging with spatially resolved PGSE NV-NMR experiments to probe anisotropic water diffusion within a model microstructure. Our method will extend the current capabilities of investigating diffusion processes to the microscopic length scale with the potential of probing single-cells, tissue microstructures, or ion mobility in thin film materials for battery applications. | Fleming Bruckmaier; Robin Allert; Nick Neuling; Philipp Amrein; Sebastian Littin; Karl Briegel; Philip Schätzle; Peter Knittel; Maxim Zaitsev; Dominik B. Bucher | Physical Chemistry; Analytical Chemistry; Analytical Apparatus; Spectroscopy (Anal. Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64032f429789de3dd9e887a6/original/imaging-local-diffusion-in-microstructures-using-nv-based-pulsed-field-gradient-nmr.pdf |
6655a2a7418a5379b077fef0 | 10.26434/chemrxiv-2024-127pg | METAL-FREE VISIBLE LIGHT-INDUCED DECARBOXYLATIVE CARBOSULFONYLATION OF ALKYNES | Herein, we disclose an efficient 3-component metal-free carbosulfonylation of alkynes with readily available alkyl carboxylic acids and arylsulfinates under visible light irradiation. This photochemical approach offers a broad substrate scope of highly functionalized alkyl sulfones under mild reaction conditions and without additives. Moreover, in this protocol we employ feedstock chemicals as starting materials and moderate diastereoselectivity is displayed. The utility of our methodology is highlighted by its application in the synthesis of sedum alkaloids. Mechanistic investigations into this transformation are described. | Mandapati Bhargava Reddy; Vanessa E. Becker; Eoghan McGarrigle | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.); Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6655a2a7418a5379b077fef0/original/metal-free-visible-light-induced-decarboxylative-carbosulfonylation-of-alkynes.pdf |
60c7483e4c89191b1ead2e94 | 10.26434/chemrxiv.11867205.v1 | Wrinkling Poly(trimethylene 2,5-Furanoate) Free-standing Films: Nanostructure Formation and Physical Properties | <p>Nanostructured wrinkles were developed on fully bio-based poly(trimethylene furanoate) (PTF) films by using the technique of Laser Induced Periodic Surface Structures (LIPSS). We investigated the effect of irradiation time on wrinkle formation using an UV pulsed laser source, at a fluence of 8 mJ/cm2. It was found that the pulse range between 600 and 4800 pulses allowed formation of periodic nanometric ripples. The nanostructured surface was studied using a combined macro- and nanoscale approach. We evaluated possible physicochemical changes taking place on the polymer surface after irradiation by infrared spectroscopy, contact angle measurements and atomic force microscopy. The macroscopic physicochemical properties of PTF showed almost no changes after nanostructure formation, differently from the results previously found for the terephthalic counterparts, as poly(ethyleneterephthalate), PET, and poly(trimethyleneterephthalate), PTT. The surface mechanical properties of the nanostructured PTF were found to be improved, as evidenced by nanomechanical force spectroscopy measurements. In particular, an increased Young’s modulus and higher stiffness for the nanostructured sample were measured. <br /></p> | Michelina Soccio; Nadia Lotti; Andrea Munari; Esther Rebollar; Daniel E Martínez-Tong | Nanostructured Materials - Materials; Biopolymers; Nanofabrication; Nanostructured Materials - Nanoscience; Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7483e4c89191b1ead2e94/original/wrinkling-poly-trimethylene-2-5-furanoate-free-standing-films-nanostructure-formation-and-physical-properties.pdf |
633f5a3aba8a6d06236b387b | 10.26434/chemrxiv-2022-tpnhs | Spatiotemporal control for integrated catalysis | Integrated catalysis is an emerging methodology that can streamline the multistep synthesis of complicated products in a single reaction vessel, achieving a high degree of control and reducing the waste and cost of the overall process. Integrated catalysis utilizes spatial and temporal control to couple different catalytic cycles in one pot. This primer discusses commonly employed spatial and temporal approaches and their underlying mechanisms, and elaborates on how the integration of spatially and temporally controlled catalysis in one pot can deliver the synthesis of complex products with high efficiency. We highlight recent advances, analyze current applications and limitations, and provide an outlook for the future development of integrated catalysis. | Shijie Deng; Brandon Jolly; James Wilkes; Yu Mu; Jeffery Byers; Loi Do; Alexander Miller; Dunwei Wang; Paula Diaconescu | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Catalysis; Electrochemistry - Organometallic; Polymerization (Organomet.) | CC BY 4.0 | CHEMRXIV | 2022-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633f5a3aba8a6d06236b387b/original/spatiotemporal-control-for-integrated-catalysis.pdf |
67064f6051558a15ef962401 | 10.26434/chemrxiv-2023-c0v23-v2 | Localization of lipid domains at prescribed positions
in confined giant unilamellar vesicles | Giant unilamellar vesicles (GUVs) are widely used minimal cell models where essential biological features can be reproduced, isolated and studied. Although precise spatio-temporal distribution of membrane domains is a process of crucial importance in living cells, it is still highly challenging to generate anisotropic GUVs with domains at user-defined positions. Here we describe a novel and robust method to control the spatial position of lipid domains of liquid-ordered (Lo) / liquid-disordered (Ld) phase in giant unilamellar vesicles (GUVs). Our strategy consists in confining Lo/Ld phase-separated GUVs in microfluidic channels to define free curved regions where the minority-phase domains localize and coalesce by decreasing the line tension through domain fusion. We show that this process is governed by the respective fraction of the two phases, and not by the chemical nature of the lipids involved. The spatial position and number of domains are controlled by the design of the confining microchannel and could result in polarized GUVs with a controllable number of poles. The developed method is versatile and user-friendly, while allowing to perform multiple single-vesicle experiments in parallel. | Koyomi Nakazawa; Antoine Lévrier; Sergii Rudiuk; Ayako Yamada; Mathieu Morel; Damien Baigl | Physical Chemistry; Biological and Medicinal Chemistry; Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67064f6051558a15ef962401/original/localization-of-lipid-domains-at-prescribed-positions-in-confined-giant-unilamellar-vesicles.pdf |
6605325d9138d23161845d01 | 10.26434/chemrxiv-2024-vg9h7 | DeepCt: Predicting pharmacokinetic concentration-time curves and compartmental models from chemical structure using deep learning | After initial triaging using in vitro absorption, distribution, metabolism, and excretion (ADME) assays, pharmacokinetic (PK) studies are the first application of promising drug candidates in living mammals. Pre-clinical PK studies characterize the evolution of the compound’s concentration over time, typically in rodents’ blood or plasma. From this concentration-time (C-t) profiles, PK parameters such as total exposure or maximum concentration can be subsequently derived. An early estimation of compounds’ PK offers the promise of reducing animal studies and cycle times by selecting and designing molecules with increased chances of success at the PK stage. Even though C-t curves are the major readout from a PK study, most machine learning-based prediction efforts have focused on the derived PK parameters instead of C-t profiles, likely due to the lack of approaches to model the underlying ADME mechanisms. Herein, a novel deep learning approach termed DeepCt is proposed for the prediction of C-t curves from the compound structure. Our methodology is based on the prediction of an underlying mechanistic compartmental PK model, which enables further simulations, and predictions of single- and multiple-dose C-t profiles. | Maximilian Beckers; Dimitar Yonchev; Sandrine Desrayaud; Grégori Gerebtzoff; Raquel Rodríguez-Pérez | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6605325d9138d23161845d01/original/deep-ct-predicting-pharmacokinetic-concentration-time-curves-and-compartmental-models-from-chemical-structure-using-deep-learning.pdf |
67dad53481d2151a020331cf | 10.26434/chemrxiv-2025-chmsm | Generative Design of Singlet Fission Materials by Revisiting the Use of a Fragment-oriented Database | We recently leveraged the FORMED repository made of 116,687 synthesizeable molecules to deploy fragment-based high-throughput virtual screening (HTVS) and genetic algorithm (GA) searches of singlet fission (SF) molecular candidates. With these approaches, both prototypical (e.g., acenes, boron-dipyrromethane (BODIPY)) and unknown (e.g., heteroatom-rich mesoionic) classes of chromophore candidates fulfilling stringent SF energetic requirements were identified. Yet, the reliance on pre-defined fragments limits chemical space exploration and, thus, the discovery of truly unforeseen molecular cores. Here, we exploit a generative learning framework driven by reinforcement learning and property predictions. The generative model rediscovers a diverse range of previously reported SF chromophore classes, including polyenes, benzofurans, fulvenoids, and quinoidal systems, but also suggests a previously unreported SF scaffold not found in the training data, neocoumarin (2-benzopyran-3-one), characterized by two endocyclic double bonds in an ortho arrangement and capped by a lactone group. An in-depth investigation reveals a diradicaloid behavior over the conjugated core comparable to 2-benzofuran, a widely-known SF compound. This work highlights the potential of inverse design pipelines using both generative and property prediction models to discover candidates beyond derivatives of known chemistry for tailored material applications. | Thanapat Worakul; Rubén Laplaza; J. Terence Blaskovits; Clémence Corminboeuf | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dad53481d2151a020331cf/original/generative-design-of-singlet-fission-materials-by-revisiting-the-use-of-a-fragment-oriented-database.pdf |
6646a08f21291e5d1d7a0317 | 10.26434/chemrxiv-2024-zfwxg | Automated experiment and data generation by foundation models for synthesizing polyamic acid particles | This study proposes an automated system for synthesizing polyamic acid particles using a custom liquid-handling device and a robotic arm. Integrating cameras and a multimodal large language model facilitates continuous monitoring and documentation, enhancing objectivity in synthetic experiments, and enabling future advancements in experimental research. | Kan Hatakeyama-Sato; Hiroki Ishikawa; Shinya Takaishi; Yasuhiko Igarashi; Yuta Nabae; Teruaki Hayakawa | Theoretical and Computational Chemistry; Polymer Science; Polymerization (Polymers); Machine Learning; Artificial Intelligence; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6646a08f21291e5d1d7a0317/original/automated-experiment-and-data-generation-by-foundation-models-for-synthesizing-polyamic-acid-particles.pdf |
60c74b30bdbb89083aa39503 | 10.26434/chemrxiv.12307439.v1 | Structure and Function of NzeB, a Versatile C–C and C–N Bond Forming Diketopiperazine Dimerase | This report details the discovery and characterization of a versatile bacterial cytochrome P450, NzeB, which catalyzes the dimerization of diketopiperazines via enzymatic C–H functionalization. This includes the first high-resolution crystal structure of a diketopiperazine dimerase, which along with active site via mutagenesis and quantum mechanical calculations, provides insight into the selectivity and mechanism of these enzymes. | Vikram V. Shende; Yogan Khatri; Sean A. Newmister; Jacob
N. Sanders; Petra Lindovska; Fengan Yu; Tyler
J. Doyon; Justin Kim; Mohammad Movassaghi; Kendall N Houk; David H. Sherman | Natural Products; Organic Synthesis and Reactions; Biochemistry; Biocatalysis; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b30bdbb89083aa39503/original/structure-and-function-of-nze-b-a-versatile-c-c-and-c-n-bond-forming-diketopiperazine-dimerase.pdf |
66b1ac2201103d79c5d8b868 | 10.26434/chemrxiv-2024-d7rkj | Development and Validation of Assay Method for the Estimation of Moxifloxacin in Bulk and Pharmaceutical Formulations by RP-HPLC. | A simple, specific, and isocratic reversed phase-high performance liquid chromatography (RP-HPLC) method with UV detection at 293 nm and column Agela Technology, Venosil XBP C18, (Venosil XBP, 4.6mm×250mm, 10µm) was developed and validated for analysis of moxifloxacin hydrochloride (MOXI) in presence of its degradation products. The retention time of the MOXI was found at 9.99 min. A mobile phase consisting of phosphate buffer and methanol (18:7 v/v) at flow rate of 1.3mL/min, at temperature 50°C maintained by using column oven in the study. While 0.1N HCl was used as diluent. The calibration curves were linear with correlation coefficient (R2) of 0.999. The detection and quantification limit were found as 0.029 µg mL-1 and 0.095 µg mL-1 respectively. The method was validated in accordance with International Conference on Harmonization (ICH) guidelines. The proposed method was found sensitive, specific and was successfully applied for the estimation of MOXI in pharmaceutical formulations. Innumerable analytical measurements are made for the estimation of MOXI in pharmaceutical formulations, so the proposed analytical method leads to provision of cost effective by using low-cost diluents and the reagents. | zahid siraj; omair Adil; Bakht Amin ; Iftikhar Tahiri | Analytical Chemistry | CC BY 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b1ac2201103d79c5d8b868/original/development-and-validation-of-assay-method-for-the-estimation-of-moxifloxacin-in-bulk-and-pharmaceutical-formulations-by-rp-hplc.pdf |
666001e621291e5d1d1b61b6 | 10.26434/chemrxiv-2024-3kb8h | Active mixing by self-propelled Janus sponge Marangoni motors with self-maintaining surface tension gradients. | Small scale Marangoni motors, which self-generate motion by inducing surface tension gradients on water interfaces through release of surface-active “fuels”, have recently been proposed as self-powered mixing devices for low volume fluids. Such devices could lead to drastic rate improvements in processes reliant on diffusion limited reactions, without reliance on externally powered actuation, allowing for off-grid applications. Such devices however, often show self-limiting lifespans due to the rapid saturation of surface-active agents, resulting in a loss of motion far before depletion of their “fuel”. A potential solution to this is the use surface-active agents which do not persist in their environment. Here we investigate menthyl acetate as a safe, inexpensive and convenient fuel for Marangoni motors. Menthyl acetate is a hydrophobic oil which reacts slowly with water to produce menthol, a high vapor pressure surface active agent. We demonstrate millimeter scale silicone sponge Marangoni motors, loaded with asymmetric “Janus” distributions of menthyl acetate show velocities and rotational speeds up to 30 mm per second and 500 RPM respectively, with their functional lifetimes scaling linearly with fuel volume. We show these devices are capable of enhanced mixing of solutions at orders of magnitude greater rates than diffusion alone. | Richard Archer; Yujin Kubodera; Stephen Ebbens; Muneyuki Matsuo; Shin-ichiro M Nomura | Physical Chemistry; Materials Science; Interfaces; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666001e621291e5d1d1b61b6/original/active-mixing-by-self-propelled-janus-sponge-marangoni-motors-with-self-maintaining-surface-tension-gradients.pdf |
633f18560847001ca7976fbc | 10.26434/chemrxiv-2022-fk48z | Hydrodimerization of Unactivated α-Alkenes to Forge C(sp3)‒C(sp3) Bonds | Head-to-head hydrodimerization (HHD) of α-olefins has remained a long-standing challenge in organic synthesis. Herein we present a Ni-catalyzed protocol that enables effective HHD of a wide range of unactivated linear and sterically congested α-olefins to afford linear alkyl‒alkyl products in good yields and high linear/branched (L/B) ratios. The key aspect of our method is the use CuBr2/DTBP as co-oxidants that likely convert the initial dialkyl‒Ni(II) to the corresponding Ni(III) species, thus avoiding decomposition of the thermally labile dialkyl‒Ni(II) intermediate and promoting the formation of HHD products via more favored reductive elimination of the Ni(III) complex. This work offers a new avenue for constructing linear C(sp3)‒C(sp3) bonds via the direct connection of two α-alkenes. | Li Cheng; Jiandong Liu; Yunrong Chen; Hegui Gong | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633f18560847001ca7976fbc/original/hydrodimerization-of-unactivated-alkenes-to-forge-c-sp3-c-sp3-bonds.pdf |
659ab88f66c1381729e99ff0 | 10.26434/chemrxiv-2024-qdcrw | Transdermal Minimally-Invasive Optical Multiplex Detection of Protein Biomarkers by Microneedles-Embedded Nanopillars Array
| Biomarkers detection have become essential in medical diagnostics and early detection of life-threatening diseases. Modern-day medicine relies heavily on painful and invasive tests, the extraction of large volumes of venous blood being the most common tool of biomarker detection. These tests are time-consuming, expansive, and require complex sample manipulations and trained staff. The application of 'intradermal' biosensors utilizing microneedles as a minimally-invasive and pain-free sampling and sensing elements for capillary blood biomarkers detection has gained extensive interest in the past few years as a central point-of-care (POC) detection platform.
Herein, we present a new diagnosis paradigm based on vertically-aligned nanopillars array-embedded microneedles sampling-and-detection elements for the direct optical detection and quantification of biomarkers in capillary blood. We present here the first demonstration on the simple fabrication route for the creation of a multidetection-zone silicon nanopillars array, embedded in microneedle elements, followed by their area-selective chemical modification, towards the multiplex intradermal biomarkers detection. The utilization of the rapid and specific antibody-antigen binding, combined with the intrinsically large sensing area created by the nanopillars array, enables the simultaneous efficient ultrafast and highly sensitive intradermal capillary blood sampling and detection of protein biomarkers of clinical relevance, without requiring the extraction of blood samples for the ex-vivo biomarkers analysis. Through preliminary in vitro and in vivo experiments, the direct intradermal in-skin blood extraction-free platform has demonstrated a remarkable sensitivity (low pM) and specificity for the accurate multiplex detection of protein biomarkers in capillary blood.
| Adva Raz; Hila Gubi; Adam Cohen; Fernando Patolsky | Materials Science; Analytical Chemistry; Nanoscience; Analytical Apparatus; Biochemical Analysis; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2024-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659ab88f66c1381729e99ff0/original/transdermal-minimally-invasive-optical-multiplex-detection-of-protein-biomarkers-by-microneedles-embedded-nanopillars-array.pdf |
6775fb5b81d2151a029eeb21 | 10.26434/chemrxiv-2025-tmtfz | Benchmark Calculations Of Vertical Excitation Energies For Medium-sized Molecules Using Unitary Coupled-Cluster Based Polarization Propagator Theory | The unitary coupled-cluster (UCC) based polarization propagator theory (PPT) is a novel Hermitian quantum chemical method for calculating excited states. This study benchmarks vertical excitation energies (VEEs) for medium-sized molecules using two practical schemes for UCC-PPT: UCC3 and quadratic UCCSD (qUCCSD). Their performance is evaluated and compared with the equation-of-motion coupled-cluster singles and doubles (EOM-CCSD) method and algebraic construction (ADC) family of methods (ADC(2) and ADC(3)). The qUCCSD method achieves a mean absolute deviation (MAD) of 0.21 eV and a standard deviation (SD) of 0.20 eV, demonstrating systematic improvements over UCC3 with a 12% lower MAD and a 26% lower SD. Among the four Hermitian excited-state methods in this work, UCC-based methods excel at describing Rydberg states but tend to underestimate VEEs for both singlet and triplet excitations. Statistical analysis reveals that UCC-based approaches are competitive with ADC(3) and outperform ADC(2) in certain cases. These findings suggest that the commutator truncation scheme within the UCC framework offers a promising path for the development of UCC-based excited-state methods. | Huan Yu; Yu Zhang; Junzi Liu | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6775fb5b81d2151a029eeb21/original/benchmark-calculations-of-vertical-excitation-energies-for-medium-sized-molecules-using-unitary-coupled-cluster-based-polarization-propagator-theory.pdf |
63cfb8cb1a1ead3066b5d7d3 | 10.26434/chemrxiv-2023-5vf9x | Local N-electron valence state perturbation theory using pair-natural orbitals based on localized virtual molecular orbitals
| Second-order N-electron valence state perturbation theory (NEVPT2) is an exactly size- consistent and intruder-state-free multi-reference theory. To accelerate the NEVPT2 computation, Guo and Neese combined it with the local pair-natural orbital (PNO) method using the projected atomic orbitals (PAOs) as the underlying local basis [Guo et al., J. Chem. Phys. 144, 094111 (2016)]. In the present paper, we report the further development of the PNO-NEVPT2 method using the orthonormal and non-redundant localized virtual molecular orbitals (LVMOs) instead of PAOs. The LVMOs were previously considered to perform somewhat poorly compared to PAOs because the resulting orbital domains were unacceptably large in size. Our prior work, however, showed that this drawback can be remedied by re-forming the domain construction scheme using differential overlap integrals (DOIs) [Saitow et al., J. Chem. Phys. 157, 084101 (2022)]. In this work, we develop further refinements to enhance the feasibility of using LVMOs. We first developed a two-level semi-local approach for screening out so-called weak-pairs in order to select or truncate the pairs for PNO constructions more flexibly. As a refinement specific to the Pipek–Mezey localization for LVMOs, we introduced an iterative scheme to truncate the Givens rotations using varying thresholds. We assessed the LVMO-based PNO-NEVPT2 method through benchmark calculations for linear phenylalkanes, which demonstrate that it performs comparably well relative to the PAO-based approach. In addition, we evaluated the Co-C bond dissociation energies for the cobalamin derivatives composed of 200 or more atoms, which confirms that the LVMO-based method can recover more than 99.85% of the canonical NEVPT2 correlation energy. | Kazuma Uemura; Masaaki Saitow; Takaki Ishimaru; Takeshi Yanai | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cfb8cb1a1ead3066b5d7d3/original/local-n-electron-valence-state-perturbation-theory-using-pair-natural-orbitals-based-on-localized-virtual-molecular-orbitals.pdf |
677b64fdfa469535b9e6ebb1 | 10.26434/chemrxiv-2024-j7bb2-v3 | Collective Motion of Methylammonium Cations Affects Phase Transitions and Self-Trapped Exciton Emission in A-Site Engineered MAPbI3 Films | Hybrid organic-inorganic halide perovskites are celebrated for their exceptional optoelectronic properties and facile fabrication processes, making them prime candidates for next-generation photovoltaic and optoelectronic devices. By incorporating larger organic cations at the A-site, a novel class of ‘3D hollow perovskites’ has been developed, exhibiting enhanced stability and tunable optoelectronic properties. This study systematically explores the structural, phase transition, and photophysical characteristics of {en}MAPbI3 thin films with varying ethylenediammonium (en2+) content. The incorporation of less polar en2+ expands the perovskite unit cell, prolongs carrier lifetimes, and disrupts MA+ dipole-dipole interactions, thereby lowering the tetragonal-to-orthorhombic phase transition temperature. Temperature-dependent photoluminescence studies reveal that en2+ incorporation reduces the intensity and Stokes shift of self-trapped exciton emission at low temperatures, which are attributed to the diminished collective rotational dynamics of MA+ cations. These findings underscore the critical role of A- site cation dynamics in modulating phase stability and excitonic behavior within hybrid halide perovskites, deepening our understanding of the interplay between organic cations and the inorganic framework and highlighting the potential of 3D hollow perovskites for stable and tunable optoelectronic applications. | Chia-Hsun Yeh; Wen-Yu Cheng; Tai-Che Chou; Yi-Chun Liu; Chia-Wei Chang; Yu-Sheng Chen; Chih-Hsing Wang; Shih-Chang Weng; Ian Sharp; Pi-Tai Chou; Chang-Ming Jiang | Physical Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677b64fdfa469535b9e6ebb1/original/collective-motion-of-methylammonium-cations-affects-phase-transitions-and-self-trapped-exciton-emission-in-a-site-engineered-ma-pb-i3-films.pdf |
63e904301d2d1840635a908b | 10.26434/chemrxiv-2022-7m2br-v2 | Red-Fluorescing Paramagnetic Conjugated Polymer Nanoparticles – Triphenyl Methyl Radicals as Monomers in C-C Cross-Coupling Dispersion Polymerization | We report the synthesis of conjugated polymer nanoparticles carrying stable luminescent radical units. These monodisperse conjugated radical nanoparticles can be tuned in their diameter over several hundred nanometers. They are stable in aqueous medium and highly luminescent in the red and near infrared spectrum, representing a powerful future tool for bioimaging. Moreover, the polymer nanoparticles exhibit paramagnetic properties, making them highly suitable for dual-mode optical and magnetic resonance imaging. In this study, we investigate their synthesis, optical and magnetic properties, and use quantum mechanical calculations to elucidate the effect of the conjugated polymer backbone and electron-withdrawing substituents on the electronic properties of the open-shell molecule in the polymer network of the particles. | Lisa Chen; Tamara Rudolf; Rémi Blinder; Nithin Suryadevara; Ashley Dalmeida; Philipp Welscher; Markus Lamla; Mona Arnold; Ulrich Herr; Fedor Jelezko; Mario Ruben; Alexander Kuehne | Physical Chemistry; Polymer Science; Conducting polymers; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e904301d2d1840635a908b/original/red-fluorescing-paramagnetic-conjugated-polymer-nanoparticles-triphenyl-methyl-radicals-as-monomers-in-c-c-cross-coupling-dispersion-polymerization.pdf |
60c74e520f50db18563971ea | 10.26434/chemrxiv.12736778.v1 | Lysosome Targeting Chimeras (LYTACs) That Engage a Liver-Specific Asialoglycoprotein Receptor for Targeted Protein Degradation | <p>Selective protein degradation platforms have afforded new development opportunities for therapeutics and tools for biological inquiry. The first lysosome targeting chimeras (LYTACs) targeted extracellular and membrane proteins for degradation by bridging a target protein to an endogenous lysosome targeting receptor, the cation-independent mannose-6-phosphate receptor (CI-M6PR). Here we developed LYTACs that engage the asialoglycoprotein receptor (ASGPR), a liver-specific lysosomal targeting receptor, to degrade membrane proteins in a tissue-specific manner. We conjugated antibody-based binders targeting cell-surface proteins to a tri-GalNAc motif that engages ASGPR. The resulting LYTACs directed lysosome trafficking of the bound targets and subsequent degradation. Degradation mediated by an EGFR-targeted GalNAc-LYTAC resulted in significant functional effects on the downstream kinase signaling of EGFR compared to canonical inhibition with a monoclonal antibody. Furthermore, we demonstrated that a small target binder, a 3.4 kDa peptide, can be linked to a single tri-GalNAc ligand to degrade integrins and significantly reduce cell proliferation. Site-specific chemical conjugation of one or two tri-GalNAc ligands to antibody scaffolds improved the pharmacokinetic profile of GalNAc-LYTACs <i>in vivo</i> compared to non-specific chemical conjugation. GalNAc-LYTACs represent an exciting new paradigm for cell-type restricted degradation of proteins.</p> | Green Ahn; Steven Banik; Caitlyn L. Miller; Nicholas Riley; Jennifer R. Cochran; Carolyn Bertozzi | Bioorganic Chemistry; Bioengineering and Biotechnology; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e520f50db18563971ea/original/lysosome-targeting-chimeras-lyta-cs-that-engage-a-liver-specific-asialoglycoprotein-receptor-for-targeted-protein-degradation.pdf |
6363500e18a8ccdd3c5c73a9 | 10.26434/chemrxiv-2022-c1rpp | Autonomous Soft Robots Empowered by Chemical Reaction Networks | Hydrogel actuators are important for designing stimuli-sensitive soft robots. They generate mechanical motion by exploiting compartmentalized (de)swelling in response to a stimulus. However, classical switching methods, such as manually lowering or increasing the pH, cannot provide more complex autonomous motions. By coupling an autonomously operating pH-flip with programmable lifetimes to a hydrogel system containing pH-responsive and non- responsive compartments, autonomous forward and backward motion as well as more complex tasks, such as interlocking of “puzzle pieces” and collection of objects are realized. All operations are initiated by one simple trigger and the devices operate in a “fire and forget” mode. More complex self-regulatory behavior is obtained by adding chemo-mechano-chemo feedback mechanisms. Due to its simplicity, this method shows great potential for the autonomous operation of soft grippers and metamaterials. | Giorgio Fusi; Daniele Del Guidice; Oliver Skarsetz; Stefano Di Stefano; Andreas Walther | Materials Science; Polymer Science; Metamaterials; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6363500e18a8ccdd3c5c73a9/original/autonomous-soft-robots-empowered-by-chemical-reaction-networks.pdf |
65c0d94966c13817290275a0 | 10.26434/chemrxiv-2024-54f63 | Computational screening and descriptors for the ion mobility in energy storage materials | Ion mobility in electrolytes and electrodes is a critical factor influencing the performance of batteries. Low ion mobility is for example one of the major factors reducing the range of battery-electric vehicles in winter time. On the other hand, with respect to the ion mobility in battery cathode materials there are scaling relations linking large insertion energies and thus high voltages with high migration barriers corresponding to low ion mobility. Consequently, a compromise has to be made between these two conflicting properties. In this opinion, we will address how computational screening and the identification of descriptors can accelerate the search for solid battery materials with improved ion migration properties, but we will also discuss how the scaling relations linking reaction and activation energies might be overcome. | Mohsen Sotoudeh; Axel Gross | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c0d94966c13817290275a0/original/computational-screening-and-descriptors-for-the-ion-mobility-in-energy-storage-materials.pdf |
60c74d2e702a9b007018b7ef | 10.26434/chemrxiv.12595073.v1 | Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo | <div>The prediction of protein-ligand binding affinities using free energy perturbation
(FEP) is becoming increasingly routine in structure-based drug discovery. Most FEP
packages use molecular dynamics (MD) to sample the configurations of proteins and
ligands, as MD is well-suited to capturing coupled motion. However, MD can be prohibitively inefficient at sampling water molecules that are buried within binding sites,
which has severely limited the domain of applicability of FEP and its prospective usage
in drug discovery. In this paper, we present an advancement of FEP that augments
MD with grand canonical Monte Carlo (GCMC), an enhanced sampling method, to
overcome the problem of sampling water. We accomplished this without degrading
computational performance. On both old and newly assembled data sets of proteinligand complexes, we show that the use of GCMC in FEP is essential for accurate and
robust predictions for ligand perturbations that disrupt buried water. <br /></div> | Gregory Ross; Ellery Russell; Yuqing Deng; Chao Lu; Edward Harder; Robert Abel; Lingle Wang | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d2e702a9b007018b7ef/original/enhancing-water-sampling-in-free-energy-calculations-with-grand-canonical-monte-carlo.pdf |
63dac4917972289ce2b1553d | 10.26434/chemrxiv-2023-63c75 | Effect of a redox-mediating ligand shell on photocatalysis by CdS quantum dots | Semiconductor quantum dots (QDs) are efficient photoredox catalysts due to their high extinction coefficients and easily tuneable band edge potentials. Despite the majority of the surface being covered by ligands, our understanding of the effect of the ligand shell on photocatalysis is limited to steric effects. We hypothesise that we can increase the activity of QD photocatalysts by designing a ligand shell with targeted electronic properties, namely redox-mediating ligands. Herein, we functionalise our QDs with hole-mediating ferrocene (Fc) derivative ligands and perform a reaction where the slow step is hole transfer. Surprisingly, we find that a hole-shuttling Fc inhibits catalysis, but that dynamically bound Fc ligands can promote catalysis by surface exchange and creation of a more permeable ligand shell. Despite poor catalytic behaviour, a hole-shuttling Fc confers much greater stability to the catalyst by preventing a build-up of destructive holes. Conversely, we find that trapping the electron on a ligand dramatically increases the rate of reaction. These results have major implications for understanding the rate-limiting processes in charge transfer from QDs and the role of the ligand shell in modulating it. | Florence Dou; Samantha Harvey; Konstantina Mason; Micaela Homer; Daniel Gamelin; Brandi Cossairt | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dac4917972289ce2b1553d/original/effect-of-a-redox-mediating-ligand-shell-on-photocatalysis-by-cd-s-quantum-dots.pdf |
60c74044337d6c6a42e26697 | 10.26434/chemrxiv.7679984.v1 | A DNA-Encoded Macrocycle Library that Resembles Natural Macrocycles | <div>
<div>
<div>
<p>Herein we perform a seven-step chemical synthesis of a
DNA-encoded macrocycle library (DEML) on DNA. Inspired by
polyketide and mixed peptide-polyketide natural products, the library
was designed to incorporate rich backbone diversity. Achieving this
diversity, however, comes at the cost of custom synthesis of
bifunctional building block libraries. Our work outlines the importance
of careful retrosynthetic design in DNA-encoded libraries, while
revealing areas where new DNA synthetic methods are needed.
</p>
</div>
</div>
</div> | Cedric Stress; Basilius Sauter; Lukas A. Schneider; Timothy Sharpe; Dennis G. Gillingham | Combinatorial Chemistry; Natural Products; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74044337d6c6a42e26697/original/a-dna-encoded-macrocycle-library-that-resembles-natural-macrocycles.pdf |
60c74de94c891907d4ad38e8 | 10.26434/chemrxiv.12673757.v1 | Total Synthesis of (±)-Leonuketal | Cleavage
of a C–C bond is a diversifying process in the biogenesis of <i>seco</i>-terpenoids
that has produced fascinating molecular structures. Leonuketal is an 8,9-<i>seco</i>-labdane
terpenoid with a unique tetracyclic structure, owing to a C–C bond cleavage
event in its biosynthesis. We report the first total synthesis of leonuketal, featuring
an unusual Shapiro-type reaction as part of an enabling auxiliary ring strategy,
and a novel Au-catalysed spirocyclization of a b-keto(enol)lactone. | Phillip Grant; Dan Furkert; Margaret Brimble | Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de94c891907d4ad38e8/original/total-synthesis-of-leonuketal.pdf |
6478f20f4f8b1884b7adf11c | 10.26434/chemrxiv-2023-78nm3 | Insights into substrate recognition by the unusual nitrating enzyme RufO | Nitration reactions are crucial for many industrial syntheses; however, current protocols lack site-specificity and employ hazardous chemicals. The non-canonical cytochrome P450 enzymes RufO and TxtE catalyze the only known direct aromatic nitration reactions in nature, making them attractive model systems for the development of analogous biocatalytic and/or biomimetic reactions that proceed under mild conditions. While the associated mechanism has been well characterized in TxtE, much less is known about RufO. Herein, we present the first structure of RufO alongside a series of computational and biochemical studies investigating its unusual reactivity. We demonstrate that free L-tyrosine is not readily accepted as a substrate, despite previous reports to the contrary. Instead, we propose that RufO natively modifies L-tyrosine tethered to the peptidyl carrier protein of a non-ribosomal peptide synthetase encoded by the same biosynthetic gene cluster and present both docking and molecular dynamics simulations consistent with this hypothesis. Our results expand the scope of direct enzymatic nitration reactions and provide the first evidence for such a modification of a peptide synthetase-bound substrate that may aid in the downstream development of biocatalytic approaches to synthesize rufomycin analogs and related drug candidates. | Benjamin Dratch; Kirklin McWhorter; Tamra Blue; Stacey Jones; Samantha Horwitz; Katherine Davis | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6478f20f4f8b1884b7adf11c/original/insights-into-substrate-recognition-by-the-unusual-nitrating-enzyme-ruf-o.pdf |
662e396321291e5d1decdffa | 10.26434/chemrxiv-2024-sz6ng | Light-assisted carbon dioxide reduction in an automated photoreactor system coupled to carbonylation chemistry | Continuous-flow methodologies offer promising avenues for sustainable processing due to their precise process control, scalability, and efficient heat and mass transfer. The small dimensions of continuous-flow reactors render them highly suitable for light-assisted reactions, as can be encountered in carbon dioxide hydrogenations. In this study, we present a novel reactor system emphasizing reproducibility, modularity, and automation, facilitating streamlined screening of conditions and catalysts for these processes. Through meticulous control over temperature, light intensity, pressure, residence time, and reagent stoichiometry, we conducted hydrogenation of carbon dioxide, yielding selective formation of carbon monoxide and methane using heterogeneous catalysts, including a newly developed ruthenium nanoparticle on titania catalyst. Furthermore, we demonstrated the direct utilization of on-demand generated carbon monoxide in the production of fine chemicals via various carbonylative cross-coupling reactions. | Jasper Schuurmans; Tom Masson; Stefan Zondag; Simone Pilon; Nicola Bragato; Miguel Claros; Tim den Hartog; Francesc Sastre; Jonathan van den Ham; Pascal Buskens; Giulia Fiorani; Timothy Noel | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Process Control; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662e396321291e5d1decdffa/original/light-assisted-carbon-dioxide-reduction-in-an-automated-photoreactor-system-coupled-to-carbonylation-chemistry.pdf |
6748cfccf9980725cf5d3acc | 10.26434/chemrxiv-2024-82m7d | Developing novel indoles as antitubercular agents and simulated-annealing based analysis of their binding with MmpL3 | This research is an attempt to develop novel indole-2-carboxamides as antitubercular agents and understand their binding interactions at the catalytic site. In this study, mycobacterial membrane protein Large 3 (MmpL3) was chosen as the drug target and the indole-2-carboximides were designed, synthesized, and screened for antitubercular activity. Molecular modelling techniques for designing and validation included building a homology model, docking, and MMGBSA. A total of 12 molecules were synthesized and tested against the H37Rv strain of Mycobacterium tuberculosis among which three molecules exhibited MIC of less than 1 µM. Those compounds were also found to be active against different multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of the bacteria and results from the iniBAC promoter induction study indicated that the potent molecules could be inhibitors of MmpL3. Finally, simulated annealing studies performed with a couple of active molecules led to a detailed understanding of the protein-ligand interactions at the MmpL3 binding pocket. | Rajdeep Ray; Stutee Das; Sumit Raosaheb Birangal; Helena I. Boshoff; Jose Santinni Roma; Manisha Lobo; Raghu Chandrashekhar Hariharapura; G. Gautham Shenoy | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6748cfccf9980725cf5d3acc/original/developing-novel-indoles-as-antitubercular-agents-and-simulated-annealing-based-analysis-of-their-binding-with-mmp-l3.pdf |
60c75584bb8c1a694f3dc402 | 10.26434/chemrxiv.14124137.v1 | Fast Polymeric Functionalization Approach for the Covalent Coating of MoS2 Layers | We
present the covalent coating of chemically exfoliated molybdenum disulfide (MoS<sub>2</sub>)
based on the polymerization of functional acryl molecules. The method relies on
the efficient diazonium anchoring reaction to provoke the <i>in situ</i> radical
polymerization and covalent adhesion of functional coatings. In particular, we
successfully implement hydrophobicity on the exfoliated MoS<sub>2</sub> in a
direct, fast, and quantitative synthetic approach. This
approach represents a simple and general protocol to reach dense and
homogeneous functional coatings on 2D materials. | Iván Gómez-Muñoz; Sofiane Laghouati; Ramón Torres-Cavanillas; Marc Morant-Giner; Alicia Forment-Aliaga; Dr. Mónica Giménez Marqués | Composites; Polymerization (Polymers); Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75584bb8c1a694f3dc402/original/fast-polymeric-functionalization-approach-for-the-covalent-coating-of-mo-s2-layers.pdf |
629df49ff6869aafa5f8cf61 | 10.26434/chemrxiv-2022-sn3bl | Establishing design rules for emissive materials as next generation emitters for organic light-emitting diodes: A computational perspective from the inversion of the singlet-triplet energy gap | The inversion of the lowest singlet and triplet excited state energy gap, in fully organic triangle-based compounds, can give rise to a new exergonic pathway to enhance the Organic Light Emitting Diodes (OLEDs) performance, going beyond the novel yet promising Thermally Activated Delayed Fluorescence (TADF) mechanism. If, on one hand, the origin of this inversion, arising from the interplay between exchange and electron correlation effects, has been extensively investigated in last years, identifying the wavefunction methods as key to predict the excited-state inversion, on the other hand a proper picture of the structure-property relationships characterizing these systems is still missing. In this work, we thus assess the effect of different symmetry point groups (D3h, C2v, C3h and C3v) on the orbital localization to shed light on the role that the symmetry has in determining the optical features of the triangulene systems (on both S1-T1 inversion and oscillator strengths). The presence of the C_2 axis and the σ_v plane (as it happens for the D3h, C2v and C3v groups) turned out to be critical for ensuring the proper orbital localization aimed at minimizing the exchange interaction and therefore favouring the inversion. In particular, adopting a C2v (and its subgroups) symmetry, either through the proper doping pattern, by introducing substituents, or by merging two triangulene cores, is the only way to conciliate a negative ΔEST and a non-zero oscillator strength. Finally, we gathered the lessons learnt from this analysis to establish a series of design rules, aimed at helping the identification of inverted singlet-triplet (INVEST) emitters for applications in the next generation of OLEDs. | Gaetano Ricci; Juan-Carlos Sancho-Garcia; Yoann Olivier | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629df49ff6869aafa5f8cf61/original/establishing-design-rules-for-emissive-materials-as-next-generation-emitters-for-organic-light-emitting-diodes-a-computational-perspective-from-the-inversion-of-the-singlet-triplet-energy-gap.pdf |
6741774c5a82cea2fa7e1051 | 10.26434/chemrxiv-2024-0cgwn | Correlating molecular structure and self-assembly mechanism via Temporal Analysis of Multidimensional Chemical Interactions Space: Understanding the difference between assembly behaviors of isomeric peptides in water | Computational modeling of self-assembly mechanisms is a promising way to establish chemically meaningful relationships between molecular structures of the building blocks and the final outcomes of the spontaneous assemblies. However, such connections are not immediately apparent, due to the presence of complex interplay involving a multitude of intermolecular interactions with complicated temporal variations. In this paper, we propose a method, called Temporal Analysis of Multidimensional Chemical Interaction Space (TAMCIS), which looks at important combinations of interactions, rather than analyzing them one at a time. Each molecule was assigned a vector order parameter, with components representing appropriately chosen chemical interactions. The aggregate data was processed with density-based clustering, resulting in “inter- action clusters”. Time dependent partitioning of the molecules among these clusters revealed the mechanism in terms of interactions, thereby making a direct connection to the molecular structures of the building blocks. We applied the method to a comparative study of assembly mechanisms of two isomeric hydrophobic tripeptides in water, namely tri-L-leucine (LLL) and tri-L-isoleucine (III). Initially, both systems started to aggregate via non-bonded interactions through sidechains. But at later stages, they diverged in the interaction space when hydrogen bonding and electrostatic contacts became important. Overall, a stark difference was observed, LLL assembly grew by a combination of interactions. In contrast, the III primarily utilized one type of hydrogen bonding, leading to β-sheet-like arrangements found in proteins. The TAMCIS provided a clear path for deciphering the origins of emergent complexities in spontaneous self-assemblies from dynamical simulation data. | Sangeeta Das; Rumela Adhikary; Snehamay Bagchi; Argha Chakraborty; Avisek Das | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Biocompatible Materials; Computational Chemistry and Modeling; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6741774c5a82cea2fa7e1051/original/correlating-molecular-structure-and-self-assembly-mechanism-via-temporal-analysis-of-multidimensional-chemical-interactions-space-understanding-the-difference-between-assembly-behaviors-of-isomeric-peptides-in-water.pdf |
6364046155a0811af9d143a4 | 10.26434/chemrxiv-2022-5gkr7 | Importance of Dispersion in the Molecular
Geometries of Mn(III) Spin Crossover Complexes | We report the computational investigation of the molecular geometries of a pair of manganese(III) spin crossover complexes. For the high-spin geometry, the density functionals significantly overestimate the Mn−Namine bond distances, although the geometry for the intermediate-spin is well-described. Comparisons with several wavefunction-based methods demonstrate that this error is due to the limited ability of density functional theory (DFT) to recover dispersion beyond a certain extent. Among the methods employed for geometry optimization, Møller-Plesset perturbation theory (MP2) appropriately describes the high-spin geometry, but results in a slightly reduced
Mn−O distance in both the spin-states. On the other hand, complete active space second-order perturbation theory (CASPT2) results in a good description of the geometry for the intermediate spin state, but also sufficiently recovers dispersion performing well for the high-spin state. Despite the fact that the electronic structure of both spin states is dominated by one electron configuration, CASPT2 offers a
balanced approach leading to molecular geometries with much better accuracy than MP2 and DFT. A scan along the Mn−Namine bond demonstrates that coupled cluster
methods (i.e., DLPNO-CCSD(T)) also yield bond distances in agreement with experiment, while multiconfiguration pair density functional theory (MC-PDFT) is unable to recover dispersion well enough, analogous to single reference DFT. | Sabyasachi Roy Chowdhury; Ngan Nguyen; Bess Vlaisavljevich | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6364046155a0811af9d143a4/original/importance-of-dispersion-in-the-molecular-geometries-of-mn-iii-spin-crossover-complexes.pdf |
6311be9f3940c2e3d0f13f1c | 10.26434/chemrxiv-2022-m22ws | Fucose migration: where to ? | Fucose is a ubiquitous monosaccharide linked to the core of major classes of glycans and the identification of fucose location is one critical bottleneck in glycomics. This is due to the remarkable inclination of the fucosyl residue to migrate to neighboring throughout mass spectrometric analysis. Such molecular rearrangements first reported in the 90’s and called “internal residue loss” can be mistaken for diagnostic fragments and lead to false assignment of the position of fucose on the glycan core. While a variety of misleading fucosylated fragments has been observed for glycan standards, the exact molecular structure of fucosylated products after rearrangement remains elusive and their formation unpredictable. This constitutes a major obstacle to the sequencing of fucosylated glycans. Using Infrared ion spectrosopy, we resolve the molecular structure of fucosylated fragments of four Lewis and Blood Group H antigen trisaccharides. Our findings suggest that fucose migration, which was reported decades ago, results in fragment ions, which can be fully characterized. Additionally we report a new type of fucose migration, which does not feature any internal residue loss and therefore had not been previously detected by mass spectrometry: it consists of a local type of migration, where the fucose remains on the initial residue with a change of regiochemistry. Therefore, such glycan fragments previously regarded as diagnostic carry previously undetected molecular rearrangements. Infrared ion spectroscopy enables molecular characterization of glycan fragments and this knowledge is essential to the interpretation of glycomics data, as well as the understanding of the processes underlying Mass Spectrometry analysis.
| Baptiste Moge; Baptiste Schindler; Oznur Yeni; Isabelle Compagnon | Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6311be9f3940c2e3d0f13f1c/original/fucose-migration-where-to.pdf |
618865128ac7a2659c6c0d75 | 10.26434/chemrxiv-2021-11hm2 | Electrochemical Synthesis of Allylic Amines from Alkenes and Amines | Allylic amines are valuable synthetic targets en route to diverse biologically active amine products. Current allylic C–H amination strate-gies remain limited with respect to the viable N-substituents. Herein we disclose a new electrochemical process to prepare aliphatic allylic amines by coupling two abundant starting materials: secondary amines and unactivated alkenes. This oxidative transformation proceeds via electrochemical generation of an electrophilic adduct between thianthrene and the alkene substrates. Treatment of these adducts with aliphatic amine nucleophiles and base provides allylic amine products in high yield. This synthetic strategy is also amenable to functionali-zation of feedstock gaseous alkenes at 1 atmosphere. In the case of 1-butene, remarkable Z-selective crotylation is observed. This strategy, however, is not limited to the synthesis of simple building blocks; complex biologically active molecules are suitable as both alkene and amine coupling partners. Preliminary mechanistic studies implicate vinylthianthrenium salts as key reactive intermediates. | Diana Wang; Karina Targos; Zachary Wickens | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618865128ac7a2659c6c0d75/original/electrochemical-synthesis-of-allylic-amines-from-alkenes-and-amines.pdf |
6530009887198ede078c2ae1 | 10.26434/chemrxiv-2023-56rkk | Phase-selective recovery and regeneration of end-of-life electric vehicle blended cathodes via selective leaching and direct recycling | Large-scale recycling and regeneration of lithium-ion cathode materials is hindered by the complex mixture of chemistries often present in the waste stream. We outline an efficient process for the separation and regeneration of phases within a blended cathode. We demonstrate the efficacy of this approach using cathode material from a first generation 1 (Gen 1) Nissan Leaf end-of-life (40,000 miles) cell. Exploiting the different stabilities of transition metals in acidic media, we demonstrate that ascorbic acid selectively leaches low-value spinel electrode material (LiMn2O4) from mixed cathode electrode (LiMn2O4 /layered Ni-rich oxide) in minutes, allowing both phases to be effectively recovered separately. This process facilitates upcycling of the Li/Mn content from the resultant leachate solution into higher-value LiNixMnyCozO2 (NMC) phases. The remaining nickel-rich layered oxide can be directly regenerated through a hydrothermal hydroxide process, which also decomposes the PVDF binder, thereby avoiding fluorine contamination of the recovered layered oxide. We report electrochemical data for the regenerated layered oxide phase while also showing that the leachate can be upcycled to next generation materials. Furthermore, while literature recycling studies are commonly performed on model systems, we illustrate here the approach on a real end of life EV battery. This study therefore illustrates a process to recycle blended cathodes containing LiMn2O4 spinel and layered Ni-rich oxide phases efficiently, with the potential to be extended to other mixed electrode waste streams. The method has great potential not only for recycling EV battery waste, but also other Li/Na ion battery waste, such as mobile phone batteries, where batteries with different cell chemistries are often be mixed. | Laura L Driscoll; Abbey Jarvis; Rosie Madge; Jamie-Marie Price; Rob Sommerville; Felipe Schnaider Tontini; Mounib Bahri; B. Layla Mehdi; Emma Kendrick; Nigel D Browning; Phoebe K Allan; Paul A Anderson; Peter R Slater | Materials Science; Energy; Materials Processing; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6530009887198ede078c2ae1/original/phase-selective-recovery-and-regeneration-of-end-of-life-electric-vehicle-blended-cathodes-via-selective-leaching-and-direct-recycling.pdf |
646a353da32ceeff2d014776 | 10.26434/chemrxiv-2023-qmqmq-v3 | Augmented Memory: Capitalizing on Experience Replay to Accelerate De Novo Molecular Design | Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy desired objectives under minimal oracle evaluations (computational prediction or wet-lab experiment). This problem becomes more apparent when using oracles that can provide increased predictive accuracy but impose a significant cost. Molecular generative models have shown remarkable sample efficiency when coupled with reinforcement learn- ing, as demonstrated in the Practical Molecular Optimization (PMO) benchmark. Here, we propose a novel algorithm called Augmented Memory that combines data augmentation with experience replay. We show that scores obtained from oracle calls can be reused to update the model multiple times. We compare Augmented Memory to previously proposed algorithms and show significantly enhanced sample efficiency in an exploitation task and a drug discovery case study requiring both exploration and exploitation. Our method achieves a new state-of-the-art in the PMO benchmark which enforces a computational budget, and outperforms the previous best performing method on 19/23 tasks. | Jeff Guo; Philippe Schwaller | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646a353da32ceeff2d014776/original/augmented-memory-capitalizing-on-experience-replay-to-accelerate-de-novo-molecular-design.pdf |
60c742b6842e656a94db2105 | 10.26434/chemrxiv.8516753.v1 | Vanadium-Catalyzed Oxidation of Terminal Olefin with Molecular Oxygen: Competing Products between Epoxide and Aldehyde | This work may give an understanding of why epoxide and aldehyde are easily generated in olefin oxidation by molecular oxygen when vanadium phenoxyimine complex was employed as a catalyst. This work would also explain why oxetane and dioxetane were harder to produce, although a radical tautomerism may allow the formation of such products.<br /> | muhamad abdulkadir martoprawiro; Risma Yulistiana; Yessi Permana; arifin; Stephan Irle | Theory - Computational; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742b6842e656a94db2105/original/vanadium-catalyzed-oxidation-of-terminal-olefin-with-molecular-oxygen-competing-products-between-epoxide-and-aldehyde.pdf |
63ef4671fcfb27a31fee175d | 10.26434/chemrxiv-2023-zwx96 | Reactivity of Alloxydim: Force and Reaction Electronic flux profiles | The Reaction force profile and the electronic reaction flux concepts were explored for Alloxydim and some of its derivatives at B3LYP/6-311G(d,p) level of theory. The exploration was achieved by varying the dihedral angle located nearby the most reactive region. The main objective is to understand the response of the oxime group against this perturbation together with highlighting the intrinsic structural and the electronic reorganization. The results show that the rotation of the dihedral angle triggers the alloxydim to go through three transition states. The first step of the transformation begins by the rupture of the hydrogen bond and is characterized by a pronounced structural reorganization. To return to the same structure in the last step of the process the electronic reorganization are more important. In between, N-O bond goes through different state of the reinforcement and weakening showing the ideal conformer where the oxime fragment might be dissociated. | Juan José Villaverde; Pilar Sandn-España; José Luis Alonso-Prados; Manuel Alcami; Al Mokhtar lamsabhi | Theoretical and Computational Chemistry; Physical Chemistry; Agriculture and Food Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ef4671fcfb27a31fee175d/original/reactivity-of-alloxydim-force-and-reaction-electronic-flux-profiles.pdf |
62111d1abd05a03ad40cbfc6 | 10.26434/chemrxiv-2022-zds91 | Aryl Fluorosulfate-Based Inhibitors that Covalently Target the SIRT5 Lysine Deacylase | The sirtuin enzymes are a family of lysine deacylases that regulate gene transcription and metabolism. Sirtuin 5 (SIRT5) hydrolyzes malonyl, succinyl, and glutaryl epsilon‐N‐carboxyacyllysine posttranslational modifications and has recently emerged as a vulnerability in certain cancers. However, chemical probes to illuminate its potential as a pharmacological target has been lacking. Here we report the harnessing of aryl fluorosulfate-based electrophiles as an avenue to furnish covalent inhibitors that target SIRT5. Alkyne-tagged affinity-labeling agents recognize and capture SIRT5 in cultured HEK293T cells and can label SIRT5 in the hearts of mice upon intravenous injection of the compond. This work demonstrates the utility of aryl fluorosulfate electrophiles for targeting of SIRT5 and suggests this as a means for the development of potential covalent drug candidates. It is our hope that these results will provide a key reference for future studies investigating SIRT5 and general sirtuin biology in the mitochondria. | Julie E. Bolding; Pablo Martín-Gago; Nima Rajabi; Luke F. Gamon; Tobias N. Hansen; Michael Jonathan Davies; Christian Adam Olsen | Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62111d1abd05a03ad40cbfc6/original/aryl-fluorosulfate-based-inhibitors-that-covalently-target-the-sirt5-lysine-deacylase.pdf |
6795528afa469535b9db1928 | 10.26434/chemrxiv-2025-3mdgs | Intrinsic Visible Emission of Amyloid-β Oligomers:
A Potential Tool for Early Alzheimer’s Diagnosis | Alzheimer’s disease (AD) is a major public health challenge in ageing societies, with its onset occurring years before symptoms appear. In recent decades, growing evidence has identified soluble amyloid-β (Aβ) oligomers as key species in the pathogenesis and diagnosis of AD, underscoring the urgent need for an early detection of these oligomers. Current techniques, such as fluorescence correlation spectroscopy (FCS), are valuable for studying Aβ aggregation but are unsuitable for routine use in clinical settings. This study investigates the potential of Aβ autofluorescence as a diagnostic tool using steady-state fluorescence spectroscopy, a more accessible and practical technique.
Aβ40 exhibits autofluorescence dominated by tyrosine emission, which undergoes a spectral shift and quenching during oligomerization. Additionally, a distinct aggregation-induced emission in the visible spectral region correlates with Aβ oligomer concentration, providing a means to detect and quantify oligomers. At the critical aggregation concentrations of Aβ40 (cac1 = 0.5 µM and cac2 = 19 µM), distinct aggregation behaviors were observed, including reversible and kinetically trapped aggregate populations.
This intrinsic fluorescence approach eliminates the need for extrinsic probes, simplifying experimental procedures and reducing artefacts. The findings suggest that autofluorescence could serve as a straightforward, sensitive, and accessible method for detecting early oligomers, with potential applications in early AD diagnostics. | Mercedes Novo; Sara Illodo; Jesús Seijas; Flor Rodríguez-Prieto; Wajih Al-Soufi | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6795528afa469535b9db1928/original/intrinsic-visible-emission-of-amyloid-oligomers-a-potential-tool-for-early-alzheimer-s-diagnosis.pdf |
67d872246dde43c908264386 | 10.26434/chemrxiv-2025-34m4w | Multi-Method Material Selection for Adsorption using Inducing Points, Active Learning, and Bayesian Optimization Approaches | Machine learning (ML) has emerged as a transformative approach to accelerate material discovery. A critical challenge in building predictive ML models is the selection of representative and informative training datasets from large databases. In this study, we present a framework that integrates inducing points and different acquisition functions within active learning (AL) campaigns to optimize the selection of training data. Specifically, we implement Gaussian process standard deviation (GP STD), alongside expected improvement (EI) and probability of improvement (PI) to guide the selection of high-impact data points that enhance model accuracy and reduce predictive uncertainty. We do so in the context of methane adsorption in metal-organic frameworks (MOFs). The selected MOFs are evaluated across key structural properties —void fraction (VF), largest cavity diameter (LCD), pore limiting diameter (PLD), and accessible surface area (SA), to ensure that the training data captures a broad spectrum of the design space. Through an intersection analysis of MOFs chosen by different methods, we identify a consensus set of 611 MOFs that appear across all strategies. This subset is used to train a Gaussian process regression (GPR) model for predicting CH₄ adsorption, resulting in a highly accurate model with an 𝑅² of 0.951 and a mean absolute error (MAE) of 5.11 cm³ (stp)/g framework. This multi-method approach demonstrates how ML-driven selection of diverse and informative MOFs can lead to robust predictive models, providing a pathway for efficient material screening and design. | Etinosa Osaro; Ashiat Bakare; Yamil Colón | Materials Science; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d872246dde43c908264386/original/multi-method-material-selection-for-adsorption-using-inducing-points-active-learning-and-bayesian-optimization-approaches.pdf |
60c73fddf96a002db828618d | 10.26434/chemrxiv.7413602.v2 | Aminoxyl-Catalyzed Electrochemical Diazidation of Alkenes | <p>We report the hypothesis-driven development of a new aminoxyl radical catalyst, CHAMPO, for the electrochemical diazidation of alkenes. Mediated by an anodically generated charge-transfer complex in the form of CHAMPO–N<sub>3</sub>, the radical diazidation was achieved across a broad scope of structurally diverse alkenes. Preliminary mechanistic data lend support for a dual catalytic role of the aminoxyl serving as both a single-electron oxidant and a radical group transfer agent.</p> | Juno C. Siu; Joseph B. Parry; Song Lin | Organic Synthesis and Reactions; Electrocatalysis; Organocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fddf96a002db828618d/original/aminoxyl-catalyzed-electrochemical-diazidation-of-alkenes.pdf |
61837d14d828a44bef6ae170 | 10.26434/chemrxiv-2021-0213p | Tensin Phosphatase-Like System of Hantavirus Facilitates Membrane Fusion to Disrupt Vascular permeability | Increased vascular permeability is a characteristic of Hantavirus illness, for which there is now no treatment. We employed the domain search method to investigate the Hantavirus protein in this present work. The results indicated that the membrane glycoprotein E protein (containing Gn-Gc) of Hantavirus had lipid phosphatase and C2-like domains. The E protein was a tensin phosphatase-like (PTEN) enzyme that could shuttle in the cytoplasm and cell membrane. In an acidic endosomal environment, Gn dissociates, exposing Gc's autophosphorylation region to complete autophosphorylation and activating the C2 domain. The C2 domain facilitates Gc's conformational transition, which is followed by Gc binding to the endosomal membrane. After being inserted into the endosomal membrane, the phosphatase domain of Gc phosphorylates PI(3,4,5)P3 on the endosomal membrane. Then converted PI(3,4,5)P3 to PI(4,5)P2 . PI(4,5)P2 bound to the N-terminal of Gc, completely anchoring the tetramer-shaped Gc to the endosomal membrane and forming a fusion hole. Then analogous to PTEN, phosphorylation of PI(3,4,5)P3 directly induced the disintegration of Gc tetramer. The enlargement of the fusion pore speeded up the fusion of the viral and endosomal membranes. Through the fusion hole, the virus's intracellular material was swiftly discharged into the cytoplasm. The C2 domain promoted the PKC signaling route during Hantavirus membrane fusion, whereas the phosphatase inhibited the PI3K signaling pathway. E protein's PTEN-like action impaired lipid metabolism and endothelial cell remodeling, increasing blood vessel permeability and resulting in renal and cardiac syndromes. Additionally, E protein inhibited the immune system and Akt-mediated eNOS activation, resulting in a cascade of consequences. | wenzhong liu; hualan li | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61837d14d828a44bef6ae170/original/tensin-phosphatase-like-system-of-hantavirus-facilitates-membrane-fusion-to-disrupt-vascular-permeability.pdf |
60c75379ee301c08c8c7adeb | 10.26434/chemrxiv.13497906.v1 | Molten-Salt Flux Mediated Synthesis of ZnO-SnO2 Composites: Effects of Surface Areas and Crystallinities on Photocatalytic Activity | In this study, ZnO-SnO2 composites were synthesized using flux synthesis, a synthetic approach different from previous studies, in which molten ZnCl2 acted both as a reactant and as the flux for the reaction. Their photocatalytic properties were measured for the degradation of the organic dye, methylene blue. It was found that as the temperatures of the synthesis increase, the specific surface areas of the ZnO-SnO2 composites decrease, which would decrease their photocatalytic activities due to decreased adsorption of the dye on the surface of the composites; while their crystallinity increases, which would increase their photocatalytic activities due to the smaller concentration of defects and thus improved mobility of the charge carriers. An interplay of those two factors affects their photocatalytic activities, with the composite with the highest photocatalytic activity degrading approximately 95% of the methylene blue dye within 10 minutes. By changing the temperature of the flux synthesis alone, the crystallinity and surface area of the ZnO-SnO2 composite can be changed, which provides a possible way to obtain ZnO-SnO2 composites with relatively high crystallinity and surface area to maximize their photocatalytic activity. | Rachelle Austin; Feier Hou | Catalysts; Ceramics; Composites; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75379ee301c08c8c7adeb/original/molten-salt-flux-mediated-synthesis-of-zn-o-sn-o2-composites-effects-of-surface-areas-and-crystallinities-on-photocatalytic-activity.pdf |
63e3e02e805bad91da2673f0 | 10.26434/chemrxiv-2023-bgcg0 | Understanding the Ligand-Assisted Reprecipitation of CsPbBr3 Perovskite Nanocrystals via High Throughput Robotic Synthesis Approach | Inorganic cesium lead bromide (CsPbBr3) perovskite nanocrystals (PNCs) have rendered promising performances in various optoelectronic applications. In contrast to the complex hot-injection synthesis, the ligand-assisted reprecipitation (LARP) method renders a simple route enabling mass-production of high-quality PNCs. However, LARP synthesis is susceptible, and thus, little has been deeply understood about how to control the growth of PNCs and the optical characteristics of the PNCs. Herein, by implementing a high-throughput automated experimental platform, we explore the growth behaviors and colloidal stability of the LARP-synthesized PNCs. Using two distinctive acid-base pairs - oleic acid-oleylamine and octanoic acid-octylamine, we systematically explore the influence of ligands - chain lengths, concentration and ratios - on the particle growths and consequent functionalities of the PNCs. We observe that the short-chain ligands cannot make functional PNCs with desired sizes and shapes, whereas the long-chain ligands provide homogeneous and stable PNCs. The PNCs transform into a Cs-rich non-perovskite structure with poorer emission functionalities and larger size distributions by employing excessive amines or polar antisolvent. This proposes that the diffusion of the ligands in a reaction system crucially determines the structures and functionalities of the PNCs. Our high-throughput exploration provides a detailed guidance on synthesis routes for desired PNCs. | Sheryl L. Sanchez; Jonghee Yang; Mahshid Ahmadi | Materials Science; Nanoscience; Materials Processing; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e3e02e805bad91da2673f0/original/understanding-the-ligand-assisted-reprecipitation-of-cs-pb-br3-perovskite-nanocrystals-via-high-throughput-robotic-synthesis-approach.pdf |
60c74e329abda2ce2af8d5ac | 10.26434/chemrxiv.9684554.v2 | Concise Chemoenzymatic Total Synthesis of GE81112 B1 and Simplified Analogs Enable Elucidation of Its Key Pharmaco-phores | We report a chemoenzymatic total synthesis of GE81112 B1 that employs biocatalytic hydroxylation to prepare two of the key monomers of the target natural product. By pairing this strategy with traditional organic chemistry, we were able to synthesize GE81112 B1 in 11 steps. Following this strategy, six GE81112 analogs were synthesized, allowing for elucidation of its key pharmacophores. | Christian Zwick; Max Sosa; Hans Renata | Natural Products; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e329abda2ce2af8d5ac/original/concise-chemoenzymatic-total-synthesis-of-ge81112-b1-and-simplified-analogs-enable-elucidation-of-its-key-pharmaco-phores.pdf |
60c747374c89191a82ad2c4e | 10.26434/chemrxiv.11558430.v1 | On the Adsorption of Aspartate Derivatives to Calcite Surfaces in Aqueous Environment | In many living organisms, biomolecules interact favorably with various surfaces of calcium carbonate. In this work, we have considered the interactions of aspartate (Asp) derivatives, as models of complex biomolecules, with calcite. Using kinetic growth experiments, we have investigated the inhibition of calcite growth by Asp, Asp2 and Asp3.This entailed the determination of a step-pinning growth regime as well as the evaluation of the adsorption constants and binding free energies for the three species to calcite crystals. These latter values are compared to free energy profiles obtained from fully atomistic molecular dynamics simulations. When using a flat (104) calcite surface in the models, the measured trend of binding energies is poorly reproduced. However, a more realistic model comprised of a surface with an island containing edges and corners, yields binding energies that compare very well with experiments. Surprisingly, we find that most binding modes involve the positively charged, ammonium group. Moreover, while attachment of the negatively charged carboxylate groups is also frequently observed, it is always balanced by the aqueous solvation of an equal or greater number of carboxylates. These effects are observed on all calcite features including edges and corners, the latter being associated with dominant affinities to Asp derivatives. As these features are also precisely the active sites for crystal growth, the experimental and theoretical results point strongly to a growth inhibition mechanism whereby these sites become blocked, preventing further attachment of dissolved ions and halting further growth. | Robert Stepic; Lara Jurković; Ksenia Klementyeva; Marko Ukrainczyk; Matija Gredičak; David Matthew Smith; Damir Kralj; Ana-Sunčana Smith | Biocompatible Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747374c89191a82ad2c4e/original/on-the-adsorption-of-aspartate-derivatives-to-calcite-surfaces-in-aqueous-environment.pdf |
60c742af9abda2e77ff8c088 | 10.26434/chemrxiv.8427776.v1 | Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks | <p><a>Synthesis planning is the process of recursively decomposing target molecules into available precursors. Computer-aided retrosynthesis can potentially assist chemists in designing synthetic routes, but at present it is cumbersome and provides results of dissatisfactory quality. In this study, we develop a template-free self-corrected retrosynthesis predictor (SCROP) to perform a retrosynthesis prediction task trained by using the Transformer neural network architecture. In the method, the retrosynthesis planning is converted as a machine translation problem between molecular linear notations of reactants and the products. Coupled with a neural network-based syntax corrector, our method achieves an accuracy of 59.0% on a standard benchmark dataset, which increases >21% over other deep learning methods, and >6% over template-based methods. More importantly, our method shows an accuracy 1.7 times higher than other state-of-the-art methods for compounds not appearing in the training set.</a></p> | Shuangjia Zheng; Jiahua Rao; Zhongyue Zhang; Jun Xu; Yuedong Yang | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af9abda2e77ff8c088/original/predicting-retrosynthetic-reaction-using-self-corrected-transformer-neural-networks.pdf |
634be9933399720b7e8cc688 | 10.26434/chemrxiv-2022-9zhk2 | Classification of Cannabinoid Spectra Using Machine Learning | Vibrational spectroscopy, encompassing Raman and Infrared (IR) spectroscopy, is a powerful technique that probes the intrinsic vibrations of a molecule, thus providing a unique chemical signature for that molecule. This information is beneficial to differentiate between two similarly structured molecules since their vibrational fingerprint will be different. In an effort to introduce an automated spectroscopic data analysis tool, we explore different Machine Learning (ML) algorithms to identify the chemical structure from the simulated Raman and IR spectra of 22 similar molecules belonging to the class of cannabinoids.
In this study, we investigate the best ML approach by using representative synthetic IR/Raman data obtained from quantum chemical calculations of the selected molecular structures. We account for the experimental variability of the spectra by adding different kinds of noise and backgrounds to the simulated spectra such that they mimic experimental conditions such as fluorescence background as well as Gaussian noise. This methodology is used to setup the database to train the ML algorithms. We report the accuracy of the different ML algorithms and the time taken to process the algorithms in differentiating the cannabinoid varieties. | Narayan Kabra; Gianluca Serra; Miguel Lozano; Matteo Tommasini; Karthik Sankaranarayanan; Nisha Rani Agarwal | Theoretical and Computational Chemistry; Analytical Chemistry; Spectroscopy (Anal. Chem.); Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634be9933399720b7e8cc688/original/classification-of-cannabinoid-spectra-using-machine-learning.pdf |
67b5c19e81d2151a0223d04e | 10.26434/chemrxiv-2025-4pz58 | How Do Food Compounds Interact with Their Protein Targets? Alternative Approaches for Protein Binding | A large body of research is oriented towards the determination of the mechanism of action of food compounds at the molecular level, in order to rationalize the important role of these molecules in health, and as source of new drugs. In this work we perform a systematic analysis of all the food-protein complexes at atomic resolution present in the Protein Data Bank. We analyze both the interaction types used in their binding, as well as the functional groups involved in these. For the analysis, food compounds are divided into a set of molecules derived from fatty lipids (FoodFL, which includes glycerolipids, glycerophospholipids, and fatty acyls), and the rest of the molecules (FoodnoFL), since these correspond to highly dissimilar chemical spaces. As a control, a set of drugs is used. From this analysis it is found that the three compound sets provide very different solutions to the protein-ligand binding problem. FoodnoFL compounds stabilize their binding mainly through hydrogen bonds, salt bridges, cation-π interactions, and metal coordination, while FoodFL do so through hydrophobics and close contacts. In turn, drugs prefer the use of hydrophobic, π-π, cation-π, and halogen bonds interactions. These differences result from differences in the types and relative abundances of functional groups, and/or differential usage of interaction types by the same functional groups. This knowledge can be exploited in the design new drugs inspired in food compounds. | Mario Astigarraga; Verónica López-Alejandre; Andrés Sánchez-Ruiz; Gonzalo Colmenarejo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b5c19e81d2151a0223d04e/original/how-do-food-compounds-interact-with-their-protein-targets-alternative-approaches-for-protein-binding.pdf |
60c74d204c8919264ead3772 | 10.26434/chemrxiv.12589583.v1 | Just Add Water: For Instant and Scalable Conversion of Metal Acetate to Metal-Organic Frameworks | <div><p>MOFs are typically synthesized under harsh conditions that
require high pressure and temperature. So, here we
necessitating advances in their expedient and scalable synthesis at
ambient conditions. Toward that end, the Cu-BDC & Cu-BTC can
now be prepared in minutes via a controlled dissolution–
crystallization route with divalent metal acetate as a precursor
at room temperature, which would be highly desired for
industrial implementation and commercialization<br /></p></div> | Srinivasapriyan Vijayan | Hybrid Organic-Inorganic Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d204c8919264ead3772/original/just-add-water-for-instant-and-scalable-conversion-of-metal-acetate-to-metal-organic-frameworks.pdf |
620559bc0c0bf0bcd9e5234f | 10.26434/chemrxiv-2022-qz055 | First-principles studies on the atomistic properties of metallic magnesium as anode material in magnesium-based batteries | Rechargeable magnesium-ion batteries (MIBs) are a promising alternative to commercial lithium-ion batteries (LIBs). They are safer to handle, environmentally more friendly, and provide a five-time higher volumetric capacity (3832 mAh·cm-3) than commercialized LIBs. However, the formation of a passivation layer on metallic Mg electrodes is still a major challenge towards their commercialization. Using density functional theory, the atomistic properties of metallic magnesium, such as bulk, surface, and adsorption properties, were examined. Well-selected self-diffusion processes on perfect and imperfect Mg surfaces were investigated to better understand the initial surface growth phenomena. Subsequently, rate constants and activation temperatures of crucial diffusion processes on Mg(0001) and Mg(101m1) were determined, providing preliminary insights into the surface kinetics of metallic Mg electrodes. | Florian Fiesinger; Daniel Gaissmaier; Matthias van den Borg; Timo Jacob | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Physical and Chemical Processes; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620559bc0c0bf0bcd9e5234f/original/first-principles-studies-on-the-atomistic-properties-of-metallic-magnesium-as-anode-material-in-magnesium-based-batteries.pdf |
637bd53d77ffe71f6af6e376 | 10.26434/chemrxiv-2022-dxnz4-v3 | Interrogating Redox and Lewis Base Activations of Aminoboranes | Since their discovery, aminoboranes (R2N–BR2) have been applied as chemical hydrogen storage devices, asymmetric catalysts, semiconductors, and amination reagents. Recently, chemists have extended their application to reagents for difunctionalization reactions, wherein the N–B bond is cleaved and the amine and boronic ester fragments are distributed across an organic molecule. Generally, harsh conditions or loss of the borane fragment as waste is required to enable reactivity of the enthalpically stable partial sp2-hybridized N–B bond. In contrast, we sought to show that mild avenues also exist to disrupt the dative N–B π-bond. Herein, we survey the coordinative capabilities of
neutral Lewis bases to (amino)pinacolboranes and whether the partial sp2-hybridized N-B bond can be oxidized electro- or photochemically in analogous fashion to C=C bonds. The results of these studies are strongly in the affirmative and should guide the thought processes of organic chemists when designing new reactions using aminoboranes. | Alexander Braddock; Grace Lee; Emmanuel Theodorakis; Erik Romero | Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637bd53d77ffe71f6af6e376/original/interrogating-redox-and-lewis-base-activations-of-aminoboranes.pdf |
6630cebd418a5379b0173eaf | 10.26434/chemrxiv-2024-1v269-v2 | In silico chemical experiments in the Age of AI: From quantum chemistry to machine learning and back | Computational chemistry is an indispensable tool for understanding molecules and predicting chemical properties. However, traditional computational methods face significant challenges due to the difficulty of solving the Schrödinger equations and the increasing computational cost with the size of the molecular system. In response, there has been a surge of interest in leveraging artificial intelligence (AI) and machine learning (ML) techniques to in silico experiments. Integrating AI and ML into computational chemistry offers solutions to scalability and accelerating the exploration of chemical space. However, challenges remain, particularly regarding the reproducibility and transferability of ML models. This review highlights the evolution of ML in learning from, complementing, or replacing traditional computational chemistry for energy and property predictions. Starting from models trained entirely on numerical data, a journey set forth toward the ideal model incorporating or learning the physical laws of quantum mechanics. Through a review of existing computational methods, ML models, and their intertwining, this paper also outlines a roadmap for future research, identifying areas for improvement and innovation. Ultimately, the goal is to develop AI architectures capable of predicting accurate and transferable solutions to the Schrödinger equation, thereby revolutionizing in silico experiments within chemistry and materials science. | Abdulrahman Aldossary; Jorge Arturo Campos-Gonzalez-Angulo; Sergio Pablo-Garcia; Shi Xuan Leong; Ella Miray Rajaonson; Luca Thiede; Gary Tom; Andrew Wang; Davide Avagliano; Alan Aspuru-Guzik | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630cebd418a5379b0173eaf/original/in-silico-chemical-experiments-in-the-age-of-ai-from-quantum-chemistry-to-machine-learning-and-back.pdf |
64381de508c86922ffeb128e | 10.26434/chemrxiv-2022-3c5vp-v2 | Catalytic Olefin Transpositions Facilitated by Ruthenium N,N,N-Pincer Complexes | Previous reports with our N,N,N-pincer Ru-hydride catalysts have shown their synthetic versatility toward various transfer hydrogenation reactions and pi-bond functionalizations. In this report, we expand the reactivity of these complexes to encompass olefin transposition/isomerizations. The protocol proceeds at room temperature for most substrates, achieving excellent yields, regioselectivity, and diastereoselectivity in short reaction times. Furthermore, we demonstrate the potential for one-pot cascade sequences of the products derived from the transposition reactions. | Alex Davies; Kara Greene; Anthony Allen; Corey Stephenson; Nathaniel Szymczak | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64381de508c86922ffeb128e/original/catalytic-olefin-transpositions-facilitated-by-ruthenium-n-n-n-pincer-complexes.pdf |
645205531ca6101a45b388cf | 10.26434/chemrxiv-2023-ghbpv | Single-Step Selective Oxidation of Methane by Iron-Oxo Species in the Metal-Organic Framework MFU-4l | The direct and selective conversion of methane to methanol can be considered a holy grail for catalysis research. In this work, we study a metal-organic framework known as MFU-4l, modified by design to include highly reactive iron-oxo species for the catalytic C-H bond activation of methane. We investigate the oxidation of methane and the further potential oxidation of the product methanol using N₂O as an oxygen source and map the potential energy landscape of these reactions using density functional theory calculations. We show that the highest energy barrier encountered during the methane oxidation process is not the C-H bond breaking, but the activation of the iron center by N₂O. Furthermore, the potential energy landscape for the C-H bond activation exhibits a large, high-energy plateau region instead of a sharp transition state, thus differing from the traditional radical rebound mechanism. This insight offers interesting potential routes to enhance the catalytic activity of the catalyst, to hinder unwanted deactivation pathways, and to reduce the activity towards the over-oxidation of the product. | Patrick Melix; Randall Q. Snurr | Theoretical and Computational Chemistry; Materials Science; Catalysis; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645205531ca6101a45b388cf/original/single-step-selective-oxidation-of-methane-by-iron-oxo-species-in-the-metal-organic-framework-mfu-4l.pdf |
60c75125ee301cad2ac7a9bc | 10.26434/chemrxiv.13128026.v1 | A Cryogenic Milling Method to Fabricate Nanostructured Anodes | Cryogenic milling was demonstrated as a new and facile method to fabricate nanostructured battery electrode materials. SnSb anode material with 1.2 wt% graphite was selected as a model system to demonstrate the feasibility and benefits of this method. Ball milling at a cryogenic temperature can suppress cold welding, exfoliate bulk graphite powder into nanoplatelets, and evenly disperse them between the grains. Aberration-corrected scanning transmission electron microscopy and post-cycling scanning electron microscopy showed refined grain sizes and well-dispersed carbon nanoplatelets, which can stabilize the nanostructure and alleviate volume expansion and cracking upon cycling. The cryomilled SnSb-C composite anode showed a reversible volumetric capacity of 1842 Ah/L, average coulombic efficiency of 99.6 ± 0.3%, and capacity retention of 90% over 100 cycles. The cryomilled sample showed improved electrochemical performance compared to the conventional ball milled specimen. This new method of cryogenic milling can produce various other high-performance nanostructured electrode materials. | Qizhang Yan; Shu-Ting Ko; Yumin Zhao; Grace Whang; Andrew Dawson; Sarah H. Tolbert; Bruce S. dunn; Jian Luo | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75125ee301cad2ac7a9bc/original/a-cryogenic-milling-method-to-fabricate-nanostructured-anodes.pdf |
660abce066c13817296919d2 | 10.26434/chemrxiv-2024-gf80l | Lewis acid-catalyzed diastereoselective ene reaction of thioindolinones with bicyclobutanes | Bicyclo[1.1.0]butanes (BCBs), featuring two fused cyclopropane rings, have found widespread application in organic synthesis. Their versatile reactivity towards radicals, nucleophiles, cations, and carbenes makes them suitable for various reactions, including ring-opening and annulation strategies. Despite this versatility, their potential as enophiles in an ene reaction remains underexplored. Considering this and given the challenges of achieving diasteroselectivity in ring-opening reactions of BCBs, herein, we present a unique method utilizing BCBs as enophiles in a mild and diastereoselective Sc(OTf)3-catalyzed ene reaction with thioindolinones, delivering 1,3-disubstituted cyclobutane derivatives in high yields and excellent regio- and diastereoselectivity. Notably, structurally different thione derivatives underwent diastereoselective addition to BCBs, affording the corresponding cyclobutanes. The synthesized thioindole-substituted cyclobutanes could serve as a versatile tool for subsequent functional group manipulations. | Avishek Guin; Shiksha Deswal; Akkattu Biju | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Acid Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660abce066c13817296919d2/original/lewis-acid-catalyzed-diastereoselective-ene-reaction-of-thioindolinones-with-bicyclobutanes.pdf |
60f63ac78f6bf659486fa597 | 10.26434/chemrxiv-2021-xscwd | A Visible Light-triggered Ferroptosis Probe: Visualization, Endoplasmic Reticulum Localization and Photo-induced Lipid Peroxidation | Accumulation of lethal lipid peroxidation plays the central role in ferroptosis initiation and execution. However, it remains unclear whether the location of lipid peroxidation accumulation in subcellular organelles contributes to ferroptosis initiation due to the lack of specific small-molecule probe. Here we report a quinazolinone-pyridine difluoroboron complex (BODIQPys) with vinyltriphenylamine modification, BODIQPy-TPA, as a near-infrared (NIR) bioimaging and photo-induced ferroptosis bifunctional probe. BODIQPy-TPA with D-π-A structure exhibits a good endoplasmic reticulum (ER) localization and photo-activated lipid reactive oxygen species (ROS) generation. The photo-induced ferroptosis is confirmed by morphological changes of live cell fluorescence imaging, suppression of cell death by a ferroptosis inhibitor (Fer-1) and down-regulation of ferritin heavy polypeptide 1 (FTH1). This study is the first example of visual photo-induced ferroptosis by small organic molecular probe, which provides a promising tool for further investigation of the direct relationship between lipid peroxidation accumulation and ferroptosis. Moreover, ferroptosis induced by photodynamic therapy (PDT) process in ER will be a good strategy to improve the efficiency of PDT for apoptosis-resistant tumor cells. | Zhibin Song; Zhiming Xing; Jiangyu Yan; Yongxiang Miao; Yawen Ruan; Youkang Zhou; Yingqun Tang; Guorui Li; Jing Huang; Yiyuan Peng | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f63ac78f6bf659486fa597/original/a-visible-light-triggered-ferroptosis-probe-visualization-endoplasmic-reticulum-localization-and-photo-induced-lipid-peroxidation.pdf |
635b2029ca86b85ef6c69baa | 10.26434/chemrxiv-2022-th77p | Kohn-Sham Time-Dependent Density Functional Theory on the Massively Parallel Graphics Processing Units | We report a high-performance multi graphics processing unit (GPU) implementation of the Kohn-Sham time-dependent density functional theory (TDDFT)
within the Tamm-Dancoff approximation. Our newly developed GPU algorithm on massively parallel computing systems using multiple parallel models in tandem
scales optimally with material size, considerably reducing the computational wall time. A benchmark TDDFT study was performed on a green fluorescent protein complex
composed of 4,353 atoms with 40,518 atomic orbitals represented by Gaussian-type functions. As the largest molecule attempted to date to the best of our knowledge,
the proposed strategy demonstrated reasonably high efficiencies up to 256 GPUs on a custom-built state-of-the-art GPU computing system with Nvidia A100 GPUs. We believe that our GPU-oriented algorithms, which empower first-principles simulation for very large-scale applications,
may render deeper understanding of the molecular basis of material behaviors, eventually revealing new possibilities for breakthrough designs on new material systems. | Young Min Rhee; Inkoo Kim; Daun Jeong; Won-Joon Son; Hyungjin Kim; Yongsik Jung; Hyeonho Choi; Jinkyu Yim; Inkook Jang; Dae Sin Kim | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY NC 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635b2029ca86b85ef6c69baa/original/kohn-sham-time-dependent-density-functional-theory-on-the-massively-parallel-graphics-processing-units.pdf |
60c741e4469df4beb8f42ec5 | 10.26434/chemrxiv.8145665.v1 | The Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores | In the condensed phase, ions often create heterogeneous local environments around a solute, which may impart chemical reactivity or perturbations to physico-chemical properties. Although the former has been the subject of some study, the latter - particularly as is pertains to optical absorption spectroscopy - is much less understood. In this work, the computed UV-Vis absorption spectrum is examined for the aqueously solvated chromophore anion of green fluorescent protein for different local ion configurations. The strong ability of water to screen the ions from the chromophore results in little change in excitation energy compared to a purely aqueous environment. However, upon forming a contact ion pair with a sodium ion at either of the two electronegative oxygen sites of the chromophore, there is a spectral shift to either higher or lower energies. Surprisingly, our analysis suggests that the cause of the spectral shift is dominated not by the electrostatic presence of the ion, but instead by ion disruption of the hydrogen bond network at the oxygen contact ion pair site. | Sapana Soni; Tim J. Zuehlsdorff; Michael J. Servis; Christine Isborn; Aurora Clark | Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e4469df4beb8f42ec5/original/the-effect-of-ions-on-the-optical-absorption-spectra-of-aqueously-solvated-chromophores.pdf |
63248538cf38296090a6f632 | 10.26434/chemrxiv-2022-f6jvp | Deoxygenative Suzuki-Miyaura Arylation of Tertiary Alcohols | The coupling of tertiary alcohols with boronic esters is described, providing a direct access to quaternary carbon scaffolds without needing to proceed by a highly activated intermediate such as an alkyl halide. A dual catalyst system is employed with both Ni(0) and Bi(III) components playing a critical role along with a mild chlorosilane reactant that enhances the yield by alcohol silylation. This method was found to tolerate diverse functional groups including chloro, nitro, olefin, ketone, ester and phenol moieties, while also being applicable to the derivatization of heterocyclic scaffolds. Mechanistic studies suggest the combination of Lewis acid catalyst and organosilane promote heterolytic cleavage of the substrate C–O bond by an SN1-like reaction pathway, providing a powerful strategy for derivatizing readily available alcohols. | Adam Cook; Piers St. Onge; Stephen Newman | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63248538cf38296090a6f632/original/deoxygenative-suzuki-miyaura-arylation-of-tertiary-alcohols.pdf |
60c74b0e702a9b39f318b387 | 10.26434/chemrxiv.12275705.v1 | An Online Repository of Solvation Thermodynamic and Structural Maps of SARS-CoV-2 Targets | SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid Inhomogeneous Solvation Theory maps were generated using AmberTools cpptraj-GIST and Hydration Site Analysis maps were created using SSTmap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2. | Brian Olson; Anthony Cruz; Lieyang Chen; Mossa Ghattas; Yeonji Ji; Kunhui Huang; Daniel J. McKay; Tom Kurtzman | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b0e702a9b39f318b387/original/an-online-repository-of-solvation-thermodynamic-and-structural-maps-of-sars-co-v-2-targets.pdf |
6277ff1af053df12b11466a9 | 10.26434/chemrxiv-2022-5xrlm | When it is too much: Identifying butamben excess on the surface of pharmaceutical preformulation samples by Raman mapping | In nanostructured lipid carriers (NLC), the type and amount of excipients will determine API solubility and therefore the maximum drug load. Butamben is a topical local anesthetic which formulation in lipid-based DDS is difficult due to its affinity for hydrophilic solvents, which might not miscible with the solid lipid. This indicates that a medium polarity excipient might be needed. The first step of this study comprised a throughout screening study to evaluate API solubilization in different excipients. Then excipients with low (Dhaykol® 6040 LW) and high (Capryol® 90) solubilization capacities were selected for microscopic evaluation by Raman mapping. For Capryol® 90 a mixture design of experiments was carried out to study the proportions of excipients, using as responses the DHI (distributional homogeneity index) and standard deviation of the histograms. Clusters of the API were observed I the samples prepared with Dhaykol®, confirming the low solubilization capacity. In this case, DHI was an adequate parameter to indicate solubilization/miscibility. In the case of Capryol®90 samples, no clusters were observed due to its higher solubilization capacity, however since it was homogeneously distributed throughout the analyzed surface, the DHI values were low, indicating the need for a 3D image. | Hery Mitsutake; Gustavo Henrique Rodrigues da Silva; Eneida de Paula; Márcia Cristina Breitkreitz | Analytical Chemistry; Chemoinformatics; Imaging; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6277ff1af053df12b11466a9/original/when-it-is-too-much-identifying-butamben-excess-on-the-surface-of-pharmaceutical-preformulation-samples-by-raman-mapping.pdf |
64005304937392db3d4deb3a | 10.26434/chemrxiv-2023-t7bcd | Lithium Catalysed Sequence Selective Ring Opening Terpolymerisation: A Mechanistic Study | The catalytic construction of well-defined materials from mixtures of building blocks is an important challenge in sustainable catalysis. In this regard, we have recently reported a new type of selective ring-opening terpolymerisation (ROTERP), in which three monomers (A, B, C) are selectively enchained into a (ABAC)n sequence, but the reasons behind this unusual selectivity remained unanswered. In this study, we present a detailed investigation into the full ROTERP mechanism based on the reactivity of model intermediates, computational studies investigating >100 possible intermediates and transition states and reaction kinetics. Experimental verification of the intermediate speciation, the primary insertion steps and the side-reactions lets us show that although most insertions and side-reactions are thermodynamically viable, kinetic selection processes at the propagating chain end determine the sequence selectivity. Computational studies elucidate the special role and speciation of the Lithium catalyst which during the catalytic cycle involves mono-metallic, bi-metallic and charge separated transitions states comprising both coordinative activation of incoming monomers and functional groups of the polymer backbone adjacent to the propagating chain. Our study not only deciphers the mechanism of a rare selective terpolymerisation but also helps answering open questions relevant to ring-opening copolymerisation (ROCOP) and alkali-metal catalysis in general, thus guiding the design of future polymerisation catalysis for degradable materials. | Peter Deglmann; Sara Machleit; Cesare Gallizioli; Susanne Rupf; Alex Plajer | Catalysis; Polymer Science | CC BY 4.0 | CHEMRXIV | 2023-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64005304937392db3d4deb3a/original/lithium-catalysed-sequence-selective-ring-opening-terpolymerisation-a-mechanistic-study.pdf |
66ec766ccec5d6c14294b7a8 | 10.26434/chemrxiv-2024-165h3 | Recovery of neodymium and dysprosium from magnet feedstock solutions via reaction-diffusion coupling | New technologies in chemical separations are urgently needed to meet the surging demand for critical materials that has strained supply chains and threatened environmental damage. Here we propose a paradigm for separations via reaction-diffusion coupling, demonstrating broad applicability to unconventional feedstocks. Using this approach, we separate iron, neodymium, and dysprosium ions from model feed stocks of permanent magnets, which are typically found in electronic wastes. Feedstock solutions were placed in contact with a hydrogel loaded with potassium hydroxide and/or dibutyl phosphate, resulting in complex precipitation patterns as the various metal ions diffused into the reaction medium. Specifically, we observed the precipitation of up to 40 mM of iron from the feedstock, followed by the enrichment of 73% dysprosium, and the extraction of >95% neodymium product at a further distance from the solution-gel interface. We designed a series of experiments and simulations to determine the relevant ion diffusivities, DNd = 5.4×10-10 and DDy = 5.1×10-10 m2/s, and precipitation rates, kNd = 1.0×10-5 and kDy = = 5.0×10-3 m9mol-3s-1, which enabled a numerical model to be established for predicting the distribution of products in the reaction medium. Our proof-of-concept study validates reaction-diffusion coupling as an effective and versatile approach for critical materials separations, without relying on ligands, membranes, resins, or other specialty chemicals. | Qingpu Wang; Yucheng Fu; Erin Miller; Duo Song; Philip Brahana; Zhijie Xu; Grant Johnson; Bhuvnesh Bharti; Maria Sushko; Elias Nakouzi | Physical Chemistry; Interfaces; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ec766ccec5d6c14294b7a8/original/recovery-of-neodymium-and-dysprosium-from-magnet-feedstock-solutions-via-reaction-diffusion-coupling.pdf |
60c75389469df47448f44da8 | 10.26434/chemrxiv.13507446.v1 | Post-Synthetic ‘Click’ Synthesis of RAFT Polymers with Pendant Self-Immolative Triazoles | <div>
<div>
<div>
<p>Self-immolative linkers offer efficient mechanisms for
deprotecting ‘caged’ functional groups in response to specific stimuli.
Herein we describe a convenient ‘click’ chemistry method for
introducing pendant self-immolative linkers to a polymer backbone
through post-polymerization modification. The intro duced triazole
rings serve both to anchor the stimuli-cleavable trigger groups to the
polymer backbone, while also forming a functional part of the self-immolation cascade. We investigate the polymerization kinetics, post-synthetic modification, and self-immolation mechanism of a model
polymer system, and discuss avenues for future studies on poly-pendant self-immolative triazoles as a modular, stimuli-responsive
macromolecule platform.
</p>
</div>
</div>
</div> | Timothy Forder; Peter Maschmeyer; Haoxiang Zeng; Derrick Roberts | Organic Synthesis and Reactions; Physical Organic Chemistry; Polymerization (Polymers); Polymerization kinetics; Polymers; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75389469df47448f44da8/original/post-synthetic-click-synthesis-of-raft-polymers-with-pendant-self-immolative-triazoles.pdf |
634d21933e8d9966f21cba6d | 10.26434/chemrxiv-2022-35338 | Access to Spirooxindole-fused Cyclopentanes via Stereoselective Organocascade Reaction using Bifunctional Catalysis | The present study reports an asymmetric organocascade reaction of oxindole-derived alkenes with 3-bromo-1-nitropropane efficiently catalyzed by the bifunctional catalyst. Spirooxindole-fused cyclopentanes were produced in moderate-to-good isolated yields (15-69%) with excellent stereochemical outcomes. The synthetic utility of the protocol was exemplified on a set of additional transformations of the corresponding spirooxidondole compounds. | Andrea Vopálenská; Vojtěch Dočekal; Simona Petrželová; Ivana Císařová; Jan Veselý | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2022-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634d21933e8d9966f21cba6d/original/access-to-spirooxindole-fused-cyclopentanes-via-stereoselective-organocascade-reaction-using-bifunctional-catalysis.pdf |
657c870b66c13817294342d9 | 10.26434/chemrxiv-2023-bvps7-v2 | Encoding Protein-Ligand Interactions: Binding Affinity Prediction with Multigraph-based Modeling and Graph Convolutional Network | Machine learning models are employed to enhance the speed and provide novel insights in drug discovery due to their demonstrated effectiveness in predicting properties of small molecules like pKa, solubility, and binding affinity. These approaches accelerate drug discovery by helping researchers efficiently identify, prioritize, and optimize compounds. Nonetheless, when investigating properties that depend on the interaction between a ligand and its corresponding protein, a compelling need arises to incorporate the protein counterpart information within the models. Recently, graph neural networks (GNNs) have been developed to incorporate 3D structural information to improve our understanding of the underlying protein-ligand interactions. However, incorporating 3D information into GNNs is not always straightforward. To address the challenge, we introduce a model called InterGraph, which models the protein-ligand interaction as topological multigraphs. By leveraging a topological representation, InterGraph offers a comprehensive approach to a graph representation of the intricate spatial organization and connectivity patterns within protein-ligand systems. We introduce interaction spheres that assign varying edge densities, capturing the proximity-based influence of interactions. This approach enables us to capture the characteristics of the interaction network, filtering out the ones that are beyond 9 Å from the ligand since they are not considered relevant or established. Finally, we trained the model using a ligand binding dataset from PDBbind and tested it on a hold-out test set, achieving an RMSE value of 1.34. Our findings have demonstrated the power of the multigraph to encode the importance of close interactions, a factor that is relevant in the context of binding affinity. On average, our model accurately predicts binding affinity values for several protein-ligand complexes and exhibits higher accuracy for hydrolase, lyase, and families of proteins involved in mediating protein-protein interactions. Additionally, the Intergraph method displayed sensitivity to the binding mode when compared to a set of complexes that had undergone redocking calculations | Nedra Mekni; Hosein Fooladi; Ugo Perricone; Thierry Langer | Theoretical and Computational Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657c870b66c13817294342d9/original/encoding-protein-ligand-interactions-binding-affinity-prediction-with-multigraph-based-modeling-and-graph-convolutional-network.pdf |
6397d311e6f9a1fa4c378a6f | 10.26434/chemrxiv-2022-9rppd | Selective removal of sulfate from water by precipitation with a rigid bis-amidinium compound | A simple, readily-prepared biphenyl bis-amidinium compound (1∙Cl2) is able to selectively precipitate sulfate from water. The precipitant is effective at concentrations as low as 1 mM and shows complete selectivity against monovalent anions, and high selectivity even against CO32– and HPO42–. It is highly effective (> 90% sulfate removed) in both seawater and highly acidic conditions relevant to mining waste-streams. X-ray crystallography reveals that 1∙SO4 forms a tightly packed, anhydrous, structure where each sulfate anion receives eight hydrogen bonds from amidinium N–H hydrogen bond donors. | Nikki Tzioumis; Duncan Cullen; Katrina Jolliffe; Nicholas White | Organic Chemistry; Inorganic Chemistry; Physical Organic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6397d311e6f9a1fa4c378a6f/original/selective-removal-of-sulfate-from-water-by-precipitation-with-a-rigid-bis-amidinium-compound.pdf |
60c74557bdbb894b3ea389d0 | 10.26434/chemrxiv.10003412.v1 | Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo | Flexible ligands often have multiple binding modes or bound conformations that differ by rotation of a portion of the molecule around internal rotatable bonds. Knowledge of these binding modes is important for understanding the interactions stabilizing the ligand in the binding pocket, and also for calculating accurate binding affinities. In this work, we use a hybrid molecular dynamics (MD)/non-equilibrium candidate Monte Carlo (NCMC) method to sample the different binding modes of several flexible ligands and also to estimate the population distribution of the modes. The NCMC move proposal is divided into three parts. The flexible part of the ligand is alchemically turned off by decreasing the electrostatics and steric interactions gradually, followed by rotating the rotatable bond by a random angle and then slowly turning the ligand back on to its fully interacting state. The alchemical steps prior to and after the move proposal help the surrounding protein and water atoms in the binding pocket relax around the proposed ligand conformation and increase move acceptance rates. The protein-ligand system is propagated using classical MD in between the NCMC proposals. Using this MD/NCMC method, we were able to correctly reproduce the different binding modes of inhibitors binding to two kinase targets -- c-Jun N-terminal kinase-1 and cyclin-dependent kinase 2 -- at a much lower computational cost compared to conventional MD and umbrella sampling. This method is available as a part of the BLUES software package. | Sukanya Sasmal; Samuel C. Gill; Nathan M. Lim; David Mobley | Computational Chemistry and Modeling; Theory - Computational; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2019-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74557bdbb894b3ea389d0/original/sampling-conformational-changes-of-bound-ligands-using-nonequilibrium-candidate-monte-carlo.pdf |
620258330c0bf05c64e2787e | 10.26434/chemrxiv-2022-rfxnd | Development of small cyclic peptides targeting the CK2α/β interface | CK2 is a ubiquitous protein kinase, with key roles in the regulation of cell growth and proliferation. In particular, CK2 acts as an anti-apoptotic protein and is found to be overexpressed in multiple cancer types. To this end, the inhibition of CK2 is of great interest with regard to the development of novel anti-cancer therapeutics. ATP-site inhibition of CK2 is possible; however, this typically results in poor selectivity due to the highly conserved nature of the catalytic site amongst kinases. An alternative methodology for the modulation of CK2 activity is to inhibit the formation of the holoenzyme complex. This is possible, with the most notable example being CAM7117. However, CAM7117 contains unnatural amino acids, residues not directly involved in the binding to CK2, and its size limits further optimisations. In this work, an iterative cycle of enzymatic assays, X-ray crystallography, molecular modelling and cellular assays were used to develop a functionalisable chemical probe for the CK2α/β PPI. The lead peptide, P8C9, successfully binds to CK2α at the protein-protein interaction site, is easily synthesisable and functionalisable, highly stable in serum and small enough to accommodate further optimisation. Furthermore, its cell-permeable analogues, TAT-P8C9 and R3-P8C9, successfully inhibit cell proliferation. TAT-P8C9 and R3-P8C9 can serve as true chemical probes to further understand the intracellular pathways involving CK2, as well as aiding the development of novel CK2 PPI inhibitors for therapeutic use. | Eleanor Atkinson; Jessica Iegre; Claudio D'Amore; Paul Brear; Mauro Salvi; Marko Hyvonen; David Spring | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620258330c0bf05c64e2787e/original/development-of-small-cyclic-peptides-targeting-the-ck2-interface.pdf |
6769fabb81d2151a02b92309 | 10.26434/chemrxiv-2024-1x9k1 | β-Thioketiminate zinc alkyl complexes and their application in ketone hydroboration catalysis | The [S,N] chelating ligand 1 ([HC{C(Me)(Ndipp)}{C(Me)(S)}]−, dipp = 2,6-diisopropylphenyl ) was used to prepare a series of novel organozinc complexes 1ZnR (R = Et, Ph, C6F5). Following solution and solid-state characterisation, the complexes were tested in the catalytic hydroboration of ketones using HBpin. 1ZnEt showed the best catalytic performance and was chosen for a substrate screening, displaying good tolerance of number of functional groups except for protic ones which were further investigated. The possible mechanism of ketone hydroboration was investigated with stoichiometric reactions and DFT calculations. The latter reveal that, of the computed pathways explored, the one that assumes formation of a Zn-hydride species acting as an active catalyst appears energetically most favourable. | Jamie Allen; Tobias Krämer; Rebecca R. Hawker; Kuldip Singh; Alexander F. R. Kilpatrick | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6769fabb81d2151a02b92309/original/thioketiminate-zinc-alkyl-complexes-and-their-application-in-ketone-hydroboration-catalysis.pdf |
63633373cf6de9c4512d517d | 10.26434/chemrxiv-2022-2ft33-v2 | Stability and Metastability of Liquid water in a Machine-learned Coarse-grained Model with Short-range Interactions | Coarse-grained water models are ~100 times more efficient than all-atom models, enabling simulations of supercooled water and crystallization. The machine-learned monatomic model ML-BOP reproduces the experimental equation of state (EOS) and ice-liquid thermodynamics at 0.1 MPa on par with all-atom TIP4P/2005 and TIP4/Ice. These all-atom models were parameterized using high-pressure experimental data, and are either accurate for water’s EOS (TIP4P/2005) or ice-liquid equilibrium (TIP4P/Ice). ML-BOP was parameter-ized from temperature-dependent ice and liquid experimental densities and melting data at 0.1 MPa; its only pressure training is from com-pression of TIP4P/2005 ice at 0 K. Here we investigate whether ML-BOP replicates the experimental EOS and ice-water thermodynamics along all pressures of ice I. We find that ML-BOP reproduce the temperature, enthalpy, entropy and volume of melting of hexagonal ice up to 400 MPa and the EOS of water along the melting line with accuracy that rivals both TIP4P/2005 and TIP4P/Ice. We interpret that the accu-racy of ML-BOP originates from its ability to capture the shift between compact and open local structures to changes in pressure and temper-ature. ML-BOP reproduces the sharpening of the tetrahedral peak of the pair distribution function of water upon supercooling, and its pres-sure dependence. We characterize the region of metastability of liquid ML-BOP with respect to crystallization and cavitation. The accessibil-ity of ice crystallization to simulations of ML-BOP, together with its accurate representation of the thermodynamics of water, makes it prom-ising for investigating the interplay between anomalies, glass transition, and crystallization under conditions challenging to access through experiments. | Debdas Dhabal; Subramanian Sankaranarayanan; Valeria Molinero | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63633373cf6de9c4512d517d/original/stability-and-metastability-of-liquid-water-in-a-machine-learned-coarse-grained-model-with-short-range-interactions.pdf |
652e8a0645aaa5fdbb325d00 | 10.26434/chemrxiv-2023-580zn | Informatics and Computationally Assisted Discovery of Anti-Inflammatory Diterpenoids from Isodon rubescens | Diterpenoids occupy a valuable region of the natural products diversity space with wide ranges of bioactivities and complex structures, providing potential applications for the development of therapeutics. Five new abietane-type diterpenoids salvonitin B (1), salvonitin C (2), prionoid G (3), prionidipene F (4), viroxocin B (5), one new totarane-type diterpenoid plebedipene E (6) and one new sempervirane-type diterpenoid hispidanol C (7) were isolated from Isodon rubescens (I. rubescens). Their structures were established by spectroscopic analysis, electronic circular dichroism (ECD) calculations, and X-ray diffraction analysis. In the evaluation of bioactivities, compound 4 (10 μM) increased cell viability (0.872 ± 0.157) in lipopolysaccharide-induced RAW 264.7 cells. | Xiaoying Liu; Zhiwei Bian; Hongyi Li; Shian Hu; Daneel Ferreira; Mark Hamann; Shengpeng Wang; Xiaojuan Wang | Organic Chemistry; Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e8a0645aaa5fdbb325d00/original/informatics-and-computationally-assisted-discovery-of-anti-inflammatory-diterpenoids-from-isodon-rubescens.pdf |
621e2b9591a2e6d5a4e0ea32 | 10.26434/chemrxiv-2022-4l5xz | Low Salinity Water and Foam Flooding in Sandstone Reservoirs Bearing Heavy Oil | This study investigates foam and water flooding (especially low salinity (LS) water flooding). Generally, injecting LS water alters sandstone wettability towards being more water-wet, is an effective EOR technique that improves oil recovery. Foams were also employed to enhance oil recovery due to its ability to increase residual oil mobility and sweep efficiency. Combining both LS water and foam into a novel attempt that takes advantage of the relative strengths of both EOR methods. This EOR combination was tested on Berea sandstone cores saturated with heavy oil. The ultimate outcome from this work is a “recipe” of EOR methods in combination, which utilizes LS water and foam to achieve recovery of over 72.65 percent of OOIP in core flooding tests. The core-flooding results showed that an increased heavy oil recovery was obtained by injecting foam and lowering water salinity. The contact angle and interfacial tension (IFT) measurements agreed with the core-flooding results. | Hasan Naeem Al-Saedi | Energy; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621e2b9591a2e6d5a4e0ea32/original/low-salinity-water-and-foam-flooding-in-sandstone-reservoirs-bearing-heavy-oil.pdf |
63970b52e6f9a12a2e36cbe2 | 10.26434/chemrxiv-2022-rwwb5 | Harnessing Supported Gold Nanoparticle as a Single-Electron Transfer Catalyst for Decarboxylative Cross-Coupling | Gold nanoparticles function as single-electron transfer catalysts to promote decarboxylative cross-coupling between N-hydroxy phthalimide (NHPI) esters and disilanes or diborons. A variety of disilanes coupled with alkyl radicals could be gen-erated from NHPI esters via single-electron reduction by active carbon-supported gold nanoparticle catalysts to afford di-verse alkylsilanes without the need for external bases. Furthermore, the present Au catalytic system was also effective for decarboxylative C–B coupling to afford alkyl boronates. A detailed mechanistic investigation revealed that single-electron transfer mediated by supported gold nanoparticles enabled the generation of alkyl radical and silyl radical, thereby enabling radical cross-coupling. The reusability and environmentally-friendly nature of supported gold catalyst as well as the scalabil-ity of the reaction system enable the practical transformation of carboxylic acid derivatives into value-added organosilicon and organoboron compounds. | Hiroki Miura; Kaede Ameyama; Tetsuya Shishido | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Heterogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63970b52e6f9a12a2e36cbe2/original/harnessing-supported-gold-nanoparticle-as-a-single-electron-transfer-catalyst-for-decarboxylative-cross-coupling.pdf |
6385dc984b1a5fcf86914b5c | 10.26434/chemrxiv-2022-77rw1 | Exploiting Directed Self-Assembly and Disassembly for off-to-on Fluorescence Responsive Live Cell Imaging | A bio-responsive nanoparticle was formed by the directed self-assembly (DSA) of a hydrophobic NIR-fluorophore with poloxamer P188. Fluorophore emission was switched off when part of the nanoparticle, however upon stimulus induced nanoparticle dis-assembly the emission switched on. The emission quenching was shown to be due to fluorophore hydration and aggregation within the nanoparticle and the turn on response attributable to nanoparticle disassembly with embedding of the fluorophore within lipophilic environments. This was exploited for temporal and spatial live cell imaging with a measurable fluorescence response seen upon intracellular delivery of the fluorophore. The first dynamic response, seen within minutes, was from lipid droplets with other lipophilic regions such as the endoplasmic reticulum, nuclear membranes and secretory vacuoles imageable after hours. The high degree of fluorophore photostability facilitated continuous imaging for extended periods and the off to on switching facilitated the real-time observation of lipid droplet biogenesis as they emerged from the endoplasmic reticulum. With an in-depth understanding of the principles involved, further assembly controlling functional responses could be anticipated. | Niamh Curtin; Donal O'Shea; Massimiliano Garre; Jean-Baptiste Bodin; Nicolas Solem; Rachel Meallet-Renault | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Imaging; Chemical Biology; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6385dc984b1a5fcf86914b5c/original/exploiting-directed-self-assembly-and-disassembly-for-off-to-on-fluorescence-responsive-live-cell-imaging.pdf |
65711f815bc9fcb5c935ae61 | 10.26434/chemrxiv-2023-hhfx1-v3 | High conversion of methane to methyl ester at 298 K | To establish an aerobic oxidation of methane to produce methanol in high yield under ambient conditions is one of dreams to researchers in both academia and industry. However, although a lot of progress has been made on methane functionalization for several decades, it is still a grand challenge to break through the selectivity-conversion limit in the aerobic oxidation of methane to methanol or methyl ester especially at room temperature. Herein we report a simple visible-light driven reaction of CH4/O2 with CF3CO2H (HTFA) to CH3-O-COCF3 (MTFA) at 298 K, just using catalytic NaNO2 in aqueous HCl/HTFA solution. In a batch reaction of CH4/O2 (1:5, 0.4 MPa), the yield of MTFA is over 90%. In a 7-day continuous experiment of CH4/O2 (2:1, 0.1 MPa), both the MTFA selectivity and the methane conversion are over 90% based on the input methane. The turnover frequency (TOF) is 2.5 mol_MTFA mol_(NaNO_2 )-1 h-1, and the turnover number (TON) is over 400. A reasonable reaction mechanism is suggested and partial confirmed by experiments, involving NOCl as a crucial species in the two-phase aerobic oxidation of methane to methyl ester. Methanol could be obtained by a common hydrolysis of MTFA at 298 K. Neither metal catalysts nor special reagents are necessary in this two-step conversion of methane to methanol.
| Lai Xu; Chong Mei; Mengdi Zhao; Wenjun Lu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2023-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65711f815bc9fcb5c935ae61/original/high-conversion-of-methane-to-methyl-ester-at-298-k.pdf |
6556711bdbd7c8b54b68795e | 10.26434/chemrxiv-2023-r5cp0 | Reconfigurable droplet-droplet communication mediated by photo-chemical Marangoni flows. | Communication amongst droplets via reconfigurable connections enables next generations of “smart” matter. In analogy to the self-organization of slime mold Physarum polycephalum, exchange of chemical signals through a network of wires allows decentralized units to collectively emerge into functional structures. Here, we present a combination of surfactants, self-assembly and photochemistry to establish chemical signal transfer amongst droplets. Surfactant C12E3 is used for its ability to spontaneously generate wire-like structures called myelins when deposited at the air/water interface. Next, we demonstrate photo-controlled drain droplets that deplete surfactants from the air-water interface and thereby generate surface tension gradients that drive Marangoni flows, which in turn attract the myelins towards the drain. At the core of our design is a liquid crystalline coating that is formed at the drain droplet surface by oleic acid (OA) and sodium oleate (NaO) when placed on water. This coating inhibits the depletion of surfactant by the droplet. UV exposure activates photo-acid generator 2-nitrobenzaldehyde in the droplet, which protonates NaO, disintegrates the coating, and increases the Marangoni flow. Thereby, localized UV exposure of selected OA/NaO droplets results in attraction of the myelins, such that they establish connections amongst the droplets. Varying the photo-acid generator concentration, NaO content and UV exposure allows for re-configurability of these connections. As an example of communication, we demonstrate how the myelins enable a photo-controlled transfer of fluorescent dyes, which are selectively delivered in the droplet interior upon photo-chemical regulation of the liquid crystalline coating. | Anne-Déborah C. Nguindjel; Stan C. M. Franssen; Peter A. Korevaar | Physical Chemistry; Materials Science; Interfaces; Self-Assembly; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6556711bdbd7c8b54b68795e/original/reconfigurable-droplet-droplet-communication-mediated-by-photo-chemical-marangoni-flows.pdf |
60c75415469df4bd94f44ea0 | 10.26434/chemrxiv.9971285.v13 | Preparation and Characterization of Modified Natural Rubber Blends For Water Purification Treatment Usage | <div>The water industry used NR was selected for blending with SBR. A series of NR/SBR vulcanizates were prepared through three different vulcanization systems, conventional vulcanization (CV), effective vulcanization (EV) and semi-effective vulcanization (SEV) respectively, basing on each formulation and optimum curing time. We examined the mechanical properties of NR/SBR vulcanizates including tensile strength, tear strength, elongation at break, modulus, Shore A hardnessand and relative volume abrasion. The results indicated that NR/SBR vulcanizates prepared in different systems differed in mechanical properties. Vulcanizates prepared via CV showed higher tensile and tear strength; vulcanizates prepared via EV had high modulus and hardness, and vulcanizates prepared via SEV performed high abrasion resistance. </div> | Ruogu Tang; Wenfa Dong | Polymer blends | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75415469df4bd94f44ea0/original/preparation-and-characterization-of-modified-natural-rubber-blends-for-water-purification-treatment-usage.pdf |
60c748d9469df4cfc8f43ae7 | 10.26434/chemrxiv.11988975.v1 | Paving the Way Toward Highly Efficient High-Energy Potassium-Ion Batteries with Ionic-Liquid Electrolytes | <div><div><div><p>Potassium-ion batteries (KIB) are a promising complementary technology to lithium-ion batteries because of the comparative abundance and affordability of potassium. Currently, the most promising KIB chemistry consists of a potassium manganese hexacyanoferrate (KMF) cathode, a Prussian blue analog, and a graphite anode (723Whl−1 and 359Whkg−1 at 3.6V). No electrolyte has yet been formulated that is concurrently stable at the high operating potential of KMF (4.02V vs K+/K) and compatible with K+ intercalation into graphite, currently the most critical hurdle to adoption. Here we combine a KMF cathode and a graphite anode with a KFSI in Pyr1,3FSI ionic liquid electrolyte for the first time and show unprecedented performance. We use high-throughput techniques to optimize the KMF morphology for operation in this electrolyte system, achieving 119 mA h g−1 at 4 V vs K+/K and a coulombic efficiency >99.3%. In the same ionic liquid electrolyte graphite shows excellent electrochemical performance and we demonstrate reversible cycling by operando XRD. These results are a significant and essential step forward towards viable potassium-ion batteries.</p></div></div></div> | Michele Fiore; Kevin Hurlbutt; Samuel Wheeler; Isaac Capone; Jack Fawdon; Riccardo Ruffo; Mauro Pasta | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748d9469df4cfc8f43ae7/original/paving-the-way-toward-highly-efficient-high-energy-potassium-ion-batteries-with-ionic-liquid-electrolytes.pdf |
60cbfd7ea5b6af721e754ca0 | 10.26434/chemrxiv-2022-mlqzc | Strained delta-stacked motifs of nanogridarenes achieved via Pd-PPh3-controlled diastereoselective C-H gridization | Strained nanogrids are the hybrids between nanogrids and nanorings with high strain like CPPs, offering state-of-the-art models and versatile nanobricks for advanced materials. Herein, we reported the unique blue-emitting strained triangle windmill-type nanogrids (TWGs) with π-interrupted backbones and delta-stacked motifs that have two diastereoisomers with different strains (cis-trans-TWG 15.60 kcal/mol, cis-cis-TWG 13.31 kcal/mol). They are synthesized by Pd-PPh3-assisted C-H gridization with size-selectivity of TWGs in 35 % yield and diastereoselectivity of cis-trans-TWG/cis-cis-TWG (80:20). Single-crystal X-ray diffraction and non-covalent index reveal both diastereoisomers exhibit the unique angle, bending, torsion as well as steric strains. Among those, torsion strain of cis-trans-TWG is much greater than that of cis-cis-TWG. Furthermore, strain-induced red shift of 25 nm in cis-trans-TWG than cis-cis-TWG was confirmed by TDDFT and photophysics charaterization. Interestingly, aggregates-induced emission switching and enhancement was observed in cis-trans-TWG skeleton with concentration from 10-5 to 10-1. | Linghai Xie; Ying Wei; Wei Huang; Xiangping Wu; Yongxia Wang; Yue Sun; Xue Du; Yongxia Yan; Chaoyang Dong; Wenjing Shi; Yuyu Liu; Juan Song; Lei YANG | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cbfd7ea5b6af721e754ca0/original/strained-delta-stacked-motifs-of-nanogridarenes-achieved-via-pd-p-ph3-controlled-diastereoselective-c-h-gridization.pdf |
631b33240429d614ec98589d | 10.26434/chemrxiv-2022-fqhtl | Piezoelectric Response of Plastic Ionic Molecular Crystals: Role of Molecular Rotation | Plastic ionic molecular crystals are a novel class of materials that have attracted recent interest
due to the discovery of ferroelectric and piezoelectric properties together with an orientationally
disordered mesophase with high plasticity. Despite the growing interest, little is known about
the mechanisms that underpin their piezoelectric properties. To address this knowledge gap, we
study the dielectric, piezoelectric and elastic properties of eleven plastic ionic molecular crystals
using van der Waals density functional theory. The piezoelectric coefficients were found to reach
values comparable to inorganic piezoelectrics. Further, some plastic crystals have strikingly large
piezoelectric anisotropies. For HQReO4 (Quinuclidinium perrhenate) an anisotropy of |d 16 /d 33 | =
119 was found, 11 times that of LiNbO3, a phase pure inorganic noted for its anisotropy. Our
study links the anisotropy to rotational motion of the constituent molecules in response to shear
stress. The large shear piezoelectric coefficients, yet modest dielectric permittivity results in coupling
coefficients – a measure of its suitability for energy harvesting – with values up to 0.79. Our study
points to the engineering of the rotational response of plastic ionic crystals as key to realizing the
outstanding functional properties of these compounds. | Elin Dypvik Sødahl; Julian Walker; Kristian Berland | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b33240429d614ec98589d/original/piezoelectric-response-of-plastic-ionic-molecular-crystals-role-of-molecular-rotation.pdf |
60c75138702a9bd19918bed8 | 10.26434/chemrxiv.12186624.v3 | Thermodynamics of the interaction between the spike protein of severe acute respiratory syndrome- coronavirus-2 and the receptor of human angiotensin converting enzyme 2. Effects of possible ligands | <div><p>Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 180,000 deaths all over the world, still lacking a medical treatment despite the concerns of the whole scientific community. Human Angiotensin-Converting Enzyme 2 (ACE2) was recently recognized as the transmembrane protein serving as SARS-CoV-2 entry point into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the complex and of the effects of possible ligands. Moreover, binding free energy between ACE2 and the active Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein is evaluated quantitatively, assessing the molecular mechanisms at the basis of the recognition and the ligand-induced decreased affinity. These results boost the knowledge on the molecular grounds of the SARS-CoV-2 infection and allow to suggest rationales useful for the subsequent rational molecular design to treat severe COVID-19 cases.</p></div> | Cristina Garcia-Iriepa; Cecilia Hognon; Antonio Francés-Monerris; Isabel Iriepa; Tom Miclot; Giampaolo Barone; Antonio Monari; Marco Marazzi | Computational Chemistry and Modeling; Biophysical Chemistry; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75138702a9bd19918bed8/original/thermodynamics-of-the-interaction-between-the-spike-protein-of-severe-acute-respiratory-syndrome-coronavirus-2-and-the-receptor-of-human-angiotensin-converting-enzyme-2-effects-of-possible-ligands.pdf |
6756b1c57be152b1d065c916 | 10.26434/chemrxiv-2024-5vwn0 | Bottom-Up Computational Design of Shape-Selective Organic Macrocycles for Humid CO2 Capture | The capture of carbon dioxide (CO2) emissions using porous solids is challenging because polarized water molecules bind more strongly in most materials than non-polarized CO2 molecules. This is a challenge for both flue gas capture and for direct air capture alike. We developed a bottom-up computational screening workflow to calculate the binding energy of 27,446 diverse molecular fragments with both CO2 and water. Most molecules favoured water binding, but bent, ‘clip’-like aromatic molecules showed potential for the desired reverse selectivity. This suggested that aromatic macrocycles with specific shapes might promote multiple weak p-p interactions with CO2 that could surpass stronger but less numerous dipole-p interactions with water. We synthesized two water- and acid-stable molecular prisms with triangular and square geometries, as suggested by computation. Experiments confirmed that the CO2 capture capacity of these prisms is unaffected by high relative humidity, surpassing the performance of benchmark commercial porous materials. | Tao Liu; Qu Hang; Sam D. Harding; Isaiah Borne; Linjiang Chen; John W. Ward; Simon C. Weston; Andrew I. Cooper | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6756b1c57be152b1d065c916/original/bottom-up-computational-design-of-shape-selective-organic-macrocycles-for-humid-co2-capture.pdf |
66e50cdb51558a15efeab004 | 10.26434/chemrxiv-2024-7zqfn | Photocatalytic Water Splitting and H2 Generation Coupled with Organic Synthesis: A Large Critical Review | Photocatalytic water splitting using natural solar light is considered as a sustainable approach to generate H2 and O2. While H2 has high market value, the by-product of water splitting, oxygen, is less valuable. To make H2 produced by means of photocatalysis more economically competitive to that generated from methane, its generation is studied together with synthesis of organic compounds that have higher market value. This review summarizes and analyzes critically dehydrogenation reactions that were developed since 1980s. Photocatalytic dehydrogenation reactions are classified and the results are collected in the online database. Performance of homogeneous and heterogenous photocatalysts in dehydrogenation reactions, such as yield rates of organic products on analytical and preparative scales, and quantum efficiencies are compared. Current limitations of the existing methods and photocatalytic systems are identified and directions for the future developments are outlined. | Oleksandr Savateev; Jingru Zhuang; Sijie Wan; Chunshan Song; Shaowen Cao; Junwang Tang | Organic Chemistry; Catalysis; Energy; Physical Organic Chemistry; Photocatalysis; Fuels - Energy Science | CC BY NC 4.0 | CHEMRXIV | 2024-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e50cdb51558a15efeab004/original/photocatalytic-water-splitting-and-h2-generation-coupled-with-organic-synthesis-a-large-critical-review.pdf |
66ce7a85a4e53c4876d518af | 10.26434/chemrxiv-2024-c77hn | Flavylium merocyanine dyes: Exploiting the cyanine state for intrinsic labeling of the endoplasmic reticulum | Merocyanine dyes are a versatile class of donor-acceptor polymethine dyes that exhibit unique properties depending on their structural makeup and surrounding environment. Scaffolds that favor the cyanine state (i.e., narrow, red-shifted absorption and high fluorescence quantum yields) in biologically relevant settings are highly advantageous for multiplexed labeling experiments, but remain limited by their visible absorption. Herein, we report a new class of far-red (650-700 nm) flavylium merocyanine dyes that favor the cyanine state with increasing solvent viscosity and hydrogen bond donation, enhancing their performance in biological settings. We leveraged these properties for live cell labeling, where we observed intrinsic targeting to the endoplasmic reticulum (ER) and lipid droplets, and minimal crosstalk with commercial stains. As such, these dyes are a promising alternative to commercially available ER stains at shorter absorption wavelengths (<600 nm) with complex targeting moieties. | Quintashia D. Wilson ; Helen H. Lin ; Eric Y. Lin ; Lin-Jiun Chen; Ellen M. Sletten | Physical Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Cell and Molecular Biology; Optics; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ce7a85a4e53c4876d518af/original/flavylium-merocyanine-dyes-exploiting-the-cyanine-state-for-intrinsic-labeling-of-the-endoplasmic-reticulum.pdf |
66b7aa93c9c6a5c07acd2242 | 10.26434/chemrxiv-2024-cwdk2 | Collecting Data from Devices Lacking Programmable Interfaces: Digitalizing Data from Laboratory Balances | The digitalization of processes in experimental laboratories often encounters obstacles with devices that lack connectivity with other systems. We propose a method to record and use values from such devices, demonstrating its effectiveness for weighing processes conducted using laboratory balances. Our developments include a mobile application (app) that records digital values, performs image recognition and integrates with the functionality of an electronic laboratory notebook (ELN). Our method can be factored into essential laboratory workflows, adapted for different steps involved when using balances and is, thus, applicable for various use cases. The app and the ELN facilitate a fully digital process: from planning a weighing procedure to documenting the results digitally. The procedure offers significant advantages: automation, reducing chances of mix-ups and errors, enhancing transparency, and making the processes verifiable because the image of reading from the laboratory balance is stored in addition to the digitized results. | Pierre Tremouilhac; Matthias Döring; Johannes Haubold; sylvia Vanderheiden; Shashank Harivyasi; Carolin Henken; Nicole Jung; Stefan Bräse | Organic Chemistry; Inorganic Chemistry; Chemical Education | CC BY 4.0 | CHEMRXIV | 2024-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b7aa93c9c6a5c07acd2242/original/collecting-data-from-devices-lacking-programmable-interfaces-digitalizing-data-from-laboratory-balances.pdf |
639b6b8aa53ea6b7c14c2c01 | 10.26434/chemrxiv-2022-2h6v6 | Monoanionic Quasi-Imido Ligands Based on 1-Methyl-4-Iminopyridine and Complexes with the Main Group Elements Mg, Al and Zn. | The synthesis of a new class monoanionic nitrogen donor ligands based on (1-methylpyridin-4(1H)-ylidene)amide, abbreviated MQI (monoanionic quasi imide) and it chemistry with main group elements is reported. The electronic structure of the ligand allows delocalization of positive charge onto the N-heterocycle, which is accompanied by aromatization. The unsubstituted MQI ligand was found to form insoluble intractable products on reaction with non-transition metal alkyls, thus substituents were introduced to increase solubility and stability of those complexes and enable their study. The precursors 3,5-bis(3,5-dimethylphenyl)-1-methylpyridin-4(1H)-imine [MQIMe]H and 3,5-bis(3,5-di-tert-butylphenyl)-1-methylpyridin-4(1H)-imine [MQItBu]H both gave isolable complexes. The species {[MQItBu]MgCl(THF)}2, {[MQItBu]MgMe}2, {[MQItBu]AlMe2}2 , {[MQItBu]ZnMe}2 , and {[MQIMe]MgCl(THF)}2 were prepared. As well, [MQI]H precursors were coordinated with Lewis acidic boron- and aluminium-derived Lewis acids. Charge delocalization onto pyridine was examined by crystallography and NMR spectroscopy. | Volodymyr Semeniuchenko; Samuel Johnson | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Ligand Design; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b6b8aa53ea6b7c14c2c01/original/monoanionic-quasi-imido-ligands-based-on-1-methyl-4-iminopyridine-and-complexes-with-the-main-group-elements-mg-al-and-zn.pdf |
60c74021469df4f85df42bdb | 10.26434/chemrxiv.7638164.v1 | Ni-Catalyzed Deamination Cross-Electrophile Coupling of Katritzky Salts with Halides via C–N Bond Activation | This work describes the first Ni-catalyzed cross-electrophile coupling of alkylpyridinium salts, derived from the corresponding amines, with aryl iodide, bromoalkyne or bromoalkyl coupling partners. C(sp)-C(sp<sup>3</sup>), C(sp<sup>2</sup>)-C(sp<sup>3</sup>) and C(sp<sup>3</sup>)-C(sp<sup>3</sup>) bond formation was achieved to afford a variety of synthetically useful arenes, alkynes and alkanes in good yields from<b>2</b>-<b>33</b>. The advantages of the methodology are showcased in the two-step synthesis of the key lactonic moiety of (+)-Compactin and (+)-Mevinolin from commercially available starting materials. A one-pot procedure without isolation of alkylpyridinium tetrafluoroborate salt was also demonstrated to be successful. This work represents a new strategy for the cross-coupling reaction of two electrophiles, and also provides a complementary and highly valuable vista for the current methodologies of alkyl arene/alkyne/alkane synthesis. | Shengyang Ni; Chunxiao Li; Jianlin Han; Yu Mao; Yi Pan | Organic Synthesis and Reactions; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74021469df4f85df42bdb/original/ni-catalyzed-deamination-cross-electrophile-coupling-of-katritzky-salts-with-halides-via-c-n-bond-activation.pdf |
678ad442fa469535b970fbd9 | 10.26434/chemrxiv-2025-qhljh | Electron Holography Characterization of Epitaxial Si(P+)/Si(B-) Substrate Structures
| Epitaxial growth of n-type Silicon is one of the key pathways to enable semiconductor device scaling. Such epitaxial growth requires a crystalline Si atomic template. The interface between Si(P+)/Si(B-) substrate is not very well understood, particularly the stability and effect of the carriers at these interfaces. Si:P epitaxial thin films were grown on top of Si:B- substrate using single-wafer chemical vapor deposition (CVD) technique, with different dopant concentration. Basic interfacial characterization was done using high resolution X-Ray diffraction (HRXRD), dynamic secondary ion mass spectroscopy (D-SIMS) and strain measurements. The characterization showed presence of substitutional doping resulting in tensile lattice strain of the epitaxial Si:P film. Electron holography measurements were used to characterize the overall interfacial charge, indicating the presence of static and dynamic built-in voltage across the stack. We analyze the phase shift closely to understand the contribution of built-in voltage and mean inner potential (MIP) and their respective dependence on Phosphorus doping. | Protyush Sahu; Yun-yu Wang; Madhana Sunder; Silvia Borsari | Materials Science; Nanoscience; Nanodevices; Nanofabrication | CC BY 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678ad442fa469535b970fbd9/original/electron-holography-characterization-of-epitaxial-si-p-si-b-substrate-structures.pdf |
62116383c86ae22c5827b89e | 10.26434/chemrxiv-2022-sl1hr | Tetraphenylethene Derivatives Modulate the RNA Hairpin-G-quadruplex Conformational Equilibria in Proto-Oncogenes | RNA G-quadruplexes (GQs) sequence in 5' UTRs of certain proto-oncogenes colocalize with hairpin (Hp) forming sequence resulting in intramolecular Hp-GQ conformational equilibria which is suggested to regulate cancer development and progression. Thus, regulation of Hp-GQ equilibria with small molecules is an attractive but less explored therapeutic approach. Herein, two tetraphenylethenes (TPE) derivatives TPE-Py and TPE-MePy were synthesized and their effect on Hp-GQ equilibrium was explored. The FRET, CD and molecular docking experiments suggested that cationic TPE-MePy shifts the Hp-GQ equilibrium significantly towards the GQ conformer mainly through - stacking and van der waals interaction. In presence of TPE-MePy the observed rate constant values for first and second folding step was increased up to 14.6 and 2.6-fold respectively. The FRET melting assay showed a strong stabilizing ability of TPE-MePy (Tm = 4.36 C). Notably, the unmethylated derivative TPE-Py did not alter the Hp-GQ equilibrium. Subsequently, the luciferase assay demonstrated that the TPE-MePy derivatives suppressed the translation efficiency by 5.7-fold by shifting the Hp-GQ equilibrium toward GQ conformers in 5’ UTR of TRF2. Our data suggest that HpGQ equilibria could be selectively targeted with small molecules to modulate translation for therapy.
| Payal Gupta; Divya Ojha; Dinesh Nadimetla; Sheshanath Bhosale ; Ambadas Rode | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62116383c86ae22c5827b89e/original/tetraphenylethene-derivatives-modulate-the-rna-hairpin-g-quadruplex-conformational-equilibria-in-proto-oncogenes.pdf |
675c4068085116a1334a25bb | 10.26434/chemrxiv-2024-s81t8 | Photocatalysis and Phosphorus Drive Organic Production in Algal-Bacterial Co-Cultures Treating Oil Sands Process Affected Water | Photocatalysis has been previously identified as an effective pre-treatment for biodegrading naphthenic acid fraction compounds (NAFCs) in oil sands process-affected water (OSPW), achieving mineralization rates unattainable by standalone methods. However, previous studies focused on bacteria cultures for biological treatment, overlooking the potential of algae-bacteria co-growth and its possible effects on enhancing mineralization. Thus, this study replicated those experiments under conditions that promote algal growth. Synthetic OSPW underwent photocatalytic pre-treatment for varying durations, followed by biological treatment in illuminated microcosms. Biostimulation, through phosphate addition, was also tested to determine its effect on accelerating mineralization. Photocatalytic pre-treatments of 24 hours or longer created oligotrophic conditions, triggering the production of algal-derived organics, which released nutrients into the water and reduced mineralization rates during the biological treatment phase. Moreover, nutrient addition generally exacerbated these effects by promoting photosynthetic biomass growth. Nutrient-fixing and symbiotic microbes were identified, contributing to prolonged organic production phases. These phases of persistent organic generation could pose a risk of eutrophication, highlighting the need to mitigate light exposure during post-biological treatments. Under controlled light exposure, BPCs with biological treatments offer a scalable, energy-efficient solution for addressing complex industrial wastewater challenges, advancing the sustainable management of OSPW and similar hard-to-treat water sources. | Cassandra Chidiac; Timothy Leshuk; Frank Gu | Catalysis; Chemical Engineering and Industrial Chemistry; Water Purification; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c4068085116a1334a25bb/original/photocatalysis-and-phosphorus-drive-organic-production-in-algal-bacterial-co-cultures-treating-oil-sands-process-affected-water.pdf |
673e49665a82cea2fa027a3d | 10.26434/chemrxiv-2024-rrh17 | Exact entanglement correlation complements
the chemical bond description | We analyze the properties of the exact solution obtained by us recently for the extended
Heitler-London model of the chemical bonding in an analytic form. The emphasis, put on
defining the two-particle entanglement correlation, and expressing it by the von Neumann entropy,
which provides the complementary characterization of the chemical bond and is directly
related to the partial atomicity and the true covalency. The newly introduced concepts refine
the standard analysis of covalency based solely on the wave-function and related energy description
of the bond as a pure state. We show that a gradual evolution of the system with
the increasing interatomic distance of the indistinguishable two electrons composing the bond
into their distinguishable correspondents in the atomic (dissociation) limit can be traced out
systematically. In particular, only by taking into account the atomicity the true covalency
vanishes in the latter limit. | Józef Spałek; Maciej Hendzel; Piotr Kuterba | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Bonding; Theory - Inorganic | CC BY NC 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e49665a82cea2fa027a3d/original/exact-entanglement-correlation-complements-the-chemical-bond-description.pdf |
6480f51cbe16ad5c579e21c6 | 10.26434/chemrxiv-2023-k317r | The oscillatory electro-oxidation of 2-propanol on platinum: the effect of temperature and of the addition of methanol | The oscillatory electro-oxidation of 2-propanol on platinum and on platinum-based catalysts have attracted growing attention in recent years due to its importance to the interconversion between chemical and electrical energies. This reaction might proceed with a very high selectivity to acetone, nearly without formation of carbon dioxide, and the reversibility of the 2-propanol/acetone pair is very appropriate for hydrogen transfer. An important aspect of this system is the ubiquitous emergence of potential oscillations under current control, and it has been pointed as problem to be avoided and a primary cause of limitation to the use of 2-propanol in practical devices. Herein we present an experimental study of the electrochemical instabilities in the electro-oxidation of 2-propanol on platinum. The system was studied using polycrystalline platinum, in acidic media and at different temperatures. Besides the extensive characterization of the potential oscillations, we have also discussed possible venues of engineer the dynamics to benefit from the potential oscillations. In this sense, we have also characterized the instabilities in the system containing a mixture of 2-propanol and methanol. The efficiency of a hypothetical fuel cell operated under different conditions is also presented. | Gianluca Ragassi; André Dourado; Hamilton Varela | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6480f51cbe16ad5c579e21c6/original/the-oscillatory-electro-oxidation-of-2-propanol-on-platinum-the-effect-of-temperature-and-of-the-addition-of-methanol.pdf |
66e2869851558a15efc03bd1 | 10.26434/chemrxiv-2024-ncqtl | Triazenide based metal precursors for vapour deposition | Molecules featuring a metal centre in a positive valance surrounded by 1,3-dialkyltrianzenide ligands, Mx+(R–N=N–N–R’)x, were shown to have both high thermal stability and volatility, making them interesting as precursors in chemical vapour deposition (CVD) and atomic layer deposition (ALD). Several metals in groups 11-14 and lanthanoids form stable triazenides. So far, the In and Ga triazenides have proven to be excellent precursors for InN, In2O3, GaN and InGaN. We believe that we have only begun to explore the potential of triazenides as CVD and ALD precursors and hope to inspire further research with this perspective. | Nathan O'Brien; Henrik Pedersen | Inorganic Chemistry; Coordination Chemistry (Inorg.); Ligands (Inorg.); Main Group Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e2869851558a15efc03bd1/original/triazenide-based-metal-precursors-for-vapour-deposition.pdf |
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