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60c7426b0f50db4981395cd6 | 10.26434/chemrxiv.8279432.v1 | Catalytic Oxidative Benzylation of Amines Enabled by Direct Ionic Decarboxylation | We report a method for the decarboxylative alkylation of amines via the direct generation of a benzylic nucleophiles. | Duanyang Kong; Patrick Moon; Odey Bsharat; Rylan Lundgren | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426b0f50db4981395cd6/original/catalytic-oxidative-benzylation-of-amines-enabled-by-direct-ionic-decarboxylation.pdf |
67d0668881d2151a0202d424 | 10.26434/chemrxiv-2025-1g7jl | ArchOnML; an open-source python package for machine-learning assisted molecular design | The python package ArchOnML ("Archive-On-Machine-Learning") is introduced, which can perform virtual screening projects covering up to millions of structural derivatives through the use of Kernel Ridge Regression models. It supports the full workflow of setting up calculation inputs for external quantum chemistry program packages and post-processesing their outputs for training and predictions. An example screening project for over 1.3 million anthraquinone derivatives is presented, where excitation energies and oscillator strengths of the first two excited singlet and triplet states are predicted from descriptors based on semi-empirical quantum chemistry results. Compared to a non-ML calculation protocol, ArchOnML achieves a speed-up factor of over 400 with mean absolute errors for excitation energies of 0.1 eV. Due to ArchOnML's modular application programming interface, new descriptors, models and interfaces to other external quantum chemistry programs can be added in a straightforward way. | Fabian Weber | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d0668881d2151a0202d424/original/arch-on-ml-an-open-source-python-package-for-machine-learning-assisted-molecular-design.pdf |
611e3d7530688d861494c222 | 10.26434/chemrxiv-2021-bf301 | Chiral Motifs in Interpenetrated Metal-Organic Frameworks Formed from Achiral Tetrahedral Ligands | We demonstrate the formation of highly interpenetrated frameworks. An interesting observation is the presence of very large adamantane-shaped cages in a single network, making these crystals new entries in the collection of diamondoid-type metal-organic frameworks (MOFs). The frameworks were constructed by assembling tetrahedral pyridine ligands and copper dichloride. Currently, the networks’ degree of interpenetration is among the highest reported and increases when the size of the ligand is increased. Usually, highly interpenetrated frameworks have low surface contact areas. In contrast, in our systems, the voids take up to 63% of the unit cell volume. The frameworks are chiral and formed from achiral components. The chirality is manifested by the coordination chemistry frameworks around the metal center, the structure of the helicoidal channels and the motifs of the individual networks. Channels with both chiralities are present within the unit cells. This phenomenon shapes the walls of the channels, which are composed of 10, 16, or 32 chains correlated to the degree of interpenetration 10-, 16- and 32-fold. By changing the distance between the center of the ligand and the coordination moieties, we succeeded to tune the diameter of the channels. Relatively large channels were formed, having diameters up to 31.0 Å × 14.8 Å. | Qiang Wen; Maria Chiara di Gregorio; Linda J. W. Shimon; Eugeny V. Alexandrov; Davide M. Proserpio; Milko E. van der Boom; Michal Lahav | Materials Science; Inorganic Chemistry; Coordination Chemistry (Inorg.); Supramolecular Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611e3d7530688d861494c222/original/chiral-motifs-in-interpenetrated-metal-organic-frameworks-formed-from-achiral-tetrahedral-ligands.pdf |
64c183c3658ec5f7e5399290 | 10.26434/chemrxiv-2023-9jkbp | Intramolecular Asymmetric Cyclopropanation Using Air Stable Alkylboronic Esters | The preparation of polysubstituted bicyclo[3.1.0]hexanes starting from air stable substituted pent-4-en-1-ylboronic esters has been investigated. The method involves a Matteson homologation with LiCHCl2 leading to intermediates 1-chlorohex-5-en-1-yl boronic esters. The intramolecular cyclopropanation step was performed in a one-pot process. With pinacol boronic esters, the cyclopropanation step was either performed thermally at 140 °C or at 70 °C after in situ transesterification to a catechol boronic ester. This last approach is suitable for the preparation of enantioenriched bicyclo[3.1.0]hexanes using either chiral auxiliary control or by taking advantage of the sparteine controlled enantioselective boroalkylation of alcohols. | Luca Vedani; Manuel Gnägi-Lux; Fabrice Dénès; Philippe Renaud | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c183c3658ec5f7e5399290/original/intramolecular-asymmetric-cyclopropanation-using-air-stable-alkylboronic-esters.pdf |
6348466e4a18765f31e29be4 | 10.26434/chemrxiv-2022-03q4x-v2 | Shearing Friction Behaviour of Synthetic Polymers Compared to a Functionalized Polysaccharide on Biomimetic Surfaces: Models for the Prediction of Performance of Eco-designed Formulations | The substitution of natural, bio-based and/or biodegradable polymers for those of petrochemical origin in consumer formulations has become an active area of research and development as the sourcing and destiny of material components becomes a more critical factor in product design. These polymers often differ from their petroleum-based counterparts in topology, raw material composition and solution behaviour. Effective and efficient reformulation that maintains comparable performance to existing products requires a deep understanding of the differences in behaviour between polymers.
In this work, we simulate the tribological behaviour of three topologically distinct polymers in simplex solutions in presence of surfactants and in contact with hair-biomimetic patterned surfaces: a strongly charged polyelectrolyte poly-(diallyldimethylammonium chloride) (Merquat 100TM, Polyquaternium 6), a zwitterionic copolymer of acrylic acid, 3-trimethylammonium propyl methacrylamide chloride and acrylamide, (Merquat 2003TM, Polyquaternium 53) and one generic functionalized polysaccharide. Merquat 100TM is a relatively simple linear cationic homopolymer. Merquat 2003TM is a pseudorandom block copolymer with a hydrophilic linear block and a brush-like cationic block. The chosen polysaccharide is a highly branched, amphiphilic and quanternized polymer with a cellulose-like backbone. Such topological differences are expected to affect rheological properties, as well as their direct interaction with structured biological substrates.
Using a refined Martini-style coarse-grained model we describe the polymer-dependent differences in aggregation behaviour as well as selective interactions with the surface depending on the structure. Finally, we introduce a formalism to characterize the response of the solution to shear as an initial study on lubrication properties, that define the sensorial performace of these systems in cosmetics (i.e. , manageability, touch, etc.).
The tools and techniques presented in this work illustrate the strength of molecular simulation in eco-design of formulation as a complement to experiment. These efforts help advance our understanding of how we can relate complex atomic-scale solution behaviour to relevant macroscopic properties. We expect these techniques to play an increasingly important role in advancing strategies for green polymer formulation design by providing an understanding for how new polymers could reach and even exceed the level of performance of existing polymers.
| Benjamin J. Coscia; John C. Shelley; Andrea R. Browning; Jeffrey M. Sanders; Robin Chaudret; Roger Rozot; Fabien Léonforte; Mathew D. Halls; Gustavo S. Luengo | Theoretical and Computational Chemistry; Materials Science; Polymer Science; Aggregates and Assemblies; Surfactants; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6348466e4a18765f31e29be4/original/shearing-friction-behaviour-of-synthetic-polymers-compared-to-a-functionalized-polysaccharide-on-biomimetic-surfaces-models-for-the-prediction-of-performance-of-eco-designed-formulations.pdf |
64a56c776e1c4c986bdab7dc | 10.26434/chemrxiv-2023-9l9dl | The multivalency game ruling the biology of immunity | Macrophages are important cells in our immune system that help maintain our tissues' health and protect us from harmful pathogens. This article explores the complexity of macrophage function, including their developmental origin and dependence on different tissues, both in normal and disease conditions. Understanding the differences between macrophages in various tissues and their unique activation states is crucial for developing effective targeted therapies, especially in diseases like tuberculosis. One approach is to use nanoparticles with ligands that can specifically target certain macrophage populations based on their receptor profiles. However, designing these nanoparticles requires overcoming challenges such as the polymer coating on the nanoparticle and the cell glycocalyx, which can impede their association. | Lara Victoria Aiassa; Giuseppe Battaglia; Loris Rizzello | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2023-07-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a56c776e1c4c986bdab7dc/original/the-multivalency-game-ruling-the-biology-of-immunity.pdf |
61c413f91e13eb703a02b5cb | 10.26434/chemrxiv-2021-p9vvs | An Easily Synthesized Covalent Nanocage that Hosts Fullerenes in Multiple Charge States and Selectively Binds C70 | Discrete nanocages provide a way to solubilize, separate, and tune the properties of molecular guests, including fullerenes and other aromatics. However, few such nanocages can be synthesized efficiently from inexpensive starting materials, limiting their practical utility. To address this limitation, we developed a new pyridinium-linked cofacial porphyrin nanocage (Cage4+) that can be prepared efficiently on a gram scale. NMR studies in CD3CN reveal that Cage4+ binds C60 and C70 with association constants >108 M-1 and complete selectivity for extracting C70 from mixtures of both fullerenes. The solubility of Cage4+ in polar solvents enabled electrochemical characterization of the host-guest complexes C60@Cage4+ and C70@Cage4+, finding that the redox properties of the encapsulated fullerenes are minimally affected despite the positive charge of the host. Complexes of the −1 and −2 charge states of the fullerenes bound in Cage4+ were subsequently characterized by UV-vis-NIR and NMR spectroscopies. The relatively easy preparation of Cage4+ and its ability to bind fullerenes without substantially affecting their redox properties suggests that C60@Cage4+ and C70@Cage4+ may be directly useful as solubilized fullerene derivatives. | Daniel A. Rothschild; Aaron Tran; William P. Kopcha; Jianyuan Zhang; Mark C. Lipke | Organic Chemistry; Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c413f91e13eb703a02b5cb/original/an-easily-synthesized-covalent-nanocage-that-hosts-fullerenes-in-multiple-charge-states-and-selectively-binds-c70.pdf |
67b6866e81d2151a0238c54c | 10.26434/chemrxiv-2024-tkvrh-v2 | FEP-SPell-ABFE: An Open-Source Automated
Alchemical Absolute Binding Free Energy
Calculation Workflow for Drug Discovery | The binding affinity between a drug molecule and its target, measured by absolute binding free energy (ABFE), is a crucial factor in the lead discovery phase of drug development. Recent research has highlighted the potential of in silico ABFE predictions to directly aid drug development by allowing for the ranking and prioritization of promising candidates. This paper introduces an open-source Python workflow called FEP-SPell-ABFE, designed to automate ABFE calculations with minimal user involvement. The workflow requires only three key inputs: a receptor protein structure in PDB format, candidate ligands in SDF format, and a configuration file (config.yaml) that governs both workflow and molecular dynamics simulation parameters. It produces a ranked list of ligands along with their binding free energies in Comma-Separated Values (CSV) format. The workflow leverages SLURM (Simple Linux Utility for Resource Management) for automating task execution and resource allocation across modules. A usage example and several benchmark systems for validation are provided. The FEP-SPell-ABFE workflow, along with a practical example, is publicly accessible on GitHub at https://github.com/freeenergylab/FEP-SPell-ABFE, distributed under the MIT License. | Pengfei Li; Tingting Pu; Ye Mei | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b6866e81d2151a0238c54c/original/fep-s-pell-abfe-an-open-source-automated-alchemical-absolute-binding-free-energy-calculation-workflow-for-drug-discovery.pdf |
634097c8ba8a6d31ef6cac2b | 10.26434/chemrxiv-2022-hdx1f | Reactive Chlorine Capture by Dichlorination of Alkene Linkers in Metal–Organic Frameworks | Chlorine (Cl2) is a toxic and corrosive gas that is both an essential reagent in industry and a potent chemical warfare agent. Materials that can strongly bind Cl2 at low pressures are essential for industrial and civilian personal protective equipment (PPE). Herein, we report the first examples of irreversible Cl2 capture via the dichlorination of alkene linkages in Zr-based metal–organic frameworks (MOFs). Frameworks constructed from fumarate (Zr-fum) and stilbene (Zr-stilbene) linkers retain long-range order and accessible porosity after alkene dichlorination. In addition, energy-dispersive X-ray spectroscopy (EDS) reveals an even distribution of Cl throughout both materials after Cl2 capture. Cl2 uptake experiments reveal high irreversible uptake of Cl2 (>10 wt %) at low partial pressures (<100 mbar), particularly in Zr-fum. In contrast, traditional porous carbons display mostly reversible Cl2 capture, representing a continued risk to users after exposure. Overall, our results support that alkene dichlorination represents a new pathway for reactive Cl2 capture, opening up new opportunities for binding this gas irreversibly in PPE. | Tyler Azbell; Ruth Mandel; Jung-Hoon Lee; Phillip Milner | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634097c8ba8a6d31ef6cac2b/original/reactive-chlorine-capture-by-dichlorination-of-alkene-linkers-in-metal-organic-frameworks.pdf |
60fdd7717bf0c90f7260b831 | 10.26434/chemrxiv-2021-cgg9j-v2 | Wetting Behavior of Zirconia Nanotubes | In this work, we investigate the wettability of ZrO2
nanotubes (ZrNT) synthesized via electrochemical
anodization of Zirconium. The ZrNT surface shows superhydrophilic behavior while the octadecylphosphonic acid
(C18H37PO(OH)2) modified surface shows superhydrophobic behavior. We demonstrate that the wetting
properties are independent of ZrO2 nanotube geometry
and length.<br /> | Swathi Naidu Vakamulla Raghu; Manuela Sonja Killian | Materials Science; Nanoscience; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60fdd7717bf0c90f7260b831/original/wetting-behavior-of-zirconia-nanotubes.pdf |
67d30c8b6dde43c908aab9b3 | 10.26434/chemrxiv-2025-38nfp | Adding the AMBER 14SB force field to the stochastic titration CpHMD method | Incorporating pH into Molecular Dynamics simulations is vital for accurately capturing the fully coupled conformational, energetic, and protonation landscape of many systems. The constant-pH molecular dynamics (CpHMD) methodologies represent state-of-the-art approaches to achieve this, with stochastic titration CpHMD (st-CpHMD) currently being one of the most well-developed and validated methods. St-CpHMD is already compatible with both the GROMOS 54A7 and CHARMM 36m force fields, and we extend it here to support the AMBER 14SB force field available in the GROMACS software package. We introduce and validate a minor modification to the official atomic partial charges of ff14SB (to achieve neutralization of the main chain) to render them compatible with st-CpHMD, and we benchmark the final implementation using lysozyme and Staphylococcal nuclease proteins. Although the root-mean-square error (RMSE) values of the predictions for pKa versus experimental data align closely with those obtained using the other supported force fields, we also identified several challenging cases where the method requires further improvement. AMBER 14SB simulations showed a lower computational cost compared to CHARMM 36m, despite being slightly higher than the GROMOS 54A7 simulations. Our findings also indicate that to further enhance computational speed, future efforts should concentrate on accelerating the PB/MC step. With this extension, we have developed the first CpHMD method implementation compatible with the three most widely used protein force fields, enabling, for the first time, a direct performance comparison among them. | João G. N. Sequeira; Adrian E. Roitberg; Miguel Machuqueiro | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d30c8b6dde43c908aab9b3/original/adding-the-amber-14sb-force-field-to-the-stochastic-titration-cp-hmd-method.pdf |
66e043bc51558a15ef97b281 | 10.26434/chemrxiv-2023-pcv6m-v2 | A radical-polar crossover approach to complex nitrogen heterocycles via the triplet state | The transition from radical to ionic reactivity is a key design feature of many photochemical reactions, enabling complex transformations not possible under either mechanistic regime alone. Ground state alkenes are common substrates in existing methods of this type, serving as radical acceptors to generate open-shell intermediates from which the radical–polar crossover (RPC) event is oxidatively or reductively triggered by a photocatalyst. Here, we describe an alternative RPC mechanism proceeding via an alkene triplet diradical. In this transformation, an iodine radical liberated during a homolytic aromatic substitution step functions as a single electron oxidant to generate an iminium electrophile that can be intercepted en route to complex natural product-like amines. An enantioselective variant of the reaction, enabled by an oxidatively installed sulfinyl leaving group, points to the generality of this underdeveloped pattern of diradical reactivity, paving the way to other triplet-state reactions that incorporate both one and two electron bond-forming processes. | Zachariah Lockhart; Mihai Popescu; Juan Alegre-Requena; Jay Ahuja; Robert Paton; Martin Smith; Shaokang Chai | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e043bc51558a15ef97b281/original/a-radical-polar-crossover-approach-to-complex-nitrogen-heterocycles-via-the-triplet-state.pdf |
651e0c2245aaa5fdbb51627c | 10.26434/chemrxiv-2023-xljnc | The decisive role of CuI-framework O binding in oxidation half cycle of selective catalytic reduction | Cu-exchanged zeolite is an efficient catalyst to remove harmful nitrogen oxides from diesel exhaust gas through the selective catalytic reduction (SCR) reaction. The SCR performance is structure dependent, in which a Cu with one adjacent framework Al (1AlCu) has lower activation energy in oxidative half-cycle than Cu with two adjacent framework Al (2AlCu). Using a combination of operando X-ray absorption spectroscopy, valence to core - X-ray emission spectroscopy and density functional theory calculations, here we showed that 1AlCu proceeds with nitrate mechanism, in which side-on coordination of O2 at a CuI(NH3)xOfw (fw = framework) is the rate-limiting step in the oxidation half-cycle. As a result, the CuI(NH3)xOfw at 1AlCu can easily yield a transient CuIINOx intermediate upon breaking of Cu-Ofw after interaction with NO. In the meantime, 2AlCu has high barriers for Cu-Ofw bond breaking and proceeds with dimer mechanism. Our results show the coexisting of both dimer and nitrate mechanism, in particular at high Cu loadings, in which controlling the strength of the Cu-Ofw coordination is key for the O-O split in the nitrate pathway. | Yiyun Liu; Jasper Berry-Gair; Zhipeng Wang ; Liqun Kang; Bolun Wang; Xuze Guan; Sushila Marlow; Junrun Feng; Loredana Mantarosie; David Thompsett; Misbah Sarwar; Maria Pia Ruggeri; Shusaku hayama; Furio Cora; Feng Ryan Wang | Inorganic Chemistry; Catalysis; Bonding; Spectroscopy (Inorg.); Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651e0c2245aaa5fdbb51627c/original/the-decisive-role-of-cu-i-framework-o-binding-in-oxidation-half-cycle-of-selective-catalytic-reduction.pdf |
65cc974166c13817299f3de8 | 10.26434/chemrxiv-2024-hw4rb | Formation of Multi-Compartment Condensates through Aging of Protein-RNA Condensates | Cells can dynamically organize reactions through the formation of biomolecular condensates. These viscoelastic networks exhibit complex material properties and mesoscale architectures, including the ability to form multi-phase assemblies. Understanding the molecular mechanisms underlying the formation of compartmentalized condensates has implications not only in biology but also in the development of advanced materials. In this study, we demonstrate that the aging of heterotypic protein-RNA condensates can lead to the formation of double-emulsion structures. By combining fluorescence-based techniques with theoretical modeling, we show that, as the condensates age, the strengthening of homotypic protein-protein interactions induces the release of RNA molecules from the dense phase. Notably, when condensates exceed a critical size, the slow diffusion of RNA molecules triggers the nucleation of a dilute phase within the protein-rich condensates, ultimately resulting in the formation of double-emulsion structures. These findings illustrate a new mechanism for a formation of dynamic multi-compartment condensates. | Katarzyna Makasewicz; Timo Schneider; Prerit Mathur; Stavros Stavrakis; Andrew deMello; Paolo Arosio | Physical Chemistry; Chemical Engineering and Industrial Chemistry; Physical and Chemical Properties; Self-Assembly; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cc974166c13817299f3de8/original/formation-of-multi-compartment-condensates-through-aging-of-protein-rna-condensates.pdf |
6343e8caf764e6186f15f316 | 10.26434/chemrxiv-2022-fn5z0 | Deep learning pipeline for statistical quantification of amorphous two-dimensional materials | Aberration-corrected transmission electron microscopy enables imaging of two-dimensional (2D) materials with atomic resolution. However, dissecting the short-range-ordered structures in radiation-sensitive and amorphous 2D materials remains a significant challenge due to low atomic contrast and laborious manual evaluation. Here, we imaged carbon-based 2D materials with strong contrast, which is enabled by chromatic and spherical aberration correction at low acceleration voltage. By constructing a deep learning pipeline, atomic registry in amorphous 2D materials can be precisely determined, providing access to a full spectrum of quantitative datasets, including bond length/angle distribution, pair distribution function, and real-space polygon mapping. Accurate segmentation of micropores and surface contamination, together with robustness against background inhomogeneity, guaranteed the quantification validity in complex experimental images. The automated image analysis provides quantitative metrics with high efficiency and throughput, which may bring new insights into the structural understanding of short-range-ordered structures. In addition, the convolutional neural network can be readily generalized to crystalline materials, allowing for automatic defect identification and strain mapping. | Christopher Leist; Meng He; Xue Liu; Ute Kaiser; Haoyuan Qi | Materials Science; Carbon-based Materials; Thin Films | CC BY NC 4.0 | CHEMRXIV | 2022-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6343e8caf764e6186f15f316/original/deep-learning-pipeline-for-statistical-quantification-of-amorphous-two-dimensional-materials.pdf |
6343fff1cf382921dac5042a | 10.26434/chemrxiv-2022-6v05x-v2 | TEtraQuinolines (TEQs): A missing link in the family of porphyrinoid macrocycles | Porphyrin contains four inwardly oriented nitrogen atoms. It is arguably the most ubiquitous multifunctional naturally occurring macrocycle that has inspired the design of novel nitrogen-containing heterocycles for decades. While cyclic tetramers of pyrrole, indole, and pyridine have been exploited as macrocycles in this category, quinoline has been largely neglected as a synthon. Herein, we report the synthesis of TEtraQuinoline (TEQ) as a ‘missing link’ in this N4 macrocycle family. In TEQs, four quinoline units are concatenated to produce an S4-symmetric architecture. TEQs are characterized by a highly rigid saddle shape, wherein the lone-pair orbitals of the four nitrogen atoms are not aligned in a planar fashion. Nevertheless, TEQs can coordinate a series of transition-metal cations. TEQs are inherently fluorescence-silent, but become strongly emissive upon protonation or complexation of Zn(II) cations ( = 0.71). TEQ/Fe(II) complexes can catalyse dehydrogenation and oxygenation reactions with catalyst loadings as low as 0.1 mol%. | Naoya Kumagai; Wei Xu; Yuuya Nagata | Organic Chemistry; Organic Compounds and Functional Groups | CC BY 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6343fff1cf382921dac5042a/original/t-etra-quinolines-te-qs-a-missing-link-in-the-family-of-porphyrinoid-macrocycles.pdf |
644ef3c60d87b493e38fd261 | 10.26434/chemrxiv-2023-c3nhg | Synthesis of artificial cells via biocatalytic polymerisation-induced self-assembly | Artificial cells are biomimetic microstructures that mimic functions of natural cells and find application, e.g., as microreactors, as building blocks for molecular systems engineering, and to host synthetic biology pathways. Here, we report enzymatically synthesised polymer-based artificial cells with the ability to express proteins. They are created by biocatalytic atom transfer radical polymerization-induced self-assembly (bioPISA). The metalloprotein myoglobin synthesises amphiphilic block copolymers that self-assemble into structures ranging from micelles over worm-like micelles to polymersomes and giant unilamellar vesicles (GUVs). The GUVs encapsulate cargo during the polymerisation, including enzymes, nanoparticles, microparticles, plasmids and cell lysate. The resulting artificial cells act as microreactors for enzymatic reactions and for osteoblast-inspired biomineralization, and could express proteins when fed with amino acids, as shown by the expression of the fluorescent protein mClover and of actin. Actin polymerises in the vesicles and alters the artificial cell’s internal structure by creating internal compartments. Thus, bioPISA-derived GUVs mimic bacteria as they are composed of a microscopic reaction compartment that contains genetic information which is able to express proteins upon induction. bioPISA not only is a powerful tool in the pursuit of artificial cells but also for the easy and highly efficient encapsulation of biological molecules under mild conditions and in biologically relevant media. Therefore, it could have significant implications for the development of biomaterials and drug-delivery systems, as well as for cell encapsulation, and the in-situ formation of nano-objects. | Sètuhn Jimaja; Andrea Belluati; Robert J. Chadwick; Christopher Glynn; Mohamed Chami; Dominic Happel; Chao Guo; Harald Kolmar; Nico Bruns | Polymer Science; Nanoscience; Biopolymers; Organic Polymers; Polymerization (Polymers); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644ef3c60d87b493e38fd261/original/synthesis-of-artificial-cells-via-biocatalytic-polymerisation-induced-self-assembly.pdf |
60c7517cbb8c1a3b9b3dbce4 | 10.26434/chemrxiv.13161956.v1 | High-Pressure Nucleation of Low-Density Polymorphs | The crystallized above
0.3 GPa polymorphs β and γ of bis-3-nitrophenyl disulphide, are less dense than
the ambient-pressure polymorph α. This
high-entropy nucleation illustrates the molecular-scale mechanism of empirical
Ostwald’s rule of stages. This method, in contrast to mechanochemical
techniques, is ideally suited the kinetic nucleation of new low-density
conformational polymorphs.<br /> | Szymon Sobczak; Paulina Ratajczyk; Andrzej Katrusiak | Process Chemistry; Stereochemistry; Chemical Kinetics; Physical and Chemical Processes; Physical and Chemical Properties; Thermodynamics (Physical Chem.); Crystallography; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7517cbb8c1a3b9b3dbce4/original/high-pressure-nucleation-of-low-density-polymorphs.pdf |
64f6899e3fdae147fa8385eb | 10.26434/chemrxiv-2023-qbrh6 | Synthesis and Characterization of Gelatin Methacryloyl: Introducing Chemistry Students to the Applications of Hydrogels in Medicine | Many undergraduate chemistry and biochemistry students pursue careers in healthcare. Biomaterials, designed to be incorporated into the human body, have become increasingly significant in medicine as drug delivery vehicles and tissue scaffolds. We believe it is essential that undergraduates are exposed to biomaterial synthesis and characterization before they pursue further graduate education or a career in pharmaceuticals. In this Laboratory Experiment, we argue that gelatin methacryloyl (GelMA) is a biomacromolecule well-suited to being synthesized and characterized in an undergraduate laboratory. We detail a protocol to graft methacrylic anhydride (MAAnh) to the gelatin backbone in a heated, buffered solution and then provide three synergistic characterization assays: NMR spectroscopy, a TNBS assay, and Fe(III)-hydroxamic acid-based assay. NMR analysis allowed the students to determine if they had achieved a successful synthesis, and the latter two colorimetric assays quantified the on-target and off-target modifications of amino and hydroxyl groups, respectively. We found that our students successfully synthesized, purified, and determined the final molecular structure of GelMA. Students indicated that the study reinforced their chemistry laboratory skills, introduced them to a new discipline, and increased their interest in the medicinal applications of materials. | Carmen Velez; Kristie Cheng; Cody Crosby | Materials Science; Polymer Science; Chemical Education; Biopolymers; Hydrogels; Polymer scaffolds | CC BY NC 4.0 | CHEMRXIV | 2023-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f6899e3fdae147fa8385eb/original/synthesis-and-characterization-of-gelatin-methacryloyl-introducing-chemistry-students-to-the-applications-of-hydrogels-in-medicine.pdf |
67acdee5fa469535b9116e3e | 10.26434/chemrxiv-2025-lz9xt | Rapid Water Permeation by Aramid Foldamer Nanochannels with Hydrophobic Interiors | Aquaporins are natural proteins that rapidly transport water across cell membranes, maintaining homeostasis, whilst strictly excluding salt. This has inspired their use in water purification and desalination, a critical emerging need. However, stability, scalability, and cost have prevented their widespread adoption in water purification membrane technologies. As such, attention has turned to the use of artificial water channels, with pore functionalized polymers and macrocycles providing a powerful alternative. Whilst impressive rates of transport have been achieved, the combination of a scalable, high-yielding synthesis and efficient transport has not yet been reported. Herein, we report such a system, with densely functionalized channel interiors, synthesized by high-yielding living polymerization with low polydispersities, showing high salt exclusion, and excellent water transport rates. Our aramid foldamers create artificial water channels with hydrophobic interiors, and single-channel water permeability rates of up to 108 water molecules per second per channel, approaching the range of natural Aquaporins (c. 109). We show that water transport rates closely correspond to the helical length, with the polymer which most closely matches bilayer thickness showing optimal efficacy, as supported by molecular dynamics simulations. Our work provides a basis for the scalable synthesis of next-generation artificial water channels. | Saquib Farooq; Javid Ahmad Malla; Miroslava Nedyalkova; Rafael Freire; Indradip Mandal; Aurelien Crochet; Stefan Salentinig; Marco Lattuada; Charlie McTernan; Andreas Kilbinger | Polymer Science; Nanoscience; Polymerization (Polymers); Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67acdee5fa469535b9116e3e/original/rapid-water-permeation-by-aramid-foldamer-nanochannels-with-hydrophobic-interiors.pdf |
652e4d5945aaa5fdbb2d1155 | 10.26434/chemrxiv-2023-ffv8z | Consensus Model of Mechanophore Sensors for Biological Force Measurement | Cellular forces regulate an untold spectrum of living processes such as cell migration, gene expression, and ion conduction. However, a quantitative description of mechanical control remains elusive due to the lack of general, live-cell tools to measure discrete forces between biomolecules. Here we introduce a computational pipeline for force measurement that leverages well-defined, tunable release of a mechanically activated small molecule fluorophore. These sensors are characterized using a consensus approach combining equilibrium and steered QM/MM molecular dynamics models to capture the chemical, mechanical, and conformational transitions underlying force activation thresholds on a pico-to-nanonewton scale. We find that chemical modification of the mechanophore and variation of its biomolecular tethers can tune the rate-determining step for fluorophore release and adjust the mechanochemical activation barrier. The models offer a new molecular framework for calibrated, programmable biomolecular force reporting within the live-cell regime, opening new opportunities to study mechanical phenomena in biological systems | Sumit Mittal; Rongsheng E. Wang; Robert Ros; Alison E. Ondrus; Abishek Singharoy | Theoretical and Computational Chemistry; Polymer Science; Biopolymers; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652e4d5945aaa5fdbb2d1155/original/consensus-model-of-mechanophore-sensors-for-biological-force-measurement.pdf |
6446b97f83fa35f8f6304caa | 10.26434/chemrxiv-2023-vpsmr | Recent Advances in Graphene-Based Electrical Glucose Monitoring | The WHO notes that diabetes can contribute to various health problems, such as blindness, lethargy, kidney failure, strokes, numbness, and heart attacks. Diabetes can be an even worthy- noting problem in developing countries. In many developing countries, there has been significant economic growth over the past decade, but current projections indicate a slowing of this trend. Thus, it is crucial to prevent missed diagnoses and delayed treatment, as these could lead to fatal consequences. Regular glucose monitoring is an indispensable diagnostic tool that allows doctors to identify early symptoms of diabetes and administer timely treatment to avert severe complications. This review provides a peek into the basics of graphene, as well as the very recent advances since 2020 utilizing graphene, GO, rGO, and other novel graphene composite to monitor glucose. | Zihan Li; Siting Liu | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Analytical Apparatus; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2023-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6446b97f83fa35f8f6304caa/original/recent-advances-in-graphene-based-electrical-glucose-monitoring.pdf |
648cb23f4f8b1884b765b7f3 | 10.26434/chemrxiv-2023-9b3g4 | Variational Active Space Selection with MC-PDFT | The selection of a good set of active orbitals for modeling strongly correlated quantum states is difficult to automate as it is highly dependent on the state and molecule of interest. As such, although many approaches have been proposed with some success, no single approach has worked in all cases. Here, we propose an improved framework for automated selection in which (i) multiple wave functions based on different active-spaces are generated, and (ii) the resulting wave functions are chosen between by some means of facile evaluation. Using this framework, we propose a method in which (i) we construct different active space orbitals through diagonalization of a parameterized operator, and (ii) we choose the state with the lowest tPBE absolute energy from multiconfigurational pair density functional theory (MC-PDFT) averaged over the targeted states of interest. We test the method using density matrix renormalization group (DMRG) wave functions with 40 active orbitals and bond index of 700, with no further orbital optimization following the active space selection. We find that with only four values of the parameter (i.e., with only four trial wave functions), we can obtain a mean unsigned error of only 0.19 eV for 199 vertical excitation energies in the QUESTDB database. Furthermore, the tPBE absolute energy proves robust in selecting between active spaces of very different sizes, over and above the wave function (CASCI/DMRG-CASCI) absolute energy. We believe this new framework is promising for the application of active space methods to chemical problems in a high-throughput fashion. | Daniel S. King; Donald G. Truhlar; Laura Gagliardi | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648cb23f4f8b1884b765b7f3/original/variational-active-space-selection-with-mc-pdft.pdf |
667df7c601103d79c55ee361 | 10.26434/chemrxiv-2024-8cm80 | Perspectives of Alkyl Introduction into Methylene-Containing Heterocycles | Two-step α-methylation via enamination with subsequent reduction was investigated on various methylene-containing heterocyclic carbonyl compounds including lactams, lactones, thiolactones etc. Outcomes or enamination with Bredereck’s reagent and DMF-DMA were compared. Optimal enamination and reduction protocols regarding solubility, reactivity and thermal stability of the substrates were elaborated. The construction of primary and secondary alkyl substituents through enaminone interaction with organometallic reagents was tested. | Andriy Frolov; Dmytro Lebid; Eugeniy Ostapchuk; Tetiana Druzhenko; Dmytro Volochnyuk; Serhiy Ryabukhin | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667df7c601103d79c55ee361/original/perspectives-of-alkyl-introduction-into-methylene-containing-heterocycles.pdf |
6560b8f0cf8b3c3cd706db85 | 10.26434/chemrxiv-2023-sz3nj | Modular synthesis of complex benzoxaboraheterocycles through chelation-assisted Rh-catalyzed [2+2+2]cycloaddition | Benzoxaboraheterocycles (BOBs) are moieties of increasing interest in the pharmaceutical industry; however, the synthesis of these compounds is often difficult or impractical due to the sensitivity of the boron moiety, the requirement for metalation-borylation protocols, and lengthy syntheses. We report a straightforward, modular approach that enables access to complex examples of the rare BOB framework through a Rh-catalyzed [2+2+2]cycloaddition using MIDA-protected alkyne boronic acids. Key to the development of this methodology was overcoming the steric barrier to catalysis by leveraging chelation assistance. We show the utility of the method through synthesis of a broad range of BOB scaffolds, mechanistic information on the chelation effect, intramolecular alcohol-assisted BMIDA hydrolysis, and the linear/cyclic BOB limits, as well as comparative binding affinities for the new BOB frameworks for ribose-derived biomolecules. | John Halford-McGuff; Marek Varga; Aidan McKay; David Cordes; Allan Watson | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560b8f0cf8b3c3cd706db85/original/modular-synthesis-of-complex-benzoxaboraheterocycles-through-chelation-assisted-rh-catalyzed-2-2-2-cycloaddition.pdf |
626168bfbdc9c21ffeddaa31 | 10.26434/chemrxiv-2022-nqn0t-v2 | Bioinspired Asymmetric Total Synthesis of Emeriones A–C | We report an asymmetric bioinspired total synthesis of the fungal metabolites emeriones A–C via stereoselective late-stage epoxidation or endoperoxidation of two bicyclo[4.2.0]octadiene diastereomers. The central bicyclic scaffold is synthesized in an 8pi/6pi electrocyclization cascade of a stereodefined (E,E,Z,Z,E)-pentaene, which contains the fully assembled and unprotected side chains of the natural products. The pentaene is constructed convergently through Stille cross-coupling of two similarly complex polyenes. The anti-aldol side chain of the emeriones is made using a Paterson-aldol approach, and the epoxide of the dioxobicyclo[3.1.0] side chain is synthesized via ring-closure onto an oxidized para-methoxyphenyl acetal. Our total synthesis has enabled the revision of the structure of emerione C and the synthesis of a “missing” family member, which we hereby call emerione D. DFT calculations indicate the two methyl groups that reside on the cyclobutene ring are critical for the stereochemical outcome of 8pi/6pi electrocyclization. | Sven Jänner; Daniel Isak; Yuli Li; K. N. Houk; Aubry Miller | Organic Chemistry; Natural Products; Organic Synthesis and Reactions; Stereochemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626168bfbdc9c21ffeddaa31/original/bioinspired-asymmetric-total-synthesis-of-emeriones-a-c.pdf |
615afc21b564b67e6a6bec45 | 10.26434/chemrxiv-2021-2c93p | Absolute optical chiral analysis using cavity-enhanced polarimetry | Chiral analysis is central for scientific advancement in the fields of chemistry, biology, and
medicine. It is also indispensable in the development and quality control of chiral compounds in
the chemical and pharmaceutical industries. Current methods for chiral analysis, namely optical
polarimetry, mass spectrometry and nuclear magnetic resonance, are either insensitive, have low
time resolution, or require preparation steps, and so are unsuited for monitoring chiral dynamics
within complex environments: the current need of both research and industry. Here we present
the concept of absolute optical chiral analysis, as enabled by cavity-enhanced polarimetry, which
allows for accurate unambiguous enantiomeric characterization and enantiomeric-excess
determination of chiral compounds within complex mixtures at trace levels, without the need for
calibration, even in the gas phase. The utility of this approach is demonstrated by post
chromatographic analysis of complex gaseous mixtures, the rapid quality control of perfume
mixtures containing chiral volatile compounds, and the online in-situ observation of chiral
volatile emissions from a plant under stress. Our approach and technology offer a step change in
chiral compound determination, enabling online quality control of complex chemical mixtures,
identification of counterfeit goods, detection of pests on plants, and assessment of chiral
emission processes from climate relevant ecosystems. | Lykourgos Bougas; Joseph Byron; Dmitry Budker; Jonathan Williams | Physical Chemistry; Organic Chemistry; Analytical Chemistry; Physical Organic Chemistry; Analytical Apparatus; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615afc21b564b67e6a6bec45/original/absolute-optical-chiral-analysis-using-cavity-enhanced-polarimetry.pdf |
67c8635a81d2151a022e299a | 10.26434/chemrxiv-2025-r9g1p | Computational design of B,N-substituted graphene ribbons exhibiting quasi-degenerate S1 and T1 states and high fluorescence rates | B,N-substituted graphene ribbons are computationally designed and their spectroscopic properties are systematically explored with wave-function based electronic-structure methods. All B,N-graphene ribbons exhibit exceptionally small S1-T1 energy gaps. The oscillator strength of the S1-S0 transition increases monotonically with the length of the ribbons. Some B,N-graphene ribbons of intermediate length (5 – 10 rings along the main axis) exhibit a negative singlet-triplet energy gap concurrently with a substantial oscillator strength. The calculated emission energies provide evidence of high rigidity of the ribbons and therefore narrow absorption/emission profiles and low radiationless quenching rates of the emissive S1 state. | Andrzej L. Sobolewski; Magdalena W. Duszka; Wolfgang Domcke | Theoretical and Computational Chemistry; Theory - Computational; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8635a81d2151a022e299a/original/computational-design-of-b-n-substituted-graphene-ribbons-exhibiting-quasi-degenerate-s1-and-t1-states-and-high-fluorescence-rates.pdf |
64d3417969bfb8925aa17d16 | 10.26434/chemrxiv-2023-wj0p6 | Synthesis of novel polymers with biodegradability from propylene and carbon monoxide | Developing novel polymers with biodegradability could mitigate polymer-related pollution. Here, polymers containing ester and ketone groups with moderate biodegradability (regardless of their chirality) were synthesized from poly(propylene-alt-carbon monoxide)s by the Baeyer–Villiger oxidation with aqueous H2O2 and AlCl3 (which increased the ester content of the as-synthesized polymers to >35 mol%). The ester groups in these polymers, showed two isomeric structures (originating from two oxygen-atom insertion modes), and 70% of the ester groups were structurally same as those in P3HB (a common biodegradable polymer). Additionally, solvent-cast blended films comprising these polymers and poly(L-lactic acid) showed a higher strain at break than pure-poly(L-lactic acid) films. Therefore, this study proposes a cost-effective strategy for the synthesis of biodegradable polymers that can be used as plasticizers of poly(L-lactic acid), facilitating a wide range of applications. | Haobo Yuan; Kohei Takahashi; Shinya Hayashi; Miwa Suzuki; Nobuhiro Fujikake; Ken-Ichi Kasuya; Jian Zhou; Shintaro Nakagawa; Naoko Yoshie; Chifeng Li; Kazuya Yamaguchi; Kyoko Nozaki | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d3417969bfb8925aa17d16/original/synthesis-of-novel-polymers-with-biodegradability-from-propylene-and-carbon-monoxide.pdf |
64e4c592dd1a73847f4d0337 | 10.26434/chemrxiv-2023-xp6v5 | 5-Nitrofuranyl Derivatives Shapeshift in Polar Aprotic Solvents Which May Give Rise to Induced Ring Currents in an Applied Magnetic Field | Anisotropically induced ring currents are not confined to Hückel’s aromatics, and many non-aromatic compounds, in particular, cyclopropane exhibit ring currents in an applied magnetic field. To this end, aromatic protons of 5-nitrofurfural give rise to two signals in its 1H NMR spectrum in CDCl3 which as expected, are only ~ ±0.1 ppm apart; however, in marked contrast to 5-nitrofurfural, the analogous aforementioned protons of (E)- 5-nitrofuran-2-yl methylene hydrazine are nearly ±1.0 ppm apart in its 1H NMR spectrum in DMSO-d6. This anomaly may, though it need not of necessity, suggest that the hydrazone moiety in (E)-5-nitrofuran-2-yl methylene hydrazine force the furan ring into a puckered non-aromatic ring so as to pave the way for an induced ring current in an applied magnetic field. 5-nitro-N'-5-nitrofuran-2-carbonyl furan-2-carbohydrazide also appears to exhibit a similar perturbation; however, to a lesser extent. | Ashley L. Dey | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.); Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e4c592dd1a73847f4d0337/original/5-nitrofuranyl-derivatives-shapeshift-in-polar-aprotic-solvents-which-may-give-rise-to-induced-ring-currents-in-an-applied-magnetic-field.pdf |
61def00690fc8a8935f4c002 | 10.26434/chemrxiv-2022-3fqfh | The effect of adding eggshell membrane to emulsified meat models with reduced salt in terms of structure, water-holding, and texture | This study was conducted to evaluate the effect of adding eggshell membrane (ESM), a by-product of the chicken egg processing industry, to emulsified meat models with different NaCl concentrations. The aim was to see if ESM could help reduce the amount of NaCl that is usually added to this type of product. The effects of ESM were investigated in terms of cooking loss, water distribution, color, and texture properties using a simplified meat emulsion model with no other additives than ESM. Emulsified meat samples were made with three different NaCl concentration (0.5, 0.1, 1.5%), without and with three levels of ESM (0.5, 1.0, 1.5%). In general addition of ESM reduced cooking loss (CL), improved texture, and increased redness. Effects of ESM were explained by structural changes in the protein matrix, as shown by two different histological methods. Addition of ESM explained 86% of the variation in LF-NMR T2 relaxation times in uncooked samples, while 97% of the variation in cooked samples was explained by the NaCl concentration. FTIR micro-spectroscopic measurements revealed that samples supplemented with ESM had a higher proportion of α-helical structures and reduced amount of protein ß-sheet aggregation in samples with 1.0 and 1.5% NaCl. It was shown that ESM increased the pH of the emulsified meat, and it was therefore suggested that increased negative repulsion effects had a positive heat stabilizing effect on the protein network. The fact that the cooked samples were redder was probably related to the antioxidant effect of ESM which was measured as MDA (malondialdehyde) equivalents after in vitro digestion of the samples. ESM can thus help reduce the salt content in sausages while ESM also has a positive antioxidant effect improving color. | Ragni Ofstad; Ulrike Böcker; Vibeke Høst; Katinka R. Dankel ; Karen Wahlstrøm Sanden; Mona E. Pedersen; Rune Rødbotten | Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61def00690fc8a8935f4c002/original/the-effect-of-adding-eggshell-membrane-to-emulsified-meat-models-with-reduced-salt-in-terms-of-structure-water-holding-and-texture.pdf |
671e7cf81fb27ce124c345df | 10.26434/chemrxiv-2024-568nn | PNGaseF-generated N-glycans adduct onto peptides in the gas phase | Glycoproteomics has recently increased in popularity due to instrumental and methodological advances. That said, O-glycoproteomic analysis is still challenging for various reasons, including signal suppression, search algorithm limitations, and co-occupancy of N- and O-glycopeptides. To decrease sample complexity and simplify analysis, most O-glycoproteomic workflows include PNGaseF digestion, which is an endoglycosidase that removes most N-glycan structures. Here, we report that N-glycans released from PNGaseF digestion were identified during data acquisition and hampered detection of O-glycopeptides. Importantly, we noted instances where free glycans adducted to unmodified peptides in the gas phase and were misidentified by search algorithms as O-glycopeptides. We confirmed the presence of free glycans in other experiments performed in our laboratory, as well as from data generated by other groups. To overcome this limitation, we demonstrated that released N-glycans can be removed using a molecular weight cut off filter prior to (glyco)protease digestion, which improves O-glycoproteomic coverage. | Valentina Rangel-Angarita; Joann Chongsaritsinsuk; Keira Mahoney; Lea Kim; Ryan Chen; Akua Appah-Sampong; Isabella Tran; Alexandra Steigmeyer; Marie Hollenhorst; Stacy Malaker | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671e7cf81fb27ce124c345df/original/pn-gase-f-generated-n-glycans-adduct-onto-peptides-in-the-gas-phase.pdf |
60c754a5567dfe7f16ec60d9 | 10.26434/chemrxiv.13681603.v1 | Benzyl and Phenyl Glucosinolates Are Metabolized by the Specific Plant Pathogen Alternaria Brassicicola but Not by the Generalist Fungal Pathogens Rhizoctonia Solani or Sclerotinia Sclerotiorum | The
metabolism of benzyl and phenyl glucosinolates by three phytopathogenic fungal
species is investigated and established that <i>A. brassicicola </i>metabolized intact benzyl and phenyl glucosinolates
and the corresponding desulfo derivatives. Syntheses and spectroscopic characterization of benzyl and
phenyl desulfo-glucosinolates are reported. Phenylacetonitrile and
benzylisothiocyanate are the first metabolic products of benzyl glucosinolate; benzyl isothiocyanate is further metabolized
to 3-benzyl-2-thioxo-2,3-dihydrothiazolidine-4-carboxylic acid. | M. Soledade C. Pedras; Chintamani Thapa; Sajjad Hossain | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754a5567dfe7f16ec60d9/original/benzyl-and-phenyl-glucosinolates-are-metabolized-by-the-specific-plant-pathogen-alternaria-brassicicola-but-not-by-the-generalist-fungal-pathogens-rhizoctonia-solani-or-sclerotinia-sclerotiorum.pdf |
62432d2b9f61ca0b65fb6612 | 10.26434/chemrxiv-2022-l9g14 | Novel (super)hard SiCN from crystal chemistry and first principles | The purpose of this work is to predict the existence of novel equiatomic SiCN based on tetragonal C6 structure (“glitter”), the elementary building unit being the 1,4 cyclohexadiene molecule comprising both tetrahedral (sp3) and trigonal (sp2) carbons. From crystal chemistry rationale the structural transformations of C6 to SiC2 and then to the ternary SiCN were fully relaxed to the ground states using first principles DFT-based calculation. Like early proposed C6 and SiC2, SiCN was found bonding and structurally stable from the elastic properties on one hand and dynamically stable from the phonons, on the other hand. The Vickers hardness of SiCN is close to that of cubic silicon carbide, a conventional superabrasive, whereas hardness of tetragonal SiC2 is slightly lower. Besides the abrasive properties, the electronic band structure indicates metal-like behavior of SiCN thus suggesting the potential for heat dissipation in operating conditions. | Samir F. Matar; Jean Etourneau; Vladimir L. Solozhenko | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62432d2b9f61ca0b65fb6612/original/novel-super-hard-si-cn-from-crystal-chemistry-and-first-principles.pdf |
655f8e0529a13c4d47d5b2e6 | 10.26434/chemrxiv-2023-w7vx9 | Canonical titration simulations | We present a Monte Carlo approach for performing titration simulations in the canonical ensemble. The standard constant pH (cpH) simulation methods are intrinsically grand canonical, allowing us to study the protonation state of molecules only as a function of pH in the reservoir. Due to the Donnan potential between a system and an (implicit) reservoir of a semi-grand canonical simulation, the pH of the reservoir can be significantly different from that of an isolated system, for an identical protonation state. The new titration method avoids this difficulty by using canonical reactive Monte Carlo algorithm to calculate the protonation state of macromolecules as a function of the total number of protons present inside the simulation cell. The pH of an equilibrated system is then calculated using a new surface insertion Widom algorithm, which bypasses the difficulties associated with the bulk Widom particle insertion for intermediate and high pH values. To properly treat the long range Coulomb force, we use Ewald summation method, showing the importance of the Bethe potential for calculating pH of canonical systems. | Amin Bakhshandeh; Yan Levin | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655f8e0529a13c4d47d5b2e6/original/canonical-titration-simulations.pdf |
60c73f22842e652620db1a2f | 10.26434/chemrxiv.7265174.v1 | Thioalkyl- and Sulfone-Substituted Poly(p-Phenylene Vinylene)s | Poly(p-phenylene vinylene)s (PPVs) have been studied for decades, but research on this interesting class of conjugated polymers is far from being completed. New applications like in bioimaging keep emerging and even simple structural variations are still waiting to be explored. Surprisingly, not even dithioalkyl-substituted PPVs (S-PPVs) have been reported in the peer-reviewed literature, although the corresponding dialkoxy-substituted PPVs (O-PPVs) like MEH-PPV or MDMO-PPV are most frequently used and although thioalkyl substituents can improve the material properties significantly. We herein report the development of a highly efficient, scalable two-step synthesis of Gilch monomers for S-PPVs starting from low-cost 1,4-diiodobenzene. A low-temperature polymerization protocol has been developed for these monomers, affording high-molecular weight S-PPVs in excellent yields. The thermal, electrochemical, and photophysical properties of S-PPVs are reported to highlight the potential of these polymers. Furthermore, treatment with dimethyldioxirane is demonstrated to result in rapid conversion into sulfone-substituted PPVs (SO<sub>2</sub>-PPVs), introducing a route to high-molecular weight SO<sub>2</sub>-PPVs with exceptional stability and solid-state photoluminescence quantum yields of up to 0.46. | Martina Rimmele; Klaus Ableidinger; Adam V. Marsh; Nathan J. Cheetham; M. Josef Taublaender; Alina Buchner; Jonathan Prinz; Johannes Fröhlich; Miriam M. Unterlass; Martin Heeney; Florian Glöcklhofer | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Thin Films; Conducting polymers; Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f22842e652620db1a2f/original/thioalkyl-and-sulfone-substituted-poly-p-phenylene-vinylene-s.pdf |
60c74f39ee301ca63ac7a66e | 10.26434/chemrxiv.12866309.v1 | A Click-Flipped Enzyme Substrate Boosts the Performance of the Diagnostic Screening for Hunter Syndrome | We report on the unexpected finding that click modification of iduronyl azides results in a conformational flip of the pyranose ring, which led to the development of a new strategy for the design of superior enzyme substrates for the diagnostic assaying of iduronate-2-sulfatase (I2S), a lysosomal enzyme related to Hunter syndrome. Synthetic substrates are essential in testing newborns for metabolic disorders to enable early initiation of therapy. Our click-flipped iduronyl triazole showed a remarkably better performance with I2S than commonly used <i>O</i>-iduronates. We found that both <i>O</i>- and triazole-linked substrates are accepted by the enzyme, irrespective of their different conformations, but only the <i>O</i>-linked product inhibits the activity of I2S. Thus, in the long reaction times required for clinical assays, the triazole substrate substantially outperforms the <i>O</i>-iduronate. Applying our click-flipped substrate to assay I2S in dried blood spots sampled from affected patients and random newborns significantly increased the confidence in discriminating between these groups, clearly indicating the potential of the click-flip strategy to control the biomolecular function of carbohydrates. | Markus Schwarz; Philipp Skrinjar; Michael J. Fink; Stefan Kronister; Thomas Mechtler; Panagiotis Koukos; Alexandre M.J.J. Bonvin; David Kasper; Hannes Mikula | Bioorganic Chemistry; Organic Compounds and Functional Groups; Biochemical Analysis; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f39ee301ca63ac7a66e/original/a-click-flipped-enzyme-substrate-boosts-the-performance-of-the-diagnostic-screening-for-hunter-syndrome.pdf |
6103204040c8bdf23d9973ed | 10.26434/chemrxiv-2021-n5mdz | Factors Controlling Oxophilicity and Carbophilicity of Transition Metals and Main Group Metals | The strength of interaction between a metal and oxygen and/or carbon is a crucial factor for catalytic performance, materials stability, and other important applications. While these are fundamental properties in materials science, there is no general understanding of what makes a metal oxophilic or carbophilic, especially for main group metals. In this work, we elucidate the factors that control how oxophilic or carbophilic a metal is by creating a predictive model and applying it to a variety of data sets for transition metals and main group metals, including DFT-calculated adsorption energies and experimental formation energies. Our model is easily interpretable and accurately describes oxophilic and carbophilic trends across different regions of the periodic table. This model captures the ionic contribution to bonding, the adsorbate-sp contribution to bonding, and the adsorbate-d contribution to bonding by using the reduction potential, matrix coupling elements, band centers, and band filling. For transition metals, the adsorbate-surface d coupling is the major factor that determines oxophilicity relative to carbophilicity. For metals that do not contain d electrons either in their core or valence shell (Li, Be, Na, Mg, Al, K, and Ca), the reduction potential and the adsorbate-surface s coupling are the major factors. As a simple application, we demonstrate the utility of oxophilicity and carbophilicity in rapidly screening metal dopants for improved selectivity for ethylene epoxidation on silver-based catalysts. Using our model, we established a direct relationship between the electronic properties of the metal dopants and their selectivity for ethylene epoxidation. The results suggest that transition metals with high adsorbate-surface d coupling and main group metals with low adsorbate-surface s coupling are good silver-dopant candidates for this reaction. Overall, the improved linkage between a metal’s electronic structure and its interaction with carbon or oxygen will be broadly useful in design of functional materials for a variety of applications. | Gbolade O. Kayode; Matthew M. Montemore | Theoretical and Computational Chemistry; Catalysis; Chemoinformatics - Computational Chemistry; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6103204040c8bdf23d9973ed/original/factors-controlling-oxophilicity-and-carbophilicity-of-transition-metals-and-main-group-metals.pdf |
676a0ce6fa469535b999990a | 10.26434/chemrxiv-2024-f17zp-v3 | A Robust Crystal Structure Prediction Method to Support Small Molecule Drug Development with Large Scale Validation and Prospective Studies | Crystal polymorphism is an important and fascinating aspect of solid state chemistry with far reaching implications in the pharmaceuticals, agrisciences, nutraceuticals, battery and aviation industries. Late appearing more stable polymorphs have caused numerous issues in the pharmaceutical industry. Experimental polymorph screening can be very expensive and time consuming, and sometimes may miss important low energy polymorphs due to an inability to exhaust all crystallization conditions. In this paper, we report a crystal structure prediction (CSP) method with state of the art accuracy and efficiency, validated on a large and diverse dataset including 66 molecules with 137 experimentally known polymorphic forms. The method combines a novel systematic crystal packing search algorithm and the use of machine learning force fields in a hierarchical crystal energy ranking. Our method not only reproduces all the experimentally known polymorphs, but also suggests new low energy polymorphs yet to be discovered by experiment that might pose potential risks to development of the currently known forms of these compounds. In addition, we report the prediction results of a blinded study, results for Target XXXI from the seventh CSP blind test, and demonstrate how the method can be used to accelerate clinical formulation design and derisk downstream processing. The high accuracy, reliability, and efficiency of our method with large scale validations, and a blinded study, position it for routine molecular crystal structure prediction in drug development. | Dong Zhou; Imanuel Bier; Biswajit Santra; Leif Jacobson; Chuanjie Wu; Adiran Suarez; Barbara Almaguer; Haoyu Yu; Robert Abel; Richard Friesner; Lingle Wang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2025-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676a0ce6fa469535b999990a/original/a-robust-crystal-structure-prediction-method-to-support-small-molecule-drug-development-with-large-scale-validation-and-prospective-studies.pdf |
60c74a0b567dfe1555ec4cb2 | 10.26434/chemrxiv.12145899.v1 | Amorphous Mixtures of Ice and C60 Fullerene | Carbon and ice make
up a substantial proportion of our Universe. Recent space exploration has shown
that these two chemical species often coexist including on comets, asteroids
and in the interstellar medium. Here we prepare mixtures of C<sub>60</sub> fullerene
and H<sub>2</sub>O by vapor co-deposition at 90 K with molar C<sub>60</sub>:H<sub>2</sub>O
ratios ranging from 1:1254 to 1:5. The C<sub>60</sub> percolation threshold is
found between the 1:132 and 1:48 samples, corresponding to a transition from
matrix-isolated C<sub>60</sub> molecules to percolating C<sub>60</sub> domains
that confine the H<sub>2</sub>O. Below this threshold, the crystallization and
thermal desorption properties of H<sub>2</sub>O are not significantly affected
by the C<sub>60</sub>, whereas the crystallization temperature of H<sub>2</sub>O
is shifted towards higher temperatures for the C<sub>60</sub>-rich samples.
These C<sub>60</sub>-rich samples also display exotherms corresponding to the
crystallization of C<sub>60</sub> as the two components undergo phase
separation. More than 60 volume percent C<sub>60</sub> is required to significantly
affect the desorption properties of H<sub>2</sub>O. A thick blanket of C<sub>60</sub>
on top of pure amorphous ice is found to display large cracks due to water
desorption. These findings may help understand the recently observed unusual surface
features and the H<sub>2</sub>O weather cycle on the 67P/Churyumov–Gerasimenko
comet. | Siriney Halukeerthi; Jacob J. Shephard; Sukhpreet Talewar; John S. O. Evans; Alexander Rosu-Finsen; Christoph Salzmann | Carbon-based Materials; Nanostructured Materials - Materials; Space Chemistry; Physical and Chemical Processes; Physical and Chemical Properties; Structure; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a0b567dfe1555ec4cb2/original/amorphous-mixtures-of-ice-and-c60-fullerene.pdf |
64c7e33f658ec5f7e5808827 | 10.26434/chemrxiv-2023-sw8wd | Direct Competitive Kinetic Isotope Effect Measurement Using Quantitative Whole Molecule MALDI-TOF Mass Spectrometry | Kinetic isotope effect (KIE) measurements are a powerful tool to interrogate the microscopic steps in enzyme catalyzed reactions and can provide detailed information about transition state structures. However, the application of KIE measurements to study enzymatic reactions is not widely applied due to the tedious and complex analytical workflows required to measure KIEs with sufficient precession. Here, we report a method for the direct measurement of competitive KIEs using a whole molecule matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS). Using isotope labeled internal standard introduced when quenching the enzyme reaction at multiple time points enables the simultaneous measurement of both the relative heavy/light isotope ratio R and fractional conversion F relative to the internal standard for each sample as the reaction progresses. We applied this approach to measure both [1'-13C]lactose and [6'-13C]lactose KIEs for the E. coli β-galactosidase (LacZ) catalyzed hydrolysis of lactose. This MALDI-TOF MS based KIE approach can measure enzymatic KIEs with precision comparable to those obtained using competitive radioisotope labelling, and NMR based approaches. | Teodora Kljaic; Merritt A. Scott; Veronica Guirguis; Michal Tyrlik; Andrew Liu; Myles B. Poulin | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c7e33f658ec5f7e5808827/original/direct-competitive-kinetic-isotope-effect-measurement-using-quantitative-whole-molecule-maldi-tof-mass-spectrometry.pdf |
65a87237e9ebbb4db967be68 | 10.26434/chemrxiv-2024-475km | A Reversible Four-electron Sn Metal Aqueous Battery | Sn is a promising metal anode for aqueous batteries due to its dendrite-free plating, large hydrogen evolution overpotential, and high theoretical capacity with up to four-electron redox per Sn atom. However, practically achieving the theoretical capacity for Sn remains challenging, with only limited cell energy densities demonstrated thus far. We validate a kinetically asymmetric [Sn(OH)6]2-/Sn redox pathway involving a direct four-electron plating and a stepwise 2+2 electron stripping through a [Sn(OH)3]- intermediate, which decreases the Coulombic efficiency (CE) by shuttling to the cathode and promoting chemical self-discharge. By using ion-selective membranes to suppress [Sn(OH)3]- crossover, we demonstrate Sn-Ni full cells with high round-trip efficiency (~80%) and energy density (143.1 Wh L-1). The results provide key understandings to the tradeoffs in engineering reversible multi-electron metal anodes and define a new benchmark for practical energy density that exceeds Sn-based aqueous batteries to date. | Jianbo Wang; Sofia K. Catalina; Zhelong Jiang; Xin Xu; Qin Tracy Zhou; William C. Chueh; J. Tyler Mefford | Inorganic Chemistry; Energy; Electrochemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a87237e9ebbb4db967be68/original/a-reversible-four-electron-sn-metal-aqueous-battery.pdf |
64e5c6a9dd1a73847f571d1e | 10.26434/chemrxiv-2023-h5h2z | HSA-hijacking nanobinders built on bioresponsive prodrugs for combined cancer chemoimmunotherapy | Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer still lacking effective treatment options. Chemotherapy in combination with immunotherapy can restrict tumor progression and repolarize the tumor microenvironment towards an anti-tumor milieu, improving clinical outcome in TNBC patients. The chemotherapeutic drug paclitaxel had been shown to induce immunogenic cell death (ICD), whereas inhibitors of the indoleamine 2,3-dioxygenase 1 (IDO1), whose expression is shared in immune regulatory and tumor cells, have been revealed to enhance the anti-tumor immune response. However, poor bioavailability and pharmacokinetic, off-target effects and hurdles in achieving therapeutic drug concentrations at the target tissue often limit the effectiveness of combination therapies. This work describes the development of novel biomimetic and carrier-free nanobinders (NB) loaded with both paclitaxel and the IDO1 inhibitor NLG919 in the form of bioresponsive prodrugs, and capable of hijacking human serum albumin (HSA). A fine tuning of the preparation conditions allowed to identify NB@5 as the best-performing prodrugs-based nanoformulation. Our data show that NB@5 effectively binds with HSA, demonstrating its protective role in the controlled release of drugs in vitro and suggesting that NB could exploit the protein as the endogenous vehicle for targeted delivery to the tumor site. Our study successfully demonstrates that the drugs encapsulated within the nanobinders are preferentially released under the altered redox conditions commonly found in the tumor microenvironment, thereby inducing cell death, promoting ICD, and inhibiting IDO1. This study highlights the potential of prodrugs-based nanobinders as a promising avenue for the targeted chemoimmunotherapy of TNBC. | Matilde Tubertini; Luca Menilli; Celeste Milani; Cecilia Martini; Maria Luisa Navacchia; Marta Nugnes; Manuela Bartolini; Marina Naldi; Daniele Tedesco; Elisa Martella; Andrea Guerrini; Claudia Ferroni; Francesca Moret; Greta Varchi | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biodegradable Materials; Controlled-Release Systems; Cell and Molecular Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e5c6a9dd1a73847f571d1e/original/hsa-hijacking-nanobinders-built-on-bioresponsive-prodrugs-for-combined-cancer-chemoimmunotherapy.pdf |
64001dc632cd591f12b4fd36 | 10.26434/chemrxiv-2023-51bqx | First Principles Reaction Discovery: From the Schrodinger Equation to Experimental Prediction for Methane Pyrolysis | Our recent success in exploiting graphical processing units (GPUs) to accelerate quantum chemistry computations led to the development of the ab initio nanoreactor, a computational framework for automatic reaction discovery and kinetic model construction. In this work, we apply the ab initio nanoreactor to methane pyrolysis, from automatic reaction discovery to path refinement and kinetic modeling. Elementary reactions occurring during methane pyrolysis are revealed using GPU-accelerated ab initio molecular dynamics simulations. Subsequently, these reaction paths are refined at a higher level of theory with optimized reactant, product, and transition state geometries. Reaction rate coefficients are calculated by transition state theory based on the optimized reaction paths. The discovered reactions lead to a kinetic model with 53 species and 134 reactions, which is validated against experimental data and simulations using literature kinetic models. We highlight the advantage of leveraging local brute force and Monte Carlo sensitivity analysis approaches for efficient identification of important reactions. Both sensitivity approaches can further improve the accuracy of methane pyrolysis kinetic model. The results in this work demonstrate the power of the ab initio nanoreactor framework for computationally affordable systematic reaction discovery and accurate kinetic modeling. | Rui Xu; Jan Meisner; Alexander Chang; Keiran Thompson; Todd Martinez | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64001dc632cd591f12b4fd36/original/first-principles-reaction-discovery-from-the-schrodinger-equation-to-experimental-prediction-for-methane-pyrolysis.pdf |
67d1c7b26dde43c9088eac89 | 10.26434/chemrxiv-2025-0ldl8 | Cation–π Interactions in Biomolecular Contexts Studied by Neutron Scattering and Molecular Dynamics: A Case Study of the Tetramethylammonium Cation | Cation–π interactions involving the tetramethylammonium motif are common in biological systems, where they play essential roles in membrane protein function, DNA expression regulation, and protein folding. However, accurately modeling cation–π interactions, where electronic polarization is crucial, presents a significant computational challenge, especially in large biomolecular systems. This study applies a physically justified electronic continuum correction (ECC) to the CHARMM36 force field, scaling ionic charges by a factor of 0.75 to effectively account for electronic polarization without adding computational overhead. While not specifically designed for cation–π interactions, this approach significantly improves predictions of the structure of an aqueous tetramethylammonium–pyridine complex compared to neutron diffraction data. These results, along with computational predictions for the structure of the aqueous tetramethylammonium–phenol complex, highlight the potential of ECC as a versatile method for improving the description of cation–π interactions in biomolecular simulations. | Matej Cervenka; Brennon Shanks; Philip Mason; Pavel Jungwirth | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d1c7b26dde43c9088eac89/original/cation-interactions-in-biomolecular-contexts-studied-by-neutron-scattering-and-molecular-dynamics-a-case-study-of-the-tetramethylammonium-cation.pdf |
60c75728337d6c3c0ae28fc5 | 10.26434/chemrxiv.14371973.v1 | Facile Conversion of Levulinic Acid and Glucose to γ-Valerolactone over Raney-Ni Catalyst Without an External Hydrogen Donor | Finding
sustainable resources has always been a strong research due to the current massive
consumption of non-renewable fossil fuels on a global scale. Recently, the
transformation of renewable biomass into value-added chemicals has become a
crucial alternative to solve this problem. Levulinic acid (LA) and glucose are
the most significant biomass-derived compounds and <i>γ</i>-valerolactone (GVL) is considered to be the important
intermediate of chemicals and fuels. However, the safety and cost of external
hydrogen are the main obstacles for the production of GVL from biomass and its
derived chemicals by catalytic transfer hydrogenation process. Herein, we
introduce the conversion of LA and glucose-derived LA into GVL without an
external hydrogen donor, respectively. One process is the production of GVL
from LA in a maximum yield of 99% at relatively mild conditions (150 <sup>o</sup>C)
for 3 h with hydrogen, which is from the decarboxylation reaction of formic
acid (FA) in water with Raney Ni. The other process is conversion of glucose
into LA and GVL in two steps. More than 50% yield of LA and 67% yield of GVL could
be obtained from glucose with 3% HCl solution and Raney Ni. | Runtian He; Zhuang Ma; Guodong Yao; Jing Xu | Environmental Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75728337d6c3c0ae28fc5/original/facile-conversion-of-levulinic-acid-and-glucose-to-valerolactone-over-raney-ni-catalyst-without-an-external-hydrogen-donor.pdf |
60c75814842e6574cfdb47d8 | 10.26434/chemrxiv.13562525.v2 | Traffic, Drugs, Mental Health, and Disinfectants: Changes in Sewage Sludge Chemical Signatures During a COVID-19 Community Lockdown | <p>The COVID-19 pandemic and related
shutdowns have caused changes in everyday activities for many people, and signs
of those changes are present in the chemical signatures of sewage sludge
produced during the pandemic. We analyzed primary sewage sludge samples from a
wastewater treatment plant in New Haven, CT USA collected between March 19 and
June 30, 2020. This time period encompassed the first wave of the COVID-19
pandemic, the initial statewide stay at home order, and the first phase of reopening.
We used liquid chromatography coupled with high resolution mass spectrometry and
targeted and suspect screening strategies to identify contaminants in the
sludge. We and found evidence of increasing opioid, cocaine, and antidepressant
use, as well as upward trends in chemicals used in disinfectants and sunscreens
during the study period. Benzotriazole, an anti-corrosion chemical associated
with traffic pollution, decreased through the stay-at-home period, and
increased during reopening. Hydroxychloroquine, a drug that received
significant attention for its potential to treat COVID-19, had elevated concentrations
in the week following the implementation of the United States Emergency Use
Authorization. Our results directly relate to nationwide reports of increased
demand for fentanyl, antidepressants, and other medications, as well as reports
of increased drug overdose deaths during the pandemic. Though wastewater surveillance during the
pandemic has largely focused on measuring SARS-CoV-2 RNA concentrations,
chemical analysis can also show trends that are important for revealing the public
and environmental health effects of the pandemic. </p> | Sara Nason; Elizabeth Lin; Brian D. Eitzer; Jeremy
P. Koelmel; Jordan Peccia | Environmental Analysis; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2021-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75814842e6574cfdb47d8/original/traffic-drugs-mental-health-and-disinfectants-changes-in-sewage-sludge-chemical-signatures-during-a-covid-19-community-lockdown.pdf |
673daadd5a82cea2fadc9884 | 10.26434/chemrxiv-2024-89xtz-v2 | THERMOMETER IONS, INTERNAL ENERGIES, AND IN-SOURCE FRAGMENTATION IN AMBIENT IONIZATION | Ionization and fragmentation are at the core of mass spectrometry. But they are not necessarily separated in space, as in-source fragmentation can also occur. Here we survey the literature published since our 2005 review on the internal energy and fragmentation in electrospray ionization sources (Gabelica, De Pauw 2005). We present new thermometer molecules to diagnose and quantify source heating, provide tables of recommended threshold (E0) and appearance energies (Eapp) for the survival yield method, and attempt to compare the softness of a variety of ambient pressure ionization sources. The droplet size distribution and desolvation dynamics play a major role: lower average internal energies are obtained when the ions remain protected by a solvation shell and spend less time nakedly exposed to activating conditions in the transfer interface. Methods based on small droplet formation without charging can thus be softer than electrospray. New dielectric barrier discharge sources can gas-phase ionize small molecules while conferring barely more internal energy than electrospray ionization. However, the tuning of the entire source interface often has an even greater influence on ion internal energies and fragmentation than on the ionization process itself. We hope that this review will facilitate further research to control and standardize in-source ion activation conditions, and to ensure the transferability of data and research results in mass spectrometry. | Emilie Bertrand; Valérie Gabelica | Physical Chemistry; Analytical Chemistry; Analytical Apparatus; Mass Spectrometry; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673daadd5a82cea2fadc9884/original/thermometer-ions-internal-energies-and-in-source-fragmentation-in-ambient-ionization.pdf |
66f678ae12ff75c3a1a78535 | 10.26434/chemrxiv-2024-crdrh | Mechanosynthesis of ruthenium trisbipyridyl complexes and application in photoredox catalysis in a ball-mill
| Herein, we developed the mechanosynthesis of ruthenium trisbipyridyl complexes. Such complexes can be difficult to prepare in solution, with long reaction times and average yields. With ball-milling, less than 3.5 hours of milling were sufficient to obtain the complexes in high yield. Such complexes were then evaluated as catalysts in the light-promoted mechanochemical reductive dehalogenation reaction. In addition to working under solvent-less conditions, the use of a Hantzsch amide instead of the classical ester allowed to drastically simplify the purification of the final compounds. | Florian Luttringer; Matthieu Lavayssiere; Enita Rastoder; Nikita Salov; Tristan Gravelet; Francois Quintin; Julien Pinaud; Frédéric Lamaty; Xavier Bantreil | Organic Chemistry; Catalysis; Organometallic Chemistry; Photochemistry (Org.); Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f678ae12ff75c3a1a78535/original/mechanosynthesis-of-ruthenium-trisbipyridyl-complexes-and-application-in-photoredox-catalysis-in-a-ball-mill.pdf |
6360990d1db0bdb469418d65 | 10.26434/chemrxiv-2022-3wg9m | A FOXC2 inhibitor, MC-1-F2, as a therapeutic candidate for targeting EMT in castration-resistant prostate cancer | Androgen deprivation therapy (ADT) is the major treatment option for advanced prostate cancer. However, prostate cancer can develop into androgen-independent castration-resistant prostate cancer (CRPC) which is resistant to ADT. Alternative treatments for CRPC have focused on targeting the epithelial-mesenchymal transition (EMT). EMT is governed by a series of transcription factors of which FOXC2 is a central mediator. Our previous research into the inhibition of FOXC2 in breast cancer cells lead to the discovery of MC-1-F2, the first direct inhibitor of FOXC2. During our current study on CRPC, MC-1-F2 has shown a decrease in mesenchymal markers, inhibition of caner stem cell (CSC) properties and decrease in invasive capabilities of CRPC cell lines. We have also demonstrated a synergistic effect between MC-1-F2 and docetaxel treatments, leading to a decrease in docetaxel dosage, suggesting the possible combination therapy of MC-1-F2 and chemotherapeutic drugs for the effective treatment of CRPC. | Maria Castaneda; Liandra Rodriguez; Jihyun Oh; Hanna Suh; Jiyong Lee | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6360990d1db0bdb469418d65/original/a-foxc2-inhibitor-mc-1-f2-as-a-therapeutic-candidate-for-targeting-emt-in-castration-resistant-prostate-cancer.pdf |
60c7518bee301c14a6c7aacf | 10.26434/chemrxiv.13093589.v3 | An Electroreductive Approach to Silyl Radical Chemistry via Strong Si–Cl Bond Activation | The construction of C(sp<sup>3</sup>)–Si bonds is important in synthetic, medicinal, and materials chemistry. In this context, reactions mediated by silyl radicals have become increasingly attractive but methods for accessing these intermediates remain limited. We present a new strategy for silyl radical generation via electroreduction of readily available chlorosilanes. At highly biased potentials, electrochemistry grants access to silyl radicals through energetically uphill reductive cleavage of strong Si–Cl bonds. This strategy proved to be general in various alkene silylation reactions including disilylation, hydrosilylation, and allylic silylation under simple and transition-metal-free conditions. | Lingxiang Lu; Juno Siu; Yihuan Lai; Song Lin | Organic Synthesis and Reactions; Physical Organic Chemistry; Electrochemistry; Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7518bee301c14a6c7aacf/original/an-electroreductive-approach-to-silyl-radical-chemistry-via-strong-si-cl-bond-activation.pdf |
60c74844702a9bf7a318af42 | 10.26434/chemrxiv.11873988.v1 | Development of an Efficient and Sustainable Synthesis of 2-(3-Methyl-1H-1,2,4-Triazol-1-Yl) Acetic Acid Under Continuous-Flow Conditions | A novel, metal-free process for the challenging synthesis of 2-(3-methyl-1<i>H</i>-1,2,4-triazol-1-yl) acetic acid (<b>1</b>) is reported, which features an efficient condensation for the triazole build-up under flow conditions. This continuous, two-step method is atom economical, highly selective and environmentally benign, due to the avoidance of chromatography and isolation steps. Compared to the earlier batch synthetic routes, higher yields were achieved in a flow reactor. In addition, a highly energetic intermediate could be controlled and handled in a safe manner. To generalize the established route, several triazoles were finally prepared under the described conditions, confirming that the methodology could find useful applications for the rapid and sustainable construction of differentially functionalized 1,2,4-triazoles. | Simone Tortoioli; Astrid Friedli; Alice Prud’homme; Sylvia Richard-Bildstein; Philipp Kohler; Stefan Abele; Gianvito Vilé | Process Chemistry; Industrial Manufacturing; Pharmaceutical Industry; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74844702a9bf7a318af42/original/development-of-an-efficient-and-sustainable-synthesis-of-2-3-methyl-1h-1-2-4-triazol-1-yl-acetic-acid-under-continuous-flow-conditions.pdf |
6679915501103d79c5053039 | 10.26434/chemrxiv-2024-cc6ct | Regioselective Palladaelectro-catalyzed Chlorination of Arenes in an Undivided Cell Setup | Chloroarenes constitute fundamental building blocks in organic synthesis and are widely applied in the synthesis of bioactive compounds, fine chemicals, materials, natural products and pharmaceuticals. Electrochemical chlorination has been recognized as a promising synthetic method for accessing chloroarenes, but it has proved challenging to achieve in practice as shown by the limited number of existing protocols. Herein, we report on a highly general electrocatalytic strategy for the regioselective chlorination of various substituted heteroaryl scaffolds in an undivided cell setup, using ethyl chloroformate as the chlorine source. This strategy offers several practical advantages over existing methodologies, including an operationally simple experimental setup, exceptional functional group tolerance, and the possibility to form either the mono- or bis-chlorinated products in high selectivity depending on the choice of catalyst loading, electric current and ethyl chloroformate equivalents. The practicality and selectivity of the protocol were demonstrated by the successful chlorination of an array of densely-substituted arene frameworks as well as by the synthesis of chlorinated bioactive molecules. | Sudipta Ponra; Ruzal Sitdikov; Alyssio Calis; Oscar Verho | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6679915501103d79c5053039/original/regioselective-palladaelectro-catalyzed-chlorination-of-arenes-in-an-undivided-cell-setup.pdf |
648b1a444f8b1884b7554b20 | 10.26434/chemrxiv-2022-00rfw-v2 | Infrared Spectroscopy Reveals Metal independent Carbonic Anhydrase Activity in Crotonyl CoA Carboxylase/Reductase | The conversion of CO2 by enzymes such as carbonic anhydrase or carboxylases plays a crucial role in many biological processes. However, methods following the conversion of CO2 at the active site in situ are limited. Here, we used infrared spectroscopy to study the interaction of CO2, water, and other reactants with β-carbonic anhydrase from Escherichia coli (EcCA) and crotonyl-CoA carboxylase/reductase from Kitasaospora setae (KsCcr), two of the fastest CO2-converting enzymes in nature. Our data reveal that KsCcr possesses a so far unknown metal-independent CA-like activity. Site-directed mutagenesis of conserved active site residues allows identifying an ‘activated’ water molecule, forming the hydroxyl anion that attacks CO2 and yields bicarbonate (HCO3–). Molecular dynamics simulations are analyzed to trace CO2 in the active site of KsCcr and explain why substrate binding inhibits the anhydrase activity. Altogether, we demonstrate how in situ infrared spectroscopy combined with molecular dynamics simulations provides a simple, yet powerful new approach to investigate the atomistic reaction mechanisms of different enzymes with CO2. | Aharon Gomez; Matthias Tinzl; Gabriele Stoffel; Hendrik Westedt; Helmut Grubmüller; Tobias J. Erb; Esteban Vöhringer-Martinez; Sven Stripp | Physical Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biocatalysis; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648b1a444f8b1884b7554b20/original/infrared-spectroscopy-reveals-metal-independent-carbonic-anhydrase-activity-in-crotonyl-co-a-carboxylase-reductase.pdf |
63ffc136897b18336f578063 | 10.26434/chemrxiv-2022-8lr3v-v2 | QM/MM Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms | The search for efficient inhibitors of the SARS-CoV-2 enzymes is ongoing due to the continuing COVID-19 pandemic. We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro ) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have been shown experimentally the ability to inhibit MPro . Two other compounds, X77A and X77C, were designed computationally in this work, derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro . We modified the X77 structure by introducing warheads capable of efficient chemical reactions with the catalytic cysteine residue in the M Pro active site. The reaction mechanisms of the four molecules with M Pro were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations using large quantum subsystems. First, at the QM/MM level, we optimized structures of stationary points on the potential energy surfaces corresponding to the reactants, products, intermediates, and transition states along the hypothesized reaction coordinates. Analysis of these structures has informed the selection of collective variables for the subsequent calculations of the Gibbs energy profiles using molecular dynamics simulations with QM/MM potentials (QM/MM MD). In these simulations, the QM part was treated by DFT with the PBE0 functional. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro . From the chemical perspective, the reactions of these four compounds with M Pro follow three distinct mechanisms. In all cases, the reaction is initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro . In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SN Ar mechanism. The reaction of M Pro with nirmatrelvir, which has a reactive nitrile group, leads to the formation of the covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. | Bella L. Grigorenko; Igor V. Polyakov; Maria G. Khrenova; Goran Giudetti; Shirin Faraji; Anna I. Krylov; Alexander V. Nemukhin | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ffc136897b18336f578063/original/qm-mm-simulations-of-the-covalent-inhibition-of-the-sars-co-v-2-main-protease-four-compounds-and-three-reaction-mechanisms.pdf |
60c75076f96a001c43287e46 | 10.26434/chemrxiv.9942095.v2 | Statistical Mechanical Model of Gas Adsorption in a Metal-Organic Framework Harboring a Rotaxane Molecular Shuttle | Metal-organic frameworks (MOFs) are modular and tunable nano-porous materials with applications in gas storage, separations, and sensing. Flexible/dynamic components that respond to adsorbed gas can give MOFs unique or enhanced adsorption properties. Here, we explore the adsorption properties that could be imparted to a MOF by a rotaxane molecular shuttle (RMS) in its pores. In the unit cell of an RMS-MOF, a macrocyclic wheel is mechanically interlocked with a strut of the MOF scaffold. The wheel shuttles between stations on the strut that are also gas adsorption sites. At a level of abstraction similar to the seminal Langmuir adsorption model, we pose and analyze a simple statistical mechanical model of gas adsorption in an RMS-MOF that accounts for (i) wheel/gas competition for sites on the strut and (ii) gas-induced changes in the configurational entropy of the shuttling wheel. We determine how the amount of gas adsorbed, position of the wheel, and differential energy of adsorption depend on temperature, pressure, and the interactions of the gas/wheel with the stations. Our model reveals that, compared to a rigid, Langmuir material, the chemistry of the RMS-MOF can be tuned to render gas adsorption more or less temperature-sensitive and to release more or less heat upon adsorption. The model also uncovers a non-monotonic relationship between the temperature and the position of the wheel if gas out-competes the wheel for its preferable station. | Jonathan Carney; David Roundy; Cory M. Simon | Nanostructured Materials - Materials; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75076f96a001c43287e46/original/statistical-mechanical-model-of-gas-adsorption-in-a-metal-organic-framework-harboring-a-rotaxane-molecular-shuttle.pdf |
642db043736114c963f884d4 | 10.26434/chemrxiv-2023-jd2m3-v2 | Metadynamics simulations with Bohmian-style bias potential | Here, we present a parametrization of the metadynamics simulations for reactions involving breaking the chemical bonds along a single collective variable coordinate. The parameterization is based on the similarity between the bias potential in metadynamics and the quantum potential in the De Broglie-Bohm formalism. We derive the method and test it on two prototypical reaction types: proton transfer and breaking of the cyclohexene cycle (reversed Diels-Alder reaction). | Denis Tikhonov | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2023-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642db043736114c963f884d4/original/metadynamics-simulations-with-bohmian-style-bias-potential.pdf |
65a7e26ce9ebbb4db95f0fcc | 10.26434/chemrxiv-2023-4dzxg-v2 | Spin Polarized Electron Dynamics Enhance Water Splitting Efficiency by Yttrium Iron Garnet Photoanodes: A New Platform for Spin Selective Photocatalysis | This work presents a spectroscopic and photocatalytic comparison of water splitting using yttrium iron
garnet (Y3Fe5O12, YIG) and hematite (α-Fe2O3) photoanodes. Despite similar electronic structures,
YIG significantly outperforms widely studied hematite, displaying more than an order of magnitude
increase in photocurrent density and a factor of two increase in Faradaic efficiency. Probing the
charge and spin dynamics by ultrafast, surface-sensitive XUV spectroscopy reveals that the enhanced
performance arises from 1) reduced polaron formation in YIG compared to hematite and 2) an intrinsic
spin polarization of catalytic photocurrents in YIG. Ultrafast XUV measurements show a reduction
in the formation of surface electron polarons compared to hematite due to site-dependent electronphonon
coupling. This leads to spin polarized photocurrents in YIG where efficient charge separation
occurs on the Td sub-lattice compared to fast trapping and electron/hole pair recombination on the
Oh sub-lattice. These lattice-dependent dynamics result in a long-lived spin aligned hole population
at the YIG surface, which is directly observed using XUV magnetic circular dichroism. Comparison
of the Fe M2,3 and O L1-edges show that spin aligned holes are hybridized between O 2p and Fe 3d
valence band states, and these holes are responsible for highly efficient, spin selective water oxidation
by YIG. Together, these results point to YIG as a new platform for highly efficient, spin selective
photocatalysis. | Harshad Gajapathy; Savini Bandaranayake; Emily Hruska; Aravind Vadakkayil; Brian P. Bloom; Stephen Londo; Jackson McClellan; Jason Guo; Daniel Russell; Frank M. F. de Groot; Fengyuan Yang; David H. Waldeck; Martin Schultze; L. Robert Baker | Physical Chemistry; Catalysis; Energy; Photocatalysis; Fuels - Energy Science; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a7e26ce9ebbb4db95f0fcc/original/spin-polarized-electron-dynamics-enhance-water-splitting-efficiency-by-yttrium-iron-garnet-photoanodes-a-new-platform-for-spin-selective-photocatalysis.pdf |
63c531a25ad3ef06879afcf2 | 10.26434/chemrxiv-2023-10jnh | Mechanical deformation affects the condensation of counterions in highly swollen polyelectrolyte hydrogels. | Polyelectrolyte gels can generate electric potentials under mechanical deformation. While the underlying mechanism of such response is often attributed to the changes in counterion-condensation levels or alterations in the ionic conditions in the pervaded volume of the hydrogel, exact molecular origins are still unknown. By using all-atom molecular dynamics simulations of a polyacrylic acid hydrogel in explicit water as a model system, we simulate the uniaxial compression and uniaxial stretching deformations of a highly-swollen (i.e., $>$90\% solvent content) hydrogel network and calculate the microscopic condensation levels of counterions around the gel chains. The counterion condensation is highly non-monotonic, and both compression and stretching increase the overall counterion condensation in the hydrogel with deformation. The effect weakens for weakly swollen hydrogels. The condensation profiles around the chains of the deformed hydrogel are highly anisotropic; the condensation tends to increase for the stretched chains of the hydrogel. However, this increase reaches a maximum and decreases as the chains are strongly stretched under uniaxial extension. Under compression, the condensation around the chains perpendicular to the deformation direction increases. For the same reason, the hydrogel chains in the constrained and unconstrained (deformation-free) directions exhibit opposing condensation behaviors. Further, the deformation-induced counterion condensation does not occur in a semi-dilute polyelectrolyte solution, suggesting the role of hydrogel topology constraining the chain ends in this phenomenon. Our results indicate that counterion condensation in a deforming polyelectrolyte hydrogel can be highly heterogeneous and depends on the conformations of constituting chains. | Muzaffar Rafique; Aykut Erbas | Materials Science; Polymer Science; Hydrogels; Polyelectrolytes - Polymers | CC BY 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c531a25ad3ef06879afcf2/original/mechanical-deformation-affects-the-condensation-of-counterions-in-highly-swollen-polyelectrolyte-hydrogels.pdf |
60c73e07337d6ce916e2627a | 10.26434/chemrxiv.6265148.v1 | N-Acylation of Oxazolidinones via Aerobic Oxidative NHC Catalysis | <p>In the ongoing quest to find alternatives to atom un-economical and forcing conditions in acylation reactions, aerobic oxidative NHC catalysis has emerged as a method to convert aldehydes to potent acylating reagents. This strategy has been utilized in the esterification of alcohols but not yet been shown for densely polyfunctionalized <i>N</i>- heterocycles such as, oxazolidinones and pyrrolidinones. Conventional acylation of oxazolidinones are typically associated with forcing reaction conditions, requiring separate activation steps and strong bases, which does not adhere to the principles of green chemistry. For reasons of waste prevention, atom economy, less hazardous syntheses and reduction of derivatives finding alternative methods are desirable.</p><p> </p>In this manuscript, we demonstrate the synthesis of several <i>N</i>-acylated oxazolidinones and pyrrolidinones that are chemically relevant, both found as pharmaceuticals and natural products as well as auxiliaries for synthesis. The developed method operates at room temperature and can be performed in ethyl acetate with open reaction vessels. The substrate scope is broad, with products isolated in good to excellent yields. The functional group tolerance is exemplified with 22 entries, where different aldehydes, oxazolidinones and pyrrolidinones are systematically investigated. Moreover, the reaction is clean as water is generated as the only byproduct. | Linda Ta; Anton Axelsson; Henrik Sundén | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2018-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e07337d6ce916e2627a/original/n-acylation-of-oxazolidinones-via-aerobic-oxidative-nhc-catalysis.pdf |
60c74da2337d6c8bdfe27e00 | 10.26434/chemrxiv.12643154.v1 | Inter- and Intramolecular Aryl-Aryl-Interactions in Partially Fluorinated Ethylenedioxy-Bridged Bisarenes | Several ethylenedioxy-bridged bisarenes with a variety of
type and number of aryl groups were synthesized to study non-covalent dispersion-driven inter- and intramolecular aryl-aryl-interactions
in the solid state and gas phase. Intramolecular interactions are preferably found in the gas phase. DFT calculations of dispersion-corrected energy scans for rotations around the ethylenedioxy-bridge
and optimized structures show larger interacting aromatic groups to
increase the dispersion energy. Single molecule structures generally
adopt folded conformations with short intramolecular aryl-aryl-contacts. Gas electron diffraction experiments were performed exemplarily for 1-(pentafluorophenoxy)-2-(phenoxy)ethane. A new procedure
for structure refinement was developed to deal with the conformational complexity of such molecules. The results are an experimental
confirmation of the existence of folded conformations of this
molecule with short -intramolecular aryl-aryl distances in the gas
phase. Solid-state structures are dominated by stretched structures
without intramolecular aryl-aryl-interactions but interactions with
neighboring molecules<br /> | Jan-Henrik Weddeling; Yury Vishnevskiy; Beate Neumann; Hans-Georg Stammler; Norbert W. Mitzel | Structure; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da2337d6c8bdfe27e00/original/inter-and-intramolecular-aryl-aryl-interactions-in-partially-fluorinated-ethylenedioxy-bridged-bisarenes.pdf |
67a0174a6dde43c90866b0f2 | 10.26434/chemrxiv-2025-5vptv | Accelerated ReaxFF Simulations of Vitrimers with Dynamic Covalent Adaptive Networks | Vitrimers are a novel class of sustainable polymers with dynamics covalent adaptive networks driven by bond exchange reactions between different constituents, making vitrimers reprocessable and recyclable. Current modeling approaches of bond exchange reactions fall short in realistically capturing the complete reaction pathways, which limit our understanding the viscoelastic properties of vitrimers. This research addresses these limitations by extending and employing Accelerated Reactive Molecular Dynamics (ReaxFF) technique, thus enabling a more accurate representation of vitrimer viscoelas- tic behavior at the molecular level. Bayesian optimization is employed to select force field parameters within the Accelerated ReaxFF framework, and an empirical function is proposed to model temperature dependency, thereby controlling reaction probabil- ities under varying temperatures. The extended framework is employed to simulate non-isothermal creep behavior of vitrimers under different applied stress levels, heating rates and numbers of reactions. The simulation results agree with experimental findings in literature, validating the robustness of the framework. | Yiwen Zheng; Vikas Varshney; Aniruddh Vashisth | Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Polymer morphology; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a0174a6dde43c90866b0f2/original/accelerated-reax-ff-simulations-of-vitrimers-with-dynamic-covalent-adaptive-networks.pdf |
62a1906ba784d14e91786193 | 10.26434/chemrxiv-2022-x9h5f | Photochemical Strategies Enable the Synthesis of Tunable Azetidine-Based Energetic Materials | Despite their favorable properties, azetidines are often overlooked as lead compounds across multiple industries. This is often attributed to the challenging synthesis of densely functionalized azetidines in an efficient manner. In this work, we report the scalable synthesis and characterization of seven azetidines with varying regio- and stereochemistry, and their application as novel azetidine-based energetic materials, enabled by the visible light-mediated aza Paternò-Büchi reaction. The performance and
stark differences in physical properties of these new compounds make them excellent potential candidates as novel solid melt-castable explosive materials, as well as potential liquid propellant plasticizers. The nitroazetidine materials synthesized exhibit reasonable sensitivities, higher densities, better oxygen balances, increased detonation pressures and velocities, as well as improved specific impulses, compared to the state-of-the-art materials. This work highlights the scalability and utility of the visible-light aza Paternò-Büchi reaction and demonstrates the impact of stereochemical considerations on the physical properties of azetidine-based energetics. Considering the versatility and efficiency of the presented synthetic strategies, we expect that this work will guide the development of new azetidine-based materials in the energetics space as well as other industries, including pharmaceuticals and agrochemicals. | Corinna Schindler; Katie Rykaczewski; Marc Becker; Manasi Anantpur; Rosario Sausa; Eric Johnson; Joshua Orlicki; Eric Bukowski; Jesse Sabatini | Organic Chemistry; Catalysis; Photochemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a1906ba784d14e91786193/original/photochemical-strategies-enable-the-synthesis-of-tunable-azetidine-based-energetic-materials.pdf |
60c74be9bdbb8972a0a396b7 | 10.26434/chemrxiv.12389585.v1 | Design and Scalable Synthesis of Novel N-Alkyl-Hydroxylamine Reagents for the Direct, Fe-Catalyzed Installation of Medicinally Relevant Amines | <p>Secondary
and tertiary alkylamines are privileged substance classes which are often found
in pharmaceuticals and other biologically active small molecules. Herein, we
report their direct synthesis from alkenes through an aminative
difunctionalization reaction enabled by iron catalysis.
A family of nine novel hydroxylamine-derived aminating
reagents was designed for the installation of several medicinally relevant amine
groups, such as methylamine, morpholine and piperazine, through the
aminochlorination of alkenes. The methodology
displays an excellent functional group tolerance, and a broad scope of alkenes was
converted to the corresponding products, including several drug-like molecules.
Besides aminochlorination, the installation of other functionalities through aminoazidation,
aminohydroxylation and even intramolecular carboamination reactions, is demonstrated,
further highlighting the broad potential of these new reagents for the discovery
of novel amination reactions.</p> | Eric Falk; Szabolcs Makai; Tristan Delcaillau; Laura Gürtler; Bill Morandi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74be9bdbb8972a0a396b7/original/design-and-scalable-synthesis-of-novel-n-alkyl-hydroxylamine-reagents-for-the-direct-fe-catalyzed-installation-of-medicinally-relevant-amines.pdf |
60c749fa337d6c8576e277d1 | 10.26434/chemrxiv.12136320.v1 | Head-to-head comparison of the penetration efficiency of lipid-based nanoparticles in a 3D tumor spheroid model | <p>Most tumor-targeted drug delivery systems must overcome a large variety of physiological barriers before reaching the tumor site and diffuse through the tight network of tumor cells. Many studies focus on optimizing the first part, the accumulation of drug carriers at the tumor site, ignoring the penetration efficiency, i.e., a measure of the ability of a drug delivery system to overcome tumor surface adherence and uptake. We used 3D tumor spheroids in combination with light-sheet fluorescence microscopy in a head-to-head comparison of a variety of commonly used lipid-based nanoparticles, including liposomes, PEGylated liposomes, lipoplexes and reconstituted high-density lipoproteins (rHDL). Whilst PEGylation of liposomes only had minor effects on the penetration efficiency, we show that lipoplexes mainly associated to the periphery of tumor spheroids, possibly due to their positive surface charge leading to fusion with the cells at the spheroid surface or aggregation. Surprisingly, the rHDL showed significantly higher penetration efficiency and high accumulation inside the spheroid. While these findings indeed could be relevant when designing novel drug delivery systems based on lipid-based nanoparticles, we stress that the used platform and detailed image analysis is a versatile tool for in vitro studies of the penetration efficiency of nanoparticles in tumors.</p><div><br /></div> | Maria Niora; Dennis Pedersbæk; Rasmus Mikkel Münter Lassen; Matilda Felicia de Val Weywadt; Thomas Lars Andresen; Jens Bæk Simonsen; Liselotte Jauffred | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749fa337d6c8576e277d1/original/head-to-head-comparison-of-the-penetration-efficiency-of-lipid-based-nanoparticles-in-a-3d-tumor-spheroid-model.pdf |
60c75046567dfe5dacec5830 | 10.26434/chemrxiv.13012895.v1 | Synthesis of Cyclopentenones with Reverse Pauson-Khand Regiocontrol via Ni-Catalyzed C–C Activation of Cyclopropanone | A formal [3+2] cycloaddition between cyclopropanone and alkynes via Ni-catalyzed C–C bond activation has been developed,
where 1-sulfonylcyclopropanols are employed as key precursors of cyclopropanone in the presence of trimethylaluminum. The transformation
provides access to 2,3-disubstituted cyclopentenones with complete regiocontrol, favoring reverse Pauson-Khand products where the large
substituent is located at the 3-position of the ring. In the process, the trimethylaluminum additive is thought to play multiple roles, including as
a Brønsted base triggering the equilibration to cyclopropanone and liberation of methane, as well as a source of Lewis acid to activate the carbonyl group toward Ni-catalyzed C–C activation. | Yujin Jang; Vincent Lindsay | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75046567dfe5dacec5830/original/synthesis-of-cyclopentenones-with-reverse-pauson-khand-regiocontrol-via-ni-catalyzed-c-c-activation-of-cyclopropanone.pdf |
6511710d60c37f4f766ab2b7 | 10.26434/chemrxiv-2023-0xhnx | Fundamental response and salinity tolerance in Brassicaceae
Plants
| This review comprehensively explores the response of Brassica sp. to saline conditions and its implications for sustainable agriculture. The detrimental effects of soil salinity on agricultural land are significant, resulting in substantial economic losses and diminished crop yields. Within this context, salinity disrupts the normal growth and development of Brassica sp. impacting crucial physiological and biochemical processes, particularly photosynthesis and water use efficiency. Understanding the mechanisms underlying these responses is critical for developing effective strategies to mitigate the adverse effects of salinity and ensure sustainable agricultural practices. Researchers have devoted considerable effort to studying salt-tolerant genotypes of Brassica sp, which exhibit improved resilience to saline environments. Through comprehensive investigations, they have elucidated the intricate molecular mechanisms responsible for conferring salt tolerance in these genotypes. These mechanisms involve the activation and/or regulation of specific salt-tolerant genes, playing a pivotal role in mitigating the harmful effects of salinity. In addition to molecular mechanisms, plants, including Brassica juncea, have evolved various morphological, physiological, and biochemical adaptations to cope with abiotic stresses like salinity. These adaptations include the deposition of organic compounds, the maintenance of ionic homeostasis, the scavenging of free radicals, and the induction of phytohormones. These complex responses collectively contribute to the plant's ability to tolerate and adapt to salinity, ultimately promoting its survival and productivity in challenging environments. By unravelling the intricacies of the response of Brassica sp. to saline conditions and understanding the underlying molecular and physiological processes, researchers and agricultural practitioners can develop targeted strategies to improve salt tolerance in this species and others facing similar challenges. Implementing these strategies can enhance long-term food production and ensure sustainable agricultural practices, even in the face of increasing global population and the adverse impacts of climate change. | Saheli Roy | Agriculture and Food Chemistry; Food | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6511710d60c37f4f766ab2b7/original/fundamental-response-and-salinity-tolerance-in-brassicaceae-plants.pdf |
665721de21291e5d1d8aba42 | 10.26434/chemrxiv-2024-bd612 | Electronic Structure of a Neodymium(III) tris(oxydiacetate) Complex from Luminescence data and ab initio Calculations | Neodymium(III) is a NIR emissive and magnetic ion, which has found use in various high-technology applications. Yet, accurate predictions of the luminescent and magnetic properties of neodymium(III) based on the coordination environment remain to be done. Guideline exists, but to build structure-property relationships for this element, more data are needed. Herein, we present a high-symmetry starting point. The tris(oxydiacetate) complex of neodymium(III) was prepared and crystallised, and access to the experimentally determined structure allows us to quantify the symmetry of the compound and to perform calculations directly on the same structure that is investigated experimentally. The luminescent properties were determined and the electronic structure was computed using state-of-the-art ab initio methods. All electronic transitions in the range from 490 to 1400 nm were mapped experimentally. Using a Boltzmann population analysis, the combination of the excitation and emission spectra revealed the crystal field splitting of the 18 lowest energy Kramers levels that experimentally could be unambiguously resolved. This assignment was supported by ab initio calculations and the crystal field splitting was well reproduced. The electronic structure reported for the tris(oxydiacetate) complex is used to deduce the coordination structure in aqueous solution. Finally, the results are compared to empirical trends in the literature for the electronic structure of neodymium(III). | Villads R. M. Nielsen; Maxime Grasser; Sabina Svava Mortensen; Boris Le Guennic; Thomas Just Sørensen | Theoretical and Computational Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665721de21291e5d1d8aba42/original/electronic-structure-of-a-neodymium-iii-tris-oxydiacetate-complex-from-luminescence-data-and-ab-initio-calculations.pdf |
647d7ef2e64f843f415a390e | 10.26434/chemrxiv-2023-khxsp-v2 | Exposomic Biomonitoring of Polyphenols by Non-Targeted Analysis and Suspect Screening | Polyphenols, prevalent in plants and fungi, are investigated intensively in nutritional and clinical settings because of their beneficial bioactive properties. Due to their complexity, analysis with untargeted approaches is favorable, which typically use high-resolution mass spectrometry (HRMS) rather than low-resolution mass spectrometry (LRMS). The advantages of HRMS were evaluated here by thoroughly testing untargeted techniques and available online resources. By applying data-dependent acquisition on real-life urine samples, 27 features were annotated with spectral libraries, 88 with in silico fragmentation, and 113 by MS1 using PhytoHub, an online database containing >2000 polyphenols. Moreover, other exogenous and endogenous molecules were screened to measure chemical exposure and a potential metabolic effect using the Exposome-Explorer database, yielding an additional 144 annotated features. Additional polyphenol-related features were explored using various non-targeted analysis techniques including MassQL for glucuronide and sulfate neutral losses, and MetaboAnalyst for statistical analysis. As HRMS typically suffers a sensitivity loss compared to state-of-the-art LRMS used in targeted workflows, this gap between the two instrumental approaches was quantified in three spiked human matrices (urine, serum, plasma) as well as real-life urine samples. Both instruments showed feasible sensitivity, with median limits of detection in the spiked samples being 10 - 18 ng/mL for HRMS and 4.8 - 5.8 ng/mL for LRMS. The results demonstrate that despite its intrinsic limitations, HRMS can readily be used for comprehensively investigating human exposure. In the future, this work is expected to allow for linking human health effects with polyphenol exposure, and toxicological mixture effects with other xenobiotics. | Ian Oesterle; Manuel Pristner; Sabrina Berger; Mingxun Wang; Vinicius Verri Hernandes; Annette Rompel; Benedikt Warth | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2023-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647d7ef2e64f843f415a390e/original/exposomic-biomonitoring-of-polyphenols-by-non-targeted-analysis-and-suspect-screening.pdf |
6563b9805bc9fcb5c97135fa | 10.26434/chemrxiv-2022-jh0h7-v2 | Flexible Nanogenerators based on Enhanced Flexoelectricity in Mn3O4 Membranes | Atomically thin, few-layered membranes of oxides show unique physical and chemical properties compared to their bulk forms. We have exfoliated manganese oxide (Mn3O4) membranes from the naturally occurring mineral Hausmannite and used them to make flexible, high-performance nanogenerators. We observe an enhanced power density in the membrane nanogenerators (NG) with the best-performing device showing a power density of 7.99 mW m-2 compared to 1.04 µW m-2 obtained from NG made up of bulk Mn3O4. We also observe a sensitivity of 108 mV kPa-1 for applied forces < 10 N in the membrane NGs. We attribute the improved performance of these NGs to enhanced flexoelectric response in few-layers of Mn3O4. Using first-principles calculations, we calculate the flexoelectric coefficients of monolayer and bilayer Mn3O4, and find them to be 50 – 100 times larger than other two-dimensional transition metal dichalcogenides (TMDCs). Using a model based on classical beam theory, we find increasing activation of the bending mode with decreasing thickness of the oxide membranes, which in turn leads to a large flexoelectric response. As a proof-of-concept, we made flexible nanogenerators using exfoliated Mn3O4 membranes and used them in self-powered paper-based devices. This research paves the way for the exploration of few-layered membranes of other centrosymmetric oxides for application as energy harvesters. | Chinmayee Gowda; John Cavin; Partha Kumbhakar; Chandra Sekhar Tiwary; Rohan Mishra | Materials Science; Nanoscience; Energy; Ceramics; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2023-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6563b9805bc9fcb5c97135fa/original/flexible-nanogenerators-based-on-enhanced-flexoelectricity-in-mn3o4-membranes.pdf |
61aa3660bc299c725f87e5ef | 10.26434/chemrxiv-2021-3lqf7 | Redox-addressable single-molecule junctions incorporating a persistent organic radical | The integration of radical (open-shell) species into single-molecule junctions at non-cryogenic temperatures is a key to unlocking the potential of molecular electronics in further applications. While many efforts have been devoted to this issue, in the absence of a chemical or electrochemical potential the open-shell character is lost when in contact with the metallic electrodes. Here, the organic 6-oxo-verdazyl radical, which is stable at ambient temperatures and atmosphere, has been functionalised by aurophilic 4-thioanisole groups at the 1,5-positions and fabricated into a molecular junction using the scanning tunnelling microscope break-junction technique. The verdazyl moiety retains open-shell character within the junction even at room temperature, and electrochemical gating permits in-situ reduction of the verdazyl to the closed-shell anionic state in a single-molecule transistor configuration. In addition, the bias-dependent alignment of the open-shell resonances with respect to the electrode Fermi levels gives rise to purely electronically-driven rectifying behaviour. The demonstration of a verdazyl-based molecular junction capable of integrating radical character, transistor-like switching behaviour, and rectification in a single molecular component under ambient conditions paves the way for further studies of the electronic, magnetic, and thermoelectric properties of open-shell species. | Saman Naghibi; Sara Sangtarash; Varshini J. Kumar; Jian-Zhong Wu; Martyna M. Judd; Xiaohang Qiao; Elena Gorenskaia; Simon J. Higgins; Nicholas Cox; Richard J. Nichols; Hatef Sadeghi; Paul J. Low; Andrea Vezzoli | Physical Chemistry; Nanoscience; Nanodevices; Physical and Chemical Processes; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61aa3660bc299c725f87e5ef/original/redox-addressable-single-molecule-junctions-incorporating-a-persistent-organic-radical.pdf |
654e5e0a6e0ec7777fb49401 | 10.26434/chemrxiv-2023-bmn60 | Contributory roles of concentration and pH in CaCO3 growth inhibition by additive Ca2+ ions | CaCO3 particles grow excessively upon chemical precipitation in the absence of impurities or growth inhibitors. Additive Ca2+ ions have been shown to preferentially adsorb on CaCO3 precipitates, effectively inhibiting their growth and promoting the crystallization of pure calcite without an observable intermediate phase. This phenomenon can be adapted towards the synthesis of small calcite particles from a conventional chemical precipitation method. Complementing such effort, this study discusses the influence of additive Ca2+ ions concentration and solution pH on the extent of CaCO3 growth inhibition. Equal volumes of equimolar CaCl2 and Na2CO3 solutions were mixed in a tubular reactor at a constant flowrate. The precipitates were continuously dispersed in Ca(OH)2 solution, where Ca2+ ions irreversibly adsorb on their surfaces. Compared to conditions where additive Ca2+ ions are absent, this method can produce more than 90% decrease in particle size. The results show the degree of growth inhibition increases as the concentration of additive Ca2+ ions increase. However, it is limited by increasing volume of precipitates. This study also reveals an unusual role of media pH. Here, growth inhibition that leads to the synthesis of monodisperse submicron CaCO3 particles is only observed in high alkaline pH conditions. This is due to the hydration of additive Ca2+ ions in low pH conditions. While additive Ca2+ ions adsorb on CaCO3 precipitates in pH conditions above the isoelectric point (pH ≈ 9), their ability to limit CaCO3 growth diminishes when pH < 12. | Olukayode Majekodunmi; Sevgi Kilic; Ekrem Ozdemir | Materials Science; Chemical Engineering and Industrial Chemistry; Biocompatible Materials; Coating Materials; Nanostructured Materials - Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654e5e0a6e0ec7777fb49401/original/contributory-roles-of-concentration-and-p-h-in-ca-co3-growth-inhibition-by-additive-ca2-ions.pdf |
6554c4c56e0ec7777ffef890 | 10.26434/chemrxiv-2023-q09db | Metastability of Protein Solution Structures in the Absence of Solvent: Rugged Energy Landscape and Glass-Like Behavior | Despite the significance of differentially modified proteins (proteoforms) to human health, it remains challenging to identify how proteoforms alter protein structural dynamics and function. Although native ion mobility/mass spectrometry is well-suited to handle proteoform heterogeneity, it characterizes protein structures in the absence of solvent. This raises long-standing, unanswered questions about the biological significance of structures identified through ion mobility/mass spectrometry. Using newly developed computational and experimental ion mobility/ion mobility/mass spectrometry methods, we investigate the structural denaturation of the protein ubiquitin in the solvent-free environment. We show that ubiquitin exists in the absence of solvent as an ensemble of kinetically stable subpopulations that are separated by substantial free energy barriers. These subpopulations unfold but do not interconvert, which indicates that the solvent-free subpopulations originate from different solution-phase conformations. The subpopulations exhibit stretched-exponential denaturation kinetics consistent with a glass transition associated with separating the C-terminal beta-strand from the N-terminal beta-hairpin occurring on the folded side of the unfolding transition state. Our data indicate that this transition state is highly polarized with significant native content in the N-terminal beta-hairpin and alpha-helix, resembling the transition state reported for the presence of a solvent. Taken together, our analysis suggests that ubiquitin in the solvent-free environment reflects the conformational ensemble of ubiquitin in solution because the initially formed solvent-free state of ubiquitin appears glass-like and “melts” over several seconds. | Tyler C. Cropley; Fanny C. Liu; Mengqi Chai; Matthew F. Bush; Christian Bleiholder | Physical Chemistry; Analytical Chemistry; Mass Spectrometry; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6554c4c56e0ec7777ffef890/original/metastability-of-protein-solution-structures-in-the-absence-of-solvent-rugged-energy-landscape-and-glass-like-behavior.pdf |
67bc113381d2151a02c85980 | 10.26434/chemrxiv-2025-xf4bl | Nitrogen Abundant Hexaazatriphenylene-diaminobenzidine Covalent Organic Framework as Promising Cathode Material in Lithium-ion Battery | In recent years, covalent organic frameworks (COFs) have emerged as promising materials because of their porosity, crystallinity, tunability and composition of lightweight elements. Conventionally, COFs have been mostly synthesized by reversible reactions to impart crystallinity. However, irreversible aromatic nucleophilic substitution reactions can lead to more stable materials which are much more relevant to electrochemical applications. Embedding nitrogen atoms in the rigid carbon framework in the form of phenazine and secondary arylamine moieties provides redox-active sites to the material which has been shown to provide impressive performance as cathode material in lithium-ion batteries. Herein, we report a nitrogen-rich, hexaazatriphenylene-diaminobenzidine based COF through -C-N- linkages synthesized via irreversible aromatic nucleophilic reactions. Due to its diverse structural features, our COF serves as a highly viable electrode material, demonstrating excellent stability and recyclability in Li-ion batteries. Our COF achieves an impressive capacity of 265 mAh/g at a current density of 0.02 A/g, with a remarkable energy density of 607 Wh/kg. Furthermore, it retains a high Coulombic efficiency of ~98% throughout the charge-discharge process even after several hundred cycles. | Korak Kar; Sabiar Rahaman; Yuchen Liu; Bhalerao Krishna ; Hiran Jyothilal; Benjamin Duff; Dinachandra Singh; Basker Sundararaju; Kumar Biradha; Ashok Keerthi | Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc113381d2151a02c85980/original/nitrogen-abundant-hexaazatriphenylene-diaminobenzidine-covalent-organic-framework-as-promising-cathode-material-in-lithium-ion-battery.pdf |
60c744bc842e65a324db24fc | 10.26434/chemrxiv.9902582.v1 | Discontinuous Behavior of the Pauli Potential in Density Functional Theory as a Function of the Electron Number | <div>The Pauli potential is an essential quantity in orbital-free density-functional theory (DFT) and in the exact electron factorization (EEF) method for many-electron systems. Knowledge of the Pauli potential allows the description of a system relying on the density alone, without the need to calculate the orbitals.</div><div>In this work we explore the behavior of the exact Pauli potential in finite systems as a function of the number of electrons, employing the ensemble approach in DFT. Assuming the system is in contact with an electron reservoir, we allow the number of electrons to vary continuously and to obtain fractional as well as integer values. We derive an expression for the Pauli potential for a spin-polarized system with a fractional number of electrons and find that when the electron number surpasses an integer, the Pauli potential jumps by a spatially uniform constant, similarly to the Kohn-Sham potential. The magnitude of the jump equals the Kohn-Sham gap. We illustrate our analytical findings by calculating the exact and approximate Pauli potentials for Li and Na atoms with fractional numbers of electrons.</div> | Eli Kraisler; Axel Schild | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744bc842e65a324db24fc/original/discontinuous-behavior-of-the-pauli-potential-in-density-functional-theory-as-a-function-of-the-electron-number.pdf |
65d22ce7e9ebbb4db9a1e9ca | 10.26434/chemrxiv-2024-pzhcs | Analysis of kinetic asymmetry in a multi-cycle chemical reaction network establishes the principles for autonomous compartmentalized molecular ratchets | Kinetic asymmetry is a key parameter describing non-equilibrium chemical systems: it indicates the directionality of a chemical reaction network under steady-state, non-equilibrium conditions. So far, kinetic asymmetry has been evaluated only in networks featuring a single cycle. Here, we have investigated kinetic asymmetry in a multi-cycle system using a combined theoretical and numerical approach. Inspired by the latest experimental developments, we selected a com-partmentalized redox-controlled network as a model system. We report the general analytical expression of kinetic asymmetry for multi-cycle networks, and specify it for the present system, which allows anticipating how key parameters influence directionality. We establish that compartmentalization can enable autonomous energy ratchet mechanisms, with directionality dictated by the system's thermodynamics. Kinetic simulations confirm analytical findings and illustrate the interplay between diffusion, chemical, and electrochemical processes. The presented treatment is general, as the same procedure can be used to assess kinetic asymmetry in other multi-cycle networks, facilitating the realization of en-dergonic processes across domains. | Emanuele Penocchio; Ahmad Bachir; Alberto Credi; R. Dean Astumian; Giulio Ragazzon | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Chemical Kinetics; Thermodynamics (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d22ce7e9ebbb4db9a1e9ca/original/analysis-of-kinetic-asymmetry-in-a-multi-cycle-chemical-reaction-network-establishes-the-principles-for-autonomous-compartmentalized-molecular-ratchets.pdf |
60c73dd4ee301ca74ec7863d | 10.26434/chemrxiv.5909824.v2 | A Blueprint for the Synthesis and Characterisation of Thin Graphene Oxide with Controlled Lateral Dimensions for Biomedicine | We report the reproducible production of graphene oxide flakes of controlled lateral dimensions under endotoxin free conditions for biomedical and hazard assessment investigations. In addition, we report the thorough characterisation of those materials, using optical, atomic force, electron microcopies; fluorescence, UV/Vis and Raman spectroscopies; Zeta potential, FTIR, TGA, and XPS. We identified that a combination of microscopic techniques are needed to fully assess the lateral dimensions of GO flakes. <br /> | Artur Rodrigues; Leon Newman; Neus Lozano; Sourav Prasanna Mukherjee; Bengt Fadeel; Cyrill Bussy; Kostas Kostarelos | Nanostructured Materials - Nanoscience; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2018-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd4ee301ca74ec7863d/original/a-blueprint-for-the-synthesis-and-characterisation-of-thin-graphene-oxide-with-controlled-lateral-dimensions-for-biomedicine.pdf |
6692501201103d79c5e6420c | 10.26434/chemrxiv-2024-1lxr0 | UMRSF-TDDFT: Unrestricted Mixed-Reference Spin-Flip-TDDFT | An unrestricted version of Mixed-Reference Spin-Flip Time-Dependent Density Functional Theory (UMRSF-TDDFT) was developed based on unrestricted Kohn-Sham orbitals (UKS) with a new molecular orbital (MO) reordering scheme. Additionally, a simple yet accurate method for estimating \( \langle S^2 \rangle \) expectation values was devised. UMRSF-TDDFT was benchmarked against cases where DFT, TDDFT, and SF-TDDFT traditionally fail to provide accurate descriptions. In an application to the ground and excited states of a Be atom, UMRSF-TDDFT successfully recovers the degenerate states, with its energies slightly reduced compared to its RO counterpart, due to the additional variational flexibility of UKS. A clear difference between UMRSF and U-SF-TDDFT is evident in the bond breaking of the hydrogen fluoride system, as the latter misses an important configuration. In the case of the Jahn-Teller distortion of trimethylenemethane (TMM), the relative singlet energy compared to the triplet is lower by 0.1 eV and 0.2 eV for UMRSF and U-SF-TDDFT, respectively, than that of MRSF-TDDFT. The reduction in UMRSF energy is attributed to spatial orbital relaxations, whereas the reduction in U-SF-TDDFT energy results from spin contamination. Overall, the additional orbital relaxations afforded by unrestricted Kohn-Sham (UKS) orbitals in UMRSF-TDDFT lead to lower total system energies compared to their restricted open-shell counterparts. This enhancement adds a practical and accurate quantum chemical theory to the existing RO variant for addressing challenging systems where traditional quantum theories suffer. | Konstantin Komarov; Minseok Oh; Hiroya Nakata; Seunghoon Lee; Cheol Ho Choi | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2024-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6692501201103d79c5e6420c/original/umrsf-tddft-unrestricted-mixed-reference-spin-flip-tddft.pdf |
65b0e1e366c138172928b246 | 10.26434/chemrxiv-2024-qlgdz-v3 | Understanding the resolution and sensitivity in photothermal nanoscale chemical imaging - a point spread function approach | Atomic force microscopy-infrared spectroscopy (AFM-IR) is a photothermal scanning probe technique that combines nanoscale spatial resolution with the chemical analysis capability of mid-infrared spectroscopy. Using this hybrid technique, chemical identification down to the single molecule level has been demonstrated. However, the mechanism at the heart of AFM-IR, the transduction of local photothermal heating to cantilever deflection, is still not fully understood. Existing physical models only describe this process in few special cases but not in many of the types of sample geometries encountered in the practical use of AFM-IR. In this work an analytical expression for modeling the temperature and photothermal expansion process is introduced, verified with finite element simulations and validated with AFM-IR experiments. This method describes AFM-IR signal amplitudes in vertically and laterally heterogeneous samples and allows us study the effect of position and size of an absorber, laser repetition rate and pulse width on AFM-IR signal amplitudes and spatial resolution. The analytical can be used to identify optimal AFM-IR experimental settings in conventional and advanced AFM-IR modes (e.g., tapping mode, surface sensitive mode). It also paves the way for signal inversion based super-resolution AFM-IR. | Yide Zhang; Ufuk Yilmaz; Gustavo Vinicius Bassi Lukasievicz; Liam O’Faolain; Bernhard Lendl; Georg Ramer | Analytical Chemistry; Nanoscience; Analytical Apparatus; Imaging | CC BY 4.0 | CHEMRXIV | 2024-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b0e1e366c138172928b246/original/understanding-the-resolution-and-sensitivity-in-photothermal-nanoscale-chemical-imaging-a-point-spread-function-approach.pdf |
652fe4a62431cc1dacd0c645 | 10.26434/chemrxiv-2023-tklk0 | Organocatalytic synthesis of δ-sultone-fused benzofurans by the tandem reaction of β-arylethenesulfonyl fluorides | An organocatalytic annulative sulfur(VI)-fluoride exchange (SuFEx) reaction of β-arylethenesulfonyl fluorides has been reported. Under the catalysis of 10 mmol% BTMG and molecular sieves 4Å, β-arylethenesulfonyl fluorides undergo Michael addition-intramolecular SuFEx click reaction with benzofuran-3(2H)-ones to give δ-sultone-fused benzofurans in 76-99% yield. Using 10 mmol% DBU and molecular sieves 4Å, β-arylethenesulfonyl fluorides coupled with oxindoles to produce δ-sultone-fused indoles in 81-85% yield. In these reactions, molecular sieves 4Å act as efficient HF scavenger, which avoid the using of stoichiometric silicon additives and bases. Importantly, density functional theory (DFT) calculations reveal that Michael addition is a decisive speed step for the reaction. | Qichao Zhang; Fang Zhang; Zhihang Wei; Jichang Liu; Lin He; Guangfen Du | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Organocatalysis | CC BY 4.0 | CHEMRXIV | 2023-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652fe4a62431cc1dacd0c645/original/organocatalytic-synthesis-of-sultone-fused-benzofurans-by-the-tandem-reaction-of-arylethenesulfonyl-fluorides.pdf |
627826fdd555500deb930a9c | 10.26434/chemrxiv-2022-jf798 | Machine Learning-assisted Exploration of a Universal Polymer Platform with Charge Transfer-dependent Full-color Emission | Understanding the color tuning of solid-state emissive materials is essential from a fundamental mechanistic viewpoint, as well as for practical applications. The development of color-tunable fluorescent materials with simple chemical compositions and easy to synthesize is highly desirable, but practically challenging. Despite copious research into molecular design and engineering, a general and facile polymer platform that offers high flexibility and broad extensibility in emission color tuning is still lacking. Here, we report a universal yet simple platform based on through-space charge transfer (TSCT) polymers, that has full-color tunable emission and was developed with the aid of predictive machine learning models. Using a single acceptor (A) fluorophore as the initiator for atom transfer radical polymerization (ATRP), a series of electron donor (D) groups containing simple polycyclic aromatic moieties (e.g., pyrene) are introduced either by one-step copolymerization or by end-group functionalization of a pre-synthesized polymer. By manipulating donor-acceptor (D-A) interactions via controlled polymer synthesis, continuous blue-to-red emission color tuning was easily achieved in solid polymers. Theoretical investigations confirm the structurally dependent TSCT-induced emission redshifts. We also exemplify how these TSCT polymers can be used as a general design platform for solid-state stimuli-responsive materials with high-contrast photochromic emission, by applying them to proof-of-concept information encryption. | suiying ye; Nastaran Meftahi ; Igor Lyskov; tian tian; Sudhir Kumar; Andrew Christofferson; David Winkler ; Chih-Jen Shih; Salvy Russo ; Jean-Christophe Leroux; Yinyin Bao | Physical Chemistry; Polymer Science; Polymer chains; Polymerization (Polymers); Physical and Chemical Properties; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627826fdd555500deb930a9c/original/machine-learning-assisted-exploration-of-a-universal-polymer-platform-with-charge-transfer-dependent-full-color-emission.pdf |
6525e109bda59ceb9a4e2ad3 | 10.26434/chemrxiv-2023-qb7cc | Synthesis, Isolation, and Study of a Heterobimetallic Uranyl Crown-Ether Complex | Although crown ethers can selectively bind many metal cations, little is known regarding the properties of crown ether complexes of the uranyl dication, UO22+. Here, the synthesis and characterization of an isolable complex in which the uranyl dication is bound in an 18-crown-6-like moiety are reported. A tailored macrocyclic complex featuring an accessory Pt(II) center was used to drive capture of UO22+ by the crown, as demonstrated by results from single-crystal X-ray diffraction analysis. The U(V) oxidation state becomes accessible at a quite positive potential (E1/2) of –0.18 V vs. Fc+/0 upon complexation, representing the most positive UVI/UV potential yet reported for the UO2n+ core moiety. Joint computational studies show that the electronic structure of the U(V) form results in significant weakening of U–Ooxo bonding despite the quite positive reduction potential at which this species can be accessed, underscoring that crown-ligated uranyl species could demonstrate unique reactivity under only modestly reducing conditions. | Riddhi Golwankar; Alexander Ervin; Malgorzata Makos; Emily Mikeska; Vassiliki-Alexandra Glezakou; James Blakemore | Inorganic Chemistry; Electrochemistry; Lanthanides and Actinides; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6525e109bda59ceb9a4e2ad3/original/synthesis-isolation-and-study-of-a-heterobimetallic-uranyl-crown-ether-complex.pdf |
60e2bf1ff7373f3c8e4525c4 | 10.26434/chemrxiv-2021-h0z4j | Results of VAMAS Survey Regarding Microplastic Issues | Trillions of tiny particles generated by our plastic-reliant society are polluting environments worldwide. An explosion of research has been devoted in the last years to detect, identify and quantify the microplastics, hidden not only in the oceans but also in the world’s rivers, lakes, air, soil as well as food and organisms. Thus, we urgently need reliable standards to support the decision-maker to handle many issues related to this question. In this paper, the results of a VAMAS survey that involved 390 experts are presented and discussed. The inter-laboratory studies urgently needed in the next future are proposed. | Stefania Federici; Monika Rani; Laura Eleonora Depero | Materials Science; Polymer Science; Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e2bf1ff7373f3c8e4525c4/original/results-of-vamas-survey-regarding-microplastic-issues.pdf |
6340690ef764e6b22712b62f | 10.26434/chemrxiv-2022-jv228 | Predictions of the poses and affinity of a ligand over the entire surface of a NEET protein: the case of human mitoNEET | Human NEET proteins contain two [2Fe–2S] iron-sulfur clusters, bound to three Cys and one His residue. They exist in two redox states. Recently, these proteins have revealed themselves as attractive drug targets for mitochondrial dysfunction-related diseases, such as type 2 diabetes, Wolfram syndrome 2, and cancers. Unfortunately, the lack of information and mechanistic understanding on ligands binding to the whole functional, cytoplasmatic domain has limited rational drug design approaches. Here we use an enhanced sampling technique, volume-based metadynamics, recently developed by a team involving some of us, to predict the poses and affinity of 2-benzamido-4-(1,2,3,4-tetrahydronaphthalen-2-yl)-thiophene-3-carboxylate ligand to the entire surface of the cytoplasmatic domain of the human NEET protein mitoNEET (mNT) in an aqueous solution. The calculations, based on the recently published X-ray structure of the complex, are consistent with the measured affinity. The calculated free energy landscape revealed that the ligand can bind in multiple sites and with poses other than the one found in the X-ray. This difference is likely to be caused by crystal packing effects that allow the ligand to interact with multiple adjacent NEET protein copies. Such extra-contacts are of course absent in solution, therefore the X-ray pose is only transient in our calculations, where the binding free energy correlate with the number of contacts. We further evaluated how the reduction and protonation of the Fe-bound histidine, as well as temperature, can affect ligand binding. Both such modifications introduce the possibility for the ligand to bind in area of the protein other than the one observed in the X-ray, with no or little impact on affinity. Overall, our study can provide insights on the molecular recognition mechanisms of ligand binding to mNT in different oxidative conditions, possibly helping rational drug design of NEET ligands. | Ke Zuo; Riccardo Capelli; Giulia Rossetti; Rachel Nechushtai; Paolo Carloni | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2022-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6340690ef764e6b22712b62f/original/predictions-of-the-poses-and-affinity-of-a-ligand-over-the-entire-surface-of-a-neet-protein-the-case-of-human-mito-neet.pdf |
6625fed391aefa6ce1125ed6 | 10.26434/chemrxiv-2024-hkqcp-v2 | 2-in-1 Phase Space Sampling for Calculating the Absorption Spectrum of the Hydrated Electron | The investigation of vibrational effects on absorption spectrum calculations often employs Wigner sampling or thermal sampling. While Wigner sampling incorporates zero-point energy, it may not be suitable for flexible systems. Thermal sampling is applicable to anharmonic systems, yet it treats nuclei classically. The application of Generalized Smoothed Trajectory Analysis (GSTA) as a post-processing method allows for the incorporation of nuclear quantum effects, combining the advantages of both sampling methods. We demonstrate this approach in computing the absorption spectrum of the hydrated electron.
Theoretical exploration of the hydrated electron and its embryonic forms, such as water cluster anions, poses a significant challenge due to the diffusivity of the excess electron and the continuous motion of water molecules. In many previous studies, the wave nature of atomic nuclei is often neglected, despite the substantial impact of nuclear quantum effects on thermodynamic and spectroscopic properties, particularly for hydrogen atoms. In our studies, we examine these nuclear quantum effects for the excess electron in various water systems.
We obtained structures from mixed classical-quantum simulations for water cluster anions and the hydrated electron, incorporating the quantum effects of atomic nuclei with the filtration of the classical trajectories. Absorption spectra were determined at different theoretical levels. Our results indicate significant nuclear quantum effects, redshift and broadening of the spectra for hydrated electron systems. This study demonstrates the applicability of GSTA to complex systems, providing insights into nuclear quantum effects on energetic and structural properties. | László Turi; Bence Baranyi; Ádám Madarász | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625fed391aefa6ce1125ed6/original/2-in-1-phase-space-sampling-for-calculating-the-absorption-spectrum-of-the-hydrated-electron.pdf |
6214b8b30c0bf003daf20e28 | 10.26434/chemrxiv-2022-cdnsx | Silver Trifluoroacetate Promoted Cycloisomerization of 3,5-diyn-1-ones: the direct observation of Ag intermediate and their application in synthesis | A simple and mild method for silver trifluoroacetate promoted cycloisomerization of 3,5-diyn-1-ones provided 2-alkynyl furans, which can be further transformed into alkyne hydration or furan-based polycyclic products was developed. It was found that tri-fluoroacetate anion plays a crucial role in the cycloisomerization reaction, and the intermediate Ag-furan complex was first directly observed by 1H-NMR spectroscopy and mass spectrometry. | Yu He; Li Xiuming; Hong Tianyu ; Yang Jing-Kui | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6214b8b30c0bf003daf20e28/original/silver-trifluoroacetate-promoted-cycloisomerization-of-3-5-diyn-1-ones-the-direct-observation-of-ag-intermediate-and-their-application-in-synthesis.pdf |
60d44324926ad0274902e4ab | 10.26434/chemrxiv-2021-jk5dq | Electrosynthesis of Green Urea by co-reduction of N2 and CO2 Using Dual Active Sites of Copper Phthalocyanine Nanotube | Green synthesis of urea under ambient conditions by electrochemical co-reduction of N2 and CO2 gases using effective electrocatalyst essentially pushes the conventional two steps (N2 + H2 = NH3 & NH3 + CO2 = CO (NH2)2) industrial process at high temperature and high pressure, to the brink. The single step urea synthesis process has hit a roadblock due to the lack of efficient and economically viable electrocatalyst with multiple active sites for dual reduction of N2 and CO2 gas molecules to urea. Herein, CuPc nanotubes having multiple active sites (such as metal center, Pyrrolic-N3, Pyrrolic-N2, and Pyridinic-N1) are reported to exhibit urea yield of 143.47 µg h-1 mg-1cat and FE of 12.99% at –0.6 V vs RHE by co-reduction of N2 and CO2. Theoretical calculation suggests that Pyridinic-N1 and Cu centers are responsible to form C-N bonds for urea by reduction of N2 to NN* and CO2 to *CO respectively. | Uttam Ghorai; Jit Mukherjee; Sourav Paul; Ashadul Adalder; Samadhan Kapse; Ranjit Thapa; Sumit Mandal; Biswajit Ghorai; Sougata Sarkar | Catalysis; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d44324926ad0274902e4ab/original/electrosynthesis-of-green-urea-by-co-reduction-of-n2-and-co2-using-dual-active-sites-of-copper-phthalocyanine-nanotube.pdf |
60c73f5d567dfe54bcec39e0 | 10.26434/chemrxiv.7338683.v1 | New Molecular Scaffolds for Fluorescent Voltage Indicators | <div>
<p>The ability to non-invasively monitor membrane potential
dynamics in excitable cells like neurons and cardiomyocytes promises to
revolutionize our understanding of the physiology and pathology of the brain
and heart. Here, we report the design, synthesis, and application of a new class
of fluorescent voltage indicator that makes use of a fluorene-based molecular
wire as a voltage sensing domain to provide fast and sensitive measurements of
membrane potential in both mammalian neurons and human-derived cardiomyocytes.
We show that the best of the new probes, fluorene VoltageFluor 2 (fVF 2)
readily reports on action potentials in mammalian neurons, detects
perturbations to cardiac action potential waveform in human induced pluripotent
stem cell (hiPSC)-derived cardiomyocytes, shows a substantial decrease in
phototoxicity compared to existing molecular wire-based indicators, and can
monitor cardiac action potentials for extended periods of time. Together, our
results demonstrate the generalizability of a molecular wire approach to
voltage sensing and highlights the utility of fVF 2 for interrogating membrane
potential dynamics.</p>
</div> | Steven Boggess; Shivaani Gandhi; Brian Siemons; Nathaniel Huebsch; Kevin Healy; Evan Miller | Bioorganic Chemistry; Organic Compounds and Functional Groups; Microscopy; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5d567dfe54bcec39e0/original/new-molecular-scaffolds-for-fluorescent-voltage-indicators.pdf |
619ff6a95f114d357f670a54 | 10.26434/chemrxiv-2021-7ls7s-v2 | Electrochemically Driven C-N Bond Formation from CO2 and Ammonia at the Triple-Phase Boundary | <p>Electrosynthetic techniques are gaining prominence
across the fields of chemistry, engineering and energy science. However, most
works within the direction of synthetic heterogeneous electrocatalysis focus on
water electrolysis and CO<sub>2</sub> reduction. In this work, we moved to
expand the scope of this technology by developing a synthetic scheme which
couples CO<sub>2</sub> and NH<sub>3</sub> at a gas-liquid-solid triple-phase
boundary to produce species with C-N bonds. Specifically, by bringing in CO<sub>2</sub>
from the gas phase and NH<sub>3</sub> from the liquid phase together over solid
copper catalysts, we have succeeded in forming formamide and acetamide products
for the first time. In a subsequent complementary step, we have combined
electrochemical analysis and a newly developed <i>operando </i>spectroelectrochemical
method, capable of probing the aforementioned triple phase boundary, to extract
an initial level of mechanistic analysis regarding the reaction pathways of
these reactions and the current system’s limitations. We believe that the
development and understanding of this set of reaction pathways will play an
exceptionally significant role in expanding the community’s understanding of
on-surface electrosynthetic reactions as well as push this set of inherently
sustainable technologies towards widespread applicability. </p> | Junnan Li; Nikolay Kornienko | Physical Chemistry; Catalysis; Nanoscience; Electrocatalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619ff6a95f114d357f670a54/original/electrochemically-driven-c-n-bond-formation-from-co2-and-ammonia-at-the-triple-phase-boundary.pdf |
60c746fd469df496a6f4375c | 10.26434/chemrxiv.11455269.v1 | Ti Catalyzed Hydroamination: A Direct Functionalization of Cu Acetylide | In the presence of a
bis-amidate-bis-amido Ti pre-catalyst, an NHC supported Cu acetylide was reacted
with <i>p</i>-toluidine to generate a new Cu containing species almost
quantitatively. The product was analyzed by NMR spectroscopy and X-ray single
crystal diffraction to be a Cu enamide. Preliminary mechanistic studies suggest
the reaction follows well accepted [2+2] cycloaddition mechanism for early
transition metal catalyzed hydroamination. Furthermore, the reaction is likely
to be a direct functionalization of the alkyne moiety of the Cu acetylide. | Han Hao; Laurel Schafer | Kinetics and Mechanism - Inorganic Reactions; Organometallic Compounds; Reaction (Inorg.); Transition Metal Complexes (Inorg.); Homogeneous Catalysis; Catalysis; Kinetics and Mechanism - Organometallic Reactions; Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746fd469df496a6f4375c/original/ti-catalyzed-hydroamination-a-direct-functionalization-of-cu-acetylide.pdf |
67c5dc9f6dde43c90850ebed | 10.26434/chemrxiv-2025-qdxf2 | Polyolefin Blends with Co-Continuous Architectures Enabled by Dynamic Covalent Crosslinking | Blending polymers produces brittle materials due to macrophase separation and poor interfacial adhesion, which is exemplified by mixtures of polyolefins. This presents a formidable challenge for the mechanical recycling of mixed plastic waste. Here, we show that dynamic covalent crosslinking of immiscible polyolefin blends at their interfaces and within the bulk creates co-continuous architectures that enhance stress transfer, toughness, and amenability to mechanical
reprocessing. Along with morphological changes and reductions in crystallite size, 4D-STEM imaging revealed shear-induced alignment of crystallite planes with strong orientational preference, particularly at polymer–polymer interfaces, contributing to advantaged blend performance. We further demonstrate that changes in crosslinker density and valency allow the properties of binary and ternary polyolefin blends to be tuned in a modular fashion from widely available polymers. | Eliza Neidhart; Stephanie Ribet; Taehyun Lee; Logan Kearney; Karen Bustillo; Mutian Hua; Colin Ophus; Erik Alexanian; Joanna Atkin; Brett Helms; Frank Leibfarth | Polymer Science; Organic Polymers; Polymer blends; Polymer morphology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c5dc9f6dde43c90850ebed/original/polyolefin-blends-with-co-continuous-architectures-enabled-by-dynamic-covalent-crosslinking.pdf |
612ccc2fac3219da106cc82d | 10.26434/chemrxiv-2021-tjgfb | Influence of the Preparation Conditions on the Reaction Performance on Steam Reforming of Methanol in a Cu/Zn/Al model catalyst | The model Cu/Zn/Al catalysts with different calcination temperature were prepared by hydrothermal method. The catalysts were characterized by XRD, BET, SEM, CO2-TPD, H2-TPR, TG, CH3OH-TPD and CO2+H2-TPSR. The effect of different calcination temperature on structure, stability and catalytic performance for methanol steam reforming at the conditions of 200-320℃ was also represented. The results of present study show that the different calcination temperature of Cu/Zn/Al catalysts had an obvious influence on the physical characteristics and catalytic performance of the methanol steam reforming. | Meng-qian Li; Sen Yao; Xing-yu Li; Fen-fen Du; Hao-ran Shi; Xu-bin Guan; Zhao-shun Zhang | Physical Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612ccc2fac3219da106cc82d/original/influence-of-the-preparation-conditions-on-the-reaction-performance-on-steam-reforming-of-methanol-in-a-cu-zn-al-model-catalyst.pdf |
60c73ed8bdbb899c2ba37eb7 | 10.26434/chemrxiv.7125107.v1 | Flow Battery Electroanalysis 2: Influence of Surface Pretreatment on Fe(III/II) Redox Chemistry at Carbon Electrodes | <p>Redox flow batteries are attractive for large-scale electrochemical energy storage, but sluggish electron transfer kinetics often limit their overall energy conversion efficiencies. In an effort to improve our understanding of these kinetic limitations in transition metal based flow batteries, we used rotating-disk electrode voltammetry to characterize the electron-transfer rates of the Fe<sup>3+/2+</sup> redox couple at glassy carbon electrodes whose surfaces were modified using several pre-treatment protocols. We found that surface activation by electrochemical cycling in H<sub>2</sub>SO<sub>4</sub>(aq) electrolyte resulted in the fastest electron-transfer kinetics: j<sub>0</sub> = 0:90 mA/cm<sup>2</sup> in an electrolyte containing 10 mM total Fe. By contrast, electrodes that were chemically treated to either remove or promote surface oxidation yielded rates that were at least an order of magnitude slower: j<sub>0</sub> = 0:07 and 0:08 mA/cm<sup>2</sup>, respectively. By correlating these findings with X-ray photoelectron spectroscopy data, we conclude that Fe<sup>3+/2+</sup> redox chemistry is catalyzed by carbonyl groups whose surface concentrations are increased by electrochemical activation.</p> | Tejal Sawant; James McKone | Carbon-based Materials; Electrochemical Analysis; Electrochemistry; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ed8bdbb899c2ba37eb7/original/flow-battery-electroanalysis-2-influence-of-surface-pretreatment-on-fe-iii-ii-redox-chemistry-at-carbon-electrodes.pdf |
60c7593c469df4e280f45813 | 10.26434/chemrxiv.14665662.v1 | Expanded Ensemble Methods Can Be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies | <p>Alchemical free energy methods have become indispensable in computational drug discovery for their ability to calculate highly accurate estimates of protein-ligand affinities. Expanded ensemble (EE) methods, which involve single simulations visiting all of the alchemical intermediates, have some key advantages for alchemical free energy calculation. However, there have been relatively few examples published in the literature of using expanded ensemble simulations for free energies of protein-ligand binding. In this paper, as a test of expanded ensemble methods, we computed relative binding free energies using the Open Force Field Initiative force field (codename “Parsley”) for twenty-four pairs of Tyk2 inhibitors derived from a congeneric series of 16 compounds. The EE predictions agree well with the experimental values (RMSE of 0.94 ± 0.13 kcal mol<sup>−1</sup> and MUE of 0.75 ± 0.12 kcal mol<sup>−1</sup>). We find that while increasing the number of alchemical intermediates can improve the phase space overlap, faster convergence can be obtained with fewer intermediates, as long as the acceptance rates are sufficient. We find that convergence can be improved using more aggressive updating of the biases, and that estimates can be improved by performing multiple independent EE calculations. This work demonstrates that EE is a viable option for alchemical free energy calculation. We discuss the implications of these findings for rational drug design, as well as future directions for improvement.</p> | Si Zhang; David Hahn; Michael R. Shirts; Vincent Voelz | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7593c469df4e280f45813/original/expanded-ensemble-methods-can-be-used-to-accurately-predict-protein-ligand-relative-binding-free-energies.pdf |
623649e2658bc0c2dbb11103 | 10.26434/chemrxiv-2022-b3cs0 | A Potential Antibacterial Wound Dressing Based on Cerium Crosslinked Alginate and Carboxymethyl Cellulose | Recently, biopolymer based wound dressing films were studied due to their biocompatibility and biodegradability. In this study, a film was prepared with alginate (Alg) and carboxymethyl cellulose (CMC) by crosslinking with Ce3+ ion to evaluate the antibacterial properties of the film. The film exhibits antibacterial activity against Gram positive (Staphylococcus aureus) and Gram negative (Escherichia coli) bacteria. Physical and chemical characterizations of the film were assessed through FT-IR spectrometry, SEM, swelling, water vapor transmission (WVT), and ultraviolet-visible light transmittance tests. The chemical and physical attributes of the film prove to be potentially advantageous for wound dressings due to its UV-protective, vapor permeable, swellable and antimicrobial properties. | Seyedeh Golnar Abtahi; Burcu Orhan; Cansu Vatansever; Hakan Kaygusuz | Biological and Medicinal Chemistry; Polymer Science; Biopolymers; Cellulosic materials; Hydrogels | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623649e2658bc0c2dbb11103/original/a-potential-antibacterial-wound-dressing-based-on-cerium-crosslinked-alginate-and-carboxymethyl-cellulose.pdf |
668d7b30c9c6a5c07ac81fee | 10.26434/chemrxiv-2024-xdq4m | Anticancer activity of 4-aryl-1,4-dihydropyridines | We have synthesized 22 symmetric and asymmetric 4-aryl-1,4-dihydropyridines (1,4-DHPs) by a “green” microwave-assisted one-pot multicomponent Hantzsch reaction and evaluated their cy-totoxicity to three human cancer cell lines viz. U-251MG (human glioblastoma), HeLa 229 (human cervical adenocarcinoma), and MCF-7 (human breast carcinoma). None of the 1,4-DHPs were cytotoxic to U-251MG cells. Most of the 1,4-DHPs did not affect HeLa 229 or MCF-7 cell viability. On the other hand, the symmetric 1,4-DHPs 18 ((±)-diethyl 4-(4-benzyloxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate), 19 ((±)-diethyl 4-(4-bromophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate), and 20 ((±)-diethyl 4-(3-fluor-4-hydroxyphenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) reduced HeLa (IC50 = 3.6, 2.3, and 4.1 µM, respectively) and MCF-7 (IC50 = 5.2, 5.7, and 11.9 µM, respectively) cell viability. These 1,4-DHPs were more cytotoxic to HeLa and MCF-7 cells than to GM07492 (normal human fibroblast) cells, as evidenced by their selectivity indexes. Therefore,1,4-DHPs 18, 19, and 20 may serve as novel lead compounds to discover other 1,4-DHP derivatives with improved anti-cancer potency and selectivity. | Thaís Oliveira; Jackson Silva; Tábata Esperandim; Nathália Acésio; Denise Tavares; Antônio Crotti | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668d7b30c9c6a5c07ac81fee/original/anticancer-activity-of-4-aryl-1-4-dihydropyridines.pdf |
674640445a82cea2fafffae9 | 10.26434/chemrxiv-2024-p132r | Unravelling the Photodissociative Mechanism of CO-Release in Re(I) Tricarbonyl Complex Using Density Functional Theory | The mechanism of the CO ligand dissociation of [Re(CO)3(Pyta)(TPP))]+ complex in aqueous medium has been investigated theoretically, as the dominant process of the photochemical ligand substitution (PLS) reaction of [Re(CO)3(Pyta)(TPP))]+, by using density functional theory (DFT). The PLS reactivity can be determined by the topology of the lowest triplet potential energy surface because the photoexcited complex is able to decay into lowest triplet state via intersystem crossing and internal conversion with sufficiently low energy barriers. The lowest triplet state has a character of metal-to-ligand-charge-transfer (3MLCT) around the Franck-Condon region, and it shifts to metal-centered (3MC) state as the axial Re-CO bond is bend and elongated. The equatorial CO ligand is not dissociated in the course of PLS reaction and only axial CO ligand is selectively dissociated. This study reveals that the 3MC connecting the 3MLCT is not dissociative in nature, rather, the dissociative 3MC is reached via multiple 3MCs. We also predict that the photoproduct [Re(CO)2(CH3CN)(Pyta)(TPP))]+ is formed via the formation of a singlet-adduct. The insights provided in this study shed light on, not-all 3MCs are dissociative in nature, and a step forward towards rationally-designing novel PhotoCORMs. | Prashant Kumar; Martial Boggio-Pasqua; Isabelle Dixon | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674640445a82cea2fafffae9/original/unravelling-the-photodissociative-mechanism-of-co-release-in-re-i-tricarbonyl-complex-using-density-functional-theory.pdf |
679c29026dde43c90809b2c7 | 10.26434/chemrxiv-2024-wqxl7-v6 | Knowledge-informed molecular design for zeolite synthesis using ChatGPT towards human-machine collaboration | The design of organic molecules lies at the heart of solving numerous chemistry-related challenges, necessitating effective collaboration between human intuition and computational power. This study demonstrates how general-purpose Large Language Models (LLMs) can facilitate the design of molecules, leveraging feedback from empirical knowledge through natural language. We used this approach to design organic structure-directing agents (OSDAs) that guide the crystallization of zeolites. In our computational workflow, the LLM proposes OSDA candidates that are evaluated by empirical knowledge and atomistic simulation. Feedback is then provided to the LLM in natural language to refine subsequent proposals, thus progressively enhancing the proposed OSDAs and promoting the exploration of chemical space. The predicted candidates encompassed experimentally validated OSDAs, structurally analogous ones, and novel ones with superior affinity scores, underscoring the robust capability of the LLM. The human-machine collaboration, utilizing natural language as the communication interface, holds potential for application in other molecular design tasks, including drug design. | Shusuke Ito; Koki Muraoka; Akira Nakayama | Theoretical and Computational Chemistry; Organic Chemistry; Materials Science; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679c29026dde43c90809b2c7/original/knowledge-informed-molecular-design-for-zeolite-synthesis-using-chat-gpt-towards-human-machine-collaboration.pdf |
644d6e8580f4b75b5356f42c | 10.26434/chemrxiv-2023-t8v3m | A comprehensive data infrastructure for redox-active organic molecules towards non-aqueous redox flow batteries | The shift of energy production towards renewable, yet at times inconsistent, resources like solar and wind have increased the need for better energy storage solutions. An emerging energy storage technology that is highly scalable and cost-effective is the redox-flow battery comprised of redox-active organic materials. Designing optimum materials for redox flow batteries involves balancing key properties such as the redox potential, stability, and solubility of the redox-active molecules. Here, we present the Data-enabled Discovery and Design to Transform Liquid-based Energy Storage (D3TaLES) database, a curated data collection of more than 43,000 redox-active organic molecules that are of potential interest as the redox-active species for redox flow batteries with the aim to offer readily accessible and uniform data for big data metanalyses. D3TaLES raw data and derived properties are organized into a molecule-centric schema, and the database ontology contributes to the establishment of community reporting standards for electrochemical data. Data are readily accessed and analyzed through an easy-to-use web interface. The data infrastructure is coupled with data upload and processing tools that extract, transform, and load relevant data from raw computation or experimental data files, all of which are available to the public via a D3TaLES API. These processing tools along with an embedded high-throughput computational workflow enable community contributions and versatile data sharing and analysis, not only in redox-flow battery research but also in any field that applies redox-active organic molecules. | Rebekah Duke; Vinayak Bhat; Parker Sornberger; Susan Odom; Chad Risko | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644d6e8580f4b75b5356f42c/original/a-comprehensive-data-infrastructure-for-redox-active-organic-molecules-towards-non-aqueous-redox-flow-batteries.pdf |
63c9aeda3e865678a888a9ec | 10.26434/chemrxiv-2023-5fkn5 | On the molecular dynamic of quercetin and chitosan behavior in water and 1-octhanol at different temperatures | rug delivery control systems allow the controlled transportation of therapeutic
agents. In order to understand the behavour of chitosan as a drug delivery system,
the behaviour of chitosan and quercetin in water and 1-octanol at 300 K and 310 K
as a complex was calculated with molecular dynamics (MD) calculations. Meanwhile,
Molecular docking (MDK) were used to make the complex of these molecules. Of nine
quercetin’s conformations around chitosan, two were chosen to make a complex due
to better energy affinity. The molecules interact between each other with hydrogen
bonds. The molecules do not interact with 1-octanol, independent of temperature. In
water, chitosan maintained insoluble with the increase of temperature. On the other
hand, quercetin demonstrated a better solubilization with temperature increasement.
The complex demonstrate a behaviour favorable to a drug delivery control system.
| Ricardo Stefani; Isabelle Silva Aguiar | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c9aeda3e865678a888a9ec/original/on-the-molecular-dynamic-of-quercetin-and-chitosan-behavior-in-water-and-1-octhanol-at-different-temperatures.pdf |
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