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62d95b84fe12e311b4ad3c2f | 10.26434/chemrxiv-2022-d2hzk-v2 | Enabling batch and microfluidic non-thermal plasma chemistry: reactor design and testing | Non-Thermal Plasma (NTP) is a promising state of matter for carrying out chemical reactions. NTP offers high densities of reactive species, without the need for a catalyst, while operating at atmospheric pressure and remaining at moderate temperature. Despite its potential, NTP cannot be used comprehensively in reactions until we understand more about the complex interactions of NTP and liquids. To achieve this, NTP reactors that can overcome challenges with solvent evaporation, enable inline data collection, and achieve high selectivity, high yield, and high throughput are required. Here, we detail the construction of i) a microfluidic reactor for chemical reactions using NTP in organic solvents and ii) a corresponding batch setup for control studies and scale-up. The use of microfluidics enables controlled generation of NTP and subsequent mixing with reaction media without loss of solvent. The construction of a low-cost custom mount enables inline optical emission spectroscopy using a fibre optic probe at points along the fluidic pathway. | Patrycja Roszkowska; Aaron Dickenson; Jonathan Higham; Timothy Easun; James Walsh; Anna Slater | Physical Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Reaction Engineering; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d95b84fe12e311b4ad3c2f/original/enabling-batch-and-microfluidic-non-thermal-plasma-chemistry-reactor-design-and-testing.pdf |
621d0cbece899b5125a762d1 | 10.26434/chemrxiv-2022-20fkz | Doping nature of group V elements in ZnO single crystals grown from melts at high pressure | ZnO single crystals doped with group-V elements have been grown from melt at high pressure. Dopants were introduced in several forms such as Sb2O3, P, As, Sb and Zn3X2 (X = P, As, Sb) in the high-pressure cell. Systematic studies of morphology were performed using optical microscopy and scanning electron microscopy. Crystal structure and lattice parameters were studied using X-ray diffraction and X-ray crystallography. Crystals exhibited distinct changes of size, shape and color compared to undoped ZnO melt-grown single crystals due to the dopants influence. X-ray photoelectron spectroscopy was used to determine valence states of group-V elements when incorporated in ZnO lattice. Photoluminescence, Raman spectroscopy and electron paramagnetic resonance spectroscopy were employed to investigate the nature of defects formed as the result of doping. Formation of VZn and VZn-complexes was confirmed and their concentrations were measured. Estimates of the number of VZn per one dopant atom showed that the ratio is noticeably higher than the one suggested for the shallow complex As(P, Sb)Zn-2VZn commonly regarded as responsible for acceptor properties in ZnO. | Nikolai O. Taibarei; Vladimir G. Kytin; Elizaveta A. Konstantinova; Vladimir A. Kulbachinskii; Olga A. Shalygina; Alexander V. Pavlikov; Serguei V. Savilov; Viktor A. Tafeenko; Vladimir A. Mukhanov; Vladimir L. Solozhenko; Andrei N. Baranov | Materials Science; Ceramics; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621d0cbece899b5125a762d1/original/doping-nature-of-group-v-elements-in-zn-o-single-crystals-grown-from-melts-at-high-pressure.pdf |
66e9cc0112ff75c3a1a11a54 | 10.26434/chemrxiv-2024-qr6kv | Integrating Path Sampling with Enhanced Sampling for Rare-event Kinetics | Studying the kinetics of long-timescale rare events is a fundamental challenge in molecular simulation. To address this problem, we propose an integration of two different rare-event sampling philosophies: biased enhanced sampling and unbiased path sampling. Enhanced sampling methods e.g. metadynamics can facilitate enthalpic barrier crossing by applying an external bias potential. On the contrary, path sampling methods like weighted ensemble (WE) lack explicit mechanisms to overcome energetic barriers. However, they can accelerate the exploration of rugged free energy surfaces through trajectory resampling. We show that a judicious combination of the weighted ensemble with a metadynamics-like algorithm, can synergize the strengths and mitigate the deficiencies of path sampling and enhanced sampling approaches. The resulting integrated sampling (IS) algorithm improves the computational efficiency of calculating the kinetics of peptide conformational transitions, protein unfolding, and the dissociation of a ligand-receptor complex. Furthermore, the IS approach can direct sampling along the minimum free energy pathway even when the collective variable used for biasing is suboptimal. These advantages make the integrated sampling algorithm suitable for studying the kinetics of complex molecular systems of biological and pharmaceutical relevance. | Dhiman Ray | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e9cc0112ff75c3a1a11a54/original/integrating-path-sampling-with-enhanced-sampling-for-rare-event-kinetics.pdf |
65768e955bc9fcb5c988aaaa | 10.26434/chemrxiv-2023-sljbt-v2 | A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery | Modern natural products (NPs) research relies on untargeted liquid chromatography coupled with mass spectrometry metabolomics. Together with cutting-edge processing and computational annotation strategies, such approaches can yield extensive spectral and structural information. However, current processing workflows require feature-alignment steps based on retention time which hinders the comparison of samples originating from different batches or analyzed using different instrumental setups. In addition, there is currently no analytical framework available to efficiently match processed metabolomics data and associated metadata with external resources. To address these limitations, we present a new sample-centric and knowledge-driven framework allowing multi-modal data alignment - e.g. through chemical structures, biological activities, or spectral features - and demonstrate its value in exploring large and chemodiverse natural extract datasets. Here, the experimental data is processed at the sample level, matched with external identifiers when possible, semantically enriched, and integrated into a unified knowledge graph. The use of semantic web technology enables comparison of processed and standardized data, information, and knowledge at the repository scale. We demonstrate the utility of the developed framework, the Experimental Natural Products Knowledge Graph (ENPKG), to leverage the results obtained from screening 1,600 plant extracts against trypanosomatids and streamline the identification of new antiparasitic compounds. Thanks to its versatility, the proposed approach allows for a radically novel exploitation of metabolomics data. Semantic web technologies are a fundamental asset and we anticipate that their adoption will strongly complement the current computational metabolomics pipelines and enable the community to advance in the description of global chemodiversity and drug discovery projects. | Arnaud Gaudry; Marco Pagni; Florence Mehl; Sébastien Moretti; Luis-Manuel Quiros-Guerrero; Luca Cappelletti; Adriano Rutz; Marcel Kaiser; Laurence Marcourt; Emerson Ferreira Queiroz; Jean-Robert Ioset; Antonio Grondin; Bruno David; Jean-Luc Wolfender; Pierre-Marie Allard | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Mass Spectrometry; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65768e955bc9fcb5c988aaaa/original/a-sample-centric-and-knowledge-driven-computational-framework-for-natural-products-drug-discovery.pdf |
663d6ade91aefa6ce19bddac | 10.26434/chemrxiv-2024-1v8gw | Current strategies to improve CAR-T cell persistence | Chimeric antigen receptor T (CAR-T) cell therapy has transformed the field of immunology by redirecting T lymphocytes toward tumor antigens. Despite successes in attaining remission rates as high as 70%, the performance of CAR therapy is limited by the survival of T cells. T cell persistence is crucial as it sustains immune response against malignancies, playing a critical role in cancer treatment outcomes. This review explores various approaches to improve CAR-T cell persistence, focusing on the choice between autologous and allogeneic cell sources, optimization of culture conditions for T cell subsets, metabolite adjustments to modify T cell metabolism, the use of oncolytic viruses, and advancements in CAR design. While these approaches are promising on their own, combining them could further enhance the persistence of T cells, particularly in targeting solid tumors. Understanding the underlying mechanisms behind these strategies is essential for maximizing the potential of CAR-T therapy in treating cancer. Further research is needed to improve safety and efficacy and seamlessly integrate the discussed strategies into the manufacturing process. | Soren Ghorai; Ashley Pearson | Biological and Medicinal Chemistry; Cell and Molecular Biology; Microbiology | CC BY 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663d6ade91aefa6ce19bddac/original/current-strategies-to-improve-car-t-cell-persistence.pdf |
661dadc6418a5379b0ec9330 | 10.26434/chemrxiv-2024-ctrnd | Killing it softly – Can soft materials play a strategic role in the eradication of tuberculosis? | Intracellular organelles can be regarded as natural vesicles essential for the organization, isolation, protection, and recycling of macromolecules within cells. Similarly, lipid and polymer-based vesicles can offer compartmentalization through the physical confinement of (macro)molecules in nanoscale dimensions, a key architectural principle to achieve biomimicry and facilitate molecular transport in organelle-like compartments. In the last few decades, the therapeutic scope of soft materials has gained significant traction, particularly in the field of bacterial infections, ranging from the prevention of biofilm formation to the development of new targeted antimicrobial agents and vaccines. This review seeks to highlight and critically discuss the potential of biomimetic synthetic vesicles in the prevention and treatment of Tuberculosis, the deadliest human bacterial infection to date, providing an overview of the clinical progress achieved thus far. | Víctor Mejías; Cátia D. F. Lopes; Iris Luz Batalha | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Nanostructured Materials - Nanoscience; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661dadc6418a5379b0ec9330/original/killing-it-softly-can-soft-materials-play-a-strategic-role-in-the-eradication-of-tuberculosis.pdf |
60c74dfaee301c34a9c7a3ef | 10.26434/chemrxiv.12683771.v1 | Mapping Mutations in Proteins of SARS CoV-2 Indian Isolates on to the Three-Dimensional Structures | <p>The amino acid residue mutations observed in SARS CoV-2 RNA dependent
RNA polymerase, helicase, endoRNAse and spike proteins from Indian isolates,
relative to the reference SARS CoV-2 proteins from the Wuhan Hu-1 isolate, were
mapped onto the protein three-dimensional structure templates available in the
Protein Data Bank.<b> </b>The secondary structure conformations corresponding to the mutations, their locations
and proximity to functionally important residues in these proteins and to the
drug binding sites in RNA dependent RNA polymerase and endoRNAse targets were
analysed. Our analyses provide structural insights into the mutations in these SARS
CoV-2 proteins.</p> | Kunchur Guruprasad | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dfaee301c34a9c7a3ef/original/mapping-mutations-in-proteins-of-sars-co-v-2-indian-isolates-on-to-the-three-dimensional-structures.pdf |
646925c8f2112b41e9e0b1f7 | 10.26434/chemrxiv-2023-lspmv | How Ligands Interact with the Kinase Hinge | ATP-competitive kinase inhibitors form hydrogen bond interactions with the kinase hinge region at the adenine binding site. Thus, it is crucial to explore hinge-ligand recognition as part of a rational drug design strategy. Here, harnessing known ligand-bound kinase structures and experimental assay resources, we first create a kinase structure-assay database (KSAD) containing 2915 nanomolar ligand-bound kinase complexes. Then, using the KSAD, we systematically investigate hinge-ligand binding patterns using interaction fingerprints, thereby delineating 15 different hydrogen-bond interaction modes. We believe these results will be valuable for de novo drug design and/or scaffold hopping of kinase-targeted drugs. | Zheng Zhao; Philip E. Bourne | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646925c8f2112b41e9e0b1f7/original/how-ligands-interact-with-the-kinase-hinge.pdf |
64c1ef55658ec5f7e53d23c8 | 10.26434/chemrxiv-2023-7f4vv | A Mild catalyzed imino Diels-Alder reaction for the synthesis of N-(2-(o-tolyl)-1,2,3,4-tetrahydroquinoline-4-yl)formamide derivatives as regulators of Quorum Sensing in Pseudomona Aeruginosa | Bacterial resistance is one of the major global public health problems. In addition, virulence factors promoted multiple drug resistance through cell-to-cell communications by molecules within microbial communities, denominated Quorum Sensing (QS). The regulation of QS by small molecules appears as a therapeutic alternative through the use of synthetic analogs of agonists. The present work developed the construction of a series of derivatives of N-(2-(o-tolyl)-1,2,3,4-tetrahydroquinoline-4-yl) formamide (1a-h) via Povarov-type sequential reactions to deliver the tetrahydroquinoline (THQ) derivatives in moderate to good yields (24-78%). To evaluate the potential in molecular diversity of THQ-type autoinducers, a study of these agents as potential inhibitors of bacterial growth and virulence factors involved in QS systems on P. aeruginosa was carried out both as antibacterial evaluation on E. coli strain. THQs showed significant activity values for molecules with halogen substituents at the C-6 position (-F, -Cl, and I), revealing at a concentration of 75 µg/mL a percentage inhibition between 27-40%. Furthermore, autoinducers with halogen substitutes in phenotypic studies on P. aeruginosa showed good results. Also, they exhibited weak formation of both biofilm and low pyocyanin formation, which are indicators of virulence in P. aeruginosa. Overall, the results suggest that compound N-(6-fluor-2-(o-tolyl)-1,2,3,4-tetrahydroquinoline-4-yl)formamide (1a) stands out as the most representative within this series of THQ derivatives. | Carlos Mario Meléndez; Leidy Johana García Maza; Dayanna F Orosco Flórez; Arturo René Mendoza Salgado; Wendy Rosales; Evelyn Mendoza-Torres | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c1ef55658ec5f7e53d23c8/original/a-mild-catalyzed-imino-diels-alder-reaction-for-the-synthesis-of-n-2-o-tolyl-1-2-3-4-tetrahydroquinoline-4-yl-formamide-derivatives-as-regulators-of-quorum-sensing-in-pseudomona-aeruginosa.pdf |
66f9d05312ff75c3a1e2143a | 10.26434/chemrxiv-2024-395q6 | Grand Canonical Monte Carlo and Deep Learning Assisted Enhanced Sampling to Characterize the Distribution of Mg2+ and Influence of the Drude Polarizable Force Field on the Stability of Folded States of the Twister Ribozyme | Molecular Dynamics (MD) simulations are crucial for understanding the structural and dynamical behavior of biomolecular systems including the impact of their environment. However, there is a gap in timescale of these simulations and that of real-world experiments. To address this problem, various enhanced simulation methods have been developed. Additionally, there has been a significant advancement of the force fields used for simulations associated with the explicit treatment of electronic polarizability. In this study, we apply oscillating chemical potential grand canonical Monte Carlo and machine learning methods to determine reaction coordinates combined with metadynamics simulations to explore the role of Mg2+ distribution and electronic polarizability in the context of the classical Drude oscillator polarizable force field on the stability of the Twister ribozyme. The introduction of electronic polarizability along with details of the distribution of Mg2+ significantly stabilize the simulations with respect to sampling the crystallographic conformation. The introduction of electronic polarizability leads to increased stability over that obtained with the additive CHARMM36 FF reported in a previous study, allowing for a wider range of ions distribution to stabilize Twister. Specific interactions contributing to stabilization are identified included both those observed in the crystal structures and additional experimentally unobserved interactions. Interactions of Mg2+ with the bases are indicated to make important contributions to stabilization. Notably, the presence of specific interactions between the Mg2+ ions and bases or the non-bridging phosphate oxygens (NBPO), lead to enhanced dipole moments of all three moieties. Mg2+-NPBO interactions led to enhanced dipoles of the phosphates but, interestingly, not in all of the participating ions. The present results further indicate the importance of electronic polarizability in stabilizing RNA in molecular simulations and the complicated nature of the relationship of Mg2+-RNA interactions with polarization response of the bases and phosphates. | Prabin Baral; Mert Sengul; Alex MacKerell | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f9d05312ff75c3a1e2143a/original/grand-canonical-monte-carlo-and-deep-learning-assisted-enhanced-sampling-to-characterize-the-distribution-of-mg2-and-influence-of-the-drude-polarizable-force-field-on-the-stability-of-folded-states-of-the-twister-ribozyme.pdf |
67dd09406dde43c908b44ad5 | 10.26434/chemrxiv-2025-c7ct3 | Covalent Organic Frameworks for Water Sorption: The Importance of Framework Physical Stability | Covalent organic frameworks (COFs) have garnered growing interest as water-sorption adsorbents. While the chemical stability of most COFs in liquid-phase water is well-established, there are limited studies on their framework physical stability in water vapor. This refers to maintaining the ordered structure of COFs without disrupting their chemical bonds, a factor that significantly influences water sorption. Here, we examined the water-vapor stability of three distinct two-dimensional COFs with various pore sizes. Microporous COFs exhibited superior stability than mesoporous COFs, albeit with reduced water-uptake capacity. Mesoporous keto-enamine-linked COFs with the intralayer hydrogen bonds between carbonyl oxygen and secondary amine hydrogen atoms exhibited markedly improved water-vapor stability compared to imine-linked COFs, which was further confirmed by molecular dynamics simulations, density functional theory calculations, and the extended water adsorption-desorption cycling test (200 cycles). Finally, a COF-coated heat exchanger was fabricated to demonstrate air dehumidification at a device level. | Wei Zhao; He Li; Bui Duc Thuan; Weidong Chen; Qiang Zhu; Mounib Bahri; Boyu Li; Kexin Yu; Chengjun Kang; Ting Chen; Zekun Wang; Nigel D. Browning; Kian Jon Chua; Dan Zhao | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67dd09406dde43c908b44ad5/original/covalent-organic-frameworks-for-water-sorption-the-importance-of-framework-physical-stability.pdf |
647a5793e64f843f4138e87d | 10.26434/chemrxiv-2023-sb2pj | Exquisite Control of Electronic and Spintronic Properties on Highly Porous Covalent Organic Frameworks (COFs): Transition Metal Intercalation in Bilayers | Two-dimensional covalent organic frameworks (2D COFs) are crystalline organic porous materials that are stacked in a layered fashion. In general, these materials have excellent structural tunability, which can be achieved through the various tools of organic synthesis. Their layered and porous nature makes them attractive candidates for electronics, optoelectronics, and catalysis. However, their application is still limited due to relatively poor $\pi$-delocalization. In this paper, we computationally explore a novel 2D COF architecture, consisting of only two crystalline atomic layers comprised of benzene, boroxine, and triazine rings. We study the intercalation of first-row transition metals in the bilayer to enhance and fine-tune their electronic behavior. Furthermore, we perform a systematic study to understand the magnetic behavior of the intercalated transition metals. We found that the concentration and position of transition metals in the structure can drastically change the 2D COFs' electronic and magnetic features. Furthermore, based on their spin-polarized electronic properties, we highlight potential applications in the fields of optoelectronics, photocatalysis, and spintronics. | Daniel Maldonado-Lopez; Jose Mendoza-Cortes | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/647a5793e64f843f4138e87d/original/exquisite-control-of-electronic-and-spintronic-properties-on-highly-porous-covalent-organic-frameworks-co-fs-transition-metal-intercalation-in-bilayers.pdf |
66cce434f3f4b052902ff08d | 10.26434/chemrxiv-2024-d2l2g | Theoretical determination of a model molecule for the catalytic upcycling of polyolefins | Considering the severe environmental and humanitarian implications of global plastic waste accumulation, understanding polyolefin catalytic degradation is essential. Accordingly, a model compound would improve experiments' reproducibility and simplify theoretical models. Therefore, this study aimed to determine the minimum number of monomers necessary to represent the degradation and upcycling of polyethylene and polypropylene over metal catalysts. Using density functional theory (DFT) calculations, we evaluated how polymer's chain length affects reaction energies and energy barriers for C-H and C-C cleavage over stepped transition metal surfaces. We found that chain length does not significantly affect the C-H and C-C cleavage reaction energies and the C-H cleavage energy barriers. Our findings suggest that ethane may be suitable as a model to study polyethylene's catalytic C-H and C-C cleavage. Although such a simple molecule cannot capture complex transport and entanglement phenomena in full polymers, it remains useful for determining reaction energetics in complex systems. | Jessica Alexandra Ortega Ramos; Mikael Maraschin; Gerardine G. Botte; Joseph A. Gauthier | Catalysis; Polymer Science; Chemical Engineering and Industrial Chemistry; Inorganic Polymers; Polymer chains; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66cce434f3f4b052902ff08d/original/theoretical-determination-of-a-model-molecule-for-the-catalytic-upcycling-of-polyolefins.pdf |
633c51a2ea6a223bde08c5df | 10.26434/chemrxiv-2022-2s6kx | ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics | Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels of noise and complexity between raw and machine learning-ready formats. While predictive proteomics is a field on the rise, when predicting peptide behavior in LC-IM-MS setups, each lab often uses unique and complex data processing pipelines in order to maximize performance, at the cost of accessibility and reproducibility. For this reason we introduce ProteomicsML, an online resource for proteomics-based datasets and tutorials across most of the currently explored physicochemical peptide properties. This community-driven resource makes it simple to access data in easy-to-process formats, and contains easy-to-follow tutorials that allow new users to interact with even the most advanced algorithms in the field. ProteomicsML provides datasets that are useful for comparing state-of-the-art (SOTA) machine learning algorithms, as well as providing introductory material for teachers and newcomers to the field alike. The platform is freely available on https://www.proteomicsml.org/ and we welcome the entire proteomics community to contribute to the project at https://github.com/proteomicsml/. | Tobias Rehfeldt; Ralf Gabriels; Robbin Bouwmeester; Siegfried Gessulat; Benjamin Neely; Magnus Palmblad; Yasset Perez-Riverol; Tobias Schmidt; Juan Antonio Vizcaíno; Eric Deutsch | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633c51a2ea6a223bde08c5df/original/proteomics-ml-an-online-platform-for-community-curated-datasets-and-tutorials-for-machine-learning-in-proteomics.pdf |
67d87fd5fa469535b98e2e4c | 10.26434/chemrxiv-2025-6l0lb | The Sabatier Principle Revisited: The Role of Electronic Properties in Simple Catalytic Reactions | We demonstrate the validity of the Sabatier principle for simple catalytic reactions using conceptual density functional theory. Our results emphasize that the Sabatier principle is based on similar adsorption and desorption energies, with the electronegativity of catalysts, reactants and products having a decisive influence. The chemical hardnesses are of minor importance and mainly regulate the value of the corresponding adsorption and desorption energies. To achieve the highest yields, nearly identical differences in electronegativity between catalysts, reactants, and products are of paramount significance. We validate our theoretical findings through experimental results for the isomerization of methyl eugenol and the catalytic cyclization of alkanes. | Ramon Miranda-Quintana; Niklas Adebar ; Moritz Schulze; Jens Smiatek | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2025-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d87fd5fa469535b98e2e4c/original/the-sabatier-principle-revisited-the-role-of-electronic-properties-in-simple-catalytic-reactions.pdf |
620e4f9b7d068a14dc22f777 | 10.26434/chemrxiv-2022-61wck | Role of a secondary coordination sphere residue in halogenation catalysis of non-heme iron enzymes | Chemo- and regio-selective catalysis of C(sp3)-H halogenation reaction is a formidable goal in chemical synthesis. 2-oxo-glutarate (2OG) dependent non-heme iron halogenases catalyze selective chlorination/bromination of C-H bonds and exhibit high sequence and structural similarities with non-heme iron hydroxylases. How the secondary coordination sphere (SCS) of these two enzyme systems differentiate and determine their reactivity is not understood. In this work, we show that tyrosine placement in the SCS of non-heme iron halogenases have a huge impact on their structure, function, and reactivity. We discover that a tyrosine mutant (F121Y) in SyrB2 halogenase undergoes post-translational oxidation to dihydroxyphenylalanine (DOPA) physiologically. A combination of spectroscopic, mass-spectrometric, and biochemical studies show that the DOPA modification in SyrB2 renders the enzyme non-functional. Further bioinformatics analysis suggests that halogenases, unlike hydroxylases, have a conserved placement of phenylalanine at position 121 to preclude such unproductive oxidation. Overall, this study demonstrates the importance of the SCS in controlling the structure and enzymatic activity of non-heme iron halogenases. Our results will have significant implications towards the design of small-molecule and protein-based halogenation catalysts. | R. Hunter Wilson; Sourav Chatterjee; Elizabeth R. Smithwick; Joe J. Dalluge; Ambika Bhagi-Damodaran | Biological and Medicinal Chemistry; Inorganic Chemistry; Catalysis; Bioinorganic Chemistry; Bioinformatics and Computational Biology; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2022-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e4f9b7d068a14dc22f777/original/role-of-a-secondary-coordination-sphere-residue-in-halogenation-catalysis-of-non-heme-iron-enzymes.pdf |
6602f79c9138d231615ba8a0 | 10.26434/chemrxiv-2024-pj4bw | Zero-Bias Anti-Ohmic Behaviour in Diradicaloid
Molecular Wires | Open-shell materials bearing multiple spin centres hold the key to efficient charge transport in singlemolecule electronic devices. They have very narrow bandgaps, and their partially occupied molecular
orbitals align very efficiently to the Fermi level of the metallic electrodes of the single-molecule junction,
thus allowing transparent electronic transport and higher conductance. Maintaining and stabilising
multiple open-shell states, especially in contact with metallic electrodes is however very challenging,
generally requiring a continuous chemical or electrochemical potential to avoid self-immolation of the
open-shell character. To overcome this issue, we designed, synthesised, and measured the
conductance of a series of bis(indeno) fused acenes, having a diradicaloid structure in resonance with
a close-shell quinoidal conformation, providing steric protection with 3,5-dimethylthioanisole anchors to
the electrodes and electronic protection against oxidation with tris(isopropyl)ethynyl substituents at the
heart of the acene. We show here that these compounds have extremely anti-ohmic behaviour, with
conductance increasing with increasing length at an unprecedented rate, across the entire bias window
(±1.3 𝑉). Density Functional Theory (DFT) calculations support our findings, showing the rapidly
narrowing bandgap unique to these diradicaloid structures is responsible for the observed behaviour.
Our results provide a framework for achieving efficient transport in neutral compounds and demonstrate
the promise that diradicaloid materials have in single-molecule electronics, owing to their great stability
and unique electronic structure. | Amit Sil; Lewis Hamilton; James Morris; Abdalghani Daaoub; James Burrows; Simon Higgins; Hatef Sadeghi; Richard Nichols; Sara Sangtarash; Andrea Vezzoli | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanodevices; Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6602f79c9138d231615ba8a0/original/zero-bias-anti-ohmic-behaviour-in-diradicaloid-molecular-wires.pdf |
61ccd5d27284d05f63fcdff6 | 10.26434/chemrxiv-2022-z53kg | PreSS/MD: Predictor of Skin Sensitization Caused by Chemicals Leaching from Medical Devices | Abstract
Safety evaluation for medical devices includes the toxicity assessment of chemicals used in device manufacturing, cleansing and/or sterilization that may leach into a patient. According to international standards on biocompatibility assessments (ISO 10993), chemicals that could be released from medical devices should be evaluated for their potential to induce skin sensitization/allergenicity, and one of the commonly used approaches is the guinea pig maximization test (GPMT). However, there is growing trend in regulatory science to move away from costly animal assays to employing New Approach Methodologies including computational methods. Herein, we developed a new computational tool for rapid and accurate prediction of the GPMT outcome that we named PreSS/MD (Predictor of Skin Sensitization for Medical Devices). To enable model development, we (i) collected, curated, and integrated the largest publicly available dataset for GPMT; (ii) succeeded in developing externally predictive (balanced accuracy of 70-74% as evaluated by both 5-fold external cross-validation and testing of novel compounds) Quantitative Structure-Activity Relationships (QSAR) models for GPMT using machine learning algorithms, including Deep Learning; and (iii) developed a publicly accessible web portal integrating PreSS/MD models that enables the prediction of GPMT outcomes for any molecules using. We expect that PreSS/MD will be used by both researchers and regulatory agencies to support safety assessment for medical devices and help replace, reduce or refine the use of animals in toxicity testing. PreSS/MD is freely available at https://pressmd.mml.unc.edu/.
Keywords: sensitization, GPMT, QSAR, deep learning,
| Joyce Borba; Vinicius Alves; Rodolpho Braga; Daniel Korn; Nicole Kleinstreuer; Kevin Causey; Alexander Tropsha; Diego Rua; Eugene Muratov | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ccd5d27284d05f63fcdff6/original/pre-ss-md-predictor-of-skin-sensitization-caused-by-chemicals-leaching-from-medical-devices.pdf |
60ee48ef0387b18363cc2c29 | 10.26434/chemrxiv-2021-43mww | Catalytic Reduction of Dinitrogen into Ammonia and Hydrazine Using Chromium Complexes Bearing PCP-Type Pincer Ligand | A series of chromium–halide, –nitride, and –dinitrogen com-plexes bearing a carbene- and phosphine-based PCP-type pin-cer ligand is newly prepared and some of them are found to work as effective catalysts to reduce dinitrogen under atmos-pheric pressure, whereby up to 8.40 equiv of ammonia and 2.46 equiv of hydrazine (13.32 equiv of fixed N atom) are produced based on the chromium atom. To the best of our knowledge, this is the first successful example of chromium-catalyzed conversion of dinitrogen to ammonia and hydrazine under mild reaction conditions. | Yuya Ashida; Akihito Egi; Kazuya Arashiba; Hiromasa Tanaka; Shogo Kuriyama; Kazunari Yoshizawa; Yoshiaki Nishibayashi | Organometallic Chemistry; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ee48ef0387b18363cc2c29/original/catalytic-reduction-of-dinitrogen-into-ammonia-and-hydrazine-using-chromium-complexes-bearing-pcp-type-pincer-ligand.pdf |
65f81495e9ebbb4db9eedc20 | 10.26434/chemrxiv-2024-qht6q | FAIMS Shotgun Lipidomics for Enhanced HILIC-like Separation and Automated Annotation of Gangliosides | The analysis of the glycosphingolipid subclass of gangliosides is extremely challenging, given their structural complexity, lack of reference standards, databases, and software solutions. Here, we introduce a fast 6 min High Field Asymmetric Ion Mobility Spectrometry (FAIMS) shotgun-based lipidomics workflow for improved ganglioside detection. By ramping compensation voltages, ideal ranges for different ganglioside classes were obtained. FAIMS revealed both class- and charge-state separation behavior based on the glycan head group moiety. The number of sialic acids attached to the glycan moiety correlated positively with their preferred charge state, i.e., trisialylated gangliosides (GT1-3) were mainly present as [M-3H]3- ions, whereas [M-4H]4- and [M 5H]5- ions were observed for GQ1 and GP1. [M-5H]5- ions were reported for the first time, primarily due to signal-to-noise enhancement and charge state filtering enabled by FAIMS. Overall, 11 ganglioside classes were covered i.e., GM1, GM2, GM3, GD1, GD2, GD3, GT1, GT2, GT3, GQ1, GP1. For data evaluation, we introduce a shotgun/FAIMS extension of the freely available, open-source Lipid Data Analyzer (LDA), which utilized combined orthogonal fragmentation spectra from CID, HCD, and 213 nm UVPD ion activation methods. Finally, 112 unique molecular gangliosides species were identified from pooled standards and porcine brain extracts. While conventional shotgun lipidomics favored the observation of singly charged ganglioside species, the incorporation of FAIMS yielded a higher number of annotated lipid species due to a gain in detection of multiply charged ion species. Therefore, this FAIMS-driven approach offers a promising strategy for complex ganglioside and glycosphingolipid characterization in shotgun lipidomics. | Katharina Hohenwallner; Leonida M. Lamp; Liuyu Peng; Madison Nuske; Jürgen Hartler; Gavin E. Reid; Evelyn Rampler | Analytical Chemistry; Chemoinformatics; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f81495e9ebbb4db9eedc20/original/faims-shotgun-lipidomics-for-enhanced-hilic-like-separation-and-automated-annotation-of-gangliosides.pdf |
66ff03e9cec5d6c14211db25 | 10.26434/chemrxiv-2024-s0ghr | C(sp3)–H Carboxylation via Carbene/Photoredox Cooperative Catalysis | C(sp3)–H bond functionalization is a powerful strategy for the synthesis of organic compounds due their abundance in simple starting materials. Photoredox catalysis has led to a diverse array of enabling C(sp3)–H activation strategies; however, the direct functionalization of C(sp3)–H to carboxylic acid derivatives remains underexplored. Disclosed herein is the development of a cooperative NHC/photoredox-catalyzed C(sp3)–H esterification transformation. This method enables access to benzylic, 𝛼–heteroatom, and formal β-esterification products in good to excellent yields under mild reaction conditions. | Karl Scheidt; Cullen Schull; Jing Cao; Sophia Mitton-Fry; Mara Mrksich | Organic Chemistry; Catalysis; Organocatalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ff03e9cec5d6c14211db25/original/c-sp3-h-carboxylation-via-carbene-photoredox-cooperative-catalysis.pdf |
654d3dc62c3c11ed7118d086 | 10.26434/chemrxiv-2023-lcsf3 | Exploring mechanochemistry of pharmaceutical cocrystals: effect of incident angle on molecular mixing during simulated indentations of two organic solids | Solid-state reaction of the active pharmaceutical ingredient theophylline with citric acid is a well-established example of a mechanochemical reaction leading to a model pharmaceutical cocrystal. Here, classical force field molecular dynamics was employed to investigate molecular mixing and structural distortion that take place upon mechanically driven indentation of a citric acid nanoparticle upon a slab of crystalline theophylline. Through non-equilibrium molecular dynamics simulations, a 6 nm diameter nanoparticle of citric acid was introduced onto an open (001) surface of a theophylline crystal, varying both the angle of incidence of the nanoparticle between 15◦ and 90◦ and the indentation speed between 1ms−1 and 16ms−1. This theoretical study enabled the evaluation of how these two parameters promote molecular mixing and overall structural deformation upon mechanical contract of theophylline and citric acid, both of which are important parameters underlying mechanochemical cocrystallisation. The results show that the angle of incidence plays a key role in the molecular transfer ability between the two species and in the structural disruption of the initially spherical nanoparticle. Changing the indentation speed, however, did not lead to a discernible trend in molecular mixing, highlighting the importance of the incident angle in mechanochemical events. | Michael Ferguson; Tomislav Friscic | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654d3dc62c3c11ed7118d086/original/exploring-mechanochemistry-of-pharmaceutical-cocrystals-effect-of-incident-angle-on-molecular-mixing-during-simulated-indentations-of-two-organic-solids.pdf |
60c74788337d6cea36e27373 | 10.26434/chemrxiv.11637312.v1 | Spontaneous Aminolytic Cyclization and Self-Assembly of Dipeptide Methyl Esters in Water | Dipeptides are known to spontaneously cyclize to
diketopiperazines, and in some cases these cyclic dipeptides have been shown to
self-assemble to form supramolecular nanostructures.<b> </b>Herein, we demonstrate the <i>in
situ</i> cyclization of dipeptide methyl esters in aqueous buffer by
intramolecular aminolysis, leading to the formation of diverse supramolecular
nanostructures. The chemical nature of the amino acid side chains dictates the
supramolecular arrangement and resulting nanoscale architectures. For c[LF],
supramolecular gels are formed, and the concentration of starting materials
influences the mechanical properties of hydrogels. Moreover, by adding
metalloporphyrin to the starting dipeptide ester solution, these become
incorporated through cooperative assembly,<b> </b>resulting in the formation of nanofibers able to
catalyse the oxidation of organic phenol in water. The approach taken here,
which combines the chemically activated assembly with the versatility of short
peptides might pave the way for achieving the spontaneous formation of
supramolecular order and function using simple building blocks.<br /> | Charalampos Pappas; Nadeesha Wijerathne; Jugal Kishore Sahoo; Ankit Jain; Daniela Kroiss; Ivan R. Sasselli; Ana Pina; Ayala Lampel; Rein V. Ulijn | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Catalysts; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74788337d6cea36e27373/original/spontaneous-aminolytic-cyclization-and-self-assembly-of-dipeptide-methyl-esters-in-water.pdf |
60c74227f96a008591286553 | 10.26434/chemrxiv.8218004.v1 | Short-Range Ordering in Battery Electrode, the ‘Cation-Disordered’ Rocksalt Li1.25Nb0.25Mn0.5O2 | We show the occurrence of local cation ordering in Li-ion battery material Li<sub>1.25</sub>Nb<sub>0.25</sub>Mn<sub>0.5</sub>O<sub>2</sub>, previously thought to be disordered. We deduce this ordering from X-ray diffraction, and test it against neutron diffraction & PDF, magnetic susceptibility and solid state NMR evidence. We identify the nature of the ordering as having a local structure related to that of gamma-LiFeO<sub>2</sub>, determine the correlation length of such ordering, and demonstrate its significant consequences for the material's electrochemistry. | Michael Jones; Philip
J. Reeves; Ieuan
D. Seymour; Matthew J. Cliffe; Siân E. Dutton; Clare P. Grey | Electrochemistry; Magnetism; Solid State Chemistry; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74227f96a008591286553/original/short-range-ordering-in-battery-electrode-the-cation-disordered-rocksalt-li1-25nb0-25mn0-5o2.pdf |
60c758f7ee301c9148c7b802 | 10.26434/chemrxiv.14608296.v1 | Prediction of Compound Synthesis Accessibility Based on Reaction Knowledge Graph | <a>With the increasing application of deep learning based generative models for <i>de novo</i> molecule design,
quantitative estimation of molecular synthetic accessibility
becomes a crucial factor for prioritizing the structures generated from
generative models. On the other hand, it is also useful for helping prioritization of hit/lead compounds and guiding retro-synthesis analysis. In current study, based on the USPTO and Pistachio reaction datasets, we created a
chemical reaction network, in which a depth-first search was performed for identification
of the reaction paths of product compounds. This reaction dataset was then used
to build predictive model for distinguishing the organic compounds either as
easy synthesize (ES) or hard-to synthesize (HS) classes. Three synthesis
accessibility (SA) models were built using deep learning/machine learning
algorithms. The comparison between our three SA scoring functions with other
existing synthesis accessibility scoring schemes, such as SYBA, SCScore,
SAScore were also carried out. and the graph based deep learning model
outperforms those existing SA scores. Our results show that prediction models
based on historical reaction knowledge could be a useful tool for measuring
molecule complexity and estimating molecule SA.</a> | Baiqing Li; Hongming Chen | Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758f7ee301c9148c7b802/original/prediction-of-compound-synthesis-accessibility-based-on-reaction-knowledge-graph.pdf |
67afb9426dde43c908e43c48 | 10.26434/chemrxiv-2024-k2k3l-v2 | Neural Mulliken Analysis: Molecular Graphs from Density Matrices for QSPR on Raw Quantum-Chemical Data | Here molecular graphs derived from the 1-electron density matrix are introduced within a more general effort to explore whether electronic structure awareness allows combining generalization from small data and optimal feature learning in a single model. Diagonal matrix blocks serve as atomic nodes embeddings, off-diagonal blocks provide embeddings for “link” nodes in-between atomic pairs. In a minimal basis, these embeddings have dimensions of only 45 and 81, still no data loss occurs. The overlap matrix is used in edge embeddings to encode structural information and as weights for pooling operations. Additionally, element-wise multiplication performed while pooling may provide access to electronic charges similar to Mulliken population analysis. A GNN trained on 94 drug-like molecules from the Solubility Challenge (2008, Llinàs et al.}) demonstrated improved solubility prediction accuracy (RMSE 0.63, R2 0.79). If combined with existing techniques for predicting electron density from molecular structure, this approach is promising for addressing various chemical machine-learning problems. | Oleg Gromov | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67afb9426dde43c908e43c48/original/neural-mulliken-analysis-molecular-graphs-from-density-matrices-for-qspr-on-raw-quantum-chemical-data.pdf |
664f13b0418a5379b013c95b | 10.26434/chemrxiv-2024-xhlgh | Dynamic Charge Distribution as a Key Driver of Catalytic Reactivity in an Artificial Metalloenzyme | Miniature artificial enzymes such as mimochromes provide a simplified platform to extract design principles for engineering rate enhancements beyond that of natural enzymes, although design optimizations have largely focused on geometric properties, leaving the impact of the electronic environment unexplored. To investigate how the electronic environment influences reactivity, we carry out classical and ab initio molecular dynamics (MD) simulations, supervised machine learning (ML), and statistical analysis of a series of mimochromes, MC6, MC6*, and MC6*a. Our classical MD simulations reveal a correlation between increased protein–heme contact and improved reactivity, confirming the importance of geometry, while ab initio MD simulations provide insight into the electronic environment, showing the electrostatic potential (ESP) at the metal center also correlates with reactivity. Quantum mechanical calculations of sulfoxidation and hydroxylation reactions demonstrate that the negative ESP at the metal center and active site electric field stabilize the highest-energy intermediate. Furthermore, using ML classifiers, we identify critical residues such as Lys12 and Asp18 in MC6*a that demonstrate charge-coupling patterns that explain differences in reactivity. This suggests that the reactivity series in mimochromes is primarily driven by key aspects of partial charge distribution dynamics, which should guide the engineering of next-generation metalloenzymes. | David Kastner; Clorice Reinhardt; Husain Adamji; Melissa Manetsch; Yuriy Roman-Leshkov; Heather Kulik | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Theory - Computational; Machine Learning; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664f13b0418a5379b013c95b/original/dynamic-charge-distribution-as-a-key-driver-of-catalytic-reactivity-in-an-artificial-metalloenzyme.pdf |
60c7535c337d6c2d3fe2885e | 10.26434/chemrxiv.13480431.v1 | One-Step Simultaneous Synthesis of Circularly Polarized Luminescent Multiple Helicenes Using a Chrysene Framework | <p>A series of multiple
helicenes was simultaneously synthesized in one step by intramolecular
cyclization of a single chrysene derivative containing two
2-[(4-alkoxyphenyl)ethynyl]phenyl units accompanied by rearrangements of the
aryl pendants. The electrophile-induced double cyclization with or without aryl
migrations proceeded efficiently under acidic conditions to afford annulative p-extension
of the chrysene units and produced quadruple (QH-<b>2</b>), triple (TH-<b>2</b>),
and double (DH-<b>2</b>)
helicenes containing [4]- and/or [5]helicene frameworks with dynamic and/or
static helicene chirality in one step. Three multiple helicenes’ structures
were determined by X-ray crystallography and/or density functional theory
calculations. The multiple TH-<b>2</b>
and DH-<b>2</b> helicenes were
separated into enantiomers because of the stable one and two [5]helicene
moieties, respectively, and showed intense circular dichroism and circularly
polarized luminescence. Although QH-<b>2</b>,
which comprises four [4]helicene subunits, was not resolved into enantiomers,
the TH-<b>2</b> enantiomers were
further separated into a pair of diastereomers at low temperature resulting
from their substituted [4]helicene chirality.</p> | Tomoyuki Ikai; Shoya Yamakawa; Nozomu Suzuki; Eiji Yashima | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7535c337d6c2d3fe2885e/original/one-step-simultaneous-synthesis-of-circularly-polarized-luminescent-multiple-helicenes-using-a-chrysene-framework.pdf |
659941fc9138d231614fd176 | 10.26434/chemrxiv-2024-4kc0h | Tuning the Interfacial Electronic Structure of MoS2 by Adsorption of Cobalt Phthalocyanine Derivatives | We investigate the interfacial electronic structure of n-type bulk MoS2 upon the adsorption of CoPc and CoPcF16 mono- and few-layers using advanced spectroscopic techniques. These include X-ray photoelectron spectroscopy (XPS), X-ray absorption spectroscopy (XAS), angle-resolved photoelectron spectroscopy (ARPES), and ultraviolet photoelectron spectroscopy (UPS). Our findings indicate that the adsorption of CoPc enhances the degree of n-doping at the interface with MoS2. In contrast, CoPcF16 results in a nearly intrinsic position of the Fermi level. Furthermore, we note the formation of an induced gap state near the valence band maximum for monolayer CoPcF16 on MoS2. These observations underscore the potential to fine-tune the interfacial electronic properties of transition metal dichalcogenides through molecular functionalization for tailored electronic applications. | Philipp Haizmann; Eric Juriatti; Maren Klein; Katharina Greulich; Ruslan Ovsyannikov; Erika Giangrisostomi; Thomas Chassé; Heiko Peisert; Marcus Scheele | Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Surface | CC BY 4.0 | CHEMRXIV | 2024-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659941fc9138d231614fd176/original/tuning-the-interfacial-electronic-structure-of-mo-s2-by-adsorption-of-cobalt-phthalocyanine-derivatives.pdf |
60c74276337d6c576ce26a86 | 10.26434/chemrxiv.8299715.v1 | Diversity Focused Semisyntheses of Tetronate Polyether Ionophores | The polyether ionophores are complex natural products capable of transporting cations across biological membranes. Many family members possess highly potent antimicrobial activity and a few selected compounds have ability to target particularly aggressive cancer cells. Despite these interesting perspectives, a detailed understanding of the cellular mode-of-action of polyether ionophores is generally lacking. In principle, broad mapping of structure-activity relationships across several biological activities could provide mechanistic insights as well as identification of lead structures but access to structural diversity within the overall class is synthetically very challenging. In this manuscript, we demonstrate that novel polyether ionophores can be constructed by recycling components of highly abundant polyethers. We provide the first examples of synthetically incorporating halogen-functionalized tetronic acids as cation-binding groups into polyether ionophores and we identify analogs with strong anti-bacterial activity and minimal effects on mammalian cells. | Shaoquan Lin; Han Liu; Esben B. Svenningsen; Christine Pedersen; Peter Nørby; Thomas Tørring; Thomas Poulsen | Natural Products; Organic Synthesis and Reactions; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74276337d6c576ce26a86/original/diversity-focused-semisyntheses-of-tetronate-polyether-ionophores.pdf |
6234a73c8ab3730425690991 | 10.26434/chemrxiv-2022-2v424 | Automated Bonding Analysis with Crystal Orbital Hamilton Populations | Understanding crystalline structures based on their chemical bonding is growing in importance. In this context, chemical bonding can be studied with the Crystal Orbital Hamilton Population (COHP), allowing to quantify interatomic bond strength. Here we present a new set of tools to automate the calculation of COHP and analyze the results. We use the program packages VASP and LOBSTER and the Python packages atomate and pymatgen. The analysis produced by our tools includes plots, a textual description, and key data in machine-readable format. To illustrate those capabilities, we have selected simple test compounds (NaCl, GaN), the oxynitrides BaTaO2N, CaTaO2N, and SrTaO2N, and the thermoelectric material Yb14Mn1Sb11. We show correlations between bond strengths and stabilities in the oxynitrides, as well as the influence of the Mn-Sb bonds on the magnetism in Yb14Mn1Sb11. Our contribution enables high-throughput bonding analysis and will facilitate the use of bonding information for machine learning studies. | Janine George; Guido Petretto; Aakash Naik; Marco Esters; Adam J. Jackson; Ryky Nelson; Richard Dronskowski; Gian-Marco Rignanese; Geoffroy Hautier | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6234a73c8ab3730425690991/original/automated-bonding-analysis-with-crystal-orbital-hamilton-populations.pdf |
60c74cdd4c8919b51cad36f3 | 10.26434/chemrxiv.12429464.v1 | Enhancing Water Sampling of Buried Binding Sites Using Nonequilibrium Candidate Monte Carlo | <div>Water molecules can be found interacting with the surface and within cavities in proteins. However, water exchange between bulk and buried hydration sites can be slow compared to simulation timescales, thus leading to the inefficient sampling of the locations of water. This can pose problems for free energy calculations for computer-aided drug design. Here, we apply a hybrid method that combines nonequilibrium candidate Monte Carlo (NCMC) simulations and molecular dynamics (MD) to enhance sampling of water in specific areas of a system, such as the binding site of a protein. Our approach uses NCMC to gradually remove interactions between a selected water molecule and its environment, then translates the water to a new region, before turning the interactions back on. This approach of gradual removal of interactions, followed by a move and then reintroduction of interactions, allows the environment relax in response to the proposed water translation, improving acceptance of moves and thereby accelerating water exchange and sampling. We validate this approach on several test systems including the ligand-bound MUP-1 and HSP90 proteins with buried crystallographic waters removed. We show that our NCMC/MD method enhances water sampling relative to normal MD when applied to these systems. Thus, this approach provides a strategy to improve water sampling in molecular simulations which may be useful in practical applications in drug discovery and biomolecular design.</div> | Teresa Danielle Bergazin; Ido Ben-Shalom; Nathan M. Lim; Samuel C. Gill; Michael K. Gilson; David Mobley | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cdd4c8919b51cad36f3/original/enhancing-water-sampling-of-buried-binding-sites-using-nonequilibrium-candidate-monte-carlo.pdf |
673d3a67f9980725cfdc3d10 | 10.26434/chemrxiv-2024-3trkk | The hole mass in Car-Parrinello molecular dynamics: insights into the dynamics of excitation | In the Car-Parrinello molecular dynamics (CPMD) formalism, orbitals can be assigned different effective masses according to whether the orbital is occupied by a hole or an electron, and such masses affect the response of the orbitals to their environment. Inspired by this, we introduce and implement a novel modification of CPMD, HoleMass CPMD, in which a hole, which is a partially empty orbital, is assigned a fictitious mass that is different from fully occupied orbitals. Despite the simplicity of the approach, we find that it solves a key problem in first principles molecule dynamics simulation: for a set of carefully assigned mass values, the method is able to successfully simulate photoinduced chemical reactions, exemplified here by the ring-opening reaction in oxirane within a few femtoseconds, and cyclobutene, within a few picoseconds. Our method can reproduce the CO ring-opening of oxirane, and the correct isomerization sequence for cyclobutene: when the ring opens, the first isomer that forms is the cis isomer, followed by the trans isomer. Our method has been implemented in the Car-Parrinello package of QuantumEspresso and is available as an open-source contribution. The HoleMass CPMD method provides a new quantum chemistry tool for the simulation of excitation dynamics in molecules, and can also be applied for modelling charge localization effects in materials systems. | Sherif Tawfik; Tiffany Walsh | Theoretical and Computational Chemistry; Organic Chemistry; Photochemistry (Org.); Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673d3a67f9980725cfdc3d10/original/the-hole-mass-in-car-parrinello-molecular-dynamics-insights-into-the-dynamics-of-excitation.pdf |
60c754ce0f50dbce7b397dc5 | 10.26434/chemrxiv.13728112.v1 | Enzymatic β-Oxidation of the Cholesterol Side Chain in Mycobacterium Tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-Cholest-4,22- Dien-24-Oyl-CoA | <p>The unique ability of <i>Mycobacterium tuberculosis </i>(Mtb) to utilize host lipids such as cholesterol for survival, persistence, and virulence has made the metabolic pathway of cholesterol an area of great interest for therapeutics development, and bioproduction of valuable sterol intermediates. Herein, we identify and characterize two genes from the <a></a><a>Cho-region of the Mtb genome</a>, <i>chsH3 </i>(Rv3538) and <i>chsB1</i> (Rv3502c). Their protein products catalyze <a></a><a>two sequential stereospecific</a>hydration and dehydrogenation steps in the b-oxidation of the cholesterol side chain. ChsH3 favors the <i>22S</i> hydration of 3-oxo-cholest-4,22-dien-24-oyl-CoA in contrast to the previously reported EchA19 (Rv3516) which catalyzes formation of the (<i>22R</i>)-hydroxy-3-oxo-cholest-4-en-24-oyl-CoA from the same enoyl-CoA substrate. ChsB1 is stereospecific and catalyzes dehydrogenation of the ChsH3 product, but not the EchA19 product. The X-ray crystallographic structure of the ChsB1 apo-protein was determined at a resolution of 2.03 Å and the holo-enzyme with bound NAD<sup>+</sup> cofactor at 2.21 Å.The homodimeric structure is representative of a classical NAD<sup>+</sup> utilizing short-chain type alcohol dehydrogenase/reductase, including a Rossmann-fold motif, but exhibits a unique substrate binding site architecture that is of greater length and width than its homologous counterparts, likely to accommodate the bulky steroid substrate. Intriguingly, Mtb utilizes MaoC-like hydratases in sterol side-chain catabolism in contrast to fatty acid b-oxidation in other species that utilize the evolutionarily distinct crotonase family of hydratases. </p> | Tianao Yuan; Joshua Werman; Xingyu Yin; Meng Yang; Miguel Garcia-Diaz; Nicole Sampson | Biochemistry; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754ce0f50dbce7b397dc5/original/enzymatic-oxidation-of-the-cholesterol-side-chain-in-mycobacterium-tuberculosis-bifurcates-stereospecifically-at-hydration-of-3-oxo-cholest-4-22-dien-24-oyl-co-a.pdf |
60c75703ee301cbd49c7b489 | 10.26434/chemrxiv.14356088.v1 | Biotechnology-Derived Chitosans with Non-Random Patterns of Acetylation Differ from Conventional Chitosans in Their Properties and Activities | Chitosans are versatile biopolymers with multiple biological activities and potential applications. They are linear copolymers of glucosamine and N-acetylglucosamine defined by their degree of polymerization (DP), fraction of acetylation (<i>F<sub>A</sub></i>), and pattern of acetylation (PA). Technical chitosans produced chemically from chitin possess defined DP and FA but random PA, while enzymatically produced natural chitosans are likely to have non-random PA. This natural process has not been replicated using biotechnology because chitin de-N-acetylases do not efficiently deacetylate crystalline chitin. Here, we show that such enzymes can partially N-acetylate polyglucosamine in the presence of excess acetate, yielding chitosans with <i>F<sub>A</sub></i> up to 0.7 and an enzyme-dependent non-random PA. The biotech chitosans differ from technical chitosans both in terms of physicochemical and nanoscale solution properties and biological activities. As with synthetic block co-polymers, controlling the distribution of building blocks within the biopolymer chain will open a new dimension of chitosan research and exploitation. | Jasper Wattjes; Sruthi Sreekumar; Anna Niehues; Tamara Mengoni; Ana Carina Loureiro Mendes; Ed Morris; Francisco Goycoolea; Bruno Moerschbacher | Biopolymers; Biochemical Analysis; Mass Spectrometry; Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75703ee301cbd49c7b489/original/biotechnology-derived-chitosans-with-non-random-patterns-of-acetylation-differ-from-conventional-chitosans-in-their-properties-and-activities.pdf |
60c745f3469df452ccf435a3 | 10.26434/chemrxiv.10299164.v1 | Using FRET to Measure the Time it Takes for a Cell to Destroy a Virus | <div><div><div><p>The emergence of viral nanotechnology over the preceding two decades has created a number of intellectually captivating possible translational applications; however, the in vitro fate of the viral nanoparticles in cells remains an open question. Herein, we investigate the stability and lifetime of virus-like particle (VLP) Qβ - a representative and popular VLP for several applications - following cellular uptake. By exploiting the available functional handles on the viral surface, we have orthogonally installed the known FRET pair, FITC and Rhodamine B, to gain insight of the particle’s behavior in vitro. Based on these data, we believe VLPs undergo aggregation in addition to the anticipated proteolysis within a few hours of cellular uptake.</p></div></div></div> | Candace E. Benjamin; Zhuo Chen; Olivia Brohlin; Hamilton Lee; Stefanie Boyd; Duane Winkler; Jeremiah J. Gassensmith | Bioengineering and Biotechnology | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745f3469df452ccf435a3/original/using-fret-to-measure-the-time-it-takes-for-a-cell-to-destroy-a-virus.pdf |
65d770ed66c1381729415bfd | 10.26434/chemrxiv-2024-dx2nv | Formation of the oxyl’s potential energy surface by the spectral kinetics of a vibrational mode | One of the most reactive intermediates for oxidative reactions is the oxyl radical, an electron-deficient oxygen atom. The discovery of a new vibration upon photoexcitation of the oxygen evolution catalysis detected the oxyl radical at the SrTiO3 surface. The vibration was assigned to a motion of the sub-surface oxygen underneath the titanium oxyl (Ti-O·-), created upon hole transfer to (or electron extraction from) a hydroxylated surface site. Evidence for such an interfacial mode derived from its spectral shape which exhibited a Fano resonance—a coupling of a sharp normal mode to continu-um excitations. Here, this Fano resonance is utilized to derive precise formation kinetics of the oxyl radical and its associ-ated potential energy surface (PES). From the Fano lineshape, the formation kinetics are obtained from the anti-resonance (the kinetics of the coupling factor), the resonance (the kinetics of the coupled continuum excitations), and the frequency integrated spectrum (the kinetics of the normal mode’s cross-section). All three perspectives yield a logistic function growth with a half-rise of 2.3 ± 0.3 ps and rate of 0.48 ± 0.09 ps. A non-equilibrium transient associated with photoexcitation is separated from the rise of the equilibrated PES. The logistic function characterizes the oxyl coverage at the very initial stages (t~0) to have an exponential growth rate that quickly decreases towards zero as a limiting coverage is reached. Such time-dependent reaction kinetics identify a dynamic activation barrier associated with the formation of a PES and quantify it for an oxyl radical coverage. | Tanja Cuk; James Stewart; Paul Zayka; Christen Courter | Physical Chemistry; Catalysis; Energy; Heterogeneous Catalysis; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d770ed66c1381729415bfd/original/formation-of-the-oxyl-s-potential-energy-surface-by-the-spectral-kinetics-of-a-vibrational-mode.pdf |
617b18049b583afce8e34f45 | 10.26434/chemrxiv-2021-dkwcm | Ionic Screening in Bulk and under Confinement | Recent experiments have shown that the repulsive force between atomically flat, like-charged surfaces confining room-temperature ionic liquids or concentrated electrolytes exhibits an anomalously large decay length.
In our previous publication [Zeman et al., Chem. Commun. 56, 15635 (2020)], we showed by means of extremely large-scale molecular dynamics simulations that this so-called underscreening effect might not be a feature of bulk electrolytes.
Herein, we corroborate these findings by providing additional results with more detailed analyses and expand our investigations to ionic liquids under confinement.
Unlike in bulk systems, where screening lengths are computed from the decay of interionic potentials of mean force (PMFs), we extract such data in confined systems from cumulative charge distributions.
At high concentrations, our simulations show increasing screening lengths with increasing electrolyte concentration, consistent with classical liquid state theories.
However, our analyses demonstrate that---also for confined systems---there is no anomalously large screening length.
As expected, the screening lengths determined for ionic liquids under confinement are in good quantitative agreement with the screening lengths of the same ionic systems in bulk.
In addition, we show that some theoretical models used in the literature to relate the measured screening lengths to other observables are inapplicable to highly concentrated electrolytes. | Johannes Zeman; Svyatoslav Kondrat; Christian Holm | Theoretical and Computational Chemistry; Physical Chemistry; Physical and Chemical Properties; Statistical Mechanics; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617b18049b583afce8e34f45/original/ionic-screening-in-bulk-and-under-confinement.pdf |
60c747080f50db0968396531 | 10.26434/chemrxiv.11494170.v1 | (2-Hydroxy-4-methoxy)benzyl Aminoadamantane Conjugates as Probes to Investigate Specificity Determinants in Blocking Influenza M2 S31N and M2 WT Channels with Binding Kinetics and Simulations | <p>In an attempt to synthesize potent blockers of the
influenza A M2 S31N proton channel with modifications of amantadine, we used MD
simulations and MM-PBSA calculations to project binding modes of compounds <b>2-5,</b> which are analogues of <b>1</b>, a dual blocker. Blocking both the
S31N mutant and the wild type (WT) M2, <b>1
</b>is composed of amantadine linked to an aryl head group, (4-methoxy-2-hydroxy)-benzyl.
Compound <b>6</b>, used as control, has an
3-(thiophenyl)isoxazolyl aryl head group, and selectively blocks M2 S31N (but
not WT) in an aryl head group “out” (i.e. N-ward) binding orientation. We then
tested <b>1</b>-<b>6</b> as anti-virals in cell culture and for M2 binding efficacy with
electrophysiology (EP). The new molecules <b>2-5</b>
have a linker between the adamantane and amino group which can be as small as a
CMe<sub>2</sub> in rimantadine derivative <b>2</b>,
or longer like phenyl in <b>3</b>.
Alternatively, we explored the impact of expanding the diameter of adamantane with
diamantyl or triamantyl in <b>4 </b>and<b> 5</b>, respectively. Antiviral effects
against A/WSN/33 and its M2 WT revertant (M2 N31S) were seen for all six
compounds except for <b>5</b> vs. the
native (S31N) virus and (as predicted from previous studies) <b>6</b> vs. the WT revertant. Compounds <b>1-5, </b>projected to bind<b> </b>in a polar head group “in” (C-ward)
orientation, strongly block<b> </b>proton
currents through M2 WT expressed in voltage-clamped oocytes with fast
association rate constants (k<sub>on</sub>), and slow dissociation rate
constants (k<sub>off</sub>). Surprisingly,<b>
2-5, </b>projected to bind<b> </b>in a
polar head group out orientation, do not effectively block M2 S31N-mediated
proton currents in EP. The results from MD and MM-PBSA calculations suggested
that compounds <b>2</b>-<b>5</b> can be fully effective at blocking
the M2 channel when present. The low degree of blocking in M2 S31N is due to
their kinetics of binding observed in EP, i.e. two orders of magnitude
reduction in k<sub>on </sub>compared to <b>6</b>,
and a fast off rate constant similar to that of <b>6</b>,<b> </b>which is consistent
with<b> </b>steered-MDsimulations. The low
k<sub>on</sub> values can be interpreted from MD simulations, which suggest
distortions to V27 cluster of the M2 S31N caused by the longer (even by one
methylene) hydrophobic segment from adamantane to aryl head group, appropriate
to fit from G34 to V27. The deformations in the N-terminus may be sufficiently
energetic for <b>2-5</b> (compared to <b>6</b>)<b>
</b>to cause the observed low k<sub>on</sub>. <br /></p> | Christina Tzitzoglaki; Kelly McGuire; Athina Konstantinidi; Panagiotis Lagarias; Anja Hoffmann; Jun Wang; Ioannis Papanastasiou; Nataliya A. Fokina; Peter R. Schreiner; Santiago Vázquez; Michaela Schmidtke; David Busath; Antonios Kolocouris | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747080f50db0968396531/original/2-hydroxy-4-methoxy-benzyl-aminoadamantane-conjugates-as-probes-to-investigate-specificity-determinants-in-blocking-influenza-m2-s31n-and-m2-wt-channels-with-binding-kinetics-and-simulations.pdf |
60c75351ee301ca997c7ada9 | 10.26434/chemrxiv.13395416.v1 | Structural Determinants for the Mode of Action of the Imidazopyridine DS2 at d-containing g-Aminobutyric Acid Type A (GABAA) Receptors | <div>A SAR study of the delta-selective positive modulators DS2 was performed to assist the quest for the binding site. The modulatory effect was measured using a fluorometric inaging plate reader (FLIPR) membrane potential (FMP) functional assay. Specific positions in the structural scaffold of DS2 was found to severly affect the pharmacological profile. <br /></div><div>Analogs superior to DS2 were identified displaying higher potency and selectivity for the alfa4beta1delta over alfa4beta1gamma.<br /></div><br /> | Bente Frølund; Frederik Rostrup; Christina Birkedahl Falk-Petersen; Kasper Harpsøe; Stine Buchleithner; Irene Conforti; Sascha Jung; David E. Gloriam; Tanja Schirmeister; Petrine Wellendorph | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75351ee301ca997c7ada9/original/structural-determinants-for-the-mode-of-action-of-the-imidazopyridine-ds2-at-d-containing-g-aminobutyric-acid-type-a-gabaa-receptors.pdf |
62beb8c213b85b4bd43b3dfc | 10.26434/chemrxiv-2022-vz4cg-v2 | How very small changes in the peptide sequence of
β-amyloids influence their redox properties. Electrochemical studies of copper complexes with Aβ(11-16) and pAβ(11-16) | Here we demonstrate a significant difference in redox behaviour of copper complexes with β-amyloids Aβ(11-x) and pAβ(11-x) which are models for important components of senile plaques. A small change in the peptide chain may enhance reactive oxygen species (ROS) formation which can severely damage nerve cells. | Magdalena Zofia Wiloch; Martin Jönsson-Niedziółka | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62beb8c213b85b4bd43b3dfc/original/how-very-small-changes-in-the-peptide-sequence-of-amyloids-influence-their-redox-properties-electrochemical-studies-of-copper-complexes-with-a-11-16-and-p-a-11-16.pdf |
60c74d77bdbb89e3d7a399ce | 10.26434/chemrxiv.12620543.v1 | Synthesis of Unsymmetrical Sulfamides and Polysulfamides Via SuFEx Click Chemistry | In this manuscript, we report practical, robust, and efficient conditions to synthesize a variety of unsymmetrical sulfamides via Sulfur(VI) Fluoride Exchange (SuFEx) click chemistry. This SuFEx strategy was subsequently harnessed to prepare a broad array of polysulfamides through polycondensation. The generality of the conditions allowed the synthesis of polymers with diverse architectures. | Ryan Kulow; Jiun Wei Wu; Cheoljae Kim; Quentin Michaudel | Organic Synthesis and Reactions; Organic Polymers; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d77bdbb89e3d7a399ce/original/synthesis-of-unsymmetrical-sulfamides-and-polysulfamides-via-su-f-ex-click-chemistry.pdf |
662af698418a5379b0bdc6f1 | 10.26434/chemrxiv-2024-c24c3 | Intelligent Photoresponsive Drug Delivery with Causal
Language Models and Chemist Instruction Training | As large-scale language models continue to expand in size and diversity, their substantial potential and the relevance of their applications are increasingly being acknowledged. The rapid advancement of these models also holds profound implications for the design of stimulus-responsive materials used in drug delivery over the long term. To optimize large models for extensive dataset processing and comprehensive learning akin to a chemist’s intuition, integrating deeper chemical insights is imperative. Our study initially contrasted the performance of Bigbrid, Gemma, GPT NeoX, etc., specifically focusing on designing photoresponsive drug delivery molecules. We gathered excitation energy data through computational chemistry tools and further explored light-driven isomerisation reaction as a critical mechanism in drug delivery. Our study explored the effectiveness of incorporating human feedback into reinforcement learning to imbue large models with chemical intuition, improving their understanding of relationships involving -N=N- groups in photoisomerisa-tion transitions of light-responsive molecules. Despite progress, the limited availability of specialized domain datasets continues to be a significant challenge in maximizing the performance of large models. | Junjie Hu; Peng Wu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662af698418a5379b0bdc6f1/original/intelligent-photoresponsive-drug-delivery-with-causal-language-models-and-chemist-instruction-training.pdf |
6638c9a7418a5379b092ec4e | 10.26434/chemrxiv-2024-p0zfm-v3 | Deciphering the Atomic Size Factor in Quasi-ternary Zintl phases RAg0.5Al0.5Ge (R = Ca, Eu) with the TiNiSi type Structure | The targeted synthesis of two analogous quasi-ternary Zintl phases CaAg0.5Al0.5Ge and EuAg0.5Al0.5Ge were conducted by direct reaction of stoichiometric mixtures of the elements at high temperature and, their crystal structures refined from single-crystal X-ray diffraction data. These pseudo-ternary structures are intended to probe the generalization of the pseudo-element concept to the small polarizing cation component of the ternary isovalent Zintl phases CaMgGe and EuMgGe, with the complete replacement of the divalent Mg position by an equiatomic mixture of monovalent Ag and trivalent Al atoms, while the TiNiSi type structure (space group Pnma) is retained. The two title phases are almost line compounds without significant experimental phase width. However, the calculated band structure of the hypothetical ordered model of Ca2AgAlGe2, based on first principles DFT method (LMTO code), predicted the compound to be metallic. The chemical bonding analysis with the help of crystal orbital Hamilton population (COHP) could confirmed that, due to the difference in atomic size between Ag and Al, the Al–Ge contacts are localized 2c-2e bonds, in contrast to the more polar and non-localized Ag–Ge bonds. Hence, the ionic formulation should be (Ca2+)2Ag+(4b-Al–)(2b-Ge2–)2, according to the Zintl-Klemm concept (2b- and 4b- indicated two bonded and four bonded atoms). This is also in agreement with an electron localization function (ELF) topology analysis, revealing monosynaptic valence basins on Ge atoms (lone pairs) and only on the Ge–Al bonds (two-center, two-electron bond). Thus, due to the similar atomic size between Al and Ge, an accumulation of charge density on the severely distorted AlGe4 tetrahedra is observed leading to strong Pauli repulsion between the localized electron pairs, while Ag–Ge bonds are depleted. These findings are interesting regarding the influence of the geometric factor on the stability and physical properties of the TiNiSi type structural family in general. | Simeon Ponou; Anja-Verena Mudring | Physical Chemistry; Inorganic Chemistry; Chemical Education; Bonding; Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6638c9a7418a5379b092ec4e/original/deciphering-the-atomic-size-factor-in-quasi-ternary-zintl-phases-r-ag0-5al0-5ge-r-ca-eu-with-the-ti-ni-si-type-structure.pdf |
67d828df81d2151a02b50f40 | 10.26434/chemrxiv-2025-c7j5z-v2 | Harnessing Self-Condensing Vinyl Copolymerization for Well-Defined Redox-Active Hyperbranched Polymers Enabled by Flow Chemistry | The increased adoption of renewable power necessitates the development of grid-scale storage solutions, with aqueous redox flow batteries (RFBs) at the forefront. Despite their potential, performance degradation due to crossover typically requires expensive specialty membranes. Previous research has demonstrated the use of cost-effective dialysis membranes, but issues of the solution viscosity and crossover continue to pose challenges. Here we use flow chemistry to create redox-active hyperbranched copolymers (HCPs) with remarkably low dispersity. The distinct reaction dynamics of flow chemistry facilitated the efficient and monomer-independent control over self-condensing vinyl polymerization. This substantially improved the suppression of crossover and enhanced rheology behaviors. RFBs equipped with our redox-active HCPs exhibited exceptional long-term stability, mapping a pathway towards more refined electrolyte design and practical application of polymer-based technologies. Meanwhile, our study underscores the significant advantages and potential of emerging flow chemistry techniques. | Yi Lv; Yuqing Zhang; Feichen Cui; Yipeng Zhang; Zixiao Wang; Junlong Yang; Qinzhe Liu; Yingshuai Zhao; Yijun Zheng; Chao Xu; Jiajun Yan | Materials Science; Polymer Science; Energy; Polyelectrolytes - Polymers; Polymerization (Polymers); Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d828df81d2151a02b50f40/original/harnessing-self-condensing-vinyl-copolymerization-for-well-defined-redox-active-hyperbranched-polymers-enabled-by-flow-chemistry.pdf |
60c7549d702a9bbbc918c573 | 10.26434/chemrxiv.13693648.v1 | Methanol Carbonylation over Acid Mordenite: Insights from Ab Initio Molecular Dynamics and Machine Learning Thermodynamic Perturbation Theory | <div>In this work we present a detailed \textit{ab initio} study of the carbonylation reaction of methoxy groups in the zeolite mordenite, as it is the rate determining step in a series of elementary reactions leading to ethanol. </div><div>For the first time we employ full molecular dynamics simulations to evaluate free energies of activation for the reactions in side pockets and main channels. Results show that the reaction in the side pocket is preferred and, when dispersion interactions are taken into account, this preference becomes even stronger. This conclusion is confirmed using multiple levels of density functional theory approximations with (PBE-D2, PBE-MBD, and vdW-DF2-B86R) or without (PBE, HSE06) dispersion corrections. These calculations, that in principle would require several demanding molecular dynamics simulations, were made possible at a minimal computational cost by using a newly developed approach that combines thermodynamic perturbation theory with machine learning.</div> | Monika Gešvandtnerová; Dario Rocca; Tomas Bucko | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7549d702a9bbbc918c573/original/methanol-carbonylation-over-acid-mordenite-insights-from-ab-initio-molecular-dynamics-and-machine-learning-thermodynamic-perturbation-theory.pdf |
65e021dd66c1381729d33fd8 | 10.26434/chemrxiv-2024-gwzfj-v2 | Enzymatically Catalyzed Molecular Aggregation | The dynamic modulation of the aggregation process of small molecules represents an important research objective for scientists. However, the complex and dynamic nature of internal environments in vivo impedes controllable aggregation processes of single molecules. In this study, we successfully achieved tumor-targeted aggregation of an aggregation-induced emission photosensitizer (AIE-PS), TBmA, with the catalysis of a tumor-overexpressed enzyme, γ-Glutamyl Transferase (GGT). Mechanistic investigations revealed that TBmA-Glu could be activated by GGT through cleavage of the -glutamyl bond and releasing TBmA. The poor water solubility of TBmA induced its aggregation, leading to an aggregation-enhanced emission and photodynamic activities of AIE-PS. The TBmA-Glu not only induced glutathione (GSH) depletion through GGT inhibition, but also triggered lipid peroxidation accumulation and ferroptosis in cancer cells through photodynamic therapy. The exceptional cancer-targeting ability and therapeutic efficiency demonstrated by this GGT activatable AIE-PS highlighted enzymatic-mediated modulation as an effective approach for regulating small molecule aggregation intracellularly, thereby advancing innovative therapeutic strategies for various diseases. | Wen-Jin Wang; Rongyuan Zhang; Liping Zhang; Liang Hao; Xu-Min Cai; Qian Wu; Zijie Qiu; Jing Feng; Shaojuan Wang; Parvej Alam; Guoqing Zhang; Zheng Zhao; Ben Zhong Tang | Biological and Medicinal Chemistry; Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e021dd66c1381729d33fd8/original/enzymatically-catalyzed-molecular-aggregation.pdf |
652d8fc045aaa5fdbb24d980 | 10.26434/chemrxiv-2023-cb5lg | 15NRORC: An Azine Labeling Protocol | A practical method for the synthesis of 15N-labeled azines with a high degree of isotopic enrichment is described. Activation of azine heterocycles with an electron-deficient arene allows for the facile substitution of the nitrogen atom with a specifically designed 15N-labeled reagent that undergoes a canonical ANRORC-type mechanism. A wide range of azines can be converted to their corresponding 15N isotopologs using this method, and it also allows for dearomative access to reduced heterocyclic congeners. A short dearomative formal synthesis of 15N-solifenacin is accomplished as well to demonstrate a practical appli-cation of this method for generating labeled pharmaceuticals. | Zachary Tolchin; Joel Smith | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d8fc045aaa5fdbb24d980/original/15nrorc-an-azine-labeling-protocol.pdf |
64bdf685b605c6803b3ed125 | 10.26434/chemrxiv-2023-v6h2h | Hybrid bronzes: mixed-valence organic-inorganic metal oxides as a tunable material platform | We demonstrate that mixed-valence layered organic-inorganic metal oxides of the form (L)zHxMO3 (L = neutral ligand; M = Mo, W; z = 0.5, 1; 0 < x < 2), which we call hybrid bronzes, can be readily synthesized through mild solution-state self-assembly reactions to integrate the stability and electronic utility of inorganic metal oxide bronzes with the chemical diversity and functionality of organic molecules. We use single-crystal and powder X-ray diffraction coupled with X-ray, electronic, and vibrational spectroscopies to show that the products of pre-, mid-, or post-synthetic reduction are mixed-valence versions of highly crystalline layered hybrid oxides. Pillared, bilayered, or canted bilayered arrangements of molecular arrays relative to inorganic sheets are dictated by judicious choice of organic ligands that can also incorporate chemical, redox, or photoactive handles. Significantly, bond-valence sum analysis and diffuse reflectance spectroscopy indicate relatively delocalized electronic behavior and four-point variable-temperature electrical transport measurements show that hybrid bronzes have comparable conductivity to their all-inorganic parent compounds. This work establishes a solution-processable, inexpensive, stable, and non-toxic material family whose electronic bands can be readily tuned and doped, thereby positioning hybrid bronzes to address myriad material challenges. | Wedage Lakna Dayaratne; Raúl Torres-Cadena; Bennett P. Schmitt; Emma M. Westrick; Adam Jaffe | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Solid State Chemistry; Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bdf685b605c6803b3ed125/original/hybrid-bronzes-mixed-valence-organic-inorganic-metal-oxides-as-a-tunable-material-platform.pdf |
60c73fdfbdbb891541a380c4 | 10.26434/chemrxiv.7480070.v1 | A Brief Pedestrian Derivation of E = mc2 for the Amateur Enthusiasts | <div>This note presents a pedestrian derivation of E=mc<sup>2</sup> for freshmen in chemistry, with a method similar to that of `handling units'. Such a picturesque derivation of the formula uses nothing but Newtonian laws of motions that do not go beyond mere definitions, together with well-known elementary physical quantities such as distance, velocity, force, momentum, and energy. The pedagogic merit of such an approach is discussed.</div><div>The following notes are stimulated from class lectures given to students in college preparing for a major in chemistry and to freshman in chemistry. While they constitute no original contribution to a subject that has been widely discussed, it is hoped that they may be of help to some teachers, students, and any enthusiast amateurs.<br /></div> | Zion Elani | Chemical Education - General; Physical and Chemical Properties; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fdfbdbb891541a380c4/original/a-brief-pedestrian-derivation-of-e-mc2-for-the-amateur-enthusiasts.pdf |
60c755a0567dfe6c9bec62f7 | 10.26434/chemrxiv.13003166.v6 | High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling | We provide an unsupervised adaptive sampling strategy capable of producing microseconds-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFF). The global exploration problem is decomposed into a set of separate MD trajectories that can be restarted within a selective process to achieve sufficient phase-space sampling. Accurate statistical properties can be obtained through reweighting. Within this highly parallel setup, the Tinker--HP package can be powered by an arbitrary large number of GPUs on supercomputers, reducing exploration time from years to days. This approach is used to tackle the urgent modeling problem of the SARS--CoV--2 Main Protease (Mpro) producing more than 38 microseconds of all-atom simulations of its apo, ligand-free, dimer using the high-resolution AMOEBA PFF. A first 15.14 microseconds simulation (physiological pH) is compared to available non--PFF long-timescale simulation data. A detailed clustering analysis exhibits striking differences between FFs, AMOEBA showing a richer conformational space. Focusing on key structural markers related to the oxyanion hole stability, we observe an asymmetry between protomers. One of them appears less structured resembling the experimentally inactive monomer for which a 6 microseconds simulation was performed as a basis of comparison. Results highlight the plasticity of Mpro active site. The C--terminal end of its less structured protomer is shown to oscillate between several states, being able to interact with the other protomer, potentially modulating its activity. Active and distal sites volumes are found to be larger in the most active protomer within our AMOEBA simulations compared to non-PFFs as additional cryptic pockets are uncovered. A second 17 microseconds AMOEBA simulation is performed with protonated His172 residues mimicking lower pH. Data show the protonation impact on the destructuring of the oxyanion loop. We finally analyze the solvation patterns around key histidine residues. The confined AMOEBA polarizable water molecules are able to explore a wide range of dipole moments, going beyond bulk values, leading to a water molecule counts consistent with experiment. Results suggest that the use of PFFs could be critical in drug discovery to accurately model the complexity of the molecular interactions structuring Mpro | Theo Jaffrelot Inizan; Frédéric Célerse; Olivier Adjoua; Dina El Ahdab; Luc-Henri Jolly; Chengwen Liu; Pengyu Ren; Matthieu Montes; Nathalie Lagarde; Louis Lagardère; Pierre Monmarché; Jean-Philip Piquemal | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755a0567dfe6c9bec62f7/original/high-resolution-mining-of-sars-co-v-2-main-protease-conformational-space-supercomputer-driven-unsupervised-adaptive-sampling.pdf |
62834d303f1e7c7510c0bac9 | 10.26434/chemrxiv-2022-nmnnd-v3 | Extraction of Chemical Structures from Literature and Patent Documents using Open Access Chemistry Toolkits: A Case Study with PFAS | The extraction of chemical information from documents is a demanding task in cheminformatics due to the variety of text and image-based representations of chemistry. The present work describes the extraction of chemical compounds with unique chemical structures from the open access CORE (COnnecting REpositories) and Google Patents full text document repositories. The importance of structure normalization is demonstrated using three open access cheminformatics toolkits: the Chemistry Development Kit (CDK), RDKit and OpenChemLib (OCL). Each toolkit was used for structure parsing, normalization and subsequent substructure searching, using SMILES as structure representations of chemical molecules and International Chemical Identifiers (InChIs) for comparison. Per- and polyfluoroalkyl substances (PFAS) were chosen as a case study to perform the substructure search, due to their high environmental relevance, their presence in both literature and patent corpuses, and the current lack of community consensus on their definition. Three different structural definitions of PFAS were chosen to highlight the implications of various definitions from a cheminformatics perspective. Since CDK, RDKit and OCL implement different criteria and methods for SMILES parsing and normalization, different numbers of parsed compounds were extracted, which were then evaluated using the three PFAS definitions. A comparison of these toolkits and definitions is provided, along with a discussion of the implications for PFAS screening and text mining efforts in cheminformatics. Finally, the extracted PFAS (~1.7 M PFAS from patents and ~27K from CORE) were compared against various existing PFAS lists and are provided in various formats for further community research efforts. | Shadrack Barnabas; Timo Böhme; Stephen Boyer; Matthias Irmer; Christoph Ruttkies; Ian Wetherbee; Todor Kondic; Emma Schymanski; Lutz Weber | Theoretical and Computational Chemistry; Analytical Chemistry; Chemoinformatics; Environmental Analysis; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2022-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62834d303f1e7c7510c0bac9/original/extraction-of-chemical-structures-from-literature-and-patent-documents-using-open-access-chemistry-toolkits-a-case-study-with-pfas.pdf |
67c6888381d2151a02f986ba | 10.26434/chemrxiv-2025-m3085-v2 | Unraveling the Surface Termination and Evolution of Topological Surface States for Electrocatalyst PtSn4 in Alkaline HER | Dirac nodal arc semimetal PtSn4 has been experimentally demonstrated as a promising electrocatalyst for hydrogen evolution reaction (HER) under both acidic and alkaline conditions. While two possible mechanisms have been proposed to explain its activity, the role of its topological surface states in HER remains unclear. It is indeed in question if the topological surface of this alloy is catalytically consequential. In this study, we investigate the surface termination that sustains topological surface states on PtSn4, and track their evolution during HER catalysis. We show that a reconstructed surface with a Sn-poor termination reproduces both the topological character and the scanning tunneling microscopy pattern observed in experiments. Through phase diagram and surface structure analysis, we outline the HER profile following the Volmer-Heyrovsky mechanism. As hydrogen atoms adsorb onto the surface, the structure undergoes further reconstruction to an equilibrium phase with a coverage of two hydrides per unit cell. Meanwhile, the surface electronic bands evolve in response to interactions with the adsorbed hydrogen atoms. We propose a hybridization diagram for understanding the surface state evolution based on wavefunction and chemical bonding analyses. While the Pt atoms serve as conventional sites for hydrogen binding, the surface states of PtSn4 are essential for stabilizing the hydrogen antibonding states via in-phase electronic interactions with the Sn components. This stabilization results in frontier surface bands that are responsible for driving the HER catalysis. Our findings provide a detailed description for the direct involvement of surface states on PtSn4 when employed as a topological catalyst for HER. | Guorong Weng; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Catalysis; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c6888381d2151a02f986ba/original/unraveling-the-surface-termination-and-evolution-of-topological-surface-states-for-electrocatalyst-pt-sn4-in-alkaline-her.pdf |
62b0698d7da6ce568c185db1 | 10.26434/chemrxiv-2022-bnxq5 | Differential Molecular Interactions of Telmisartan: Molecular-Level Insights from Spectral and Computational Studies | In this study, we investigated differential molecular interactions of crystalline and amorphous
forms of telmisartan (TEL), which is a non-peptide angiotensin-II receptor antagonist
commonly used in the management of hypertension. Amorphous telmisartan (AM-TEL) was
prepared using quench cooling of the melt. The analysis of solid-state properties of AM-TEL
using differential scanning calorimetry (DSC) and X-ray powder diffraction (XRD) confirmed
formation of AM-TEL. Based on a comparative analysis of molecular interactions using spectral
(FTIR and 13C solid-state NMR) and computational tools, we demonstrated that amorphous
telmisartan shows altered molecular interactions. Molecular dynamics simulation of amorphous
and crystalline forms demonstrate that the amorphous form retained some of the molecular
interactions in its disordered molecular arrangement, with a relatively stronger (decrease in bond
length) but lesser (up to only 2.6 % of the population) hydrogen bonding network as compared
with the crystalline counterpart (up to 76% of the population) | Mahendra Singh; Jacob Kongsted; Peng Zhan; Uttam Chand Banerjee; Vasanthanathan Poongavanam; N. Arul Murugan | Physical Chemistry; Materials Science; Biocompatible Materials; Materials Processing; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b0698d7da6ce568c185db1/original/differential-molecular-interactions-of-telmisartan-molecular-level-insights-from-spectral-and-computational-studies.pdf |
66b0957501103d79c5c85c65 | 10.26434/chemrxiv-2024-p2pqx | Dearomative Spirocyclization of Ynamides | Spiro N-heterocycles, particularly aza-spiro piperidines, have shown significant promise in pharmaceutical applications due to their ability to enhance physicochemical properties. Despite their potential, the preparation of these complex structures poses significant challenges. To address this, we propose a one-pot dearomative spirocyclization reaction of ynamides. This method involves a copper-catalyzed carbomagnesiation reaction, achieving chemo-, regio-, and stereoselective formation of (Z)-vinyl metal intermediates. Upon the addition of a Lewis acid, these intermediates undergo a regioselective nucleophilic dearomatization event, facilitating the synthesis of diverse aza-spiro piperidine scaffolds with multiple functional handles. Various Grignard reagents, diverse ynamides, and acylating reagents, have been explored, producing complex spirocyclic structures with potential medicinal relevance. | Mohamed Agbaria; Nwar Egbaria; Zackaria Nairoukh | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b0957501103d79c5c85c65/original/dearomative-spirocyclization-of-ynamides.pdf |
63757a6c0821299853fa1049 | 10.26434/chemrxiv-2022-kgz7g | 3D-Printed Microfluidic Device for High-Throughput Production of Lipid Nanoparticles Incorporating SARS-CoV-2 Spike Protein mRNA | Lipid nanoparticles (LNPs) are drug carriers for protecting nucleic acids for cellular delivery. The first mRNA vaccines authorized by the United States Food and Drug Administration are the mRNA-1273 (Moderna) and BNT162b (BioNTech/Pfizer) vaccines against coronavirus disease 2019 (COVID-19). We designed a 3D printed Omnidirectional Sheath-flow Enabled Microfluidics (OSEM) Device for producing mRNA-loaded LNPs that closely resemble the Moderna vaccine: we used the same lipid formulations to encapsulate mRNA encoding SARS-CoV-2 spike protein. The OSEM device is made of durable methacrylate-based materials that can support flow rates in the mL/min range and was fabricated by stereolithography (SLA), incorporating readily adaptable interfaces using commercial fluidic connectors. Two key features of the OSEM device are: 1) a 4-way hydrodynamic flow focusing region and 2) a staggered herringbone mixer (SHM). Superior to conventional planar fluid junctions, the 4-way sheath flow channel generates an evenly focused, circular center flow that facilitates the formation of LNPs with low polydispersity. Downstream, fluid mixing in the SHM is intensified by incorporating a zig-zag fluidic pathway to deliver high mRNA encapsulation efficiency. We characterized the mRNA-loaded LNPs produced in the OSEM device and showed that the enhanced 3D microfluidic structures enable a 5-fold higher throughput production rate (60 mL/min) of LNPs than commercial multi-thousand-dollar micromixers. The device produced LNPs of diameter less than 90 nm, with low polydispersity (2-8%) and high mRNA encapsulation efficiency (> 90%). At a significantly lower cost (US $1.5) compared to commercial instruments, the OSEM device provides an unprecedented all-in-one solution to LNP production from lab to market. | Wan-Zhen Lin; W. Kristian Bostic; Noah Malmstadt | Biological and Medicinal Chemistry; Nanoscience; Nanofabrication; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63757a6c0821299853fa1049/original/3d-printed-microfluidic-device-for-high-throughput-production-of-lipid-nanoparticles-incorporating-sars-co-v-2-spike-protein-m-rna.pdf |
64667406a32ceeff2ddb3f0b | 10.26434/chemrxiv-2023-2qldt | Effect of Surface Functionality on the Rheological and Self-Assembly Properties of Chitin and Chitosan Nanocrystals and Use in Biopolymer Films | Chitin nanocrystals (ChNCs) are unique to all other bio-derived nanomaterials in one aspect: the inherent presence of a nitrogen moiety. By tuning the chemical functionality of this nanomaterial, and thus its charge and hydrogen bonding capacity, one can heavily impact its macroscopic properties such as its rheological and self-assembly characteristics. In this study, two types of ChNCs are made using acid hydrolysis (AH-ChNCs) and oxidative (OX-ChNCs) pathways, unto which deacetylation using a solvent-free procedure is utilized to create chitosan nanocrystals (ChsNCs) of varying degree of deacetylation (DDA). These nanocrystals were then studied for their rheological behaviour and liquid crystalline ordering. It was found that with both deacetylation and carboxylation of OX-ChNCs, viscosity continually increased with increasing concentrations from 2-8 wt. %, contrary to AH-ChNC suspensions in the same range. Interestingly, increasing the amine content of ChNCs was not proportional to the storage modulus, where a peak saturation of amines provided the most stiffness. Conversely, while the introduction of carboxylation increased the elastic modulus of OX-ChNCs by an order of magnitude from that of AH-ChNCs, it was degraded by increasing DDA. Deacetylation and carboxylation both inhibited the formation of a chiral nematic phase. Finally, these series of nanocrystals were incorporated into biodegradable pectin-alginate films as a physical reinforcement, which showed increased tensile strength and Young’s modulus values for the films incorporated with ChsNCs. Overall, this study is the first to investigate how surface functionalization of chitin-derived nanocrystals can affect their rheological and liquid-crystalline properties, and how it augments starch-based pectin/alginate films as a physical reinforcement nanofiller. | Madison Santos; Olivia Del Carlo; Jasmine Hong; Ziruo Liu; Shuaibing Jiang; Edmond Lam; Tony Jin; Audrey Moores | Polymer Science; Nanoscience; Biopolymers; Cellulosic materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64667406a32ceeff2ddb3f0b/original/effect-of-surface-functionality-on-the-rheological-and-self-assembly-properties-of-chitin-and-chitosan-nanocrystals-and-use-in-biopolymer-films.pdf |
6512407060c37f4f76755f54 | 10.26434/chemrxiv-2023-1lprg | Chemical bonding and the role of node-induced electron confinement | The chemical bond is the cornerstone of chemistry, providing a conceptual framework to understand and predict the behavior of molecules in complex systems. However, the fundamental origin of chemical bonding remains controversial, and has been responsible for fierce debate over the past century. Here we present a unified theory of bonding, using a separation of electron delocalization effects from orbital relaxation to identify four mechanisms – node-induced electron confinement, Pauli repulsion, orbital contraction and polarization – that each modulate kinetic energy during bond formation. Through analysis of a series of archetypal bonds, we show that electron delocalization is not the universal driving force for bonding. Instead, an exquisite balance of delocalizing and localizing effects are dictated simply by atomic electron configurations, nodal structure and electronegativities. The utility of this unified bonding theory is demonstrated by its application to explain observed trends in bond strengths throughout the periodic table, including main group and transition metal elements. | Alistair J. Sterling; Daniel S. Levine; Abdulrahman Aldossary; Martin Head-Gordon | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6512407060c37f4f76755f54/original/chemical-bonding-and-the-role-of-node-induced-electron-confinement.pdf |
65649477cf8b3c3cd73c3949 | 10.26434/chemrxiv-2023-tl4v1 | Impact of Viscosity on Human Hepatoma Spheroids in Soft Core-Shell Microcapsules | Extracellular environment regulates structures and functions of cells, from molecular up to the tissue level. However, underlying mechanisms that influence organization and adaptation of cancer in 3D environments are not yet fully understood. In this study, we investigate the influence of viscosity of the environment on the mechanical adaptability of human hepatoma cell (HepG2) spheroids in vitro, using hybrid 3D microcapsule reactors formed with droplet-based microfluidics. To mimic the environment with different mechanical properties, HepG2 cells are encapsulated in hybrid alginate core- shell microcapsules with tunable core viscosities achieved by incorporating carboxymethylcellulose. The significant changes in cell and spheroid distribution, proliferation, and cytoskeleton are observed and quantified. Importantly, changes in expression and distribution of F-actin and keratin 8 indicate that the spheroid stiffness varies with viscosity of the surrounding medium. The increase in F-actin levels in viscous medium can be indicative of enhanced tumor cell ability to traverse dense tissue. These results demonstrate that cancer cell assemblies (scale ca. 200-300μm) are able to dynamically adapt to the changes of extracellular viscosity, which holds promise for advancing our understanding of the mechanical characteristics of cancer entities development. | Xuan Peng; Željko Janićijević; Sandy Lemm; Sandra Hauser; Michael Knobel; Jens Pietzsch; Michael Bachmann; Larysa Baraban | Biological and Medicinal Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65649477cf8b3c3cd73c3949/original/impact-of-viscosity-on-human-hepatoma-spheroids-in-soft-core-shell-microcapsules.pdf |
6636860c418a5379b07172fc | 10.26434/chemrxiv-2024-wljm9 | Techno-economic Analysis and Life Cycle Assessment of Biomass-Derived Polyhydroxyurethane and Non-Isocyanate Polythiourethane Production and Reprocessing | Non-isocyanate polyurethanes (NIPUs) show promise as more sustainable alternatives to conventional, isocyanate-based polyurethanes (PUs). In this study, polyhydroxyurethane (PHU) and non-isocyanate polythiourethane (NIPTU) production and reprocessing models inform the results of a techno-economic analysis and a life cycle assessment. The profitability of selling PHU and NIPTU is rationalized by identifying significant production costs, indicating that raw materials drive the costs of PHU and NIPTU production and reprocessing. After stepping along a path of process improvements, PHU and NIPTU can achieve minimum selling prices (MSPs) of 3.15 USD kg-1 and 4.39 USD kg-1, respectively. Depolymerization yields need to be optimized and polycondensation reactions need to be investigated for the reprocessing of NIPUs into secondary (2°) NIPUs. Of the NIPUs examined here, PHU has a low depolymerization yield and NIPTU has a high depolymerization yield. Fossil energy use, greenhouse gas (GHG) emissions, and water consumption are reported for the bio-based production of PHU, NIPTU, 2° PHU, and 2° NIPTU and compared with baseline values for fossil-based PU production. There are options for reducing environmental impacts which could make these pathways more sustainable. If barriers to implementation are overcome, 2° NIPUs can be manufactured at lower cost and environmental impacts than virgin NIPUs. | Chloe Liang; Yasheen Jadidi; Yixuan Chen; Ulises Gracida-Alvarez; John Torkelson; Troy Hawkins; Jennifer Dunn | Polymer Science; Chemical Engineering and Industrial Chemistry; Biopolymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6636860c418a5379b07172fc/original/techno-economic-analysis-and-life-cycle-assessment-of-biomass-derived-polyhydroxyurethane-and-non-isocyanate-polythiourethane-production-and-reprocessing.pdf |
6352d3831db0bd58fd33dffd | 10.26434/chemrxiv-2021-lmlmg-v2 | Assessing Catalytic Rates of Bimetallic Nanoparticles with Active Site Specificity - A Case Study using NO Decomposition | Bimetallic alloys have emerged as an important class of catalytic materials, spanning a wide range of shapes, sizes, and compositions. The combinatorics across this wide materials space makes predicting catalytic turnovers of individual active sites challenging. Herein, we introduce the stability of active sites as a descriptor for site-resolved reaction rates. The site stability unifies structural and compositional variations in a single descriptor. We compute this descriptor using coordination-based models trained with DFT calculations. Our approach enables instantaneous predictions of catalytic turnovers for nanostructures up to 12 nm in size. Using NO decomposition as probe reaction, we identify sites on Au-Pt nanoparticles that, because of local structure and composition, yield one-to-two orders of magnitude increase in rate compared to sites on monometallic Pt. By prescribing specific sizes, morphologies, and compositions of optimal catalytic nanoparticles, our method guides experiments towards designing bimetallic catalysts with optimal turnovers. | Joakim Halldin Stenlid; Verena Streibel; Tej S. Choksi; Frank Abild-Pedersen | Theoretical and Computational Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6352d3831db0bd58fd33dffd/original/assessing-catalytic-rates-of-bimetallic-nanoparticles-with-active-site-specificity-a-case-study-using-no-decomposition.pdf |
64db79cf4a3f7d0c0d34f389 | 10.26434/chemrxiv-2023-sq846 | Synthesis, Characterization, and Single-Crystal X-ray Structures of d0 Refractory Metal Compounds as Precursors for the Single-Source Chemical Vapor Deposition of Metal Nitrides | The chemical vapor deposition of refractory metal nitrides requires volatile precursors and has previously been achieved using metal complexes containing a variety of imide ligands. Recently the 1,4-di-tert-butyl-1,3-diazabutadiene (DAD) adduct of bis(tert-butylimide)dichloridemolybdenum(VI) was shown to be an excellent precursor for the single-source CVD of Mo2N thin films. Leveraging the success of this work, we have prepared chromium and tungsten compounds with the same framework. Additionally, the framework has been modified slightly to allow the isolation of mono(tert-butylimide)trichloride complexes of vanadium, niobium, tantalum, and molybdenum(V) to extend the search for new vapor phase precursors. These compounds were all fully characterized using the standard methods of multi-nuclear magnetic resonance spectroscopy, combustion analysis, and single-crystal X-ray diffraction. Their thermal properties were determined using thermogravimetric analysis and differential scanning colorimetry to assess their utility as vapor phase precursors. Finally, preliminary deposition studies were carried out to investigate their potential as single-source CVD precursors. | Kieran Lawford; Michael Land; Eden Goodwin; Katherine Robertson; Seán Barry | Inorganic Chemistry; Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64db79cf4a3f7d0c0d34f389/original/synthesis-characterization-and-single-crystal-x-ray-structures-of-d0-refractory-metal-compounds-as-precursors-for-the-single-source-chemical-vapor-deposition-of-metal-nitrides.pdf |
6182d7f381c4fcb45bebc5a2 | 10.26434/chemrxiv-2021-sf92q | Carbonate-Catalyzed Reverse Water-Gas Shift to Produce Gas Fermentation Feedstocks for Renewable Liquid Fuel Synthesis | Carbon-neutral liquid fuel generation is essential for decarbonizing sectors that cannot readily electrify. Recently commercialized acetogenic gas fermentation offers an alternative to conventional biofuels that circumvents efficiency limitations and land requirements, provided the requisite H2/CO feedstocks can be generated efficiently using renewable inputs. CO2 electrolysis to CO is under development for this purpose, but suffers from scalability challenges and impurity sensitivity. We describe an alternative that utilizes dispersed alkali carbonates as reverse water-gas shift (RWGS) catalysts to convert H2 and CO2 to an appropriate ratio of CO/CO2/H2 for acetogenic fermentation. Using a fixed bed reactor operating at industrially relevant space velocity, we demonstrate equilibrium RWGS conversion starting at 410 °C that remains stable over days, even with 50 ppm H2S impurity. The combination of carbonate-catalyzed RWGS, water electrolysis, and gas fermentation could convert electricity to ethanol with nearly 50% energy efficiency, providing a compelling option for renewable liquid fuel production. | Chastity Li; Amy Frankhouser; Matthew Kanan | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Base Catalysis; Heterogeneous Catalysis; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182d7f381c4fcb45bebc5a2/original/carbonate-catalyzed-reverse-water-gas-shift-to-produce-gas-fermentation-feedstocks-for-renewable-liquid-fuel-synthesis.pdf |
66bafd03a4e53c48763a05d6 | 10.26434/chemrxiv-2024-sz8x8 | Electronically transparent Ag-C(sp3) contacts result in
low conductance junctions | Chemical groups capable of connecting molecules physically and electrically between electrodes are of critical importance in molecular-scale electronics, influencing junction conductance, variability, and function. While the development of such linkage chemistries has focused on interactions at gold, the distinct reactivity and electronic structure of other electrode metals provides underexplored opportunities to characterize and exploit new binding motifs. In this work we show that 𝛼,ω-alkanedibromides spontaneously form well-defined junctions using silver, but not gold, electrodes. Through application of the glovebox-based scanning tunneling microscope-based break junction method, we find that the same junctions form when using different halide, or trimethyltin, terminal groups, suggestive of an electronically transparent silver-carbon(sp3) contact chemistry. However, the conductance of these junctions is ~30× lower than for analogous junctions formed on gold and does not align with predictions based on first-principles calculations. Through insights provided from prior temperature-programmed desorption studies and a robust series of atomistic simulations and control experiments, we propose that in these experiments we measure alkoxide-terminated junctions formed through the reaction of unstable silver-alkyl species with adsorbed surface oxygen. This study, in demonstrating that high conductance contact chemistries established using model gold electrodes may not be readily transferred to other metals, underscores the need to directly characterize the interfacial electronic properties and reactivity of electrode metals of wider technological relevance. | Thomas Czyszczon-Burton; Enrique Montes; Jazmine Prana; Sawyer Lazar; Nils Rotthowe; Sully Chen; Hector Vazquez; Michael Inkpen | Physical Chemistry; Nanoscience; Nanodevices; Interfaces; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bafd03a4e53c48763a05d6/original/electronically-transparent-ag-c-sp3-contacts-result-in-low-conductance-junctions.pdf |
60d715ada5b6af768976c459 | 10.26434/chemrxiv-2021-l2mbl | Deprotonation and Cation Adsorption on the NiOOH/Water Interface: A Grand-Canonical First-Principles Investigation | Nickel-based oxides are highly active, cost effective materials for the oxygen evolution reaction in alkaline conditions. Recent experimental studies have revealed the importance of surface deprotonation and alkali metal cation adsorption on the activity of Ni oxide surfaces, in contact with aqueous alkaline electrolyte. As a first step to elucidate the role of the alkali adsorption for the activity, we performed first-principles electronic structure calculations to address the stable surface structures of beta-NiOOH(0001) as a function of the operating conditions in an electrochemical environment. We present a grand-canonical approach to compute the surface Pourbaix diagram of the beta-NiOOH/water interface for the processes of deprotonation and alkali metal cation adsorption. The results of this study emphasize the importance of double layer effects, including the adsorbate-induced change of surface dipole moments and the rearrangement of water molecules due to their strong interaction with the adsorbed species, for the most stable interface structure. | Mohammad Eslamibidgoli; Jun Huang; Piotr Kowalski; Michael Eikerling; Axel Gross | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2021-06-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d715ada5b6af768976c459/original/deprotonation-and-cation-adsorption-on-the-ni-ooh-water-interface-a-grand-canonical-first-principles-investigation.pdf |
62f54fb8e78f70920637f0e9 | 10.26434/chemrxiv-2022-zn3mn | Molecular Capacitors: Accessible 6- and 8-electron Redox Chemistry from Dimeric “Ti(I)” and “Ti(0)” Synthons Support-ed by Imidazolin-2-Iminato Ligands. | Reduction of the diamagnetic Ti(III)/Ti(III) dimer [Cl2Ti(μ-NImDipp)]2 (1) (NImDipp = [1,3-bis(Dipp)imidazolin-2-iminato]-, Dipp = NC6H3-2,6-Pri2) with 4 and 6 equiv of KC8 generates the intramolecularly arene-masked, dinuclear titanium com-pounds [(μ-N-μ-η6-ImDipp)Ti]2 (2) and {[(Et2O)2K](μ-N-μ-η6:η6-ImDipp)Ti}2 (3), respectively, in modest yields. The compounds have been structurally characterized by X-ray crystallographic analysis and inspection of the bond metrics within the η6-coordinated aryl substituent of the bridging imidazolin-2-iminato ligand show perturbation of the aromatic system most consistent with two-electron reduction of the ring. As such, 2 and 3 can be assigned respectively as possessing metal centers in formal Ti(III)/Ti(III) and Ti(II)/Ti(II) oxidation states. Exploration of their redox chemistry reveal the ability to reduce several substrate equivalents. For instance, treatment of 2 with excess C8H8 (COT) forms the novel COT-bridged complex [(ImDippN)(η8-COT)Ti](μ-η2:η3-COT)[Ti(η4-COT)(NImDipp)] (4) that dissociates in THF solutions to give mononuclear (ImDippN)Ti(η8-COT)(THF) (5). Addition of COT to 3 yields heterometallic [(ImDippN)(η4-COT)Ti(μ-η4:η5-COT)K(THF)(μ-η6:η4-COT)Ti(NImDipp)(μ-η4:η4-COT)K(THF)2]n (6). Compounds 2 and 5 are the products of the 4-electron oxidation of 2, while 6 stands as the 8-electron oxidation product of 3. Reduction of organozides was also explored. Low temperature reaction of 2 with 4 equiv of AdN3 gives the terminal and bridged imido complex [(ImDippN)Ti(=NAd)](μ-NAd)2[Ti(NImDipp)(N3Ad)] (7) that undergoes intermolecular C-H activation of toluene at room temperature to afford the amido compound [(ImDippN)Ti(NHAd)](μ-NAd)2[Ti(C6H4Me)(NImDipp)] (8-tol). These complexes are the 6-electron oxidation products of the reaction of 2 with AdN3. Furthermore, treatment of 3 with 4 equiv of AdN3 produces the thermally sta-ble Ti(III)/Ti(III) terminal and bridged imido [K(18-crown-6)(THF)2]{[(ImDippN)Ti(NAd)](μ-NAd)2K[Ti(NImDipp)]} (10). Alto-gether, these reactions firmly establish 2 and 3 as unprecedented Ti(I)/Ti(I) and Ti(0)/Ti(0) synthons with the clear ca-pacity to effect multi-electron reductions ranging from 4 – 8 electrons. | Alejandra Gomez-Torres; Niki Mavragani; Alejandro Metta-Magana; Muralee Murugesu; Skye Fortier | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f54fb8e78f70920637f0e9/original/molecular-capacitors-accessible-6-and-8-electron-redox-chemistry-from-dimeric-ti-i-and-ti-0-synthons-support-ed-by-imidazolin-2-iminato-ligands.pdf |
60c7503c9abda2066ff8d9be | 10.26434/chemrxiv.12971624.v2 | Shape-Selective Synthesis of Pentacene Macrocycles and the Effect of Geometry on Singlet Fission | <p>Pentacene’s extraordinary photophysical and electronic properties are highly dependent on intermolecular, through-space interactions. Macrocyclic arrangements of chromophores have been shown to provide a high level of control over these interactions, but few examples exist for pentacene due to inherent synthetic challenges. In this work, zirconocene-mediated alkyne coupling was used as a dynamic covalent C-C bond forming reaction to synthesize two geometrically distinct, pentacene-containing macrocycles on a gram scale and in four or fewer steps. Both macrocycles undergo singlet fission in solution, with rates that differ by an order of magnitude while the rate of triplet recombination is approximately the same. This independent modulation of singlet and triplet decay rates is highly desirable for the design of efficient singlet fission materials. The dimeric macrocycle adopts a columnar packing motif in the solid state, with large void spaces between pentacene units of the crystal lattice.</p> | Harrison Bergman; Gavin Kiel; Ryan J. Witzke; David P. Nenon; Adam M. Schwartzberg; Yi Liu; T. Don Tilley | Supramolecular Chemistry (Org.); Carbon-based Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7503c9abda2066ff8d9be/original/shape-selective-synthesis-of-pentacene-macrocycles-and-the-effect-of-geometry-on-singlet-fission.pdf |
619f01aac481c3c544f7ffbc | 10.26434/chemrxiv-2021-0rfst | Photochemical [2+1]-Cycloadditions of Nucleophilic Carbenes | Visible light induced singlet nucleophilic carbene intermediates undergo rapid [2+1]-cycloaddition with tethered olefins to afford unique bicyclo[3.1.0]hexane and bicyclo[4.1.0]heptane scaffolds. This cyclopropanation proceeds using only visible light irradiation, circumventing the use of exogenous (photo)catalysts or sensitisers and showcases an underexplored mode of reactivity for nucleophilic carbenes in chemical synthesis. The discovery of additional transformations including a cyclopropanation/retro-Michael/Michael cascade reaction to afford chromanone derivatives are also described. | Amanda Bunyamin; Anastasios Polyzos; Daniel Priebbenow | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619f01aac481c3c544f7ffbc/original/photochemical-2-1-cycloadditions-of-nucleophilic-carbenes.pdf |
60c7525a469df4a07af44b53 | 10.26434/chemrxiv.13288463.v1 | Covalent and Non-Covalent Binding Free Energy Calculations for Peptidomimetic Inhibitors of SARS-CoV-2 Main Protease | COVID-19, the disease caused by the newly discovered coronavirus — SARS-CoV-2, has created global health, social, and economic crisis. At the time of writing (November 12, 2020), there are over 50 million confirmed cases and more than 1 million reported deaths due to COVID-19. Currently, there are no approved vaccines, and recently Veklury (remdesivir) was approved for the treatment of COVID-19 requiring hospitalization. The main protease (M<sup>pro</sup>) of the virus is an attractive target for the development of effective antiviral therapeutics because it is required for proteolytic cleavage of viral polyproteins. Furthermore, the M<sup>pro</sup> has no human homologues, so drugs designed to bind to this target directly have less risk for off-target reactivity. Recently, several high-resolution crystallographic structures of the M<sup>pro</sup> in complex with inhibitors have been determined — to guide drug development and to spur efforts in structure-based drug design. One of the primary objectives of modern structure-based drug design is the accurate prediction of receptor-ligand binding affinities for rational drug design and discovery. Here, we perform rigorous alchemical absolute binding free energy calculations and QM/MM calculations to give insight into the total binding energy of two recently crystallized inhibitors of SARS-CoV-2 M<sup>pro</sup>, namely, N3 and α-ketoamide 13b. The total binding energy consists of both covalent and non-covalent binding components since both compounds are covalent inhibitors of the M<sup>pro</sup>. Our results indicate that the covalent and non-covalent binding free energy contributions of both inhibitors to the M<sup>pro</sup> target differ significantly. The N3 inhibitor has more favourable non-covalent interactions, particularly hydrogen bonding, in the binding site of the M<sup>pro</sup> than the α-ketoamide inhibitor. But the Gibbs energy of reaction for the M<sup>pro</sup>–α-ketoamide covalent adduct is greater than the Gibbs reaction energy for the M<sup>pro</sup>–N3 covalent adduct. These differences in the covalent and non-covalent binding free energy contributions for both inhibitors could be a plausible explanation for their in vitro differences in antiviral activity. Our findings highlight the importance of both covalent and non-covalent binding free energy contributions to the absolute binding affinity of a covalent inhibitor towards its target. | Ernest Awoonor-Williams; Abd Al-Aziz A. Abu-Saleh | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7525a469df4a07af44b53/original/covalent-and-non-covalent-binding-free-energy-calculations-for-peptidomimetic-inhibitors-of-sars-co-v-2-main-protease.pdf |
678902f5fa469535b9450d8b | 10.26434/chemrxiv-2025-spzw3-v2 | Theoretical Investigation of the Photochemistry and Phototoxicity of Aloe-Emodin as a Natural Sensitizing Dye in Photodynamic Therapy | The photosensitizing properties of aloe-emodin, linked to its anticancer and antimicrobial effects in photodynamic therapy, were investigated under physiological conditions using computational chemistry tools. Neutral and monoanionic species of aloe-emodin were found to coexist in a ratio of approximately 1:3. Dissociation leads to a rearrangement of molecular orbitals, resulting in a redshift of the absorption spectrum. Excited-state dynamics analysis revealed an average triplet state quantum yield of 0.76, with triplet lifetimes of 78.3 ns for the neutral species and 2.08 ns for the anionic species. Both species exhibit comparable propensities for type I photoreactivity, although the neutral species more readily oxidizes biomolecules during type III photoreactivity. Additionally, the neutral form effectively intercalates DNA, preferentially at the AT–TA site, altering the absorption profile and inducing eventually cytotoxic structural rearrangements to the nucleotides. | Maciej Spiegel | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Natural Products; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678902f5fa469535b9450d8b/original/theoretical-investigation-of-the-photochemistry-and-phototoxicity-of-aloe-emodin-as-a-natural-sensitizing-dye-in-photodynamic-therapy.pdf |
66c4cff8f3f4b052907b5e9d | 10.26434/chemrxiv-2024-8hv7c | Computational Design of Gallium Imides for Methane Activation | Activation of the strong non-polar C-H bonds in methane is difficult, especially in solution. In this work, computational modeling is used to modify NacNac gallium imide, which has recently been shown to cleave unactivated sp3 C-H bonds in organic substrates with the aim of making it suitable for methane activation. Density functional theory predicts that the 123 kJ mol−1 methane activation barrier for the experimentally employed gallium imide can be reduced to 93 kJ mol−1 by changing substituents around the active gallium center. Furthermore, pre-straining the gallium imide reduces the reaction barrier to just 62 kJ mol−1. Dimerization of the gallium imides can be prevented with bulky groups that do not affect the reaction barrier. Several modified NacNac gallium imides are thus shown to be viable for the homogeneous activation of methane and higher alkanes. | Sylvester Zhang; Peter McBreen; Chao-Jun Li; Rustam Khaliullin | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c4cff8f3f4b052907b5e9d/original/computational-design-of-gallium-imides-for-methane-activation.pdf |
63e2e6ca068fd759792cbdca | 10.26434/chemrxiv-2023-cf0t3 | Rational Design of Molecular Cavity Polariton Relaxation | Maximizing the coherence between the constituents of molecular materials remains a crucial goal towards the implementation of these systems into everyday optoelectronic technologies operating at room temperature. In this study we experimentally assess the ability of strong light-matter coupling in the collective limit to reduce the impact of energetic disorder on polariton relaxation using multiple porphyrin-based chromophores in different Fabry-Perot (FP) micro-resonator structures. Following characterization of cavity polaritons formed from spatially separated porphyrin monomers and uniformly dispersed porphyrin dimers, we find the peak corresponding to the lower polariton (LP) state in each sample does not possess a width consistent with con- ventional theories of the dispersive energetics in these systems. We model the anomalous, dispersive behavior of the LP peak width in each sample effectively using the results of a Greens function theory used to explain motional narrowing of polariton luminescence spectra in high quality, fully inorganic micro-cavities. We correlate differences in the suppression of excitonic energetic disorder between our samples with macroscopic aspects of specific FP micro-resonators and microscopic attributes of the distinct porphyrin species we use to form cavity polaritons. Our results demonstrate how researchers can design coherence into hybrid molecular material systems to improve their suitability for next generation optoelectronic technologies. | Sachithra Wanasinghe; Wade Burson; Adelina Gjoni; Caris Majeski; Bradly Zaslona; Aleksandr Avramenko; Aaron Rury | Physical Chemistry; Nanoscience; Optics; Quantum Mechanics; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e2e6ca068fd759792cbdca/original/rational-design-of-molecular-cavity-polariton-relaxation.pdf |
60c7464f702a9bbf9818abad | 10.26434/chemrxiv.11302295.v1 | A General Protocol for the Accurate Predictions of Molecular 13C/1H NMR Chemical Shifts via Machine Learning | Accurate prediction of NMR chemical shifts with affordable computational cost is of great importance for rigorous structural assignments of experimental studies. However, the most popular computational schemes for NMR calculation—based on density functional theory (DFT) and gauge-including atomic orbital (GIAO) methods—still suffer from ambiguities in structural assignments. Using state-of-the-art machine learning (ML) techniques, we have developed a DFT+ML model that is capable of predicting 13C/1H NMR chemical shifts of organic molecules with high accuracy. The input for this generalizable DFT+ML model contains two critical parts: one is a vector providing insights into chemical environments, which can be evaluated without knowing the exact geometry of the molecule; the other one is the DFT-calculated isotropic shielding constant. The DFT+ML model was trained with a dataset containing 476 13C and 270 1H experimental chemical shifts. For the DFT methods used here, the root-mean-square-derivations (RMSDs) for the errors between predicted and experimental 13C/1H chemical shifts are as small as 2.10/0.18 ppm, which is much lower than the typical DFT (5.54/0.25 ppm), or DFT+linear regression (4.77/0.23 ppm) approaches. It also has smaller RMSDs and maximum absolute errors than two previously reported NMR-predicting ML models. We test the robustness of the model on two classes of organic molecules (TIC10 and hyacinthacines), where we unambiguously assigned the correct isomers to the experimental ones. This DFT+ML model is a promising way of predicting NMR chemical shifts and can be easily adapted to calculated shifts for any chemical compound.<br /> | Peng Gao; Jun Zhang; Qian Peng; Vassiliki-Alexandra Glezakou | Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7464f702a9bbf9818abad/original/a-general-protocol-for-the-accurate-predictions-of-molecular-13c-1h-nmr-chemical-shifts-via-machine-learning.pdf |
6165df90a3d2c90a7ed49f7c | 10.26434/chemrxiv-2021-77bdj | Into the Facet-Selectivity of Sequenced Amphiphilic Peptoids at the Au-Water Interface | Shape-controlled colloidal nanocrystal syntheses often require aid from facet-selective solution-phase chemical additives to regulate atom addition/migration fluxes or oriented particle attachment. Because of their highly tunable chemical property and robustness to a wide range of experimental conditions, peptoids contribute to a very promising group of next-generation functional chemical additives. To generalize the design philosophy, it is critical to understand the origin of facet selectivity at the molecular level. We employ molecular dynamics simulations and biased sampling methods to investigate the origin of Au(111)-favored adsorption of a peptoid, Nce3Ncp6, that is evidenced to assist the formation of five-fold twinned nanostructures. We find that the facet-selectivity is achieved through a synergistic effect of both molecule-surface and solvent-surface interactions. Extending beyond the single-chain scenario, the order of peptoid-peptoid and peptoid-surface energetics, i.e., peptoid-Au(100) < peptoid-peptoid < peptoid-Au(111), further amplifies the distinct behavior of Nce3Ncp6 chains on different Au surfaces. Our studies set the stage for future peptoid design in shape-controlled nanocrystal syntheses by probing the facet selectivity from various perspectives. | Xin Qi; Biao Jin; Bin Cai; Feng Yan; James De Yoreo; Chun-Long Chen; Jim Pfaendtner | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Nanocatalysis - Catalysts & Materials; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6165df90a3d2c90a7ed49f7c/original/into-the-facet-selectivity-of-sequenced-amphiphilic-peptoids-at-the-au-water-interface.pdf |
66e81e2dcec5d6c1423a3461 | 10.26434/chemrxiv-2024-x3sn8 | Molecular basis of the CYFIP2 and NCKAP1 autism-linked variants in the WAVE regulatory complex | The WAVE regulatory pentameric complex regulates actin remodeling. Two components of it (CYFIP2 and NCKAP1) are encoded by genes whose genetic mutations increase the risk for Autism Spectrum Disorder (ASD) and related neurodevelopmental disorders. Here, we use a newly developed computational protocol and hotspot analysis to uncover the functional impact of these mutations at the interface of the correct isoforms of the two proteins into the complex. The mutations turn out to be located on the surfaces involving the largest number of hotspots of the complex. Most of them decrease the affinity of the proteins for the rest of the complex, but some have the opposite effect. The results are fully consistent with the available experimental data. The observed changes in the WAVE regulatory complex stability might impact on complex activation and ultimately play a role in the aberrant pathway of the complex, leading to the cell derangement associated with the disease. | Song Xie; Ke Zuo; Silvia De Rubeis; Paolo Ruggerone; Paolo Carloni | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e81e2dcec5d6c1423a3461/original/molecular-basis-of-the-cyfip2-and-nckap1-autism-linked-variants-in-the-wave-regulatory-complex.pdf |
62e4cd705be0417e50a1d248 | 10.26434/chemrxiv-2022-2bddz | Access to sensitive near infrared circularly polarized light detection via non-fullerene acceptor blends | Circularly polarized light (CPL), as a light source, offers greater light persistence than both non-polarized light and linearly polarized light, and is widely used for high-contrast sensing technologies. An everlasting challenge in realizing full-spectrum CPL detection when using chiral organic semiconductors is to achieve strong chiroptical activities in the near infrared (NIR) region. The conventional approaches to reducing the band gap of organic semiconductors are based on co-planar backbones and lead to molecular symmetries incompatible with the presence of chirality; thus, the strategies to design chiral molecules rely on twisted stereogenic moieties. Here, instead of a de novo design of chiral molecular structures, we introduce a widely applicable strategy to directly induce chiroptical activity in planar non-fullerene acceptors (NFAs), which have been largely developed in the framework of organic photovoltaics and provide a wealth of opportunities to fill the spectral gap of CPL detection in the NIR. We demonstrate proof-of-concept circularly polarized organic photodiodes (CP-OPDs) using chiroptically active NFA blends, which exhibit strong circular dichroism (CD) and hence great sensitivity to CPL in the NIR region. Importantly, this strategy is found to be effective in a wide series of state-of-the-art NFA families, i.e., ITIC, o-IDTBR, and Y6 analogs, which significantly broadens the range of materials applicable to NIR CPL detection and can inspire further designs of strongly CPL-active systems for chiropto-electronics. | Li Wan; Rui Zhang; Eunkyung Cho; Hongxiang Li; Veaceslav Coropceanu; Jean-Luc Bredas; Feng Gao | Materials Science; Materials Processing; Optical Materials; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e4cd705be0417e50a1d248/original/access-to-sensitive-near-infrared-circularly-polarized-light-detection-via-non-fullerene-acceptor-blends.pdf |
65a00ab6e9ebbb4db9efe2b4 | 10.26434/chemrxiv-2024-w2f4s | Diborane Reductions of CO2 and CS2 Mediated by Dicopper μ-Boryl Complexes of a Robust Bis(Phosphino)-1,8-Napthyridine Ligand | A symmetrical dinucleating 1,8-naphthyridine ligand featuring phosphino side arms linked through fluorene-9,9-diyl moieties (PNNPFlu) was synthesized and used to obtain the cationic organodicopper complexes 2, [(PNNPFlu)Cu2(µ‐Ph)][NTf2]; [NTf2] = bis(trifluoromethane)sulfonimide, and 6, [(PNNPFlu)Cu2(µ‐CCPh)][NTf2], as well as the µ‐tert-butoxide 3, [(PNNPFlu)Cu2(µ‐OtBu)][NTf2]. Complex 3 reacted with diboranes to afford dicopper µ‐boryl species (4, with µ‐Bcat; cat = catecholate and 5, with µ‐Bpin; pin = pinacolate). Complexes 4 and 5 are more reactive in C–H bond activations of terminal alkynes and toward activations of CO2 and CS2, in comparison to dicopper µ‐boryl complexes supported by a 1,8-naphthyridine-based ligand with two di(pyridyl) side arms. The molecular structures (determined by X-ray crystallography) and DFT analysis indicate that the higher reactivity of 4 and 5 relate to changes in the coordination sphere of copper, rather than to perturbations on the Cu–B bonding interactions. Addition of xylyl isocyanide (CNXyl) to 4 gave 7, [(PNNPFlu)Cu2(µ‐Bcat)(CNXyl)][NTf2], demonstrating that the lower coordination number at copper is chemically significant. Reactions of 4 and 5 with CO2 yielded the corresponding dicopper borate complexes (8, [(PNNPFlu)Cu2(µ‐OBcat)][NTf2]; 9, [(PNNPFlu)Cu2(µ‐OBpin)][NTf2]), with 4 demonstrating catalytic CO2 reduction in the presence of excess diborane. Related reactions of 4 and 5 with CS2 provided the insertion products 10, {[(PNNPFlu)Cu2]2[µ‐S2C(Bcat)2]}[NTf2]2 and 11, [(PNNPFlu)Cu2(µ,κ2‐S2CBpin)][NTf2], respectively. These insertion products feature Cu–S–C–B linkages analogous to those of proposed, analogous CO2 insertion intermediates. | Matthew See; Pablo Ríos; T. Don Tilley | Inorganic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a00ab6e9ebbb4db9efe2b4/original/diborane-reductions-of-co2-and-cs2-mediated-by-dicopper-boryl-complexes-of-a-robust-bis-phosphino-1-8-napthyridine-ligand.pdf |
6274961b87d01f8259da5c86 | 10.26434/chemrxiv-2022-917k5 | Exploring the Combinatorial Explosion of Amine–Acid Reaction Space via Graph Editing | Amines and carboxylic acids are abundant chemical feedstocks that are nearly exclusively united via the amide coupling. The disproportionate use of the amide coupling leaves a large section of unexplored reaction space between two of the most common chemical building blocks. Herein we conduct a thorough exploration of amine–acid reaction space via systematic enumeration of reactions involving a simple amine–carboxylic acid pair. This approach to chemical space exploration investigates the coarse and fine modulation of physicochemical properties and molecular shapes. While the invention of reaction methods becomes increasingly automated bringing conceptual reactions into reality, our map will provide an entirely new axis of chemical space exploration for rational property design. | Rui Zhang; Babak Mahjour; Tim Cernak | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Combinatorial Chemistry; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6274961b87d01f8259da5c86/original/exploring-the-combinatorial-explosion-of-amine-acid-reaction-space-via-graph-editing.pdf |
642f5918a41dec1a569b674d | 10.26434/chemrxiv-2023-tntkg-v2 | Chemical Reaction Networks Explain Gas Evolution Mechanisms in Mg-Ion Batteries | Out-of-equilibrium electrochemical reaction mechanisms are notoriously difficult to characterize. However, such reactions are critical for a range of technological applications. For instance, in metal-ion batteries, spontaneous electrolyte degradation controls electrode passivation and battery cycle life. Here, to improve on our ability to elucidate electrochemical reactivity, we for the first time combine computational chemical reaction network (CRN) analysis based on density functional theory (DFT) and differential electrochemical mass spectroscopy (DEMS) to study gas evolution from a model Mg- ion battery electrolyte — magnesium bistriflimide (Mg(TFSI)2) dissolved in diglyme (G2). Automated CRN analysis allows for facile interpretation of DEMS data, revealing H2O, C2H4, and CH3OH as major products of G2 decomposition. These findings are further explained by identifying elementary mechanisms using DFT. While TFSI– is reactive at Mg electrodes, we find that it does not meaningfully contribute to gas evolution. The combined theoretical-experimental approach developed here provides a means to effectively predict electrolyte decomposition products and pathways when initially unknown. | Evan Walter Clark Spotte-Smith; Samuel M. Blau; Daniel Barter; Noel J. Leon; Nathan T. Hahn; Nikita S. Redkar; Kevin R. Zavadil; Chen Liao; Kristin A. Persson | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Electrochemistry - Mechanisms, Theory & Study | CC BY NC 4.0 | CHEMRXIV | 2023-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642f5918a41dec1a569b674d/original/chemical-reaction-networks-explain-gas-evolution-mechanisms-in-mg-ion-batteries.pdf |
62d90c454e76bf2cb1992635 | 10.26434/chemrxiv-2022-cwccz | A State-of-the-Art Review of Graphene-Based Corrosion Resistant Coatings for Metal Protection | Protection of metal is primary undertaking for any design engineer and coating formulator. Construction of large scale equipment and structure involves huge investment in terms of money, time, manpower and other resources. In economic aspects, the life of such structure must as long as possible to get the best return on its investment. To improve the life of such huge structures, it is becomes mandatory to protect the metal substrates from corrosion. Application of corrosion resistant coating is one of the most intriguing, robust, practical and efficient techniques to safeguard the metal from corrosion. Graphene is novel material and got prodigious application due to its extraordinary features. Lot of research has been conducted since last decade for modifying the graphene and making the best use to formulate corrosion resistant coating. The use of graphene in the coating creates an obstacle and increases the convoluted path for corrosive medium to reach the metal. As the path to reach to metal is increased, it delays the corrosion medium to reach up to the metal and thus corrosion of metal can be avoided. In this literature review is conducted for various aspects of corrosion, importance of graphene in coating formulation is discussed, which includes chemical modifications of graphene, effect of graphene concentration on corrosion inhibition and contact angle of coating. This review also discussed about the importance of water based corrosion resistant coating to avoid the environmental damages.
Keywords: Graphene, Corrosion resistance, contact angle, water base coating, metal protection, corrosive media, corrosion inhibition.
| Ganesh Zade; Kiran Patil | Materials Science; Coating Materials | CC BY 4.0 | CHEMRXIV | 2022-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d90c454e76bf2cb1992635/original/a-state-of-the-art-review-of-graphene-based-corrosion-resistant-coatings-for-metal-protection.pdf |
648f1ed54f8b1884b77afb25 | 10.26434/chemrxiv-2023-z34m0-v2 | Serendipitous Triplet Harvesting in Donor-acceptor Dyads with Low Spin-orbit Coupling | Here, we present a heuristic mechanism for efficient intersystem crossing (ISC) between singlet and triplet states with low spin-orbit coupling (SOC) in molecules having donor-acceptor (D-A) moieties separated by a sigma bond. We show that SOC between the first singlet and the higher-lying triplet states, together with nuclear motion-driven coupling of this triplet state with lower-lying triplet state during the free rotation about a sigma bond is the only plausible way to achieve the experimentally observed ISC rate for a class of D-A type photoredox catalysts. We found this mechanism to be the dominant contributor to the ISC process with the corresponding rate reaching maximum at an optimal dihedral angle between D-A moieties. An extension to this is provided by discovering the same mechanism to be operative in a specific spirobis[anthracene]diones molecule where the D and A moieties are interlocked near to the optimal dihedral angle,
indicating the plausible universality of the proposed mechanism. The present finding is expected to have implications in strategies for the synthesis of a new generation of triplet-harvesting organic molecules. | Pijush Karak; Torsha Moitra; Ambar Banerjee; Kenneth Ruud; Swapan Chakrabarti | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Theory - Computational; Photochemistry (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2023-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648f1ed54f8b1884b77afb25/original/serendipitous-triplet-harvesting-in-donor-acceptor-dyads-with-low-spin-orbit-coupling.pdf |
62ddab7cb464fa8e7a71895e | 10.26434/chemrxiv-2022-jmc23 | Mechanical Properties of Microspheres Assembled from Carboxylated Cellulose Nanocrystal Rods | The elastic modulus of carboxylated cellulose nanocrystal (cCNC) microbeads made by spray-drying were measured by Atomic Force Microscopy (AFM) combined with a 1 μm Si microsphere probe method. Use of a Si microsphere on the cantilever probe tip to measure deformations of cCNC microbeads is shown to eliminate spurious contributions from localized mechanical responses that plague conventional cantilever sharp probe tips. The findings are consistent with the Hertz model. The the Young’s modulus of cCNC microbeads depends on spray drying parameters. Spray drying from dilute cCNC suspensions yields particles with a Young’s modulus of 18.02 MPa. Higher cCNC feed concentrations yield denser particles characterized by an elastic modulus of 24.55 MPa. Doping dilute cCNC suspensions with citric acid results in aerosol-phase esterification and crosslinking of the cCNC microbeads. Crosslinking in this manner yields a stiffer microbead with a Young’s modulus of 27.97 MPa. cCNC-derived microbeads are stiffer than microbeads derived from collagen, hyaluronic acid, alginate, dextran or pectin, but they are more elastic than urethane-acrylate crosslinked beads, and cellulose beads reconstituted from dissolved cellulose by emulsion-precipitation. | Junqi Wu; Mark Andrews | Materials Science; Biodegradable Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ddab7cb464fa8e7a71895e/original/mechanical-properties-of-microspheres-assembled-from-carboxylated-cellulose-nanocrystal-rods.pdf |
60c7467bee301c028ec79517 | 10.26434/chemrxiv.11336612.v1 | Synthesis, Characterization and Unusual Near-Infrared Luminescence of 1,1,4,4-Tetracyanobutadienes | <p>
Two
1,1,4,4-tetracyanobutadiene (TCBD) derivatives were prepared by [2+2]cycloaddition-retroelectrocyclization
from ynamides bearing either a pyrene (<b>1</b>) or a perylene unit (<b>2</b>). In addition
to panchromatic absorptions in <b>2</b>, in the solid state, both compounds
unexpectedly display NIR photoluminescence that could be detected up to about
1350 nm. <br /></p> | Anh Thy Bui; Clotilde Philippe; Maxime Beau; Nicolas Richy; Marie Cordier; Thierry Roisnel; Loïc Lemiègre; Olivier Mongin; Frédéric Paul; Yann Trolez | Organic Synthesis and Reactions; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.); Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7467bee301c028ec79517/original/synthesis-characterization-and-unusual-near-infrared-luminescence-of-1-1-4-4-tetracyanobutadienes.pdf |
63237129e665bdfd620613d5 | 10.26434/chemrxiv-2022-9r564 | Determination of Bioactive Compounds Suppressing SARS-CoV-2 in Wastewater Using High Pressure Liquid Chromatography - Tandem Mass Spectrometry | Recent SARS-CoV-2 wastewater-based epidemiology (WBE) surveillance studies have reported that several bioactive ingredients formulated in detergents, surface active agents, emulsifiers, and disinfection products in wastewater could significantly compromise WBE efforts by suppressing SARS-CoV-2 signals. A comprehensive, reliable, and robust analytical method is needed to quantify these bioactive molecules to assess the impacts of these compounds on SARS-CoV-2 wastewater surveillance results, and to evaluate the required action (e.g., correction factor) to achieve more reliable and unbiased surveillance results. In this study, a multi-residue analytical method was developed to quantify a selection of 19 bioactive compounds commonly found in the wastewater discharged from industrial facilities. The analytes were identified and quantified by high-performance liquid chromatography–tandem mass spectrometry (HPLC–MS/MS) using multiple reaction monitoring (MRM) or single ion recording (SIR). The recovery rate (%) ranged from 60±0.64% to 112.5 ± 12.7%. The detection limit of the developed method ranged from 0.4 µg/L to 57.7 µg/L. The developed analytical method was applied to quantify these reactive molecules in the effluent of 65 wastewater treatment facilities located in Missouri, USA. The stability of SARS-CoV-2 in wastewater was evaluated in the presence of 4-nonylphenol (4-NOPH), dodecylbenzenesulfonic acid (DBSA), bisoctyldimethyl ammonium chloride (BDAC), C12-C14-Alkyl(ethylbenzyl)dimethylammonium chloride (C12-C14-AEDC) and lauroyl peroxide (LAPE). The compounds were reacted with wastewater containing SARS-CoV-2 for 24h. The suppression rates (SR%) were 35%, 51%, 62.1% and 66% when 4-NOPH, BDAC, C12-C14-AEDC and LAPE were added, respectively. The developed robust and sensitive analytical method could be incorporated into SARS-CoV-2 wastewater-based epidemiology surveillance studies to determine the concentrations of these chemical suppressors. Correction factors could then be developed to achieve more reliable and unbiased surveillance results for wastewater treatment facilities that receive wastewater from industries. | Mohamed Bayati; Chenhui Li; Shu-Yu Hsu; Elizabeth Rogers; Ryan Vinhal; Hsin-Yeh Hsieh; Lindsi Wilfing; Jeff Wenzel; Chris G. Wieberg; Marc C. Johnson; Chung-Ho Lin | Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63237129e665bdfd620613d5/original/determination-of-bioactive-compounds-suppressing-sars-co-v-2-in-wastewater-using-high-pressure-liquid-chromatography-tandem-mass-spectrometry.pdf |
66a95622c9c6a5c07a8a7f2f | 10.26434/chemrxiv-2023-f5ktf-v2 | Two-dimensional antimonene as a potential candidate for dioxin capture | Among the serious environmental problems that attracted much attention from the broader public is the high toxicity of dioxins. Considerable efforts have been made to develop techniques and materials that could help in their efficient removal from the environment. Due to its high specific surface area and numerous active sites, outstanding structural and electronic proper- ties antimonene is considered for a variety of potential applications in different fields such as energy storage, electrocatalysis, and biomedicine. The present study adds to this portfolio by suggesting antimonene as a promising candidate for dioxin capture. Using density functional theory (DFT) calculations, we studied the adsorption of 2, 3, 7, 8-tetrachlorodibenzo-p-dioxin (TCDD) on pristine as well as Ca-, Ti-, and Ni-doped antimonene. Three configurations of the adsorption of TCDD on antimonene were analyzed. The results obtained from calculating ad- sorption energies, charge transfer, charge density differences, and densities of states (DOS) give evidence that antimonene outperforms other nanomaterials that have been previously suggested for dioxin capture applications. Therefore, we propose these substrates (i.e., pristine and doped antimonene) as potential capture agents for removing such toxic organic pollutants. | Moyassar Meshhal; Ashour Ahmed; Mohamed Shibl; Saadullah Aziz; Oliver Kühn; Kamal Soliman | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a95622c9c6a5c07a8a7f2f/original/two-dimensional-antimonene-as-a-potential-candidate-for-dioxin-capture.pdf |
60c74db1f96a0049ad2879b5 | 10.26434/chemrxiv.12652361.v1 | CO2-Enabled Cyanohydrin Synthesis and Facile Homologation Reactions | Thermodynamic and kinetic control of a chemical process is the key to access desired products and states. Changes are made when desired product is not accessible; one may manipulate the reaction with additional reagents, catalysts and/or protecting groups. Here we report the use of carbon dioxide to direct reaction pathways in order to selectively afford desired products in high reaction rates while avoiding the formation of byproducts. The utility of CO<sub>2</sub>-mediated selective cyanohydrin synthesis was further showcased by broadening Kiliani-Fischer synthesis to offer an easy access to variety of polyols, cyanohydrins, linear alkylnitriles, by simply starting from alkyl- and arylaldehydes, KCN and atmospheric pressure of CO<sub>2</sub>. | Martin Juhl; Allan Petersen; JIWOONG LEE | Organic Synthesis and Reactions; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74db1f96a0049ad2879b5/original/co2-enabled-cyanohydrin-synthesis-and-facile-homologation-reactions.pdf |
66fef047cec5d6c14210b8cb | 10.26434/chemrxiv-2024-5twl7 | Self-assembly of halloysite nanotubes in water modulated via heterogeneous surface charge and transparent exopolymer particles | Halloysite clay nanotubes are a viable model to investigate the colloid behaviour of particles dispersed in water. They demonstrate excellent colloid stability in water due to the strong overall negative surface charge. We performed detailed characterisation of halloysite surface inhomogeneity and in situ observations of diluted halloysite water suspensions behaviour. Using dark-field microscopy, we detected an aggregation between individual halloysite rods, behaving unlike the bulk majority of the non-aggregating nanoparticles. The stochastic distribution of positively charged patches on overall smooth halloysite surfaces facilitates the electrostatic clustering of individual clay nanotubes into stable aggregates having end-to-end and end-to-side configurations. Another pattern of halloysite aggregation through seemingly long-range attraction of like-charged colloids was attributed to trace amounts of transparent exopolymer particles (TEP), ubiquitous microgels of biogenic origin, persisting in purified deionised water and bridging individual halloysites into long-standing coordinated clusters. These aggregates demonstrate the earlier unknown role of water-suspended nanoscale particulate organic matter in counterintuitive long-range aggregation of like-charged colloids. We also found that microbial biopolymer mucospheres attract halloysite rods, forming unusual sea urchin-like motile microstructures, confirming the participation of TEP in natural colloids self-assembly. The persistence of barely detectable amounts of TEP in sterile purified deionised water suggests their important role in colloids interactions and other nano/micro scale processes. | Ilnur Ishmukhametov; Svetlana Batasheva; Svetlana Konnova; Yuri Lvov; Rawil Fakhrullin | Physical Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fef047cec5d6c14210b8cb/original/self-assembly-of-halloysite-nanotubes-in-water-modulated-via-heterogeneous-surface-charge-and-transparent-exopolymer-particles.pdf |
67af40bb81d2151a026b9d19 | 10.26434/chemrxiv-2025-46341 | Optimizing Lubricant Deposition on Hair-like Substrates Using Cationic Polymer/Anionic Surfactant Complexes | Oppositely charged polymer-surfactant mixtures exhibit unique bulk and interfacial properties with many applications. For instance, cationic polymers paired with anionic surfactants are often used to deposit oils and lubricants on hair and skin upon dilution. These dilution-deposition systems are widely studied in simple mixtures but rarely in complex formulations. Thus, our paper focuses on cationic polysaccharides (cat-Guars and cat-HECs) paired with the anionic surfactant SLES-1EO (sodium laureth-1 sulfate) and incorporated into shampoos. We analyzed the polymer-surfactant complexes’ (PSCs) phase behavior, adsorption at the silicone/water interface, stickiness to bubbles (and drops), and deposition on hair-like substrates via phase behavior analysis, zeta potential measurements, foam film experiments, and imaging ellipsometry. Our results showed that the cat-Guar/SLES-1EO complexes exhibit wider precipitation regions and higher adsorption at the silicone/water interface than the cat-HEC/SLES-1EO complexes. The foam film experiments implied that only the cat-Guar/SLES-1EO complexes bridge the air bubbles as they form sticky PSCs. Imaging ellipsometry revealed that cat-Guars deposit thick, inhomogeneous layers of PSCs and silicone on the hair-like substrates, whereas cat-HECs deposit thinner layers or nothing. Together, these findings elucidate the underlying deposition mechanism and offer strategies to optimize the polymer performance in shampoo formulations via a comprehensive experimental protocol. | Nikol K. Dimitrova; Mihail T. Georgiev; Svetoslav E. Anachkov | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Aggregates and Assemblies; Polyelectrolytes - Materials; Thin Films | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67af40bb81d2151a026b9d19/original/optimizing-lubricant-deposition-on-hair-like-substrates-using-cationic-polymer-anionic-surfactant-complexes.pdf |
6489cfca4f8b1884b74a247d | 10.26434/chemrxiv-2023-znb8j-v2 | Understanding Sensitivity and Cross-Reactivity of Xylazine Lateral Flow Immunoassay Test Strips for Drug Checking Applications | The continued prevalence of xylazine in the illicit drug market has necessitated the development of quick and simple methods for identification of adulterated materials. One method that could be employed is lateral flow immunoassays (also known as test strips), which are similar to those frequently used to determine the presence of fentanyl. In this work, we explored the use of xylazine test strips (XTS) for the detection of xylazine in drug residue samples and investigated their sensitivity and cross-reactivity. XTS were found to detect xylazine at concentrations as low as 0.5 µg/mL in solution and consistently produced a positive result at concentrations as low as 2.5 µg/mL. Cross-reactivity with other α2-agonists, α2-antagonists, commonly encountered drugs and cutting agents, and other structurally similar compounds was minimal, with lidocaine being the only compound of the 77 studied to illicit a positive response. When XTS were used to detect xylazine in real-world drug residue samples, xylazine was consistently detected in samples where the concentration was above 2 µg/mL and mixed results were obtained when the concentration ranged between 0.1 µg/mL and 2 µg/mL. When considering samples that were negative for xylazine or had xylazine present at a concentration above the 1 µg/mL cut-off, an overall accuracy of 98.6% was achieved. | Edward Sisco; Danielle F. Nestadt; Madeline B. Bloom; Kristin E. Schneider; Rae A. Elkasabany; Saba Rouhani; Susan G. Sherman | Analytical Chemistry; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6489cfca4f8b1884b74a247d/original/understanding-sensitivity-and-cross-reactivity-of-xylazine-lateral-flow-immunoassay-test-strips-for-drug-checking-applications.pdf |
60c74c37bdbb89fde3a3972c | 10.26434/chemrxiv.12455357.v1 | Highly Luminescent 4-Pyridyl-Extended Dithieno[3,2-b:2′,3′-d]phospholes | The unexpectedly challenging synthesis of 4-pyridyl-extended dithienophospholes is reported. The optical and electrochemical properties of the phosphoryl-bridged species were studied experimentally and computationally, and their properties compared to their non-<i>P</i>-bridged congeners. The 4-pyridyl-extended dithieno-phospholes display quantitative luminescence quantum yields in solution.<br /><br /> | Thomas Baumgartner; Paul Demay-Drouhard | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c37bdbb89fde3a3972c/original/highly-luminescent-4-pyridyl-extended-dithieno-3-2-b-2-3-d-phospholes.pdf |
61fc8601a6fb4d21684a16fc | 10.26434/chemrxiv-2022-mvdk0 | Fluorofoldamer-Based Salt- and Proton-Rejecting Artificial Water Channels for Ultrafast Water Transport | Here, we report on a novel class of fluorofoldamer-based artificial water channels (AWCs) that combines excellent water over ion selectivity with extraordinarily high water transport efficiency and structural simplicity and robustness. These AWCs were produced by a facile one-pot copolymerization reaction under mild conditions. Among these channels, the best-performing channel (AWC 1) is a n-C8H17-decorated foldamer nanotube with an average channel length of 2.8 nm and a pore diameter of 5.2 Å. AWC 1 demonstrates an ultrafast water conduction rate of 1.4 × 1010 H2O/s per channel, outperforming the archetypal biological water channel, aquaporin 1, by 27%, while excluding salts (i.e., NaCl and KCl) and protons. Unique to this class of channels, the inwardly facing C(sp2)-F moieties are proposed as being critical to enabling the ultrafast and superselective water transport properties observed. | Jie SHEN; Arundhati Roy; Himanshu Joshi; Laxmicharan Samineni; Ruijuan Ye; Yu-Ming Tu; Woochul Song; Matthew Skiles; Manish Kumar; Aleksei Aksimentiev; Huaqiang Zeng | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fc8601a6fb4d21684a16fc/original/fluorofoldamer-based-salt-and-proton-rejecting-artificial-water-channels-for-ultrafast-water-transport.pdf |
65d344ef9138d2316172e36a | 10.26434/chemrxiv-2024-jh876 | Aqueous Micellar Environment Impacts the Co-Catalyzed Phototransformation: A Case Study | In recent years, methodologies that rely on water as the reaction medium have gained considerable attention. The unique properties of micellar solutions were shown to improve the regio-, stereo-, and chemoselectivity of different transformations. Herein, we demonstrate that the aqueous environment is a suitable medium for a visible light driven cobalt-catalyzed reaction involving radical species. In this system, reduced vitamin B12 reacts with alkyl halides, gen-erating radicals that are trapped by the lipophilic olefin present in the Stern layer. A series of NMR measurements and theoretical studies revealed the location of reaction components in the micellar system. | Aleksandra Wincenciuk; Piotr Cmoch; Maciej Giedyk; Martin Andersson; Dorota Gryko | Organic Chemistry; Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d344ef9138d2316172e36a/original/aqueous-micellar-environment-impacts-the-co-catalyzed-phototransformation-a-case-study.pdf |
624ffab302f701487ddb475e | 10.26434/chemrxiv-2022-x1tl0 | Sensors and energy harvesting devices applicable on cellulose products – a literature survey | This literature survey, conducted by the Digital Cellulose Center, details sensors and energy harvesting technologies capable of being integrated in, or on, cellulose-based materials such as paper or board. The goal of the survey is to identify how full sensor system integration can be performed on environmentally friendly substrates. Using cellulose and other bio-based materials from the forest is a promising way of making electronics greener. Also, such system integration can add new intelligence to existing cellulose products such as packages for food and logistics. The survey focuses on moisture sensors, temperature sensors, pressure and strain sensors, piezoelectric cellulose, patterning methods, and triboelectric nanogenerators, each one divided into separate chapters. The outcome of the survey is considered in the light of connected cellulose-based sensor applications, identifying the most pertinent scientific questions and remaining challenges. We particularly consider the results in light of sensors integrated into pressboard. | Tiffany Abitbol; Dagmawi Belaineh; Valerio Beni; Robert Brooke; Jesper Edberg; Omid Hosseinaei; Karl Håkansson; Yusuf Mulla; Mats Sandberg; Xin Wang | Materials Science; Energy; Biological Materials; Carbon-based Materials; Power; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624ffab302f701487ddb475e/original/sensors-and-energy-harvesting-devices-applicable-on-cellulose-products-a-literature-survey.pdf |
66681a18e7ccf7753a7f3023 | 10.26434/chemrxiv-2024-zh6t7 | Isothiocyanate Enabled Versatile Cyclizations of Phage Dis-played Peptides for the Discovery of Macrocyclic Binders | Cyclic peptides exhibit advantages in binding protein targets with high affinity and competency in inhibiting protein-protein interactions (PPIs). Cyclic peptide phage display with over a billion variants is an invaluable tool in drug discovery. However, achieving efficient peptide cyclization on phages remains a challenge due to the limited availability of reaction sites, which also restricts scaffold diversity. Here, we report an isothiocyanate-derived crosslinker featuring dual reactive groups: a bro-mide that covalently attaches to cysteine thiols, and a thiocyanogen that selectively forms a thiourea bridge with either the N-terminal amino group or ε-amines of lysine, depending on pH. This strategy enables pH-modulated cyclization, with head-to-side chain cyclization at pH 6.5 and side chain-to-side chain ligation at pH 9.5, simultaneously generating thiourea scaffolds. To demonstrate the versatility and biocompatibility of this approach, we constructed cyclic peptide libraries using both cy-clization methods and successfully selected binders for several targets, including Cyp D, TNF, MDM2, and Keap1, with disso-ciation constants (KD) ranging from micromolar to nanomolar. Given the broad pharmacological potential of the thiourea moiety, this phage display library opens new chemical space with high scaffold diversity and the integration of a proven pharmacophore for the development of cyclic peptide therapeutics. | Xinxiang Lei; Liwen Bai; Ting Dan; Peng Cheng; Xiaoqin Yang; Hua Xiang; Rong Huang; Qi Wang; Kai Li; JinMing Gao | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66681a18e7ccf7753a7f3023/original/isothiocyanate-enabled-versatile-cyclizations-of-phage-dis-played-peptides-for-the-discovery-of-macrocyclic-binders.pdf |
625721625b9009633c0cfd7d | 10.26434/chemrxiv-2022-drdkg | On the ambiphilic character of phosphanylidenephosphoranes and
manipulation of phosphinidenoid reactivity with Lewis acids | Phosphanylidenephosphoranes of the type R−P(PR’3), also known as phospha-Wittig reagents, can be utilized in a variety of bond activation reactions pursuing their phosphinidenoid reactivity. In here, we thoroughly show that a facile PMe3 for H2O exchange gives access to various primary phosphine oxides of the general formula RP(H)2O (R = Mes*, MesTer, DipTer). The molecular structure of DipTerP(H)2O was determined and provided the first picture of such species in the solid state. However, phosphanylidenephosphoranes are described to be highly nucleophilic as well. We show that the attachment of main group Lewis acids such as GaCl3 and GaI3 to2 R−P(PMe3) yielded highly sensitive, yet stable coordination compounds [RP(GaX3)PMe3] (R = Mes*, DipTer) or [(RPPMe3)2GaCl2]GaCl4 (R = MesTer). In contrast to the free phosphanylidenephosphoranes, these species reacted differently with H2O which was demonstrated for [(Mes*PPMe3)GaI3]. Here the formation of the phosphinophosphonium cation [Mes*P(H)PMe3]+ and different anions was observed with combined NMR spectroscopic and SC-XRD (SC-XRD = single crystal diffraction analysis) studies. This work demonstrates that the ambiphilic character of phosphanylidenephosphoranes can be utilized to manipulate the reactivity of R−P(PMe3) towards water, giving primary phosphine oxides, whereas the Lewis acid adducts [(RPPMe3)GaX3] gave phosphino-phosphonium species. | Fabian Dankert; Malte Fischer; Christian Hering-Junghans | Inorganic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625721625b9009633c0cfd7d/original/on-the-ambiphilic-character-of-phosphanylidenephosphoranes-and-manipulation-of-phosphinidenoid-reactivity-with-lewis-acids.pdf |
6544304ea8b423585ad53eaa | 10.26434/chemrxiv-2023-t6xm5 | Overcoming The Low Initial Coulombic Efficiency of Si Anodes Through Prelithiation in All-solid-state Batteries | All-solid-state batteries using Si as the anode have shown promising performance without continual solid-electrolyte interface (SEI) growth. However, the low initial Coulombic efficiency (ICE) of Si limits their energy density. In this work, a prelithiation strategy was adopted to improve the ICE and conductivity of Si all-solid-state cells. Lithiated Si anodes were examined in symmetric-, half-, and full-cell configurations to understand the cell-level improvement. A full cell comprising a Li1Si anode achieved over 95% of ICE when paired with a lithium cobalt oxide (LCO) cathode. Additionally, a comparison of cells containing either a lithium nickel manganese cobalt oxide (NCM) or LCO cathode paired with either Si or LixSi at the anode revealed performance improvements with Si prelithiation only in anode-limited cases. Rate and long-term cycling capabilities were evaluated for Si- and Li1Si-containing cells, showing higher discharge capacities at all rates for Li1Si than Si. With Li1Si, 73.8% capacity retention was achieved after 1000 cycles, a 15% improvement when compared to a pure Si anode. With Li1Si, a high areal capacity of up to 10 mAh cm-2 was attained using a dry-processed LCO cathode film, suggesting that the prelithiation method may be suitable for high loading next-generation all-solid-state batteries. | So-Yeon Ham; Elias Sebti; Ashley Cronk; Tyler Pennebaker; Grayson Deysher; Yu-Ting Chen; Jin An Sam Oh; Jeong Beom Lee; Min Sang Song; Phillip Ridley; Darren H. S. Tan; Raphaële J. Clément; Jihyun Jang; Ying Shirley Meng | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6544304ea8b423585ad53eaa/original/overcoming-the-low-initial-coulombic-efficiency-of-si-anodes-through-prelithiation-in-all-solid-state-batteries.pdf |
62b2be7a486c9899b3ae52a6 | 10.26434/chemrxiv-2022-013k3 | Biomolecular Condensates Formed by Designer Minimalistic Peptides | Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of such biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities and responsiveness to specific stimuli a significant challenge. To address this need we have designed a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by specific changes to the peptide composition at the single amino acids level, with Raman and NMR spectroscopy proving instrumental in determining the molecular contribution of each side chain to droplet formation. The resulting sequence-structure-function correlation is mandatory for future development of compartments for a variety of applications. | Avigail Baruch Leshem; Sian Sloan-Dennison; Tlalit Massarano; Shavit Ben-David; Duncan Graham; Karen Faulds ; Hugo Gottlieb; Jordan Chill; Ayala Lampel | Materials Science; Aggregates and Assemblies; Biological Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b2be7a486c9899b3ae52a6/original/biomolecular-condensates-formed-by-designer-minimalistic-peptides.pdf |
60c75307f96a003f8b288388 | 10.26434/chemrxiv.13385114.v1 | Gold(III) Aryl Complexes as Reagents for Constructing Hybrid Peptide-Based Assemblies via Cysteine S-Arylation | <p>Organometallic complexes have recently gained attention as competent bioconjugation reagents capable of introducing a diverse array of substrates to biomolecule substrates. Here, we detail the synthesis and characterization of an
aminophosphine-supported Au(III) platform that provides rapid and convenient access to a wide array of peptide-based assemblies via cysteine S-arylation. This strategy results in the formation of robust C‒S covalent linkages and is an attractive
method for the modification of complex biomolecules due to the high functional group tolerance, chemoselectivity, and rapid
reaction kinetics associated with these arylation reactions. This work expands upon existing metal-mediated cysteine arylation by introducing a class of air-stable organometallic complexes that serve as competent bioconjugation reagents enabling
the synthesis of conjugates of higher structural complexity including macrocyclic stapled and bicyclic peptides, as well as a
peptide-functionalized multivalent hybrid nanocluster. This organometallic-based approach provides a convenient, one-step
method of peptide functionalization and macrocyclization, and has the potential to contribute to efforts directed towards
developing efficient synthetic strategies of building new and diverse hybrid peptide-based assemblies of high complexit<br /></p> | Julia M. Stauber; Arnold L. Rheingold; Alexander Spokoyny | Organometallic Compounds | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75307f96a003f8b288388/original/gold-iii-aryl-complexes-as-reagents-for-constructing-hybrid-peptide-based-assemblies-via-cysteine-s-arylation.pdf |
60c743ecbdbb89255aa386e3 | 10.26434/chemrxiv.9199889.v2 | On the Inverted Singlet-Triplet Gaps and Their Relevance to Organic Light-Emitting Diodes | The basic design principle for emitters exhibiting thermally activated delayed fluorescence (TADF) is the minimization of the singlet-triplet gap. While typically this gap is positive, a possible inversion of states has been proposed as a pathway to improve the efficiency of organic light-emitting diodes. Despite the efforts to design such emitters, there are very few reports indicating that it is at all possible. We analyze the problem of gap inversion from the perspective of the electronic structure theory. The key result is that inversion is possible but requires a substantial contribution of double excitations and that commonly used cheap electronic structure methods would fail to predict it. | Piotr de Silva | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743ecbdbb89255aa386e3/original/on-the-inverted-singlet-triplet-gaps-and-their-relevance-to-organic-light-emitting-diodes.pdf |
67b46c56fa469535b9d8e6c1 | 10.26434/chemrxiv-2025-70p06 | Assessing non-bonded aggregates populations: application to the concentration-dependent IR O-H band of phenol | In this work, we present two alternative computational strategies to determine the populations of non-bonded aggregates. One approach extracts these populations from molecular dynamics (MD) simulations, while the other employs quantum mechanical partition functions for the most relevant minima of the multimolecular potential energy surfaces (PESs), identified by automated conformational sampling. In both cases, we adopt a common graph-theory-based framework, introduced in this work, for identifying aggregate conformations, which enables a consistent comparative assessment of both methodologies and provides insight into the underlying approximations. We apply both strategies to investigate phenol aggregates, up to the tetramer, at different concentrations in phenol/carbon tetrachloride mixtures. Subsequently, we simulate the concentration-dependent OH stretching IR region by averaging the harmonic IR spectra of aggregates using the populations predicted by each strategy. Our results indicate that the populations extracted from MD trajectories yield OH stretching signals that closely follow the experimental trends, outperforming the spectra from populations obtained by systematic conformational searches. Such a better performance of MD is attributed to a better description of the entropic contributions. Moreover, the proposed protocol not only successfully addresses a very challenging problem but also offers a benchmark to assess the accuracy of intermolecular force fields. | J. Pablo Galvez; José Zúñiga; Javier Cerezo | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b46c56fa469535b9d8e6c1/original/assessing-non-bonded-aggregates-populations-application-to-the-concentration-dependent-ir-o-h-band-of-phenol.pdf |
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