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60c7548dbdbb8942cba3a67f | 10.26434/chemrxiv.13681432.v1 | Nickel-Catalyzed Benzylic Alkynylation: Migratory Hydroalkynylation and Enantioselective Hydroalkynylation of Olefins with Bromoalkynes | A nickel-hydride catalyzed reductive migratory
hydroalkynylation of olefins with bromoalkynes that delivers the corresponding
benzylic alkynylation products in high yield and with excellent regioselectivity
has been developed. Catalytic enantioselective hydroalkynylation of styrenes
has been realized using a simple chiral PyrOx ligand. The obtained
enantioenriched benzylic alkynes are versatile synthetic intermediates and can
be readily transformed into synthetically useful chiral synthons | Xiaoli Jiang; Bo Han; Yuhang Xue; Mei Duan; Zhuofan Gui; You Wang; Shaolin Zhu | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7548dbdbb8942cba3a67f/original/nickel-catalyzed-benzylic-alkynylation-migratory-hydroalkynylation-and-enantioselective-hydroalkynylation-of-olefins-with-bromoalkynes.pdf |
67191d4d12ff75c3a14f4b20 | 10.26434/chemrxiv-2024-nfsqn-v3 | Efficient Constitution of a Library of Rotenoid Analogs Active against Trypanosoma cruzi from a Digitalized Plant Extract Collection | Natural products (NP) have proven to be a rich source of potentially bioactive compounds, and metabolomics is the current method of choice for characterizing natural extracts. To integrate the vast amount of data and information produced by modern metabolomics workflows, we recently developed a sample-centric approach for the semantic enrichment and alignment of metabolomics datasets. The resulting Experimental Natural Products Knowledge Graph (ENPKG) is queryable and integrates both newly acquired digitalized experimental data and information, and previously reported knowledge. It allows the highlighting of putative bioactive compounds at the extract level by comparing, for example, the occurrence of compounds of a given chemical class with bioactivity results. Using this approach, we recently described potent anti-Trypanosoma cruzi activity of two rotenoids, deguelin and rotenone. These compounds were identified in six active extracts from four plant species: Cnestis palala (Connaraceae), Chadsia grevei, Pachyrhizus erosus, and Desmodium heterophylum (Fabaceae). In this work, we present the results of the phytochemical investigation of four of these extracts and the establishment of a library of structural analogs for in vitro bioactivity testing. This work led to the isolation, characterization, and biological evaluation of the anti-T. cruzi potential of 41 compounds, including 11 rotenoids and seven compounds reported for the first time. Thanks to modern metabolite annotation and single-step isolation procedures, this work also demonstrates the possibility of considering natural extract libraries as a reservoir of rapidly accessible pure NPs. This perspective could increase the options for NP research and help accelerate NP drug discovery efforts. | Arnaud Gaudry; Laurence Marcourt; Marcel Kaiser; Julien Flückiger; Bruno David; Antonio Grondin; Jean-Robert Ioset; Pascal Mäser; Emerson Ferreira Queiroz; Pierre-Marie Allard; Jean-Luc Wolfender | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Natural Products; Mass Spectrometry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67191d4d12ff75c3a14f4b20/original/efficient-constitution-of-a-library-of-rotenoid-analogs-active-against-trypanosoma-cruzi-from-a-digitalized-plant-extract-collection.pdf |
65c1857de9ebbb4db9bff80f | 10.26434/chemrxiv-2024-tc9hm | The impact of earth-abundant metals as a replacement for Pd in cross coupling reactions
| Substitution of one metal catalyst for another is not straightforward as simply justifying this change based on the availability and/or cost of the metals. A life cycle-like assessment was performed leading to the conclusion that the commonly held view that use of earth-abundant metals (and in this case study, Ni) are replacements for palladium most notably in cross coupling reactions, and Suzuki-Miyaura couplings, in particular, is an incomplete analysis of the entire picture. This notion can be misleading, and unfortunately derives nowadays mainly from the standpoint of cost, and to some degree, the relative natural abundance and mining impact of each metal. However, a more realistic appreciation emerges when several additional reaction parameters involved in the couplings are considered. Such an analysis unequivocally points to the major impact on climate change brought about by use of organic solvents, while the metals actually play subordinate roles in terms of CO2-release into the environment. Clearly, this study reveals that several factors contribute in various ways to the overall carbon footprint. Hence, a far more detailed analysis is required than that typically being utilized! | Bruce Lipshutz; Fabrice Gallou; Michael Luescher | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c1857de9ebbb4db9bff80f/original/the-impact-of-earth-abundant-metals-as-a-replacement-for-pd-in-cross-coupling-reactions.pdf |
60c748069abda22037f8c9e3 | 10.26434/chemrxiv.11836137.v1 | Tailoring Polymer Dispersity by Controlled Radical Polymerization: A Versatile Approach | <p>Dispersity (<i>Ɖ</i>) can significantly affect
polymer properties and is a key parameter in materials design; however, current
methods do not allow for the comprehensive control of dispersity. They are limited in monomer scope, may require the use of flow-based systems and/or additional
reagents (<i>e.g.</i> termination agents or co-monomers), and are often
accompanied by multimodal molecular weight distributions, low initiator
efficiencies or poor end-group fidelity. Herein, we
report a straightforward and versatile batch method based on reversible
addition-fragmentation chain transfer (RAFT) polymerization which enables
good control over <i>Ɖ</i> of a wide
range of monomer classes, including acrylates, acrylamides, methacrylates and
styrene. In addition, our methodology is compatible with more challenging
monomers such as methacrylic acid, vinyl ketone and vinyl acetate. Control over
<i>Ɖ</i> is achieved by mixing two RAFT
agents with sufficiently different transfer activities in various ratios,
affording polymers with monomodal molecular weight distributions over a broad
dispersity range (<i>Ɖ</i> ~ 1.09-2.10). Our findings were further supported by simulations
through the use of deterministic kinetic modelling which was fully in line with
our experimental data, further confirming the power of our methodology. The
robustness of the concept is further demonstrated by the preparation of well-defined
block copolymers via chain extension of all polymers regardless of the initial <i>Ɖ</i>.</p> | Richard Whitfield; Kostas Parkatzidis; Nghia Truong; Tanja Junkers; Athina Anastasaki | Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748069abda22037f8c9e3/original/tailoring-polymer-dispersity-by-controlled-radical-polymerization-a-versatile-approach.pdf |
66f5321812ff75c3a18553fd | 10.26434/chemrxiv-2024-1zwr6-v2 | Machine Learning Applications in Drug Discovery | Integrating machine learning (ML) into drug discovery has ushered in a new era of innovation, dramatically enhancing the efficiency and precision of identifying and developing new therapeutics. This review provides a comprehensive analysis of the current applications of machine learning in drug discovery, focusing on its transformative impact across various stages of the drug development pipeline. We delve into key ML methodologies, including supervised and unsupervised learning, neural networks, and reinforcement learning, examining their underlying principles and specific contributions to drug discovery processes. By exploring case studies and recent advancements, this review illustrates how ML algorithms have been utilized to predict drug-target interactions, optimize drug design, and streamline clinical trial processes. Furthermore, we discuss the challenges and limitations of implementing ML techniques in this field and highlight emerging trends and future directions. This review aims to offer researchers a thorough understanding of ML's potential to revolutionize drug discovery and equip them with the insights needed to leverage these technologies effectively. | Sadettin Y Ugurlu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2024-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f5321812ff75c3a18553fd/original/machine-learning-applications-in-drug-discovery.pdf |
60c74cdbf96a00d67828784f | 10.26434/chemrxiv.12290621.v2 | Dry Heat as a Decontamination Method for N95 Respirator Reuse | <div>
<div>
<p>A pandemic such as COVID-19 can cause a sudden depletion in the worldwide supply of respirators, forcing healthcare providers to reuse them. In this study, we systematically evaluated dry heat treatment as a viable option for the safe decontamination of N95 respirators (1860, 3M) before its reuse. We found that the dry heat generated by an electric cooker (100°C, 5% relative humidity, 50 min) effectively inactivated Tulane virus (>5.2-log<sub>10</sub> reduction), rotavirus (>6.6-log<sub>10</sub> reduction), adenovirus (>4.0-log<sub>10</sub> reduction), and transmissible gastroenteritis virus (>4.7-log<sub>10</sub> reduction). The respirator integrity (determined based on the particle filtration efficiency and quantitative fit testing) was not compromised after 20 cycles of 50-min dry heat treatment. Based on these results, we propose dry heat decontamination generated by an electric cooker (e.g., rice cookers, instant pots, ovens) to be an effective and accessible decontamination method for the safe reuse of N95 respirators.<br /></p>
</div>
</div> | Chamteut Oh; Elbashir Araud; Joseph V. Puthussery; Hezi Bai; Gemma G. Clark; Vishal Verma; Thanh H. Nguyen | Environmental biology | CC BY NC 4.0 | CHEMRXIV | 2020-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cdbf96a00d67828784f/original/dry-heat-as-a-decontamination-method-for-n95-respirator-reuse.pdf |
62eccfced131b7fc100d316a | 10.26434/chemrxiv-2022-1js1h | A Modular Polymer for Nanoparticle Supports | Nanoparticles are key to a range of applications, due to the properties that emerge as a result of their small size. However, their size also presents challenges to their processing and use, especially in relation to their immobilization on solid supports without losing their favourable functionalities. Here, we present a multifunctional polymer-bridge-based approach to attach a range of pre-synthesised nanoparticles onto microparticle supports. We demonstrate the attachment of mixtures of different types of metal-oxide nanoparticles, as well as metal-oxide nanoparticles modified with standard wet chemistry approaches. We then show that our method can also create composite films of metal and metal-oxide nanoparticles by exploiting different chemistries simultaneously. We finally apply our approach to the synthesis of designer microswimmers with decoupled mechanisms of steering (magnetic) and propulsion (light) via asymmetric nanoparticle binding, aka Toposelective Nanoparticle Attachment.
We envision that the ability to freely mix available nanoparticles to produce composite films will help bridge the fields of catalysis, nanochemistry, and active matter towards new materials and applications. | Maximilian Bailey; Tobias Gmür; Fabio Grillo; Lucio Isa | Materials Science; Catalysis; Nanoscience; Composites; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2022-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eccfced131b7fc100d316a/original/a-modular-polymer-for-nanoparticle-supports.pdf |
620e9c9f0aec1a0d6a2143b2 | 10.26434/chemrxiv-2022-2s2z7 | Selective Electrochemical Reductive Amination of Benzaldehyde at Heterogeneous Metal Surfaces | Ammonia is one of the largest volume commodity chemicals, and electrochemical routes to ammonia utilization are appealing due to increasingly available renewable electricity. In this work, we demonstrate an electrochemical analogue to reductive amination for the synthesis of benzylamine from benzaldehyde and ammonia. Previous works on electrochemical reductive amination generally focus on proof-of-concept outer-sphere routes. We demonstrate an inner-sphere route, opening a large phase space of heterogeneous electrocatalysts that can direct selectivity and drive the reaction. In our system, imine hydrogenation proceeds on a silver electrocatalyst at ambient conditions in methanol with an initial Faradaic efficiency toward the primary amine product of ~80% and partial current greater than 4 mA/cm2 at -1.96 V vs. Fc/Fc+ (-1.36 V vs. NHE). Silver was selected after evaluating diverse transition metal electrocatalysts, and with density functional theory, we found that the reaction rate on various metals is best described by the charge density distribution above the metal surface, independent of molecular adsorption energies. On silver, the catalyst that promotes amination with the highest Faradaic efficiency and one of the highest partial currents, the rate-determining step was found to be the initial electron transfer to the imine. Overall, this work on the kinetics of electrochemical reductive amination represents a step toward inner-sphere electrochemical reductive amination systems for the synthesis of amines that currently rely on thermochemical reductive amination. | Zachary Schiffer; Minju Chung; Katherine Steinberg; Karthish Manthiram | Physical Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620e9c9f0aec1a0d6a2143b2/original/selective-electrochemical-reductive-amination-of-benzaldehyde-at-heterogeneous-metal-surfaces.pdf |
678e10e781d2151a02e081bc | 10.26434/chemrxiv-2025-0lxhw | Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-objective molecular optimization | The rapid and economical synthesis of novel bioactive compounds remains a significant hurdle in drug discovery efforts. This study demonstrates an integrated medicinal chemistry workflow that effectively diversifies hit and lead structures, enabling an efficient acceleration of the critical hit-to-lead optimization phase. Employing high-throughput experimentation (HTE), we generated a comprehensive data set encompassing 13,490 novel Minisci-type C-H alkylation reactions. This data set served as the foundation for training deep graph neural networks to accurately predict reaction outcomes. Scaffold-based enumeration of potential Minisci reaction products, starting from moderate inhibitors of monoacylglycerol lipase (MAGL), yielded a virtual library containing 26,375 molecules. This virtual chemical library was evaluated using reaction prediction, physicochemical property assessment, and structure-based scoring, identifying 212 potential MAGL inhibitor candidates. Of these, 14 ligands were synthesized and exhibited subnanomolar activity, representing a potency improvement of up to 4500 times over the original hit compound. These compounds also displayed favorable pharmacological profiles. Co-crystallization of three computationally designed ligands with the MAGL protein provided valuable structural insights into their preferred binding poses. This study demonstrates the potential of combining miniaturized HTE with deep learning and molecular property optimization to reduce cycle times in drug discovery. | David F. Nippa; Kenneth Atz; Yannick Stenzhorn; Alex T. Müller; Andreas Tosstorff; Jörg Benz; Hayley Binch; Markus Bürkler; Achi Haider; Dominik Heer; Remo Hochstrasser; Christian Kramer; Michael Reutlinger; Petra Schneider; Thierry Shem; Andreas Topp; Alexander Walter; Matthias B. Wittwer; Jens Wolfard; Bernd Kuhn; Mario van der Stelt; Rainer E. Martin; Uwe Grether; Gisbert Schneider | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678e10e781d2151a02e081bc/original/expediting-hit-to-lead-progression-in-drug-discovery-through-reaction-prediction-and-multi-objective-molecular-optimization.pdf |
620a8b03bd05a0b72b069d5f | 10.26434/chemrxiv-2022-w059p | Analysis of Laboratory-Evolved Flavin-Dependent Halogenases Affords a Computational Model for Predicting Halogenase Site Selectivity | Flavin-dependent halogenases catalyze selective halogenation of electron-rich aromatic compounds without the need for harsh oxidants required by conventional oxidative halogenation reactions. Predictive models for halogenase site selectivity would greatly improve their utility for chemical synthesis. Toward this end, we analyzed the structures and selectivity of three halogenase variants evolved to halogenate tryptamine with orthogonal selectivity. Crystal structures and reversion mutations revealed key residues involved in altering halogenase selectivity. Density functional theory calculations and molecular dynamics simulations are both consistent with hypohalous acid as the active halogenating species in FDH catalysis. This model was used to accurately predict the site selectivity of halogenase variants toward different synthetic substrates, providing a valuable tool for implementing halogenases in biocatalysis efforts. | Mary C. Andorfer; Declan Evans; Song Yang; Cyndi Q. He; Anna M. Girlich; Jaylie Vergara-Coll; Narayanasami Sukumar; K. N. Houk; Jared C. Lewis | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Computational Chemistry and Modeling; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620a8b03bd05a0b72b069d5f/original/analysis-of-laboratory-evolved-flavin-dependent-halogenases-affords-a-computational-model-for-predicting-halogenase-site-selectivity.pdf |
6711845f51558a15ef60c919 | 10.26434/chemrxiv-2024-bjl82 | Acid-Cleavable Poly(Oxazoline) Surfactants | The low pH of the cancer tumor microenvironment and the late endosome is a tantilizing target for stimuli-responsive nanotherapeutics due to the accessibilility of these particular chemical differences to nanomaterials. Acid-cleavable surfactants are well-established for the formulation of stimuli-responsive nanoparticles and much work has been done to tune the sensitivity of these motifs to match their intended application. Acid-labile hydrazone-linked surfactants, specifically display increased stability over the more common imine linkage to prevent premature release outside of the cell, but remain labile enough for effective payload release once endocytosed. Furthermore, their cationic byproducts are known to facilitate enhanced endosomal escape through membrane disruption. Herein, we report the synthesis of a hydrazone-linked poly(oxazoline)-based diblock copolymer surfactant. This surfactant cleaves in a pH-dependent manner both in solution, and at the perfluorocarbon-water interface. We then demonstrate the ability of nanoemulsion encapsulated payloads to partition into cell membrane mimics only after cleavage of the surfactant. In all, this work demonstrates a viable route to create POx-based nanomaterials with controlled release capabilities in biologically relevant conditions and is a promising platform for advancing the endosomal escape and cancer targeting of nanomaterials. | Joseph Garcia; Ashley Vergara Mendez; Ellen Sletten | Polymer Science; Nanoscience; Drug delivery systems; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6711845f51558a15ef60c919/original/acid-cleavable-poly-oxazoline-surfactants.pdf |
65254965bda59ceb9a42f567 | 10.26434/chemrxiv-2021-rbj0t-v2 | In-Situ Monitoring of Mechanochemical MOF Formation by NMR Relaxation Time Correlation | In this paper, we present a new approach to monitoring mechanochemical transformations, based on a magnetic resonance method in which relaxation time correlation maps are used to track the formation of the popular metal-organic framework (MOF) materials Zn-MOF-74 and ZIF-8. The two-dimensional (2D) relaxation correlation measurement employed yields a T1-T2* spectrum which visually and analytically identifies different 1H environments in the sample of interest. The measurement is well-suited to analyzing solid mixtures, and liquids, in complex systems. Application in this work to monitoring MOF formation shows changes in signal amplitudes, and their MR lifetime coordinates, within the 2D plots as the reaction progresses, confirming reaction completion. This new measurement provides a simple way to analyse solid-state reactions without dissolution, and there is a logical pathway to benchtop measurement with a new generation of permanent magnet-based MR instruments. The methodology described permits measurement in an MR compatible milling container, which may be directly transferred from the shaker assembly to the MR magnet for in-situ measurement of the entire reaction mixture. | Madeleine Leger; Jiangfeng Guo; Bryce MacMillan; Hatem Titi; Tomislav Friscic; Barry Blight; Bruce Balcom | Physical Chemistry; Inorganic Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65254965bda59ceb9a42f567/original/in-situ-monitoring-of-mechanochemical-mof-formation-by-nmr-relaxation-time-correlation.pdf |
65eedc9a9138d23161338d33 | 10.26434/chemrxiv-2024-0jxr0-v2 | New insights in the mechanism of the SARS-CoV-2 Mpro inhibition by benzisoselenazolones and diselenides | Although global vaccination campaigns relieved the SARS-CoV-2 pandemic in terms of morbidity and mortality, the capability of the virus to originate mutants may reduce vaccines efficiency, posing a serious risk to fall into the pandemic again. As a result, there is the need to develop small molecules able to tackle conserved viral targets, such as the main protease (Mpro). Here a series of benzisoselenazolones and diselenides were tested for their ability to inhibit Mpro, then, for the most potent compounds, the antiviral activity was measured in vitro, and the mechanism of action was investigated. Density functional theory and molecular docking procedures were also implemented to shed a light into the protein/compound interaction. Finally, a bioorganic model was set up to investigate the reaction between selenorganic compounds and biologically relevant thiols, to unravel possible metabolic pathways of such compounds. The overall results contribute to identify a series of novel compounds active against SARS-CoV-2, and to clarify some important aspects in the mechanisms of action of Se-containing inhibitors targeting the SARS-CoV-2 main protease (Mpro). | Luca Sancineto; Francesca Mangiavacchi; Agnieszka Dąbrowska; Agata Pacuła; Magdalena Obieziurska-Fabisiak; Veronica Ceccucci; Cecilia Scimmi; Juan Kong; Yao Zhao; Gianluca Ciancaleoni; Vanessa Nascimento; Bruno Rizzuti; Anna Kula-Pacurar; Haitao Yang; Jacek Ścianowski; Ying Lei; Krzysztof Pyrc; Claudio Santi | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eedc9a9138d23161338d33/original/new-insights-in-the-mechanism-of-the-sars-co-v-2-mpro-inhibition-by-benzisoselenazolones-and-diselenides.pdf |
60c758419abda2fa4df8e896 | 10.26434/chemrxiv.14529315.v1 | Incorporation of [Cp*Rh] and [Cp*Ir] Species into Heterobimetallic Complexes via Protonolysis Reactivity and Dioximato Chelation | <p><a></a>Synthesis
of multimetallic compounds can enable placement of two or more metals in close
proximity, but efforts in this area are often hindered by reagent
incompatibilities and lack of selectivity. Here, we show that organometallic half-sandwich
[Cp*M] (M = Rh, Ir) fragments (where Cp* is <i>η</i><sup>5</sup>-pentamethylcyclopentadienyl)
can be cleanly installed into metallomacrocyclic structures based on the
workhorse diimine-monooxime-monooximato ligand system. Six new heterobimetallic
compounds have been prepared to explore this synthetic chemistry, which relies
on <i>in situ </i>protonolysis reactivity with precursor Ni(II) or Co(III) monometallic
complexes in the presence of suitable [Cp*M] species. Solid-state X-ray
diffraction studies confirm installation of the [Cp*M] fragments into the
metallomacrocyles via effective chelation of the Rh(III) and Ir(III) centers by
the nascent dioximato site. Contrasting with square-planar Ni(II) centers, the Co(III)
centers prefer octahedral geometry in the heterobimetallic compounds, promoting
bridging ligation of acetate across the two metals. Spectroscopic and
electrochemical studies reveal subtle influences of the metals on each other’s
properties, consistent with the moderate M′•••M distances of ca. 3.6–3.7 Å in
the modular compounds. The [Co,Rh] complex was found to catalyze hydrogenation
of <i>p</i>-trifluoromethylbenzaldehyde to <i>p</i>-trifluoromethylbenzyl
alcohol more cleanly than a 1:1 mixture of the individual monometallic
precursor complexes, suggesting that this family of heterobimetallic complexes could be useful in
future studies of multimetallic chemistry, especially in light of the starring
role of other [Cp*M] complexes in diverse catalytic systems.</p><br /> | Amit Kumar; Daniel King; Victor W. Day; James Blakemore | Transition Metal Complexes (Inorg.); Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758419abda2fa4df8e896/original/incorporation-of-cp-rh-and-cp-ir-species-into-heterobimetallic-complexes-via-protonolysis-reactivity-and-dioximato-chelation.pdf |
66684bf2e7ccf7753a81a125 | 10.26434/chemrxiv-2024-sq3xn | Computer-Aided Retrosynthesis for Greener and Optimal Total Synthesis of a Helicase-primase Inhibitor Active Pharmaceutical Ingredient | This study explores the application of computer-aided retrosynthesis (CAR) for developing greener and more efficient synthetic routes for the active pharmaceutical ingredient (API) IM-204, a helicase primase inhibitor with potential against Herpes simplex virus (HSV) infections. Using various CAR tools, several total synthetic routes were identified, evaluated, and experimentally validated, with the goal to maximize selectivity and yield and minimize the environmental impact. The selected route achieved a significant improvement in the overall yield of IM-204 synthesis from 8% to 35% while also enhancing GreenMotion metrics from 0 to 18 overall and reducing the cost of building blocks by 300-fold. This work demonstrates the potential of CAR in drug development, highlighting its capacity to streamline synthesis processes, reduce environmental footprint, and lower production costs, thereby advancing the field towards more efficient and sustainable practices. | Rodolfo Teixeira; Michael Andresini; Renzo Luisi; Brahim Benyahia | Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Pharmaceutical Industry; Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66684bf2e7ccf7753a81a125/original/computer-aided-retrosynthesis-for-greener-and-optimal-total-synthesis-of-a-helicase-primase-inhibitor-active-pharmaceutical-ingredient.pdf |
66423d6a21291e5d1d262885 | 10.26434/chemrxiv-2024-xxvdt | Controlling molar mass and dispersity in polymers through deuteration: the case of poly(phenyl D3-vinyl sulfide) | Polymer properties can be defned by functionalizing the monomer and tuned by modifying key properties, such as, molar mass and dispersity. Typically, these modification approaches require significant alterations to the synthesis process, or even re-optimization of the whole process. In this study, we demonstrate that deuteration, a mainly overlooked method, can significantly influence the properties without altering the chemical structure of the monomer or the synthesis procedure. For the poly(phenyl vinyl sulfide), we introduce a technique for integrating deuterium into a monomer, providing a novel way to adjust the properties of the resulting polymer without changing its chemical nature. This method is both accessible and cost-effective, adhering to the principles of green chemistry. Quantum chemical analysis revealed that this control over properties is due to a reduction in the rate of the polymerization deactivation, which proceeds through the chain transfer mechanism. The opportunity hgighlighted in the present study may be well-applicable for a number of ohter polyemrs, leading to a new approach to pracical tuning of polymer properties and developing materials with enhanced properties. | Anastasia Kutskaya; Mikhail Polynski; Konstantin Rodygin; Nina Demchenko; Valentine Ananikov | Physical Chemistry; Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Physical Organic Chemistry; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66423d6a21291e5d1d262885/original/controlling-molar-mass-and-dispersity-in-polymers-through-deuteration-the-case-of-poly-phenyl-d3-vinyl-sulfide.pdf |
63d3f9d210cb6ae6a2e8cb3a | 10.26434/chemrxiv-2023-7l7d0 | Selective Carbonic Anhydrase IX and XII Inhibitors Based Around a Functionalized Coumarin Scaffold | Inhibition of specific carbonic anhydrase (CA) enzymes is a validated strategy for the development of agents to target cancer. The CA isoforms IX and XII are overexpressed in various human solid tumors wherein they play a critical role in regulating extracellular tumor acidification, proliferation, and progression. A series of novel sulfonamides based on the coumarin scaffold were designed, synthesized and characterized as potent and selective CA inhibitors. Selected compounds show significant activity and selectivity over CA I and CA II to target the tumor-associated CA IX and CA XII with high inhibition activity at the single digit nanomolar level. Twelve compounds were identified to be more potent compared with acetazolamide (AAZ) control to inhibit CA IX while one was also more potent than AAZ to inhibit CA XII. Compound 18f (Ki’s = 955 nM, 515 nM, 21 nM and 5 nM for CA’s I, II, IX and XII respectively) is highlighted as a novel CA IX and XII inhibitor for further development. | Bader Huwaimel; Sravan Jonnalagadda; Shirisha Jonnalagadda; Shikha Kumari; Alessio Nocentinic; Claudiu Supuran; Trippier Paul | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d3f9d210cb6ae6a2e8cb3a/original/selective-carbonic-anhydrase-ix-and-xii-inhibitors-based-around-a-functionalized-coumarin-scaffold.pdf |
6701d678cec5d6c1424c01b1 | 10.26434/chemrxiv-2024-zthw9 | Lewis-acid mediated reactivity in single-molecule junctions | Recent work has shown that solution-based chemical reactions at a gold electrode can be monitored using molecular conductance and driven by extrinsic stimuli, such as an electric field or electrochemical potential. However, the intrinsic properties of the nanostructured interface may be expected to play important additional functions that are not yet well understood. Here we study single-molecule junctions formed from components having the same molecular backbone functionalized with 12 different sulfur-based linker groups to determine the influence of sulfur-substituent on junction conductance and stability. Remarkably, we find evidence for in situ S–C(sp3) bond breaking, and C(sp2)–C(sp3) bond forming, reactions that are consistent with the ex situ transformations expected for those systems in the presence of a Lewis acid. We also find we approach the limits of substituent influence on the conductance of physisorbed sulfur-bound junctions. As an illustrative example, we show that a tert-butylthio-functionalized 4,4’-biphenyl precursor can form both chemisorbed (Au−S) junctions, consistent with heterolytic S−C(sp3) bond cleavage to generate the stable tert-butyl carbocation, as well as physisorbed junctions that are >1 order of magnitude lower than analogous junctions comprising cyclic “locked” thioether contacts. Our findings are supported by a systematic analysis of model thioether components comprising different simple hydrocarbon substituents of intermediate size, which do not form chemisorbed contacts and further clarify the inverse relationship between conductance and substituent steric bulk. First-principles calculations based on density-functional theory also confirm that bulky sulfur-substituents increase the probability of forming junction geometries with reduced electronic coupling between the electrode and π-conjugated molecular backbone. Together, this work helps to rationalize the dual roles that linker molecular structure and metal electrode Lewis character play in mediating interfacial reactions in break-junction experiments. The insights provided may be applied to advance our understanding of heterogeneous chemical processes or develop new molecular electronic components with improved or novel functionality. | Jazmine Prana; Leopold Kim; Thomas Czyszczon-Burton; Grace Homann; Sully Chen; Zelin Miao; Maria Camarasa-Gomez; Michael Inkpen | Physical Chemistry; Organic Chemistry; Nanoscience; Physical Organic Chemistry; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6701d678cec5d6c1424c01b1/original/lewis-acid-mediated-reactivity-in-single-molecule-junctions.pdf |
67da5d256dde43c9085ff076 | 10.26434/chemrxiv-2025-1x7pv | Dual-sites for low-concentration NO to NH3 electrosynthesis in neutral media: promoting NO adsorption and water dissociation | The electrosynthesis of NH3 from low-concentration NO (NORR) in neutral media is a promising strategy for sustainable nitrogen fixation. However, the inherently weak adsorption of NO on traditional catalysts, coupled with the challenging water dissociation and NO hydrogenation kinetics, limits the efficiency of this reaction. Herein, we introduce a novel strategy by loading Pt nanoparticles (PtNPs) as electron donor onto an Fe single-atom catalyst (FeSAC) to form a strong electronic interaction between PtNPs and FeSAC. This electronically engineered architecture creates dual active site that significantly improves neutral low concentration NORR performance. In situ X-ray absorption spectroscopy (XAS), in situ attenuated total reflection-infrared spectroscopy (ATR-IR), and theoretical calculations reveal that PtNPs, acting as an electron reservoir, donate electrons to the FeSAC sites. This electron donation increases electron density at the Fe sites, promoting NO adsorption. Additionally, the PtNPs facilitate water dissociation, providing protons that greatly decrease the activation barrier for NO hydrogenation. Thus, the PtNPs/FeSAC dual-sites activated a synergistic cascade mechanism in neutral media during NORR process, with a Faradaic efficiency (FE) of 90.3% and an NH3 yield rate of 709.7 µg h-1 mgcat.-1 under 1.0 vol% NO, outperforming pure FeSAC (NH3 yield rate: 444.2 µg h-1 mgcat.-1, FE: 56.6%) and previously reported systems operating at high NO concentrations. Remarkably, this neutral NORR process achieved a record NH3 yield of 3023.8 μg h-1 mgcat.-1 in a membrane electrode assembly (MEA) electrolyzer under a 1.0 vol% NO atmosphere. This work develops a new class of electron-donating nanoparticles-mediated dual-sites that simultaneously enhance NO adsorption and facilitate water dissociation, significantly improving neutral low concentration NORR performance and paving the way for large-scale sustainable NH3 electrosynthesis. | Tongwei Wu; Xiaoxi Guo; Hengfeng Li; Yanning Zhang; Chao Ma; Hongmei Li; Haitao Zhao; Liyuan Chai; Min Liu | Theoretical and Computational Chemistry; Materials Science; Catalysis; Catalysts; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67da5d256dde43c9085ff076/original/dual-sites-for-low-concentration-no-to-nh3-electrosynthesis-in-neutral-media-promoting-no-adsorption-and-water-dissociation.pdf |
60c74521842e655f32db25a9 | 10.26434/chemrxiv.9971741.v1 | An Autonomous Electrochemical Test stand for Machine Learning Informed Electrolyte Optimization | <div>
<div>
<p>A fully automated, computer-controlled test stand capable of rapidly creating and electrochemically characterizing any arbitrary liquid electrolyte solution is described. Hundreds of different electrolytes were studied, and the results were used to verify the precision and accuracy of the system. To test the functionality of the approach, several 2-dimensional co-solvated electrolyte solutions containing blends of aqueous sulfates and nitrates were rapidly created and examined automatically. The test stand took less than a day to conduct these searches, while conventional manual methods would have taken much longer. The demonstrated standard error of the test-stand was 0.5 mS/cm on conductivity and 0.02 V for voltage stability window measurements, and several of the combinations studied revealing surprisingly high voltage stability and conductivity values. The demonstrated success of the test-stand in a 2-dimensional search spaces shows the promise of conducting high speed co-optimization studies of liquid electrolytes in particular when used in concert with a machine learning-based real time/in-loop data assessment computational package. </p><div><br /></div>
</div>
</div> | Jay Whitacre; Jared Mitchell; Adarsh Dave; Sven Burke; Venkatasubramanian Viswanathan | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74521842e655f32db25a9/original/an-autonomous-electrochemical-test-stand-for-machine-learning-informed-electrolyte-optimization.pdf |
60c74f599abda2354df8d830 | 10.26434/chemrxiv.12894056.v1 | Engineering of Saccharomyces pastorianus Old Yellow Enzyme 1 for the Synthesis of Pharmacologically Active (S)-Profen Derivatives | <a>2-Arylpropionic acid </a><a>derivatives</a>, such as ibuprofen, constitute
an important group of non-steroidal anti-inflammatory drugs (NSAIDs). Biocatalytic
asymmetric reduction of<a> 2-arylacrylic acid</a> derivatives by ene reductases (EREDs) is a
valuable approach for synthesis of these derivatives. However, previous bioreduction
of <a>2-arylacrylic acid derivatives</a> by either ERED wild-types
or variants resulted solely in nonpharmacological (<i>R</i>)-enantiomers as the products. <a></a><a>Here,
</a>we present the engineering
of <i>Saccharomyces pastorianus</i> old yellow
enzyme 1 (OYE1) into (<i>S</i>)-stereoselective
enzymes, which afford pharmacologically active (<i>S</i>)-profen derivatives. By structural comparison of substrate
recognition in related EREDs and analysis of non-covalent contacts in the pro-<i>S</i> model
of OYE1, the key residues of OYE1 that switch its stereoselectivity
to an (<i>S</i>)-stereopreference were
identified. Systematic site-directed mutagenesis screening at these positions successfully
provided the (<i>S</i>)-stereoselective OYE1
variants, which catalyzed stereoselective bioreduction of various profen
precursors to afford pharmacologically active (<i>S</i>)-derivatives including (<i>S</i>)-ibuprofen
and (<i>S</i>)-naproxen methyl esters with
up to >99% <i>ee</i> values. <a>Moreover, the key
residues and mutation strategy obtained from OYE1 </a>could be further
transferred to OYE 2.6 (from <i>Pichia
stipitis</i>) and KnOYE1 (from <i>Kazachstania
naganishii</i>) to create the (<i>S</i>)-stereoselective
EREDs. Our results may
provide a generalizable strategy for stereocontrol of OYEs and set the basis
for biocatalytic production of (<i>S</i>)-profens. | Guigao Liu; Shang Li; Qinghua Shi; Hengyu Li; Jiyang Guo; Jingping Ouyang; Xian Jia; Lihan Zhang; Song You; Bin Qin | Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f599abda2354df8d830/original/engineering-of-saccharomyces-pastorianus-old-yellow-enzyme-1-for-the-synthesis-of-pharmacologically-active-s-profen-derivatives.pdf |
60c74902f96a0046ab28717e | 10.26434/chemrxiv.12009582.v1 | Homology Modeling of TMPRSS2 Yields Candidate Drugs That May Inhibit Entry of SARS-CoV-2 into Human Cells | The most rapid path to discovering treatment options for the novel coronavirus SARS-CoV-2 is to find existing medications that are active against the virus. We have focused on identifying repurposing candidates for the transmembrane serine protease family member II (TMPRSS2), which is critical for entry of coronaviruses into cells. Using known 3D structures of close homologs, we created seven homology models. We also identified a set of serine protease inhibitor drugs, generated several conformations of each, and docked them into our models. We used three known chemical (non-drug) inhibitors and one validated inhibitor of TMPRSS2 in MERS as benchmark compounds and found six compounds with predicted high binding affinity in the range of the known inhibitors. We also showed that a previously published weak inhibitor, Camostat, had a significantly lower binding score than our six compounds. All six compounds are anticoagulants with significant and potentially dangerous clinical effects and side effects. Nonetheless, if these compounds significantly inhibit SARS-CoV-2 infection, they could represent a potentially useful clinical tool. | Stefano Rensi; Russ B Altman; Tianyun Liu; Yu-Chen Lo; Greg McInnes; Alex Derry; Allison Keys | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74902f96a0046ab28717e/original/homology-modeling-of-tmprss2-yields-candidate-drugs-that-may-inhibit-entry-of-sars-co-v-2-into-human-cells.pdf |
60c7585d842e6596c9db4838 | 10.26434/chemrxiv.14535930.v1 | Self-sustained Marangoni Flows Driven by Chemical Reactions | Out-of-equilibrium chemical systems, comprising
reaction networks and molecular self-assembly pathways, rely on the delivery of
reagents. Rather than via external flow, diffusion or convection, we aim at
self-sustained reagent delivery. Therefore, we explore how the coupling of
Marangoni flow with chemical reactions can generate self-sustained flows,
driven by said chemical reactions, and – in turn – sustained by the delivery of
reagents for this reaction. We combine a photoacid generator with a
pH-responsive surfactant, such that local UV exposure decreases the pH,
increases the surface tension and triggers the emergence of a Marangoni flow.
We study the impact of reagent concentrations and identify threshold conditions
at which flow can emerge. Surprisingly, we unraveled an antagonistic influence
of the reagents on key features of the flow such as interfacial velocity and
duration, and rationalize these findings via a kinetic model. Our study
displays the potential of reaction-driven flow to establish autonomous control
in fuel delivery of out-of-equilibrium systems. | Anne-Déborah C. Nguindjel; Peter A. Korevaar | Surfactants; Interfaces; Photochemistry (Physical Chem.); Self-Assembly; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7585d842e6596c9db4838/original/self-sustained-marangoni-flows-driven-by-chemical-reactions.pdf |
6229c4a657a9d2ce207a3a33 | 10.26434/chemrxiv-2022-kbglv | Calibrating catalytic DNA nanostructures for site-selective protein modification | Many biomedical fields rely on proteins that are selectively modified with novel chemical entities. These are often attached using reactive or catalytic moieties, but the position where these moieties are attached is often poorly controlled. In this work, we assess how catalyst position affects the efficiency and selectivity of protein modification. For this, we anchored a template DNA strand to the active site of three different proteins, which were subsequently hybridized to DNA strands that contained catalysts at different positions. We found that catalysts operating via a covalently bound reactant intermediate show a strong correlation between their distance to the protein surface and their efficiency and that the site-selectivity of the modification is affected by the position of the catalyst. Our results are rationalized using computational simulations, showing that one-point anchoring of the DNA construct leads to notable differences in the site of modification. | Jordi Keijzer; Han Zuilhof; HB Albada | Organic Chemistry; Catalysis; Bioorganic Chemistry; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229c4a657a9d2ce207a3a33/original/calibrating-catalytic-dna-nanostructures-for-site-selective-protein-modification.pdf |
6543524bc573f893f1a61575 | 10.26434/chemrxiv-2023-tg83z | Micro-Solvation of Propofol in Propylene Glycol-Water Binary Mixtures: Molecular Dynamics Simulation Studies | The water micro-structure around propofol plays a crucial role in controlling their solubility in the binary mixture. The unusual nature of such water micro-structure can influence both translational and reorientational dynamics, as well as the water hydrogen bond network near propofol. We have carried out the all atom molecular dynamics (MD) simulations of five different compositions of propylene glycol (PG): water binary mixture containing propofol (PFL) molecules to investigate the differential behavior of water micro-solvation shells around propofol, which is likely to control the propofol solubility. It is evident from the simulation snapshots for various composition that the PG at high molecular ration favors the water cluster and extended chainlike net- work that percolates within the PG matrix, where the propofol is in the disperse state. We estimated the radial distribution function indicates higher ordered water micro- structure around propofol for high PG content, as compared to the lower PG content 1in the PG:Water mixture. So, the hydrophilic propylene glycol regulates the stability of water micro-network around propofol and their solubility in the binary mixture. We observed the translational and rotational mobility of water belonging to the propofol micro-solvation shell is hindered for high propylene glycol content, and relaxed towards the low propylene glycol molecular ration in the PG:Water mixture. It has been noticed that the structural relaxation of the hydrogen bond formed between the propofol and the water molecules present in the propofol micro-solvation shell for all five compositions, is found slower for high PG content, and becomes faster on the way to low PG content in the mixture. Simultaneously, we calculated the intermittent residence time correlation function of the water molecules belonging to the micro-solvation shell around the propofol for five different compositions, and found a faster short time decay followed up with a long time components. Again, the origin of such long time decay primarily from the structural relaxation of the micro-solvation shell around the propofol, where the high propylene glycol content shows the slower structural relaxation that turns faster as the propylene glycol content approaches to the other end of the compositions. So, our studies showed that the slower structural relaxation of the micro-solvation shell around propofol for high propylene glycol molecular ration in the PG:Water mixture, correlate well with the extensive ordering of water micro-structure and restricted water mobility, facilitates the dissolution process of propofol in the binary mixture. | ANUPAMA SHARMA; Vishal Kumar; Sudip Chakraborty | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6543524bc573f893f1a61575/original/micro-solvation-of-propofol-in-propylene-glycol-water-binary-mixtures-molecular-dynamics-simulation-studies.pdf |
6195365858bc4b945c96bf26 | 10.26434/chemrxiv-2021-zpz3b | Forced unfolding of protein-inspired single-chain random heteropolymers | Synthetic random heteropolymers (RHPs) with high chemical heterogeneity can self-assemble into single-chain nanoparticles that exhibit features reminiscent of natural proteins, such as topological polymorphism. Using all-atom molecular dynamics simulations, this work investigates the structure and single-chain mechanical unfolding of a library of four-component RHPs in water, studying the effects of sequence, composition, configuration, and molecular weight. Results show that compactified RHPs can have highly dynamic unfolding behaviors which are dominated by complex side-chain interactions and prove markedly different from their homopolymer counterparts. For a given sequence and conformation, an RHP’s backbone topology can strongly impact its unfolding response, hinting at the importance of topological design in the nanoscale mechanics of heteropolymers. In addition, we identify enthalpically-driven reconfiguration upon unfolding, observing a solvent-shielding protection mechanism similar to protein stabilization by PEGylation. This work provides the first computational evidence for the force-induced unfolding of protein-inspired multicomponent heteropolymers. | Zexiang Han; Shayna Hilburg; Alfredo Alexander-Katz | Polymer Science; Polymer chains; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6195365858bc4b945c96bf26/original/forced-unfolding-of-protein-inspired-single-chain-random-heteropolymers.pdf |
66ca7e1cf3f4b05290096556 | 10.26434/chemrxiv-2024-vqn0q-v3 | Protocol for Evaluating Anion Exchange Membranes for Nonaqueous Redox Flow Batteries | Nonaqueous redox flow batteries (NARFBs) often suffer from reduced battery lifetime and decreased coulombic effi-ciency due to crossover of the redox-active species through the membrane. One method to mitigate this undesired crossover is to judiciously choose a membrane based on several criteria: swelling and structural integrity, size and charge(s) of redox active species, and ionic conductivity. Most research to date has focused on reducing crossover by synthesizing modified redox-active molecules and/or new membranes. However, no standard protocol exists to com-pare membranes and a comprehensive study comparing membranes has yet to be done. To address both these limita-tions, we evaluate herein 26 commercial anion exchange membranes (AEMs) to assess their compatibility with com-mon nonaqueous solvents and their resistance to crossover by using neutral and cationic redox-active molecules. Ul-timately, we found that all the evaluated AEMs perform poorly in organic solvents due to uncontrolled swelling, low ionic conductivity, and/or high crossover rates. We believe that this method, and the generated data, will be useful to evaluate and compare the performance of all anion exchange membranes—commercial and newly synthesized—and should be implemented as a standard protocol for all future work. | Jessica Tami; MD Motiur Mazumder; Grace Cook; Shelley Minteer; Anne McNeil | Materials Science; Polymer Science; Energy; Polyelectrolytes - Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ca7e1cf3f4b05290096556/original/protocol-for-evaluating-anion-exchange-membranes-for-nonaqueous-redox-flow-batteries.pdf |
65cfe909e9ebbb4db987e305 | 10.26434/chemrxiv-2024-gtmx2 | Impact of Sr-Containing Secondary Phases on Oxide Conductivity in Solid-Oxide Electrolyzer Cells | Solid-oxide electrolyzer cells (SOECs) based on yttria-stabilized zirconia (YSZ) oxide electrolytes are devices capable of producing hydrogen with excess thermal energy. However, beginning with initial materials sintering and extending through electrochemical aging, Sr diffusion within the Gd-doped CeO2 (GDC) barrier layer has been observed to lead to the formation of unwanted secondary phases such as SrO and SrZrO3. To establish the impact of these phases on SOEC performance, we perform firstprinciples calculations to determine secondary phase bulk oxide conductivities and compared them to that of the YSZ electrolyte. We find that SrO has a low conductivity arising from poor mobility and a low concentration of oxygen vacancies (V_O^2+), and its presence in SOECs should therefore be avoided as much as possible. SrZrO3 also has a lower oxide conductivity than YSZ; however, this discrepancy is primarily due to lower V_O^2+ concentrations, not V_O^2+ mobility. We find Y-doping to be a viable strategy to increase V_O^2+ concentrations in SrZrO3, with 16% substitution of Y on the Zr site leading to an ionic conductivity on par with that of YSZ. Energy dispersive x-ray spectroscopy obtained using scanning transmission electron microscropy on cross-sections of SOECs indicates that Y is the most common minority element present in SrZrO3 forming near the GDC—YSZ interface. Thus, we expect SrZrO3 to be rich in V_O^2+ and not to hinder long-term device performance. These results from our combined computational–experimental analysis can inform future materials engineering strategies designed to limit the detrimental effects of Sr-induced secondary phase formation on SOEC performance. | Andrew Rowberg; Heather Slomski; Namhoon Kim; Nicholas Strange; Brian Gorman; Sarah Shulda; David Ginley; Kyoung Kweon; Brandon Wood | Theoretical and Computational Chemistry; Materials Science; Energy; Fuels - Materials; Computational Chemistry and Modeling; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cfe909e9ebbb4db987e305/original/impact-of-sr-containing-secondary-phases-on-oxide-conductivity-in-solid-oxide-electrolyzer-cells.pdf |
61bb909ca53f1b9ee09e4658 | 10.26434/chemrxiv-2021-r590w | Site-selective Amide Functionalization by Catalytic Azoline Engrafting | Amide activation is a challenging transformation due to the stabilizing effect of the amide group. While enzymes can be considered as prototypical systems that have evolved to achieve high selectivity and specificity, small-molecule catalysts that functionalize the amide group may accommodate a much larger selection of substrates but currently re-main scarce. Here, by combining the desired features from both catalytic regimes we designed an artificial cyclodehy-dratase, a catalytic system for site-selective modification of peptides and natural products by engrafting heterocyclic into their scaffolds. The catalytic system features molybdenum(VI) center that was decorated with a sterically congest-ed tripod ligand. The optimized catalyst can introduce azolines into small molecules, natural products, and oligopeptides with high efficiency and minimal waste. We further demonstrate the utility of the new protocol in direct func-tionalization of a single amide group in the presence of up to seven other chemically similar positions, and direct conversion into amines and thioamides. This new mechanistic paradigm may address an unmet need for a general method for selective and sustainable functionalization of peptides and natural products. | Wyatt Powell; Garrett Evenson; Maciej Walczak | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Physical Organic Chemistry; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2021-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bb909ca53f1b9ee09e4658/original/site-selective-amide-functionalization-by-catalytic-azoline-engrafting.pdf |
66b1c75301103d79c5dc6df6 | 10.26434/chemrxiv-2024-shm27 | Sensitivity analysis of kinetic, thermodynamic, and transport parameters in HMX (1,3,5,7- tetranitro-1,3,5,7-tetrazocane) combustion modeling | Chemical kinetic mechanisms are crucial for modeling the combustion processes of solid propellants, but the specific impacts of these mechanism’s parameters on combustion have not been fully assessed. This study conducted a comprehensive sensitivity analysis on kinetics, thermodynamics, and transport parameters affecting solid propellant mechanisms, exemplified with HMX as a case study. A onedimensional steady-state numerical model incorporating gas and liquid phase mechanisms of HMX was developed and validated against experimental data. This model enables a thorough sensitivity analysis to evaluate the influence of various parameters, including the reaction constant (k) of each elementary reaction, enthalpy of formation (hf), entropy (s), heat capacity (cp), collision diameter (σ), and potential well-depth (ε) of each species, on key combustion characteristics over a wide range of pressure. The analysis revealed that gas kinetics predominantly govern the HMX combustion compared to the liquid kinetics, particularly at high pressures. Notably, the decomposition reactions of H2CNNO2 and N2O in the gas phase were identified as highly sensitive reactions that control the r and the pressure exponent of HMX. By calculating the normalized sensitivity coefficients of all parameters, the cp values of small gaseous molecules were found to be the most significant factors affecting combustion, indicating a role played by the thermodynamic properties of small species. This research could enhance our understanding of HMX combustion mechanisms and underscore critical areas for future development and refinement of detailed kinetic mechanisms of solid propellants. | Jie-Yao Lyu; Qiren Zhu; Geng Xu; Fangmian Dong; Xin Wang; Song He; Xinyi Zhou; Yichen Zong; Markus Kraft; Yang Li; Wenming Yang | Theoretical and Computational Chemistry; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b1c75301103d79c5dc6df6/original/sensitivity-analysis-of-kinetic-thermodynamic-and-transport-parameters-in-hmx-1-3-5-7-tetranitro-1-3-5-7-tetrazocane-combustion-modeling.pdf |
6710455951558a15ef4aade2 | 10.26434/chemrxiv-2024-7ssm5-v2 | Ion Mobility-Assisted Free Radical Initiated Peptide Sequencing | Free radical-initiated peptide sequencing (FRIPS) is a tandem mass spectrometry technique (MS/MS) that enables radical-based dissociation on instruments only capable of collisional activation. In FRIPS, peptides are chemically-derivatized with a compound that undergoes homolytic cleavage and generates radicals upon collisional activation. These radicals then propagate through the peptide backbone enabling the sequencing of peptide ions. This MS/MS technique has shown promise in sequencing post-translationally modified peptides, but it is typically performed in an MS3 workflow and single-step MS/MS approaches result in the generation of both collisional- and radical-driven dissociation products and highly complex spectra. Recently, our group developed a method to dissociate peptide ions prior to ion mobility analysis within a trapped-ion mobility spectrometry (TIMS) device. In this work, we examine if this “CIDtims” technique can initiate the homolytic cleavage of the FRIPS precursor. We then examine if the resultant ion mobility separation results in additional assignments of product ions and improved sequence coverage. We demonstrate that activation within the TIMS device does indeed promote robust radical initiation and fragmentation of peptide cations and that the generated product ions are mobility separated enabling facile assignment and increased sequence coverage. | Kemi Osho; Keshari Kunwor; Nicholas Borotto | Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710455951558a15ef4aade2/original/ion-mobility-assisted-free-radical-initiated-peptide-sequencing.pdf |
64d375a94a3f7d0c0ddfc9d6 | 10.26434/chemrxiv-2023-g8435 | The nanoscale ordering of cellulose in a hierarchically structured hybrid material revealed using scanning electron diffraction | Cellulose, being a renewable and abundant biopolymer, has garnered significant attention for its unique properties and potential applications in hybrid materials. Understanding the hierarchical arrangement of cellulose nanofibers is crucial for developing cellulose-based materials with enhanced mechanical properties. In this study, we present the use of Scanning Electron Diffraction (SED) to map the nanoscale orientation of cellulose fibers in a bio-composite material with a preserved wood cell structure. The SED data provides insights into the ordering of cellulose and enables quantitative analysis of the fiber orientation within the composite with a resolution of ~15 nm. We observed a highly organized arrangement of cellulose fibers within the secondary cell wall, with a gradient of orientations towards the outer part of the wall. The in-plane fiber rotation was quantified, revealing a uniform orientation close to the middle lamella. Transversely sectioned material exhibited similar trends, suggesting a layered cell wall structure. Based on the SED data, we constructed a 3D model depicting the complex helical alignment of fibers throughout the cell wall. This study demonstrates the unique opportunities SED provides for characterizing the nanoscale hierarchical arrangement of cellulose nanofibers, empowering further research on a range of hybrid materials. | Mathias Nero; Hasan Ali; Yuanyuan Li; Tom Willhammar | Materials Science; Nanoscience; Composites; Fibers; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d375a94a3f7d0c0ddfc9d6/original/the-nanoscale-ordering-of-cellulose-in-a-hierarchically-structured-hybrid-material-revealed-using-scanning-electron-diffraction.pdf |
62ec4b0eadfd35eddd272954 | 10.26434/chemrxiv-2022-z4j2p-v2 | Data-driven Generation of Perturbation Networks for Relative Binding Free Energy Calculations | Relative binding free energy (RBFE) calculations are increasingly used to support the ligand optimisation problem in early-stage drug discovery. Because RBFE calculations frequently rely on alchemical perturbations between ligands in a congeneric series, practitioners are required to estimate an optimal combination of pairwise perturbations for each series. RBFE networks constitute in a collection of edges chosen such that all ligands (nodes) are included in the network, where each edge represents a pairwise RBFE calculation. As there is a vast number of possible configurations it is not trivial to select an optimal perturbation network. Current approaches rely on human intuition and rule-based expert systems for proposing RBFE perturbation networks. This work presents a data-driven alternative to rule-based approaches by using a graph siamese neural network architecture. A novel dataset, RBFE-Space, is presented as a representative and transferable training domain for RBFE machine learning research. The workflow presented in this work matches state-of-the-art programmatic RBFE network generation performance with several key benefits. The workflow provides full transferability of the network generator because RBFE-Space is open-sourced and ready to be applied to other RBFE software. Additionally, the deep learning model represents the first machine-learned predictor of perturbation reliability in RBFE calculations. | Jenke Scheen; Mark Mackey; Julien Michel | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2022-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ec4b0eadfd35eddd272954/original/data-driven-generation-of-perturbation-networks-for-relative-binding-free-energy-calculations.pdf |
61cd11b61e13ebdf8b0a2f91 | 10.26434/chemrxiv-2021-n949l | Cy-clo-tetrakis(μ-diphenylphosphido)-1,5-bis(tri-tert-butylphosphine-tetracopper(I) | Copper phosphido cluster Cu4(μ-PPh2)4(PtBu3)2 was synthesized by three synthetic methods and structurally characterized by X-ray diffraction and 1H, 31P, 13C and 31P HMBC NMR spectroscopy. Cu4(μ-PPh2)4(PtBu3)2 was also demonstrated to be a hydrophosphination pre-catalyst. | Steven Dannenberg; Rory Waterman | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Catalysis; Main Group Chemistry (Organomet.); Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2021-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61cd11b61e13ebdf8b0a2f91/original/cy-clo-tetrakis-diphenylphosphido-1-5-bis-tri-tert-butylphosphine-tetracopper-i.pdf |
60c75481ee301c7365c7af93 | 10.26434/chemrxiv.13664678.v1 | Phytochemical Analysis and Cellular Uptake Study of an Ayurvedic Formulation, Vyaghryadi Kashayam Used in the Clinical Management of COVID-19. | Repurposing of drugs is one of the ways to combat COVID-19 and Traditional Chinese
Medicine set a precedence for such an approach at the outset of the pandemic. In India, the Ministry of
AYUSH has recommended a number of formulations in clinical management of COVID-19. Vyaghryadi
Kashayam (VK) is a classical formulation indicated in the management of Vatakaphajvara (a type of
fever) which is amongst the medicines recommended for management of COVID-19. The constituents of
VK are Zingiber officinale Roscoe, Tinospora cordifolia (Thunb.) Miers and Solanum xanthocarpum
Schrad & Wendl. A chemical profile of VK was generated using HPTLC and LC-MS/MS QTOF. Out of
the 31 identified phytochemicals in VK, it was found that seven have been reported to have activity against
SARS-CoV-2 in prior docking studies. Cellular uptake studies of VK in Caco2 cells showed that all these
seven phytochemicals were absorbed by the cells. These findings provide preliminary hints about the
potential of VK in clinical management of COVID-19. Further confirmatory in-vitro studies are warranted
before large scale clinical studies are initiated. | Nandakumar G; Deepu Mohanan; Minsha MG; Rammanohar P | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75481ee301c7365c7af93/original/phytochemical-analysis-and-cellular-uptake-study-of-an-ayurvedic-formulation-vyaghryadi-kashayam-used-in-the-clinical-management-of-covid-19.pdf |
60c74aa64c8919c13cad329d | 10.26434/chemrxiv.12129201.v2 | Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease | <p></p><p>The
recent pandemic of novel corona virus (nCoV) infections (COVID19) has put the
world on serious alert. The main protease of nCov (nCov-MP) cleaves the long
polyprotein chains to release functional proteins required for replication of
the virus and thus is a potential drug target to design new chemical entities
in order to inhibit the viral replication in human cells. The current study
employs state of art computational methods to design novel molecules by linking
molecular fragments which specifically bind to different constituent sub-pockets
of the nCov-MP binding site. A huge library of 191678 fragments was screened
against the binding cavity of nCov-MP and high affinity fragments binding to
adjacent sub-pockets were tailored to generate new molecules. These newly
formed molecules were further subjected to molecular docking, ADMET property
filters and MM-GBSA binding free energy calculations to select 17 best
molecules (named as MP-In1 to Mp-In17), which showed comparable binding
affinities and interactions with the key binding site residues as the reference
ligand. The complexes of these 17 molecules and the reference molecule with
nCov-MP, were subjected to molecular dynamics simulations, which assessed the
stabilities of their binding with nCov-MP. Fifteen molecules were found to form
stable complexes with nCov-MP. These novel chemical entities designed
specifically according to the pharmacophoric requirements of nCov-MP binding
pockets showed good synthetic feasibility and returned no exact match when
searched against chemical databases. Considering their interactions, binding
efficiencies and novel chemotypes, they can be further evaluated as potential
starting points for nCov drug discovery.
</p><br /><p></p> | Chinmayee Choudhury | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa64c8919c13cad329d/original/fragment-tailoring-strategy-to-design-novel-chemical-entities-as-potential-binders-of-novel-corona-virus-main-protease.pdf |
62e5f40d5be04101fca2f7d4 | 10.26434/chemrxiv-2022-ttwkd | Amplitude Reordering Accelerates the Adaptive Variational Quantum Eigensolver Algorithms
| The variational quantum eigensolver (VQE) algorithm can simulate the chemical systems such as molecules in the noisy intermediate-scale quantum devices and shows promising applications in quantum chemistry simulations. The accuracy and computational cost of the VQE simulations are determined by the underlying Ansätze.
Therefore, the most important issue is to generate a compact and accurate Ansätze which requires a shallower parametric quantum circuit and can achieve an acceptable accuracy. The newly developed adaptive algorithms (AAs) such as the adaptive derivative-assembled pseudo-Trotter VQE (ADAPT-VQE) can solve this issue via generating compact and accurate Ansätze. However, these AAs show very low computational efficiency because they require a large number of additional measurements. Here we propose an amplitude reordering (AR) strategy to accelerate the promising but expensive AAs by adding operators in a "batched" fashion in a way that their order is still quasi-optimal. We first introduce the AR method into ADAPT-VQE and build the AR-ADAPT-VQE algorithm. We then endow the energy-sorting VQE (ES-VQE) algorithm with the adaptive feature, and introduce the AR into AES-VQE to form the AR-AES-VQE algorithm. To demonstrate the performance of these algorithms, we calculate the dissociation curves of three small molecules, LiH, linear BeH2, and linear H6, by using (AR-)ADAPT-VQE and (AR-)AES-VQE algorithms. It is found that all the AR-equipped AAs (AR-AAs) can significantly reduce the number of iterations and subsequently accelerate the calculations with a speedup of up to more than ten times without the obvious loss of the accuracy. The final Ansätze generated by the AR-AAs not only avoids extra circuit depth but also maintains the computational accuracy, sometimes the AR-AAs even outperforms their original counterparts. | Zhihao Lan; WanZhen Liang | Theoretical and Computational Chemistry; Quantum Computing | CC BY 4.0 | CHEMRXIV | 2022-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e5f40d5be04101fca2f7d4/original/amplitude-reordering-accelerates-the-adaptive-variational-quantum-eigensolver-algorithms.pdf |
67989a7b6dde43c908b03f06 | 10.26434/chemrxiv-2025-h92dd | On-the-fly synthesis of freestanding spin-crossover architectures with tunable magnetic properties | Spin-crossover (SCO) molecular-based switches displaying magnetic bistability have shown promise across a range of applications since their discovery, including sensors, memory storage devices, actuators, or displays. Yet, limited processability remains a substantial barrier to their real-world implementation. Efforts to overcome this limitation by integrating SCO materials into polymer matrices have often been constrained by complex, costly, and time-consuming multi-step methods, which tend to produce inhomogeneous particle distributions within the matrix. Herein, we demonstrate how three-dimensional (3D) flow-focusing chemistry provides unprecedented control for the direct fabrication of SCO composite materials, effectively addressing key challenges in processability, scalability, and cost. By using a continuous 3D coaxial flow-focusing microfluidic device, we simultaneously synthesize [Fe(Htrz)2(trz)](BF4) and achieve its homogeneous incorporation into alginate fibers in a seamless continuous manner. The versatility of the microfluidic device allows for precise manipulation of the reaction-diffusion (RD) zone, resulting in SCO composite fibers with tunable physicochemical and magnetic properties. Additionally, we demonstrate the ability to isolate these fibers as freestanding architectures and highlight the potential for printing them with defined shapes. Finally, we show that the 3D control of the RD zone granted by continuous flow microfluidic devices offers precise spatiotemporal control over the distribution of SCO complexes within the fibers, effectively encoding SCO materials into them. SCO-encoded fibers can seamlessly combine adaptability and functionality, offering innovative solutions for application-specific customization. | Anh Tuan Ngo; David Aguilà; João Pedro Vale; Semih Sevim; Michele Mattera; Ramón Pons; Guillem Aromí; Bumjin Jang; Salvador Pané; Tiago Sotto Mayor; Mario Palacios-Corella; Josep Puigmartí-Luis | Materials Science; Nanoscience; Fibers; Magnetic Materials; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67989a7b6dde43c908b03f06/original/on-the-fly-synthesis-of-freestanding-spin-crossover-architectures-with-tunable-magnetic-properties.pdf |
6345662d4165cf40f3a1c948 | 10.26434/chemrxiv-2022-vz44z-v3 | Template-free synthesis of mesoporous and amorphous transition metal phosphate materials | We present how mesoporosity can be engineered in transition metal phosphate (TMPs) materials in a template-free manner. The method involves a transformation of a precursor metal phosphate phase, M-struvite (NH4MPO4·6H2O, M = Mg2+, Ni2+, Co2+, Nix2+Co1-x2+), and it relies on the thermal decomposition of crystalline M-struvite precursors to an amorphous and simultaneously mesoporous phase, which forms while degassing of NH3 and H2O from crystals. The temporal evolution of mesoporous frameworks and the response of the metal coordination environment were followed with in-situ and ex-situ scattering and diffraction, as well as X -ray spectroscopy. Despite sharing the same precursor struvite structure, different amorphous and mesoporous structures were obtained. We highlight the systematic differences in absolute surface area, pore shape, pore size, and phase transitions depending on a metal cation present in the analogous M-struvites. The amorphous structures of thermally decomposed Mg-, Ni- and NixCo1-x-struvites exhibit high surface areas and pore volumes (240 m²g-1 and 0.32 cm-3 g-1 for Mg and 90 m²g-1 and 0.13 cm-3 g-1 for Ni). We propose that the low-cost, environmentally friendly M-struvites could be obtained as recycling products from industrial and agricultural wastewaters. These waste products could be then upcycled into mesoporous TMPs through a simple thermal treatment for further applications, for instance, in in (electro)catalysis.
| Stephanos Karafiludis; Ana Guilherme Buzanich; Christian Heinekamp; Annett Zimathies; Glen Smales; Vasile-Dan Hodoroaba; Johan ten Elshof; Franziska Emmerling; Tomasz Stawski | Physical Chemistry; Materials Science; Materials Processing; Nanostructured Materials - Materials; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6345662d4165cf40f3a1c948/original/template-free-synthesis-of-mesoporous-and-amorphous-transition-metal-phosphate-materials.pdf |
64a88adb6e1c4c986b00a3af | 10.26434/chemrxiv-2022-tfdn8-v2 | Measuring Tryptophan Dynamics Using Fast Scan Cyclic Voltammetry at Carbon Fiber Microelectrodes with Improved Sensitivity and Selectivity | Despite the fact that tryptophan is an essential amino acid that humans typically obtain through diet, there are several interesting tryptophan dynamics at play in the body. Quantifying and understanding these dynamics are crucial in studies of depression, autism spectrum disorder, and other disorders that involve neurotransmitters directly synthesized from tryptophan. Here we detail the optimization of waveform parameters in fast scan cyclic voltammetry at carbon fiber microelectrodes to yield four-fold higher sensitivity and six-fold higher selectivity compared to previously reported methods. We demonstrate the utility of our method in measuring tryptophan dynamics in two cell model systems. | Isabella Schapira; Maggie O'Neill; Lillian Russo-Savage; Terdha Narla; Kathryn Laprade; James Stafford; Yangguang Ou | Analytical Chemistry; Electrochemical Analysis | CC BY 4.0 | CHEMRXIV | 2023-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a88adb6e1c4c986b00a3af/original/measuring-tryptophan-dynamics-using-fast-scan-cyclic-voltammetry-at-carbon-fiber-microelectrodes-with-improved-sensitivity-and-selectivity.pdf |
60c755bf842e65adc6db4393 | 10.26434/chemrxiv.14153819.v1 | Efficient Exploration of Chemical Space with Docking and Deep-Learning | With the advent of make-on-demand commercial libraries, the number of purchasable compounds available for virtual screening and assay has grown explosively in recent years, with several libraries eclipsing one billion compounds. Today’s screening libraries are larger and more diverse, enabling discovery of more potent hit compounds and unlocking new areas of chemical space, represented by new core scaffolds. Applying physics-based in-silico screening methods in an exhaustive manner, where every molecule in the library must be enumerated and evaluated independently, is increasingly cost-prohibitive. Here, we introduce a protocol for machine learning-enhanced molecular docking based on active learning to dramatically increase throughput over traditional docking. We leverage a novel selection protocol that strikes a balance between two objectives: (1) Identifying the best scoring compounds and (2) exploring a large region of chemical space, demonstrating superior performance compared to a purely greedy approach. Together with automated redocking of the top compounds, this method captures nearly all the high scoring scaffolds in the library found by exhaustive docking. This protocol is applied to our recent virtual screening campaigns against the D4 and AMPC targets that produced dozens of highly potent, novel inhibitors, and a blinded test against the MT1 target. Our protocol recovers more than 80% of the experimentally confirmed hits with a 14-fold reduction in compute cost, and more than 90% of the hit scaffolds in the top 5% of model predictions, preserving the diversity of the experimentally confirmed hit compounds. | Ying Yang; Kun Yao; Matthew P. Repasky; Karl Leswing; Robert Abel; Brian Shoichet; Steven Jerome | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Pharmaceutical Industry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755bf842e65adc6db4393/original/efficient-exploration-of-chemical-space-with-docking-and-deep-learning.pdf |
66f1b82a51558a15efe7f841 | 10.26434/chemrxiv-2024-9wc7v | Uranyl Fluorescence in Acidic Solution: Quenching Effects by Tetramethylammonium (TMA+) | The quenching of uranyl luminescence by various cation species was studied in aqueous media at low pH. Solutions with different nitrate salts, held at constant uranyl nitrate, nitric acid, and ion concentration, were tested to examine the quenching effects of the cations from the nitrate salts. Alkali metal (Li+, Na+, Rb+) and quaternary ammonium cations (NH4+, (CH3)4N+ (TMA+), (C2H5)4N+ (TEA+) were investigated. Solutions containing TMA+ reduced the lifetime of uranyl fluorescence significantly more than the other cations. Uranyl emission spectra also showed that TMA+ increased the complex formation between uranyl and nitrate ions. Fluorescence decay lifetime measurements for most solutions yielded values between 1.4–1.9 µs at 20 C, while 1.8 M TMA+ reduced the lifetime of uranyl fluorescence to 0.6 µs. Decay rate versus concentration data (Stern-Volmer plots) indicated a dynamic quenching process with increasing fluorescence decay rates at higher cation concentrations for Li+, TMA+, and TEA+. The temperature dependencies of the decay rates and the kinetics in D2O were also examined. | Thomas Persinger; Michael Heaven; Richard Wilson | Physical Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f1b82a51558a15efe7f841/original/uranyl-fluorescence-in-acidic-solution-quenching-effects-by-tetramethylammonium-tma.pdf |
641200c2dab08ad68f2b2064 | 10.26434/chemrxiv-2023-w9dr8 | Ab Initio-Based Metric for Predicting the Protectiveness of Surface Films in Aqueous Media | Materials can passivate by forming surface films when placed in aqueous media. However, these films may or may not be stable, and their stability can be predicted by a metric called the Pilling-Bedworth Ratio (PBR). In this article, we extend PBR to predict passivation protectiveness of multi-component materials. We then evaluate this new PBR (ePBR)'s effectiveness by comparing its predictions against experimental studies of 21 multi-element materials of diverse chemistries, with agreement for 17 of the materials. Finally, we encode the methodology to compute ePBR in a web-application to predict the protectiveness of 140,000+ materials in the Materials Project database. | Rachel Gorelik; Arunima Singh | Theoretical and Computational Chemistry; Materials Science; Energy; Alloys; Ceramics; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641200c2dab08ad68f2b2064/original/ab-initio-based-metric-for-predicting-the-protectiveness-of-surface-films-in-aqueous-media.pdf |
643fa96083fa35f8f6e4b44a | 10.26434/chemrxiv-2023-2g0d8 | Practical aspects concerning catalysis with molecularly doped metals | Ranging from silver-entrapped dyes and gold-entrapped enzymes through palladium-entrapped graphene oxide, molecularly doped metals (or metal organic alloys, MORALs) are active, stable and uniquely versatile catalysts in a number of reactions of relevance to the chemical industry. Reactions successfully catalyzed by MORALs concern both industry’s main sectors, producing bulk and fine chemicals. Though first reported in 2005, and clearly holding a great applicative potential, their use in catalysis is still surprisingly limited. This study investigates a number of practical aspects concerning molecularly doped metals as heterogeneous catalysts. | Rosaria Ciriminna; Matteo Formenti; Mario Pagliaro; Cristina Della Pina | Catalysis; Heterogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643fa96083fa35f8f6e4b44a/original/practical-aspects-concerning-catalysis-with-molecularly-doped-metals.pdf |
65bd55c3e9ebbb4db98a19bd | 10.26434/chemrxiv-2024-121k1 | Unveiling the role of termination groups in stabilizing MXenes in contact with water | MXenes are versatile 2D materials demonstrating outstanding electrochemical and physical properties, but their practical use is limited because of fast degradation in an aqueous environment. To prevent the degradation of MXenes, it is essential to understand the atomistic details of the reaction and identify active sites. In this letter, we provided a computational analysis of the degradation processes at the interface between MXene basal planes and water using enhanced sampling ab initio molecular dynamics simulations and symbolic regression analysis. Our results indicate that the reactivity of Ti sites toward water attack reaction depends on both local coordination and chemical composition of the MXene surfaces. Decreasing the work function of Ti3C2Tx surfaces and avoiding Ti sites that are loosely anchored to the subsurface (e.g., O-coordinated) can improve surface stability. The developed computational framework can be further used to investigate other possible culprits of degradation reaction, including the role of defects and edges. | Valentina Nesterova; Vladislav Korostelev; Konstantin Klyukin | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bd55c3e9ebbb4db98a19bd/original/unveiling-the-role-of-termination-groups-in-stabilizing-m-xenes-in-contact-with-water.pdf |
60c7457b337d6c5d0ae26fa4 | 10.26434/chemrxiv.10029224.v1 | A Molecular-Level Mechanism of the Biological N2 Fixation | We present a detailed molecular-level mechanism for the biological fixation of atmospheric nitrogen into ammonia. The mechanism is based on a series of electronic structure calculations and provides insight into the key question of what it is that the enzyme does to enable selective N<sub>2</sub> reduction that cannot be mimicked by simple electrochemical processes. | Vanessa Jane Bukas; Jens Kehlet Nørskov | Computational Chemistry and Modeling; Biocatalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457b337d6c5d0ae26fa4/original/a-molecular-level-mechanism-of-the-biological-n2-fixation.pdf |
64de820d694bf1540c84d805 | 10.26434/chemrxiv-2023-21rp0 | Harnessing Transaminases to Construct Azacyclic Non-Canonical Amino Acids | Non-canonical amino acids (ncAAs) are prized building blocks in the synthesis of natural products, designer peptides and drug molecules. Despite their general utility, the complex structure of these molecules still presents an enormous challenge for chemical synthesis. Here, we develop a one-pot chemoenzymatic approach for the construction of azacyclic ncAAs with multiple substitutions and various ring sizes. A promiscuous transaminase was identified to convert a wide range of diketoacids to the corresponding α-amino acids. A spontaneous cyclic imine formation was followed by a stereocontrolled chemical reduction to generate the corresponding products in one-pot with high stereoselectivity. More than twenty azacyclic ncAAs were successfully prepared with this approach. This work demonstrates the value of developing hybrid biocatalytic-chemocatalytic approaches to privileged small molecule motifs. | Tsung-Han Chao; Xiangyu Wu; Yu Fu; Licheng Yang; Hans Renata | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64de820d694bf1540c84d805/original/harnessing-transaminases-to-construct-azacyclic-non-canonical-amino-acids.pdf |
64109101b5d5dbe9e83f5a72 | 10.26434/chemrxiv-2023-444s3 | Machine learning predictions of low thermal conductivity: comparing TaVO5 and GdTaO4 | Advancements in materials discovery tend to rely disproportionately on happenstance and luck rather than employing a systematic approach. Recently, advances in computational power have allowed researchers to build computer models to predict the material properties of any chemical formula. From energy minimization techniques to machine learning based models, these algorithms have unique strengths and weaknesses. However, a computational model is only as good as its accuracy when compared to real-world measurements. In this work, we take two recommendations from a thermoelectric machine learning model, TaVO5 and GdTaO4, and test their thermoelectric properties of Seebeck coefficient, thermal conductivity, and electrical conductivity. We see that the predictions are mixed; thermal conductivities are correctly predicted, while electrical conductivities and Seebeck coefficients are not. Furthermore, we discover a possible new avenue of research of a low thermal conductivity oxide family. | Travis Allen; Jake Graser; Ramsey Issa; Taylor Sparks | Materials Science; Energy; Ceramics; Piezoelectricity and Thermoelectricity | CC BY NC 4.0 | CHEMRXIV | 2023-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64109101b5d5dbe9e83f5a72/original/machine-learning-predictions-of-low-thermal-conductivity-comparing-ta-vo5-and-gd-ta-o4.pdf |
60c74679469df49ef2f4364c | 10.26434/chemrxiv.11330561.v1 | A Tetranuclear Cobalt (II) Phosphate Possessing a D4R Core: An Efficient Water Oxidation Catalyst | <p>The
reaction of Co(OAc)<sub>2</sub>·4H<sub>2</sub>O
with the sterically hindered phosphate ester, LH<sub>2</sub>, afforded
the tetranuclear complex, [Co<sup>II</sup>(L)(CH<sub>3</sub>CN)]<sub>4</sub>∙5CH<sub>3</sub>CN
(<b>1</b>) [LH<sub>2</sub> = <a>2,6</a>‐(diphenylmethyl)‐4‐isopropyl‐phenyl phosphate]. The molecular structure of <b>1</b> reveals
that it is a tetranuclear assembly where the Co(II) centers are present in the
alternate corners of a cube. The four Co(II) centers are held together by four
di-anionic [L]<sup>2-</sup> ligands. The fourth coordination site on Co(II) is
taken by an acetonitrile ligand. Changing
the Co(II) precursor from Co(OAc)<sub>2</sub>·4H<sub>2</sub>O
to Co(NO<sub>3</sub>)<sub>2</sub>.6H<sub>2</sub>O
afforded the mononuclear complex [Co<sup>II</sup>(LH)<sub>2</sub>(CH<sub>3</sub>CN)<sub>2</sub>(MeOH)<sub>2</sub>](MeOH)<sub>2
</sub>(<b>2). </b>In<b> 2, </b>the Co(II) is surrounded by two monoanionic
[LH]<sup>‒</sup> ligands, and a pair of methanol and acetonitrile solvents in a
six-coordinate arrangement. <b>1</b> has been
found to be an efficient catalyst for the electrochemical water oxidation under
high basic conditions while the mononuclear analogue, <b>2</b>, does not respond towards
electrochemical water oxidation. The
tetranuclear catalyst has excellent electrochemcial stability and longevity, as
established by the chronoamperometry and >1000 cycles durability test in
high alkaline conditions. Excellent current densities of 1 and 10 mAcm<sup>‒2</sup>
were achieved with the overpotential of 354 and 452 mV respectively. The turnover
frequency of this catalyst was calculated as 5.23 s<sup>−1 </sup>with
excellent faradaic efficiency of 97%, indicating the selective oxygen evolution
(OER) process happening with the aid of this catalyst. A mechanistic insight in
to the higher activity of complex <b>1</b>
towards OER compared to complex <b>2 </b>is
also provided with the help of density functional theory based calculations.</p> | Atanu Dey; Virendra Kumar; Shubhadeep Pal; Anku Guha; Sumit Bawari; Tharangattu Narayanan; Vadapalli Chandrasekhar | Base Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74679469df49ef2f4364c/original/a-tetranuclear-cobalt-ii-phosphate-possessing-a-d4r-core-an-efficient-water-oxidation-catalyst.pdf |
60c7591bbb8c1af3363dcb5c | 10.26434/chemrxiv.14650302.v1 | Stacking Gaussian Processes to Improve pKa Predictions in the SAMPL7 Challenge | Accurate predictions of acid dissociation constants are essential to rational molecular design in the pharmaceutical industry and elsewhere. There has been much interest in developing new machine learning methods that can produce fast and accurate pK<sub>a</sub> predictions for arbitrary species, as well as estimates of prediction uncertainty. Previously, as part of the SAMPL6 community-wide blind challenge, Bannan et al. approached the problem of predicting pK<sub>a</sub>s by using a Gaussian process regression to predict microscopic pK<sub>a</sub>s, from which macroscopic pK<sub>a</sub> values can be analytically computed. While this method can make reasonably quick and accurate predictions using a small training set, accuracy was limited by the lack of a sufficiently broad range of chemical space in the training set (e.g., the inclusion of polyprotic acids). Here, to address this issue, we construct a deep Gaussian Process (GP) model that can include more features without invoking the curse of dimensionality. We trained both a standard GP and a deep GP model using a database of approximately 3500 small molecules curated from public sources, filtered by similarity to targets. We tested the model on both the SAMPL6 and more recent SAMPL7 challenge, which introduced a similar lack of ionizable sites and/or environments found between the test set and the previous training set. The results show that while the deep GP model made only minor improvements over the standard GP model for SAMPL6 predictions, it made significant improvements over the standard GP model in SAMPL7 macroscopic predictions, achieving a MAE of 1.5 pK<sub>a</sub>. | Robert Raddi; Vincent Voelz | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7591bbb8c1af3363dcb5c/original/stacking-gaussian-processes-to-improve-p-ka-predictions-in-the-sampl7-challenge.pdf |
664cbb6591aefa6ce1985da2 | 10.26434/chemrxiv-2024-2zvbm | Molecular Recognition in Mechanochemistry: Insights from Solid-State NMR Spectroscopy | Molecular-recognition events are highly relevant in biology and chemistry. In the present study, we investigated such processes in the solid state under mechanochemical conditions using the formation of racemic phases upon reacting enantiopure entities as example. As test systems, a-(trifluoromethyl)lactic acid (TFLA) and the amino acids serine and alanine were used. The effects of ball-milling and resonant acoustic mixing (RAM) on the formation of racemic phases were probed by using solid-state Nuclear Magnetic Resonance (NMR) spectroscopy. In a mixer mill, a highly efficient and fast racemic phase formation occurred for both TFLA and the two amino acids. RAM led to the racemic phase for TFLA also, and this process was facilitated upon employing pre-milled enantiopure entities. In contrast, under comparable conditions RAM did not result in the formation of racemic phases for serine and alanine. | Calogero Quaranta; Igor d'Anciães Almeida Silva; Sven Moos; Ettore Bartalucci; Leeroy Hendrickx; Benjamin M. D. Fahl; Claudia Pasqualini; Francesco Puccetti; Mirijam Zobel; Carsten Bolm; Thomas Wiegand | Physical Chemistry; Organic Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664cbb6591aefa6ce1985da2/original/molecular-recognition-in-mechanochemistry-insights-from-solid-state-nmr-spectroscopy.pdf |
65f8ba4f66c13817294301d0 | 10.26434/chemrxiv-2023-qq206-v3 | Reweighting from Molecular Mechanics Force Fields to the ANI-2x Neural Network Potential | To achieve chemical accuracy in free energy calculations, it is necessary to accurately describe the system's potential energy surface and efficiently sample configurations from its Boltzmann distribution. While neural network potentials (NNPs) have shown significantly higher accuracy than classical molecular mechanics (MM) force fields, they have limited range of applicability and are significantly slower than MM potentials, often by orders of magnitude. To address this challenge, Rufa et al suggested a two-stage approach that uses a fast and established MM alchemical energy protocol, followed by reweighting the results using NNPs, known as endstate correction or indirect free energy calculation. In this study, we systematically investigate the accuracy, robustness, and efficiency of free energy calculations between a MM reference and a neural network target potential (ANI-2x) using free energy perturbation (FEP) and non-equilibrium (NEQ) switching simulation in vacuum. We investigate the influence of longer switching lengths and the impact of slow degrees of freedom on outliers in the work distribution. We compare the results to multistage equilibrium free energy calculations (MFES) for an established dataset. Our results demonstrate that free energy calculations between NNPs and MM potentials should not be performed using FEP but require NEQ switching simulations to obtain accurate free energy estimates. NEQ switching simulations between MM and NNPs are highly efficient, robust, and trivial to implement. | Sara Tkaczyk; Johannes Karwounopoulos; Andreas Schöller; H. Lee Woodcock; Thierry Langer; Stefan Boresch; Marcus Wieder | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f8ba4f66c13817294301d0/original/reweighting-from-molecular-mechanics-force-fields-to-the-ani-2x-neural-network-potential.pdf |
644bad630d87b493e36ef583 | 10.26434/chemrxiv-2023-w0p5m | Thiomethyltetrazines are Reversible Covalent Cysteine Warheads whose Dynamic Behavior can be "Switched off” via Bioorthogonal Chemistry Inside Live Cells | Electrophilic small molecules that can reversibly modify proteins are of growing interest in drug discovery. However, the ability to study reversible covalent probes in live cells can be limited by their reversible reactivity after cell lysis and in proteomic workflows, leading to scrambling and signal loss. We describe how thiomethyltetrazines function as reversible covalent warheads for cysteine modification and this dynamic labeling behavior can be "switched off” via bioorthogonal chemistry inside live cells. Simultaneously, the tetrazine serves as bioorthogonal reporter enabling the introduction of tags for fluorescent imaging or affinity purification. Thiomethyltetrazines can label isolated proteins, proteins in cellular lysates, and proteins in live cells with second-order rate constants spanning two orders of magnitude (k2 1–100 M-1s-1). Reversible modification by thiomethyltetrazines can be switched off upon the addition of trans-cyclooctene in live cells, converting the dynamic thiomethyltetrazine tag into a Diels-Alder adduct which is stable to lysis and proteomic workflows. Time-course quenching experiments were used to demonstrate temporal control over electrophilic modification. Moreover, it is shown that “locking in” the tag through Diels-Alder chemistry enables the identification of protein targets that are otherwise lost during sample processing. Three probes were further evaluated to identify unique pathways in a live-cell proteomic study. We anticipate that discovery efforts will be enabled by the trifold function of thiomethyltetrazines as electrophilic warheads, bioorthogonal reporters, and switches for “locking in” stability. | Amanda Tallon; Yingrong Xu; Graham West; Christopher am Ende; Joseph Fox | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Mass Spectrometry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644bad630d87b493e36ef583/original/thiomethyltetrazines-are-reversible-covalent-cysteine-warheads-whose-dynamic-behavior-can-be-switched-off-via-bioorthogonal-chemistry-inside-live-cells.pdf |
61de30e7db142e3b84bd6a92 | 10.26434/chemrxiv-2022-jlqbb | Acid-in-clay electrolyte for wide-temperature-range and
long-cycle proton batteries | Proton conduction underlies many important electrochemical technologies. We report a series of new proton electrolytes: acid-in-clay electrolyte termed AiCE, prepared by integrating fast proton carriers in a natural phyllosilicate clay network, that can be made into thin-film (tens of microns) fluid-impervious membranes. The chosen example systems (sepiolite-phosphoric acid) rank top among the solid proton conductors in consideration of proton conductivities (15 mS cm−1 at 25 °C, 0.023 mS cm−1 at −82 °C), the stability window (3.35 V), and reduced chemical activity. A solid-state proton battery was assembled using AiCE as the electrolyte to demonstrate the performance of these electrolytes. Benefitting from the wider electrochemical stability window, reduced corrosivity, and excellent ionic selectivity of AiCE, the two main problems (gasification and cyclability) of proton batteries have been successfully solved. This work also draws the attention of elemental cross-over in proton batteries and illustrates a simple “acid-in-clay” approach to synthesize a series of solid proton electrolytes with a superfast proton permeability, outstanding selectivity, and improved stability for many potential applications associated with protons. | Shitong Wang; Heng Jiang; Yanhao Dong; David Clarkson; He Zhu; Charles Settens; Yang Ren; Thanh Nguyen; Fei Han; Weiwei Fan; So Yeon Kim; Jianan Zhang; Weijiang Xue; Sean Sandstrom; Guiyin Xu; Emre Tekoglu; Mingda Li; Sili Deng; Qi Liu; Steven Greenbaum; Xiulei Ji; Tao Gao; Ju Li | Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61de30e7db142e3b84bd6a92/original/acid-in-clay-electrolyte-for-wide-temperature-range-and-long-cycle-proton-batteries.pdf |
60c73cc04c89195cdcad1aed | 10.26434/chemrxiv.14762478.v1 | Convergent Azaspirocyclization of Bromoarenes with N-Tosylhydrazones by a Palladium Catalyst | 1-Azaspirocyclic compounds have gained attention in chemistry and drug discovery fields. In this manuscript, the development of a Pd-catalyzed dearomative azaspirocyclization of bromoarenes bearing an aminoalkyl group with <i>N</i>-tosylhydrazones is described. The present method enables azaspirocyclization with the introduction of carbon substituents, achieving the convergent synthesis of 1-azaspirocycles. This method allowed furan, thiophene, and naphthalene cores to generate the corresponding 1-azaspirocycles. The obtained azaspirocycles from furans were further elaborated <i>via</i> an acid-catalyzed rearrangement to afford 1-azaspirocyclopentenones. | Aika Yanagimoto; Yota Uwabe; Qikun Wu; Kei Muto; Junichiro Yamaguchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc04c89195cdcad1aed/original/convergent-azaspirocyclization-of-bromoarenes-with-n-tosylhydrazones-by-a-palladium-catalyst.pdf |
63c2c3af3af973e0f5688fcc | 10.26434/chemrxiv-2023-xdqzr | Laser-Induced Nitrogen Fixation | Industrial ammonia production is currently performed at 400–500 °C and 100–200 bar with fossil–fuel–involved power and hydrogen feedstock by the Haber-Bosch method, which enabled the growth of humanity beyond previous limits but demands larger infrastructure, capital investments and causes substantial emissions of carbon dioxide. For distributed ammonia production and decarbonization of this process by exploiting renewable energy sources, alternative methods, such as the electrochemical approach or using plasma on a small–scale, have been explored. Nonetheless, they still lack yield and efficiency to be industrially relevant. Here, we demonstrate a new approach of nitrogen fixation to synthesize ammonia at ambient conditions via laser–induced multiphoton dissociation of lithium oxide. Lithium oxide is dissociated under non–equilibrium multiphoton absorption and high temperatures under focused infrared light, and the generated zero–valent metal spontaneously fixes nitrogen and forms a lithium nitride, which upon subsequent hydrolysis generates ammonia. The highest ammonia yield rate of 30.9 micromoles per second per square centimeter is achieved at 25 °C and 1.0 bar nitrogen. This is two orders of magnitude higher than state–of–the–art ammonia synthesis at ambient conditions. The focused infrared light here is produced by a commercial simple CO2 laser, serving as a demonstration of potentially solar pumped lasers for nitrogen fixation and other high excitation chemistry. We anticipate such solar-laser-involved technology will bring unprecedented opportunities to realize not only local ammonia production but also other new chemistry. | Huize Wang; Gaofeng Chen; Volker Strauss; Oleksandr Savateev; Guangtong Hai; Liangxin Ding; Haihui Wang; Markus Antonietti | Physical Chemistry; Energy; Energy Storage; Photochemistry (Physical Chem.); Physical and Chemical Processes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c2c3af3af973e0f5688fcc/original/laser-induced-nitrogen-fixation.pdf |
6729ff9bf9980725cf287396 | 10.26434/chemrxiv-2024-sjwlb-v2 | Reactions of cold argon plasmas with condensed-phase peptides and proteins for mass spectrometry imaging and structural elucidation | The analysis of macromolecules - such as proteins - pose a significant bottleneck in analytical science. We have developed surface treatment techniques utilising direct and radiofrequency current argon plasmas, able to quickly digest condensed-phase macromolecules while maintaining spatial resolution of analytes. We show here that these plasmas can be powerful tools for mass spectrometry imaging of peptides and proteins. | Dan McGill; Daniel Simon; Siva Ramadurai; Zoltan Takats | Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6729ff9bf9980725cf287396/original/reactions-of-cold-argon-plasmas-with-condensed-phase-peptides-and-proteins-for-mass-spectrometry-imaging-and-structural-elucidation.pdf |
62444d3b7ffb63714ef08f1c | 10.26434/chemrxiv-2022-744pt | Probing Thermodynamics, Kinetics and Structural Details of Multivalent Lectin-Glycan Interactions by Quantum Dot-FRET | Multivalent lectin-glycan interactions (MLGIs) are widely employed for bio- recognition and discrimination, but they are also exploited by pathogens to infect host cells. Their biophysical details (e.g. thermodynamics, kinetics, binding modes and binding site orientation) are thus highly valuable, not only for elucidating the underlying mechanisms, but also for guiding the design of multivalent therapeutics against specific MLGIs. However, these details are not readily available due to the limitations of conventional biophysical techniques in probing such complex, flexible interactions. We have recently established densely glycosylated quantum dots (glycan-QDs) as novel structural probes for MLGIs. Using a pair of important, almost identical tetrameric lectins, DC-SIGN and DC-SIGNR, as the model lectins, we have shown that glycan-QDs can not only provide quantitative binding affinities but also dissect their distinct binding modes: DC-SIGN binds simultaneously with one glycan-QD whereas DC-SIGNR inter-cross-links. Herein, we further extend the capacity of the glycan-QD probes to investigate how binding mode affects the binding thermodynamics and kinetics, and probe a structural basis of their binding nature. We show that, while both lectin-glycan-QD interactions are enthalpy driven, with similar binding enthalpy changes (~4 times that of monovalent binding measured by ITC), DC-SIGN binding pays a lesser entropy penalty than DC-SIGNR, giving rise to a stronger affinity. We also reveal that a short C-terminal segment at the flexible junction between the tetramerization domain and glycan binding domain in DC-SIGN, absent in DC-SIGNR, plays a critical role in maintaining DC-SIGN’s glycan-QD binding properties: its removal leads to an entirely different binding enthalpy and entropy profile, despite maintaining the same binding mode. Furthermore, we show that the simultaneous lectin-glycan-QD binding partners give single 2nd-order kon rates which rapidly reach saturation, whereas cross-linking partners give two distinct on-rates: a rapid initial association step, followed by a much slower secondary interaction. Together, our work have established glycan-QDs as a powerful new biophysical platform for solution-based MLGI studies which can provide a wide range of important biophysical parameters. | James Hooper; Yuanyuan Liu; Darshita Budhadev; Dejian Zhou; Yuan Guo | Physical Chemistry; Analytical Chemistry; Nanoscience; Biochemical Analysis; Biophysical Chemistry; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-03-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62444d3b7ffb63714ef08f1c/original/probing-thermodynamics-kinetics-and-structural-details-of-multivalent-lectin-glycan-interactions-by-quantum-dot-fret.pdf |
6472121dbe16ad5c57017ecf | 10.26434/chemrxiv-2023-ddv9j | A carbon-efficient bicarbonate electrolyzer | CO2 electroreduction (CO2ER) is a promising route to carbon-neutral production of various chemicals and fuels. Carbon efficiency is one of the most pressing problems for CO2ER today. While there have been studies on anion exchange membrane (AEM) electrolyzers with CO2(gas) and bipolar membrane (BPM) electrolyzers with HCO3–(aq) feedstock, both suffer from significant carbon efficiency loss. In AEM electrolyzers, this is due to carbonate anion crossover, whereas in BPM electrolyzers, the exsolution of CO2(gas) from the bicarbonate solution is the culprit. Here, we first elucidate the root cause of the low carbon efficiency of liquid bicarbonate electrolyzers with thermodynamic calculations, then achieve carbon-efficient CO2ER by adopting a near-neutral-pH cation exchange membrane (CEM) and CO2(gas) partial pressure management, with tin nanoparticle catalysts. We have converted highly concentrated bicarbonate solution to solid formate fuel with a yield (carbon efficiency) of > 96%. The device test was demonstrated at 100 mA cm–2 with a full-cell voltage of 3.1 V for over 100 h. This strategy enables full conversion of HCO3–(aq) feedstock to energy-dense solid formate fuel at ambient pressure and temperature with renewable electricity. Importantly, it can power direct formate fuel cells (DFFCs) which exhibit promising power density for seasonal energy storage. | Ju Li; Zhen Zhang; Dawei Xi; Zhichu Ren | Materials Science; Catalysis; Energy; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6472121dbe16ad5c57017ecf/original/a-carbon-efficient-bicarbonate-electrolyzer.pdf |
6153f7c5aade360d04c61d54 | 10.26434/chemrxiv-2021-nlht1 | Evidence for an N-halohistidyl Intermediate in the Catalytic Cycle of Vanadium Chloroperoxidase (VCPO) and an Artificial Enzyme derived from VCPO: A Computational Investigation | Vanadium haloperoxidases play an important catalytic role in the natural production of antibiotics which are difficult to make in the laboratory. Understanding the catalytic mechanism of these enzymes will aide in the production of artificial enzymes useful in bioengineering the synthesis of drugs and useful chemicals. However, the catalytic mechanism remains not fully understood yet. In this paper, we investigate one of the key steps of the catalytic mechanism using QM/MM. Our investigation reveals a new N-haloxy histidyl intermediate in the catalytic cycle of vanadium chloroperoxidase (VCPO). This new intermediate, in turn, yields an explanation for the known inhibition of the enzyme by substrate under acidic conditions (pH<4). Additionally, we examine the possibility of replacing V in VCPO by Nb or Ta using QM modeling. We report the new result that the Gibbs free energy barrier of several steps of the catalytic cycle are lower in the case of artificial enzymes, incorporating NbO43- or TaO43- instead of VO43-. Our results suggest that these new artificial enzymes may catalyze the oxidation of halide faster than the natural enzyme. | Gregory Anderson; Raghu Nath Behera; Ravi Gomatam | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6153f7c5aade360d04c61d54/original/evidence-for-an-n-halohistidyl-intermediate-in-the-catalytic-cycle-of-vanadium-chloroperoxidase-vcpo-and-an-artificial-enzyme-derived-from-vcpo-a-computational-investigation.pdf |
637e54681234cb05b82074ac | 10.26434/chemrxiv-2022-h697n | Synthesis, Isolation and Characterization of Two Cationic Organo-bismuth(II) Pincer Complexes Relevant in Radical Redox Chemistry | Herein, we report the synthesis, isolation and characterization of two cationic organobismuth(II) compounds bearing N,C,N pincer frameworks, which are crucial intermediates in bismuth radical processes. X-ray crystallography uncovered a monomeric Bi(II) structure, while SQUID magnetometry in combination with NMR and EPR spectroscopy provide evidence for a para-magnetic S = 1/2 state. High resolution multifrequency EPR at X, Q, and W-band enable the precise assignment of the full g- and 209Bi A-tensors. Experimental data and DFT calculations reveal both complexes are metal-centered radicals with little delocalization onto the ligands. | Xiuxiu Yang; Edward Reijerse; Nils Nöthling; Daniel SantaLucia; Markus Leutzsch; Alexander Schnegg; Josep Cornella | Physical Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Main Group Chemistry (Organomet.); Spectroscopy (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637e54681234cb05b82074ac/original/synthesis-isolation-and-characterization-of-two-cationic-organo-bismuth-ii-pincer-complexes-relevant-in-radical-redox-chemistry.pdf |
60c742af337d6c01b9e26ac2 | 10.26434/chemrxiv.8075222.v2 | Mechanosynthesis of Sydnone-Containing Coordination Complexes | <p><i>N</i>-Phenyl-4-(2-pyridinyl)
sydnone was shown to act as a four-electron donor <i>N</i>,<i>O</i>-ligand in unprecedented
coordination complexes featuring four different metallic centers (Co, Cu, Zn).
Starting from various anilines, the use of ball-mill enabled efficiently the
synthesis of <i>N</i>-arylglycines, subsequent
nitrosylation and cyclization into sydnone, and further metalation.</p> | Nicolas Petry; Thibaut Vanderbeeken; Astrid Malher; Yoan Bringer; Pascal Retailleau; Xavier Bantreil; Frédéric Lamaty | Coordination Chemistry (Organomet.); Ligand Design; Ligands (Organomet.); Main Group Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af337d6c01b9e26ac2/original/mechanosynthesis-of-sydnone-containing-coordination-complexes.pdf |
6452799227fccdb3ea6e866b | 10.26434/chemrxiv-2023-32k8h | Photophysical Properties of Sulfone-Based TADF Emitters In Relation To Their Structural Properties | In this work, Thermally Activated Delayed Fluorescence (TADF) of a series of emitters with sulfone-based acceptor moieties were studied by Density Functional Theory (DFT) methods. Sulfone derivatives were shown to be high performing TADF emitters over recent years. When discussing the TADF efficiency, various properties, such as, singlet–triplet energy gap (∆EST), spin–orbit coupling (SOC), nature of states and the hyperfine coupling (HF) stand out due to their roles in reverse intersystem crossing (RISC). Here, we mainly focused on three important structural parameters that affect the intersystem crossing (ISC) and RISC pathways and their efficiencies. These three parameters are: 1) effect of meta- and para- conjugation, 2) effect of rigid acceptor moieties and 3) effect of phenyl bridge on photophysical properties. | Aslıhan Hepguler; Pelin Ulukan; Saron Catak | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6452799227fccdb3ea6e866b/original/photophysical-properties-of-sulfone-based-tadf-emitters-in-relation-to-their-structural-properties.pdf |
679aad01fa469535b95b279a | 10.26434/chemrxiv-2025-5tk44 | 5'-Guanidino Xylofuranosyl Nucleosides as Novel Types of 5'-Functionalized Nucleosides with Therapeutic Potential | The synthesis and biological evaluation of 5′-guanidino furanosyl nucleosides comprising 6-chloropurine and uracil moieties and a 3-O-benzyl xylofuranosyl unit is presented. Their access was based on the N-glycosylation of a 5-azido 3-O-benzyl xylofuranosyl acetate donor with the silylated nucleobase and a subsequent one-pot sequential two-step protocol involving Staudinger reduction of the thus obtained 5-azido uracil and N7/N9-linked purine nucleosides followed by guanidinylation with N,N’-bis(tert-butoxycarbonyl)-N’’-triflylguanidine.
Bioactivity screening revealed the significant activities exhibited among the synthesized compounds, namely abilities to inhibit butyrylcholinesterase (BChE), a therapeutic target for the symptomatic treatment of latter stages of Alzheimer’s disease, cytotoxic activities against cancer cells, and/or neuroprotective effects.
5′-Guanidino 6-chloropurine nucleosides were shown to act as mixed-type and selective submicromolar or micromolar BChE inhibitors, from which the N9 nucleoside was the most prominent compound with inhibition constants Ki / Ki' of 0.89 μM / 2.96 μM, besides showing low cytotoxicity to FL83B hepatocytes and no significant cytotoxicity to human neuroblastoma cells (SH-SY5Y). Moreover, the N9-linked nucleoside exhibited selective cytotoxic activity to prostate cancer cells (DU-145, IC50 = 27.63 μM), while its N7 regioisomer was active against all cancer cells tested [DU-145, IC50 = 24.48 μM; colorectal adenocarcinoma (HCT-15, IC50 = 64.07 μM); and breast adenocarcinoma (MCF-7, IC50 = 43.67 μM)]. In turn, the 5'-guanidino uracil nucleoside displayed selective cytotoxicity to HCT-15 cells (IC50 = 76.02 μM) and showed also neuroprotective potential in a Parkinson’s disease SH-SY5Y cells’ damage model. The active molecules exhibited IC50 values to the affected cancer cells close or lower than those of standard drugs, and comparable or not significant neuro- and hepatotoxicity. | Nuno Manuel Xavier; Jennifer Szilagyi; Tânia Moreira; Rafael Santana Nunes; Joana Silva; Celso Celso Alves; Alice I. Martins; Rebeca Alvariño; Niels V. Heise; René Csuk | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679aad01fa469535b95b279a/original/5-guanidino-xylofuranosyl-nucleosides-as-novel-types-of-5-functionalized-nucleosides-with-therapeutic-potential.pdf |
61b05fa86927e34b3afc3735 | 10.26434/chemrxiv-2021-9gxpp | Highly Chemo-, Regio- and Stereoselective Cysteine Modification of Peptides and Proteins with Ynamides | Chemoselective modification of peptides and proteins has wide applications in chemical biology and pharmaceutical development. An efficient cysteine (Cys) precise modification protocol via rationally designed β-addition of ynamides is reported. The strong electron-withdrawing triflyl group on the nitrogen atom of ynamides plays a crucial role for controlling the chemo-, stereo- and regioselectivities of this protocol. Another substituent of the terminal ynamides offers a handle for functionality diversification. This Cys modification with ynamides proceeds efficiently in a slightly basic aqueous media (pH 8) to provide a series of Z-isomer of the corresponding conjugated products with excellent stereoselectivity (> 99%) and superior stability. All the reactive peptide side chain functional groups such as amino, carboxyl, primary amide, and hydroxyl groups, as well as the unprotected imidazole and indole rings are compatible. This method displays a broad substrates scope including linear and cyclic peptides and proteins. The potential application of this method in peptide and protein chemical biology was exemplified by Cys-bioconjugation with ynamides containing different functional molecules, including drug, fluorescent and affinity tags. In addition, this strategy is also compatible with click chemistry (performed in one pot), which remarkably extends the toolbox for further applications. The chemoselective biotinylation of ubiquitin(G47C) variant with a biotinylated ynamide, as well as the regioselective modification of Cys14 and Cys38 in bovine pancreatic trypsin inhibitor (BPTI) were accomplished under the optimized conditions and in high yield, without perturbation of disulfide bonds. | Changliu Wang; Zhenguang Zhao; Reem Ghadir; Yuqing Li; Yongli Zhao; Norman Metanis; Junfeng Zhao | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2021-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b05fa86927e34b3afc3735/original/highly-chemo-regio-and-stereoselective-cysteine-modification-of-peptides-and-proteins-with-ynamides.pdf |
67b9f8c26dde43c908014c4a | 10.26434/chemrxiv-2025-5tlrl | Predicting the stability of base-mediated C–H carboxylation adducts using data science tools | Base-mediated C–H carboxylation is a versatile pathway for utilizing carbon dioxide (CO2) as a C1 building block in organic synthesis. However, CO2 constitutes a notorious thermodynamic sink, which restricts this approach to activated or intrinsically reactive nucleophiles. To qualitatively assess the stability of CO2 adducts, we present a computational approach that integrates quantum chemistry with statistical modeling to build a predictive workflow. The target property is the CO2 affinity, specifically the negative Gibbs free reaction energy. This predictive workflow has been applied to 60 novel carbon-centered nucleophiles, suggesting reactions that yield stable carboxylation adducts. The results have been validated through experimental methods for five predicted nucleophiles, which include three stable and two unstable adducts. | Maike Eckhoff; Aleria Garcia-Roca; Shubham Deolka; Liudmila Seidel; Matthew S. Sigman; Jonny Proppe | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b9f8c26dde43c908014c4a/original/predicting-the-stability-of-base-mediated-c-h-carboxylation-adducts-using-data-science-tools.pdf |
6775e7f3fa469535b97ec414 | 10.26434/chemrxiv-2025-67s9h | Harness first principles thinking in problem-based learning for chemical education | In philosophy and science, a first principle is a basic proposition or assumption that cannot be deduced from any other proposition or assumption. Ancient Greek philosophy Aristotle defined the first principle as “the first basis from which a thing is known.” First principles thinking (or reasoning from first principles) is a way of thinking and problem-solving that breaks down a complex problem into its most basic assumptions, facts, concepts, or ideas and then reassembles them from the bottom-up. In this paper, we reported our attempts to harness first principles thinking into problem-based learning (PBL) in chemistry education. Two PBL projects were elaborately designed respectively for two student groups. By utilizing the inquiry-based technique and jigsaw technique, the understanding of the fundamental principles of chemistry was employed to guide the students´ research activity and strengthen the learning of chemistry. We also observed signs of increased creativity during the process. This communication indicated that first principles thinking could be harnessed to increase students´ learning depth and promote creativity in chemical education. | Junjun Tan; Xinxin Xiao | Chemical Education | CC BY 4.0 | CHEMRXIV | 2025-01-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6775e7f3fa469535b97ec414/original/harness-first-principles-thinking-in-problem-based-learning-for-chemical-education.pdf |
63a97d3fe8047ac705f618da | 10.26434/chemrxiv-2022-brbgj | G-Quadruplex-Protein Interactions: Screening, Characterization and Regulation | G-quadruplex (G4) is a kind of peculiar nucleic acid secondary structure formed by DNA or RNA, which is considered as a fundamental feature of the genome. Many proteins can specifically bind to G4 structures. There is increasing evidence that G4-protein interactions involve in the regulation of important cellular processes such as DNA replication, transcription, RNA splicing and translation. Besides, G4-protein interactions have been proved to be potential targets for disease treatment. In order to unravel the detailed bioregulatory mechanisms of G4-binding proteins (G4BPs), biochemical methods for detecting G4-protein interactions with high specificity and sensitivity are highly demanded. Here, we review recent advances in the screening and validation of new G4BPs and bioregulatory tools of G4BPs. | Yicong Dai; Xucong Teng; Qiushuang Zhang; Hongwei Hou; Jinghong Li | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a97d3fe8047ac705f618da/original/g-quadruplex-protein-interactions-screening-characterization-and-regulation.pdf |
60c74fda567dfe4074ec576b | 10.26434/chemrxiv.12951083.v1 | Copper (II) Phthalocyanine Effects On Solid Propellant Combustion | <p>In the present work, the effects of copper (II) phthalocyanine, CuP (C<sub>32</sub>H<sub>16</sub>CuN<sub>8</sub>)
on the combustion of rocket solid propellant is investigated. For this purpose,
parameters such as ignition temperature, mass and volume of generated gases are
measured. For such purpose, the sucrose-potassium nitrate (KNSu) was employed
as a “model system”. It was found that CuP interferes with the combustion of
the KNSu propellant, inhibiting the thermal degradation of potassium carbonate
and also decreasing the ignition temperature of KNSu. It was identified that,
in a percentage of 50%, CuP reduces the ignition temperature of KNSu by ~ 60
ºC.</p> | George Santos Marinho; Robson de Farias | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fda567dfe4074ec576b/original/copper-ii-phthalocyanine-effects-on-solid-propellant-combustion.pdf |
62c45c5ebe884b65adfba156 | 10.26434/chemrxiv-2022-hqgjv-v2 | How to Dope the Basal Plane of 2H-MoS2 to Boost the Hydrogen Evolution Reaction? | Molybdenum disulfide (MoS2) is considered one of the most likely materials that could be turned into low-cost hydrogen evolution reaction (HER) catalysts to replace noble metals in acidic medium. However, several challenges prevent MoS2 from being truly applicable, including limited number of active sites (typically only the edges are active) and poor conductivity. In this work, we perform an extensive density func- tional theory (DFT) screening of substitutional doping as a possibility to activate the otherwise inert basal surface. We assess 17 Earth abundant elements for molybdenum doping and 5 elements (N, O, P, Se and Te) for sulfur substitution. Systematically de- termining the preference of the metallic dopants to be located on the edges rather than in the basal plane, we reveal that most dopants are much more likely to be incorpo- rated at the edges, suggesting that advanced synthesis methods are required to obtain basal-plane doped catalysts. The latter may, however, feature many more active sites per MoS2 formula unit, motivating our study on the properties of such substitutionally doped surfaces. For the first time for such a screening study, we explore not only the adsorption of H, but also of OH and H2O to explore the solvent effect since the reac- tion takes place in an aqueous medium. Two additional phenomena that could hinder the hydrogen production at these sites are investigated, namely H2S release and the (local) segregation/dispersion tendency of the dopants in the basal surface. Moreover, to assess the electrocatalytic activity, we take the electrochemical potential explicitly into account via grand canonical DFT in combinations. Compared with pristine MoS2 nanosheets, our results show that most doping elements significantly enhanced the elec- trocatalytic activity. Considering all assessed factors, we identify the most promising systems: Dimers of Ti, Zr and Hf and the substitution of S by P are predicted to lead to stable active sites on the basal plane with overpotentials of about 0.2 V. | Nawras Abidi; Audrey Bonduelle-Skrzypczak; Stephan N. Steinmann | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c45c5ebe884b65adfba156/original/how-to-dope-the-basal-plane-of-2h-mo-s2-to-boost-the-hydrogen-evolution-reaction.pdf |
62671ef8742e9fd9176b907b | 10.26434/chemrxiv-2021-pplfs-v2 | SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine | We present SEEKR2 (Simulation-Enabled Estimation of Kinetic Rates version 2) – the latest iteration in the family of SEEKR programs for using multiscale simulation methods to computationally estimate the kinetics and thermodynamics of molecular processes, in particular, ligand-receptor binding. SEEKR2 generates equivalent, or improved, results compared to the earlier versions of SEEKR, but with significant increases in speed and capabilities. SEEKR2 has also been built with greater ease of usability with extensible features to enable future expansions of the method. Now, in addition to supporting simulations using NAMD, calculations may be run with the fast and extensible OpenMM simulation engine. The Brownian dynamics portion of the calculation has also been upgraded to Browndye 2. In addition, this version of SEEKR supports hydrogen mass repartitioning to significantly reduce computational cost. | Lane Votapka; Andrew Stokely; Anupam Ojha; Rommie Amaro | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62671ef8742e9fd9176b907b/original/seekr2-versatile-multiscale-milestoning-utilizing-the-open-mm-molecular-dynamics-engine.pdf |
60c752de337d6c957be2879d | 10.26434/chemrxiv.13296389.v1 | Phytochemical Screening, Antioxidant and Antibacterial Activity of the Root Extract of Cyphostemma Adenocaule (Steud. Ex A. Rich.) Wild & R.B.Drumm | <p><b>ABSTRACT</b></p><p></p><p>Plant secondary
metabolites had provided important bioactive principles for developing new lead
compounds. Within their confinement, they exhibit unique chemical diversity,
which influence their diverse biological properties. The <i>vitaceae</i> family are known for their potent antioxidant and
antibacterial phytoconstituents, among other biological properties. <i>Cyphostemma adenocaule</i> is one of the
family members explored for its ethnomedicinal properties. This study undertook the evaluation of the phytochemical,
antioxidant and antibacterial properties of the root extract of <i>Cyphostemma adenocaule</i>, as well as, evaluating their Biological
properties; antioxidant activity (DPPH assay) and antibacterial activity (agar
well diffusion test). Preliminary phytochemical screening revealed the
presence of flavonoids, alkaloids,
carbohydrates & glycoside, alkaloids, saponins and tannins. The
methanol root extract had the highest percentage in the DPPH assay, providing
50% inhibition IC<sub>50 </sub>of
10.87µg/ml, followed by nHexane (IC<sub>50</sub> 74.10µg/ml) and
chloroform (IC<sub>50</sub> 74.31µg/ml) extract. In the antibacterial assay,
the chloroform extract was active against <i>E. coli</i> (24.00±0.15) and moderate activity against <i>Staph. aureus</i> (12.5±0.18). The nHex extract was completely inactive
against the test organism while the methanol extract showed poor activity
against the test organism. The present study adds to the existing literature on
<i>Cyphostemma adenocaule</i>
with scientific evidence into its biological properties. </p>
<p>Keywords: <i>Cyphostemma adenocaule</i>, Phytochemical screening,
antioxidant and antibacterial activity</p><b></b><p></p> | Abdulbasit Haliru Yakubu; Mohammed Mustapha Mohammed; Abdulqadir bukar bababe; Hassan Yesufu | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752de337d6c957be2879d/original/phytochemical-screening-antioxidant-and-antibacterial-activity-of-the-root-extract-of-cyphostemma-adenocaule-steud-ex-a-rich-wild-r-b-drumm.pdf |
6414d7e72bfb3dc251f0c0aa | 10.26434/chemrxiv-2023-20bx2 | Unanticipated Thio-oxidation of Organophosphite Chemical Additives in PVC Microplastics Following In-Situ Weathering | Microplastics have emerged as contaminants of concern due to their worldwide distribution and persistence. Following environmental weathering the chemical composition of microplastics may be altered by physicochemical processes. In this study, nontargeted analysis was employed to examine changes in the chemical composition of five different types of microplastics that had been subjected to 16 weeks of in-situ exposure to flowing river water. The highest number of observed peak features was associated with PVC (12,043), among which 2,086 were newly formed. It was unanticipated that three organothiophosphates, including triphenyl thiophosphate (TPTP), would have the highest abundance following in-situ exposure of PVC microplastics. The abiotic formation of organothiophosphates was confirmed via in-lab simulation trials following 6 weeks of artificial weathering. To further investigate potential reaction mechanisms, triphenyl phosphite (TPPi) and PVC microplastic particles were individually incubated along with five major sulfur species. Elementary sulfur (S8) and sulfide (S2-) were observed to be responsible for the formation of TPTP via the thio-oxidation of TPPi. This is the first known report of thio-oxidation as a transformation pathway, highlighting the importance of considering chemical transformations when conducting microplastic risk assessments. | Wanzhen Chen; Husein Almuhtaram; Robert Andrews; Hui Peng | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6414d7e72bfb3dc251f0c0aa/original/unanticipated-thio-oxidation-of-organophosphite-chemical-additives-in-pvc-microplastics-following-in-situ-weathering.pdf |
632ddee90e3c6a285026073d | 10.26434/chemrxiv-2022-h2mrp | Size-modified Poisson-Nernst-Planck approach for modeling a local electrode environment in CO2 electrolysis | Electrochemical reduction of CO2 heavily depends on the reaction conditions found near the electrode surface. These local conditions are affected by phenomena such as electric double layer formation and steric effects of the solution species, which in turn impact the passage of CO2 molecules to the catalytic surface. Most models for CO2 reduction ignore these effects, leading to an incomplete understanding of the local electrode environment. In this work, we present an modeling approach consisting of a set of size-modified Poisson-Nernst-Planck equations and the Frumkin interpretation of Tafel kinetics. We introduce a modification to the steric effects inside the transport equations which results in more realistic concentration profiles. We also show how the modification lends the model numerical stability without adopting any separate stabilization technique. The model can replicate experimental current densities and Faradaic efficiencies till -1.5 vs SHE/V of applied electrode potential. We also show the utility of this approach for systems operating at elevated CO2 pressures. Using Frumkin-corrected kinetics gels well with the theoretical understanding of the double layer. Hence, this work provides a sound mechanistic understanding of the CO2 reduction process, from which new insights on key performance controlling parameters can be obtained. | Esaar Naeem Butt; Johan Padding; Remco Hartkamp | Energy; Energy Storage | CC BY NC 4.0 | CHEMRXIV | 2022-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632ddee90e3c6a285026073d/original/size-modified-poisson-nernst-planck-approach-for-modeling-a-local-electrode-environment-in-co2-electrolysis.pdf |
60c756bc702a9b508318c985 | 10.26434/chemrxiv.14315579.v1 | Metabolite Identification Using Infrared Ion Spectroscopy – Novel Biomarkers for Pyridoxine-Dependent Epilepsy | Untargeted LC-MS based metabolomics strategies are being increasingly applied in metabolite screening for a wide variety of medical conditions. The long-standing “grand challenge” in the utilization of this approach is metabolite identification – confidently determining the chemical structures of m/z-detected unknowns. Here, we use a novel workflow based on the detection of molecular features of interest by high-throughput untargeted LC-MS analysis of patient body fluids combined with targeted molecular identification of those features using infrared ion spectroscopy (IRIS), effectively providing diagnostic IR fingerprints for mass-isolated targets. A significant advantage of this approach is that in silico predicted IR spectra of candidate chemical structures can be used to suggest the molecular structure of unknown features, thus mitigating the need for the synthesis of a broad range of physical reference standards. Pyridoxine dependent epilepsy (PDE-ALDH7A1) is an inborn error of lysine metabolism, resulting from a mutation in the ALDH7A1 gene that leads to an accumulation of toxic levels of α-aminoadipic semialdehyde (α-AASA), piperideine-6-carboxylate (P6C), and pipecolic acid in body fluids. While α-AASA and P6C are known biomarkers for PDE in urine, their instability makes them poor candidates for diagnostic analysis from blood, which would be required for application in newborn screening protocols. Here, we use combined untargeted metabolomics-IRIS to identify several new biomarkers for PDE-ALDH7A1 that can be used for diagnostic analysis in urine, plasma, and cerebrospinal fluids, and are compatible with analysis in dried blood spots for newborn screening. The identification of these novel metabolites has directly rendered novel insights in the pathophysiology of PDE-ALDH7A1. | Rianne E. van Outersterp; Udo F. H. Engelke; Jona Merx; Giel Berden; Mathias Paul; Thomas Thomulka; Albrecht Berkessel; Marleen C. D. G. Huigen; Leo A. J. Kluijtmans; Jasmin Mecinović; Floris P. J. T. Rutjes; Clara D.M. van Karnebeek; Ron A. Wevers; Thomas
J. Boltje; Karlien L.M. Coene; Jonathan Martens; Jos Oomens | Organic Synthesis and Reactions; Mass Spectrometry; Spectroscopy (Anal. Chem.); Biochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756bc702a9b508318c985/original/metabolite-identification-using-infrared-ion-spectroscopy-novel-biomarkers-for-pyridoxine-dependent-epilepsy.pdf |
675833cb7be152b1d080d39e | 10.26434/chemrxiv-2023-3r8sf-v2 | Catalytic efficiencies for atmospheric methane removal in the high-chlorine regime | Catalytic production of chlorine atoms from iron salt aerosols (ISA) has been suggested as a means of achieving atmospheric methane reduction (AMR). The feasibility of this approach its efficiency and the optimum conditions
for deployment must be determined. Success is not obvious because it depends on nonlinear atmospheric free radical chain reactions; under some conditions added chlorine is known to increase methane lifetime. Here we evaluate the catalytic efficiency of atmospheric methane oxidation, initiated by the photocatalytic conversion of chloride to chlorine by iron chlorides Fe(III)Cl(3−n)n , using a OD box model. While HOx and high NOx behaviours are well known, a new regime is characterized by high ClOx conditions ypified by CH3O2 reacting with ClO rather than NO or HO2. We find that at NOx mixing ratios below 50 ppt or above
390 ppt, methane removal per iron atom is always net positive regardless of the Cl2 addition rate. However, between these NOx mixing ratios and for a chlorine production rate below 1×10^6 Cl2 /(cm3 s) the net effect is negative, increasing CH4 concentrations. The efficiencies seen in the model range from -0.26 to 2.63 CH4/Cl. | Luisa Pennacchio; Maarten van Herpen; Daphne Meidan; Alfonso Saiz-Lopez; Matthew S. Johnson | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675833cb7be152b1d080d39e/original/catalytic-efficiencies-for-atmospheric-methane-removal-in-the-high-chlorine-regime.pdf |
642501b262fecd2a83a827f6 | 10.26434/chemrxiv-2023-vmmht-v2 | Electronic and Magnetic Properties of Oligomers and Chains of Poly(benzodifurandione) (PBDF), A Highly Conducting n-Type Polymer | The seminal development of highly electrically conducting polyacetylene via oxidative or reductive treatment (“doping”) has continuously inspired the search for other conducting π-conjugated polymers. Recently, poly(benzodifurandione), PBDF, was reported to have unexpected solubility given the absence of side chains and to exhibit an unprecedented, high electrical conductivity upon reduction (“n-doping”), with protons acting as counter-ions. Here, we theoretically investigate the electronic and magnetic properties of PBDF by taking long oligomers and one-dimensional (1D) periodic chains as model systems. With the oligomer models, we characterize the formation of polarons and bipolarons in n-doped PBDF. Our results indicate that singlet bipolarons tend to be the energetically most favorable species when protons bind to two adjacent carbonyl groups in nearest-neighbor benzodifuran moieties. The calculations on the 1D periodic chain models show that the positions of the protonated carbonyl groups determine the metallic, semiconducting, or insulating nature of a PBDF chain. When the protonated carbonyl groups are all situated on the same side of a PBDF chain, a stable helical chain configuration is found that exhibits ferromagnetic behavior. Our findings elucidate the mechanism of polaron and bipolaron formation in long oligomers of n-doped PBDF and highlight the fascinating electronic and magnetic properties of periodic 1D chains. These studies also provide a steppingstone for the investigations of PBDF thin films, for which two- and three-dimensional structures must be considered. | Xiaojuan Ni; Hong Li; Jean-Luc Bredas | Materials Science; Nanostructured Materials - Materials; Oligomers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642501b262fecd2a83a827f6/original/electronic-and-magnetic-properties-of-oligomers-and-chains-of-poly-benzodifurandione-pbdf-a-highly-conducting-n-type-polymer.pdf |
668282b85101a2ffa8fe776c | 10.26434/chemrxiv-2024-1k5kc | Unmasking the Reverse Catalytic Activity of ‘Ene’-Reductases for Asymmetric Carbonyl Desaturation | Carbonyl desaturation is a fundamental reaction widely practiced in organic synthesis. While numerous methods have been developed to expand the scope of this important transformation, most of them necessitate multistep protocols, or suffer from the use of high loadings of metal or strong oxidizing conditions. Moreover, approaches that can achieve precise stereochemical control of the desaturation process are extremely rare. We report herein a novel biocatalytic platform for desymmetrizing desaturation of cyclohexanones to generate diverse cyclohexenones bearing a remote quaternary stereogenic center, by reengineering ‘ene’-reductases (EREDs) to efficiently mediate dehydrogenation, the reverse process of their native activity. This ERED-based desaturation system operates under mild conditions with air as the terminal oxidant, tolerates oxidation-sensitive or metal-incompatible functional groups, and more importantly, exhibits unparalleled stereoselectivity comparing to those achieved with small-molecule catalysts. Mechanistic investigations suggested that the reaction proceeded through a-deprotonation followed by a rate-determining b-hydride transfer. | Hui Wang; Bin Gao; Heli Cheng; Shixuan Cao; Xinyi Ma; Yinjuan Chen; Yuxuan Ye | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668282b85101a2ffa8fe776c/original/unmasking-the-reverse-catalytic-activity-of-ene-reductases-for-asymmetric-carbonyl-desaturation.pdf |
60c74919ee301caa87c799f0 | 10.26434/chemrxiv.12026904.v1 | Fatty Liver and Impaired Hepatic Metabolism Alters the Congener-Specific Distribution of Polychlorinated Biphenyls (PCBs) in Mice with a Liver-Specific Deletion of Cytochrome P450 Reductase | Polychlorinated biphenyls (PCBs) are persistent organic pollutants that are linked to adverse health outcomes. PCB tissue levels are determinants of PCB toxicity; however, it is unclear how factors, such as an altered metabolism and/or a fatty liver, affect PCB distribution in vivo. We determined the congener-specific disposition of PCBs in mice with a liver specific deletion of cytochrome P450 reductase (KO), a model of fatty liver with impaired hepatic metabolism, and wildtype (WT) mice. Male and female KO and WT mice were exposed orally to Aroclor 1254, a technical PCB mixture. PCBs were quantified in adipose, blood, brain and liver tissues by gas chromatography-mass spectrometry. PCB profiles and levels in tissues were genotype and sex dependent. PCB levels were higher in the liver from KO compared to WT mice. PCB profiles showed clear differences between tissues from the same exposure group. While experimental tissue : blood partition coefficients in KO and WT mice did not follow the trends predicted using a composition-based model, the agreement between experimental and calculated partition coefficients was still reasonable. Thus, a fatty liver and/or an impaired hepatic metabolism alter the distribution of PCBs in mice and the magnitude of the partitioning of PCBs from blood into tissues can be approximated using composition-based models.<br /> | Xueshu Li; Chun-Yun Zhang; Hans-Joachim Lehmler | Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74919ee301caa87c799f0/original/fatty-liver-and-impaired-hepatic-metabolism-alters-the-congener-specific-distribution-of-polychlorinated-biphenyls-pc-bs-in-mice-with-a-liver-specific-deletion-of-cytochrome-p450-reductase.pdf |
657775867acf130c320354cf | 10.26434/chemrxiv-2023-56frn | The determination of free energy of hydration of water ions from first principles. | We model the auto-ionization of water by determining the free energy of hydration of the major intermediate species of water ions. We represent the smallest ions - the hydroxide ion OH- , the hydronium ion H3O+, and the Zundel ion H5O2+, - by bonded models; and the more extended ionic structures by strong non-bonded interactions (e.g. the Eigen H9O4+ = H3O+ +3(H2O) and the Stoyanov H13O6+ = H5O2+ + 4(H2O)). Our models are faithful to the precise QM energies and their components to within 1% or less. Using the calculated free energies and atomization energies, we compute the pKa of pure water from first principles as a consistency check, and arrive at a value within 1.3 log units of the experimental one. From these calculations we conclude that the hydronium ion, and its hydrated state, the Eigen cation, are the dominant species in the water auto-ionization process. | Oleg Butin; Leonid Pereyaslavets; Ganesh Kamath; Alexey Illarionov; Serzhan Sakipov; Igor Kurnikov; Ekaterina Voronina; Ilya Ivahnenko; Igor Leontyev; Grzegorz Nawrocki; Mikhail Darkhovskiy; Michael Olevanov; Yevhen Cherniavskyi; Christopher Lock; Sean Greenslade; Roger Kornberg; Michael Levitt; Boris Fain | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657775867acf130c320354cf/original/the-determination-of-free-energy-of-hydration-of-water-ions-from-first-principles.pdf |
62c302e27b3b3079bc0cb448 | 10.26434/chemrxiv-2022-3v785 | Nuclear Magnetic Resonance Studies of Carbon Dioxide Capture | Carbon dioxide capture is an important greenhouse gas mitigation technology that can help limit climate change. The design of improved capture materials requires a detailed understanding of the mechanisms by which carbon dioxide is bound. Nuclear magnetic resonance (NMR) spectroscopy methods have emerged as a powerful probe of CO2 sorption and diffusion in carbon capture materials. In this article, we first review the practical considerations for carrying out NMR measurements on capture materials dosed with CO2 and we then present three case studies that review our recent work on NMR studies of CO2 binding in metal-organic framework materials. We show that simple 13C NMR experiments are often inadequate to determine CO2 binding modes, but that more advanced experiments such as multidimensional NMR experiments and 17O NMR experiments can lead to more conclusive structural assignments. We further discuss how pulsed field gradient (PFG) NMR can be used to explore diffusion of adsorbed CO2 through the porous framework. Finally, we provide an outlook on the challenges and opportunities for the further development of NMR methodologies that can improve our understanding of carbon capture. | Suzi Pugh; Alexander Forse | Inorganic Chemistry; Chemical Engineering and Industrial Chemistry; Spectroscopy (Inorg.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c302e27b3b3079bc0cb448/original/nuclear-magnetic-resonance-studies-of-carbon-dioxide-capture.pdf |
6287fedf7087677ac359e867 | 10.26434/chemrxiv-2022-rzt27 | Introducing the role of metals in biology to high school and undergraduate students
| Metals enable numerous physiological processes ranging from respiration to nitrogen fixation. However, the role of metals in biology and biocatalysis is not appreciated by the general public. This lack of knowledge around biological metals can lead to misinformation, especially regarding vaccines and health products. Here, we present a series of easy-to-implement experiments and demonstrations that can be incorporated in high school and undergraduate curricula to introduce students to the role of metals in biology. Our results from running these experiments/demonstrations in virtual (N = 6-10) and in-person (N = 22) formats reveal that only 9-30% of high school students are aware of the presence of metals in humans. These statistics can be changed to 48-100% by incorporating proposed experiments and content in the curriculum. | Eaindra Yee; Murphi T. Williams; Ambika Bhagi-Damodaran | Biological and Medicinal Chemistry; Inorganic Chemistry; Chemical Education; Chemical Education - General; Bioinorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287fedf7087677ac359e867/original/introducing-the-role-of-metals-in-biology-to-high-school-and-undergraduate-students.pdf |
60c7443cf96a004a6228697c | 10.26434/chemrxiv.9767504.v1 | Mechanistic Insight into Biopolymer Induced Iron Oxide Mineralization Through Quantification of Molecular Bonding | Microbial production of iron (oxy)hydroxides on polysaccharide rich biopolymers occurs on such a vast scale that it impacts the global iron cycle and has been responsible for major biogeochemical events. Yet the physiochemical controls these biopolymers exert on iron (oxy)hydroxide formation are poorly understood. Here we used dynamic force spectroscopy to directly probe binding between complex, model and natural microbial polysaccharides and common iron (oxy)hydroxides. Applying nucleation theory to our results demonstrates that if there is a strong attractive interaction between biopolymers and iron (oxy)hydroxides, the biopolymers decrease the nucleation barriers, thus promoting mineral nucleation. These results are also supported by nucleation studies and density functional theory. Spectroscopic and thermogravimetric data provide insight into the subsequent growth dynamics and show that the degree and strength of water association with the polymers can explain the influence on iron (oxy)hydroxide transformation rates. <br /> | K.K. Sand; Stanislav Jelavic; Sören Dobberschütz; P.D. Ashby; Matthew J. Marshall; Knud Dideriksen; S.L.S. Stipp; S.N. Kerisit; R.W. Friddle; J.J. DeYoreo | Biological Materials; Geological Materials; Environmental Science; Geochemistry; Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7443cf96a004a6228697c/original/mechanistic-insight-into-biopolymer-induced-iron-oxide-mineralization-through-quantification-of-molecular-bonding.pdf |
626f70d8ebac3a2af4eac074 | 10.26434/chemrxiv-2022-t2lkm | A Highly Stereoselective Claisen-Sakurai Approach to Densely Functionalized Cyclopentenols | The formation of highly substitiuted cyclopentenols was developed using a Claisen-Sakurai reaction. Both elements of the reaction can be performed in a one-pot sequence that provides the corresponding cyclized products in high stereoselectivity. The stereochemical outcome is defined by a combination of Claisen stereospecificity and stereoelectronic effects in the Sakurai cyclization that promotes reactivity via a syn-SE’ antiperiplanar transition-state. This was determined by examination of the product stereochemistry and through detailed DFT analysis. | Matthew Cook; Ksenia Stankevich | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626f70d8ebac3a2af4eac074/original/a-highly-stereoselective-claisen-sakurai-approach-to-densely-functionalized-cyclopentenols.pdf |
628b8671809e3218f599b33b | 10.26434/chemrxiv-2022-frz75 | Fluorescence sensing of picomolar ammonia by covalent organic framework | Fluorescence sensing has exhibited its power in analytical sciences due to its sensitivity, selectivity and convenience. However, it is still challenging to further improve the sensitivity to picomolar (pM) and sub-pM level as LPRS- and SERS-enhanced electrochemical, ELISA and aptamer-based highly sensitive methods. The main obstacle lies that even if strongly absorbing fluorophores with 100% photoluminescence quantum yield, the signals it generates at pM level still cannot exceed the background noise by solvent and particle Rayleigh and Raman scattering and detector dark current and a satisfactory signal to noise ratio cannot be achieved. To overcome this issue, non-linear amplification strategies were undertaken such as enzyme catalyzed processes such as ELISA and aptamer-based fluorescence sensing. However, due to the rigorous physiological conditions enzyme required, it is highly desired to develop artificial catalytic amplification method to non-linearly enhance the weak fluorescence signals generated by the fluorophores, which responds to pM level analytes. Here, we developed a TAPA-BTD-COF, which complexes with NH3 by its C=N-H bond, and the as-formed strong interaction strengthen the C=N imine bond and fix the trans-configuration. Given the infinite extending two-dimensional network by strong covalent bond, the fixation of a single imine bond to trans-configuration leads to a domino effect rendering the C=N bond in the two-dimensional plane to be locked one by one to trans-configuration. Since trans-configuration bears stronger fluorescence than cis-configuration because of more rigidified and conjugated structures. This domino amplification effect by a single NH3 molecule drives about 10 million TAPA-BTD-COF C=N-H bond be locked due to the whole rigid two-dimensional COF structure not allowing the flexible configuration isomerization and blocked the non-radiative channel realizing unprecedented pM concentration fluorescence sensing by common chemical sensors without pursuing to biologically enzyme catalyzed amplification process such as ELISA or aptamer. | Yuhang Qian; Jiani Li; Mingyang Ji; Jundan Li; Anan Liu; Dongge Ma; Yaohui Zhu | Analytical Chemistry; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628b8671809e3218f599b33b/original/fluorescence-sensing-of-picomolar-ammonia-by-covalent-organic-framework.pdf |
67240516f9980725cfba3171 | 10.26434/chemrxiv-2024-87hn7 | Enantioselectivity in Metabolism and Toxicity of 6PPD-Quinone in Salmonids | The toxicity of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-Q) in salmonids has been found to be sensitive to even minor structural changes on its alkyl side chain. Inspired by this, we herein isolated the enantiomers of 6PPD-Q and tested their in vitro metabolism in liver S9 of rainbow trout (O. mykiss), along with their toxicity in a coho salmon (O. kisutch) embryo (CSE-119) cell line. (R)-6PPD-Q was found to be rapidly metabolized in rainbow trout liver S9 with a half-life (t1/2) of 12.3 minutes, which was 2.92 times faster than that of (S)-6PPD-Q. This was further evidenced by the preferential formation of an (R)-aryl-OH-6PPD-Q metabolite. Supporting this, enantioselective accumulation of (S)-6PPD-Q was found in rainbow trout in vivo. To further distinguish between kinetics and intrinsic toxicity, we tested the toxicity of 6PPD-Q enantiomers in the CSE-119 cell line with minimal metabolism of 6PPD-Q. (R)-6PPD-Q was found to strongly induce cytotoxicity in CSE-119 cells with an IC50 of 17.7 µg/L, which was 3.94 times stronger than that of (S)-6PPD-Q. In summary, this study reported the enantioselectivity in both the toxicity and metabolism of 6PPD-Q, demonstrating that its toxicity should be mediated by specific protein binding. | Rui Li; Holly Barrett; Pranav Nair; Minghua Wang; Linna Xie; Hui Peng | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67240516f9980725cfba3171/original/enantioselectivity-in-metabolism-and-toxicity-of-6ppd-quinone-in-salmonids.pdf |
60c742af4c89198686ad24ee | 10.26434/chemrxiv.8425400.v1 | Role of Guanidinium-Carboxylate Interaction in Enzyme Inhibition with Implication for Drug Design | Guanidinium cation (Gdm<sup>+</sup>) interacts strongly with amino acids of different polarities modulating protein structure and function. Using density functional theory calculations and molecular dynamics simulations we studied the interaction of Gdm<sup>+</sup> with carboxylate ions mimicking its interaction with acidic amino acids and explored its effect in enzymatic folding and activity. We show that in low concentrations, Gdm<sup>+</sup> stabilizes carboxylate ion dimers by acting as a bridge between them thereby reducing the electrostatic repulsion. We further show that this carboxylate-Gdm<sup>+</sup>-carboxylate interaction can have an effect on the structure-activity relationship in enzymes with active sites containing two acidic residues. Using five enzymes (hen egg white lysozyme, T4 lysozyme, HIV-1 protease, pepsin and creatine kinase), which have two acidic amino acids in their active sites, we show that in low concentrations (< 0.5 M), Gdm<sup>+</sup> strongly binds to the enzyme active site, thereby potentially inhibiting its activity without unfolding it. This can lead to misleading conclusions in experiments, which infer the extent of enzyme unfolding from activity measurements. However, the carboxylate-Gdm<sup>+</sup>-carboxylate specific interaction can be exploited in drug discovery as drugs based on guanidinium derivatives are already being used to treat various maladies related to muscle weakness, cancer, diabetes etc. Guanidinium derivatives can be designed as potential drug molecules to inhibit activity or functioning of enzymes, which have binding pockets with two acidic residues in close vicinity.<br /> | Aswathy Muttathukattil; Sriraksha Srinivasan; Antarip Halder; Govardhan Reddy | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742af4c89198686ad24ee/original/role-of-guanidinium-carboxylate-interaction-in-enzyme-inhibition-with-implication-for-drug-design.pdf |
60c756ab469df43740f4534b | 10.26434/chemrxiv.14292293.v1 | Polydimethyl siloxane/MIL-101 Composites for Enhanced Toluene Adsorption in the Presence of Humidity | <div><b>ABSTRACT</b> <br /></div><div><br /></div><div>
Competition
between atmospheric moisture and volatile organic compounds (VOCs) for an
adsorbent’s sites can significantly impact its VOC removal efficiency. The
development of moisture-tolerant adsorbents is essential to address this issue.
A vapor phase deposition process using polydimethylsiloxane (PDMS) has created
a hydrophobic form of the highly porous, normally hydrophilic, MOF MIL-101.
After optimizing the PDMS vapor deposition time and molecular weights,
hydrophobicity index calculations verified the improved hydrophobicity of the
coated MOF (MIL-PDMS-Sigma-0.25) over its pristine form. The surface area, pore
volume as well as single component vapor adsorption of water and toluene
capacities were also preserved, resulting to similar performance to MIL-101.
Toluene-water vapor co-adsorption experiments were conducted at 40% RH using
two toluene concentrations: 0.5% P/P<sub>0</sub> and 10% P/P<sub>0</sub>,
mimicking environmental VOC and industrial concentrations, respectively. At
0.5% P/P<sub>0</sub>, MIL-PDMS-Sigma-0.25 exhibited 60% higher adsorption
capacity and twice the rate of toluene capture relative to pristine MIL-101, as
well as a 3-fold higher toluene uptake relative to a commercial activated
carbon. Preliminary adsorbent regeneration experiments confirm the stability
and performance of MIL-PDMS-Sigma-0.25. Using a simple vapor phase
modification, this new MOF-composite material offers superior competitive
toluene vapor uptake in humidified real-world conditions at VOC concentrations. </div> | Luqman Hakim Mohd Azmi; Pavani Cherukupally; Elwin Hunter-Sellars; Bradley P. Ladewig; Daryl R. Williams | Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756ab469df43740f4534b/original/polydimethyl-siloxane-mil-101-composites-for-enhanced-toluene-adsorption-in-the-presence-of-humidity.pdf |
67d052c26dde43c9086c70f5 | 10.26434/chemrxiv-2025-rv1m0 | Organic Cage Rotaxanes | Organic cages are a robust class of molecular hosts with a myriad of applications in materials science.
Despite this, there has been a paucity of explorations into the modification of their properties via external
functionalization. In this work, [n]rotaxanes featuring unoccupied organic cages as stopper components and a small 2,2’-bipyridine macrocycle were constructed using the active metal template approach. By exploiting a scrambling
methodology, it was possible to synthesise cages with a defined number of interlocked components (n = 2-4). The
gas uptake, solubility and thermal properties of the interlocked systems were compared against those of their
constituent, non-interlocked components. In this manner, we were able to demonstrate the potential of exploiting
the mechanical bond for modulating the physiochemical properties of these molecular materials. | Zarik Yusaf; Benjamin Egleston; Gokay Avci; Kim Jelfs; James Lewis; Rebecca Greenaway | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d052c26dde43c9086c70f5/original/organic-cage-rotaxanes.pdf |
6221ae30ce899b04f6ab7f8c | 10.26434/chemrxiv-2022-gkk7l | Hydride-like NH2δ- species-driven reductive amination over Co@CoO catalyst | Selective synthesis of primary amines via reductive amination becomes an important research topic due to their wide applications. Various metal-based catalysts (Ru, Ir, Pt, Rh, etc.) have been developed; however, most systems suffer from low efficiency and poor stability. Here, we revealed that the hydride-like NH2δ- species, generated by the dissociation of NH3 over a core-shell structured Co@CoO catalyst is capable of accelerating the ammonolysis of Schiff bases, the reaction intermediates. This catalyst can handle various reductive aminations of aldehydes and ketones under mild conditions and run 21 times without deactivation. The combination of various spectroscopic measurements and computational modelling illustrated that this catalyst not only drives the dissociation of H2 to active Hδ- species, it also enables the homolytic and heterolytic cleavages of NH3 to NH2δ- species. D2 isotopic tracing experiment provided further evidence of the direct participation of hydride-like NH2δ- species in the ammonolysis of the Schiff bases. Theoretical calculations also verified the stable co-adsorption state of the Hδ- and NH2δ- species which allows the Schiff base to move freely on the surface of the CoO shell, resulting in the exceptional catalytic activity. This study demonstrates, for the first time, the potential of metal-oxide catalysts for the production of primary amines through reductive amination. | Wanjun Guo; Zhiqiang Wang; Shuang Xiang; Yaxuan Jing; Yong Guo; Xiaohui Liu; Xue-qing Gong; Yanqin Wang | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6221ae30ce899b04f6ab7f8c/original/hydride-like-nh2-species-driven-reductive-amination-over-co-co-o-catalyst.pdf |
623d7611658bc04041b7844b | 10.26434/chemrxiv-2022-m56st | Nitrogen-doped, proton-exchanged Dion-Jacobson layered niobate perovskites for photocatalytic hydrogen generation in solar light | Wide band gap semiconductor niobate photocatalysts with Dion-Jacobson layered perovskite structure were nitrogen-doped via simple gas-solid reaction to extend their absorption into the visible light range. Nitrogen doping was performed using ammonia as precursor, resulting in decreased band gaps of doped AB2Nb3O10 compounds (A = Cs, Rb, K; B = Ca, Sr) down to 2.5 eV. The resulting materials were investigated concerning their chemical and electronic structures. Nitrogen-doped AB2Nb3O10 crystals showed a clear red shift in absorption. Photocatalytic performance tests for the doped materials evaluated the capability of H2 production under simulated solar irradiation. The addition of carbonates to the gas-solid reaction turned out to be advantageous for the reduction of defects and the preservation of photocatalytic activity of nitrogen-doped layered niobates AB2Nb3O10. | Natalia Kulischow; Roland Marschall | Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623d7611658bc04041b7844b/original/nitrogen-doped-proton-exchanged-dion-jacobson-layered-niobate-perovskites-for-photocatalytic-hydrogen-generation-in-solar-light.pdf |
62028b0a0aec1a32b3169508 | 10.26434/chemrxiv-2022-b69v7 | Molecular docking studies of Alpinia galanga metabolites against human placental aromatase for estrogen-dependent breast cancer treatment | Breast cancer is the leading cause of cancer-related deaths among women. With the clinical success of several synthetic aromatase inhibitors (AIs) as therapeutic agents in post-menopausal estrogen receptor-positive breast cancer, natural products have been tapped in search of chemically diverse compounds with potential better effectiveness against aromatase while conferring reduced adverse effects. Alpinia galanga is among the Philippine native medicinal plants with extensive studies on its phytopharmacological properties yet reports on its human placental aromatase inhibitory activity remain rudimentary. Thus, a total of 119 database-derived A. galanga secondary metabolites was molecularly docked onto the catalytic site of human placental aromatase using the UCSF Chimera platforms according to the AutoDock Vina Broyden-Fletcher-Goldfarb-Shanoo (BFGS) algorithm. Drug-likeness was assessed in silico using SwissADME. Of the screened compounds, galanolactone (1), 4-(3,4-dimethoxy-trans-cinnamoyl)-trans-cinnamic acid (2), isocoronarin D (3), quercetin (4), β-sitosterol (5), (E)-8ß,17-epoxylabd-12-ene-15,16-dial (6), galangin (7), labda-8(17),12-diene-15,16-dial (8), 7-(4-Hydroxy-3-methoxyphenyl)-1-phenylhept-4-en-3-one (9), and 3,5,7-trihydroxy-4-methoxyflavanone (10) conferred highest binding affinities against aromatase ranging from binding energies of -8.7 to -8.0 kcal/mol with notable formed hydrogen bonds and interactions against key amino acid residues. Top-ranked compounds exhibited druggability with at most one violation of the Lipinski Rule of Five (LRo5). Overall, the study indicates the potential of top A. galanga secondary metabolites as promising drug pharmacophores in developing therapeutics against breast cancer. | JOE ANTHONY MANZANO; CECIL LAURENCE III CRUZ; ALLAN PATRICK MACABEO | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62028b0a0aec1a32b3169508/original/molecular-docking-studies-of-alpinia-galanga-metabolites-against-human-placental-aromatase-for-estrogen-dependent-breast-cancer-treatment.pdf |
62eb865badfd35cfb826843e | 10.26434/chemrxiv-2022-hxldq-v3 | A computational tool to accurately and quickly predict 19F NMR chemical shifts of molecules with fluorine-carbon and fluorine-boron bonds | We report the evaluation of density-functional-theory (DFT) based procedures for predicting 19F NMR
chemical shifts at modest computational cost for a range of molecules with fluorine bonds, to be used as a
tool for assisting the characterisation of reaction intermediates and products and as an aid to identifying
mechanistic pathways. The results for a balanced learning set of molecules were then checked using two
further testing sets, resulting in the recommendation of the ωB97XD/aug-cc-pvdz DFT method and basis
set as having the best combination of accuracy and computational time, with a RMS error of 3.57 ppm.
Cationic molecules calculated without counter-anion showed normal errors, whilst anionic molecules showed
larger errors, possibly due to omission of the counter-cation. The method was applied to the prediction of
the conformationally averaged 19F chemical shifts of 2,2,3,3,4,4,5,5-octafluoropentan-1-ol, in which gauche
stereoelectronic effects involving fluorine dominate and to determining the position of coordination equilibria
of fluorinated boranes as an aid to verifying the relative energies of intermediate species involved in catalytic
amidation reactions involving boron catalysts.
| Alexandre Dumon; Henry Rzepa; Carla Alamillo-Ferrer; Jordi Bures; Richard Procter; Tom Sheppard; Andrew Whiting | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eb865badfd35cfb826843e/original/a-computational-tool-to-accurately-and-quickly-predict-19f-nmr-chemical-shifts-of-molecules-with-fluorine-carbon-and-fluorine-boron-bonds.pdf |
661c6d4e21291e5d1dd79e3c | 10.26434/chemrxiv-2024-jffkv-v2 | Flash Sequence-Defined Molecular Synthesis Enabled by Living Anionic Monoaddition of Polymerizable Alkenes | The selective monoaddition of polymerizable vinyl monomers like styrenes and methacrylates in a living manner has been achieved for the flash-flow preparation of molecules in a defined sequence with high selectivity. We demonstrated the sequence-defined synthesis of multifunctional molecules using an initiator, functionalized styrenes, diarylethylenes, various methacrylates, and an electrophilic trapping reagent at the living terminus (six-component sequential connection at maximum) without any intermediate purification steps. The anionic living terminus of the vinyl monomers in the flow system described herein is active for polymerization, such that the styrene or methacrylate sequence can be expanded to afford highly dispersed oligomers without affecting other single units, which means that the unequivocal sequences were successfully inserted into the internal or terminal positions. The methodology described herein provides an adaptable method for the construction of new molecular spaces based on unimolecular sequence control and pinpoint functionalization. | Kazuhiro Okamoto; Dong-eun Yoo; Rikako Yoshioka; Ryohei Nakasato; Yosuke Ashikari; Kenji Kitayama; aiichiro nagaki | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661c6d4e21291e5d1dd79e3c/original/flash-sequence-defined-molecular-synthesis-enabled-by-living-anionic-monoaddition-of-polymerizable-alkenes.pdf |
615fb318a3d2c93606cf790e | 10.26434/chemrxiv-2021-3hj92 | Independent component analysis combined with Laplace inversion of spectrally resolved spin-alignment echo/T1 3D 7Li NMR of superionic Li10GeP2S12 | The use of independent component analysis (ICA) for the analysis of two-dimensional (2D) spin-alignment echo--T1 7Li NMR correlation data with transient echo detection as a third dimension is demonstrated for the superionic conductor Li10GeP2S12 (LGPS). ICA was combined with Laplace inversion, or discrete inverse Laplace transform (ILT), to obtain spectrally resolved 2D correlation maps. Robust results were obtained with the spectra as well as the vectorized correlation maps as independent components. It was also shown that the order of ICA and ILT steps can be swapped. While performing the ILT step before ICA provided better contrast, a substantial data compression can be achieved if ICA is executed first. Thereby the overall computation time could be reduced by one to two orders of magnitude, since the number of computationally expensive ILT steps is limited to the number of retained independent components.
For LGPS, it was demonstrated that physically meaningful independent components and mixing matrices are obtained, which could be correlated with previously investigated material properties yet provided a clearer, better separation of features in the data. LGPS from two different batches was investigated, which showed substantial differences in their spectral and relaxation behavior. While in both cases this could be attributed to ionic mobility, the presented analysis may also clear the way for a more in-depth theoretical analysis based on numerical simulations.
The presented method appears to be particularly suitable for samples with at least partially resolved static quadrupolar spectra, such as alkali metal ions in superionic conductors. The good stability of the ICA analysis makes this a prospect algorithm for preprocessing of data for a subsequent automatized analysis using machine learning concepts. | Marc C. Paulus; Anja Paulus; Rüdiger-A. Eichel; Josef Granwehr | Physical Chemistry; Analytical Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615fb318a3d2c93606cf790e/original/independent-component-analysis-combined-with-laplace-inversion-of-spectrally-resolved-spin-alignment-echo-t1-3d-7li-nmr-of-superionic-li10ge-p2s12.pdf |
672c6d8b5a82cea2fa5a4e5d | 10.26434/chemrxiv-2024-51wmm-v2 | Role of Cavity Strong Coupling on Single Electron Transfer Reaction at Electrode-Electrolyte Interface | Physicochemical properties of molecules can be modulated through the polariton formation under strong electromagnetic confinement. Here, we discuss the possibility of exploiting this phenomenon to increase the electron transfer rate at an electrode–electrolyte interface. Electron transfer theory under strong electromagnetic confinement can be extended to the electrode–electrolyte interface, and single–electron transfer reaction can be simulated using Gerischer’s theory. Although single electron transfer in free space is well described using Marcus theory, the vacuum electric field can facilitate an additional electron transfer pathway via virtual photon excitation under cavity strong coupling conditions. Therefore, this binary reaction pathway for single electron transfer can yield a quasi-two-particle electron transfer process. This quantum behavior can dominate when the mode volume is small and there is a large number of molecules in the vacuum electric field. Exploitation of polaritons in single electron transfer reactions can lead to enhanced electrochemical energy conversion systems. | Takahiro Hayashi; Tomohiro Fukushima; Kei Murakoshi | Physical Chemistry; Chemical Kinetics; Interfaces; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672c6d8b5a82cea2fa5a4e5d/original/role-of-cavity-strong-coupling-on-single-electron-transfer-reaction-at-electrode-electrolyte-interface.pdf |
665a3f2421291e5d1dc4cf5a | 10.26434/chemrxiv-2023-rpbs4-v2 | Sulfone Electrophiles in Cross-Electrophile Coupling: Nickel-Catalyzed Difluoromethylation of Aryl Bromides | Fluoroalkyl fragments have played a critical role in the design of pharmaceutical and agrochemical molecules in recent years due to the enhanced biological properties of fluorinated molecules compared to their non-fluorinated analogues. Despite the potential advantages conferred by incorporating a difluoromethyl group in organic compounds, industrial adoption of difluoromethylation methods lags be-hind fluorination and trifluoromethylation. This is due in part to challenges in applying common difluoromethyl sources towards indus-trial applications. We report here the nickel-catalyzed cross-electrophile coupling of (hetero)aryl bromides with difluoromethyl 2-pyridyl sulfone, a sustainably sourced, crystalline difluoromethylation reagent. The scope of this reaction is demonstrated with 24 examples (67 ± 16% average yield) including a diverse array of heteroaryl bromides and precursors to difluoromethyl-containing preclinical pharmaceuti-cals. This reaction can be applied to small-scale parallel synthesis and benchtop scale-up under mild conditions. As sulfone reagents are uncommon electrophiles in cross-electrophile coupling, the mechanism of this process was investigated. Studies confirmed the formation of •CF2H instead of difluorocarbene. A series of modified difluoromethyl sulfones revealed that sulfone reactivity does not correlate ex-clusively with reduction potential and that coordination of cations or nickel to the pyridyl group is essential to reactivity, setting out pa-rameters for matching the reactivity of sulfones in cross-electrophile coupling. | Benjamin Chi; Samantha Gavin; Benjamin Ahern; Nikita Peperni; Sebastien Monfette; Daniel Weix | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665a3f2421291e5d1dc4cf5a/original/sulfone-electrophiles-in-cross-electrophile-coupling-nickel-catalyzed-difluoromethylation-of-aryl-bromides.pdf |
66425aba21291e5d1d286a95 | 10.26434/chemrxiv-2024-cw501 | Modular, Atroposelective Total Synthesis of Micitide 982 | A modular, atroposelective total synthesis of micitide 982 (1) is reported. The feature of this report is the gram-scale C-H biarylation of N-phthaloyl-L-alanine followed by atroposelective Larock macrocyclization. This modular approach allowed the construction of a highly strained atrop-Tyr-Trp cross-linkage with unprecedented atropisomerism, as well as the first total synthesis of micitide 982 (1). | Hiroshige Ogawa; Longhui Yu; Shangzhao Li; Yuuya Nagata; Tsz Ki Chan; Yudai Matsuda; Jing Liu; Yong-Xin Li; Hugh Nakamura | Organic Chemistry; Catalysis; Organometallic Chemistry; Natural Products; Organic Synthesis and Reactions; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66425aba21291e5d1d286a95/original/modular-atroposelective-total-synthesis-of-micitide-982.pdf |
60c752c3337d6c510be28779 | 10.26434/chemrxiv.13347107.v1 | Unraveling the Activity of Iron Carbide Clusters Embedded in Silica for Thermocatalytic Conversion of Methane | <p>Isolated Fe-sites on silica substrate have recently been reported for direct and non-oxidative</p>
<p>conversion of gaseous methane with high selectivity. The activated catalyst was proposed to be</p>
<p>FeC2 cluster embedded in silica. Using a combination of density-functional theoretic methods</p>
<p>and micro-kinetic modeling, we show that under the same reaction conditions (1223 K , 1 atm)</p>
<p>FeC2 sites convert to FeC3 and the latter is instead responsible for the observed activity. We</p>
<p>investigate the detailed mechanism of conversion of methane to methyl radical and hydrogen</p>
<p>on FeC3@SiO2 under different conditions of methane partial pressure. We find that methyl</p>
<p>radical evolution is the rate-determining step for the overall conversion. Our calculations also</p>
<p>indicate that the conversion of embedded FeC3 to FeC4 competes with methyl radical evolution</p>
<p>from the active catalyst. However, due to the higher stability of FeC3 sites, we anticipate that</p>
<p>formation of higher carbides can be inhibited by controlling the hydrogen partial pressure.</p> | Gopal K. Dixit; Manish Kumar; Ankita Katiyar; Antonius P. J. Jansen; Alexander van Bavel; Ravi Agrawal; Prathamesh M. Shenai; Varadharajan Srinivasan | Catalysts; Heterogeneous Catalysis; Chemical Kinetics; Surface; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752c3337d6c510be28779/original/unraveling-the-activity-of-iron-carbide-clusters-embedded-in-silica-for-thermocatalytic-conversion-of-methane.pdf |
60c7491b702a9be88718b0e9 | 10.26434/chemrxiv.12029709.v1 | Interstitial vs. Substitutional Metal Insertion in V2O5 as Post-Lithium Ion Battery Cathode: A Comparative GGA/GGA+U Study with Localized Bases | <p></p><p>The generalized gradient approximation
(GGA) often fails to correctly describe the electronic structure and
thermochemistry of transition metal oxides and is commonly improved using an
inexpensive correction term with a scaling parameter <i>U</i>. We tune <i>U</i>
to reproduce experimental vanadium oxide redox energetics with a localized basis
and a GGA functional. We find the value for <i>U</i> to be significantly lower
than what is generally reported with plane-wave bases, with the uncorrected GGA
results being in reasonable agreement with experiments. We use this
computational setup to calculate interstitial and substitutional <a>insertion energies of main group metals in vanadium
pentoxide</a> and find <a>interstitial doping to be
thermodynamically favored</a>.</p><p></p> | Daniel Koch; Sergei Manzhos | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7491b702a9be88718b0e9/original/interstitial-vs-substitutional-metal-insertion-in-v2o5-as-post-lithium-ion-battery-cathode-a-comparative-gga-gga-u-study-with-localized-bases.pdf |
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