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6766b26d81d2151a027bab03 | 10.26434/chemrxiv-2024-khszr | Improving hydrogen generation from biomass and solid waste by combining sonophotocatalysis through carbon-based materials: challenges and future perspectives | Abstract
Environmental pollution is becoming one of the main issues facing human civilisation as a result of
the world's growing industrialisation. Using limitless solar energy, photocatalysis may be used to
address environmental issues. Whilst, the incorporation of ultrasonic cavitation in various processes
such as the Fenton-like process, electrochemical process, and especially sono-photocatalysis offer
ideal conditions for increasing biomass fragmentation and conversion into target products and green
hydrogen within a lesser reaction time. The scientific community and industry have taken a serious
interest in the intensification of ultrasonic processes for a variety of applications, as well as the
resulting synergistic effects based on conventional comparisons in literature. In light of this, the
purpose of this review is to summarize the current research in the field, provide an overview of the
recent studies on ultrasound-assisted different catalytic processes for hydrogen production and
discuss their limits and validity, comparing them to conventional techniques. Finally, a few future
perspectives in the form of suggestions on ultrasound-assisted photocatalysis for hydrogen production
from various biomass models and different wastes, and highlighting the role and recent evolution of
carbon-based materials in this field, are presented together with current issues and challenges to
clarify future attitudes in the hopes of exploring this ideal combination for large-scale H2 production. | DJABALLAH Ahmed Malek; Behdokht Hashemi Hosseini; Ramón Fernando Colmenares-Quintero; Dariusz Łomot; Juan Carlos Colmenares | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis; Photocatalysis; Power | CC BY 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6766b26d81d2151a027bab03/original/improving-hydrogen-generation-from-biomass-and-solid-waste-by-combining-sonophotocatalysis-through-carbon-based-materials-challenges-and-future-perspectives.pdf |
60c74392f96a0080e8286837 | 10.26434/chemrxiv.9034178.v2 | Solvent Dynamics and Thermodynamics at the Crystal-Solution Interface of Ibuprofen | In this paper we apply molecular simulation techniques to analyse the dynamics and thermodynamics of nine solvents, i.e. water, 1-butanol, toluene, cyclohexanone, cyclohexane, acetonitrile, trichloromethane, methanol and ethyl acetate, at the interface with the morphologically relevant crystal faces {100}, {002}, {011} and {110} of ibuprofen. <div>The insight obtained from this analysis is used to rationalise the impact of the solvent choice on the growth shape of crystals. <br /><div><br /></div></div> | Veselina Marinova; Geoffrey P. F. Wood; Ivan Marziano; Matteo Salvalaglio | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74392f96a0080e8286837/original/solvent-dynamics-and-thermodynamics-at-the-crystal-solution-interface-of-ibuprofen.pdf |
60c73f5d469df493dbf42a93 | 10.26434/chemrxiv.7346693.v1 | Turning a Methanation Catalyst into a Methanol Producer: In-Co Catalysts for the Direct Hydrogenation of CO2 to Methanol | <div>
<div>
<div>
<p>The direct hydrogenation of CO2 to methanol using green hydrogen is
regarded as a potential technology to reduce greenhouse gas emissions and the
dependence on fossil fuels. For this technology to become feasible, highly selective
and productive catalysts that can operate under a wide range of reaction conditions
near thermodynamic conversion are required. Here, we demonstrate that indium in
close contact with cobalt catalyses the formation of methanol from CO2 with high
selectivity (>80%) and productivity (0.86 gCH3OH.gcatalyst-1.h-1) at conversion levels close
to thermodynamic equilibrium, even at temperatures as high as 300 °C and at
moderate pressures (50 bar). The studied In@Co system, obtained via co-
precipitation, undergoes in situ transformation under the reaction conditions to form
the active phase. Extensive characterization demonstrates that the active catalyst is
composed of a mixed metal carbide (Co3InC0.75), indium oxide (In2O3) and metallic Co.
</p>
</div>
</div>
</div> | Anastasiya Bavykina; Irina Yarulina; Lieven Gevers; Mohamed
Nejib Hedhili; Xiaohe Miao; Adrian Ramirez; Oleksii Pustovarenko; Alla Dikhtiarenko; Amandine Cadiau; Samy Ould-Chikh; Jorge Gascon | Heterogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5d469df493dbf42a93/original/turning-a-methanation-catalyst-into-a-methanol-producer-in-co-catalysts-for-the-direct-hydrogenation-of-co2-to-methanol.pdf |
64cba5fe4a3f7d0c0d86b452 | 10.26434/chemrxiv-2023-lck31-v2 | Cost Estimation of the Sustainable Production of MIL-100(Fe) at Industrial Scale from two upscaled synthesis routes | Understanding the impact of MOF synthesis conditions on the production cost is vital in order to have a competitive product in a view of industrial applications. Here, considering the benchmark mesoporous iron(III) trimesate MIL-100(Fe) as a prototypical example, we show that the production cost can reach <30 $/kg if a careful selection of the synthetic route is made. Two routes were considered in the analysis, using sulfate and nitrate as iron sources. A new optimized synthesis protocol in a laboratory pilot-scale reactor of 5 liters based on iron sulfate was developed using optimized sustainable ambient pressure conditions, leading to larger particles and a higher STY. Based on reliable pilot-scale data and established chemical engineering estimation methods, this leads to a significantly low production cost of high quality MIL-100(Fe) achieving a potential competitive product. | farid Nouar; christian Serre; Moisés L. Pinto; Maria Inês Severino; Vanessa Pimenta; Catia Freitas | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64cba5fe4a3f7d0c0d86b452/original/cost-estimation-of-the-sustainable-production-of-mil-100-fe-at-industrial-scale-from-two-upscaled-synthesis-routes.pdf |
638d0d3c836ceb41c873788d | 10.26434/chemrxiv-2022-jbc9n | Evidence for Ligand- and Metal-Centered
Reduction in Polypyridyl Dicarboxylate Complexes of Ru(II) and U(VI) | Polypyridyl dicarboxylates have been established as oxidatively robust ligands capable of effectively binding heavy metals, but the reductive electrochemical properties of complexes supported by these ligands have not been explored to date. Here, the redox properties of Ru(II) and uranyl(VI) (UO22+) complexes of 2,2′-bipyridyl-6,6′-dicarboxylate (bdc), 2,2′:6′,2″-terpyridyl-6,6″-dicarboxylate (tdc), and 4′-phenyl-2,2′:6′,2″-terpyridyl-6,6″-dicarboxylate (Phtdc) have been investigated, revealing that these ligands can enable both ligand- and metal-centered reductions. In control ruthenium complexes, electrochemical and spectroelectrochemical data supported by theoretical findings from density functional theory suggest electron density in the reduced forms primarily resides on the ligands. In bdc complexes of uranyl, electrochemical data and theoretical findings support the involvement of both ligand- and metal-centered reductive behavior. This “non-innocent” redox chemistry, along with support for the assertion that these ligands bind large metals effectively, suggests that polypyridyl dicarboxylates could be useful in new schemes for reductive activation of challenging metal-containing species. The observation of ligand-centered reduction events is also in agreement with the recognized “non-innocent” redox activity of related 2,2′-bipyridyl systems that lack appended carboxylate functionalities. | Emily Mikeska; Gabriel Benitez; Kaihua Zhang; Allen Oliver; Marco Caricato; Chelsea Comadoll; James Blakemore | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Ligands (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638d0d3c836ceb41c873788d/original/evidence-for-ligand-and-metal-centered-reduction-in-polypyridyl-dicarboxylate-complexes-of-ru-ii-and-u-vi.pdf |
60c743be9abda229e7f8c23e | 10.26434/chemrxiv.9206417.v2 | Reciprocal Polarizable Embedding with a Transferable H2O Potential Function I: Formulation & Tests on Dimer | This work describes a general energy functional formulation of a polarizable embedding QM/MM scheme, as well as an implementation where a real-space Grid-based Projector Augmented Wave (GPAW) DFT method is coupled with a potential function for H<sub>2</sub>O based on a Single Center Multipole Expansion (SCME) of the electrostatics, including anisotropic dipole and quadrupole polarizability. | Elvar Jónsson; Asmus Ougaard Dohn; Hannes Jonsson | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743be9abda229e7f8c23e/original/reciprocal-polarizable-embedding-with-a-transferable-h2o-potential-function-i-formulation-tests-on-dimer.pdf |
637eb2a61234cb2cfb20c7be | 10.26434/chemrxiv-2022-d56f5 | Signatures of Chemical Dopants in Simulated Resonance Raman Spectroscopy of Carbon Nanotubes | Single-walled carbon nanotubes (SWCNTs) with organic sp2- or sp3-hybdridization defects allow for robust tunability in many optoelectronic properties in these topologically interesting quasi-one-dimensional materials. Recent resonant Raman experiments have discovered new features in the intermediate frequency region upon functionalization and change with the degree of functionalization as well as with interactions between defect sites. In this letter, we report ab initio simulated near-resonant Raman spectroscopy results for pristine and chemically functionalized SWCNT models and find new features concomitant to experimental observations. We are able to assign the character of these features by varying the frequency of the external Raman laser frequency near the defect-induced E11* optical transition using a perturbative treatment to the electronic structure of the system. Obtained insights establish relationships between nanotube atomistic structure and Raman spectra facilitating further exploration of SWCNTs with tunable optical properties tuned by chemical doping. | Braden Weight; Ming Zheng; Sergei Tretiak | Theoretical and Computational Chemistry; Nanoscience; Nanodevices; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637eb2a61234cb2cfb20c7be/original/signatures-of-chemical-dopants-in-simulated-resonance-raman-spectroscopy-of-carbon-nanotubes.pdf |
65a7fc3e66c1381729aa8d77 | 10.26434/chemrxiv-2024-7gb3v | Nickel Perfluoroalkyl Complexes Supported by Simple Acetate Co-Ligands | The interaction of tetramethylammonium acetate with [(MeCN)2Ni(CF3)2], [(MeCN)2Ni(C2F5)2], and [NMe4][(MeCN)Ni(CF3)3] was explored by 19F NMR spectroscopy. We show that, depending on the nature of the nickel complex, one or two acetate ligands can add to the metal center and replace the nickel-bound acetonitriles, depending on the acetate concentration. The number of acetates that could bind to nickel, and whether the resulting complex exists as a monomer or dimer, was determined to be dependent on the nature of the fluoroalkyl ligand. Moreover, we observe that oxidation of the nickel center of [(MeCN)2Ni(CF3)2] in the presence of two equivalents of acetate leads cleanly to the octahedral, paramagnetic, and anionic nickel(III) complex [NMe4][(OAc)2Ni(CF3)2. | Cherry Ravidas; Scott Shreiber; David Vicic | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a7fc3e66c1381729aa8d77/original/nickel-perfluoroalkyl-complexes-supported-by-simple-acetate-co-ligands.pdf |
65fc89109138d23161f7dac1 | 10.26434/chemrxiv-2024-cb6lx | Photocatalytic treatment of diverse contaminants of potential concern in oil sands process-affected water | Oil sands process-affected water (OSPW), generated by surface mining in Canada’s oil sands, require treatment of environmentally persistent dissolved organic compounds before release to the watershed. Conventional chemical and mechanical treatments have not proved suitable for treating the large quantities of stored OSPW, and the biological recalcitrance of some dissolved organics may not be adequately addressed by conventional passive treatment systems. Previous work has evaluated photocatalytic treatment as a passive advanced oxidation process (P-AOP) for OSPW remediation. This work expands upon this prior research to further characterize the effects of water chemistry on the treatment rate and detoxification threshold. Under artificial sunlight, buoyant photocatalysts (BPCs) detoxified all OSPW samples within 1 week of treatment time with simultaneous treatment of polycyclic aromatic hydrocarbons, naphthenic acid fraction components (NAFCs), and un-ionized ammonia. Overall, these results further demonstrate passive photocatalysis as an effective method for treatment of OSPW contaminants of potential concern (COPCs). | Jeffrey T. Martin; Timothy M. C. Leshuk; Kieran Armstrong; Tia Chai; Zachary W. Young; Theo Paradis; Asfaw Bekele; Todd White; Frank Gu | Catalysis; Earth, Space, and Environmental Chemistry; Environmental Science; Wastes; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fc89109138d23161f7dac1/original/photocatalytic-treatment-of-diverse-contaminants-of-potential-concern-in-oil-sands-process-affected-water.pdf |
60c74df6469df47f27f4439d | 10.26434/chemrxiv.12152970.v4 | A Predictive Model of the Temperature-Dependent Inactivation of Coronaviruses | The
COVID-19 pandemic has stressed healthcare systems and supply lines, forcing
medical doctors to risk infection by decontaminating and reusing single-use
medical personal protective equipment. The uncertain future of the pandemic is
compounded by limited data on the ability of the responsible virus, SARS-CoV-2,
to survive across various climates, preventing epidemiologists from accurately
modeling its spread. However, a detailed thermodynamic analysis of experimental
data on the inactivation of SARS-CoV-2 and related coronaviruses can enable a
fundamental understanding of their thermal degradation that will help model the
COVID-19 pandemic and mitigate future outbreaks. This paper introduces a
thermodynamic model that synthesizes existing data into an analytical framework
built on first principles, including the rate law and the Arrhenius equation,
to accurately predict the temperature-dependent inactivation of coronaviruses.
The model provides much-needed thermal decontamination guidelines for personal
protective equipment, including masks. For example, at 70 °C, a 3-log (99.9%)
reduction in virus concentration can be achieved in ≈ 3 minutes and can be
performed in most home ovens without reducing the efficacy of typical N95
masks. The model will also allow for epidemiologists to incorporate the
lifetime of SARS-CoV-2 as a continuous function of environmental temperature
into models forecasting the spread of coronaviruses across different climates
and seasons. | Te Faye Yap; Zhen Liu; Rachel A. Shveda; Daniel Preston | Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74df6469df47f27f4439d/original/a-predictive-model-of-the-temperature-dependent-inactivation-of-coronaviruses.pdf |
67b542b6fa469535b9f0060a | 10.26434/chemrxiv-2025-9dw51 | A Compartmentalized Model of Multiphase Chemical Kinetics | There are significant challenges in predicting multiphase chemical kinetics due to the complex coupling of reaction and mass transport across a phase boundary (i.e. interface). Here we describe a framework for predicting multiphase kinetics that embeds the elementary kinetic steps of reaction, solvation and diffusion into a coarse grain spatial description of two phases. The model is constructed to bridge the short-timescale interfacial dynamics observed in molecular simulations with the longer timescales observed in kinetic experiments. A simple set of governing differential equations is presented, which when solved numerically or analytically, yield accurate predictions of multiphase kinetics in microdroplets. Although the equations are formulated for gas-liquid reactions, the underlying conceptual framework is general and can be applied to transformations in other two-phase systems (solid-liquid, liquid-liquid, etc.). | Alexander Prophet; Kevin Wilson | Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Chemical Kinetics; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b542b6fa469535b9f0060a/original/a-compartmentalized-model-of-multiphase-chemical-kinetics.pdf |
67b3e046fa469535b9c919ea | 10.26434/chemrxiv-2025-b7z0z | Visible-Light Induced “Photo-Click” Reactions of Acylsilanes with Pyruvate Electrophiles
| Siloxycarbenes induced via the visible light irradiation of acylsilanes undergo highly efficient “photo-click” chemistry reactions with electron deficient ketones. This process requires no reagents other than visible light, proceeds with high efficiency and is tolerant of a wide range of functional groups. Pyruvate esters, thioesters, amides, nitriles and phosphonates were all suitable electrophiles including those tethered to complex drug or biomolecule scaffolds. The “photo-click” chemistry process was achieved on larger scale using both batch and flow methodologies, accompanied by diversification studies on the corresponding addition products. Mechanistic insights into siloxycarbene reactivity were also obtained by DFT analysis. | Rowan Pilkington; Rosa Koessler; Jesse Molloy; Stefan Braese; Daniel Priebbenow | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b3e046fa469535b9c919ea/original/visible-light-induced-photo-click-reactions-of-acylsilanes-with-pyruvate-electrophiles.pdf |
679622dbfa469535b9eb52f5 | 10.26434/chemrxiv-2025-7fhz2 | Human Serum Albumin Loaded with Fatty Acids Reveals Complex Protein-Ligand Thermodynamics and Boleadora-Type Solution Dynamics Leading to Gelation | Using an electron paramagnetic resonance (EPR) spectroscopic strategy that has been developed for core-shell polymers, the complexity of the binding of fatty acids to human serum albumin (HSA) is characterized in detail. We unravel the internal dynamics of HSA solutions with fatty acids by applying continuous wave EPR (CW EPR) from which we derive a consistent thermodynamic interpretation about fatty acid interactions with HSA in the investigated temperature range of 5 °C – 97 °C. Additionally, data from CW EPR are corroborated by dynamic light scattering (DLS), differential scanning calorimetry (DSC) and nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy. We discuss our data in light of decades of biophysical studies on albumin and aim at drawing a complete functional and dynamic picture of HSA “at work”. This picture suggests that HSA is built from modular, rotationally-decoupled domains that resemble an entangled three-piece boleadora in solution. | Dariush Hinderberger; Jörg Reichenwallner; Sebastian Michler; Christian Schwieger | Physical Chemistry; Biological and Medicinal Chemistry; Biophysical Chemistry; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/679622dbfa469535b9eb52f5/original/human-serum-albumin-loaded-with-fatty-acids-reveals-complex-protein-ligand-thermodynamics-and-boleadora-type-solution-dynamics-leading-to-gelation.pdf |
60c73e99bb8c1a9f6a3d9929 | 10.26434/chemrxiv.7043927.v1 | Synthesis of Phosphonic Acid Ligands for Nanocrystal Surface Functionalization and Solution Processed Memristors | <p>Here
we synthesize 2-ethylhexyl, 2-hexyldecyl, 2-[2-(2-methoxyethoxy)ethoxy]ethyl,
oleyl and <i>n</i>-octadecyl phosphonic acid
and use them to functionalize CdSe and HfO<sub>2</sub> nanocrystals. In
contrast to branched carboxylic acids, post-synthetic surface functionalization
of CdSe and HfO<sub>2</sub> nanocrystals is readily achieved with branched
phosphonic acids. A simple flow coating process is used to deposit ribbons of
individual phosphonic acid capped HfO<sub>2</sub> nanocrystals, which are
subsequently evaluated as a memristor using conductive atomic force microscopy
(c-AFM). We find that 2-ethylhexyl phosphonic acid is a superior ligand,
combining a high colloidal stability with a compact ligand shell that results
in a record-low operating voltage that is promising for application in flexible
electronics. </p> | Jonathan De Roo; Zimu Zhou; Jiaying Wang; Loren Deblock; Alfred J. Crosby; Jonathan S. Owen; Stephen
S. Nonnenmann | Organic Synthesis and Reactions; Ceramics; Materials Processing; Nanostructured Materials - Materials; Surfactants; Thin Films; Nanodevices; Nanostructured Materials - Nanoscience; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e99bb8c1a9f6a3d9929/original/synthesis-of-phosphonic-acid-ligands-for-nanocrystal-surface-functionalization-and-solution-processed-memristors.pdf |
66e90ffacec5d6c1424b73dd | 10.26434/chemrxiv-2024-nx3vg | Experimental Demonstration of Humid Post-Combustion CO2 Capture by Vacuum Swing Adsorption Using CALF-20 | Calgary Framework 20 (CALF-20) is a metal-organic framework deployed for industrial post-combustion CO2 capture. This work explores capturing CO2 from a humid stream using CALF-20. A four-step vacuum swing adsorption (VSA) cycle incorporating a light product pressurization step was examined. Two columns packed with structured CALF-20 were used to perform VSA experiments over a wide range of relative humidity (RH) values (13%, 25%, 45% and 70% RH). Key process performance indicators, purity, recovery and productivity were measured and compared with the dry case basis. At low to intermediate relative humidity (13%-45% RH), the difference between the dry and the wet VSA cycle was minimal. The purity and recovery were approximately 95% and 71% in Case Study 1, and 92% and 81% in Case Study 2, respectively. The temperature and composition histories were similar to the dry. At high relative humidity (70% RH), while CALF-20 could still achieve similar purity, recovery and productivity, reaching low pressure during the evacuation step was difficult due to the water condensation. Each experiment was run for several days (hundreds of cycles) to confirm the long-term stability of the material. CALF-20 also showed good cyclic durability; minimal loss in the CO2 capacity from the used CALF-20 sample (~10,000 cycles) was observed | Tai Nguyen; George Shimizu; Arvind Rajendran | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e90ffacec5d6c1424b73dd/original/experimental-demonstration-of-humid-post-combustion-co2-capture-by-vacuum-swing-adsorption-using-calf-20.pdf |
6506c35699918fe5371a827a | 10.26434/chemrxiv-2023-cbq9k | Deep interactome learning for de novo drug design | De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It allows for the construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma were generated. The top-ranking designs were chemically synthesized and biophysically and biochemically characterized. Potent PPAR partial agonists were identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirmed the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules. | Kenneth Atz; Leandro Cotos Muñoz; Clemens Isert; Maria Håkansson; Dorota Focht; David F. Nippa; Mattis Hilleke; Michael Iff; Jann Ledergerber; Carl C. G. Schiebroek; Jan A. Hiss; Daniel Merk; Petra Schneider; Bernd Kuhn; Uwe Grether; Gisbert Schneider | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6506c35699918fe5371a827a/original/deep-interactome-learning-for-de-novo-drug-design.pdf |
63480e663e8d99aea61870e7 | 10.26434/chemrxiv-2022-c9gkl | Polyketones from Carbon Dioxide and Ethylene by Integrating Electrochemical and Organometallic Catalysis | The utilization of carbon dioxide in polymer synthesis is an attractive strategy for sustainable materials. Electrochemical CO2 reduction would offer a natural starting point for producing monomers, but the conditions of electrocatalysis are often drastically different from the conditions of organometallic coordination-insertion polymerization. Reported here is a strategy for integrating electrochemical and organometallic catalysts that enables polyketone synthesis from CO2 and ethylene in a single multicompartment reactor. Polyketone materials that are up to 50% derived from CO2 can be prepared in this way. Potentiostatic control over the CO-producing catalyst enables the controlled generation of low-pressure CO, which in conjunction with a palladium phosphine sulfonate organometallic catalyst enables copolymerization to nonalternating polyketones with the CO content tuned based on the applied current density | Henry Dodge; Benjamin Natinsky; Brandon Jolly; Haochuan Zhang; Yu Mu; Scott Chapp; Thi Tran; Paula Diaconescu; Loi Do; Dunwei Wang; Chong Liu; Alexander Miller | Catalysis; Organometallic Chemistry; Polymer Science; Polymerization catalysts; Electrocatalysis; Electrochemistry - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63480e663e8d99aea61870e7/original/polyketones-from-carbon-dioxide-and-ethylene-by-integrating-electrochemical-and-organometallic-catalysis.pdf |
60c73e10842e65ec97db184c | 10.26434/chemrxiv.6287810.v1 | Structure and Dynamics of Water Confined in Imogolite Nanotubes | We have studied the properties of water adsorbed inside nanotubes of hydrophilic imogolite, an aluminium silicate clay mineral, by means of molecular simulations. We used a classical force field to describe the water and the flexible imogolite nanotube, and validated it against data obtained from first-principles molecular dynamics. With it, we observe a strong structuration of the water confined in the nanotube, with specific adsorption sites and a distribution of hydrogen bond patterns. The combination of number of adsorption sites, their geometry and the preferential tetrahedral hydrogen bonding pattern of water leads to frustration and disorder. We further characterize the dynamics of the water, as well as the hydrogen bonds formed between water molecules and the nanotube, which are found to be more than one order of magnitude longer than water–water hydrogen bonds. | Laura Scalfi; Guillaume Fraux; Anne Boutin; François-Xavier Coudert | Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e10842e65ec97db184c/original/structure-and-dynamics-of-water-confined-in-imogolite-nanotubes.pdf |
65c49e5566c13817293472a1 | 10.26434/chemrxiv-2024-6l2q7 | An extremely electron poor Au(III) trication bearing acetonitrile ligands | The synthesis and structural characterization of an electron poor Au(III) trication bearing 2 imidazole and 2 acetonitrile ligands is described. The new complex is capable of aryl C-H metalation with the formation of a monomesitylene species and also demonstrated to be highly oxidizing in facilitating the rapid room temperature conversion of cyclohexene to benzene. | Jason Dutton; Lachlan Barwise; Bibidh Dhakal; Keith White | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Coordination Chemistry (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-02-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c49e5566c13817293472a1/original/an-extremely-electron-poor-au-iii-trication-bearing-acetonitrile-ligands.pdf |
60c755e7f96a0074af288992 | 10.26434/chemrxiv.13341659.v2 | How Wide Is the Window Opened by High-Resolution Relaxometry on the Internal Dynamics of Proteins in Solution? | Here we apply the detectors approach to probe the amount of information in high-resolution relaxometry measurements in biological macromolecules in solution. We show that high-resolution relaxometry provides new relevant information in the nanosecond range and that the additional range of information is all the more large as the overall rotational diffusion is slow. | Albert Smith; Nicolas Bolik-Coulon; Matthias Ernst; Beat Meier; Fabien Ferrage | Biophysical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755e7f96a0074af288992/original/how-wide-is-the-window-opened-by-high-resolution-relaxometry-on-the-internal-dynamics-of-proteins-in-solution.pdf |
6234cac28ab3730baa69580a | 10.26434/chemrxiv-2022-4jdc5 | QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases | β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered ‘last resort’ antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to the deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes activation free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency towards carbapenems. | Ewa Chudyk; Michael Beer; Michael A.L. Limb; Charlotte A. Jones; James Spencer; Mark W. van der Kamp; Adrian Mulholland | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Biochemistry; Biophysics; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6234cac28ab3730baa69580a/original/qm-mm-simulations-reveal-the-determinants-of-carbapenemase-activity-in-class-a-lactamases.pdf |
6212a8857d068aa1a326e062 | 10.26434/chemrxiv-2021-wn21q-v3 | Global, High-Resolution, Reduced-Complexity Air Quality Modeling for PM2.5 Using InMAP (Intervention Model for Air Pollution) | Each year, millions of premature deaths worldwide are caused by exposure to outdoor air pollution, especially fine particulate matter (PM2.5). Designing policies to reduce these deaths relies on air quality modeling for estimating changes in PM2.5 concentrations from many scenarios at high spatial resolution. However, air quality modeling typically has substantial requirements for computation and expertise, which limits policy design, especially in countries where most PM2.5-related deaths occur. Lower requirement reduced-complexity models exist but are generally unavailable worldwide. Here, we adapt InMAP, a reduced-complexity model originally developed for the United States, to simulate annual-average primary and secondary PM2.5 concentrations across a global-through-urban spatial domain: “Global InMAP”. Global InMAP uses a variable resolution grid, with horizontal grid cell widths ranging from 500 km in remote locations to 4km in urban locations. We evaluate Global InMAP performance against both measurements and a state-of-the-science chemical transport model, GEOS-Chem. Against measurements, InMAP predicts total PM2.5 concentrations with a normalized mean error of 62%, compared to 41% for GEOS-Chem. For the emission scenarios considered, Global InMAP reproduced GEOS-Chem pollutant concentrations with a normalized mean bias of 59%–121%, which is sufficient for initial policy assessment and scoping. Global InMAP can be run on a desktop computer; simulations here took 2.6–8.4 hours. This work presents a global, open-source, reduced-complexity air quality model to facilitate policy assessment worldwide, providing a screening tool for reducing air pollution-related deaths where they occur most. | Sumil Thakrar; Christopher Tessum; Joshua Apte; Srinidhi Balasubramanian; Dylan B Millet; Spyros Pandis; Julian D. Marshall; Jason Hill | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6212a8857d068aa1a326e062/original/global-high-resolution-reduced-complexity-air-quality-modeling-for-pm2-5-using-in-map-intervention-model-for-air-pollution.pdf |
60c752d2842e65c0eddb3e21 | 10.26434/chemrxiv.13340711.v1 | Efficient PCA-Exploration of High-Dimensional Datasets | <div><div><div><p>Basic tools for exploration and interpretation of Principal Component Analysis (PCA) results are well- known and thoroughly described in many comprehensive tutorials. However, in the recent decade, several new tools have been developed. Some of them were originally created for solving authentication and classification tasks. In this paper we demonstrate that they can also be useful for the exploratory data analysis.</p><p><br /></p><p>We discuss several important aspects of the PCA exploration of high dimensional datasets, such as estimation of a proper complexity of PCA model, dependence on the data structure, presence of outliers, etc. We introduce new tools for the assessment of the PCA model complexity such as the plots of the degrees of freedom developed for the orthogonal and score distances, as well as the Extreme and Distance plots, which present a new look at the features of the training and test (new) data. These tools are simple and fast in computation. In some cases, they are more efficient than the conventional PCA tools. A simulated example provides an intuitive illustration of their application. Three real-world examples originated from various fields are employed to demonstrate capabilities of the new tools and ways they can be used. The first example considers the reproducibility of a handheld spectrometer using a dataset that is presented for the first time. The other two datasets, which describe the authentication of olives in brine and classification of wines by their geographical origin, are already known and are often used for the illustrative purposes.</p><p><br /></p><p>The paper does not touch upon the well-known things, such as the algorithms for the PCA decomposition, or interpretation of scores and loadings. Instead, we pay attention primarily to more advanced topics, such as exploration of data homogeneity, understanding and evaluation of an optimal model complexity. The examples are accompanied by links to free software that implements the tools.</p></div></div></div> | Oxana Ye. Rodionova; Sergey Kucheryavskiy; Alexey L. Pomerantsev | Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752d2842e65c0eddb3e21/original/efficient-pca-exploration-of-high-dimensional-datasets.pdf |
6145b3d7d9c956140dd69207 | 10.26434/chemrxiv-2021-43vr3 | The DNA–carbon nanotube binding mode determines the efficiency of carbon nanotube-mediated DNA delivery to intact plants | Efficient delivery of DNA, RNA, and genome engineering machinery to plant cells will enable efforts to genetically modify plants for global food security, sustainable energy production, synthetic biology applications, and climate change resilience. For the delivery of functional genetic units into plant cells, charged nanoparticles, particularly carbon nanotubes (CNT), have attracted considerable interest. Although some success has been achieved using CNT-based approaches, the efficiency, batch reproducibility, and the limits of their applicability remain to be assessed. Here, we provide a mechanistic understanding of plasmid DNA-loaded CNTs based transfection of plant cells, and factors affecting the expression of the transformed plasmid. We show that transfection is inherently limited by the presence of the cell wall, Coulomb interactions between DNA and polymer coated CNT, and DNA size, whereas expression of the transformed plasmid is limited by relative gene-to-plasmid size and the intracellular accessibility of DNA. We further show that the formation of partially condensed DNA on the CNT surface is a prerequisite for successful transfection and expression. Furthermore, DNA does not detach completely from the CNT, so the accessibility of the transcription machinery to DNA is the key for transformation efficiency. This irreversible DNA plasmid binding and partial condensation limit the length of DNA that can be expressed, thus negatively affecting efficiency and reproducibility. Understanding the underlying mechanisms and limitations of CNT-mediated delivery of DNA through the plant cell wall is of considerable importance in guiding efforts to design nanomaterials for efficient transformation, trait engineering, and synthetic biology applications. | Zahir Ali; Maged Serag; Gozde Demirer; Bruno Torre; Enzo di Fabrizio; Markita Landry; Satoshi Habuchi; Magdy Mahfouz | Nanoscience; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6145b3d7d9c956140dd69207/original/the-dna-carbon-nanotube-binding-mode-determines-the-efficiency-of-carbon-nanotube-mediated-dna-delivery-to-intact-plants.pdf |
60c74686ee301c012ac79545 | 10.26434/chemrxiv.11342096.v1 | Ru-Catalyzed Carbonylative Murai Reaction: Directed C3-Acylation of Biomass-Derived 2-Formyl Heteroaromatics | <p>We describe
here the carbonylative Murai reaction applied to 2-formylfurans,
2-formylpyrrols and 2-formylthiophenes. Thanks to the installation of removable
imine directing groups, this acylation reaction takes place
regioselectively at C3 position of the heterocyclopentadienes. It can be achieved by treating the two reaction partners with a
catalytic amount of Ru<sub>3</sub>(CO)<sub>12</sub>, in toluene at 120-150 °C,
after CO bubbling, at atmospheric pressure. DFT computations of the full
catalytic cycle help in deciphering the mechanism of this transformation, and
to rationalize the different behaviors depending on the nature of imine
directing groups.</p> | Roberto Sala; Fares Roudesly; Luis F. Veiros; Gianluigi Broggini; Julie Oble; Giovanni Poli | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74686ee301c012ac79545/original/ru-catalyzed-carbonylative-murai-reaction-directed-c3-acylation-of-biomass-derived-2-formyl-heteroaromatics.pdf |
667179675101a2ffa8dc7586 | 10.26434/chemrxiv-2023-mx4m7-v2 | pH drives electron density fluctuations that enhance electric field-induced liquid flow | Liquid flow along a charged interface is commonly described by classical continuum theory, which represents the electric double layer by uniformly distributed point charges. The electrophoretic mobility of hydrophobic nanodroplets in water doubles in magnitude when the pH is varied from neutral to mildly basic (pH 7 to pH 11). Classical continuum theory predicts that this increase in mobility is due to an increased surface charge. Here, by combining all-optical measurements of surface charge and molecular structure, as well as electronic structure calculations, we show that surface charge and molecular structure at the nanodroplet surface are identical at neutral and mildly basic pH. We propose that the force that propels the droplets originates from two factors: Negative charge on the droplet surface due to charge transfer from and within water, and anisotropic gradients in the fluctuating polarization induced by the electric field. Both charge density fluctuations couple with the external electric field, and lead to droplet flow. Replacing chloride by hydroxide doubles both the charge conductivity via the Grotthuss mechanism, and the droplet mobility. This general mechanism deeply impacts a plethora of processes in biology, chemistry, and nanotechnology and provides an explanation of how pH influences hydrodynamic phenomena and the limitations of classical continuum theory currently used to rationalize these effects. | Saranya Pullanchery; Sergey Kulik; Tereza Schönfeldová; Colin Egan; Giuseppe Cassone; Ali Hassanali; Sylvie Roke | Theoretical and Computational Chemistry; Physical Chemistry; Interfaces; Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667179675101a2ffa8dc7586/original/p-h-drives-electron-density-fluctuations-that-enhance-electric-field-induced-liquid-flow.pdf |
648306fae64f843f418b906a | 10.26434/chemrxiv-2023-zpk29-v5 | Synthesis and Binding Profile Using Simulations of New Building Blocks for PSMA Theranostics Against Prostate Cancer | GCPII also known as Prostate Specific Membrane Antigen (PSMA), is overexpressed in prostate cancer (PCa) cells and provide a biomarker for tumor targeting PSMA receptor. The development of lysine-urea-glutamate pharmacophore based inhibitors targeting PSMA for theranostics applications led to PSMA11 and PSMA617. In PSMA11, this pharmacophore is attached via aminohexanoic acid (Ahx) spacer to a chelator while in PSMA617 the pharmacophore is connecting with the linker 2-naphthyl-L-Ala, trans-4-(aminomethyl)cyclohexanecarboxylic acid and then to chelator. Here, we synthesized: (a) a squaramide analog of lysine-urea-glutamic acid; (b) two new building blocks for PSMA theranostics in which lysine-urea-glutamic acid was attached with two (i) phenyl alanine residues and (ii) amino hexanoic acid residues. Induced fit docking explored the binding profile of the new molecules. Biological experiments will provide data on the significance of the new molecules. | Evangelos Machairas; George Laros; George Lambrinidis; Maria Halabalaki; Christos Liolios; Antonios Kolocouris | Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2023-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648306fae64f843f418b906a/original/synthesis-and-binding-profile-using-simulations-of-new-building-blocks-for-psma-theranostics-against-prostate-cancer.pdf |
64357573a41dec1a56e16f8a | 10.26434/chemrxiv-2023-82fqp | Cobalt(III)-Catalyzed Free Amine Directed Site-Selective Allylation in 2-Aminobiaryls with Vinyl Cyclopropanes | 2-Aminobiaryls are privileged scaffolds and their cogent synthesis and diversifications, particularly through the C-H bond activation strategy, is a continuous enterprise in organic synthesis. In this realm, capitalization on susceptible native amine (-NH2) directing group is beneficial but increasingly challenging owing to its innate nucleophilic reactivity. Also, the C-H activation reactions of this class of substrates have traditionally been restricted to the cross-ring C-H bond as the ortho C-H functionalization presumably requires the formation of a strained high-energy four-membered metallacycle. Herein, we report the first example of free amine-directed ortho C-H activation reaction of 2-aminobiaryls under high-valent Cp*Co(III)-catalysis, enabling regio- and stereoselective allylation reaction in high yields. The protocol engages vinyl cyclopropanes as allyl synthons where the C-C bond construction event was tunneled to a C-C activation process to forge internal olefin with exclusive (E)-selectivity. The products were judicially used to access high-value benzo[d]isoxazoles and dihydro phenanthridine derivatives. Mechanistic experiments and DFT calculations have also been conducted to unravel the rationale behind the unique site selectivity, where the thermodynamic constraints of the corresponding intermediates favoring the ortho C-H activation over cross-ring functionalization. | Deepan Chowdhury; Suman Ghosh; K.S.S.V. Prasad Reddy; Sharma S.R.K.C. Yamijala ; Mahiuddin Baidya | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64357573a41dec1a56e16f8a/original/cobalt-iii-catalyzed-free-amine-directed-site-selective-allylation-in-2-aminobiaryls-with-vinyl-cyclopropanes.pdf |
67c8728d6dde43c9089b6eb3 | 10.26434/chemrxiv-2025-v14p7 | A Perspective Marking 20 Years of Using
Permutationally Invariant Polynomials for
Molecular Potentials | This Perspective is focused on Permutationally invariant polynomials (PIPs). Since their introduction in 2004 and first use in developing a fully permutationally invariant
potential for the highly fluxional cation CH+5 , PIPs have found widespread use in developing machine learned potentials (MLPs) for isolated molecules, chemical reactions, clusters, condensed phase, and materials. More than 100 potentials have been reported using PIPs. The popularity of PIPs for MLPs stems from their fundamental property of being invariant with respect to permutations of like atoms; this is a fundamental property of potential energy surfaces. This is achieved using global descriptors and thus without using an atom-centered approach (which is manifestly fully permutationally invariant). PIPs have been used directly for Linear Regression fitting of electronic energies and gradients for complex energy landscapes to chemical reactions with numerous
product channels. PIPs have also been used as inputs to Neural Network and Gaussian Process Regression methods and in many-body (atom-centered, water monomer, etc) applications, notably for gold standard potentials for water. Here we focus on the progress and usage of PIPs since 2018, when the last review of PIPs was done by our group. | Joel Bowman; Chen Qu; Riccardo Conte ; Apurba Nandi; Paul Houston ; Qi Yu | Theoretical and Computational Chemistry; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2025-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c8728d6dde43c9089b6eb3/original/a-perspective-marking-20-years-of-using-permutationally-invariant-polynomials-for-molecular-potentials.pdf |
6182adc2d828a4704d6a0591 | 10.26434/chemrxiv-2021-269vx | Difluoroalkylation of tertiary amides and lactams by an iridium-catalyzed reductive Reformatsky reaction | The synthesis of medicinally relevant α-difluoroalkylated amines by an iridium-catalyzed reductive alkylation of tertiary amides and lactams with difluoro-Reformatsky reagents, is described. This report features the introduction of various geminal difluoro-acetates and -acetamides as well as late stage derivatization of APIs, gram scale synthesis and downstream functionalizations. | Phillip Biallas; Ken Yamazaki; Darren J. Dixon | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6182adc2d828a4704d6a0591/original/difluoroalkylation-of-tertiary-amides-and-lactams-by-an-iridium-catalyzed-reductive-reformatsky-reaction.pdf |
665f6f49418a5379b016927b | 10.26434/chemrxiv-2024-5xsp5-v2 | Corrosion and Enhanced Hydrogen Evolution in Electrochemical Reduction of Ammonium Carbamate on Transition Metal Surfaces | Experiments and theory are combined to search for catalyst activity and stability descriptors for the direct reactive capture and conversion (RCC) of CO2 in ammonia capture solutions using Cu, Ag, Au, Sn and Ti electrodes. Two major phenomena emerge in RCC that are not predominant in the electrochemical CO2 reduction (CO2R) reaction, namely, the rapid corrosion and restructuring of the catalyst in the presence of the CO2-ammonia adducts, and the promotion of the competing hydrogen evolution reaction (HER). The prevalence of HER in RCC is correlated to the electrostatic attraction of the protonated amine to the electrode and the repulsion of the captured CO2, using the potential of zero charge (PZC). The stability of catalysts under RCC conditions is a function of the applied potential and cannot be readily predicted using binding energy descriptors commonly used in the prediction of CO2R activity. Three different trends are experimentally observed under RCC testing: i) Cu, and Sn corrode under open circuit potential and produce predominantly hydrogen, ii) Au and Ag show activity for the reduction of dissolved CO2 and restructure under cathodic potentials, and iii) Ti does not corrode under open circuit conditions and only generated hydrogen as reduction product. This work shows that a direct correlation between calculated binding energies of CO2R intermediates, atomic oxygen, hydrogen, and ammonia, and the activity and stability of transition metal for RCC cannot be found, highlighting the need for further development of activity and stability descriptors beyond those known for CO2R. | Jounghwan Choi; Shawn Chiu; Avishek Banerjee; Robert L. Sacci; Gabriel M. Veith; Chantal Stieber; Christopher Hahn; Anastassia N. Alexandrova; Carlos G. Morales-Guio | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665f6f49418a5379b016927b/original/corrosion-and-enhanced-hydrogen-evolution-in-electrochemical-reduction-of-ammonium-carbamate-on-transition-metal-surfaces.pdf |
64ccb75269bfb8925a55be64 | 10.26434/chemrxiv-2023-cpvp6 | Three-Dimensional Covalent Organic Frameworks with nia Nets for Efficient Separation of Benzene/Cyclohexane Mixtures | The synthesis of three-dimensional (3D) covalent organic frameworks (COFs) with highly connected building blocks presents a significant challenge. In this study, we report two novel 3D COFs with the nia topology, named JUC-641 and JUC-642, by introducing planar hexagonal and triangular prism nodes for the first time. The resulting materials display high crystallinity, excellent thermal/chemical stability, a through-hole structure, and a large specific surface area. Notably, our adsorption studies and breakthrough experiments reveal that both COFs exhibit exceptional separation capabilities, surpassing previously reported 3D COFs and most porous organic polymers, with a separation factor of up to 2.02 for benzene and cyclohexane. Additionally, dispersion-corrected density functional theory analysis suggests that the outstanding performance of these 3D COFs can be attributed to the incorporation of highly aromatic building blocks and the presence of extensive pore structures. Consequently, this research not only expands the diversity of COFs but also highlights the potential of functional COF materials as promising candidates for environmentally-friendly separation applications. | Jianhong Chang; Fengqian Chen; Hui Li; Jinquan Suo; Haorui Zheng; Jie Zhang; Zitao Wang; Liangkui Zhu; Valentin Valtchev; Shilun Qiu; Qianrong Fang | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ccb75269bfb8925a55be64/original/three-dimensional-covalent-organic-frameworks-with-nia-nets-for-efficient-separation-of-benzene-cyclohexane-mixtures.pdf |
6365369fac45c70cd9a583bc | 10.26434/chemrxiv-2022-gn5sp | 4D Printed Programmable Shape-morphing Hydrogels as Intraoperative Self-folding Nerve Conduits for Sutureless Neurorrhaphy | Even as four-dimensional (4D) printing of biomaterials evolves as a fascinating technology to engineer complex and dynamic biomimetic parts, the utility of 4D printed hydrogels in addressing clinical needs in vivo has not been established. In this study, a hydrogel system was engineered from tailored concentrations of alginate and methyl cellulose with defined swelling behaviors, which demonstrated excellent printability in extrusion-based three-dimensional (3D) printing and programmed shape deformations post-printing. Shape deformations of the spatially patterned hydrogels with defined infill angles were computationally predicted for a variety of 3D printed structures, which were subsequently validated experimentally. The gels were further coated with gelatin-rich nanofibers by airbrushing to augment cell attachment and growth. 3D printed hydrogel sheets with pre-programmed infill patterns rapidly self-rolled into hollow tubes in vivo to serve as nerve guiding conduits for repairing sciatic nerve defects in a rat model. These 4D printed hydrogels minimized the complexity of surgeries by tightly clamping the resected ends of the nerves to assist in the healing of peripheral nerve damage, as revealed by histological evaluation and functional assessments for up to 45 days. This work demonstrates that 3D printed hydrogels can be designed for programmed shape changes by swelling in vivo to yield 4D printed tissue constructs for the repair of peripheral nerve damage with a potential to be extended in other areas of regenerative medicine. | Akshat Joshi; Saswat Choudhury; Vageesh Baghel; Souvik Ghosh; Sumeet Gupta; Debrupa Lahiri; G Ananthasuresh; Kaushik Chatterjee | Materials Science; Polymer Science; Biocompatible Materials; Materials Processing; Hydrogels | CC BY NC 4.0 | CHEMRXIV | 2022-11-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6365369fac45c70cd9a583bc/original/4d-printed-programmable-shape-morphing-hydrogels-as-intraoperative-self-folding-nerve-conduits-for-sutureless-neurorrhaphy.pdf |
6530ff2087198ede079c49d6 | 10.26434/chemrxiv-2023-2zrw8 | The sensitive aspects of modelling polymer-ceramic composite solid-state electrolytes by molecular dynamics simulations | Solid-state composite electrolytes have arisen as one of the most promising mate- rials classes for the next-generation Li-ion battery technology. These composites mix ceramic and solid-polymer ion conductors with the aim of combining the advantages of each material. The ion-transport mechanisms within such materials, however, remain elusive. This knowledge gap can to a large part be attributed to difficulties in studying processes at the ceramic−polymer interface, which are expected to play a major role in the overall ion transport through the electrolyte. Computational efforts have the po- tential of providing significant insight to these processes. One of the main challenges to overcome is then to understand how a sufficiently robust model can be constructed in order to provide reliable results. To this end, a series of molecular dynamics simu- lations are here carried out with a variation of certain structural (surface termination and polymer length) and pair potential (van der Waals parameters and partial charges) models of the Li7La3Zr2O12 (LLZO) poly(ethylene oxide) (PEO) system, in order to test how sensitive the outcome is to each variation. The study shows that the static and dynamic properties of Li+ are significantly affected by van der Waals parameters as well as the surface terminations, while the thickness of the interfacial region - where the structure-dynamic properties are different as compared to the bulk-like regime - is the same irrespective of the simulation setup. | Melania Kozdra; Daniel Brandell; C. Moyses Araujo; Amber Mace | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6530ff2087198ede079c49d6/original/the-sensitive-aspects-of-modelling-polymer-ceramic-composite-solid-state-electrolytes-by-molecular-dynamics-simulations.pdf |
64f841923fdae147fa99bb90 | 10.26434/chemrxiv-2023-nss4q-v2 | Bifunctional Co0.75Fe0.25@C nanocomposite towards zero waste approach: Organic pollutants removal and OER electrocatalysis | Here, we report synthesis of magnetic nanocomposite with zero-waste approach for organic pollutant removal and oxygen evolution reaction. The nanocomposite was synthesized using agriculture waste soaked with Co2+-Fe3+ metal ions at 900 °C and characterized using FESEM, HRTEM, PXRD, Zeta-potential, and VSM techniques. The nanocomposite shows an impressive adsorbent property for organic dyes (90-96 % removal), and pharmaceutical drug (paracetamol, 84% removal), along with individually used ‘hair dye’ (95% removal) in 5 min only. The recyclability of the nanocomposite demonstrates the practical benefits of the material for waste water remediation. Interestingly, after the adsorption, the generated secondary waste (exhausted dye adsorbed nanocomposite) is used as oxygen evolution reaction (OER) electrocatalyst. The dye-adsorbed nanocomposite shows good OER activity with an overpotential of 264 mV at 10 mA/cm2 with good stability upto 10 h. This study sheds light on the reuse and recycling of the secondary waste of the adsorption process to develop efficient OER electrocatalysts and shows a zero-waste approach towards the environment. | Sai Rashmi M.; Sayali Patil; Akhila S.; Velvita Duas; Akshaya Samal; Rupesh Devan; Manav Saxena | Materials Science; Energy; Carbon-based Materials; Composites; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f841923fdae147fa99bb90/original/bifunctional-co0-75fe0-25-c-nanocomposite-towards-zero-waste-approach-organic-pollutants-removal-and-oer-electrocatalysis.pdf |
6741154df9980725cf879c5d | 10.26434/chemrxiv-2024-q8ztn-v2 | The Chemistry of Henna: A Module for High School Students | Here we present a hands-on module for high school students to explore the chemistry of henna dye. This lesson is affordable, accessible, adaptable, and engaging for students. In this lesson, students are shown how henna paste is derived from the henna shrub, discuss the chemical structure of the main dye component lawsone (2-hydroxy-1,4-napthoquinone), apply the henna paste to their skin, and discuss the darkening of the dye over time as a result of lawsone oxidation. Through understanding the chemistry of henna, students are encouraged to consider the influence of chemical reactions in their daily lives. This module also promotes diversity and inclusion in science by increasing the representation of non-Western cultures in the chemistry curriculum. In this work, the module is presented in detail, and student reactions are discussed. | Shoshana Williams; Eric Appel | Chemical Education | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6741154df9980725cf879c5d/original/the-chemistry-of-henna-a-module-for-high-school-students.pdf |
63a40ccbdadddc118e975b31 | 10.26434/chemrxiv-2022-7h8vn | Fungal Anthraquinone Photoantimicrobials Challenge the Dogma of Cationic Photosensitizers | The photoantimicrobial potential of four mushroom species (i.e., Cortinarius cinnabarinus, C. sanguineus, C. rubrophyllus, and C. holoxanthus) was explored based on a light modified EUCAST protocol. The extracts were tested against Candida albicans, Escherichia coli, and Staphylococcus aureus under blue (λ = 428 nm and λ = 478 nm, H = 30 J cm-2) and green light (λ = 528 nm, H = 30 J cm-2) irradiation. Three extracts showed significant photoantimicrobial effects at concentrations below 25 µg/mL. Targeted isolation of the major pigments from C. sanguineus led to the identification of two new potent photoantimicrobials, one of them (i.e., dermocybin) being active against S. aureus and C. albicans under green light irradiation (PhotoMIC523 = 39.5 µM and 2.3 µM, respectively) and the other one (i.e., emodin) being active against E. coli in a low micromolar range
(PhotoMIC428 = 11.1 µM). Intriguingly, dermocybin was not (photo)cytotoxic against three tested cell lines adding an additional level of selectivity. Since both photoantimicrobials are not charged, this discovery shifts the paradigm of cationic photosensitizers.
| Fabian Hammerle; Johannes Fiala; Anja Höck; Lesley Huymann; Pamela Vrabl; Yurii Husiev; Sylvestre Bonnet; Ursula Peintner; Bianka Siewert | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a40ccbdadddc118e975b31/original/fungal-anthraquinone-photoantimicrobials-challenge-the-dogma-of-cationic-photosensitizers.pdf |
6642039a91aefa6ce1dbf5d2 | 10.26434/chemrxiv-2024-d4klb-v2 | Chemically Recyclable and Enzymatically Degradable Polyesters from α-Pinene-Derived Chiral Diols | Accelerated production of recyclable and biodegradable biopolymers is crucial in combating the socio-economic and environmental issues of fossil-based plastics. While renewable diacids have been in the spotlight for the generation of bio-based polyesters with tailored properties by varying the alkyl chain length, capitalizing on diols from biomass for this purpose is underexplored and has mainly focused on linear and branched shorter chain alcohols. Here we explored the potential of two (ꟷ)-α-pinene-derived diols (PDOs) as building blocks to generate polyesters that mimic the properties of aromatic fossil-based polymers when combined with renewable diesters. The semi-crystalline or amorphous nature of the resulting polymers is tunable with the appropriate choice of diester. We demonstrate a concise synthesis of two novel unsymmetrical chiral PDOs on 20-40 g scale, together with eight structurally differing polyesters with excellent thermal stability; as reflected by high melting (270 oC, 277 oC), and glass transition temperatures (90 oC, 121 oC) for two of the polymers. The steric hindrance of the intact bicyclic α-pinene ring structure protruding from the backbone of the polymers can also aid in the degradation process, manifested by facile chemical recycling of these polyesters under mild conditions to recover both monomers. Finally, our results show how the generated rigid polymers are prone to enzymatic degradation by PETase and cutinase without any chemical pre-treatment. Our results illuminate the potential of expanding the currently available chemical space in bio-based monomers to bicyclic diols to generate biomaterials with tailormade properties. | Ganapathy Ranjani; Ximena Lopez-Lorenzo; Sathiyaraj Subramaniyan; Minna Hakkarainen; Per-Olof Syrén | Polymer Science; Biopolymers | CC BY 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6642039a91aefa6ce1dbf5d2/original/chemically-recyclable-and-enzymatically-degradable-polyesters-from-pinene-derived-chiral-diols.pdf |
60c75361bb8c1a86f23dc024 | 10.26434/chemrxiv.13483185.v1 | TorsionNet: A Deep Neural Network to Rapidly Predict Small Molecule Torsion Energy Profiles with the Accuracy of Quantum Mechanics | <p></p><p>TorsionNet: A Deep Neural Network to Rapidly Predict Small
Molecule Torsion Energy Profiles with the Accuracy of Quantum
Mechanics </p>
<p> </p>
<p>Brajesh K. Rai<sup>*,1</sup>,
Vishnu Sresht<sup>1</sup>, Qingyi Yang<sup>2</sup>, Ray Unwalla<sup>2</sup>,
Meihua Tu<sup>2</sup>, Alan M. Mathiowetz<sup>2</sup>, and Gregory A. Bakken<sup>3</sup></p>
<p><sup>1</sup>Simulation
and Modeling Sciences and <sup>2</sup>Medicine Design, Pfizer Worldwide
Research Development and Medical, 610 Main Street, Cambridge, Massachusetts
02139, United States</p>
<p><sup>3</sup>Digital, Pfizer, Eastern Point Road,
Groton, Connecticut 06340, United States</p>
<p> </p>
<p> </p>
<p><b>ABSTRACT</b><b> </b><b></b></p>
<p>Fast and accurate assessment of small
molecule dihedral energetics is crucial for molecular design and optimization
in medicinal chemistry. Yet, accurate prediction of torsion energy
profiles remains a challenging task as current molecular mechanics methods are
limited by insufficient coverage of druglike chemical space and accurate quantum
mechanical (QM) methods are too expensive. To address this limitation,
we introduce TorsionNet, a deep neural network (DNN) model
specifically developed to predict small molecule torsion energy profiles
with QM-level accuracy. We applied active learning to identify nearly 50k
fragments (with elements H, C, N, O, F, S, and Cl) that maximized the coverage
of our corporate library and leveraged massively parallel cloud computing
resources to perform DFT torsion scan of these fragments, generating a training
dataset of 1.2 million DFT energies. By training TorsionNet on this dataset, we
obtain a model that can rapidly predict the torsion energy profile of typical
druglike fragments with DFT-level accuracy. Importantly, our method also provides
a direct estimate of the uncertainty in the predicted profiles without any
additional calculations. In this report, we show that TorsionNet can reliably identify
the preferred dihedral geometries observed in crystal structures. We also present
practical applications of TorsionNet that demonstrate how consideration of DNN-based
strain energy leads to substantial improvement in existing lead discovery and
design workflows. A benchmark dataset (TorsionNet500) comprising 500 chemically
diverse fragments with DFT torsion profiles (12k DFT-optimized geometries and
energies) has been created and is made freely available.</p><br /><p></p> | Brajesh Rai; Vishnu Sresht; Qingyi Yang; Rayomond J. Unwalla; Meihua Tu; Alan M. Mathiowetz; Gregory A. Bakken | Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75361bb8c1a86f23dc024/original/torsion-net-a-deep-neural-network-to-rapidly-predict-small-molecule-torsion-energy-profiles-with-the-accuracy-of-quantum-mechanics.pdf |
65ba029766c1381729a1fb9a | 10.26434/chemrxiv-2023-l6f1v-v2 | Photocatalytic H2O2 Production Over Photocatalysts Prepared By Phosphine-protected Au101 Nanoparticles on WO3 | Photocatalytic H2O2 synthesis is an appealing and feasible strategy to replace the energy- intensive, tedious, and waste-generating anthraquinone process. Often, pure metal oxides show low activity in photocatalytic H2O2 production and therefore metal co-catalysts are required to improve the photoactivity. This work investigated photocatalytic H2O2 production using monodisperse gold nanoclusters Au101(PPh3)21Cl5 supported on WO3. From HRTEM imaging, the Au101 size in the uncalcined samples is in the cluster regime (<2 nm) and after calcination at 200 °C the size increases to ca. 4.5 nm. The roles of Au101 have been identified to reduce the charge carrier recombination and provide the active sites for O2 reduction which significantly enhances the photoactivity. Both uncalcined and calcined Au101/WO3 photocatalysts produce over 75 mM g-1 h-1 of H2O2 under UV light irradiation while the pure WO3 is inactive. At early times (up to 30 min), the production rate of H2O2 from calcined Au101/WO3 reaches 173 mM g-1 h-1 and is almost double the rate of the uncalcined catalyst (93 mM g-1 h-1). The higher photoactivity of calcined versus uncalcined Au101/WO3 can be attributed to the aggregated Au101 and removal of phosphine ligands from the Au core as verified by HRTEM and XPS. The reaction rate decreases over time which is attributed to the reverse reaction. Using a simple kinetic model, the rate constant of the H2O2 formation (kf) for uncalcined and calcined Au101/WO3 are 2.07 and 6.31 mM h-1, while the rate constant of the H2O2 decomposition (kd) for uncalcined and calcined Au101/WO3 are 0.49 and 2.93 h-1, respectively. This work highlights a simple preparation of highly active photocatalysts to produce H2O2 derived from Au101 clusters and WO3. | Imran Hakim Abd Rahim; Xuan Yin Lee; Abdulrahman S. Alotabi; D. J. Osborn; Gunther G. Andersson; Gregory F. Metha; Rohul H. Adnan | Physical Chemistry; Catalysis; Photocatalysis; Chemical Kinetics; Clusters; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba029766c1381729a1fb9a/original/photocatalytic-h2o2-production-over-photocatalysts-prepared-by-phosphine-protected-au101-nanoparticles-on-wo3.pdf |
62b86acd7da6ce24b62105a7 | 10.26434/chemrxiv-2022-8m46q-v3 | Critical role of water on the synthesis and gelling of gamma-In2S3 nanoribbons with giant aspect ratio | We report the synthesis of ultrathin indium sulfide In<sub>2</sub>S<sub>3</sub> nanoribbons which display a giant aspect ratio using a simple and fast solvothermal method. They have a sub-nanometer thickness controlled at the atomic level, a width of (8.7 <font face=symbol>±</font> 0.1) nm and a length which can reach several micrometers. We determine the atomic composition of the inorganic core by Rutherford backscattering spectrometry (RBS) and measure by X-ray photoelectron spectrometry (XPS) an oleylamine surface coverage of 2.3 ligands per nm<sup>2</sup>. X-ray diffraction experiments and simulations as well as high-resolution dark-field STEM point toward a P<span style="border-top:1 solid black;">3</span>m1 trigonal crystallographic structure (<font face=symbol>g</font> phase). Transport measurements show that the nanoribbons display n-type semiconductor unipolar behavior. Their lateral dimensions can be tuned by reaction time, temperature and by the amount of water present in the reaction medium: anhydrous synthesis conditions lead to hexagonal nanoplates, whereas controlled addition of water induces a symmetry break yielding long rectangular nanoribbons. Depending on the dispersion solvent, these long ribbon-like nanoparticles can form either well-dispersed colloids or bundles in which they stack face-to-face. Their large aspect ratio induces the formation of gels at volume fractions as low as 1.3 × 10<sup><font face=symbol>-</font>4</sup>
</td>
<td nowrap align=center>
making them supergelators. The kinetics of gelation is strongly accelerated by an increase in the relative humidity of the ambient atmosphere. | Lilian Guillemeney; Laurent Lermusiaux; Patrick Davidson; Austin Hubley; Stefano Pierini; Debora Pierucci; Gilles Patriarche; Bruno Canut; Emmanuel Lhuillier; Benoit Mahler; Benjamin ABECASSIS | Nanoscience; Nanostructured Materials - Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b86acd7da6ce24b62105a7/original/critical-role-of-water-on-the-synthesis-and-gelling-of-gamma-in2s3-nanoribbons-with-giant-aspect-ratio.pdf |
66e3741451558a15efd1d9d3 | 10.26434/chemrxiv-2024-4wz03 | Detection and Structural Elucidation of Copper Binding Tri- and Tetrapyrrole Ligands Produced by the marine diatom Phaeodactylum Tricornutum | In seawater most dissolved copper (Cu) is complexed by organic ligands, many of which are thought to be produced by phytoplankton. Although very little is known about the composition and structure of these ligands, they play an important role in determining the reactivity and bioavailability of Cu. In this study, Phaeodactylum tricornutum, a marine diatom known to produce Cu ligands (CuLs), was grown in laboratory pure culture and the CuLs recovered from the growth media. Using liquid chromatography coupled to ultrahigh resolution tandem mass spectrometry, eleven Cu ligand complexes were identified and assigned molecular formulae. Molecular formulae were confirmed by comparing the expected and observed relative abundances of 15N, 13C, 65Cu, and 18O isotopologues. The CuLs had molecular weights from 520 to 719 Da and molecular formulae of C26-35H23-36O5-9N3-4Cu with an average assignment error of 56 ppb. High-resolution tandem mass spectrometry of the Cu-bound and metal-free ligands revealed these to be a suite of tri- and tetrapyrroles stabilized through complexation of Cu by N. The ligands share similar parent structures but differ in the number, type, and arrangement of functional groups that decorate the pyrroles. The similarity of CuL structures with known catabolites of chlorophyll suggests these ligands may be widely produced by marine photoautotrophs. | Lydia Babcock-Adams; Jingxuan Li; Amy McKenna; Christopher Hendrickson; Daniel Repeta | Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry | CC BY 4.0 | CHEMRXIV | 2024-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e3741451558a15efd1d9d3/original/detection-and-structural-elucidation-of-copper-binding-tri-and-tetrapyrrole-ligands-produced-by-the-marine-diatom-phaeodactylum-tricornutum.pdf |
67a674aafa469535b9727e10 | 10.26434/chemrxiv-2025-jwkz1 | Impact of Timestep on Energy Drift and Accuracy of Alchemical Free Energy Calculations | Molecular dynamics (MD) simulations are essential for investigating complex bi- ological systems. Timestep selection is crucial for accuracy and efficiency, yet the common practice of using a 4 fs timestep with hydrogen mass repartitioning (HMR) and SHAKE for alchemical free energy (AFE) calculations requires further scrutiny. This study investigates the impact of timestep on energy drift and AFE calculations across three molecular systems: cAMP, ethane, and the protein-ligand system Tyk2 (emj 42 to emj 55), exploring timesteps from 0.5 to 4 fs. NVE simulations revealed a strong correlation between increasing timestep and energy drift, with and without HMR. Simulations without SHAKE were unstable at larger timesteps. Thermody- namic integration (TI) simulations in the NPT ensemble showed consistent dU dλ values for 0.5, 1, and 2 fs timesteps, but deviations up to 3 kcal/mol were observed at 4 fs in some cases. Statistical t-tests (p < 0.05) confirmed significant differences between the 4 fs timestep and the 0.5 fs reference, especially in aqueous solution. These findings, based on analyses across various λ states (0-1) and softcore treatments, highlight the importance of careful timestep selection. We recommend limiting the timestep to a maximum of 2 fs for accurate and reliable AFE calculations using HMR and SHAKE. | Saikat Pal; Omid Jahanmahin; Shi Zhang; Tai-Sung Lee | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a674aafa469535b9727e10/original/impact-of-timestep-on-energy-drift-and-accuracy-of-alchemical-free-energy-calculations.pdf |
60c74f129abda2551cf8d794 | 10.26434/chemrxiv.12844715.v1 | Bayesian Data Analysis Reveals No Preference for Cardinal Tafel Slopes in CO2 Reduction Electrocatalysis | In this paper, we develop a Bayesian data analysis approach to estimate the Tafel slope from experimentally-measured current-voltage data. Our approach obviates the human intervention required by current literature practice for Tafel estimation, and provides robust, distributional uncertainty estimates. Using synthetic data, we illustrate how data insufficiency can unknowingly influence current fitting approaches, and how our approach allays these concerns. We apply our approach to conduct a comprehensive re-analysis of data from the CO<sub>2</sub> reduction literature. This analysis reveals no systematic preference for Tafel slopes to cluster around certain "cardinal values" (e.g. 60 or 120 mV/decade). We hypothesize several plausible physical explanations for this observation, and discuss the implications of our finding for mechanistic analysis in electrochemical kinetic investigations. | Aditya Limaye; Joy S. Zeng; Adam Willard; Karthish Manthiram | Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f129abda2551cf8d794/original/bayesian-data-analysis-reveals-no-preference-for-cardinal-tafel-slopes-in-co2-reduction-electrocatalysis.pdf |
60c759abbb8c1a0fce3dcc73 | 10.26434/chemrxiv.14721111.v1 | Structural Evolution of Pt, Au, and Cu Anodes by Electrolysis up to Contact Glow Discharge Electrolysis in Alkaline Electrolytes | <div>Applying a voltage to metal electrodes in contact with aqueous electrolytes results in the electrolysis of water at low voltages and plasma formation in the electrolyte at high voltages referred to as contact glow discharge electrolysis (CGDE). While several studies explore parameters that lead to changes in the I-U characteristics in this voltage range, little is known about the evolution of the structural properties of the electrodes. Here we study this aspect on materials essential to electrocatalysis, namely Pt, Au, and Cu. The stationary I-U characteristics are almost identical for all electrodes. Detailed structural characterization by optical microscopy, scanning electron microscopy, and electrochemical approaches reveal that Pt is stable during electrolysis and CGDE, while Au and Cu exhibit a voltage-dependent oxide formation. More importantly, oxides are reduced when the Au and Cu electrodes are kept in the electrolysis solution. We suspect that H<sub>2</sub>O<sub>2 </sub>(formed during electrolysis) is responsible for the oxide reduction. The reduced oxides (which are also accessible <i>via</i> electrochemical reduction) form a porous film, representing a possible new class of materials in energy storage and conversion studies.</div> | Evelyn Artmann; Pramod V. Menezes; Lukas Forschner; Mohamed Elnagar; Ludwig A. Kibler; Timo Jacob; Albert Engstfeld | Catalysts; Nanocatalysis - Catalysts & Materials; Electrochemistry; Electrochemistry - Mechanisms, Theory & Study; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759abbb8c1a0fce3dcc73/original/structural-evolution-of-pt-au-and-cu-anodes-by-electrolysis-up-to-contact-glow-discharge-electrolysis-in-alkaline-electrolytes.pdf |
67024c1151558a15ef3ea382 | 10.26434/chemrxiv-2024-2hcg4 | Thymidine Phosphodiester Chemiluminescent Probe for Sensitive and Selective Detection of Ectonucleotide Pyrophosphatase 1 | ENPP-1 is a transmembrane enzyme involved in nucleotide metabolism, and its overexpression is associated with various cancers, making it a potential therapeutic target and biomarker for early tumor diagnosis. Current detection methods for ENPP-1 utilize a colorimetric probe, TMP-pNP, which has significant limitations in sensitivity. Here, we present probe CL-ENPP-1, the first nucleic acid-based chemiluminescent probe designed for rapid and highly sensitive detection of ENPP-1 activity. The design of probe CL-ENPP-1 features a phenoxy-adamantyl-1,2-dioxetane luminophore linked to thymidine via a phosphodiesteric bond. Upon cleavage of the enzymatic substrate by ENPP-1, the probe undergoes an efficient chemiexcitation process to emit a green photon. Probe CL-ENPP-1 demonstrates an exceptional signal-to-noise ratio of 15000 and a limit of detection value approximately 4500-fold lower than the widely used colorimetric probe TMP-pNP. A comparison of TMP-pNP activation by ENPP-1 versus alkaline phosphatase (ALP) reveals a complete lack of selectivity. Removal of the self-immolative spacer from probe CL-ENPP-1 resulted in a new chemiluminescent probe, CL-ENPP-2, with an 18.4-fold increase in selectivity for ENPP-1 over ALP. As far as we know, to date, CL-ENPP-1 and CL-ENPP-2 are the most sensitive probes for the detection of ENPP-1 catalytic activity. We anticipate that our new chemiluminescent probes will be valuable for various applications requiring ENPP-1 detection, including enzyme inhibitor-based drug discovery assays. The insights gained from our probe design principles could advance the development of more selective probes for ENPP-1 and contribute to future innovations in chemiluminescence research. | Omri Shelef; Sara Gutkin; Molhm Nassir; Phil S. Baran; Doron Shabat | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67024c1151558a15ef3ea382/original/thymidine-phosphodiester-chemiluminescent-probe-for-sensitive-and-selective-detection-of-ectonucleotide-pyrophosphatase-1.pdf |
662695d4418a5379b066638f | 10.26434/chemrxiv-2024-41r63 | Visualizing and understanding batch heterogeneity during freeze-drying using shelf-scale infrared thermography | Freeze-drying is widely used for manufacturing biopharmaceuticals in vials. One significant challenge in process design and optimization is heterogeneity among vials across a batch, which has been difficult to investigate due to the lack of adequate monitoring techniques. Here we leverage infrared thermography to quantify the freezing and drying behavior of all vials, hence enabling comprehensive studies of batch heterogeneity. Surprisingly, the stochasticity of nucleation, commonly considered the main driver of batch heterogeneity, only causes little heterogeneity. Instead, heterogeneity originates from heat transfer between vials: when ice is formed in one vial, the release of latent heat governs the freezing behavior of its neighboring vials. Guided by a mechanistic model and confirmed by experiments, the cooling rate and geometrical arrangement of the vials are identified as main drivers of batch heterogeneity. In conclusion, this contribution reports transformational insights into freeze-drying and supports practitioners in process design and optimization. | Leif-Thore Deck; Nicole Ferru; Andraž Košir; Marco Mazzotti | Chemical Engineering and Industrial Chemistry; Industrial Manufacturing; Pharmaceutical Industry; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662695d4418a5379b066638f/original/visualizing-and-understanding-batch-heterogeneity-during-freeze-drying-using-shelf-scale-infrared-thermography.pdf |
60c744b5bdbb8901e2a3888a | 10.26434/chemrxiv.9889994.v1 | Molecular Interactions Using New Technology: A Virtual Reality Gaming Platform to Visualize and Manipulate Molecules | <p>The representation of complex biomolecular structures and interactions is a difficult challenge across life sciences. Researchers and students use unintuitive 2D representations to gain an intuitive understanding of 3D space and molecular interactions. Since this is cumbersome for complex structures, such as protein-ligand interactions, several solutions have been proposed to help elucidate the 3D space. However, these representations are often static or do not fully leverage the interactivity that modern computing systems can provide. Our solution, Molecular Interaction using New Technology (MINT), is the first “gaming” platform to effectively represent and manipulate structures in 3D space using virtual reality while simultaneously scoring biomolecular interactions in real-time. Utilizing this combination of manipulation and real-time feedback, MINT provides scientists with an intuitive and effective method for drug discovery. We hope the combination of an intuitive interface with a powerful chemistry backend will expand molecular understanding and drug discovery for scientists and non-scientists.</p> | Wei Zhang; Jonathan A Fine; Christopher Sculley; Jordon McGraw; Gaurav Chopra | Chemical Education - General; Biochemistry; Bioinformatics and Computational Biology; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry; Structure | CC BY 4.0 | CHEMRXIV | 2019-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744b5bdbb8901e2a3888a/original/molecular-interactions-using-new-technology-a-virtual-reality-gaming-platform-to-visualize-and-manipulate-molecules.pdf |
62208892c3e9dad9337e8889 | 10.26434/chemrxiv-2022-c69mz-v2 | Umpolung of Indoles: Triflic Acid-Mediated C3-Regioselective Hydroarylation of N-H Indoles | The direct dearomative addition of arenes to the C3-position of unprotected indoles is reported under operationally simple condi-tions, using triflic acid at room temperature. The present regioselective hydroarylation is a straightforward manner to generate an electrophilic indole at the C3-position without the need of a deactivating acetyl group at the indolic nitrogen as in previously reported strategies. This atom economical method delivers biologically relevant 3-arylindolines and 3,3-spiroindolines in high yields and regioselectivities from both intra- and intermolecular processes. DFT computations suggest the stabilization of cationic or dicationic intermediates with H-bonded (TfOH)n clusters. | Nazarii Sabat; Weiping Zhou; Vincent Gandon; Xavier Guinchard; Guillaume VINCENT | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62208892c3e9dad9337e8889/original/umpolung-of-indoles-triflic-acid-mediated-c3-regioselective-hydroarylation-of-n-h-indoles.pdf |
60c74c9f469df43bbcf44100 | 10.26434/chemrxiv.12496547.v1 | Identification of Diphenoxylate as an Antiviral Agent Against Severe Acute Respiratory Syndrome Coronavirus 2 | This
is the first report to show that diphenoxylate is highly active against
SARS-CoV-2 with EC<sub>50</sub> of 1.4 μM, CC<sub>50</sub> over 100 μM and selectivity index over 71.4
after screening of 14 diphenyl derivatives. Our results with highly purified
solid diphenoxylate confirmatively demonstrate that the viral S protein is
reduced in the virus-infected cells in a dose-dependent manner. It could provide
insights for antiviral treatment of COVID-19 with diphenoxylate or its chemical
derivatives | Jin Soo Shin; Eunhye Jung; Yejin Jang; Soo Bong Han; Meehyein Kim | Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c9f469df43bbcf44100/original/identification-of-diphenoxylate-as-an-antiviral-agent-against-severe-acute-respiratory-syndrome-coronavirus-2.pdf |
623213d7d6d3edfc4893dee6 | 10.26434/chemrxiv-2022-0j830 | Uncovering the Structure of Heterogeneous Catalysts Using Atomic Pair Distribution Function Analysis | Heterogeneous catalysts are complex materials, often containing multiple atomic species and phases with various degrees of structural order. The identification of structure – performance relationships that rely on the availability of advanced structural characterization tools, is key for a rational catalyst design. Structural descriptors in catalysts can be defined over different length scales from several Å up to several nanometers (crystalline structure), requiring structural characterization techniques covering these different length scales. Pair distribution function (PDF) analysis is a powerful method to extract structural information spanning from the atomic to the nanoscale under in situ or operando conditions. We discuss recent advances using PDF to provide insight into the atomic-to-nanoscale structure of heterogeneous catalysts. | Nora Zimmerli; Christoph R. Müller; Paula Abdala | Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623213d7d6d3edfc4893dee6/original/uncovering-the-structure-of-heterogeneous-catalysts-using-atomic-pair-distribution-function-analysis.pdf |
668b400ec9c6a5c07a9d9269 | 10.26434/chemrxiv-2021-qqhs8-v2 | Expedient decagram-scale synthesis of robust organic cages that bind sulfate strongly and selectively in water | Selective anion recognition remains a key challenge in supramolecular chemistry: only a very small number of systems that can function in water are known, and these nearly always preferentially bind hydrophobic anions. In this work, we report three robust hexa-cationic cages that can be prepared on scales up to 14 g in two simple and high-yielding steps from commercially-available materials. One of these cages displays unusually strong sulfate binding in water (Ka = 12,000 M–1), and demonstrates high selectivity for this anion over H2PO4–/HPO42– in DMSO/buffer mixtures. These results demonstrate that relatively large, three-dimensional supramolecular hosts can be prepared in high yields and on large scales, and can be highly potent receptors. | Emer Foyle; Rosemary Goodwin; Cameron Cox; Bailee Smith; Annie Colebatch; Nicholas White | Organic Chemistry; Inorganic Chemistry; Supramolecular Chemistry (Org.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668b400ec9c6a5c07a9d9269/original/expedient-decagram-scale-synthesis-of-robust-organic-cages-that-bind-sulfate-strongly-and-selectively-in-water.pdf |
62e0ec207f3aa6f697f9300b | 10.26434/chemrxiv-2022-4rz5q | Importance and Impact of International Agreements or Protocols to Protect Ozone and Beyond | Synchronized control of both global warming and ozone depletion is prerequisite for the sustainable stability of our bio-diversity. Here we uncover the importance of Paris Agreement and Kyoto Protocol and the new impact of Montreal Protocol to protect stratospheric ozone by considering the prototype H₂O + O(¹D) → 2OH insertion/addition reaction as the representative reaction of potent GHG molecules with steady state O(¹D). While CO₂ via its continuous regeneration CO₂ + O(¹D) → CO₂ + O(³P) reaction in stratosphere is involved in ozone hole formation, the geoengineering via nonstop CaCO₃ injections in stratosphere in future would also be responsible for ozone hole formation. Moreover, the classical nature of single potential wells of single step exothermic barrierless reactions governed by quantum mechanics de-energizes the energized adducts or products analogous to energy conservation of a falling mass from some height under gravity and plays decisive role in the extent of pressure independency of rate constants. | Montu K. Hazra; Soumen Mondal; Saikat Sadhukhan | Theoretical and Computational Chemistry; Physical Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e0ec207f3aa6f697f9300b/original/importance-and-impact-of-international-agreements-or-protocols-to-protect-ozone-and-beyond.pdf |
61c2c07d75c57234a4f3f51b | 10.26434/chemrxiv-2021-g6hvv | Entanglement of Square Nets in Covalent Organic Frameworks | Two entangled 2D square COFs have been synthesized from 4,4',4'',4'''-(9,9'-spirobi[fluorene]-2,2',7,7'-tetrayl)-tetrabenzaldehhyde (SFTB) and p-phenylenediamine (PPA) and benzidine (BZD) to form COF-38, [(SFTB)(PPA)2]imine and its isoreticular form COF-39, [(SFTB)(BZD)2]imine. We also report the single crystal electron diffraction structure of COF-39 and find that it is composed of mutually entangled 2D square nets (sql). These COFs represent the first examples of entangled 2D COF structures, which as we illustrate were made possible by our strategy of using the distorted tetrahedral SFTB building unit. SFTB overcomes the propencity of 2D COFs to stack through π-π stacking and allows for entanglements to form. This work adds significantly to the design principles of COFs. | Fangying Jin; Lac Ha Nguyen; Zhiye Zhong; Xing Han; Chenhui Zhu; Xiaokun Pei; Yanhang Ma; Omar Yaghi | Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c2c07d75c57234a4f3f51b/original/entanglement-of-square-nets-in-covalent-organic-frameworks.pdf |
627a5b2ca42e9c1f963b70c2 | 10.26434/chemrxiv-2022-db090-v2 | How Accurate is Density Functional Theory
for Molecules in Electric Fields? | The use of oriented external electric fields (OEEFs) as a potential tool for catalyzing chemical
reactions has gained traction in recent years. Electronic structure calculations using OEEFs are
commonly done using methods based on density functional theory (DFT), but until now, the
performance of DFT methods for calculating molecules in OEEFs had not been assessed in a more
general scope. Looking at the accuracy of both molecular geometries and electronic energies, we
have investigated a wide variety of density functionals using different basis sets to determine how
well the individual functionals perform on various types of chemical bonds. We found that most
functionals accurately calculate geometries in OEEFs, and that small basis sets are sufficient in
many cases. Calculations of electronic energies show a significant error introduced by the OEEF,
which the use of a larger basis set helps mitigate. Our findings show that DFT methods can be
used for accurate calculations in OEEFs, allowing researchers to make full use of the advantages
that they bring. | Tarek Scheele; Tim Neudecker | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/627a5b2ca42e9c1f963b70c2/original/how-accurate-is-density-functional-theory-for-molecules-in-electric-fields.pdf |
63fa4c46937392db3d0d603d | 10.26434/chemrxiv-2023-ssf53-v3 | Dissent in the Sediment? – Lake sediments as archives of short- and long-range impact of anthropogenic activities in northeastern Germany | The suitability of lake sediment cores to reconstruct past inputs, regional pollution, and usage patterns of pesticides has been shown previously. Until now, no such data exist for lakes in eastern Germany. Therefore, ten sediment cores (length 1 m) of ten lakes in eastern Germany, the territory of the former German Democratic Republic (GDR), were collected and cut into 5-10 mm layers. In each layer, concentrations of trace elements (TEs) As, Cd, Cr, Cu, Ni, Pb, S, Zn, as well as of organochlorine pesticides (OCPs) were analyzed. A miniaturized solid-liquid extraction technique in conjunction with headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) was used for the latter. Of OCPs, only transformation products of dichlorodiphenyltrichloroethane (DDT) were found. Congener ratios indicate a mainly aerial input. In the lakes’ profiles, several regional features and also responses to national policies and measures are visible. Dichlorodiphenyldichloroethane (DDD) concentrations reflect the history of DDT use in the GDR. TEs show a uniform progression over time. They follow a trans-regional pattern and are indicative of activity and policy making in West Germany before 1990 instead of those in the GDR. Lake sediments proved to be suitable to archive short- and long-range impacts of anthropogenic activity. Our data can be used to complement and validate other forms of environmental pollution long-term monitoring and check for the efficiency of pollution counter measures in the past. | Marcel Pierre Simon; Marlene Schatz; Leonard Böhm; István Papp; Hans-Peter Grossart; Thorbjørn Joest Andersen; Miklós Bálint; Rolf-Alexander Düring | Earth, Space, and Environmental Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fa4c46937392db3d0d603d/original/dissent-in-the-sediment-lake-sediments-as-archives-of-short-and-long-range-impact-of-anthropogenic-activities-in-northeastern-germany.pdf |
6373a90677ffe77da4ef0608 | 10.26434/chemrxiv-2022-g91vh | Modeling Light-Induced Chromophore Hydration in the Reversibly Photoswitchable Fluorescent Protein Dreiklang | We report the results of a computational study of the mechanism of the light-induced chemical reaction of chromophore hydration in the fluorescent protein Dreiklang responsible for its switching from the fluorescent ON-state to the dark OFF-state. We explore the relief of the potential energy surface from the excited-state level of the charge-transfer character in the ON-state to locate conical intersection points with the ground state energy surface. Simulations of further evolution of model systems allow us to characterize the ground-state reaction intermediate tentatively suggested in the femtosecond studies of the light-induced dynamics in Dreiklang and finally to arrive to the reaction product. The obtained results clarify the details of the photoswitching mechanism in Dreiklang, which is due to the chemical modification of the fluorescent protein chromophore. | Bella Grigorenko; Igor Polyakov; Alexander Nemukhin | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6373a90677ffe77da4ef0608/original/modeling-light-induced-chromophore-hydration-in-the-reversibly-photoswitchable-fluorescent-protein-dreiklang.pdf |
6336c1980e3c6a13c72e48c1 | 10.26434/chemrxiv-2022-3rw52 | Origin of the volcano-like ethanol oxidative dehydrogenation activity trend for VOx/CeO2 catalysts uncovered by operando time-resolved XAS | Supported vanadia (VOx) is a versatile catalyst for various redox processes, where ceria-supported VOx have shown to be particularly active in oxidative dehydrogenation (ODH) of alcohols. In this work, we clarify the origin of the volcano-shaped ethanol ODH activity trend for VOx/CeOx catalysts using operando quick V K- and Ce L3- edge XAS experiments performed under transient conditions. We quantitatively demonstrate that both vanadium and cerium are synergistically involved in alcohol ODH. The concentration of reversible Ce4+/Ce3+ species was identified as the main descriptor of the alcohol ODH activity. The activity drop in the volcano plot, observed at above ca. 3 V/nm2 surface loading (ca. 30% of VOx monolayer coverage), is related to the formation of spectator V4+ and Ce3+ species, which were identified here for the first time. These results might prove to be helpful for the rational optimization of VOx/CeO2 catalysts and the refinement of the theoretical models. | Olga V. Safonova; Anna Zabilska; Maxim Zabilskiy; Rob Jeremiah G. Nuguid; Adam H. Clark; Maarten Nachtegaal; Oliver Kröcher | Physical Chemistry; Catalysis; Heterogeneous Catalysis; Redox Catalysis; Chemical Kinetics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6336c1980e3c6a13c72e48c1/original/origin-of-the-volcano-like-ethanol-oxidative-dehydrogenation-activity-trend-for-v-ox-ce-o2-catalysts-uncovered-by-operando-time-resolved-xas.pdf |
6436751073c6563f14b5264c | 10.26434/chemrxiv-2023-whjkw | Saddles as rotational locks within shape-assisted self-assembled nanosheets | Two-dimensional (2D) materials are a key target for many applications in the modern day. Self-assembly is one approach that can bring us closer to this goal, which usually relies upon strong, directional interactions instead of covalent bonds. Control over less directional forces is more challenging and usually does not result in as well-defined materials. Explicitly incorporating topography into the design as a guiding effect to enhance the interacting forces can help to form highly ordered structures. Herein, we show the process of shape-assisted self-assembly to be consistent across a range of derivatives that highlights the restriction of rotational motion. A shape governed angle distribution nurtures monomers into loose columns that then arrange to form 2D structures with long-range order observed in both crystalline and soft materials. These features strengthen the idea that shape becomes an important design principle leading towards precise molecular self-assembly and the inception of new materials. | Joseph F. Woods; Lucía Gallego; Amira Maisch; Dominik Renggli; Corrado Cuocci; Olivier Blacque; Gunther Steinfeld; Andres Kaech; Bernhard Spingler; Andreas Vargas Jentzsch; Michel Rickhaus | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6436751073c6563f14b5264c/original/saddles-as-rotational-locks-within-shape-assisted-self-assembled-nanosheets.pdf |
641a7f88aad2a62ca124bb27 | 10.26434/chemrxiv-2023-pzkl0 | SESAMI APP: An Accessible Interface for Surface Area Calculation of Materials from Adsorption Isotherms | The most widely used approach to calculate a material’s gravimetric surface area, i.e. surface area per unit mass, is the Brunauer-Emmett-Teller (BET) method. The BET method computes the surface area of a material given the adsorption isotherm of a probe gas (i.e., N2 or Ar) in that material. Many researchers either obtain the BET area from commercial software that comes with measurement equipment, or perform the analyses manually on a spreadsheet, which is time-consuming and nearly impossible for some types of isotherms. Furthermore, these two approaches lead to large variability in BET-calculated areas. These challenges have motivated the development of programs for the automated and standardized calculation of BET areas. The SESAMI web interface allows a user to make surface area calculations on their web browser simply by uploading isotherm data. The motivation for this interface is to lower the barrier of entry for research groups seeking to use SESAMI code, which was previously packaged in Python and Jupyter Notebook scripts. | Gianmarco Terrones; Yu Chen; Archit Datar; Li-Chiang Lin; Heather Kulik; Yongchul Chung | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Machine Learning; Surface | CC BY NC 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641a7f88aad2a62ca124bb27/original/sesami-app-an-accessible-interface-for-surface-area-calculation-of-materials-from-adsorption-isotherms.pdf |
60c754f64c89192d59ad45db | 10.26434/chemrxiv.13217432.v2 | Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases | <p>Protein tyrosine phosphatases (PTPs) play an important role in cellular signalling and have been implicated in human cancers, diabetes, and obesity. Despite shared catalytic mechanisms and transition states for the chemical steps of catalysis, catalytic rates within the PTP family vary over several orders of magnitude. These rate differences have been implied to arise from differing conformational dynamics of the closure of a protein loop, the WPD-loop, which carries a catalytically critical residue. The present work reports computational studies of the human protein tyrosine phosphatase 1B (PTP1B), and YopH from <i>Yersinia pestis</i>, for which NMR has demonstrated a link between both their respective rates of WPD-loop motion and catalysis rates, which differ by an order of magnitude. We have performed detailed structural analysis, both conventional and enhanced sampling simulations of their loop dynamics, as well as empirical valence bond simulations of the chemical step of catalysis. These analyses revealed the key residues and structural features responsible for these differences, as well as the residues and pathways that facilitate allosteric communication in these enzymes. Curiously, our wild-type YopH simulations also identify a catalytically incompetent hyper-open conformation of its WPD-loop, sampled as a rare event, previously only experimentally observed in YopH-based chimeras. The effect of differences within the WPD-loop and its neighbouring loops on the modulation of loop dynamics, as revealed in this work, may provide a facile means for the family of PTP enzymes to respond to environmental changes and regulate their catalytic activities. </p> | Rory Crean; Michal Biler; Marc van der Kamp; Alvan C. Hengge; Shina Caroline Lynn Kamerlin | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c754f64c89192d59ad45db/original/loop-dynamics-and-enzyme-catalysis-in-protein-tyrosine-phosphatases.pdf |
60c74f02702a9b2a7918badb | 10.26434/chemrxiv.12837524.v1 | Real-Space X-Ray Pair Distribution Function Analysis and Molecular-Dynamics Modelling of Diflunisal Channel Hydrates | X-ray pair distribution function analysis is used with first-principles molecular dynamics simulations to study the co-operative H<sub>2</sub>O binding, structural dynamics and host-guest interactions in the channel hydrate of diflunisal. | Anuradha Pallipurath; Francesco Civati; Jonathan Skelton; Dean Keeble; Clare Crowley; Mary-Ellen Crowley; Patrick McArdle; Andrea Erxleben | Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f02702a9b2a7918badb/original/real-space-x-ray-pair-distribution-function-analysis-and-molecular-dynamics-modelling-of-diflunisal-channel-hydrates.pdf |
60c741740f50db9bad395b07 | 10.26434/chemrxiv.8055773.v1 | A Micellar Mitotane Formulation with High Drug Loading and Solubility: Physico-Chemical Characterization and Cytotoxicity Studies in 2D and 3D in Vitro Tumor Models. | Adrenocortical carcinoma (ACC) is a rare tumor and prognosis is overall poor but heterogeneous. Mitotane (MT) has been used for treatment of ACC for decades, either alone or in combination with cytotoxic chemotherapy. Even at doses up to 6 g per day, more than half of the patients do not achieve targeted plasma concentration (14-20 mg/L) even after many months of treatment which is caused by low water solubility and unfavorable pharmacokinetic properties such as poor bioavailability and high volume of distribution of MT. The clinical need and previously reported extraordinary high drug loading of poly(2-methyl-2-oxazoline)-block-poly(2-butyl-2-oxazoline)-block-poly(2-methyl-2-oxazoline) (A-pBuOx-A) based micelles for paclitaxel (PTX), led us to develop MT loaded micelles which may enable an injectable formulation. We successfully solubilized up to 6 g/L of MT in an aqueous formulation. The MT loaded nanoformulations were characterized by Fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and powder X-ray<br />
<p>diffraction (XRD), confirmed the amorphous nature of drug in the formulations. The polymer itself did not show cytotoxicity in adrenal and liver cell lines. By using the ACC model cell line NCI-H295 both in monolayers and tumor cell spheroids, we demonstrated micellar MT to exhibit comparable efficacy to its ethanol solution. We postulate that this formulation would be suitable for i.v. application and more rapid attainment of therapeutic plasma concentrations. In conclusion, we consider our micellar formulation a promising tool to alleviate major drawbacks of current MT treatment while retaining bioactivity towards ACC in vitro.</p> | Malik Salman Haider; Jochen Schreiner; Sabine Kendl; Matthias Kroiß; Robert Luxenhofer | Biocompatible Materials; Surfactants; Drug delivery systems; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741740f50db9bad395b07/original/a-micellar-mitotane-formulation-with-high-drug-loading-and-solubility-physico-chemical-characterization-and-cytotoxicity-studies-in-2d-and-3d-in-vitro-tumor-models.pdf |
64bed05bae3d1a7b0d45fd1e | 10.26434/chemrxiv-2023-70gkd | Nanocomposite Dielectric Elastomer Actuator for Micropump Diaphragms- Material Fabrication and Simulation Studies | Electroactive polymers are a class of materials that deform when an electric field is applied. Dielectric elastomers are classified under electroactive polymers that are capable of producing very large deformations and this is due to their elastomeric nature. The fabrication of a dielectric elastomeric actuator based on a polymer nanocomposite with ceramic fillers is reported here. Polydimethylsiloxane (PDMS) was the choice of dielectric elastomer and hexagonal boron nitride (hBN) was used as dielectric fillers, which was added in weight percentages to the polymer. An amorphous carbon-filled polyvinyl acetate composite was used as the compliant electrode. Altering the stiffness of the polymer gives the ability to bring about small actuations, achieved by adding nanofillers to the polymer matrix. The incorporation of hBN into the matrix increased the tensile modulus of the pure PDMS from 0.297 MPa to a maximum of 0.535 MPa with a marginal rise in tensile strength. Scanning electron microscopy and elemental mapping were carried out to understand the morphology and filler distribution in the nanocomposites. From the experiments, the actual voltage (in kV) which was necessary to induce visible actuations in the nanocomposites was determined. Data from the experiments were used in the simulation studies. Finite element analysis was performed on the diaphragm model to predict the behavior of the material and active area displacement of the diaphragm was 1 mm at 8 kV, and deformation of 78 % was achieved. The simulation studies showed that the nanocomposite was perfectly suitable to be used as a pumping mechanism in micropumps. | Adithya Lenin; Pandurangan Arumugam | Materials Science; Polymer Science; Nanoscience; Composites; Elastic Materials; Inorganic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bed05bae3d1a7b0d45fd1e/original/nanocomposite-dielectric-elastomer-actuator-for-micropump-diaphragms-material-fabrication-and-simulation-studies.pdf |
67b3669b6dde43c90848c729 | 10.26434/chemrxiv-2025-q2t1b | Versatile bifunctional PYTA derivatives for actinium-225 radiolabeling: a comparison to gold standards | We report the synthesis of the first PYTA bifunctional chelators designed for the coordination of actinium-225 and their bioconjugation to biovectors of interest. Three PYTA bifunctional chelators, PY3A, PYTA-GA, and PYTA-PE, were synthesized. A comparative study with current gold standards, MacropaTM, DOTA and Crown derivatives, highlights the excellent radiochemical properties and prolonged in vitro stability of PYTA derivatives. These exceptional performances were validated further through conjugation to a small PSMA ligand and two antibodies with quantitative radiolabeling under smooth conditions (37°C, low concentration). In vivo evaluation of radioimmunoconjugates further confirmed the prolonged stability of PYTA conjugates, yielding pharmacokinetic results comparable to Macropa™, while revealing clear in vivo instability of the Crown derivative. These findings underscore the potential of PYTA to emerge as the next gold-standard chelator for actinium-225, comparable to Macropa™, with the added advantages of easier synthesis of bifunctional derivatives and greater versatility for radiolabeling with other radionuclides. | Maxime Cheveau; Mathieu Moreau; Anna Grohmann; Sarah Robert; Alexandre Cochet; Bertrand Collin; Frédéric Boschetti; Sophie Poty; Franck Denat | Organic Chemistry; Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b3669b6dde43c90848c729/original/versatile-bifunctional-pyta-derivatives-for-actinium-225-radiolabeling-a-comparison-to-gold-standards.pdf |
64e345f3694bf1540cb8544d | 10.26434/chemrxiv-2023-5kzdk-v2 | Unravelling Irreversible Adsorbate Thermodynamics through Adsorption Assisted Desorption | Strongly bound surface species like alkylamines adsorbed on the Brønsted acid site of aluminosilicate zeolites exhibit negligible rates of molecular desorption, preventing them from achieving an equilibrated state on experimentally relevant timescales that limit the measurement of their adsorption thermodynamics. Through adsorption-assisted desorption, whereby distinct alkylamines facilitate desorption from Brønsted acid sites, we demonstrate that equilibrated states are achieved. Breakthrough adsorption measurements reveal that while 2-butylammonium on a Brønsted acid site is irreversibly adsorbed, it readily undergoes molecular desorption when exposed to a distinct alkylamine like 2-propylamine. As a result, two-adsorbate equilibrium was achieved when exposing Brønsted acid sites of aluminosilicate zeolites to a binary vapor phase alkylamine mixture. By varying relative vapor phase partial pressures and temperatures, we demonstrate the ability to experimentally measure the adsorption enthalpy and entropy of alkylammonium adsorbates on mostly isolated Brønsted acid sites in H-ZSM-5 (Si/Al = 140). A multi-adsorbate Langmuir isotherm was found to quantitatively describe the co-adsorption of alkylamines varying in size and basicity over a wide range of conditions, through which the relative adsorption enthalpy and entropy of alkylamines were measured. Across a homologous family of sec-alkylamines (C3-C5) adsorbed on isolated Brønsted acid sites, a fixed contribution to the enthalpy (19 ± 4 kJ mol CH2-1) and entropy (25 ± 4 J mol CH2-1 K-1) of adsorption per methylene unit of was found to exist, likely resulting from electrostatic interactions between the alkyl chain and surrounding pore environment. | Omar Abdelrahman; Ajibola Lawal | Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e345f3694bf1540cb8544d/original/unravelling-irreversible-adsorbate-thermodynamics-through-adsorption-assisted-desorption.pdf |
62ece624d131b7d8740d49c5 | 10.26434/chemrxiv-2022-6d0l1 | Exclusive Solution Discharge in Li-O2 Batteries? | Capacity, rate performance, and cycle life of aprotic Li-O2 batteries critically depend on reversible electrodeposition of Li2O2. Current understanding states surface adsorbed versus solvated LiO2 to control Li2O2 growth as surface film or as large particles. Here we show that Li2O2 forms across a wide range of electrolytes, carbons, and current densities as particles via solution mediated LiO2 disproportionation, questioning the prevalence of any surface growth under practical conditions. We describe a unified O2 reduction mechanism, which can explain all found capacity relations and Li2O2 morphologies with exclusive solution discharge. Deciding for particle morphology and achievable capacities are species mobilities, true areal rate and the degree of LiO2 association in solution. Capacity is conclusively limited by mass transport through the tortuous Li2O2 rather than electron transport through a passivating Li2O2 film. Provided that species mobilities and surface are high, high capacities are also achieved with weakly solvating electrolytes, previously considered prototypical for low capacity via surface growth. | Christian Prehal; Soumyadip Mondal; Ludek Lovicar; Stefan Freunberger | Physical Chemistry; Energy; Energy Storage; Chemical Kinetics; Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62ece624d131b7d8740d49c5/original/exclusive-solution-discharge-in-li-o2-batteries.pdf |
60c755044c891948d4ad4600 | 10.26434/chemrxiv.13956122.v1 | Structure Revision of the Lomaiviticins | The lomaiviticins are dimeric genotoxic bacterial metabolites that contain unusual diazocyclopentadiene functional groups and 2–4 deoxyglycoside residues. Because only 6 of 19 carbon atoms in the monomeric aglycon unit are proton-attached, their structure determination by NMR spectroscopic analysis is non-trivial. Prior structure elucidation efforts established that the two halves of the lomaiviticins are joined by a single carbon–carbon bond appended to an oxidized cyclohexenone ring. This ring was believed to comprise a 4,5-dihydroxycyclohex-2-en-1-one. The bridging bond was positioned at C6. This structure proposal has not been tested because none of the lomaiviticins have been prepared by total chemical synthesis or (to the best of our knowledge) successfully analyzed by X-ray crystallography. Here we disclose microED studies which establish that (–)-lomaiviticin C contains a 4,6-dihydroxy-cyclohex-2-en-1-one residue, that the bridging carbon–carbon bond is located at C5, and that the orientation of the cyclohexenone ring and configuration of the secondary glycoside are reversed, relative to their original assignment. High-field (800 MHz) NMR analysis supports the revised assignment and suggests earlier efforts were misled by a fortuitous combination of a nearzero 3JH4,H5 coupling constant and a 4-bond HMBC correlation that was interpreted as a 3-bond coupling. DFT calculations of the expected 13C chemical shifts of the original and revised structures of the aglycon and (–)-lomaiviticin B provide further robust support for the structure revision. Because the interconversion of lomaiviticins A, B, and C has been demonstrated, these findings apply to each isolate. These studies clarify the structures of this family of metabolites and underscore the power of microED analysis in natural products structure determination. | Lee Joon Kim; Mengzhao Xue; Xin Li; Zhi Xu; Eric Paulson; Brandon Q. Mercado; Hosea Nelson; Seth Herzon | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755044c891948d4ad4600/original/structure-revision-of-the-lomaiviticins.pdf |
65651f275bc9fcb5c98637e6 | 10.26434/chemrxiv-2023-59dcd | Probing Ion-Receptor Interactions in Halide Complexes of Octamethyl Calix[4]Pyrrole | The interplay of solvation and ion binding in anion host-guest complexes in solution governs the binding efficiency and selectivity of ion receptors. To gain molecular-level insight into the intrinsic binding properties of octamethyl calix[4]pyrrole (omC4P) host molecules with halide guest ions, we performed cryogenic ion vibrational spectroscopy (CIVS) of omC4P in complexes with fluoride, chloride, and bromide ions. We interpret the spectra using density functional theory, describing the infrared spectra of these complexes with both harmonic and anharmonic VPT2 calculations. The NH stretching modes of the pyrrole moieties serve as sensitive probes of the ion binding properties, as their frequencies encode the ion-receptor interactions. While scaled harmonic spectra reproduce the experimental NH stretching modes of the chloride and bromide complexes in broad strokes, the high proton affinity of fluoride introduces strong anharmonic effects. As a result, the spectrum of F−·omC4P is not even qualitatively captured by harmonic calculations, but it is recovered very well by VPT2 calculations. In addition, the VPT2 calculations recover the intricate coupling of the NH stretching modes with overtones and combination bands of CH stretching and NH bending modes and with low-frequency vibrations of the omC4P macrocycle, which are apparent for all halide ion complexes investigated here. A comparison of the CIVS spectra with infrared spectra of solutions of the same ion-receptor complexes shows how ion solvation changes the ion-receptor interactions for the different halide ions. | Lane M. Terry; Madison M Foreman; Anne P Rasmussen; Anne B McCoy; J. Mathias WEBER | Physical Chemistry; Clusters; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65651f275bc9fcb5c98637e6/original/probing-ion-receptor-interactions-in-halide-complexes-of-octamethyl-calix-4-pyrrole.pdf |
67114655cec5d6c142706eef | 10.26434/chemrxiv-2024-k4mqv | digitalMALDI: A single particle-based mass spectrometric detection system for biomolecules | The development of a real-time system to analyze individual biomolecule-containing aerosol particles could provide a critical capability to diagnose lung disease rapidly. However, currently available technologies are mainly based on molecular assays, require costly reagents, and are relatively slow and challenging to multiplex. To address these limitations, we developed digitalMALDI™, a laser-based mass spectrometry-based system. In particular, digitalMALDI™ is a near real-time system that directly samples aerosols, eliminating the need for complex and time-consuming sample preparation and producing MALDI-MS spectra for individual aerosol particles. In this study, an intact insulin protein was used to demonstrate the feasibility of this approach. Results showed that digitalMALDI™ is sensitive to detecting ~1 picogram of insulin protein in single particles in real-time, suggesting that the system has a broad application for disease diagnosis, environmental monitoring, and biosecurity management. | Dapeng Chen; Wayne Bryden; Michael McLoughlin ; Scott Ecelberger; Timothy Cornish; Lara Moore | Analytical Chemistry; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67114655cec5d6c142706eef/original/digital-maldi-a-single-particle-based-mass-spectrometric-detection-system-for-biomolecules.pdf |
65fd889ae9ebbb4db944ed88 | 10.26434/chemrxiv-2024-433hj | Counteranion-Controlled Chemodivergent Transfer-Hydrothiolation/Carbothiolation Utilizing Thioethers as Bifunctional Reagents | The pursuit of catalysis capable of forging C(sp3)-S bonds is extremely desired because these bonds have substantial importance in pharmaceuticals, functional materials, and organic synthesis. Hydrothiolation and carbothiolation of feedstock alkenes are among the most straightforward and prominent approaches to C(sp3)-S bond formations. However, hydrothiolation of unactivated alkenes typically proceeds in an anti-Markovnikov fashion, and carbothiolation relied on three-component coupling strategies using highly reactive pre-functionalized electrophilic sulfur sources and nucleophilic carbon sources. While carbothiolation of alkenes with a single, bifunctional reagent represents a concise and streamlined synthetic strategy for -alkyl organosulfur compounds, it has not been reported. Herein, by strategically using heterolytic cleavage of C(sp3)−S bond, we report a chemodivergent transfer-hydrothiolation and carbothiolation of alkenes with thioethers serving as bifunctional reagents. These catalytic systems can control the cleavage and reformation of strong C(sp3)−S -bonds. The chemo-control is achieved through careful selection of the counteranion associated with the Rh-centre. Counteranions with relatively strong basicity and coordinating ability, such as TfO-, promote an unusual Markovnikov transfer-thiol-ene reaction. Conversely, less basic and non-coordinating counteranions, such as BF4-, enable an unprecedented thioether-ene reaction, directly adding thioethers across alkenes. Mechanistic and computational studies elucidated that the coordination or non-coordination of counteranions on Rh can alter the basicity of thiolate, resulting in chemodivergence. | Zhen Wang; Hao-Dong Tan; Yao-Xin Wang; Qi Li; Xiao-Song Xue; Xiao-Hui Yang | Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fd889ae9ebbb4db944ed88/original/counteranion-controlled-chemodivergent-transfer-hydrothiolation-carbothiolation-utilizing-thioethers-as-bifunctional-reagents.pdf |
60c75225337d6c4f45e2868e | 10.26434/chemrxiv.13215167.v1 | An Activity-Based Fluorescent Sensor for the Detection of the Phenol Sulfotransferase SULT1A1 in Living Cells | <p>The biological activation and incorporation of inorganic sulfate proceeds via a process known as sulfurylation. Transfer of a sulfuryl moiety from the activated sulfate donor, 3’-phosphoadenosine-5’-phosphosulfate (PAPS), to hydroxy-containing substrates by human phenol sulfotransferases (SULT1 family) alters substrate solubility and charge to affect the metabolism of endogenous metabolites, xenobiotics, and drugs. Current methods to monitor SULT1 activity in living cells primarily rely on radiolabeling and/or cell extractions, but these methods do not provide a direct readout of enzyme activity with a dynamic, temporally resolved spatial map in live, intact cells. To fill this gap, here, we present the development, computational modeling, <i>in vitro</i> enzymology, and biological application of Sulfotransferase Sensor-3, STS-3, an activity-based fluorescent sensor for SULT1A1, the most widely expressed and promiscuous SULT1 isoform. </p> | Regina
A. Baglia; Kira Mills; Koushambi Mitra; Jasmine Tutol; Darby Ball; Kierstin Page; Jyothi Kallu; Sriharika Gottipolu; Sheena D’Arcy; Steven O. Nielsen; Sheel Dodani | Imaging; Sensors; Biochemistry; Chemical Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75225337d6c4f45e2868e/original/an-activity-based-fluorescent-sensor-for-the-detection-of-the-phenol-sulfotransferase-sult1a1-in-living-cells.pdf |
63e26ec9f1da89c683812227 | 10.26434/chemrxiv-2023-trx9k | Towards the detection limit of electrochemistry: Studying anodic processes with a fluorogenic reporting reaction | Recently, shot noise has been shown to be an inherent part of all charge transfer processes, leading to a practical limit of quantification of 2100 electrons (~0.34 fC) (Curr. Opin. Electrochem. 2020, 22, 170177). Attainable limits of quantification are made much larger by greater background currents and insufficient instrumentation, which restricts progress in sensing and single-entity applications. This limitation can be overcome by converting electrochemical charges into photons, which can be detected with much greater sensitivity, even down to a single-photon level. In this work, we demonstrate the use of fluorescence, induced through a closed-bipolar set-up, to monitor charge transfer processes below the detection limit of electrochemical workstations. During this process, the oxidation of ferrocenemethanol (FcMeOH) in one cell is used to concurrently drive the oxidation of Amplex Red (AR), a fluorogenic redox molecule, in another cell. The spectroelectrochemistry of AR is investigated and new insights on the commonplace practise of using deprotonated glucose to limit AR photooxidation are presented. The closed-bipolar set-up was used to produce fluorescent signals corresponding to the steady-state voltammetry of FcMeOH on a microelectrode. Chronopotentiometry is then used to show a linear relationship between the charge passed through FcMeOH oxidation and the integrated AR fluorescence signal. The sensitivity of the measurements obtained at different timescales varies between 2200 - 500 electrons per detected photon. The electrochemical detection limit is approached using a diluted FcMeOH solution in which no current signal is observed. Nevertheless, a fluorescence signal corresponding to FcMeOH oxidation is still seen, and detection of charges down to 300 fC is demonstrated. | Steven Linfield; Sylwester Gawinkowski; Wojciech Nogala | Physical Chemistry; Analytical Chemistry; Electrochemical Analysis; Electrochemistry - Mechanisms, Theory & Study | CC BY 4.0 | CHEMRXIV | 2023-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e26ec9f1da89c683812227/original/towards-the-detection-limit-of-electrochemistry-studying-anodic-processes-with-a-fluorogenic-reporting-reaction.pdf |
6290dcad2f3a0533600692cb | 10.26434/chemrxiv-2022-pvcmg-v2 | Photoelectron spectroscopy of cryogenically cooled NiO2¯ via slow photoelectron velocity-map imaging | High-resolution anion photoelectron spectra of cryogenically cooled NiO2¯ anions, obtained using slow photoelectron velocity-map imaging (cryo-SEVI), are presented in tandem with coupled cluster electronic structure calculations including relativistic effects. The experimental spectra encompass the , , and photodetachment transitions of linear ONiO0/-, revealing previously unobserved vibrational structure in all three electronic bands. The high-resolution afforded by cryo-SEVI allows for the extraction of vibrational frequencies for each state, congruent with those previously measured in the ground state and in good agreement with scalar-relativistic coupled-cluster calculations. Previously unobserved vibrational structure is observed in the and states and is tentatively assigned. Further, a refined electron affinity of 3.0464(7) eV for NiO2 is obtained as well as precise term energies for the and states of NiO2 of 0.3982(7) and 0.7422(10) eV, respectively. Numerous Franck-Condon forbidden transitions involving the doubly degenerate v2 bending mode are observed and ascribed to Herzberg-Teller coupling to an excited electronic state. | Mark Babin; Martin DeWitt; Jascha Lau; Marissa Weichman; Jongjin Kim; Lan Cheng; Daniel Neumark | Physical Chemistry; Spectroscopy (Physical Chem.); Surface | CC BY 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6290dcad2f3a0533600692cb/original/photoelectron-spectroscopy-of-cryogenically-cooled-ni-o2-via-slow-photoelectron-velocity-map-imaging.pdf |
61705ba264e2af4fa50b4626 | 10.26434/chemrxiv-2021-dr8n6 | Controlling the Optical and Catalytic Properties of Artificial Metalloenzyme Photocatalysts Using Chemogenetic Engineering |
Visible light photocatalysis enables a broad range of organic transformations that proceed via single electron or energy transfer. Metal polypyridyl complexes are among the most commonly employed visible light photocatalysts. The photophysical properties of these complexes have been extensively studied and can be tuned by modifying the substituents on the pyridine ligands. On the other hand, ligand modifications that enable substrate binding to control reaction selectivity remain rare. Given the exquisite control that enzymes exert over electron and energy transfer processes in nature, we envisioned that artificial metalloenzymes (ArMs) created by incorporating Ru(II) polypyridyl complexes into a suitable protein scaffold could provide a means to control photocatalyst properties. This study describes approaches to create covalent and non-covalent ArMs from a variety of Ru(II) polypyridyl cofactors and a prolyl oligopeptidase scaffold. A panel of ArMs with enhanced photophysical properties were engineered, and the nature of the scaffold/cofactor interactions in these systems was investigated. These ArMs provided higher yields and rates than Ru(Bpy)32+ for the reductive cyclization of dienones and the [2+2] photocycloaddition between C-cinnamoyl imidazole and 4-methoxystyrene, suggesting that protein scaffolds could provide a means to improve the efficiency of visible light photocatalysts. | Yasmine S. Zubi; Bingqing Liu; Yifan Gu; Dipankar Sahoo; Jared Lewis | Biological and Medicinal Chemistry; Catalysis; Bioengineering and Biotechnology; Biocatalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61705ba264e2af4fa50b4626/original/controlling-the-optical-and-catalytic-properties-of-artificial-metalloenzyme-photocatalysts-using-chemogenetic-engineering.pdf |
65d592f566c138172923eb4f | 10.26434/chemrxiv-2024-7zqx1 | Quasi-degenerate extension of local N-electron valence state perturbation theory with pair-natural orbital method based on localized virtual molecular orbitals | Chemical phenomena involving near-degenerate electronic states, such as conical intersections or avoided crossing, can be properly described using quasi-degenerate perturbation theory (QDPT). This study proposed a highly scalable quasi-degenerate second-order N-electron valence state perturbation theory (QD-NEVPT2) using the local pair-natural orbital (PNO) method. Our recent study showed an efficient implementation of the PNO-based state-specific (SS) NEVPT2 method using orthonormal localized virtual molecular orbitals (LVMOs) as an intermediate local basis. This study derived the state-coupling (or off-diagonal) terms to implement QD-NEVPT2 in an alternative manner to enhance efficiency based on the internally contracted basis (ICB) and PNO overlap matrices between different references. To facilitate further acceleration, a local resolution-of-the-identity (RI) three-index integral generation algorithm was developed using LMOs and LVMOs. Although the NEVPT2 theory is considered to be less susceptible to the intruder-state problem (ISP), this study revealed that it can easily suffer from ISP when calculating high-lying excited states. We ameliorated this instability using the imaginary level shift (LS) technique. The PNO-QD-NEVPT2 calculations were performed on small organic molecules for the 30 lowest-lying states, as well as photoisomerization involving the conical intersection of 1,1-dimethyldibenzo[b,f] silepin with a cis-stilbene skeleton. These calculations revealed that the PNO-QD-NEVPT2 method yielded negligible errors compared to the canonical QD-NEVPT2 results. Furthermore, we tested its applicability to a large photoisomerization system using the green fluorescent protein model and the 10-state calculation of the large transition metal complex, showcasing that off-diagonal elements can be evaluated at a relatively low cost. | Manami Hayashi; Masaaki Saitow; Kazuma Uemura; Takeshi Yanai | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d592f566c138172923eb4f/original/quasi-degenerate-extension-of-local-n-electron-valence-state-perturbation-theory-with-pair-natural-orbital-method-based-on-localized-virtual-molecular-orbitals.pdf |
60c74f3e842e6579d9db37c0 | 10.26434/chemrxiv.12865490.v1 | Borophosphate Glass as an Active Media for CuO Nanoparticle Growth: An Efficient Catalyst for Selenylation of Oxadiazoles and Application in Redox Reactions | <div>Herein, we report the preparation of CuO@ borophosphate nanoparticles (CuOnano@glass) and their wide catalytic applications.The glass annealing, under a controlled atmosphere, enables the growth of copper nanoparticles on the glass surface (not within) by an uncommon bottom-up process. Following the thermal annealing of metallic nanoparticles under air atmosphere, supported copper oxide nanoparticles CuONPs on the glass surface can be obtained. The approach enables the glass matrix to be explored as a precursor and a route for the synthesis of supported copper-based nanoparticles in a solvent-free process without immobilization steps or stabilizing agents. In order to demonstrate the wide synthetic utility of this CuONPs glass-based catalyst, one-pot three-component domino reactions were performed under an air atmosphere, affording the desired selenylated oxadiazoles in good to excellent yields. We also extended the application of these new materials as a glass-based catalyst in the phenol hydroxylation and the reduction of 4-nitrophenol.</div> | Marcos R. Scheide; Marcos M. Peterle; Sumbal Saba; Jos´e S. S. Neto; Guilherme F. Lenz; Rosane Dias Cezar; Jorlandio F. Felix; Giancarlo V. Botteselle; Ricardo Schneider; Jamal Rafique; antonio luiz braga | Organic Synthesis and Reactions; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f3e842e6579d9db37c0/original/borophosphate-glass-as-an-active-media-for-cu-o-nanoparticle-growth-an-efficient-catalyst-for-selenylation-of-oxadiazoles-and-application-in-redox-reactions.pdf |
661d69f3418a5379b0e89e3e | 10.26434/chemrxiv-2024-cpf4j | Direct in situ NMR observation of lithium plating, corrosion, nitridation and protonolysis for ammonia synthesis | As a low-carbon and decentralized ammonia synthetic method, lithium-mediated electrochemical synthesis has shown promising efficiencies and reaction rates. Nevertheless, many mechanistic questions need to be addressed to optimize the process and in situ characterizations are in great need. Here we develop in situ NMR methodology that allows us to directly observe each reaction step of the catalytic cycle, including plating of metallic lithium and the concurrent corrosion, nitrogen splitting on lithium metal and protonolysis of lithium nitride. The in situ NMR methods are general and can be broadly applied for screening and understanding Li and beyond-Li catalysts for nitrogen splitting, accelerating the materials discovery for ammonia synthesis. | Ruipeng Luo; Anna Bergljót Gunnarsdóttir; Evan Wenbo Zhao | Physical Chemistry; Catalysis; Energy; Electrocatalysis; Electrochemistry - Mechanisms, Theory & Study; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661d69f3418a5379b0e89e3e/original/direct-in-situ-nmr-observation-of-lithium-plating-corrosion-nitridation-and-protonolysis-for-ammonia-synthesis.pdf |
65fba95d9138d23161e8ee73 | 10.26434/chemrxiv-2024-sm0gd | Many-body interactions and deep neural network potentials for water | We present a detailed assessment of deep neural network potentials developed within the DeePMD framework and trained on the MB-pol data-driven many-body potential energy function. Specific focus is directed at the ability of DeePMD-based potentials to correctly reproduce the accuracy of MB-pol across various water systems. Analyses of bulk and interfacial properties as well as many-body interactions characteristic of water elucidate inherent limitations in the transferability and predictive accuracy of DeePMD-based potentials. These limitations can be traced back to an incomplete implementation of the “nearsightedness of electronic matter” principle, which may be common throughout machine learning potentials that do not include a proper representation of self-consistently determined long-range electric fields. These findings provide further support for the "short-blanket dilemma" faced by DeePMD-based potentials, highlighting the challenges in achieving a balance between computational efficiency and a rigorous, physics-based representation of the properties of water. Finally, we believe that our study contributes to the ongoing discourse on the de- velopment and application of machine learning models in simulating water systems, offering insights that could guide future improvements in the field. | Yaoguang Zhai; Richa Rashmi; Etienne Palos; Francesco Paesani | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fba95d9138d23161e8ee73/original/many-body-interactions-and-deep-neural-network-potentials-for-water.pdf |
633a40800e3c6ab7f43125fe | 10.26434/chemrxiv-2022-drf9p | Switchable Decarboxylation by Energy- or Electron-Transfer Photocatalysis | Kolbe dimerization and Hofer-Moest reactions are well-investigated carboxylic acid transformations, wherein new carbon–carbon and carbon–heteroatom bonds are constructed via electrochemical decarboxylation. These transformations can be switched by choosing an electrode that allows control of the reactive intermediate such as carbon radical or carbocation. However, the requirement of a high current density diminishes the functional group compatibility with these electrochemical reactions. Here, we demonstrate the photocatalytic decarboxylative transformation of carboxylic acids in a switchable and functional group-compatible manner. We discovered that switching between Kolbe-type or Hofer-Moest-type reactions can be accomplished with suitable photocatalysts by controlling the reaction pathways: energy transfer (EnT) and single-electron transfer (SET). The EnT pathway promoted by an organo-photocatalyst yielded 1,2-diarylethane from arylacetic acids, whereas the ruthenium photoredox catalyst allows the construction of an ester scaffold with two arylmethyl moieties via the SET pathway. The resulting radical intermediates were coupled with olefins to realize multicomponent reactions. Consequently, four different products were selectively obtained from a simple carboxylic acid. This discovery offers new opportunities for selectively synthesizing multiple products via switchable reactions using identical substrates with minimum cost and effort. | Yota Sakakibara; Kenichiro Itami; Kei Murakami | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633a40800e3c6ab7f43125fe/original/switchable-decarboxylation-by-energy-or-electron-transfer-photocatalysis.pdf |
60c74b66ee301cb031c79e61 | 10.26434/chemrxiv.12326399.v1 | Repurposing the Natural Compound for Antiviral During an Epidemic -a Case Study on the Drug Repurpose of Natural Compounds to Treat COVID-19 | <p>The pandemic caused by the novel coronavirus
SARS-CoV-2 is rapidly spreading and infecting the population on the global
scale, it is a global health threat due to its high infection rate, high mortality
and the lack of clinically approved drugs and vaccines for treating the disease
(COVID-19). Utilising the published structures and homologue remodelling for
proteins from SARS-CoV-2, an <i>in silico</i> molecular docking based screening
was conducted and deposited in the Shennong project database. The results from
the screening could be used to explain the clinical observation of repurposing
the Ritonavir and Lopinavir to treat patients in the early stage of COVID-19
infection, and the prescription of Remdisivir in the United States as the
therapy. Additionally, this molecular docking identified natural compound
candidates for drug repurposing. This <i>in silico </i>molecular docking screen
may be used for the initatial evaluation and rationalisation for drug
repurposing of other potential candidates, especially other natural compounds
from traditional Chinese medicines.</p> | Zhihao Wang; Chi Xu; Bing Liu; Nan Qiao | Biochemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b66ee301cb031c79e61/original/repurposing-the-natural-compound-for-antiviral-during-an-epidemic-a-case-study-on-the-drug-repurpose-of-natural-compounds-to-treat-covid-19.pdf |
66168f6821291e5d1d887100 | 10.26434/chemrxiv-2024-dhhk8 | UV photochemistry of the L-cystine disulfide bridge in aqueous solution investigated by femtosecond X-ray absorption spectroscopy | Despite the biological relevance of the disulfide bond as the motive, which stabilizes the tertiary structure of many proteins, its photostability, UV-induced bond cleavage mechanisms and secondary photochemistry are still contested after decades of research. In this study, we employed femtosecond X-ray absorption spectroscopy to unravel the photochemistry of the aliphatic disulfide bridge of the semi-essential proteinogenic amino acid L-cysteine (L-cystine) in aqueous solution. We observe homolytic bond cleavage upon UV irradiation and the emergence of thiyl radicals as the single primary photoproduct and its ultrafast decay due to geminate recombination at remarkably high quantum yield in excess of 80% within 20 ps. These dynamics coincide with the emergence of a secondary product, attributed to the perthiyl radical. More than 70% of broken disulfide bridges form within the first nanosecond after bond cleavage. From these observations, we establish a dynamic photostability of the disulfide bridge and a mechanism of perthiyl radical formation from a 'hot' ground-state parent molecule that asymmetrically fragments along a carbon-sulfur bond, resolving long-standing questions in the photochemistry of disulfide bridges in condensed phase. | Miguel Ochmann; Jessica Harich; Rory Ma; Antonia Freibert; Jae Hyuk Lee; Daewoong Nam; Sangsoo Kim; Intae Eom; Minseok Kim; Yujin Kim; Madhusudana Gopannagari; Da Hye Hong; Briony A. Yorke; Tae Kyu Kim; Nils Huse | Physical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66168f6821291e5d1d887100/original/uv-photochemistry-of-the-l-cystine-disulfide-bridge-in-aqueous-solution-investigated-by-femtosecond-x-ray-absorption-spectroscopy.pdf |
60c73d93ee301cb073c785cc | 10.26434/chemrxiv.5962240.v1 | Adsorption Contraction Mechanics: Understanding Breathing Energetics in Isoreticular Metal-Organic Frameworks | In this article we report the synthesis and detailed analysis of the highly porous metal-organic framework DUT-48, isoreticular to DUT-49 a material which shows an adsorption-induced structural transition. DUT-48 has impressive porosity and methane storage capacity, however displays conventional adsorption behaviour. The contrasting flexibility of DUT-48 and DUT-49 were analysed and rationalised using a combination of novel experimental and computational techniques. Microcalorimetry measurements, in conjunction with molecular simulations, demonstrate that DUT-48 has a significantly lower adsorption enthalpy difference and a higher framework stiffness which leads to an absence of adsorption-induced transitions and negative gas adsorption (NGA). However, by analysing the mechanical behaviour of both DUT-48 and DUT-49, employing mercury porosimetry experiments, we discovered that both materials exhibit large volume changes under hydrostatic compression, demonstrating noteworthy potential as shock absorbers, and directly linking internal adsorption-induced contraction to external hydrostatic compression. | Simon Krause; Jack D. Evans; Volodymyr Bon; Irena Senkovska; Sebastian Ehrling; Ulrich Stoeck; Pascal Yot; Paul Iacomi; Philip Llewellyn; Guillaume Maurin; François-Xavier Coudert; Stefan Kaskel | Elastic Materials; Hybrid Organic-Inorganic Materials; Metamaterials; Coordination Chemistry (Inorg.); Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d93ee301cb073c785cc/original/adsorption-contraction-mechanics-understanding-breathing-energetics-in-isoreticular-metal-organic-frameworks.pdf |
621cf47757a9d2c4146e257a | 10.26434/chemrxiv-2022-h0rrx | Resonance between dithiocarbamates and thioureide mesomeres coupled to metal−hydrogen anagostic bond transforming under pressure | The pressure-induced transformation of plane-square complex nickel(II) bis(N,N-diethyldithiocarbamate) between its soft dithiocarbamate (form I) and thioureide (form II) mesomeres is coupled to the interchange of anagostic Ni‧‧‧H−C interactions from methylene to the methyl group, respectively. At 1.23 GPa, the clearly visible giant anomalous compressibility of the crystal reveals a potential-energy difference of 5.4 kJmol-1 between the two complex forms. The structural and spectroscopic results, which are supported by quantum-mechanical calculations, connect this solid-state phase transition with the mesomeric transition, and this is accompanied by the conformational transformation of anagostic Ni‧‧‧H−C rearrangement and formation of the charge–assisted S-‧‧‧H−C bond under pressure. | Szymon Sobczak; Kinga Roszak; Andrzej Katrusiak | Physical Chemistry; Materials Science; Physical and Chemical Properties; Materials Chemistry; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621cf47757a9d2c4146e257a/original/resonance-between-dithiocarbamates-and-thioureide-mesomeres-coupled-to-metal-hydrogen-anagostic-bond-transforming-under-pressure.pdf |
6447ee86df78ec50155eb778 | 10.26434/chemrxiv-2023-mv05n | CO2 permeation through fusion-bonded epoxy coating in humid environments | This study investigates the effect of water and CO2 exposure on the performance of epoxy-based coatings under conditions commonly found in pipeline applications. The permeability of fusion bonded epoxy (FBE) decreases as CO2 pressure increases and the presence of water facilitates gas transport through the coating. The latter is in conflict with theories of membrane selectivity and competitive transport in gas/vapor systems, in which water is the predominant permeant for its lower kinetic diameter and higher condensability. Our results show that this anomaly was due to the dynamic transformation of permeable channels in the coating structure. Microstructural characterization of FBE after exposure to CO2/H2O mixtures showed that carbonation of wollastonite filler particles results in a change in shape, volume, and chemical composition of these filler particles. The chemical reaction between wollastonite and CO2 in the presence of water led to a degradation that caused changes in porosity, permeability, and filler volume. To verify these findings for the coating in the presence of adhesion forces, electrochemical impedance spectroscopy (EIS) was also used. The tests conducted showed that exposure to a CO2/H2O mixture causes filler particles within the coating to undergo carbonation, leading to the formation of new microchannels within the epoxy network. Initially, the carbonation of fillers led to an increase in the pore resistance of the coating, which was attributed to the plugging of micropore channels on the coating surface. However, the subsequent decreasing trend of this parameter suggested that water infiltration into the coating had increased due to this degradation. The carbonation of wollastonite within the FBE coating leads to a volume change in the fillers, resulting in the creation of small voids or gaps in the epoxy matrix. This, in turn, facilitates the easier penetration of water and dissolved gas to the underlying substrate. Consequently, the accumulation of water inside coating increases the dielectric constant, resulting in a higher capacitance of the coating. It appears that high concentrations of CO2 in wet conditions, even at low pressures, can have negative impacts on the barrier performance of the coating. | Hossein Zargarnezhad; Kashif Mairaj Deen ; Dennis Wong; C. N. Catherine Lam; Edouard Asselin | Materials Science; Polymer Science; Chemical Engineering and Industrial Chemistry; Coating Materials; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6447ee86df78ec50155eb778/original/co2-permeation-through-fusion-bonded-epoxy-coating-in-humid-environments.pdf |
670a1d0751558a15efd578f3 | 10.26434/chemrxiv-2024-s1436 | Highly Strained Tricyclic Oxanorbornenes with Uncommon Reactivity Enable Rapid ROMP for High-Performance Polyenes | Bio-derived monomers, readily available from biomass via atom- and redox-efficient processes, will need to play a major role in the development of sustainable polymeric materials. Here, we show that a family of tricyclic monomers, efficiently made from bio-based furans via Diels-Alder chemistry, allows the production of polyenes with diverse thermo/physical properties through Ring Opening Metathesis Polymerization (ROMP). Via small structure variations, we offer insight into the intricacies of monomer design and implications for polymerization. Notably, the thermostable polyenes all show very similarly high Head-to-Tail regioregularities, trans-linkage isomerism distributions and narrow dispersities. In addition, the monomers exhibit rare reactivity with ethyl vinyl ether, which can be used chain transfer agent, making telechelic polyenes accessible. The monomers do differ substantially in polymerization rate, spanning two orders of magnitude, in extent of molecular weight control and in the properties of the resulting amorphous polymers. With glass transition temperatures ranging from 116 to 217 °C and degradation temperatures succeeding 350 °C, these materials are among the highest performing biobased homopolymers reported. We elucidate these variations, demonstrating that ROMP is profoundly influenced by subtle structural changes in the monomers. | Björn Grabbet; Abdullah Taiem; Răzvan Cioc; Pieter Bruijnincx; Arnaud Thevenon | Polymer Science; Organic Polymers; Polymerization (Polymers); Polymerization catalysts | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670a1d0751558a15efd578f3/original/highly-strained-tricyclic-oxanorbornenes-with-uncommon-reactivity-enable-rapid-romp-for-high-performance-polyenes.pdf |
60c75195ee301c4912c7aae4 | 10.26434/chemrxiv.13182965.v1 | Identification of Potential Phytochemical Inhibitors as Promising Therapeutics Against SARS-CoV-2 and Molecular Dynamics Simulation | The high infectivity and mortality of novel coronavirus has caused a serious concern all over the
world. Still, there is no specific drug or preventive medication to treat SARS-CoV-2 infection
despite comprehensive analysis by the researchers. This study was designed to demonstrate the
efficacy of some phyto-chemical compounds against SARS-CoV-2 by using both structure and
ligand based virtual screening methods. A total of 33 plant metabolites were screened against
SARS-CoV-2 main protease proteins (MPP), Nsp9 RNA binding protein, spike receptor binding
domain and HR2 domain using a molecular docking approach. Results showed that three
metabolites, i.e., Limonin, Isoflavone, and Coumadin conferred maximum binding affinity with
all key proteins of SARS-CoV-2. For each viral protein, the critical binding sites and drug surface
hotspots have been unraveled. ADME analysis indicated that none of the compounds have adverse
effects that could decrease their drug-like properties. Moreover, toxicity pattern analysis also
unmasked the non-toxic nature of the top drug candidates. The RMSD values of top ligandmacromolecule complexes were less than 2 Å, while RMSF values showed regular atomic
fluctuations in the molecular dynamics study. Notably, most of the target class by top drug
candidates belonged to enzyme groups (e.g. oxidoreductases, protease, Kinase). Results of drug
similarity prediction revealed two approved structural analogs of Coumadin named Warfarin
(DB00682) and Phenprocoumon (DB00946) from DrugBank. In addition, Isoformononetin an
experimental drug analog of isoflavone could also be an option for the treatment of viral infections.
For limonin there was no analog found in drugbank. The study can pave the way for the creation
of effective SARS-CoV-2 medications and preventive measures. We highly recommend further in
vivo trials for the experimental validation of our findings | Anik Banik; Emran Sajib; Anamika Deb; Sheikh Rashel Ahmed; Md- Tariqul Islam; Soykot Roy; Shiuly Sinha; Hlamrasong Marma; Kazi Faizul Azim | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75195ee301c4912c7aae4/original/identification-of-potential-phytochemical-inhibitors-as-promising-therapeutics-against-sars-co-v-2-and-molecular-dynamics-simulation.pdf |
60c74f000f50db19fa397306 | 10.26434/chemrxiv.11938182.v3 | Ion-Specific Clustering of Metal-Amphiphile Complexes in Rare Earth Separations | <p>The nanoscale structure of a complex fluid can play a major
role in the selective adsorption of ions at the nanometric interfaces, which
are crucial in industrial and technological applications. Here we study the
effect of anions and lanthanide ions on the nanoscale structure of a complex
fluid formed by metal-amphiphile complexes, using small angle X-ray scattering.
The nano- and mesoscale structures we observe can be directly connected to
preferential transfer of light (La, Nd) or heavy (Er, Lu) lanthanides into the
complex fluid from an aqueous solution. While the toluene-based complex fluids
containing trioctylmethylammonium-nitrate (TOMA-nitrate) always show the same
mesoscale hierarchical structure regardless of lanthanide loading and prefer
light lanthanides, those containing TOMA-thiocyanate show an evolution of
mesoscale structure as a function of the lanthanide loading and prefer heavy
lanthanides. The hierarchical structuring indicates the presence of attractive
interactions between ion-amphiphile aggregates, causing them to form clusters.
A clustering model, that accounts for the hard sphere repulsions and
short-range attractions between the aggregates, has been adapted to model the
X-ray scattering results. The new model successfully describes the nanoscale
structure and helps in understanding the mechanisms responsible for amphiphile
assisted ion transport between immiscible liquids. Accordingly, our results
imply different mechanisms of lanthanide transport depending on the anion present in the
complex fluid and correspond with anion-dependent trends in rare-earth
separations. </p> | Srikanth Nayak; Kaitlin Lovering; Ahmet Uysal | Nanostructured Materials - Nanoscience; Clusters; Physical and Chemical Processes; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f000f50db19fa397306/original/ion-specific-clustering-of-metal-amphiphile-complexes-in-rare-earth-separations.pdf |
60c74b31bb8c1a022a3db162 | 10.26434/chemrxiv.12264308.v2 | Ion Coordination and Chelation in a Glycolated Polymer Semiconductor: Molecular Dynamics and X-Ray Fluorescence Study | <p>Organic electrochemical transistors (OECTs) are based on the doping of a semiconducting polymer by an electrolyte. Due to their ability to conjugate volumetric ion penetration with high hole mobility and charge density, polythiophenes bearing glycolated side chains have rapidly surged as the highest performing materials for OECTs; amongst them, p(g2T-TT) is amongst those with the highest figure of merit. While recent studies have shown how different doping anions tend to affect the polymer microstructure, only a handful of electrolytes have been tested in mixed conduction devices. Our work provides an atomistic picture of the p(g2T-TT) -electrolyte interface in the ‘off’ state of an OECT, expected to be dominated by cation-polymer interactions. Using a combination of molecular dynamics simulations and X-ray fluorescence, we show how different anions effectively tune the coordination and chelation of cations by glycolated polymers. At the same time, softer and hydrophobic anions such as TFSI and ClO<sub>4</sub> are found to preferentially interact with the p(g2T-TT) phase, further enhancing polymer-cation coordination. Besides opening the way for a full study of electrolyte doping mechanisms in operating devices, our results suggest that tailoring the electrolyte for different applications and materials might be a viable strategy to tune the performance of mixed conducting devices.</p> | Micaela Matta; Ruiheng Wu; Bryan D. Paulsen; Anthony Petty; Rajendar Sheelamanthula; Iain McCulloch; George C Schatz; Jonathan Rivnay | Conducting polymers; Polymer morphology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b31bb8c1a022a3db162/original/ion-coordination-and-chelation-in-a-glycolated-polymer-semiconductor-molecular-dynamics-and-x-ray-fluorescence-study.pdf |
66155909418a5379b078e69d | 10.26434/chemrxiv-2024-wp0vg | Exceptions, Paradoxes, and Their Resolutions in Chemical Reactivities | Chemists have long utilized theories and models to rationalize empirical data and predict outcomes in new chemical systems. Unexpected reactivities often present themselves as exceptions or paradoxes, highlighting gaps in our current understanding and the limitations of (then) existing models. Rather than something to be disregarded, these exceptions offer valuable insights that can lead to the refinement of theories and the resolution of paradoxes, ultimately fostering scientific discovery. While the concept of scientific discovery described is not new, practically, it remains significantly underappreciated in the field of organic chemistry. This perspective article postulates possible epistemic origins of such unexpected chemical reactivities across various contexts, proposing a systematic approach to addressing these anomalies. Through a compilation of origins, supported by specific modern examples, this work aims to lay the groundwork for more comprehensive thinking that will help the field navigate future exploration. While the illustrative examples presented herein focus on physical organic chemistry, the concepts discussed are universally applicable across different fields in chemical science. | Guanqi Qiu | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66155909418a5379b078e69d/original/exceptions-paradoxes-and-their-resolutions-in-chemical-reactivities.pdf |
678d1bad6dde43c9083104c3 | 10.26434/chemrxiv-2025-v1jd8 | Oxidant-Free Amidation of Aldehydes Enabled by Electrophotocatalysis | Electrophotocatalysis (EPC) is emerging as a powerful tool in organic synthesis, offering unique redox transformations without the need for sacrificial oxidants or reductants. Building on this activation mode, we have developed an electrophotocatalytic method for the direct amidation of aldehydes, utilizing electricity as the sole oxidant and light to generate chlorine radicals for hydrogen atom transfer. This sustainable approach is compatible with a wide range of aldehydes and nitrogen-based nucleophiles, performing efficiently under batch conditions and demonstrating scalability with flow technology. The mild reaction conditions, excellent functional group tolerance, and versatility make this EPC protocol particularly suitable for C–N bond formation, enabling functionalization of diverse organic compounds and facilitating late-stage modifications in drug development. | Dimitris Ioannou; Elena Bombonato; Jiri Sanramat; Joost Reek; Timothy Noel | Organic Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Organic Compounds and Functional Groups; Electrocatalysis; Photocatalysis | CC BY 4.0 | CHEMRXIV | 2025-01-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678d1bad6dde43c9083104c3/original/oxidant-free-amidation-of-aldehydes-enabled-by-electrophotocatalysis.pdf |
669a87a501103d79c5985128 | 10.26434/chemrxiv-2024-g8tl8-v3 | Non-deterministic Dynamics in η-to-θ Phase Transition of Alumina Nanoparticles | Phase diagrams and crystallography are standard tools for studying structural phase transitions while acquiring kinetic information at the atomistic level has been considered essential but challenging. Here, we report a rare example of a statistical kinetics study, showing that the η-to-θ phase transition of alumina, unidirectional in bulk and retaining the crystal lattice orientation, occurs non-deterministically via an ergodic equilibrium via molten state, as observed for nanoparticles on bulk Al(OH)3 surface. The memory of the lattice orientation is lost. The rate of the interconversion was insensitive to the electron dose rate, and it is a thermal process with a small Gibbs free energy of activation. This non-deterministic kinetics should be a key feature of crystal nucleation occurring in high surface energy regions of bulk crystals. | Masaya Sakakibara; Minoru Hanaya; Takayuki Nakamuro; Eiichi Nakamura | Physical Chemistry; Analytical Chemistry; Microscopy; Clusters; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669a87a501103d79c5985128/original/non-deterministic-dynamics-in-to-phase-transition-of-alumina-nanoparticles.pdf |
67a76c366dde43c90811a855 | 10.26434/chemrxiv-2025-rdgd5 | Modifying polyelectrolyte charge density and surface coverage for enhanced polyelectrolyte-surfactant lubrication of biomimetic interfaces | Mixtures of polyelectrolytes and surfactants are useful components of many fluid formulations, including shampoos and conditioners. These mixtures form polyelectrolyte-surfactant complexes in solution that can adsorb on solid surfaces and significantly reduce friction. Experiments have shown that the charge density of polyelectrolytes affects their adsorption and conformation on the surface, which are expected to strongly influence their lubrication performance. Here, we use coarse-grained, non-equilibrium molecular dynamics simulations to study how different charge densities and surface coverages of a polyelectrolyte, cationic guar gum, in the presence of an anionic surfactant, sodium dodecyl sulfate, influence hair friction. We observe improved lubrication for polyelectrolytes with higher charge densities on biomimetic surfaces representative of both virgin and bleached hair. This is attributed to an increase in surface separation, which is facilitated by higher retention of interfacial surfactants and water. Higher polyelectrolyte surface coverages also result in lower friction through this mechanism. At sufficiently high polyelectrolyte surface coverages, friction becomes insensitive to the level of chemical damage on the hair surface. Most polyelectrolytes have flat, train-like conformations, particularly at high charge density and low surface coverage. The number of tail and loop conformations increases at lower charge density and higher surface coverage, but this has a minor effect on friction compared to the amount of water and surfactant trapped inside the contact. These simulations show considerable promise for virtual screening of polyelectrolytes with optimal lubricity performance in liquid formulations. | Erik Weiand; Francisco Rodriguez-Ropero; Stefano Angioletti-Uberti; Daniele Dini; James P. Ewen | Theoretical and Computational Chemistry; Physical Chemistry; Polymer Science; Polyelectrolytes - Polymers; Computational Chemistry and Modeling; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a76c366dde43c90811a855/original/modifying-polyelectrolyte-charge-density-and-surface-coverage-for-enhanced-polyelectrolyte-surfactant-lubrication-of-biomimetic-interfaces.pdf |
643aeb0773c6563f14f0d582 | 10.26434/chemrxiv-2023-2ckbx | Binding Pocket Response of EDTA Complexes with Alkaline Earth Dications to Stepwise Hydration – Structural Insight from Infrared Spectra | We investigate the microhydration structures of complexes of alkaline earth dications and ethylenediaminetetraacetic acid (EDTA) for up to two water molecules, using cryogenic ion vibrational spectroscopy in concert with density functional theory. The interaction with water shows a clear dependence on the chemical identity of the bound ion. For Mg2+, microhydration mostly involves the carboxylate groups of EDTA and does not entail direct contact with the dication. In contrast, the larger ions (Ca2+, Sr2+, and Ba2+) interact electrostatically with the microhydration environment, and this interaction increases in importance with the size of the ion. This trend reflects the ion position in the EDTA binding pocket, which comes closer to the rim of the pocket with increasing ion size. | Madison M. Foreman; Lane M. Terry; J. Mathias Weber | Physical Chemistry; Clusters; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643aeb0773c6563f14f0d582/original/binding-pocket-response-of-edta-complexes-with-alkaline-earth-dications-to-stepwise-hydration-structural-insight-from-infrared-spectra.pdf |
635e55fbcf6de9f65e2857c3 | 10.26434/chemrxiv-2022-mxtm4 | Bridging Nanocrystals to Robust, Multifunctional, Bulk Materials through Nature-Inspired, Hierarchical Design | Self-assembly of nano-building blocks has emerged as a key tool to direct the arrangement and the collective properties of nanomaterials.
Nevertheless, the lack of control over larger length scales when nanomaterials are processed typically leads to defects which scale with the dimensions of the specimen. This ultimately limits their structural integrity and hence their development beyond microscale materials and devices.
Herein, we propose a new, versatile approach to fabricate at low temperatures a nature-inspired composite material based on self-similar, hard, inorganic structures interconnected via soft, organic layers on two hierarchy levels.
The final macroscale composite material presents a robust architecture while still maintaining the instrinsic nano-characteristic, functional properties derived from its nano-building blocks. The obtained nanocrystalline magnetite-based material has a high bending strength, significantly improved fracture toughness, high saturation magnetization and a low coercivity while portraying an adjustable, macroscopic shape in the cm-scale. The presented nanocomposite design, therefore, allows to obtain macroscale components with multifunctional properties fostered through nanoscale features and hence enables advancing nanomaterials towards large-scale engineering applications. | Alexander Plunkett; Kaan Temiz; Chad Warren; Valea Wisniewski; Kaline P. Furlan; Javier Garay; Diletta Giuntini; Berta Domènech; Gerold A. Schneider | Materials Science; Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635e55fbcf6de9f65e2857c3/original/bridging-nanocrystals-to-robust-multifunctional-bulk-materials-through-nature-inspired-hierarchical-design.pdf |
60c73ffbf96a0086c32861e0 | 10.26434/chemrxiv.7578599.v1 | Macrocellular Titanosilicate Monoliths as Highly Efficient Structured Olefin Epoxidation Catalysts | Self-standing macrocellular titanosilicate monolith foams are obtained using a one-pot sol-gel route and show excellent performance in the epoxidation of cyclohexene. Thanks to the High Internal Phase Emulsion (HIPE) templating method, the materials feature a high void fraction, a hierarchically porous texture and good mechanical strength. Highly dispersed Ti species can be incorporated in tetrahedral coordination the silica matrix. These characteristics allow the obtained ‘SiTi(HIPE)’ materials to reach high catalytic turnover in the epoxidation of cyclohexene. The monoliths can advantageously be used to run the reaction in continuous flow mode.<br /> | Valentin Smeets; Ludivine van den Biggelaar; Tarek Barakat; Eric M. Gaigneaux; Damien Debecker | Catalysts; Reaction Engineering; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73ffbf96a0086c32861e0/original/macrocellular-titanosilicate-monoliths-as-highly-efficient-structured-olefin-epoxidation-catalysts.pdf |
60c73f5abdbb894132a37fac | 10.26434/chemrxiv.7313657.v1 | Spying on Neuronal Membrane Potential with Genetically Targetable Voltage Indicators | Methods for optical measurement of voltage dynamics in
living cells are attractive because they provide spatial resolution surpassing
traditional electrode-based measurements and temporal resolution exceeding that
of widely-used Ca<sup>2+</sup>-imaging. Chemically-synthesized
voltage-sensitive dyes that use photoinduced electron transfer (PeT) as a
voltage-sensing trigger offer high voltage sensitivity and fast response
kinetics, but targeting chemical indicators to specific cells remains an
outstanding challenge. Here, we present a new family of readily
functionalizable, fluorescein-based voltage sensitive fluorescent dyes
(sarcosine-VoltageFluors) that can be covalently attached to a
genetically-encoded cell surface receptor to achieve voltage imaging from
genetically defined neurons. We synthesized four new VoltageFluor derivatives
that possess carboxylic acid functionality for simple conjugation to flexible
tethers. The best of this new group of dyes was conjugated via a
polyethyleneglycol (PEG) linker to a small peptide (SpyTag, 13 amino acids)
that directs binding and formation of a covalent bond with its binding partner,
SpyCatcher (15 kDa). The new VoltageSpy dyes effectively label cells expressing
cell-surface SpyCatcher, display good voltage sensitivity, and maintain fast
response kinetics. In cultured neurons, VoltageSpy dyes enable robust,
single-trial optical detection of action potentials at neuronal soma with
sensitivity exceeding genetically encoded voltage indicators. Importantly,
genetic targeting of chemically synthesized dyes enables VoltageSpy to report
on action potentials in axons and dendrites in single trials, tens to hundreds
of micrometers away from the cell body. | Vincent Grenier; Brittany Daws; Pei Liu; Evan Miller | Bioorganic Chemistry; Organic Synthesis and Reactions; Imaging; Biophysics; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f5abdbb894132a37fac/original/spying-on-neuronal-membrane-potential-with-genetically-targetable-voltage-indicators.pdf |
60c9b9951fd533ec6c56ac29 | 10.26434/chemrxiv.7892870.v3 | Tropolone-Based Treatments for Visualising Latent Fingermarks on Porous Surfaces | The work describes a new chemical means of visualising latent fingerprints (fingermarks) using tropolone. Tropolone reacts with amino acids within the fingermark residue to form adducts that absorb UV radiation. These adducts provide useful contrast on highly-fluorescent prous surfaces will illuminated with UV radiation. The conjugated seven-membered ring of the tropolone adduct can be reacted further diazonium salts, which is demonstrated here with formation of two dyes. The methodology is extremely rapid, occurring in minutes with mild heating, and can be applied before ninhydrin in a chemical detection sequence. <br /> | Clara M. Agapie; Melissa Sampson; William Gee | Dyes and Chromophores; Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9b9951fd533ec6c56ac29/original/tropolone-based-treatments-for-visualising-latent-fingermarks-on-porous-surfaces.pdf |
64b795eaae3d1a7b0df9a6df | 10.26434/chemrxiv-2023-wc8sl | Synthesis of penta- and hexa(3,4-thienylene): Size-dependent structural properties of cyclic oligothiophenes | Penta- and hexa(3,4-thienylene)s were synthesized via sequential coupling reactions, and the structures were detemined by X-ray crystallography. NMR spectroscopic analysis revealed that the interconversion of thiophene rings is fast in penta(3,4-thienylene), and slow in hexa(3,4-thienylene) reflecting the activation energy for enantiomerization. Size-dependent bathochromic shift was observed in UV-vis absorption spectra. | Mai Nagase; Sachiko Nakano; Yasutomo Segawa | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b795eaae3d1a7b0df9a6df/original/synthesis-of-penta-and-hexa-3-4-thienylene-size-dependent-structural-properties-of-cyclic-oligothiophenes.pdf |
671b534283f22e4214273d68 | 10.26434/chemrxiv-2024-80r5m-v2 | Probing the Intramolecular Folding of Nucleic Acids with Native Ion Mobility Mass Spectrometry: Strategies and Caveats | The goal of native mass spectrometry is to obtain information on non-covalent interactions in solution through mass spectrometry measurements in the gas phase. Characterizing intramolecular folding re-quires using structural probing techniques such as ion mobility spectrometry. However, inferring solu-tion structures of nucleic acids is difficult because the low-charge state ions produced from aqueous solutions at physiological ionic strength get compacted during electrospray. Here we explored whether native supercharging could produce higher charge states that would better reflect solution folding, and whether the voltage required for collision-induced unfolding (CIU) could reflect preserved intramolecu-lar hydrogen bonds. We studied pH-responsive i-motif structures with different loops, and unstructured controls. We also implemented a multivariate curve resolution procedure to extract physically meaning-ful pure components from the CIU data and reconstruct unfolding curves. We found that the relative unfolding voltages reflect to some extent, but not always unambiguously, the number of intramolecular hydrogen bonds that were present in solution. Reaching phosphate charging densities over 0.25 makes it easier to discriminate between structures, and the use of native supercharging agents is thus essential. We also uncovered several caveats in data interpretation: (1) when different structures (for example the i-motif with and without hairpin) unfold via different pathways, the unfolding voltages do not necessari-ly reflect the number of hydrogen bonds, (2) unstructured controls also undergo unfolding, and the base composition influences the unfolding voltage, (3) changing the solution pH also unexpectedly changed the unfolding voltage, and (4) the ion mobility patterns become more complicated when two structures are present simultaneously, such as an i-motif and a harpin, because of opposite effects on the collision cross section upon activation. | Sanae Benabou; Anna de Juan; Valérie Gabelica | Physical Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Biophysics | CC BY 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671b534283f22e4214273d68/original/probing-the-intramolecular-folding-of-nucleic-acids-with-native-ion-mobility-mass-spectrometry-strategies-and-caveats.pdf |
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