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64197a0adab08ad68f7547b0 | 10.26434/chemrxiv-2023-4cdx6-v2 | Naked-eye thiol analyte detection via self-propagating, amplified reaction cycle | We introduce naked-eye thiol analyte detection through signal-triggered macroscopic degradation of a hydrogel scaffold using a molecular self-propagating amplification cycle. This system contains an allylic phosphonium salt coupled to a disulfide-crosslinked hydrogel, which is triggered by thiol-analytes to undergo physical degradation through chemical cascade reactions within the gel matrix. We constructed a numerical model to predict the behaviour of the signal-triggered amplification cycle applied to small molecules by varying the input concentration of thiol trigger. The model is validated using experimental data. Using the amplification system embedded within the hydrogel, multiple thiol analytes, including a small molecule probe, an amino acid, DNA and a protein, could be detected at concentrations ranging from 132 to 0.132 µM. Furthermore, we found that force-generated disulfide scission can initiate the cycle, enabling damage-triggered hydrogel destruction via the self-propagating amplification system. | Benjamin Klemm; Ardeshir Roshanasan; Irene Piergentili; Jan van Esch; Rienk Eelkema | Physical Chemistry; Organic Chemistry; Polymer Science | CC BY 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64197a0adab08ad68f7547b0/original/naked-eye-thiol-analyte-detection-via-self-propagating-amplified-reaction-cycle.pdf |
60c75390567dfe1287ec5f00 | 10.26434/chemrxiv.13350728.v1 | Exfoliation and Optical Properties of Near-Infrared Fluorescent Silicate Nanosheets | <div><div><div><p>The silicates Egyptian Blue (CaCuSi4O10, EB), Han Blue (BaCuSi4O10, HB) and Han Purple (BaCuSi2O6, HP) emit in bulk bright and stable fluorescence in the near-infrared (NIR), which is of high interest for (bio)photonics due to minimal scattering, absorption and phototoxicity in this spectral range. So far the optical properties of nanosheets (NS) of these silicates are poorly understood. Here, we exfoliate them into nanosheets and report their physicochemical properties. The approach uses ball milling followed by tip sonication and centrifugation steps to exfoliate the silicates into NS with a lateral size ≈ 16-27 nm and thickness ≈ 1-4 nm. They emit at ≈ 927 nm (EB-NS), 953 nm (HB-NS) and 924 nm (HP-NS) and single NS can be resolved in the NIR. Fluorescence lifetimes decrease from ≈ 30-100 μs (bulk) to 17 μs (EB- NS), 8 μs (HB-NS) and 7 μs (HP-NS). NS of different composition/size can be imaged by fluorescence lifetime imaging, which enables lifetime-encoded multicolor imaging both on the microscopic and the macroscopic scale. Finally, remote imaging through tissue phantoms reveals the potential for bioimaging. In summary, we report a procedure to gain NIR fluorescent silicate nanosheets, characterize their photophysical properties and show their potential for NIR photonics.</p></div></div></div> | Gabriele Selvaggio; Milan Weitzel; Nazar Oleksiievets; Tabea A. Oswald; Robert Nißler; Ingo Mey; Volker Karius; Jörg Enderlein; Roman Tsukanov; Sebastian Kruss | Biocompatible Materials; Materials Processing; Nanostructured Materials - Materials; Optical Materials; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Minerals; Solid State Chemistry; Spectroscopy (Inorg.); Bioengineering and Biotechnology; Biophysics; Biophysical Chemistry; Optics; Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75390567dfe1287ec5f00/original/exfoliation-and-optical-properties-of-near-infrared-fluorescent-silicate-nanosheets.pdf |
628f113c6cae1c9c2118002b | 10.26434/chemrxiv-2022-w1t0g-v2 | Analytic First-Order Derivatives of (X)MS, XDW, and RMS Variants of the CASPT2 and RASPT2 Methods | Crossings between states involve complex electronic structures, making the accurate characterization of the crossing point difficult. In this study, the analytic derivatives
of three complete active space second-order perturbation theory (CASPT2) variants as well as an extension of the restricted active space (RASPT2) are developed. These variants
are applied to locating minimum energy conical intersections. Our results demonstrate that the three CASPT2 variants predict qualitatively similar results, but a recently developed variant, the rotated multistate CASPT2 (RMS-CASPT2), is least sensitive to the number of states considered in the calculation. We demonstrate that CASPT2 and the reference self-consistent field calculations predict qualitatively different energetics and bond lengths. | Yoshio Nishimoto; Stefano Battaglia; Roland Lindh | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628f113c6cae1c9c2118002b/original/analytic-first-order-derivatives-of-x-ms-xdw-and-rms-variants-of-the-caspt2-and-raspt2-methods.pdf |
60c74de8469df493faf4438d | 10.26434/chemrxiv.12671069.v1 | Phase Behavior that Enables Solvent-Free Carbonate-Promoted Furoate Carboxylation | <div><div><div><p>A solvent-free transformation that enables production of polyester precursors from inedible biomass proceeds from a heterogeneous reaction mixture containing both solid and molten components. Characterization of the evolution of these component phases over the course of the reaction provides insight relevant to process design and scale-up.</p></div></div></div> | Amy Frankhouser; Matthew Kanan | Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74de8469df493faf4438d/original/phase-behavior-that-enables-solvent-free-carbonate-promoted-furoate-carboxylation.pdf |
635816d7ecdad53910ec98f1 | 10.26434/chemrxiv-2022-7tf0h-v2 | Scaffold Generator - A Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK) | The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the generation, handling, and display of molecular scaffolds, scaffold trees and networks. The new library is based on the Chemistry Development Kit (CDK) and highly customisable through multiple settings, e.g. five different structural framework definitions are available. For display of scaffold hierarchies, the open GraphStream Java library is utilised. Performance snapshots with natural products (NP) from the COCONUT (COlleCtion of Open Natural prodUcTs) database and drug molecules from DrugBank are reported. The generation of a scaffold network from more than 450,000 NP can be achieved within a single day. | Jonas Schaub; Julian Zander; Achim Zielesny; Christoph Steinbeck | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Natural Products; Organic Compounds and Functional Groups; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/635816d7ecdad53910ec98f1/original/scaffold-generator-a-java-library-implementing-molecular-scaffold-functionalities-in-the-chemistry-development-kit-cdk.pdf |
60c74ae1702a9b584718b35e | 10.26434/chemrxiv.12263837.v1 | Band Positions of Anatase (001) and (101) Surfaces in Contact with Water from Density Functional Theory | Titanium dioxide in the anatase configuration plays an increasingly important role for photo(electro)catalytic applications due to its superior electronic properties when compared to rutile. In aqueous environments, the surface chemistry and energetic band positions upon contact with water determine charge-transfer processes over solid--solid or solid--electrolyte interfaces. Here, we study the interaction of anatase (001) and (101) surfaces with water and the resulting energetic alignment by means of hybrid density functional theory. While the alignment of band positions favours charge-transfer processes between the two facets for the pristine surfaces, we find the magnitude of this underlying driving force to crucially depend on water coverage and degree of dissociation. It can be largely alleviated for intermediate water coverages. Surface states and their passivation by dissociatively adsorbed water play an important role here. Our results suggest that anatase band positions can be controlled over a range of almost one eV via its surface chemistry. | Julian Geiger; Michiel Sprik; Matthias May | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae1702a9b584718b35e/original/band-positions-of-anatase-001-and-101-surfaces-in-contact-with-water-from-density-functional-theory.pdf |
65a740cd9138d2316116d92b | 10.26434/chemrxiv-2024-mrfwv | Enforcing Metal‒Arene Interactions in Bulky p-Terphenyl Bis(anilide) Complexes of Group 2 Metals (Be‒Ba): Potential Precursors for Low Oxidation State Alkaline Earth Metal Systems | An extremely bulky p-terphenyl bis(aniline), p-C6H4{C6H4[N(H)TCHP]-2}2 (TCHP = 2,4,6-tricyclohexylphenyl) TCHPTerphH2, has been developed. Deprotonation of a less bulky analogue, DipTerphH2 (Dip = 2,6-diisopropylphenyl), with BePh2 affords the bimetallic system, [(BePh)2(-DipTerph)] 1. Treating either TCHPTerphH2 or DipTerphH2 with Mg{CH2(SiMe3)}2 gives the monomeric bis(anilide) complexes [Mg(ArTerph)] (Ar = Dip 2, TCHP 3) which display rare examples of eta-6-arene coordination to the metal centre. Treating 2 with THF leads to partial dissociation of the Mg···arene interaction, and formation of [Mg(DipTerph)(THF)] 4. Reactions of the bis(aniline)s with the group 2 metal amides [M{N(SiMe3)2}2] affords dimeric, isostructural compounds [{M(ArTerph)}2] (Ar = Dip, M= Ca 5, Sr 6, Ba 7; Ar = TCHP, M= Ca 8, Sr 9, Ba 10) which display intermolecular M···arene interactions in the solid-state. Computational studies have shown that the intramolecular M···arene interactions in models of the ether free metal bis(anilide) compounds are largely electrostatic in nature. Reductions of these compounds with alkali metals led to mixtures of unidentified products. | Dat Nguyen; Christoph Helling; Matthew Evans; Cameron Jones | Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a740cd9138d2316116d92b/original/enforcing-metal-arene-interactions-in-bulky-p-terphenyl-bis-anilide-complexes-of-group-2-metals-be-ba-potential-precursors-for-low-oxidation-state-alkaline-earth-metal-systems.pdf |
645dfeaefb40f6b3ee74b4fc | 10.26434/chemrxiv-2023-sp7ls | Understanding the Electronic Structure of Y2Ti2O5S2 for Green Hydrogen Production: A Hybrid-DFT and GW Study | Utilising photocatalytic water splitting to produce green hydrogen is the key to reducing the carbon footprint of this crucial chemical feedstock. In this study, density functional theory (DFT) is employed to gain insights into the photocatalytic performance of an up-and-coming photocatalyst Y2Ti2O5S2 from first principles. Eleven non-polar clean surfaces are evaluated at the generalised gradient approximation level to obtain a plate-like Wulff shape that agrees well with the experimental data. The (001), (101) and (211) surfaces are considered further at hybrid-DFT level to determine their band alignments with respect to vacuum. The large band offset between the basal (001) and side (101) and (211) surfaces confirms experimentally observed spatial separation of hydrogen and oxygen evolution facets. Furthermore, relevant optoelectronic bulk properties were established using a combination of hybrid-DFT and many-body perturbation theory. The optical absorption of Y2Ti2O5S2 weakly onsets due to dipole-forbidden transitions, and hybrid Wannier-Mott/Frenkel excitonic behaviour is predicted to occur due to the two-dimensional electronic structure, with an exciton binding energy of 0.4 eV. | Katarina Brlec; Christopher N. Savory; David O. Scanlon | Theoretical and Computational Chemistry; Materials Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645dfeaefb40f6b3ee74b4fc/original/understanding-the-electronic-structure-of-y2ti2o5s2-for-green-hydrogen-production-a-hybrid-dft-and-gw-study.pdf |
60c759c5f96a001737289089 | 10.26434/chemrxiv.14687151.v2 | A Nanoscale Model System for the Human Myelin Sheath | Here, we for the first time establish nanodiscs with the challenging lipid
composition of myelin of the peripheral or central nervous systems,
respectively (PNS and CNS, both containing >40% cholesterol, which so far
has been thought to be detrimental for nanodisc formation).Thus, we prove that
more complex lipid model membrane systems are in general accessible through
nanodiscs and can study protein-lipid interactions in myelin and factors
driving myelin formation or degradation using combinations of myelin proteins
in a highly controlled lipid environment resembling myelin’s cytoplasmic leaflet.
For the functional studies, initial proof-of-principle experiments using myelin
basic protein have been performed. <br /> | Matthias Hoffmann; David Haselberger; Tommy Hofmann; Lisa Müller; Kevin Janson; Annette Meister; manabendra das; Carolyn Vargas; Sandro Keller; Panagiotis L. Kastritis; Carla Schmidt; Dariush Hinderberger | Polyelectrolytes - Materials; Organic Polymers; Polymer scaffolds; Biochemistry; Biophysics; Biophysical Chemistry; Interfaces; Self-Assembly; Spectroscopy (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759c5f96a001737289089/original/a-nanoscale-model-system-for-the-human-myelin-sheath.pdf |
631a935a3e2e3647d82fe0ce | 10.26434/chemrxiv-2022-n5468 | Building a high-performance organic cathode material containing electron-withdrawing groups for lithium-ion batteries | Abstract: The capacity of cathode materials is one of the main factors to limit the performance of lithium-ion batteries (LIBs), so it is urgent to develop high-performance cathode materials. Herein, trinitrohexaazatrinaphthalene (TNHATN) including an electron-withdrawing group (nitro, -NO2) was synthesized by the condensation reaction between hexaketocyclohexane and 4-nitro-o-phenylenediamine, and it was first investigated as a cathode material for lithium-ion batteries. The TNHATN electrode displays a high discharge specific capacity of 361.7 mAh g-1 at 0.05 A g-1 and a superior cycling stability, remaining the capacity retention of 97.9 % after 200 cycles. The excellent behaviors may be ascribed to its π-conjugated structure including electron-withdrawing groups and multiple redox active sites. The experimental resultes reveal the redox active sites are pyrazine nitrogen atoms and oxygen atoms from nitrio groups. This work confirms that it is an effective route to introduce an electron-withdrawing group into a π-conjugated compound for obtaining high-performance organic cathode materials of LIBs. | Qi Liu; Daozhen Shen; Xiaojuan Chen; Chen Chen; Qingyan Jiang; Lixin Su; Hongren Rong; Hongjiang Liu | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631a935a3e2e3647d82fe0ce/original/building-a-high-performance-organic-cathode-material-containing-electron-withdrawing-groups-for-lithium-ion-batteries.pdf |
60c7512f337d6c7a1be284bc | 10.26434/chemrxiv.13133291.v1 | Simultaneous Measurement of Ionic and Electronic Conductivities of Conductive Polymers as a Function of Electrochemical Doping in Battery Electrolyte | We show that the ionic and electronic conductivity of a wide range of p-type and n-type conducting polymer thin films can be reliably measured as a function of electrochemical doping in relevant battery electrolytes by impedance spectroscopy on interdigitated electrodes by combining two separate electrode geometries. The results demonstrate the broad applicability of the methodology for gaining insights into the electrical conduction in polymers in relevant environments, particularly for batteries and other electrochemical devices | Billal Zayat; Pratyusha Das; Barry C. Thompson; Sri Narayan | Conducting polymers; Electrochemical Analysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7512f337d6c7a1be284bc/original/simultaneous-measurement-of-ionic-and-electronic-conductivities-of-conductive-polymers-as-a-function-of-electrochemical-doping-in-battery-electrolyte.pdf |
65984cb2e9ebbb4db981b197 | 10.26434/chemrxiv-2024-zm5d0 | A Perspective on the Simulation of ECD and CPL Spectra in Chiral Solid Materials | Chiral materials have shown tremendous potential for many technological applications, like optoelectronics, sensing, magnetism, information technology, and imaging. Characterization of these materials is mostly based on chiroptical spectroscopies such as electronic circular dichroism (ECD) and circularly polarized luminescence (CPL). These experimental measurements would greatly benefit from theoretical simulations for the interpretation of the spectra as well as for predictions on new materials. While ECD and CPL simulations are well established for molecular systems, they are not for materials. In this perspective, we describe the theoretical quantities necessary to simulate ECD and CPL spectra in oriented systems. Then, we discuss the approximate strategies currently used to perform these calculations, what computational machinery is already available to develop more general approaches, and some of the open challenges for the simulation of ECD and CPL spectra in solid materials. When methods that are as reliable and computationally efficient as for molecules are developed, these simulations will provide invaluable insight and guidance for the rational design of optically active materials. | Marco Caricato | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65984cb2e9ebbb4db981b197/original/a-perspective-on-the-simulation-of-ecd-and-cpl-spectra-in-chiral-solid-materials.pdf |
60c74a1b469df43aacf43cac | 10.26434/chemrxiv.12155286.v1 | HPM-14, a New Germanosilicate Zeolite with Interconnected Extra-Large Pores Plus Odd-Membered and Small Pores | We describe HPM-14, a new extra-large pore zeolite synthesized using imidazolium-based organic structure-directing agents, fluoride anions and germanium and silicon as tetrahedral components of the framework. Due to the presence of stacking disorder, the structure elucidation of HPM-14 was challenging, and different techniques were necessary to clarify the details of the structure and to understand the nature of the disorder. The structure has been solved by three-dimensional electron diffraction technique (3D ED) and consists of an intergrowth of two polymorphs possessing a three-dimensional channel system, including an extra-large pore opened through windows made up of sixteen tetrahedral atoms (16-membered ring, 16MR) as well as two additional sets of odd-membered (9MR) and small (8MR) pores. The intergrowth has been studied by scanning transmission electron microscopy (C s -STEM) and powder X-ray diffraction simulations (DIFFaX), which show a large predominance of the monoclinic polymorph A.<br /> | Zihao Gao; Jian Li; Cong Lin; Alvaro Mayoral; Junliang Sun; Miguel Camblor | Catalysts; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a1b469df43aacf43cac/original/hpm-14-a-new-germanosilicate-zeolite-with-interconnected-extra-large-pores-plus-odd-membered-and-small-pores.pdf |
67a995e86dde43c9083f817a | 10.26434/chemrxiv-2025-w3k4n | PyDescriptorC*: A Descriptor Calculation Tool for Decoding Chirality Cliffs and Revealing Hidden Patterns in Drug Discovery | Chirality plays a crucial role in the biological activity and pharmacological properties of molecules, often leading to significant differences in activity profiles, referred to as chirality cliffs or activity cliffs. To address this challenge, we introduce PyDescriptorC*, a novel Python-based script designed to calculate thousands of chirality-aware descriptors and other molecular descriptors using molecular 3D structures (total 112,194 molecular descriptors). PyDescriptorC* leverages multiprocessing, PyMOL integration, and compatibility with mol2 file formats, ensuring computational efficiency and broad applicability. The tool was rigorously tested on two structurally diverse datasets (HDAC4 and ADM17) for regression analysis, demonstrating exceptional performance in capturing chirality-driven insights and elucidating the molecular basis of chirality cliffs. These chirality descriptors provided a deeper understanding of activity patterns, significantly enhancing the predictive accuracy and interpretability of QSAR models. PyDescriptorC* has been validated across multiple operating systems, ensuring platform independence and user accessibility. This work highlights the potential of PyDescriptorC*, an extended version of PyDescriptor, to advance drug discovery and development by unlocking hidden chirality patterns and bridging the gap between structural data and predictive modelling. Its seamless integration of chirality-specific descriptors into QSAR workflows offers a powerful resource for cheminformatics, machine learning, and molecular design. | Vijay Masand; Gaurav Masand; Sami A. Al-Hussain; Rahul Jawarkar; Vesna Rastija; Magdi E.A. Zaki | Theoretical and Computational Chemistry; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a995e86dde43c9083f817a/original/py-descriptor-c-a-descriptor-calculation-tool-for-decoding-chirality-cliffs-and-revealing-hidden-patterns-in-drug-discovery.pdf |
60c742ac702a9b27ac18a4c6 | 10.26434/chemrxiv.8342408.v1 | Modification of Chitosan Based on Computer Simulation and Its Application as Biomaterial | <p>Modification
of chitosan has become an important means to obtain chitosan polymers with
better properties. In recent years, the application properties of chitosan have
been greatly improved by modification, crosslinking, grafting and other
modification methods. In order to improve its poor solubility and weak
stability and expand its application scope, physical and chemical methods are
often used to modify chitosan. As an important natural biomaterial, the
modification and application of chitosan have attracted wide attention. This
paper briefly summarizes the degradation and modification methods of chitosan
at home and abroad and its research results in biomedicine. The interaction of
the interface of the knife polymer composite system and the bonding effect of
the coupling agent on the interface of the composite were analyzed by computer
simulation. The simulation results show that the interaction between the
surface and the three polymer segments is the strongest. These results indicate
that chitosan is a kind of biomaterial with excellent performance and has broad
application prospects.</p> | Gurmohinder Heggnnavar | Biopolymers; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ac702a9b27ac18a4c6/original/modification-of-chitosan-based-on-computer-simulation-and-its-application-as-biomaterial.pdf |
6163e754a3d2c9c34cd2cf58 | 10.26434/chemrxiv-2021-j1t52 | Data Synchronization in Operando Gas and Heating TEM | Time-resolved correlations between the environment, the reaction products, the energy transfer and the material structures during the reaction processes make operando gas and heating TEM more and more attractive in recent years. The intrinsic time delays that exist among parameter measurement locations need to be calibrated for valid correlations. Otherwise, erroneous conclusions would be drawn, such as over-estimating the critical temperatures, or mismatching the structure and composition relationships to activities. Herein, we report on a method measuring and calibrating the time delays involved in operando TEM. This method relies on the unique capability of on-chip calorimetry of the gas Nano-Reactor. It is shown that the time delay depends on the gas flow rate and pressure, and has little dependence on the gas type. A functional relationship fitted between the time delay and the gas flow rate can automize the time delay calibration and thus synchronize the data from different locations. Based on the investigations, we developed algorithms and scripts to enable the automatic data synchronization in operando gas and heating TEM in both real time experiments and post experiments. | Fan Zhang; Merijn Pen; Ronald G. Spruit; Hugo Perez Garza; Wei Liu; Dan Zhou | Analytical Chemistry; Nanoscience; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6163e754a3d2c9c34cd2cf58/original/data-synchronization-in-operando-gas-and-heating-tem.pdf |
672a296b7be152b1d00fcc60 | 10.26434/chemrxiv-2023-hc95q-v3 | Filling a critical need: a lightweight and fast Gaussian puff model implementation | Atmospheric dispersion models are a key component for characterizing methane emissions on oil and gas sites. While some model implementations with varying degrees of complexity are available, existing regulatory-grade dispersion models are cumbersome to apply within an inversion framework on a routine operational level or at scale, and require a gamut of meteorologic information that is typically not available in field operations. Simple Gaussian plume models on the other hand, fail to incorporate changing wind regimes that are routinely observed and prove relevant in practice. Filling this critical need, we provide a computationally efficient and scalable version of the Gaussian puff model with a thresholding algorithm that is two orders of magnitude faster than a naive implementation and only requires readily available meteorological data. Our comparison shows that the Gaussian puff model is higher fidelity and able to capture temporal variation in atmospheric transport better than the commonly used Gaussian plume model. This computationally-efficient and scalable Gaussian puff implementation can be applied to model near-field atmospheric transport in a broad range of applications including the timely call to quickly infer methane emissions from measurements on oil and gas sites for efficient mitigation. | Meng Jia; Ryker Fish; William Daniels; Brennan Sprinkle; Dorit Hammerling | Physical Chemistry; Energy; Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672a296b7be152b1d00fcc60/original/filling-a-critical-need-a-lightweight-and-fast-gaussian-puff-model-implementation.pdf |
67926c97fa469535b97ef308 | 10.26434/chemrxiv-2025-677hc | Enabling Stereoselective Fluoroalkyl-Sulfonylalkylation of Alkenes and Alkynes Via Photoredox Catalysis | We describe a versatile photocatalytic approach for inter- and intramolecular fluoroalkyl-sulfonylalkylation of carbon−carbon bonds in activated and unactivated alkenes and alkynes. We employ fluoroalkyl sulfinate salts as bifunctional reagents to intro-duce fluoroalkyl and SO2 groups, and alkyl halides to intercept the ensuing sulfonyl intermediates in a process that creates one C(sp3)-C(sp3) and two C(sp3)-S bonds in one step. This method is applicable for the fluoroalkyl-sulfonylalkylation of both alkenes and alkynes bearing a diverse set of functional groups and unsaturated gaseous hydrocarbons. The robustness of the method is also demonstrated by the late-stage diversification of steroids, alkaloids and pharmaceuticals. Mechanistic insights reveal a photoredox-mediated sequential process involving fluoroalkyl radical addition, SO2 incorporation, and subsequent SN2-type displacement. | Supuni I. N. Hewa Inaththappulige; Ayush Acharya; A. Nipuna D. De Zoysa; Harshvardhan Singh; Ramesh Giri | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67926c97fa469535b97ef308/original/enabling-stereoselective-fluoroalkyl-sulfonylalkylation-of-alkenes-and-alkynes-via-photoredox-catalysis.pdf |
63a5aaf916e9a82ac93285f4 | 10.26434/chemrxiv-2022-jm92g | Photoelectrocatalytic conversion of CO2 by transition metal functionalized diamond nanoparticles under solar illumination | Overcoming the energy barrier in CO2 reduction is a key avenue in the development of sustainable carbon capture and recycling systems spearheading against the climate emergency. Diamond, a wide-bandgap material, has shown promise in this aspect due its ability to produce highly reductive solvated electrons when irradiated with deep UV light. This requirement for high-energy optical illumination, however, hampers its sustainable application and limits its useful lifetime. Here we show the photosensitization of nanoscale detonation diamond in reductive photoelectrocatalysis through surface functionalisation with a ruthenium-based dye, demonstrating solar-light driven turnover of CO2 using the unique properties of diamond. The hybrid photosensitizer-nanodiamond materials demonstrated good colloidal and photochemical stability. The nature of electronic conjugation between diamond and photosensitizer was elucidated through X-ray absorption, transient optical absorption, and ultraviolet photoemission spectroscopies, with CO2 turnover significantly improved under solar conditions for photosensitized systems. The potential for photoexcited electron transfer (PET) mediated photosensitization in reductive diamond catalysis opens the way for further sustainable applications using diamond as a sustainable photoelectrocatalyst. | Benjamin Kiendl; Adam Day; Sneha Choudhury; Franziska Buchner; Kaan Atak; Arsene Chemin; Christoph Merschjann; Emina Hadzifejzovic; Tim Claridge; Karin Larsson; Amelie Venerosy; Mailis Lounasvuori; Natalia Zabarska; Boyan Iliev; Thomas Schubert; Hugues Girard; Jean-Charles Arnault; Tristan Petit; John Foord; Anke Krueger | Organic Chemistry; Materials Science; Catalysis; Carbon-based Materials; Photosensitizers; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a5aaf916e9a82ac93285f4/original/photoelectrocatalytic-conversion-of-co2-by-transition-metal-functionalized-diamond-nanoparticles-under-solar-illumination.pdf |
60c74ef24c8919526cad3b06 | 10.26434/chemrxiv.12824522.v1 | Optimization of the Bulk Heterojunction of All-smallmolecule Organic Photovoltaics Using Design of Experiment and Machine Learning Approaches | All-small-molecule organic photovoltaic (OPV) cells based upon the small molecule donor, DRCN5T, and non-fullerene acceptors, ITIC, IT-M, and IT-4F, were optimized using Design of Experiments (DOE) and machine learning (ML) approaches. This combination enables rational sampling of large parameter spaces in a sparse but mathematically deliberate fashion and promises economies of precious resources and time. The work focused upon the optimization of the core layer of the OPV device, the bulk heterojunction (BHJ). Many experimental processing parameters play critical roles in the overall efficiency of a given device and are often correlated, and thus are difficult to parse individually. DOE was applied to the (i) solution concentration of the donor and acceptor ink used for spin-coating, (ii) the donor fraction, and (iii) the temperature and (iv) duration of the annealing of these films. The ML-based approach was then used to derive maps of the PCE landscape for the first and second rounds of optimization to be used as guides to determine the optimal values of experimental processing parameters with respect to device efficiency. This work shows that with little knowledge of a potential combination of components for a given BHJ, a large parameter space can be effectively screened and investigated to rapidly determine its potential for high efficiency OPVs. | Aaron Kirkey; Erik Luber; Bing Cao; Brian Olsen; Jillian Buriak | Materials Processing; Nanostructured Materials - Materials; Thin Films; Photovoltaics | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ef24c8919526cad3b06/original/optimization-of-the-bulk-heterojunction-of-all-smallmolecule-organic-photovoltaics-using-design-of-experiment-and-machine-learning-approaches.pdf |
662b5b8a21291e5d1dc24821 | 10.26434/chemrxiv-2024-1q7wk | Spontaneous Elliptical Polarization of Racemic Multilayer Polymers and Oligomers | It is well-known that racemic molecules are elliptically inactive. Herein, we found novel racemic multilayer polymers and oligomers that are generated from catalytic polymerization can asymmetrically rotate the plane-polarized circular light to the right-handed direction in THF-H2O cosolvents. The specific rotation depends on the water ratios (fw) of co-solvents and UV-vis radiation time inside polarimeter. The aggregation of polymers and oligomers was proven via AIE (aggregation-induced emission) appeared as they dissolved in THF-H2O co-solvents, which would be responsible for this abnormal phenomenon. This discovery is anticipated to lead to a new research topic in chemical, medical, and materials sciences, and provide an alternative clue to the origin of life on earth in the future. | Sai Zhang; Qingkai Yuan; Yu Wang; Yao Tang; Anis. U Rahman; Shengzhou Jin; Jiayin Wang; Ting Xu; Guigen Li | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/662b5b8a21291e5d1dc24821/original/spontaneous-elliptical-polarization-of-racemic-multilayer-polymers-and-oligomers.pdf |
63a0e62716e9a8b2092e31f5 | 10.26434/chemrxiv-2022-rljqn | Per-/Poly-fluoroalkyl Substances (PFASs) Treatment and Mechanistic Insights: Photo-catalyst and Photo-Electro-catalyst Materials Application | The PFASs contamination (Per-/Poly-fluoroalkyl Substances ~ 4000 compounds) is influencing the humane through soil and aquifers contamination, resulting in the endocrine-disrupting symptoms (EDS). PFASs decontamination involves both (i) Capture/non-degradation techniques and (ii) Degradation techniques. In the present work, a detailed discussion on various photo-catalytic/electrocatalytic electrode materials (Fe/Ti/Zn/Bi/C etc.) over PFASs degradation is provided. The authors have focused onto the recent literature published in the last couple of years for citing research outputs and schematic figures. The analysis of both radical species (e.g., hydroxyl/sulphate species) and direct electron transfer (DET) mechanisms are given. An insightful discussion of the impact on various degradation mechanisms (decarboxylation, and hydrodefluorination) onto various PFASs has been provided. A different set of examples are provided in describing both electron (e-) based oxidation and hole (h+) based oxidation phenomenon. The state-of-the-art novel inventions towards pilot-scale studies and field-level applications are discussed with explaining the possible limitations (e.g., light source etc.). The factors influencing the degradation process (i.e., Electrode potential, Current density, Impact of dosage, pH, Radical species, Competing ions, Temperature and light source) are also detailed prior to the future perspective and conclusions. | Yaswanth Penke; Kamal Kar | Catalysis; Earth, Space, and Environmental Chemistry; Environmental Science; Photocatalysis; Redox Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a0e62716e9a8b2092e31f5/original/per-poly-fluoroalkyl-substances-pfa-ss-treatment-and-mechanistic-insights-photo-catalyst-and-photo-electro-catalyst-materials-application.pdf |
60db364e6e388bba366ff395 | 10.26434/chemrxiv-2021-0cch4 | Is ice formation by sea spray particles at cirrus temperatures controlled by crystalline salts? | The ice nucleating ability of sea spray aerosols (SSA) has been explored in recent years due to the abundance of SSA in the atmosphere. The role of SSA in ice nucleation extends to cirrus clouds, due to processes that loft SSA to the upper troposphere. This is of special relevance because of the frequent occurrence of cirrus in the atmosphere, their role in the Earth’s radiative balance, and uncertainties regarding how aerosols may affect their formation and evolution. In this study, a continuous flow diffusion chamber (CFDC) is used to investigate the ice nucleating ability of size-selected particle distributions of SSA and its primary constituent sodium chloride (NaCl) at temperatures < 235 K. Results show that above ~220 K, the majority of SSA and NaCl particles fully deliquesce and freeze via homogeneous nucleation at or below water relative humidities, RHw, of ~ 95%. However, below 220 K, the onset RHw of freezing for NaCl and SSA is much lower, at ~75%, where strong heterogeneous freezing of 10% of the aerosol population occurs. Similar heterogeneous freezing behavior for NaCl and SSA aerosols, occurring near their predicted deliquescence RHw, points towards SSA freezing at the lowest temperatures being controlled by the crystalline salts. Finally, calculations of ice nucleation active surface site densities show that particle size does not dictate the efficiency of freezing for NaCl and SSA. These results indicate SSA as a potentially significant source of ice nucleating particles at cirrus temperatures, with the ability to contribute to cirrus-mediated climate impacts if sea spray emission and transport scenarios change in the future. | Ryan Patnaude; Russell Perkins; Sonia Kreidenweis; Paul DeMott | Earth, Space, and Environmental Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60db364e6e388bba366ff395/original/is-ice-formation-by-sea-spray-particles-at-cirrus-temperatures-controlled-by-crystalline-salts.pdf |
671a35e098c8527d9e335924 | 10.26434/chemrxiv-2024-nf2j2 | Rauhut–Currier Polyaddition: Self-Polymerization of Divalent Aryl Vinyl Ketones for Unsaturated Polyketones | The self-polyaddition of divalent vinyl ketones (VKs) by the Rauhut-Currier (RC) reaction is investigated to synthesize polymers composed of a carbon backbone. 2,7-Diacryloyl-9,9-dimethylfluorene is treated with 1,4-diazabicyclo[2.2.2]octane (DABCO) (20 mol%) and phenol (20 mol%), resulting in an improved degree of polymerization (Mn = 13800, Ð = 4.21). The polymerization is under kinetic control, probably due to the excellent electrophilicity of the VKs. However, the cyclization reaction becomes competitive during the latter stage of polymerization (conv. > 96.1%), whereas branch formation is implied by the dimerization of VK skeletons in the generated polymers. Thus, the polymerization should be controlled by the appropriate reaction time. Despite such potential side reactions, RC polymerization is notably attractive, as the resulting polyketones exhibit high thermal resistance with a 5% weight-loss temperature (Td5) of 389 °C and a remaining residue of 50 wt% even at 1000 °C. Furthermore, the VK skeletons of the polymer are quantitatively modifiable using thiol–ene click chemistry. Hence, RC polymerization affords polyketones with stable carbon backbones and reactive side-groups. | Masatoshi Ohyama; Rie Yasuda; Hirotsugu Kuratani; Shinsuke Miyauchi; Yasuhiro Kohsaka | Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671a35e098c8527d9e335924/original/rauhut-currier-polyaddition-self-polymerization-of-divalent-aryl-vinyl-ketones-for-unsaturated-polyketones.pdf |
652d5661bda59ceb9ab3e7d8 | 10.26434/chemrxiv-2023-kl8vh | Binding Sites of Bicarbonate in PEP Carboxylase | PhosphoEnolPyruvate Carboxylase is used in plant metabolism for fruit maturation or seed development, as well as in the C4 and CAM mechanisms in photosynthesis where it is used for the capture of hydrated CO2 (bicarbonate). To find the yet unknown binding site of bicarbonate in this enzyme, we have first identified putative binding sites with non-equilibrium molecular dynamics simulations, and then ranked these sites with alchemical free energy calculations with corrections of computational artefacts. 14 pockets where bicarbonate could bind were identified, with three having realistic binding free energies with differences with the experimental value below 1 kcal/mol. One of these pockets is found far from the active site at 14 Å, whereas in the two others bicarbonate is in direct interaction with the magnesium ion. The study of mutant K606N allowed to discriminate between these two pockets and to identify the binding site of bicarbonate in PhosphoEnolPyruvate Carboxylase. | Nicolas Chéron | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2023-10-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652d5661bda59ceb9ab3e7d8/original/binding-sites-of-bicarbonate-in-pep-carboxylase.pdf |
60c74423842e6516f5db23c3 | 10.26434/chemrxiv.9747674.v1 | A Triazole-Substituted Aryl Iodide with Omnipotent Reactivity in Enantioselective Oxidative Couplings | A triazole-substituted chiral aryl iodide is described as an efficient catalyst for a variety of diverse oxidative coupling reactions such as the Kita-spirocyclization, phenol-dearomatizations, alpha-oxygenations and oxidative rearrangements. Structures of the in situ oxidized hydroxy(tosyloxy)iodoarenes are discussed based on DFT-calculations.<br /> | Ayham Abazid; Boris Nachtsheim | Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74423842e6516f5db23c3/original/a-triazole-substituted-aryl-iodide-with-omnipotent-reactivity-in-enantioselective-oxidative-couplings.pdf |
63127a9f5351a31eefed04dc | 10.26434/chemrxiv-2022-jrq2q | Computational investigations of the excited state dynamics and quenching mechanisms of polycyclic aromatic hydrocarbon DNA adducts in solution | Synthetically modified fluorescent nucleotides (SFNs) are highly popular in a variety of experiments to explore biochemistry in molecular imaging, but their photodynamics and quenching mechanisms remain relatively unstudied computationally. We combine various levels of theory, including classical force field dynamics and excited state QM/MM Born-Oppenheimer dynamics to characterize a set of polycyclic aromatic hydrocarbon based substituents bound to cytidine (dC) and guanine (dG) nucleobases. We specifically focus on perylene (P) bound to C5 and C6 of dC, and the naturally occurring benzo[a]pyrene diol epoxide (B[a]PDE) on dG. We find that specific angles of the connection points between them modulate mechanisms of intramolecular charge transfer, where an electron moves from P to dC and dG to B[a]PDE once an optimal angle is reached. Functionalization location and flexibility of the substituent affect access to these angles and, therefore, the amount of rapid charge transfer quenching of the fluorescence that we observe. This work gives new insight into how these systems might be tuned for desired photophysical properties. | Solomon Yamoah Effah; W. K. D. N. Kaushalya; Mark A. Hix; Alice R. Walker | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Biophysical Chemistry; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63127a9f5351a31eefed04dc/original/computational-investigations-of-the-excited-state-dynamics-and-quenching-mechanisms-of-polycyclic-aromatic-hydrocarbon-dna-adducts-in-solution.pdf |
65d644e7e9ebbb4db9e589d0 | 10.26434/chemrxiv-2024-18sbg | The Case of the Q(5) Raman Line of Carbon Monoxide and its Fitted q-Gaussian Function | In an article by Thibault et al., 2002, we can find measurements of Raman linewidths in the Q branch of carbon monoxide, for mixtures with Argon at different temperatures. A plot is available for the Q(5) line with a fitted Voigt function. Here we show that a q-Gaussian Tsallis function can be used for fitting this line too. We will note that the fitted q-Gaussian has the wings which are not Lorentzian. At the same time, the wings are not Gaussian. Besides the use of q-Gaussians, a discussion will be proposed about the time correlation functions related to different line shapes (q-Gaussian, Egelstaff-Schofield, Kubo, BWF, Voigt, speed-dependent Voigt, Galatry, Rautian, HTP). Some of these line shapes have been proposed for the high-resolution spectroscopy of gases; however, their knowledge can be relevant also for the condensed matter spectroscopy. | Amelia Carolina Sparavigna | Materials Science | CC BY 4.0 | CHEMRXIV | 2024-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d644e7e9ebbb4db9e589d0/original/the-case-of-the-q-5-raman-line-of-carbon-monoxide-and-its-fitted-q-gaussian-function.pdf |
67ddbe1f81d2151a0257f3e6 | 10.26434/chemrxiv-2025-w1563 | Design of Tough 3D Printable Elastomers with Human-in-the-Loop Reinforcement Learning | The development of high-performance elastomers for additive manufacturing requires overcoming complex property trade-offs that challenge conventional material discovery pipelines. Here, a human-in-the-loop reinforcement learning (RL) approach is used to discover exceptional polyurethane elastomers that overcome pervasive stress–strain property tradeoffs. Starting with a diverse training set of 92 formulations, a coupled multi-component reward system was identified that guides RL agents toward materials with both high strength and extensibility. Through three rounds of iterative optimization combining RL predictions with human chemical intuition, we identified elastomers with more than double the average toughness compared to the initial training set. The final exploitation round, aided by solubility prescreening, predicted twelve materials exhibiting both high strength (>10 MPa) and high engineering strain (>200%). Analysis of the high performing materials revealed structure–property insights, including the benefits of high molar mass urethane oligomers, a high density of urethane functional groups, and incorporation of rigid low molecular weight diols and unsymmetric diisocyanates. These findings demonstrate that machine-guided, human-augmented design is a powerful strategy for accelerating polymer discovery in applications where data is scarce and expensive to acquire, with broad applicability to multi-objective materials optimization. | Johann Rapp; Dylan Anstine; Filipp Gusev; Filipp Nikitin; Kelly Yun; Mia Borden; Vittal Bhat; Olexandr Isayev; Frank Leibfarth | Materials Science; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ddbe1f81d2151a0257f3e6/original/design-of-tough-3d-printable-elastomers-with-human-in-the-loop-reinforcement-learning.pdf |
661cd188418a5379b0df32c2 | 10.26434/chemrxiv-2024-jt46s | Enabling pan-repository reanalysis for big data science of public metabolomics data | Public untargeted metabolomics data is a growing resource for metabolite and phenotype discovery; however, accessing and utilizing these data across repositories pose significant challenges. Therefore, we've developed pan-repository universal identifiers and harmonized cross-repository metadata. This novel ecosystem facilitates discovery by integrating diverse data sources from public repositories including MetaboLights, Metabolomics Workbench, and GNPS/MassIVE. Our approach simplifies data handling and unlocks previously inaccessible reanalysis workflows, fostering unmatched research opportunities. | Yasin El Abiead; Michael Strobel; Thomas Payne; Eoin Fahy; Claire O’Donovan; Shankar Subramamiam; Juan Antonio Vizcaino; Simone Zuffa; Shipei Xing; Helena Mannochio-Russo; Ipsita Mohanty; Haoqi Nina Zhao; Andres Mauricio Caraballo-Rodriguez; Paulo Wender Portal Gomes; Nicole Elizabeth Avalon; Pieter C Dorrestein; Mingxun Wang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Mass Spectrometry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2024-04-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661cd188418a5379b0df32c2/original/enabling-pan-repository-reanalysis-for-big-data-science-of-public-metabolomics-data.pdf |
63edc76cfcfb27a31fdedfde | 10.26434/chemrxiv-2022-w4h3t-v2 | CysDB: A Human Cysteine Database based on Experimental Quantitative Chemoproteomics | Cysteine chemoproteomics studies provide proteome-wide portraits of the ligandability or potential ‘druggability’ of thousands of cysteine residues. Consequently, these studies are enabling resources for closing the druggability gap, namely achieving pharmacological manipulation of ~99% of the human proteome that remains untargeted by FDA approved small molecules. Recent interactive dataset repositories, such as OxiMouse and SLCABPP, have enabled users to interface more readily with cysteine chemoproteomics studies1,2. However, these databases remain limited to single studies and therefore do not provide a mechanism to perform cross-study analyses. Here we report CysDB as a curated community-wide repository of cysteine chemoproteomics data that incorporates high coverage data derived from nine studies generated by the Backus, Cravatt, Gygi, Wang, and Yang research groups. CysDB is a SQL relational database that is publicly available at https://backuslab.shinyapps.io/cysdb/ and features chemoproteomic measures of identification, hyperreactivity, and ligandability for 62,888 cysteines (24% of all cysteines the human proteome). The CysDB web application also includes annotations of functionality (UniProtKB/Swiss-Prot, Pfam, Panther), known druggability (FDA approved targets, DrugBank, ChEMBL), disease-relevance and genetic variation (ClinVar, Cancer Gene Census, Online Mendelian Inheritance in Man), and structural features (Protein Data Bank). Showcasing the utility of CysDB, here we report the discovery and enrichment of ligandable cysteines in undruggable classes of proteins, the observation that a subset of cysteines showed marked preference for specific classes of electrophiles (chloroacetamide vs acrylamide), and that ligandable cysteines are present in numerous undrugged disease-relevant proteins. Most importantly, we have designed CysDB for the incorporation of new datasets and features to support the continued growth of the druggable cysteineome. | Lisa Boatner; Maria Palafox; Devin Schweppe; Keriann Backus | Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63edc76cfcfb27a31fdedfde/original/cys-db-a-human-cysteine-database-based-on-experimental-quantitative-chemoproteomics.pdf |
65eed743e9ebbb4db970888f | 10.26434/chemrxiv-2024-6pg8b | Solvent effects in hyperpolarization of 15N nuclei in [15N3]metronidazole and [15N3]nimorazole antibiotics via SABRE-SHEATH | Metronidazole and nimorazole are antibiotics of a nitroimidazole group originally designed for acting on anaerobic bacteria. These antibiotics may be potentially utilized as hypoxia radiosensitizers for the treatment of cancerous tumors. Hyperpolarization of 15N nuclei in these compounds using SABRE-SHEATH (Signal Amplification By Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei) approach provides dramatic enhancement of detection sensitivity of these analytes using magnetic resonance spectroscopy and imaging. Methanol-d4 is conventionally employed as a solvent in SABRE hyperpolarization process. Herein, we investigate SABRE-SHEATH hyperpolarization of isotopically labeled [15N3]metronidazole and [15N3]nimorazole in nondeuterated methanol-h4 and ethanol-h6 solvents (with the latter one being more preferable for biomedical applications due to its significantly lower toxicity). Optimization of hyperpolarization parameters, such as polarization transfer magnetic field, temperature, parahydrogen flow rate and pressure, allowed us to obtain an average 15N polarization of up to ca. 7.6% for both substrates. The highest 15N polarizations were observed in methanol-d4 for [15N3]metronidazole and in ethanol-h6 for [15N3]nimorazole. At a clinically relevant magnetic field of 1.4 T the 15N nuclei of these substrates possess long characteristic hyperpolarization lifetimes (T1) in the range from ca. 1 to ca. 7 min, with the longest relaxation observed for 15NO2 sites. This study represents a major step toward SABRE in more biocompatible solvents, such as ethanol, and also paves the way for future utilization of these hyperpolarized nitroimidazoles as molecular contrast agents for MRI visualization of tumors. | Anna P. Yi; Oleg G. Salnikov; Dudari B. Burueva; Nikita V. Chukanov; Eduard Y. Chekmenev; Igor V. Koptyug | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eed743e9ebbb4db970888f/original/solvent-effects-in-hyperpolarization-of-15n-nuclei-in-15n3-metronidazole-and-15n3-nimorazole-antibiotics-via-sabre-sheath.pdf |
64e807143fdae147fac27acb | 10.26434/chemrxiv-2023-mrm25 | Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions | In enzyme mechanistic studies and mutant design, it is highly desirable to know the individual residue contributions to the reaction free energy barrier. In this work, we show that such free energy contributions from each residue can be readily obtained by post-processing ab initio quantum mechanical molecular mechanical (ai-QM/MM) free energy simulation trajectories. Specifically, through a mean force integration along the minimum free energy pathway, one can obtain the electrostatic, polarization, and van der Waals contributions from each residue to the free energy barrier. Separately, a similar analysis procedure allows us to assess the contribution from different collective variables along the reaction coordinate. The chorismate mutase reaction is used to demonstrate the utilization of these two trajectory analysis tools. | Xiaoliang Pan; Richard Van; Jingzhi Pu; Kwangho Nam; Yuezhi Mao; Yihan Shao | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e807143fdae147fac27acb/original/free-energy-profile-decomposition-analysis-for-qm-mm-simulations-of-enzymatic-reactions.pdf |
60c740e4ee301cf6e1c78b31 | 10.26434/chemrxiv.7263596.v2 | Machine Learning for Acute Toxicity Prediction Using High-Throughput Enzyme-Reaction Chip | <p>Machine
learning (ML) has brought significant technological innovations in many fields,
but it has not been widely embraced by most researchers of natural sciences to
date. Traditional understanding and
promotion of chemical analysis cannot meet the definition and requirement of
big data for running of ML. Over the years, we focused on building a more
versatile and low-cost approach to the acquisition of copious amounts of data
containing in a chemical reaction. The generated data meet exclusively the
thirst of ML when swimming in the vast space of chemical effect. As
proof in this study, we carried out a case for acute toxicity test throughout
the whole routine, from model building, chip preparation, data collection, and
ML training. Such a strategy will probably play an important role in connecting
ML with much research in natural science in the future.</p> | Qiannan Duan; Jianchao Lee; Jinhong Gao; Jiayuan Chen; Yachao Lian; Zoudi Wang; Can Wang; Zhaoyi Xu; Juan Ren; Sifan Bi | Biochemical Analysis; Imaging; Chemical Biology; Environmental biology; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e4ee301cf6e1c78b31/original/machine-learning-for-acute-toxicity-prediction-using-high-throughput-enzyme-reaction-chip.pdf |
642faa3e736114c9630e5df7 | 10.26434/chemrxiv-2023-wkjmm | Ionic Blockades Control the Efficiency of Energy Recovery in Forward Bias Bipolar Membranes | Limited understanding exists about the operation of bipolar membranes (BPMs) in forward bias to convert protonic gradients into electrical work, despite its emerging role in many electrochemical devices. In these device contexts, the BPM is typically exposed to complex electrolyte mixtures, but their impact on polarization remains poorly understood. Herein, we develop a mechanistic model explaining the forward bias polarization behavior of BPMs in mixed electrolytes with different acidities/basicities. This model invokes that weak acids/bases accumulate in the BPM and impose an ionic blockade that inhibits the recombination of stronger acids/bases, resulting in a substantial neutralization overpotential. We demonstrate the utility of our model to fuel cells and redox flow batteries, and introduce two materials design strategies for mitigating this inhibition. Lastly, we apply our findings to enhance the energy efficiency of carbonate management in CO2 electrolyzers. This work highlights how non-equilibrium local environments at membrane-membrane interfaces can define the efficiency of protonic-to-electrical energy conversion. | Wei Lun Toh; Hieu Dinh; An Chu; Ethan Sauvé; Yogesh Surendranath | Physical Chemistry; Energy; Fuel Cells; Interfaces; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642faa3e736114c9630e5df7/original/ionic-blockades-control-the-efficiency-of-energy-recovery-in-forward-bias-bipolar-membranes.pdf |
60c74f7f337d6cf0c2e28150 | 10.26434/chemrxiv.12911168.v1 | Time-Resolved X-ray Phase-Contrast Imaging (XPCI) of Nucleation and Crystal Growth in the Anti-Solvent Crystallization of Lovastatin | <p>X-ray phase contrast imaging (XPCI) of anti-solvent
crystallization of lovastatin from an acetone/water solution was carried out in
a concentric flow mixing device, using water as the anti-solvent. Spinodal
decomposition of the solution is observed to give rise to ‘oiled out’ phases
that undergo heterogeneous nucleation at the interface with the flowing
solution. Heterogeneous nucleation is also observed on the walls of the reactor
walls in the form of what appears to be Stranski–Krastanov
growth of plate-like crystals. XPCI together with Eulerian video magnification
forms a powerful tool for the spatio-temporal analysis, revealing mechanistic
details of a non-equilibrium process such as anti-solvent crystallization.</p> | Gunjan Das; Anuradha Pallipurath; Joanna Leng; Kazimir Wanelik; John McGinty; Russell Miller; Thokozile Kathyola; Sin-Yuen Chang; Laila H. Al-Madhagi; Shashidhara Marathae; Christoph Rau; Jan Sefcik; Sven L.M. Schroeder | Pharmaceutical Industry; Process Control | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f7f337d6cf0c2e28150/original/time-resolved-x-ray-phase-contrast-imaging-xpci-of-nucleation-and-crystal-growth-in-the-anti-solvent-crystallization-of-lovastatin.pdf |
62e00678a8e4dc7d521d996a | 10.26434/chemrxiv-2022-xpv04 | Effect of Rheology and Role of External Forces on Indigenous Melt Centrifugal Spinning of PP fibers and their Transcrystalline Composites | This paper discusses the use of polypropylene fiber as a reinforcing agent in a HDPE matrix. The PP fiber has been prepared by a Novel and Patented Melt Centrifugal Spinning Machine, developed by me. It is well known that fibers and other fillers can cause trans-crystallization in HDPE, resulting in improvement of mechanical properties. Firstly, I have proposed a force balance which helps in understanding the role of external forces on the spinning of fibers. Thereafter, the fibers have been synthesized and effects of parameters such as temperature & RPM on the morphology of the fibers have been studied. Further, composites of synthesized PP fibers with HDPE have been prepared and characterized for their mechanical property with corroboration to DSC. Also, I have attempted to make use of Ethylene – Propylene Copolymer as a compatibilizer for the PP fibers & HDPE, and have studied the effect of the addition of the same on the mechanical properties of the prepared composites. | Manoj Praharaj Bhatnagar | Materials Science; Polymer Science; Nanoscience; Composites; Fibers; Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e00678a8e4dc7d521d996a/original/effect-of-rheology-and-role-of-external-forces-on-indigenous-melt-centrifugal-spinning-of-pp-fibers-and-their-transcrystalline-composites.pdf |
624d7ec5855ee52f2ce39798 | 10.26434/chemrxiv-2022-xjvpw | Biased Borate Esterification during Nucleoside Phosphorylase-Catalyzed Reactions: Apparent Equilibrium Shifts and Kinetic Implications | Biocatalytic nucleoside (trans-)glycosylations catalyzed by nucleoside phosphorylases have graduated to a practical and convenient approach to the preparation of modified nucleosides, which are important pharmaceuticals for the treatment of various cancers and viral infections. However, the obtained yields in these reactions are generally determined exclusively by the innate thermodynamic properties of the nucleosides involved, hampering the biocatalytic access to many sought-after target nucleosides. We herein report an orthogonal dimension for reaction engineering of these systems. We show how apparent equilibrium shifts in phosphorolysis and glycosylation reactions can be effected through entropically driven, biased esterification of nucleosides with inorganic borate. Our multifaceted analysis further describes the kinetic implications of this in situ reactant esterification for a model phosphorylase. Our results suggest an unusual pseudo-non-competitive inhibitory mechanism where
reversible binding of the borate ester of the nucleoside substrate yields a non-productive inhibitor-enzyme complex. This complex exhibits constricted molecular dynamics and exists in a rapid equilibrium with the productive enzyme-substrate complex via hydrolytic interconversion. Collectively, this report presents a partial departure from the stringent thermodynamic constraints of nucleoside phosphorolysis reactions and shines light on the molecular processes regulating the activity of nucleoside-binding
enzymes in the presence of borate. | Felix Kaspar; Felix Brandt; Sarah Westarp; Lea Eilert; Sebastian Kemper; Anke Kurreck; Peter Neubauer; Christoph Jacob; Anett Schallmey | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Physical Organic Chemistry; Biochemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2022-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624d7ec5855ee52f2ce39798/original/biased-borate-esterification-during-nucleoside-phosphorylase-catalyzed-reactions-apparent-equilibrium-shifts-and-kinetic-implications.pdf |
61e1454bf2bef72f1ba13637 | 10.26434/chemrxiv-2022-p2kt2 | Synthesis, Reactivity, and Properties of Benz[a]azulenes via [8 + 2] Cycloaddition of 2H-cyclohepta[b]furan-2-ones with an Enamine | Starting with the reaction of 2H-cyclohepta[b]furan-2-ones with an enamine, which was prepared from 4-tert-butylcyclohexanone and pyrrolidine, benz[a]azulenes having both formyl and tert-butyl groups were obtained in the three-step sequence. Subsequently, both the formyl and tert-butyl groups were eliminated by heating the benz[a]azulene derivatives in 100% H3PO4 to give benz[a]azulenes without these substituents in high yields. In terms of the product yield, this method is the best one ever reported for the synthesis of the parent benz[a]azulene so far. The conversion of the benz[a]azulene derivatives with a formyl group into cyclohept[a]acenaphthylen-3-one derivatives was also investigated via Knoevenagel condensation with dimethyl malonate, followed by Brønsted acid-mediated intramolecular cyclization. The structural features including the bond alternation in the benz[a]azulene derivatives were revealed by NMR studies, NICS calculations, and a single-crystal X-ray structural analysis. The optical and electrochemical properties of a series of benz[a]azulene derivatives were evaluated by UV/Vis, fluorescence spectroscopy and voltammetry experiments. As a result, we found that some benz[a]azulene derivatives showed remarkable luminescence in acidic media. In addition, the benz[a]azulene derivatives with the electron-withdrawing group and cyclohept[a]acenaphthylen-3-one derivative displayed good reversibility in the spectral changes under the electrochemical redox conditions. | Taku Shoji; Akari Yamazaki; Ryuzi Katoh; Konomi Shimamura; Rina Sakai; Masafumi Yasunami; Tetsuo Okujima; Shunji Ito | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e1454bf2bef72f1ba13637/original/synthesis-reactivity-and-properties-of-benz-a-azulenes-via-8-2-cycloaddition-of-2h-cyclohepta-b-furan-2-ones-with-an-enamine.pdf |
625e400f88636c2225175101 | 10.26434/chemrxiv-2022-qqt4d | A Data-Driven and Topological Mapping Approach for the A Priori Prediction of Stable Molecular Crystalline Hydrates | Predictions of the structures of stoichiometric, fractional, or non-stoichiometric hydrates of organic molecular crystals is immensely challenging due to the extensive search space of different water contents, host molecular placements throughout the crystal, and internal molecular conformations. However, the dry frameworks of these hydrates, especially for non-stoichiometric or isostructural dehydrates, can often be predicted from a standard anhydrous crystal structure prediction (CSP). Inspired by developments in the field of drug binding, we introduce an efficient data-driven and topologically aware approach for predicting organic molecular crystal hydrate structures through a mapping of water positions within the crystal structures. As such, the method does not require a priori specification of water content and can, therefore, predict stoichiometric, fractional, and non-stoichiometric hydrate structures. This approach, which we term MACH (Mapping of Crystalline Hydrates), establishes a set of rules for systematic determination of favorable positions for water insertion within predicted or experimental crystal structures based on considerations of the chemical features of local environments and void regions. The proposed approach is tested on hydrates of three pharmaceutically relevant compounds that exhibit diverse crystal packing motifs and void environments characteristic of hydrate structures. Overall, we show that this mapping approach introduces a new advance in the efficient performance of hydrate CSP through generation of stable hydrate stoichiometries at low cost and should be considered an integral component for CSP workflows. | Richard Hong; Alessandra Mattei; Ahmad Sheikh; Mark Tuckerman | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Computational Chemistry and Modeling; Theory - Computational; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625e400f88636c2225175101/original/a-data-driven-and-topological-mapping-approach-for-the-a-priori-prediction-of-stable-molecular-crystalline-hydrates.pdf |
65ea9d7ee9ebbb4db93b1a28 | 10.26434/chemrxiv-2024-kdg1s | Unraveling the Superior Stability of 3–5-Layer α7-Borophene | The discovery of bilayer borophene has highlighted the importance of interlayer covalent B−B bonds in addressing the stability challenges of air-sensitive monolayer borophene, which showcases promising attributes for diverse electronic and energy applications. Yet, investigations into multilayer borophene structures, particularly beyond the bilayer, are sparse. In this study, we conducted a systematic investigation of the geometries, stabilities, electronic structures, and work functions of 2- to 5-layer α7- and α8-borophene using density functional theory calculations, based on different stacking modes. Remarkably, we identified metallic 3- to 5-layer configurations of α7-borophene (α7ABA, α7ABAbB, and α7ABABA), each demonstrating the highest thermodynamic stability reported to date for their respective layer numbers. Additionally, the 3- to 5-layer α8-borophene variants, including α8AAB, α8AABbA, and α8AABAB, also exhibited significant thermodynamic stability, ranking second highest among the borophene configurations examined. With increasing layer number from 2 to 5, the influence of in-plane orbitals (s, px, and py) on in-plane bonding became more pronounced, while their effect on interlayer interactions diminished. This evolution led to greater geometric distortion within the layers and enhanced in-plane binding, resulting in higher overall binding energies in both the α7- and α8-borophene series. Importantly, the calculated work functions for the 3- to 5-layer α7- and α8-borophene were found to be comparable to that of graphene (4.37–4.60 eV), suggesting that these multilayer borophene materials could potentially serve as viable alternatives to graphene. Overall, these findings offer valuable insights into the structural and electronic properties of multilayer borophene, paving the way for its integration into future nanotechnology applications. | Bing Zheng; Zhe Wang; Ying Xie; Jiao Zhang; Yan-chang Zhang; Li-ying Cui; Yong-jie Liu | Theoretical and Computational Chemistry; Materials Science; Nanoscience; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ea9d7ee9ebbb4db93b1a28/original/unraveling-the-superior-stability-of-3-5-layer-7-borophene.pdf |
6547c6c0c573f893f1dd7718 | 10.26434/chemrxiv-2023-0pjxv | Learning Stability Scores from Computationally Generated Kinetic Data | The absence of computational methods to predict stressor-specific degradation susceptibilities represents a significant and costly challenge to the introduction of new materials into applications. Here, a machine-learning framework is developed that predicts stressor-specific stability scores from computationally generated reaction data. Thermal degradation of alkanes was studied as an exemplary system to demonstrate the approach. The half-lives of ~32k alkanes were simulated under pyrolysis conditions using 59 model reactions. Using a hinge-loss function, this half-life data was used to train machine learning models to predict a scalar representing the relative stability based only on the molecular graph. These models were successful in transferability case-studies using distinct train:test splits to recapitulate known stability trends with respect to the degree of branching and alkane size. Even the simplest models showed excellent performance in these case studies, demonstrating the relative ease with which thermal stability can be learned. The stability score is also shown to be useful in a design study, where it is used as part of the objective function of a genetic algorithm to guide the search towards more stable species. This work provides a framework for converting kinetic reaction data into stability scores that provide actionable design information and opens avenues for exploring more complex chemistries and stressors. | Veerupaksh Singla; Qiyuan Zhao; Brett Savoie | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6547c6c0c573f893f1dd7718/original/learning-stability-scores-from-computationally-generated-kinetic-data.pdf |
62f14617e78f70445f33ec4d | 10.26434/chemrxiv-2022-trzlf | Facile Deoxygenative Reduction of a Bridging Carbonato Ligand with Silyl and Boryl 4,4’-Bipyridinylidene Reagents | The reactivity of CO2 with a previously described PCcarbeneP cobalt(I) hydroxide is reported. Insertion of CO2 into the Co-OH bond followed by a dehydration reaction releasing water results in a cobalt(I) bridging carbonate species featuring fluctional κ1: κ1 and κ1: κ2 coordination of the central carbonate moiety. The reduction chemistry of the resulting cobalt(I) bridging carbonate species is explored utilizing deoxygenative reducing agents N,N′-bis(trimethylsilyl)- and N,N′-bis(pinacolatoboryl)-4,4′-bipyridinylidene. The three-electron reduction produces the corresponding PCcarbeneP cobalt(I) siloxide or boroxide complex alongside a PCcarbeneP cobalt(0) monocarbonyl, silyl/boryl ether, and 4,4’-bipyridine. | Warren Piers; Marissa Clapson; Zachary Dubrawski; Benjamin Gelfand | Inorganic Chemistry; Organometallic Compounds; Small Molecule Activation (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62f14617e78f70445f33ec4d/original/facile-deoxygenative-reduction-of-a-bridging-carbonato-ligand-with-silyl-and-boryl-4-4-bipyridinylidene-reagents.pdf |
60c74d0d4c8919271dad3753 | 10.26434/chemrxiv.12213914.v2 | Minisci C-H Alkylation of Heteroarenes Enabled by Dual Photoredox/bromide Catalysis in Micellar Solutions | Microstructured
aqueous solutions were employed to engage non-activated alkyl bromides in the
visible-light-promoted C‑H functionalization of heteroarenes. The reactive
carbon-centered alkyl radicals were generated by merging the photoredox
approach, bromide anion co-catalysis and spatial pre-aggregation of reacting
species in the mixture. The presented methodology allowed obtaining alkylated
heteroarenes without stoichiometric radical-promoters, in acid-free conditions
and using blue LEDs as the light source. | Marila S. Santos; Martyna Cybularczyk-Cecotka; Burkhard Koenig; Maciej Giedyk | Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d0d4c8919271dad3753/original/minisci-c-h-alkylation-of-heteroarenes-enabled-by-dual-photoredox-bromide-catalysis-in-micellar-solutions.pdf |
646cef0eb3dd6a65309b8d0d | 10.26434/chemrxiv-2023-wdjqm-v3 | Planar Confined Water Organisation in Lipid Bilayer Stacks of Phosphatidylcholine and Phosphatidylethanolamine | Phospholipid-based liposomes are abundantly studied in biomembrane research and used in numerous medical and biotechnological applications. Despite current extensive knowledge on membrane nanostructure and its mechanical properties under various environmental conditions, there is still a lack of understanding on interfacial lipid-water interactions. In this work, the nature of the confined water layer for L-α-phosphatidylcholine (egg-PC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dimyristoyl-sn-glycerol-3-phosphocholine (DMPC) and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE) in the fluid lamellar phase of multilamellar vesicles was investigated. A new model for describing three different water regions is proposed, which have been characterised using a combination of small angle X-ray scattering (SAXS) and densitometry. The three regions concern (i) ‘the headgroup water’, (ii) ‘perturbed water’ near the membrane/water interface and (iii) a core layer of ‘free water’ (unperturbed water). The behaviour of all three layers is discussed as a function of temperature, concerning influences of chain saturation and headgroup type. While the overall water layer and perturbed water layer thickness increase with temperature, the free water layer displays the opposite trend for PCs, and in PEs is completely absent. Furthermore, an estimate of the temperature dependent headgroup orientation is given for both, PCs and PEs. The newly presented structural data deduced from the three-water region model will be useful for future refined molecular dynamics simulations and allow a better theoretical understanding of the attractive van der Waals force between adjacent membranes. | Gerome Vancuylenberg; Amin Sadeghpour; Arwen Tyler; Michael Rappolt | Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646cef0eb3dd6a65309b8d0d/original/planar-confined-water-organisation-in-lipid-bilayer-stacks-of-phosphatidylcholine-and-phosphatidylethanolamine.pdf |
6723878ef9980725cfb03e4c | 10.26434/chemrxiv-2024-zfhsx | Self-Assembly, Rearrangement and Disassembly of {Cr6} Horseshoe Oligomers | Molecular assemblies are commonly found in biological systems; designing and reporting on synthetic mimics of these is a challenge for modern chemistry. Here, we apply ion mobility mass spectrometry (IM-MS), density functional theory calculations and mass-selective electrospray ion beam deposition followed by low temperature scanning tunnelling microscopy (STM) to decipher the self-assembly, rearrangement and disassembly processes of {Cr6}n horseshoe oligomers (n = 1 - 5). Activated tandem IM-MS reveals the oligomer disassembly in detail, highlighting the stability of the dimer unit. When n = 2 and 3 oligomers are deposited on surfaces, we observe the rearrangement of dimers and trimers to dimers of dimers, as characterised by low temperature STM. In its entirety, the experimental and computational data provide a convincing framework for the analysis of supramolecular assembly processes in non-crystalline phases that could be used in future design strategies | Niklas Geue; Dhaneesh Gopalakrishnan; Jimin Ham; Shengpeng Huang; Grigore Timco; Neil Burton; Richard Winpenny; Kelvin Anggara; Perdita Barran | Physical Chemistry; Analytical Chemistry; Organometallic Chemistry; Mass Spectrometry; Microscopy | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6723878ef9980725cfb03e4c/original/self-assembly-rearrangement-and-disassembly-of-cr6-horseshoe-oligomers.pdf |
6544ea8948dad23120fe8d2a | 10.26434/chemrxiv-2023-r54g8 | MXene-induced nonradiative energy transfer | Since their discovery in 2011, MXenes have risen to prominence for energy storage, electromagnetic shielding, and optoelectronics. Yet, the nonradiative energy transfer properties of this family of 2D materials remain elusive, which may have implications in optoelectronics, photovoltaics and biosensing. Here, we use single-molecule fluorescence confocal microscopy and DNA origami nanopositioners to investigate, for the first time, the distance-dependent energy transfer of an organic emitter (ATTO 542) placed on transparent thin films made of spincast Ti3C2Tx flakes. We propose a specific immobilization chemistry for DNA origami nanostructures based on glycine-MXene interaction, allowing us to precisely control their orientation on the surface. Each DNA origami structure is designed to carry a single dye molecule at predetermined heights. Our findings reveal that when the dye is located at distances of 1 nm < d < 8 nm from the surface, the fluorescence is quenched following a distance dependence of d-3. This is in agreement with the Förster-type mechanism of energy transfer in transparent conductors at the bulk level. 50% of energy transfer efficiency is reached at 2.7 nm (d0). MXenes could therefore be used as short-distance spectroscopic nanorulers, sensitive at a distance regime that common energy transfer tools cannot access. | Carmen Lorena Manzanares Palenzuela; Dahnan Spurling; Alan Szalai; Tim Schröder; Valeria Nicolosi; Philip Tinnefeld | Materials Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6544ea8948dad23120fe8d2a/original/m-xene-induced-nonradiative-energy-transfer.pdf |
6734e612f9980725cf1695e5 | 10.26434/chemrxiv-2024-nsd7r-v2 | Reversible Small Molecule pan-Ras Inhibitors Display Tunable Affinity for the Active and Inactive forms of Ras. | Activating mutations of Ras are one of the most prevalent drivers of cancer and are often associated with poor clinical outcomes. Despite FDA approval for two irreversible inhibitors that target the inactive state of KRasG12C, significant unmet clinical need still exists, and the susceptibility of non-G12C mutants to inactive-state inhibition remains unclear. Here we report the discovery of a novel series of reversible inhibitors that bind in an enlarged version of the switch I-II pocket with nanomolar affinities. Dependent on chemotype these can either preferentially bind to the inactive or active state or bind both with similar affinity. The active-state binders inhibit the Raf interaction for wild-type Ras, and a broad range of oncogenic KRas mutants with nanomolar potency. A sub-series of these molecules displays cellular inhibition of Ras-Raf binding, as well as decreased phosphorylation of the downstream protein ERK, demonstrating that potent pan-Ras inhibitors can be accessed from this novel pocket. | Charles Parry; Francesca Pellicano; Alexander W. Schüttelkopf; Kim Beyer; Justin Bower; Amy Bryson; Kenneth S. Cameron; Nichole M. Cerutti; Jonathan P. Clark; Stuart Davidson; Keneth Davies; Martin J. Drysdale; Jeffrey Engelman; Anna Estevan-Barber; Andrea Gohlke; Christopher H. Gray; Daniel A. Guthy; Min Hong; Alana Hopkins; Luke Hutchinson; Jennifer Konczal; Michel Maira; Duncan McArthur; Mokdad Mezna; Heather McKinnon; Ridvan Nepravishta; Nils Ostermann; Camila Pasquali; Katie Pollock; Angelo Pugliese; Nicholas Rooney; Niko Schmiedeberg; Paul Shaw; Camilo Velez-Vega; Christopher West; Ryan West; Frederic Zecri; John B. Taylor | Biological and Medicinal Chemistry; Organic Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6734e612f9980725cf1695e5/original/reversible-small-molecule-pan-ras-inhibitors-display-tunable-affinity-for-the-active-and-inactive-forms-of-ras.pdf |
66df4a9f12ff75c3a1e281b3 | 10.26434/chemrxiv-2024-nq72z-v2 | Grignard Reagents as Simple Preatalysts for the Dehydrocoupling of Amines and Silanes | Methyl magnesium bromide is a precatalyst for the dehydrocoupling of silanes and amines to produce aminosilane products under mild conditions. As a commercially available Grignard reagent, this precatalyst represents a simplification over previous magnesium-containing catalysts for Si–N bond formation while displaying similar activity to other magnesium-based precatalysts. This observation is consistent with the hypothesis that competitive Schlenk equilibrium can be addressed by not using an ancillary ligand. While the activity of MeMgBr is lower than some reported catalysts, including other commercially available catalysts, unique selectivity was observed for MeMgBr that may allow for selective synthesis of aminosilane products. This work continues to increase the accessibility of Si–N heterodehydrocoupling through a growing family of commercially available precatalysts that balance activity and selectivity. | Claire Bushey; Diego Javier-Jimenez; Matthew Reuter; Rory Waterman | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66df4a9f12ff75c3a1e281b3/original/grignard-reagents-as-simple-preatalysts-for-the-dehydrocoupling-of-amines-and-silanes.pdf |
661ed29b418a5379b0fc6724 | 10.26434/chemrxiv-2024-jt42x | Buildup and Consumption of Species in Emulsion Droplets during Aqueous Suzuki Coupling Correlate with Yield | Fluorescence lifetime imaging microscopy (FLIM) provides spatiotemporal resolution of the changing composition of emulsion droplets during an aqueous–surfactant Suzuki coupling. In contrast to previous investigations, the present experiments characterize the full course of a catalytic chemical reaction, addressing key questions about if and where reaction species build up, and correlating these microscale behaviors with bench-scale product yields. At low concentrations of (active) catalyst, droplet environments are stable; however, at higher concentrations, emulsion droplet environments change markedly, as indi-cated by the rise and fall of fluorescence lifetimes. These changes are consistent with buildup and consumption of reaction species inside the droplets. A combination of FLIM and brightfield imaging pinpoint limitations in catalyst solubility as controlling the rate and degree of buildup of species in droplets. These solubility limitations are also identified as the cause of a reaction induction period, and an origin of the rate-and-reproducibility advantage obtained by adding a THF as a cosolvent. The subsequent mechanistic model from these data led to a bench-scale reaction optimization, wherein premixing the catalyst components bypasses the catalyst induction period, resulting in a faster reaction at otherwise constant catalyst load-ing. The understanding generated by FLIM thus provides an early example of how understanding changes in droplet compo-sitions on the microscale during ongoing aqueous–organic reactions can be leveraged for enhancing efficiencies in bench-scale reactions. | Hannah Peacock; Suzanne Blum | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661ed29b418a5379b0fc6724/original/buildup-and-consumption-of-species-in-emulsion-droplets-during-aqueous-suzuki-coupling-correlate-with-yield.pdf |
60c74eed337d6ce671e28054 | 10.26434/chemrxiv.12332678.v2 | Drug Binding Dynamics of the Dimeric SARS-CoV-2 Main Protease, Determined by Molecular Dynamics Simulation | <div>
<div>
<div>
<p>We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute
respiratory syndrome corona virus 2) main protease (Mpro) to examine the binding
dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir,
lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead
drugs to investigate access to the drug binding sites in Mpro. The frequently accessed sites
on Mpro were classified based on contacts between the ligands and the protein, and the
differences in site distributions of the encounter complex were observed among the
ligands. All seven ligands showed binding to the active site at least twice in 28 simulations
of 200 ns each. We further investigated the variations in the complex structure of the
active site with the ligands, using microsecond order simulations. Results revealed a wide
variation in the shapes of the binding sites and binding poses of the ligands. Additionally,
the C-terminal region of the other chain often interacted with the ligands and the active
site. Collectively, these findings indicate the importance of dynamic sampling of protein-
ligand complexes and suggest the possibilities of further drug optimisations. <br /></p><p><br /></p><p><br />
</p><div>
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<div>
<p>Raw trajectory data analysed in this paper and movie examples are available at the zenodo
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</div> | Teruhisa S. KOMATSU; Noriaki Okimoto; Yohei M. KOYAMA; Yoshinori HIRANO; Gentaro MORIMOTO; Yousuke OHNO; Makoto Taiji | Bioinformatics and Computational Biology; Biophysics; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eed337d6ce671e28054/original/drug-binding-dynamics-of-the-dimeric-sars-co-v-2-main-protease-determined-by-molecular-dynamics-simulation.pdf |
66f6f046cec5d6c1426e7c6c | 10.26434/chemrxiv-2024-xhrbz | Self-Immolative Polymers from Bio-based Monomers via Thiol−Ene Click Chemistry | The use of bio-based polymers is a promising approach to reduce reliance on petrochemicals. In addition, depolymerization is attracting significant attention for the breakdown of polymers at their end-of-life or to achieve specific stimuli-responsive functions. However, the design of polymers incorporating both of these features remains a challenge. Herein, we report a new class of self-immolative polymers based on lignin-derived aldehydes via thiol-ene click polymerization. These polymers can be further used in polymer-polymer coupling to access block copolymers. Moreover, diverse responsive end-caps can be introduced through post-polymerization functionalization from a single polymer precursor. These bio-based self-immolative polymers undergo cascade degradation in response to specific stimuli through alternating 1,6-elimination and cyclization reactions. | Zhengyu Deng; Elizabeth R. Gillies | Polymer Science; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f6f046cec5d6c1426e7c6c/original/self-immolative-polymers-from-bio-based-monomers-via-thiol-ene-click-chemistry.pdf |
660feb7e418a5379b02630e0 | 10.26434/chemrxiv-2024-ltkxm-v2 | Woolitmus: An Approach to Minimize E-waste using Wool-Based Wearable Sensor for Sweat pH Detection | This study introduces "Woolitmus" a textile-based wearable sweat pH indicator developed using pyranine, also known as HPTS (8-Hydroxypyrene-1,3,6-trisulfonic acid) and naturally occurring wool as substrate. Sweat pH analysis is crucial for monitoring health conditions associated with pH imbalance. The sensor exhibits pH responsiveness under both visible and UV light, offering potential as a real-time sweat patch for pH monitoring. The interaction of pyranine with wool substrate is detailed, elucidating the mechanism behind the pH sensitivity backed up by photophysical characterizations. Stability and reversibility tests also confirm the sensor's robustness and performance. The reported sensor also can simultaneously collect and detect pH levels without support of any additional accessories like electrodes, display, etc. It also offers sensitivity, real-time response, and non-invasive detection. But more importantly it stands out for its biodegradability, reusability, zero e-waste, and biocompatibility of the substrate. The wool fabric-based pH sensor holds promising applications, including health monitoring and lifestyle management. | Shruti Ghadge; Aditya Marathe; Ravindra Adivarekar; Sandeep More | Materials Science; Biocompatible Materials; Fibers | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660feb7e418a5379b02630e0/original/woolitmus-an-approach-to-minimize-e-waste-using-wool-based-wearable-sensor-for-sweat-p-h-detection.pdf |
66b3af46c9c6a5c07a574ba1 | 10.26434/chemrxiv-2024-wxj86-v2 | UniChromCD for Demultiplexing Time-resolved Charge Detection-Mass Spectrometry Data | Charge detection mass spectrometry (CD-MS) enables characterization of large, heterogeneous analytes through the analysis of individual ion signals. Because hundreds to thousands of scans must be acquired to produce adequate ion statistics, CD-MS generally requires long analysis times. The slow acquisition speed of CD-MS complicates efforts to couple it with time-dispersive techniques, such as chromatography and ion mobility, because it is not always possible to acquire enough scans from a single sample injection to generate sufficient ion statistics. Multiplexing methods based on Hadamard and Fourier transforms offer an attractive solution to this problem by improving the duty cycle of the separation while preserving retention/drift time information. However, integrating multiplexing with CD-MS data processing is complex. Here, we present UniChromCD, a new module in the open-source UniDec package that incorporates CD-MS time-domain data processing with demultiplexing tools. Following a detailed description of the algorithm, we demonstrate its capabilities using two multiplexed CD-MS workflows: Hadamard-transform size-exclusion chromatography and Fourier-transform ion mobility. Overall, UniChromCD provides a user-friendly interface for analysis and visualization of time-resolved CD-MS data. | James Sanders; October Owen; Brian Tran; Kyle Juetten; Michael Marty | Analytical Chemistry; Chemoinformatics; Mass Spectrometry; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b3af46c9c6a5c07a574ba1/original/uni-chrom-cd-for-demultiplexing-time-resolved-charge-detection-mass-spectrometry-data.pdf |
613ae191abeb636d50ce676f | 10.26434/chemrxiv-2021-6617l | Accelerated Design of Near-Infrared-II Molecular Fluorophores via First-Principles Understanding and Machine Learning | Organic molecular fluorophores in the second near-infrared window (NIR-II) have attracted much attention in the recent decade due to their great potentials in both fundamental research and practical applications. This is especially true for biomedical research, owing to their deep light penetration depth and low bioluminescence background at the long wavelength. However, the fluorescence quantum yields (QY) of most NIR-II materials are very low, which are not ideal for practical applications. Although there is a growing need to discover new NIR-II fluorophores, most of them were designed based on experience, and the structures were limited to few molecular motifs. Herein, we report the design of high QY NIR-II fluorophores in solutions based on enhancing the rigidity of the conjugated backbones, which could be quantified by the Seminario method. A deep neural network was trained to predict the HOMO-LUMO energy gaps for a chemical library of NIR-II backbone structures. Hundreds of new NIR-II cores with low energy gap were discovered, and eight of them across different acceptor cores are found to have relatively rigid conjugated backbones. With further molecular processing or formulation, the proposed new fluorophores should boost the development of NIR-II materials for applications in a wide range of fields. | Shidang Xu; Pengfei Cai; Jiali Li; Xianhe Zhang; Xianglong Liu; Xiaonan Wang; Bin Liu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/613ae191abeb636d50ce676f/original/accelerated-design-of-near-infrared-ii-molecular-fluorophores-via-first-principles-understanding-and-machine-learning.pdf |
60cf5893b912f856de5aad85 | 10.26434/chemrxiv-2021-1lw5t | Defect Chemistry and Doping of BiCuSeO | While p-type BiCuSeO is a well-known mid-temperature oxide thermoelectric (TE) material, computations predict that superior TE performance can be realized through n-type doping. In this study, we use first-principles defect calculations to show that Cu vacancies are responsible for the native p-type self doping; yet, we find that BiCuSeO is n-type dopable under Cu-rich growth conditions, where the formation of Cu vacancies is suppressed. We computationally survey a broad suite of 23 dopants and find that only Cl and Br are effective n-type dopants. Therefore, we recommend that future experimental doping efforts utilize phase boundary mapping to optimize the electron concentration and resolve the anomalous p-n-p transitions observed in halogen-doped BiCuSeO. The prospects of n-type doping, as revealed by our defect calculations, paves the path for rational design of BiCuSeO chemical analogues with similar doping behavior and even better TE performance. | Michael Toriyama; Jiaxing Qu; G. Jeffrey Snyder; Prashun Gorai | Theoretical and Computational Chemistry; Energy; Theory - Computational; Piezoelectricity and Thermoelectricity; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cf5893b912f856de5aad85/original/defect-chemistry-and-doping-of-bi-cu-se-o.pdf |
65fb346ae9ebbb4db920d6bf | 10.26434/chemrxiv-2024-zgn9m | Shallow Rate-Overpotential Scaling in Aqueous Molecular Oxygen Reduction Electrocatalysis Across a Family of Iron Macrocycles | Rate-overpotential scaling relationships have been employed widely to understand trends in oxygen reduction reaction (ORR) electrocatalysis by dissolved metal macrocycles in organic electrolytes. Similar scaling relationships remain unknown for surface-adsorbed ORR electrocatalysts in the acidic aqueous environments germane to proton-exchange membrane (PEM) fuel cells. Herein, we examine ORR catalysis in aqueous perchloric acid media for a structurally diverse array of iron macrocycle complexes adsorbed on Vulcan carbon black. The macrocycles encompass Fe–N4, Fe–N2N′2 and Fe–NxC4−x motifs bearing pyrrolic, pyridinic, and N-heterocyclic carbene (NHC) moieties in the primary ligation sphere, giving rise to a 530 mV range in Fe(III/II) redox potentials, EFe(III/II). Experimental Tafel data in the micropolarization regime were extrapolated to the EFe(III/II) to furnish estimated TOF values that span ~3 orders of magnitude across the family of compounds. Despite the structural diversity of this family of compounds, extrapolated TOF values correlate with Fe(III/II) redox potentials in a roughly log-linear fashion with a shallow scaling factor of approximately 180 mV/decade. These findings highlight that negative shifts in EFe(III/II) lead to diminishing returns in catalytic rate promotion and suggest that changes to the primary ligating environment in a macrocycle are insufficient to break fundamental rate-overpotential scaling relationships in aqueous ORR catalysis. Together these studies motivate the development of new higher-potential iron complexes that employ motifs beyond the equatorial ligation plane to enhance ORR catalysis. | Travis Marshall-Roth; Liang Liu; Vennela Mannava; Deiaa Harraz; Brian Cook; Morris Bullock; Yogesh Surendranath | Inorganic Chemistry; Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fb346ae9ebbb4db920d6bf/original/shallow-rate-overpotential-scaling-in-aqueous-molecular-oxygen-reduction-electrocatalysis-across-a-family-of-iron-macrocycles.pdf |
65d3582366c1381729fb9ab1 | 10.26434/chemrxiv-2024-z65f0 | Rh(III)-Catalyzed Regioselective C8-alkenylation of isoquinolones with methoxyallene: A Facile Access to aldehyde bearing isoquin-olones | A simple and facile access to isoquinolone aldehyde scaffolds has been achieved through a rhodium-catalyzed reaction between isoquinolone and methoxyallene. Herein, methoxyallene serves as an acrolein equivalent, resulting in this unique functionalization. Furthermore, the compatibility with natural complex and drug molecules underscores the sig-nificance of this developed protocol. Based on kinetic studies and several control reactions, a plausible reaction mecha-nism has also been proposed for this regioselective transformation. | Ankita Thakur; Devesh Chandra; Upendra Sharma | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d3582366c1381729fb9ab1/original/rh-iii-catalyzed-regioselective-c8-alkenylation-of-isoquinolones-with-methoxyallene-a-facile-access-to-aldehyde-bearing-isoquin-olones.pdf |
66b36a3301103d79c5075f55 | 10.26434/chemrxiv-2024-st9qn | [ECCE]-Coordinated (E = P, As) Ruthenium Complexes in Different Oxidation States: Ru(I) (E = P), Ru(II) (E = P, As) and Ru(III) (E = As) | Targeting Ru(III) and Ru(I) η2-alkyne complexes, 2,2’-(iPr2E)2-substituted diphenylacetylenes (1-E, E = P, As) were employed for the prepara-tion of [ECCE]-coordinated Ru(II) complexes, which were examined with respect to 1e− oxidation and reduction. Starting from [(η6-cymene)RuCl2]2 and 1-E, ligand cyclization reactions (via attack of one iPr2E moiety at the alkyne) were observed and found to afford cyclic aryl ylidic mesoionic carbenes (2-E). Attempts to ring-open these complexes were unsuccessful for E = P, but found to proceed smoothly for E = As, which led to the isolation of cis-[AsCCAs]RuCl2(MeCN) (3-As). To also gain access to the corresponding [PCCP]-coordinated derivative (3-P), the reactions between 1-E (E = P, As) and cis-(MeCN)2(COD)RuCl2 ∙ 2 MeCN were examined, which led to the envisioned complexes 3-E for E = As and E = P. Compounds cis-[ECCE]RuCl2(MeCN) (3-E) and their carbonyl derivatives cis-[ECCE]RuCl2(CO) (5-E) were oxidized using PhICl2, which led to an oxidative dichlorination of the alkyne in the case of 5-E. The latter dichlorination was found to occur trans-selective to afford complexes of the type [trans-E(Cl)C=C(Cl)E]RuCl2(CO) (6-E), while unselective oxidation processes set in upon treatment of 3-E with PhICl2. Although the envisioned Ru(III) complexes [ECCE]RuCl3 (7-E) were detectable for E = P and E = As, only the arsa-derivative 7-As was obtained in a pure form, namely via oxidation of cis-[ECCE]RuCl2(THT) (8), which is accessible for E = As only. Upon reduction of compounds 3-E, a hitherto unprecedented Ru(I) η2-alkyne complex, [PCCP]RuCl (9), was obtained for E = P, while multi-ple attempts to also isolate the corresponding arsa-derivative met with failure. The former square planar Ru(I) complex (9) was characterized comprehensibly and examined in detail by means of DFT and CASSCF calculation. Upon treatment of 9 with TlPF6, a diamagnetic µ-Tl-bridged compound (10) with a nearly linear Ru−Tl−Ru array was formed and isolated in high yields. Careful analysis of the bonding situation suggested that the Ru−Tl−Ru moiety in 10 is best interpreted in terms of a 3c-4e− bond. | Benjamin Rudin; Carolin A. M. Stein; Joachim Ballmann | Organometallic Chemistry; Coordination Chemistry (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b36a3301103d79c5075f55/original/ecce-coordinated-e-p-as-ruthenium-complexes-in-different-oxidation-states-ru-i-e-p-ru-ii-e-p-as-and-ru-iii-e-as.pdf |
60c74a8eee301c483fc79c87 | 10.26434/chemrxiv.12218426.v1 | DpgC-Catalyzed Peroxidation of DPA-CoA: Insights onto the Spin-Forbidden Transition and Charge Transfer Mechanisms | Oxygenases are a family of enzymes that catalyse the breaking of molecular oxygen with incorporation of, at least, one oxygen atom into an organic substrate. Since molecular oxygen is a diradical and most organic molecules have no unpaired-electrons, reactions catalysed by oxygenases involve changes in the spin state of the system that are forbidden in non-relativistic quantum theory. To overcome this limitation, oxygenases usually require metal or redox cofactors for catalysis. Intriguingly, some oxygenases can catalyse oxygen incorporation reactions even in the absence of any cofactor, but the detailed mechanism followed by these enzymes to overcome this limitation is still unknown. In the present work we give insight onto the mechanism for the enzymatic cofactor-independent oxidation of 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) by the combination of multi-reference calculations on a model system, with QM/MM calculations for the enzymatic reaction. Our results reveal that intersystem crossing takes place without requiring concerted protonation of molecular oxygen. We characterized and identifed the nine concurrent electronic states, showing that a first electron transfer is concomitant with the triplet-singlet transition (intersystem crossing). The enzyme apparently plays a passive role in promoting the intersystem crossing, although spontaneous reorganization of the water-wire connecting the active site with the bulk presets the substrate for subsequent chemical transformations. We believe that our results are fairly general showing that stabilization of the singlet radical-pair state between molecular oxygen and enolates is enough to promote spin-forbidden reaction without the need of neither metal cofactors nor basic residues in the active site. | Pablo Ortega; Alexandre Zanchet; Cristina Sanz-Sanz; Susana Gómez-Carrasco; Lola González-Sánchez; Pablo G. Jambrina | Chemical Biology; Computational Chemistry and Modeling; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a8eee301c483fc79c87/original/dpg-c-catalyzed-peroxidation-of-dpa-co-a-insights-onto-the-spin-forbidden-transition-and-charge-transfer-mechanisms.pdf |
626731f0ef2ade18543d643b | 10.26434/chemrxiv-2022-3jv2h | Teaching undergraduate physical chemistry lab with kinetic analysis of COVID-19 in the United States | A physical chemistry lab for undergraduate students described in this report is about applying kinetic models to analyze the spread of COVID-19 in the United States and obtain the reproduction numbers. The susceptible-infectious-recovery (SIR) model and the SIR-vaccinated (SIRV) model are explained to the students and are used to analyze the COVID-19 spread data from U.S. Centers for Disease Control and Prevention (CDC). The basic reproduction number R0 and the real-time reproduction number Rt of COVID-19 are extracted by fitting the data with the models, which explains the spreading kinetics and provides a prediction of the spreading trend in a given state. The procedure outlined here shows the differences between the SIR model and the SIRV model. The SIRV model considers the effect of vaccination which helps explain the later stages of the ongoing pandemic. The predictive power of the models is also shown giving the students some certainty in the predictions they made for the following months. | Dylan Smith; Kristin Lauro; Dymond Kelly; Joel Fish; Emma Lintelman; David McEwen; Corrin Smith; Max Stecz; Tharushi Ambagaspitiya; Jixin Chen | Physical Chemistry; Analytical Chemistry; Chemical Education; Chemical Kinetics | CC BY 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626731f0ef2ade18543d643b/original/teaching-undergraduate-physical-chemistry-lab-with-kinetic-analysis-of-covid-19-in-the-united-states.pdf |
60c745abbb8c1aef853da713 | 10.26434/chemrxiv.10093610.v1 | Supramolecular Polymerization Provides Non-Equilibrium Product Distributions of Imine-Linked Macrocycles | Supramolecular polymerization of imine-linked macrocycles has been coupled to dynamic imine bond exchange within a series of macrocycles and oligomers. In this way, macrocycle synthesis is driven by supramolecular assembly, either into small aggregates supported by π-π interactions, or high-aspect ratio nanotubes stabilized primarily by electrostatic and solvophobic interactions. For the latter, supramolecular polymerization into nanotubes restricts imine exchange, thereby conferring chemical stability to the assemblies and their constituent macrocycles. Competition in the formation and component exchange among macrocycles favored pyridine-2,6-diimine-linked species due to their rapid synthesis, thermodynamic stability, and assembly into high-aspect ratio nanotubes under the reaction conditions. In addition, the pyridine-containing nanotubes inhibit the formation of similar macrocycles containing benzene-1,3-diimine-linkages, presumably by disrupting their assembly and templation. Finally, we exploit rapid imine exchange within weak, low-aspect ratio macrocycle aggregates to carry out monomer exchange reactions to macrocycles bearing pyridine moieties. Once a pyridine-containing dialdehyde has exchanged into a macrocycle, the macrocycle becomes capable of nanotube formation, which dramatically slows further imine exchange. This kinetic trap provides chemically diverse macrocycles that are not attainable by direct synthetic methods. Together these findings provide new insights into coupling supramolecular polymerization and dynamic covalent bond-forming processes and leverages this opportunity to target asymmetric nanotubes. We envision these findings spurring further research efforts in the synthesis of nanostructures with designed and emergent properties. | Michael Strauss; Austin Evans; Ioannina Castano; Rebecca Li; William Dichtel | Physical Organic Chemistry; Supramolecular Chemistry (Org.); Aggregates and Assemblies; Nanostructured Materials - Materials; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745abbb8c1aef853da713/original/supramolecular-polymerization-provides-non-equilibrium-product-distributions-of-imine-linked-macrocycles.pdf |
640cbe92b5d5dbe9e81abe36 | 10.26434/chemrxiv-2023-w5tgk | Overall controlling factor in R1-R2-D reactions-diffusion phenomena in two-reactions-in-series systems for selectivity enhancement | The secondary internal effectiveness factor in a two-reaction-in-series system (A + B -> C + D, C + B -> E+F) can be above unity for positive-order reaction kinetics. While the controlling factor in the reaction-diffusion phenomenon for the first reaction can be determined using the Weisz criterion based on the value of the primary internal effectiveness factor, the criteria to assign the secondary effectiveness factor that is above unity do not exist yet, making difficult the development of determinable overall controlling factors in the R1-R2-D phenomena in the two-reaction-in-series system. Here, using a two-step methanol oxidation reaction as a case study, we combined an analytically derived criterion for R1-R2 phenomenon with the Weisz criterion for R1-D phenomenon to allow the development of assignment criteria for four overall controlling factors. The overall assignment criteria are found to be dependent on the internal effectiveness factors , as well as the rate of the individual reactions at the catalyst surface. When the assignments criteria are re-decomposed using assignable criteria that are based on only the two internal effectiveness factors, a child component criterion is confirmed to satisfy the overall assignment criteria. Based on the sensitivity of the overall controlling factor with respect to the reaction temperature and catalyst size, the selectivity of the formaldehyde intermediate species in methanol oxidation reaction can be enhanced at high reaction temperature when catalysts are specifically designed to enhance the rate of formaldehyde formation (rate of the first reaction). However, CO formation (the rate of the second reaction) needs to be suppressed to enhance selectivity towards formaldehyde at moderately low temperature. This reaction-diffusion theoretical framework provides guidance for the development of highly selective catalyst for two-reactions-in-series systems and can be extended for higher-number multiple reactions in series and in parallel. | Musa Najimu; Lateef Kareem; Sagir Adamu; Kandis Gilliard-AbdulAziz | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640cbe92b5d5dbe9e81abe36/original/overall-controlling-factor-in-r1-r2-d-reactions-diffusion-phenomena-in-two-reactions-in-series-systems-for-selectivity-enhancement.pdf |
66ac55fcc9c6a5c07ac8a598 | 10.26434/chemrxiv-2024-fds9x | Theoretical exploration of 4π-Photocyclization Mechanism of α-Tropone Derivatives | In this study, we employed ab initio methods to investigate the 4π-photocyclization process of substituted α-tropones. Our findings suggest that the initial stages of this reaction occur from low-energy excited states such as S2 and S3, as the barriers in higher-energy excited states are prohibi-tively high. Additionally, we observed that the presence of acid catalysts or substitution of tro-pones with electron-donating groups reduces the energy barriers. Regarding the formation of bicy-clo[3.2.0]hepta-3,6-dien-2-one derivatives, both T1/S0 and S1/S0 crossings were identified as plau-sible pathways for this deactivation process. Specifically, electron-donating groups on the tro-pones promote degeneracy between S1 and S0 states during the return to the ground state. Moreo-ver, T1/S0 crossing systems were consistently observed across all investigated scenarios. | Cristian Guerra; Yeray A. Rogriguez-Nuñez; Manuel Taborda-Martinez; Mitchell Bacho; Rafael Miranda-Pastrana; Adolfo Ensuncho | Physical Chemistry; Organic Chemistry; Photochemistry (Org.); Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ac55fcc9c6a5c07ac8a598/original/theoretical-exploration-of-4-photocyclization-mechanism-of-tropone-derivatives.pdf |
63127c2449042a456ec9fa4c | 10.26434/chemrxiv-2022-kqmfc | An Alternative Strategy for Spectral Tuning of Flavin-binding Fluorescent Proteins | iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin’s C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin’s N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation in iLOV results in a slight change in absorption and a 4-8 nm redshift in the fluorescence relative to iLOV, in good agreement with the computational prediction. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red-shifting may be achieved by bringing the side chain closer to the cofactor. | Mohammad Pabel Kabir; Daniel Ouedraogo; Yoelvis Orozco-Gonzalez; Giovanni Gadda; Samer Gozem | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biochemistry; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63127c2449042a456ec9fa4c/original/an-alternative-strategy-for-spectral-tuning-of-flavin-binding-fluorescent-proteins.pdf |
639ed629e9d0fdadc3213b52 | 10.26434/chemrxiv-2022-vgr23 | Benzylic C-H Arylation with Dicyanoarenes via Convergent Paired-Electrolysis | We describe the convergent paired electrolysis of methylarene derivatives and 1,4-dicyanoarenes to perform the arylative functionalization of a benzylic C(sp3)-H bond to form 1,1-biarylmethane derivatives which motif is found in several drugs and biologically active compounds. This electrochemical process proceeds via the coupling of a benzylic radical and a 1,4-dicyanoarene radical anion to form the desired C-C bond followed by elimination of cyanide anion which woud be trapped as a cyanhydrin by an aldehyde. These radical species are produced by respectively oxidation of the benzylic substrate at the anode and reduction of the dicyanoarene at the cathode. One of the key challenge that we overcame is to avoid the formation of overoxidized coupling products at the bisbenzylic position of the biarylmethane products obtained. | Shanyu Tang; Guillaume Vincent | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639ed629e9d0fdadc3213b52/original/benzylic-c-h-arylation-with-dicyanoarenes-via-convergent-paired-electrolysis.pdf |
62628aa5d048edcdf94d1171 | 10.26434/chemrxiv-2021-gk1gt-v2 | In silico drug repurposing of anticancer drug 5-FU and analogues against SARS-CoV-2 main protease: molecular docking, pharmacokinetics and chemical reactivity | Since the last COVID-19 outbreak, several approaches have been put forward to quickly tackle this global calamity. One of the strategies employed by a handful of researchers is the so-called drug repurposing, which consists in finding new therapeutic uses for approved drugs. Following the same paradigm, we report in the present study an investigation of the potential inhibitory activity of 5-FU and nineteen of its analogues against the SARS-CoV-2 main protease in the framework of molecular docking. This work also discusses the profile of druggability of the best binding candidates as well as their inherent reactivity using ADMET and quantum mechanics methods respectively. From the calculations performed, four candidates show promising results with respect to the binding affinity to the target protease, 3CLpro, the therapeutic profile of druggability and safety. Molecular electrostatic potential, Fukui functions and frontier molecular orbitals are scrutinized to discuss the global and local reactivity of these candidates. Further in-vitro and in-vivo investigations are needed to shed light on the possible mechanism of pharmacological action of the proposed ligands. | Aristote Matondo; Washington Dendera; Bienfait K. Isamura; Koto-te-Nyiwa Ngbolua; Hilaire V.S. Mambo; Mayaliwa Muzomwe; Virima Mudogo | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62628aa5d048edcdf94d1171/original/in-silico-drug-repurposing-of-anticancer-drug-5-fu-and-analogues-against-sars-co-v-2-main-protease-molecular-docking-pharmacokinetics-and-chemical-reactivity.pdf |
6654450391aefa6ce1183331 | 10.26434/chemrxiv-2024-lf3jn-v2 | Analytical Model for the Molecular Ionization Energy in an External Electric Field | A model for the molecular ionization energy in an applied electric field is presented based on a perturbation expansion in the electric field. The leading term arises from the Frenkel approach, which is the same for all molecules, normally used in the Poole-Frenkel model for the conductivity in an electric field. For a set of test molecules, the results are of comparable quality to previous results using constrained density functional theory. It is concluded that the Frenkel term is dominant and sufficient at relatively low fields and that the dipole and polarizability terms, the leading terms dependent on the properties of the individual molecule, give a significant contribution only at high fields and for relatively large molecules. Since the presented model is analytical, quantum chemical calculations are avoided for a variety of electric field strengths and molecular orientations, and the model can therefore be applied directly in coarse-grained models for electronic processes in dielectric condensed phases. | Per-Olof Åstrand | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Theory - Computational; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654450391aefa6ce1183331/original/analytical-model-for-the-molecular-ionization-energy-in-an-external-electric-field.pdf |
61d4db7cf52bc4a520d826a5 | 10.26434/chemrxiv-2022-s5j9h | Kinetic Monte Carlo Modeling of Graphene Sheet Growth During CVD | Graphene is a material of key interest across several research fields. Bulk graphene synthesis, however, has long remained a challenge for larger-scale projects and real-world manufacturability. This work seeks an improved understanding of graphene sheet growth via computational modeling, with the objective of maximizing grain size. To this end, the kinetic Monte Carlo method is used to simulate chemical vapor deposition under various configurations of carbon flow and graphene seeding. Ultimately, both quantitative and qualitative results are obtained to shed light on graphene growth mechanisms, with insights into real-world synthesis and future computational models. | Hironori Kondo | Theoretical and Computational Chemistry; Nanoscience; Nanofabrication; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61d4db7cf52bc4a520d826a5/original/kinetic-monte-carlo-modeling-of-graphene-sheet-growth-during-cvd.pdf |
6250253885bc59fcb2801af1 | 10.26434/chemrxiv-2022-k4f4w | Enhanced Exosome Immunodetection by Integration of Silica Inverse Opal Architectures as Nanostructured Sensors in Quartz Crystal Microbalance with Dissipation Monitoring | Exosomes are nanosized circulating vesicles that contain biomarkers considered promising for early diagnosis within neurology, cardiology and oncology. Recently, acoustic wave biosensors, in particular based on quartz crystal microbalance with dissipation monitoring (QCM-D), have emerged as a sensitive, label-free, and selective exosome characterisation platform. A rational approach to further improving sensing detection limits relies on the nanostructuration of the sensor surfaces. To this end, inorganic inverse opals (IOs) derived from colloidal self-assembly present a highly tuneable and scalable nanoarchitecture of suitable feature sizes and surface chemistry. This work systematically investigates their use in 2D and 3D for enhanced QCM-D exosome detection. Precise tuning of the architecture parameters delivered improvements in detection performance to sensitivities as low as 6.24 x 10^7 particles/ml. Our findings emphasise that attempts to enhance acoustic immunosensing via increasing the surface area by 3D nanostructuration need to be carefully analyzed in order to exclude solvent and artefact entrapment effects. Moreover, the use of 2D nanostructured electrodes to compartmentalise analyte anchoring presents a particularly promising design principle. | Jugal Suthar; Alberto Alvarez-Fernandez; Alaric Taylor; Gareth R Williams; Stefan Guldin | Materials Science; Analytical Chemistry; Nanoscience; Nanostructured Materials - Materials; Analytical Chemistry - General; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6250253885bc59fcb2801af1/original/enhanced-exosome-immunodetection-by-integration-of-silica-inverse-opal-architectures-as-nanostructured-sensors-in-quartz-crystal-microbalance-with-dissipation-monitoring.pdf |
65b0f06466c1381729298531 | 10.26434/chemrxiv-2024-gk620 | Sodium Triflate Water-in-Salt Electrolyte in Advanced Battery Applications: A First-principles Based Molecular Dynamics Study | Offering a compelling combination of safety and cost-effectiveness, Water-in-Salt (WiS) electrolytes have emerged as promising frontiers in energy storage technology. Still, there is a strong demand for research and development efforts to make these electrolytes ripe for commercialization. Here we present a first-principles based molecular dynamics study addressing in detail the properties of a sodium triflate WiS electrolyte for Na-ion batteries. We have developed a workflow based on a machine learning (ML) potential derived from ab initio molecular dynamics simulations. As ML potentials are typically restricted to the interpolation of the data points of the training set and have hardly any predictive properties, we subsequently optimize a classical force field based on physics principles to ensure broad applicability and high performance. Performing and analysing detailed molecular dynamics simulations, we identify several very promising properties of the sodium triflate as a WiS electrolyte, but also indicate some potential stability challenges associated with its use as a battery electrolyte. | Majid Rezaei; Sung Sakong; Axel Groß | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Machine Learning; Electrochemistry - Mechanisms, Theory & Study; Statistical Mechanics | CC BY NC 4.0 | CHEMRXIV | 2024-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b0f06466c1381729298531/original/sodium-triflate-water-in-salt-electrolyte-in-advanced-battery-applications-a-first-principles-based-molecular-dynamics-study.pdf |
60c73d4f567dfe3aa9ec35f0 | 10.26434/chemrxiv.5330794.v2 | Excitonic Coupled-cluster Theory: Part II, Electronic Hamiltonian | <div>
<div>
<div>Generic equations were presented in a companion article for a variant of coupled-cluster theory that operates directly on fragment excitation coordinates (excitonic CC),
and its promise was illustrated on model systems. Three conditions were asserted for the
excitonic CC framework to be valid and practicable; these concerned (1) the existence of
an appropriate fragment-decomposed complete basis, (2) the existence of single-fragment
fluctuation operators referencing that basis, and (3) the existence and complexity of the
Hamiltonian resolved in terms of strings of those operators. In this article, we take
on these assertions specificially for fragment-decomposed electronic systems, proceeding
ultimately to explicit recipes for resolving the Hamiltonian in a systematically improvable
manner. Though framed in the context of excitonic CC theory, the derivations here are
applicable to the general inter-fragment electron-exchange problem. The number of terms
in the exactly transformed Hamiltonian formally scales quartically, but this can be reduced
to quadratic within an arbitrary error tolerance. The vast majority of these terms are
outside of exchange range and may be decomposed efficiently in terms of single-fragment
information.
</div>
</div>
</div> | Anthony Dutoi; Yuhong Liu | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2017-08-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d4f567dfe3aa9ec35f0/original/excitonic-coupled-cluster-theory-part-ii-electronic-hamiltonian.pdf |
631ed9a103e27d16bcd19505 | 10.26434/chemrxiv-2022-wt3fb | Predicting mechanochemical reactivity with the method of Constrained Geometries Simulate External Force | Mechanochemistry is a fast-developing field of interdisciplinary research with a growing number of applications. Therefore, many theoretical methods have been developed to quickly predict the outcome of mechanically induced reactions. Constrained geometries simulate External Force (CoGEF) is one of the pioneering methods in this field. It is easily implemented and can be conducted with most DFT codes. However, recently, we observed totally different predictions for model systems of epoxy resins in different conformations and with different density functionals. To better understand the conformational and functional dependence in typical CoGEF calculations we present a systematic evaluation of the CoGEF method for different model systems covering homolytic and heterolytic bond cleavage reactions, electrocyclic ring opening reactions and scission of non-covalent interactions in hydrogen-bond complexes. From our calculations we observe that many mechanochemical descriptors strongly depend on the functional used, however, a systematic trend exists for the relative maximum Force. In general, we observe that the CoGEF procedure is forcing the system to high energetic regions on the molecular potential energy profiles, which can lead to unexpected and uncorrelated predictions of mechanochemical reactions. This is questioning the true predictive character of the method. | Christian R. Wick; Ece Topraksal; David M. Smith; Ana-Sunčana Smith | Theoretical and Computational Chemistry; Polymer Science; Organic Polymers; Polymer chains; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631ed9a103e27d16bcd19505/original/predicting-mechanochemical-reactivity-with-the-method-of-constrained-geometries-simulate-external-force.pdf |
66d36b3af3f4b05290c05709 | 10.26434/chemrxiv-2024-wtmf0 | Treatment of Glioblastoma tumors using photoactivated chemotherapy | Glioblastoma multiforme (GBM) is highly aggressive and difficult to treat, necessitating the development of new therapies. Photoactivated chemotherapy (PACT) has emerged as a promising method, where biologically active compounds are “caged” into inactive prodrugs, and re-activated by visible light irradiation at the tumor site, potentially offering more patient-friendly treatments without compromising antitumor efficacy. In this study, we investigated the activity of a series of ruthenium-based PACT compounds [1](PF6)2-[3](PF6)2 in U-87MG glioblastoma cells, a common in vitro model for glioblastoma, and the safety of these compounds in SH-SY5Y cells, which is a recognized model for healthy neurons. The action of these compounds was compared to that of Donepezil, a known acetylcholinesterase inhibitor used in the treatment of brain disorders. Promising light-activated anticancer activity was observed in U-87MG cells for [3](PF6)2 while the two other compounds were inactive([1](PF6)2) or non-activated ([2](PF6)2). In non-cancerous SH-SY5Y cells the light-activated complexes surprisingly enhanced cell proliferation in a manner similar to Donepezil. While significantly higher amounts of Ru were found in SH-SY5Y cells upon green light irradiation, in particular for [3](PF6)2, this cell proliferation effect was independent from ruthenium cellular uptake. Given the importance of Ca2+ levels for the normal function of neurons, we also examined Ca2+ accumulation upon treatment with ruthenium and light. Increased Ca2+ uptake was found in cells treated with inactivated [1](PF6)2 , [2](PF6)2 , or with green light only. Upon treatment with [3](PF6)2 intracellular Ca2+ content was not changed in the dark but it significantly increased upon light activation, without observable sign of cell death. The structure-dependent action of the ruthenium compounds on Ca2+ homeostasis suggested a docking studies with the NMDA, serotonin, and AMPA receptors, which all act on calcium levels. Docking revealed that [3](PF6)2 interacts with the NMDA receptor, which might be responsible for the enhanced Ca2+ uptake upon light activation in SH-SY5Y cells. Overall, although [3](PF6)2 was phototoxic to U-87MG cells, the combination of this prodrug and green light irradiation enhanced the survival of neuronal-like cells and increased intracellular Ca2+ levels, probably via interaction with the NMDA receptor. These findings highlight the potential of ruthenium-based PACT prodrugs in treating glioblastoma cells while maintaining the viability of nearby, healthy neuronal cells | Sina Katharina Goetzfried; Matthijs L. A. Hakkennes; Anja Busemann; Sylvestre Bonnet | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Inorganic Chemistry; Bioinorganic Chemistry; Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2024-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d36b3af3f4b05290c05709/original/treatment-of-glioblastoma-tumors-using-photoactivated-chemotherapy.pdf |
670c192f51558a15eff5c275 | 10.26434/chemrxiv-2024-w4dtr | Generation of connections between protein sequence space and chemical space to enable a predictive model for biocatalysis | The application of biocatalysis in synthesis has the potential to offer dramatically streamlined routes toward target molecules, exquisite and tunable catalyst-controlled selectivity, as well as more sustainable processes. Despite these advantages, biocatalytic synthetic strategies can be high risk to implement. Successful execution of these approaches requires identifying an enzyme capable of performing chemistry on a specific intermediate in a synthesis which often calls for extensive screening of enzymes and protein engineering. Strategies for predicting which enzyme is most likely to be compatible with a given small molecule have been hindered by the lack of well-studied biocatalytic reactions. The under exploration of connections between chemical and protein sequence spaces constrains navigation between these two landscapes. Herein, this longstanding challenge is overcome in a two-phase effort relying on high throughput experimentation to populate connections between substrate chemical space and biocatalyst sequence space, and the subsequent development of machine learning models that enable the navigation between these two landscapes. Using a curated library of α-ketoglutarate-dependent non-heme iron (NHI) enzymes, the BioCatSet1 dataset was generated to capture the reactivity of each biocatalyst with >100 substrates. In addition to the discovery of novel chemistry, BioCatSet1 was leveraged to develop a predictive workflow that provides a ranked list of enzymes that have the greatest compatibility with a given substrate. To make this tool accessible to the community, we built CATNIP, an open access web interface to our predictive workflows. We anticipate our approach can be readily expanded to additional enzyme and transformation classes, and will derisk the application of biocatalysis in chemical synthesis. | Alexandra Paton; Daniil Boiko; Jonathan Perkins; Nicholas Cemalovic; Thiago Reschützegger; Gabe Gomes; Alison Narayan | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670c192f51558a15eff5c275/original/generation-of-connections-between-protein-sequence-space-and-chemical-space-to-enable-a-predictive-model-for-biocatalysis.pdf |
6255ff70d048edc6f140c152 | 10.26434/chemrxiv-2022-s7thf | Redox-triggerable Luciferin-Bioinspired Hydrogels as Injectable and Cell-encapsulating Matrices | Over the past few decades there has been a great interest in developing smart hydrogels that are stimuli-responsive, due to their ability to respond to variations caused by external stimuli. These materials are exploited for biomedical applications such as biosensors, injectable scaffolds, drug delivery and tissue engineering. Recently, our group reported firefly-inspired hydrogel matrices for 3D cell culture. This platform exhibited certain advantages like rapid gelation rate and tunability of mechanical and biological properties. However, this firstly reported system did not allow for fine control of the gelation onset because the crosslinking reaction started as soon as the two precursors were mixed. Moreover, one of its precursors demonstrated poor storage stability in aqueous solution. These limitations restrict its application as injectable matrices. In this article, we endow the luciferin-inspired hydrogels with redox-triggering capability, to overcome the limitations of the previous system and to widen its application range. We achieve this goal by introducing protected macromers as hydrogel polymeric precursors that can be activated in the presence of a mild reductant, to trigger gel formation in situ with high degree of control. We demonstrate that the regulation of intrinsic (e.g., structure of protecting group, reductant type) and extrinsic (e.g., pH, temperature) parameters of the triggering reaction can be used to modulate key materials properties. This novel upgraded redox-triggerable system enables precise control over gelation onset and kinetics, thus facilitating its utilization as injectable hydrogel without negatively impacting its cytocompatibility. Our findings expand the current toolkit of chemically-based stimuli-responsive hydrogels. | Minye Jin; Alisa Gläser; Julieta I. Paez | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Hydrogels; Polymerization kinetics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6255ff70d048edc6f140c152/original/redox-triggerable-luciferin-bioinspired-hydrogels-as-injectable-and-cell-encapsulating-matrices.pdf |
60c74ea40f50db7a1239728c | 10.26434/chemrxiv.12780482.v1 | Primary Prevention of Outdoor Lead (Pb) Exposure on Residential Properties in Rochester, NY, and Potential of a Sustainable Remediation Solution Involving the Reuse of Drinking Water Treatment Residual (WTR), a Waste Generated Daily by the City | Prevention of lead (Pb) poisoning is imperative for public health and environmental justice. This study presents both assessment and affordable mitigation of Pb exposure risks at individual yard scales, which are critically important to homeowners to attain primary prevention, but not yet explored thoroughly.<br /> | Padmini Das; Stephanie Zamule; Deanna R. Bolduc; Michelle J. Patton; Meghan L. Mendola; Julia Penoyer; Benjamin Lyon; Hanna M. Chittenden; Alexander C. Hoyt; Cassandra V. Dupre; Jack J. Wessel; Ivan Gergi; Charlotte V. Buechi; Jane A. Shebert; Mandeep Chauhan; David Giacherio; Jacob C. Phouthavong-Murphy | Environmental Science; Geochemistry; Soil Science; Wastes | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ea40f50db7a1239728c/original/primary-prevention-of-outdoor-lead-pb-exposure-on-residential-properties-in-rochester-ny-and-potential-of-a-sustainable-remediation-solution-involving-the-reuse-of-drinking-water-treatment-residual-wtr-a-waste-generated-daily-by-the-city.pdf |
65f2b8519138d231616f1145 | 10.26434/chemrxiv-2024-pddc0 | Singlet Oxygen Insertion into Hydrocarbons: The
Role of First- and Second-Generation Pathways in
Astronomically Relevant Ices | Complex organic molecules are widespread in different areas of the interstellar medium, including cold areas such as molecular clouds where chemical reactions occur in ice. The underlying molecular mechanisms responsible for the observed rich chemistry are still not understood. O(1D) atom reactions provide a pathway for chemical complexity even in cold areas, as the reactions are typically barrierless, and O(1D) is a photofragmented product of astronomically relevant ices such as CO2. In this work, we use quantum chemistry methods to model reactions in astronomical ices containing oxygen with small C1 and C2 hydrocarbons in the presence of UV radiation. Our results demonstrate that the underlying molecular mechanism of reactions in ice includes the oxygen insertion reaction (first-generation reactions), photofragmentation of products and radical recombination reactions (second-generation reactions). The mechanism explains the formation of formaldehyde in methane ice, acetaldehyde in ethane ice, CO in acetylene ice and the consumption of alcohol in all systems. This work demonstrates the important role of first- and second-generation reactions in the unique chemical processes in astronomical ices; where basic molecular building blocks are fragmented and recombined into new molecules resulting in enhanced chemical complexity. | Amit Daniely; Alon Zamir; Helen R. Eisenberg; Ester Livshits; Elettra Piacentino; Jennifer B. Bergner; Karin Oberg; Tamar Stein | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Photochemistry (Physical Chem.); Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f2b8519138d231616f1145/original/singlet-oxygen-insertion-into-hydrocarbons-the-role-of-first-and-second-generation-pathways-in-astronomically-relevant-ices.pdf |
66415bb6418a5379b01adb7b | 10.26434/chemrxiv-2024-60m8b | Promoting effect of Pd nanoparticles on SrTi0.8Mn0.2O3 in the reverse water-gas shift reaction via the Mars–van Krevelen mechanism | The reverse water-gas shift (RWGS) reaction serves as a critical pathway for converting CO2 into diverse chemicals. The Mars–van Krevelen (MvK) mechanism, which leverages lattice oxygen as the oxidant and oxygen vacancies as reductants, offers an alternative catalytic strategy for the selective RWGS reaction. While Mn-substituted SrTiO3 (i.e., SrTi0.8Mn0.2O3) has been shown to promote the RWGS reaction selectively via the MvK mechanism, achieving a sufficient conversion of CO2 necessitates elevated temperatures. This study investigated the effect of Pd-loaded SrTi0.8Mn0.2O3 on the activation of adsorbed H2 molecules, which generated oxygen vacancies and enhanced CO2 conversion. Notably, 1.0 wt% Pd-loaded SrTi0.8Mn0.2O3 yielded 13.4% of CO at 673 K, whereas pristine SrTi0.8Mn0.2O3 and Pd-loaded SrTiO3 yielded negligible or minimal amount of CO. Hydrogen temperature-programmed reduction and X-ray absorption spectroscopy measurements revealed that Pd promoted the formation of oxygen vacancies via both thermodynamic and kinetic mechanisms. Fourier transform infrared spectroscopy and kinetic studies revealed that the RWGS reaction over Pd-loaded SrTi0.8Mn0.2O3 proceeded primarily via the MvK mechanism with a partial contribution from the Langmuir–Hinshelwood mechanism. This study underscores the effectiveness of combining metal and MvK-type catalysts to enhance the efficiency of the RWGS reaction. | Minori Kobayashi; Shimpei Naniwa; Hiroki Matsuo; Shoji Iguchi; Tsunehiro Tanaka; Kentaro Teramura | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66415bb6418a5379b01adb7b/original/promoting-effect-of-pd-nanoparticles-on-sr-ti0-8mn0-2o3-in-the-reverse-water-gas-shift-reaction-via-the-mars-van-krevelen-mechanism.pdf |
645513871ca6101a45d39ce0 | 10.26434/chemrxiv-2023-cghv4 | Combining multi-modal non-destructive techniques to investigate ageing and orientation effects in automotive Li-ion pouch cells | As the electrification of the transport sector progresses, an abundance of lithium-ion batteries inside electric vehicles (EVs) will reach their end-of-life (EoL). The cells inside battery packs will age differently depending on multiple factors during their use. Currently, there is limited publicly available research on the degradation of the individual cells recovered from real-world EV usage. Once they have been recovered from the vehicle, large-format pouch cells are challenging to characterise, measure their internal structure and determine state-of-health (SoH). Here, large-format (261 x 216 x 7.91 mm) Nissan Leaf cells are harvested from an EV and four complementary non-destructive techniques are used to distinguish the ageing of cells arranged in varying orientations and locations within the pack. The measurement suite includes infrared thermography, ultrasonic mapping, X-ray computed tomography, and synchrotron X-ray diffraction, and represents a unique combination of characterisation techniques. We found that each of the non-destructive diagnostic techniques corroborated each other yet provide different complementary insights. The influence of orientation and location of the cells is significant, with the rotated/vertically aligned cells differing significantly from the flat/horizontally aligned cells in mode and degree of ageing. These insights provide new information on cell degradation that can help to influence pack design and illustrates how rapid and relatively inexpensive technology can provide sufficient information for practical assessment compared to costly synchrotron studies. Such an approach can inform decision support at EoL and more efficient battery production reducing the wastage of raw materials. | Arthur Fordham; Zoran Milojevic; Emily Giles; Wenjia Du; Rhodri E. Owen; Stefan Michalik; Philip Chater; Prodip Das; Pierrot S. Attidekou; Simon M. Lambert ; Phoebe K. Allan; Peter R. Slater; Paul A. Anderson; Rhodri Jervis; Paul R. Shearing; Dan J. L. Brett | Inorganic Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Electrochemistry; Energy Storage; Power | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645513871ca6101a45d39ce0/original/combining-multi-modal-non-destructive-techniques-to-investigate-ageing-and-orientation-effects-in-automotive-li-ion-pouch-cells.pdf |
62272df3ce899bea2db03e8e | 10.26434/chemrxiv-2022-lqjqr | Transition Metal-catalyzed C-H /C-C Activation and Coupling with 1, 3-diyne | This review focuses on providing a broad overview of the recent developments in the field of transition metal-catalyzed C-H bond activation and coupling with 1,3-diyne for assembling alkynylated heterocycles and bis-heterocycles. In recent years the use of 2π-unsaturated units as coupling partners for the synthesis of heterocycles through C-H bond activation and an-nulation sequence has received immense attention. Among the unsaturated units employed for assembling heterocycles, the use of 1,3-diynes has garnered significant attention due to its ability in rendering the straightforward bis-heterocycles. Earlier methods employed to assemble bis-heterocycle include the use of preformed and pre-functionalized heterocycles via transi-tion metal-catalyzed coupling reactions. The expensive pre-functionalized halo-heterocycles and sensitive & expensive heterocyclic metal reagents limit its use. However, the transition metal-catalyzed C-H activation obviates the need for expensive heterocyclic metal reagents and pre-functionalized halo-heterocycles. The C-H bond activation strategy makes use of C-H bonds as functional groups for effecting the transformation. This renders the overall synthetic sequence both step and costs economic. Hence, this strategy of C-H activation and subsequent reaction with 1,3-diyne is useful for the larger-scale synthesis of chemicals in the pharmaceutical industry. Despite these advances, there is still the possibility of exploration of earth-abundant, and cost-effective first-row transition metals (Ni, Cu, Mn. Fe, etc.) for the synthesis of bis-heterocycles. Moreover, the Cp* ligand free, simple metal salt mediated synthesis of bis-heterocycles is also less explored. Thus, more exploration of reaction conditions for the Cp* free synthesis of bis-heterocycles is called for. We hope this review will inspire scientists to explore the unexplored domains. | Bedadyuti Vedvyas Pati; Nitha Nahan Puthalath; Shyam Kumar Banjare; Tanmayee Nanda; Ponneri C. Ravikumar | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62272df3ce899bea2db03e8e/original/transition-metal-catalyzed-c-h-c-c-activation-and-coupling-with-1-3-diyne.pdf |
60c744f1469df45d40f433f5 | 10.26434/chemrxiv.9925145.v1 | Reductive Cleavage of Secondary Sulfonamides: Converting Terminal Functional Groups into Versatile Synthetic Handles | Sulfonamides are pervasive in drugs and agrochemicals,
yet are typically considered as terminal functional groups rather than
synthetic handles. To enable the general late-stage functionalization of
secondary sulfonamides, we have developed a mild and general method to
reductively cleave the N-S bonds of sulfonamides to generate sulfinates and
amines, components which can further react <i>in-situ</i>
to access a variety of other medicinally relevant functional groups. The
utility of this platform is highlighted by the selective manipulation of
several complex bioactive molecules. | Patrick Fier; Suhong Kim; Kevin M. Maloney | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744f1469df45d40f433f5/original/reductive-cleavage-of-secondary-sulfonamides-converting-terminal-functional-groups-into-versatile-synthetic-handles.pdf |
60c73edb842e652464db19b9 | 10.26434/chemrxiv.7159682.v1 | Evolutionarily Conserved Allosteric Communication in Protein Tyrosine Phosphatases | Protein tyrosine phosphatases (PTPs) are an important class of regulatory enzymes that exhibit aberrant activities in a wide range of diseases. A detailed mapping of allosteric communication in these enzymes could, thus, reveal the structural basis of physiologically relevant—and, perhaps, therapeutically informative—perturbations (i.e., mutations, post-translational modifications, or binding events) that influence their catalytic states. This study combines detailed biophysical studies of protein tyrosine phosphatase 1B (PTP1B) with bioinformatic analyses of the PTP family to examine allosteric communication in PTPs. Results of X-ray crystallography, molecular dynamics simulations, and sequence-based statistical analyses indicate that PTP1B possesses a broadly distributed allosteric network that is evolutionarily conserved across the PTP family, and findings from kinetic studies and mutational analyses show that this network is functionally intact in sequence-diverse PTPs. The allosteric network resolved in this study reveals new sites for targeting allosteric inhibitors of PTPs and helps explain the functional influence of a diverse set of disease-associated mutations. | Michael K. Hjortness; Laura Riccardi; Akarawin Hongdusit; Peter
H. Zwart; Banumathi Sankaran; Marco De Vivo; Jerome Fox | Biochemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edb842e652464db19b9/original/evolutionarily-conserved-allosteric-communication-in-protein-tyrosine-phosphatases.pdf |
651713f1ade1178b245e6e88 | 10.26434/chemrxiv-2023-qwmb2-v4 | Life cycle comparison of industrial-scale lithium-ion battery recycling and mining supply chains | Recycling lithium-ion batteries (LIBs) can supplement existing supplies of critical materials and improve the environmental sustainability of LIB supply chains. In this work, environmental impacts (greenhouse gas emissions, water consumption, energy consumption) of industrial-scale production of battery-grade cathode materials from used LIBs are compared to the environmental impacts of conventional mining supply chains. Refining mixed-stream LIBs into battery-grade materials reduces these environmental impacts by at least 59%. Recycling batteries to mixed metal products instead of discrete salts further reduces environmental impacts. Electricity consumption is identified as the principal contributor to all LIB recycling environmental impacts, and different electricity sources can change greenhouse gas emissions up to eight times. Supply chain steps that precede refinement (material extraction and transport) contribute marginally to the environmental impacts of circular LIB supply chains (<5%), but are more significant in conventional supply chains (31%). This analysis disaggregates conventional and circular steps based on material extraction, transport, and industrial refinement operations; provides important insights for advancing sustainable LIB supply chains; and informs optimization of industrial-scale environmental impacts for emerging battery recycling efforts. | Michael Machala; Xi Chen; Samantha Bunke; Gregory Forbes; Akarys Yegizbay; Jacques de Chalendar; Inês Azevedo; Sally Benson; William Tarpeh | Energy; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651713f1ade1178b245e6e88/original/life-cycle-comparison-of-industrial-scale-lithium-ion-battery-recycling-and-mining-supply-chains.pdf |
60c746874c89191cc3ad2b76 | 10.26434/chemrxiv.11342471.v1 | Water-Compatible Cycloadditions of Oligonucleotide-Conjugated Strained Allenes for DNA-Encoded Library Synthesis | DNA-encoded libraries of small molecules are being explored extensively for the identification of binders in early drug-discovery efforts. Combinatorial syntheses of such libraries require water- and DNA-compatible reactions, and the paucity of these reactions currently limit the chemical features of resulting barcoded products. The present work introduces strain-promoted cycloadditions of cyclic allenes under mild conditions to DNA-encoded library synthesis. Owing to distinct cycloaddition modes of these reactive intermediates with activated olefins, 1,3-dipoles and dienes, the process generates diverse molecular architectures from a single precursor. The resulting DNA-barcoded compounds exhibit unprecedented ring and topographic features—related to elements found to be powerful in phenotypic screening. | Matthias V. Westphal; Liam Hudson; Jeremy W. Mason; Frédéric J. Zécri; Karin Briner; Stuart L. Schreiber | Combinatorial Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746874c89191cc3ad2b76/original/water-compatible-cycloadditions-of-oligonucleotide-conjugated-strained-allenes-for-dna-encoded-library-synthesis.pdf |
60c74da0bdbb894456a39a15 | 10.26434/chemrxiv.12642803.v1 | Sulfonamide Directivity Enables Ni-Catalyzed 1,2-Diarylation of Diverse Alkenyl Amines | 1,2-Diarylation of alkenyl sulfonamides with aryl iodides and aryl boronic esters under nickel catalysis is reported. The developed method tolerates coupling partners with disparate electronic properties and substitution patterns. 1,2- and 1,1-Disubstituted alkenes, as well as alkenes distal from the directing group, are all accommodated. Control experiments are consistent with a N–Ni coordination mode of the directing group, which stands in contrast to earlier reports on amide-directed 1,2-diarylation that involve carbonyl coordination. The synthetic utility of the method arises from the dual function of the sulfonamide as both a directing group and masked amine nucleophile. This is highlighted by various product diversifications where complex amine compounds are synthesized in a two-step sequence of <i>N</i>-functionalization and deprotection of the sulfonyl group. | Omar Apolinar; Van Tran; Michael A. Schmidt; Joseph Derosa; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74da0bdbb894456a39a15/original/sulfonamide-directivity-enables-ni-catalyzed-1-2-diarylation-of-diverse-alkenyl-amines.pdf |
60c7598ebb8c1acb813dcc3a | 10.26434/chemrxiv.14707251.v1 | Novel β-Cyclodextrin Functionalized Core-Shell Fe3O4 Magnetic Nanoparticles for the Removal of Toxic Metals from Water | Herein we report the synthesis and characterization of β-CD functionalized core-shell Fe3O4 magnetic nanoparticles which were used as an adsorbent for removal of Lead (II) and Copper (II) ions from aqueous solution. Various characterization techniques including FTIR, TGA analysis, SEM, TEM, X-Ray diffraction patterns (XRD) and nitrogen adsorption- desorption measurements were employed to investigate the properties of the synthesized material. The influence of pH, contact time, metal ion concentration, adsorbent dosage of Lead (II) and Copper (II) ion removal were also studied. The isotherm models for both ions showed a fit to the Langmuir model. Thermodynamic parameters such as enthalpy, entropy and Gibbs free energy were also evaluated and the negative values of ΔH for both Lead (II) and Copper (II) ions indicated the exothermic nature their sorption. | Babak Kaboudin; Torabi Momen; Foad Kazemi; Priyanka Ray | Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Environmental Science; Analytical Chemistry - General; Separation Science; Nanofabrication; Nanostructured Materials - Nanoscience; Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7598ebb8c1acb813dcc3a/original/novel-cyclodextrin-functionalized-core-shell-fe3o4-magnetic-nanoparticles-for-the-removal-of-toxic-metals-from-water.pdf |
651d52358bab5d2055a136b0 | 10.26434/chemrxiv-2023-7kllx | On the traditional medicinal plants and plant derived natural drugs used by indigenous people of Nagaland, India | An ethnobotanical documentation on the medicinal plants used by local people of Nagaland, (North-east India) has been presented here. The study explored 33 plant species (with their local names, indigenous applications, sources/origins, parts of plants used, bioactive compounds present, process of preparing medicines from the plants) belonging to 28 families have been reviewed thoroughly. Some examples are, Catharanthus roseus (Tsuinrinaro, Periwinkle), Acacia pennata (Chakrangaing, Ballikhadira), Adhatoda vasica (Kicharangnaro, Malabar-nut), Ageratum conzyoides (Imchenriza, Billy-goat-weed, /Tropical-white-weed), Alstonia scholaris (Lazarongpang, Blackboard), Rauvolfia serpentina (Per-mozutong, Indian-snakeroot) etc. Plant based drugs are very popular and effective in Nagaland from ancient times but thorough-documentation with scientific-background of effectiveness, active chemical-compounds present, their action-mechanism etc. are still scanty. Such review can be of useful for pharmacologist, phyto-chemists to a broad group of researchers and may lead to discovery of new sources of novel medicines through traditional therapeutic knowledge. | Soching Luikham; Jhimli Bhattacharyya | Biological and Medicinal Chemistry; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651d52358bab5d2055a136b0/original/on-the-traditional-medicinal-plants-and-plant-derived-natural-drugs-used-by-indigenous-people-of-nagaland-india.pdf |
67bdca3381d2151a02ff5d03 | 10.26434/chemrxiv-2025-tnhwp | Tuning Magnetic Anisotropy and Luminescence Thermometry in a Series of Dysprosium Complexes containing β-diimine Ligand | Understanding spin dynamics in molecular systems is critical for developing advanced quantum materials, where optimizing structural parameters plays a pivotal role. Although significant progress has been made in studying the spin dynamics of β-diketone-Dysprosium(III) complexes with α-diimine bidentate ligands, the exploration of β-diimine-based ligands to elucidate the structure-property relationship in spin dynamics remains limited. Here, we report three Dysprosium complexes containing -diimine based bidentate ligands, [Dy(dbm)3(bik-Et)] (1), [Dy(dbm)3(bik-Me)] (2), and [Dy(acac)3(bik-Et)] (3) (dbm = 1,3-diphenyl-1,3-propanedione, acac = acetylacetonate, bik-Et = bis(1-ethyl-1H-imidazol-2-yl)methanone), and bik-Me = bis(1-methyl-1H-imidazol-2-yl)methanone)), which were synthesized and characterized by single crystal X-ray diffraction analysis, spectroscopic, magnetic and theoretical investigations. Structural investigations showed a distorted square antiprism geometry in 1 and 3 and a trigonal bipyramidal geometry in 2 in a DyO6N2 environment. Magnetic studies reveal slow magnetic relaxation behaviour under a zero-applied DC field for all three complexes. Theoretical calculations at the DFT and CASSCF level of theory were carried out to find a better correlation between the electronic structure and magnetism of the reported complexes. Moreover, the variable temperature photoluminescence study of the complexes reveals these complexes performed significantly well in the application of luminescent thermometry. | Sukanya Bagchi; Sakshi Mehta; Sujit Kamilya; Mathieu Rouzières; Radovan Herchel; Mikhail Kiskin; Subrata Ghosh; Abhishake Mondal | Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Magnetism | CC BY 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bdca3381d2151a02ff5d03/original/tuning-magnetic-anisotropy-and-luminescence-thermometry-in-a-series-of-dysprosium-complexes-containing-diimine-ligand.pdf |
6560c405cf8b3c3cd7077a00 | 10.26434/chemrxiv-2023-234d6 | Non-destructive egg breed separation using advanced VOC analytical techniques HSSE-GC-MS, PTR-TOF-MS, and SIFT-MS: assessment of performance and systems’ complementarity | Over the past decade, advanced analytical techniques have been utilized to examine volatile organic compounds (VOCs) in eggs. These VOCs offer valuable insights into factors such as freshness, fertility, the presence of cracks, embryo sex, and breed. In our study, we assessed three mass spectrometry-based systems (headspace sorptive extraction gas chromatography-mass spectrometry; HSSE-GC-MS, proton transfer reaction time-of-flight-mass spectrometry; PTR-TOF-MS; and selected ion flow tube mass spectrometry; SIFT-MS) to analyze and identify VOCs present in intact hatching eggs from three distinct breeds (Dekalb white layer, Shaver brown layer, and Ross 308 broiler). The eggs were sampled on incubation days 2 and 8, to identify VOCs that distinguish breeds irrespective of incubation day. VOC measurements were conducted on 15 eggs per breed by placing them together with PDMS-coated stir bars inside inert Teflon® air sampling bags. After an accumulation period of 2 hours, the headspace was analyzed using PTR-TOF-MS and SIFT-MS, while the VOCs adsorbed onto the stir bars were analyzed using GC-MS for additional compound identification. Partial least squares discriminant analysis (PLS-DA) models were constructed for breed differentiation, and variable selection was performed. As a result, 111 VOCs were identified using HSSE-GC-MS, with alcohols and esters being the most abundant. The PLS-DA models demonstrated the efficacy of breed discrimination, with the HSSE-GC-MS and the PTR-TOF-MS exhibiting the highest balanced accuracy of 95.5% using a reduced set of 11 VOCs and 5 product ion masses, respectively. The SIFT-MS model had a balanced accuracy of 92.8% with a reduced set of 11 product ion masses. Furthermore, complementarity was observed between HSSE-GC-MS, which primarily selected higher molecular weight VOCs, and PTR-TOF-MS and SIFT-MS. A higher correlation was found for compound abundances between the HSSE-GC-MS and the PTR-TOF-MS relative to the SIFT-MS, indicating that the PTR-TOF-MS was better suited to quantify specific compounds identified by the HSSE-GC-MS. Finally, the findings support the presence of VOCs originating from both synthetic and natural sources, highlighting the ability of the VOC analysis systems to non-destructively perform quality control and reveal differences in management practices or biological information encoded in eggs. | Matthias Corion; Miguel Portillo-Estrada; Simão Santos; Jeroen Lammertyn; Bart De Ketelaere; Maarten Hertog | Analytical Chemistry; Agriculture and Food Chemistry; Analytical Chemistry - General; Analytical Apparatus; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6560c405cf8b3c3cd7077a00/original/non-destructive-egg-breed-separation-using-advanced-voc-analytical-techniques-hsse-gc-ms-ptr-tof-ms-and-sift-ms-assessment-of-performance-and-systems-complementarity.pdf |
60c743494c89192130ad25ff | 10.26434/chemrxiv.9033953.v1 | Computational Modeling Reveals the Mechanism of Fluorescent State Recovery in the Reversibly Photoswitchable Protein Dreiklang | <p>The unique properties of the photoswitchable protein Dreiklang are attributed
to a reversible hydration/dehydration reaction at the
imidazolinone ring of the chromophore. Recovery of the fluorescent state, which
is associated with a chemical reaction of chromophore dehydration, is an
important part of the photocycle of this protein. Here we characterize
the fluorescent (ON) and non-fluorescent (OFF) states of Dreiklang and simulate
the thermal recovery reaction OFF → ON using
computational approaches. By using molecular modeling methods including the quantum
mechanics/molecular mechanics (QM/MM) technique, we characterize the structures
and spectra of the ON- and OFF-states. The results are consistent with relevant
experimental data. The computed reaction profile explains the observed recovery
reaction and clarifies the mechanism of chemical transformations in the
chromophore-containing pocket in Dreiklang. </p> | Bella Grigorenko; Igor Polyakov; Anna I. Krylov; Alexander Nemukhin | Biochemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743494c89192130ad25ff/original/computational-modeling-reveals-the-mechanism-of-fluorescent-state-recovery-in-the-reversibly-photoswitchable-protein-dreiklang.pdf |
65f321099138d23161741bae | 10.26434/chemrxiv-2024-jj94j | Efficient Integration of Molecular Representation and Message-Passing Neural Networks for Predicting Small Molecule Drug-like Properties | The physicochemical properties of a drug molecule determine its metabolism properties. There have been hybrid quantum mechanics approaches with computer-aided drug design and recent supervised machine-learning approaches to predict these properties of small-molecule drugs. However, these methods are low in accuracy and computationally expensive. To get around this problem and improve the performance of a model that predicts the properties of drug molecules, we came up with a novel architecture that uses a "bond order matrix" and structural information to improve molecular graph representations and information in the molecule. Message-passing neural networks (MPNNs) are a framework used to learn local and global features from irregularly formed data invariant to permutations. We take advantage of MPNN architecture and introduce a “semi-master node,” a unique way of representing the functional groups in a small molecule and aggregating features obtained from the functional groups, in anticipation of reverse engineering small molecules given the desired physicochemical properties. This novel architecture and molecule representation were evaluated on the QM9 dataset, which has 133,000 stable small organic molecules with nine heavy atoms (CONF) out of the GDB-17 chemical universe. The metric for evaluating the model's performance is DFT error, an estimated average error of the properties of each molecule. Our models have shown a performance gain of ~10%. | Shreyas Bhat Brahmavar; Mrunmay Mohan Shelar; Revanth Harinarthini; Bandaru Hemanth Sai Krishna; Nahush Harihar Kumta; Ojas Wadhwani; Raviprasad Aduri | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f321099138d23161741bae/original/efficient-integration-of-molecular-representation-and-message-passing-neural-networks-for-predicting-small-molecule-drug-like-properties.pdf |
6197a26d2e10ad6eb44dd9a6 | 10.26434/chemrxiv-2021-blvfj | Comparison of coarse-grained and all-atom
representations by explicit energy landscape
explorations | Computational studies of large molecular systems are often hindered by resource constraints, such as the available computational time. A common approach to reduce the computational cost is to use a coarse-grained description instead of an all-atom representation. However, such a simpli cation requires careful consideration of the coarse-graining scheme to identify potential artefacts introduced and the limitations of the model. In this contribution, we use the computational energy landscape framework to explicitly explore the energy landscapes for a coarse-grained (HiRE-RNA) and an all-atom potential (AMBER) for an example system, the Aquifex aeolicus tmRNA
pseudoknot PK1. The method provides insight into structural, thermodynamic and kinetic properties within a common framework, and allows for a comparison of a variety of commonly computed observables, demonstrating the usefulness of this approach.
For the speci c case study, we observe that both potentials exhibit a number of common features, highlighting that the coarse-grained model captures essential physical features of the system. Nonetheless, we observe shortcomings, and we demonstrate how our approach allows us to improve the model based on the insight obtained from the computational modelling. | Yuxin Ma; Antoine Monsavior; Samuela Pasquali; Konstantin Roeder | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2021-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6197a26d2e10ad6eb44dd9a6/original/comparison-of-coarse-grained-and-all-atom-representations-by-explicit-energy-landscape-explorations.pdf |
623d81dda4ed95febb2ced68 | 10.26434/chemrxiv-2022-2rt0t | A tracer gas study of ventilation and air movement to inform potential SARS-CoV-2 airborne transmission | Tracer gas studies were carried out to investigate the potential for airborne transmission of SARS-CoV-2 variants, and to inform work practises to reduce COVID-19 exposure and transmission. The air exchange of a meeting room was determined in accordance with ASTM E741-11 using sulfur hexafluoride (SF6), a colourless, odorless, non-flammable, and non-toxic tracer gas. Air was generally well mixed in the room, and very little tracer gas escaped through the closed door. The calculated air changes per hour (ACH) of the meeting room (5.8 h-1) was higher than the value recommended for offices (2-3 h-1) and used to assess potential COVID-19 infection risk and calculate maximum occupancy rates using the Airborne Infection Risk Calculator (AIRC) V3 Beta. Results showed that the previous guidance for maximum occupancy rates provided by many Australian States and Territories (the 2 or 4 square meters rule) provides a conservative estimate of the maximum number of occupants within a room for exposure events of up to 2 hours. However, for longer periods, such as a full working day (7.5 hours), and for more infectious strains of SARS-CoV-2, the 2 or 4 square meter rule did not adequately address infection risk. Use of two additional controls, mask wearing and ensuring that all occupants had received a third boosted vaccine dose, was estimated to reduce the probability of infection by 3.75-fold assuming infection with the Omicron variant. Including both controls increased the predicted maximum occupancy to values greater than the 2 and 4 square meter rule for most scenarios. Air movement outside the meeting room was investigated by filling the room with tracer gas and allowing the air to move freely by keeping the door open. Airflow was most influenced by the ventilation system of the laboratories in the north wing of building, rather than laboratories in the south wing. The plug of tracer gas was largely removed from the building within 30 minutes, although detectable concentrations were measured in some areas with lower air flow at the end of the 2-hour experiment. High concentrations were also noted in front of the elevators, however tracer gas concentrations were below detection on other floors. The techniques employed in this study are suitable for measuring air movement and ventilation in other buildings where aerosol transmission of COVID-19 is of concern. | Kathryn Linge; Julian Palmer; Angela Downey; Karina Soukos; Jacky Cailes; Michael Walker; Ewald Swinny | Analytical Chemistry; Environmental Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623d81dda4ed95febb2ced68/original/a-tracer-gas-study-of-ventilation-and-air-movement-to-inform-potential-sars-co-v-2-airborne-transmission.pdf |
66ea801612ff75c3a1ad9674 | 10.26434/chemrxiv-2024-ls0j0 | Temperature Correction of Near-Infrared Spectra of Raw Milk | Accurate milk composition analysis is crucial for improving product quality, economic efficiency, and animal health in the dairy industry. Near-infrared (NIR) spectroscopy can quantify milk composition quickly and nondestructively. However, external factors, such as temperature fluctuations, can alter the molecular vibrations and hydrogen bonding in milk, altering the NIR spectra and leading to errors in predicting key constituents such as fat, protein, and lactose. This study compares the effectiveness of Piecewise Direct Standardization (PDS), Continuous PDS (CPDS), External Parameter Orthogonalization (EPO), and Dynamic Orthogonal Projection (DOP in correcting the impact of temperature-induced variations on predictions in milk long-wave NIR spectra (LW-NIR, 1000 to 1700 nm).
A total of 270 raw milk samples were analyzed, collecting both reflectance and transmittance spectra at five different temperatures (20°C, 25°C, 30°C, 35°C, and 40°C). The experimental setup ensured precise temperature control and accurate spectral measurements. PLSR models were calibrated at 30°C to predict milk fat, protein, and lactose content. The performance of these models was assessed before and after applying the temperature correction methods, with a primary focus on reflectance spectra.
Results indicate that EPO and DOP significantly enhance model robustness and prediction accuracy across all temperatures, outperforming PDS and CPDS, especially for lactose prediction. These orthogonalization methods were compared against PLSR models calibrated with spectra from all temperatures. EPO and DOP showed comparable or superior performance, highlighting their effectiveness without requiring extensive temperature-specific calibration data. These findings suggest that orthogonalization methods are particularly suitable for in-line milk quality measurements under farm conditions where temperature control is challenging. This study highlights the potential of advanced chemometric techniques to improve real- time, on-farm milk composition analysis, facilitating better farm management and enhanced dairy product quality. | José Antonio Díaz Olivares; Stef Grauwels; Xinyue Fu; Ines Adriaens; Wouter Saeys; Ryad Bendoula; Jean-Michel Roger; Ben Aernouts | Analytical Chemistry; Agriculture and Food Chemistry; Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ea801612ff75c3a1ad9674/original/temperature-correction-of-near-infrared-spectra-of-raw-milk.pdf |
654b37e32c3c11ed71f37347 | 10.26434/chemrxiv-2023-bt2rq | Designing Organic π-Conjugated Molecules for Crystalline Solid Solutions: Adamantane-substituted Naphthalenes | We showcase herein organic crystalline solid solutions (CSSs) based on the simplest polycyclic aromatic hydrocarbon (PAH) scaffold, naphthalene, stabilized by dispersion forces induced by adamantane substitution. High thermal stability of the host and guest molecules synthesized by cross-coupling of dibromonaphthalene derivatives and 4-(1-adamantyl)phenyl boronic ester enabled formation of crystals by sublimation. We could generate binary monocrystalline solid solution systems proven by X-ray crystallography, the first system of designed CSSs stabilized exclusively via dispersion forces with structural evidence. These observations are additionally supported by lattice energy calculations and spectroscopic examinations. For the generation of CSSs, it is of utmost importance that the host and guest molecules have similar lattice energies and spatial compatibility. We anticipate that the thermostable organic CSS design demonstrated herein would be beneficial for functional materials and further investigation towards materials with unique properties. | Benedikt Herbert; Janis Walpuski; Matthias Stolte; Kazutaka Shoyama | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/654b37e32c3c11ed71f37347/original/designing-organic-conjugated-molecules-for-crystalline-solid-solutions-adamantane-substituted-naphthalenes.pdf |
66f14b9951558a15efda7c34 | 10.26434/chemrxiv-2024-ph882-v3 | Porous molecular crystals derived from cofacial porphyrin/phthalocyanine heterodimers. | Porphyrin-based porous materials are of growing interest as heterogeneous catalysts especially for reactions that are of importance to sustainability. Here we demonstrate that porous molecular crystals can be prepared by the simple co-crystallisation of tetraphenylporphyrin (TPP) with octa(2’,6’-di-iso-propylphenoxy)phthalocyanine or some of its metal complexes [(dipPhO)8PcM; M = H2, Al-OH, Ti=O, Mn-Cl, Fe-Cl, Co, Ni, Cu, Zn, Ga-Cl, Ag, In-Cl or Au-Cl]. This process is facilitated by the efficient formation of the supramolecular heterodimer between TPP and (dipPhO)8PcM, which is driven by the complementary shape and symmetry of the two macrocycles. The (dipPhO)8PcM component directs the crystal structure of the heterodimers to form Phthalocyanine Nanoporous Crystals (PNCs) of similar structure to those formed by (dipPhO)8PcM alone. The incorporation of TPP appears to partially stabilise the PNCs towards the removal of included solvent and for cocrystals containing (dipPhO)8PcCo stability can be enhanced further by the in-situ addition of 4,4-bipyridyl to act as a “molecular wall tie”. These stabilised PNC/TPP cocrystals have a Brunauer-Emmett-Teller surface area (SABET) of 454 m2 g-1 and a micropore volume (Vmp) of 0.22 ml g-1. The reactivity of both macrocycles within the PNC/TPP co-crystals are demonstrated by in-situ metal insertion. | Nikolaos-Angelos Stamos; Shannah Kerrigan; Alexander Stiven; Gary Nichol; C. Grazia Bezzu; Luke Burt; Stephen Moggach; Gemma Turner; Neil McKeown | Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f14b9951558a15efda7c34/original/porous-molecular-crystals-derived-from-cofacial-porphyrin-phthalocyanine-heterodimers.pdf |
60c740e69abda209cdf8bda8 | 10.26434/chemrxiv.7874453.v1 | Straightforward Background Depletion Unlocks Transaminase Evolution Through Solid-Phase Screening | Here we report a rapid, reliable, and <b>widely applicable</b> <b>solid-phase screening</b> method for transaminase variants, which was successfully applied to a transaminase from Halomonas elongata (HEWT), evolved through rounds of random mutagenesis towards a series of diverse prochiral ketones. Key element of this work is the effective and long lasting <b>background depletion</b> which enhances discrimination and minimised false positive hits. | Matteo Planchestainer; Eimear Hegarty; Christian Heckmann; Louise Gourlay; Francesca Paradisi | Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e69abda209cdf8bda8/original/straightforward-background-depletion-unlocks-transaminase-evolution-through-solid-phase-screening.pdf |
60c75770469df4939ef45484 | 10.26434/chemrxiv.14402366.v1 | Six-Step Gram Scale Synthesis of the HIV Integrase Inhibitor Dolutegravir Sodium | A short and practical synthesis for preparing the active pharmaceutical ingredient dolutegravir
sodium was investigated. The convergent strategy developed herein starts from 3-(R)-amino-1-
butanol and builds up the BC ring system in 76% isolated yield over four steps. Ring A was
constructed by a one-pot 1,4-addition to diethyl-(2E/Z)-2-(ethoxymethylidene)-3-oxobutandioate
and subsequent MgBr2·OEt2-mediated regioselective cyclization. Amide formation with 2,4-
difluorobenzylamine was either performed from the carboxylic acid or through aminolysis of the
corresponding ester precursor. Final salt formation afforded dolutegravir sodium in 48–51%
isolated yield (HPLC-purity: 99.7–99.9%) over six linear steps.<br /> | Jule-Phillip Dietz; Tobias Lucas; Jonathan Groß; Sebastian Seitel; Jan Brauer; Dorota Ferenc; B. Frank Gupton; Till Opatz | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75770469df4939ef45484/original/six-step-gram-scale-synthesis-of-the-hiv-integrase-inhibitor-dolutegravir-sodium.pdf |
619320262bf8a9f740de0019 | 10.26434/chemrxiv-2021-kp3v9-v2 | Cationic DABCO-based Catalyst for Site-Selective C−H Alkylation via Photoinduced Hydrogen-Atom Transfer | A novel class of hydrogen-atom transfer (HAT) catalysts based on the readily available and tunable 1,4-diazabicyclo[2.2.2]octane (DABCO) structure was designed, and their photoinduced HAT catalysis ability was demonstrated. The combination of the optimal HAT catalyst with an acridinium-based organophotoredox catalyst enables highly efficient and site-selective C−H alkylation of substrates ranging from unactivated hydrocarbons to complex molecules. Notably, a HAT catalyst with additional substituents adjacent to a nitrogen atom further improved the site-selectivity. Mechanistic studies suggested that the N-substituent of the catalyst plays a crucial role, assisting in the generation of a dicationic aminium radical as an active species for the HAT process. | Akira Matsumoto; Keiji Maruoka | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/619320262bf8a9f740de0019/original/cationic-dabco-based-catalyst-for-site-selective-c-h-alkylation-via-photoinduced-hydrogen-atom-transfer.pdf |
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