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63f449f0fcfb27a31f231c61 | 10.26434/chemrxiv-2023-dxtt7 | Superior Photoprotection of Cyanine Dyes with Thio-imidazole Amino Acids | Preventing fluorophore photobleaching and unwanted blinking is crucial for singlemolecule
fluorescence studies. Reductants achieve photoprotection via quenching excited tripletstates,
yet either require counteragents, or for popular alkyl-thiols, are limited to cyanine dye Cy3
protection. Here we provide mechanistic and imaging results showing that the naturally occurring
amino acid ergothioneine and its analogue dramatically enhance photostability for Cy3, Cy5 and
their conformationally restrained congeners, providing a biocompatible universal solution for
demanding fluorescence imaging. | Yasser Gidi; Jorge Ramos-Sanchez; Terri C. Lovell; Viktorija Glembockyte; Irwin K. Cheah; Martin J. Schnermann; Barry Halliwell; Cosa Gonzalo | Physical Chemistry; Biological and Medicinal Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f449f0fcfb27a31f231c61/original/superior-photoprotection-of-cyanine-dyes-with-thio-imidazole-amino-acids.pdf |
60c74645bdbb895bc1a38bc0 | 10.26434/chemrxiv.11294780.v1 | A Single-Component Photorheological Fluid with Light-Responsive Viscosity | Manuscript and supporting information detailing characterisation of photoresponsive viscoelastic fluids prepared from wormlike micelles composed of azobenzene surfactants. Data includes results from rheology, UV/vis absorption, transmission electron microscopy and small-angle X-ray scattering measurements. | Elaine A. Kelly; Niamh Willis-Fox; Judith E. Houston; Camille Blayo; Giorgio Divitini; Nathan Cowieson; Ronan Daly; Rachel Evans | Nanostructured Materials - Materials; Surfactants; Photochemistry (Physical Chem.); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74645bdbb895bc1a38bc0/original/a-single-component-photorheological-fluid-with-light-responsive-viscosity.pdf |
60c75206702a9b5ddc18c052 | 10.26434/chemrxiv.13241228.v1 | Switch Chemistry at Cryogenic Conditions: Quantum Tunnelling under Electric Fields | While the influence of intramolecular electric fields is a known feature in enzymes, the use of oriented external electric fields (EEF) to enhance or inhibit molecular reactivity is a promising topic still in its infancy. Herein we will explore computationally the effects that EEF can provoke in simple molecules close to the absolute zero, where quantum tunnelling (QT) is the sole mechanistic option. We studied three exemplary systems, each one with different reactivity features and known QT kinetics: bond-shifting in pentalene, Cope rearrangement in semibullvalene, and cycloreversion of diazabicyclohexadiene. The kinetics of these cases depdend both on the field strength and its direction, usually giving subtle but remarkable changes. However, for the cycloreversion, which suffers large changes on the dipole through the reaction, we also observed striking results. Between the effects caused by the EEF on the QT we observed an inversion of the Arrhenius equation, deactivation of the molecular fluxionality, and stabilization or instantaneous decomposition of the system. All these effects may well be achieved, literally, at the flick of a switch.<br /> | Omer Kirshenboim; Alexander Frenklah; Sebastian Kozuch | Physical Organic Chemistry; Computational Chemistry and Modeling; Chemical Kinetics; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75206702a9b5ddc18c052/original/switch-chemistry-at-cryogenic-conditions-quantum-tunnelling-under-electric-fields.pdf |
60c74459842e650e62db242b | 10.26434/chemrxiv.9638633.v2 | Dibenzochrysene Enables Tightly Controlled Docking and Stabilizes Photoexcited States in Dual-Pore Covalent Organic Frameworks | Covalent
organic frameworks (COFs), consisting of covalently connected organic building
units, combine attractive features such as crystallinity, open porosity and
widely tunable physical properties. For optoelectronic applications, the
incorporation of heteroatoms into a 2D COF has the potential to yield desired
photophysical properties such as lower band gaps, but can also cause lateral
offsets of adjacent layers. Here, we introduce dibenzo[g,p]chrysene (DBC) as a
novel building block for the synthesis of highly crystalline and porous 2D
dual-pore COFs showing interesting properties for optoelectronic applications.
The newly synthesized terephthalaldehyde (TA), biphenyl (Biph), and
thienothiophene (TT) DBC-COFs combine conjugation in the a,b-plane with a tight
packing of adjacent layers guided through the molecular DBC node serving a
specific docking site for successive layers. The resulting DBC-COFs exhibit a
hexagonal dual-pore kagome geometry, which is comparable to COFs containing
another molecular docking site, namely
4,4′,4″,4‴-(ethylene-1,1,2,2-tetrayl)-tetraaniline (ETTA). In this context, the
respective interlayer distances decrease from about 4.60 Å in ETTA-COFs to
about 3.6 Å in DBC-COFs, leading to well-defined hexagonally faceted single
crystals sized about 50-100 nm. The TT DBC-COFs feature broad light absorption
covering large parts of the visible spectrum, while Biph DBC-COF shows extraordinary
excited state lifetimes exceeding 10 ns. In combination with the large number
of recently developed linear conjugated building blocks, the new DBC
tetra-connected node is expected to enable the synthesis of a large family of
strongly p-stacked, highly ordered 2D COFs with promising
optoelectronic properties. | Niklas Keller; Torben Sick; Nicolai Bach; Andreas Koszalkowski; Julian Rotter; Dana D. Medina; Thomas Bein | Carbon-based Materials; Nanostructured Materials - Materials; Optical Materials; Conducting polymers; Organic Polymers; Physical and Chemical Properties; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74459842e650e62db242b/original/dibenzochrysene-enables-tightly-controlled-docking-and-stabilizes-photoexcited-states-in-dual-pore-covalent-organic-frameworks.pdf |
6165f62235b406a76a11cbd5 | 10.26434/chemrxiv-2021-kr87t | Enabling modular autonomous feedback-loops in materials science through hierarchical experimental laboratory automation and orchestration | Materials acceleration platforms (MAPs) operate on the paradigm of integrating combinatorial synthesis, high-throughput characterization, automatic analysis, and machine learning. Within these MAPs, one or multiple autonomous feedback loops may aim to optimize materials for certain functional properties or generate new insights. The scope of a given experiment campaign is defined by the range of experiment and analysis actions that are integrated into the experiment framework. Herein we present a method for integrating many actions within a hierarchical experimental laboratory automation and orchestration (HELAO) framework. We demonstrate the capability of orchestrating distributed research instruments that can incorporate data from experiments, simulations, and databases. HELAO interfaces laboratory hardware and software that are distributed across several computers and operating systems for executing experiments, data analysis, provenance tracking, and autonomous planning. Parallelization is an effective approach for accelerating knowledge generation provided that multiple instruments can be effectively coordinated, which we demonstrate with parallel electrochemistry experiments orchestrated by HELAO. Efficient implementation of autonomous research strategies requires device sharing, asynchronous multithreading, and full integration of data management in experiment orchestration, which to the best of our knowledge, is demonstrated for the first time herein. | Fuzhan Rahmanian; Jackson Flowers; Dan Guevarra; Matthias Richter; Maximilian Fichtner; John Gregoire; Helge Sören Stein | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6165f62235b406a76a11cbd5/original/enabling-modular-autonomous-feedback-loops-in-materials-science-through-hierarchical-experimental-laboratory-automation-and-orchestration.pdf |
63b775354a7fa1dc8f11d27a | 10.26434/chemrxiv-2023-zd1nd | Synthesis and Self-assembly of Limonene Oxide - Lactide Block Copolymers | The reaction of limonene oxide with a zirconium complex led to polymers with a molar mass up to 4.0 kDa, the largest limonene oxide homopolymer reported so far. Diblock, triblock, and tetrablock copolymers of limonene oxide and L-lactide were also prepared using a redox switchable catalyst based on the same zirconium complex; the obtained copolymers are the first-ever reported limonene oxide-lactide block copolymers. The solid-state self-assembly properties of the copolymers were characterized by small angle X-ray scattering and rheology measurements, giving a self-assembly domain radius of 11, 25, and 35 nm for the diblock, triblock, and tetrablock copolymers, respectively. | Ruxi Dai; Shah Valloppilly; Nethmi De Alwis Watuthanthrige; Progyateg Chakma; Shijie Deng; Dominik Konkolewicz; Paula Diaconescu | Polymer Science; Biopolymers; Polymerization catalysts | CC BY NC 4.0 | CHEMRXIV | 2023-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b775354a7fa1dc8f11d27a/original/synthesis-and-self-assembly-of-limonene-oxide-lactide-block-copolymers.pdf |
65784919bec7913d276db0d3 | 10.26434/chemrxiv-2023-gnh1v-v2 | Visualizing and Characterizing Excited States from Time-Dependent Density Functional Theory | Time-dependent density functional theory (TD-DFT) is the most widely-used electronic structure method for excited states, due to a favorable combination of low cost and (in many contexts) semi-quantitative accuracy. This Perspective describes various ways in which excited states from TD-DFT calculations can be visualized and analyzed, both qualitatively and quantitatively. This includes not just orbitals and densities but also well-defined statistical measures of electron-hole separation and of Frenkel-type exciton delocalization. Emphasis is placed on mathematical connections between methods that have often been discussed separately. Particular attention is paid to charge-transfer diagnostics, which provide indicators to diagnose when TD-DFT may not be trustworthy due to its categorical failure to describe long-range electron transfer. Measures of exciton size and charge separation that are directly connected to the underlying transition density are recommended over more ad hoc metrics for quantifying charge-transfer character. | John Herbert | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2023-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65784919bec7913d276db0d3/original/visualizing-and-characterizing-excited-states-from-time-dependent-density-functional-theory.pdf |
6627f39621291e5d1d8150e6 | 10.26434/chemrxiv-2024-zl8dw | Intermolecular Formal [2π+2σ] Cycloaddition of Enol Silyl Ethers with Bicyclo[1.1.0]butanes Promoted by Lewis acids | A new approach to directly access bicyclo[2.1.1]hexanes (BCHs) from easily prepared enol silyl ethers and bicyclo[1.1.0]butanes (BCBs) through formal [2π+2σ] cycloaddition was developed involving two-electron mediated process promoted by commercially available Lewis acids. This new reaction tolerated a wide range of enol silyl ethers and BCBs. In addition, a scale-up experiment and the synthetic transformations of the cycloadducts further highlighted the synthetic utility. | Shi-Wu Li; Shi-Jie Zhu; Xue Tian | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6627f39621291e5d1d8150e6/original/intermolecular-formal-2-2-cycloaddition-of-enol-silyl-ethers-with-bicyclo-1-1-0-butanes-promoted-by-lewis-acids.pdf |
60c75300702a9b1bc118c2ac | 10.26434/chemrxiv.13373837.v1 | A Floating Mould Technique for the Programmed Assembly of Protocells into Protocellular Materials Capable of Non-Equilibrium Biochemical Sensing | Despite important breakthroughs in bottom-up synthetic biology have recently been achieved, a major challenge still remains the construction of free-standing, macroscopic and robust materials from protocell building blocks that are stable in water and capable of emergent behaviours. Herein we report a new floating mould technique for the fabrication of millimetre- to centimetre-sized protocellular materials (PCMs) of any shape that overcomes most of the current challenges in prototissue engineering. Significantly, this technique also allowed us to generate 2D periodic arrays of PCMs that displayed an emergent non-equilibrium spatiotemporal sensing behaviour. These arrays were capable of collectively translating the information provided by the external environment and encoded in the form of propagating reaction-diffusion fronts into a readable dynamic signal output. Overall, our methodology opens up a route to the fabrication of macroscopicand robust tissue-like materials with emergent behaviours, providing a new paradigm of bottom-up synthetic biology and biomimetic materials science. | Agostino Galanti; Rafael Moreno Tortolero; Raihan Azad; Stephen Cross; Sean Davis; Pierangelo Gobbo | Biocompatible Materials; Biological Materials; Biodegradable Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75300702a9b1bc118c2ac/original/a-floating-mould-technique-for-the-programmed-assembly-of-protocells-into-protocellular-materials-capable-of-non-equilibrium-biochemical-sensing.pdf |
64ffef77b6ab98a41c4ba62f | 10.26434/chemrxiv-2023-swlfz | Atom Transfer Radical Addition to Alkenes using Fukuzumi Photocatalyst for Regioselective Functionalization of Quinoxalin-2(1H)-ones | The atom transfer radical addition (ATRA) reaction is defined as a method for introducing halogenated compounds into alkenes via a radical mechanism. In this study, we present an ATRA approach for achieving regioselective functionalization of quinoxalin-2(1H)-ones by activating C-Br bonds of CBr4, and subsequent trihaloalkyl-carbofunctionalization of styrenes employing the 9-mesityl-10-methylacridinium perchlorate (Fukuzumi) photocatalyst under 3W blue LED (450-470 nm) irradiation. This three-component radical cascade process demonstrates remarkable efficiency in the synthesis of 1-methyl-3-(3,3,3-tribromo-1-(4-chlorophenyl)propyl)quinoxalin-2(1H)-one derivatives.
| Buddhadeb Pal; Sathi Sahoo; Prasenjit Mal | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ffef77b6ab98a41c4ba62f/original/atom-transfer-radical-addition-to-alkenes-using-fukuzumi-photocatalyst-for-regioselective-functionalization-of-quinoxalin-2-1h-ones.pdf |
61bdf082f52bc4325fc56647 | 10.26434/chemrxiv-2021-f8rv5-v2 | C2H5NO Isomers: from Acetamide to1,2-Oxazetidine and Beyond | This work documents the properties of a number of isomers of molecular formula C2H5NO from the most stable, acetamide, through 1,2-oxazetidine and including even higher energy species largely of a dipolar nature. Only two of the isomers have been detected in emissions
from the interstellar medium (ISM); possible further candidates are identifi ed and the likelihood of their being detectable are considered. In general hardly any of these compounds have featured in the existing chemical literature so this work represents an important contribution
extending the canon of chemical bonding which can contribute to machine-learning
| providing a more exacting test of AI applications.
The presence of acetamide, CH3C(O)NH2, is the subject of current debate with no clear and obvious paths to its formation; it is shown that a 1,3[H]-transfer from (E,Z ) ethanimidic acid, CH3C(OH){{NH, is feasible in spite of an energy barrier of 130 kJ/mol. It is speculated
that the imidic acid can itself be formed from abundant precursors, H2O and CH3C{{{N, in an acid-induced, water addition, auto-catalytic reaction on water-ice grains. | John Simmie | Physical Chemistry; Earth, Space, and Environmental Chemistry; Space Chemistry; Physical and Chemical Properties; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2021-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61bdf082f52bc4325fc56647/original/c2h5no-isomers-from-acetamide-to1-2-oxazetidine-and-beyond.pdf |
60c74c2f9abda27cb0f8d228 | 10.26434/chemrxiv.12374900.v2 | Conformal Coating of Orthopedic Plates with X-Ray Scintillators and pH Indicators for X-Ray Excited Luminescence Chemical Imaging Through Tissue. | We describe a material that allows for high spatial resolution pH mapping through tissue using X-ray excited luminescence chemical imaging (XELCI). This is especially useful for detecting implant associated infection and elucidating how the local biochemical environment changes during infection and treatment. To acquire one pixel in the image, a focused X-ray beam irradiates a small region of scintillators coated on the implant and the X-ray excited optical luminescence spectrum is modulated by indicator dyes to provide a chemically sensitive measurement with low background. Scanning the X-ray beam across the implant surface generates high spatial resolution chemical measurements. Two associated challenges are 1) to make robust sensors that can be implanted in tissue to measure local chemical concentrations and specifically for metal orthopedic implants, and 2) to conformally coat the implant surface with scintillators and pH indicator dyes in order to make measurements over a large area. Previously, we have physically pressed or glued a pH-sensitive hydrogel sensor to the surface of an implant, but this is impractical for imaging over large irregular device areas such as an orthopedic plate with holes and edges. Herein we describe a chemically sensitive and biocompatible XELI sensor material containing scintillator particles (Gd<sub>2</sub>O<sub>2</sub>S:Eu) and a pH sensitive hydrogel coating using a roughened epoxy coating. A two-part commercial grade epoxy film was tested and found to make the coating of pH sensitive layer adhere better to the titanium surface. Sugar and salt particles were added to the surface of the epoxy as it cured to create a roughened surface and increase surface area. On this roughened surface, a secondary layer of diacrylated polyethylene glycol (PEG) hydrogel, containing a pH sensitive dye, was polymerized. This layer was found to adhere well to the epoxy-coated implant unlike other previously tested polymer surfaces which delaminated when exposed to water or humidity. The focused X-ray beam enabled 0.5 mm spatial resolution through 1 cm thick tissue. The pH sensor coated orthopedic plate was imaged with XELCI through tissue with different pH to acquire a calibration curve. The plates were also imaged through tissue with low pH region from a Staphylococcus aureus biofilm grown on one section. These studies demonstrate the use of pH sensor coated orthopedic plates for mapping the surface pH through tissue during biofilm formation using XELCI. | Unaiza Uzair; Chloe Johnson; Shayesteh Beladi-Behbahani; Donald Benza; Yash Raval; Meenakshi Ranasinghe; Gretchen Schober; Tzuen-Rong Tzeng; Jeffrey Anker | Biocompatible Materials; Coating Materials; Biopolymers; Hydrogels; Analytical Chemistry - General; Imaging; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c2f9abda27cb0f8d228/original/conformal-coating-of-orthopedic-plates-with-x-ray-scintillators-and-p-h-indicators-for-x-ray-excited-luminescence-chemical-imaging-through-tissue.pdf |
63d9408cd1632f652beb94b0 | 10.26434/chemrxiv-2023-3nm93 | RFNET: Integrating Rich Features into Neural Networks for Band Gap Prediction of Perovskite Crystals | Perovskite crystals with simplicity in manufacturing and tuneable band gaps attracted wide attention in material science. Currently, the development of materials with specific band gaps remains difficult and consumes significant manufacturing resources. Therefore, demand keeps increasing in the context of material property prediction through machine learning in order to refine the discovery process. Herein, we proposed a novel model RFNET which integrated rich features into neural networks for predicting band gaps of Perovskite crystals. A virtual screen was studied to showcase the effectiveness of RFNET model in identifying the narrowest band gap perovskite crystals. We comprehensively compared the RFNET with nine other common machine learning and deep learning methods. The experimental result demonstrated that RFNET could reduce the number of candidate materials by 8% to 14%. We also offered a highly practical hands-on tutorial for material science researchers to reproduce the code of this work. Overall, this unprecedented model guaranteed the implications for enhancing virtual screening performance and minimizing workload. | Kun Zhang; Yang Yu; Minyan Li; Yifan Pang; Zhi Xu; Tao You; Kai Wang; Hui Liu | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d9408cd1632f652beb94b0/original/rfnet-integrating-rich-features-into-neural-networks-for-band-gap-prediction-of-perovskite-crystals.pdf |
636cfcc9c4c8791908250940 | 10.26434/chemrxiv-2022-hpf6f-v2 | Label-free measurement of antimicrobial peptide interactions with lipid vesicles and nanodiscs using microscale thermophoresis | Antimicrobial peptides (AMPs) are a promising source of inspiration for new antibiotic discovery, in part because they believed to not trigger rapid resistance. AMPs can target many features of the cell surface, and effective resistance development may require multiple mutations in parallel that have large fitness costs. Although they have diverse modes of action, AMPs will often begin by binding to the membrane; cell-penetrating peptides will subsequently need to cross it. Characterization of AMP activity can thus be inferred by the determination of KD (dissociation constant for binding affinity) and KP (partitioning constant).
Here we demonstrate that microscale thermophoresis (MST) can be used for reliable label-free measurement of KD and KP utilising the intrinsic tryptophan fluorescence - removing the need for chromophore labelling. The MST results of binding to small unilamellar vesicles (SUVs) and styrene maleic acid (SMA) based nanodiscs are compared to the corresponding surface plasmon resonance (SPR) measurements. SMA-QA nanodiscs are shown to be best suited for accurate measurements, while vesicles are a viable alternative. Unmodified SMA-nanodiscs proved unsuitable due to interactions between the cationic AMPs and the anionic polymer belt.
Significant reduction of KD was observed when 5% anionic lipids were included in the lipid composition of the membrane models. This highlights the preference of the tested AMPs for anionic bacterial membranes, and the measured KD and KP values correlate well with their activity towards S. aureus and E. coli. We conclude that MST is a promising method for fast and efficient detection of peptide-lipid interactions, and the relative strength of the interactions can be reliably ranked within a library of screened compounds.
| Philip Rainsford; Fredrik Rylandsholm; Martin Jakubec; Eric Juskewitz; Mitchell Silk; Richard A. Engh; Johan Isaksson | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Analytical Apparatus; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2022-11-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636cfcc9c4c8791908250940/original/label-free-measurement-of-antimicrobial-peptide-interactions-with-lipid-vesicles-and-nanodiscs-using-microscale-thermophoresis.pdf |
623ae2d9658bc0a01fb504f4 | 10.26434/chemrxiv-2022-9164j | Electrochemical Depolymerization of Lignin in a Biomass-based Solvent | The successive breakdown of the lignin macromolecule into smaller units is the key to generate high value-added products from this complex plant polyphenol. Obtaining well-defined aromatic compounds is, therefore, an important step towards the production of biobased chemicals for the fuel, coating and lubricant industries. Nevertheless, processes requiring lignin dissolution are always challenging. Dissolving this macromolecule in an environment-friendly way takes this challenge to a whole new level. Levulinic acid, an organic compound formed during the hydrothermal processing of lignocellulosic biomass, has been shown to efficiently dissolve lignin. Herein, we describe a system consisting of levulinic acid as a biobased solvent for the reductive electrochemical depolymerization of lignin. Copper was used as an electrocatalyst due to the economic feasibility and low activity towards the hydrogen evolution reaction. After depolymerization, high-resolution mass spectrometry and NMR structural characterization revealed lignin-derived monomers and dimers. A predominance of aryl ether and phenolic groups was observed. The effect of the depolymerized lignin as an anti-corrosion coating was assessed, revealing enhancements on the electrochemical stability of the metal. Via a simple depolymerization process of biomass waste in a biomass-based solvent, these results demonstrate a straightforward approach to produce high value-added compounds or tailored biobased materials. | Márcia Gabriely Alves da Cruz; Robin Gueret; Jianhong Chen; Jędrzej Piątek; Mika Sipponen; Marcella Frauscher; Serhiy Budnyk; Bruno Rodrigues; Adam Slabon | Polymer Science; Earth, Space, and Environmental Chemistry; Biopolymers; Environmental Science; Wastes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623ae2d9658bc0a01fb504f4/original/electrochemical-depolymerization-of-lignin-in-a-biomass-based-solvent.pdf |
60c743b64c89198115ad26c2 | 10.26434/chemrxiv.9619772.v1 | Absolute Autocatalytic Amplification Under Heterogenous Conditions Involving Subsequent Hydride Transfer and Hemiacetal Intermediate. | Absolute asymmetric amplification is observed for
pyridine alkanol by reaction with iPr<sub>2</sub>Zn vapor under heterogenous
conditions. Beside the chiral alkanol, formation of a chiral ester is observed
and identified as a subsequent Claisen-Tishchenko product of a hemiacetal
intermediate during a Soai absolute amplification. | Giuesppe rotunno; Dirk Petersen; Mohamed Amedjkouh | Heterogeneous Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743b64c89198115ad26c2/original/absolute-autocatalytic-amplification-under-heterogenous-conditions-involving-subsequent-hydride-transfer-and-hemiacetal-intermediate.pdf |
6555b55ddbd7c8b54b5cf6e9 | 10.26434/chemrxiv-2023-7n8kp | Mechanically-controlled multifaceted dynamic transformations in twisted organic crystal waveguides | This study introduces mechanically induced novel phenomena such as standing, leaning, stacking, and interlocking behaviors in naturally twisted optical waveguiding microcrystals on a substrate. The twisted crystal self-assembled from 2,4-dibromo-6-(((2-bromo-5-fluorophenyl)imino)methyl)phenol is flexible and emits orange fluorescence. Crystal’s mechanical flexibility in the perpendicular direction to (001) and (010) planes can be attributed to intermolecular interactions, including C-H···Br, N-H···O, C-H···O, and π···π stacking interactions. Through a systematic process involving step-by-step bending and subsequent optical waveguiding experiments at each bent position, a linear relationship between optical loss and mechanical strain is established. Additionally, the vertical standing and leaning of these crystals at different angles on a flat surface and the vertical stacking of multiple crystals reveal the three-dimensional aspects of organic crystal waveguides, introducing light trajectories in a 3D space. Furthermore, the integration of two axially interlocked twisted crystals enables the coupling of polarization along their long axis. These novel crystal dynamics expand the horizons of crystal behavior and have the potential to revolutionize various applications, rendering these crystals invaluable in the realm of crystal-related science and technology.
| Rajadurai Chandrasekar; Mehdi Rohullah; Vuppu Vinay Pradeep; Shruti Singh | Nanoscience; Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6555b55ddbd7c8b54b5cf6e9/original/mechanically-controlled-multifaceted-dynamic-transformations-in-twisted-organic-crystal-waveguides.pdf |
630d0682d147b2fe1bbd3553 | 10.26434/chemrxiv-2022-d2xnf | Thiamyxins: Structure and Biosynthesis of Myxobacterial RNA-Virus-Inhibitors | During our search for novel myxobacterial natural products, we discovered the Thiamyxins: thiazole- and thiazoline-rich non-ribosomal peptide-polyketide hybrids with potent antiviral activity. We isolated two cyclized and two open-chain congeners of this unprecedented natural product family, whereof the non-cyclized Thiamyxin D was found to be fused to a glycerol unit attached to the C-terminal carboxyl function. Alongside their structure elucidation and absolute stereochemistry, we present the biosynthetic origin of the Thiamyxins supported by a concise biosynthesis model based on biosynthetic gene cluster analysis and feeding experiments with isotope labelled precursors. We report an unprecedented incorporation of a 2-(hydroxymethyl)-4-methylpent-3-enoic acid moiety originating from the involved polyketide synthase featuring a rare GCN5-related N-acetyltransferase-like decarboxylase domain. The Thiamyxins showed potent inhibition of different RNA-viruses as analysed in cell culture models of corona, zika and dengue virus infection. Their potency up to a half maximal inhibitory concentration of 560 nM combined with milder cytotoxic effects on human cell lines indicate a potential for further development of the Thiamyxins as broad-spectrum antivirals targeting RNA-viruses. | Patrick Haack; Kirsten Harmrolfs; Chantal Bader; Ronald Garcia; Antonia Gunesch; Sibylle Haid; Alexander Popoff; Alexander Voltz; Heeyoung Kim; Ralf Bartenschlager; Thomas Pietschmann; Rolf Müller | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry; Bioorganic Chemistry; Natural Products; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630d0682d147b2fe1bbd3553/original/thiamyxins-structure-and-biosynthesis-of-myxobacterial-rna-virus-inhibitors.pdf |
66ff3879cec5d6c14214c331 | 10.26434/chemrxiv-2024-5rwk3-v2 | Hydroalkylation of Vinylarenes via Transition Metal-Free In-Situ Generation of Benzylic Nucleophiles using Tetramethyldisiloxane and KOtBu | Hydrosilanes and Lewis bases are known to promote various reductive defunctionalizations, rearrangements, and silylation reactions, facilitated by enigmatic silicon/Lewis base-derived reactive intermediates. Despite the wide variety of transformations enabled by this reagent combination, no examples of intermolecular C(sp3)–C(sp3) forming reactions have been reported. In this work, we’ve identified 1,1,3,3-tetramethyldisiloxane (TMDSO) and KOtBu as a unique reagent combination capable of generating benzylic nucleophiles in-situ from styrene derivatives, which can subsequently react with alkyl halides to give a new C(sp3)–C(sp3) linkage via formal hydroalkylation. Mechanistic experiments suggest that the reaction proceeds through a key hydrogen atom transfer (HAT) step from a hydrosilane reducing agent to styrene, affording a benzylic radical that undergoes reductive radical polar crossover (RRPC) and subsequent SN2 alkylation. | Piers St-Onge; Hana Nugraha; Stephen Newman | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ff3879cec5d6c14214c331/original/hydroalkylation-of-vinylarenes-via-transition-metal-free-in-situ-generation-of-benzylic-nucleophiles-using-tetramethyldisiloxane-and-k-ot-bu.pdf |
642b33a7a029a26b4cdcd8b4 | 10.26434/chemrxiv-2022-ddlc9-v2 | Thermoset Polymers Characterization as a Function of Cure State Using Off-stoichiometry Proxies | Rapid reaction kinetics often produce drastic changes in the thermo-chemo-mechanical characteristics of thermoset polymers over short time periods. Thus, it is a major challenge to quantify material properties over the entire spectrum of cure states at relevant temperatures with both efficiency and accuracy. This work presents a novel characterization technique as a function of the cure state of a difunctional epoxy with amine curing agent through off-stoichiometry mixing formulations that serve as proxies for the intermediately crosslinked polymer. Mass density, cure kinetics, and elastic and strength properties are characterized across four mixing ratios, and relative cure/crosslinked states of off-stoichiometry cases are quantified. Essential to this unique approach is the capability to eliminate time dependence resulting from reaction kinetics on characterizing intermediate crosslinking states. The procedure reported herein facilitates efficient and accurate measurement of properties of curing epoxies for building and validating computational process modeling frameworks developed for optimizing material performance. | Michael Olaya; Sagar Shah; Marianna Maiaru | Materials Science; Polymer Science; Composites; Materials Processing; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642b33a7a029a26b4cdcd8b4/original/thermoset-polymers-characterization-as-a-function-of-cure-state-using-off-stoichiometry-proxies.pdf |
6344477bba8a6d6c2b702b32 | 10.26434/chemrxiv-2022-drhkn-v2 | Mechanics of lithium metal at the nanoscale | The fracture of ceramic solid electrolytes, driven by the plating of lithium within cracks, has been identified as one of the fundamental issues to successfully develop solid-state batteries. Understanding the mechanics of lithium at the nanoscale is therefore essential. In this work, the elastic and plastic properties of lithium are measured by nanoindentation within an electron microscope. Lithium metal samples are characterised by electron backscattered diffraction (EBSD) before and after indentation to understand the dependence of the mechanical properties on crystallographic orientation, and determine the stiffness tensor components, moduli and Poisson’s ratio using a method first proposed by Vlassak and Nix. The measured stiffness tensor components are C11=13.3, C12=11.2, and C44=8.8 GPa. Hardness measurements show a clear size effect with hardness in excess of 100 MPa observed for indent depths below 300 nm, which could contribute toward observed lithium filament propagation. | Jack Aspinall; David Armstrong; Mauro Pasta | Materials Science; Energy | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6344477bba8a6d6c2b702b32/original/mechanics-of-lithium-metal-at-the-nanoscale.pdf |
63e0e84afcfb27a31f6742d2 | 10.26434/chemrxiv-2023-tnggx | Monodisperse size-controlled 1T'-WS2 nano-monolayers with high colloidal stability | The difference between in-plane and out-of-plane bonding energy of transition metal dichalcogenides has provided the possibility of isolating single layers. A one step synthesis protocol to produce size-controlled single layers has always been challenging. Here we developed a new colloidal synthesis to produce monodisperse size-controlled 1T'-WS2 nano-monolayers with outstanding colloidal stability by using 1-octadecanethiol as the coordinating agent. Changes in the reaction time and amount of coordinating agent regulate the mean size of the nanosheets. We investigated the effect of octadecanethiol and injection rate on the dispersion and mean-size, using UV-Vis spectroscopy, X-ray diffraction techniques, and transmission electron microscopy. Furthermore, thermogravimetric analysis and Fourier transform infrared spectroscopy allow for ligands detection and analysis at the surface of the nanosheets. These results open a new pathway to synthesize, control and explore the properties of nanoscale transition metal dichalcogenides. | Ashkan Shahmanesh; Austin Hubley; Pierre Bauer; Yannick Guyot; Benjamin Abecassis; Benoit Mahler | Materials Science; Nanoscience; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63e0e84afcfb27a31f6742d2/original/monodisperse-size-controlled-1t-ws2-nano-monolayers-with-high-colloidal-stability.pdf |
60c753c8337d6cbe7ce288eb | 10.26434/chemrxiv.13550054.v1 | Norm-Conserving Pseudopotentials and Basis Sets to Explore Actinide Chemistry in Complex Environments | We have developed a new set of norm-conserving pseudopotentials and companion Gaussian basis sets for the actinide (An) series (Ac - Lr) using the Goedecker, Teter and Hutter (GTH) formalism with the Perdew, Burke and Ernzerhof (PBE) exchange-correlation functional of generalized gradient approximation (GGA). To test the accuracy and reliability of the newly parameterized An-GTH pseudopotentials and basis sets, a variety of benchmarks on actinide-containing molecules are carried out and compared to all-electron and available experimental results. The new pseudopotentials include both medium- ([Xe]4f14) and large-core ([Xe]4f145d10) options that have successfully reproduced structures and energetics, particularly redox processes. The medium-core size set, in particular, reproduce all-electron calculations over multiple oxidation states from 0 to VII, whereas the large-core set is suitable only for the early series elements and low oxidation states. The underlying reason for these transferability issues are discussed in detail. This work fills a critical void in the literature for studying the chemistry of 5f-block elements in condensed phase. | Jun-Bo Lu; David Cantu; Cong-Qiao Xu; Manh-Thuong Nguyen; Han-Shi Hu; Vassiliki-Alexandra Glezakou; Roger Rousseau; Jun Li | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753c8337d6cbe7ce288eb/original/norm-conserving-pseudopotentials-and-basis-sets-to-explore-actinide-chemistry-in-complex-environments.pdf |
60c741a90f50db84e6395b89 | 10.26434/chemrxiv.8089307.v1 | A General Approach for Multireference Ground and Excited States using Non-Orthogonal Configuration Interaction | A
balanced description of ground and excited states is essential for the
description of many chemical processes. However, few methods can handle cases
where static correlation is present, and often these scale very unfavourably
with system size. Recently, multiple Hartree-Fock (HF) solutions have been
proposed as a basis for non-orthogonal configuration interaction (NOCI) to
provide multireference ground and excited state energies, although applications
across multiple geometries have been limited by the coalescence of HF
solutions. Holomorphic HF (h-HF) theory allows solutions to be analytically
continued beyond the Coulson-Fischer
points at which they vanish but, until now, this has only been demonstrated for
small model systems. In this work, we propose a general protocol for computing
NOCI ground and excited state energies using multiple HF solutions. To do so,
we outline an active space variation of SCF metadynamics that allows a
chemically relevant set of HF states to be identified, and describe how these
states can be routinely traced across all molecular geometries by exploiting
the topology of h-HF solutions in the complex plane. Finally, we illustrate our
approach using the dissociation of the fluorine dimer and the
pseudo-Jahn-Teller distortion of cyclobutadiene, demonstrating its
applicability for multireference ground and excited states. <br /> | Hugh G.
A. Burton; Alex Thom | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741a90f50db84e6395b89/original/a-general-approach-for-multireference-ground-and-excited-states-using-non-orthogonal-configuration-interaction.pdf |
60c74628842e65d7cadb2743 | 10.26434/chemrxiv.8967941.v2 | Structure-Based Design of a Macrocyclic PROTAC | Constraining a molecule in its bioactive conformation via macrocyclization represents an attractive strategy to rationally design functional chemical probes. While this approach has been applied to enzyme inhibitors or receptor antagonists, to date it remains unprecedented for bifunctional molecules that bring proteins together, such as PROTAC degraders. Here, we report the design and synthesis of a first macrocyclic PROTAC by adding a second cyclizing linker to the BET degrader MZ1. A co-crystal structure of macroPROTAC-1 bound in a ternary complex with VHL and the second Brd4 bromodomain validated the rational design. Biophysical studies revealed enhanced discrimination between the second and the first bromodomains of BET proteins. Despite a 12-fold loss of binary binding affinity for Brd4, macroPROTAC-1 exhibited cellular activity comparable to MZ1. Our findings support macrocyclization as an advantageous strategy to enhance PROTAC degradation potency and selectivity between homologous targets. | Andrea Testa; Scott J. Hughes; Xavier Lucas; Jane E. Wright; Alessio Ciulli | Biochemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74628842e65d7cadb2743/original/structure-based-design-of-a-macrocyclic-protac.pdf |
6148f1fb1df4a1ea157634a2 | 10.26434/chemrxiv-2021-ln16w | Behavior of Linear and Nonlinear Dimensionality
Reduction for Collective Variable Identi cation of
Small Molecule Solution-Phase Reactions | Identifying collective variables for chemical reactions is essential to reduce the 3$N$ dimensional energy landscape into lower dimensional basins and barriers of interest. However in condensed phase processes, the non-meaningful motions of bulk solvent often overpower the ability of dimensionality reduction methods to identify correlated motions that underpin collective variables. Yet solvent can play important indirect or direct roles in reactivity and much can be lost through treatments that remove or dampen solvent motion. This has been amply demonstrated within principal component analysis, although less is known about the behavior of nonlinear dimensionality reduction methods, e.g., UMAP, that have become more popular recently. The latter presents an interesting alternative to linear methods though often at the expense of interpretability. This work presents distance attenuated projection methods of atomic coordinates that facilitate the application of both PCA and UMAP to identify collective variables in solution, and further the specific identity of solvent molecules that participate in chemical reactions. The performance of both methods is examined in detail for two reactions where the explicit solvent plays very different roles within the collective variables. The first reaction consists of the dynamic exchange of a cation about a polyhydroxy anion that is facilitated by waters of solvation, while the second reaction consists of a nucleophilic attack of water upon ethylene to initiate cis/trans isomerization.
When applied to raw data, both PCA and UMAP representations are dominated by bulk solvent motions.
On the other hand, when applied to data preprocessed by our attenuated projection methods, both PCA and UMAP identify the appropriate collective variables in solution. | Hung Le; Sushant Kumar; Nathan May; Ernesto Martinez-Baez; Ravishankar Sundararaman; Bala Krishnamoorthy; Aurora Clark | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6148f1fb1df4a1ea157634a2/original/behavior-of-linear-and-nonlinear-dimensionality-reduction-for-collective-variable-identi-cation-of-small-molecule-solution-phase-reactions.pdf |
60d1c092b912f814925afbfc | 10.26434/chemrxiv-2021-2gk1r | Electrochromism or Water Splitting in Neutral Aqueous Solutions by a Metallo-Organic Assembly | We describe two different functionalities of one metallo-organic film assembled on the surface of a transparent metal-oxide electrode. Two redox-active elements, electrochromic iron-polypyridyl complexes and catalytically-active palladium centers, operate by applying different potentials in aqueous solutions. The color of the material can be cycled 1500 times from dark purple to colorless by electrochemically addressing the Fe2+/3+ centers at 0.0-1.0 V (vs Ag/Ag+). The differences between the transmittance of these two states is high: ΔT = 52%. Catalytic water oxidation can occur by palladium oxide particles that form in-situ by applying a higher potential (1.22-2.0 V vs Ag/Ag+), resulting in the formation of dihydrogen and oxygen. The product output is stable for at least 7 hours in an aqueous electrolyte at pH = 6.9, with a Faradaic efficiency (FE) of ~70%. | Naveen Malik; Tatyana Bendikov; Michal Lahav; Milko van der Boom | Catalysis; Energy; Electrocatalysis; Heterogeneous Catalysis; Redox Catalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d1c092b912f814925afbfc/original/electrochromism-or-water-splitting-in-neutral-aqueous-solutions-by-a-metallo-organic-assembly.pdf |
60c75551ee301c5acac7b16a | 10.26434/chemrxiv.14074070.v1 | Polysulfates Block SARS-CoV-2 Uptake via Electrostatic Interactions | <p><a>Here we report that
negatively charged polysulfates can bind to the spike protein of SARS-CoV-2 via
electrostatic interactions</a>. Using a plaque reduction assay, we compare inhibition of SARS-CoV-2 by
heparin, pentosan sulfate, linear polyglycerol sulfate (LPGS) and hyperbranched
polyglycerol sulfate (HPGS). Highly sulfated LPGS is the optimal inhibitor,
with a half-maximal inhibitory concentration (IC<sub>50</sub>) of 67 μg/mL (approx. 1.6 μM). This
synthetic polysulfates exhibit more than 60-fold higher virus inhibitory
activity than heparin (IC<sub>50</sub>: 4084 μg/mL), along
with much lower anticoagulant activity. Furthermore, in molecular dynamics
simulations, we verified that LPGS can bind stronger to the spike protein than
heparin, and that LPGS can interact even more with the spike protein of the new
N501Y and E484K variants. Our study demonstrates that the entry of SARS-CoV-2 into
host cells can be blocked via electrostatic interaction, therefore LPGS can serve
as a blueprint for the design of novel viral inhibitors of SARS-CoV-2. </p> | Chuanxiong Nie; Paria Pouyan; Daniel Lauster; Jakob Trimpert; Yannic Kerkhoff; Gergo Peter Szekeres; Matthias Wallert; Stephan Block; Anil Kumar Sahoo; Jens Dernedde; Kevin Pagel; Benedikt B. Kaufer; Roland
R. Netz; Matthias Ballauff; Rainer Haag | Biochemistry; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75551ee301c5acac7b16a/original/polysulfates-block-sars-co-v-2-uptake-via-electrostatic-interactions.pdf |
67ca74906dde43c908d9bb06 | 10.26434/chemrxiv-2025-8t4c7 | Unlocking Dual Functionality in Triazine-Based Emitters: Synergistic
Enhancement of Two-Photon Absorption and TADF-OLED Performance with
Electron-Withdrawing Substituents | The simultaneous realization of two-photon absorption (2PA) and thermally activated delayed fluorescence (TADF) in a single molecular system is challenging due to the inherent trade-off in their molecular design. In this study, we develop a strategy to enhance both properties by introducing electron-withdrawing substituents into the CzTRZ scaffold. The TRZCF3 and TRZCN units effectively enhance the charge-transfer (CT) character of CzTRZ, resulting in high 2PA cross-sections (156 GM for CzTRZCF3 and 200 GM for CzTRZCN) and a reduced singlet-triplet energy gap (ΔEST = ES1 – ET1). Computational and experimental studies reveal that incorporating TRZCF3 and TRZCN units selectively stabilizes the S1 state and reduces ΔEST, significantly facilitating the reversed intersystem crossing (RISC) process. Notably, 1c exhibits the fastest RISC rate (kRISC), leading to superior TADF properties and an external quantum efficiency (EQE) of 13.5% in OLEDs. These findings demonstrate a rational molecular design strategy for the synergistic enhancement of 2PA cross-sections and excellent OLED performance, paving the way for applications in advanced imaging probes and organic semiconductors. | Youhei Chitose; Gomathi Vinayakam Mageswari; Ryota Zenke; Toshiharu Ide; Shintaro Kohata; Ja-Hon Lin; Youichi Tsuchiya; Chihaya Adachi | Organic Chemistry; Materials Science; Photochemistry (Org.); Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca74906dde43c908d9bb06/original/unlocking-dual-functionality-in-triazine-based-emitters-synergistic-enhancement-of-two-photon-absorption-and-tadf-oled-performance-with-electron-withdrawing-substituents.pdf |
610c4b3cd800ad44a4405a6a | 10.26434/chemrxiv-2021-r1dmp-v3 | Geometry Optimization Speedup Through a Geodesic Approach to Internal Coordinates | We present a new geodesic-based method for geometry optimization in a basis of redundant internal coordinates. Our method updates the molecular geometry by following the geodesic generated by a displacement vector on the internal coordinate manifold, which dramatically reduces the number of steps required to converge to a minimum. Our method can be implemented in any existing optimization code, requiring only implementation of derivatives of the Wilson B-matrix and the ability to numerically solve an ordinary differential equation. | Eric Hermes; Khachik Sargsyan; Habib Najm; Judit Zádor | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610c4b3cd800ad44a4405a6a/original/geometry-optimization-speedup-through-a-geodesic-approach-to-internal-coordinates.pdf |
651b238400659409124fd9f9 | 10.26434/chemrxiv-2023-zrtdk | Coarse-Grained Model-Assisted Design of Optimized Polymer Prodrug Nanoparticles: A Combined Theoretical and Experimental Study | To achieve efficient drug release from polymer prodrug nanoparticles, the drug-polymer linker must be accessible for cleavage to release the drug, which can occur under certain physiological conditions (e.g., presence of specific enzymes). Supramolecular organization of polymer prodrug nanoparticles is crucial as it greatly affects the location of the linker, its surface exposure/solvation and thus its cleavage to release the drug. Since experimental access to this data is not straightforward, a new methodology is critically needed to access this information and to accelerate the development of more effective polymer prodrug nanoparticles, and replace the time-consuming and resource-intensive traditional trial-and-error strategy. In this context, we developed a coarse-grained model-assisted design of optimized polymer prodrug nanoparticles. By choosing the solvent accessible surface area as the critical parameter for predicting drug release and hence cytotoxicity of polymer prodrug nanoparticles, we developed an optimized polymer-drug linker with enhanced hydrophilicity and solvation. Our hypothesis was then experimentally validated by the synthesis of the corresponding polymer prodrugs based on two different drugs (gemcitabine and paclitaxel), which demonstrated greater performances in terms of drug release and cytotoxicity on two cancer cell lines. Interestingly, our methodology can be easily applied to other polymer prodrug structures, which would contribute to the development of more efficient drug delivery systems. | Ping Gao; Tâp Ha-Duong; Julien Nicolas | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Polymer Science; Drug delivery systems; Polymerization (Polymers); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651b238400659409124fd9f9/original/coarse-grained-model-assisted-design-of-optimized-polymer-prodrug-nanoparticles-a-combined-theoretical-and-experimental-study.pdf |
63501328a2c7901fae4e070c | 10.26434/chemrxiv-2022-b916c | Mechanistic Investigations into the Selective Reduction of Oxygen by a MCO T3 site-inspired Copper Complex | Understanding how multicopper oxidases (MCOs) efficiently and selectively reduce oxygen in the trinuclear copper cluster (TNC) is of great importance. Previously it was reported that when the T2-site is removed from the TNC, all O2 binding activity at the dinuclear T3-site is lost. Computational studies attribute this loss of activity to the flexibility of the protein active site, where the T3-copper centers move apart to minimize electrostatic repulsions. To address the question if and how a more constrained T3-site will catalyze the reduction of oxygen, we herein report a mechanistic investigation into the oxygen reduction reaction (ORR) activity of the dinuclear copper complex [Cu2L(μ-OH)]3+ (L=2,7-bis[bis(2-pyridylmethyl)aminomethyl]-1,8-naphthyridine). This T3-inspired complex confines the Cu centers in a rigid scaffold in close proximity instead of the flexible scaffold found in the protein active site and we demonstrate that under these constraints the dinuclear copper site displays ORR activity. Compared to the ORR mechanism of MCOs, we show that electrochemical reduction of [Cu2L(μ-OH)]3+ follows a similar pathway as the reduction of the resting enzyme due to the presence of the Cu-OH-Cu motif. By identification of key intermediates along the catalytic cycle of [Cu2L(μ-OH)]3+ we provide for the first time evidence that metal-metal cooperativity takes place during electrocatalysis of the ORR by a copper-based catalyst, which is achieved by the ability of the rigid ligand framework to bind two copper atoms in close proximity. Electrochemical studies show that the mechanisms of the ORR and hydrogen peroxide reduction reaction (HPRR) found for [Cu2L(μ-OH)]3+ are different from the ones found for analogous mononuclear copper catalysts. In addition, the metal-metal cooperativity results in an improved selectivity for the four-electron ORR of more than 70%. This selectivity is achieved by better stabilization of reaction intermediates between both copper centers, which is also essential for the ORR mechanism observed in MCOs. Overall, the mechanism of the [Cu2L(μ-OH)]3+-catalyzed ORR in this work gives insight into the ORR activity of a T3-site and contributes to understanding of how the ORR activity and selectivity are established in MCOs. | Phebe H. Langevelde; Errikos Kounalis; Lars Killian; Emily Monkcom; Daniel L. J. Broere; Dennis G. H. Hetterscheid | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Bioinorganic Chemistry; Electrocatalysis; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63501328a2c7901fae4e070c/original/mechanistic-investigations-into-the-selective-reduction-of-oxygen-by-a-mco-t3-site-inspired-copper-complex.pdf |
61fc000a216867384a6a0f43 | 10.26434/chemrxiv-2022-02hlc | Synthesis and copolymerization of novel oxy ring-substituted isopropyl cyanoarylacrylates | Novel oxy ring-substituted isopropyl 2-cyano-3-arylacrylates, RPhCH=C(CN)CO2CH(CH3)2 (where R is 3-phenoxy, 4-phenoxy, 2-benzyloxy, 3-benzyloxy, 4-benzyloxy, 4-acetyloxy, 3-acetyl, 4-acetyl, 4-acetylamino, 4-methoxy-2-methyl, 4-methoxy-3-methyl, 3-ethoxy-4-methoxy, 3,4-dibenzyloxy, 3-benzyloxy-4-methoxy, 4-benzyloxy-3-methoxy, 2,3-dimethyl-4-methoxy, 2,5-dimethyl-4-methoxy, 2,4-dimethoxy-3-methyl, 2,4-dimethoxy-6-methyl, 3,5-dimethoxy-4-hydroxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of oxy ring-substituted benzaldehydes and isopropyl cyanoacetate and characterized by CHN elemental analysis, FTIR, 1H and 13C-NMR. All the acrylates were copolymerized with styrene in solution with radical initiation at 70C. The composition of the copolymers was calculated from nitrogen analysis, and the structures were analyzed by FTIR, 1H and 13C-NMR. Thermal properties of the copolymers are characterized by DSC and TGA. Decomposition of the copolymers in nitrogen occurred in two steps, first in the 200-500ºC range with a residue, which then decomposed in the 500-800ºC range. | Kumail M. Hussain; Joshua J. Ludtke; Jose L. Zepeda; Sara Rocus; William Schjerven; Gregory B Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fc000a216867384a6a0f43/original/synthesis-and-copolymerization-of-novel-oxy-ring-substituted-isopropyl-cyanoarylacrylates.pdf |
6438f02373c6563f14d40de1 | 10.26434/chemrxiv-2022-1q6gb-v4 | Angstrom-confined electrochemical synthesis of sub-unit cell non van der Waals 2D metal oxides | Bottom-up electrochemical synthesis of atomically thin materials is desirable yet challenging, especially for non-van der Waals (vdW) materials. Thicknesses below few nm have not been reported yet, posing the question how thin can non-vdW materials be electrochemically synthesized? This is important as materials with (sub-) unit cell thickness often show remarkably different properties compared to their bulk form or thin films of several nm thickness. Here, we introduce a straightforward electrochemical method utilizing the angstrom-confinement of laminar reduced graphene oxide (rGO) nanochannels to obtain a centimeter-scale network of atomically thin (< 0.43nm) 2D-transition metal oxides (2D-TMO). The angstrom-confinement provides a thickness limitation, forcing sub-unit cell growth of 2D-TMO with oxygen and metal vacancies. We showcase that Cr2O3, a material without significant catalytic activity for OER in bulk form, can be activated as a high-performing catalyst if synthesized in the 2D sub-unit cell form. Our method displays the high activity of sub-unit cell form while retaining the stability of bulk form, promising to yield unexplored fundamental science and applications. We show that while retaining the advantages of bottom-up electrochemical synthesis like simplicity, high yield, and mild conditions, the thickness of TMO can be limited to sub-unit cell dimensions. | Dali Ji; Yunah Lee; Yuta Nishina; Kazuhide Kamiya; Rahman Daiyan; Xinyue Wen; Dewei Chu; Masamichi Yoshimura; Priyank Kumar; Daria Andreeva; Kostya Novoselov; Gwan-Hyoung Lee; Rakesh Joshi; Tobias Foller | Materials Science; Nanoscience; Carbon-based Materials; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438f02373c6563f14d40de1/original/angstrom-confined-electrochemical-synthesis-of-sub-unit-cell-non-van-der-waals-2d-metal-oxides.pdf |
630d13f090802ddf8d6ec794 | 10.26434/chemrxiv-2022-th2wh | Unravelling Water and Salt transport in Polyamide with Nuclear Magnetic Resonance Spectroscopy | Unraveling water and salt transport in polyamide is of growing importance as the use of reverse osmosis membranes grows in many industries. Here, using solid-state nuclear magnetic resonance (NMR) spectroscopy, we measure the translational diffusion coefficients using pulsed-field gradient NMR, examine ion dynamics with NMR relaxometry, and determine activation energy barriers of hydrogen and sodium ions in ion-exchanged polyamide using variable-temperature NMR. We identify two predominant diffusion components within the spectra associated with bound and unbound hydrogen and sodium ions. We show that the diffusion coefficient of the bound hydrogen ions decreases by 46% while the free hydrogen diffusion coefficient remained constant as the salinity of the mixture increases from 1 M to 2 M. Conversely, the diffusion coefficient of bounded sodium did not change while the unbounded sodium diffusion coefficient decreased by 38% as the salinity of the mixture increases from 1 M to 2 M. Through examining the spin-lattice relaxation time (T1) at various temperatures we reveal that the sodium and hydrogen ion motion decreases with an increase in salinity, and we also report the associated activation energy. We believe these molecular-scale measurements can aid in extending the solution-diffusion model of reverse osmosis membranes. | Mahsa Abbaszadeh; Ji LL Choi; Yudan Chen; Johannes Leisen; Madeline Garell; Seung Soon Jang; Yan-Yan Hu; Marta Hatzell | Polymer Science; Energy; Chemical Engineering and Industrial Chemistry; Transport Phenomena (Chem. Eng.); Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630d13f090802ddf8d6ec794/original/unravelling-water-and-salt-transport-in-polyamide-with-nuclear-magnetic-resonance-spectroscopy.pdf |
6116a01f424ea3ed758921a7 | 10.26434/chemrxiv-2021-9f2m5 | Making it rain: cloud-based molecular simulations for everyone | We present a user-friendly front-end for running molecular dynamics (MD) simulations using OpenMM toolkit on the Google Colab framework. Our goals are: 1) to highlight the usage of a cloud-computing scheme for educational purposes for a hands-on approach when learning MD simulations and 2) to exemplify how low-income research groups can perform MD simulations in the microsecond timescale. We hope this work facilitates teaching and learning of molecular simulation throughout the community. | Pablo Ricardo Arantes; Marcelo Depólo Polêto; Conrado Pedebos; Rodrigo Ligabue-Braun | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6116a01f424ea3ed758921a7/original/making-it-rain-cloud-based-molecular-simulations-for-everyone.pdf |
64ca9d2169bfb8925a3f9aa8 | 10.26434/chemrxiv-2023-rzn2r-v3 | Emergence of Anionic Counterparts of Divalent Metal Salts as the Fine-Tuners of Alginate Hydrogel Properties for Tissue Engineering and Drug Delivery Applications | The role of anionic counter ions of divalent metal salts in alginate gelation and hydrogel properties was thoroughly investigated. Three anions were selected from the Hofmeister series viz. sulphates, acetates and chlorides paired in all permutations and combinations with calcium, zinc and copper divalent metals. Spectroscopic analysis revealed the presence of anions and their interaction with the metal atoms post-gelation. Data showed gelation time and other hydrogel properties were mostly governed by the cations. However, subtle yet significant variations in viscoelastic, water-uptake, drug-release and cytocompatibility properties were anion dependent in a cationic group. Computational modelling study showed metal-anion-alginate configurations were energetically more stable than metal-alginate models. The in vitro and in silico studies conclude that acetate anions precede the chlorides in the drug-delivery, swelling, and cytocompatibility fronts, followed by sulphate anions in each cationic group. Overall, the data provided affirmation that anions are integral part of the metal-alginate complex. Furthermore, anions offer a novel option to further fine-tune the properties of alginate hydrogels for tissue engineering and drug delivery applications. Moreover, extensive exploration of this novel avenue would enhance the usability of alginate polymers in pharma, environmental, biomedical and food industries. | Subhasis Dash; Pavan Gutti; Birendra Behera; Debasish Mishra | Biological and Medicinal Chemistry; Materials Science; Biocompatible Materials; Controlled-Release Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca9d2169bfb8925a3f9aa8/original/emergence-of-anionic-counterparts-of-divalent-metal-salts-as-the-fine-tuners-of-alginate-hydrogel-properties-for-tissue-engineering-and-drug-delivery-applications.pdf |
60c73f75337d6ce6fbe2651e | 10.26434/chemrxiv.7381025.v1 | Photocatalytically Active Ladder Polymers | <p>Conjugated ladder polymers
(cLaPs) are introduced as organic semiconductors for photocatalytic hydrogen
evolution from water under sacrificial conditions. Starting from a linear
conjugated polymer (cLiP1), two ladder polymers are synthesized via
post-polymerization annulation and oxidation techniques to generate rigidified,
planarized materials bearing dibenzo[<i>b</i>,<i>d</i>]thiophene (<b>cLaP1</b>) and dibenzo[<i>b</i>,<i>d</i>]thiophene sulfone subunits (<b>cLaP2</b>). The high photocatalytic
activity of <b>cLaP1</b>
(1307 μmol h<sup>−1</sup> g<sup>−1</sup>) in comparison to <b>cLaP2</b> (18 μmol h<sup>−1</sup> g<sup>−1</sup>)
under broadband illumination (λ >295 nm) in presence of a
hole-scavenger is attributed to a higher yield of long-lived charges (µs–ms
timescale), as evidenced by transient absorption spectroscopy. Additionally, <b>cLaP1</b> has a larger overpotential for
proton reduction and thus an increased driving force for the evolution of
hydrogen under sacrificial conditions.</p> | Anastasia Vogel; Mark forster; Liam Wilbraham; Charlotte Smith; Alexander Cowan; Martijn Zwijnenburg; Seb Sprick; Andrew
I. Cooper | Conducting polymers; Organic Polymers; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f75337d6ce6fbe2651e/original/photocatalytically-active-ladder-polymers.pdf |
60c757d5702a9be84318cb9a | 10.26434/chemrxiv.14464980.v1 | Is Configurational Entropy the Main Stabilizing Term in Rock-Salt Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O High-Entropy Oxide? | We question the conclusions reported in the paper "Entropy-stabilized Oxides, by C. Rost et al., by looking into the role of configurational entropy as the stabilization of the rock-salt cubic structure of the Mg0.2Co0.2Ni0.2Cu0.2Zn0.2O (HEO) solid solution (SS). First, we demonstrate that configurational entropy can be reduced from 1.61R for HEO to 0.5R for a two-member SS, still obtaining a single-phase material if the molar fractions of ZnO and CuO are 0.2. These SSs behave identically as HEO regarding the reversible transformation between a multi- and single-phase states when temperatures are cycled between 800 and 1000 °C. Second, we demonstrate that the different SSs presenting a configurational entropy significantly lower than HEO, are less prone to the cubic to tetragonal structural distortion, suggesting that the configurational entropy has not the central role as stabilizing factor of the rock-salt structure.<br /> | Martina Fracchia; Mauro Coduri; Maela Manzoli; Paolo Ghigna; Umberto Anselmi-Tamburini | Ceramics; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757d5702a9be84318cb9a/original/is-configurational-entropy-the-main-stabilizing-term-in-rock-salt-mg0-2co0-2ni0-2cu0-2zn0-2o-high-entropy-oxide.pdf |
60c745cf337d6c1431e27060 | 10.26434/chemrxiv.10119230.v1 | Strain Induced Tunability of the Electronic Properties of SrTiO3 Interfaces | SrTiO 3 (STO) films are widely used as substrates in oxide devices. Although STO is one of the most studied materials, both experimentally and computationally, the effect of strain at the interface is almost completely ignored. In this work, we perform Density Functional Theory (DFT) calculations using the SCAN meta-GGA exchange-correlation functional to study the effect of uniaxial- and biaxial-strain on structural and electronic properties of STO interfaces. We find that under tensile uniaxial-strain, the band gap increases significantly, as a consequence of a large tilting in the octahedra. On the other side, under compression, the band gap is almost constant. Similar effects are seen for tensile biaxial strain, while for compressive strain, the gap first increases and then decreases, due to the temporary appearance of a polar distortion. In addition, we observe an orbital inversion at the conduction-band edge under different uni/bi-axial-strain conditions. This work provides a new perspective of the use of strain to modulate the structural and electronic properties of perovskite film materials for multiple applications. | Zhenyun Lan; Tejs Vegge; Ivano E. Castelli | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745cf337d6c1431e27060/original/strain-induced-tunability-of-the-electronic-properties-of-sr-ti-o3-interfaces.pdf |
665c891121291e5d1de5ae7a | 10.26434/chemrxiv-2024-v8mmt | ∆DFT predicts inverted singlet-triplet gaps with chemical accuracy at a fraction of the cost of wavefunction-based approaches | Efficient OLEDs must quickly convert singlet and triplet excitons into photons. Molecules with an inverted singlet-triplet energy gap (INVEST) are promising candidates for this task. However, typical INVEST molecules have drawbacks like too low oscillator strengths and excitation energies. High-throughput screening could identify suitable INVEST molecules, but existing methods are problematic: The workhorse method TD-DFT cannot reproduce gap inversion, while wavefunction-based methods are too slow. This study proposes a state-specific method based on unrestricted Kohn-Sham DFT with common hybrid functionals. Tuned on the new INVEST15 benchmark set, this method achieves an error of less than 1 kcal/mol, which is traced back to error cancellation between spin contamination and dynamic correlation. Applied to the larger and structurally diverse NAH159 set in a black-box fashion, the method maintains a small error (1.2 kcal/mol) and accurately predicts gap signs in 83% of cases, confirming its robustness and suitability for screening workflows. | Lukas Kunze; Thomas Froitzheim; Andreas Hansen; Stefan Grimme; Jan-Michael Mewes | Theoretical and Computational Chemistry; Materials Science; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665c891121291e5d1de5ae7a/original/dft-predicts-inverted-singlet-triplet-gaps-with-chemical-accuracy-at-a-fraction-of-the-cost-of-wavefunction-based-approaches.pdf |
64ca90e569bfb8925a3f3280 | 10.26434/chemrxiv-2023-tg7fj-v2 | Long Lifetime Mild pH-decoupling Aqueous Flow Battery with Practical in Situ pH Recovery | Aqueous redox flow batteries (ARFBs) constitute a promising technology for grid-scale electricity storage, but it is challenging to implement cell voltages exceeding the 1.23 V thermodynamic water splitting window with high Coulombic efficiency and long lifetime. pH decoupling – the creation of a pH difference between the negolyte and posolyte – can broaden the operating voltage window and improve long-term operational stability. This penalizes the efficiency, however, due to acid-base crossover induced by the pH gradient. As the voltage of the water splitting window varies linearly with pH whereas crossover fluxes vary exponentially, we employed mildly acidic and mildly basic electrolytes to develop a cell with high round-trip energy efficiency at an open-circuit voltage > 1.7 V. Moreover, we implemented an in situ acid-base regeneration system to periodically restore the negolyte and posolyte pH to their initial values. The combined system exhibits a capacity fade rate of less than 0.07% per day, a roundtrip energy efficiency of over 85%, and a Coulombic efficiency of approximately 99%. This work demonstrates principles for addressing critical issues such as lifespan, rate capability, long-term practicability, and energy efficiency in pH-decoupling ARFBs, providing guidance for the design of the next generation of high-voltage ARFBs. | Dawei Xi; Abdulrahman Alfaraidi; Jinxu Gao; Thomas Cochard; Luana Faria; Thomas George; Taobo Wang; Roy Gordon; Richard Liu; Michael Aziz | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-08-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ca90e569bfb8925a3f3280/original/long-lifetime-mild-p-h-decoupling-aqueous-flow-battery-with-practical-in-situ-p-h-recovery.pdf |
60c746bc4c891941d1ad2bb9 | 10.26434/chemrxiv.11372022.v1 | Understanding Thermal and Organic Solvent Stability of Thermoalkalophilic Lipases: Insights from Computational Predictions and Experiments | The study enclosed herein reports computational
and experimental findings on the active and inactive conformations of the
lipase from the family I.5. Given their high stability under extreme
conditions, this lipase family, also called thermoalkalophilic liapses, are of
high potential for industrial reactions. To this end, this study investigated
the structural impact of 5 different organic solvents that are commonly used in
industrial reactions, on the active and inactive conformations <i>in silico</i>. These findings were validated
by the experiments which recruited the recombinant enzyme and analyzed organic
solvent stability at different temperatures. <br /> | Mohamed Shehata; Emel Timucin; Alessandro Venturini; Osman Ugur Sezerman | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746bc4c891941d1ad2bb9/original/understanding-thermal-and-organic-solvent-stability-of-thermoalkalophilic-lipases-insights-from-computational-predictions-and-experiments.pdf |
65c2abace9ebbb4db9cf1a24 | 10.26434/chemrxiv-2023-j62ft-v2 | Taming The Third Order Cumulant Approximation to Linear Optical Spectroscopy | The second order cumulant method offers a promising pathway to predicting optical properties in condensed phase systems. It allows for the computation of linear absorption spectra from excitation energy fluctuations sampled along molecular dynamics (MD) trajectories, fully accounting for vibronic effects, direct solute-solvent interactions, and environmental polarization effects. However, the second order cumulant approximation only guarantees accurate lineshapes for energy gap fluctuations obeying Gaussian statistics. A third order correction has been derived recently [J. Chem. Phys. {151}, 074111 (2019)], but often yields unphysical spectra or divergent lineshapes for moderately non-Gaussian fluctuations, due to the neglect of higher order terms in the cumulant expansion. In this work, we develop a corrected cumulant approach, where the collective effect of neglected higher order contributions is approximately accounted for through a dampening factor applied to the third order cumulant term. We show that this dampening factor can be expressed as a function of the skewness and kurtosis of the energy gap fluctuations and can be parameterized from a large set of randomly sampled model Hamiltonians for which exact spectral lineshapes are known. The approach is shown to systematically remove unphysical contributions in the form of negative absorbances from cumulant spectra in both model Hamiltonians and condensed phase systems sampled from MD, and dramatically improves over the second order cumulant method in describing systems exhibiting Duschinsky mode mixing effects. We successfully apply the approach to the coumarin-153 dye in toluene, obtaining an | Luke Allan; Tim Zuehlsdorff | Theoretical and Computational Chemistry; Physical Chemistry; Theory - Computational; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c2abace9ebbb4db9cf1a24/original/taming-the-third-order-cumulant-approximation-to-linear-optical-spectroscopy.pdf |
66e87daacec5d6c142425aad | 10.26434/chemrxiv-2024-j0229-v2 | Directed Evolution Enables Dynamic Control of Transient Intermediates for Anti-Markovnikov Wacker-Tsuji-Type Oxidation of Unactivated Alkenes | Controlling the dynamic behavior of highly reactive fleeting intermediates is an intriguing concept to generate selectivity in competing reaction pathways. Here we report the directed evolution of a P450 enzyme for anti-Markovnikov-selective Wacker-Tsuji-type oxidation of unactivated alkenes. This reaction is a long-standing challenge in catalysis due to its unfavorable energetics and competing reactions. The evolved aMOx-A enzyme performs anti-Markovnikov oxidation of unactivated alkenes with several hundred turnovers and possesses kinetic parameters comparable to those of average natural enzymes. The biocatalyst guides an oxo-transfer process through multiple competing reactions, including bifurcating reaction pathways that originate after a rate-limiting transition state. Chemoselectivity of aMOx-A arises from controlling substrate conformations as well as dynamics of reactive intermediates. This includes accessing and controlling a fleeting carbocation intermediate that does not correspond to a minimum on the potential energy surface. Engineering of aMOx-A highlights how directed enzyme evolution optimizes unique catalytic processes that have largely eluded efficient catalysis. | Cindy Klaus; Jordi Soler; Grzegorz Kubik; Yosephine Gumulya; Yue Hui; Ella J. Watkins-Dulaney; Max-Luca Heitland; Marc Sommer; Alina Klein; Julia L. Kowal; Hartmut H. Niemann; Frances H. Arnold; Marc Garcia-Borràs; Stephan C. Hammer | Organic Chemistry; Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e87daacec5d6c142425aad/original/directed-evolution-enables-dynamic-control-of-transient-intermediates-for-anti-markovnikov-wacker-tsuji-type-oxidation-of-unactivated-alkenes.pdf |
64ff350999918fe537c3b3b8 | 10.26434/chemrxiv-2023-pf1kh | Polymer-assisted microcontact printing: Using a tailor-made polydimethylsiloxane (PDMS) stamp for precise patterning of rough surfaces | Rough, capillary-active surfaces remain demanding substrates for microcontact printing (µCP), as the diffusive mobility of the ink thereon drastically limits the printing resolution. To reduce ink smearing, we developed a polymer-supported μCP, which includes a stamp with a polymer brush-decorated surface. The ink molecules are thereby bound into the stamp-bound brush matrix, from where they may be transferred to the substrate, which exclusively occurs during the contact of both interfaces. Conventionally, Slygard184-based polydimethylsiloxane (PDMS) stamps are used for µCP. The material’s surface must be functionalized in a multi-step procedure for the protocol. In addition, Sylgard comes along with a drawback of a persistent leakage oligomeric PDMS (oPDMS), which can contaminate the substrate. To circumvent these problems, we developed a novel stamp material, that (i) enables a straightforward polymer grafting, and (ii) shows a low tendency of oPDMS leakage. We prepare the stamp with a commercially available amino-functional PDMS prepolymer, and a polymer-ic crosslinker that can be used for a controlled photoiniferter reversible addition and fragmentation chain transfer (PI-RAFT) polymerization. The prepared stamp shows elastic properties at the relevant strain region, is compatible with brush formation, and has been demonstrated demonstrated suitable to transfer precise patterns on rough capillary-active oxide surfaces. | Nazim Pallab; Stefan Reinicke; Johannes Gurke; Rainer Rihm; Sergio Kogikoski Jr.; Matthias Hartlieb; Martin Reifarth | Polymer Science; Polymer brushes | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ff350999918fe537c3b3b8/original/polymer-assisted-microcontact-printing-using-a-tailor-made-polydimethylsiloxane-pdms-stamp-for-precise-patterning-of-rough-surfaces.pdf |
60c73d51469df44598f426d2 | 10.26434/chemrxiv.5712217.v1 | Solar Synthesis of Limonene Epoxide | The silylation of crystalline
titania P25, commonly used for photocatalytic degradation of pollutants,
results in an exceptionally selective catalyst for the aerobic limonene epoxidation
to 1,2-limonene oxide under solar light irradiation. The hypothesized mechanism
involves the singlet oxygen generated through energy transfer from the excited
TiO<sub>2</sub> to adsorbed O<sub>2</sub> molecules. The reaction product is the
valued precursor of bio-based poly(limonene carbonate), a thermoplastic polymer
of superior thermal and optical properties whose industrial production is in
need of an efficient green synthesis of limonene oxide. | Rosaria Ciriminna; Francesco Parrino; Claudio De Pasquale; Leonardo Palmisano; Mario Pagliaro | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d51469df44598f426d2/original/solar-synthesis-of-limonene-epoxide.pdf |
64b97e0eae3d1a7b0d102135 | 10.26434/chemrxiv-2023-vz994-v2 | Simultaneous Electrochemical Exfoliation and Functionalization of 2H-MoS2 | MoS2 is a promising semiconducting material that has been widely studied for applications in catalysis and energy storage. The covalent chemical functionalization of MoS2 can be used to tune the optoelectronic and chemical properties of MoS2 for different applications. However, 2H-MoS2 is typically chemically inert and difficult to functionalize directly and thus requires pre-treatments such as a phase transition to 1T-MoS2 or argon plasma bombardment to introduce reactive defects. Apart from being inefficient and inconvenient, these methods can cause a degradation of the desirable properties and introduce unwanted defects. Here, we report a facile and scalable procedure of fabricating functionalized thin (~4 nm) MoS2 layers. We demonstrate that 2H-MoS2 can be simultaneously electrochemically exfoliated and functionalized. The aryl diazonium salts used for functionalization have not only been successfully grafted onto the 2H-MoS2, as verified by X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy, but also aid the exfoliation. Electrochemical characterization of MoS2 supercapacitors revealed that the specific capacitance of electrodes produced using this material was increased by 25% when functionalized. This electrochemical functionalization technique could possibly be extended to other types of transition metal dichalcogenides (TMDs), which are also chemically inert, with different functional species to adjust to specific applications. | Yuling Zhuo; Ian Kinloch; Mark Bissett | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanocatalysis - Catalysts & Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b97e0eae3d1a7b0d102135/original/simultaneous-electrochemical-exfoliation-and-functionalization-of-2h-mo-s2.pdf |
637764a055455e1e9c89f824 | 10.26434/chemrxiv-2022-41pf6 | A Donor-Acceptor 10-Cycloparaphenylene and Its Use as an Emitter in an Organic Light-Emitting Diodes | Here, we explored the possibility of using radial conjugated π-system of cycloparaphenylenes (CPP) within a donor-acceptor TADF emitter design. 4PXZPh-[10]CPP contains four electron-donating moieties connected to a [10]CPP. In the 15 wt% doped in CzSi film, 4PXZPh-[10]CPP showed sky-blue emission with λPL = 475 nm, ΦPL = 29%, and triexponential emis-sion decays with τPL of 4.4, 46.3 and 907.8 ns. Solution-processed OLEDs using 4PXZPh-[10]CPP exhibited sky-blue emission with an λEL of 465 nm and an EQEmax of 1.0%. | Dongyang Chen; Yoshimasa Wada; Yu Kusakabe; Ei-ichi Kayahara; Liangsheng Sun; Katsuaki Suzuki; Hiroyuki Tanaka; Shigeru Yamago; Hironori Kaji; Eli Zysman-Colman | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637764a055455e1e9c89f824/original/a-donor-acceptor-10-cycloparaphenylene-and-its-use-as-an-emitter-in-an-organic-light-emitting-diodes.pdf |
6458c70c27fccdb3eab194ad | 10.26434/chemrxiv-2023-trm05-v3 | Benzimidazoles and Imidazo[1,2-a]pyridines : Biological Activities, Method of Synthesis and Perspectives on Combination of Deuce Pharmacophore | N-Heterocyclic scaffolds have generated significant interest among medicinal chemists. Among
these potential heterocyclic drugs, benzimidazole and imidazopyridine scaffolds are the most
prevalent. Over the past few decades, it has gained immense attention. Both are important classes
of molecules owing to their wide spectrum of biological activities and clinical applications. Both
are used in fashion design and the development of novel synthetic analogs for various therapeutic
disorders. A wide variety of derivatives have been developed as potential anticancer, antimicrobial,
antiviral, and anti-inflammatory agents in addition to other chemotherapeutic agents. The
benzimidazole core is found in a natural system, displaying a wide range of pharmaceutical
properties, and has gained significant attention in medicinal chemistry, as reported in several full
articles and communications. Imidazopyridines are widely distributed in many pharmacologically
important compounds, as shown by their frequent occurrence in a large number of marketed drug
formulations and drug candidates, as well as in other fields such as material and organometallic
chemistry. These scaffolds have been structurally characterized as ligands that can bind to different
receptor sites for the discovery of various emerging drugs. They act as key pharmacophore motifs
for the identification and optimization of lead structures to increase the medicinal chemistry
toolbox. This review outlines the synthesis and medicinal significance of benzimidazoles and
imidazopyridines for their development as lead molecules with improved therapeutic efficiency.
Here, we cover the various designs used to obtain both heterocycles to establish a relationship
between their combination and biological activities. | Souleymane Coulibaly; Ablo Evrard; Amit Kumar; Drissa Sissouma | Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6458c70c27fccdb3eab194ad/original/benzimidazoles-and-imidazo-1-2-a-pyridines-biological-activities-method-of-synthesis-and-perspectives-on-combination-of-deuce-pharmacophore.pdf |
63f7976932cd591f125ff401 | 10.26434/chemrxiv-2023-l1n1p | Intramolecular and Intermolecular Hole Delocalization Rules the Reducer Character of Isolated Nucleobases and Homogeneous Single-Stranded DNA | The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization. | Jesús Lucia-Tamudo; Sergio Díaz-Tendero; Juan Jose Nogueira | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f7976932cd591f125ff401/original/intramolecular-and-intermolecular-hole-delocalization-rules-the-reducer-character-of-isolated-nucleobases-and-homogeneous-single-stranded-dna.pdf |
6752fe177be152b1d0246e7b | 10.26434/chemrxiv-2024-bgzv3 | Green light activated dual-action Pt(IV) prodrug with enhanced PDT activity | Light induced release of cisplatin from Pt(IV) prodrugs is a promising tool for precise spatiotemporal control over the antiproliferative activity of Pt-based chemotherapeutic drugs. A combination of light-controlled chemotherapy (PACT) and photodynamic therapy (PDT) in one molecule has the potential to overcome crucial drawbacks of both Pt-based chemotherapy and PDT via synergetic effect. Herein we report green-light activated Pt(IV) prodrugs GreenPt with BODIPY-based photosentitizer in axial position with incredible high light response and singlet oxygen generation ability. GreenPt demonstrated the ability to release cisplatin under low-dose green light irradiation up to 1 J/cm2. The investigation of the photoreduction mechanism of GreenPt prodrug using DFT modeling and ΔG0 PET estimation revealed that the anion-radical formation and substituent photoinduced electron transfer from the triplet excited state of the BODIPY axial ligand to the Pt(IV) center is the key step in the light-induced release of cisplatin. Green-light activated BODIPY-based photosentitizers 5 and 8 demonstrated outstanding photosensitizing properties with extraordinary phototoxicity index (PI) >1300. GreenPt prodrug demonstrated gradual intracellular accumulation and light-induced phototoxicity with PI > 100, thus demonstrating dual action through light-controlled release of both cisplatin and a potent BODIPY-based photosensitizer. | Olga Krasnovskaya; Daniil Spector; Vladislav Bykusov; Yulia Isaeva; Roman Akasov; Anastasia Zharova; Igor Rodin; Mikhail Vokuev; Vita Nikitina; Alexander Martynov; Elena Beloglazkina | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6752fe177be152b1d0246e7b/original/green-light-activated-dual-action-pt-iv-prodrug-with-enhanced-pdt-activity.pdf |
60c73cc90f50dbb8423953bb | 10.26434/chemrxiv.14756190.v1 | Biofunctionalisation of Gallium Arsenide with Neutravidin | <div>We report a study presenting a physicochemical surface characterisation of the GaAs surface along the functionalisation with a high-affinity bioconjugation pair widely explored in the life</div><div>sciences: biotin and neutravidin. Combined X-ray photoelectron spectroscopy (XPS), wettability measurements and spectroscopic ellipsometry were used for a reliable characterisation of the surface functionalisation process. The results suggest that a film with a thickness lower than 10nm was formed, with a neutravidin to biotin ratio of 1:25 on the GaAs surface. Reduction of non-specific binding of the protein to the surface was achieved by optimising the protein buffer and rinsing steps. This study shows the feasibility of using GaAs as a platform for specific biomolecular recognition, paving the way to a new generation of optoelectronic biosensors.</div> | Barbara Santos Gomes; David Morgan; Wolfgang Langbein; Paola Borri; Francesco Masia | Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc90f50dbb8423953bb/original/biofunctionalisation-of-gallium-arsenide-with-neutravidin.pdf |
60c74eedbdbb8931eda39c83 | 10.26434/chemrxiv.12820502.v1 | Asymmetric Bis-PNP Pincer Complexes of Zirconium and Hafnium - a Measure of Hemilability | Asymmetrically-bound pyrrollide-based bis-PNP pincer complexes of zirconium and hafnium<br />have been formed. The [κ2-PNPPh][κ3-PNPPh]MCl2 species are in direct contrast to previous<br />zirconium PNP pincer complexes. The pincer ligands are fluxional in their binding and the<br />energy barrier for exchange has been approximated using VT-NMR spectroscopy and the<br />result validated by DFT calculations. | Celia Idelson; Leah Webster; Tobias Krämer; Mark Chadwick | Coordination Chemistry (Organomet.); Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eedbdbb8931eda39c83/original/asymmetric-bis-pnp-pincer-complexes-of-zirconium-and-hafnium-a-measure-of-hemilability.pdf |
631ca0b50429d63a0e9998b8 | 10.26434/chemrxiv-2022-qt49t | Explainable Uncertainty Quantifications for Deep Learning-Based Molecular Property Prediction | Quantifying uncertainty in machine learning is important in new research areas with scarce high-quality data. In this work, we develop an explainable uncertainty quantification method for deep learning-based molecular property prediction. This method can capture aleatoric and epistemic uncertainties separately and attribute the uncertainties to atoms present in the molecule. The atom-based uncertainty method provides an extra layer of explainability to the estimated uncertainties, i.e., one can analyze individual atomic uncertainty values to diagnose the chemical component that introduces uncertainty to the prediction. Our experiments demonstrate that atomic uncertainty can detect unseen chemical structures and identify chemical species whose data are potentially associated with significant noise. Furthermore, we propose a post-hoc calibration method to refine the uncertainty quantified by ensemble models for better confidence interval estimates. This work improves uncertainty calibration and provides a framework for assessing whether and why a prediction should be considered unreliable. | Chu-I Yang; Yi-Pei Li | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631ca0b50429d63a0e9998b8/original/explainable-uncertainty-quantifications-for-deep-learning-based-molecular-property-prediction.pdf |
67d167d4fa469535b9f7a99f | 10.26434/chemrxiv-2025-qxc9b | Solid-state formation reactions of (Ba,Ca)(Zr,Ti)O3 piezoceramics | The lead-free piezoceramic (Ba,Ca)(Zr,Ti)O3 system has been a focus of scientific research due to its outstanding electromechanical properties, rivaling those of conventional lead-based materials. However, poor reproducibility and unwanted secondary phases are major obstacles to the further development of these materials. Here, we used thermal analysis and high-temperature in-situ X-ray diffraction to identify the chemical reactions taking place during the solid-state synthesis of (Ba,Ca)(Zr,Ti)O3. We identified the reaction sequence, discovered novel and formerly unknown intermediate phases, and defined the conditions for secondary phase formation. Strategies for the removal of the main secondary phases, namely CaTiO3 and a polytitanate phase, were proposed. This resulted in an increase of the small-signal piezoelectric coefficient d33 by 28%. The reaction sequence generated in this study will help to improve the processing conditions for this material system to allow for controlled microstructure engineering and enhanced electromechanical properties. | Anna Margarethe Paulik; Sylvia Kunz; Marc Widenmeyer; Oliver Clemens; Anke Weidenkaff; Jurij Koruza | Materials Science; Ceramics; Materials Processing; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d167d4fa469535b9f7a99f/original/solid-state-formation-reactions-of-ba-ca-zr-ti-o3-piezoceramics.pdf |
61547e8cef08e6f5e61cb266 | 10.26434/chemrxiv-2021-r55x3 | Profiling of D-alanine production by the microbial isolates of rat gut microbiota | D-alanine (D-Ala) and several other D-amino acids (D-AAs), unusual amino acids present in mammals, act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized D-serine in animals, D-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce D-Ala and other D-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their D-AA secretion in vitro, focusing on D-Ala. Serial dilutions of intestinal content from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial D-AA secretion, combining a D-amino acid oxidase-based enzymatic assay for rapid assessment of overall D-AA amount, followed by chiral LC-MS/MS to quantify individual D-AAs, revealing 19 out of the 38 isolated strains as D-AA producers. LC-MS/MS analysis of the eight top D-AA producers showed high levels of D-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of D-glutamate and D-aspartate, which are poor substrates for enzymatic assay. We observed large inter- and intra-species variation of D-AA secretion profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology. | Cindy J. Lee; Tian A. Qiu; Zhilai Hong; Zhenkun Zhang; Yuhao Min; Linzixuan Zhang; Lei Dai; Huimin Zhao; Tong Si; Jonathan V. Sweedler | Biological and Medicinal Chemistry; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61547e8cef08e6f5e61cb266/original/profiling-of-d-alanine-production-by-the-microbial-isolates-of-rat-gut-microbiota.pdf |
60c73f1c842e65136ddb1a1a | 10.26434/chemrxiv.7250201.v1 | Bioinspired Thiophosphorodichloridate Reagents for Chemoselective Histidine Bioconjugation | Site-selective bioconjugation to native protein
residues is a powerful tool for protein functionalization, with cysteine and
lysine side chains being the most common points for attachment owing to their
high nucleophilicity. We now report a strategy for histidine modification using
thiophosphorodichloridate reagents that mimic post-translational histidine
phosphorylation, enabling fast and selective labeling of protein histidines
under mild conditions where various payloads can be introduced via copper-assisted
alkyne-azide cycloaddition (CuAAC) chemistry. We establish that these reagents
are particularly effective at covalent modification of His-tags, which are
common motifs to facilitate protein purification, as illustrated by selective
attachment of polyarginine cargoes to enhance the uptake of proteins into
living cells. This work provides a starting point for probing and enhancing protein
function using histidine-directed chemistry. | Shang Jia; Christopher Chang | Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1c842e65136ddb1a1a/original/bioinspired-thiophosphorodichloridate-reagents-for-chemoselective-histidine-bioconjugation.pdf |
60c75185ee301c5912c7aaca | 10.26434/chemrxiv.13175012.v1 | Global Diastereoconvergence in the Ireland–Claisen Rearrangement of Isomeric Enolates: Synthesis of Tetrasubstituted -Amino Acids | <div><div><div><p>A dual experimental/theoretical investigation of the Ireland–Claisen rearrangement of tetrasubstituted a-phthalimido ester enolates to afford a-tetrasubstituted, b-trisubstituted a-amino acids (generally >20:1 dr) is described. For trans allylic olefins, the Z and E-enol ethers proceed through chair and boat transition states, respectively. For cis allylic olefins, the trend is reversed. As a result, the diastereochemical outcome of the reaction is preserved regardless of the geometry of the enolate or the accompanying allylic olefin. We term this unique convergence of all possible olefin isomers as global diastereoconvergence. This reaction manifold circumvents limitations in present-day technologies for the stereoselective enolization of a,a-disubstituted allyl esters. Density func- tional theory paired with state-of-the-art local coupled-cluster theory (DLPNO-CCSD(T)) was employed for the accurate determina- tion of quantum mechanical energies.</p></div></div></div> | Tyler J. Fulton; Alexander Cusumano; Eric J. Alexy; Yun Emily Du; Haiming Zhang; Kendall N Houk; Brian Stoltz | Organic Synthesis and Reactions; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75185ee301c5912c7aaca/original/global-diastereoconvergence-in-the-ireland-claisen-rearrangement-of-isomeric-enolates-synthesis-of-tetrasubstituted-amino-acids.pdf |
634ff28786473a1f2819925c | 10.26434/chemrxiv-2022-7k032 | Multifunctional Helicene-Based Ytterbium(III) Coordination Polymer Displaying Circularly Polarized Luminescence, Slow Magnetic Relaxation and Room Temperature Magneto-Chiral Dichroism | The combination of physical properties sensitive to molecular chirality in a single system allows the observation of fascinating phenomena such as Magneto-Chiral Dichroism (MChD) and Circularly Polarized Luminescence (CPL) having potential applications for optical data readout and display technology. Homochiral monodimensional coordination polymers of YbIII were designed from a 2,15-bis-ethynyl-hexahelicenic scaffold decorated with two terminal 4-pyridyl units. Thanks to the coordination of the chiral organic chromophore to Yb(hfac)3 units, efficient NIR-CPL activity is observed. Moreover, the specific crystal field around the YbIII induces a strong magnetic anisotropy which leads to a slow magnetic relaxation (SMM) and a remarkable room temperature MChD. The MChD-structural correlation is supported by computational investigations. | Kais Dhbaibi; Maxime Grasser; Haiet Douib; Vincent Dorcet; Olivier Cador; Nicolas Vanthuyne; françois Riobé; Olivier Maury; Stéphan Guy; Amina Bensalah-Ledoux; Bruno Baguenard; Geert Rikken; Cyrille Train; Boris Le Guennic; Matteo Atzori; Fabrice Pointillart; Jeanne Crassous | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/634ff28786473a1f2819925c/original/multifunctional-helicene-based-ytterbium-iii-coordination-polymer-displaying-circularly-polarized-luminescence-slow-magnetic-relaxation-and-room-temperature-magneto-chiral-dichroism.pdf |
60c74bb3702a9b8b8818b4db | 10.26434/chemrxiv.12324353.v2 | Synthesis of a Zigzag Carbon Nanobelt | <div>
<div>
<div>
<p>The structure-selective precise synthesis of carbon nanotubes (CNTs) has been long
sought in materials science. The aromatic molecules corresponding to segment
structures of CNTs, i.e. carbon nanobelts (CNBs), have been of interest as templates
for CNT growth. Although two of three types, armchair and chiral CNBs, have been
synthesized recently, zigzag CNBs remain elusive. Herein we report the synthesis and
isolation of a zigzag CNB. The synthesis involves an iterative Diels–Alder reaction
sequence followed by reductive aromatization of oxygen-bridged moieties. As
predicted by theoretical calculations, this CNB was isolated as a stable compound. The
structure of the zigzag CNB was fully characterized by X-ray crystallography, and its
wide energy gap with blue fluorescence properties were revealed by photophysical
measurement. With synthetic strategies towards all three types of CNBs in hand, the
road to the precise synthesis of CNTs can now proceed to the next stage.
</p>
</div>
</div>
</div> | Kwan Yin Cheung; Kosuke Watanabe; Yasutomo Segawa; Kenichiro Itami | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb3702a9b8b8818b4db/original/synthesis-of-a-zigzag-carbon-nanobelt.pdf |
63a03ecd16e9a8812a2d9da4 | 10.26434/chemrxiv-2022-k9fs9 | Solvent-free synthesis of zeolites: new insights into the mechanism and non-mechanochemical route | The solvent-free (SF) synthesis is a green alternative to the conventional method of synthesis
for zeolites. In this study, we show for the first time the feasibility of carrying out the SF synthesis
of silicalite-1 (F- route) without any grinding. We also monitor the changes during the synthesis
thanks to multiple characterization techniques: XRD, TGA, SEM, EDX, and multinuclear NMR (13C,
19F, 29Si). We show how the duration of the thermal treatment impacts the zeolite crystal size
and morphology, as well as the local degree of order probed by solid-state NMR. The obtained
results provide new insights on the SF formation mechanism based on solid phase
transformations. Our findings also show that once the organic structure directing agent (OSDA),
here tetrapropylammonium, is incorporated, the crystals are formed and no other intermediate
phases incorporating the OSDA exist. Further, we study the role of water in the synthesis using
17O NMR. For this purpose, we develop a simple and efficient 17O enrichment method of zeolite
frameworks. The efficiency of this enrichment demonstrates the role of water in the hydrolysis
and condensation reactions and its need for a successful synthesis. | Shadi Al-Nahari; Danielle Laurencin; Bruno Alonso | Physical Chemistry; Inorganic Chemistry; Reaction (Inorg.); Solid State Chemistry; Spectroscopy (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a03ecd16e9a8812a2d9da4/original/solvent-free-synthesis-of-zeolites-new-insights-into-the-mechanism-and-non-mechanochemical-route.pdf |
60c73fde9abda2fc7cf8bb6d | 10.26434/chemrxiv.7506023.v1 | Spin-Crossover Phenomena of Ni(cyclam)I2 Complex: Magnetostructural Correlations in Two Polymorphs | <div>Two crystal polymorphs of Ni(cyclam)I<sub>2</sub> (cyclam = 1,4,8,11-</div><div>tetraazacyclotetradecane) were identified by X-ray structural analysis and their magnetic properties were investigated. Gradual spin-crossover behaviors were found in both polymorphs. Entropy differences between high- and low-spin states obtained by assuming the spin equilibrium model reflected subtle difference of the coordination environment of nickel(II) ion in two polymorphs.</div> | Yoji Horii; Yuki Kanegae; Kiyonori Takahashi; Akira Fuyuhiro; Hal Suzuki; Motohiro Nakano | Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fde9abda2fc7cf8bb6d/original/spin-crossover-phenomena-of-ni-cyclam-i2-complex-magnetostructural-correlations-in-two-polymorphs.pdf |
60c7582a842e652dd2db47f3 | 10.26434/chemrxiv.14515014.v1 | Total Synthesis of (+)-Spiroindimicin A via Asymmetric Palladium-Catalyzed Spirocyclization | <p>The spiroindimicins are a unique class of chlorinated indole alkaloids characterized by three heteroaromatic rings structured around a congested spirocyclic stereocenter. Here, we report the first total synthesis of (+)-spiroindimicin A, which bears a challenging C-3’/C-5’’-linked spiroindolenine. We detail our initial efforts to effect a biomimetic oxidative spirocyclization from its proposed natural precursor, lynamicin D, and describe how these studies shaped our final abiotic 9-step solution to this complex alkaloid built around a key asymmetric Pd-catalyzed spirocyclization. Scalable access to spiroindimicins A, H, and their congeners has enabled discovery of their activity against several parasites relevant to human health, providing potential starting points for new therapeutics for the neglected tropical diseases leishmaniasis and African sleeping sickness.</p> | Zhen Zhang; Sneha Ray; Leah Imlay; Lauren Callaghan; Hanspeter Niederstrasser; Prema Latha Mallipeddi; Bruce A. Posner; Dawn Wetzel; Margaret Phillips; Myles Smith | Natural Products; Organic Synthesis and Reactions; Biochemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7582a842e652dd2db47f3/original/total-synthesis-of-spiroindimicin-a-via-asymmetric-palladium-catalyzed-spirocyclization.pdf |
615604d2cc53d981d9b847c0 | 10.26434/chemrxiv-2021-wdrwc | Upper Secondary School and University Level Students’ Perceptions of Extractions in Context: Experiences from a Simple Laboratory Experiment
| We discuss the pedagogical challenges associated with the current way of introducing extraction in upper secondary school chemistry education. These challenges were identified based on a survey of upper secondary school textbooks and verified through a questionnaire study. To address the identified challenges, we introduce a simple and effective extraction experiment which focuses on building a deeper conceptual understanding of extraction processes. The operationally simple extraction experiment and the accompanying questionnaire revealed that while students have several chemical misconceptions arising from the use of superficial everyday examples, they have all the necessary knowledge for developing a deeper understanding of chemistry. Providing a suitable experimental platform for developing and re-evaluating their knowledge allows the students to reasonably independently re-conceptualize their thinking toward a more coherent view of the surrounding world and the related scientific models. Furthermore, the work analyses the challenges that can be encountered when using everyday examples in
teaching, and demonstrates that student-discovered examples of chemical systems can be a powerful method for generating meaningful and relevant ways to introduce scientific phenomena in STEM education.
| Tuomas Nurmi; Juha Siitonen | Chemical Education | CC BY NC 4.0 | CHEMRXIV | 2021-10-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615604d2cc53d981d9b847c0/original/upper-secondary-school-and-university-level-students-perceptions-of-extractions-in-context-experiences-from-a-simple-laboratory-experiment.pdf |
60c758ad702a9befce18cd8a | 10.26434/chemrxiv.14574315.v1 | Template Instrumentation for "Accurate Constant via Transient Incomplete Separation" (ACTIS) | <p>ACTIS
is a new method for finding the equilibrium dissociation constant <i>K</i><sub>d</sub>
of a protein–small molecule complex based on transient incomplete
separation of the complex from the unbound small molecule in a
capillary. This separation is caused by differential transverse
diffusion of the complex and the small molecule in a pressure-driven
flow. The advection-diffusion processes underlying ACTIS can be
described by a system of partial differential equations allowing for
a virtual ACTIS instrument to be built and ACTIS to be studied in
silico. The previous in-silico studies show that large variations in
the fluidic system geometry do not affect the accuracy of <i>K</i><sub>d</sub>
determination, thus, proving that ACTIS is conceptually accurate. The
conceptual accuracy does not preclude, however, instrumental
inaccuracy caused by run-to-run signal drifts. Here we report on
assembling a physical ACTIS instrument with a fluidic system that
mimics the virtual one and proving the absence of signal drifts.
Furthermore, we confirmed method ruggedness by assembling a second
ACTIS instrument and comparing the results of experiments performed
with both instruments in parallel. Despite some differences between
the instruments and, accordingly, significant differences in their
respective separagrams, we found that the <i>K</i><sub>d</sub>
values determined for identical samples with these instruments were
equal. Conclusively, the fluidic system presented here can serve as a
template for reliable ACTIS instrumentation.</p> | Jean-Luc Rukundo; Sven Kochmann; Tong Ye Wang; Nikita A. Ivanov; J.C. Yves Le Blanc; Boris I. Gorin; Sergey N. Krylov | Analytical Chemistry - General; Analytical Apparatus; Biochemical Analysis; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ad702a9befce18cd8a/original/template-instrumentation-for-accurate-constant-via-transient-incomplete-separation-actis.pdf |
64b63739ae3d1a7b0de7264f | 10.26434/chemrxiv-2023-bhzjb | Transmembrane transport by platinum-based metal-organic anionophores | A series of Pt(II) metal complexes with urea-appended isoquinoline ligands act as efficient transmembrane chloride transporters and operate via classical hydrogen bonding interactions rather than ligand exchange. A number of the complexes exhibited potent transmembrane chloride transport activity. | Patrick Wang; Mohamed Fares; Xin Wu; William Lewis; Stephen Loeb; Lauren Macreadie; Philip Alan Gale | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b63739ae3d1a7b0de7264f/original/transmembrane-transport-by-platinum-based-metal-organic-anionophores.pdf |
641b3827aad2a62ca12e0141 | 10.26434/chemrxiv-2023-1rvh3 | A Fluctuating Density Energy Model for RNA Nucleobase Interactions | A new potential termed the Fluctuating Density (FD) model is presented as an alternative to traditional fixed partial-charge force fields for describing RNA nucleobase interactions within a molecular mechanics framework. Instead of atom-centered point charges, we take inspiration from fluctuating charge models and use a site-centered density representation for electron distributions to account for charge penetration effects present in both frozen and polarizable electrostatic interactions. A parameterization procedure is established to fit the FD model against energy decomposition analysis (EDA) for density functional theory (DFT) computations of both hydrogen-bonded and stacked RNA base pairs. Additionally, the FD model's ability to replicate intermolecular interactions of NMR resolved base pairs from the RSCB Protein Data Bank, as well as a comparison against the CHARMM Drude oscillator and AMOEBA force fields, is also presented. We find that charge penetration effects, when used as a cornerstone for parameterization, have strong influences on the remaining force field energy terms such as polarization and charge transfer. Furthermore, the FD model is able to produce polarization energetic contributions from electron density changes of similar magnitude as predicted by DFT computations. | Christopher Myers; Alan Chen | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641b3827aad2a62ca12e0141/original/a-fluctuating-density-energy-model-for-rna-nucleobase-interactions.pdf |
66463bd3418a5379b0756f55 | 10.26434/chemrxiv-2024-nd80s-v2 | Precise and accurate determination of the pKw of water via a new protocol within the Blue Moon ensemble | Water self-dissociation is one of the most studied reactions in aqueous medium, having received a special attention from the computational chemistry community. However, a precise and accurate in silico estimation of the pKw remained elusive for a long time, until very recent works finally reached this goal with a strong technical effort. In this work, I define a very accessible procedure within the Blue Moon ensemble approach that allows a precise determination of the pKw , correcting two effects present in the regular application of different constrained MD methods that caused a wrong description of the dissociated state. This approach, together with an extremely efficient ab initio setup within the Second-generation Car–Parrinello MD scheme, and a description of the electronic structure at the RPBE-D3 level, yields an estimation of the pKw that is practically equal to the experimental value of heavy water. | Daniel Muñoz-Santiburcio | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Physical and Chemical Properties; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66463bd3418a5379b0756f55/original/precise-and-accurate-determination-of-the-p-kw-of-water-via-a-new-protocol-within-the-blue-moon-ensemble.pdf |
666c2ee201103d79c534c2a1 | 10.26434/chemrxiv-2024-x2jl2 | Comprehensive Screening of Conditions for Block Copolymer Nanoaggregate Formation via Automated DLS | A fully automated robotic synthesizer for the screening of amphiphilic block copolymer nanoparticle synthesis is presented. To reach this aim, block copolymer solutions are mixed in continuous flow with water, allowing for the automated variation of overall polymer concentration, mixing ratio of the water and organic solvent phase and the overall flow rate of the system. Particle sizes are monitored online via a commercial DLS instrument, and the obtained data is automatically analyzed. While the machine generally allows to produce particles with a 10% standard deviation, the control software performs automatic outlier detection based on measurement of data in triplicates, and repeats experiments until a statistically robust result is obtained. The synthesis platform was tested on 5 individual block copolymers, namely poly(ethyl methacrylate)-block-poly(2-(dimethylamino)ethyl acrylate) (PEMA75-b-PDMAEA50), polystyrene-block-poly(2-(dimethylamino)ethyl acrylate) (PS50-b-PDMAEA25), polystyrene-block-poly(poly(ethylene glycol) methyl ether acrylate) (PS40-b-PPEGMEA35, PS90-b-PPEGMEA23) and polystyrene-block-poly(2-hydroxy ethyl acrylate) (PS90-b-PHEA14), which were obtained from RAFT polymerization. | Lakshani Weerarathna; Oliver Weismantel; Tanja Junkers | Polymer Science | CC BY 4.0 | CHEMRXIV | 2024-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/666c2ee201103d79c534c2a1/original/comprehensive-screening-of-conditions-for-block-copolymer-nanoaggregate-formation-via-automated-dls.pdf |
66d00fd4a4e53c4876f7d17b | 10.26434/chemrxiv-2024-4xgd6 | Structure and thermal stability of phosphorus-iodonium ylids | Hypervalent iodine(III) reagents have become indispensable tools in organic synthesis, but gaps remain
in the functionalities they can transfer. In this study, a fundamental understanding of the thermal stability
of phosphorus-iodonium ylids is obtained through X-ray diffraction, differential scanning calorimetry
(DSC) and thermogravimetric analysis (TGA). Insights into the structural factors affecting thermal
stability and potential decomposition pathways will enable the future design and development of new
reagents. | Andrew Greener; Stephen P. Argent; Coby Clarke; Miriam L. O'Duill | Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2024-08-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d00fd4a4e53c4876f7d17b/original/structure-and-thermal-stability-of-phosphorus-iodonium-ylids.pdf |
60c74ebeee301c6eecc7a581 | 10.26434/chemrxiv.12376094.v3 | Profiling Molecular Simulations of SARS-CoV-2 Main Protease (Mpro) Binding to Repurposed Drugs Using Neural Network Force Fields | <p>
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<p>With the current pandemic situation caused by a novel coronavirus disease (COVID-19), there is an urgent call to develop a working therapeutic against it. Efficient computations can minimize the efforts by identifying a subset of drugs that can potentially bind to the COVID-19 main protease or target protein (M<sup>PRO</sup>). The results of computations are accompanied by an evaluation of their accuracy, which depends on the details described by the model used. Neural network models trained on millions of points and with unmatched accuracies are the best approach to employ in this process. In this work, I first identified and described the interaction sites of the M<sup>PRO</sup> protein using a geometric deep learning model. Second, I conducted virtual screening (at one of the sites identified) on FDA-approved drugs and selected 91 drugs with the highest binding affinities (below -8.0 kcal/mol). Then, I conducted 10 ns of molecular dynamics (MD) simulations using classical force fields and classified 37 drugs to be binding (including Lopinavir, Saquinavir, and Indinavir) based on the RMSD between MD-binding trajectories. To drastically improve the dynamics profile of the 37 selected drugs, I used the highly accurate neural network force field (ANI) method trained on coupled-cluster method (CCSD(T)/CBS) data points and performed 1 ns of binding dynamics for each drug with the protein. Using this approach, 19 drugs were qualified based on their RMSD cutoffs, and based on free energy (ANI/MM/PBSA) computations, 7 of the drugs were rejected. The final selection of 12 drugs was validated based on an MD trajectory clustering approach where 11 of the 12 drugs (Targretin, Eltrombopag, Rifaximin, Deflazacort, Ergotamine, Doxazosin, Lastacaft, Rifampicin, Victrelis, Trajenta, Toposar, and Indinavir) were confirmed to exhibit binding. Further investigations were performed to study their interactions with the protein and an accurate 2D-interaction map was generated. These findings and mappings of drug-protein interactions are highly accurate and may be potentially used to guide rational drug discovery against COVID-19.</p>
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</div> | Aayush Gupta | Biochemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ebeee301c6eecc7a581/original/profiling-molecular-simulations-of-sars-co-v-2-main-protease-mpro-binding-to-repurposed-drugs-using-neural-network-force-fields.pdf |
60c740c8842e655c74db1d5d | 10.26434/chemrxiv.7796543.v1 | Towards General Network Architecture Design Criteria for Negative Gas Adsorption Transitions in Ultraporous Frameworks | <p>Critical design criteria for negative gas
adsorption (NGA), a counterintuitive feature of pressure amplifying materials,
hitherto uniquely observed in a highly porous framework compound (DUT-49), are
derived by analysing the physical effects of micromechanics, pore size,
interpenetration, adsorption enthalpies, and the pore filling mechanism using
advanced in situ X-ray and neutron diffraction, NMR spectroscopy, and
calorimetric techniques parallelized to adsorption for a series of six
isoreticular networks. Aided by computational
modelling, we identify DUT-50 as a new pressure amplifying material featuring
distinct NGA transitions upon methane and argon adsorption. In situ neutron
diffraction analysis of the methane (CD4) adsorption sites at 111 K supported
by grand canonical Monte Carlo simulations reveals a sudden population of the
largest mesopore to be the critical filling step initiating structural contraction
and NGA. In contrast, interpenetration leads to framework stiffening and
specific pore volume reduction, both factors effectively suppressing NGA
transitions.</p> | Simon Krause; Jack D. Evans; Volodymyr Bon; Irena Senkovska; Paul Iacomi; Felicitas Kolbe; Sebastian Ehrling; Erik Troschke; Jürgen Getzschmann; Daniel D. Többens; Alexandra Franz; Dirk Wallacher; Pascal
G. Yot; Guillaume Maurin; Eike Brunner; Philip L. Llewellyn; François-Xavier Coudert; Stefan Kaskel | Elastic Materials; Hybrid Organic-Inorganic Materials; Metamaterials; Computational Chemistry and Modeling; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740c8842e655c74db1d5d/original/towards-general-network-architecture-design-criteria-for-negative-gas-adsorption-transitions-in-ultraporous-frameworks.pdf |
66700185c9c6a5c07aa619ce | 10.26434/chemrxiv-2024-wpz3z-v2 | High-speed Ball Milling Enables an Ultra-fast Wittig Olefination Under Ambient and Solvent-free Conditions Without Ylide Pre-formation | 30 Seconds to success! – The Wittig reaction, a fundamental and extensively utilized reaction in organic chemistry, enables the efficient conversion of carbonyl compounds to olefins using phosphonium salts. Traditionally, meticulous reaction setup, including the pre-formation of a reactive ylide species via deprotonation of a phosphonium salt, is crucial for achieving high-yielding reactions under classical solution-based conditions. In this report, we present an unprecedented protocol for an ultra-fast mechanochemically driven Wittig reaction under solvent-free and ambient conditions, eliminating the need for tedious ylide pre-formation under strict air and moisture exclusion. A range of aldehydes and ketones were reacted with diverse phosphonium salts under high-speed ball milling conditions, giving access to the respective olefins in only 30 seconds. | Johanna Templ; Michael Schnürch | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-06-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66700185c9c6a5c07aa619ce/original/high-speed-ball-milling-enables-an-ultra-fast-wittig-olefination-under-ambient-and-solvent-free-conditions-without-ylide-pre-formation.pdf |
67bffeba81d2151a02408897 | 10.26434/chemrxiv-2025-q9s64 | Introducing Ylides as Charge-Neutral Termini for Poly(Ethylene Glycol) with Applications in Nanomedicine | The widespread use of polyethylene glycol (PEG) in biomedical applications has led to the emergence of anti-PEG antibodies, which accelerate systemic clearance and undermine the performance of PEGylated systems including those of nanomedicines. Antibody recognition often involves the hydrophobic PEG terminus, highlighting the need for alternative end-functionalization strategies that enhance hydrophilicity while maintaining stealth properties. Here, we introduce a novel PEGylation concept using sulfur ylides bearing tri- and pentapeptides as terminal modifications. These ylide-PEG (yPEGs) conjugates were integrated into polymeric nanoparticles as a model system, demonstrating that ylide-functionalization maintains key physicochemical properties such as ζ-potential and antifouling behavior. Crucially, antibody binding assays with monoclonal IgM and IgG anti-PEG antibodies revealed that the ylide terminus significantly reduces recognition by both main chain and terminus-specific anti-PEG antibodies. Experiments with polyclonal anti-PEG antibodies from mPEG-immunized mice suggest that increasing the chemical complexity of the ylide terminus with a highly polar – yet overall charge-neutral – terminus effectively prevents antigenicity from extending to the terminus, ultimately reducing PEG-specific recognition. This modular and scalable strategy offers a new paradigm for engineering stealth-functionalized polymers, with broad implications for nanomedicine, biomaterials, and surface coatings. | Dulce M. Sánchez-Cerrillo; Kouichi Shiraishi; Lucía Mallen-Huertas; Remi Peters; Daniela A. Wilson; Kevin Neumann | Organic Chemistry; Polymer Science; Bioorganic Chemistry; Drug delivery systems; Polymer scaffolds; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bffeba81d2151a02408897/original/introducing-ylides-as-charge-neutral-termini-for-poly-ethylene-glycol-with-applications-in-nanomedicine.pdf |
60c741230f50db0d88395a63 | 10.26434/chemrxiv.7945379.v1 | Electrochemically Gated Long Distance Charge Transport in Photosystem I | <p>The transport of electrons along photosynthetic and
respiratory chains involves a series of
enzymatic reactions that are coupled through
redox mediators, including proteins and small molecules. The use of native and
synthetic redox probes is key to
understand charge transport mechanisms, and to design bioelectronic sensors and solar energy conversion devices. However,
redox probes have limited tunability to exchange charge at the desired
electrochemical potentials (energy levels) and at different protein sites.
Here, we take advantage of electrochemical scanning tunneling microscopy
(ECSTM) to control the Fermi energy and nanometric position of the ECSTM probe in order to study electron transport in
individual photosystem I (PSI) complexes. Current-distance measurements at
different potentiostatic conditions
indicate that PSI supports long-distance
transport that is electrochemically gated near the redox potential of P700,
with current extending farther under hole injection conditions.</p> | Montserrat López Martínez; Manuel López Ortiz; Maria Elena Antinori; Emilie Wientjes; Roberta Croce; Ismael Díez-Pérez; Pau Gorostiza | Biophysics; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741230f50db0d88395a63/original/electrochemically-gated-long-distance-charge-transport-in-photosystem-i.pdf |
63c6fa9830e3e565ee93d841 | 10.26434/chemrxiv-2023-090f6 | Room Temperature Cu-Catalyzed Amination of Aryl Bromides Enabled by DFT-Guided Ligand Design | Ullman-type C–N coupling reactions represent an important alternative to well-established Pd-catalyzed approaches due to the differing reactivity and the lower cost of Cu. While the design of anionic Cu ligands, particularly those by Ma, has enabled the coupling of various classes of aryl halides and alkyl amines, most methods require conditions that can limit their utility on complex substrates. Herein, we disclose the development of anionic N1,N2-diarylbenzene-1,2-diamine ligands that promote the Cu-catalyzed amination of aryl bromides under mild conditions. Guided by DFT-calculations, these ligands were designed to (1) increase the electron density on Cu, thereby facilitating the rate of oxidative addition of aryl bromides, and (2) stabilize the active anionic CuI complex via a π-interaction. Under optimized conditions, structurally diverse aryl and heteroaryl bromides and a broad range of alkyl amine nucleophiles, including pharmaceuticals bearing multiple functional groups, were efficiently coupled at room temperature. Combined computational and experimental studies support a mechanism of C–N bond formation that follows a catalytic cycle akin to the well-explored Pd-catalyzed variants. Modification of the ligand structure to include a naphthyl residue resulted in a lower energy barrier to oxidative addition, providing a 30-fold rate increase relative to what is seen with other ligands. Collectively, these results establish a new class of anionic ligands for Cu-catalyzed C–N couplings which we anticipate may be extended to other Cu-catalyzed C–heteroatom and C–C bond-forming reactions. | Seoung-Tae Kim; Michael J. Strauss; Albert Cabré; Stephen L. Buchwald | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Catalysis; Ligand Design | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c6fa9830e3e565ee93d841/original/room-temperature-cu-catalyzed-amination-of-aryl-bromides-enabled-by-dft-guided-ligand-design.pdf |
66c37a6320ac769e5f16b413 | 10.26434/chemrxiv-2024-hm61k | Separation of Lithium from Ores in Seconds | Lithium (Li) is the lowest density metal, and therefore an optimal element in most battery designs1,2. With the increasing demand for Li, metallurgical techniques using excess acid leaching of mineral ores are common. However, these techniques are limited by complex, multi-step processes with adverse environmental impacts caused by secondary waste streams1,3. Here, we show that flash Joule heating (FJH) can convert the earth-abundant Li ore, alpha-spodumene, into beta-spodumene in seconds, making LiCl extractable with 1 M HCl (Method A). Even more simply, we show that a one-step FJH of alpha-spodumene under an atmosphere of Cl2 (FJH-Cl2) can afford high-purity and high-yield LiCl in seconds without any acid treatment (Method B). This capitalizes upon the lower DeltaGform of the LiCl over the competing aluminum and silicon chlorides. Spodumene undergoes the FJH-Cl2 reaction at 1550 °C in seconds, whereupon LiCl immediately distills from the remaining non-volatile aluminum oxide and silicon oxide. LiCl with a 96% purity and 94% yield can be achieved in this rapid one-step process, enormously reducing costs and waste emissions. Local processing with FJH-Cl2 can dramatically lessen the complexity and cost in obtaining Li, obviating remote mining, and facilitating the world’s progression toward cleaner renewable energies2,3. | Shichen Xu; Justin Sharp; Alex Lathem; Qiming Liu; Lucas Eddy; Shihui Chen; Bowen Li; Tengda Si; Jaeho Shin; Chi Choi; Yimo Han; Boris Yakobson; Yufeng Zhao; James Tour | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Wastes; Natural Resource Recovery; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c37a6320ac769e5f16b413/original/separation-of-lithium-from-ores-in-seconds.pdf |
64d3e3c4dfabaf06ff008dd7 | 10.26434/chemrxiv-2023-02t0k | Rapid Formation of Non-canonical Phospholipid Membranes by Chemoselective Amide-forming Ligations with Hydroxylamines | There has been increasing interest in methods to generate synthetic lipid membranes as key constituents of artificial cells or to develop new tools for remodeling membranes in living cells. However, the biosynthesis of phospholipids involves elaborate enzymatic pathways that are challenging to reconstitute in vitro. An alternative approach is to use chemical reactions to non-enzymatically generate natural or non-canonical phospholipids de novo. Previous reports have shown that synthetic lipid membranes can be formed in situ using various ligation chemistries, but these methods lack biocompatibility and/or suffer from slow kinetics at physiological pH. Thus, it would be valuable to develop chemoselective strategies for synthesizing phospholipids from water-soluble precursors that are compatible with synthetic or living cells Here, we demonstrate that amide-forming ligations between lipid precursors bearing hydroxylamines and α-ketoacids (KAs) or potassium acyltrifluoroborates (KATs) can be used to prepare non-canonical phospholipids in physiologically relevant conditions. The generated amide-linked phospholipids spontaneously self-assemble into cell-like micron-sized vesicles similar to natural phospholipid membranes. We show that lipid synthesis using KAT ligation proceeds extremely rapidly, and the high selectivity and biocompatibility of the approach facilitates the in situ synthesis of phospholipids and associated membranes in living cells. | Jiyue Chen; Roberto J. Brea; Alessandro Fracassi ; Christy J. Cho ; Adrian M. Wong ; Marta Salvador-Castell ; Sunil K. Sinha ; Itay Budin ; Neal K. Devaraj | Biological and Medicinal Chemistry; Organic Chemistry; Biochemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d3e3c4dfabaf06ff008dd7/original/rapid-formation-of-non-canonical-phospholipid-membranes-by-chemoselective-amide-forming-ligations-with-hydroxylamines.pdf |
60c74bd8bb8c1a65403db2dd | 10.26434/chemrxiv.12383522.v1 | On the Role of Entropy in the Stabilization of α-Helixes | Protein folding evolves by exploring the conformational space with a subtle balance between enthalpy and entropy changes which eventually leads to a decrease of the free energy upon reaching the folded structure. <br />A complete understanding of this process requires, therefore, a deep insight into both contributions to the free energy.<br />In this work, we clarify the role of entropy in favoring the stabilization of folded structures in polyalanine peptides with up to 12 residues . We use a novel method referred to as K2V that allows us to obtain the potential energy landscapes in terms of residue conformations extracted from molecular dynamics simulations at conformational equilibrium, and yields folding thermodynamic magnitudes in agreement with the experimental data available. <br />Our results demonstrate that the folded structures of the larger polyalanine chains are stabilized with respect to the folded structures of the shorter chains mostly by an increase of the entropic contribution of the solvent, which compensates the decrease of conformational entropy of the polypeptide, thus unveiling a key piece in the puzzle of protein folding.<br />In addition, the ability of the K2V method to provide the enthalpic and entropic contributions for individual residues along the peptide chain makes it clear that the entropic stabilization is basically governed by the nearest neighbor residues conformations, with the folding propensity being rationalized in terms of triads of residues.<br /><br /> | Adolfo Bastida; José Zúñiga; Alberto Requena; Beatriz Miguel; Javier Cerezo | Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bd8bb8c1a65403db2dd/original/on-the-role-of-entropy-in-the-stabilization-of-helixes.pdf |
661e2f7a418a5379b0f35623 | 10.26434/chemrxiv-2023-b7l81-v2 | Combining Bayesian optimization with sequence- or structure-based strategies for optimization of protein-peptide binding | This study introduces a novel Bayesian Optimization (BO) method to support the design and optimization of bioactive peptide sequences in the context of a fully automated closed-loop Design-Make-Test (DMT) pipeline. Using the major histocompatibility complex class I receptor system as test case, we showed that BO is capable to efficiently navigate vast sequence spaces. Starting from a single peptide-lead sequence in the $\mu$M IC50 range, the method is able to optimize a peptide sequence to its optimal binding affinity in less than 5 DMT cycles, with 96 peptide sequences per batch. We extensively evaluated its performance, in various conditions and with different parameters, providing valuable insights for peptide optimization tasks in future closed-loop DMT environments. Different sequence- and structure-based initialization strategies were also tested, to generate the initial batch of peptide sequences, as well as different molecular fingerprints and protein language models. Additionally, the method developed here can natively handle various peptide sequence lengths and scaffolds (e.g. macrocycles) and support any arbitrary non-standard amino acids or residue modifications. The source code of our method, Mobius, is publicly available under the Apache license at https://git.scicore.unibas.ch/schwede/mobius. | Jérôme Eberhardt; Aidan Lees; Markus Lill; Torsten Schwede | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661e2f7a418a5379b0f35623/original/combining-bayesian-optimization-with-sequence-or-structure-based-strategies-for-optimization-of-protein-peptide-binding.pdf |
60c74c13ee301cc830c79fd7 | 10.26434/chemrxiv.12420242.v1 | α-Bi2Sn2O7: A Potential Room Temperature n-type Oxide Thermoelectric | <p>Interest in oxide thermoelectrics has been building due to their high thermal stability and earth-abundant constituent elements. However, the thermoelectric efficiency of flagship oxide materials remains comparatively low, and most materials only reach the maximum figure of merit, <i>ZT</i>, at very high temperatures, above those where the majority of low-grade industrial heat is emitted. It is important to identify thermoelectrics with high conversion efficiency closer to room temperature, particularly for lower-temperature applications such as in domestic heating, consumer electronics and electric vehicles. One of the main factors limiting the efficiency of oxide thermoelectrics is their large lattice thermal conductivities, which has inspired research into more structurally complex materials. In this study, we apply first-principles modelling to assess the low-temperature polymorph of Bi<sub>2</sub>Sn<sub>2</sub>O<sub>7</sub> (α-Bi<sub>2</sub>Sn<sub>2</sub>O<sub>7</sub>) as a potential thermoelectric material, due to its complex crystal structure, which should suppress phonon transport, and the presence of Bi <i>p</i> and Sn <i>s</i> states in the conduction band, which should yield high electrical conductivity when donor (<i>n</i>) doped. Lattice-dynamics calculations using third-order perturbation theory predict an ultralow room-temperature lattice thermal conductivity of 0.4 W m<sup>-1</sup> K<sup>-1</sup>, the lowest ever predicted for an oxide material, and suggest that nanostructuring to a grain size of 5 nm could further decrease this to 0.28 W m<sup>-1</sup> K<sup>-1</sup>. The ultralow lattice thermal conductivity gives α-Bi<sub>2</sub>Sn<sub>2</sub>O<sub>7 </sub>a maximum <i>ZT</i> of 0.36 at 385 K (0.46 with nanostructuring), which is the highest low-temperature value predicted for an oxide thermoelectric. Most importantly, our analysis highlights the relationship between the structural complexity, the chemical nature of the cation, and the short phonon lifetimes, and thus provides guidelines for identifying other novel high-performance oxide thermoelectrics.</p> | Warda Rahim; Jonathan Skelton; David Scanlon | Theory - Inorganic | CC BY NC 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c13ee301cc830c79fd7/original/bi2sn2o7-a-potential-room-temperature-n-type-oxide-thermoelectric.pdf |
63a6015f16e9a80c7d32d81a | 10.26434/chemrxiv-2022-5s955 | Density Functional Tight-Binding Model for Lithium-Silicon Alloys. | The predictive power of molecular dynamic simulations is mainly restricted by the time scale and model accuracy. Many systems of current relevance are of such complexity that requires addressing both issues simultaneously. This is the case of silicon electrodes in Li-ion batteries, where different Li$_x$Si alloys are formed during charge/discharge cycles. While first-principles treatments for this system are seriously limited by the computational cost of exploring its large conformational space, classical force-fields are not transferable enough to represent it accurately. Density Functional Tight-Binding (DFTB) is an intermediate complexity approach capable of capturing the electronic nature of different environments with a relatively low computational cost. In this work, we present a new set of DFTB parameters suited to model amorphous Li$_x$Si alloys. The latter is the usual finding upon cycling the Si electrodes in the presence of Li-ions. The model parameters are constructed with a particular emphasis on their transferability for the entire Li$_x$Si composition range. This is achieved by introducing a new optimization procedure that weights stoichiometries differently to improve the prediction of their formation energies. The resulting model is shown to be robust for predicting crystal and amorphous structures for the different compositions, giving excellent agreement with DFT calculations and outperforming state-of-the-art ReaxFF potentials. | Ma. Belén Oviedo; Francisco Fernandez; Manuel Otero; Ezequiel Leiva; S. Alexis Paz | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Alloys; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY 4.0 | CHEMRXIV | 2022-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a6015f16e9a80c7d32d81a/original/density-functional-tight-binding-model-for-lithium-silicon-alloys.pdf |
61c13982d6dcc2bdc93fb896 | 10.26434/chemrxiv-2021-mfflc | Large-Scale Preparation of Low-Cost Nonfullerene Acceptors for Stable and Efficient Organic Solar Cells | Despite the development of nonfullerene acceptors (NFAs) that have made a breakthrough in the photovoltaic performance, large-scale preparation of NFAs that is prerequisite for commercial application has never been explored. Herein, we designed two dodecacyclic all-fused-ring electron acceptors, F11 and F13, and develop a whole set of synthetic procedures, achieving unprecedented scalable preparation of NFAs in the lab at a 10-g scale notably within one day. The single-crystal structures of F11 reveals the 3D network packing. F11 and F13 display the lowest costs among reported NFAs, even comparable with the classical donor material, P3HT. By matching a medium-bandgap polymer donor, F13 delivers power conversion efficiencies of over 13%, which is an efficiency record for non-INCN acceptors. Benefiting from the intrinsically high stability, OSCs based on F11 and F13 show device stability superior to the typical ITIC- and Y6-based OSCs as evidenced by the tiny burn-in losses. The current work presents a first example for large-scale preparation of low-cost NFAs with good efficiency and high device stability, which is significant for OSC commercialization in near future. | Wenrui Liu; Shengjie Xu; Wuyue Liu; Xiaozhang Zhu | Materials Science; Energy; Photovoltaics; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c13982d6dcc2bdc93fb896/original/large-scale-preparation-of-low-cost-nonfullerene-acceptors-for-stable-and-efficient-organic-solar-cells.pdf |
6791112881d2151a025efb6c | 10.26434/chemrxiv-2025-0fp67 | Hydrogenation of Mixed Ir-Ti Oxide, a Powerful Concept to Promote the Oxygen Evolution Reaction in Acidic Water Electrolysis | A novel and simple strategy of catalytic promotion is presented that is able to significantly improve the oxygen evolution reaction (OER) activity of phase-pure Ir0.30Ti0.7O2 by hydrogen incorporation of 26 at% into Ir0.30Ti0.7O2 through H2 exposure at 150 °C without compromising the long-term stability in acidic water electrolysis. The most attractive feature of hydrogen promotion is the prospect of improving oxidation catalysis for an entire class of materials, namely mixed oxides, and for various oxidation reactions, regardless whether they belong to thermal- or to electrocatalysis. | Herbert Over; Wei Wang; Matej Zlatar; Yu Wang; Phillip Timmer; Alexander Spriewald-Luciano; Lorena Glatthaar; Serhiy Cherevko | Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6791112881d2151a025efb6c/original/hydrogenation-of-mixed-ir-ti-oxide-a-powerful-concept-to-promote-the-oxygen-evolution-reaction-in-acidic-water-electrolysis.pdf |
60c748b5bb8c1a74f63dad18 | 10.26434/chemrxiv.11959323.v1 | D3Similarity: A Ligand-Based Approach for Predicting Drug Targets and for Virtual Screening of Active Compounds Against COVID-19 | <p>Discovering
efficient drugs and identifying target proteins are still an unmet but urgent need
for curing COVID-19. Protein structure based docking is a widely applied
approach for discovering active compounds against drug targets and for
predicting potential targets of active compounds. However, this approach has
its inherent deficiency caused by, e.g., various different conformations with
largely varied binding pockets adopted by proteins, or the lack of true target
proteins in the database. This deficiency may result in false negative results.
As a complementary approach to the protein structure based platform for
COVID-19, termed as D3Docking in our recent work, we developed the ligand-based
method, named D3Similarity, which is based on the molecular similarity
evaluation between the submitted molecule(s) and those in an active compound
database. The database is constituted by all the reported bioactive molecules against
the coronaviruses SARS, MERS and SARS-CoV-2, some of which have target or
mechanism information but some don’t. Based on the two-dimensional and
three-dimensional similarity evaluation of molecular structures, virtual
screening and target prediction could be performed according to similarity ranking
results. With two examples, we demonstrated the reliability and efficiency of D3Similarity
for drug discovery and target prediction against COVID-19. D3Similarity is
available free of charge at <a href="https://www.d3pharma.com/D3Targets-2019-nCoV/D3Similarity/index.php">https://www.d3pharma.com/D3Targets-2019-nCoV/D3Similarity/index.php</a>.</p> | Zhengdan Zhu; Xiaoyu Wang; Yanqing Yang; Xinben Zhang; Kaijie Mu; Yulong Shi; Cheng Peng; Zhijian Xu; weiliang zhu | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748b5bb8c1a74f63dad18/original/d3similarity-a-ligand-based-approach-for-predicting-drug-targets-and-for-virtual-screening-of-active-compounds-against-covid-19.pdf |
67a17d4381d2151a02182f36 | 10.26434/chemrxiv-2025-qx1h3 | The Optimal Arm Length for Star Polymer Electrolytes | The wide application of lithium batteries requires safe and stable electrolyte materials. Recently, there has been an emergence of advanced polymer electrolytes that combine polyethylene oxide with other components in complex architectures including block, bottlebrush, and star structures. However, the conduction mechanisms within these non-linear architectures are yet to be rigorously examined and there lack transferable principles to aid the design and optimization of polymer electrolytes with non-linear architectures. Therefore, in this work, we utilized star polymer as an example to obtain fundamental understandings on how the desired high ionic conductivity evolves with the changes in the arm structures of star polymers. Specifically, we identified a delicate balance between the high flexibility provided by long arms and the low crystallinity caused by shorter arms, leading to an optimal chain length for ion-conduction. Based upon this finding, we proposed a set of general design rules that we anticipate could inform the designs of other polymer electrolytes with complex architectures moving forward. | Feichen Cui; Zhi-Kun Xie; Jixin Wu; Yue Zhang; Zhengyang Zhang; Jun Fu; Rongliang Shang; Yifu Ruan; Gengxin Liu; Yanming Wang; Jin Xie; Jiajun Yan; Bo Qiao | Polymer Science; Energy; Energy Storage; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a17d4381d2151a02182f36/original/the-optimal-arm-length-for-star-polymer-electrolytes.pdf |
60c7593a702a9bdc6e18ce79 | 10.26434/chemrxiv.14672691.v1 | Hydroxylamine as a Superior Organocatalyst for Morita-Baylis-Hillman Reaction | Computational investigations indicate that the use of <i>N</i>,<i>N</i>-dimethylhydroxylamine as organocatalyst enhances
the rate of Morita-Baylis-Hillman reaction by lowering the activation energy of
the rate-controlling aldol step. The rate enhancement is understood to
originate from the a-effect of oxygen on nitrogen in hydroxylamine, which enhances the
nucleophilicity of the nitrogen and results in its more effective conjugate
addition to the enone to form an advanced and, thus, reactive enolate to
participate in the aldol process. The activation energy of the aldol reaction
is therefore reduced. | Veejendra Yadav | Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7593a702a9bdc6e18ce79/original/hydroxylamine-as-a-superior-organocatalyst-for-morita-baylis-hillman-reaction.pdf |
60c743e2f96a0082e52868b4 | 10.26434/chemrxiv.7037699.v1 | Multi-Stimuli-Responsive Mesoporous Membranes and Effect of Molecular Architecture on Thermo- and pH-Responsive Behavior of the grafted Block Copolymer brushes | In
this study, we prepared ultrafiltration membranes with a decoupled responses of
filtration property to temperature and pH. The membrane preparation method was
developed based on our previous work. We utilized methanol-supercritical carbon dioxide (methanol-scCO<sub>2</sub>)
selective swelling method to introduce nanopores to block copolymers containing poly(diethylene glycol) methyl
ether methacrylate (PMEO<sub>2</sub>MA), poly(N,N-dimethylaminoethyl methacrylate)
(PDMAEMA) and polystyrene (PS) blocks. Formation of the mesoporous barrier layer with PS being the
mechanically stable part of the matrix was driven by selective swelling of the
PMEO<sub>2</sub>MA-b-PDMAEMA domains. Due to the selective swelling of PMEO<sub>2</sub>MA or PDMAEMA domains to introduce
pores, the interior of the pores are covered with PMEO<sub>2</sub>MA or PDMAEMA blocks after pore
formation. The PMEO<sub>2</sub>MA-b-PDMAEMA polymer brushes are naturally attached on the pore walls and worked
as functional gates. PMEO<sub>2</sub>MA is a non-toxic, neutral thermo-responsive polymer with LCST at 26 ᴼC. PDMAEMA is a typical weak polyelectrolyte with pK<sub>a</sub> value
at 7.0-7.5 and also a thermo-responsive polymer revealed a LCST of 20-80 °C in
aqueous solution. Therefore, these membranes were expected to have multi dimensions as
function of the combination of temperature and pH. Moreover, to understand the
detail of the temperature and pH depended conformation transitions of PMEO<sub>2</sub>MA-b-PDMAEMA brushes, those diblock
copolymers were end-tethered on flat substrates and analyzed via neutron
reflectivity (NR). | Yanchun Tang; Kohzo Ito; Hideaki Yokoyama | Nanostructured Materials - Materials; Polymer brushes; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743e2f96a0082e52868b4/original/multi-stimuli-responsive-mesoporous-membranes-and-effect-of-molecular-architecture-on-thermo-and-p-h-responsive-behavior-of-the-grafted-block-copolymer-brushes.pdf |
66d5e9b9cec5d6c142ec05b0 | 10.26434/chemrxiv-2024-hnswv | Sulfoximine Aided d-1,1-Cascade Heterocyclization of Unactivated Alkenes | A palladium-catalyzed -annulative 1,1-difunctionalization of unactivated alkene was achieved through the merging of C(alkenyl)H activation and Wacker-type nucleometallation. The 2-pyridyl methyl sulfoximine (MPyS) bidentate directing group in combination with the 2-hydroxy-5-methylpyridine ligand plays a significant in making the transformation viable under mild conditions. The process enables the cascade formation of CC/CN & CC/CO bonds in a single operation, as evidenced by bi-functional reagents (BFRs) from the 2-iodobenzamide, and 2-iodobenzoic acid series. Notably, the de-novo synthesis of -branched isoindolinones/phthalides motifs highlights its practicality. Mechanistic studies uncover the intricacies of the catalytic cycle. Moreover, the ‘N’ to ‘O’ atom swap showcases the skeletal editing of these complex molecular entities; this process provides direct access to the synthesis of monoamine oxidase A inhibitor. | Arghadip Ghosh; koneti kondalarao; Akhila Kumar Sahoo | Organic Chemistry; Catalysis; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d5e9b9cec5d6c142ec05b0/original/sulfoximine-aided-d-1-1-cascade-heterocyclization-of-unactivated-alkenes.pdf |
62c710ed5163111ddc15255f | 10.26434/chemrxiv-2022-2m3qb | Identification of Potential Solid-State Li-Ion Conductors with Semi-Supervised Learning | Despite ongoing efforts to identify high-performance electrolytes for solid-state Li-ion batteries, thousands of prospective Li-containing structures remain unexplored. Here, we employ a semi-supervised learning approach to expedite identification of ionic conductors. We screen 180 unique descriptor representations and use agglomerative clustering to cluster ~26,000 Li-containing structures. The clusters are then labeled with experimental ionic conductivity data to assess the fitness of the descriptors. By inspecting clusters containing the highest conductivity labels, we identify 212 promising structures that are further screened using bond valence site energy and nudged elastic band calculations. Li3BS3 is identified as a potential high-conductivity material and selected for experimental characterization. With sufficient defect engineering, we show that Li3BS3 is a superionic conductor with room temperature ionic conductivity greater than 1 mS cm-1. While the semi-supervised method shows promise for identification of superionic conductors, the results illustrate a continued need for descriptors that explicitly encode for defects. | Forrest A. L. Laskowski ; Daniel B. McHaffie; Kimberly A. See | Inorganic Chemistry; Energy; Electrochemistry; Solid State Chemistry; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c710ed5163111ddc15255f/original/identification-of-potential-solid-state-li-ion-conductors-with-semi-supervised-learning.pdf |
60c750a8f96a006873287e9a | 10.26434/chemrxiv.11950665.v2 | Design Considerations for Oligo(p-Phenyleneethynylene) Organic Radicals in Molecular Junctions | Spin polarization in the electron transmission of radicals is important for understanding single-molecule conductance experiments focusing on shot noise, Kondo properties or magnetoresistance. We study how stable radical substituents can affect such spin polarization when attached to oligo(p- phenyleneethynylene) (OPE) backbones. We find that it is not straightforward to translate the spin density on a stable radical substituent into spin-dependent transmission for the para-connected wires under study here, owing to increased steric interactions compared with meta-connected wires, and a resulting twisting of the radical substituent and OPE π systems. The most promising example is a t-butyl nitroxide substituent, which, despite little pronounced spin delocalization onto the backbone, yields a spin-dependent transmission feature which one might be able to shift towards the Fermi energy by additional substituents. We also find that for bulkier substituents, dispersion interactions with the substituent can lead to twisting of one of the outer OPE rings, reducing the overall conductance. As a further potential design consideration, attaching radicals via linkers might increase the possibilities for spin-dependent intermolecular and molecule-electrode interactions. | Martin Sebastian Zöllner; Rukan Nasri; Haitao Zhang; Carmen Herrmann | Computational Chemistry and Modeling; Theory - Computational; Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750a8f96a006873287e9a/original/design-considerations-for-oligo-p-phenyleneethynylene-organic-radicals-in-molecular-junctions.pdf |
66ce7856a4e53c4876d4dcbc | 10.26434/chemrxiv-2024-ntqw9 | Competition between dissolution vs. ion exchange during low temperature synthesis of LiCoO2 on carbon scaffolds | Deterministic design of electrodes is the concept of intentionally designing and controlling the electrode architecture to achieve high capacity and rate capability, leading to high power and high energy devices. Utilizing 3D conductive scaffolds for deterministic electrode design could unlock new applications for energy storage devices in structural energy storage and wearable electronics. One challenge is to obtain direct wiring of commercially-relevant electrode materials to 3D scaffolds such as porous carbon materials. For example, the synthesis of lithium metal oxide cathode materials requires high temperatures (>700°C) that exceed the stability of conductive carbon-based scaffolds (~400°C). In this work, we studied the aqueous chemistry of Co(OH)2 to build a mechanistic understanding of a combined electrodeposition-hydrothermal synthesis along with mild heat treatment (<300°C) to obtain crystalline, layered LCO on 3D carbon scaffolds using only 3 feedstock materials. We established an understanding of how hydrothermal treatment pressure, temperature, duration, and LiOH concentration modulate the active synthesis mechanism and resulting LCO morphology. We find that in particular low hydrothermal pressure and high LiOH concentration prevent dissolution of precursor Co(OH)2 to enable an ion-exchange of H+ from Co(OH)2 with Li+ from solution to produce layered LCO while preserving the nanoflake architecture on the scaffold. We demonstrated the versatility of the ion-exchange process to coat a variety of electrode geometries and architectures. Overall, this research provides insight into the versatility, and limitations, of soft chemistry strategies to crystallize commercially relevant Li-ion cathode materials directly onto unique geometries for wide-ranging applications. | Ishita Kamboj; Seongbak Moon; Hannah Teeters; Veronica Augustyn | Materials Science; Carbon-based Materials; Materials Processing; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ce7856a4e53c4876d4dcbc/original/competition-between-dissolution-vs-ion-exchange-during-low-temperature-synthesis-of-li-co-o2-on-carbon-scaffolds.pdf |
6438059108c86922ffea0a42 | 10.26434/chemrxiv-2023-3w2cn-v2 | H2-Mediated Copper Catalyzed C–C Coupling Reactions – Selective Formation of Skipped Dienes | A simple copper(I)/N-heterocyclic carbene complex facilitates a H2-mediated C–C coupling reaction of internal alkynes and allylic chlorides. The catalytic protocol delivers the corresponding 1,4-dienes (skipped dienes) with high chemo-, regio- and stereoselectivity without any isomerization to the thermodynamically more stable 1,3-dienes or overreduction to the corre-sponding alkanes. The H2-mediated C–C coupling reaction allows for the exploitation “copper hydride catalysis” with H2 as terminal reducing agent and source of hydrides for forging of new C–C bonds. In this way, this approach gives rise to C–C bond forming reactions with a 3d metal without the need for a stoichiometric organometallic reducing agent. | Lea Brechmann; Teichert Johannes | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438059108c86922ffea0a42/original/h2-mediated-copper-catalyzed-c-c-coupling-reactions-selective-formation-of-skipped-dienes.pdf |
60c74374842e65e1fcdb22ad | 10.26434/chemrxiv.9205853.v1 | Modeling Physico-Chemical ADMET Endpoints With Multitask Graph Convolutional Networks | Simple physico-chemical properties like logD, solubility or serum albumin binding have a direct impact on the likelihood of success of compounds in clinical trials. Here, we collected all the Bayer in house data related to these properties and applied machine learning techniques to predict them for new compounds. We report that, for the endpoints studied here, a multitask graph convolutional network appears a highly competitive choice. The new model shows increased predictive performance on all endpoints compared to previous modeling methods.<br /> | Floriane Montanari; Lara Kuhnke; Antonius ter Laak; Djork-Arné Clevert | Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74374842e65e1fcdb22ad/original/modeling-physico-chemical-admet-endpoints-with-multitask-graph-convolutional-networks.pdf |
60c74eecbdbb89188ba39c82 | 10.26434/chemrxiv.12820244.v1 | Operando X-Ray Absorption Spectroscopy (XAS) Observation of Photoinduced Oxidation in FeNi (Oxy)hydroxide Overlayers on Hematite (α-Fe2O3) Photoanodes for Solar Water Splitting | A FeNi (oxy)hydroxide co-catalyst overlayer was photoelectrochemically deposited on a thin film hematite
(α-Fe2O3) photoanode, leading to a cathodic shift of ~100 mV in the photocurrent onset potential.
Operando X-ray absorption spectroscopy (XAS) at the Fe and Ni K-edges was used to study the changes in
the overlayer with potential, in dark and under illumination conditions. Potential or illumination only had
a minor effect on the Fe oxidation state, suggesting that Fe atoms do not accumulate significant amount
of charge over the whole potential range. In contrast, the Ni K-edge spectra showed pronounced
dependence on potential in dark and under illumination. The effect of illumination is to shift the onset for
the Ni oxidation because of the generated photovoltage, and suggests that holes which are
photogenerated in hematite are transferred mainly to the Ni atoms in the overlayer. The increase in the
oxidation state of Ni proceeds at potentials corresponding to the redox wave of Ni, which occurs
immediately prior to the onset of the oxygen evolution reaction (OER). Linear fitting analysis of the
obtained spectra suggests that the overlayer does not have to be fully oxidized to promote oxygen
evolution. Cathodic discharge measurements show that the photogenerated charge is stored almost
exclusively in the Ni atoms within the volume of the overlayer. <br /> | Anton Tsyganok; Paolo Ghigna; Alessandro Minguzzi; Alberto Naldoni; Vadim Murzin; Wolfgang Caliebe; Avner Rothschild; David Ellis | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74eecbdbb89188ba39c82/original/operando-x-ray-absorption-spectroscopy-xas-observation-of-photoinduced-oxidation-in-fe-ni-oxy-hydroxide-overlayers-on-hematite-fe2o3-photoanodes-for-solar-water-splitting.pdf |
67db462881d2151a020d244a | 10.26434/chemrxiv-2025-8bpqx | Difluoroacetamide: A Selectively Tunable, Universal 1H and 19F Quantitative NMR Calibrant | Quantitative NMR (qNMR) is a robust technique used in a variety of chemical industries due to its numerous analytical advantages. It exhibits a universal response, a broad linear range, diverse compound applicability, and allows for facile method development. The most accurate qNMR results are obtained with an internal calibrant, but no truly universal calibrant currently is known that is stable, non-toxic, commercially available, exhibits a unique chemical shift, is highly soluble in both aqueous and non-polar solvents, and exists as a non-hygroscopic solid for accurate weighing. In this study, we investigated several potential qNMR calibrants and identified 2,2-difluoroacetamide (DFA), which meets all the aforementioned criteria. This calibrant is soluble in a wide polarity range of both protic and aprotic solvents from D2O to CD2Cl2, and it exhibits selectively tunable 1H and 19F chemical shifts via decoupling that resonate in sparse regions of the typical NMR spectrum. We evaluated the broad utility of this calibrant by assaying 13 active pharmaceutical ingredients in 12 different deuterated solvents. Our results demonstrate excellent measured accuracies and precisions of 100 ± 1% and % RSD (n=3) less than 1%, respectively. Therefore, we recommend difluoroacetamide as a reliable and generally applicable internal calibrant for qNMR analysis. | Jared Wood; Ryan Cohen; Xiao Wang; Robert Thomas Williamson; Mikhail Reibarkh | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67db462881d2151a020d244a/original/difluoroacetamide-a-selectively-tunable-universal-1h-and-19f-quantitative-nmr-calibrant.pdf |
60c7520fbb8c1ad51a3dbdfb | 10.26434/chemrxiv.13249631.v1 | Rapid Access to Diverse Potassium Acyltrifluoroborates (KATs) Through Late-Stage Chemoselective Cross-Coupling Reactions | Potassium acyltrifluoroborates (KATs) are opening up new avenues in chemical biology, materials science and synthetic organic chemistry due to their intriguing reactivities. However, the synthesis of these compounds remains mostly complicated and time-consuming. This lack of a rapid and facile synthetic route has hindered the widespread adoption of KAT-based chemistry, especially in the areas of compound library synthesis and drug discovery. Herein, we have developed chemoselective Pd-catalyzed approaches for the late-stage diversification of arenes bearing pre-functionalized KATs. These approaches feature chemoselective cross-coupling, rapid diversification, functional group tolerance, mild reaction conditions, and high yields. | Xingwang Deng; Guan Zhou; Xiao Han; Khadim Ullah; Rajavel Srinivasan | Combinatorial Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7520fbb8c1ad51a3dbdfb/original/rapid-access-to-diverse-potassium-acyltrifluoroborates-ka-ts-through-late-stage-chemoselective-cross-coupling-reactions.pdf |
66aa3d955101a2ffa8b24944 | 10.26434/chemrxiv-2024-5f0cv-v2 | Gold-Catalyzed Migratory Insertion of Alkynes | Herein, for the first time, we disclose the migratory insertion of alkynes into Au(III)‒C bonds in a catalytic fashion. Experimental results clearly suggest that the migratory insertion pathway predominates over the π-activation pathway - a finding further supported by the Density Functional Theory (DFT) calculations. The observed regioselectivity underscores the distinct advantages and complementarity of gold catalysis in comparison to palladium catalysis. | Avishek Das; Biswajit Biswas; Vincent Gandon; Nitin T. Patil | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66aa3d955101a2ffa8b24944/original/gold-catalyzed-migratory-insertion-of-alkynes.pdf |
62a521fa2e6269ab067ff2d9 | 10.26434/chemrxiv-2022-h8w0k | Enantioselective Hydroalkenylation and Hydroalkynylation of Alkenes Enabled by a Transient Directing Group | The catalytic enantioselective synthesis of α-chiral alkenes and alkynes represents a powerful strategy for rapid generation of molecular complexity. Herein, we report a transient directing group facilitated site-selective palladium-catalyzed reductive Heck-type hydroalkenylation and hydroalkynylation of alkenylaldehyes using alkenyl and alkynyl bromides, respectively, allowing for construction of a stereocenters at the δ position with respect to the aldehyde. | Amit Simlandy; Johny Nguyen; Lucas Oxtoby; Quynh Wong; Jason Chen; Keary Engle | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a521fa2e6269ab067ff2d9/original/enantioselective-hydroalkenylation-and-hydroalkynylation-of-alkenes-enabled-by-a-transient-directing-group.pdf |
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