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66d4647120ac769e5f87e5be | 10.26434/chemrxiv-2024-3jxwn | Have we been wrong all along about the luminescence of iridium(III) complexes? | We demonstrate that the photoluminescence of certain types of iridium(III) complexes displays a substantial contribution from thermally activated delayed fluorescence (TADF), which enhances the efficiency of emission. The careful assessment of a range of literature data allowed TADF-emitting complexes to be identified, having a singlet-triplet energy gap ΔEST in the range 14 to 100 meV. The TADF contribution at room temperature (RT) is assessed from experimental data and computational modelling. While typically characterised by a relatively fast metal-facilitated phosphorescence, Ir(III) complexes may additionally benefit from the TADF mechanism, leading to even larger radiative rate constants kr. The typical features of such complexes that emerge are (i) dinuclearity, (ii) significant overlap between the absorption and emission spectra, and (iii) radiative decay rates kr > 106 s–1 at RT. Our findings suggest that, due to the presence of 1,3MLCT states the ΔEST of many Ir(III) complexes is sufficiently small to allow the re-population of their S1 states at RT. Nevertheless, if the f(S1->S0) has low singlet oscillator strength, the effect of TADF on the luminescence may be insignificant. Hence, whilst TADF might be widespread among Ir(III) complexes, its effect on photoluminescence may often be negligible. As luminescent iridium(III) complexes are common in various areas of study, this work may disrupt research on a broader scale beyond the immediate realm of photophysics. | Dawid Nastula; J.A. Gareth Williams; Piotr Pander | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Organometallic Compounds; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d4647120ac769e5f87e5be/original/have-we-been-wrong-all-along-about-the-luminescence-of-iridium-iii-complexes.pdf |
617cec4f3c169d781287c928 | 10.26434/chemrxiv-2021-t9878 | Use of Marine biotoxins to modulate the tyrosine kinase domain of the human epidermal growth factor receptor | Inappropriate activation of the Epidermal growth factor receptor (EGFR) group of kinases has been identified in a variety of tumour cells, either due to mutation or overexpression. Although the tumour is a fatal disease, significant therapy discoveries have lately been made. The human EGFR and this family of kinases have emerged as promising targets for cancer therapy. In this molecular docking study, Natural marine toxins are employed to regulate the activity of the human EGFR tyrosine kinase domain (EGFRtkd) in the molecular docking investigation (PDB ID5JEB). Marine biotoxins can cause neurological, gastrointestinal, and cardiovascular problems, as well as severe mortality and long-term morbidity in some situations. Because there is no antidote for any of the natural marine poisons, supportive care is the mainstay of treatment. Paralytic shellfish poisoning, in particular, and puffer fish poisoning, in particular, can result in death within hours of exposure to the poisons and may require immediate medical intervention. However, this research found that marine biotoxins can modulate EGFRtkd. Furthermore, homoyessotoxin was anticipated to be an EGFRtkd modulator with a binding affinity as -9.584 kcal/mol. To employ the homoyessotoxin in tumour therapies, further knowledge of natural marine biotoxins and further toxicological research is required. | Charli Deepak Arulanandam; Ramesh Dharmara; Prathiviraj Ragothaman; Samuel Gnana Prakash Vincent | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617cec4f3c169d781287c928/original/use-of-marine-biotoxins-to-modulate-the-tyrosine-kinase-domain-of-the-human-epidermal-growth-factor-receptor.pdf |
60ee78cba4e06b149a72854c | 10.26434/chemrxiv-2021-bgdql | All Are Aromatic: A 3D Globally Aromatic Cage Containing Five Types of 2D Aromatic Macrocycles | The studies on three-dimensional (3D) aromaticity have been mainly focused on fullerenes, boron-based deltahedrons/clusters, metal clusters and polyhedral hydrocarbons, but there are very limited researches on the fundamental aromaticity rule for 3D fully π-conjugated molecules. Herein, we report a π-conjugated molecular cage in which two aromatic porphyrin units are bridged by four thiophene-based arms. Two-electron chemical oxidation leads to a 3D globally aromatic cage with a C2 symmetry according to X-ray diffraction, NMR, electronic absorption spectra, and theoretical calculations. Detailed magnetic shielding response analysis along different axes reveal that all the possible five types of two-dimensional (2D) macrocycles in the cage skeleton are aromatic and follow Hückel rule. The switch from localized aromaticity to global aromaticity upon chemical oxidation is also observed in a tricyclic model compound. The study indicates that to attain 3D global aromaticity in a molecular cage, all the formally available π-conjugated macrocycles should be 2D aromatic. | Longbin Ren; Yi Han; Xudong Hou; Yong Ni; Jishan Wu | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ee78cba4e06b149a72854c/original/all-are-aromatic-a-3d-globally-aromatic-cage-containing-five-types-of-2d-aromatic-macrocycles.pdf |
6248eda1739db1322c219a72 | 10.26434/chemrxiv-2022-6x1lm | Towards Efficient Direct Dynamics Studies of
Chemical Reactions: A Novel Matrix Completion Algorithm | This paper describes the development and testing of a polynomial variety-based matrix completion (PVMC) algorithm towards reducing computational effort associated with reaction rate coefficient calculations using variational transition state theory with multidimensional tunneling (VTST-MT). The algorithm recovers eigenvalues of quantum mechanical Hessians constituting the minimum energy path (MEP) of a reaction using only a small sample of the information, by leveraging underlying properties of these eigenvalues. In addition to the low-rank property that constitutes the basis for most matrix completion (MC) algorithms, this work introduces a polynomial constraint in the objective function. This enables us to sample matrix columns unlike most conventional MC methods that can only sample elements, which makes PVMC readily compatible with quantum chemistry calculations as sampling a single column requires 1 Hessian calculation. For various types of reactions – SN2, hydrogen atom transfer, metal-ligand cooperative catalysis, and enzyme chemistry – we demonstrate that PVMC on average requires only 6-7 Hessian calculations to accurately predict both quantum and variational effects. | Stephen Jon Quiton; Jeongmin Chae; Selin Bac; Kareesa Kron; Urbashi Mitra; Shaama Mallikarjun Sharada | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6248eda1739db1322c219a72/original/towards-efficient-direct-dynamics-studies-of-chemical-reactions-a-novel-matrix-completion-algorithm.pdf |
616b7bbaf718df39c1e141fe | 10.26434/chemrxiv-2021-7zh15 | In-situ fabrication of metal oxide nanocaps based on biphasic reactions with surface nanodroplets | Surface-bound nanomaterials are widely used in clean energy techniques from lithium batteries, solar-driven evaporation in desalination to hydrogen production by photocatalytic electrolysis. Reactive surface nanodroplets may potentially streamline the process of fabrication of a range of surface-bound nanomaterials invoking biphasic reactions at interfaces. In this work, we demonstrate the feasibility of reactive surface nanodroplets for in-situ synthesis and anchoring of nanocaps of metal oxides with tailored porous structures. Spatial arrangement and surface coverage of nanocaps are predetermined during the formation of reactive nanodroplets, while the crystalline structures of metal oxides can be controlled by thermal treatment of organometallic nanodroplets produced from the biphasic reactions. Notably, tuning the ratio of reactive and non-reactive components in surface nanodroplets enables the formation of porous nanocaps that can double photocatalytic efficiency in the degradation of organic contaminants in water, compared to smooth nanocaps. In total, we demonstrate in-situ fabrication of four types of metal oxides in the shape of nanocaps. Our work shows that reactive surface nanodroplets may open a door to a general, fast and tuneable route for preparing surface-bound metal oxides. This fabrication approach may help develop new nanomaterials
needed for photocatalytic reactions, wastewater treatment, optical focusing, solar energy conversion and other clean energy techniques. | Zixiang Wei; Tulsi Dabodiya; Jian Chen; Qiuyun Lu; Jiasheng Qian; Jia Meng; Hongbo Zeng; Hui Qian; Xuehua Zhang | Energy; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616b7bbaf718df39c1e141fe/original/in-situ-fabrication-of-metal-oxide-nanocaps-based-on-biphasic-reactions-with-surface-nanodroplets.pdf |
66d840e851558a15ef03833c | 10.26434/chemrxiv-2024-btp37 | Dynamic phase behavior of amorphous solid dispersions revealed with in situ stimulated Raman scattering microscopy | This study reports the application of in situ stimulated Raman scattering (SRS) microscopy for real-time chemically-specific imaging of dynamic phase phenomena in amorphous solid dispersions (ASD). Using binary ritonavir and poly(vinylpyrrolidone-vinyl acetate) films with different drug loadings (0-100% w/w) as model systems, we employed SRS microscopy with fast spectral focusing to analyze ASD behavior upon contact with dissolution medium. Multivariate unmixing of the SRS spectra allowed changes in the distributions of the drug, polymer and water to be (semi-)quantitatively imaged in real time, both in the film and the adjacent dissolution medium. The SRS analyses were further augmented with complementary correlative sum frequency generation and confocal reflection, for additional crystallinity and phase sensitivity. In the ASDs with drug loadings of 20, 40 and 60% w/w, the water penetration front within the film, followed by both surface-directed and bulk phase separation in the film were apparent, but differed quantitatively. Additionally, drug-loading and phase dependent polymer and drug release behavior was imaged, and liquid-liquid phase separation was observed for the 20% drug loading ASD. Overall, SRS microscopy with fast spectral focusing provides quantitative insights into water-induced ASD phase phenomena, with chemical, solid-state, temporal and spatial resolution. These insights are important for optimal ASD formulation development. | Teemu Tomberg; Ilona Hämäläinen; Clare Strachan; Bert van Veen | Analytical Chemistry; Polymer Science; Drug delivery systems; Microscopy; Spectroscopy (Anal. Chem.) | CC BY 4.0 | CHEMRXIV | 2024-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d840e851558a15ef03833c/original/dynamic-phase-behavior-of-amorphous-solid-dispersions-revealed-with-in-situ-stimulated-raman-scattering-microscopy.pdf |
60c74b26337d6c3f76e27a44 | 10.26434/chemrxiv.12292514.v1 | Structure Based Drug Repurposing Through Targeting Nsp9 Replicase and Spike Proteins of SARS-CoV-2 | <p>Due to unavailability of therapeutic
approach for the novel coronavirus disease (COVID-19), the drug repurposing
approach would be the fastest and efficient way of drug development against this
deadly disease. We have applied bioinformatics approach for structure-based
drug repurposing to identify the potential inhibitors through drug screening,
molecular docking and molecular dynamics against non-structural
protein 9 (Nsp9) replicase and spike proteins of the SARS-CoV-2 from the
FDA approved drugs. We have performed virtual screening of 2000
FDA approved compounds including antiviral, anti-malarial, anti-parasitic,
anti-fungal, anti-tuberculosis and active phytochemicals against Nsp9 replicase and spike proteins of
SARS-CoV-2. Molecular docking was performed using Autodock-Vina. Selected hit compounds
were identified based on their highest binding energy and favourable ADME
profile. Notably, Conivaptan, an arginine vasopressin antagonist drug exhibited
highest binding energy (-8.4 Kcal/mol) and maximum stability with the amino
acid residues present on the active site of Nsp9 replicase. Additionally,
Tegobuvir, a non-nucleoside inhibitor of hepatitis C virus exhibited maximum
stability with highest binding energy (-8.1 Kcal/mol) on the active site of spike
protein. Molecular docking scores were further validated with the molecular
dynamics using Schrodinger, which supported strong stability of ligands with
proteins at their active site through water bridges, hydrophobic interactions,
H-bond. Overall, our findings highlight the fact that Conivaptan and Tegobuvir could
be used to control the infection and propagation of SARS-CoV-2 targeting Nsp9
replicase and spike protein, respectively. Moreover, <i>in vitro</i> and <i>in vivo</i>
validation of these findings will be helpful in bringing these molecules at the
clinical settings.</p> | Vaishali Chandel; Prem Prakash Sharma; Sibin Raj; Brijesh Rathi; Dhruv Kumar | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b26337d6c3f76e27a44/original/structure-based-drug-repurposing-through-targeting-nsp9-replicase-and-spike-proteins-of-sars-co-v-2.pdf |
66801cc5c9c6a5c07abffe10 | 10.26434/chemrxiv-2024-k5r0p-v2 | Identifying and Engineering Flavin Dependent Halogenases for Selective Biocatalysis | Organohalogen compounds are extensively used as building blocks, intermediates, pharmaceuticals, and agrochemicals due to their unique chemical and biological properties. Installing halogen substituents, however, frequently requires functionalized starting materials and multistep functional group interconversion. Several classes of halogenases evolved in nature to enable halogenation of a different classes of substrates; for example, site-selective halogenation of electron rich aromatic compounds is catalyzed by flavin-dependent halogenases (FDHs). Mechanistic studies have shown that these enzymes use FADH2 to reduce O2 to water with concomitant oxidation of X- to HOX (X = Cl, Br, I). This species travels through a tunnel within the enzyme to access the FDH active site. Here, it is believed to interact with an active site lysine proximal to bound substrate, enabling electrophilic halogenation with selectivity imparted via molecular recognition, rather than directing groups or strong electronic activation.
The unique selectivity of FDHs led to several early biocatalysis efforts, preparative halogenation was rare, and the hallmark catalyst-controlled selectivity of FDHs did not translate to non-native substrates. FDH engineering was limited to site-directed mutagenesis, which resulted in modest changes in site-selectivity or substrate preference. To address these limitations, we optimized expression conditions for the FDH RebH and its cognate flavin reductase (FRed), RebF. We then showed that RebH could be used for preparative halogenation of non-native substrates with catalyst-controlled selectivity. We reported the first examples in which the stability, substrate scope, and site selectivity of an FDH were improved to synthetically useful levels via directed evolution. X-ray crystal structures of evolved FDHs and reversion mutations showed that random mutations throughout the RebH structure were critical to achieving high levels of activity and selectivity on diverse aromatic substrates, and these data were used in combination with molecular dynamics simulations to develop predictive model for FDH selectivity. Finally, we used family-wide genome mining to identify a diverse set of FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds.
The diversity of our evolved and mined FDHs allowed us to pursue synthetic applications beyond simple aromatic halogenation. For example, we established that FDHs catalyze enantioselective reactions involving desymmetrization, atroposelective halogenation, and halocyclization. These results highlight the ability of FDH active sites to tolerate different substrate topologies. This utility was further expanded by our recent studies on the single component FDH/FRed, AetF. While we were initially drawn to AetF because it does not require a separate FRed, we found that it halogenates substrates that are not halogenated efficiently or at all by other FDHs and provides high enantioselectivity for reactions that could only be achieved using RebH variants after extensive mutagenesis. Perhaps most notably, AetF catalyzes site-selective aromatic iodination and enantioselective iodoetherification. Together, these studies highlight the origins of FDH engineering, the utility and limitations of the enzymes developed to date, and the promise of FDHs for an ever-expanding range of biocatalytic halogenation reactions. | Jared C. Lewis | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Bioengineering and Biotechnology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66801cc5c9c6a5c07abffe10/original/identifying-and-engineering-flavin-dependent-halogenases-for-selective-biocatalysis.pdf |
65e498cf9138d23161946ae8 | 10.26434/chemrxiv-2024-wb68d | Elucidating Heavy Atom Tunneling Kinetics | In this work, we characterize the temperature dependence of kinetic properties in heavy atom tunneling reactions by means of molecular dynamics simulations, including nuclear quantum effects (NQEs) via Path Integral theory. To this end, we consider the prototypical Cope rearrangement of semibullvalene.
The reaction was studied in the 25--300~K temperature range observing that the inclusion of NQEs modifies the temperature behavior of both free energy barriers and dynamical recrossing factors with respect to classical dynamics. Notably, while in classical simulations the activation free energy shows a very weak temperature dependence, it becomes strongly dependent on temperature when NQEs are included. This temperature behavior shows a transition from a regime where the quantum effects are limited and can mainly be traced back to zero point energy, to a low temperature regime where tunneling plays a dominant role. In this regime, the free energy curve literally tunnels below the potential energy barrier along the reaction coordinate, allowing much faster reaction rates.
Finally, the temperature dependence of the rate constants obtained from molecular dynamics simulations was compared with available experimental data and with semi-classical transition state theory calculations, showing comparable behaviors and similar transition temperatures from thermal to (deep) tunneling regime. | Federica Angiolari; Giacomo Mandelli; Simon Huppert; Chiara Aieta; Riccardo Spezia | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e498cf9138d23161946ae8/original/elucidating-heavy-atom-tunneling-kinetics.pdf |
60c759850f50db431f3986c1 | 10.26434/chemrxiv.14706612.v1 | Bleaching the Record: After 200 Years, Single Crystal X-Ray Crystallography Reveals the Structure and Hydrogen-Bonding Properties of Hypochlorite and Hypobromite Ions in the Solid State | <div>We report the first single crystal structures of hypochlorite and hypobromite salts, including hydrated sodium hypochlorite - a ubiquitous bleaching and disinfection agent in use for almost 200 years. The structures represent the first characterization of fundamentally important hypochlorite and hypobromite anions in the solid state, by X-ray crystallography and are supported by Raman spectroscopy on individual crystals. The structural analysis provides insight into supramolecular chemistry of the hypohalite ions in the hydrated environment of the NaOCl<sup>.</sup>5H<sub>2</sub>O and NaOBr<sup>.</sup>5H<sub>2</sub>O solid salts, and reveals measured Cl-O and Br-O bond lengths of 1.69 A and 1.82 A, respectively, which are significantly longer than those for corresponding higher-valence oxoanions, and in agreement with the values spectroscopically determined for hypohalous acids and corresponding oxides in the gas phase.<br /></div> | Filip Topic; Joseph Marrett; Tristan Borchers; Hatem M. Titi; Christopher J. Barrett; Tomislav Friscic | Bonding; Main Group Chemistry (Inorg.); Solid State Chemistry; Solvates; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759850f50db431f3986c1/original/bleaching-the-record-after-200-years-single-crystal-x-ray-crystallography-reveals-the-structure-and-hydrogen-bonding-properties-of-hypochlorite-and-hypobromite-ions-in-the-solid-state.pdf |
6438ea5e1d262d40ea6cc7cf | 10.26434/chemrxiv-2023-qk8zn | Paper-Based Electrical Sensors for Aqueous Heavy Metal Ion Detections | Trace levels of heavy metals such as lead, cadmium, mercury, and arsenic can have harmful effects on human health, causing damage to organs and the nervous system. As a result, it is essential to monitor heavy metal concentrations continuously and in real-time, with detection limits of less than nanomolar to reduce their impact on the environment and human health. The development of paper-based microfluidics in recent years has made it a promising platform for lab-on-a-chip devices capable of detecting heavy metals on a large scale and on-site for environmental purposes. This review article will introduce commonly used paper-based electrical sensing (including electrochemical, FETs, and chemiresistive sensors), existing fabrication and analysis techniques, and various application areas for these heavy metal ion sensors. Additionally, the challenges that must be addressed for paper-based sensors to realize their full potential and future outlooks will be discussed. | Su Sun; Jing Chen; Wei Wong | Analytical Chemistry; Analytical Chemistry - General | CC BY 4.0 | CHEMRXIV | 2023-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6438ea5e1d262d40ea6cc7cf/original/paper-based-electrical-sensors-for-aqueous-heavy-metal-ion-detections.pdf |
6185ffc27a00215319482387 | 10.26434/chemrxiv-2021-2ps1v | Accelerated Discovery of CH4 Uptake Capacity MOFs using Bayesian Optimization | High-throughput computational studies for discovery of metal-organic frameworks (MOFs) for separations and storage applications are often limited by the costs of computing thermodynamic quantities, with recent studies reliant ab initio results for a narrow selection of MOFs and empirical force-field methods for larger selections. Here, we conduct a proof-of-concept study using Bayesian optimization on CH4 uptake capacity of hypothetical MOFs for an existing dataset (Wilmer et al, Nature Chem. 2012, 4, 83). We show that less than 0.1% of the database needs to be screened with our Bayesian optimization approach to recover the top candidate MOFs. This opens the possibility of efficient screening of MOF databases using accurate ab-initio calculations for future adsorption studies on a minimal subset of MOFs. Furthermore, Bayesian optimization and the surrogate model presented here can offer interpretable material design insights and our framework will be applicable in the context of other target properties. | Eric Taw; Jeffrey Neaton | Theoretical and Computational Chemistry; Machine Learning; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6185ffc27a00215319482387/original/accelerated-discovery-of-ch4-uptake-capacity-mo-fs-using-bayesian-optimization.pdf |
66ac30ac01103d79c5835f73 | 10.26434/chemrxiv-2024-nmrqj | Phosphorylation Strongly Affects the Inhibition of Human Carbonic Anhydrase I CO2 Hydration Activity | Human carbonic anhydrases (hCAs) have essential roles in respiration, acid-base balance, and fluid secretion, with implications in diseases such as glaucoma, epilepsy, obesity, and cancer. Of the fifteen known hCAs, human CA I (hCA I) is particularly abundant in erythrocytes, playing a critical role in CO2 transport. Despite extensive research on hCA I, the impact of post-translational modifications (PTMs), particularly phosphorylation, on its catalytic activity and inhibitor binding remains poorly understood. Although multiple phosphorylation sites have been identified in hCA I in vivo through high-throughput proteomics studies including at the highly conserved Ser51 residue, the functional consequences of these modifications are not well characterized. We investigated the effects of a phosphomimic mutation at Ser51 on hCA I, examining its catalytic efficiency and susceptibility to inhibition by sulfonamides and anions. Using a recombinant expression system and a stopped-flow kinetic assay, we characterized the CO2 hydration activity and inhibition profiles of S51E hCA I compared to the wild type enzyme. Our results demonstrate that the S51E mutation increases the catalytic turnover rate (kcat) from 2.0 × 105 s-1 to 2.6 × 105 s-1 but significantly decreases substrate affinity, raising the Michaelis constant (KM) from 4.0 mM to 13.9 mM, reducing overall catalytic efficiency by over 50%. Inhibition studies with a panel of 41 sulfonamides revealed that the S51E mutation dramatically alters inhibitor sensitivity, particularly for the most effective inhibitors. For example, 15 of the 16 most effective sulfonamide inhibitors for hCA I (with KIs <350 nM) were an average of over 35-fold less effective in inhibiting S51E hCA I than the wild type. For example, the KI of the anticonvulsant zonisamide increased from 31 nM for the wild type hCA I to 4 µM. The inhibition profile with a panel of 37 small anions further indicated that the S51E mutant exhibited significantly reduced susceptibility to inhibition by 24 out of 37 tested anions, with some KI values increasing by up to 11,000-fold for inhibitors like hydrogen sulfide. This study underscores the significant impact that phosphorylation may have on hCA I function and inhibition. By characterizing the effects of phosphorylation on the CO2 hydration activity and inhibitor sensitivity of hCA I, these findings represent early steps in developing more selective proteoform-specific inhibitors, which could lead to more effective treatments for diseases involving carbonic anhydrases. | Andrea Angeli; Vivian De Luca; Xiaojing Huang; Daniel Winter; Clemente Capasso; Claudiu Supuran; William Donald | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ac30ac01103d79c5835f73/original/phosphorylation-strongly-affects-the-inhibition-of-human-carbonic-anhydrase-i-co2-hydration-activity.pdf |
64a84f676e1c4c986bfa4298 | 10.26434/chemrxiv-2023-g1b52 | Detection and Characterization of Rapidly Equilibrating Glycosylation Reaction Intermediates Using Exchange NMR | The stereoselective introduction of glycosidic bonds (glycosylation) is one of the main challenges in the chemical synthesis of carbohydrates. Glycosylation reaction mechanisms are difficult to control because in many cases the exact reactive species driving product formation cannot be detected and the product outcome cannot be explained by the primary reaction intermediate observed. In these cases, reactions are expected to take place via other low-abundance reaction intermediates that are in rapid equilibrium with the primary reaction intermediate via a Curtin-Hammett scenario. Despite this principle being well-known in organic synthesis, mechanistic studies investigating this model in glycosylation reactions are complicated by the challenge of detecting the extremely short-lived reactive species responsible for product formation. Herein, we report the utilization of the chemical equilibrium between low abundance reaction intermediates and the stable, readily observed α-glycosyl triflate intermediate in order to infer the structure of the former species by employing exchange NMR. Using this technique, we enabled the detection of reaction intermediates such as β-glycosyl triflates and glycosyl dioxanium ions. This demonstrates the power of exchange NMR to unravel reaction mechanisms as we aim to build a catalogue of kinetic parameters allowing for the understanding and the eventual prediction of glycosylation reactions | Frank de Kleijne; Floor ter Braak; Dimitrios Piperoudis; Peter Moons; Sam Moons; Hidde Elferink; Paul White; Thomas Boltje | Organic Chemistry; Physical Organic Chemistry; Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64a84f676e1c4c986bfa4298/original/detection-and-characterization-of-rapidly-equilibrating-glycosylation-reaction-intermediates-using-exchange-nmr.pdf |
64808812be16ad5c579aa4ad | 10.26434/chemrxiv-2023-l3gsz | Cu(I)-catalysed enantioselective chlorine atom transfer with vinyl radicals | Enantioselective intermolecular atom transfer reactions of vinyl radicals have hitherto remained elusive mainly due to their inherently high instability and reactivity which significantly compromises the stereodiscriminating substrate-catalyst interactions. Herein, we describe Cu(I)-catalyzed enantioselective chlorine atom transfer with vinyl radicals using tailormade tridentate anionic N,N,N-ligands featuring bulky peripheral substituents. This reaction readily accommodates (hetero)aryl and alkyl sulfonyl chlorides as radical precursors and more importantly, a large panel of 2-aminoaryl and 2-oxyaryl alkynes as substrates, providing highly transformable axially chiral vinyl chlorides in moderate to good yield with excellent enantioselectivity. The reaction can be easily scaled up to gram scales and straightforward manipulations of the thus obtained vinyl halides lead to axially chiral thiourea, pyridyl carboxamide, and quinolyl sulfonamide compounds, which are promising chiral reagents for asymmetric catalysis. Both experimental and theoretical mechanistic studies supported the proposed chlorine atom transfer reaction mechanism. | Jun-Bin Tang; Jun-Qian Bian; Zhihan Zhang; Yong-Feng Cheng; Li Qin; Qiang-Shuai Gu; Peiyuan Yu; Xin-Yuan Liu | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64808812be16ad5c579aa4ad/original/cu-i-catalysed-enantioselective-chlorine-atom-transfer-with-vinyl-radicals.pdf |
63c0551f4fba707bd4034577 | 10.26434/chemrxiv-2023-2lgkg | Fragment-based approaches to identify RNA binders | Although fragment-based drug discovery (FBDD) has been successfully implemented and
well-explored for protein targets, its feasibility for RNA targets is emerging. Despite the
challenges associate with the selective targeting of RNA, efforts to integrate known methods of
RNA binder discovery with fragment-based approaches has been fruitful, as a few bioactive
ligands have been identified. Here, we review various fragment-based approaches implemented
for RNA targets and provide insight into experimental design and outcomes, to guide future work
in the area. Indeed, investigations surrounding the molecular recognition of RNA by fragments
address rather important questions such as the limits of molecular weight that confers selective
binding and the physicochemical properties favorable for RNA binding and bioactivity. | Blessy M. Suresh; Amirhossein Taghavi; Jessica L. Childs-Disney; Matthew D. Disney | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c0551f4fba707bd4034577/original/fragment-based-approaches-to-identify-rna-binders.pdf |
665f3de121291e5d1d0f25e4 | 10.26434/chemrxiv-2024-kp2cw | Probability distributions of phases I | This article presents the mathematical foundation for calculating PD's (probability distributions) for some set of phases needed for the structure determination of a crystal. We can obtain PD's of the phases that can contain N, or without N . A former paper [3] could only obtain PD's of the phases containing N . Here we have the two possibilities. | Jan Brosius ; Walter Brosius | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665f3de121291e5d1d0f25e4/original/probability-distributions-of-phases-i.pdf |
60c74c499abda22d89f8d254 | 10.26434/chemrxiv.12411020.v2 | Isonitrile Ruthenium and Iron PNP Complexes: Synthesis, Characterization and Catalytic Assessment for Base-Free Dehydrogenative Coupling of Alcohols | Neutral and ionic ruthenium and iron aliphatic PNPH-type pincer complexes (PNPH= NH(CH2CH2PiPr2)2) bearing benzyl, n-butyl or tert-butyl isocyanide ancillary ligands have been prepared and characterized. Reaction of [RuCl2(PNPH)]2 with one equivalent CN-R per ruthe-nium center affords complexes [Ru(PNPH)Cl2(CNR)] (R= benzyl, 1a, R= n-butyl, 1b, R= t-butyl, 1c), with cationic [Ru(PNPH)(Cl)(CNR)2]Cl 2a-c as side-products. Complexes 2a-c are selectively prepared upon reaction of [RuCl2(PNPH)]2 with 2 equiva-lents of isonitrile per ruthenium center. Dichloride species 1a-c react with excess NaBH4 to afford [Ru(PNPH)(H)(BH4)(CN-R)] 3a-c, analogues to benchmark Takasago catalyst [Ru(PNP)(H)(BH4)(CO)]. Reaction of 1a-c with a single equivalent of NaBH4 under protic conditions results in formation of hydrido chloride derivatives [Ru(PNPH)(H)(Cl)(CN-R)] (4a-c), from which 3a-c can be prepared upon reaction with excess NaBH4. Use of one equivalent of NaHBEt3 with 4a and 4c affords bishydrides [Ru(PNPH)(H)2(CN-R)] 5a and 5c. In the case of bulkier t-butylisonitrile, two isomers were observed by NMR, with the PNP framework in either meridional or facial confor-mation. Deprotonation of 4c by KOtBu generates amido derivative [Ru(PNP’)(H)(CN-t-Bu)] (6, PNP’= -N(CH2CH2PiPr2)2), unstable in solution. Addition of excess benzylisonitrile to 4a provides cationic hydride [Ru(PNPH)(H)(CN-CH2Ph)2]Cl (7). Concerning iron chemis-try, [Fe(PNPH)Br2] reacts one equivalent benzylisonitrile to afford [Fe(PNPH)(Br)(CNCH2Ph)2]Br (8). The outer-sphere bromide anion can be exchanged by salt metathesis with NaBPh4 to generate [Fe(PNPH)(Br)(CNCH2Ph)2](BPh4) (9). Cationic hydride species [Fe(PNPH)(H)(CN-t-Bu)2](BH4) (10) is prepared from consecutive addition of excess CN-t-Bu and NaBH4 on [Fe(PNPH)Br2]. Ruthenium complexes 3a-c are active in acceptorless alcohol dehydrogenative coupling into ester under base-free conditions. From kinetic follow-up, the trend in initial activity is 3a ≈ 3b > [Ru(PNPH)(H)(BH4)(CO)] >> 3c; for robustness, [Ru(H)(BH4)(CO)(PNPH)] > 3a > 3b >> 3c. Hy-potheses are given to account for the observed deactivation. Complexes 3b, 3c, 4a, 4c, 5c, 7, cis-8 and 9 were characterized by X-ray crystallography. | Duc Hanh Nguyen; Delphine Merel; Nicolas Merle; Xavier Trivelli; Frederic Capet; Regis Gauvin | Homogeneous Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c499abda22d89f8d254/original/isonitrile-ruthenium-and-iron-pnp-complexes-synthesis-characterization-and-catalytic-assessment-for-base-free-dehydrogenative-coupling-of-alcohols.pdf |
60c73d91469df4bc74f42726 | 10.26434/chemrxiv.5362630.v2 | Relaxed structure of typical nitro explosives in the excited state: observation, implication and application | <a></a><a></a><a></a><a>U</a><a></a><a></a><a></a><a></a><a></a><a>nderstanding the structural, geometrical and
chemical changes that occur after electronic excitation is essential to unraveling
the inherent mechanism of nitro
explosives. In
this work, relaxed structures of typical nitro explosives in the excited state are
investigated by time-dependent density functional theory. During the excitation
process, nitro group becomes activated and then relaxes,
leading to a relaxed structure. </a><a></a><a>All five nitro explosives exhibit a similar
behavior, and impact sensitivity is related to excitation energy of relaxed structure.</a> <a></a><a>H</a>igh sensitivity d-HMX has a lower excitation energy for relaxed
structure than b-HMX. This work offers a novel insight into energetic
material.<a></a> | Genbai Chu; Zuhua Yang; Tao Xi; Jianting Xin; Yongqiang Zhao; Weihua He; Min Shui; Yuqiu Gu; Ying Xiong; Tao Xu | Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2017-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d91469df4bc74f42726/original/relaxed-structure-of-typical-nitro-explosives-in-the-excited-state-observation-implication-and-application.pdf |
661463eb418a5379b06c1ee4 | 10.26434/chemrxiv-2024-2g3kn | Electrodialysis and Nitrate Reduction to Enable Distributed Ammonia Manufacturing from Wastewaters | Underutilized wastewaters containing dilute levels of reactive nitrogen (Nr) can help rebalance the nitrogen cycle. This study describes electrodialysis and nitrate reduction (EDNR), a reactive electrochemical separation architecture that combines catalysis and separations to remediate nitrate and ammonium-polluted wastewaters while recovering ammonia. By engineering operating parameters (e.g., background electrolyte, applied potential, electrolyte flow rate), we achieved near-complete recovery and conversion of Nr in both simulated and real wastewaters. EDNR process demonstrated long-term robustness and recovered >100 mM ammonium fertilizer solution from 8.2 mM Nr-containing agricultural runoff. EDNR is the first reported process to our knowledge that remediates dilute real wastewater and recovers ammonia from multiple Nr pollutants, with an energy consumption (245 MJ/kg NH3-N in simulated wastewater, 920 MJ/kg NH3-N in agricultural runoff) on par with the state-of-the-art. Demonstrated first at proof-of-concept and engineered to technology readiness level (TRL) 5, EDNR shows great promise for distributed wastewater treatment and sustainable ammonia manufacturing. | Jinyu Guo; Matthew Liu; Chloe Laguna; Dean Miller; Kindle Williams; Brandon Clark; Carolina Munoz; Sarah Blair; Adam Nielander; Thomas Jaramillo; William Tarpeh | Catalysis; Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Water Purification; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661463eb418a5379b06c1ee4/original/electrodialysis-and-nitrate-reduction-to-enable-distributed-ammonia-manufacturing-from-wastewaters.pdf |
6474a06a4f8b1884b778e9a0 | 10.26434/chemrxiv-2023-vkw87 | DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking | To allow DOCK 6 access to unprecedented chemical space for screening billions of small molecules, we have implemented features from DOCK 3.7 into DOCK 6, including a search routine that traverses precomputed ligand conformations stored in a hierarchical database. We tested them on the DUDE-Z and SB2012 test sets. The hierarchical database search routine is 16 times faster than anchor-and-grow. However, the ability of hierarchical database search to reproduce the experimental pose is 16% worse than that of anchor-and-grow. The enrichment performance is on average similar, but DOCK 3.7 has better enrichment than DOCK 6, and DOCK 6 is on average 1.7 times slower. However, with post-docking torsion minimization, DOCK 6 surpasses DOCK 3.7. A large-scale virtual screen is performed with DOCK 6 on 23 million fragment molecules. We use current features in DOCK 6 to complement hierarchical database calculations, including torsion minimization, which is not available in DOCK 3.7. | Trent E. Balius; Mayukh Chakrabarti; Y. Stanley Tan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6474a06a4f8b1884b778e9a0/original/dock-6-incorporating-hierarchical-traversal-through-precomputed-ligand-conformations-to-enable-large-scale-docking.pdf |
6559a0b16e0ec7777f3f3191 | 10.26434/chemrxiv-2023-nk6wj | Physics-Informed Design of Hybrid Pulse Power Characterization (HPPC) Tests for Rechargeable Batteries | Industry-standard diagnostic methods for rechargeable batteries, such as hybrid pulse power characterization (HPPC) tests for hybrid electric vehicles, provide some indications of state of health (SoH), but lack a physical basis to guide protocol design and identify degradation mechanisms. We develop a physics-based theoretical framework for HPPC tests, which accurately determines kinetic parameters that capture root causes of battery degradation. We show that voltage pulses are generally preferable to current pulses, since voltage-resolved linearization more rapidly quantifies degradation without sacrificing accuracy or allowing significant state changes during the measurement. In addition, asymmetric amounts of information gain between (dis)charge pulses were found from differences in electrode kinetic scales. We demonstrate our approach of physics-informed HPPC on simulated Li-ion batteries with nickel-rich cathodes and graphite anodes. Multivariable optimization by physics-informed HPCC rapidly determines kinetic parameters that correlate with degradation phenomena at the anode, such as solid-electrolyte interphase (SEI) growth and lithium plating, as well as at the cathode, such as oxidation-induced cation disorder. Standardized voltage protocols for HPPC tests could play a pivotal role in expediting battery SoH assessment and accelerating materials design by providing new electrochemical features for interpretable machine learning of battery degradation. | Debbie Zhuang; Michael Li; Vivek Lam; Richard Braatz; William Chueh; Martin Bazant | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage | CC BY 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6559a0b16e0ec7777f3f3191/original/physics-informed-design-of-hybrid-pulse-power-characterization-hppc-tests-for-rechargeable-batteries.pdf |
65411a9fc573f893f183c73e | 10.26434/chemrxiv-2023-73tl7 | Understanding the effects of forced and bubble-induced convection in transport-limited organic electrosynthesis | Organic electrosynthesis offers a sustainable path to decarbonize the chemical industry by integrating renewable energy into chemical manufacturing. However, achieving the selectivity and energy efficiency required for industrial applications is challenging due to the inherent mass transport limitations. Convection can mitigate mass transport limitations, but its impact on organic electrochemical processes remains poorly understood. We investigate the interplay between mass transport and electrochemical reaction rates under convective flows in the context of the electrosynthesis of adiponitrile, one of the largest organic electrochemical processes in the industry. We use experiments and data-driven predictive models to demonstrate that forced liquid convection and bubble-induced convection produce near-identical mass transport conditions when the corresponding Sherwood numbers—the ratio of convective mass transport to diffusive mass transport—are equal. Moreover, we show that the Faradaic efficiency (i.e., the electrochemical selectivity) scales with the Sherwood number for a given current density and reactant concentration. This scalability enables performance to be predicted irrespective of the convection mode employed to enhance mass transport. Our results provide a deeper understanding of mass transport in organic electrosynthesis and offer guidelines to enable more sustainable chemical manufacturing practices. | Casey Bloomquist; Melisa Dogan; James Harris; Benjamin Herzog; William Tenn; Eray Aydil; Miguel Modestino | Chemical Engineering and Industrial Chemistry; Reaction Engineering; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65411a9fc573f893f183c73e/original/understanding-the-effects-of-forced-and-bubble-induced-convection-in-transport-limited-organic-electrosynthesis.pdf |
6355cb451db0bd8f0336a51a | 10.26434/chemrxiv-2022-l7rmf | Heterogeneity in Cation Exchange Ag+ Doping of CdSe Nanocrystals
| Cation exchange is becoming extensively used for nanocrystal (NC) doping in order to produce NCs with unique optical and electronic properties. However, despite its ever-increasing use, the relationships between the cation exchange process, its doped NC products, and the resulting NC photophysics are not well characterized. For example, similar doping procedures on NCs with the same chemical compositions have resulted in quite different photophysics. Through a detailed single molecule investigation of a post-synthesis Ag+ doping of CdSe NCs, a number of species were identified within a single doped NC sample, suggesting the differences in the optical properties of the various synthesis methods are due to the varied contributions of each species. Electrostatic force microscopy (EFM), electron energy loss spectroscopy (EELS) mapping, and single molecule photoluminescence (PL) studies were used to identify four possible species resulting from the Ag+-CdSe cation exchange doping process. The heterogeneity of these samples shows the difficulty in controlling a post-synthesis cation exchange method to produce homogenous samples needed for use in any potential application. Additionally, the heterogeneity in the doped samples demonstrates that significant care must be taken in describing the ensemble or average characteristics of the sample. | Abigail R Freyer; Trevor Tumiel; Michelle Smeaton; Benjamin H Savitzky; Lena F Kourkoutis; Todd D Krauss | Physical Chemistry; Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6355cb451db0bd8f0336a51a/original/heterogeneity-in-cation-exchange-ag-doping-of-cd-se-nanocrystals.pdf |
67bf3845fa469535b90b4a49 | 10.26434/chemrxiv-2025-psg4n | Direct Synthesis of Amorphous Metal–Organic Frameworks from Nanoclusters | The direct synthesis of amorphous metal–organic frameworks (aMOFs) is an appealing yet often avoided approach due to the perceived unpredictability of amorphous network formation. In this study, we develop a strategy for aMOF synthesis using pre-formed nanoclusters and rigid organic linkers, providing enhanced control over disorder and defect chemistry while bypassing the traditional ‘crystallise–amorphise’ approach. By systematically comparing this nanocluster-based method to other direct synthesis routes and using X-ray pair distribution function, thermogravimetric and statistical analyses, we establish key design principles governing aMOF formation. We demonstrate that kinetic control—fast reactions under basic conditions at room temperature—suppresses crystallisation and drives amorphous network formation. Using nanoclusters as synthetic precursors consistently yields highly disordered frameworks with the shortest coherence lengths among direct synthesis methods. Additionally, we show that tuning metal composition through doping with kinetically inert cations restricts coordination reversibility, significantly increasing defect density and structural disorder. Structural analysis reveals that while aMOFs share motifs with crystalline polymorphs, they cannot be directly mapped onto known structures, highlighting the importance for more nuanced characterisation approaches. Just as crystal engineering was instrumental in the expansion of crystalline MOFs, new synthetic strategies are essential for advancing the aMOF field. By developing a systematic approach to aMOF design, this work provides a foundation for tailoring structural disorder and functional properties, expanding the potential of aMOFs for catalysis, adsorption, and transport applications. | Nanna Lærke Baun; Sabina Svava Mortensen; Heloisa Bordallo; Kirsten Jensen; Adam Sapnik | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bf3845fa469535b90b4a49/original/direct-synthesis-of-amorphous-metal-organic-frameworks-from-nanoclusters.pdf |
63317f03f764e67e1b03bba5 | 10.26434/chemrxiv-2022-lhm0z | Structural and Optical Properties of Ni and Zn co-doped Copper Oxide nanoparticles | Ni doping in CuO showed successful replacement of Cu+2 ions by Ni+2 ions. Evidence of strain being developed due to doping was seen. Change in crystallite size was observed depending upon the role of Ni as a nucleating center. Intensity variations in absorption and emission spectra were observed which were related to the amount of defects or formation of new phases in the materials. A wide absorption window was observed due to exciton. A change in band gap was observed corresponding to the change in particle size. Zn doping in CuO caused a variation in crystallite size and incorporated defects which had effect on the optical properties. A change in band gap due to defect generated energy levels as well as quantum size effect was seen. | Ritambhara Dash; Arnab Bhattacharyya | Materials Science; Aggregates and Assemblies; Materials Processing; Nanostructured Materials - Materials | CC BY NC 4.0 | CHEMRXIV | 2022-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63317f03f764e67e1b03bba5/original/structural-and-optical-properties-of-ni-and-zn-co-doped-copper-oxide-nanoparticles.pdf |
65bf34379138d2316165e366 | 10.26434/chemrxiv-2024-jch7t | Nearly all-active-material cathodes free of nickel and cobalt for Li-ion batteries | The global transition to electric vehicles and large-scale energy storage systems requires cost-effective and abundant alternatives to commercial Co/Ni-based cathodes (e.g., LiNi0.6Mn0.2Co0.2O2) for Li-ion batteries (LIBs). Manganese-based disordered rock-salts (Mn-DRXs) can outperform conventional cathodes at lower cost, achieving >900 Wh/kg-AM (per active material, AM), but such performance has been demonstrated exclusively in cell constructions far removed from commercial viability, namely with diluted electrode films (~70 wt%-AM) containing excessive carbon and binder. Herein, our work involves a comprehensive study to attain AM-concentrated Mn-DRX cathodes (>95 wt%-AM), covering from inherent material properties to the microstructure of electrodes, to address the formidable challenges in Mn-DRX research. We reveal that Mn-DRXs’ failures in AM-concentrated electrodes originate from their extremely low electrical conductivity (10^-10-10^-8 S/cm) and the collapse of the electrical network with volume change over cycling. These failure modes are resolved through electrical percolation engineering and enhancement of electrode mechanical properties, allowing our demonstration of nearly all-AM Mn-DRX cathodes (~96 wt%-AM) and the highest application-level energy density (~1050 Wh/kg-cathode) reported to date. This work further unveils the trade-off role of Mn-content on Mn-DRXs’ electrical conductivity and volume change, providing guidelines for material design to 33 advance Co/Ni-free LIB's technology readiness. | Eunryeol Lee; Dae-Hyung Lee; Stéphanie Bessette; Sang-Wook Park; Nicolas Brodusch; Gregory Lazaris; Hojoon Kim; Rahul Malik; Raynald Gauvin; Dong-Hwa Seo; Jinhyuk Lee | Materials Science; Energy; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65bf34379138d2316165e366/original/nearly-all-active-material-cathodes-free-of-nickel-and-cobalt-for-li-ion-batteries.pdf |
66f2f9e312ff75c3a157ef25 | 10.26434/chemrxiv-2024-jl2jr | Plasmon-enhanced multiphoton polymer crosslinking for selective modification of plasmonic hotspots | A novel approach to selectively modify narrow sub-areas of metallic nanostructures adjacent to plasmonic hotspots, where strong electromagnetic field amplification occurs upon localized surface plasmon (LSP) excitation, is reported. In contrast to plasmon-driven polymerization, it relies on plasmonically enhanced multiphoton crosslinking (MPC) of polymer chains carrying photoactive moieties. When attached to metallic nanostructures and irradiated with a femtosecond near-infrared beam resonantly coupled with LSPs, the enhanced field intensity locally exceeds the threshold and initiates MPC at plasmonic hotspots. This concept is demonstrated using gold nanoparticle arrays coated with two specifically designed polymers. Local MPC of a poly(N,N-dimethyl acrylamide)-based copolymer with an anthraquinone crosslinker is shown via atomic force microscopy. Additionally, MPC is tested with a thermoresponsive poly(N-isopropyl acrylamide)-based terpolymer. The reversible thermal collapsing and swelling of the MPC-formed hydrogel at specific nanoparticle locations are confirmed by polarization-resolved LSPR spectroscopy. These hybrid metallic/hydrogel materials can be further post-modified offering attractive characteristics for future spectroscopic/bioanalytical applications. | Yevhenii Morozov; Nestor Gisbert Quilis; Stefan Fossati; Laura de Laporte; Claudia Gusenbauer; Andreas Weber; Jose Luis Toca-Herrera; Fiona Wiesner (née Diehl); Ulrich Jonas; Jakub Dostalek | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Processes; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f2f9e312ff75c3a157ef25/original/plasmon-enhanced-multiphoton-polymer-crosslinking-for-selective-modification-of-plasmonic-hotspots.pdf |
62a03fc8f85b591413016e9b | 10.26434/chemrxiv-2022-hlfkq | Identification of Styryl Sulfonyl Fluoride (SSF) as An Efficient, Robust and Irreversible Cysteine-specific Protein Bioconjugation Reagent | Cysteine (Cys)-specific bioconjugation has found wide application in the synthesis of protein conjugates, particularly for the functionalization of antibody. Here, through direct assessment on protein substrate, we report the discovery of trans-styryl sulfonyl fluoride (SSF) as a near perfect Michael acceptor (MA) for cysteine-specific protein bioconjugation. Com-pared to predominantly used maleimides, SSF exhibited better chemoselectivity, self-stability and conjugate-stability while kept comparable reactivity. Using SSF-derived probes, proteins can be readily modified on the Cys residue(s) to install functionalities, e.g., fluorescent dyes, toxins and oligonucleotides (oligos), without the influence of activity. Fur-ther applications of SSF derived serum stable antibody-drug conjugates and PD-L1 nanobody-oligo conjugates demon-strate the great translational value of SSF-based bioconjugation in the drug development and single-cell sequencing. | Jie Li; Qingsong Wu; Xue Qi; Ji Li; Qinheng Zheng; Xinlu Zhao; Wannan Li; Shiming Sun; Wanxing Sha; Yang Yang; Yi Yang | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a03fc8f85b591413016e9b/original/identification-of-styryl-sulfonyl-fluoride-ssf-as-an-efficient-robust-and-irreversible-cysteine-specific-protein-bioconjugation-reagent.pdf |
67619bfbfa469535b9e823c9 | 10.26434/chemrxiv-2024-ng990-v2 | C6 to C17 Organic Products from Artificial Photosynthesis Catalyzed by 2-Phenyl Indole (PI) Titanium Tetrachloride Complex (PI)2TiCl4. The Synergism of Hydroxyl Radicals. |
The newly discovered artificial photosynthesis process catalyzed by 2-phenyl indole (PI) and TiCl₄ complexes activated by visible light, produces long-chain oxygenated hydrocarbons up to C17. This process begins with the formation of α-carboxylic acid-ω-aldehyde compounds (C6 to C9), arising from a cascade of autocatalytic organotitanium complexes derived from (PI)₂TiCl₄. These complexes are formed via hydrolysis by ambient air humidity and the direct atmospheric capture (DAC) of CO₂. Carbon chain growth utilizes system-generated formaldehyde as a feedstock. The initial C6 to C9 compounds can further couple to C12 to C17 derivatives through a radical mechanism initiated by hydroxyl radicals. A proposed mechanism explores the synergistic interaction between organotitanium catalysis and hydroxyl radicals. This development represents the only known heterogeneous catalytic system that autonomously captures CO₂ and humidity from the atmosphere to produce long-chain oxygenated hydrocarbons using solar energy.
| Gregory Arzoumanidis; Michail Paraskevas | Catalysis; Organometallic Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science; Ligands (Organomet.) | CC BY 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67619bfbfa469535b9e823c9/original/c6-to-c17-organic-products-from-artificial-photosynthesis-catalyzed-by-2-phenyl-indole-pi-titanium-tetrachloride-complex-pi-2ti-cl4-the-synergism-of-hydroxyl-radicals.pdf |
60c73edd0f50db71b639570d | 10.26434/chemrxiv.7171736.v1 | Performance of Microporous Carbon Electrodes for Supercapacitors: Comparing Graphene with Disordered Materials | Over the past decades, the specific surface area and the pore size distribution have been identified as the main structural features that govern the performance of carbon-based supercapacitors. As a consequence, graphene nanostructures have been identified as strong candidates for maximizing their capacitance. However, this hypothesis could not be thoroughly tested so far due to the difficulty of synthesizing perfect materials with high pore accesibility and a sufficiently large density. Here we perform molecular simulations of a series of perforated graphene electrodes with single pore sizes ranging from 7 to 10 Angstroms in contact with an adsorbed ionic liquid, and compare the capacitances (using various metrics) to the one obtained with a typical disordered nanoporous carbon. The latter displays better performances, an observation that we explain by analyzing the structure of the liquid inside the pores. It appears that although the smaller pores are responsible for the largest surface charges, larger ones are also necessary to store the counter-ions and avoid the formation of detrimental opposite charges on the carbon. These results rationalize the need for disordered or activated carbon materials to design efficient supercapacitors. | Trinidad Mendez-Morales; Nidhal Ganfoud; Zhujie Li; Matthieu Haefele; Benjamin Rotenberg; Mathieu Salanne | Carbon-based Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edd0f50db71b639570d/original/performance-of-microporous-carbon-electrodes-for-supercapacitors-comparing-graphene-with-disordered-materials.pdf |
6561ab3829a13c4d47f1eaf4 | 10.26434/chemrxiv-2023-5bj9j | HandMol: Coupling WebXR, AI and HCI technologies for Immersive, Natural, Collaborative and Inclusive Molecular Modeling | Except for isolated developments and specific software extensions, molecular graphics and modeling have historically been stuck at flat screens for visualization, mouse operations for molecular manipulation, menus and command line interfaces for controls, and single-user interfaces that only allow collaboration by streaming video hence limited to just sharing the view of the user operating the software. We demonstrate here how various technologies are ripe enough to enable much more fluent, immersive and natural human-computer interactions that in turn facilitate collaboration between human users, using affordable hardware through the internet and without even installing any specialized programs. For this, we introduce HandMol, a web app that exploits (i) WebXR for molecular visualization and manipulation in virtual reality, (ii) speech recognition coupled to a large language model to pass commands orally, (iii) speech synthesis for auditory feedback, (iv) WebRTC to communicate multiple instances of the tool without even requiring a server, and (v) external APIs to flexibly account for molecular mechanics, exemplified here with an endpoint running an AMBER forcefield for protein and nucleic acids and another running a DFT-trained neural network, ANI-2x, to allow exploration of conformation and some simple reactivity at high speed and accuracy. We show example applications to situations from daily work and education in chemistry and structural biology where HandMol can provide an advantage over traditional software: exploring and explaining molecular conformations and reactivity, docking and undocking small molecules into/out of protein pockets, threading molecules through nanopores, preparing systems for molecular simulations and for protein design, etc. We also present a brief study showing how users, even with limited or even no experience in VR, can significantly benefit from these kinds of technologies. As a draft prototype for the moment, HandMol is made available free of charge and without registration at https://go.epfl.ch/handmol, in (optional but greatly appreciated) exchange for feedback on usability and on features expected for this kind of tools. | Fabio Cortes Rodriguez; Lucien Krapp; Matteo Dal Peraro; Luciano Abriata | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Education; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6561ab3829a13c4d47f1eaf4/original/hand-mol-coupling-web-xr-ai-and-hci-technologies-for-immersive-natural-collaborative-and-inclusive-molecular-modeling.pdf |
675a7a387be152b1d0b440de | 10.26434/chemrxiv-2024-nmnlk-v2 | Advancing Vapor Pressure Prediction: A Machine Learning Approach with Directed Message Passing Neural Networks | Background:
Vapor pressure is a critical property in chemical and environmental engineering. Accurately predicting vapor pressure across a range of temperatures is vital for various applications, but traditional methods rely on critical property measurements or quantum mechanical calculations, which can be limiting, especially for new or under-characterized chemicals.
Methods:
This study employs a machine learning model based on the directed message passing neural network (D-MPNN) architecture to predict the vapor pressure of organic molecules. Various strategies to incorporate temperature effects into the model are explored to improve prediction accuracy.
Significant findings:
The D-MPNN model achieves significantly better accuracy than the traditional PR + COSMOSAC method, with a lower average absolute relative deviation (AARD) of 0.617 compared to 1.36 for the traditional method, using a dataset of 19,079 molecules. The machine learning approach offers a robust alternative that does not require additional critical property data or quantum mechanical calculations. | Yen-Hsiang Lin; Hsin-Hao Liang; Shiang-Tai Lin; Yi-Pei Li | Theoretical and Computational Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Artificial Intelligence; Thermodynamics (Chem. Eng.) | CC BY NC 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675a7a387be152b1d0b440de/original/advancing-vapor-pressure-prediction-a-machine-learning-approach-with-directed-message-passing-neural-networks.pdf |
60c758529abda20866f8e8b8 | 10.26434/chemrxiv.14538267.v1 | Lipid Transporters: From Bacteria, Protozoa, Fungi and Plants, to Mice and Men | <p>The tuberculosis drug candidate SQ109 targets the trehalose monomycolate transporter MmpL3 in <i>Mycobacterium tuberculosis </i>and also has activity against other pathogens. We found related proteins in 22 protozoa, including <i>Trypanosoma cruzi </i>and <i>Entamoeba histolytica, </i>as well as in archaea and other bacteria, including the fatty acid transporter, FarE. We show these proteins, alpha-MMPL proteins, adopt similar structures to that of MsMmpL3 having two sets (P1 and P2) of conserved active site/H<sup>+</sup>-transporter Asp, Tyr and Phe residues in “pentad” motifs (DYxxF) that can bind to the SQ109 ethylenediamine and adamantyl moieties. Based on structural comparisons with MsMmpL3, we find that there are superimposable transmembrane and H<sup>+</sup>-transporter structures in much larger proteins, beta-MMPLs, found in apicomplexan parasites, fungi, plants and animals. They also contain double “pentad” motifs in which the P1 Asp is totally conserved, but the P2 Asp may also be a Glu, and the P2 Phe seen in the alpha-MMPLs is a His that H-bonds to the P1 and P2 Asp/Glu residues. There are also 5 conserved Ser/Thr residues that extend the H-bond/H<sup>+</sup>-transporter network with 2 interacting directly with the P1 Asp, and the His. We propose that all MMPL proteins are involved in proton motive force-mediated lipid (phospholipid, glycolipid, sterol, fatty acid) transport, and that SQ109 may target some pathogens directly, by binding to the P1/P2 motifs. Overall, the results are of general interest since they indicate that there are two major classes of lipid transporters: alpha-MMPL proteins found in many bacteria and protozoa, and much larger, beta-MMPL proteins, found in fungi, apicomplexa, plants and animals and, in some cases, they are potential drug targets. </p> | Satish Malwal; Kyung-Hwa Baek; Trong-Nhat Phan; Hyeryon Lee; Zhu-Hong Li; Silvia N. J. Moreno; Joo Hwan No; Eric Oldfield | Bioorganic Chemistry; Biochemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758529abda20866f8e8b8/original/lipid-transporters-from-bacteria-protozoa-fungi-and-plants-to-mice-and-men.pdf |
674c48757be152b1d091eb5f | 10.26434/chemrxiv-2024-h7jqg | Defect Layer at the Surface of BaTaO2N and Implications for Photocatalysis | BaTaO2N has a valence and conduction band position which make the material a promising candidate for photocatalytic water splitting. However, the material shows a very low solar to hydrogen (STH) efficiency. It is generally assessed that the reason for the low STH is the presence of defects at the surface of the material which act as recombination centers for the excited electrons and holes. Here we show with high resolution transmission electron microscopy (HR TEM) an amorphous layer at the surface BaTaO2N which may be a cause of low STH. We demonstrate the amorphous layer can be removed through etching. Subsequently, the valence band structure is analyzed with UV photoelectron spectroscopy (UPS) and valence band X-ray photoelectron spectroscopy (VBXPS), where the latter has a significantly larger probing depth than the first. UPS reveals that non-etched BaTaO2N has a low density of states (DOS) whereas the VBXPS results are compatible with the optical band gap of the material. However, the DOS of BaTaO2N samples etched with H2SO4 solution were consistent with the optical band gap for both UPS and VBXPS measurements, indicating that after removal of the amorphous layer BaTaO2N is a suitable candidate for photocatalytic water splitting. | Matthew Smith; Wenpeng Li; Gregory Metha; Takashi Hisatomi; Kazunari Domen; Gunther Andersson | Physical Chemistry; Interfaces; Physical and Chemical Processes; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/674c48757be152b1d091eb5f/original/defect-layer-at-the-surface-of-ba-ta-o2n-and-implications-for-photocatalysis.pdf |
675c167f7be152b1d0d9e4e5 | 10.26434/chemrxiv-2024-8s4w3 | Attenuated Total Reflection Mid-Infrared Spectroscopy to Screen Austrian and French Wheat from Multiple Years for Deoxynivalenol | The high-throughput capabilities of attenuated total reflection mid-infrared spectroscopy (ATR-MIRS) make it a promising analytical technique for rapid and green mycotoxin screening. In ATR-MIRS, changes in samples induced by mycotoxigenic fungi are correlated with mycotoxin concentrations obtained through reference analysis, using multivariate statistical methods. Due to its indirect nature, limited research has explored the applicability of this technique for complex sample sets. In this study, we demonstrate that ATR-MIRS can effectively screen for deoxynivalenol (DON) contamination in wheat samples collected across two countries over multiple years. A total of 320 naturally contaminated samples from Austria and France were utilized to develop screening models. Partial least squares discriminant analysis (PLS-DA), combined with various spectral preprocessing strategies and dataset balancing, was explored to classify samples as compliant or non-compliant with the European Commission (EC) limit of 1000 µg/kg DON in unprocessed wheat. Model performance during repeated nested cross-validation exhibited a true positive rate ranging from 0.32 to 1. This variability was primarily influenced by sample splitting, as well as by dataset balancing and spectral preprocessing approaches. These findings underscore the critical importance of sample selection when developing chemometric models for mycotoxin screening. Analysis of variable importance in projection (VIP) scores revealed that PLS-DA predominantly selected wavenumbers associated with dissolved carbohydrates in the MIRS spectra to discriminate between compliant and non-compliant samples. Overall, our results demonstrate the feasibility of using ATR-MIRS to assess DON contamination in complex, multiyear wheat sample sets as exemplified for samples obtained from Austria and France while adhering to regulatory limits. Additionally, this study highlights the potential of ATR-MIRS for investigating the effects of mycotoxigenic fungi on wheat composition during the development of DON screening models. | Stephan Freitag; Maximilian Anlanger; Polina Fomina; Antoni Femenias; Miriam Aledda; Boris Mizaikoff; Achim Kohler; Michael Sulyok; Rudolf Krska | Analytical Chemistry; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675c167f7be152b1d0d9e4e5/original/attenuated-total-reflection-mid-infrared-spectroscopy-to-screen-austrian-and-french-wheat-from-multiple-years-for-deoxynivalenol.pdf |
661a18e221291e5d1dbce893 | 10.26434/chemrxiv-2024-t97z6 | Silane-mediated, Facile and Selective C(sp²)−H and N−Methylation using Formaldehyde | The use of (para)-formaldehyde for the selective reductive methylation of C(sp²)−H and N−H bonds, utilizing a combination of silane and hexafluoroisopropanol (HFIP) as activators, is reported. Overcoming the complexity of C(sp²)−H methylation on aryl and heteroaryl substrates, the process utilizes Friedel–Crafts alkylation, followed by silane as a hydride donor under mild acidic medium. The developed protocol offers a promising avenue for converting amines into their monomethylated counterparts with excellent yields. Mechanistic insights into the reductive methylation process are provided, highlighting the role of silane and HFIP in achieving good selectivity. This scalable transformation is well-suited for general alkylation using various non-activated aliphatic aldehydes under mild conditions in a shorter reaction time and is also adaptable for the late-stage methylation of pharmaceuticals and natural products. Notably, the method has been successfully employed for the efficient synthesis of the antifungal drug Butenafine and non-steroidal anti-inflammatory drug (NSAID) Flurbiprofen derivative. | Jabir Khan; Neha Taneja; Naveen Yadav; Chinmoy Hazra | Organic Chemistry; Catalysis; Chemical Education; Organic Synthesis and Reactions; Acid Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661a18e221291e5d1dbce893/original/silane-mediated-facile-and-selective-c-sp2-h-and-n-methylation-using-formaldehyde.pdf |
65f9cea366c138172955ab5a | 10.26434/chemrxiv-2024-q70p1 | Extended sulfo-pillar[6]arenes – a new host family and its application in the binding of direct oral anticoagulants | Herein we report the synthesis of extended sulfo-pillar[6]arenes, a new supramolecular host class with a pedigree in salt tolerance and ultra-high binding affinity towards multiple drug classes. The parent sulfo-pillar[6]arene (sP6) is a high affinity host with the potential to act as a supramolecular reversal agent. However, it lacks synthetic diversification of the core scaffold. The new extended sulfo-pillar[6]arenes have either a mono-directional (A1sP6) or bi-directional (A1A2sP6) extension of the hydrophobic cavity. This new functionality enables more non-covalent interactions and strong affinity towards guests, which we demonstrate using the direct oral anticoagulants (DOACs) dabigatran, betrixaban, and edoxaban. DOACs are highly prescribed therapeutics that are underexplored in host-guest chemistry. These agents prevent the formation of blood clots and reversing their action during emergencies is paramount. We show that the new hosts have ultra-high affinity to-wards dabigatran (Kd = 27 nM, A1A2sP6) in salty solutions. Their increased functionality resulted in a 6- and 2.5-fold in-crease in affinity towards betrixaban (Kd = 230 nM, A1A2sP6) and edoxaban (Kd = 800 nM, A1sP6), relative to the unfunctionalized sulfo-pillar[6]arene. | Chelsea R. Wilson; Austia O. Puckett; Allen G. Oliver; Fraser Hof | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f9cea366c138172955ab5a/original/extended-sulfo-pillar-6-arenes-a-new-host-family-and-its-application-in-the-binding-of-direct-oral-anticoagulants.pdf |
6287a601809e32858d9673ce | 10.26434/chemrxiv-2022-2z60p | Using diketopyrrolopyrroles to stabilize double excitation and control internal conversion | Diketopyrrolopyrrole (DPP) is a pivotal functional group to tune the physicochemical properties of novel organic photoelectronic materials. Among its multiple uses, DPP-thiophene derivatives forming a dimer through a vinyl linker were recently shown to quench the fluorescence observed
in their isolated monomers. Here, we explain this fluorescence quenching using computational chemistry. The DPP-thiophene dimer has a low-lying doubly excited state that is not energetically accessible for the monomer. This state delays the fluorescence allowing internal conversion to occur first. We characterize the doubly excited state wavefunction by systematically changing the derivatives to tune the pi-scaffold size and the acceptor and donor characters. The origin of this state's stabilization is related to the increase in the π-system and not to the charge-transfer features. This analysis delivers core conceptual information on the electronic properties of organic chromophores arranged symmetrically around a vinyl linker, opening new ways to control the balance between luminescence and internal conversion. | Mariana T. do Casal; Josene M. Toldo; Felix Plasser; Mario Barbatti | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6287a601809e32858d9673ce/original/using-diketopyrrolopyrroles-to-stabilize-double-excitation-and-control-internal-conversion.pdf |
67c811f66dde43c90891cc5f | 10.26434/chemrxiv-2025-g6lr3 | Light-triggered quenching of the 19F-MRI signal from micelle-encapsulated PERFECTA | We report the development of a fluorinated micellar nanosystem whose 19F-MRI signal can be selectively dimmed by application of an external stimulus. A photo-activatable quencher unit (ferrocene) was co-encapsulated with the superfluorinated PERFECTA probe in colloidal micelles. While pristine micelles were MRI responsive and were readily imaged (“On” state), their irradiation by light triggered the conversion of ferrocene to ferrocenium. The generation of paramagnetic ferrocenium resulted in shorter T2 relaxation time of the 19F-nuclei and fading of the MRI signal of PERFECTA (“Off” state). | Claire Leterrier; Sébastien Mériaux; Edmond Gravel; Eric Doris | Organic Chemistry; Nanoscience; Bioorganic Chemistry; Organic Compounds and Functional Groups; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c811f66dde43c90891cc5f/original/light-triggered-quenching-of-the-19f-mri-signal-from-micelle-encapsulated-perfecta.pdf |
60c75332ee301c3b83c7ad7f | 10.26434/chemrxiv.13425005.v1 | In Silico Drug Repositioning Against Human NRP1 to Block SARS-CoV-2 Host Entry | Despite
COVID-19 turned into a pandemic, no approved drug for the treatment or globally
available vaccine is out yet. In such a global emergency, drug repurposing
approach that bypasses a costly and long-time demanding drug discovery process
is an effective way in search of finding drugs for the COVID-19 treatment.
Recent studies showed that SARS-CoV-2 uses neuropilin-1 (NRP1) for host entry.
Here I took advantage of structural information of the NRP1 in complex with
C-terminal of spike (S) protein of SARS-CoV-2 to identify drugs that may
inhibit NRP1 and S protein interaction. U.S. Food and Drug Administration (FDA)
approved drugs were screened using docking simulations. Among top drugs,
well-tolerated drugs were selected for further analysis. Molecular dynamics
(MD) simulations of drugs-NRP1 complexes were run for 100 ns to assess the
persistency of binding. MM/GBSA calculations from MD simulations showed that
eltrombopag, glimepiride, sitagliptin, dutasteride, and ergotamine stably and
strongly bind to NRP1. In silico Alanine scanning analysis revealed that Tyr<sup>297</sup>,
Trp<sup>301</sup>, and Tyr<sup>353</sup> amino acids of NRP1 are critical for
drug binding. Validating the effect of drugs analyzed in this paper by
experimental studies and clinical trials will expedite the drug discovery
process for COVID-19. | Seref Gul | Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75332ee301c3b83c7ad7f/original/in-silico-drug-repositioning-against-human-nrp1-to-block-sars-co-v-2-host-entry.pdf |
6299c9d5468a08292b4a1328 | 10.26434/chemrxiv-2022-9313q | Quasi-continuous cooperative adsorption mechanism in crystalline nanoporous materials | Phase behavior of confined fluids adsorbed in na-nopores differs significantly from their bulk coun-terparts and depends on the chemical and structural properties of the confining structures. In general, phase transitions in nanoconfined fluids are reflect-ed in stepwise adsorption isotherms with a pro-nounced hysteresis. Here, we show experimental evidence and in silico interpretation of the reversi-ble stepwise adsorption isotherm which is observed when methane is adsorbed in the rigid, crystalline metal-organic framework IRMOF-1 (MOF-5). In a very narrow range of pressures, the adsorbed fluid undergoes a structural and highly cooperative re-construction and transition between low-density and high-density nanophases, as a result of the competition between the fluid-framework and flu-id-fluid interactions. This mechanism evolves with temperature: below 110 K a reversible stepwise iso-therm is observed, which is a result of the bimodal distribution of the coexisting nanophases. This temperature may be considered as a critical temper-ature of methane confined to nanopores of IRMOF-1. Above 110 K, as the entropy contribution in-creases, the isotherm shape transforms to a common continuous S-shaped form that is characteristic to a gradual densification of the adsorbed phase as the pressure increases. | Bartosz Mazur; Filip Formalik; Kornel Roztocki; Volodymyr Bon; Stefan Kaskel; Alexander V. Neimark; Lucyna Firlej; Bogdan Kuchta | Theoretical and Computational Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6299c9d5468a08292b4a1328/original/quasi-continuous-cooperative-adsorption-mechanism-in-crystalline-nanoporous-materials.pdf |
67850d2ffa469535b9cb7936 | 10.26434/chemrxiv-2025-57jk1 | Tailoring Spectral Response and First Hyperpolarizability of Aryl-Substituted BODIPY-based 'Push-Pull’ Chromophores: Influence of Medium and Structural Modifications | The medium plays a pivotal role in dictating the extent of intramolecular charge transfer (ICT) in a molecule, which in turn could be useful in tuning its spectral as well as nonlinear optical (NLO) response properties. Tuning of ICT in a 𝜋-conjugated electronic donor-accepter molecule has been utlized to modulate the absorption and emission maxima as well as the first hyperpolarizability (𝛽) of the so-called ’push-pull’ chromophores. Molecules with boron dipyrromethene (BODIPY)-based acceptors became popular in recent years for their unique photophysical properties, ease of synthesis, and high thermal stability. In this article, we present a quantum chemical investigation of the influence of the medium on the ICT process of some novel aryl-substituted BODIPY molecules. This influence ultimately modulates their absorption, emission, and nonlinear optical (NLO) properties. Both static and frequency-dependent 𝛽 for the second harmonic generation are investigated along with the the Pockels effect. Density functional theory (DFT) and time-dependent DFT (TDDFT) calculations using long-range corrected CAM-B3LYP functional was employed in the present study. Restricting
the rotation of the aryl ring through the incorporation of methyl groups to the BODIPY moiety enhances the fluorescence decay rate of the molecule. Both electronic and vibrational contributions to the static 𝛽 are considered. A significant increase in 𝛽 has been observed in polar solvents, compared to that in the gas phase. An interplay between structural and electronic effects was found to dictate the properties investigated. Our results sheds light on the ICT process in the studied BODIPY dyes and could be useful in tuning their spectral properties as well as formulating design principles of novel NLO materials for future technological applications. | Anushree Dutta; Alex Iglesias-Reguant; Josep M. Luis; Ramprasad Misra; Nabanita Deb | Physical Chemistry; Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67850d2ffa469535b9cb7936/original/tailoring-spectral-response-and-first-hyperpolarizability-of-aryl-substituted-bodipy-based-push-pull-chromophores-influence-of-medium-and-structural-modifications.pdf |
60c748e3469df426c9f43b06 | 10.26434/chemrxiv.11994471.v1 | Reaction of H2 with Mitochondria-Relevant Metabolites Using a Multifunctional Molecular Catalyst | The Krebs cycle is the fuel/energy source for cellular activity, and therefore of paramount importance for oxygen-based life. The cycle occurs in the mitochondrial matrix, where it produces and transfers electrons to generate energy-rich NADH and FADH<sub>2</sub>, as well as C<sub>4</sub>-, C<sub>5</sub>-, and C<sub>6</sub>-polycarboxylic acids as energy-poor metabolites. These metabolites are bio-renewable resources that represent potential sustainable carbon feedstocks, provided that carbon–hydrogen bonds are restored to these molecules. In the present study, polycarboxylic acids of the Krebs cycle and other mitochondria-relevant metabolites are dehydrated and reduced to diols or triols upon reaction with H<sub>2</sub>, catalyzed by sterically confined iridium-bipyridyl complexes. | Sota Nimura; Shota Yoshioka; Masayuki Naruto; Susumu Saito | Bond Activation; Catalysis; Ligand Design; Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748e3469df426c9f43b06/original/reaction-of-h2-with-mitochondria-relevant-metabolites-using-a-multifunctional-molecular-catalyst.pdf |
60c74436bdbb895fdea387a2 | 10.26434/chemrxiv.9701789.v2 | A Mechanically Planar Chiral Rotaxane Ligand for Enantioselective Catalysis | <p>
<b>Rotaxanes are interlocked molecules in which a
molecular ring is trapped on a dumbbell-shaped axle due to its inability to
escape over the bulky end groups, resulting in a so-called mechanical bond. Interlocked
molecules have mainly been studied as components of molecular machines, but the crowded, flexible environment created by threading one molecule through
another, reminiscent of the active site of an enzyme, has also been explored in
catalysis and sensing. However, so far the applications of one of the most
intriguing properties of interlocked molecules, their ability to display
stereogenic units that do not rely on the stereochemistry of their covalent
subunits, termed "mechanical chirality", have yet to be properly
explored and prototypical demonstration of the applications of mechanically
chiral rotaxanes remain scarce. Here we describe a mechanically planar chiral
rotaxane-based Au complex that mediates a cyclopropanation reaction with
stereoselectivities that are comparable with conventional covalent catalyst
reported for this reaction.</b></p> | Andrew Heard; Stephen Goldup | Organic Synthesis and Reactions; Stereochemistry; Supramolecular Chemistry (Org.); Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74436bdbb895fdea387a2/original/a-mechanically-planar-chiral-rotaxane-ligand-for-enantioselective-catalysis.pdf |
62eba28015fdae7f542200aa | 10.26434/chemrxiv-2022-dr5cd | A study of Cu-Rh electrodeposition | This manuscript reports the simultaneous electrodeposition of Cu and Rh from an aqueous nitrate solution. The early stages of nucleation and growth of the bimetallic layer were explored using techniques such as cyclic voltammetry and current transients. Non-dimensional Scharifker–Hills graphs showed the occurrence of diffusion-controlled three-dimensional nucleation and growth best described by the Volmer-Weber mechanism. Additionally, different ratios of Cu-Rh catalysts were synthesized by varying the potential of deposition and the Rh content in the deposition bath. Characterization techniques including electron microscopy, x-ray diffraction, and x-ray photoelectron spectroscopy were employed to investigate the chemical composition and structure of the deposits. The results showed a higher amount of Cu2+ species in the layer than Cu+/Cu0 when a more negative potential was applied, and when Rh was present in high amounts in the deposition bath The final morphology of the obtained catalyst proved to be dependent on the deposition potentials and the Cu:Rh content, showing interdependence between the metals. | Dimitra Anastasiadou; Jasmijn Janssen ; Emiel Hensen; Marta Costa Figueiredo | Physical Chemistry; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62eba28015fdae7f542200aa/original/a-study-of-cu-rh-electrodeposition.pdf |
6400e84e37e01856dc08de29 | 10.26434/chemrxiv-2023-nvxkg | Digital pipette: Open hardware for liquid transfer in self-driving laboratories | Self-driving laboratories promise to democratize automated chemical laboratories. Accurate liquid handling is an essential operation in the context of chemical labs, and consequently a self-driving laboratory will require a robotic liquid handling and transfer. Although many pipettes are available for human scientists, robots cannot manipulate these pipettes due to the limitations of current robot gripper morphology. We propose an intuitive yet elegant design for a 3D-printed digital pipette designed for robots to carry out chemical experiments. Performance-evaluation experiments were carried out liquid transfer tasks. Our results show that robots with digital pipette could transfer liquids within 0.5% error. This error is comparable to the baseline set by commercially available human-handled pipettes. | Naruki Yoshikawa; Kourosh Darvish; Animesh Garg; Alan Aspuru-Guzik | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2023-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6400e84e37e01856dc08de29/original/digital-pipette-open-hardware-for-liquid-transfer-in-self-driving-laboratories.pdf |
632ab0b4ba8a6ddb4d5713a2 | 10.26434/chemrxiv-2022-vqct8 | Assessing detection efficiencies for continuous methane emission monitoring systems at oil and gas production sites | Continuous monitoring systems, consisting of multiple fixed sensors, are increasingly being deployed at oil and gas production sites to detect methane emissions. While these monitoring systems operate continuously, their efficiency in detecting emissions will depend on meteorological conditions, sensor detection limits, the number of sensors deployed, and sensor placement strategies. This work demonstrates an approach to assess the effectiveness of continuous sensor networks in detecting infinite duration and fixed duration emission events from a point source, using a case study in west Texas. The case study examines a 10 kg/hr source at a height of 5.5m, representative of the emission pattern from a liquid storage tank. Using site specific meteorological data and dispersion modeling, emission detection performance was characterized. For this case study, infinite duration emission events were detected within 1 hour to multiple days, depending on the numbers of sensors deployed. The percentage of fixed duration emission events that were detected ranged from less than 30% to more than 90%, depending on the emission event duration and the number of sensors deployed. Because the dispersion modeling for the case study region predicted relatively narrow plumes, with steep concentration gradients, the benefit of using sensors with low detection thresholds was less important to system performance than the number of sensors deployed and the positioning of the sensors. While these results are specific to this case study, the analysis framework described in this work can be broadly applied in the evaluation of continuous emission monitoring network designs. Overall, while there can be time delays in continuous monitoring systems detecting continuous infinite duration emission events, and while some fixed duration emission events may not be detected, the detection efficiencies for continuous monitoring networks are greater than efficiencies for periodic short duration measurements, such as monthly or quarterly inspections. | Qining Chen; Colette Schissel; Yosuke Kimura; Gary McGaughey; Elena McDonald-Buller; David T. Allen | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/632ab0b4ba8a6ddb4d5713a2/original/assessing-detection-efficiencies-for-continuous-methane-emission-monitoring-systems-at-oil-and-gas-production-sites.pdf |
60c74ef6469df44f59f445b5 | 10.26434/chemrxiv.12409382.v2 | Effect of Surface Chemistry on Islet Amyloid Polypeptide Conformation | <div>The formation of dense, linear protein arrays (fibrils) is the hallmark of a number of degenerative</div><div>diseases, such as Alzheimer’s and type-2 diabetes. Protein fibrils have also attracted interest</div><div>as building blocks for new materials. It has long been recognised that surfaces can affect the</div><div>fibrillation process. Recent work on the model fibril forming protein human islet polypeptide</div><div>(hIAPP) has shown that while the protein concentration is highest at hydrophobic surfaces, the</div><div>rate of fibril formation is lower than on other surfaces. To understand this, replica exchange</div><div>molecular dynamics simulations were used to investigate the conformations that hIAPP adopts on</div><div>surfaces of di↵erent hydrophobicity. The hydrophobic surface stabilizes ↵-helical structures, which</div><div>are quite di↵erent to those found on the hydrophilic surface and in bulk solution. There is also</div><div>a greatly reduced conformational ensemble on the hydrophobic surface, due to long-lived contacts</div><div>between hydrophobic residues on the protein and the surface. This new microscopic information</div><div>will help us determine the mechanism of the enhancement of fibril formation on surfaces.</div> | David Cheung | Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ef6469df44f59f445b5/original/effect-of-surface-chemistry-on-islet-amyloid-polypeptide-conformation.pdf |
60c74e99469df44f7bf444e1 | 10.26434/chemrxiv.12777062.v1 | Emission Color-Tunable Oxazol(in)yl-Substituted Excited-State Intramolecular Proton Transfer (ESIPT)-Based Luminophores | Oxazolinyl- and arylchalcogenyl-substituted hydroxyfluorenes exhibiting
excited-state intramolecular proton transfer (ESIPT) are described as
potent and highly modular luminophores. Emission color-tuning was
achived by benzannulation of the oxazline and insertion of different
chalcogens. | Dominik Göbel; Pascal Rusch; Daniel Duvinage; Nadja C. Bigall; Boris Nachtsheim | Organic Compounds and Functional Groups; Photochemistry (Org.); Dyes and Chromophores; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e99469df44f7bf444e1/original/emission-color-tunable-oxazol-in-yl-substituted-excited-state-intramolecular-proton-transfer-esipt-based-luminophores.pdf |
626bf9eced4d8840641cfb4c | 10.26434/chemrxiv-2022-vkm6h | One Stone Three Birds: Regiodivergent Access to Amino-Substituted Benzophospholes and Their Structure–Property Relationships | Three series new NH2-benzophosphole oxides were synthesized from cycloaddition of o-aminophenyl phosphine oxide with alkynes. Photophysics investigation and theoretical calculation indicate that the position of amino group in these benzophosphole oxides obviously regulate their properties. 4-NH2-benzo[b]phosphole oxides show strong fluorescence emission and high fluorescence quantum efficiency. This “One stone three birds” process provides rapid access to multiple organophosphorus based luminogens for the structure–property relationship study. | Jiahao Zhu; Lili Wang; Zheng Duan | Organic Chemistry; Organic Compounds and Functional Groups | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626bf9eced4d8840641cfb4c/original/one-stone-three-birds-regiodivergent-access-to-amino-substituted-benzophospholes-and-their-structure-property-relationships.pdf |
60c773d3f96a00b50328915f | 10.26434/chemrxiv.14695674.v1 | Towards the Understanding of Water-in-Salt Electrolytes: Individual Ion Activities and Liquid Junction Potentials in Highly Concentrated Aqueous Solutions | Highly concentrated electrolytes were recently proposed to improve the performances of aqueous electrochemical systems by delaying the water splitting and increasing the operating voltage for battery applications. While advances were made regarding their implementation in practical devices, debate exists regarding the physical origin for the delayed water reduction occurring at the electrode/electrolyte interface. Evidently, one difficulty resides in our lack of knowledge regarding ions activity arising from this novel class of electrolyte, it being necessary to estimate the Nernst potential of associated redox reactions such as Li<sup>+</sup> intercalation or the hydrogen evolution reaction. In this work, we first measured the potential shift of electrodes selective to either Li<sup>+</sup>, H<sup>+</sup> or Zn<sup>2+</sup> ions from diluted to highly concentrated regimes in LiCl or LiTFSI solutions. Observing similar shifts for these different cations and environments, we establish that shifts in redox potentials from diluted to highly concentrated regime originates in large from an increase junction potential, it being dependent on the ions activity coefficients that increase with concentration. While our study shows that single ion activity coefficients, unlike mean ion activity coefficients, cannot be captured by any electrochemical means, we demonstrate that protons concentration increases by approximatively two orders of magnitude from 1 mol.kg<sup>-1</sup> to 15-20 mol.kg<sup>-1</sup> solutions. Combined with the increased activity coefficients, this increases the activity of protons and thus the pH of highly concentrated solutions which appears acidic. | Damien Degoulange; Nicolas Dubouis; Alexis Grimaud | Energy Storage; Solution Chemistry; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c773d3f96a00b50328915f/original/towards-the-understanding-of-water-in-salt-electrolytes-individual-ion-activities-and-liquid-junction-potentials-in-highly-concentrated-aqueous-solutions.pdf |
60c73d75702a9bbc6a189ba1 | 10.26434/chemrxiv.5797995.v1 | Unrestrictive protein modification localization and quality control for open search of mass spectra | We have
developed PTMiner, a first software tool for automated, confident filtering, localization and
annotation of protein post-translational modifications identified by open (mass-tolerant)
search of large tandem mass spectrometry
datasets. The performance of
the software was validated on carefully designed simulation data. <br /> | Zhiwu An; Fuzhou Gong; Yan Fu | Analytical Chemistry - General; Chemoinformatics; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d75702a9bbc6a189ba1/original/unrestrictive-protein-modification-localization-and-quality-control-for-open-search-of-mass-spectra.pdf |
612ecd5f8e38a37feb45b9d7 | 10.26434/chemrxiv-2021-ksld6 | Novel functional copolymers of vinyl acetate: 1. Alkyl ring-substituted ethyl 2-cyano-3-phenyl-2-propenoates | Alkyl ring-substituted ethyl 2-cyano-3-phenyl-2-propenoates, RPhCH=C(CN)CO2C2H5 (where R is 2-methyl, 3-methyl, 4-methyl, 4-ethyl, 4-isopropyl, 4-t-butyl, 4-trifluoromethyl, 2-trifluoromethyl) were prepared and copolymerized with vinyl acetate in solution with radical initiation. The compositions of the copolymers were calculated from nitrogen analysis and the structures were analyzed by IR, 1H and 13C-NMR. Thermal behavior of the copolymers was studied by DSC and TGA. Decomposition of the copolymers in nitrogen occurred in two steps, first in the 200-500ºC range with residue (13-16 wt%), which then decomposed in the 500-800ºC range. | Benjamin Y. Killam; Rima T. Barkauskas; Daniel P. Dembiec; Rebecca S. Farrell; Maritza A. Gallego; Kelly A. Kaiser; Michelle L. Keeling; Kari Y. Kang; Gretchen R. Verdoorn; Gregory Kharas | Polymer Science; Organic Polymers | CC BY NC 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612ecd5f8e38a37feb45b9d7/original/novel-functional-copolymers-of-vinyl-acetate-1-alkyl-ring-substituted-ethyl-2-cyano-3-phenyl-2-propenoates.pdf |
6543ad6ec573f893f1aae379 | 10.26434/chemrxiv-2023-l4psd | Ion-combination specific effects driving enzymatic activity of halophilic Alcohol Dehydrogenase 2 from Haloferax volcanii in aqueous ionic liquid solvent mixtures | Biocatalysis in ionic liquids enables novel routes for bioprocessing. Enzymes derived from extremophiles promise greater stability and activity under ionic liquid (IL) influence. Here, we probe the enzyme Alcohol Dehydrogenase 2 from the halophilic archaeon Haloferax volcanii in thirteen different ion combinations for relative specific activity and analyse the results against MD simulations of the same IL systems. We probe the ionic liquid property space based on ion polarizability and molecular electrostatic potential. Using radial distribution functions, survival probabilities and spatial distribution functions of ions we show that cooperative ion-ion interactions determine ion-protein interaction, specifically, strong ion-ion interactions equate to higher enzymatic activity if neither of the ions interact strongly with the protein surface. We further demonstrate a tendency for ions interacting with the protein surface to be least detrimental to enzymatic activity if they show a low polarizability and a small range of molecular electrostatic potential. We also find that the IL ion influence is not mitigated by the surplus of negatively charged residues of the halophilic enzyme. This is shown by free energy landscape analysis in root mean square deviation and distance variation plots of active site gating residues (Trp43 and His273) demonstrating no protection of specific structural elements relevant to preserving enzymatic activity. On the other hand, we observe a general effect across all IL systems that a tight binding of water at acidic residues is preferentially interrupted at these residues through the increased presence of potassium ions.
Overall, this study demonstrates a co-ion interaction dependent influence on allosteric surface residues controlling the active/inactive conformation of halophilic Alcohol Dehydrogenase 2 and the necessity to engineer ionic liquid systems for enzymes that rely on the integrity of functional surface residues regardless of their halophilicity or thermophilicity for use in bioprocessing. | Alexandra Schindl; M. Lawrence Hagen; Christof M. Jäger; Andrew C. Warden; Mischa Zelzer; Thorsten Allers; Anna K. Croft | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Catalysis; Bioengineering and Biotechnology; Computational Chemistry and Modeling; Biocatalysis | CC BY NC 4.0 | CHEMRXIV | 2023-11-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6543ad6ec573f893f1aae379/original/ion-combination-specific-effects-driving-enzymatic-activity-of-halophilic-alcohol-dehydrogenase-2-from-haloferax-volcanii-in-aqueous-ionic-liquid-solvent-mixtures.pdf |
62695375bdc9c275d0e4bcfd | 10.26434/chemrxiv-2022-xlddl | Ni-Catalyzed Enantioselective Dialkyl Carbinol Synthesis via Decarboxylative Cross Coupling: Development, Scope, and Applications | The first enantioselective decarboxylative Negishi-type alkylations of a-oxy carboxylic acids is reported via the intermediacy of redox-active esters (RAEs). This transformation enables a radical-based retrosynthesis of seemingly trivial enantiopure dialkylcarbinols. This article includes a discussion of the history of such couplings, the retrosynthetic ramifications of such a coupling, the development of general conditions, and an extensive series of applications that vividly demonstrate how it can simplify synthesis.
| yang gao; benxiang zhang; laura levy; haijun zhang; chi he; phil baran | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2022-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62695375bdc9c275d0e4bcfd/original/ni-catalyzed-enantioselective-dialkyl-carbinol-synthesis-via-decarboxylative-cross-coupling-development-scope-and-applications.pdf |
67a46a7dfa469535b93bdd92 | 10.26434/chemrxiv-2025-9hpvb | Asymmetric Ring Contraction of 2-Hydroxypyranones by Borrowing Hydrogen Biocatalysis | Ring contraction reactions facilitate easy access to carbo- and heterocyclic scaffolds from readily available precursors and have therefore enjoyed great popularity as a strategy in organic synthesis for a long time. By repurposing commercial alcohol dehydrogenases as borrowing hydrogen biocatalysts, we were able to develop a rare example of an enzymatic ring contraction methodology, where racemic 2-hydroxypyranones can be converted in an enantioconvergent manner to the corresponding 5-membered butenolides. The redox self-sufficient transformation delivers gamma-lactones in excellent optical purities and was successfully employed in the total synthesis of an Osmunda metabolite. Moreover, the biocatalytic tool was incorporated into a multi-step cascade consisting of six enzymes, achieving the formal enantioselective dearomatization of a furfuryl alcohol to deliver the corresponding saturated gamma-lactone in >99% ee. | Yuchang Liu; J. D. Rolfes; Jan Deska | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Natural Products; Organic Synthesis and Reactions; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2025-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a46a7dfa469535b93bdd92/original/asymmetric-ring-contraction-of-2-hydroxypyranones-by-borrowing-hydrogen-biocatalysis.pdf |
62669f6a5b900964f71b8da7 | 10.26434/chemrxiv-2022-s0sxl | Decarbonylative Reductive Coupling of Aromatic Esters by Nickel and Palladium Catalyst | Ni or Pd-catalyzed decarbonylative reductive couplings of aromatic esters were developed. A range of (hetero)aromatic esters was applicable to these reductive homocoupling reactions. Moreover, it was found that Pd-catalysis enables a reductive decarbonylative cross-coupling between two different aromatic esters to afford a nonsymmetrical biaryls system. | Yunfei Peng; Ryota Isshiki; Kei Muto; Junichiro Yamaguchi | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62669f6a5b900964f71b8da7/original/decarbonylative-reductive-coupling-of-aromatic-esters-by-nickel-and-palladium-catalyst.pdf |
60c7426ef96a00451a286600 | 10.26434/chemrxiv.8293952.v1 | The Endocyclic Carbon Substituent of Guanidinate and Amidinate Precursors Controlling ALD of InN Films | <p>Indium nitride (InN) is an
interesting material for future high frequency electronics, due to its high
electron mobility. The problematic deposition of InN films currently prevents
full exploration of InN based electronics. We present studies of atomic layer
deposition (ALD) of InN using In precursors with bidentate ligands forming In–N
bonds; tris(<i>N</i>,<i>N</i>-dimethyl-<i>N</i>’,<i>N</i>’’-diisoproprylguanidinato)indium(III),
tris(<i>N</i>,<i>N</i>’-diisopropylamidinato)indium(III) and tris(<i>N</i>,<i>N</i>’-diisopropylformamidinato)indium(III).
These compounds form a series were the size of the substituent in the
endocyclic position decreases from –NMe<sub>2</sub>, to –Me
and to –H, respectively. We show that when the size of the substituent decreases, InN films with higher crystalline-
and optical quality, lower roughness and an In/N ratio closer to unity is achieved.
From quantum chemical calculations we show that the smaller substituents lead
to less steric repulsion and weaker bonds between the ligand and In centre. We
propose that these effects render a more favoured surface chemistry for the
nitidisation step in the ALD cycle which explains the improved film properties.
</p> | Polla Rouf; Nathan J O'Brien; Karl Rönnby; Rouzbeh Samii; Ivan G. Ivanov; Lars Ojamäe; Henrik Pedersen | Thin Films; Organometallic Compounds; Computational Chemistry and Modeling; Ligand Design; Ligands (Organomet.); Main Group Chemistry (Organomet.); Surface | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426ef96a00451a286600/original/the-endocyclic-carbon-substituent-of-guanidinate-and-amidinate-precursors-controlling-ald-of-in-n-films.pdf |
6336ec4e975e94e3fc8e9219 | 10.26434/chemrxiv-2022-9506r | psm_utils: A high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results | A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream processing of peptide-spectrum matches (PSMs) and PSM files. While standards exist to solve this problem, these are far from universally supported by search engines. Moreover, software libraries are available to read a selection of PSM file formats, but a light-weight package to parse PSM files into a unified data structure has been missing. Here, we present psm_utils, a Python package to read and write various PSM file formats and to handle peptidoforms, PSMs, and PSM lists in a unified and user-friendly Python-, command line-, and web-interface. psm_utils was developed with pragmatism and maintainability in mind, adhering to community standards and relying on existing packages where possible. The Python API and command line interface greatly facilitate handling various PSM file formats. Moreover, a user-friendly web application was built using psm_utils that allows anyone to interconvert PSM files and retrieve basic PSM statistics. psm_utils is freely available under the permissive Apache2 license at https://github.com/compomics/psm_utils. | Ralf Gabriels; Arthur Declercq; Robbin Bouwmeester; Sven Degroeve; Lennart Martens | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Analytical Chemistry; Mass Spectrometry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6336ec4e975e94e3fc8e9219/original/psm-utils-a-high-level-python-api-for-parsing-and-handling-peptide-spectrum-matches-and-proteomics-search-results.pdf |
60c74cca4c89191ac5ad36dd | 10.26434/chemrxiv.12546572.v1 | The Synthesis of Peptide-Conjugated Poly(2-Ethyl-2-Oxazoline)-bpoly(L-Lactide) (PEtOx-B-PLA) Polymeric Systems Through the Combination of Controlled Polymerization Techniques and Click Reactions | To optimize the therapeutic effect of pharmaceutical agents, drug delivery systems tailored from FDA-approved polymers like poly(L-lactide) (PLA) is an effective strategy. Because of their hydrophobic character, these systems greatly suffer from reduced circulation time thus, amphiphilic block copolymers became favourable to overcome this limitation. Of them, poly(oxazoline)-b-poly(L-lactide) are of choice as poly(oxazoline) (PEtOx) is compatibile, biodegradable, while exhibiting minimum cytotoxicity. To tailor selective drug targeting drug delivery systems, whereby their selectivity for tumour tissues is maximised, these polymers should be decorated with so-called tumour-homing agents, such as antibodies, peptides and so forth. To this respect, we designed a new block copolymer, allyl-poly(2-ethyl-2-oxazoline)-b-poly(L-lactide) allyl-(PEtOx-b-PLA) and its subsequent conjugation to tumour-homing peptides, peptide-18 and peptide-563 at the terminal position. In this manuscript, we report our synthetic route to obtain this building block and its conjugation to tumour-homing agents. | Umut Ugur Ozkose; Sevgi Gulyuz; Melek Parlak Khalily; Salih Ozcubukcu; Asuman Bozkır; Mehmet Atilla Taşdelen; onur alpturk; Özgür Yılmaz | Drug delivery systems; Organic Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cca4c89191ac5ad36dd/original/the-synthesis-of-peptide-conjugated-poly-2-ethyl-2-oxazoline-bpoly-l-lactide-p-et-ox-b-pla-polymeric-systems-through-the-combination-of-controlled-polymerization-techniques-and-click-reactions.pdf |
67bc45b0fa469535b9b38277 | 10.26434/chemrxiv-2025-jgx5p | The density-based many-body expansion for polypeptides and proteins | Fragmentation schemes enable the efficient quantum-chemical treatment of large biomolecular systems, and provide an ideal starting point for the development of accurate machine-learning potentials for proteins. Here, we present a fragment-based method that only used calculations for single-amino acids and their dimers, and is able to reduce the fragmentation error in total energies to ca. 1 kJ/mol per amino acid for polypeptides and proteins across different structural motifs. This is achieved by combining a two-body extension of the molecular fractionation with conjugate caps (MFCC) scheme with the density-based many-body expansion (db-MBE), thus extending the applicability of the db-MBE from molecular clusters to polypeptides and proteins. | Johannes R. Vornweg; Toni M. Maier; Christoph R. Jacob | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2025-02-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67bc45b0fa469535b9b38277/original/the-density-based-many-body-expansion-for-polypeptides-and-proteins.pdf |
62cd0b23cd7a998873c4ad2c | 10.26434/chemrxiv-2022-07q8z-v4 | Understanding Nonlinear Composition Dependency of Enantioselectivity in Chiral Separation Using Mixed Micelle | Hypothesis:
Mixtures of chiral and achiral building blocks of supramolecules exhibit interesting cooperative phenomena, indicat-ed by the nonlinear composition dependence of the chiral properties. However, the nonlinear composition depend-ence of the enantioselectivity of mixed micelles is not well understood. It was hypothesized that in-depth understand-ing can be achieved by carefully investigating the composition dependence of the properties.
Experiments:
In this work, the nonlinear composition dependence of the enantioselectivity was found for the mixed micelle of achi-ral and chiral N-acyl amino acids by micellar electrokinetic chromatography (MEKC). Capillary electrophoresis, circu-lar dichroism (CD) spectroscopy, surface tension measurement, and fluorescence spectroscopy were used to investi-gate the mechanisms.
Findings:
Four mechanisms that could be causing the nonlinearity were investigated: (i) synergistic and antagonistic interac-tions of the surfactants; (ii) the chiral transfer from chiral to achiral surfactant; (iii) differences in the retention factor; and (iv) cooperative chiral recognition of the chiral and achiral surfactant. The investigation of the composition de-pendency of critical micelle concentration (CMC) and molar circular dichroism revealed that the effect of (i) and (ii) was negligibly small. The newly derived equations for (iii) and (iv) revealed that (iii) and (iv) have a major or medi-um effect on the nonlinear enantioselectivity. | Nozomu Suzuki | Organic Chemistry; Analytical Chemistry; Polymer Science; Stereochemistry; Analytical Chemistry - General; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cd0b23cd7a998873c4ad2c/original/understanding-nonlinear-composition-dependency-of-enantioselectivity-in-chiral-separation-using-mixed-micelle.pdf |
60c74a7dee301ce23ec79c71 | 10.26434/chemrxiv.11710137.v2 | Ten Facets, One Force Field: The GAL19 Force Field for Water - Noble Metal Interfaces | <div>Understanding the structure of the water/metal interfaces plays an important role in many are as ranging from surface chemistry to environmental processes. Due to their intrinsic complexity, the water/metal interfaces cannot yet be adequately described by quantum mechanical approaches and accurate force-fields are therefore needed. We develop and parametrize GAL19, a novel force-field to describe the interaction of water with two facets (111 and 100) of five metals (Pt, Pd, Au, Ag, Cu). To increase transferability compared to its predecessor GAL17, the water-metal interaction is described as a sum of pair-wise terms. The interaction energy has three contributions: (i) physisorption is described via a Tang and Toennies potential, (ii) chemisorption and surface corrugation relies on an attractive Gaussian term and (iii) the angular dependence is explicitly included as a truncated Fourier series. 13 parameters are used for each metal surface and were fitted on 250 water adsorption energies computed at the PBE+dDsC level. </div><div>The performance of GAL19 was evaluated on a set of more than 600 DFT adsorption energies for each surface, leading to an average root mean square deviation (RMSD) of only 1 kcal/mol, correctly reproducing the adsorption trends: strong on Pt and Pd but weaker on Ag, Au and Cu. This force-field was then used to simulate the water/metal interface for all ten surfaces for 1 ns. Structural analyses reveal similar tendencies for all surfaces: a first, dense water layer that is mostly adsorbed on the metal top sites, and a second layer up to around 6 Å, which is less structured. On Pt and Pd, the first layer is strongly organized with water lying flat on the surface. The pairwise additive functional form allows to simulate the water adsorption on alloys, which is demonstrated at the example of Ag/Cu and Au/Pt alloys. The water/Ag-Cu interface is predicted to be disordered with water mostly adsorbed on Cu which should exacerbate the Ag reactivity. On the contrary, incorporating Pt into Au materials leads to a structuring of the water interface. Our promising results make GAL19 an ideal candidate to get representative sampling of complex metal/water interfaces as a first step towards accurate estimation of free energies of reactions in solution at the metal interface.</div> | Paul Clabaut; Paul Fleurat-Lessard; Carine Michel; Stephan Steinmann | Computational Chemistry and Modeling; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a7dee301ce23ec79c71/original/ten-facets-one-force-field-the-gal19-force-field-for-water-noble-metal-interfaces.pdf |
61a8f88148e4bc2900f89426 | 10.26434/chemrxiv-2021-rk2lf-v2 | Computational Spectroscopy of the Cr–Cr Bond in Coordination Complexes | We report the accurate computational vibrational analysis of the Cr–Cr bond in dichromium complexes using second-order multireference complete active space methods (CASPT2), allowing direct comparison with experimental spectroscopic data both to facilitate interpreting the low-energy region of the spectra and to provide insights into the nature of the bonds themselves. Recent technological development by the authors has realized such computation for the first time. Accurate simulation of the vibrational structure of these compounds has been hampered by their notorious multiconfigurational electronic structure that yields bond distances that do not correlate with bond order. Some measured Cr–Cr vibrational stretching modes, ν(Cr2), have suggested weaker bonding, even for so-called ultrashort Cr–Cr bonds, while others are in line with the bond distance. Here we optimize the geometries and compute ν(Cr2) with CASPT2 for three well-characterized complexes, Cr2(O2CCH3)4(H2O)2, Cr2(mhp)4, and Cr2(dmp)4. We obtain CASPT2 harmonic ν(Cr2) modes in good agreement with experiment at 282 cm−1 for Cr2(mhp)4 and 353 cm−1 for Cr2(dmp)4, compute 50Cr and 54Cr isotope shifts, and demonstrate that the use of the so-called IPEA shift leads to improved Cr–Cr distances. Additionally, normal mode sampling was used to estimate anharmonicity along ν(Cr2) leading to an anharmonic mode of 272 cm−1 for Cr2(mhp)4 and 333 cm−1 for Cr2(dmp)4. | Toru Shiozaki; Bess Vlaisavljevich | Theoretical and Computational Chemistry; Physical Chemistry; Inorganic Chemistry; Theory - Inorganic; Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a8f88148e4bc2900f89426/original/computational-spectroscopy-of-the-cr-cr-bond-in-coordination-complexes.pdf |
60c74582337d6ca863e26fc2 | 10.26434/chemrxiv.10050575.v1 | Can Doping of Transition Metal Oxide Cathode Materials Increase Achievable Voltages with Multivalent Metals? | We investigate from first principles the use of
substitutional p-doping as a means to enhance the insertion energies of
multivalent metals in transition metal oxides, and therefore the resulting
voltages in an electrochemical cell, due to bandstructure modulation.
Multivalent and earth-abundant metals such as magnesium or aluminium are
attractive candidates to replace lithium in future high-performance secondary
batteries with intercalation-type electrodes. Unfortunately, the achievable
voltages obtained with this kind of elements still remain uncompetitively low.
We study and compare the changes in insertion energetics (voltages) of single-
and multivalent metals in semiconducting and insulating transition metal oxides
upon substitutional p-doping with different metals, introducing different
numbers of hole states. We use a single vanadium pentoxide monolayer as model
system to study the effect of p-doping on achievable voltages and deduce
general trends for transition metal oxides. Our investigations reveal the
formation of n-hole polarons (with n>1) in form of oxygen dimers in p-doped
vanadia caused by localized <i>p</i> holes
on oxide ions in agreement with previous findings. We find that the oxygen
dimer formation has an adverse effect on adsorption energetics compared to the
single-hole case without dimerization. We find an analogous oxygen dimerization
in other TMOs with oxygen-dominated valence bands like molybdenum trioxide and
titanium dioxide, while strained systems like trigonal nickel- or titanium
dioxide, or Mott-type systems like monoclinic vanadium dioxide with
qualitatively different valence band composition do not exhibit oxygen
dimerization with multi-hole doping. Our results demonstrate the advantages and
limitations of TMO electrode p-doping and show a path to possible strategies to
overcome detrimental effects. | Daniel Koch; Sergei Manzhos | Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74582337d6ca863e26fc2/original/can-doping-of-transition-metal-oxide-cathode-materials-increase-achievable-voltages-with-multivalent-metals.pdf |
67d0d41a81d2151a020f0915 | 10.26434/chemrxiv-2025-xzv83 | Explaining the Broad Raman Peak for Alkynes Solvated in Triethylamine | The terminal alkyne C≡C stretch has a large Raman scattering cross section in the “silent” region for biomolecules. Experimental work taking advantage of this property provide an impetus for the development of theoretical tools addressing the vibration. In prior work, we have developed a localized normal mode method for computing terminal alkyne vibrational frequencies using a discrete variable representation of the potential energy surface. Using this method and molecular dynamics simulations, we interpret the unusually broad Raman spectrum of alkynes solvated in triethylamine. Energy decomposition analysis is performed on alkyne-triethylamine dimers to determine that like charge transfer, electrostatics, and Pauli exclusion have large effects on the frequency. Molecular dynamics simulations are performed and uncover that the terminal alkyne hydrogen interacts strongly with the triethylamine nitrogen when the alkynes are solvated in triethylamine. Using this data, a spectroscopic map for terminal alkynes in triethylamine is developed and used to compute Raman spectra. We find that the broad experimental spectra result from the combination of a population of alkynes associated with the solvent nitrogens and a population not associated with those nitrogens. This work sets the stage for investigations of alkynes in more complex environments. | Anagha Aneesh; Kristina Streu; Clyde Daly | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.); Transport phenomena (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2025-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d0d41a81d2151a020f0915/original/explaining-the-broad-raman-peak-for-alkynes-solvated-in-triethylamine.pdf |
67051094cec5d6c14293a9ce | 10.26434/chemrxiv-2024-1g8tf | Metal-free, Selective Ortho-Deuteration of N-heterocyclic oxides | Replacing hydrogen with deuterium raises the activation energy for C‒D bond cleavage. This approach has gained attention in drug design, especially to protect the ortho-position of pyridines, which are susceptible to enzymatic oxidation. Until now, direct hydrogen isotope exchange has been largely restricted to the use of reactive organolithium reagents or metal-catalysed deuteration methods. In this work, we present a metal-free, selective ortho-deuteration of N-heterocycles starting from their N-oxides, proceeding at room temperature in just 5 minutes. This method achieves high deuterium incorporation across a broad range of N-heterocycles, including bioactive compounds. Experimental and computational studies have elucidated the mechanism of the reaction, showing that regioselectivity is driven by a successful increase in acidity at the ortho-position, enabling deprotonation by the in-situ generated dimsyl anion. | Arianna Montoli; Alessandro Dimasi; Andrea Citarella; Paolo Ronchi; Daniele Passarella; Valerio Fasano | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67051094cec5d6c14293a9ce/original/metal-free-selective-ortho-deuteration-of-n-heterocyclic-oxides.pdf |
61f422dd71868da1fac1a336 | 10.26434/chemrxiv-2022-0x2r1 | Synthesis and styrene copolymerization of novel phenoxy ring-substituted isopropyl phenylcyanoacrylates | Phenoxy ring-substituted isopropyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH(CH3)2, where R is 2-(3-methoxyphenoxy), 2-(4-methoxyphenoxy), 3-(4-methoxyphenoxy), 3-(4-methylphenoxy), 4-(4-bromophenoxy), 4-(4-fluorophenoxy), 2-(4-chlorophenoxy), 3-(4-chlorophenoxy), 4-(3-chlorophenoxy), 4-(4-chlorophenoxy), 3-(3,4-dichlorophenoxy), 3-(3,5-dichlorophenoxy), 4-(2,4-dichlorophenoxy) were prepared and copolymerized with styrene. The acrylates were synthesized
by the piperidine catalyzed Knoevenagel condensation of phenoxy ring-substituted benzaldehydes and isopropyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C-NMR. All the acrylates were copolymerized with styrene in solution with radical initiation at 70C. The compositions of the copolymers were calculated from nitrogen analysis and the structures were analyzed by IR, 1H and 13C-NMR. Decomposition of the copolymers in nitrogen occurred in two steps, first in the 129-500ºC range with residue (2-10% wt.), which then decomposed in the 500-800ºC range.
| Paige M. Whelpley; Jose L. Zepeda; William S. Schjerven; Sara M Rocus; Gregory B. Kharas | Organic Chemistry; Polymer Science; Organic Compounds and Functional Groups; Organic Polymers; Polymerization (Polymers) | CC BY 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f422dd71868da1fac1a336/original/synthesis-and-styrene-copolymerization-of-novel-phenoxy-ring-substituted-isopropyl-phenylcyanoacrylates.pdf |
6571efe65bc9fcb5c949ee8b | 10.26434/chemrxiv-2023-18c5k | Electron Tug Effect in Ni Single Atoms for Carbon Dioxide Electroreduction over a Wide Potential Range | Atomically dispersed symmetrical NiN4 moieties represent a promising category of catalysts for electrochemical reduction of carbon dioxide (eCO2RR). Nonetheless, their practical application is constrained by challenges such as high overpotentials and limited potential ranges. Here, we report Ni active sites with unique electron distribution realized by minute amounts of Au nanoparticles decoration and lateral oxygen coordination (Au/Ni-N-O-C) for achieving a low overpotential while widening the applied potential ranges. The optimized Au0.5/Ni-N-O-C catalyst exhibits an outstanding eCO2RR performance, achieving over 95% Faradaic efficiency (FE) of CO within a broad potential window from −0.50 to −0.85 V vs. reversible hydrogen electrode, notably, 93% FECO at an overpotential of 340 mV. Theoretical calculations demonstrate that additional electron tug effect on Ni single atoms, induced by the oxygen in the lateral coordination configuration and introduced Au nanoparticles, effectively lower the free energy for *COOH formation by redistributing the electronic distribution of Ni active sites, thus significantly promoting the eCO2RR across a wide applied potential range. This strategy not only presents an efficient pathway to regulate the electron distribution of single atom catalysts, but also is potentially adaptable for diverse catalytic reactions. | Xu Han; Ting Zhang; Martí Biset-Peiró; Chaoyue Zhang; Ke Xiao; Pengfei Cao; Marc Heggen; Weiqiang Tang; Miquel Vega-Paredes; Alba Garzón-Manjón; Lirong Zheng; Rafal E. Dunin-Borkowski; Andreu Cabot; Kim Daasbjerg; Joan R. Morante; Jordi Arbiol | Materials Science; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-12-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6571efe65bc9fcb5c949ee8b/original/electron-tug-effect-in-ni-single-atoms-for-carbon-dioxide-electroreduction-over-a-wide-potential-range.pdf |
60c74d49842e65efa5db344d | 10.26434/chemrxiv.12609545.v1 | Possibilities and Limitations of Photoactivatable Cytochalasin D for the Spatiotemporal Regulation of Actin Dynamics | <div>The study of the actin cytoskeleton and related cellular processes requires tools to specifically
interfere with actin dynamics in living cell cultures, ideally with spatiotemporal control and
compatible with real time imaging. A phototriggerable derivative of the actin disruptor
Cytochalasin D (CytoD) is described and tested here. It includes a nitroveratryloxycarbonyl
(Nvoc) photoremovable protecting group (PPG) at the hydroxyl group at C7 of CytoD.
The attachment of the PPG renders Nvoc-CytoD temporarily inactive, and enables light-dosed
delivery of the active drug CytoD to living cells. This article presents the full structural and
physicochemical characterization, the toxicity analysis. It is complemented with biological
tests to show the time scales (seconds) and spatial resolution (cellular level) achievable with a
UV source in a regular microscopy setup<br /></div> | Roshna V. Nair; Shifang Zhao; Emmanuel Terriac; Franziska Lautenschläger; Joseph H.R. Hetmanski; Patrick T. Caswell; Aranzazu del Campo | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d49842e65efa5db344d/original/possibilities-and-limitations-of-photoactivatable-cytochalasin-d-for-the-spatiotemporal-regulation-of-actin-dynamics.pdf |
60c73d50469df4cf62f426a3 | 10.26434/chemrxiv.5662474.v1 | Phase behaviour and applications of a binary liquid-liquid mixture of methanol and a thermotropic liquid crystal | Herein, we report on the phase behaviour of a binary liquid-liquid mixture composed of methanol (MeOH) and the thermotropic liquid crystal 4-Cyano-4'-pentylbiphenyl (5CB). The corresponding phase diagram combines features of a conventional liquid-liquid mixture with characteristics that are particular to the nematic liquid crystal. We observe four arrangements as a function of composition and temperature, namely monophasic isotropic, monophasic nematic, biphasic isotropic-isotropic and biphasic isotropic-nematic, with an upper critical solution temperature of 298 K. The interplay of nematogenic and non-nematogenic species offers a number of applications. Dilution of mesogens with MeOH allows to control the isotropic-to-nematic phase transition of 5CB over a range of 35 K. The tunability of phase mixing and phase composition in an accessible temperature window provides novel routes for the extraction of target compounds, here shown for Eosin Y, Doxorubicin, Crystal Violet and Sudan IV. | Luis A Serrano; Maximiliano J Fornerod; Ye Yang; Simon Gaisford; Francesco Stellacci; Stefan Guldin | Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d50469df4cf62f426a3/original/phase-behaviour-and-applications-of-a-binary-liquid-liquid-mixture-of-methanol-and-a-thermotropic-liquid-crystal.pdf |
637888d33551196f1d38e00b | 10.26434/chemrxiv-2022-mnn0k | Co-crystals of NHC Au(I) Aryl Complexes with Iodoperfluoroarenes as a Platform for the Study of Au(I) Involving Halogen Bonding | Among the known types of non-covalent interactions with Au(I) metal center, Au(I) involving halogen bonding (XB) remains a rare phenomenon that has not been studied systematically. Herein, using five N-heterocyclic carbene (NHC) Au(I) aryl complexes and two iodoperfluoroarenes as XB donors, we demonstrated that the XB involving the Au(I) metal center can be predictably obtained for neutral Au(I) complexes using the example of nine co-crystals. The presence of XBs involving the Au(I) center was experimentally investigated by single-crystal X-ray diffraction and solid-state 13C CP-MAS NMR methods, and their nature was elucidated through DFT calculations, followed by electron density, electrostatic potential, and orbital analyses. The obtained results revealed the connection between the structure of Au(I) complexes as XB acceptors and the geometrical, electronic, and spectroscopic features of XB interactions, as well as the supramolecular structure of the co-crystals | Alexander Mikherdov; Mingoo Jin; Hajime Ito | Theoretical and Computational Chemistry; Physical Chemistry; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637888d33551196f1d38e00b/original/co-crystals-of-nhc-au-i-aryl-complexes-with-iodoperfluoroarenes-as-a-platform-for-the-study-of-au-i-involving-halogen-bonding.pdf |
65e718eee9ebbb4db9f21886 | 10.26434/chemrxiv-2024-z5jnt | PromptSMILES: Prompting for scaffold decoration and fragment linking in chemical language models | SMILES-based generative models are amongst the most robust and successful recent methods used to augment drug design. They are typically used for complete de novo generation, however, scaffold decoration and fragment linking applications are sometimes desirable which requires a different architecture, a different training dataset and therefore, re-training of a new model. In this work, we describe a simple procedure to conduct constrained molecule generation with a SMILES-based generative model to extend applicability to scaffold decoration and fragment linking by providing SMILES prompts, without the need for re-training. In combination with reinforcement learning, we show that pre-trained, decoder-only models adapt to these applications quickly and can further optimize molecule generation towards a specified objective. We compare the performance of this approach to a variety of orthogonal approaches and show that performance is comparable or better. This approach enables the unification of de novo generation, scaffold decoration, and fragment linking into one chemical language model, without the need to use a bespoke grammar, curate a custom dataset or train a separate model. For convenience, we provide an easy-to-use python package to facilitate model sampling which can be found on GitHub and the Python Package Index. | Morgan Thomas; Mazen Ahmad; Gary Tresadern; Gianni de Fabritiis | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e718eee9ebbb4db9f21886/original/prompt-smiles-prompting-for-scaffold-decoration-and-fragment-linking-in-chemical-language-models.pdf |
60c74fcaee301c2a89c7a766 | 10.26434/chemrxiv.12941819.v1 | Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity | The SARS-CoV-2 main protease (M<sup>pro</sup>) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 M<sup>pro</sup> with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 M<sup>pro</sup>, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of M<sup>pro</sup> by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor. | Kemel Arafet; Natalia Serrano-Aparicio; Alessio Lodola; Adrian Mulholland; Florenci V. González; Katarzyna Swiderek; Vicent Moliner | Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fcaee301c2a89c7a766/original/mechanism-of-inhibition-of-sars-co-v-2-mpro-by-n3-peptidyl-michael-acceptor-explained-by-qm-mm-simulations-and-design-of-new-derivatives-with-tunable-chemical-reactivity.pdf |
66435894418a5379b03d7d71 | 10.26434/chemrxiv-2024-f8bnk-v2 | Deciphering molecular embeddings with centered kernel alignment | The creation of effective models is of utmost importance in various scientific and engineering domains. However, analyzing such models, especially nonlinear ones, poses significant challenges. In this context, centered kernel alignment (CKA) has emerged as a promising model analysis tool that assesses the independence between two embeddings. CKA's efficacy depends on the selection of a kernel that adequately captures the underlying properties of the compared models. We examine the properties of the linear and random forest (RF) kernel with respect to multilayer perceptrons (MLPs) and RFs to adapt the model analysis tool CKA to cheminformatics. Furthermore, we demonstrate the utility of CKA in cheminformatics in three case studies in which we (1) investigate why optimizing the radius of circular fingerprints beyond two bonds results in only minor changes in the performance of models, (2) analyze the dependence between physicochemical properties and the molecular representations induced by graph neural networks (GNNs) that use addition as readout operation, and (3) compare different graph readout operations in GNNs. | Matthias Welsch; Steffen Hirte; Johannes Kirchmair | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66435894418a5379b03d7d71/original/deciphering-molecular-embeddings-with-centered-kernel-alignment.pdf |
65cac9c8e9ebbb4db93752df | 10.26434/chemrxiv-2024-xnzfm | Cooperative catalysis in a crystalline framework with templated acid–base sites | Nature uses weakly basic residues in conjunction with weakly acidic residues to catalyze challenging heterolytic bond transformations. Here, we show that these cooperative effects can be replicated in a metal–organic framework containing bifunctional Brønsted acid–base sites. Using a templating strategy, we show, unambiguously, that the co-localization of acid and base sites is key to catalytic activity. Specifically, a thermolabile crosslinker containing tertiary ester and tertiary carbamate linkages is used to tether carboxylic acid and benzylamine pairs in close proximity during framework synthesis. These templated materials are over four-fold more active aldol condensation catalysts than non-templated materials containing randomly distributed acid and base sites. Together, this work establishes metal–organic frameworks as an exciting platform for cooperative acid–base catalysis that couples the advantages of heterogeneous catalysts with the structural precision of enzymes. | Devin Rollins; Jackson Geary; Kamaya Ronning; Kathleen Snook; Dianne Xiao | Inorganic Chemistry; Catalysis; Heterogeneous Catalysis; Organocatalysis; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cac9c8e9ebbb4db93752df/original/cooperative-catalysis-in-a-crystalline-framework-with-templated-acid-base-sites.pdf |
62286980c3e9da184c85c1a0 | 10.26434/chemrxiv-2021-qlh3r-v4 | Addition Coupled Electron Transfer (ACET) and Addition Coupled Electron Coupled Proton Transfer (ACPCET) | The new types of elementary reaction in which a nucleophilic addition (A) to quinones is coupled with electron transfer (ET) and even further proton transfer (PT) are suggested herein by density functional theory calculation, which are called Addition Coupled Electron Transfer (ACET) and Addition Coupled Proton Coupled Electron Transfer (ACPCET). With a [2.2]paracyclophane-derived biquinone as the substrate, the nature of nucleophilic addition onto its sp2 carbons exhibits a change from stepwise A-ET-PT to ACET-PT and further to ACPCET, in parallel with the decreased nucleophilicity of the attacking reagent. In addition, we further proposed six possible potential energy surfaces and the coupling modes among A, ET and PT, among which three have been found in this work. Quasi-classical trajectory shows that the ACET and PT event can also be dynamically concerted even for an ACET-PT mechanism. | Yumiao Ma; Aqeel Hussein | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62286980c3e9da184c85c1a0/original/addition-coupled-electron-transfer-acet-and-addition-coupled-electron-coupled-proton-transfer-acpcet.pdf |
6195615178db4e5b9111eb86 | 10.26434/chemrxiv-2021-8bl44 | Heterogeneous Pair Approximation of Methanol
Oxidation on TiO2 Reveals Two Reaction
Pathways | We propose a novel method to simulate the chemical kinetics of methanol oxidation on the rutile TiO2(110) surface. This method must be able to capture the effects of static disorder (site-to-site variations in the rate constants), as well as dynamic correlation (interdependent probabilities of finding reactants and products next to each other). Combining the intuitions of the mean-field steady state (MFSS) method and the pair approximation (PA), we consider representative pairs of sites in a self-consistent bath of the average pairwise correlation. Pre-averaging over the static disorder in one site of each pair makes this half heterogeneous pair approximation (HHPA) efficient enough to simulate systems of several species and calibrate rate constants. According to the simulated kinetics, a static disorder in the hole transfer steps suffices to reproduce the stretched exponentials in the observed kinetics. The identity of the dominant hole scavenger is found to be temperature-dependent -- the methoxy anion at 80 K and the methanol molecule at 180 K. Moreover, two distinct groups of 5-coordinate titanium (Ti5c) sites emerge -- a high-activity group and a low-activity group -- even though no such division exists in the rate constants. Since the division is quite insensitive to the type of static disorder, the emergence of the two groups might play a significant role in a variety of photocatalytic processes on TiO2. | Changhae Andrew Kim; Troy Van Voorhis | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Chemical Kinetics; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6195615178db4e5b9111eb86/original/heterogeneous-pair-approximation-of-methanol-oxidation-on-ti-o2-reveals-two-reaction-pathways.pdf |
60c752adf96a00424b2882d0 | 10.26434/chemrxiv.13335428.v1 | Efficient and Flexible Synthesis of New Photoactivatable Propofol Analogs | Propofol is a widely used general anesthetic, which acts by binding to and modulating several
neuronal ion channels. We describe the synthesis of photoactivatable propofol analogs
functionalized with an alkyne handle for bioorthogonal chemistry. Such tools are useful for
detecting and isolating photolabeled proteins. We designed expedient and flexible synthetic
routes to three new diazirine-based crosslinkable propofol derivatives, two of which have alkyne
handles. As a proof of principle, we show that these compounds activate heterologously
expressed Transient Receptor Potential Ankyrin 1 (TRPA1), a key ion channel of the pain
pathway, with a similar potency as propofol in fluorescence-based functional assays. This work
demonstrates that installation of the crosslinkable and clickable group on a short nonpolar spacer
at the para position of propofol does not affect TRPA1 activation, supporting the utility of these
chemical tools in identifying and characterizing potentially druggable binding sites in propofolinteracting proteins. | Kenneth Skinner; Joseph Wzorek; Daniel Kahne; Rachelle Gaudet | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752adf96a00424b2882d0/original/efficient-and-flexible-synthesis-of-new-photoactivatable-propofol-analogs.pdf |
6253f5f66c989c04f6b40986 | 10.26434/chemrxiv-2022-prz2r | Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation | A plethora of AI-based techniques now exists to conduct de novo molecule generation that can devise molecules conditioned towards a particular endpoint in the context of drug design. One popular approach is using reinforcement learning to update a recurrent neural network or language-based de novo molecule generator. However, reinforcement learning can be inefficient, sometimes requiring up to 10^5 molecules to be sampled to optimize more complex objectives, which poses a limitation when using computationally expensive scoring functions like docking or computer-aided synthesis planning models. In this work, we propose a reinforcement learning strategy called Augmented Hill-Climb based on a simple, hypothesis-driven hybrid between REINVENT and Hill-Climb that improves sample-efficiency by addressing the limitations of both currently used strategies. We compare its ability to optimize several docking tasks with REINVENT and benchmark this strategy against other commonly used reinforcement learning strategies including REINFORCE, REINVENT (version 1 & 2), Hill-Climb and best agent reminder. We find that optimization ability is improved ~1.5-fold and sample-efficiency is improved ~45-fold compared to REINVENT while still delivering appealing chemistry as output. Diversity filters were used, and their parameters were tuned to overcome observed failure modes that take advantage of certain diversity filter configurations. Lastly, we find that Augmented Hill-Climb outperforms the other reinforcement learning strategies used on six tasks, especially in the early stages of training or for more difficult objectives. Overall, we hence show that AHC improves sample-efficiency for language-based de novo molecule generation conditioning via reinforcement learning, compared to the current state-of-the-art. This makes more computationally expensive scoring functions, such as docking, more accessible on a relevant timescale. | Morgan Thomas; Noel M. O'Boyle; Andreas Bender; Chris de Graaf | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6253f5f66c989c04f6b40986/original/augmented-hill-climb-increases-reinforcement-learning-efficiency-for-language-based-de-novo-molecule-generation.pdf |
62fea80b90802d2cb8611d12 | 10.26434/chemrxiv-2022-c0plp-v2 | Enhanced structural control of soft-templated mesoporous inorganic thin films by inert processing conditions | Mesoporous thin films are widely used for applications in need of high surface area and good mass and charge transport properties. A well-established fabrication process involves the supramolecular assembly of organic molecules (e.g. block copolymers, and surfactants) with inorganic materials obtained by sol-gel chemistry. Typically, subsequent calcination in air serves to remove the organic template and reveal the pores. A major challenge for such coatings is the anisotropic shrinkage due to the volume contraction related to solvent evaporation, inorganic condensation, and template removal, affecting the final porosity as well as pore shape, size, arrangement and accessibility. Here, we show that a two-step calcination process, composed of high-temperature treatment in argon followed by air calcination, leads to reduced film contraction and enhanced structural control. Crucially, the formation of a transient carbonaceous scaffold enables the inorganic matrix to fully condense before template removal. The resulting mesoporous films retain a higher porosity as well as larger, more uniform pores with extended hexagonally closed-packed order. Such films present favorable characteristics for a variety of applications, such as improved mass transport of large biomolecules. This is demonstrated for the adsorption and desorption of lysozyme into the mesoporous thin films as an example of enzyme storage. | Maximiliano Jara Fornerod; Alberto Alvarez-Fernandez; Eric Williams; Maximilian W. A. Skoda; Beatriz Prieto-Simon; Nicolas H. Voelcker; Morgan Stefik; Marc-Olivier Coppens; Stefan Guldin | Materials Science; Nanoscience; Coating Materials; Nanostructured Materials - Materials; Nanofabrication; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fea80b90802d2cb8611d12/original/enhanced-structural-control-of-soft-templated-mesoporous-inorganic-thin-films-by-inert-processing-conditions.pdf |
641c26b162fecd2a834ca096 | 10.26434/chemrxiv-2023-zzt1v-v2 | Into the Dynamics of Rotaxanes at Atomistic Resolution | Mechanically-interlocked molecules (MIMs) are at the basis of artificial molecular machines and are attracting increasing interest for various applications, from catalysis to drug delivery and nanoelectronics. MIMs are composed of mechanically-interconnected molecular sub-parts that can move with respect to each other, imparting these systems innately dynamical behaviors and interesting stimuli-responsive properties. The rational design of MIMs with desired functionalities requires studying their dynamics at sub-molecular resolution and on relevant timescales, which is challenging experimentally and computationally. Here, we combine molecular dynamics and metadynamics simulations to reconstruct the thermodynamics and kinetics of different types of MIMs at atomistic resolution under different conditions. As representative case studies, we use rotaxanes and molecular shuttles substantially differing in structure, architecture, and dynamical behavior. Our computational approach provides results in optimal agreement with available experimental evidence and a direct demonstration of the critical effect of the solvent on the dynamics of the MIMs. At the same time, our simulations unveil key factors controlling the dynamics of these systems, providing submolecular-level insights into the mechanisms and kinetics of shuttling. Reconstruction of the free-energy profiles from the simulations reveals details of the conformations of macrocycles on the binding site that are difficult to access via routine experiments and precious for understanding the MIMs’ behavior, while their decomposition in enthalpic and entropic contributions unveils the mechanisms and key transitions ruling the intermolecular movements between metastable states within them. The computational framework presented herein is flexible and can be used, in principle, to study a variety of mechanically-interlocked systems. | Luigi Leanza; Claudio Perego; Luca Pesce; Matteo Salvalaglio; Max von Delius; Giovanni M. Pavan | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Self-Assembly; Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2023-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c26b162fecd2a834ca096/original/into-the-dynamics-of-rotaxanes-at-atomistic-resolution.pdf |
6547bac148dad23120203208 | 10.26434/chemrxiv-2023-0ths1 | cis-Azo-Promoted Construction of Vinylene-Linked Covalent Organic Frameworks with Exceptional Capability of Stepwise Water Harvesting | sp2-nitrogen atom holds a promising role either in promoting the construction of covalent organic frameworks (COFs) or tailoring their properties and functions. Herein, starting from 3,6-dimethylpyridazine as the linear ditopic monomer embedded with two adjacent sp2-nitrogen atoms, we successfully built up two novel vinylene-linked COFs upon Knoevenagel condensation with triformyl substituted aromatic derivatives. The finely-resolved powder X-ray diffraction (PXRD) patterns demonstrated their high crystalline structures with a hexagonal lattice in AA mode stacking along vertical direction. The resultant one-dimensional channels possess fruitful strong hydrogen-bond accepting sites arising from the decorated cis-azo units with two pair of the fully exposed lone pair electrons. In combination with their finely tailored micro-/nano-pore sizes, high surface areas and stable nonpolar vinylene linkages, as-prepared COFs enable exceptionally stepwise water harvesting from air, as shown by their water sorption isotherms consisting of successive steep water uptake steps even starting from a very low humidity (~10%), and reaching the largest water uptake capacity up to 1.26 g/g at P/PSTA = 0.95 (25 °C), representing the record values among the reported COF materials so far. Dynamic vapor sorption measurements confidently revealed the fast kinetics of such kinds of COFs, even in the cluster formation process. Water uptake and release cycling test manifested their outstanding hydrolytic stability, durability and adsorption-desorption retention ability. | Kaiwen Mou; Fancheng Meng; Zixing Zhang; Xiaomeng Li; Mengqi Li; Yang Jiao; Zhiheng Wang; Bai Xue; Fan Zhang | Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6547bac148dad23120203208/original/cis-azo-promoted-construction-of-vinylene-linked-covalent-organic-frameworks-with-exceptional-capability-of-stepwise-water-harvesting.pdf |
66da32c5cec5d6c14242c560 | 10.26434/chemrxiv-2024-llkmj-v2 | Dynamics of Photoexcited 5-Bromouracil and 5-Bromo-2'-Deoxyuridine Studied by Extreme Ultraviolet Time-resolved Photoelectron Spectroscopy in Liquid Flat Jets | The UV-induced photo-relaxation dynamics of 5-bromouracil (BrU) and 5-bromo-2’-deoxyuridine (BrUrd) in aqueous solution were investigated using femtosecond time-resolved photoelectron spectroscopy with an extreme ultraviolet (XUV) probe in a flat liquid jet. Upon excitation to the 1ππ* state by 4.66 eV UV photons, both molecules exhibited rapid relaxation into lower-lying electronic states followed by decay to the S0 ground state. By employing a 21.7 eV XUV probe pulse, we were able to differentiate the relaxation of the excited state population from the initially excited 1ππ* state to an intermediate electronic state with 100 fs. Computational results identify this intermediate as the 1πσ* excited state, accessed by a 1ππ*/1πσ* conical intersection, and the signal from this intermediate state disappears within 200 fs. In contrast to thymine, formation of neither the 1nπ* state nor a long-lived triplet state was observed. Although the 1πσ* state is largely repulsive, prior studies have reported a low quantum yield for dissociation, and we observe weak signals that are consistent with production of hot S0 ground state (for BrUrd) on a time scale of 1.5-2 ps. It thus appears that solvent caging effects limit the dissociation yield in solution. | Do Hyung Kang; Masafumi Koga; Neal Haldar; Daniel M. Neumark | Physical Chemistry; Chemical Kinetics; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66da32c5cec5d6c14242c560/original/dynamics-of-photoexcited-5-bromouracil-and-5-bromo-2-deoxyuridine-studied-by-extreme-ultraviolet-time-resolved-photoelectron-spectroscopy-in-liquid-flat-jets.pdf |
66729e49c9c6a5c07ad1b0a8 | 10.26434/chemrxiv-2024-kxlgm | Excuse me, there is a mutant in my bioactivity soup!
A comprehensive analysis of the genetic variability landscape of bioactivity databases and its effect on activity modelling | Bioactivity prediction is essential in computational drug discovery, particularly within virtual screening campaigns. Despite advancements in model architectures and features, the sparsity and quality of relevant training data remain a major bottleneck. Notably, genetic variance annotation, crucial for understanding variant-specific bioactivity, is often neglected. Key efforts to tackle these issues are conducted by public bioactivity databases such as ChEMBL, but these are not free of challenges. Here, a comprehensive analysis of the extent and distribution of bioactivity data tested on genetic variants across organisms, protein families, individual targets, and specific variants, for the first time characterises in detail the genetic variability landscape in the ChEMBL database and sheds light on the range and consequences of protein amino acid substitutions in bioactivity data distribution and modelling. Furthermore, an extensive set of analysis resources (Python package and notebooks) and a variant-annotated bioactivity dataset are made available to help replicate the analyses described here for any protein of interest and make informed decisions regarding the quality of data for modelling. Finally, the potential to extract variants and subsets of the chemical space with desirable inter-variant bioactivity profiles is demonstrated for data-rich proteins. This approach contributes to more reliable bioactivity modelling, aids noise reduction and informs decision-making in computational drug discovery. | Marina Gorostiola González; Olivier J. M. Béquignon; Emma Manners; Anna Gaulton; Prudence Mutowo; Elisabeth Dawson; Barbara Zdrazil; Andrew R. Leach; Adriaan P. IJzerman; Laura H. Heitman; Gerard J. P. van Westen | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology | CC BY 4.0 | CHEMRXIV | 2024-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66729e49c9c6a5c07ad1b0a8/original/excuse-me-there-is-a-mutant-in-my-bioactivity-soup-a-comprehensive-analysis-of-the-genetic-variability-landscape-of-bioactivity-databases-and-its-effect-on-activity-modelling.pdf |
668c338b01103d79c5685fa8 | 10.26434/chemrxiv-2021-htz42-v4 | Orbital Exchange Calculations of Chemical Bonding in Some Molecules Containing Carbon | The purpose of this paper is to extend the application of the orbital exchange method to a series of molecules containing carbon. The paper describes the calculation of bond length, bond strength and dipole moment in ethane, ethylene, acetylene, benzene, allene, hydrogen cyanide, formaldehyde, floromethane, tetrafloromethane and floromethylidyne (CF). This work explains how the s bonding orbital coefficients in such molecules as ethylene and acetylene are maximized to enable shorter and stronger carbon-carbon bonds. Pi orbital resonance of the form [C-C+,CC,C+C-] in ethylene, acetylene, and benzene is described and quantified. Pi orbital resonance in HCN [CN,C+N-] and H2CO [CO,C+O-] and sigma orbital resonance in H3CF [H3CF, H3C+F-], CF4 and CF is quantified. Secondary interactions are described. Calculated bond lengths are generally within 0.003Å of observed values. Calculated molecular energies are within 2%. | Paul Merrithew | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668c338b01103d79c5685fa8/original/orbital-exchange-calculations-of-chemical-bonding-in-some-molecules-containing-carbon.pdf |
60c74e5a469df44ac3f44472 | 10.26434/chemrxiv.12287576.v2 | Antibacterial Properties of Glycosylated Surfaces: Variation of the Glucosidal Moiety and Fatty Acid Conformation of Grafted Microbial Glycolipids | <div>Glycosylated surfaces can display antimicrobial properties. It has been shown that sophorolipids can be used to develop biocidal coatings against Gram-positive and Gramnegative bacteria, but with a limited efficiency so far. Therefore, it appears necessary to further investigate the surface antibacterial activity of a broader set of structurally related glycolipids.</div><div>The present work explores the influence of the glucosidic moiety (gluco-, sophoro-, cellobio-)</div><div>and the fatty acid backbone (saturated, cis or trans monounsaturated). We show that the fatty</div><div>acid backbone plays an important role: cis derivative of sophorolipids (SL) grafted onto model</div><div>gold surfaces has better biocidal properties than saturated (SL0) and trans monounsaturated</div><div>(SLt) molecules, which appear to be inefficient. The number of glucose units is also a key factor:</div><div>a one-third decrease in antibacterial activity is observed when having one glucose unit (GL)</div><div>compared to two (SL).Sugar acetylation (SLa) does not seem to have an impact on the biocidal</div><div>properties of surfaces. These results are not limited to sophorolipids, cellobioselipids (CL)</div><div>leading to similar antibacterial observations. </div> | Claire Valotteau; Sophie L. K. W. Roelants; Prabhu Dasaiyan; Susanne Zibek; Michael Günther; Wim Soetaert; Bernd Everaert; Claire-Marie Pradier; Florence Babonneau; Niki Baccile; Vincent Humblot | Biocompatible Materials; Coating Materials; Surfactants | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e5a469df44ac3f44472/original/antibacterial-properties-of-glycosylated-surfaces-variation-of-the-glucosidal-moiety-and-fatty-acid-conformation-of-grafted-microbial-glycolipids.pdf |
63fbdfb032cd591f1284483a | 10.26434/chemrxiv-2023-slfmk | Recent Advances in Discovery, Biosynthesis and
Therapeutic Potentialities of Isocoumarins Derived from Fungi: A Comprehensive Update | Microorganisms still remain as main hotspots in the global drug discovery avenue. In particular, fungi are highly prolific producers of a vast of structurally divers specialised secondary metabolites, which have displayed a myriad of biomedical potentialities. Intriguingly, isocoumarins is one distinctive class of fungal natural products polyketides, which demonstrated numerous remarkable biological and pharmacological activities. This review article provides a comprehensive state of the art over the period 2000-2022 about the discovery, isolation, classifications, and therapeutic potentialities of isocoumarins exclusively reported from fungi. Indeed, a comprehensive list of 351 structurally diverse isocoumarins were documented, classified according to their fungal sources [16 order/ 28 family/ 55 genera] where they have been originally discovered, alongside, their reported pharmacological activities wherever applicable. Also, recent insights around their proposed and experimentally proven biosynthetic pathways are also briefly discussed. | Mohamed A. Tammam; Mariam I. Gamal El-Din; Amira Abood; Amr El-Demerdash | Biological and Medicinal Chemistry; Organic Chemistry; Natural Products | CC BY NC 4.0 | CHEMRXIV | 2023-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63fbdfb032cd591f1284483a/original/recent-advances-in-discovery-biosynthesis-and-therapeutic-potentialities-of-isocoumarins-derived-from-fungi-a-comprehensive-update.pdf |
612cba54fc08e3b98f864749 | 10.26434/chemrxiv-2021-4fmmn | A scalable galvanic approach to microswimmer synthesis | Microswimmers are small particles capable of converting available energy sources into propulsion owing to their compositional asymmetry and are promising for applications ranging from targeted delivery to enhanced mixing at the microscale. However, current fabrication techniques demonstrate limited scalability and/or rely on the excessive use of expensive precursor materials. Here, a scalable Pickering-wax emulsion technique is combined with galvanic electrochemistry, to grow platinum films from copper nanoparticles asymmetrically seeded onto SiO\textsubscript{2} microparticle supports. In this manner, large quantities of Pt-SiO\textsubscript{2} Janus microswimmers are obtained. Utilising copper as a templating material not only reduces synthesis time, material costs, and toxic waste, but also facilitates the further extension of this methodology to a range of functional materials. This electrochemical approach builds upon previous attempts to overcome the current limitations in microswimmer synthesis and offers exciting opportunities for their future development. | Maximilian Bailey; Nico Reichholf; Anne Flechsig; Fabio Grillo; Lucio Isa | Materials Science; Inorganic Chemistry; Core-Shell Materials; Nanostructured Materials - Materials; Electrochemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/612cba54fc08e3b98f864749/original/a-scalable-galvanic-approach-to-microswimmer-synthesis.pdf |
65ae234e9138d231617732e6 | 10.26434/chemrxiv-2024-l48f9 | Finding relevant retrosynthetic disconnections for stereocontrolled reactions | Machine learning driven Computer Aided Synthesis Planning (CASP) tools have become important tools for idea generation in the design of complex molecule synthesis but do not adequately address stereochemical features of the target compounds. A novel approach to automated extraction of templates used in CASP that includes stereochemical information included in the USPTO and an internal AstraZeneca database containing reactions from Reaxys, Pistachio, and AstraZeneca electronic lab notebooks is implemented in the freely available AiZynthFinder software. 367 templates covering reagent- and substrate controlled as well as stereospecific reactions were extracted from the USPTO while 20,724 templates were from the AstraZeneca database. The performance of these templates in multi-step CASP are evaluated for 936 targets from the ChEMBL database and an in-house selection of 791 AZ compounds. The potential and limitations are discussed for four case studies from the ChEMBL and examples of FDA-approved drugs. | Olaf Wiest; Christoph Bauer; Paul Helquist; Per-Ola Norrby; Samuel Genheden | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ae234e9138d231617732e6/original/finding-relevant-retrosynthetic-disconnections-for-stereocontrolled-reactions.pdf |
63455f1b2e6e7cd52b56f373 | 10.26434/chemrxiv-2022-fp5g4 | Wet chemical fabricating of 3D printed electrodes for overall water splitting | Electrocatalytic water splitting is a key technology for sustainable energy. To-date, designing electrodes from the atomic level to the nano- and microstructure is a promising route to address challenges ranging from catalytic activity and stability to mass transport and gaseous product release. Thus, developing facile routes to well-defined electrodes with high activity and stability is still a challenge. As an additive fabrication technology, 3D printing enables the fabrication of electrochemical devices and electrodes in a novel way. Here, we developed wet chemical methods, including simple electroless plating and corrosion, for the preparation of metallized 3D printed electrodes for the hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). By doing HER on Ni-plated electrodes, an unexpected activation process was observed to be facilitated by W and P dopants. The electrodes for OER were prepared by corroding Ni-plated electrodes in an aqueous solution containing Fe3+. The resulting electrodes exhibit relatively low overpotentials in alkaline aqueous solution for HER (42 mV, current density j = 10 mA/cm2) and OER (220 mV, current density j = 10 mA/cm2), respectively. | Si Liu; Dandan Gao; Joachim Bansmann; Yupeng Zhao; Adam Clark; Johannes Biskupek; Ute Kaiser; Rongji Liu; Carsten Streb | Catalysis; Electrocatalysis | CC BY NC 4.0 | CHEMRXIV | 2022-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63455f1b2e6e7cd52b56f373/original/wet-chemical-fabricating-of-3d-printed-electrodes-for-overall-water-splitting.pdf |
65cfccc2e9ebbb4db986b451 | 10.26434/chemrxiv-2024-3wdwv | Improved Estimates of Folding Stabilities and Kinetics with Multiensemble Markov Models | Markov State Models (MSMs) have been widely applied to understand folding mechanisms and predict long timescale dynamics from ensembles of short molecular simulations. Most MSM estimators enforce detailed balance, assuming that trajectory data is sampled at equilibrium. This is rarely the case for ab initio folding studies, however, and as a result, MSMs can severely underestimate protein folding stabilities from such data. To remedy this problem, we have developed an enhanced-sampling protocol in which (1) unbiased folding simulations are performed and sparse tICA is used to obtain features that best capture the slowest events in folding, (2) umbrella sampling along this reaction coordinate is performed to observe folding and unfolding transitions, and (3) the thermodynamics and kinetics of folding are estimated using multiensemble Markov models (MEMMs). Using this protocol, folding pathways, rates, and stabilities of a designed alpha-helical hairpin, Z34C, can be predicted in good agreement with experimental measurements. These results indicate that accurate simulation-based estimates of absolute folding stabilities are within reach, with implications for the computational design of folded mini-proteins and peptidomimetics. | Si Zhang; Yunhui Ge; Vincent Voelz | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Theory - Computational; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cfccc2e9ebbb4db986b451/original/improved-estimates-of-folding-stabilities-and-kinetics-with-multiensemble-markov-models.pdf |
60c758269abda2bc72f8e86c | 10.26434/chemrxiv.14510664.v1 | Structure and Properties of Electrochemically Synthesized Silver Nanoparticles in Aqueous Solution by High Resolution Techniques | <p>In this work high resolution
techniques as transmission electron microscopy (TEM), scanning electron
microscopy (SEM), Zeta Potential measurements, and matrix-assisted laser
desorption/ionization time of flight mass spectrometry (MALDI-TOF) have been
employed to deeply investigate about silver nanoparticles (AgNPs)
electrochemically synthesized and successfully applied in biological and
chemical fields. Strong brightness, as well as the tendency to generate odd
number nanoclusters, and the absence of free silver ion in solution have been
observed. The chemical and physical properties of the AgNPs seem to be related
to their peculiar oxidative state as suggested by X-ray photoelectron
spectroscopy (XPS) and X-ray powder diffraction analysis (XRPD). Finally,
cytotoxicity of the investigated AgNPs has been tested by MTT assay.</p> | carla gasbarri; maurizio ronci; antonio aceto; tullio florio; Federica Barbieri; Roshan Vasani; Gianluca iezz; Guido Angelini; Luca Scotti | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758269abda2bc72f8e86c/original/structure-and-properties-of-electrochemically-synthesized-silver-nanoparticles-in-aqueous-solution-by-high-resolution-techniques.pdf |
6648902d21291e5d1d9db807 | 10.26434/chemrxiv-2024-w0j9n | Inverse Photoemission Spectroscopy of Coinage Metal Corroles: Comparison with Solution-Phase Electrochemistry | A combined direct and inverse photoemission study of coinage metal corroles suggests that the latter technique, in favorable cases, can provide some additional information relative to electrochemical measurements. Thus, whereas inverse photoemission spectroscopy (IPES) provides relative electron affinities for electron addition to different unoccupied orbitals, electrochemical reduction potentials sheds light on the energetics of successive electron additions. While all three coinage metal triphenylcorrole (TPC) complexes exhibit similar ionization potentials, they exhibit dramatically different inverse photoemission spectra. For Cu[TPC], the lowest-energy IPES feature (0.74 eV) is found to be exceedingly close to the Fermi level; it is significantly higher for Ag[TPC] (1.65 eV) and much higher for Au[TPC] (2.40 eV). These differences qualitatively mirror those observed for electrochemical reduction potentials and are related to a partially metal-centered LUMO in the case of Cu- and Ag[TPC] and a fully corrole-based LUMO in the case of Au[TPC]; the latter orbital corresponds to the LUMO+1 in the case of Ag[TPC]. | Luca Giovanelli; Younal Ksari; Hela Mrezguia ; Eric Salomon; Marco Minissale; Abraham Alemayehu; Abhik Ghosh | Theoretical and Computational Chemistry; Materials Science; Inorganic Chemistry; Electrochemistry; Spectroscopy (Inorg.); Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6648902d21291e5d1d9db807/original/inverse-photoemission-spectroscopy-of-coinage-metal-corroles-comparison-with-solution-phase-electrochemistry.pdf |
60c75006ee301c7adac7a7d5 | 10.26434/chemrxiv.12924974.v2 | Microscopic Factors Modulating the Interactions Between the SARS-CoV-2 Main Protease and α−Ketoamide Inhibitors | <p>We performed 10 ns scale molecular dynamics simulations of 6 SARS-CoV-2 main protease/alpha-ketoamide inhibitor complexes in aqueous solution, in the phase before the inhibitor covalently binds to the protease's catalytic cysteine, using a polarizable multi-scale molecular modeling approach. For each simulation, 100 Mpro/inhibitor snapshots</p><p>(about 4 800 atoms) were extracted along the last 2 ns simulation segments. They were post processed using a fully quantum mechanical O(N) approach to decompose the protease in sets of fragments from which we computed the mean local interaction energies between the inhibitors and the different pockets of the protease catalytic domain. Contrary to earlier results, our analysis shows that the protease pocket S2 to be a key anchoring site able to lock within the catalytic domain an alpha-ketoamide inhibitor even before covalent bonding to the protease catalytic cysteine occurs. To target that pocket our computations suggest to consider hydrophobic groups, like cyclo-propyl or cyclo-hexyl.</p> | Luigi Genovese; William Dawson; Takahito Nakajima; Viviana Cristiglio; Valérie Vallet; Michel Masella | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75006ee301c7adac7a7d5/original/microscopic-factors-modulating-the-interactions-between-the-sars-co-v-2-main-protease-and-ketoamide-inhibitors.pdf |
67b4ca9f6dde43c9086eb5ae | 10.26434/chemrxiv-2025-h8rwj | Frontal Polymerization of Hydroxylated Norbornene: Fabrication of Functional Foams for Catalytic Applications | Polymeric foams are versatile materials with direct applications in numerous fields, including insulation and heterogeneous catalysis. Existing polymeric foam production processes include several stages, many of which are energy intensive. Herein, we report the single-step fabrication of polymeric foams using the low energy technique, frontal ring opening metathesis polymerization (FROMP), and demonstrate their use as scaffolds for the deposition of palladium nanoparticles. Initially, we studied FROMP of 5-hydroxymethyl-2-norbornene (HMNB) monomer using the second-generation Grubbs catalyst (G2) as initiator. In contrast with the model FROMP system of dicyclopentadiene (DCPD), HMNB is a liquid that contains hydroxyl groups capable of inhibiting G2. By incorporating 10 wt% n-pentane within FROMP mixtures, we successfully fabricated hydroxyl-containing foams with high porosities. The presence of hydroxyl groups enhanced the material’s ability to bind and uniformly disperse palladium nanoparticles (Pd NPs) as compared to DCPD foams. Coupled with a more hydrophilic surface, the generated foams were demonstrated as efficient catalytic scaffolds for cross-coupling reactions with activities comparable to that of free NPs. Our results demonstrate that HMNB can be polymerized using FROMP in the presence of a blowing agent to make functional foams that serve as a platform for heterogeneous catalysts development. We envision that these novel foams have potential use as scaffolds in flow chemistry. | Andrew Vogler; Tina Dinh; Hanlin Wang; Ghaida Aldhahri; Arfa Abrar Malik; Diego Alzate-Sanchez | Catalysis; Polymer Science; Polymerization (Polymers); Polymer scaffolds; Heterogeneous Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67b4ca9f6dde43c9086eb5ae/original/frontal-polymerization-of-hydroxylated-norbornene-fabrication-of-functional-foams-for-catalytic-applications.pdf |
653e383648dad23120a2c1bf | 10.26434/chemrxiv-2023-v368j | Studies on a Type III Atropisomeric Colchicine Analog Enabled by an Intermolecular Oxidopyrylium (5 + 2) Cycloaddition/Reductive Ring-Opening Sequence | Colchicine is one of the oldest known microtubule-targeting agents, and the development of clinically viable colchicine binding site inhibitors (CBSIs) remains of high interest to the medicinal chemistry community. Colchicine’s binding to tubulin is the result of its biaryl methoxytropone-trimethoxybenzene system (called the AC ring), which binds in a preferred aR conformation. In the natural source, this axial chiral form is favored thermodynamically by approximately 3 kcal/mol as a result of nearby point chirality on its B ring, and without this point chirality the AC ring will racemize within minutes to hours at room temperature (∆G ~ 22 kcal/mol, t1/2, 298K ~ 30 min). Herein, we describe the synthesis and evaluation of a novel acyclic AC analog of colchicine that is highly stable to epimerization based not on thermodynamic stabilization, but rather a high rotational barrier energy (∆G‡ = 31.2 kcal/mol, t1/2, 298K ~ 300 y). Access to this molecule, as well as several structural homologs, was enabled through the development of a convenient intermolecular oxidopyrylium (5 + 2) cycloaddition/reductive ring-opening approach from 3-hydroxy-4-pyrones. Profiling and characterization of the dihedral angles were carried out computationally and experimentally using vibrational circular dichroism (VCD), demonstrating that the ground state dihedral angles of the new molecules differ significantly from colchicine and MTC. However, despite this difference, the molecule retained anti-cancer, tubulin-binding, and tubulin polymerization inhibitory activity. | Lauren Bejcek; Orugbani Eli; Anastasiya Lyubibova; Diana Kapkayeva; Jordan Nafie; John Beutler; Emilio Gallicchio; Dan Sackett; Ryan Murelli | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653e383648dad23120a2c1bf/original/studies-on-a-type-iii-atropisomeric-colchicine-analog-enabled-by-an-intermolecular-oxidopyrylium-5-2-cycloaddition-reductive-ring-opening-sequence.pdf |
667628f0c9c6a5c07a1153e7 | 10.26434/chemrxiv-2024-3f78l | Fragment correlation mass spectrometry enables direct characterization of di-sulfide cleavage pathways of therapeutic peptides | Therapeutic peptides that are connected by disulfide bonds are often difficult to analyze by traditional tandem mass spec-trometry without chemical modification. Using fragment correlation mass spectrometry, we measured 56 pairs of fragment ions from an equimolar (10 µM) mixture of three cyclic peptides, with sequence coverages for octreotide, desmopressin, and the structural analog of desmopressin to be 86%, 100%, and 75%, respectively. In all detected fragment ion pairs, only 20% of the fragments are terminal ions, with most of the measured MS2 signals only made available by fragment correlation mass spectrometry. From the peak volumes in the covariance map, we calculated branching ratios of each disulfide fragmentation pathway, providing direct measures of disulfide fragmentation probabilities without altering analytes’ chemical structures. | Yangjie Li; Guy Cavet; Richard Zare; Taran Driver | Analytical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-06-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667628f0c9c6a5c07a1153e7/original/fragment-correlation-mass-spectrometry-enables-direct-characterization-of-di-sulfide-cleavage-pathways-of-therapeutic-peptides.pdf |
63ed88601d2d184063919570 | 10.26434/chemrxiv-2022-crwxr-v2 | Structures of LaH10, EuH9, and UH8 superhydrides rationalized by electron counting and Jahn-Teller distortions in a covalent cluster model | The superconducting hydrides LaH10, EuH9 and UH8 are studied using chemically intuitive bonding analysis of periodic and molecular models. We find trends in the crystallographic and electronic structures of the materials by focusing on chemically meaningful building blocks in the predicted H sublattices. Atomic charge calculations, using two complementary techniques, allow us to assign oxidation states to the metals and divide the H sublattice into neutral and anionic components. Cubic [H8]q- clusters are an important structural motif, and molecular orbital analysis of this cluster in isolation shows the crystal structures to be consistent with our oxidation state assignments. Crystal orbital Hamilton population analysis confirms the applicability of the cluster model to the periodic electronic structure. A Jahn-Teller distortion predicted by MO analysis rationalises the distortion observed in a prior study of EuH9. The impact of this distortion on superconductivity is determined, and implications for crystal structure prediction in other metal-hydrogen systems are discussed. Additionally, the performance of electronic structure analysis methods at high pressures are tested and recommendations for future studies are given. These results demonstrate the value of simple bonding models in rationalizing chemical structures under extreme conditions. | Harry Morgan; Anastassia Alexandrova | Theoretical and Computational Chemistry; Inorganic Chemistry; Bonding; Solid State Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ed88601d2d184063919570/original/structures-of-la-h10-eu-h9-and-uh8-superhydrides-rationalized-by-electron-counting-and-jahn-teller-distortions-in-a-covalent-cluster-model.pdf |
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