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60c73e5a0f50dbb40f395649 | 10.26434/chemrxiv.6960404.v1 | Highly Enantioselective Hiyama Cross-Coupling via Rh-Catalyzed Allylic Arylation of Racemic Allyl Chlorides | <div><div><div><p>Highly enantioselective Hiyama cross-coupling reactions have been achieved through rhodium(I)-catalyzed dynamic kinetic asymmetric transformations between aryl siloxanes and racemic allyl halides. This process affords valuable enantiomerically enriched allyl arenes and is compatible with heterocyclic allyl chloride electrophiles.</p></div></div></div> | Jesus Gonzalez; Philipp Schäfer; Stephen P. Fletcher | Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-08-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e5a0f50dbb40f395649/original/highly-enantioselective-hiyama-cross-coupling-via-rh-catalyzed-allylic-arylation-of-racemic-allyl-chlorides.pdf |
62565e9a5b9009673f0c2989 | 10.26434/chemrxiv-2022-6xwd7 | smProdrugs: A repository of small molecule prodrugs | In modern drug discovery and development, the prodrug approach has become a crucial strategy for enhancing the pharmacokinetic profiles of drugs. A prodrug is a chemical compound, which gets metabolized into a pharmacologically active form (drug) inside the body after its administration. In the current work, we report ‘smProdrugs’, which is one of the first exclusive databases on small molecule prodrugs, which stores the structures, physicochemical properties and experimental ADMET data manually curated from literature. SmProdrugs lists 626 small molecule prodrugs and their active compounds with the above mentioned experimental data from 1808 research articles and 61 patents have been stored. The information page of each record gives the structures and properties of the prodrug and the active drug side by side which makes it easy for the user to instantly compare them. The structural modifications in the prodrug/active drugs are highlighted in a different colour for easy comparison. Experimental data has been curated from the downloaded PubMed and patent articles and were catalogued in a tabular form with more than 25 fields under sub-sections i) name and structures of the prodrugs and their active compounds, ii) mode of activation of the prodrug and enzyme/biocatalyst involved in the conversion, iii) indications/disease, iv) pharmacological target, v) experimental pharmacokinetic properties such as solubility, absorption, volume of distribution, half-life, clearance etc. and vi) information on the purpose/gain from the prodrug strategies. Considering the ever expanding utility of the prodrug approach smProdrugs will be of great use to the scientific community working on rational design of small molecule prodrugs. | Chinmayee Choudhury; Vivek Kumar | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62565e9a5b9009673f0c2989/original/sm-prodrugs-a-repository-of-small-molecule-prodrugs.pdf |
61a4f31d836f65c501818b21 | 10.26434/chemrxiv-2021-49lwd | Flexible operation of modular electrochemical CO2 reduction processes | Electrochemical CO2 reduction (eCO2R) is an emerging technology that is capable of producing various organic chemicals from CO2, but its high electricity cost is a big economic obstacle. One solution to reduce the cumulative
electricity cost is demand side management, i.e., to adjust the power load based on time-variant electricity prices. However, varying the power load of CO2-electrolyzers often leads to changes in Faraday efficiency towards target components and thereby influences the product composition. Such deviations from the target product composition may be undesired for downstream processes. We tackle this challenge by proposing a flexible operating scheme for a modular eCO2R process. We formulate the economically optimal operation of an eCO2R process with multiple electrolyzer stacks as a parallel-machine scheduling problem. Adjusting the power load of each sub-process properly, we can save electricity costs while the desired product composition is met at any time. We apply an algorithm based on wavelet transform to solve the resulting large-scale nonlinear scheduling problem in tractable time. We solve each optimization problem with a deterministic global optimization software MAiNGO. We examine flexible operation of a modular eCO2R process for syngas production. The case studies show that the modular structure enables savings in the cumulative electricity cost of the eCO2R process via flexible operation while deviations in the syngas composition could be reduced. Also, the maximum ramping speed of the entire process is found to be a key parameter that strongly influences the cost saving. | Kosan Roh; Luisa Brée; Pascal Schäfer; Daniel Strohmeier; Alexander Mitsos | Chemical Engineering and Industrial Chemistry | CC BY 4.0 | CHEMRXIV | 2021-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a4f31d836f65c501818b21/original/flexible-operation-of-modular-electrochemical-co2-reduction-processes.pdf |
67405d827be152b1d0533388 | 10.26434/chemrxiv-2024-j9g93-v3 | Competitive Strain Modulation of Oxygen Reduction Reaction in Monolayer Binary Alloy Surfaces | Binary alloys of transition metals show great promise as catalyst materials for the cathodic oxygen-reduction reaction (ORR) in polymer-electrolyte-membrane fuel cells. However, their catalytic application is limited by a lack of understanding of the factors influencing the ORR performance. To improve this understanding, we examine the activity of monolayer AuxPt1-x surface alloys supported on Pt(111) using density functional theory. We found that the catalytic activity of AuxPt1-x/Pt(111) alloys varies significantly with the surface atomic arrangements, where phase-segregated surfaces show higher activity than those with random atomic arrangements. A key factor is a competitive strain influencing the Pt adsorption site activity. Distant Au atoms induce a long-range compressive strain that enhances Pt site activity, while adjacent Au atoms generate tensile strain that slightly reduces the Pt site activity. These findings suggest that surface alloys of elements with dissimilar lattice constants can generate competitive strain effects that modulate the activity of different adsorption sites. Our findings underscore the importance of understanding and controlling atomic arrangements in alloys to ensure good catalytic performance. | Mailde S. Ozório; Marcus Frahm Nygaard; Jan Rossmeisl | Materials Science; Catalysis; Energy; Alloys; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67405d827be152b1d0533388/original/competitive-strain-modulation-of-oxygen-reduction-reaction-in-monolayer-binary-alloy-surfaces.pdf |
638b92c30a81271a19d20708 | 10.26434/chemrxiv-2022-c8dbz | Mechanochemical interconversion reactions of halogen-bonded cocrystals inspired by theoretical calculations | Periodic density-functional theory (DFT) calculations were used to predict the thermodynamic stability and the likelihood of interconversion between a series of halogen-bonded cocrystals. The outcomes of mechanochemical transformations were in excellent agreement with the theoretical predictions, demonstrating the power of periodic DFT as a method for designing solid-state mechanochemical reactions prior to experimental work. Furthermore, the calculated DFT energies were compared with experimental dissolution calorimetry measurements, marking the first such benchmark for the accuracy of periodic DFT calculations in modelling transformations of halogen-bonded molecular crystals. | Lavanya Kumar; Katarina Leko; Vinko Nemec; Damian Trzybiński; Nikola Bregović; Dominik Cinčić; Mihails Arhangelskis | Theoretical and Computational Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638b92c30a81271a19d20708/original/mechanochemical-interconversion-reactions-of-halogen-bonded-cocrystals-inspired-by-theoretical-calculations.pdf |
645ec680a32ceeff2d8b91e8 | 10.26434/chemrxiv-2023-1lx2v | A comprehensive analysis of charge transfer effects on donor-pyrene (bridge)-acceptor systems using different substituents | The alternant polycyclic aromatic hydrocarbon pyrene has photophysical properties that can be tuned with different donor and acceptor substituents. Recently, a D (donor) – Pyrene (bridge) – A (acceptor) system, DPA, with the electron donor N,N-dimethylaniline (DMA), and the electron acceptor trifluoromethylphenyl (TFM), was investigated by means of time-resolved spectroscopic measurements (J. Phys. Chem. Lett. 2021, 12, 2226−2231). DPA shows great promise for potential applications in organic electronic devices. In this work, we used the ab initio second-order algebraic diagrammatic construction method ADC(2) to investigate the excited-state properties of a series of analogous DPA systems, including the originally synthesized DPAs. The additionally investigated substituents were amino, fluorine, and methoxy as donors and nitrile and nitro groups as acceptors. The focus of this work was on characterizing the lowest excited singlet states regarding charge transfer (CT) and local excitation (LE) characters. For the DMA-pyrene-TFM system, the ADC(2) calculations show two initial electronic states relevant for interpreting the photodynamics. The bright S1 state is locally excited within the pyrene moiety, and an S2 state is localized ~0.5 eV above S1 and characterized as a donor to pyrene charge transfer state. Density functional theory HOMO and LUMO energies were employed to assess the efficiency of the DPA compounds for organic photovoltaics. HOMO-LUMO and optical gaps were used to estimate power conversion and light-harvesting efficiencies for practical applications in organic solar cells. From the systems using smaller D/A substituents, compounds with the strong acceptor NO2 substituent group show enhanced CT and promising properties for use in organic photovoltaics. | Itamar Borges Jr.; Roberta Guimarães; Gabriel Monteiro-de-Castro; Nathalia Rosa; Reed Niemann; Hans Lischka; Adelia Aquino | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645ec680a32ceeff2d8b91e8/original/a-comprehensive-analysis-of-charge-transfer-effects-on-donor-pyrene-bridge-acceptor-systems-using-different-substituents.pdf |
67d06040fa469535b9dff783 | 10.26434/chemrxiv-2025-x15nw | Hydrogen scrambling and high propensity for multiple neutral emissions from 1,3-butadiene dication | The two-body dissociation of the dications formed after double ionization of the smallest conjugated
diene, the 1,3-butadiene, C4H6, is studied using the coincidence time-of-flight technique and
quantum chemistry calculations. The dication was formed by ion-impact ionization using energetic
Xe3+ projectiles. Our results show that butadiene dication has a high propensity of neutral particle
emission (H/H2/C2H2) prior to two-body dissociation leading to two singly charged fragments.
The asymmetric two-body breakup, after the emission of neutral fragments from parent butadiene
dication, is observed to be ≈200% more likely than the asymmetric two-body breakup of intact butadiene
dication. Evidence is recorded for formation of multiple structures for the several different
precursor dications formed after loss of neutral particles, which is indicative of the strong role of
hydrogen scrambling. The internal energy dependence and time evolution of the interplay between
neutral particle emission, hydrogen scrambling and hydrogen migration is explored using ab-initio
molecular dynamics simulations to support the experimental observations. | Pooja Kumari; C.P. Safvan; Aakash Dixit; Jatin Yadav; Dariusz G. Piekarski; Jyoti Rajput | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d06040fa469535b9dff783/original/hydrogen-scrambling-and-high-propensity-for-multiple-neutral-emissions-from-1-3-butadiene-dication.pdf |
6312186f5351a3f3b9ec98cb | 10.26434/chemrxiv-2022-fhq71 | Photoelectrochemical detection of calcium ions based on hematite nanorod sensor substrates | α-Fe2O3 (hematite) thin films have been shown to be a robust sensor substrate for photoelectrochemical imaging with good stability and high spatial resolution. Herein, one-dimensional (1D) hematite nanorods (NRs) synthesized via a simple hydrothermal method are proposed as a substrate, which provides nanostructured surfaces with enhanced photocurrent responses, good stability and excellent spatial resolution for potential imaging applications. The photoelectrochemical sensing capability of hematite NRs was demonstrated by a high pH sensitivity without modification and by an amperometric response to calcium ions (Ca2+) when modified with a thin ion-sensitive membrane. | Bo Zhou; Yunlu Jiang; Qian Guo; Anirban Das; Ana Sobrido; Karin Hing; Anatoly Zayats; Steffi Krause | Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Electrochemical Analysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6312186f5351a3f3b9ec98cb/original/photoelectrochemical-detection-of-calcium-ions-based-on-hematite-nanorod-sensor-substrates.pdf |
64504e5f80f4b75b53745c09 | 10.26434/chemrxiv-2023-s1460 | Prolonged Circulation and Enhanced Tumor Uptake of PEGylated Nanoparticles by Manipulation of Nanoscale Surface Topography | Improving the performance of nanocarriers remains a major challenge in the clinical translation of nanomedicine. Efforts to optimize nanoparticle formulations typically rely on tuning the surface density and thickness of stealthy polymer coatings such as poly(ethylene glycol) (PEG). Here, we show that modulating the surface topography of PEGylated nanoparticles using bottlebrush block copolymer (BBCP) significantly enhances circulation and tumor accumulation providing an alternative strategy to improve nanoparticle coatings. Specifically, nanoparticles with rough surface topography achieve high tumor cell uptake in vivo due to superior tumor extravasation and distribution compared to conventional smooth-surfaced nanoparticles. Furthermore, surface topography profoundly impacts the interaction with serum proteins resulting in the adsorption of fundamentally different proteins onto the surface of rough-surfaced nanoparticles formed from BBCPs. We envision that controlling the nanoparticle surface topography of PEGylated nanoparticles will enable the design of improved nanocarriers in various biomedical applications. | Julian Grundler; Kwangsoo Shin; Hee-Won Suh; Chang-Hee Whang; W. Mark Saltzman | Polymer Science; Nanoscience; Drug delivery systems; Polymer brushes; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64504e5f80f4b75b53745c09/original/prolonged-circulation-and-enhanced-tumor-uptake-of-pe-gylated-nanoparticles-by-manipulation-of-nanoscale-surface-topography.pdf |
6149e73818be8540822ae7d1 | 10.26434/chemrxiv-2021-zpbqb-v3 | Exploring the Relationship between the CO Oxidation Reaction and the Elemental Composition in Electrocatalysts with Machine Learning - a Case Study of PtRuPdRhAu High Entropy Alloys | In recent years, the development of complex multi-metallic nanomaterials like high entropy alloy (HEA) catalysts has gained popularity. Composed of 5 or more metals, the compositions of HEAs exhibit extreme diversity. This is both a promising avenue to identify new catalysts and a severe constraint on their preparation and study. To address the challenges related to the preparation, study and optimization of HEAs, machine learning solutions are attractive. In this paper, the composition of PtRuPdRhAu hydrogen oxidation catalysts is optimized for the CO oxidation reaction. This is achieved by constructing a dataset using Bayesian optimization as guidance. For this quinary nanomaterial, the best performing composition was found within the first 35 experiments. However, the dataset was expanded until a total of 68 samples were investigated. This final dataset was used to construct a random forest regression model and a linear model. These machine learned models were used to assess the relationships between the concentrations of the consituent elements and the CO oxidation reaction onset potential. The onset potentials were found to correlate with the composition dependent adsorption energy of *OH obtained from density functional theory. This study demonstrates, how machine learning can be employed in an experimental setting to investigate the vast compositional space of HEAs. | Vladislav Mints; Jack Pedersen; Alexander Bagger; Jonathan Quinson; Andy Anker; Kirsten Jensen; Jan Rossmeisl; Matthias Arenz | Physical Chemistry; Catalysis; Nanoscience; Nanocatalysis - Catalysts & Materials; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6149e73818be8540822ae7d1/original/exploring-the-relationship-between-the-co-oxidation-reaction-and-the-elemental-composition-in-electrocatalysts-with-machine-learning-a-case-study-of-pt-ru-pd-rh-au-high-entropy-alloys.pdf |
6784dfde6dde43c9084c6fc8 | 10.26434/chemrxiv-2025-sx9jq | Low-cost optical multi-wavelength sensor for accurate real-time state-of-charge monitoring in vanadium flow batteries | We presents a novel, low-cost optical sensor for accurate real-time monitoring of state of charge (SoC) and total vanadium concentration in vanadium flow batteries. Using only six discrete wavelengths, the sensor achieves precision comparable to full-spectrum methods while significantly reducing equipment costs and complexity. A general deconvolution method is used to measure both the SoC and the total vanadium concentration in both the posolyte and negolyte, with calibration covering concentrations from 1.2 to 1.8 M. We achieve an overall accuracy of 2.4% for the SoC and 70 mM for the total vanadium concentration. Additionally, an optimization study is proposed to determine the optimal number and placement of spectral channels, providing a basis for designing tailored optical sensors for vanadium electrolytes. | Ange A. Maurice; Pablo A. Prieto-Díaz; Marcos Vera | Analytical Chemistry; Energy; Chemical Engineering and Industrial Chemistry; Spectroscopy (Anal. Chem.); Energy Storage | CC BY 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6784dfde6dde43c9084c6fc8/original/low-cost-optical-multi-wavelength-sensor-for-accurate-real-time-state-of-charge-monitoring-in-vanadium-flow-batteries.pdf |
65a14db466c13817294b1e9b | 10.26434/chemrxiv-2023-zn5w7-v2 | How 2D nanoflakes improve transport in mixed matrix membranes: insights from a simple lattice model and dynamic mean field theory | Mixed matrix membranes (MMMs), incorporating graphene and graphene oxide structural fragments, have emerged as promising materials for challenging gas separation processes. What remains unclear is the actual molecular mechanism responsible for the enhanced permeability and perm- selectivity of these materials. With the fully atomistic models still unable to handle the required time and length scales, here we employ a simple qualitative model based on the lattice representa- tion of the physical system and Dynamic Mean Field theory. We demonstrate that the performance enhancement results from the flux-regularization impact of the 2D nanoflakes, and that this effect sensitively depends on the orientation of the nanoflakes and the properties of the interface between the nanoflakes and the polymer. | Tianmu Yuan; Lev Sarkisov | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Thermodynamics (Chem. Eng.); Transport Phenomena (Chem. Eng.); Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a14db466c13817294b1e9b/original/how-2d-nanoflakes-improve-transport-in-mixed-matrix-membranes-insights-from-a-simple-lattice-model-and-dynamic-mean-field-theory.pdf |
60c746794c89192f45ad2b50 | 10.26434/chemrxiv.11324504.v1 | Selective Metathesis Synthesis of MgCr2S4 by Control of Thermodynamic Driving Forces | MgCr<sub>2</sub>S<sub>4</sub> thiospinel is predicted to be a compelling Mg-cathode material, but its preparation via traditional solid-state synthesis methods has proven challenging. Wustrow et al. [Inorg. Chem. 57, 14 (2018)] found that the formation of MgCr<sub>2</sub>S<sub>4</sub> from MgS + Cr<sub>2</sub>S<sub>3</sub> binaries requires weeks of annealing at 800 ℃ with numerous intermediate regrinds. The slow reaction kinetics of MgS + Cr<sub>2</sub>S<sub>3 </sub>--> MgCr<sub>2</sub>S<sub>4</sub> can be attributed to a miniscule thermodynamic driving force of ΔH = –2 kJ/mol. Here, we demonstrate that the double ion-exchange metathesis reaction, MgCl<sub>2</sub> + 2 NaCrS<sub>2</sub> --> MgCr<sub>2</sub>S<sub>4</sub> + 2 NaCl, has a reaction enthalpy of ΔH = –47 kJ/mol, which is thermodynamically driven by the large exothermicity of NaCl formation. Using this metathesis reaction, we successfully synthesized MgCr<sub>2</sub>S<sub>4</sub> nanoparticles (< 200 nm) from MgCl<sub>2</sub> and NaCrS<sub>2</sub> precursors in a KCl flux at 500 °C in only 30 minutes. NaCl and other metathesis byproducts are then easily washed away by water. We rationalize the selectivity of MgCr<sub>2</sub>S<sub>4</sub> in the metathesis reaction from the topology of the DFT-calculated pseudo-ternary MgCl<sub>2</sub>-CrCl<sub>3</sub>-Na<sub>2</sub>S phase diagram. Our work helps to establish metathesis reactions as a powerful alternative synthesis route to inorganic materials that have otherwise small reaction energies from conventional precursors.<br /> | akira miura; Hiroaki Ito; Christopher Bartel; Wenhao Sun; Nataly Carolina Rosero-Navarro; Kiyoharu Tadanaga; Hiroko Nakata; Kazuhiko Maeda; Gerbrand Ceder | Reaction (Inorg.); Solid State Chemistry; Theory - Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746794c89192f45ad2b50/original/selective-metathesis-synthesis-of-mg-cr2s4-by-control-of-thermodynamic-driving-forces.pdf |
621da82d5f1d9a2275ac5044 | 10.26434/chemrxiv-2022-0zlr3 | Potential COVID-19 therapies from computational repurposing of drugs and natural products against the SARS-CoV-2 helicase | Repurposing of existing drugs is a rapid way to find potential new treatments for SARS-CoV-2. Here we applied a virtual screening approach using Autodock Vina and molecular dynamic simulation in tandem to screen and calculate binding energies of repurposed drugs against the SARS-CoV-2 helicase protein (non-structural protein nsp13). Amongst the top hits from our study were antivirals, antihistamines, and antipsychotics plus a range of other drugs. Approximately 30% of our top 87 hits had published evidence indicating in vivo or in vitro SARS-CoV-2 activity. Top hits not previously reported to have SARS-CoV-2 activity included the antiviral agents, cabotegravir and RSV-604, the NK1 antagonist, aprepitant, the trypanocidal drug, aminoquinuride, the analgesic antrafenine, the anticancer intercalator, epirubicin, the antihistamine, fexofenadine, and the anticoagulant, dicoumarol. These hits from our in silico SARS-CoV-2 helicase screen warrant further testing as potential COVID-19 treatments | Sakshi Piplani; Puneet Singh; David Winkler; Nikolai Petrovsky | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621da82d5f1d9a2275ac5044/original/potential-covid-19-therapies-from-computational-repurposing-of-drugs-and-natural-products-against-the-sars-co-v-2-helicase.pdf |
66fe375651558a15efeab3a6 | 10.26434/chemrxiv-2024-cw1tt-v2 | GOCIA: grand canonical Global Optimizer for Clusters, Interfaces, and Adsorbates | Restructuring of surfaces and interfaces underlie the activation and/or deactivation of a wide spectrum of heterogeneous catalysts and functional materials. The statistical ensemble representation can provide unique atomistic insights into this fluxional and metastable realm, but constructing the ensemble is very challenging, especially for the systems with off-stoichiometric reconstruction and varying coverage of mixed adsorbates. Here we report GOCIA, a general-purpose global optimizer for exploring the chemical space of these systems. It features the grand canonical genetic algorithm (GCGA), which bases the target function on the grand potential and evolves across the compositional space, as well as many useful functionalities and implementation details. GOCIA has been applied to various systems in catalysis, from cluster to surfaces, and from thermal to electro-catalysis. | Zisheng Zhang; Winston Gee; Robert H. Lavroff; Anastassia N. Alexandrova | Theoretical and Computational Chemistry; Catalysis; Chemical Engineering and Industrial Chemistry; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66fe375651558a15efeab3a6/original/gocia-grand-canonical-global-optimizer-for-clusters-interfaces-and-adsorbates.pdf |
60c75241bdbb895fd2a3a240 | 10.26434/chemrxiv.12768353.v2 | SAMPL7 Host-Guest Challenge Overview: Assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations | The SAMPL challenges focus on testing and driving progress of computational methods to help guide pharmaceutical drug discovery. However, assessment of methods for predicting binding affinities is often hampered by computational challenges such as conformational sampling, protonation state uncertainties, variation in test sets selected, and even lack of high quality experimental data. SAMPL blind challenges have thus frequently included a component focusing on host-guest binding, which removes some of these challenges while still focusing on molecular recognition. Here, we report on the results of the SAMPL7 blind prediction challenge for host-guest affinity prediction. In this study, we focused on three different host-guest categories -- a familiar deep cavity cavitand series which has been featured in several prior challenges (where we examine binding of a series of guests to two hosts), a new series of cyclodextrin derivatives which are monofunctionalized around the rim to add amino acid-like functionality (where we examine binding of two guests to a series of hosts), and binding of a series of guests to a new acyclic TrimerTrip host which is related to previous cucurbituril hosts. Many predictions used methods based on molecular simulations, and overall success was mixed, though several methods stood out. As in SAMPL6, we find that one strategy for achieving reasonable accuracy here was to make empirical corrections to binding predictions based on previous data for host categories which have been studied well before, though this can be of limited value when new systems are included. Additionally, we found that alchemical free energy methods using the AMOEBA polarizable force field had considerable success for the two host categories in which they participated. The new TrimerTrip system was also found to introduce some sampling problems, because multiple conformations may be relevant to binding and interconvert only slowly. Overall, results in this challenge tentatively suggest that further investigation of polarizable force fields for these challenges may be warranted. | Martin Amezcua; Léa El Khoury; David Mobley | Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2020-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75241bdbb895fd2a3a240/original/sampl7-host-guest-challenge-overview-assessing-the-reliability-of-polarizable-and-non-polarizable-methods-for-binding-free-energy-calculations.pdf |
60c74ce3469df42ebef4419a | 10.26434/chemrxiv.12555419.v1 | Crack Tip Field of a Double-Network Gel: Visualizing Covalent Bond Scission by Mechanoradical Polymerization | Quantitative characterization of the energy dissipative zone around the crack tip is the central issue in fracture mechanics of soft materials. In this research, we present a mechanochemical technique to visualize the bond scission of the first network in the damage zone of tough double-network hydrogels. The mechanoradicals generated by polymer chain scission are employed to initiate polymerization of a thermoresponsive polymer, which is visualized by a fluorophore. This technique records the spatial distribution of internal fracturing from the fractured surface to the bulk, which provides the spatial profiles of stress, strain, and energy dissipation around the crack-tip. The characterized results suggest that, in addition to the dissipation in relatively narrow yielded zone which is mostly focused in the previous works, the dissipation in wide pre-yielding zone and the intrinsic fracture energy have also significant contribution to the fracture energy of a DN gel. | Takahiro Matsuda; Runa Kawakami; Tasuku Nakajima; Jian Ping Gong | Polymers | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ce3469df42ebef4419a/original/crack-tip-field-of-a-double-network-gel-visualizing-covalent-bond-scission-by-mechanoradical-polymerization.pdf |
61195e2e18911d3204e13f03 | 10.26434/chemrxiv-2021-s5qp7 | De novo Sequencing and Native Mass Spectrometry Reveals Hetero-Association of Dirigent Protein Homologs and Potential Interacting Proteins in Forsythia × intermedia | The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro was then reported to afford the optically active lignan, (+)-pinoresinol from coniferyl alcohol, provided one-electron oxidase/oxidant capacity was present. It later became evident that DPs have several distinct sub-families. In vascular plants, DPs hypothetically function, along with other essential enzymes/proteins (e.g. oxidases), as part of lignin/lignan forming complexes (LFCs). Herein, we used an integrated bottom-up, top-down, and native mass spectrometry approach to detect potential interacting proteins in a DP-enriched solubilized protein fraction from Forsythia × intermedia, via adaptation of our initial report of DP solubilization and purification. Because this hybrid species lacks a published genome, de novo sequencing was performed using publicly available transcriptome and genomic data from closely related species. We detected and identified two new DP homologs, which appear to form hetero-trimers. Molecular dynamics simulations suggest that similar hetero-trimers were possible between Arabidopsis DP homologs with comparable sequence similarity. Other identified proteins in the DP-enriched preparation were putatively associated with DP function or the cell wall. Although their co-occurrence after extraction and chromatographic separation is suggestive for components of a protein complex in vivo, none were found to form stable complexes with DPs under the specific experimental conditions we have explored. Nevertheless, our integrated mass spectrometry method development helps prepare for future investigations directed to detect hypothetical LFCs and other related complexes isolated from plant biomass fractionation. | Mowei Zhou; Joseph Laureanti; Callum Bell; Mi Kwon; Qingyan Meng; Irina Novikova; Dennis Thomas; Carrie Nicora; Ryan Sontag; Diana Bedgar; Isabelle O’Bryon; Eric Merkley; Bojana Ginovska; John Cort; Laurence Davin; Norman Lewis | Biological and Medicinal Chemistry; Analytical Chemistry; Analytical Chemistry - General; Mass Spectrometry; Plant Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61195e2e18911d3204e13f03/original/de-novo-sequencing-and-native-mass-spectrometry-reveals-hetero-association-of-dirigent-protein-homologs-and-potential-interacting-proteins-in-forsythia-intermedia.pdf |
60c75756469df458c5f45457 | 10.26434/chemrxiv.14394284.v1 | COVID-19: CRISPR/Cas-like System of nsp3 Promotes the Mutant Recombination and Drug Resistance | <p>Patients with novel coronavirus pneumonia usually suffer from bacterial and fungal infections, and the drug resistance problem caused by the pandemic is becoming more and more serious. Simultaneously, the SARS-COV-2 virus has a rapid mutation phenomenon, and somegene coding regions by mutation and recombination may be related to the drug resistance of the virus. Therefore, studying the relationship between the co-infection of bacteria and fungi and the evolution of SARS-COV-2 has important guiding significance for preventing a pandemic. We found that the SARS-COV-2 virus's nsp3 protein had a CRISPR/Cas 9 (II-B)-like function by searching for conserved domains. The system could target and edit the negative-strand RNA of SARS-COV-2. We speculated that the crRNA (CRISPR RNA) produced by the CRISPR/Cas system of Pseudomonas aeruginosa carried the genetic information of the conserved domains of bacteriophages and Pseudomonas, including drug resistance. After the phage lysed the Pseudomonas, the crRNA was released and attached to the fungal spores, and then invaded the patient's cells along with the spores or hyphae. nsp3 synthesized and assembled 4Fe-4S, iron-containing molecules bound to the cas4 domain, in the mitochondria of phagocytes. The iron came from hemoglobin attacked by the SARS-COV-2 virus protein. The nsp3 protein bound the crRNA in the phagocytic cytoplasm. It targeted the negative-strand RNA of SARS-COV-2, inserting conserved domain gene fragments into the negative-strand RNA through editing and splicing. Since the Cas protein had no codon checking function, the cutting and splicing would destroy the protein-coding information in the original RNA coding region, causing mutation and recombination of the SARS-COV-2 virus genome. If crRNA carried the drug resistance gene fragments of bacteria or phage, SARS-COV-2 would have similar drug resistance. Because of the growing problem of drug resistance in COVID-19 patients, we should pay attention to preventing fungi and bacteria co-infection. Avoid the CRISPR/Cas-like system of the novel coronavirus to cause rapid mutation and recombination and increased the drug resistance problem of SARS-COV-2.</p> | liu wenzhong; Li hualan | Bioinformatics and Computational Biology; Biophysics; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75756469df458c5f45457/original/covid-19-crispr-cas-like-system-of-nsp3-promotes-the-mutant-recombination-and-drug-resistance.pdf |
60c75923842e65f64edb49a4 | 10.26434/chemrxiv.14662932.v1 | Alumination of Aryl Methyl Ethers: Switching Between Sp2 and Sp3 C–O Bond Functionalisation with Pd-Catalysis | The reaction of [{(ArNCMe)2CH}Al] (Ar = 2,6-di-iso-propylphenyl, 1) with aryl methyl ethers proceeded with alumination of the sp3 C–O bond by a presumed SN2 pathway. The selectivity of this reaction could be switched by inclusion of a catalyst. In the presence of [Pd(PCy3)2], chemoselective sp2 C–O bond functionalisation was observed. Kinetic isotope experiments and DFT calculations support a catalytic pathway involving the ligand-assisted oxidative addition of the sp2 C–O bond to a Pd---Al intermetallic complex. The net result of both non-catalysed and catalytic pathways is the generation of polar organoaluminium complexes from aryl methyl ethers with complete atom-efficiency. Switches in selectivity yield isomeric products from a single starting material. The methodology (and mechanistic insight) holds promise as a means to functionalise aromatic molecules derived from lignin depolymerisation and we demonstrate an application to a derivative of vanillin. | Ryan Brown; Thomas N hooper; Feriel Rekroukh; Andrew J. P. White; Paulo J. Costa; Mark Crimmin | Organic Synthesis and Reactions; Organometallic Compounds; Transition Metal Complexes (Inorg.); Homogeneous Catalysis; Bond Activation; Catalysis; Kinetics and Mechanism - Organometallic Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75923842e65f64edb49a4/original/alumination-of-aryl-methyl-ethers-switching-between-sp2-and-sp3-c-o-bond-functionalisation-with-pd-catalysis.pdf |
646311fca32ceeff2db89f20 | 10.26434/chemrxiv-2023-v9l5v | Stereoselective Baeyer–Villiger oxidation of 3-substituted cyclobu-tanones promoted by flavinium-cinchona alkaloid ion-pair catalyst | The previously reported asymmetric Baeyer–Villiger (BV) oxidation of 3-substituted cyclobutanones promoted by a co-factor flavin derivative was revisited to broaden its scope. The correlation between the stereochemical outcome and the catalyst structure was examined, and only one stereocenter was found to be critical for achieving high stereoselectivity. This observa-tion led to the identification of a new, simpler catalyst with improved selectivity. By positioning a lone pair donor on the substrate, the selectivity was further enhanced to 95% ee using the original catalyst or >99% ee with the new catalyst, among the highest selectivities achieved for the BV reaction using a small-molecule catalyst. This observation supports our hypoth-esis that the H-bonding network is central to the catalyst. This study demonstrates the power of mechanistic investigation to broaden the scope of catalytic systems and aid in catalyst design. We are currently exploring methods to expand the applica-bility of this catalyst and demonstrate its use. | Junya Fujimoto; Eika Surga; Kana Yamamoto | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/646311fca32ceeff2db89f20/original/stereoselective-baeyer-villiger-oxidation-of-3-substituted-cyclobu-tanones-promoted-by-flavinium-cinchona-alkaloid-ion-pair-catalyst.pdf |
60c752f7ee301c1dedc7acd6 | 10.26434/chemrxiv.13370414.v1 | Anisotropic Band-Edge Absorption of Millimeter-Size Zn(3-Ptz)2 Single Crystal Metal-Organic Frameworks | <div><div><div><p>Metal-organic frameworks (MOF) have emerged as promising tailor-design materials for developing next-generation solid-state devices with applications in linear and non-linear coherent optics. However, the implementation of functional devices is challenged by the notoriously difficult process of growing large MOF single-crystals of high optical quality. By controlling the solvo-thermal synthesis conditions, we succeed in producing large individual single crystals of the non-centrosymmetric MOF Zn(3-ptz)2 (MIRO-101) with deformed octahedron habit, and unprecedented surface areas of up to 37 mm<sup>2</sup>. We measure the polarized UV-visible absorption spectrum of individual Zn(3- ptz)2 single crystals across different lateral incidence planes. Millimeter size single crystals have band gap <i>E</i><i>g</i> = 3.32 eV, and exhibit anisotropic absorption in the band edge region near 350 nm, whereas polycrystalline samples are fully transparent in the same frequency range. Using solid-state density functional theory (DFT), the observed size dependence of the optical anisotropy is correlated with the preferred orientation adopted by freely rotating pyridyl groups under conditions of slow crystal self-assembly. Our work thus paves the way for the development of optical polarization switches based on metal-organic frameworks.</p></div></div></div> | Ignacio Chi-Duran; Ruben Fritz; Vanessa Olaya; Rodrigo Urzua-Leiva; Gloria I. Cárdenas-Jirón; Dinesh Pratap Singh; Felipe Herrera | Optical Materials; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752f7ee301c1dedc7acd6/original/anisotropic-band-edge-absorption-of-millimeter-size-zn-3-ptz-2-single-crystal-metal-organic-frameworks.pdf |
60c74951469df435a1f43baa | 10.26434/chemrxiv.12052443.v1 | Impact of Binding to the Multidrug Resistant Regulator Protein LmrR on the Photo-Physics and -Chemistry of Photosensitizers | Light activated photosensitizers generate reactive oxygen species (ROS) that interfere with cellular components and can induce cell death, e.g., in photodynamic therapy (PDT). The effect of cellular components and especially proteins on the photochemistry and photophysics of the sensitizers is a key aspect in drug design and the correlating cellular response with the generation of specific ROS species. Here, we show the complex range of effects of binding of photosensitizer to a multidrug resistance protein, produced by bacteria, on the formers reactivity. We show that recruitment of drug like molecules by LmrR (Lactococcal multidrug resistance Regulator) modifies their photophysical properties and their capacity to induce oxidative stress especially in 1O2 generation, including rose bengal (RB), protoporphyrin IX (PpIX), bodipy, eosin Y (EY), riboflavin (RBF), and rhodamine (Rh6G). The range of neutral and charged dyes with different exited redox potentials, are broadly representative of the dyes used in PDT. | Sara H Mejías; Gerard Roelfes; wesley browne | Spectroscopy (Anal. Chem.); Chemical Biology; Photochemistry (Physical Chem.); Physical and Chemical Processes; Physical and Chemical Properties; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74951469df435a1f43baa/original/impact-of-binding-to-the-multidrug-resistant-regulator-protein-lmr-r-on-the-photo-physics-and-chemistry-of-photosensitizers.pdf |
60c73fd2bdbb898261a38084 | 10.26434/chemrxiv.7496102.v1 | Simulating Water Exchange to Buried Binding Sites | Traditional molecular dynamics (MD) simulations of proteins, which rely on integration of Newton’s equations of motion, cannot efficiently equilibrate water occupancy for buried cavities in proteins. This leads to slow convergence of thermodynamic averages for such systems. We have addressed this challenge by efficiently integrating standard Metropolis Monte Carlo (MC) translational water moves with MD in the AMBER simulation package. The translational moves allow water to easily enter or exit buried sites in a thermodynamically correct way during a simulation. To maximize efficiency, the algorithm avoids moves that only interchange waters within the bulk around the protein, instead focusing on moves that can transfer water between bulk and the protein interior. In addition, a steric grid allows avoidance of moves that would lead to obvious steric clashes, and a fast grid-based energy evaluation is used to reduce the number of expensive full energy calculations. The potential energy distribution produced using MC/MD was found to be statistically indistinguishable from that of control simulations using only MD, and the algorithm effectively equilibrated water across steric barriers and into binding pockets that are not accessible with pure MD. The MC/MD method introduced here should be of increasing utility for applications spanning protein folding, the elucidation of protein mechanisms, and free energy calculations for computer-aided drug design. It is available in version 18 release of the widely disseminated AMBER simulation package. | Ido Ben-Shalom; charles Lin; Tom Kurtzman; ross walker; Michael Gilson | Biophysics; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fd2bdbb898261a38084/original/simulating-water-exchange-to-buried-binding-sites.pdf |
60c7544c337d6c4f5ae28a00 | 10.26434/chemrxiv.13643693.v1 | On-Demand Electrochemical Synthesis of copper(I) Triflate and Its Application in the Aerobic Oxidation of Alcohols | <p>An on-demand electrochemical
synthesis of copper(I) triflate under both batch and continuous flow conditions
has been developed. A major benefit of the electrochemical methodology is that
the only by-product of the reaction is hydrogen gas which obviates the need for
work-up and purification, and water is not incorporated into the product. Upon
completion of the electrochemical synthesis, solutions are directly transferred
or dispensed into reaction mixtures for the catalytic oxidation of alcohols
with no requirement for work-up or purification. </p> | Thomas P. Nicholls; Richard A. Bourne; Bao N. Nguyen; Nikil Kapur; Charlotte Willans | Electrochemistry; Ligands (Inorg.); Transition Metal Complexes (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7544c337d6c4f5ae28a00/original/on-demand-electrochemical-synthesis-of-copper-i-triflate-and-its-application-in-the-aerobic-oxidation-of-alcohols.pdf |
60c74653ee301ccd68c794e8 | 10.26434/chemrxiv.9943961.v2 | Defect-Mediated Conductivity Enhancements in Na3-xPn1-xWxS4 (Pn = P, Sb) using Aliovalent Substitutions | <p>The sodium-ion conducting family of Na<sub>3</sub><i>Pn</i>S<sub>4</sub>, with <i>Pn</i> = P, Sb, have gained interest for the use in solid-state batteries due to their high ionic conductivity. However, significant improvements to the conductivity have been hampered by the lack of aliovalent dopants that can introduce vacancies into the structure. Inspired by the need for vacancy introduction into Na<sub>3</sub><i>Pn</i>S<sub>4</sub>, the solid solutions with WS<sub>4</sub><sup>2-</sup> introduction are explored. The influence of the substitution with WS<sub>4</sub><sup>2-</sup> for PS<sub>4</sub><sup>3-</sup> and SbS<sub>4</sub><sup>3-</sup>, respectively, is monitored using a combination of X-ray diffraction, Raman and impedance spectroscopy. With increasing vacancy concentration improvements resulting in a very high ionic conductivity of 13 ± 3 mS·cm<sup>-1</sup> for Na<sub>2.9</sub>P<sub>0.9</sub>W<sub>0.1</sub>S<sub>4</sub> and 41 ± 8 mS·cm<sup>-1</sup> for Na<sub>2.9</sub>Sb<sub>0.9</sub>W<sub>0.1</sub>S<sub>4</sub> can be observed. This work acts as a stepping-stone towards further engineering of ionic conductors using vacancy-injection via aliovalent substituents.</p> | Till Fuchs; Sean Culver; Paul Till; Wolfgang Zeier | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74653ee301ccd68c794e8/original/defect-mediated-conductivity-enhancements-in-na3-x-pn1-x-wx-s4-pn-p-sb-using-aliovalent-substitutions.pdf |
67a2fb1881d2151a0238c1ab | 10.26434/chemrxiv-2025-sz3pn | Efficient Automated Workflow for Radical Reaction Networks in Environmental Disinfectants: A Peroxyacetic Acid Case Study with Machine Learning Interatomic Potentials | Peroxy-type disinfectants initiate chain reactions upon activation, but the underlying mechanisms of organic radical formation remain difficult to fully elucidate. In this study, we combine Density Functional Theory (DFT) with machine learning-based interatomic potentials to automate the construction of the reaction network for peroxyacetic acid (PAA). Using double-hybrid functionals, wavefunction analysis, we reveal that peroxide bond cleavage is primarily driven by an electronic excitation from the HOMO to the LUMO+1 orbital, resulting in bond dissociation. A pretrained machine learning model, refined through active learning, efficiently captures reaction pathways in molecular dynamics simulations. Conventional gas-phase calculations often neglect solvent effects and environmental factors, such as explicit solvation and dissolved oxygen, both of which are essential for accurately predicting chemical reactivity. Notably, O₂ facilitates the formation of CH₃OO·, which in turn produces CH₂O and ·OH radicals, further propagating the radical network. N₂/O₂ aeration experiments further highlight the crucial role of oxygen in driving reactivity, consistent with our computational predictions. The integrated approach of this study can readily be extended to issues of reaction mechanisms under microscopic media in environmental systems. Accordingly, we provide a research framework and have developed accompanying software for use. | Fulin Shao; Weiying Li | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a2fb1881d2151a0238c1ab/original/efficient-automated-workflow-for-radical-reaction-networks-in-environmental-disinfectants-a-peroxyacetic-acid-case-study-with-machine-learning-interatomic-potentials.pdf |
60c74d25567dfe7184ec52d5 | 10.26434/chemrxiv.12591629.v1 | t1-Noise Eliminated Dipolar Heteronuclear Multiple-Quantum Coherence Solid-State NMR Spectroscopy | <p>Heteronuclear correlation (HETCOR) spectroscopy is one of the key tools in the arsenal of the solid-state NMR spectroscopist to probe spatial proximity between two different nuclei and enhance spectral resolution. Dipolar heteronuclear multiple-quantum coherence (D-HMQC) is a powerful technique that can be potentially utilized to obtain <sup>1</sup>H detected 2D HETCOR solid-state NMR spectra of any NMR active nucleus. A long-standing problem in <sup>1</sup>H detected D-HMQC solid-state NMR experiments is the presence of <i>t</i><sub>1</sub>-noise which reduces sensitivity and impedes spectral interpretation. In this contribution, we describe novel pulse sequences, termed <i>t</i><sub>1</sub>-noise eliminated (TONE) D-HMQC, that suppress <i>t</i><sub>1</sub>-noise and can provide higher sensitivity and resolution than conventional D-HMQC. Monte-Carlo and numerical simulations confirm that <i>t</i><sub>1</sub>-noise in conventional D-HMQC primarily occurs because random MAS frequency fluctuations cause variations in the NMR signal amplitude from scan to scan, leading to imperfect cancellation of uncorrelated signals by phase cycling. The TONE D-HMQC sequence uses <sup>1</sup>H p-pulses to refocus the evolution of <sup>1</sup>H CSA across each recoupling block, improving the stability of the pulse sequence to random MAS frequency fluctuations. The <sup>1</sup>H refocusing pulses also restore the orthogonality of in-phase and anti-phase magnetization for all crystallite orientations, enabling the use of 90° flip-back or LG spin-lock trim pulses to reduce the intensity of uncorrelated signals. We demonstrate the application of these methods to acquire detected 2D <sup>1</sup>H-<sup>35</sup>Cl and <sup>1</sup>H-<sup>13</sup>C HETCOR spectra of histidine•HCl•H<sub>2</sub>O with reduced <i>t</i><sub>1</sub>-noise. To show generality, we also apply these methods to obtain 2D <sup>1</sup>H-<sup>17</sup>O spectra of 20%-<sup>17</sup>O fmoc-alanine and for the first time at natural abundance, 2D <sup>1</sup>H-<sup>25</sup>Mg HETCOR spectra of magnesium hydroxide. The TONE D-HMQC sequences are also used to probe <sup>1</sup>H-<sup>25</sup>Mg and <sup>1</sup>H-<sup>27</sup>Al proximities in Mg-Al layered double hydroxides and confirm the even mixing of Mg and Al in these materials.</p> | Amrit Venkatesh; Xuechen Luan; Frédéric Perras; Ivan Hung; Wenyu Huang; Aaron Rossini | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d25567dfe7184ec52d5/original/t1-noise-eliminated-dipolar-heteronuclear-multiple-quantum-coherence-solid-state-nmr-spectroscopy.pdf |
64d660394a3f7d0c0d01f530 | 10.26434/chemrxiv-2023-9f7qq | Conjugated Polymer Process Ontology and Experimental Data Repository for Organic Field-Effect Transistors | Polymer-based semiconductors and organic electronics encapsulate a significant research thrust for informatics-driven materials development. However, device measurements are described by a complex array of design and parameter choices, many of which are sparsely reported. For example, the mobility of a polymer-based organic field-effect transistor (OFET) may vary by several orders of magnitude for a given polymer, as a plethora of parameters related to solution processing, interface design/surface treatment, thin-film deposition, post-processing, and measurement settings have a profound effect on the value of the final measurement. Incomplete contextual, experimental details hamper the availability of reusable data applicable for data-driven optimization, modeling (e.g., machine learning), and analysis of new organic devices. To curate organic device databases that contain reproducible and Findable, Accessible, Interoperable, and Reusable (FAIR) experimental data records, data ontologies that fully describe sample provenance and process history are required. However, standards for generating such process ontologies are not widely adopted for experimental materials domains. In this work, we design and implement an object-relational database for storing experimental records of OFETs. A data structure is generated by drawing on an international standard for batch process control (ISA-88) to facilitate the design. We then mobilize these representative data records, curated from literature and laboratory experiments, to enable data-driven learning of process-structure-property relationships. The work presented herein opens the door for the broader adoption of data management practices and design standards for both the organic electronics and the wider materials community. | Aaron Liu; Myeongyeon Lee; Rahul Venkatesh; Jessica Bonsu; Ron Volkovinsky; Carson Meredith; Elsa Reichmanis; Martha Grover | Polymer Science; Conducting polymers | CC BY 4.0 | CHEMRXIV | 2023-08-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64d660394a3f7d0c0d01f530/original/conjugated-polymer-process-ontology-and-experimental-data-repository-for-organic-field-effect-transistors.pdf |
64186d92dab08ad68f69feb0 | 10.26434/chemrxiv-2023-8l8nw | Potential energy surface of Li–O2 system for cold collisions | This paper explores the interactions between Li and oxygen in their van der Waals state for the study of cold collisions between these two species. The quartet surface was calculated using a basis set converged spin-restricted CCSD(T) method, while for the doublet state, we obtained energy splitting with respect to high-spin using both CASSCF and MRCI approaches. Our findings suggest that the interaction in the quartet state of Li–O2 is weak, with a shallow and nearly isotropic well depth of 37.5 cm−1. The shallow potential well and small reduced mass of the system allow us to predict the scattering length for all possible combinations of 6Li and 7Li with 16O2 and 17O2. This result could be useful for understanding the collision dynamics of Li-O2 in ultra-cold regime. | Piotr Zuchowski; Katarzyna Madajczyk | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64186d92dab08ad68f69feb0/original/potential-energy-surface-of-li-o2-system-for-cold-collisions.pdf |
60c73cc0ee301c3e84c7848f | 10.26434/chemrxiv.14739348.v1 | Simplified Colloidal Method to Produce Nanostructured Au-Ag Films with Superconductivity in the Ambient | This article presents a detailed synthetic strategy to enable preparation of Au-Ag structures with optical and electrical anomalies | Subham Kumar Saha; Rekha Mahadevu; Pritha Mondal; Anand Sharma; Navyashree Vasudeva; Anshu Pandey | Nanostructured Materials - Nanoscience; Plasmonic and Photonic Structures and Devices | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc0ee301c3e84c7848f/original/simplified-colloidal-method-to-produce-nanostructured-au-ag-films-with-superconductivity-in-the-ambient.pdf |
60c751049abda2a3cff8db24 | 10.26434/chemrxiv.13108382.v1 | Enantioselective Coupling of Nitroesters and Alkynes | <div><div><div><p>By using Rh-H catalysis, we couple α-nitroesters and alkynes to prepare α-amino acid surrogates. This atom-economical strategy generates two contiguous stereocenters, with high enantio- and diastereocontrol. In this transformation, the alkyne undergoes isomerization to generate a Rh(III)-π-allyl electrophile, which is trapped by an α-nitroester nucleophile. A subsequent reduction with In powder transforms the allylic α-nitroesters to the corresponding α,α- disubstituted α-amino esters.</p></div></div></div> | Ryan Davison; Patrick Parker; Xintong Hou; Crystal Chung; Sara Augustine; Vy M. Dong | Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751049abda2a3cff8db24/original/enantioselective-coupling-of-nitroesters-and-alkynes.pdf |
62cfa0a77aab582954bd100d | 10.26434/chemrxiv-2022-5l430 | In-depth analysis on photocatalysts related research trends about polyoxometalate-based materials: A bibliometric study | In recent years, polyoxometalate-based materials have attracted wide attention in heterogeneous photocatalysis due to their various structure types and controllable redox properties. In this review, 1382 scientific publications related to polyoxometalate-based photocatalysts in the Web of Science database were investigated by a bibliometric method. The number of annual publications, journals, countries, institutions, authors, research hotspots, and references were analyzed. Through VOSviewer and CiteSpace software, the average publication time and citation frequency networks of journals, the cooperation network of different countries and institutions, the co-occurrence network of keywords, and the co-citation network of references were clustered and visualized to examine their contributions to related fields. The results could show the evolution of research hotspots in the past decades and provide reference and inspiration for researchers in polyoxometalate-based photocatalysis. | Rongqing Tang; Jianhui Zhou; Nan Zhang | Inorganic Chemistry; Catalysis; Nuclear Chemistry; Photocatalysis; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2022-07-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cfa0a77aab582954bd100d/original/in-depth-analysis-on-photocatalysts-related-research-trends-about-polyoxometalate-based-materials-a-bibliometric-study.pdf |
6189d4579b583a6e02f0fd17 | 10.26434/chemrxiv-2021-fk5c0-v2 | Synthesis of (±)-Emtricitabine and (±)-Lamivudine by Chlorotrimethylsilane-Sodium Iodide Promoted Vorbrüggen Glycosylation | By simply adding water and sodium iodide (NaI) to chlorotrimethylsilane (TMSCl), promotion of a Vorbrüggen glycosylation en route to essential HIV drugs emtricitabine (FTC) and lamivudine (3TC) is achieved. TMSCl-NaI in wet solvent (0.1 M water) activates a 1,3-oxathiolanyl acetate donor for N-glycosylation of silylated cytosine derivatives, leading to cis ox-athiolane products with up to 95% yield and >20:1 dr. This telescoped sequence is followed by recrystallization and borohydride reduction, resulting in rapid synthesis of (±)-FTC/3TC from an achiral tartrate ester. | Sarah Jane Mear; Long V. Nguyen; Ashley J. Rochford; Timothy F. Jamison | Organic Chemistry; Organic Synthesis and Reactions; Process Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6189d4579b583a6e02f0fd17/original/synthesis-of-emtricitabine-and-lamivudine-by-chlorotrimethylsilane-sodium-iodide-promoted-vorbruggen-glycosylation.pdf |
61131e9345805d2c5984f8c9 | 10.26434/chemrxiv-2021-fdd2c | Studies on the Synthesis of Perfluoroaryl Sulfides and their Application in Desulfurative Nickel-Catalyzed Reductive Cross-Coupling | The C−S activation and sulfur removal from native thiols is challenging and limits the application of thiols as typical feedstock materials in organic synthesis despite their natural abundance. Herein, we describe a simple procedure to introduce a per-/polyfluoroaryl moiety, which serves as a redox-active scaffold, into alkyl/aryl thiols using nucleophilic aromatic substitution (SNAr) chemistry to activate the C−S bond. The per-/polyfluoroaryl group acts as an electron acceptor in single electron transfer events to generate radical intermediates through cleavage of the C−S bond of mercaptans and utilize them in nickel-catalyzed reductive cross-coupling reactions. In addition, using computational methods, we shed light on the mechanism of this class of SNAr reaction and show that the preference for a concerted or stepwise mechanistic pathway can be easily rationalized through a Marcus-type argument, as well as consideration of the relative stability of the potential energy surfaces. | Shao-Chi Lee; Che-Ming Hsu; Hsin Kao; Li-Yun Li; Zong-Nan Tsai; Yong-Ting Tsao; Yu-Ling Hsu; Shinje Miñoza; Cheng-chau Chiu; Hsuan-Hung Liao | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61131e9345805d2c5984f8c9/original/studies-on-the-synthesis-of-perfluoroaryl-sulfides-and-their-application-in-desulfurative-nickel-catalyzed-reductive-cross-coupling.pdf |
66c67032a4e53c48762fb9e3 | 10.26434/chemrxiv-2024-h4flq | Multi-scale Measurements of Greenhouse Gas Emissions at U.S. Natural Gas Liquefaction Terminals | Addressing methane emissions across the liquefied natural gas (LNG) supply chain is key to reducing climate impacts of LNG. Actions to address methane emissions have emphasized the importance of the use of measurement-informed emissions inventories, given the systematic underestimation in official GHG emission inventories. Despite significant progress in field measurements of GHG emissions across the natural gas supply chain, no detailed measurements at US liquefaction terminals are publicly available. In this work, we conduct multiscale, periodic measurements of methane and carbon dioxide emissions at two US LNG terminals over a 16-month campaign. We find that methane emissions intensity varied from 0.007% to 0.045%, normalized to LNG production. Carbon dioxide emissions accounted for over 95% of total GHG emissions using 100-year global warming potential for methane. Thus, contrary to observations across other natural gas supply chain segments, we find that reported GHG emissions intensity closely matches measurement informed GHG emissions intensity of 0.24 – 0.27 kg CO2e/kg CH4. In the context of developing LNG supply chain emissions intensity, we conclude that the use of Greenhouse Gas Reporting Program emissions intensity provides reasonably accurate estimates of total GHG emissions at LNG terminals. | Yuanrui Zhu; Greg Ross; Olga Khaliukova; Selina Roman-White; Fiji George; Dorit Hammerling; Arvind Ravikumar | Energy; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c67032a4e53c48762fb9e3/original/multi-scale-measurements-of-greenhouse-gas-emissions-at-u-s-natural-gas-liquefaction-terminals.pdf |
63691760bef5d4a65f49d220 | 10.26434/chemrxiv-2022-9b47d | Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes | Cyclic peptides are able to extend the druggable space of pharmaceutical targets, due to their size, conformational behavior, and high proportion of hydrogen bond donors and acceptors. However, for the same reasons, they often suffer from poor membrane permeation and thus low oral bioavailability. As permeability assays do not allow to monitor the pathway and behavior of cyclic peptides on their “journey” trough lipid membranes, little is known about the underlying permeation process, which poses a major obstacle for their rational design. Here, we use molecular dynamics (MD) simulations as a computational microscope to uncover how large and conformationally flexible cyclic peptides enter and cross a lipid bilayer. In a first step, we performed unbiased MD simulations to elucidate the permeation pathway. Subsequently, this pathway knowledge was utilized to seed biased simulations to further enrich for permeation events. Based on our simulations, we show how specific side-chain residues can act as ’molecular anchors’, which establish the first contact between the peptides and the membrane, and consequently enable membrane insertion. Inside the membrane, the cyclic peptides are positioned directly between the polar headgroup and the apolar tail region, where they are subjected to a unique polar/apolar interface environment. In this environment, the cyclic peptides show a preference for one of two distinct orientations. We observe that only one of these orientations allows the formation of the permeable ’closed’ conformation, and only in this ’closed’ conformation the cyclic peptides can cross from the upper to the lower membrane leaflet, which again requires a unique anchoring and flipping mechanism. Our findings provide atomistic insights into the permeation process of flexible cyclic peptides and reveal unique design considerations for each step of the process. | Stephanie M. Linker; Christian Schellhaas; Anna S. Kamenik; Hans-Joerg Roth; Marianne Fouche; Stephane Rodde; Sereina Riniker | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC 4.0 | CHEMRXIV | 2022-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63691760bef5d4a65f49d220/original/lessons-for-oral-bioavailability-how-conformationally-flexible-cyclic-peptides-enter-and-cross-lipid-membranes.pdf |
60c74f7bbb8c1a11d43db942 | 10.26434/chemrxiv.12909593.v1 | Broad and Comprehensive Approach to Evaluate Infrared Intensities at Atomic Level: The AC/DC Analysis | <div>We present a complete theoretical protocol to split infrared intensity in terms owing to individual atoms in two different but related approaches: the Atomic Contributions (AC's) how how the entire molecule motion is noticed by the electronic structure of a single atom, and therefore reflected on the intensity. On the other hand, the Dynamic Contributions (DC's) show how the displacement of a single atom is noticed by the electronic structure of the entire molecule, and reflected on the IR intensity. The two analyses are complementary ways of partitioning the same total intensity, and conserve most of the features of the total intensity itself. Combined they are called the AC/DC analysis. These can be further partitioned following the CCTDP (or CCT) models regarding the population analysis chosen by the researcher. The main conceptual features of the equations are highlighted and representative numerical results are shown to support the interpretation of the equations. The results are invariant to rotation and translation and can readily be extended to molecules of any size, shape or symmetry. A fully automated protocol managed by Placzek program is made available, free of charge.</div> | Wagner Richter; Leonardo Duarte; Luciano N. Vidal; Roy E. Bruns | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f7bbb8c1a11d43db942/original/broad-and-comprehensive-approach-to-evaluate-infrared-intensities-at-atomic-level-the-ac-dc-analysis.pdf |
60c74933337d6c089ce276af | 10.26434/chemrxiv.12040173.v1 | Virtual Reality Educational Tool for Connecting Chemistry Lecture with Remote Laboratory Demonstrations | <p>Providing access to up-to-date and expensive instruments
for a large classroom is challenging for courses of analytical chemistry and
physical chemistry, where knowledge on analytical methods or demonstration of
phenomena is associated with a specialized instrument. In this technology
report, we present our solution to this challenge: a virtual reality (VR)
chemical educational tool that provides <i>in
situ</i> user experience on research equipment to a large classroom. The VR
educational tool consists of a VR camera in the laboratory attached to a
teaching assistant who performs the experiment and many virtual reality playing
devices in a classroom watched by students. The experience of experimenting is shared
with the students in the classroom. Moreover, the VR educational tool can also
provide an immersive experience on laboratory demonstrations to the general
audience for outreach, without the constraint from safety concerns. Further
utilization of the VR educational tool is expected to remove the barrier
between the lecture room and the laboratory and enable new pedagogical methods
for lectures in STEM education.</p> | Yuming Tian; Haoluo Fu; Jiawei Liu; Le Wang; Xiaoji Xu | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74933337d6c089ce276af/original/virtual-reality-educational-tool-for-connecting-chemistry-lecture-with-remote-laboratory-demonstrations.pdf |
60c74a71f96a0016cb287417 | 10.26434/chemrxiv.12204668.v1 | Possibility of HIV-1 Protease Inhibitors-Clinical Trial Drugs as Repurposed Drugs for SARSCoV-2 Main Protease: A Molecular Docking, Molecular Dynamics and Binding Free Energy Simulation Study | <p>Initially,
the SARS-CoV-2 virus was emerged from Wuhan, China and rapidly spreading across
the world and urges the scientific community to develop antiviral therapeutic
agents. Among several strategies, drug repurposing will help to react
immediately to overcome COVID-19 pandemic. In the present study, we have chosen
two clinical trial drugs TMB607 and TMC310911 are the inhibitors of HIV-1
protease to use as the inhibitors of SARS-CoV-2 main protease (M<sup>pro</sup>)
enzyme. To make use of these two inhibitors as the repurposed drugs for
COVID-19, it is essential to know the molecular basis of binding mechanism of
these two molecules with the SARS-CoV-2 main protease (M<sup>pro</sup>).
Understand the binding mechanism; we performed the molecular docking, molecular
dynamics (MD) simulations and binding free energy calculations against the
SARS-CoV-2 M<sup>pro</sup>. The docking results indicate that both molecules
form intermolecular interactions with the active site amino acids of M<sup>pro</sup>
enzyme. However, during the MD simulations, TMB607 forms strong interactions
with the key amino acids of M<sup>pro</sup> and remains intact. The RMSD and
RMSF values of both complexes were stable throughout the MD simulations. The
MM-GBSA binding free energy values of both complexes are -43.7 and -34.9
kcal/mol, respectively. This <i>in silico</i>
study proves that the TMB607 molecule binds strongly with the SARS-CoV-2 M<sup>pro</sup>
enzyme and it is suitable for the drug repurposing of COVID-19 and further drug
designing.</p> | Ancy Iruthayaraj; Sivanandam Magudeeswaran; Kumaradhas Poomani | Bioinformatics and Computational Biology; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a71f96a0016cb287417/original/possibility-of-hiv-1-protease-inhibitors-clinical-trial-drugs-as-repurposed-drugs-for-sars-co-v-2-main-protease-a-molecular-docking-molecular-dynamics-and-binding-free-energy-simulation-study.pdf |
6500228ab6ab98a41c4ec87f | 10.26434/chemrxiv-2023-dj2wg | Non-classical crystallization pathway of transition metal phosphate compounds | Here, we elucidate non-classical multistep crystallization pathways of transition metal phosphates from aqueous solutions. We followed precipitation processes of M-struvites, NH4MPO4∙6H2O, and M-phosphate octahydrates, M3(PO4)2∙8H2O, where M = Ni, Co, NixCo1-x by using in-situ scattering and spectroscopy-based techniques, supported by elemental mass spectrometry analyses and advanced electron microscopy. Ni- and Co-phosphates crystallize via intermediate colloidal amorphous nanophases which subsequently change their complex structures while agglomerating, condensing, and densifying throughout the extended reaction times. We reconstructed the three-dimensional morphology of these precursors by employing cryo-electron tomography (cryo-ET). We found that the complex interplay between metastable amorphous colloids and proto-crystalline units determines the reaction pathways. Ultimately, the same crystalline structure, such as struvite, is formed. However, the multistep process stages vary in complexity and can last from a few minutes to several hours depending on the selected transition metal(s), their concentration, and the Ni:Co ratio. | Stephanos Karafiludis; Zdravko Kochovski; Ernesto Scoppola; Anika Retzmann; Vasile-Dan Hodoroaba; Johan ten Elshof; Franziska Emmerling; Tomasz Stawski | Physical Chemistry; Inorganic Chemistry; Kinetics and Mechanism - Inorganic Reactions; Minerals; Physical and Chemical Processes; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6500228ab6ab98a41c4ec87f/original/non-classical-crystallization-pathway-of-transition-metal-phosphate-compounds.pdf |
60c75919842e6599a7db4990 | 10.26434/chemrxiv.14639007.v1 | Molecular Transformer-aided Biocatalysed Synthesis Planning | Enzyme catalysts are an integral part of green chemistry strategies towards a more sustainable and resource-efficient chemical synthesis. However, the use of enzymes on unreported substrates and their specific stereo- and regioselectivity are domain-specific knowledge factors that require decades of field experience to master. This makes the retrosynthesis of given targets with biocatalysed reactions a significant challenge. Here, we use the molecular transformer architecture to capture the latent knowledge about enzymatic activity from a large data set of publicly available biochemical reactions, extending forward reaction and retrosynthetic pathway prediction to the domain of biocatalysis. We introduce the use of a class token based on the EC classification scheme that allows to capture catalysis patterns among different enzymes belonging to the same hierarchical families. The forward prediction model achieves an accuracy of 49.6% and 62.7%, top-1 and top-5 respectively, while the single-step retrosynthetic model shows a round-trip accuracy of 39.6% and 42.6%, top-1 and top-10 respectively. Trained models and curated data are made publicly available with the hope of promoting enzymatic catalysis and making green chemistry more accessible through the use of digital technologies. | Daniel Probst; Matteo Manica; Yves Gaëtan Nana Teukam; Alessandro Castrogiovanni; Federico Paratore; Teodoro Laino | Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75919842e6599a7db4990/original/molecular-transformer-aided-biocatalysed-synthesis-planning.pdf |
616116c5a3d2c9866bd0addb | 10.26434/chemrxiv-2021-srdt7 | Experimental and DFT Studies on Cp*Co(III)-Catalyzed Selective C8-Olefination and Oxyarylation of Quinoline N-Oxides with Terminal Alkynes | Herein we report Cp*Co(III)-catalysed site-selective (C8)-H olefination and oxyarylation of quinoline N-oxides with terminal alkynes. The selectivity for C8-olefination and oxyarylation is sterically and electronically controlled. In case of quinoline N-oxides (unsubstituted at C2-position), only olefination product is obtained irrespective of the nature of alkynes. In contrast, majorly oxyarylation is observed when 2-substituted quinoline N-oxides are reacted with bulkier alkynes such as 9-ethynyl phenanthrene. However, alkynes with electron-withdrawing groups provided only olefination products with 2-substituted quinoline N-oxides also. The developed strategy allowed a facile functionalization of naturally derived quinoline N-oxides and terminal alkynes to deliver corresponding olefinated and oxyarylated products. In the developed protocol, the 'N-O’ bond played a dual role i.e., as a traceless directing group and an oxygen atom source (in case of oxyarylation), which is confirmed by 18O-labeling and crossover experiments. In addition, control experiments, deuterium labeling experiments, KIE studies and DFT studies are performed to understand the mechanism and origin of selectivity for different substrates. DFT studies revealed that the alkyne addition into Co-C bond is the rate limiting step. The observed product selectivity is reproduced by DFT methods. Furthermore, the energy decomposition analysis is performed to understand the origin of selec-tivity. | Upendra Sharma; Diksha Parmar; Ankit Kumar Dhiman; Rohit Kumar; Akhhilesh K Sharma | Organic Chemistry; Catalysis; Natural Products; Organic Compounds and Functional Groups; Redox Catalysis | CC BY NC 4.0 | CHEMRXIV | 2021-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/616116c5a3d2c9866bd0addb/original/experimental-and-dft-studies-on-cp-co-iii-catalyzed-selective-c8-olefination-and-oxyarylation-of-quinoline-n-oxides-with-terminal-alkynes.pdf |
60c758bf4c891967f1ad4c4c | 10.26434/chemrxiv.14593740.v1 | Exchange Functionals and Basis Set Comparisons for Theoretical Studies of ZnO Nonoclusters | Catalysts made of nano-scaled metal oxide clusters can push the
limits of chemical reactions in the manufacture of paints, cosmetics,
and pharmaceuticals. The ZnO clusters can also act as semiconductors with a wide band gap of 3.4 eV at 300 K, and are prospective phoocatalysts in many reactions including H2 production in water splitting reactions. In this project, we studied the structural (geometry)
and electronic properties (vertical detachment energy and electron
affinity) of ZnO monomers and dimers that form model ZnO clusters,
using density functional theory (DFT) with many different exchange
functionals and 29 basis sets to optimize their choice. We compared
the singlet-triplet energy gaps of small ZnO clusters to find the optimal ZnO cluster size and the best theoretical method to investigate
their photocatalytic water splitting activity. Our results show that B3LYP/DGDZVP2 level of exchange functional/basis set theory is the most efficient and fastest of the ones
considered. Comparison of the singlet-triplet energy gaps shows
that the trimer (ZnO)3, with an energy gap of 58.66 k cal/mol, is approximately equal to the energy of a visible photon at 555 nm and
a HOMO-LUMO gap of 4.4 eV, and is the best choice amongst the
(ZnO)n clusters of different sizes when the number of monomers n
in the clusters ranges from 1 to 6. We used the Gaussian16 software
package for all the calculations. | Duwage Perera; jayendran Rasaiah | Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758bf4c891967f1ad4c4c/original/exchange-functionals-and-basis-set-comparisons-for-theoretical-studies-of-zn-o-nonoclusters.pdf |
60c75338567dfe662cec5dfc | 10.26434/chemrxiv.13395383.v1 | Structural Revisions of Diterpenoid Alkaloids | Twelve diterpenoid alkaloids aconicarmichosides
A–L (<b>1</b>–<b>12</b>) reported in the journals <i>Chinese
Chemical Letters</i> (<b>2017</b>, <i>28</i>, 1705–1710) and <i>Acta Pharmaceutica Sinica B </i>(<b>2018</b>,
<i>8</i>, 409–419) have been revised as
their corresponding trifluoroacetates (<b>1a</b>–<b>12a</b>) based on the known literature as
well as careful analysis. | Feng-Peng Wang | Natural Products | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75338567dfe662cec5dfc/original/structural-revisions-of-diterpenoid-alkaloids.pdf |
66d889fe51558a15ef0a2b76 | 10.26434/chemrxiv-2024-3dttc | Fenton-Enhanced zero-valent iron powder oxidation: Investigating transformation products of antimicrobials and its removal | The occurrence of pharmaceuticals and pesticides in water is of concern due to their hazardous effect on the environment. Such micropollutants deteriorate environmental quality and can induce antimicrobial resistance in pathogenic bacteria. Thus, removal of these emerging contaminants is a necessity and thus requires a clear understanding of the effective treatment and mechanistic approach utilized in degradation and removal. Frequently, treatment systems are optimized for the removal of contaminants while the formation of transformation products and their removal are not targeted. We utilized our established iron powder catalyzed Fe (0) Fenton Oxidation treatment to study the degradation of emerging contaminants — sulfamethoxazole, gabapentin, diuron, and triazine class pesticides. We used state-of-the-art mass spectrometry to establish the common oxidative mechanistic approach after identifying the transformation products formed during the Fe (0) Fenton Oxidation processes. Fenton transformed product was produced after 60 min reaction time when treatment was initiated after adding the optimized H2O2 and iron powder Fe (0)) in a micropollutant solution adjusted to pH 5. About 5-to-7 transformed products of each micropollutant were identified and predicted to have low toxicity risk to aquatic organisms. The oxidative degradation pathway of micropollutants illustrates the shared oxidative mechanism where the aliphatic chain of the heteroatom: Sulphur (R—S—R as thiosulphate), functional groups (R—C=O, R—COOR, R—NH2, R— NH=O—N) and alkyl chain present in the target compound was suggested as the prime region of hydroxyl radicle (•OH) attack. The tandem mass spectrometry estimated the evolution of sulfamethoxazole-transformed product formation and removal during the treatment. The informed optimization of Fe (0) Fenton treatment, confirmed through MS2 was established at 40 min reaction time at which both the sulfamethoxazole and its transformed product were reduced to trace levels (ngL-1). | Anuradha Goswami; Jia-Qian Jiang; Roberts Joanne; Michael Petri | Organic Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Organic Compounds and Functional Groups; Environmental Analysis; Mass Spectrometry | CC BY NC 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d889fe51558a15ef0a2b76/original/fenton-enhanced-zero-valent-iron-powder-oxidation-investigating-transformation-products-of-antimicrobials-and-its-removal.pdf |
60c7422b702a9b4e4218a3e3 | 10.26434/chemrxiv.8230235.v1 | Photocatalytic Alkylation of Pyrroles and Indoles with α-Diazo Esters | This article describes direct photoalkylation of electron-rich aromatic compounds with diazo compoiunds. C-2 alkylated indoles and pyrroles are obtained with good yields even though the photocatalyst (Ru(bpy)3Cl2) loading is as low as 0.075 mol %. For substrates bearing electron-withdrawing substituents the addition of a catalytic amount of N,N-dimethyl-4-methoxyaniline is required. Both EWG-EWG and EWG-EDG substituted diazo esters are suitable as alkylating agents. The reaction selectivity and mechanistic experiments suggest that carbenes/carbenoid intermediates are not involved in the reaction pathway, instead radical formation is proposed. | Łukasz Ciszewski; Jakub Durka; Dorota Gryko | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7422b702a9b4e4218a3e3/original/photocatalytic-alkylation-of-pyrroles-and-indoles-with-diazo-esters.pdf |
62a148192e626964587cc0af | 10.26434/chemrxiv-2022-jndlx | Predicting the properties of salt water using neural network potentials and continuum solvent theory | Electrolyte solutions play a fundamental role in a vast range of important industrial and biological applications. Yet their thermodynamic and kinetic properties still can not be predicted from first principles. There are three central challenges that need to be overcome to achieve this. Firstly, the dynamic nature of these solutions requires long time scale simulations. Secondly, the long-range Coulomb interactions require large spatial scales. Thirdly, the short-range quantum mechanical (QM) interactions require an expensive level of QM theory. Here, we demonstrate a methodology to address these challenges. Data from a short \emph{ab initio} molecular dynamics (AIMD) simulation of aqueous sodium chloride is used to train an equivariant graph neural network interatomic potential (NNP) that can reliably reproduce the short-range QM forces and energies at a moderate computational cost. This NNP is combined with a continuum solvent description of the long-range electrostatic interactions to enable stable long time and large spatial scale simulations. From these simulations, ion-water and ion-ion radial distribution functions (RDFs), as well as ionic diffusivities, can be determined. The ion-ion RDFs are then used in a continuum solvent approach to calculate the osmotic and activity coefficients. Good experimental agreement is demonstrated up to the solubility limit of sodium chloride in water. This result implies that classical electrostatic theory can describe electrolyte solution over a remarkably wide concentration range as long as it is combined with an accurate description of the short-range interactions. This approach should be applicable to determine the thermodynamic and kinetic properties of many important electrolyte solutions for which experimental data is insufficient. | Joshua Pagotto; Junji Zhang; Timothy Duignan | Theoretical and Computational Chemistry; Physical Chemistry; Artificial Intelligence; Solution Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a148192e626964587cc0af/original/predicting-the-properties-of-salt-water-using-neural-network-potentials-and-continuum-solvent-theory.pdf |
61e6922f4a603dffc034078c | 10.26434/chemrxiv-2022-fsbk4 | One-Pot Chemical Protein Synthesis Utilizing Fmoc-Masked Selenazolidine to Address the Redox Functionality of Human Selenoprotein F | Human SELENOF is an endoplasmic reticulum (ER) selenoprotein that contains the redox active motif CXU (C is cysteine and U is selenocysteine), resembling the redox motif of thiol-disulfide oxidoreductases (CXXC). Like other selenoproteins, the challenge in accessing SELENOF has somewhat limited its full biological characterization thus far. Here we present the one-pot chemical synthesis of the thioredoxin-like domain of SELENOF, highlighted by the use of Fmoc-protected selenazolidine, native chemical ligations and deselenization reactions. The redox potential of the CXU motif, together with insulin turbidimetric assay suggested that SELENOF may catalyze the reduction of disulfides in misfolded proteins. Furthermore, we demonstrate that SELENOF is not a protein disulfide isomerase (PDI)-like enzyme, as it did not enhance the folding of the two protein models; bovine pancreatic trypsin inhibitor and hirudin. These studies suggest that SELENOF may be responsible for reducing the non-native disulfide bonds of misfolded glycoproteins as part of the quality control system in the ER. | Zhenguang Zhao; Reem Mousa; Norman Metanis | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e6922f4a603dffc034078c/original/one-pot-chemical-protein-synthesis-utilizing-fmoc-masked-selenazolidine-to-address-the-redox-functionality-of-human-selenoprotein-f.pdf |
6150c49f1df4a189f17d87a4 | 10.26434/chemrxiv-2021-fvcph | High precision evaluation of the combustion enthalpy by
ab-intio computations | Accurate evaluation of combustion enthalpy is of high scientific and industrial importance. Although
via ab-initio computation of heat of reactions, as one of the promising and well-established approaches
in computational chemistry, this goal should in principle be achievable, examples of reliable and
precise evaluation of heat of combustion by ab-initio methods has surprisingly not yet been reported.
A handful of works carried out for this purpose report significant inconsistencies between the ab-initio
evaluated and experimentally determined combustion enthalpies and suggest empirical corrections
to improve the accuracy of predicted data. With this background, the main aims of the present
study is to investigate the reasons behind those reported inconsistencies and propose guidelines for
highly accurate evaluation of combustion enthalpy via ab-initio computations. Through the provided
guidelines, the most accurate results ever reported, with average absolute deviation, mean unsigned
error and correlation coefficient of 1.556 kJ/mole, 0.072% and 0.99999, respectively, is achieved for
theoretically computed combustion enthalpies of 40 studied hydrocarbons. | Amin Alibakhshi | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Education; Chemical Education - General; Chemoinformatics - Computational Chemistry; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6150c49f1df4a189f17d87a4/original/high-precision-evaluation-of-the-combustion-enthalpy-by-ab-intio-computations.pdf |
62fb178a0ce00a2a9c8f146a | 10.26434/chemrxiv-2022-bcnf9-v3 | Si-based Composite Anode for Li-ion Batteries with Enhanced Cycle Stability via Doping Cu3Si Phase Achieved by Modified Coating of PDA | Silicon (Si) is a promising anode material for Li-ion batteries but its application is limited due to its severe volume change during the lithiation/delithiation process, leading to a fast degradation of cycle performance. Applying transition metals to dope into the bulk Si forming active/inactive silicide phase is proved as an effective and practical method to solve the issue. However, the classic high-energy ball milling method is faced with the challenges of strict requirements to the machine, long-time working and difficulty to control the morphology of the product. Aiming to this point, the present study proposes a facile and “softer” method via coating the polydopamine (PDA) with the assistance of CuCl2·2H2O followed by a high-temperature annealing process to successfully fabricate the Si-based anode material with a unique structure of Si-Cu3Si@c-PDA. We firstly achieved the doping of Cu3Si and the coating of carbon layer simultaneously on the surface of Si. Owing to the synergistic effect of carbonized PDA layer and doped Cu3Si phase, both structural stability and electronic conductivity of electrode have been significantly enhanced. The Si-Cu3Si@c-PDA composite anode not only exhibited a high initial reversible capacity of 2356.7 mAh·g-1 with an initial coulombic efficiency of 83.6%, but also demonstrated a good capacity retention of 89.7% after 100 cycles at the current density of 400 mA·g-1. We believe this work would pave a novel way to improve the Si-based anode material. | Xingyu_Polyu Zhang; Ying Li; Tianye Zheng; Ruitao Zhou; Kwok Ho Lam | Materials Science; Inorganic Chemistry; Energy; Coating Materials; Core-Shell Materials; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fb178a0ce00a2a9c8f146a/original/si-based-composite-anode-for-li-ion-batteries-with-enhanced-cycle-stability-via-doping-cu3si-phase-achieved-by-modified-coating-of-pda.pdf |
6786763dfa469535b9f20b59 | 10.26434/chemrxiv-2025-s26cq | Macrocycles for Conventionally Druggable Targets: Lessons from Macrocyclic Kinase Inhibitors | Macrocycles are emerging as a prominent modality in drug discovery, including for conventionally druggable targets for which simpler, acyclic ligands are readily discoverable. Given the additional synthetic challenges of macrocyclic chemotypes, we ask what benefits macrocycles provided for these highly druggable targets. To do this, we examine the effects of macrocyclization on inhibitors of highly druggable kinase targets. For each example, we isolate closely matched acyclic/macrocyclic compound pairs, allowing us to precisely identify the effects of macrocyclization on binding affinity, selectivity, and ADME properties absent other confounding factors. Our findings show that, while the impact of macrocyclization on potency is variable, a profound effect on selectivity is common. Macrocyclization can also bring benefits for membrane permeability, efflux ratio, blood-brain barrier penetrance, and metabolic stability. These findings lead us to propose specific circumstances in which a drug discoverer targeting kinases or other conventionally druggable target classes should consider a macrocycle approach. | Lauren Viarengo-Baker; Adrian Whitty | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY 4.0 | CHEMRXIV | 2025-01-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6786763dfa469535b9f20b59/original/macrocycles-for-conventionally-druggable-targets-lessons-from-macrocyclic-kinase-inhibitors.pdf |
60c74a69bb8c1a70053db002 | 10.26434/chemrxiv.12185535.v1 | Direct Access to Highly Enantioenriched α-Branched Acrylonitriles through a Formal Cross Rauhut-Currier Reaction | A highly enantioselective synthesis of α-branched acrylonitriles is reported featuring an unprecedented formal cross Rauhut-Currier reaction consisting of an asymmetric Michael addition/retro-Dieckmann/retro-Michael fragmentation cascade. The method, which involves the use of an acrylonitrile surrogate, is practical, scalable and highly versatile, and provides a straightforward access to a wide range of enantioenriched nitrile-containing building blocks without using acrylonitrile or any source of cyanide. Most importantly, it offers a new tool to incorporate an acrylonitrile moiety in an asymmetric fashion.<br /> | Nicolas Duchemin; Martin Cattoen; Oscar Gayraud; Silvia Anselmi; Bilal Siddiq; Roberto Buccafusca; Marc Daumas; Vincent Ferey; Michael Smietana; Stellios Arseniyadis | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a69bb8c1a70053db002/original/direct-access-to-highly-enantioenriched-branched-acrylonitriles-through-a-formal-cross-rauhut-currier-reaction.pdf |
65e80b439138d23161c57e53 | 10.26434/chemrxiv-2024-z8blq | The role of fine particles in the stability of emulsion in the naphthenic froth treatment (NFT) process | This study investigates the role of fine particles in stabilizing emulsion in the naphthenic froth treatment (NFT) process. The characterization results of different types of solids collected from the diluted bitumen froth indicate that kaolinite is the dominant clay mineral in the composition of NFT solids. There were differences in the mineralogy of the fine samples depending on the phase (carrier fluid) from which the samples were collected. FTIR analysis shows that the fines that remain in the diluted bitumen even after several hours of sample retention time are mainly kaolinite, though the presence of other minerals such as siderite is very likely. Moreover, the presence of organic functional groups on the surface of the particles is confirmed for all types of solids in the FTIR analysis, regardless of the washing and drying procedures employed. Inspection of the different layers of the diluted bitumen via micrography and measurement of the solids concentration shows higher fine content and smaller particles in the top layer, a dire situation for destabilizing the emulsion in the top layer, supported by the observation that the water droplets in this layer are tiny. Solid partitioning tests revealed the solid particles migrate to the interfacial region and the aqueous phase. The concentration of particles increased in the interfacial region with the presence of asphaltene in the oil phase (dominant effect) and the increased polarity of the oil. The wettability measurements show that without the coverage of solid particles with organics (asphaltene-resin molecules), the fine particles are extremely hydrophilic. The adsorption of asphaltene-resin matter on the fine particles increased the hydrophobicity of the fines, a situation that promotes the partitioning of the fine particles at the interfacial region and the stability of the droplets. It was observed that the contact angle increased with the decreasing polarity of the oil phase. In the interfacial tension measurements, the fine solids with minimal asphaltic matter coverage did not remain suspended in the oil phase and either sedimented rapidly or migrated to the air-oil interface, unlike the organics-covered solids which remained immersed in oil. No decrease in the interfacial tension was recorded for the water-oil systems in the presence of fine solids. Interfacial rheology measurements illustrate the viscoelastic behavior of the interfacial film at lower frequencies and higher fine particle concentrations. We conclude that if not for the interaction between the asphaltic matter and the fine particles, the emulsion stability by fine particles would have been very unlikely. | Arian Velayati; Hongbo Zeng | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e80b439138d23161c57e53/original/the-role-of-fine-particles-in-the-stability-of-emulsion-in-the-naphthenic-froth-treatment-nft-process.pdf |
64af8f4bba3e99daef042489 | 10.26434/chemrxiv-2023-25b7m | Pd-Catalyzed picolinamide directed late-stage chalcogenation of tryp-tophan containing peptides | This report describes the Pd-catalyzed late-stage chalcogenation of tryptophan containing peptides with disulfides/diselenides in moderate to good yields. It comprises broad substrate scope, functional group diversity, late-stage mutation of drug mole-cules and various valuable synthetic transformations including room temperature easy removal of picolinamide auxiliary, which could be applicable to tune the structure and function of peptides. | Nagendra Sharma; Raghunath Bag | Organic Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64af8f4bba3e99daef042489/original/pd-catalyzed-picolinamide-directed-late-stage-chalcogenation-of-tryp-tophan-containing-peptides.pdf |
6769af7281d2151a02b4b2d6 | 10.26434/chemrxiv-2024-57p0l | Potent Analogues of Clovibactin from Commercially Available Amino Acid Building Blocks | This paper reports highly active analogues of clovibactin in which the rare, non-canonical amino acid D-hydroxyasparagine is replaced with the commercially available amino acid D-threonine. Sequential mutation of leucines 2, 7, and 8 to the more hydrophobic homologue cyclohexylalanine dramatically increases the antibiotic activity of D-Thr5-clovibactin. The resulting analogues (D-Cha2,D-Thr5-clovibactin, Cha7,D-Thr5-clovibactin, and Cha8,D-Thr5-clovibactin) are readily prepared by standard peptide synthesis techniques and exhibit excellent activity (≤ 1 μg/mL) against the Gram-positive, drug-resistant pathogens MRSA and VRE. | Jackson Brunicardi; Jeramiah Small; Maria Sophia Teresa Lee Padilla; Jovanna Carrera Plancarte; James Nowick | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Drug Discovery and Drug Delivery Systems; Microbiology | CC BY 4.0 | CHEMRXIV | 2024-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6769af7281d2151a02b4b2d6/original/potent-analogues-of-clovibactin-from-commercially-available-amino-acid-building-blocks.pdf |
60c73fc2469df42a4df42b2b | 10.26434/chemrxiv.7479944.v1 | The Total Synthesis of Rhabdastrellic Acid A | <div>The first total synthesis of rhabdastrellic acid A, a highly cytotoxic isomalabaricane triterpenoid, has been accomplished in a linear sequence of 14 steps from commercial geranylacetone. The prominently strained <i>trans-syn-trans</i>-perhydrobenz[<i>e</i>]indene core characteristic of the isomalabaricanes is efficiently accessed in a selective manner for the first time through a rapid, complexity-generating sequence incorporating a reductive radical polyene cyclization, an unprecedented oxidative Rautenstrauch cycloisomerization, and umpolung 𝛼-substitution of a <i>p</i>-toluenesulfonylhydrazone with in situ reductive transposition. A late-stage cross-coupling in concert with a modular approach to polyunsaturated side chains renders this a general strategy for the synthesis of numerous family members of these synthetically challenging and hitherto inaccessible marine triterpenoids.</div> | Yaroslav Boyko; Christopher Huck; David Sarlah | Natural Products; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fc2469df42a4df42b2b/original/the-total-synthesis-of-rhabdastrellic-acid-a.pdf |
65a023a49138d23161b4db0f | 10.26434/chemrxiv-2024-ftlw1 | CARBON FIBER PRODUCTION FROM LIGNIN: A PRECURSOR OF FUTURE | Carbon fibers have recently attracted tremendous attention, and many industries have adopted them. However, high manufacturing costs and complex processes still limit their widespread use in large-scale applications. The cost of current precursors, namely PAN and Pitch, alone accounts for more than half of the total cost of carbon fiber manufacturing. Therefore, a new, cost-efficient, renewable, and abundantly available precursor should be investigated to overcome these challenges. Lignin serves all these purposes and is a promising substitute for convectional precursors. It can be processed using melt spinning, solution spinning, or electrospinning. This paper reviews the published research on lignin structure, the production of lignin precursor fibers, their conversion into carbon fibers, and future directions. | Nishant Chaudhari | Polymer Science; Biopolymers | CC BY 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a023a49138d23161b4db0f/original/carbon-fiber-production-from-lignin-a-precursor-of-future.pdf |
615b4206a3d2c9046bcbafd5 | 10.26434/chemrxiv-2021-qwcg3 | Substituents of life: The most common substituent patterns present in natural products | Comparison of substituents present in natural products with the substituents found in average synthetic molecules revealed considerable differences between these 2 groups. The natural products substituents contain mostly oxygen atoms and very little other heteroatoms, are structurally more complex, often containing double bonds and are rich in stereocenters. Substituents found in synthetic molecules contain nitrogen and sulfur atoms, halogenes and more aromatic and particularly heteroaromatic rings. The characteristics of substituents typical for natural products identified here can be useful in the medicinal chemistry context, for example to guide the synthesis of natural product-like libraries and natural product-inspired fragment collections. The results may be used also to support compound derivatization strategies and the design of pseudo-natural natural products. | Peter Ertl | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615b4206a3d2c9046bcbafd5/original/substituents-of-life-the-most-common-substituent-patterns-present-in-natural-products.pdf |
63ee94459da0bc6b330bdc80 | 10.26434/chemrxiv-2023-q12b3 | A Surprising Use of the Business Innovation Bass Diffusion Model to Accurately Describe Adsorption Isotherm Types I, III, and V | Using adsorption isotherm data to determine heats of adsorption or predict mixture adsorption using the Ideal Adsorbed Solution Theory (IAST) relies on accurate fits of the data with continuous, mathematical models. Here, we derive an empirical two-parameter model to fit isotherm data of IUPAC types I, III, and V in a descriptive way based on the Bass model for innovation diffusion. We report 31 isotherm fits to existing literature data covering all six types of isotherms, various adsorbents, such as carbons, zeolites, and metal-organic frameworks (MOF), as well as different adsorbing gases (water, carbon dioxide, methane, nitrogen). We find several cases, especially for flexible MOFs, where previously reported isotherm models reached their limits and either failed to fit the data or could not sufficiently be fitted due to stepped type V isotherms. Moreover, in two instances models specifically developed for distinct systems are fitted with a higher R2 value compared to the models in the original reports. Using these fits, it is demonstrated how the new Bingel-Walton isotherm can be used to qualitatively assess the hydrophilic or hydrophobic behavior of porous materials from the relative magnitude of the two fitting parameters. The model can also be employed to find matching heats of adsorption values for systems with isotherm steps using one, continuous fit instead of partial, stepwise fits or interpolation. Additionally, using our single, continuous fit to model stepped isotherms in IAST mixture adsorption predictions leads to good agreement with results from the Osmotic Framework Adsorbed Solution Theory (OFAST) that was specifically developed for these systems using a stepwise, approximate fitting, yet is far more complex. Our new isotherm equation accomplishes all of these tasks with only two fitted parameters, providing a simple, accurate method for modeling a variety of adsorption behavior. | Lukas Willi Bingel; Krista S Walton | Physical Chemistry; Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ee94459da0bc6b330bdc80/original/a-surprising-use-of-the-business-innovation-bass-diffusion-model-to-accurately-describe-adsorption-isotherm-types-i-iii-and-v.pdf |
673e7a297be152b1d003cc99 | 10.26434/chemrxiv-2024-sw04g | Pose Ensemble Graph Neural Networks to Improve Docking Performances. | The prediction of the geometry and strength governing small molecule-protein interactions remains a paramount challenge in drug discovery due to their complex and dynamic nature. A number of machine learning (ML) methods have been proposed to complement and improve on physics-based tools such as molecular docking, usually by mapping three dimensional features of individual poses to their closeness to experimental structures and/or to binding affinities. Here, we introduce Dockbox2 (DBX2), a novel approach that encodes ensembles of computational poses within a graph neural network architecture via simple energy-based features derived from molecular docking. The model was jointly trained to predict binding pose likelihood as a node-level task and binding affinity as a graph-level task using the PDBbind dataset and demonstrated significant performance in comprehensive, retrospective docking and virtual screening experiments. Our results encourage further exploration of ML models based on conformational ensembles to provide more accurate estimates of small molecule-protein interactions and thermodynamics. The DBX2 code is available at https://github.com/jp43/DockBox2. | Thanawat Thaingtamtanha; Jordane Preto; Francesco Gentile | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673e7a297be152b1d003cc99/original/pose-ensemble-graph-neural-networks-to-improve-docking-performances.pdf |
6724cb817be152b1d0ab1cef | 10.26434/chemrxiv-2023-vg68p-v2 | Architectured Silicone Vitrimers with Light-Tunable Mechanical and Self-Healing Behavior | Architectured materials synergistically harness chemical and microstructural features to create monoliths with antagonistic properties. Although it is a hallmark of biological composites, this material design concept has only recently been applied to synthetic elastomers and vitrimers. Here, we propose a light-based platform to manufacture architectured silicone vitrimers with locally tunable mechanical properties. Vitrimers are created through photocuring of polymer mixtures containing silica particles, silicone prepolymers and thiol crosslinkers. Dioxaborolane groups are incorporated in the silicone prepolymers to form dynamic bonds in the covalent adaptive network. Experiments showed that the mechanical properties and self-healing behavior of the silicone vitrimers are strongly influenced by the illumination conditions used during photo-curing. This dependence is exploited to manufacture architectured silicone vitrimers combining high stretchability and locally programmable mechanical stiffness. The high stretchability, tunable local properties and adaptive nature of these polymers makes them attractive for applications in soft robots, biomedical implants, and wearable devices. | Stefano Menasce; Fergal Coulter; Rafael Libanori | Materials Science | CC BY NC 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6724cb817be152b1d0ab1cef/original/architectured-silicone-vitrimers-with-light-tunable-mechanical-and-self-healing-behavior.pdf |
650ea12760c37f4f764b733b | 10.26434/chemrxiv-2023-hn02p | Exo-Cleavable Linkers: A Paradigm Shift for Enhanced Stability and Therapeutic Efficacy in Antibody-Drug Conjugates | Customized drug delivery systems have become paramount in the rapidly evolving field of precision medicine, and at the forefront of advances in this regard, antibody-drug conjugates (ADCs) present a symbiotic fusion of cytotoxic payloads and monoclonal antibodies (mAbs) facilitated by intricate chemical linkers. The search for ideal linkers that can dexterously provide the dual functionalities of enhancing circulatory stability and facilitating the effective release of the tumor payload is a present and formidable challenge. The valine-citrulline (Val-Cit) linker, which is used in a wide range of ADCs, despite its approval by the Food and Drug Administration, is associated with several inherent drawbacks, including hydrophobicity-induced aggregation, limited payload capacity, and premature payload release. This study presents a paradigm shift from the conventional linear linker archetype by introducing an exo-linker avant-garde approach that repositions the cleavable peptide linker at the exo-position of the PAB moiety. This molecular refinement not only offered the possibility to overcome the intrinsic drawbacks of the Val-Cit platform, but also significantly improved ADC stability, therapeutic efficacy, and pharmacokinetics. In vitro and in vivo biological evaluations, confirmed that ADCs designed using the exo-linker blueprint significantly attenuated premature payload release, while increasing the drug-to-antibody ratio, even with hydrophobic payloads, and this without inducing pronounced aggregation. Therefore, the fabricated exo-linker represents a significant improvement with respect to traditional Val-Cit ADCs. Moreover, under the influence of enzymes, such as carboxylesterases and human neutrophil elastase, the payload remained stably conjugated to the ADC, underscoring a favorable safety profile and highlighting potential for clinical translatability. Thus, our findings also demonstrate the potential of the novel exo-linker paradigm as well as the profound implications of nuanced molecular modifications for reshaping ADC design and functionality. | Tomohiro Watanabe; Naoko Arashida; Tomohiro Fujii; Natsuki Shikida; Kenichiro Ito; Kazutaka Shimbo; Takuya Seki; Yusuke Iwai; Ryusuke Hirama; Noriko Hatada; Akira Nakayama; Tatsuya Okuzumi; Yutaka Matsuda | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650ea12760c37f4f764b733b/original/exo-cleavable-linkers-a-paradigm-shift-for-enhanced-stability-and-therapeutic-efficacy-in-antibody-drug-conjugates.pdf |
64eab87b79853bbd78811452 | 10.26434/chemrxiv-2023-smhv5 | Compound similarity network as a novel data mining strategy for high-throughput investigation of degradation pathways of organic pollutants in industrial wastewater treatment | The identification of degradation products and pathways is crucial for investigating emerging pollutants and evaluating wastewater treatment methods. Non-targeted analysis is a powerful tool to systematically investigate the degradation pathways of organic pollutants in real wastewater samples, but often generate large data sets making it difficult to effectively find information of interests. Here, we propose that that it is possible to establish the linkages among compounds in the same degradation pathways based on their structure similarity. Using this principle, we introduce compound similarity network (CSN) as a novel data mining strategy to identify degradation pathways using MS data collected in LC-MS based non-targeted analysis of complex wastewater samples. We demonstrated this strategy by non-targeted identifying potential degradation products of organic pollutants in leather industrial wastewater during laboratory-scale activated carbon adsorption (ACD) and ozonation processes. Using LC-MS based non-targeted analysis and the CSN strategy, we putatively identified 4324 compounds in the untreated leather industrial wastewater, 3246 after ACD, and 3777 after ACD/ozonation. We located 145 potential degradation pathways of organic pollutants in the ACD/ozonation process using CSN and validated 9 pathways with 21 commercial standard compounds. Our CSN strategy for LC-MS based non-targeted analysis provides a highly efficient way to investigate degradation pathways of complicated organic pollutants in authentic wastewater. | Lirong An; Bin Chen; Yuchen Zhang; Rongfu Huang; Feng Li; Yanan Tang | Analytical Chemistry; Environmental Analysis; Mass Spectrometry; High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64eab87b79853bbd78811452/original/compound-similarity-network-as-a-novel-data-mining-strategy-for-high-throughput-investigation-of-degradation-pathways-of-organic-pollutants-in-industrial-wastewater-treatment.pdf |
60c753aaf96a0043f32884e1 | 10.26434/chemrxiv.13524191.v1 | Providing Adverse Outcome Pathways from the AOP-Wiki in Semantic Web Format to Increase Usability and Accessibility of the Content | <div>The AOP-Wiki is the main environment for the development and storage of Adverse Outcome Pathways. These Adverse Outcome Pathways describe mechanistic information about toxicodynamic processes and can be used to develop effective risk assessment strategies. However, it is challenging to automatically and systematically parse, filter, and use its contents. We explored solutions to better structure the AOP-Wiki content and to link it with chemical and biological resources. Together this allows more detailed exploration which can be automated.</div><div><br /></div><div>We converted the complete AOP-Wiki content into Resource Description Framework. We used over twenty ontologies for the semantic annotation of property-object relations, including the ChemInformatics Ontology, Dublin Core, and the Adverse Outcome Pathway Ontology. The latter was used over 8,000 times. Furthermore, over 3,500 link-outs were added to twelve chemical databases and over 6,500 link-outs to four gene and protein databases. </div><div><br /></div><div>SPARQL queries can be used against the Resource Description Framework to answer biological and toxicological questions, such as listing measurement methods for all Key Events leading to an Adverse Outcome of interest. The full power that the use of this new resource provides becomes apparent when combining the content with external databases using federated queries. For example, we can link genes related to Key Events with molecular pathway on WikiPathways in which they occur and find all Adverse Outcome Pathways caused by stressors that are part of a particular chemical group. Overall, the AOP-Wiki Resource Description Framework allows new ways to explore the rapidly growing Adverse Outcome Pathway knowledge and makes the integration of this database in automated workflows possible.</div> | Marvin Martens; Chris Evelo; Egon Willighagen | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753aaf96a0043f32884e1/original/providing-adverse-outcome-pathways-from-the-aop-wiki-in-semantic-web-format-to-increase-usability-and-accessibility-of-the-content.pdf |
638dbb087b7c917c25e3fd87 | 10.26434/chemrxiv-2022-6ksq3 | Trithiolato-Bridged Dinuclear Ruthenium(II)-Arene Conjugates Tethered with Lipophilic Units: Synthesis and Antiparasitic Activity | Trithiolato-bridged dinuclear ruthenium(II)-arene complexes are active against various parasites including Toxoplasma gondii. Lipids, isoprenoids and lipoate are metabolites scavenged by T. gondii from the host cell but also synthesized by the parasite, and these molecules can be appended to the diruthenium moiety in a conjugate approach aiming at compounds with improved antiparasitic activity and selectivity. The synthesis and in vitro T. gondii activity evaluation of 23 new trithiolato diruthenium complexes bearing various lipophilic units are reported. The influence of several structural elements as the nature of the lipophilic pendant and the type of the connecting bond between the two units on the conjugates’ biological properties were examined. In a primary screening, the antiparasitic efficacy and cytotoxicity were assessed at 0.1 and 1 µM against transgenic T. gondii tachyzoites constitutively expressing β-galactosidase and on human foreskin fibroblasts (HFF) host cells. For 14 selected conjugates the half-maximal inhibitory concentration (IC50) on T. gondii and their effect on HFF viability at 2.5 µM were determined. The decanoic, oleic and elaidic ester conjugates 13a, 16a and 17a efficiently inhibited parasite proliferation (IC50 values of 0.065, 0.127 and 0.123 µM, respectively) with no effect on HFF viability at 2.5 µM and deserve further attention. | Oksana Desiatkina; Nicoleta Anghel; Ghalia Boubaker; Yosra Amdouni; Andrew Hemphill; julien Furrer; Emilia Paunescu | Inorganic Chemistry; Bioinorganic Chemistry; Organometallic Compounds | CC BY NC 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638dbb087b7c917c25e3fd87/original/trithiolato-bridged-dinuclear-ruthenium-ii-arene-conjugates-tethered-with-lipophilic-units-synthesis-and-antiparasitic-activity.pdf |
671f57b483f22e42146cdf58 | 10.26434/chemrxiv-2024-khzdk | Polarization Induced Quantum Confinement of Negative Charge Carriers by Organic Nanoporous Frameworks | We characterize the attachment of excess-electrons to organic nanoporous systems including molecular nanohoops and models of covalent organic frameworks (COFs) using many-body methods. \emph{All} the nanopore systems exhibit diffuse electronic states where the excess-electron is bound to the molecular scaffold via long-range polarization forces, and the excess-electron is predominantly localized in the interior of the nanopore or away from the molecular scaffold. Such ``nanopore-bound'' states show an enhanced electron-transfer coupling compared to more strongly-bound skeletal-states (or valence-bound states), where the excess-electron is confined to the molecular skeleton. For 1D assemblies of nanohoops, the bands formed from nanopore-bound states have a consistent nearly-free-electron character, indicating an efficient excited-state pathway for charge-carriers, while the bands from skeletal-states have higher effective mass along certain lattice directions. The nanopore-bound states show distinct size-dependent variations in electron affinities compared to skeletal-states and previously observed molecular quantum corral states. We conclude that nanopore-bound states emerge from polarization-induced quantum confinement, forming a distinct common feature of organic nanoporous matter with potential for efficient electron-transport. | Ritaj Tyagi; Vamsee Voora | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671f57b483f22e42146cdf58/original/polarization-induced-quantum-confinement-of-negative-charge-carriers-by-organic-nanoporous-frameworks.pdf |
637bb9ff20798147012f8870 | 10.26434/chemrxiv-2022-404jn | Re-investigating the structure-property relationship of the solid electrolyte Li 3-xIn1-xZrxCl6 and the impact of In-Zr(IV) substitution
| Chloride based solid electrolytes are considered interesting candidates for catholytes in all-solid-state batteries due to their high electrochemical stability, which allows the use of high-voltage cathodes without protective coatings. Aliovalent Zr(IV) substitution is a widely applicable strategy to increase the ionic conductivity of Li3M(III)Cl6 solid electrolytes. In this study, we investigate how Zr(IV) substitution affects the structure and ion conduction in
Li3-xIn1-xZrxCl6 (0 ≤ x ≤ 0.5). Combined refinement of x-ray and neutron diffraction is used to make a structural model based on both scattering contrasts, and AC-impedance measurements and solid-state NMR relaxometry measurements at multiple Larmor frequencies are used to study the Li-ion dynamics. Hereby the diffusion mechanism and its correlation with the structure are explored and compared to previous studies, advancing the understanding of these complex and difficult to characterize materials. It is found that the diffusion in Li3InCl6 is most ikely anisotropic considering the crystal structure and two distinct jump processes found by solid-state NMR. Zr-substitution improves ionic conductivity by tuning the charge carrier concentration, accompanied by small changes in the crystal structure which affect ion-transport even on short timescales, likely reducing the anisotropy. | Eveline Maas; Theodosios Famprikis; Saskia Pieters; Jonas P. Dijkstra; Zhaolong Li; Steven Parnell; Ron Smith; Ernst van Eck; Swapna Ganapathy; Marnix Wagemaker | Inorganic Chemistry; Energy; Solid State Chemistry; Energy Storage; Materials Chemistry; Crystallography – Inorganic | CC BY 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637bb9ff20798147012f8870/original/re-investigating-the-structure-property-relationship-of-the-solid-electrolyte-li-3-x-in1-x-zrx-cl6-and-the-impact-of-in-zr-iv-substitution.pdf |
650afb9eed7d0eccc3e2b9af | 10.26434/chemrxiv-2023-4nswv | An At-Home Compatible Calorimetry Experiment Using Drug Store Clinical Thermometers | Calorimetry is one of the best experiments to do in an introductory level chemistry laboratory course as it has high accuracy and requires relatively inexpensive materials. However, like other traditional general chemistry lab experiments, it is not easily converted with at-home or remote experimentation. The traditional experiment requires thermometers for a range of at least 20 to 110° Celsius, precise balances, and either Bunsen burners or hot plates for heating. Here we present a modified calorimetry experiment designed with an accessibility-first approach during remote lab instruction in response to the COVID-19 pandemic. The approach uses drug store thermometers, hanger balances, and microwaves to determine the specific heat of metals. A majority of the reported specific heat values fell within a 40-60% range from the literature value, compared to 16-94% when using traditional methods. This presents an opportunity for our accessibility designed at-home lab to be used as a prelab or make up assignment as part of an inclusive lab course. | Oğuz Kuçukosman; Jaren Harrell; Donna Garandouka; Ashutosh Sahoo; Ageliki Karagiannis; Courtney Sobers | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650afb9eed7d0eccc3e2b9af/original/an-at-home-compatible-calorimetry-experiment-using-drug-store-clinical-thermometers.pdf |
67ca3b59fa469535b947c899 | 10.26434/chemrxiv-2025-83d8x | Framework for De novo Sequencing of Peptide Mixtures via Network Analysis and Two-Dimensional Tandem Mass Spectrometry | Two-dimensional tandem mass spectrometry (2D MS/MS) provides in-depth biopolymer structural information previously not directly accessible with traditional one-dimensional MS/MS workflows, and in significantly less time (<1 second per sample). In this study, we enhance analysis of 2D MS/MS data for greater applicability in omics workflows and address challenges in sequencing peptide of mixtures. We designed a graph-theory-based framework to efficiently manage, visualize, and maximize the structural information extractable from 2D MS/MS spectra. Graph analysis algorithms, including a PageRank-based method, are shown to deconvolve MS/MS signals and group together product ions from the same peptide precursor, enabling the reconstruction of peptide fragmentation trees. From this, MSn information can be extracted to improve sequencing accuracy relative to current MS/MS methods. We also introduce a computationally efficient de novo sequencing approach that leverages this structural information to reduce reliance on databases and sample separation, while also enabling the rapid sequencing of post-translationally modified peptides. Tests on simulated 2D MS/MS spectra, designed to mimic those from proteomic samples, achieved high precision in signal assignment. Proof-of-concept studies were conducted on real data from simple mixtures of short chain peptides, showing the potential applicability of combining network analysis with de novo sequencing to analyze unknown peptide mixtures. We anticipate that this technique will complement proteomics workflows and facilitate direct biopolymer structural analysis. | MyPhuong Le; Yu Zhu; Eric Dziekonski; Dylan Holden; David Gleich; R. Graham Cooks | Analytical Chemistry; Biochemical Analysis; Chemoinformatics; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ca3b59fa469535b947c899/original/framework-for-de-novo-sequencing-of-peptide-mixtures-via-network-analysis-and-two-dimensional-tandem-mass-spectrometry.pdf |
60e7051e0387b17547ca5aea | 10.26434/chemrxiv-2021-zs4pl-v2 | Virtual Homonuclear Decoupling in Direct Detection NMR Experiments using Deep Neural Networks | Nuclear magnetic resonance (NMR) experiments are frequently complicated by the presence of homonuclear scalar couplings. For the growing body of biomolecular 13C-detected NMR methods, one-bond 13C-13C couplings significantly reduce sensitivity and resolution. The solution to this problem has typically been to perform virtual decoupling by recording multiple spectra and taking linear combinations. Here, we propose an alternative method of virtual decoupling using deep neural networks, which only requires a single spectrum and gives a significant boost in resolution while reducing the effective phase cycles of the experiments by at least a factor of two. We successfully apply this methodology to virtually decouple in-phase CON (13CO-15N) protein NMR spectra, 13C-13C correlation spectra of protein side chains, and 13Cα-detected protein 13Cα-13CO spectra where two large homonuclear couplings are present. The deep neural network approach effectively decouples spectra with a high degree of flexibility, including in cases where existing methods fail, facilitates the use of simpler pulse sequences, and yields spectra with comparable quality to traditional virtual decoupling schemes in half the time or less. | Gogulan Karunanithy; Harry Mackenzie; D Flemming Hansen | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Machine Learning; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e7051e0387b17547ca5aea/original/virtual-homonuclear-decoupling-in-direct-detection-nmr-experiments-using-deep-neural-networks.pdf |
60c757ee0f50db731f39835c | 10.26434/chemrxiv.14483124.v1 | Easy Access To Allylic Sulfones Through Transition Metal-Free Hydrosulfonylation Of Allenes | A Brønsted acid-mediated addition of (hetero)aryl and (cyclo)alkyl sodium sulfinates to <i>N</i>-allenyl derivatives is described under very smooth conditions. This reaction provided a practical and efficient protocol for the synthesis of allylic sulfones in an atom- and step-economic fashion. In addition, an one-step double hydrosulfonylation has also been demonstrated, affording the corresponding 1,3-disulfone in to good yield.<br /> | Lucas Pages; Sebastien Lemouzy; Marc Taillefer; Florian Monnier | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757ee0f50db731f39835c/original/easy-access-to-allylic-sulfones-through-transition-metal-free-hydrosulfonylation-of-allenes.pdf |
678a97bd81d2151a028bb921 | 10.26434/chemrxiv-2024-qrxg7-v2 | Crosslinked polyisoprene networks: linker architecture and elastomer properties | Crosslinking macromolecules is an important process that aims to modulate mechanical properties of elastomers and meet desired specifications based on the application sought. The impact of crosslinking density on rubber moduli has been well established by theory, experiments and computational studies. However, several reports imply a role for the length of the sulfide bond and the attachment location. In this study, we construct all-atom models of polyisoprene (PI) networks using equilibrated precursor melts and sulfide crosslinks of a specific chemical architecture. We first examine network characteristics which follow expectations based on our random crosslinking approach. We report the presence of a substantial number of intramolecular connections formed. Thermodynamics and microscopic dynamics of the resulting networks are also probed. Comparing systems with the same number of crosslinks, we find that local mobility is most decelerated in the presence of long quaternary connections. To resolve any impact on mechanical properties we resorted to extensive characterization of moduli via equilibrium (stress-stress fluctuations) and non-equilibrium processes (constant-rate and oscillatory deformations). Both equilibrium and non-equilibrium simulations (at times/frequencies accessible to our all-atom models) confirm that quaternary linkages provide for the highest moduli with linker length holding a secondary role during moderate deformations. | Rohit Ghanta; George Papakonstantopoulos; Jan Domurath; Patrycja Polińska; Craig Burkhart; Vagelis Harmandaris; Manolis Doxastakis | Theoretical and Computational Chemistry; Polymer Science; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678a97bd81d2151a028bb921/original/crosslinked-polyisoprene-networks-linker-architecture-and-elastomer-properties.pdf |
6659a555418a5379b0be2d55 | 10.26434/chemrxiv-2024-bxr4n | Intermolecular Anionic Mixed-Valence and π-Dimer Complexes of Ortho-Pentannulated BisAzaCoroneneDiimides | This study reports the serendipitous discovery of intermolecular anionic mixed-valence (MV) and π-dimer species in ortho-pentannulated BisAzaCoroneneDiimides (BACDs) during their electrochemical reduction in a non-aqueous solvent. A library of nitrogen-containing extended PDIs was synthesized via an aza-benzannulation reaction followed by a Pd-catalysed ortho-pentannulation reaction. Ortho-pentannulated BACDs revealed strong aggregation abilities in solution. Concentration-dependent UV-vis absorption spectra, variable temperature 1H NMR experiments, and atomic force microscopy coupled to molecular dynamics support their self-assembly into columnar aggregates. Cyclic voltammetry experiments in dichloromethane reveal prominent splitting of the first reduction wave, attributed to the formation of unprecedented intermolecular anionic MV and π-dimers in organic solvent. These species were thoroughly characterized by real-time spectroelectrochemistry, electrochemical simulations and theoretical calculations. Remarkably, this work underscores the tuneable nature of AzaBenzannulatedPerylene Diimides (AzaBPDIs) and BACDs, emphasizing their potential as a promising scaffold for designing supramolecular materials with long-range radical anion delocalization. The observation of this phenomenon provides insights into the fundamental behaviour of supramolecular organic semiconductors, thereby paving the way for the development of novel electronic devices and electron-deficient materials. | Arthur David; Maxime Roger; Olivier Alévêque; Heorhii Melnychenko; Laura Le Bras; Magali Allain; Adèle Gapin; David Canevet; Olivier Ségut; Eric Levillain; Antoine Goujon | Physical Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.); Electrochemistry - Mechanisms, Theory & Study; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659a555418a5379b0be2d55/original/intermolecular-anionic-mixed-valence-and-dimer-complexes-of-ortho-pentannulated-bis-aza-coronene-diimides.pdf |
66a2643f5101a2ffa8061019 | 10.26434/chemrxiv-2024-2c5j2 | Highly Enantioselective Organocatalysis with Bidentate Halogen Bond Donors | As the employment of ”non-classical” non-covalent interactions like halogen bonding (XB) in asymmetric catalysis is still at a very early stage, there are significant challenges to overcome. In some reported cases, the relevance of halogen bonding to the catalytic action is unclear, while in others, catalyst activity is limited. Herein, we present the second generation of a bidentate iodine(I)-based halogen bond donor as a modifiable and highly active chiral halogen bonding catalyst. With these modified derivatives, high stereocontrol of up to 98% ee could be achieved in a model Mukaiyama aldol reaction for a range of different substrates. Importantly, the crucial role of halogen bonding in this catalytic process was demonstrated by the low performance of the non-iodinated variants. | Julian Wolf; Meghana Poliyodath Mohanan; Revannath Sutar; Elric Engelage; Stefan M. Huber | Organic Chemistry; Catalysis; Supramolecular Chemistry (Org.); Homogeneous Catalysis; Organocatalysis | CC BY NC 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a2643f5101a2ffa8061019/original/highly-enantioselective-organocatalysis-with-bidentate-halogen-bond-donors.pdf |
6751cc927be152b1d00e55c6 | 10.26434/chemrxiv-2025-pnh6l | Data-driven massive reaction networks reveal new pathways underlying catalytic CO2 hydrogenation | Heterogeneous catalytic pathways for clean energy conversion involve thousands of elementary steps, but most quantum-mechanical models involve only a few dozen reactions. We combine extensive density functional theory (DFT) calculations, machine learning (ML) for activation barrier prediction, and human intelligence-inspired reaction enumeration and elementary reaction identification. This enables automated kinetic modeling of CO2 hydrogenation on copper, a key process to produce fuels and chemicals. We construct the largest dataset of 152 elementary CO2 reduction reactions and experimentally determine CO2 conversion, finding that even large networks with 100+ reactions are insufficient. In contrast, our approach reveals 9389 elementary reactions, reducing human bias in the reaction pathway. We unravel 40-fold higher CO2 conversion rates, following experimental trends of methanol and CO production. We establish the crucial role of intermolecular hydrogen transfer and hydrogenation by molecular hydrogen, a surprising ML-enabled discovery validated post-facto. The proposed strategy to comprehensively model complex catalytic mechanisms will significantly advance catalysis research and carbon conversion processes. | Anand M. Verma; Shivam Chaturvedi; Swastik Paul; Srinibas Nandi; Rahul Sheshanarayana; Kotni Santhosh; G Valavarasu; Ambedkar Dukkipati; Chuandayani Gunawan Gwie; Pei Ying Moo; Chun Qi Joy Ng; Amol Amrute; Ananth Govind Rajan | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Machine Learning; Nanocatalysis - Reactions & Mechanisms; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6751cc927be152b1d00e55c6/original/data-driven-massive-reaction-networks-reveal-new-pathways-underlying-catalytic-co2-hydrogenation.pdf |
67de5434fa469535b92e0302 | 10.26434/chemrxiv-2025-lxdks | Thioether-linked single-molecule junctions with coinage metal contacts | The influence of changing electrode material on the electrical and mechanical properties of metal-molecule-metal junctions is relatively poorly understood, yet an improved understanding of these interfaces remains critical to the implementation of such systems as active elements in real-world circuits. Accordingly, here we study single-molecule junctions comprising thioether-linked alkane and oligophenyl wires formed under an inert atmosphere using gold, silver, and copper electrodes. Break junction experiments and computational simulations reveal that the conductance of junctions with different contacts typically decreases in the order gold > silver ≥ copper. Notably, such trends cannot be explained solely from the differences in work function for these metals. Transport calculations reveal the role of electronic coupling to the electrodes, which is strongest for gold. Together, this study charts a coherent path towards a more complete understanding of the role of the electrode in single-molecule devices. | Thomas Czyszczon-Burton; Enrique Montes; Jazmine Prana; Sully Chen; Christopher Pakhanyan; Héctor Vázquez; Michael Inkpen | Physical Chemistry; Nanoscience; Nanodevices; Interfaces; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67de5434fa469535b92e0302/original/thioether-linked-single-molecule-junctions-with-coinage-metal-contacts.pdf |
65dbe50066c13817298b6f76 | 10.26434/chemrxiv-2024-7j0wl | Cobalt-Catalyzed Domino Transformations via Enantioselective C–H Activation/Nucleophilic [3+2] Annulation Towards Chiral Bridged Bicycles | Selective synthesis of chiral bridged (hetero)bicyclic scaffolds via asymmetric C–H activation constitutes substantial chal-lenges, due to the multiple reactivities of strained bicyclic structures. Herein, we develop the domino transformations through an unprecedent cobalt-catalyzed enantioselective C–H activation/nucleophilic [3+2] annulation with symmetrical bicyclic alkenes. The methods offer straightforward accesses to a wide range of chiral molecules bearing [2.2.1]-bridged bicy-clic cores with four and five consecutive stereocenters in a single step. Two elaborated salicyloxazoline (Salox) ligands were synthesized based on the rational design and mechanistic understanding. The well-defined chiral pockets generated from asymmetric coordination around trivalent cobalt catalyst direct the orientation of bicyclic alkenes, leading to the excellent enantioselectivity. | Fan-Rui Huang; Qi-Jun Yao; Peng Zhang; Ming-Ya Teng; Jia-Hao Chen; Lu-Chen Jiang; Bing-Feng Shi | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65dbe50066c13817298b6f76/original/cobalt-catalyzed-domino-transformations-via-enantioselective-c-h-activation-nucleophilic-3-2-annulation-towards-chiral-bridged-bicycles.pdf |
65d74326e9ebbb4db9f38c0f | 10.26434/chemrxiv-2024-s98nt | Printing Green: Microalgae-based materials for 3D printing with light | Microalgae offer significant advantages as a renewable resource due to their ability to fix CO2 during cultivation, rapid growth rates and the production of relevant metabolites. In particular, several microalgae accumulate lipids in high concentration, especially triglycerides, which can be used as feedstock for new high-value materials such as fuel. However, despite their great potential, microalgae remain unexplored in other fields, such as additive manufacturing. Herein, we exploit for the first time microalgae-based materials for high-resolution 3D printing using two-photon polymerization. In this study, Odontella aurita (BEA 0921B) and Tetraselmis striata (BEA 1102B) have been selected and cultivated as suitable microalgae accumulating high content of lipids. The extracts obtained from the microalgae (mainly triglycerides) have been functionalized with photopolymerizable groups and used directly as printable materials (inks). Notably, 3D printing is facilitated solely by the chlorophylls inherently contained in the microalgae extracts, without the need for further additives. We demonstrate the potential of the developed microalgae-based inks for the fabrication of complex 3D microstructures with sub-micron resolution. Furthermore, the 3D printed materials show biocompatibility. Our findings establish a new route for the next generation of sustainable, biobased, and biocompatible materials with great potential in life science applications. | Clara Vazquez-Martel; Lilliana Florido Martins; Elisa Genthner; Carlos Almeida; Antera Martel Quintana; Martin Bastmeyer; Juan Luis Gómez Pinchetti; Eva Blasco | Materials Science; Polymer Science; Biocompatible Materials | CC BY 4.0 | CHEMRXIV | 2024-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d74326e9ebbb4db9f38c0f/original/printing-green-microalgae-based-materials-for-3d-printing-with-light.pdf |
6746321af9980725cf0f27bc | 10.26434/chemrxiv-2024-jfjt1-v2 | Roughhousing with Ions: Surface-Induced Dissociation and Electron Capture Dissociation as Diagnostics of Q-Cyclic IMS-TOF Instrument Tuning Gentleness | Native mass spectrometry can characterize a range of biomolecular features pertinent to structural biology, including intact mass, stoichiometry, ligand-bound states, and topology. However, when an instrument’s ionization source is tuned to max-imize signal intensity or adduct removal, it is possible that the biomolecular complex’s tertiary and quaternary structures can be rearranged in a way that no longer reflect its native-like conformation. This could affect downstream ion activation exper-iments, leading to erroneous conclusions about the native-like structure. One such activation strategy is surface-induced dis-sociation (SID), which generally causes native-like protein complexes to dissociate along the weakest subunit interfaces, re-vealing critical information about the complex’s native-like topology and subunit connectivity. If the quaternary structure has been disturbed then the SID fingerprint will shift as well. Thus, SID was used diagnose source-induced quaternary struc-ture rearrangement and help tune an instrument’s source and other upstream transmission regions to strike the balance be-tween signal intensity, adduct removal, and conserving the native-like structure. Complementary to SID, electron-capture dissociation (ECD) can also diagnose rearranged quaternary structures and was used after in-source activation to confirm that the subunit interfaces were rearranged, opening the structure to electron capture and subsequent dissociation. These results provide a valuable guide for new practitioners to native mass spectrometry and highlight the importance of using standard protein complexes when tuning new instrument platforms for optimal native mass spectrometry performance. | Andrew Arslanian; Vicki Wysocki | Analytical Chemistry; Mass Spectrometry | CC BY 4.0 | CHEMRXIV | 2024-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6746321af9980725cf0f27bc/original/roughhousing-with-ions-surface-induced-dissociation-and-electron-capture-dissociation-as-diagnostics-of-q-cyclic-ims-tof-instrument-tuning-gentleness.pdf |
60c73efeee301c2168c787db | 10.26434/chemrxiv.7083257.v2 | Fluorescence Enhancement of a Microbial Rhodopsin via Electronic Reprogramming | The manuscript reports on two mutations of the photo-sensory protein Anabaena Sensory Rhodopsin and how these mutations modify the fluorescence quantum yield with respect to the wild-type protein. Experimental results are presented and explained theoretically on the basis of mixing of the S1 and S2 excited states. This mixing modulated by electrostatic and steric effects, tunes the excited state potential energy surface, and thereby the excited state lifetime and the fluorescence quantum yield.<br /> | Maria del Carmen Marin; Damianos Agathangelou; Yoelvis Orozco-González; Alessio Valentini; Yoshitaka Kato; Rei Abe-Yoshizumi; Hideki Kandori; Ahreum Choi; Kwang-Hwan Jung; Stefan Haacke | Microbiology; Biophysical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-09-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73efeee301c2168c787db/original/fluorescence-enhancement-of-a-microbial-rhodopsin-via-electronic-reprogramming.pdf |
60c755dc469df45961f451ec | 10.26434/chemrxiv.14130596.v2 | Bottom-up Fabrication and Atomic-scale Characterization of Triply-linked, Laterally π-Extended Porphyrin Nanotapes | <p>Porphyrin nanotapes (Por NTs) have attracted vast interest
as potential molecular wires thanks to their exceptional electronic properties.
Recently, Por NTs have been synthesized by solution-based methods,
demonstrating high versatility and great potential for technological
applications. However, their synthesis is tedious and their characterization
limited by low solubility and stability. Here, we report the first example of
meso-meso triply-fused Por NTs, which are prepared from a readily available Por
precursor through a two-step synthesis on Au(111). The structural and
electronic properties of individual Por NTs are addressed, both on Au(111) and
on a thin insulating NaCl layer, by high-resolution scanning probe
microscopy/spectroscopy complemented by density functional theory calculations.<br /></p> | Qiang Sun; Luis M. Mateos; Roberto Robles; Nicolas Lorente; Pascal Ruffieux; Giovanni Bottari; Tomás Torres; Roman Fasel | Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755dc469df45961f451ec/original/bottom-up-fabrication-and-atomic-scale-characterization-of-triply-linked-laterally-extended-porphyrin-nanotapes.pdf |
61ef90f51fd2741feb1a517d | 10.26434/chemrxiv-2022-7nh6d | Feedback-Controlled Topological Reconfiguration of Molecular Assemblies for Programming Supramolecular Structures | In biology, nonequilibrium assembly is characterized by fuel-driven switching between associating and nonassociating states of biomolecules. This dynamic assembly model has been used routinely to describe the nonequilibrium processes in synthetic systems. Here, we present a G-quartet-based nonequilibrium system mediated by fuel-driven co-assembly of guanosine 5’-monophosphate disodium salt hydrate and urease. Addition of lanthanum(III) ions to the system caused macroscopic dynamic switching between precipitates and hydrogels. Interestingly, combined analyses of the nonequilibrium systems demonstrated that molecules could switch between two distinct associating states without undergoing a nonassociating state, suggesting a nonequilibrium assembly mechanism of topological reconfiguration of molecular assemblies. We detailed quantitatively the nonequilibrium assembly mechanism to precisely control the phase behaviors of the active materials and, therefore, were able to apply the materials for transient-gel-templated polymerization and transient circuit connection. This work presents a new nonequilibrium system with unusual phase behavior, and the resultant active hydrogels hold substantial promise in applications including fluid confinements and transient electronics. | Panpan Li; Aixin Song; Jingcheng Hao; Xu Wang | Physical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ef90f51fd2741feb1a517d/original/feedback-controlled-topological-reconfiguration-of-molecular-assemblies-for-programming-supramolecular-structures.pdf |
60c75665702a9b1bc618c8e4 | 10.26434/chemrxiv.14228576.v1 | Circularity in Mixed Plastics Chemical Recycling Enabled by Variable Rates of Polydiketoenamine Hydrolysis | <div>Footwear, carpet, soft furnishings, automotive interiors, and multi-layer packaging are examples of products manufactured from several types of polymers whose inextricability poses significant challenges for recycling at end-of-life. Here, we show that chemical circularity in mixed-polymer recycling becomes possible by controlling the rates of depolymerization of polydiketoenamines (PDKs) over several orders of magnitude through molecular engineering. Stepwise deconstruction of mixed-PDK composites, laminates, and assemblies is chemospecific, allowing a prescribed subset of monomers, fillers, and additives to be recovered in pristine condition at each stage of the recycling process. We provide a theoretical framework to understand PDK depolymerization via acid-catalyzed hydrolysis and experimentally validate trends predicted for the rate-limiting step. The control achieved by PDKs in managing thermal and materials entropy points to new opportunities for pairing circular design with sustainable manufacturing.</div> | Jeremy Demarteau; alexander epstein; Peter Christensen; Mark Abubekerov; hai wang; Simon J Teat; Trevor Seguin; Christopher Chan; Corinne D. Scown; Thomas Russell; Jay Keasling; Kristin Persson; Brett Helms | Organic Polymers; Polymers | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75665702a9b1bc618c8e4/original/circularity-in-mixed-plastics-chemical-recycling-enabled-by-variable-rates-of-polydiketoenamine-hydrolysis.pdf |
60c73cc9f96a0069e8285ca0 | 10.26434/chemrxiv.14739486.v1 | Discovery of a Highly Potent and Selective Degrader Targeting Hematopoietic Prostaglandin D Synthase via in Silico Design | <p>Hematopoietic prostaglandin D synthase (H-PGDS) is an attractive target for the development of therapeutic agents for Duchenne muscular dystrophy (DMD) and other H-PGDS-related diseases. We have recently developed the H-PGDS degrader <b>PROTAC(H-PGDS)-1</b>, which is a chimeric molecule in which TFC-007 (that binds to H-PGDS) and pomalidomide (that binds to cereblon [CRBN]) were conjugated to the PEG5 linker. Herein, using a docking simulation of the ternary complex of the H-PGDS degrader, H-PGDS, and CRBN, we have succeeded in developing <b>PROTAC(H-PGDS)-7, </b>a new H-PGDS degrader that does not contain a linker. <b>PROTAC(H-PGDS)-7</b> showed potent and selective degradation activity (DC<sub>50</sub> = 17.3 pM), and potent suppression of prostaglandin D<sub>2</sub> (PGD<sub>2</sub>) production in KU812 cells. Additionally, in a DMD model using <i>mdx</i>mice with cardiac hypertrophy, <b>PROTAC(H-PGDS)-7</b> showed better inhibition of inflammatory cytokines than TFC-007. <b>PROTAC(H-PGDS)-7</b> is expected to be a promising candidate for the treatment of DMD and other H-PGDS-related diseases.</p> | Hidetomo Yokoo; Norihito Shibata; Akinori Endo; Takahito Ito; Yuta Yanase; Yuki Murakami; Kiyonaga Fujii; Yasushi Saeki; Mikihiko Naito; Kosuke Aritake; Yosuke Demizu | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9f96a0069e8285ca0/original/discovery-of-a-highly-potent-and-selective-degrader-targeting-hematopoietic-prostaglandin-d-synthase-via-in-silico-design.pdf |
6271528b5b9009189a25f318 | 10.26434/chemrxiv-2022-2gg11 | Linker-dependent folding rationalizes PROTAC cell permeability | Proteolysis targeting chimeras (PROTACs) must be cell permeable to reach their target proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical space at, or beyond, the outer limits of oral druggable space. We used NMR spectroscopy and MD simulations independently to gain insight into the origin of the differences in cell permeability displayed by three flexible cereblon PROTACs having closely related structures. Both methods revealed that the propensity of the PROTACs to adopt folded conformations with low solvent accessible 3D polar surface area in an apolar environment correlated to high cell permeability. The flexibility of the linker appeared essential for the PROTACs to populate folded conformations stabilized by intramolecular hydrogen bonds, pi-pi and van der Waals interactions. We conclude that MD simulations may be used for the prospective ranking of cell permeability in the design of cereblon PROTACs. | Vasanthanathan Poongavanam; Yoseph Atilaw; Stephan Siegel; Anja Giese; Lutz Lehmann; Daniel Meibom; Mate Erdelyi; Jan Kihlberg | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Chemical Biology; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6271528b5b9009189a25f318/original/linker-dependent-folding-rationalizes-protac-cell-permeability.pdf |
651496d8ade1178b243d81b7 | 10.26434/chemrxiv-2023-sxbg6 | Innate Reprocessability in Engineering Thermosets | While valued for their durability and exceptional performance, crosslinked thermosets are challenging to recycle and reuse. Here, we unveil inherent reprocessability in industrially relevant polyolefin thermosets. Unlike prior methods, our approach eliminates the need to introduce exchangeable functionality to regenerate the material, relying instead on preserving the activity of the metathesis catalyst employed in the curing reaction. Frontal ring opening metathesis polymerization (FROMP) proves critical to preserving this activity. We explore conditions controlling catalytic viability to successfully reclaim performance across multiple generations of material, thus demonstrating long-term reprocessability. This straightforward and scalable remolding strategy is poised for widespread adoption. Given the anticipated growth in polyolefin thermosets, our findings represent an important conceptual advance in the pursuit of a fully circular lifecycle for thermoset polymers. | Julian Cooper; Justine Paul; Nabil Ramlawi; Chaimongkol Saengow; Anisha Sharma; Benjamin Suslick; Randy Ewoldt; Nancy Sottos; Jeffrey Moore | Materials Science; Polymer Science; Materials Processing; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/651496d8ade1178b243d81b7/original/innate-reprocessability-in-engineering-thermosets.pdf |
60c74aa64c89195347ad32d3 | 10.26434/chemrxiv.12235928.v1 | A Multiphoton Single-Electron Reduction of Olefins via Tandem Photoredox Catalysis | <p><a></a>Herein we report a visible light multiphoton tandem photoredox catalysis strategy enabling a distinctive mode of olefin activation via a one electron reduction to the corresponding radical anion. This highly nucleophilic intermediate was harnessed to develop a method for the formal hydrogenation of unactivated alkenes under mild reaction conditions, in the absence of hydrogen gas or dissolving metals. <b></b></p> | Tyra Horngren; Mitchell S. Taylor; Milena Czyz; Anastasios Polyzos | Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aa64c89195347ad32d3/original/a-multiphoton-single-electron-reduction-of-olefins-via-tandem-photoredox-catalysis.pdf |
655b6a862c3c11ed71c6bb05 | 10.26434/chemrxiv-2023-k0fqx | Fluorescence lifetime imaging unravels the pathway of glioma cell death upon hypericin-induced photodynamic therapy | Malignant primary brain tumors are a group of highly aggressive and often infiltrating tumors that lack adequate therapeutic treatments to achieve long time survival. Complete tumor removal is one precondition to reach this goal. A promising approach to optimize resection margins and eliminate remaining infiltrative so-called guerilla cells is photodynamic therapy (PDT) using organic photosensitizers that can pass the disrupted blood-brain-barrier and selectively accumulate in tumor tissue. Hypericin fulfills these conditions and additionally offers outstanding photophysical properties, making it an excellent choice as a photosensitizing molecule for PDT. However, the actual hypericin-induced PDT cell death mechanism is still under debate. In this work, hypericin-induced PDT was investigated by employing the three distinct fluorescent probes hypericin, resorufin and propidium iodide (PI) in fluorescence-lifetime imaging microscopy (FLIM). This approach enables visualizing the PDT-induced photodamaging and dying of single, living glioma cells, as an in vitro tumor model for glioblastoma. Hypericin PDT and FLIM image acquisition were simultaneously induced by 405 nm laser irradiation and sequences of FLIM images and fluorescence spectra were recorded to analyze the PDT progression. The reproducibly observed cellular changes provide insight into the mechanism of cell death during PDT and suggest that apoptosis is the initial mechanism followed by necrosis after continued irradiation. These new insights into the mechanism of hypericin PDT of single glioma cells may help to adjust irradiation doses and improve the implementation as a therapy for primary brain tumors. | Miriam Bassler; Jonas Hiller; Frank Wackenhut; Sven zur Oven-Krockhaus; Philipp Frech; Felix Schmidt; Christoph Kertzscher; Tim Rammler; Rainer Ritz; Kai Braun; Marcus Scheele; Alfred J. Meixner; Marc Brecht | Physical Chemistry; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2023-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655b6a862c3c11ed71c6bb05/original/fluorescence-lifetime-imaging-unravels-the-pathway-of-glioma-cell-death-upon-hypericin-induced-photodynamic-therapy.pdf |
64ba3386b053dad33aa22f6d | 10.26434/chemrxiv-2023-qvb0g | Intermediate Transfer Rates and Solid-State Ion Exchange are Key Factors Determining the Bifunctionality of a Tandem CO2 Hydrogenation Catalyst | Probing the interaction between different active sites and transfer of reaction intermediates in bifunctional catalysts for tandem hydrogenation of CO2 is crucial for optimal catalyst design that maximize synergy to achieve high rates and product selectivity. Herein, thermocatalytic conversion of CO2 to hydrocarbon (HC) via a methanol (CH3OH) intermediate was investigated by modulating the placement of In2O3 and HZSM-5 in bifunctional admixtures at temperatures between 350 to 450 °C and 500 psig, to probe the key factors that drive synergy in these bifunctional systems. Analysis of the intermediate CH3OH transfer rates showed that although a millimeter scale placement of In2O3 and HZSM-5 yields a simple tandem reaction with a total HC and methanol CH3OH space-time yield of 8×10-6 molCgcat-1min-1, a microscale placement exhibits a ten-fold increase in catalytic activity with a total HC and CH3OH space-time yield of 8×10-5 molCgcat-1min-1 (at 400 °C) due to a faster advective and diffusive transfer rate of CH3OH. A combination of reactivity, spectroscopy with Raman, X-ray photoelectron spectroscopy (XPS), powder X-ray diffraction (PXRD) patterns, microscopy with scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and control experiments on methanol to hydrocarbons (MTH) revealed that further enhancing the reaction intermediate transfer at a nanoscale placement was counteracted by solid-state ion exchange (SSIE) between Brønsted acid sites (H+) of the HZSM-5 with the Inδ+ ions from In2O3, and that the formation of CH4 at the nanoscale placement was likely through CH3OH hydrogenolysis and not CO2 methanation at these intimate distances. Overall, our data showed the interconnected and subtle ways through which bifunctionality of catalysts could be regulated and paves the way for the development of design principles for designing more effective bifunctional catalysts for tandem CO2 hydrogenation. | Fatima Mahnaz; Jasan Mangalindan; Jenna Vito; Yu-Ting Lin; Mustafa Akbulut; Manish Shetty | Materials Science; Catalysis; Chemical Engineering and Industrial Chemistry; Acid Catalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ba3386b053dad33aa22f6d/original/intermediate-transfer-rates-and-solid-state-ion-exchange-are-key-factors-determining-the-bifunctionality-of-a-tandem-co2-hydrogenation-catalyst.pdf |
660bf8839138d23161f4abbe | 10.26434/chemrxiv-2024-7hwf7 | Protein Representations: Encoding Biological Information for Machine Learning in Biocatalysis | Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for industrial settings, an endeavor that is challenging and laborious. To address this issue, the power of machine learning can be harnessed to produce predictive models that facilitate in silico study and engineering of novel enzymatic properties. However, the conversion from the biological domain to the computational realm requires special attention to ensure the training of accurate and precise models. In this review, we examine the critical step of encoding protein information to numeric representations for use in machine learning. We selected the most important approaches for encoding the three distinct biological protein representations — primary sequence, 3D structure, and dynamics — to explore their requirements for employment and inherent biases. Combined representations of proteins and substrates are also introduced as emergent tools in biocatalysis. We propose the division of fixed representations, a collection of rule-based encoding strategies, and learned representations extracted from the latent spaces of large neural networks. To select the most suitable protein representation, we propose two main factors governing this choice. The first one is the model setup, being influenced by the size of the training dataset and the choice of architecture. The second factor is the model objectives, concerning the assayed property, the difference between wild-type models and mutant predictors, and requirements for explainability. This review is aimed at serving as a source of information and guidance for properly representing enzymes in future machine learning models for biocatalysis. | David Harding-Larsen; Jonathan Funk; Niklas Gesmar Madsen; Hani Gharabli; Carlos G. Acevedo-Rocha; Stanislav Mazurenko; Ditte Hededam Welner | Biological and Medicinal Chemistry; Catalysis; Biochemistry; Bioinformatics and Computational Biology; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660bf8839138d23161f4abbe/original/protein-representations-encoding-biological-information-for-machine-learning-in-biocatalysis.pdf |
65ba8d2866c1381729ac4cd6 | 10.26434/chemrxiv-2024-nn6xc | Identifying SARS-CoV-2 Variants using Single-Molecule Conductance Measurements | The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we i) select target sequences of interest for specific variants, ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS CoV-2 variants, as well as recognizes the emergence of new variants as they arise. | Zahra Aminiranjbar; Caglanaz Akin Gultakti; Mashari Nasser Alangari; Yiren Wang; Busra Demir ; Zeynep Koker; Arindam K. Das; M. P. Anantram; Ersin Emre Oren Emre Oren; Josh Hihath | Theoretical and Computational Chemistry; Nanoscience; Nanodevices; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ba8d2866c1381729ac4cd6/original/identifying-sars-co-v-2-variants-using-single-molecule-conductance-measurements.pdf |
65de9b5f66c1381729b95a67 | 10.26434/chemrxiv-2024-9pf8d | Put a Ring on It: Improving the Thermal Stability of Molybdenum Imides Through Ligand Rigidification | Volatile bis(tert-butylimido)-dichloromolybdenum(VI) compounds containing N,N’-chelating ligands, (tBuN)2MoCl2·L, have previously been used as single-source precursors for the chemical vapor deposition of high-purity Mo2N thin films. The first step in the thermolysis of these compounds is the partial dissociation of the chelating ligand to yield (tBuN)2MoCl2, which further decomposes by eliminating isobutylene and tBuNH2. The rate determining step in this process is the formation of a pentacoordinate intermediate where the previously bidentate ligand adopts a κ1-coordination. Here we show that rigidification of the ligand backbone, by incorporating various heterocycles, led to an overall increase in thermal stability (21−38 °C) of these complexes by preventing the formation of the κ1-intermediate. Formation of the κ1-intermediates is highlighted by high level calculations and is supported by experimental activation barriers. Finally, a model for the κ1-bipyridine adduct was isolated and characterized using 2-phenylpyridine. This careful control of the thermal stabilities of these compounds can lead to new vapor-phase deposition precursors for the preparation of Mo2N films. | Michael Land; Kieran Lawford; Lara Watanabe; Marshall Atherton; Sean Barry | Physical Chemistry; Inorganic Chemistry; Transition Metal Complexes (Inorg.); Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65de9b5f66c1381729b95a67/original/put-a-ring-on-it-improving-the-thermal-stability-of-molybdenum-imides-through-ligand-rigidification.pdf |
6654b5d091aefa6ce120d455 | 10.26434/chemrxiv-2024-fjrpp | NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation | We present the Netsci program - an open-source scientific software package that leverages GPU acceleration and a k-nearest-neighbor algorithm in order to estimate the mutual information (MI) between data in a set. The GPU acceleration presented here, as an improvement upon existing estimators, enables calculation speeds several orders of magnitude faster than CPU-based implementations, all with dataset size limits determined only by the available hardware. To demonstrate the validity and usefulness of Netsci, we show that the MI is correctly computed for the analytically-verifiable two-dimensional Gaussian distribution, and we also reproduce the generalized correlation (GC) analysis performed in an earlier study on the B1 domain of protein G. In addition, we apply Netsci to the analysis of molecular dynamics simulations of the Sarcoendoplasmic Reticulum Calcium-ATPase (SERCA) pump. Specifically, we use Netsci to understand the allosteric mechanisms and pathways of SERCA, and compare the differential effects of the binding of two nucleotides, ATP and 2'-deoxy-ATP (dATP). We determine that ATP binding to SERCA, compared to dATP, induces differential allosteric effects. The most likely information pathways from the bound nucleotide to the calcium binding domain are also predicted using our MI estimator in combination with network analysis tools on the SERCA pump, which differs based on the bound nucleotide. Netsci is shown to be a useful program for the estimation of MI and GC within general datasets, and for the analysis of intraprotein communication and information transfer, in particular. | Andrew Stokely; Lane Votapka; Marcus Hock; Abigail Teitgen; J Andrew McCammon; Andrew McCullough; Rommie Amaro | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6654b5d091aefa6ce120d455/original/net-sci-a-library-for-high-performance-biomolecular-simulation-network-analysis-computation.pdf |
6633a33191aefa6ce1fa00b4 | 10.26434/chemrxiv-2024-l76ph-v2 | Preparation and biochemical evaluation of diallyl-thiosulfinate/polyoxyethylene conjugated pH-responsive micelle with enhanced stability, hydrosolubility and antibacterial properties | Diallyl-thiosulfinate (allicin) is a major bioactive chemical with several notable therapeutic characteristics of garlic (Allium sativum). Nonetheless, one of the biggest concerns regarding the extensive use of allicin in biopharmaceutical commodities is its unstable characteristics. Therefore, utilizing Polyoxyethylene (Brij S20 and Brij 58), appropriate pH-responsive micelle carrier systems have been designed to entrap and improve allicin's stability at an ambient temperature (25 °C) while preserving its quantity and biological activity. Comparing the Brij S20 with the Brij 58 micelle carrier system, the latter demonstrated superior stability and entrapment. In addition, it was found that allicin's stability in micellized condition is significantly influenced by both pH and temperature (p<0.05). Additionally, the liberation of allicin from micelle is greatly aided by acidic pH 1.5. The liberation of allicin from the micelle in a controlled manner using lower pH as stimuli may facilitate its biological action at an individual's gastrointestinal lumen or near cancer cell environment having lower pH. Additionally, it was made sure that the micellization method did not impair allicin's bioactivity or reduce appropriate biocompatibility. The current study increases the likelihood of creating a commercially available allicin-loaded, micelle-based formulation for application in biopharma and food related industries. | Souptik Bhattacharya; Sayamdipta DasChowdhury | Biological and Medicinal Chemistry; Chemical Engineering and Industrial Chemistry; Agriculture and Food Chemistry; Food; Industrial Manufacturing; Pharmaceutical Industry | CC BY 4.0 | CHEMRXIV | 2024-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6633a33191aefa6ce1fa00b4/original/preparation-and-biochemical-evaluation-of-diallyl-thiosulfinate-polyoxyethylene-conjugated-p-h-responsive-micelle-with-enhanced-stability-hydrosolubility-and-antibacterial-properties.pdf |
6758b33a085116a133fd1356 | 10.26434/chemrxiv-2024-5ss7j | Bias Enhanced Electro-Photocatalysis on TiO2 Nanoporous Materials for Decomposition of Forever Chemicals in Saltwater | In this study, a TiO2-based bias-enhanced photocatalytic system was prepared with the aim of achieving high photocatalytic activity in deionized as well as in saltwater systems. Highly ordered TiO2 nanoporous materials were fabricated via a double-anodization method. A small potential bias was applied that suppresses electron-hole recombination and deters interference from the ions present in the solution while minimizing electrochemical reactions. Photodegradation reactions involving Rhodamine B (RhB) were conducted to evaluate the efficacy of the nanomaterials with and without the applied bias. Our experimental results revealed that the synthesized TiO2 nanomaterials possessed high photochemical activity under UVA light, substantially enhanced with the applied bias. A very significant enhancement was observed when the Bias Enhanced Electrolytic Photocatalysis (BEEP) system was used in saline solutions. Higher photocatalytic efficiency was achieved with the increase in the salinity level in the reaction mixture. These bias-enhanced nanomaterials were successfully tested for the degradation of per- and polyfluorinated substances (PFAS), recognized as a significant threat to the environment and human health. The results indicated that the presented technology could eliminate a wide range of fluorinated molecules. The simplicity, efficacy and scalability of the new BEEP approach described in this study make the use of TiO2-based advanced oxidation process (AOP) possible in designing high-performance water purification technologies applicable to fresh and salt water. | Sapanbir Thind; Bobby Ryane; John Hayden; Ian Chagunda; Mathias Paul; Jackie Hayden; Scott McIndoe | Catalysis; Chemical Engineering and Industrial Chemistry; Electrocatalysis; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6758b33a085116a133fd1356/original/bias-enhanced-electro-photocatalysis-on-ti-o2-nanoporous-materials-for-decomposition-of-forever-chemicals-in-saltwater.pdf |
63101526d858fbac8e63f565 | 10.26434/chemrxiv-2022-djw3f | (Alkali metal)decarboxylation reaction: Lone pair participation and design of diastereoselective enolate formation | Recently, we demonstrated that, contrary to the explanation in most textbooks on organic chemistry, the mechanism of the decarboxylation reaction can be more appropriately explained by the orbital theory, since the most electrondonating bond orbital, i.e., the highest occupied bond orbital, in a carbonyl group should be the lone pair on the oxygen, not the .pi.-bond orbital of the C=O bond. Thus, the electron moves from the lone pair to the .sigma.*-orbital of the OH bond, not from the .pi.-orbital of the carbonyl group. With this insight, we succeeded in developing the boradecarboxylation reaction. In our initial screening, the alkali metals were not so promising since they decomposed in TSs. However, the calculations were performed without considering solvation in the gas phase. We supposed that this was influenced by the strongly ionic character of the alkali metal ions. We reconsidered the calculations including those involv-ing the solvent molecules, dimethyl ether (DME) and THF. | Yuji Naruse; Tsubasa Ando | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63101526d858fbac8e63f565/original/alkali-metal-decarboxylation-reaction-lone-pair-participation-and-design-of-diastereoselective-enolate-formation.pdf |
6731f40e7be152b1d0b70c2e | 10.26434/chemrxiv-2024-0cvjg | Fluorescence Microscopy Imaging of Light-Harvesting in Self-Assembled Nanofibers of Naphthalenediimides towards Perylenediimide Guests | The self-assembly of a bichromophoric naphthalenediimide (NDI) into nanofibers showed efficient energy transfer (light-harvesting) to perylenediimide (PDI) molecules through host-guest interaction, which can be visualized by microscopy using samples deposited on glass surfaces. In combination with atomic force microscopy (AFM), spectral and polarization analyses, fluorescence imaging unveiled the inhomogeneity, packing defects, and relative spatial arrangement of PDI and NDI molecular units, which were found to affect the exciton mobility along the NDI nanofibers and the energy transfer efficiency from NDI to PDI guests. Fluorescence micro-spectroscopy shows that efficient energy transfer occurs from NDI nanofibers to isolated PDI molecules and their partial self-aggregates. The NDI nanofibers emit strong blue polarized emission, while the emission corresponding to PDI guest molecules is weakly polarized, indicating the local disruption of NDI chromophores-ordering upon PDI guest binding. | Ramarani Sethy; Arnaud Brosseau; Takuya Nakashima; Tsuyoshi Kawai; Rémi Métivier | Physical Chemistry; Photochemistry (Physical Chem.); Self-Assembly; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-11-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6731f40e7be152b1d0b70c2e/original/fluorescence-microscopy-imaging-of-light-harvesting-in-self-assembled-nanofibers-of-naphthalenediimides-towards-perylenediimide-guests.pdf |
615eead5a3d2c96139ceab44 | 10.26434/chemrxiv-2021-4dnn0 | A comprehensive investigation of Li-ion conductivity in lithium hydroxy halide antiperovskite solid electrolytes | Lithium hydroxide halide antiperovskite Li-ion conductors are ideal model systems for the systematic investigation of the effect of grain, grain boundary and interfacial resistance on the total Li-ion conductivity in solid-state batteries. Their low melting point (<300°C) empowers the use of melting and solidification to prepare pellets with high relative density without additional sintering steps and with control over grain size. The tunability of the halogen anion site enables control over grain conductivity and interfacial chemistry, with minimal structural perturbation. In this study, we conduct a comprehensive investigation of Li-ion conduction in Li2OHCl(1-x)Brx antiperovskites. We identify Li2OHCl0.9Br0.1 as the composition with the highest Li-ion conductivity of 2.52 E-3 mS/cm at room temperature. We highlight how the thermal expansion coefficient can serve as an indicator for the presence of structural defects hard to probe directly with X-ray techniques and essential in improving bulk Li-ion conduction. The detrimental effect of grain boundaries on ionic conductivity is demonstrated by atomistic calculations and validated experimentally by electrochemical impedance spectroscopy on pellets with controlled grain size. In-situ X-ray photoelectron spectroscopy experiments of Li2OHCl0.9Br0.1 demonstrate its chemical stability in contact with metallic lithium at room temperature. These insights provide design principles to improve Li-ion conductivity of lithium hydroxide halide antiperovskites. | Hyeon Jeong Lee; Brigita Darminto; Sudarshan Narayanan; Maria Diaz-Lopez; Albert Xiao; Yvonne Chart; Ji Hoon Lee; James Dawson; Mauro Pasta | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615eead5a3d2c96139ceab44/original/a-comprehensive-investigation-of-li-ion-conductivity-in-lithium-hydroxy-halide-antiperovskite-solid-electrolytes.pdf |
637e26260058eb266c623cca | 10.26434/chemrxiv-2023-0fqvw | Methanation of CO/CO2 mixtures: Evaluation of pellet size effect on methane formation rate and reactant selectivity | In the present contribution, numerical experiments are used to interpret results obtained from physical diffusion-influenced experiments for the CO and CO2 co-methanation. Physical and numerical experiments are conducted in the temperature range from 513 to 573 K and different CO/CO2 ratios. It is revealed that CO and CO2 behave very differently when both are simultaneously converted into CH4, which is mainly due to the competing reaction kinetics. Since CO inhibits the methanation of both CO2 and itself, large pellets and the associated diffusion limitation can be used to reduce the concentration of CO inside the pellets and hence its overall inhibiting effect. This catalyst design aspect can be used to increase the effective methane formation rate up to 35 % for a co-methanation of CO and CO2, while larger pellets allow to reduce the pressure drop in the reactor at the same time, which provides further advantages for reactor operation. Moreover, it is found that a selective CO methanation can be conducted with low-loading (nickel) catalysts, as long as the catalyst is operated in the low-temperature region (T << 300 °C) with small particle sizes below 1.5 mm. In addition, it is shown that industrially relevant catalysts significantly affect the reactant selectivity. | Jannik Schumacher; Dominik Meyer; Jens Friedland; Robert Güttel | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Transport Phenomena (Chem. Eng.); Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2023-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637e26260058eb266c623cca/original/methanation-of-co-co2-mixtures-evaluation-of-pellet-size-effect-on-methane-formation-rate-and-reactant-selectivity.pdf |
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