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60c73dd5bb8c1a61fe3d9815 | 10.26434/chemrxiv.6199280.v1 | Probing the Basis Set Limit for Thermochemical Contributions of Inner-Shell Correlation: Balance of Core-Core and Core-Valence Contributions | The inner-shell correlation contributions to the total atomization energies of the W4-17 computational thermochemistry benchmark have been determined at the CCSD(T) level near the basis set limit using several families of core correlation basis sets, such as aug-cc-pCVnZ (n=3-6), aug-cc-pwCVnZ (n=3-5), and nZaPa-CV (n=3-5). The three families of basis sets agree very well with each other (0.01 kcal/mol RMS) when extrapolating from the two largest available basis sets: however, there are considerable differences in convergence behavior for the smaller basis sets. nZaPa-CV is superior for the core-core term and awCVnZ for the core-valence term. While the aug-cc-pwCV(T+d)Z basis set of Yockel and Wilson is superior to aug-cc-pwCVTZ, further extension of this family proved unproductive. The best compromise between accuracy and computational cost, in the context of high-accuracy computational thermochemistry methods such as W4 theory, is CCSD(T)/awCV{T,Q}Z, where the {T,Q} notation stands for extrapolation from the awCVTZ and awCVQZ basis set pair. For lower-cost calculations, a previously proposed combination of CCSD-F12b/cc-pCVTZ-F12 and CCSD(T)/pwCVTZ(no f) appears to ‘give the best bang for the buck’. While core-valence correlation accounts for the lion’s share of the inner shell contribution in first-row molecules, for second-row molecules core-core contributions may become important, particularly in systems like P<sub>4</sub>and S<sub>4</sub>with multiple adjacent second-row atoms.<div>[In memory of Dieter Cremer, 1944-2017]</div> | Nitai Sylvetsky; Gershom Martin | Computational Chemistry and Modeling; Theory - Computational; Clusters | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd5bb8c1a61fe3d9815/original/probing-the-basis-set-limit-for-thermochemical-contributions-of-inner-shell-correlation-balance-of-core-core-and-core-valence-contributions.pdf |
677d6687fa469535b91b48ba | 10.26434/chemrxiv-2024-0h9t2-v3 | Photosulfoxidation catalysis as the driving principle for the deazaoxaflavin photoredox catalyst formation | Catalysts are essential for sustainability because they decrease the energy and resource consumption in the production of high value-added products. The design of a novel catalyst is a challenging and expensive target, and a simplified methodology for catalyst development can trigger burgeoning progress in both academic and applied research. Here, we demonstrate a reaction network that autonomously yields the photoredoxcatalyst for transformation of the provided substrate under applied catalytic conditions. The system stems from the reversible condensation pathway leading to deazaoxaflavins, 2H-chromeno[2,3-d]pyrimidine synthetic analogs of flavins, with which they share photoorganocatalytic activity. We report on the photocatalytic activity of deazaoxaflavins and their covalently dynamic behavior. The reversibility principle allows for the exchange of one of the deazaoxaflavin constituents for a different moiety, thus leading to the adaptability of the catalyst. We argue that the observed phenomenon is of thermodynamic origin and thus can be applied to other photo/organocatalytic reactions, in which the combination of a suitable substrate and conditions are the governing principle for catalyst formation. | Karolína Křížová; Rimeh Ismail; Tung Anh Nguyen; Marek Bříza; Anna Geleverya; Valentino Guerra; Petr Kovaricek | Organic Chemistry; Catalysis; Organocatalysis; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d6687fa469535b91b48ba/original/photosulfoxidation-catalysis-as-the-driving-principle-for-the-deazaoxaflavin-photoredox-catalyst-formation.pdf |
67364af2f9980725cf35c53d | 10.26434/chemrxiv-2024-x1nfd | Realizing Ultra-Fine Color Tuning of Organic Electronics Materials by Electronic State Informatics | One of the challenges in materials informatics is establishing a way to describe molecular functions governed by multi-electronic states. Here, we show a study of advanced spectral optimization including beyond 20 electronic states toward ordinally uncolored organic electrochromic material design, where the color (magenta) is one of the three primary colors that had never been achieved due to the advanced spectroscopic requirements in a redox process. Using qualitatively accurate and computationally cheap semiempirical molecular orbital descriptors, desired structures were efficiently narrowed from 1.2 million triphenylamine derivatives and realized by subsequent organic syntheses with spectroelectrochemical experiments. The universality of the protocol would allow the simultaneous optimization of multiple functions in organic electronics materials. | Daisuke Goto; Yusuke Kanebako; Kengo Takashima; Nahoko Kuroki; Hirotoshi Mori | Theoretical and Computational Chemistry; Materials Science; Dyes and Chromophores; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67364af2f9980725cf35c53d/original/realizing-ultra-fine-color-tuning-of-organic-electronics-materials-by-electronic-state-informatics.pdf |
60c73d92469df41ff9f42743 | 10.26434/chemrxiv.5917114.v1 | Are Dispersion Corrections Accurate Outside Equilibrium? A Case Study on Benzene | Modern approaches to modelling dispersion forces are becoming increasingly accurate, and can predict accurate binding distances and energies. However, it is possible that these successes reflect a fortuitous cancellation of errors at equilibrium. Thus, in this work we investigate whether a selection of modern dispersion methods agree with benchmark calculations across several potential-energy curves of the benzene dimer to determine if they are capable of describing forces and energies outside equilibrium. We find the exchange-hold dipole moment (XDM) model describes most cases with the highest overall agreement with reference data for energies and forces, with many-body dispersion (MBD) and its fractionally ionic (FI) variant performing essentially as well. Popular approaches, such as Grimme-D and van der Waals density functional approximations (vdW-DFAs) underperform on our tests. The meta-GGA M06-L is surprisingly good for a method without explicit dispersion corrections. Some problems with SCAN+rVV10 are uncovered and briefly discussed.<br /> | Tim Gould; Erin R. Johnson; Sherif Abdulkader Tawfik | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2018-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d92469df41ff9f42743/original/are-dispersion-corrections-accurate-outside-equilibrium-a-case-study-on-benzene.pdf |
60c73dfcbdbb890ef4a37d58 | 10.26434/chemrxiv.5831751.v2 | The tetragonal elastic dipole Cr5+ in SrTiO3 | Tetragonal Cr<sup>5+</sup> impurity centre in single crystals
of the perovskite SrTiO<sub>3</sub>. After careful analyses we came to the
conclusion that this centre is an off-centre system and no Jahn-Teller
impurity. From the previous stress experiments in EPR we calculated the linear
stress coupling tensor as β = 3.56×10<sup>-30</sup> m<sup>3</sup>, which is in
agreement with other stress coupling tensors of off-centre systems in SrTiO<sub>3</sub>
as well as BaTiO<sub>3</sub>. | Thomas (Tom) Kool | Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2018-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dfcbdbb890ef4a37d58/original/the-tetragonal-elastic-dipole-cr5-in-sr-ti-o3.pdf |
66c576a4f3f4b052908ddaab | 10.26434/chemrxiv-2024-rpml5-v2 | Frustrated van der Waals heterostructures | Geometrical frustration results from the packing of constituents in a lattice, where the constituents have conflicting forces. The phenomenon is known in glass materials, and this work expands the concept of geometrical frustration into the realm of van der Waals two-dimensional materials. Using density functional theory with the r$^2$SCAN+rVV10 exchange-correlation potential, we find a number of two-dimensional heterostructures with alternating strains, where one layer is strained and the adjacent layer is compressed. We adopted three structural stability criteria to find synthesisable candidate materials: phonon dispersion of the individual layers, comparing the thermodynamic stability of this class of materials, frustrated van der Waals heterostructures, with the non-frustrated counterparts, and \textit{ab initio} molecular dynamics simulations. These criteria were applied to 9 frustrated van der Waals heterostructures, identifying two materials that are potentially stable. We discuss possible fabrication pathways for creating this class of materials. | Sherif Abdulkader Tawfik | Materials Science; Nanostructured Materials - Materials | CC BY 4.0 | CHEMRXIV | 2024-08-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c576a4f3f4b052908ddaab/original/frustrated-van-der-waals-heterostructures.pdf |
6463c10aa32ceeff2dc08c49 | 10.26434/chemrxiv-2023-k73qz-v2 | NP-SAM: Implementing the Segment Anything Model for Easy Nanoparticle Segmentation in Electron Microscopy Images | Despite the numerous existing (semi)automated workflows for image segmentation of electron microscopy pictures of nanoparticles for statistical size and shape determination the prevalent approach to particle counting still is doing so in cumbersome manual fashion. Here, we present an easily implementable, low entry barrier workflow for nanoparticle segmentation, which eliminates the need for manual particle counting. It is based on the recently released segment anything model and widely distributed, well maintained, python libraries. We explore the impressive zero shot performance of the segment anything model and present approaches for subsequent filtering of outputs to minimize over and under segmentation on a range of different electron microscopy images of nanoparticles. Furthermore, we introduce a novel methodology for handling partial overlap between nanoparticles, which comprise one of the biggest obstacles for many automated segmentation algorithms. Our presented workflow is easily adaptable, and we encourage the community to further build on the work we present here. | Rasmus Larsen; Torben L. Villadsen; Jette K. Mathiesen; Kirsten M. Ø. Jensen; Espen D. Boejesen | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6463c10aa32ceeff2dc08c49/original/np-sam-implementing-the-segment-anything-model-for-easy-nanoparticle-segmentation-in-electron-microscopy-images.pdf |
673ca5d47be152b1d09fc528 | 10.26434/chemrxiv-2024-vx797-v3 | pKa Prediction in Non-Aqueous Solvents | Acid dissociation constants (pKa) are widely measured and studied, most typically in water. Comparatively few datasets and models for non-aqueous pKa values exist. In this work, we demonstrate how the pKa in one solvent can be accurately determined using reference data in another solvent, corrected by solvation energy calculations from the COSMO-RS method. We benchmark this approach in ten different solvents, and find that pKa values calculated in six solvents deviate from experimental data on average by less than 1 pKa unit. We observe comparable performance on a more diverse test set including amino acids and drug molecules, with higher error for large molecules. The model performance in four other solvents is worse, with some MAEs exceeding 3 pKa units; we discuss how such errors arise due to both model error and inconsistency in obtaining experimental data. Finally, we demonstrate how this technique can be used to estimate the proton transfer energy between different solvents, and use this to report a value of the proton’s solvation energy in formamide, a quantity that does not have a consensus value in literature. | Jonathan W. Zheng; Emad Al Ibrahim; Ivari Kaljurand; Ivo Leito; William H. Green | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Organic Compounds and Functional Groups; Computational Chemistry and Modeling; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673ca5d47be152b1d09fc528/original/p-ka-prediction-in-non-aqueous-solvents.pdf |
63b5845b81e4ba1bdc659e89 | 10.26434/chemrxiv-2023-cn4q1 | Competitive Aminal Formation during the Synthesis of a Highly Soluble, Isopropyl-Decorated Imine Porous Organic Cage | The synthesis of a new porous organic cage decorated with isopropyl moieties (CC21) was achieved from the reaction of triformylbenzene and an isopropyl functionalised diamine. Unlike structurally analogous porous organic cages, its synthesis proved challenging due to competitive aminal formation, rationalised using control experiments and computational modelling. The use of an additional amine was found to increase conversion to the desired cage. | Rachel Kearsey; Andrew Tarzia; Marc Little; Michael Brand; Rob Clowes; Kim Jelfs; Andrew Cooper; Rebecca Greenaway | Organic Chemistry; Supramolecular Chemistry (Org.); Materials Chemistry; Crystallography – Organic | CC BY 4.0 | CHEMRXIV | 2023-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63b5845b81e4ba1bdc659e89/original/competitive-aminal-formation-during-the-synthesis-of-a-highly-soluble-isopropyl-decorated-imine-porous-organic-cage.pdf |
60c74a0a4c891995baad315c | 10.26434/chemrxiv.12086565.v2 | Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach | <p>In this work, computer-aided drug design method has been implemented to
quickly identify promising drug repurposing
candidates against COVID-19 main protease (M<sup>pro</sup>)<sup> </sup>. The world is facing an epidemic and in absence of
vaccine or any effective treatment, it has created a sense of urgency for novel
drug discovery approaches. We have made an immediate effort by performing
virtual screening of clinically approved drugs or molecules under clinical
trials against COVID-19 M<sup>pro</sup> to identify potential drug molecules. With given knowledge of this system, N3 and 13B
compounds have shown inhibitory effect against COVID-19 M<sup>pro</sup>. Both the compounds were
considered as control to filter out the screened molecules. Overall, we have identified six potential compounds, Leupeptin
Hemisulphate, Pepstatin A, Nelfinavir , Birinapant, Lypression and Octeotide which
have shown the docking energy > -8.0 kcal/mol and MMGBSA > -68.0 kcal/mol.
The binding pattern of these compounds suggests that they interacted with key <i>hot-spot</i> residues. Also, their pharmacokinetic annotations and therapeutic importance have indicated that
they possess drug-like properties and could pave their way for<i> in-vitro</i> studies. The findings of this work will be significant for structure and
pharmacophore-based designing. </p> | Lovika Mittal; Anita Kumari; Mitul Srivastava; Mrityunjay Singh; Shailendra Asthana | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a0a4c891995baad315c/original/identification-of-potential-molecules-against-covid-19-main-protease-through-structure-guided-virtual-screening-approach.pdf |
645db7c5a32ceeff2d802583 | 10.26434/chemrxiv-2023-6tgkh | A novel “activation switch” motif common to all aminergic receptors | Aminergic receptors are G protein-coupled receptors (GPCRs) that transduce signals from small endogenous biogenic amines to regulate intracellular signaling pathways. Agonist binding in the ligand binding pocket on the extracellular side opens and prepares a cavity on the intracellular face of the receptors to interact with and activate G proteins and β-arrestins. Here, by reviewing and analyzing all available aminergic receptor structures, we seek to identify activation-related conformational changes that are independent of the specific scaffold of bound agonist, which we define as “activation conformational changes” (ACCs). While some common intracellular ACCs have been well-documented, identifying common extracellular ACCs, including those in the ligand binding pocket, is complicated by local adjustments to different ligand scaffolds. Our analysis shows no common ACCs at the extracellular ends of the transmembrane helices. Furthermore, the restricted access to the ligand binding pocket identified previously in some receptors is not universal. Notably, the Trp6.48 toggle switch and the Pro5.50-Ile3.40-Phe6.44 (PIF) motif at the bottom of the ligand binding pocket have previously been proposed to mediate the conformational consequences of ligand binding to the intracellular side of the receptors. Our analysis shows that common ACCs in the ligand binding pocket are associated with the PIF motif and nearby residues, including Trp6.48, but fails to support a shared rotamer toggle associated with activation. However, we identify two common rearrangements between the extracellular and middle subsegments, and propose a novel “activation switch” motif common to all aminergic receptors. This motif includes the middle subsegments of transmembrane helices 3, 5, and 6, and integrates both the PIF motif and Trp6.48. | Kuo Hao Lee; Jamie Manning; Jonathan Javitch; Lei Shi | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645db7c5a32ceeff2d802583/original/a-novel-activation-switch-motif-common-to-all-aminergic-receptors.pdf |
65265eccbda59ceb9a54a222 | 10.26434/chemrxiv-2023-x4b1g | HSQC Spectra Simulation and Matching for Molecular Identification | In the pursuit of improved compound identification and database search tasks, this study explores Heteronuclear Single Quantum Coherence (HSQC) spectra simulation and matching methodologies. HSQC spectra serve as unique molecular fingerprints, enabling a valuable balance of data collection time and information richness. We conducted a comprehensive evaluation of four HSQC simulation techniques: ACD-Labs (ACD), MestReNova (MNova), Gaussian NMR calculations (DFT), and a graph-based neural network (ML). For with the latter two techniques, we developed a reconstruction logic to combine proton and carbon 1D spectra into HSQC spectra.
The methodology involved the implementation of three peak-matching strategies (Minimum-Sum, Euclidean-Distance, and Hungarian-Distance) combined with three padding strategies (zero-padding, peak-truncated, and nearest-neighbor double assignment). We found that coupling these strategies with a robust simulation technique facilitates the accurate identification of correct molecules from similar analogues (regio- and stereoisomers) and allows for fast and accurate large database searches. Furthermore, we demonstrated the efficacy of the best-performing methodology by rectifying the structures of a set of previously misidentified molecules.
This research indicates that effective HSQC spectra simulation and matching methodologies significantly facilitate molecular structure elucidation. Furthermore, we offer a Google Colab notebook for researchers to use our methods on their own data.
| Martin Priessner; Anna Tomberg; Jon Paul Janet; Richard J. Lewis; Jonathan M. Goodman; Magnus J. Jonahnsson | Theoretical and Computational Chemistry; Analytical Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65265eccbda59ceb9a54a222/original/hsqc-spectra-simulation-and-matching-for-molecular-identification.pdf |
60c742ef567dfe0f8bec3fdf | 10.26434/chemrxiv.8856146.v1 | Thiourea and Guanidine Compounds and their Iridium Complexes in Drug-Resistant Cancer Cell Lines: Structure-Activity Relationships and Direct Luminescent Imaging | <p>Thiourea and guanidine units are found in
nature, medicine, and materials. Their continued exploration in applications as
diverse as cancer therapy, sensors, and electronics means that their toxicity
is an important consideration. We have systematically synthesised a set of
thiourea compounds and their guanidine analogues, and elucidated
structure-activity relationships in terms of cellular toxicity in three ovarian
cancer cell lines and their cisplatin-resistant sub-lines. We have been able to
use the intrinsic luminescence of iridium complexes to visualise the effect of
both structure alteration and cellular resistance mechanisms. These findings
provide starting points for the development of new drugs and consideration of
safety issues for novel thiourea- and guanidine-based materials.</p> | Samuel J. Thomas; Barbora Balonova; Jindrich Cinatl; Mark Wass; Christopher Serpell; Barry Blight; Martin Michaelis | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ef567dfe0f8bec3fdf/original/thiourea-and-guanidine-compounds-and-their-iridium-complexes-in-drug-resistant-cancer-cell-lines-structure-activity-relationships-and-direct-luminescent-imaging.pdf |
60c749c0bdbb896342a39230 | 10.26434/chemrxiv.12090408.v1 | Drug Repurposing to Identify Therapeutics Against COVID 19 with SARS-Cov-2 Spike Glycoprotein and Main Protease as Targets: An in Silico Study | <p>The
total cases of novel corona virus (SARS-CoV-2)
infections is more than one million and total deaths recorded is more than fifty thousand.
The research for developing vaccines and drugs against SARS-CoV-2 is going on in different parts of the world. Aim
of the present study was
to identify
potential drug
candidates against
SARS-CoV-2 from existing drugs using <i>in silico</i> molecular modeling and
docking. The targets for the present study was the spike
protein and the main
protease of SARS-CoV-2. The study was able to identify some drugs that can either bind to the spike protein receptor
binding domain or the main protease of SARS-CoV-2. These include some of the antiviral drugs. These
drugs might have the potential
to inhibit the infection and viral replication.</p> | arun kumar; Sharanya C.S; Abhithaj J; Sadasivan C | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749c0bdbb896342a39230/original/drug-repurposing-to-identify-therapeutics-against-covid-19-with-sars-cov-2-spike-glycoprotein-and-main-protease-as-targets-an-in-silico-study.pdf |
6761896781d2151a02079948 | 10.26434/chemrxiv-2024-h5zgs | Discovery and Optimization of a Novel Carboxamide Scaffold with Selective Antimalarial Activity | Artemisinin combination therapies (ACTs) are critical components of malaria control worldwide. Alarmingly, ACTs have begun to fail, owing to the rise in artemisinin resistance. Thus, there is an urgent need for an expanded set of novel antimalarials to generate new combination therapies. Herein, through a virtual high-throughput screen (vHTS), cheminformatics-driven down-selection, and structure-activity relationship (SAR) studies, we have identified a 1,2,4-triazole-containing carboxamide scaffold; while the most promising triazole displayed 519 nM potency against the asexual blood stages of the parasite, this activity was unable to be surpassed. Scaffold hopping efforts then revealed three alternative cores with up to a 2.5-fold increase in potency from the aforementioned front-runner triazole. The lead compound of this class, a deuterated picolinamide, displays moderate aqueous solubility (13.4 µM) and metabolic stability (CLintapp HLM 17.3 µL/min/mg) in vitro, as well as moderate oral bioavailability (% F 16.2) in in vivo pharmacokinetic studies. Front-runners representing three cores were confirmed potent against a panel of three clinical isolates harboring different resistance profiles, suggesting a novel mechanism of action, and the lead compound displayed a slow-to-moderate rate of killing (average PRR 2.4) in a parasite reduction ratio assay, making the series appealing for further development. | Alicia Wagner; Roger Trombley; Maris Podgurski; Anthony A. Ruberto; Meng Cui; Caitlin A. Cooper; William E. Long; Gia-Bao Nguyen; Adriana A. Marin; Sarah Lee Mai; Franco Lombardo; Steven P. Maher; Dennis E. Kyle; Roman Manetsch | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6761896781d2151a02079948/original/discovery-and-optimization-of-a-novel-carboxamide-scaffold-with-selective-antimalarial-activity.pdf |
66307f9b21291e5d1d0f98cb | 10.26434/chemrxiv-2024-5jl5n | Towards the Atomic-Level Analysis of Ground-State Electronic Structures of Solid Materials via Prediction from Core-Loss Spectra | Local electronic structure at the ground state is essential for understanding the stability and properties of materials. Core-loss spectroscopy using electron or X-ray provides the insights into the local electronic structure, but directly observable information is limited to the partial density of state (PDOS) of the conduction band at the excited state. To overcome this limitation, we developed a machine learning (ML) approach by creating a database of Si-K core-loss spectra and corresponding ground-state PDOS for various silicon structures. Using this database, we constructed an ML model capable of predicting atom-specific ground-state PDOS of the valence and conduction bands from Si-K edges. Our model demonstrated the ability of ML to extract the complex correlation between ground-state PDOS and Si -K edges. This study provides crucial insights into achieving atomic-level analysis of ground-state electronic structures, paving the way for a deeper understanding of stability and properties of materials. | Izumi Takahara; Kiyou Shibata; Teruyasu Mizoguchi | Physical Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66307f9b21291e5d1d0f98cb/original/towards-the-atomic-level-analysis-of-ground-state-electronic-structures-of-solid-materials-via-prediction-from-core-loss-spectra.pdf |
60c75474f96a001f8f28866f | 10.26434/chemrxiv.13619180.v2 | Aminobismuthination of CO2 | We report the facile (25 <sup>o</sup>C, 1 atm, <5 minutes) and selective insertion of CO<sub>2</sub> into Bi-N bonds to yield bismuth carbamates. The role of ligand and substituent on promoting the controlled aminobismuthination of CO<sub>2</sub> and rendering the bismuth carbamate products stable against thermal decomposition and ligand degradation is revealed. <br /> | Katherine Marczenko; Saurabh Chitnis | Kinetics and Mechanism - Inorganic Reactions; Theory - Inorganic; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75474f96a001f8f28866f/original/aminobismuthination-of-co2.pdf |
67a18a7dfa469535b9fb6fd4 | 10.26434/chemrxiv-2023-48zsc-v2 | Battery Electric Long-Haul Trucking in the United States: A Comprehensive Costing and Emissions Analysis | This work presents a costing and emissions analysis of long-haul battery electric trucks (BETs) with overnight charging for the U.S. market. First, we compute the energy
requirements of a long-haul truck for a 600-mile (966 km) real-world driving range and perform battery sizing. The battery sizes are used along with a fleet-replacement
model and the U.S. payload distribution to compute payload losses for two different chemistries, Nickel-Manganese-Cobalt (NMC) and Lithium-Iron-Phosphate (LFP). Given present battery energy densities, BET fleets will require 1.06 and 1.27 times the trucks of a diesel fleet to provide the same cargo capacity. Next, we perform electricity pricing analysis for high-power applications. Our baseline scenario estimates a price of 0.32 USD/kWh, and it only decreases to 0.15 USD/kWh for the optimistic scenario. Currently, we compute the total cost of ownership for BETs to be more than twice (>2x) that of diesel trucks, however, the price premium is projected to decrease significantly to 1.2x in the long term. BETs could become economically competitive with diesel if the delivered cost of electricity for high-power applications drops below 0.1 USD/kWh, and if we realize projected improvements in battery energy density and cost. Our emissions analysis shows negligible present-day greenhouse gas (GHG) benefits from switching to BETs, primarily due to the carbon intensity of electricity generation. In the long term, we project BETs to have 40% less GHG emissions than diesel. Today, BETs are not well-suited for the long-haul trucking sector. However, our sensitivity analysis shows that operating with battery swapping and short-haul applications could potentially benefit from electrification, hence we encourage further investigation. Our analysis framework is provided as a Google Colab Notebook that can be modified to
assist these needed future studies. | Kariana Moreno Sader; Sayandeep Biswas; Rob Jones; Marian Mennig; Reza Rezaei; William H. Green | Energy; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2025-02-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a18a7dfa469535b9fb6fd4/original/battery-electric-long-haul-trucking-in-the-united-states-a-comprehensive-costing-and-emissions-analysis.pdf |
61ee04a671868d22fdbc8856 | 10.26434/chemrxiv-2022-w1c6h | Exploration of organic superionic glassy conductors by process and materials informatics with lossless graph database | Data-driven material exploration is a ground-breaking research style; however, daily experimental results are difficult to record, analyze, and share. We report a new data platform that losslessly describes the relationships of structures, properties, and processes as graphs in electronic laboratory notebooks. As a model project, organic superionic glassy conductors were explored by recording over 500 different experiments. Automated data analysis revealed the essential factors for a remarkable room temperature ionic conductivity of 10^−4-10^−3 S/cm and a lithium transference number of around 0.8. In contrast to previous materials research, everyone can access all the experimental results, including graphs, raw measurement data, and data processing systems, at a public repository. Direct data sharing will improve scientific communication and accelerate integration of material knowledge. | Kan Hatakeyama-Sato; Momoka Umeki; Hiroki Adachi; Naoaki Kuwata; Gen Hasegawa; Kenichi Oyaizu | Theoretical and Computational Chemistry; Materials Science; Composites; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ee04a671868d22fdbc8856/original/exploration-of-organic-superionic-glassy-conductors-by-process-and-materials-informatics-with-lossless-graph-database.pdf |
648c448de64f843f41df6375 | 10.26434/chemrxiv-2023-6rbfj | Recommending Multiple Reaction Conditions Using
Two-Stage Deep Neural Networks | The temperatures, prices of reagent and solvent and the yields influence the feasibility of the
synthetic pathway. Therefore, predicting reaction condition is an important topic when designing
a profitable synthetic pathway. For a single-step reaction, there are sometimes more than one
suitable reaction contexts. Different reaction conditions result in different reaction rate and
selectivity, and the design should comply with the requirement of the chemists. Providing diverse
alternatives could help design the more economic synthesis pathway. However, recent literature
has only tried to predict one best reaction condition. To improve this situation, we construct a twostage
listwise ranking model to recommend multiple reaction conditions, and the ranking metrics
are based on the yield level. The model is trained on the dataset consisting of ten representative
types of reaction exported from Reaxys, and it recommends the reaction conditions with the top-
20 mean average precision (MAP) equal to 0.2723. The MAE of the temperature prediction is 11.1
°C. Besides, we used t-SNE to reduce the dimensionality of the embeddings and found that the
model implicitly learns the pattern of reaction classification when predicting the reaction
conditions. | Lung-Yi Chen; Yi-Pei Li | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648c448de64f843f41df6375/original/recommending-multiple-reaction-conditions-using-two-stage-deep-neural-networks.pdf |
656dfe045bc9fcb5c907eb93 | 10.26434/chemrxiv-2023-c24qz | Structure-Guided Investigation of Fungal Adenylation Domain Substrate Selectivity | Adenylation (A) domains are the primary gatekeepers to substrate selectivity in nonribosomal peptide synthetases (NRPSs). A significant body of work has investigated key structural motifs contributing to substrate activation in bacterial A domains, but these findings have often failed to hold true in fungal systems. Here, we employed homology modeling to interrogate the structures of bacterial and fungal A domains, aiming to improve bioinformatic predictions of substrate selectivity “codes,” particularly for uncommon and nonproteinogenic building blocks. After comparing five different homology modeling tools to an existing crystal structure, we generated 46 structural models for a variety of bacterial and fungal A domains, both characterized and uncharacterized. We were able to identify an 18 amino acid code by distance-mapping residues within 5 Å of a docked substrate, which acts as a more reliable predictor of substrate binding than existing in silico methods. This new 18 residue code was then confirmed through mutagenesis experiments, allowing for the activation of non-native substrates by a previously characterized fungal A domain. | Stephanie Heard; Jaclyn Winter | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656dfe045bc9fcb5c907eb93/original/structure-guided-investigation-of-fungal-adenylation-domain-substrate-selectivity.pdf |
667e9c8c5101a2ffa8c914ad | 10.26434/chemrxiv-2024-fj8s9 | Ab Initio Molecular Dynamics Simulations of Atmospheric Molecular Clusters Boosted by Neural Networks | The computational cost of accurate quantum chemistry (QC) calculations of large molecular systems can often be unbearably high. Machine learning offers a lower computational cost compared to QC methods while maintaining their accuracy. In this study, we employ the polarizable atom interaction neural network (PaiNN) architecture to train and model the potential energy surface of molecular clusters relevant to atmospheric new particle formation, such as sulfuric acid–ammonia clusters. We compare the differences between the neural network and previous kernel ridge regression modeling for the Clusteromics I–V data sets. We showcase three models capable of predicting electronic binding energies and interatomic forces with mean absolute errors of <0.3 kcal/mol and <0.2 kcal/mol/ ̊A, respectively. Furthermore, we demonstrate that the error of the modeled properties remains below the chemical accuracy of 1 kcal/mol even for clusters vastly larger than those in the training database (up to (H2SO4)15(NH3)15 clusters, containing 30 molecules). Consequently, we emphasize the potential applications of these models for faster and more thorough configurational sampling and for boosting molecular dynamics studies of large atmospheric molecular clusters. | Jakub Kubečka; Daniel Ayoubi; Zeyuan Tang; Yosef Knattrup; Morten Engsvang; Haide Wu; Jonas Elm | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667e9c8c5101a2ffa8c914ad/original/ab-initio-molecular-dynamics-simulations-of-atmospheric-molecular-clusters-boosted-by-neural-networks.pdf |
61b77cf1dce1793bce0dc763 | 10.26434/chemrxiv-2021-jm3p8 | Multi-objective goal-directed optimization of de novo stable organic radicals for aqueous redox flow batteries | Advances in the field of goal-directed molecular optimization offer the promise to find feasible candidates for even the most challenging molecular design applications. However, several obstacles remain in applying these tools to practical problems, including lengthy computational or experimental evaluation, synthesizability considerations, and a vast potential search space. As an example of a fundamental design challenge with industrial relevance, we search for novel stable radical scaffolds for an aqueous redox flow battery that simultaneously satisfy redox requirements at the anode and cathode. To meet this challenge, we develop a new open-source molecular optimization framework based on AlphaZero coupled with a fast, machine learning-derived surrogate objective trained with nearly 100,000 quantum chemistry simulations. The objective function comprises two graph neural networks: one that predicts adiabatic oxidation and reduction potentials and a second that predicts electron density and local 3D environment, previously shown to be correlated with radical persistence and stability. With no hand-coded knowledge of organic chemistry, the reinforcement learning agent finds molecule candidates that satisfy a precise combination of redox, stability, and synthesizability requirements defined at the quantum chemistry level, many of which have reasonable predicted retrosynthetic pathways. The optimized molecules show that alternative stable radical scaffolds may offer a unique profile of stability and redox potentials to enable low-cost symmetric aqueous redox flow batteries. | Shree Sowndarya S. V.; Jeffrey Law; Charles Tripp; Dmitry Duplyakin; Erotokritos Skordilis; David Biagioni; Robert Paton; Peter St. John | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY 4.0 | CHEMRXIV | 2021-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b77cf1dce1793bce0dc763/original/multi-objective-goal-directed-optimization-of-de-novo-stable-organic-radicals-for-aqueous-redox-flow-batteries.pdf |
66c71e0520ac769e5f72d17e | 10.26434/chemrxiv-2024-l7jcn | Claisen-Schmidt condensation: an interdisciplinary journey in the organic synthesis laboratory | In general, students face great difficulty in understanding certain topics in organic chemistry, which is why the teacher's role in offering new methodologies is necessary. By using practical laboratory classes in Organic Chemistry, it is possible to connect these strategies in the teaching
of chemistry at the undergraduate level. Contextualizing problems is essential to link theoretical concepts to laboratory practice and their resolution based on interdisciplinarity, promoting a more comprehensive understanding by relating chemistry to other areas of
knowledge. | Wender Alves Silva; Felipe M. Nogueira; Sayuri C. S. Takada | Chemical Education; Chemical Education - General | CC BY NC 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c71e0520ac769e5f72d17e/original/claisen-schmidt-condensation-an-interdisciplinary-journey-in-the-organic-synthesis-laboratory.pdf |
67a14ab2fa469535b9f7373c | 10.26434/chemrxiv-2025-xhrdt | Label-Free Detection of Virus-Membrane Interactions Using Surface-Enhanced Infrared Absorption (SEIRA) Spectroscopy | Viral binding and membrane fusion are essential steps in viral infection, mediated by viral proteins that bind to host cell receptors and facilitate the fusion between viral and host membranes. Targeting these steps for the development of new antiviral strategies requires methods that enable investigating virus-membrane interactions under in-situ conditions, while providing mechanistic insights on a molecular level. Here, we demonstrate the use of surface-enhanced infrared absorption (SEIRA) spectroscopy combined with tethered bilayer lipid membranes (tBLMs) for the label-free detection of virus-membrane interactions, using the Influenza A/X-31 virus (IAV) as a model. Exploiting the nanometer-scale surface-sensitivity of SEIRA, we detect the vibrational fingerprint of IAV’s hemagglutinin (HA) glycoprotein as it specifically binds to sialic acid receptors of the ganglioside GD1a in the tBLM, mimicking the host membrane. Triggering viral fusion via a pH change, we identify structural changes of HA as it engages with the host membrane model. Moreover, by constructing the tBLM from deuterated lipids, we utilize the vibrational isotope effect and distinguish between viral and model membrane, providing a basis to track lipid mixing. This approach establishes a powerful tool for spectroscopic studies of the function and inhibition of viral proteins, while still embedded in intact virus particles. | Amelie Teresa Heinen; Saskia Heermant; Daniel Christian Lauster; Stephan Block; Jacek Kozuch | Physical Chemistry; Biophysical Chemistry; Interfaces; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-02-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67a14ab2fa469535b9f7373c/original/label-free-detection-of-virus-membrane-interactions-using-surface-enhanced-infrared-absorption-seira-spectroscopy.pdf |
60c74e94bdbb89785ca39bcb | 10.26434/chemrxiv.12762179.v1 | Evaluating the “Darkness” of Melanin Materials. | <p>We developed a
mathematical process to quantify the apparent darkness of solutions containing
melanin-like materials. The visible portion of their UV-Vis spectra is model
using an exponential equation. Linear regression analysis provides the
constants that define this exponential equation. Using these constants, the
exponential equation is integrated between 400nm to 900nm to obtain the
area-under-the-curve (AUC) of the visible portion of the UV-Vis spectra. This
process was applied to data collected from various melanin-like materials
discussed in earlier reports. By comparing the AUC values of different samples
one can readily compare the “darkness” of melanins and evaluate the impact varying
reaction conditions may have on this physical property. We revisited the
results of earlier reports and discuss additional points related to the UV-protective
properties attributed to melanins.</p> | Koen Vercruysse | Biochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e94bdbb89785ca39bcb/original/evaluating-the-darkness-of-melanin-materials.pdf |
60c74644567dfe81efec45c0 | 10.26434/chemrxiv.11294543.v1 | Iron(III)-Mediated Oxy-Sulfonylation of Enamides with Sodium and Lithium Sulfinates | <p>An iron-mediated vicinal difunctionalization of enamides and enecarbamates with sulfinic acid salts and alcohols is described. This reaction proceeds under mild conditions and furnishes the oxy-sulfonylated products in moderate to excellent yields. Moreover, the direct incorporation of sulfur dioxide into the sulfonylated products via organolithium chemistry has been achieved. The formed <i>N</i>-<i>O</i>-acetals are competent acylimine precursors. Their utilization as building block for the synthesis of biologically relevant β-amidosulfones is described as well. <br /></p> | Philipp Kramer; Miro Halaczkiewicz; Yu Sun; Harald Kelm; Georg Manolikakes | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74644567dfe81efec45c0/original/iron-iii-mediated-oxy-sulfonylation-of-enamides-with-sodium-and-lithium-sulfinates.pdf |
62062e0d0aec1aa14f19bd2a | 10.26434/chemrxiv-2022-cbp87 | Mechanochemical reaction kinetics scales linearly with impact energy | Inelastic collisions of the milling media in ball milling provide energy to the reaction mixture required for a chemical transformations. However, movement of the milling media results also in physical mixing of reactants, which too may enable a chemical reaction. Separating the two contributions is challenging and gaining a direct insight into the purely mechanochemically driven reactivity is accordingly hindered. Here, we have applied in situ reaction monitoring by Raman spectroscopy to a suitable, purely mechanically activated, chemical reaction and combined kinetic analysis with numerical simulations to access experimentally unattainable milling parameters. The breadth of milling conditions allow us to establish a linear relationship between the reaction rate and the energy dose received by the sample. Consequently, different kinetic profiles in time scale to the same profile when plotted against the energy dose, which increases with the ball mass, the average ball velocity and the frequency of impacts, but it decreases with the hardness of the milling media due to more elastic collisions. The fundamental relationship between kinetics and energy input provides the basis for planning and optimisation of mechanochemical reactions and is essential for transferability of mechanochemical reactions across different milling platforms. | Leonarda Vugrin; Maria Carta; Stipe Lukin; Ernest Meštrović; Francesco Delogu; Ivan Halasz | Physical Chemistry; Chemical Kinetics; Physical and Chemical Processes | CC BY NC 4.0 | CHEMRXIV | 2022-02-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62062e0d0aec1aa14f19bd2a/original/mechanochemical-reaction-kinetics-scales-linearly-with-impact-energy.pdf |
663ed26521291e5d1df7bca9 | 10.26434/chemrxiv-2024-vfgq0 | Thiourea-based Rotaxanes Transport Anions across Membranes of Different Fluidity | We report the synthesis of two rotaxanes (1 and 2) whose rings have appended thiourea units for the selective recognition of Cl− anions. Two-dimensional exchange spectroscopy indicates the ring can shuttle much faster within rotaxanes featuring an axle similar to the one in 1 than in 2 when investigated in solution. Furthermore, rotaxane 1 transports Cl− anions across lipid bilayers more efficiently than 2, exhibiting EC50 values of 0.76 µM versus 2.30 µM respectively, which might be related to the difference in the shuttling rate. Moreover, control rotaxane (3) without the thiourea units and the individual axle (4) also showed Cl− transport, although with a much lower efficiency (EC50 values of 12.64 µM and 15.58 µM). Thus, it is plausible that in addition to shuttling, other pathways, such as a relay process, might contribute to the observed anion transport of 1 and 2. Our studies also suggest that rotaxane 1 could behave as a Cl−/NO3− antiport. Additionally, the transport activity 1 is significantly influenced by the membrane composition, exhibiting higher transport in membranes with higher fluidity. Our study provides new insights into the structural features of rotaxanes required for efficient anion transport and a better understanding of their functioning in different membranes. This will help in developing future rotaxane-based transporters for applications in biomedicine and bioengineering, purification technologies, and energy storage and conversion devices. | Nasim Akhtar; Udyogi N. K. Conthagamage; Macallister L. Davis; Víctor García-López | Biological and Medicinal Chemistry; Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Bioengineering and Biotechnology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/663ed26521291e5d1df7bca9/original/thiourea-based-rotaxanes-transport-anions-across-membranes-of-different-fluidity.pdf |
62e23aff7f3aa6020efac954 | 10.26434/chemrxiv-2022-dbcvc | Promoting Halogen-Bonding Catalyzed Living Radical Polymerization through Ion-Pair Strain | Discovering efficient catalysts is highly desired in expanding the application of halogen-bonding catalysis. We herein report our findings on applying triaminocyclopropenium (TAC) iodides as highly potent catalysts for halogen-bonding catalyzed living radical polymerization. Promoted by the unique effect of ion-pair strain between the TAC cation and the iodide anion, the TAC iodides showed high catalytic efficiency in the halogen-bonding catalysis toward radical generation, and surpassed the previously reported organic iodide catalysts. With the TAC iodide as catalyst, radical polymerization with a living feature was successfully realized, which shows general applicability with a variety of monomers and produced block copolymers. In addition, the TAC-iodides also showed promising feasibility in catalyzing the radical depolymerization of iodo-terminated polymethacrylates. Noteworthily, the catalytic capacity of the TAC iodides is demonstrated to be closely related to the electronic properties of the TAC cation, which offers a molecular platform for further catalyst screening and optimization. | Shiwen Huang; Xinjian Su; Yanzhen Wu; Xiao-Gen Xiong; Yiliu Liu | Catalysis; Polymer Science; Polymerization (Polymers); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62e23aff7f3aa6020efac954/original/promoting-halogen-bonding-catalyzed-living-radical-polymerization-through-ion-pair-strain.pdf |
6540052e48dad23120b8763f | 10.26434/chemrxiv-2023-23s14 | Nondestructive flash cathode recycling | Effective recycling of end-of-life Li-ion batteries (LIBs) is essential due to continuous accumulation of battery waste and gradual depletion of battery metal resources. The present closed-loop solutions include destructive conversion to metal compounds, by destroying the entire three-dimensional morphology of the cathode through continuous thermal treatment or harsh wet extraction methods, and direct regeneration by lithium replenishment. Here, we report a solvent- and water-free flash Joule heating (FJH) method combined with magnetic separation to restore fresh cathodes from waste cathodes, followed by solid-state relithiation. The entire process is called flash recycling. This FJH method exhibits the merits of milliseconds of duration and high battery metal recovery yields of ~98%. After FJH, the cathodes reveal intact core structures with hierarchical features, implying the feasibility of their reconstituting into new cathodes. Relithiated cathodes are further used in LIBs, and show good electrochemical performance, comparable to new commercial counterparts. Life-cycle-analysis highlights that flash recycling has higher environmental and economic benefits over traditional cathode recycling processes. | Weiyin Chen; Yi Cheng; Jinhang Chen; Ksenia Bets; Rodrigo Salvatierra; Chang Ge; John Li; Duy Luong; Carter Kittrell; Emily McHugh; Guanhui Gao; Bing Deng; Yimo Han; Boris Yakobson; James Tour | Materials Science; Energy; Earth, Space, and Environmental Chemistry; Materials Processing; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6540052e48dad23120b8763f/original/nondestructive-flash-cathode-recycling.pdf |
6204f2f649bd325b344b5d01 | 10.26434/chemrxiv-2022-cb6p7 | Palladium-Catalyzed Three-Component Selective Aminoallylation of Diazo Compounds | In spite of the valuable perspective on rapid accessing α,α-disubstituted α-amino acid derivatives, a three-component reaction of diazo compounds, amines and allyl esters remains as an unexplored challenge, probably because of the fore-seeable side reactions arising from each two reactants. In this work, we describe a novel Xantphos-containing dinuclear palladium complex enabled geminal aminoallylation of diazocarbonyl compounds, which provides a range of quaternary α-amino esters selectively. Direct N-H insertion, allylic alkylation of amino nucleophiles and diene formation were not observed under standard conditions. Mechanistic studies indicated that the Xantphos-containing palladium complex with a Pd/P ratio of 1/1 was optimal to enable the reaction to achieve high selectivity. A relayed pathway via allylation of N-H insertion product or [2,3]-sigmatropic rearrangement of a ylide intermediate was unlikely. We believe that the current strategy on palladium-catalyzed selective carbene difunctionalization could be general to construct quaternary carbon centers, and inspire more transformations in related field. | Pengcheng Ou; Lei Zhu; Yinghua Yu; Liyao Ma; Xueliang Huang | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2022-02-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6204f2f649bd325b344b5d01/original/palladium-catalyzed-three-component-selective-aminoallylation-of-diazo-compounds.pdf |
652b9626bda59ceb9a9f3abd | 10.26434/chemrxiv-2023-v9pgb | Co-transcriptional allosteric regulation of synthetic nucleic acid receptors | We present a strategy to control allosterically the loading and release of molecular ligands from synthetic nucleic acid receptors using in vitro transcription. We demonstrate this by engineering three model synthetic DNA-based receptors: a triplex-forming DNA complex, an ATP-binding aptamer, and a hairpin strand, whose ability to bind their specific ligands can be tuned (activated or inhibited) in response to the binding of a specific RNA strand acting as allosteric effector. We then show that the receptor loading/release of ligands can be controlled co-transcriptionally by allosteric RNA regulators produced by rationally designed synthetic genes. This approach shows that highly programmable nucleic acid receptors can be controlled with molecular instructions provided by dynamic transcriptional systems, illustrating their promise in the context of coupling DNA nanotechnology with biological signaling. The kinetics of our allosteric sensors and their genetically generated inputs can be captured using differential equation models, corroborating the predictability of the approach used. | Daniela Sorrentino; Simona Ranallo; Eiji Nakamura; Elisa Franco; Francesco Ricci | Analytical Chemistry; Nanoscience; Nanodevices; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652b9626bda59ceb9a9f3abd/original/co-transcriptional-allosteric-regulation-of-synthetic-nucleic-acid-receptors.pdf |
62fcbd837cdc0557969fb2e8 | 10.26434/chemrxiv-2022-3vwp3 | Rapid Electrochemical Detection of Levodopa using Polyaniline-Modified Screen-Printed Electrodes for the Improved Management of Parkinson's Disease | A portable test to rapidly determine levels of levodopa, the drug used to treat Parkinson’s disease, can improve clinical management of the disease. In this study, screen-printed
electrodes were modified with polymers to facilitate the electrochemical detection of levodopa. Cyclic voltammetry was used to deposit a thin layer of polyaniline on the electrode surface. Scanning electron microscopy revealed high surface coverage, which did not impact the
electrode's conductivity. Differential pulse voltammetry measurements with the polyaniline-modified electrodes enabled the measurement of levodopa at physiologically relevant concentrations with discrimination between a common interferent (ascorbic acid) and a structurally similar compound (L-tyrosine). However, the use of the polymer layer did not permit differentiation between levodopa and dopamine; the only difference in these molecules is that levodopa has an amino acid moiety whereas dopamine has a free amine group. Density
functional theory calculations demonstrated that aniline formed a hydrogen bond between the amino group of the monomer and the meta-hydroxyl group, which is present in both levodopa and dopamine, with similar binding energies (-53.36 vs -50.08 kJ mol-1). Thus, the polymer-functionalised SPEs are a valuable tool to measure compounds important in Parkinson’s disease, but further refinement is needed to achieve selective detection. | Henrique Noguchi; Sarbjeet Kaur; Luiza Krettli; Pankaj Singla; Jake McClements; Helena Snyder; Robert Crapnell; Craig Banks; Katarina Novakovic; Inderpreet Kaur; Jonas Gruber; James Dawson; Marloes Peeters | Analytical Chemistry; Polymer Science; Conducting polymers; Analytical Chemistry - General; Electrochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-08-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62fcbd837cdc0557969fb2e8/original/rapid-electrochemical-detection-of-levodopa-using-polyaniline-modified-screen-printed-electrodes-for-the-improved-management-of-parkinson-s-disease.pdf |
60c74021ee301cc90ec78a00 | 10.26434/chemrxiv.7635980.v1 | Tortuosity but not Percolation: Design of Graphene Nanocomposite Coatings for the Extended Corrosion Protection of Aluminum Alloys | Corrosion inhibition offered by unfunctionalized exfoliated graphite polymer composite coatings for protection of aluminum alloy 7075 substrates is described. | Rachel Davidson; Yenny Cubides; Coleman Fincher; Chelsea McLain; Matt Pharr; Homero Castaneda; Sarbajit Banerjee | Carbon-based Materials; Coating Materials; Composites | CC BY NC ND 4.0 | CHEMRXIV | 2019-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74021ee301cc90ec78a00/original/tortuosity-but-not-percolation-design-of-graphene-nanocomposite-coatings-for-the-extended-corrosion-protection-of-aluminum-alloys.pdf |
658589039138d2316141e5ef | 10.26434/chemrxiv-2023-3n8xt | Comprehensive Photophysical and Nonlinear Spectroscopic Study of Thioanisolyl-Picolinate Triazacyclononane Lanthanide Complexes | Detailed photophysical studies of luminescent lanthanide complexes are presented and elaborated using a newly developed thioanisolyl-picolinate antenna and the related tacn macrocyclic ligand. The new ligand proved to sensitise Nd(III), Sm(III), Eu(III) and Yb(III) emission. Eu(III) complex showed complete energy transfer, yielding high quantum yield (44%) and brightness, while the Tb(III) analogue underwent a thermally activated back-energy transfer, resulting in a strong oxygen quenching of the triplet excited state. Transient absorption spectroscopy measurements of Gd(III), Tb(III) and Eu(III) compounds confirmed the sensitization processes upon the charge-transfer antenna excitation. The triplet excited state lifetime of the Tb(III) complex was 5-times longer than that of the Gd(III) analogue. In contrast, the triplet state was totally quenched by the energy transfer to the 4f-metal ion in the Eu(III) species. Nonlinear two-photon absorption highlighted efficient biphotonic sensitization in Eu(III) and Sm(III) complexes. In case of the Nd(III) compound, one-photon absorption in 4f-4f transitions was predominant, despite the excitation at the antenna two-photon band. This phenomenon was due to the Nd(III) 4f-4f transitions overlapping with the wavelength-doubled absorption of the complex. | Dina Akl; Lucile Bridou; Maher Hojorat; Guillaume Micouin; Salauat Kiraev; François Riobé; Sandrine Denis-Quanquin; Akos Banyasz; Olivier Maury | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Lanthanides and Actinides; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658589039138d2316141e5ef/original/comprehensive-photophysical-and-nonlinear-spectroscopic-study-of-thioanisolyl-picolinate-triazacyclononane-lanthanide-complexes.pdf |
60c74a069abda2615cf8cd58 | 10.26434/chemrxiv.12141894.v1 | Electronic Structure Benchmark Calculations of CO2 Fixing Elementary Chemical Steps in RuBisCO Using the Projector-Based Embedding Approach | <div>Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO<sub>2</sub>) fixation in the biosphere. This enzyme catalyses a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready <i>et al.</i> by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory. </div><div><br /></div><div>The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions.</div><div><br /></div><div>However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing and potentially adding to modelling of enzyme reaction mechanisms with DFT methods.</div> | Oscar A. Douglas-Gallardo; Ian J. Shepherd; Simon Bennie; Kara Ranaghan; Adrian Mulholland; Esteban Vöhringer-Martinez | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a069abda2615cf8cd58/original/electronic-structure-benchmark-calculations-of-co2-fixing-elementary-chemical-steps-in-ru-bis-co-using-the-projector-based-embedding-approach.pdf |
66558c39418a5379b0760433 | 10.26434/chemrxiv-2024-zb5t4 | Tuning the electronic properties of Zr UiO-66 through defect-functionalised multivariate modulation. | The multivariate modulation of Metal-Organic Frameworks is presented as a valuable tool to introduce multiple functional units into UiO-66 while increasing its porosity. This manuscript encloses a comprehensive study using p-functionalised benzoate -NO2, -SO3 and -SH modulators, rationalizing the defects introduced and their impact on properties. | Carmen Rosales-Martínez; Marcelo Assis; Celia Castillo-Blas; Isabel Abánades Lázaro | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66558c39418a5379b0760433/original/tuning-the-electronic-properties-of-zr-ui-o-66-through-defect-functionalised-multivariate-modulation.pdf |
6659d87a21291e5d1dbe9849 | 10.26434/chemrxiv-2024-0sk35 | Nonenzymatic Hydration of Phosphoenolpyruvate: General Conditions for Hydration in Protometabolism by Searching Across Pathways | Numerous reactions within metabolic pathways have been reported to occur nonenzymatically, supporting the hypothesis that life began from a primitive nonenzymatic precursor to metabolism. However, most of those studies reproduce individual transformations or segments of pathways without providing a common set of conditions for classes of reactions that span multiple pathways. In this study, we search across pathways for common nonenzymatic conditions for a recurring chemical transformation in metabolism: alkene hydration. The mild conditions that we identify (Fe oxides such as green rust) apply to all hydration reactions of the rTCA cycle and gluconeogenesis, including the hydration of phosphoenolpyruvate (PEP) to 2-phosphoglycerate (2PGA), which had not previously been reported under nonenzymatic conditions. Mechanistic insights were obtained by studying analogous substrates and through anoxic and radical trapping experiments. Searching for nonenzymatic conditions across pathways provides a complementary strategy to triangulate conditions conducive to the nonenzymatic emergence of a protometabolism. | Joris Zimmermann; Atalay Bora Basar; Joseph Moran | Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6659d87a21291e5d1dbe9849/original/nonenzymatic-hydration-of-phosphoenolpyruvate-general-conditions-for-hydration-in-protometabolism-by-searching-across-pathways.pdf |
628f0088a42e9cf60c4e8736 | 10.26434/chemrxiv-2022-rpnp8 | Overcoming Limitations in Decarboxylative Arylation via Ag-Ni Electrocatalysis | A useful protocol for achieving decarboxylative cross coupling (DCC) of redox-active esters (RAE, isolated or generated in situ) and halo(hetero)arenes is reported. This pragmatically focused study employs a unique Ag-Ni electrocatalytic platform to overcome numerous limitations that have plagued this strategically powerful transformation. In its optimized form coupling partners can be combined in a surprisingly simple way: open to the air, technical grade solvents, an inexpensive ligand and Ni source, substoichiometric AgNO3, proceeding at room temperature with a simple commercial potentiostat. Most importantly all of the results are placed into context by benchmarking with state-of-the-art methods. Applications are presented that simplify synthesis and rapidly enable access to challenging chemical space. Finally, adaptation to multiple scale regimes, ranging from parallel mg-based synthesis to decagram recirculating flow is presented | Maximilian Palkowitz; Gabriele Laudadio; Simon Kolb; Jin Choi; Martins Oderinde; Tamara Ewing; Philippe Bolduc; TeYu Chen; Hao Zhang; Peter Cheng; Benxiang Zhang; Michael Mandler; Jeremy Richter; Michael Collins; Ryan Schioldager; Murali Dhar; Benjamin Vokits; Yeheng Zhu; Pierre-Georges Echeverria; Michael Poss; Scott Shaw; Sebastian Clementson; Nadia Petersen; Pavel Mykhailiuk; Phil Baran | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2022-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/628f0088a42e9cf60c4e8736/original/overcoming-limitations-in-decarboxylative-arylation-via-ag-ni-electrocatalysis.pdf |
60c7501b9abda23ee4f8d98b | 10.26434/chemrxiv.12993371.v1 | Chemical Tools for Study of Phosphohistidine: Generation of Selective τ-Phosphohistidine and π-Phosphohistidine Antibodies | Non-hydrolysable
stable analogues of τ-pHis and π-pHis have been designed using electrostatic
surface potential calculations, and subsequently synthesized. The τ-pHis and
π-pHis analogues (phosphopyrazole <b>8 </b>and pyridyl amino amide <b>13</b>,
respectively)<b> </b>were used as haptens to generate pHis polyclonal
antibodies. <a>Both τ-pHis and π-pHis conjugates in the
form of a BSA-glutaraldehyde-τ-pHis and BSA-glutaraldehyde-π-pHis</a> were
synthesized and characterized by <sup>31</sup>P NMR spectroscopy. Commercially
available τ-pHis (SC56-2) and π-pHis (SC1-1; SC50-3) monoclonal antibodies were
used to show that the BSA-G-τ-pHis and BSA-G-π-pHis conjugates could be used to assess the selectivity of pHis antibodies in a
competitive ELISA. Subsequently, the selectivity of the generated pHis
antibodies generated using phosphopyrazole <b>8 </b>and pyridyl amino amide <b>13</b>
as haptens was assessed by competitive ELISA against His, pSer, pThr, pTyr,
τ-pHis and π-pHis. Antibodies generated using the phosphopyrazole <b>8</b> as a
hapten were found to be selective for τ-pHis, and antibodies generated using
the <a>pyridyl amino amide <b>13</b> </a>were found to be
selective for π-pHis. Both τ- and π-pHis antibodies were shown to be effective in immunological experiments, including ELISA,
western blot, and immunofluorescence. The τ-pHis antibody was also shown to be
useful in the immunoprecipitation of proteins containing pHis | Mehul Makwana; Cleide Dos Santos Souza; Barry T. Pickup; Mark J. Thompson; Santosh Kumar Lomada; Yushi Feng; Thomas Wieland; Richard F. W. Jackson; Richmond MUIMO | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7501b9abda23ee4f8d98b/original/chemical-tools-for-study-of-phosphohistidine-generation-of-selective-phosphohistidine-and-phosphohistidine-antibodies.pdf |
60c74827702a9b5b3518af13 | 10.26434/chemrxiv.11860077.v1 | Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds | <div>The recently emerged 2019 Novel Coronavirus (SARS-CoV-2) and associated COVID-19 disease cause serious or even fatal respiratory tract infection and yet no FDA-approved therapeutics or effective treatment is currently available to effectively combat the outbreak. This urgent situation is pressing the world to respond with the development of novel vaccine or a small molecule therapeutics for SARS-CoV-2. Along these efforts, the structure of SARS-CoV-2 main protease (Mpro) has been rapidly resolved and made publicly available to facilitate global efforts to develop novel drug candidates.</div><div>In recent month, our group has developed a novel deep learning platform – Deep Docking (DD) which enables very fast docking of billions of molecular structures and provides up to 6,000X enrichment on the top-predicted ligands compared to conventional docking workflow (without notable loss of information on potential hits). In the current work we applied DD to entire 1.3 billion compounds from ZINC15 library to identify top 1,000 potential ligands for SARS-CoV-2 Mpro. The compounds are made publicly available for further characterization and development by scientific community.</div> | Anh-Tien Ton; Francesco Gentile; Michael Hsing; Fuqiang Ban; Artem Cherkasov | Bioinformatics and Computational Biology; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74827702a9b5b3518af13/original/rapid-identification-of-potential-inhibitors-of-sars-co-v-2-main-protease-by-deep-docking-of-1-3-billion-compounds.pdf |
6293e739d3c73a2f26d4f3e8 | 10.26434/chemrxiv-2022-cf0c3-v2 | Direct alpha-Amination of Amides and Lactams Enabled by the (3+2) Vinyl Azide-Enolate Cycloaddition Manifold | Direct alpha-amination of carbonyl compounds remains an important yet synthetically challenging transformation. Here we report a solution for direct alpha-amination of amides and lactams, identified through fundamental exploration of (3+2) vinyl azide-enolate cycloaddition chemistry. Initial cycloadducts undergo rearrangement via 1,2-N-migration to afford imine intermediates that are readily converted to the target alpha-amino amides or lactams. The sequence requires no pre-functionalisation, can be performed on a range of substrates, including compound classes unsuccessful using reported methods, and delivers primary or secondary alpha-amines. This work highlights the diversity and synthetic potential of the rapidly expanding (3+2) azide-enolate cycloaddition manifold. | Joseph Bell-Tyrer; Paul Hume; Phillip Grant; Margaret Brimble; Daniel Furkert | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6293e739d3c73a2f26d4f3e8/original/direct-alpha-amination-of-amides-and-lactams-enabled-by-the-3-2-vinyl-azide-enolate-cycloaddition-manifold.pdf |
63903eee92f084c9612a9086 | 10.26434/chemrxiv-2022-g9lr7 | Theoretical Advances in Polariton Chemistry and Molecular Cavity Quantum Electrodynamics | When molecules are coupled to an optical cavity, new light-matter hybrid states, so-called polaritons, are formed due to quantum light-matter interactions. With the experimental demonstrations of modifying chemical reactivities by forming polaritons under strong light-matter interactions, theorists have been encouraged to develop new methods to simulate these systems and discover new strategies to tune and control reactions. This review summarizes some of these exciting theoretical advances in polariton chemistry, in methods ranging from the fundamental framework to computational techniques and applications spanning from photochemistry to vibrational strong coupling. Even though the theory of quantum light-matter interactions goes back to the mid-twentieth century, the gaps in the knowledge of molecular quantum electrodynamics (QED) have only recently been filled. We review recent advances made in resolving gauge ambiguities, the correct form of different QED Hamiltonians under different gauges, and their connections to various quantum optics models. Then, we review recently developed {\it ab-initio} QED approaches which can accurately describe polariton states in a realistic molecule-cavity hybrid system. We then discuss applications using these method advancements. We review advancements in polariton photochemistry where the cavity is made resonant to electronic transitions to control molecular non-adiabatic excited state dynamics and enable new photochemical reactivities. When the cavity resonance is tuned to the molecular vibrations instead, ground-state chemical reaction modifications have been demonstrated experimentally, though its mechanistic principle remains unclear. We present some recent theoretical progress in resolving this mystery. Finally, we review the recent advances in understanding the collective coupling regime between light and matter, where many molecules can collectively couple to a single cavity mode or many cavity modes. We also lay out the current challenges in theory to explain the observed experimental results. We hope that this review will serve as a useful document for anyone who wants to become familiar with the context of polariton chemistry and molecular cavity QED and thus significantly benefit the entire community. | Arkajit Mandal; Michael Taylor; Braden Weight; Eric Koessler; Xinyang Li; Pengfei Huo | Theoretical and Computational Chemistry; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2022-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63903eee92f084c9612a9086/original/theoretical-advances-in-polariton-chemistry-and-molecular-cavity-quantum-electrodynamics.pdf |
60c73fbd842e654164db1b6a | 10.26434/chemrxiv.7476347.v1 | Synthesis and Catalytic Activity of Rhodium(I) and Iridium(I) 4,5-Dibrominated N-Heterocyclic Carbenes | The synthesis and characterisation of another example of an air-stable carbene is described, in addition to the preparation of rhodium and iridium olefin and carbonyl complexes. The spectroscopic data indicates that these air-stable carbenes do not display reduced sigma-donor capacity of the carbenic centre. The catalytic applications of these carbenes are explored in the hydrosilylation and transfer hydrogenation processes. | Samantha Furfari; Matthew Gyton; Marcus Cole | Coordination Chemistry (Organomet.); Ligands (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fbd842e654164db1b6a/original/synthesis-and-catalytic-activity-of-rhodium-i-and-iridium-i-4-5-dibrominated-n-heterocyclic-carbenes.pdf |
60c752dfee301c04bcc7acb2 | 10.26434/chemrxiv.13318421.v2 | Catalytic Synthesis of Cyclic Guanidines via Hydrogen Atom Transfer and Radical-Polar Crossover | Cyclic guanidines are found in many biologically active compounds and natural products. Further, the for-mation of the atypical 7-membered ring of cyclic guanidine remains challenging due to a lack of efficient preparation strategies and low yield. Herein, a catalytic synthetic method for cyclic guanidines was developed via transition-metal hydrogen atom transfer and radical-polar crossover. This mild and functional-group tolerant process enabled the cycliza-tion of an alkenyl guanidines bearing common protective groups, such as Cbz and Boc groups. This powerful method not only provided typical 5- and 6-membered rings but also the atypical 7-membered ring. The derivatization of the products afforded various heterocycles. We also investigated the selective cyclization of mono-protected or hetero-protected (TFA and Boc) alkenyl guanidines and their further derivatizations. | Shunya Ohuchi; Hiroki Koyama; Hiroki Shigehisa | Organic Synthesis and Reactions; Homogeneous Catalysis; Catalysis; Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752dfee301c04bcc7acb2/original/catalytic-synthesis-of-cyclic-guanidines-via-hydrogen-atom-transfer-and-radical-polar-crossover.pdf |
636e6572b588505428483fa4 | 10.26434/chemrxiv-2022-6jm2g | Metal-Free Molecular Catalysts for Oxygen Reduction Reaction: Electron Affinity as Activity Descriptor | Heteroatom-doped polyaromatic hydrocarbons (or nanographenes) are promising molecular electrocatalysts for the oxygen reduction reaction (ORR). Here, we use density functional theory to investigate the first step of the ORR pathway (chemisorption) for a set of molecules with experimentally determined catalytic activities. Weak chemisorptions are found only for negatively charged catalysts, and a strong correlation is observed between computed electron affinities and experimental catalytic activities for a range of B- and B,N-doped polyaromatic hydrocarbons. The electron affinity is put forward as a simple activity descriptor of charged (activated) catalysts on an electrode. | Christopher Ehlert; Anna Piras; Juliette Schleicher; Ganna Gryn'ova | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636e6572b588505428483fa4/original/metal-free-molecular-catalysts-for-oxygen-reduction-reaction-electron-affinity-as-activity-descriptor.pdf |
6615f3b2418a5379b0805cd9 | 10.26434/chemrxiv-2024-pt7wp | Polyglutamine (PolyQ) Diseases: Navigating the Landscape of Neurodegeneration | Polyglutamine (polyQ) diseases are a group of inherited neurodegenerative disorders caused by expanded cytosine-adenine-guanine (CAG) repeats encoding proteins with abnormally expanded polyglutamine tract. A total of nine polyQ disorders have been identified, including Huntington's disease, six spinocerebellar ataxias, dentatorubral pallidoluysian atrophy (DRPLA), and spinal and bulbar muscular atrophy (SBMA). The diseases of this class are each considered rare, yet polyQ diseases constitute the largest group of monogenic neurodegenerative disorders. While each subtype of polyQ diseases has its own causative gene, certain pathologic molecular attributes have been implicated in virtually all of the polyQ diseases, including protein aggregation, proteolytic cleavage, neuronal dysfunction, transcription dysregulation, autophagy impairment, and mitochondrial dysfunction. Although animal models of polyQ disease are available helping to understand their pathogenesis and access disease-modifying therapies, there is neither a cure nor prevention for these diseases, with only symptomatic treatments available.
In this paper, we analyze data from the CAS Content Collection to summarize the research progress in the class of polyQ diseases. We examine the publication landscape in the area in effort to provide insights into current knowledge advances and developments. We review the most discussed concepts and assess the strategies to combat these diseases. Finally, we inspect clinical applications of products against polyQ diseases with their development pipelines. The objective of this review is to provide a broad overview of the evolving landscape of current knowledge regarding the class of polyQ diseases, to outline challenges, and evaluate growth opportunities to further efforts in combating the diseases.
| Rumiana Tenchov; Janet Sasso; Qiongqiong Angela Zhou | Biological and Medicinal Chemistry; Biochemistry | CC BY 4.0 | CHEMRXIV | 2024-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6615f3b2418a5379b0805cd9/original/polyglutamine-poly-q-diseases-navigating-the-landscape-of-neurodegeneration.pdf |
65b261ab9138d23161b931bd | 10.26434/chemrxiv-2023-9v2dw-v3 | Phase segregation and nanoconfined fluid O2 in a lithium-rich oxide cathode | Lithium-rich oxide cathodes lose energy density during cycling due to atomic disordering and nanoscale structural rearrangements, both of which are challenging to characterise. Here, we resolve the kinetics and thermodynamics of these processes in an exemplar layered Li-rich cathode, Li1.2–xMn0.8O2 by using a combined approach of ab initio molecular dynamics and cluster-expansion-based Monte Carlo simulations. We identify a kinetically accessible and thermodynamically favoured mechanism to form O2 molecules in the bulk, involving Mn migration and driven by interlayer oxygen dimerisation. At the top of charge the bulk structure locally phase-segregates into MnO2-rich regions and Mn-deficient nanovoids, which contain O2 molecules as a nanoconfined fluid. These nanovoids are connected in a percolating network, potentially allowing long-range oxygen transport, and linking bulk O2 formation to surface O2 loss. These insights highlight the importance of future strategies to kinetically stabilise the bulk structure of Li-rich O-redox cathodes to maintain their high energy densities. | Kit McColl; Samuel W. Coles; Pezhman Zarabadi–Poor; Benjamin J. Morgan; M. Saiful Islam | Theoretical and Computational Chemistry; Energy; Theory - Computational; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b261ab9138d23161b931bd/original/phase-segregation-and-nanoconfined-fluid-o2-in-a-lithium-rich-oxide-cathode.pdf |
65f8e0119138d23161bd3c6f | 10.26434/chemrxiv-2024-4px5b-v2 | Organic carbon sink dynamics and carbon sink-source balance in global lakes during the Anthropocene | The carbon burial and greenhouse gas emissions of lakes are pivotal in the global carbon cycle to offset or accelerate global warming. However, their balance or the magnitude of anthropogenic increase of carbon burial remains uncertain in global lakes. Here, we quantified the carbon sink dynamics and the sink-source balance in global lakes with effect size metrics, that is, the log-response ratio of organic carbon burial between post-1950 and pre-1900 periods and the carbon balance ratio between carbon burial and greenhouse gas emissions, respectively. The organic carbon burial ratios revealed an average increase of 2.44 times in carbon burial rates during the Anthropocene, while the carbon balance ratios were negative in 82.68% of lakes, indicating that most lakes had lower burial rates than emission rates and acted as carbon sources rather than carbon sinks. The organic carbon burial ratios exhibited a significantly decreasing latitudinal trend and were mainly influenced by its trophic state with the explained variation of 44.79%. They were also indirectly influenced by climate, lake morphometry and catchment properties through their interactions with the lake’s trophic state. The carbon balance ratios however showed nonsignificant latitudinal trend. They were primarily affected by lake catchment properties with the explained variation of 26.21% and were also indirectly affected by climate variables via the interactions with catchment properties. Overall, our study highlights that human activities such as lake eutrophication and catchment changes have altered the carbon sink and source in global lakes during the Anthropocene, and are essential drivers for future evaluations of lake carbon budgets. | Fanfan Meng; Ang Hu; Hao Wu; Kyoung-Soon Jang; Bo Liu; Tianheng Gao; Qinglong Wu; Jianjun Wang | Earth, Space, and Environmental Chemistry; Environmental Science; Geochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f8e0119138d23161bd3c6f/original/organic-carbon-sink-dynamics-and-carbon-sink-source-balance-in-global-lakes-during-the-anthropocene.pdf |
6414f4cb2bfb3dc251f176d5 | 10.26434/chemrxiv-2023-njptl | Photosensitized Dioxygen Enables Intermolecular Cyclopropanation of Alkenes Directly with Active Methylene Compounds | Cyclopropane, a versatile synthetic intermediate, is forged as a key structural feature in many preclinical, clinical and commercial drugs, and occur as a skeletal motif in numerous natural products. The most prolific technique for its synthesis is the metal-catalyzed reaction of an alkene with a diazoalkane, a highly energetic, reactive and explosive reagent requiring stringent safety precautions. The expedient construction of cyclopropyl ring on alkenes with convenient and innocuous reagents under nonhazardous conditions remains an ongoing challenge. Herein, we report a simple photoredox-catalyzed intermolecular cyclopropanation of unactivated alkenes with a diverse set of active methylene compounds that demonstrates striking conceptual and practical synthetic advances over the known methods. The reaction proceeds with a photoredox catalyst (PC*) excited under a blue LED light in air/O2 and neutral reaction conditions in the presence of catalytic amounts of iodine, either in the form of added molecular I2 or generated in situ from alkyl iodides. . The reaction demonstrates a remarkably broad scope on the applicability of 19 different active methylene compounds in 5 different clusters from the standpoint of synthetic tolerability, and tolerates a wide range of functional groups. Moreover, the reaction is also amenable for the cyclopropanation of alkenes in complex molecular architectures, pharmaceuticals and natural products. Mechanistic investigation through the isolation of a series of intermediate products, probes, control experiments, UV-Vis and fluorescence studies indicate that photosensitized dioxygen plays a vital role in the generation of carbon-centered radicals for both the addition of active methylene compounds to alkenes and ring closure, and catalytically generated iodine recycles the PC. | Dhruba P. Poudel; Amrit Pokhrel; Raj Kumar Tak; Shankar Majji; Ramesh Giri | Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6414f4cb2bfb3dc251f176d5/original/photosensitized-dioxygen-enables-intermolecular-cyclopropanation-of-alkenes-directly-with-active-methylene-compounds.pdf |
653bede548dad231208425dc | 10.26434/chemrxiv-2023-l4fwt | Determining the Key Vibrations for Spin Relaxation in Ruffled Cu(II) Porphyrins via Resonance Raman Spectroscopy | Pinpointing vibrational mode contributions to electron spin relaxation (T1) constitutes a key goal for developing molecular quantum bits (qubits) with long room temperature coherence times. However, there remains no consensus to date as to the energy and symmetry of the relevant modes that drive relaxation. Here, we analyze a series of three geometrically-tunable S = ½ Cu(II) porphyrins with varying degrees of ruffling distortion in the ground state. Theoretical calculations predict that increased distortion should activate low-energy ruffling modes (~50 cm-1) for spin-phonon coupling, thereby causing faster spin relaxation in distorted porphyrins. However, experimental T1 times do not follow the degree of ruffling, with the highly distorted copper tetraisopropylporphyrin (CuTiPP) even displaying room-temperature coherence. Local mode fitting indicates that the true vibrations dominating T1 lie in the energy regime of bond stretches (~200 – 300 cm-1), which are comparatively insensitive to the degree of ruffling. We employ resonance Raman (rR) spectroscopy to determine vibrational modes possessing both the correct energy and symmetry to drive spin-phonon coupling. The rR spectra uncover a set of mixed symmetric stretch vibrations from 200 – 250 cm-1 that explain the trends in temperature-dependent T1. These results indicate that molecular spin-phonon coupling models systematically overestimate the contribution of ultra-low-energy distortion modes to T1, pointing out a key deficiency of existing theory. Furthermore, this work highlights the untapped power of rR spectroscopy as a tool for building spin-dynamics structure-function relationships in molecular quantum information science. | Nathanael Kazmierczak; Nathan Lopez; Kaitlin Luedecke; Ryan Hadt | Physical Chemistry; Inorganic Chemistry; Magnetism; Spectroscopy (Inorg.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653bede548dad231208425dc/original/determining-the-key-vibrations-for-spin-relaxation-in-ruffled-cu-ii-porphyrins-via-resonance-raman-spectroscopy.pdf |
63a33573a53ea6cb53532aa4 | 10.26434/chemrxiv-2022-djdtz | C-H Bond Activation via Concerted Metalation-Deprotonation at a Palladium(III) Center | Herein we report the direct observation of C-H bond activation at an isolated mononuclear Pd(III) center. The oxidation of the Pd(II) complex (MeN4)PdII(neophyl)Cl (neophyl = -CH2C(CH3)2Ph; MeN4 = N,N′-di-tert-butyl-2,11-diaza[3.3](2,6)pyridinophane) using the mild oxidant ferrocenium hexafluorophosphate (FcPF6) yields the stable Pd(III) complex [(MeN4)PdIII(neophyl)Cl]PF6. Upon the addition of an acetate source, [(MeN4)PdIII(neophyl)Cl]PF6 undergoes Csp2-H bond activation to yield the cyclometalated product [(MeN4)PdIII(cycloneophyl)]PF6. This metallacycle can be independently prepared, allowing for a complete characterization of both the starting and final Pd(III) complexes. The C-H activation step can be monitored directly by EPR and UV-Vis spectroscopies, and kinetic isotope effect (KIE) studies suggest the C-H activation likely occurs after the rate determining step. Density functional theory calculations support that molecular isomerization/ligand rearrangement is rate limiting and proceeds through a κ3 ligand geometry. Overall, this study represents the first example of discrete C-H bond activation occurring at a Pd(III) center through a concerted metalation-deprotonation mechanism, akin to that observed for Pd(II) and Pd(IV) centers. | Bailey Bouley; Fengzhi Tang; Dae Young Bae; Liviu Mirica | Organic Chemistry; Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a33573a53ea6cb53532aa4/original/c-h-bond-activation-via-concerted-metalation-deprotonation-at-a-palladium-iii-center.pdf |
60cb5d54a5b6af65837538d3 | 10.26434/chemrxiv-2021-zmp0l | Real-time Prediction of 1H and 13C Chemical Shifts with DFT accuracy using a 3D Graph Neural Network | The computational prediction of NMR chemical shifts using quantum mechanical calculations is now commonplace in aiding organic structural assignment since spectra can be computed for several candidate structures and then compared with experimental values to find the best possible match. However, the computational demands of calculating multiple structural- and stereo-isomers, each of which may typically exist as an ensemble of rapidly-interconverting conformations calculations, are expensive. In this work, we address both of these shortcomings by developing a rapid machine learning (ML) protocol to predict 1H and 13C chemical shifts through an efficient graph neural network (GNN) using 3D structures as input. Transfer learning with experimental data is used to improve the final prediction accuracy of a model training using QM calculations. When tested on the CHESHIRE dataset, the 13C chemical shifts are predicted with comparable accuracy to the best-performing DFT functionals (1.5 ppm) in around 1/6000 of the CPU time. | Yanfei Guan; Shree Sowndarya SV; Liliana Gallegos; Peter St. John; Robert Paton | Theoretical and Computational Chemistry; Organic Chemistry; Natural Products; Stereochemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2021-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cb5d54a5b6af65837538d3/original/real-time-prediction-of-1h-and-13c-chemical-shifts-with-dft-accuracy-using-a-3d-graph-neural-network.pdf |
60c74f284c8919a4d4ad3b52 | 10.26434/chemrxiv.12858044.v1 | Bulk and Surface Chemistry of the Niobium MAX and MXene Phases from Multinuclear Solid-State NMR Spectroscopy | MXenes, derived from layered MAX phases, are a class of two-dimensional materials with
emerging applications in energy storage, electronics, catalysis, and other fields due to their
high surface areas, metallic conductivity, biocompatibility and attractive optoelectronic
properties. MXene properties are heavily influenced by their surface chemistry, but a detailed
understanding of the surface functionalization is still lacking. Solid-state nuclear magnetic
resonance (NMR) spectroscopy is sensitive to the interfacial chemistry, the phase purity
including the presence of amorphous/nanocrystalline phases, and the electronic properties of
the MXene and MAX phases. In this work, we systematically study the chemistry of Nb MAX
and MXene phases, Nb2CTx and Nb4C3Tx, with their unique electronic and mechanical
properties, using solid-state NMR spectroscopy and examine a variety of nuclei (
1
H, 13C, 19F,
27Al and 93Nb) with a range of one- and two-dimensional correlation, wideline, high-sensitivity,
high-resolution, and/or relaxation-filtered experiments. Hydroxide and fluoride terminations
are identified, found to be intimately mixed, and their chemical shifts are compared with other
MXenes. This multinuclear NMR study demonstrates that diffraction alone is insufficient to
characterize the phase composition of MAX and MXene samples as numerous amorphous or nanocrystalline phases are identified including NbC, AlO6 species, aluminum nitride or
oxycarbide, AlF3×nH2O, Nb metal, and unreacted MAX phase. To the best of our knowledge,
this is the first study to examine the transition-metal resonances directly in MXene samples,
and the first 93Nb NMR of any MAX phase. The insights from this work are employed to enable
the previously-elusive assignment of the complex overlapping 47/49Ti NMR spectrum of
Ti3AlC2. The results and methodology presented here provide fundamental insights on MAX
and MXene phases and can be used to obtain a more complete picture of MAX and MXene
chemistry, to prepare realistic structure models for computational screening, and to guide the
analysis of property measurements.<br /> | Kent Griffith; Michael Hope; Philip
J. Reeves; Mark Anayee; Yury Gogotsi; Clare P. Grey | Nanostructured Materials - Materials; Spectroscopy (Anal. Chem.); Solid State Chemistry; Spectroscopy (Inorg.); Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2020-08-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f284c8919a4d4ad3b52/original/bulk-and-surface-chemistry-of-the-niobium-max-and-m-xene-phases-from-multinuclear-solid-state-nmr-spectroscopy.pdf |
60c74a98469df46760f43d9b | 10.26434/chemrxiv.12226946.v1 | Sensitivity of Pore Collapse Heating to the Melting Temperature and Liquid-phase Shear Viscosity of HMX | A multiscale modeling strategy is used to quantify factors governing the temperature rise in hot spots formed by pore collapse from supported and unsupported shock waves in the high explosive HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine). Two physical aspects are examined in detail, namely the melting temperature and liquid shear viscosity. All-atom molecular dynamics simulations of phase coexistence are used to predict the pressure-dependent melting temperature up to 5~GPa. Equilibrium simulations and the Green-Kubo formalism are used to obtain the temperature- and pressure-dependent liquid shear viscosity. Starting from a simplified continuum-based grain-scale model for HMX, we systematically increase the complexity of treatments for the solid-liquid phase transition and liquid shear viscosity in simulations of pore collapse. Using a realistic pressure-dependent melting temperature completely suppresses melting for supported shocks, which is otherwise predicted when treating it as a constant determined at atmospheric pressure. Alternatively, large melt pools form around pores during pressure release in unsupported shocks, even with a pressure-dependent melting temperature. Capturing the pressure dependence of the shear viscosity increases the peak temperature of melt pools by hundreds of Kelvin through viscous work. The complicated interplay of the solid-phase plastic work, solid-liquid phase transition, and liquid-phase viscous work identified here motivate taking a systematic approach to building increasingly complex grain-scale models and for guiding interpretation of predictions made using them. | Matthew Kroonblawd; Ryan Austin | Carbon-based Materials; Computational Chemistry and Modeling; Physical and Chemical Processes; Physical and Chemical Properties; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a98469df46760f43d9b/original/sensitivity-of-pore-collapse-heating-to-the-melting-temperature-and-liquid-phase-shear-viscosity-of-hmx.pdf |
6242e091a432253960432d07 | 10.26434/chemrxiv-2022-mpc1s | Time-independent desorption hysteresis in liquid phase sorption experiments: the concept and the models based on gate-sorption site coupling | Sorption-desorption hysteresis (SDH) is often observed in liquid phase (solution) sorption experiments with various chemicals on complex natural materials, including soils and sediments. Sorption-desorption interactions with soils and sediments are of significant fundamental and applied interest since they control the transport and fate of chemicals in environmental systems. SDH expressed as a difference between sorption and desorption isotherms determined in solutions may demonstrate time-independent behavior. This work aims to propose a concept that could mechanistically explain and allow predictions of time-independent SDH in three different scenarios: (1) sorbed molecules are entrapped and physically blocked from their exchange with the environment; (2) sorbed molecules are irreversibly bound to sorbent matrix such that the sorption sites capable of irreversible binding are not fully occupied in the presence of non-zero concentrations of solutes; (3) SDH is associated with forming of a non-relaxed sorbent state where the free exchange of sorbate molecules with the environment occurs. The proposed concept introduces the gates present in a sorbent matrix and capable of concentration-dependent cooperative opening/closure, thus acting as a switch: sorbate interactions with sorption sites are allowed at increased solute concentrations but not the opposite. Coupling the gates distribution with the distribution of sorption sites allows addressing each scenario of interest and explaining time-independent SDH. The models developed within the concept can represent and even predict desorption data using a minimal number of adjustable parameters. This predictive potential may be improved by accounting for the assumptions introduced while developing the models. | Mikhail Borisover | Physical Chemistry; Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Environmental Science; Soil Science; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6242e091a432253960432d07/original/time-independent-desorption-hysteresis-in-liquid-phase-sorption-experiments-the-concept-and-the-models-based-on-gate-sorption-site-coupling.pdf |
645dbf4efb40f6b3ee705f45 | 10.26434/chemrxiv-2023-qs4jw | Creation of Polymer Datasets with Targeted Backbones for Screening of Gas Permeability and Selectivity | A simple approach was developed to computationally construct a polymer by composing simplified molecular-input line-entry system (SMILES) strings of a polymer backbone and a molecular fragment. This method was used to create 14 polymer datasets by combining seven polymer backbones and two large molecular datasets (ZINC and QM9). Polymer backbones that were studied include four polydimethylsiloxane (PDMS) based backbones, polyethylene oxide (PEO), poly-allyl glycidyl ether, and polyphosphazene. The generated polymer datasets can be used for various cheminformatics tasks, including high-throughput screening for gas permeability and selectivity. This study used machine learning (ML) models to screen the polymers for CO2/CH4 and CO2/N2 gas separation using membranes and several polymers of interest were identified. | Surya Prakash Tiwari; Wei Shi; Samir Budhathoki; James Baker; David Hopkinson; Janice Steckel | Theoretical and Computational Chemistry; Polymer Science; Energy; Polymer scaffolds; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/645dbf4efb40f6b3ee705f45/original/creation-of-polymer-datasets-with-targeted-backbones-for-screening-of-gas-permeability-and-selectivity.pdf |
60c9e3b17980187658c766ea | 10.26434/chemrxiv.14769987.v1 | Density of Phonon States in Cubic Ice Ic | The measurement of the H-projected density of phonon states (H-DOPS) of polycrystalline ice Ic has been performed with an unprecedented accuracy, and in a sample having an almost perfect crystallographic purity, as it was obtained from the transformation of ice XVII. Results are compared with new accurate measurements of H-DOPS in ice Ih, and with centroid molecular-dynamics (MD) computations. The differences between the experimental H-DOPS in these two forms of ice are subtle, but quantitatively measurable. In addition, they are reproduced semi-quantitatively by computational methods, demonstrating the effectiveness of this innovative simulation tool for reproducing the dynamical properties of the ice structures. | Leonardo del Rosso; Milva Celli; Daniele Colognesi; Svemir Rudic; Niall J. English; Lorenzo Ulivi | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b17980187658c766ea/original/density-of-phonon-states-in-cubic-ice-ic.pdf |
65ef26eb66c1381729bfcb1b | 10.26434/chemrxiv-2024-9ms0m | Contemporary forest harvesting impacts
on water quality and treatability | Forested landscapes are critical source regions for the supply of drinking water globally. The increasing frequency and severity of climate shocks (e.g., wildfire, floods) in these regions can deteriorate source water quality. Forest harvesting has been proposed as an allied component of forest fuel management and pre-emptive mitigation of disturbance impacts on source water quality and treatability; however, forest harvesting can also deteriorate source quality and compromise treatability in the absence of sufficient operational response capacity. Critically, the impacts of forest harvesting on drinking water treatability have not been reported. Here, drinking water source quality and treatability impacts of three contemporary forest harvesting approaches (clear-cut with patch retention, strip-shelterwood cut, and partial cut) were evaluated in Alberta, Canada. Stream water turbidity, the concentration and character of dissolved organic matter, and disinfection by-product formation potential were evaluated over four years, in harvested and reference watersheds. No appreciable impacts of forest harvesting on water quality and treatability were observed. The results suggest that contemporary forest harvesting approaches may show promise as source water protection technologies for mitigating climate-exacerbated disturbance threats to drinking water treatability; however, further study is needed to establish causality and the contributions of other biotic and abiotic factors. | Soosan Bahramian; Shoeleh Shams; Chris Williams; Uldis Silins; Micheal Stone; Monica Emelko | Earth, Space, and Environmental Chemistry; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef26eb66c1381729bfcb1b/original/contemporary-forest-harvesting-impacts-on-water-quality-and-treatability.pdf |
67888c1a6dde43c908c33ffa | 10.26434/chemrxiv-2025-mzjd7 | Modeling of cement clinker production in a rotary kiln incorporating melting and aggregation of particles | Cement clinker is produced in rotary kilns operating at high temperature. The harsh internal conditions in the kiln prevent direct measurements of key process variables. Digital twins that use mathematical models to mimic and emulate the process in real time are viable alternatives to track equipment performance and product quality. Building on the past modeling efforts for rotary kilns, this work brings in two important and interacting phenomena of melting and aggregation that have often been ignored in the literature. Some of the components that form in the solid phase, melt due to the high temperature in the kiln. The melt aids smaller particles to aggregate and grow to form large clinker chunks. In this work, a core-shell model is used to capture the melting process along with a population balance model to track the particle size distribution of the aggregates. The model predicts melting and aggregation to take place nearly after 75\% of the kiln length from the feed end. The model is first validated with published chemical analysis of clinker in an industrial kiln. Simulations reveal that as melting lowers the bed temperature, it reduces $\rm C_{3}S$ production and increases $\rm C_{2}S$ production. Aggregation somewhat reverses the trend, bringing out the interactions among particle size, melting and reaction kinetics. | Akanksha Dhayal; Mohammed Suhail; Sivakumar Subramanian; Venkataramana Runkana | Chemical Engineering and Industrial Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67888c1a6dde43c908c33ffa/original/modeling-of-cement-clinker-production-in-a-rotary-kiln-incorporating-melting-and-aggregation-of-particles.pdf |
60d2ee6b926ad0f81102b52b | 10.26434/chemrxiv-2021-k3szw-v2 | Surface NMR Using Quantum Sensors in Diamond | Characterization of the molecular properties of surfaces under ambient or chemically reactive conditions is a fundamental scientific challenge. Nuclear magnetic resonance (NMR) spectroscopy would be the ideal technique, however it lacks the sen-sitivity to probe the small number of spins at interfaces. Here we use nitrogen vacancy (NV) centers in diamond as quantum sensors to optically detect NMR signals from chemically modified thin films. Aluminum oxide (Al2O3) layers, common supports in catalysis and materials science, are prepared by atomic layer deposition and are subsequently functionalized by phosphonate chemistry to form self-assembled monolayers (SAMs). The surface NV-NMR technique detects NMR signals from the monolayer, indicates chemical binding, and quantifies molecular coverage. In addition, it can monitor in real-time the formation kinetics at the solid-liquid interface. This work demonstrates the capability of NV quantum sensors as a sur-face-sensitive (femtomole) NMR tool for in-situ analysis in catalysis, materials and biological research. | Kristina Liu; Alex Henning; Markus W. Heindl; Robin Allert; Johannes D. Bartl; Ian D. Sharp; Roberto Rizzato; Dominik Benjamin Bucher | Physical Chemistry; Materials Science; Chemical Kinetics; Spectroscopy (Physical Chem.); Surface; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60d2ee6b926ad0f81102b52b/original/surface-nmr-using-quantum-sensors-in-diamond.pdf |
64bbd73eae3d1a7b0d276bce | 10.26434/chemrxiv-2023-jd2pn | Phosphonate and Thia-Sugar Analogs of Glucosamine-6-phosphate: Activation of the glmS Riboswitch | The glmS riboswitch is a motif found in 5’-untranslated regions of bacterial mRNA that controls the synthesis of glucosamine-6-phosphate (GlcN6P), an essential building block for the bacterial cell wall, by a feed-back mechanism. Activation of the glmS riboswitch by GlcN6P mimics interferes with the bacterial ability to synthesize its cell wall. Accordingly, GlcN6P mimics acting as glmS activators are promising candidates for future antibiotic drugs that may overcome emerging bacterial resistance against established antibiotics. We describe the synthesis of a series of phosphonate mimics of GlcN6P as well as the thia-sugar analogue of GlcN6P. The phosphonate mimics differ in their pKa value to answer the question whether derivatives with a pKa matching that of GlcN6P would be efficient glmS activators. We found that all derivatives activate the riboswitch, however, less efficiently than GlcN6P. This observation can be explained by missing hydrogen bonds in the case of phosphonates and is a valuable information for the design of future GlcN6P mimics. The thia-sugar analogue of GlcN6P on the other hand turned out to be a glmS riboswitch activator with the same activity as the natural metabolite GlcN6P. Therefore, the compound is a promising lead structure for the development of future antibiotics with a novel mode of action. | Bjarne Silkenath; Dennis Kläge; Hanna Altwein; Nina Schmidthäuser; Günter Mayer; Jörg S. Hartig; Valentin Wittmann | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64bbd73eae3d1a7b0d276bce/original/phosphonate-and-thia-sugar-analogs-of-glucosamine-6-phosphate-activation-of-the-glm-s-riboswitch.pdf |
664cece791aefa6ce19ba4f1 | 10.26434/chemrxiv-2024-xfvq9 | Reconciling Experiment with Quantum Chemical Calculations: Electron Iso-Density Surfaces Represent Atomic and Molecular Surfaces | The surface area of atoms and molecules plays a crucial role in shaping many physiochemical properties of materials. Despite its fundamental importance, precisely defining atomic and molecular surfaces has long been a puzzle. Among the available definitions, a straightforward and elegant approach by Bader describes a molecular surface as an iso-density surface beyond which electron density drops below a certain cut-off. However, so far neither this theory nor a decisive value for the density cut-off have been amenable to experimental verification due to the limitations of conventional experimental methods. In the present study, we employ a state-of-the-art experimental method based on the recently developed concept of thermodynamically effective (TE) surfaces to tackle this longstanding problem. By studying a set of 104 molecules, a close to perfect agreement between quantum chemical evaluations of iso-density surfaces for a cut-off density of 0.0016 a.u. and experimental results obtained via thermodynamic phase change data is demonstrated, with a mean unsigned percentage deviation of 1.6% and a correlation coefficient of 0.995. Accordingly, we suggest the iso-density surface contoured at an electron density value of 0.0016 a.u. as a representation of the surface of atoms and molecules. | Amin Alibakhshi; Lars V. Schäfer | Physical Chemistry; Interfaces; Quantum Mechanics; Structure; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664cece791aefa6ce19ba4f1/original/reconciling-experiment-with-quantum-chemical-calculations-electron-iso-density-surfaces-represent-atomic-and-molecular-surfaces.pdf |
65cf05a89138d231613d6b74 | 10.26434/chemrxiv-2024-k768m-v2 | Beyond Electrons: Correlation and Self-Energy in Multicomponent Density Functional Theory | Post-Kohn-Sham methods are used to evaluate the ground-state correlation energy and the orbital self-energy of systems consisting of multiple flavors of different fermions. Starting from multicomponent density functional theory, suitable ways to arrive at the corresponding multicomponent random-phase approximation and the multicomponent Green's function GW approximation, including relativistic effects, are outlined. Given the importance of both of this methods in the development of modern Kohn-Sham density functional approximations, this work will provide a foundation to design advanced multicomponent density functional approximations. Additionally, the GW quasiparticle energies are needed to study light-matter interactions with the Bethe-Salpeter equation. | Christof Holzer; Yannick J. Franzke | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65cf05a89138d231613d6b74/original/beyond-electrons-correlation-and-self-energy-in-multicomponent-density-functional-theory.pdf |
669e57c2c9c6a5c07a77e8d1 | 10.26434/chemrxiv-2024-mrdg3 | Identification of a privileged scaffold for inhibition of sterol transport proteins through the synthesis and ring distortion of diverse, pseudo-natural products | Sterol transport proteins mediate intracellular sterol transport, organelle contact sites, and lipid metabolism. Despite their importance, the similarities in their sterol-binding domains have made the identification of selective modulators difficult. Herein we report a combination of different compound library synthesis strategies to prepare a cholic-acid inspired compound collection for the identification of potent and selective inhibitors of sterol transport proteins. The fusion of a primary sterol scaffold with a range of different fragments found in natural products followed by various ring distortions allowed the synthesis of diverse sterol-inspired compounds. This led to the identification of a complex and three-dimensional spirooxepinoindole as a privileged scaffold for sterol transport proteins. With careful optimisation of the scaffold the selectivity could be directed towards a single transporter, as showcased by the development of a potent and selective Aster-A inhibitor. We suggest that the combination of different strategies can be used to identify potent and selective bioactive compounds with drug-like properties. | Frederik Simonsen Bro; Laura Depta; Nienke Dekker; Hogan Bryce-Rogers; Kaia Præstegaard; Tino Petersson; Thomas Whitmarsh-Everiss; Mariusz Kubus; Luca Laraia | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2024-07-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e57c2c9c6a5c07a77e8d1/original/identification-of-a-privileged-scaffold-for-inhibition-of-sterol-transport-proteins-through-the-synthesis-and-ring-distortion-of-diverse-pseudo-natural-products.pdf |
65669c87cf8b3c3cd75bda42 | 10.26434/chemrxiv-2023-p8x2v | Gravity separation of fine itabirite iron ore using the Reflux Classifier – Part II – Establishing the underpinning partition surface | This work assessed the potential of a single stage Reflux Classifier to upgrade itabirite iron ore to high grade at satisfactory recovery. Part I reported on the detailed findings of the experimental program and the physical transport of the particles through the system. A key purpose of the present paper was to deduce the underlying partition surface from relatively basic feed information on the Fe assays obtained as a function of the particle size. Conversion of the feed data into a simple binary description based on the density of hematite and density of silicates was used. This approach then provided a basis for applying the partition surface to a given feed to predict the separation performance. Data from the experiments were compared to values predicted from the partition surface. A least squares objective function was used to deduce the parameters governing the partition surface. Across 12 of the experiments, the key exponent, n, governing the partition surface was found to be 0.26+/-0.02. This result was in very good agreement with the value of 0.28 determined previously. The second key parameter, the Ep, was also determined for each of the experiments. The lowest Ep, found to be 365 kg/m3 for a low slimes viscosity, was also in good agreement with the result reported previously for a deslimed feed. This work provides confidence in the application of the partition surface to predict similar dense mineral separations, and stronger insights into the mechanisms responsible for the separation. | Armando Rodrigues; Homero Delboni Jr; James Zhou; Kevin Galvin | Chemical Engineering and Industrial Chemistry; Fluid Mechanics; Natural Resource Recovery | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65669c87cf8b3c3cd75bda42/original/gravity-separation-of-fine-itabirite-iron-ore-using-the-reflux-classifier-part-ii-establishing-the-underpinning-partition-surface.pdf |
66595a2891aefa6ce16e2a93 | 10.26434/chemrxiv-2024-18s8z | Compositional Design of Spontaneous Heterointerface Modulators for Perovskite Solar Cells Allowing a Broad Process Window | Spontaneous heterointerface modulation techniques have significantly contributed to the rapid development of perovskite solar cells (PSCs), and alkyl-primary-ammonium bis(trifluoromethanesulfonyl)imides (RA–TFSIs), whose archetype is n-octylammonium bis(trifluoromethanesulfonyl)imides (OA–TFSI), have recently emerged as functional additives for hole transport materials (HTMs). RA–TFSIs are designed to allow spontaneous perovskite passivation via the HTM deposition process; leveraging the high reactivity of RA cations toward the perovskite surface, these additives spontaneously and effectively suppress the defects over the perovskite surface and thereby enhance photovoltaic (PV) performance. Moreover, this perovskite passivation negates the need for conventional post-passivation processes, thereby improving the fabrication efficiency of PSCs. Although the advantages of these PSC fabrication processes have been less discussed than methods aimed at enhancing PV performance, they are crucial for further advancement of PSCs, especially in the context of spontaneous heterointerface modulation techniques. A key aspect is the concentration sensitivity of RA–TFSI; excessive OA–TFSI in the HTM solution leads to some OA cations failing to attach to the perovskite surface during spontaneous passivation, remaining in the HTM core and hindering carrier collection. To address this issue, we herein developed RA–TFSIs and synthesized ethylammonium bis(trifluoromethanesulfonyl)imide (EA–TFSI) for the first time. EA–TFSI not only enhanced the PV properties of PSCs but also significantly mitigated the concentration sensitivity owing to its small cation size, reducing the risk of poor carrier collection. In the case of OA–TFSI, increasing its concentration to twice the optimal amount decreased power conversion efficiency (PCE) by 14%, accompanied by drops in fill factor (FF). However, upon EA–TFSI addition, PCE decreased by only 4%, with FF values remaining unchanged (i.e., nearly 100% retention). This research offers insights into designing nascent yet potent spontaneous heterointerface modulators for PSCs, including RA–TFSI, to facilitate a broad process window, which is critical yet rarely discussed aspect. Therefore, this study will contribute to the further development of PSCs. | Naoyuki Nishimura; Hiroyuki Kanda; Takurou N. Murakami | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66595a2891aefa6ce16e2a93/original/compositional-design-of-spontaneous-heterointerface-modulators-for-perovskite-solar-cells-allowing-a-broad-process-window.pdf |
61b7608f476fcd6dae137a3c | 10.26434/chemrxiv-2022-x4p38 | Novel ultra-hard hexacarbon allotropes from first principles | Novel ultra-hard hexacarbon C6 allotropes are proposed based on crystal chemistry rationale and geometry optimization onto ground state structures. Similar to diamond, the orthorhombic, tetragonal and trigonal C6 are cohesive networks of C4 tetrahedra illustrated by charge density projections exhibiting sp3-like carbon hybridization. All three allotropes are identified as mechanically (elastic constants) and dynamically (phonons) stable. The electronic band structures are characteristic of insulators with large band gaps of 4 to 5 eV, like diamond. From three different models evaluating Vickers hardness HV, all new carbon allotropes are identified as ultra-hard. | Samir F. Matar; Vladimir L. Solozhenko | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2022-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61b7608f476fcd6dae137a3c/original/novel-ultra-hard-hexacarbon-allotropes-from-first-principles.pdf |
65284077bda59ceb9a745098 | 10.26434/chemrxiv-2023-1k9ls | Synthesis and Biological Activity of Penaresidins A and B, Penazetidine A, and Related Analogs | Since the first reports of their isolation, the penaresidins A and B together with penazetidine A and related analogs have attracted interest from the synthetic community for their unique structural features, specifically the highly functionalized azetidine core. This review provides a comprehensive overview of the biological activity of the penaresidins, penazetidine, and their analogs together with reported synthetic strategies developed since their isolation. | Corinna Schindler; Sean Burns; Timothy McClure; Seren Parikh | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65284077bda59ceb9a745098/original/synthesis-and-biological-activity-of-penaresidins-a-and-b-penazetidine-a-and-related-analogs.pdf |
643147e3a41dec1a56b34d32 | 10.26434/chemrxiv-2022-cn3qd-v3 | Electrochemical Formation of C-S Bonds from CO2 and Small Molecule Sulfur Species | The formation of C-S bonds is an important step in the synthesis of pharmaceutical, biological, and chemical products. A very attractive green route to C-S bond containing species would be one driven through electrocatalysis using abundant small molecule precursors but examples within this context are largely absent from the literature. To this end, this work demonstrates the use of CO2 and SO32- as cheap building blocks that couple on the surface Cu-based heterogeneous catalysts to form hydroxymethanesulfonate, sulfoacetate and methane sulfonate for the first time, with Faradaic efficiencies of up to 9.5%. A combination of operando measurements and computational modelling reveal that *CHOH formed on metallic Cu is a key electrophilic intermediate that is nucleophilically attacked by SO32- in the principal C-S bond forming step. In all, the proof-of-concept for electrocatalytic C-S bond formation and mechanistic insights gained stand to substantially broaden the scope of the emerging field of electrosynthesis. | Junnan Li; Hasan Al-Mahayni; Daniel Chartrand; Ali Seifitokaldani; Nikolay Kornienko | Physical Chemistry; Catalysis; Energy; Heterogeneous Catalysis; Energy Storage; Fuels - Energy Science | CC BY 4.0 | CHEMRXIV | 2023-04-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/643147e3a41dec1a56b34d32/original/electrochemical-formation-of-c-s-bonds-from-co2-and-small-molecule-sulfur-species.pdf |
6706feb2cec5d6c142b9329d | 10.26434/chemrxiv-2024-bjvr7 | Fabrication of Low-Cost, High-Resolution Open Capillary Microfluidics towards Self-Sustaining, Long-Term Hydration of Engineered Living Materials | Engineered living materials (ELMs) are an emerging class of biohybrid materials that have shown great promise with advanced capabilities unachievable by conventional materials. However, application of ELMs outside of the laboratory has been limited due to the need for periodic media replenishment or complete media immersion. We herein demonstrated the integration of capillary microfluidics for the autonomous and pump-free hydration of ELM hydrogels. We optimized 3D printing parameters, including exposure time and build plate lift and retract distances, to obtain microchannel dimensions capable of spontaneous capillary flow using a low-cost liquid crystal display stereolithographic apparatus (LCD-SLA) 3D printer and two hydrogel resins that are suitable for ELMs. Microchannel dimensions were accurate with ≤ 10% deviation between designed and measured widths and precise with coefficients of variation (CVs) <5% for microchannels ≥ 206.4 μm. We demonstrated proof-of-concept spontaneous capillary flow in 3D printed microfluidic devices using dye-incorporated lysogeny broth (LB). Snapshots of the devices captured up to 24 hours showed the diffusion of dye-incorporated LB throughout the bulk material. Through this proof-of-concept study, we have showcased the feasibility of integrating capillary microfluidics with ELMs for the autonomous and pump-free flow of fluids towards self-sustaining and long-term hydration. | Aileen Y. Sun; Carrie H. Lin; John A. Tatka; Kinsey Drake; Shannon Daily; Megan Castellanos; Alshakim Nelson; Ayokunle O. Olanrewaju | Materials Science; Biocompatible Materials; Materials Processing | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706feb2cec5d6c142b9329d/original/fabrication-of-low-cost-high-resolution-open-capillary-microfluidics-towards-self-sustaining-long-term-hydration-of-engineered-living-materials.pdf |
65f33a269138d23161766921 | 10.26434/chemrxiv-2024-nfsqp | Preparing initial conditions for excited-state dynamics in solvated systems | Performing excited-state dynamics or computing spectra on solvated systems requires sampling the ground state to generate initial conditions. Initial conditions (or snapshots for spectra) are typically produced by QM/MM Boltzmann sampling (following MM equilibration or optimization). It is now becoming clear that one should wait for a set period of time, which we call the healing time, before beginning to sample from the QM/MM trajectory. An appropriate healing time should be as short as possible (to avoid unnecessary computational effort), but long enough to equilibrate to the QM/MM ground state distribution. Healing times in previous studies range from tens of femtoseconds to tens of picoseconds, suggesting the need for guidelines to choose a healing time. We examine the effect of healing trajectory length on the nonadiabatic dynamics and spectrum of a first-generation Donor-Acceptor Stenhouse Adduct in chloroform. Insufficient healing times skew the branching ratio of relaxation back to the ground state and alter the relaxation time for one pathway. The healing time exerts a weaker influence on the spectrum: an insufficient healing time may cause a slight red shift. Monitoring the solute temperature during the healing trajectory provides a reasonable estimate for the healing time. Last, we apply the solute temperature metric to other common equilibration methods for solvated systems. | Ethan Curtis; Chey Jones; Todd Martinez | Theoretical and Computational Chemistry; Physical Chemistry; Photochemistry (Physical Chem.); Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f33a269138d23161766921/original/preparing-initial-conditions-for-excited-state-dynamics-in-solvated-systems.pdf |
67769779fa469535b98bbb25 | 10.26434/chemrxiv-2025-lrx59 | Revealing the Photochemical Pathways of Nitrate in Water through First-Principles Simulations | Nitrate anion (NO3-) is a ubiquitous species in aqueous phases in the environment, including atmospheric particles, aerosol droplets, surface waters, and snow. The photolysis of nitrate is a 'renoxification' process, which converts \nitrate solvated in water or deposited on surfaces back into NOx to the atmosphere. Nitrate photolysis under environmental conditions can follow two channels: (1) NO2 and O-; (2) nitrite and O. Despite the well-studied macroscopic kinetics of the two channels, the microscopic picture of the photolysis still needs to be explored. Furthermore, previous experiments have shown that nitrate photolysis in aqueous solutions has a low quantum yield of ~1% leading to a solvation cage effect hypothesis. A previous theoretical study has indicated that the low quantum yield may be due to the direct spin-forbidden absorption of \nitrate to its triplet state. Here, we employ first-principles molecular dynamics simulations at the level of hybrid DFT with enhanced sampling to explore the two channels in an aqueous solution to unravel the atomistic and electronic structure details of the photolysis, as well as investigate the causes of its low quantum yield under a solvation environment. The direct spin-forbidden absorption to T1 state is viable through spin-orbit coupling and is ~15 times weaker than the spin-allowed absorption to S1 state. A solvation cage complex is identified as a metastable state that requires additional thermal energy to complete the dissociation of the N-O bond at the triplet state. This metastable state allows the photo fragments to recombine or deactivate through non-radiative processes. Our simulations also qualitatively explain the temperature dependence of the two channels observed in experiments based on the rearrangement of H-bonds. This work provides a novel molecular picture illustrating the significantly low quantum yield and temperature dependence of nitrate photolysis under environmental conditions and a starting point for future studies of environmental nitrate photochemistry. | Kam-Tung Chan; Margaret Berrens; Zekun Chen; C. William McCurdy; Cort Anastasio; Davide Donadio | Theoretical and Computational Chemistry; Earth, Space, and Environmental Chemistry; Atmospheric Chemistry; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67769779fa469535b98bbb25/original/revealing-the-photochemical-pathways-of-nitrate-in-water-through-first-principles-simulations.pdf |
60c74479702a9b1f7918a84a | 10.26434/chemrxiv.9823667.v1 | Application of the Spatial Distribution Function to Colloidal Ordering | 2D colloidal assembly is a vital process in the fabrication of nanostructured devices and remains of widespread interest in fundamental research. Characterising the ordering is crucial to develop an understanding of the driving forces behind the assembly and to optimise processing conditions. Image analysis offers a direct evaluation pathway, typically via the radial distribution function or the 2D-fast Fourier transform. Both methods have inherent limitations; the former provides no angular dependence while the latter is challenged when confronted with imperfection on the mean size, spacing and coverage of the building blocks. Here, we introduce the 2D spatial distribution function (SDF) as an alternative pathway to evaluate colloidal ordering. We benchmark the method in case studies of prominent examples and provide a tool-kit for implementation, either as imageJ plugin or standalone software. Application and interpretation is straightforward and particularly powerful to analyse and compare colloidal assemblies with limited order. | Niamh Mac Fhionnlaoich; Runzhang Qi; Stefan Guldin | Materials Processing; Nanostructured Materials - Materials; Optical Materials; Nanofabrication; Nanostructured Materials - Nanoscience; Interfaces; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74479702a9b1f7918a84a/original/application-of-the-spatial-distribution-function-to-colloidal-ordering.pdf |
61a09645568d339902473319 | 10.26434/chemrxiv-2021-wnqd3-v3 | Boosting efficiency in light-driven water splitting by dynamic irradiation through synchronizing reaction and transport processes | This work elaborates the effect of dynamic irradiation on light-driven molecular water oxidation to counteract catalyst deactivation. It highlights the importance of overall reaction engineering to overcome limiting factors in artificial photosynthesis reactions. Systematic investigation of a homogenous three component ruthenium-based water oxidation system revealed significant potential to enhance the overall catalytic efficiency by synchronizing the timescales of photoreaction and mass transport in a capillary flow reactor. The overall activity could be improved by a factor of more than 10 with respect to the turnover number and a factor of 31 referring to the external energy efficiency by controlling the local availability of photons. Detailed insights into the mechanism of light driven water oxidation could be obtained using complementary methods of investigation like Raman, IR and UV-vis/emission spectroscopy, unraveling the importance of avoiding high concentrations of excited photosensitizers. | Maximilian Sender; Fabian Huber; Maximilian Moersch; Daniel Kowalczyk; Julian Hniopek; Sarah Klingler; Michael Schmitt; Simon Kaufhold; Kevin Siewerth; Jürgen Popp; Boris Mizaikoff; Dirk Ziegenbalg; Sven Rau | Catalysis; Energy; Chemical Engineering and Industrial Chemistry; Reaction Engineering; Homogeneous Catalysis; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a09645568d339902473319/original/boosting-efficiency-in-light-driven-water-splitting-by-dynamic-irradiation-through-synchronizing-reaction-and-transport-processes.pdf |
60c74907bdbb89ab36a390a2 | 10.26434/chemrxiv.12015663.v1 | Pd-Catalyzed C4-Dearomative Allylation of Benzyl Ammoniums with Allylstannanes | A dearomative C4-allylation of benzyl ammoniums with allylstannanes by a palladium catalysis is described. A triarylphosphine-ligated palladium catalyst, which is capable of cleaving benzylic C–N bonds, realized facile dearomative reactions with C4 selectivity. Combined with precedented C2- and C3-selective functionalizations of benzyl amine derivatives, the present reaction can provide a new synthetic option for the synthesis of multi-substituted alicyclic compounds as well as aromatic compounds. | Yuki Kayashima; Masaaki Komatsuda; Kei Muto; Junichiro Yamaguchi | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74907bdbb89ab36a390a2/original/pd-catalyzed-c4-dearomative-allylation-of-benzyl-ammoniums-with-allylstannanes.pdf |
677d85cc6dde43c908a633ec | 10.26434/chemrxiv-2025-l1bzs | Autonomous Organic Synthesis for Redox Flow Batteries via Flexible Batch Bayesian Optimization | Traditional trial-and-error methods for materials discovery are too slow to meet the urgent demands posed by the rapid progression of climate change. This urgency has driven the increasing interest in integrating robotics and machine learning into materials research to accelerate experimental learning. However, idealized decision-making frameworks to achieve maximum sampling efficiency are not always compatible with high-throughput experimental workflows inside a laboratory. For multistep chemical processes, differences in hardware capacities can complicate the digital framework by introducing constraints on the maximum number of samples in each step of the experiment, hence causing varying batch sizes in variable selection within the same batch. Therefore, designing flexible sampling algorithms is necessary to accommodate the multi-step synthesis with practical sampling constraints unique to each high-throughput workflow. In this work, we designed and employed three strategies on a high-throughput robotic platform to optimize the sulfonation reaction of redox-active molecules used in flow batteries. Our strategies adapt to the multi-step experimental workflow, where their formulation and heating steps are separate, causing varying batch size requirements. By strategically sampling using clustering and mixed-variable batch Bayesian optimization, we were able to iteratively identify optimal conditions that maximize the yields. Our work presents a new approach that allows tailoring the ML decision-making to suit the practical constraints in individual HTP platforms, followed by performing resource-efficient yield optimization using already existing and available open-source Python libraries. | Clara Tamura; Heather Job; Henry Chang; Wei Wang; Yangang Liang; Shijing Sun | Organic Chemistry; Materials Science; Energy; Organic Synthesis and Reactions; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677d85cc6dde43c908a633ec/original/autonomous-organic-synthesis-for-redox-flow-batteries-via-flexible-batch-bayesian-optimization.pdf |
676495946dde43c908ac9ca5 | 10.26434/chemrxiv-2024-0wqc3 | From Slit Pores to 3D Frameworks: Advances in Molecular Modeling of Adsorption in Nanoporous Carbons | Recent advances in computational capabilities have revolutionized the modeling of nanoporous carbons, enabling a transition from idealized pore descriptions to versatile three-dimensional molecular models. This review traces the evolution from traditional continuous potential methods and elementary pore models to modern simulation techniques that generate realistic carbon structures incorporating surface heterogeneity, pore connectivity, and framework flexibility. We examine various approaches including Hybrid Reverse Monte Carlo, Quench Molecular Dynamics, and Annealed Molecular Dynamics methods, discussing their relative strengths and limitations. Particular attention is given to the choice of interatomic potentials and their impact on structural predictions. The development of million-atom models captures long-range ordering effects previously inaccessible to simulation. Applications of the 3D models demonstrate their capability to predict adsorption behavior quantitatively and provide improved characterization of practical carbons through novel methods such as 3D-VIS and APDM. Recent hybrid MD/MC approaches incorporate the effects of structure flexibility and offer new insights into adsorbate-induced structural changes. This review highlights how advancing computational methods are bridging the gap between molecular-level understanding and practical applications in the carbon materials design and modeling of adsorption processes. | Nicholas Corrente; Alexander Neimark | Theoretical and Computational Chemistry; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Nanoscience; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676495946dde43c908ac9ca5/original/from-slit-pores-to-3d-frameworks-advances-in-molecular-modeling-of-adsorption-in-nanoporous-carbons.pdf |
636911d6c4c8796db11ee856 | 10.26434/chemrxiv-2022-rtc8h | A radioiodinated rucaparib analogue as an Auger electron emitter for cancer therapy. | Introduction: Radioligand therapy (RLT) is an expanding field that has shown great potential in the fight against cancer. Radionuclides that can be carried by selective ligands such as antibodies, peptides, and small molecules targeting cancerous cells have demonstrated a clear improvement in the move towards precision medicine. Poly (ADP-ribose) polymerase (PARP) is a family of enzymes involved in DNA damage repair signalling pathway, with PARP inhibitors olaparib, talazoparib, niraparib, veliparib, and rucaparib having FDA approval for cancer therapy in routine clinical use. Based on our previous work with the radiolabelled PARP inhibitor [18F]rucaparib, we replaced the fluorine-18 moiety, used for PET imaging, with iodine-123, a radionuclide used for SPECT imaging and Auger electron therapy, resulting in 8-[123I]iodo-5-(4-((methylamino)methyl)phenyl)-2,3,4,6-tetrahydro-1H-azepino[5,4,3-cd]indol-1-one, ([123I]GD1), as a potential radiopharmaceutical for RLT.
Methods: [123I]GD1 was synthesised via copper-mediated radioiodination from a selected boronic esters precursor. In vitro uptake, retention, blocking, and effects on clonogenic survival with [123I]GD1 treatment were tested in a panel of cancer cell lines. The enzymatic inhibition of PARP by GD1 was also tested in a cell-free system. The biodistribution of [123I]GD1 was investigated by SPECT/CT in mice following intravenous administration.
Results: Cell-free enzymatic inhibition and in vitro blocking experiments confirmed a modest ability of GD1 to inhibit PARP-1, IC50= 239 nM. In vitro uptake of [123I]GD1 in different cell lines was dose-dependent, and the radiolabelled compound was retained in cells for more than 2 h. Significantly reduced clonogenic survival was observed in vitro after exposure of cells for 1 h with as low as 50 kBq of [123I]GD1. The biodistribution of [123I]GD1 was further characterized in vivo showing both renal and hepatobiliary clearance pathways with a biphasic blood clearance.
Conclusion: We present the development of a new theragnostic agent based on the rucaparib scaffold and its evaluation in in vitro and in vivo models. The data reported show that [123I]GD1 may have the potential to be used as a theragnostic agent.
| Gianluca Destro; Zijiun Chen; Chung Ying Chang; Claudia Fraser; Gemma Dias; Michael Mosley; Florian Guibbal; Veronique Gouverneur; Bart Cornelissen | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/636911d6c4c8796db11ee856/original/a-radioiodinated-rucaparib-analogue-as-an-auger-electron-emitter-for-cancer-therapy.pdf |
66f677b751558a15ef4cf5f7 | 10.26434/chemrxiv-2024-tkm36 | SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases | SynTemp is a framework designed to extract and hierarchically cluster reaction templates from large-scale reaction data repositories. Reaction templates are partial Imaginary Transition State graphs representing the reaction center as well as surrounding context. These graphs are equivalent to Double Pushout graph rewriting rules and thus can be applied directly to predict reaction outcomes at structural formula level. Rule inference is based on a consensus of multiple atom-atom mapping (AAM) tools integrating predictions RXNMapper, GraphormerMapper, and LocalMapper based on a robust graph-theoretic methodology for comparing partial atom-atom mappings. SynTemp achieves an exceptional accuracy of 99.5% and a success rate of 71.23% in obtaining AAMs on the Chemical Reaction Dataset. Reaction centers with surrounding contexts are extracted and completed with mechanistically relevant hydrogen atoms to obtain complete reaction templates. Subsequently, they were categorized into distinct groups based on topological features using hierarchical clustering, resulting in a library of 311 transformation rules that explains 86% of the reaction data set. A residual of 14% remained unresolved due to non-equivalent AAMs and ambiguous hydrogen placements. Despite these challenges, the coverage of our templates remains high at approximately 93.5-94.5%, surpassing that of RDChiral using SMARTS templates. | Tieu-Long Phan; Klaus Weinbauer; Marcos E. Gonzalez Laffitte; Yingjie Pan; Daniel Merkle; Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Peter F. Stadler | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f677b751558a15ef4cf5f7/original/syn-temp-efficient-extraction-of-graph-based-reaction-rules-from-large-scale-reaction-databases.pdf |
60c7542ebb8c1ac3353dc1be | 10.26434/chemrxiv.13621421.v1 | Testing the Limitations of MD-based Local Electric Fields Using the Vibrational Stark Effect in Solution: Penicillin G as a Test Case | <div>Non-covalent interactions underlie nearly all molecular processes in the condensed phase from solvation to</div><div>catalysis. Their quantification within a physically consistent framework remains challenging. Experimental vibrational Stark effect (VSE)-based solvatochromism can be combined with molecular dynamics (MD) simulations to quantify the electrostatic forces in solute-solvent interactions for small rigid molecules and, by extension, when these solutes bind in enzyme active sites. While generalizing this approach towards more complex (bio)molecules, such as the conformationally flexible and charged penicillin G (PenG), we were surprised to observe inconsistencies in MD-based electric fields. Combining synthesis, VSE spectroscopy, and computational methods, we provide an intimate view on the origins of these discrepancies. We observe that the electrics fields are correlated to conformation-dependent effects of the flexible PenG side-chain, including both local solvation structure and solute conformational sampling in MD. Additionally, we identified that MD-based electric fields are consistently overestimated in 3-point water models in the vicinity of charged groups; this cannot be entirely ameliorated using polarizable force fields (AMOEBA) or advanced water models. This work demonstrates the value of the VSE as a direct method for experiment-guided refinements of MD force fields and establishes a general reductionist approach to calibrating vibrational probes for complex (bio)molecules.</div> | Jacek Kozuch; Samuel Schneider; Chu Zheng; Zhe Ji; Richard T Bradshaw; Steven Boxer | Biophysical Chemistry; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7542ebb8c1ac3353dc1be/original/testing-the-limitations-of-md-based-local-electric-fields-using-the-vibrational-stark-effect-in-solution-penicillin-g-as-a-test-case.pdf |
66ca7c4c20ac769e5fc44a45 | 10.26434/chemrxiv-2024-0h0hn | Revisiting the influence of acid-base equilibrium and tautomerism on the free radical scavenging activities of curcumin derivatives in the physiological environment – A mechanistic and kinetic study | Curcumin has been believed to have effective medicinal properties such as anti-cancer, anti-Alzheimer, anti-inflammatory, and antioxidant…, in which the free radical scavenging activities play a crucial role in its treating mechanisms. Although the antioxidant properties of curcumin and its derivatives have been widely studied in the literature, a systematical investigation of the thermodynamics and kinetics of the reaction towards hydroperoxide (HOO•), the standardized free radicals, has still been lacking. This work investigated the HOO• radical scavenging activities of two curcumin derivatives, namely curcumin I (Cur-I) and curcumin III (Cur-III), in water and pentyl ethanoate (PEA) solutions using Density functional theory (DFT) approaches. The antioxidant properties of the neutral and anionic forms of two tautomers, including keto-enol and diketone of curcumin, were investigated via three common mechanisms, i.e., hydrogen transfer (HT), radical adduct formation (RAF) and single electron transfer (SET). Intrinsic parameters, thermochemical parameters, and kinetics of the curcumin-HOO radical reactions were systematically characterized. As a result, the overall rate constant for the reaction in the water of Cur-I (9.36 107 M-1 s-1) is about three times higher than the one of Cur-III (2.60 107 M-1 s-1). Meanwhile, the ones in the PEA solvent are less significant, being 4.02 101 M-1 s-1 and 8.16 102 M-1 s-1, respectively. Because of the dominant molar fraction of the keto-enol form compared to that of the diketone, the reaction rates were contributed mainly by the keto-enol form. Finally, the chemical nature of the HT processes was analyzed in detail, and it was found that all the most predominant HT reactions at the phenolic -OH groups (i.e., O22H and O23H) occurred via the proton-coupled electron transfer (PCET) process. | Dinh Hieu Truong; Thi Tu Dinh ; Thi My Duyen Trinh; Thi Hong Minh Pham; Minh Quan Pham; Urszula Gawlik-Dziki; Duy Quang Dao | Physical Chemistry; Organic Chemistry; Agriculture and Food Chemistry; Physical Organic Chemistry; Chemical Kinetics; Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66ca7c4c20ac769e5fc44a45/original/revisiting-the-influence-of-acid-base-equilibrium-and-tautomerism-on-the-free-radical-scavenging-activities-of-curcumin-derivatives-in-the-physiological-environment-a-mechanistic-and-kinetic-study.pdf |
60c74bb5337d6c895fe27b0f | 10.26434/chemrxiv.12370334.v1 | Phase Behavior in NaSiCON Electrolytes and Electrodes | <p>The replacement of the presently used liquid electrolytes by a non-flammable solid electrolyte is an important avenue to create safer batteries. The Natrium Superionic CONductor<b> </b>(NaSiCON) Na<sub>1+x</sub>Zr<sub>2</sub>Si<sub>x</sub>P<sub>3-x</sub>O<sub>12</sub> (0 < x < 3) that displays high bulk ionic conductivity and good stability towards other NaSiCON-based electrodes is a good solid electrolyte in NaSiCON-based batteries. Despite the sizeable share of research on Na<sub>1+x</sub>Zr<sub>2</sub>Si<sub>x</sub>P<sub>3-x</sub>O<sub>12</sub>, the structural and thermodynamic properties of NaSiCON require better understanding for more efficient synthesis and optimization as a solid electrolyte, which often follows chemical intuition. Here, we analyze the thermodynamic properties of the NaSiCON electrolyte by constructing the Na<sub>1+x</sub>Zr<sub>2</sub>Si<sub>x</sub>P<sub>3-x</sub>O<sub>12</sub> phase diagram, based on density functional theory calculations, a cluster expansion framework, and Monte Carlo simulations. Specifically, we build the phase diagram as a function of temperature and composition (0 < x < 3) for the high-temperature rhombohedral structure, which has been also observed in several positive electrode materials, such as Na<sub>3</sub>Ti<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>, Na<sub>3</sub>V<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub> and Na<sub>3</sub>Cr<sub>2</sub>(PO<sub>4</sub>)<sub>3</sub>. Through the phase diagram, we identify the concentration domains providing the highest Na<sup>+</sup>-ion conductivity and previously unreported phase-separation behavior across three different single-phase regions. Further, we note the similarities in the phase behavior between Na<sub>1+x</sub>Zr<sub>2</sub>Si<sub>x</sub>P<sub>3-x</sub>O<sub>12</sub> and other NaSiCON-based mono-transition metal electrodes and discuss the potential competition between thermodynamics and kinetics in experimentally observed phase separation. Our work is an important addition in understanding the thermodynamics of NaSiCON-based materials and in the development of inexpensive Na-ion batteries. From our results we propose that the addition of SiO<sub>4</sub><sup>4–</sup> moieties to single-transition metal NaSiCON-phosphate-based electrodes will slow significantly the kinetics toward phase separation. </p> | Zeyu Deng; Gopalakrishnan Sai Gautam; Sanjeev Krishna Kolli; Jean-Nöel Chotard; Anthony K. Cheetham; Christian Masquelier; Pieremanuele Canepa | Nanostructured Materials - Materials; Computational Chemistry and Modeling; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bb5337d6c895fe27b0f/original/phase-behavior-in-na-si-con-electrolytes-and-electrodes.pdf |
60c749e9469df4a658f43c5a | 10.26434/chemrxiv.12118857.v1 | Main Protease Inhibitors and Drug Surface Hotspot for the Treatment of COVID-19: Drug Repurposing and Molecular Docking Approach | <div>The world is facing an unprecedented global pandemic caused by the novel SARS-CoV-2. In the absence</div><div>of a specific therapeutic agent to treat COVID-19 patients, the present study aimed to virtually screen out</div><div>the effective drug candidates from the approved main protease protein (MPP) inhibitors and their</div><div>derivatives for the treatment of SARS-CoV-2. Here, drug repurposing and molecular docking were</div><div>employed to screen approved MPP inhibitors and their derivatives. The approved MPP inhibitors against</div><div>HIV and HCV were prioritized, whilst hydroxychloroquine, favipiravir, remdesivir, and alpha-ketoamide</div><div>were studied as control. The target drug surface hotspot was also investigated through the molecular</div><div>docking technique. ADME analysis was conducted to understand the pharmacokinetics and drug-likeness</div><div>of the screened MPP inhibitors. The result of this study revealed that Paritaprevir (-10.9 kcal/mol), and its</div><div>analog (CID 131982844)(-16.3 kcal/mol) showed better binding affinity than the approved MPP inhibitor</div><div>compared in this study including favipiravir, remdesivir, and alpha-ketoamide. A comparative study among</div><div>the screened putative MPP inhibitors revealed that amino acids T25, T26, H41, M49, L141, N142, G143,</div><div>C145, H164, M165, E166, D187, R188, and Q189 are at critical positions for becoming the surface hotspot</div><div>in the MPP of SARS-CoV-2. The study also suggested that paritaprevir and its' analog (CID 131982844),</div><div>may be effective against SARS-CoV-2 as these molecules had the common drug-surface hotspots on the</div><div>main protease protein of SARS-CoV-2. Other pharmacokinetic parameters also indicate that paritaprevir</div><div>and its top analog (CID 131982844) will be either similar or better-repurposed drugs than already approved</div><div>MPP inhibitors. </div><div><br /></div> | Mahmudul Hasan; Md Sorwer Alam Parvez; Kazi Faizul Azim; Abdus Shukur Imran; Topu Raihan; Airin Gulshan; Samuel Muhit; Rubaiat Nazneen Akhand; Md Bashir Uddin; Syed Sayeem Uddin Ahmed | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749e9469df4a658f43c5a/original/main-protease-inhibitors-and-drug-surface-hotspot-for-the-treatment-of-covid-19-drug-repurposing-and-molecular-docking-approach.pdf |
62d06fb5fe12e35c2ca1decf | 10.26434/chemrxiv-2022-tvlp7 | Designing Efficient Tandem Organic Solar Cells with Machine Learning and Genetic Algorithms | Tandem organic solar cells can potentially drastically improve the PCE over single-junction devices. However, there is limited research on device development and often only ca. 1% improvement over single-junction devices. Because of the complex nature of organic material compatibility and properties, such as energy-level alignment and maximizing absorption spectra, and the vastness of chemical space, computational guidance is vital. The first part of this work uses a new data set of 1,225 donor/non-fullerene acceptor (NFA) pairs containing 1,001 unique pairs, one of the largest to date, to train an ensemble machine learning model to predict device efficiency (RMSE =1.60 +/- 0.14%). Next, a series of genetic algorithms (GA) are used to discover high-performing NFAs and polymer donors, and then combinations of them for potential high-efficiency tandem cells. Interesting design motifs show up in high-performing NFAs, such as diphenylamine substituents on the core and 3D terminal groups. The donor polymers from the GA reveal that it may be beneficial to arrange the monomers as a small-block copolymer instead of the common alternating copolymer. The GAs for selection of tandem cell materials successfully find material combinations, that when in a device together, have strong absorption across the entire visible-near-IR spectrum. Computational guidance is critical for the selection of tandem OSC materials, with genetic algorithms proving a highly successful technique. | Brianna Greenstein; Geoffrey Hutchison | Theoretical and Computational Chemistry; Energy; Computational Chemistry and Modeling; Machine Learning; Photovoltaics; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d06fb5fe12e35c2ca1decf/original/designing-efficient-tandem-organic-solar-cells-with-machine-learning-and-genetic-algorithms.pdf |
6194db48b039f27304a803fa | 10.26434/chemrxiv-2021-mgmw0 | Evaluating a dispersion of sodium in sodium chloride for the synthesis of low-valent nickel complexes | The use of a sodium in sodium chloride dispersion is systematically evaluated for the synthesis of nickel(0) and nickel(I) complexes from readily-prepared nickel(II) precursors. A variety of complexes with phosphine and bipyridine-type ligands were accessed, although some reactions were found to produce mixtures of nickel(0) and nickel(I), and yields were highly variable. Several new nickel(I) complexes were obtained, and these were characterised using techniques including NMR spectroscopy, EPR spectroscopy, and single crystal X-ray diffraction analysis. | Elliot Johnson Humphrey; Alan Kennedy; Stephen Sproules; David Nelson | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Reaction (Organomet.); Transition Metal Complexes (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6194db48b039f27304a803fa/original/evaluating-a-dispersion-of-sodium-in-sodium-chloride-for-the-synthesis-of-low-valent-nickel-complexes.pdf |
6188bf88ad7f7c28825941e3 | 10.26434/chemrxiv-2021-6f71d-v3 | Flexible boundary layer using exchange for embedding theories. II. QM/MM dynamics of the hydrated electron | The FlexiBLE embedding method introduced in the preceding companion paper [Z. Shen and W. J. Glover, J. Chem. Phys. X, X (2021)] is applied to explore the structure and dynamics of the aqueous solvated electron at an all-electron density functional theory QM/MM level. Compared to a one-electron mixed quantum/classical description, we find the dynamics of the many-electron model of the hydrated electron exhibits enhanced coupling to water OH stretch modes. Natural Bond Orbital analysis reveals this coupling is due to significant population of water OH σ* orbitals, reaching 20%. Based on this, we develop a minimal frontier orbital picture of the hydrated electron involving a cavity orbital and important coupling to 4-5 coordinating OH σ* orbitals. Implications for the interpretation of the spectroscopy of this interesting species are discussed. | Zhuofan Shen; Shaoting Peng; William Glover | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Solution Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-11-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6188bf88ad7f7c28825941e3/original/flexible-boundary-layer-using-exchange-for-embedding-theories-ii-qm-mm-dynamics-of-the-hydrated-electron.pdf |
61e128f077a416272ad0b912 | 10.26434/chemrxiv-2022-v708l | Construction of axial chirality via asymmetric radical
trapping by cobalt under visible light | 3d-Metals have been identified as economic and sustainable alternatives to palladium, the frequently used metal in transition-metal-catalyzed cross-couplings. However, cobalt has long stood behind its neighboring elements, nickel and copper, in asymmetric radical couplings, owing to its high catalytic activity in the absence of ligands. Here, we disclose an asymmetric metallaphotoredox catalysis (AMPC) strategy for the dynamic kinetic resolution (DKR) of racemic heterobiaryls, which represents the first example of visible-light-induced, asymmetric radical couplings for the construction of axial chirality. This success can also be extended to the reductive cross-coupling variant featuring on more easily available feedstocks. The keys to these successes are the rational design of a sustainable AMPC system by merging asymmetric cobalt catalysis with organic photoredox catalysis and, perhaps more importantly, the identification of an efficient chiral polydentate ligand. | Liang-Qiu Lu; Wen-Jing Xiao; Xuan Jiang; Wei Xiong; Shuang Deng; Fu-Dong Lu; Yue Jia ; Qian Yang; Li-Yuan Xue; Xiaotian Qi; Jon A. Tunge | Organic Chemistry; Organic Synthesis and Reactions; Photochemistry (Org.); Stereochemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61e128f077a416272ad0b912/original/construction-of-axial-chirality-via-asymmetric-radical-trapping-by-cobalt-under-visible-light.pdf |
60c74279bb8c1a2f503da148 | 10.26434/chemrxiv.8295878.v1 | Assessing Negative Thermal Expansion in Mesoporous Metal-Organic Frameworks by Molecular Simulation | Most conventional materials display expansion upon heating, so there is considerable interest in identifying materials that display the opposite behavior, negative thermal expansion (NTE). In the current study, seven mesoporous metal-organic frameworks (MOFs) of varying topology and composition, which exhibit outstanding porosity, were investigated using molecular simulation for temperature-induced contraction. We find exceptional NTE for the most porous MOFs and a correlation between the coefficient of NTE and porosity. The large molecular subunits of the MOFs were further studied to find they intrinsically display NTE, corresponding to terahertz vibrational modes. As a result, NTE has a considerable effect on the mechanical properties of these MOFs and is an important consideration for understanding the mechanical stability of new extremely porous materials. | Jack D. Evans; Johannes P. Dürholt; Stefan Kaskel; Rochus Schmid | Nanostructured Materials - Materials; Computational Chemistry and Modeling; Physical and Chemical Properties; Structure; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74279bb8c1a2f503da148/original/assessing-negative-thermal-expansion-in-mesoporous-metal-organic-frameworks-by-molecular-simulation.pdf |
60c757719abda2d6fcf8e71a | 10.26434/chemrxiv.14369726.v1 | Towards an Atomistic Understanding of Polymorphism in Molecular Solids | Many chemical
phenomena are ultimately due to energy balances between atoms. In order to
reach firm and clear conclusions one needs a reliable energy decomposition
analysis (EDA). The Interacting Quantum Atoms (IQA) energy partitioning method is one of the most
recent EDA methods. IQA is a topological energy partitioning that generates
well-defined intra- and interatomic contributions, of steric, electrostatic or
covalent (exchange) character. IQA has a minimal and powerful architecture and
does not suffer from a number of conceptual and practical problems that plague the more traditional non-topological EDAs
(<i>Chem.
Soc. Rev.</i>, <b>44</b> (2015) 3177).<div><br /></div><div>For the first time,
our manuscript reports on a protocol for using the IQA to understand polymorphism,
which we apply to the three polymorphs of succinic acid (SA), including the
unusual polymorph that
was recently discovered serendipitously (<i>CrystEngComm</i>, <b>20</b> (2018) 3971). The many intra- and interatomic energy terms from the EDA scheme are processed using
a new technique that we developed called the Relative Energy Gradient (REG)
method, which clearly identifies the atoms and corresponding energetic terms
that govern the behaviour of the total system, in a minimal and unbiased way. <br /></div> | Arturo Sauza-de la Vega; Leonardo
J. Duarte; arnaldo silva; Jonathan Skelton; Tomás Rocha-Rinza; Paul Popelier | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757719abda2d6fcf8e71a/original/towards-an-atomistic-understanding-of-polymorphism-in-molecular-solids.pdf |
60c74ae8bdbb891f82a39479 | 10.26434/chemrxiv.12272861.v1 | Amide-to-Ester Substitution Improves Membrane Permeability of a Cyclic Peptide Without Altering Its Three-Dimensional Structure | <div>
<div>
<div>
<p>Cyclic peptides are attractive molecules as inhibitors with high affinity and selectivity against intracellular protein-protein interactions (PPIs). On the other hand, cyclic peptides generally have low passive cell-membrane permeability, which makes it difficult to discover cyclic peptides that efficiently
permeate into cells and inhibit intracellular PPIs. Here, we show that backbone amide-to-ester substitutions are useful for improving membrane permeability of peptides. Permeability in a series of model dipeptides increased upon amide-to-ester substitution. Amide-to-ester substitutions increased permeability
in the same manner as amide-to-N-methyl amide substitutions, which are conventionally used for increasing permeability. Furthermore, amide-to-ester substitutions of exposed amides of a cyclic peptide
successfully improved permeability. Conformational studies of the cyclic peptides using NMR and molecular mechanics calculations revealed that an amide-to-ester substitution of an exposed amide bond
did not affect its low-energy conformation in CDCl<sub>3</sub>, in contrast with an N-methyl amide substitution.
We envision that amide-to-ester substitution will be a potentially useful strategy for rational design of
bioactive peptides with high membrane permeability.
</p>
</div>
</div>
</div> | Yuki Hosono; Jumpei Morimoto; Chad Townsend; Colin N. Kelly; Matthew R. Naylor; Hsiau-Wei Lee; R. Scott Lokey; Shinsuke Sando | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae8bdbb891f82a39479/original/amide-to-ester-substitution-improves-membrane-permeability-of-a-cyclic-peptide-without-altering-its-three-dimensional-structure.pdf |
64efac5079853bbd78c10569 | 10.26434/chemrxiv-2023-pbr32 | Solvation of Nanoions in Aqueous Solutions | In recent years it has been increasingly recognized that different classes of large ions with multiple valency have effects conceptually similar to weakly solvated ions in the Hofmeister series, also labeled by the term chaotropic. The term “super- chaotropic effect” has been coined, because these effects are much stronger pronounced for nanometer-sized ions, whose adsorption properties often resemble typical surfac- tants. Despite this growing interest in these nanometer-sized ions, a simple conceptual extension of the Hofmeister series towards nanoions has not been achieved, because an extrapolation of the one-dimensional surface charge density scale does not lead to the superchaotropic regime. In this work, we discuss a generic model that is broadly appli- cable to ions of nearly shperical shape and thus includes polyoxometallates and boron clusters. We present a qualitative classification scheme, in which the ion size appears as a second dimension. Ions of different size but same charge density differ in their bulk solvation free energy. As the ions grow bigger at constant surface charge density, they become more stable in solution, but the adsorption behavior is still governed by the surface charge density. A detailed molecular dynamics simulation study of large ions that is based on a shifted Lennard-Jones potential is presented that supports the presented classification scheme. | Philipp Dullinger; Dominik Horinek | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Solution Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64efac5079853bbd78c10569/original/solvation-of-nanoions-in-aqueous-solutions.pdf |
655918482c3c11ed71aa6567 | 10.26434/chemrxiv-2023-ll6p7 | Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach | Unraveling the reaction pathway of photoinduced reactions poses a great challenge owing to its complexity. Recently, graph theory-based machine learning combined with non-adiabatic molecular dynamics (NAMD) has been applied to obtain the global reaction coordinate of the photoisomerization of azobenzene. However, NAMD simulations are computationally expensive as they require calculating the non-adiabatic coupling vectors at each time step. Here we showed that ab initio molecular dynamics (AIMD) can be used as an alternative to NAMD by choosing an appropriate initial condition for the simulation. We applied our methodology to determine a plausible global reaction coordinate of retinal photoisomerization, which is essential for human vision. On rank-ordering the internal coordinates, based on the mutual information (MI) between the internal coordinates and the HOMO energy, NAMD and AIMD give a similar trend. Our results demonstrate that instead of NAMD, AIMD-based machine learning is a computationally more affordable approach to study reaction coordinates. | Goran Giudetti; Madhubani Mukherjee; Samprita Nandi; Sraddha Agrawal; Oleg Prezhdo; Aiichiro Nakano | Theoretical and Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/655918482c3c11ed71aa6567/original/exploring-the-global-reaction-coordinate-for-retinal-photoisomerization-a-graph-theory-based-machine-learning-approach.pdf |
62be0385d66f68ee9bb89111 | 10.26434/chemrxiv-2022-mfmc5 | The role of organic cations as additives in photovoltaic perovskites. | The design of additives for perovskite-based solar cells seeks to improve the balance between stability and power conversion efficiency. Organic molecules such as theophylline, theobromine and caffeine (xanthines) have proved to be a good engineering solution. As an alternative, we present a first-principle study of the use of organic cations as additives. These cations are got when the free nitrogen of the imidazole unit of the aforementioned molecules is quaternized. We have found that the interaction between the organic cations and the MAPbI3 perovskite surface is stronger compared to the organic molecules. The Pb-O and I-H bonds of the interface dominated these interactions. In addition, organic cations showed higher charge transfer through the interface and shallow states that are harmless and could improve the charge carrier mobility. These characteristics show that quaternized xanthines should be a promising additive for perovskite materials in photovoltaic applications. | alejandra tayde cadillo; alejandra vargas; arian roa; Andres M. Garay-Tapia | Theoretical and Computational Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Optical Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62be0385d66f68ee9bb89111/original/the-role-of-organic-cations-as-additives-in-photovoltaic-perovskites.pdf |
638efe2ecfb5ffb6fd5ef0fa | 10.26434/chemrxiv-2022-2s60l | Differential contributions of distinct free radical peroxidation mechanisms to the induction of ferroptosis | Ferroptosis is a form of regulated cell death driven by lipid peroxidation of polyunsaturated fatty acids (PUFAs). Lipid peroxidation can propagate through either hydrogen-atom transfer (HAT) or peroxyl radical addition (PRA) mechanism. However, the contribution of the PRA mechanism to the induction of ferroptosis has not been studied. In this study, we aim to elucidate the relationship between the reactivity and mechanisms of lipid peroxidation and ferroptosis induction. We found that while some peroxidation-reactive lipids, such as 7-dehydrocholesterol, vitamins D3 and A, and coenzyme Q10, suppress ferroptosis, both nonconjugated and conjugated PUFAs enhanced cell death induced by RSL3, a ferroptosis inducer. Importantly, we found that conjugated polyunsaturated fatty acids (PUFAs), including conjugated linolenic acid (CLA 18:3) and conjugated linoleic acid (CLA 18:2) can induce or potentiate ferroptosis much more potently than nonconjugated PUFAs. We next sought to elucidate the mechanism underlying the different ferroptosis-inducing potency of conjugated and nonconjugated PUFAs. Lipidomics revealed that conjugated and nonconjugated PUFAs are incorporated into distinct cellular lipid species. The different peroxidation mechanisms predict the formation of higher levels of reactive electrophilic aldehydes from conjugated PUFAs than nonconjugated PUFAs, which was confirmed by aldehyde-trapping and mass spectrometry. RNA sequencing revealed that protein processing in the endoplasmic reticulum and proteasome are among the most significantly upregulated pathways in cells treated with CLA 18:3, suggesting increased ER stress and activation of unfolded protein response. Significantly, using click chemistry, we observed increased protein adduction by oxidized lipids in cells treated with an alkynylated CLA 18:2 probe. These results suggest that protein damage by lipid electrophiles is a key step in ferroptosis. | Quynh Do; Rutan Zhang; Gavin Hooper; Libin Xu | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638efe2ecfb5ffb6fd5ef0fa/original/differential-contributions-of-distinct-free-radical-peroxidation-mechanisms-to-the-induction-of-ferroptosis.pdf |
6642639f21291e5d1d28dc14 | 10.26434/chemrxiv-2024-zfvbq | Second Coordination Sphere Effects in an Earth-Abundant Monometallic Complex as Catalyst Dictate Highly Selective Photochemical Conversion of CO2 to HCOOH | Photochemical reduction of CO2 to formic acid (HCOOH) using molecular transition metal complexes as catalysts has been previously documented to proceed via either of the two mechanisms: CO2 insertion into metal hydride bonds, or hydrogenation of CO2. We present herein photoreduction of CO2 to HCOOH that adopts both these pathways by a single monometallic molecular catalyst featuring earth-abundant cobalt - a characteristic not observed in other molecular catalysts for CO2 photoreduction to date. This dual functionality stems from distinctly different, active forms of the catalyst, at different temporal stages of irradiation. We employ in situ NMR spectroscopy to monitor potential catalytic intermediates at various time points of irradiation by visible light. These observed states align with the kinetic profiles of product evolution, proving instrumental in revealing the catalyst's unique behavior. We advocate for the integration of such in situ NMR monitoring in future studies as it provides a valuable tool for an informed design of photochemical CO2 reduction by molecular catalysts. | Hemlata Agarwala; Vincent Artero; Marc Fontecave | Inorganic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Photocatalysis; Small Molecule Activation (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6642639f21291e5d1d28dc14/original/second-coordination-sphere-effects-in-an-earth-abundant-monometallic-complex-as-catalyst-dictate-highly-selective-photochemical-conversion-of-co2-to-hcooh.pdf |
65549f52dbd7c8b54b4e8ed3 | 10.26434/chemrxiv-2023-3fgrr-v2 | Modeling pH-dependent biomolecular photochemistry | The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics, using a combination of constant-pH molecular dynamics and semi-classical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena Sensory Rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties such as the isomerization quantum yield or decay rates. We decompose our results in single titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy. | Elisa Pieri; Oliver Weingart; Miquel Huix-Rotllant; Vincent Ledentu; Marco Garavelli; Nicolas Ferré | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65549f52dbd7c8b54b4e8ed3/original/modeling-p-h-dependent-biomolecular-photochemistry.pdf |
6446e81ee4bbbe4bbf31d060 | 10.26434/chemrxiv-2023-g56rp | Sublimation Thermodynamics of 5,10,15,20–Tetraphenyl-21-X, 23-Y-Heteroporphyrins (X=O or S; Y= N or S). The Molecular structure of 5,10,15,20-Tetraphenyl-21-thiaporphyrin | Sublimation enthalpies of 10,15,20–tetraphenyl-21-oxa- (I), 5,10,15,20-tetraphenyl-21-thia- (II) and 5,10,15,20-tetraphenyl-21,23-dithia- (III) porphyrines were measured by Knudsen effusion mass spectrometry: ΔHsubl.(T) = 209±2 (561 K), 224±2 (552 K) and 219±2 (577 K) kJ/mol, respectively. A structure of a free molecule of II was studied by quantum chemistry and gas-phase electron diffraction. The molecular structures of the dimeric associates of I-III were tested by quantum chemical calculations. | Ilya Kuzmin; Sergey Shlykov; Alexander Krasnov; Svetlana Pukhovskaya; Sergey Syrbu; Yulia Ivanova | Physical Chemistry; Organic Chemistry; Physical Organic Chemistry; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6446e81ee4bbbe4bbf31d060/original/sublimation-thermodynamics-of-5-10-15-20-tetraphenyl-21-x-23-y-heteroporphyrins-x-o-or-s-y-n-or-s-the-molecular-structure-of-5-10-15-20-tetraphenyl-21-thiaporphyrin.pdf |
644bc2756ee8e6b5ed4014a9 | 10.26434/chemrxiv-2023-1k3bw | Trapping of Photoluminescent Kinetic Intermediates During High-Concentration Synthesis of Non-Emissive Metal-Organic Frameworks | Metal-organic frameworks (MOFs) are porous, crystalline materials constructed from organic linkers and inorganic nodes with potential utility in gas separations, drug delivery, sensing, and catalysis. Small variations in MOF synthesis conditions can lead to a range of accessible frameworks with divergent chemical or photophysical properties. New meth-ods to controllably access phases with tailored properties would broaden the scope of MOFs that can be reliably prepared for specific applications. Herein, we demonstrate that simply increasing the reaction concentration during the solvother-mal synthesis of M2(dobdc) (M = Mg, Mn, Ni; dobdc4− = 2,5-dioxido-1,4-benzenedicarboxylate), also known as MOF-74, unexpectedly leads to trapping of a kinetic intermediate termed CORN-MOF-1 (CORN = Cornell University). In-depth spec-troscopic, crystallographic, and computational studies support that CORN-MOF-1 has a similar structure to M2(dobdc) but with partially protonated linkers and charge-balancing or coordinated formate groups in the pores. The resultant vari-ation in linker spacings causes CORN-MOF-1 (Mg) to be strongly photoluminescent in the solid state, whereas H4dobdc and Mg2(dobdc) are weakly emissive due to excimer formation. In addition, CORN-MOF-1 variants can be converted into high-quality samples of the thermodynamic M2(dobdc) phases by heating in N,N-dimethylformamide (DMF). Overall, our findings support that high-concentration synthesis provides a straightforward method to identify new kinetic MOF phas-es with different properties from known materials and to produce highly porous samples of MOFs, paving the way for the discovery and gram-scale synthesis of framework materials. | Arjun Halder; David Bain; Tristan Pitt; Zixiao Shi; Julia Oktawiec; Jung-Hoon Lee; Stavrini Tsangari; Marcus Ng; Jose Fuentes-Rivera; Alexander Forse; Tomce Runcevski; David Muller; Andrew Musser; Phillip Milner | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644bc2756ee8e6b5ed4014a9/original/trapping-of-photoluminescent-kinetic-intermediates-during-high-concentration-synthesis-of-non-emissive-metal-organic-frameworks.pdf |
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