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62372d6dd75627a1ca1ed7eb | 10.26434/chemrxiv-2022-gqtr6 | Simultaneously Tuning the Conductance of Multiple Embedded Circuits in Bis-Terpyridine-Based Single Molecule Breadboard Junctions | Assembling and prototyping multiple circuits on a common breadboard scaffold is critical for developing functional single molecule electronic devices. However, at present, controlling and combining the electronic properties of multiple circuits within a single-molecule junction remains an unresolved challenge. Here, we describe the molecular conductance distributions for five single terminal circuits each within three constitutional isomers of a bis-terpyridine-based molecular breadboard junction through a rigorous computational framework which accounts for molecular conformational flexibility and the relative electrode accessibility (REA) of anchoring groups. The isomers, termed TPo, TPm, and TPp, differ in the relative placement of the linking nitrogen (N) atoms at ortho, meta, and para positions, respectively, of the peripheral pyridyl rings. We demonstrate that quantum interference effects (QIE) and REA of the anchoring N atoms can be exploited to alter the relative conductance of the five single terminal circuits within the molecular breadboards by ~ 4–32 times. We introduce a phase-plot-analysis to highlight the interdependence of QIE- and REA-induced changes in the conductance states of the basis circuits across breadboard pairs. Our studies predict that REA should not impact the QIE-induced boost in circuit conductance for TPp relative to that in TPm. In contrast, REA suppresses the QIE boost for circuit conductance in TPo relative to that in TPm. Our results showcase the possibility of accessing the combined effect of QIE and REA within an experimental break-junction setup to develop diverse molecular electronic breadboards with multiple embedded circuits and distinct electronic properties. | Ravinder Kumar; Charu Seth; Veerabhadrarao Kaliginedi; Ravindra Venkatramani | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Theory - Computational; Quantum Mechanics; Transport phenomena (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62372d6dd75627a1ca1ed7eb/original/simultaneously-tuning-the-conductance-of-multiple-embedded-circuits-in-bis-terpyridine-based-single-molecule-breadboard-junctions.pdf |
610ab70b18911d4c50d9e794 | 10.26434/chemrxiv-2021-2tkt2 | Leaflet Asymmetry Modeling in Lipid Composition of Escherichia coli Cytoplasmic Membrane | Lipid composition asymmetry between leaflets is important to cell function and plays a key role in the “positive inside” rule in transmembrane proteins. In this work, E. coli inner plasma membrane models reflecting this asymmetry have been investigated at the early-log and stationary stages during the bacterial lifecycle using all-atom molecular dynamics simulations. The CHARMM36 lipid force field is used, and selected membrane properties are tested for variations between two leaflets and whole membranes. Our models include bacterial lipids containing cyclopropane moiety on the sn-2 acyl chain in the stationary membrane. The PE:PG ratio in two leaflets reflects the “positive inside” rule of membrane proteins, set to 6.8 and 2.8 for the inner and outer leaflets of the two models. We are the first to model leaflet asymmetry in lipid composition on E. Coli cytoplasmic membrane and observe the effect on membrane properties in leaflets and whole membranes. Specifically, our results show that for the stationary phase bilayer, the surface area per lipid (SA/lipid) is larger, the thickness (2DC and DB) is thinner, the tilt angle is larger, the tilt modulus is smaller, and the deuterium order parameter (SCD) of sn-1 and sn-2 tails are lower, compared to the early-log stage. Moreover, the stationary stage bilayer has a negative spontaneous curvature while the early-log stage is near flat spontaneous curvature. For leaflet asymmetry, the inner leaflet has a larger SA/lipid, a smaller thickness, a smaller elastic tilt modulus (a larger tilt angle), and low SCD, compared to the outer leaflet in both stages. Moreover, asymmetric membrane involves a lipid tilt and a lateral extension, varying from a reference state of pre-equilibrium membrane. This work encourages a more profound exploration of leaflet asymmetry in various other membrane models and specifically how this might affect structure and function of membrane-associated peptides and proteins. | Min-Kang Hsieh; Jeffery Klauda | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610ab70b18911d4c50d9e794/original/leaflet-asymmetry-modeling-in-lipid-composition-of-escherichia-coli-cytoplasmic-membrane.pdf |
60c74b6b4c89191d05ad3452 | 10.26434/chemrxiv.12331025.v1 | Prediction of Drug Metabolites Using Neural Machine Translation | <div>We present an end-to-end learning-based method for predicting possible human metabolites of small molecules including drugs. The metabolite prediction task is approached as a sequence translation problem with chemical compounds represented using the SMILES notation. We perform transfer leaning on a Seq2Seq Transformer model originally trained on chemical reaction data to predict the outcome of human metabolic reactions. We further build an ensemble model to account for multiple and diverse metabolites. <br /></div><div>Extensive evaluation reveals that the proposed method generalizes well to different enzyme families, as it can correctly predict metabolites for phase I and phase II drug metabolism reactions as well as for other enzymes. </div> | Eleni Litsa; Payel Das; Lydia Kavraki | Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b6b4c89191d05ad3452/original/prediction-of-drug-metabolites-using-neural-machine-translation.pdf |
67c0518081d2151a024875ed | 10.26434/chemrxiv-2025-6hhn1 | SEISMiQ: de novo impurity structure elucidation from tandem mass spectra boosts drug development | Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is an essential analytical technique in the pharmaceutical industry, used particularly for elucidating the structure of unknown impurities in the synthesis of active pharmaceutical ingredients. However, the interpretation of mass spectra is challenging and time-consuming, requiring significant expertise. While recent computational tools aimed at automating this process have been developed, their accuracy in determining the chemical structure is limited. In this paper, we introduce a new method for elucidating unknown impurities from their MS/MS spectra. We are able to significantly improve elucidation accuracy by integrating domain experts’ knowledge, specifically the impurity sum formula and known substructure, into the model's training and inference process. Further performance improvements can be achieved through transfer learning from simulated MS/MS spectra of impurities from an in-house database. Finally, the need for any experimental data collection for finetuning can be circumvented by simulating the entire drug substance synthesis process in silico via reaction templates. | Emilio Dorigatti; Jonathan Groß; Jonas Kühlborn; Robert Möckel; Frank Maier; Julian Keupp | Theoretical and Computational Chemistry; Organic Chemistry; Analytical Chemistry; Mass Spectrometry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c0518081d2151a024875ed/original/seis-mi-q-de-novo-impurity-structure-elucidation-from-tandem-mass-spectra-boosts-drug-development.pdf |
6526541745aaa5fdbbc1aa99 | 10.26434/chemrxiv-2023-ds62s-v2 | Prediction of Order Parameters based on Protein NMR Structure Ensemble and Machine Learning | The fast motions of proteins at the picosecond to nanosecond timescale, known as fast dynamics, are closely related to protein conformational entropy and rearrangement, which in turn affect catalysis, ligand binding and protein allosteric effects. The most used NMR approach to study fast protein dynamics is the model free method, which uses order parameter S2 to describe the amplitude of the internal motion of local group. However, to obtain order parameter through NMR experiments is quite complex and lengthy. In this paper, we present a machine learning approach for predicting order parameters based on protein NMR structure ensemble. A random forest model is used to learn the relationship between order parameters and structural features. Our method achieves high accuracy in predicting order parameters for a test dataset of 10 proteins, with a Pearson correlation coefficient of 0.817 and a root-mean-square error of 0.131. | Qianqian Wang; Zhiwei Miao; Xiongjie Xiao; Xu Zhang; Daiwen Yang; Bin Jiang; Maili Liu | Analytical Chemistry; Analytical Chemistry - General; Chemoinformatics; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6526541745aaa5fdbbc1aa99/original/prediction-of-order-parameters-based-on-protein-nmr-structure-ensemble-and-machine-learning.pdf |
60c75129842e656f65db3b50 | 10.26434/chemrxiv.12526277.v3 | Dose COVID-19 Uncovered a New Feature of Metronidazole Drug?Dose COVID-19 Uncover a New Feature of Metronidazole Drug? | Studies of coronavirus disease 2019 (COVID-19) as a current global health problem shown the
initial plasma levels of most pro-inflammatory cytokines increased during the infection, which
leads to patient countless complications. Previous studies also demonstrated that the
metronidazole (MTZ) administration reduced related cytokines and improved treatment in
patients. However, the effect of this drug on cytokines has not been determined. In the present
study, the interaction of MTZ with cytokines was investigated using molecular docking as one of
the principal methods in drug discovery and design. According to the obtained results, the IL12-metronidazole complex is more stable than other cytokines, and an increase in the surface and
volume leads to prevent to bind to receptors. Moreover, ligand-based virtual screening of several
libraries showed metronidazole phosphate, metronidazole benzoate, 1-[1-(2-Hydroxyethyl)-5-
nitroimidazol-2-yl]-N-methylmethanimine oxide, acyclovir, and tetrahydrobiopterin (THB or
BH4) like MTZ by changing the surface and volume prevents binding IL-12 to the receptor.
Finally, the inhibition of the active sites of IL-12 occurred by modifying the position of the
methyl and hydroxyl functional groups in MTZ. <br /> | Mohammad Seyedhamzeh; Bahareh Farasati Far; Mehdi Shafiee Ardestani; Shahrzad Javanshir; Fatemeh Aliabadi; Hamed Reyhanfard; Hamidreza Pazoki-Toroudi | Bioengineering and Biotechnology; Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75129842e656f65db3b50/original/dose-covid-19-uncovered-a-new-feature-of-metronidazole-drug-dose-covid-19-uncover-a-new-feature-of-metronidazole-drug.pdf |
60c74dd79abda248d9f8d529 | 10.26434/chemrxiv.12593765.v2 | Computational Studies to Identify Potential Main Protease Inhibitors for SARS-CoV-2 | The Coronavirus pandemic has put the entire humanity in total shock and has forced the world to go under total
lockdown. It is time for the entire scientific community across the globe to find a solution for this deadly and
unseen enemy. In silico studies play a vital role in situations like this, as experimental studies are not feasible by
all researchers particularly with relevance to BSL4 procedures. In this study, using the high resolution crystal
structure of SARS-CoV-2 main protease (PDB: 5R82), we have identified molecules which can potentially
inhibit the main protease (Mpro). We used a three-tier docking protocol making use of three different databases.
We analysed the residues which are lying near the ligand binding pocket of the main protease structure and it
shows a wide cavity, which can accommodate chemically diverse ligands, occupying different sub-pockets.
Using the small fragment bound in the 5R82, we have identified several larger molecules whose functional
groups make interactions with the active site residues covering. This study also presumably steers the structure
determination of many ligand-main protease complexes using x- ray diffraction methods. These molecules can
be used as ‘in silico leads’ and further be explored in the development of SARS-CoV-2 drugs. | M. Elizabeth Sobhia; Ketan Ghosh; Srikanth Sivangula; Harmanpreet Singh; Siva Kumar | Bioinformatics and Computational Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74dd79abda248d9f8d529/original/computational-studies-to-identify-potential-main-protease-inhibitors-for-sars-co-v-2.pdf |
64ddd6e84a3f7d0c0d4e6372 | 10.26434/chemrxiv-2023-1rvq5 | Negative result: Application of Raman spectroscopy to the forensic analysis of an arid, sandy, soil | Previous studies have demonstrated the utility of Raman spectroscopy for forensic discrimination of soils after appropriate sample preparation to negate the effects of fluorescence. In this study, the application of Raman spectroscopy for the examination of the quartz-recovered fine fraction of arid, sandy soils is presented for the first time. The initial recovery of the quartz fine fraction is detailed, as well as its analysis using a Raman spectrometer. The aim was to explore whether the technique would allow for the initial screening of samples, with the goal to further extend the technique to allow for in-situ analysis of the coatings on the quartz grains. Despite investigation of a variety of experimental conditions and different approaches to data correction, Raman analysis of the quartz-recovered fine fraction of sandy soils showed high levels of fluorescence, which masked all potential characterisation data captured within the spectra. | Talia Newland; Kari Pitts; Simon Lewis | Analytical Chemistry; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ddd6e84a3f7d0c0d4e6372/original/negative-result-application-of-raman-spectroscopy-to-the-forensic-analysis-of-an-arid-sandy-soil.pdf |
62d1938d581987d6ea411290 | 10.26434/chemrxiv-2022-7gt0s-v4 | Breaking the Histone Code with Two-Dimensional Partial Covariance Mass Spectrometry | Combinatorial post-translational modifications (PTMs) of proteins, such as histones, govern cell differentiation and organismal development, and are widely thought to play a key role in aging, development of cancers, neurodevelopmental disorders, neurodegenerative and other diseases. Nonetheless, current understanding of the precise biological function of different modification patterns is limited by the difficulty of mass spectrometry to identify and quantify different combinatorial isomers in their mixtures as they naturally occur. This profound difficulty is a result of the fundamental incompleteness of the information contained in a one-dimensional mass spectrum featuring the mass-to-charge ratios and relative abundances of the individual peptide fragments. Here we demonstrate that the fragment-fragment correlations revealed by the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS) allow one to solve the combinatorial PTM puzzles that cannot be tackled by the standard mass spectrometry as a matter of principle. We introduce the concept of 2D-PC-MS marker ion correlations and show that they can provide the missing PTM location information that enables identification of co-fragmentated combinatorially modified isomers in their mixtures. We demonstrate experimentally the use of the marker ion correlations to fully analyze and resolve mixtures of doubly acetylated histone H4 peptides, a problem that was previously branded “mathematically impossible”. Our accompanying comprehensive in silico study reveals that the marker ion correlations can be used to unambiguously identify five times more combinatorially modified tryptic peptides and three times more combinatorially modified Glu-C peptides of human histones than is possible using the standard MS/MS. | Taran Driver; Ruediger Pipkorn; Vitali Averbukh; Leszek Frasinski; Jon P. Marangos; Marina Edelson-Averbukh | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d1938d581987d6ea411290/original/breaking-the-histone-code-with-two-dimensional-partial-covariance-mass-spectrometry.pdf |
65522ab92c3c11ed714eb6e9 | 10.26434/chemrxiv-2023-jbz23 | Supported metal catalysts with single-atom promoters via reductive atom trapping | Nanosized cerium oxide (CeO2) has been extensively used as an oxygen storage component in automotive emission control systems. However, the possible involvement of atomically dispersed cerium (Ce) has not been explored. Here, we demonstrate the controllable transformation of CeO2 nanoparticles into isolated Ce1 cations on the surface of gamma-type alumina (γ-Al2O3) via reductive atom trapping, achieving over half-monolayer coverage. Supported single-atom rhodium (Rh1) surrounded by dispersed Ce1 shows superior performance to Rh1 on bare Al2O3 or crystalline CeO2 in catalyzing NO reduction, exhibiting a striking one-order-of-magnitude increase in turnover frequency. Dispersed Ce1 also exhibits greatly enhanced oxygen transfer capability and introduces a modified reaction mechanism that involves adjacent Rh1-Ce1 dual-sites, resulting in a greatly decreased activation barrier (96 vs. 192 kJ/mol). The understanding of reductive atom trapping of Ce1 as well as its structure-property relationships obtained in this work could be implemented in the rational design of Ce1-promoted catalysts for many other applications. Benefiting from the greatly enhanced OSC, activity enhancements are also seen with Ce1-promoted platinum nanoparticles for the oxidation of CO and hydrocarbons. Additionally, dispersing Ce1 on Al2O3 results in modified surface properties, which could be further utilized to explore the field of acid-base catalysis | Dong Jiang; Hien Pham; Yixiao Li; Yubing Lu; Wenda Hu; Gang Wan; Chaochao Dun; Junrui Li; Carlos García-Vargas; Yipeng Sun; Anthony Savoy; Weixin Huang; Rui Zhang; Andrew DeLaRiva; R. Soyoung Kim; Xiang Li; Jeffrey Urban; Junko Yano; Kelly Shelly; Chengjun Sun; Konstantin Khivantsev; Christopher Tassone; Jianzhi Hu; Janos Szanyi; Abhaya Datye; Yong Wang | Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Redox Catalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65522ab92c3c11ed714eb6e9/original/supported-metal-catalysts-with-single-atom-promoters-via-reductive-atom-trapping.pdf |
67cf1c706dde43c9084ba9f6 | 10.26434/chemrxiv-2025-5d76r | Co-Intelligent Design of Catalysis Research with Large Language Models: Hype or Reality? | Large language models are making a strong impact on broad fields of science and technology. Initial concerns like hallucinations have been largely mitigated in the latest models, enhancing their reliability. Co-intelligence, the synergy between human and artificial intelligences, has a strong potential in research when using large language models. This analysis focused on the question: Can large language models collaborate with chemists in the design of catalysis research? In a conversation where the author made a few prompts giving minimal guidance, GPT proved its ability to co-design a research project at different levels of detail. Besides a few, non-critical flaws, the project concept and workflows were provided by the model, making a major contribution to the research design. The assessment of the project by a committee including other models (DeepSeek and Gemini) was also investigated. | David Balcells | Theoretical and Computational Chemistry; Catalysis; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf1c706dde43c9084ba9f6/original/co-intelligent-design-of-catalysis-research-with-large-language-models-hype-or-reality.pdf |
60c73d97337d6c4d9be261c7 | 10.26434/chemrxiv.6011096.v1 | Iron-Catalyzed C—H Insertions: Organometallic and Enzymatic Carbene Transfer Reactions | <p>C—H insertion reactions with organometallic and enzymatic catalysts based on earth-abundant iron complexes remain one of the major challenges in organic synthesis. In this report, we describe the development and application of these iron-based catalysts in the reaction of two different carbene precursors with <i>N-</i>heterocycles for the first time. While FeTPPCl showed excellent reactivity in the Fe(III) state with diazoacetonitrile, the highest activities of the YfeX enzyme could be achieved upon heme-iron reduction to Fe(II) with both diazoacetonitrile and ethyl diazoacetate. This highlights unexpected and subtle differences in reactivity of both iron catalysts. Deuterium labeling studies indicated a C—H insertion pathway and a marked kinetic isotope effect. This transformation features mild reaction conditions, excellent yields or turnover numbers with broad functional group tolerance, including gram-scale applications giving a unique access to functionalized <i>N</i>-heterocycles.</p> | Katharina
J. Hock; Anja Knorrscheidt; Renè Hommelsheim; Junming Ho; Martin
J. Weissenborn; Rene M. Koenigs | Biocatalysis; Homogeneous Catalysis; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2018-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d97337d6c4d9be261c7/original/iron-catalyzed-c-h-insertions-organometallic-and-enzymatic-carbene-transfer-reactions.pdf |
60cc526cb912f8356b5a53f9 | 10.26434/chemrxiv-2021-t5zt2 | Surface properties modulate protein corona formation and determine cellular uptake and cytotoxicity of silver nanoparticles | The lack of the basic understanding of how NPs interact with the biological environment has severely limited their delivery efficiency to target tissue and clinical translation. Here, we show the effective regulation of the surface properties of NPs, cellular uptake and cytotoxicity. Surface properties of NPs are tuned through the controlled replacement of native ligands, which favor protein adsorption, with ligands able to increase protein adsorption resistance. The extent and composition of the protein layer adsorbed on NPs are strongly correlated to the degree of ligands replaced on their surface and, while BSA is the most abundant protein detected, ApoE is the one whose amount is most affected by surface properties. Increasing the protein resistance, cellular uptake and cytotoxicity in mouse embryonic fibroblasts of NPs are drastically reduced, but surface coating has not effects on the process by which NPs mainly induce cell death. | Marianna Barbalinardo; Jessika Bertacchini; Linda Bergamini; Maria Sara Magarò; Luca Ortolani; Alessandra Sanson; Carla Palumbo; Massimiliano Cavallini; Denis Gentili | Materials Science; Nanoscience; Nanostructured Materials - Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60cc526cb912f8356b5a53f9/original/surface-properties-modulate-protein-corona-formation-and-determine-cellular-uptake-and-cytotoxicity-of-silver-nanoparticles.pdf |
65c1541f66c138172909d93a | 10.26434/chemrxiv-2024-pskzz | Gravesoil derived postmortem interval using attenuated total reflectance-Fourier transform infrared spectroscopy and the influence of carrion-associated fabric. | Establishing time elapsed for unattended death scenes is crucial in formulating a timeline of events facilitating death investigations. However, traditional postmortem interval (PMI) methods rely on visually evaluating physical atrophy and are closely influenced by both biotic and abiotic variables associated with carrion. During the bloat stage, carrion produces a characteristic landscape known as the cadaver decomposition island (CDI), through the
propagation of fluids rich in decomposition by-products. Here, attenuated total reflectance- Fourier transform infrared spectroscopy (ATR-FT-IR) was employed as a non-invasive, low input, low preparation interface for determining PMI from simulated Mus musculus burial gravesoil. Furthermore, understanding the influences of environmental and inter-individual differences in gaining accurate PMI is important to validate, prior to implementation to enhance the current forensic toolkit. It is documented that the presence, type and weight of clothing interferes with progression through decomposition. The subsequent impacts of clothing material (cotton, polyester, viscose) on CDI footprint development will be reflected in the biological and chemical characteristics of this ecosystem. Principal component analysis (PCA) of the IR spectra showed two clusters of samples corresponding to control and gravesoil. PC loadings plot showed that the 3100 - 1000 cm-1 spectral range attributed for over 95% of the variance. Bands within this range are ascribed to the presence of lipids, proteins and volatile organic compounds (VOCs) as byproducts of mammalian decomposition. Overall, presence and fabric type impacted decomposition, spectral CDI detection and grave discrimination. This
study questions the efficacy of proxy size and microcosm design in conducting applicable forensic research in lieu of taphonomy facilities or ethical constraints. | Phebie Watson; Sulaf Assi ; T. Komang Ralebitso Senior | Analytical Chemistry; Earth, Space, and Environmental Chemistry; Soil Science; Environmental Analysis; Spectroscopy (Anal. Chem.) | CC BY NC 4.0 | CHEMRXIV | 2024-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c1541f66c138172909d93a/original/gravesoil-derived-postmortem-interval-using-attenuated-total-reflectance-fourier-transform-infrared-spectroscopy-and-the-influence-of-carrion-associated-fabric.pdf |
677e36e56dde43c908b499d0 | 10.26434/chemrxiv-2025-g86dx | Automation of the Antisolvent Method via an Automated Spin-coating System and the Effects of Reduced Surface Roughness and Depth Distribution of Residual PbI2 on Reproducibility | Perovskite solar cells often exhibit performance variability even under identical experimental conditions. One of the reasons of this inconsistency is attributed to manual interventions such as the application of antisolvents. To address these challenges, we develop an automated system to precisely control the solvent dropping and substrate heating processes. Spin coating is performed by using an automated system comprising a robot arm, spin coater, automatic solution dropping part, hot plate, and substrate storage area. Manual fabrication is conducted simultaneously to compare the outcomes. The reproducibility of devices fabricated by using the system and intra- and interbatch consistency are assessed. The automated system considerably diminishes performance fluctuations across batches conducted on different dates from 2.2 to 0.4%. Especially, the automated, uniform application of an antisolvent considerably minimize surface roughness variability in perovskite films. X-ray diffraction analyses further reveal differences between the residual PbI2 contents of perovskite films fabricated via automated and manual methods. Additionally, grazing incidence wide-angle X-ray scattering measurements indicate that the residual PbI2 depth distribution in the perovskite layer was influenced by the antisolvent drop rate and timing. The results suggest that precise control of antisolvent drop rates and drop timings can improve the reproducibility of perovskite solar cells. | Naoto Eguchi; Kohei Yamamoto; Hiroyuki Kanda; Santa Mondal; Takurou Murakami | Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677e36e56dde43c908b499d0/original/automation-of-the-antisolvent-method-via-an-automated-spin-coating-system-and-the-effects-of-reduced-surface-roughness-and-depth-distribution-of-residual-pb-i2-on-reproducibility.pdf |
6329f539fee74ec73d43c431 | 10.26434/chemrxiv-2022-rtzqm-v3 | Sodium silicate and hexametaphosphate promote the release of (oxyhydr)oxide nanoparticles from corroding iron | Sequestrants such as polyphosphate and sodium silicate are used widely to control iron precipitation in drinking water, but less is known about their impacts on iron corrosion scale. Here we characterize the nanoparticulate iron (oxyhydr)oxide suspensions that result from corroding cast iron coupons in solutions containing either sodium hexametaphosphate (3 mg P L-1) or sodium silicate (100 mg SiO2 L-1). We determined the elemental composition and size distribution of these suspensions using flow field-flow fractionation with ultraviolet, multielement, and multiangle light scattering detection (FFF-UV-MALS-ICP-MS). Both sequestrants yielded stable iron suspensions, and the pooled median radius of gyration at peak 57Fe intensity was 22 nm, corresponding to a sphere-equivalent geometric diameter of 57 nm. The median Feret diameter and ASTM roundness were 50 nm and 0.4, respectively, as determined by transmission electron microscopy. Lead associated readily with iron nanoparticles, and in the hexametaphosphate suspension it associated preferentially with iron over free hexametaphosphate. Sequestrants then, may interact with iron corrosion scale to yield effective transport vectors for lead in drinking water systems, even when complexation of free lead by the sequestrant is negligible. | Benjamin F Trueman; Javier M Locsin; Evelyne Doré; Kalli Hood; Graham A Gagnon | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY 4.0 | CHEMRXIV | 2022-09-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6329f539fee74ec73d43c431/original/sodium-silicate-and-hexametaphosphate-promote-the-release-of-oxyhydr-oxide-nanoparticles-from-corroding-iron.pdf |
67c4f369fa469535b9a9c05f | 10.26434/chemrxiv-2025-mcrsz | CovCIFDock: Covalent Docking with CIFDock and Hybrid QM/MM Minimizations | Although reversible inhibitors represent the majority of approved and investigational drug therapeutics, irreversible inhibitors (or targeted covalent inhibitors, TCIs) are increasingly being considered due to a greater potency and higher selectivity. Many currently available commercial programs excel at modeling traditional reversible inhibitors. However, many of these non-covalent docking programs are unsuitable for docking TCIs because they do not model the post-reaction protein-ligand structure. Attempts to modify existing methods or formulate new ones that can simulate covalent docking often utilize classical mechanical potentials that inherently lack the ability to modulate bonding topologies in an effort to reduce computational overhead. Not only are such modifications ill-suited to covalent docking, they can lead to a reduction in docking accuracy and impose limitations on the transferrability of a method to other protein systems. Herein we aim to address these shortcomings by utilizing a hybrid simulation workflow that employs both classical and quantum mechanical (QM/MM) potentials capable of bond rearrangement. The workflow, named CovCIFDock, is comprised of modules natively available in CHARMM and is an extension of the recently published CIFDock flexible docking method. Protein-ligand complexes are docked classically in the pre-reactive state in order to facilitate computational speed, after which a QM/MM minimization is conducted to form the protein-ligand bond and refine the final pose. CovCIFDock was validated against 46 protein receptors belonging to Cathepsin K, HCV NS3, EGFR, and XPO1 targets. Results show that CovCIFDock is able to replicate the binding mode of these TCI complexes within 2 Angstrom of the crystal structure, and is comparable in accuracy to leading commercial docking programs. | Luke Warrensford; Amanda Rose Pittman; Steven Austin; H. Lee Woodcock | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c4f369fa469535b9a9c05f/original/cov-cif-dock-covalent-docking-with-cif-dock-and-hybrid-qm-mm-minimizations.pdf |
614145d7ac32195b5d7bf8b7 | 10.26434/chemrxiv-2021-s94jc-v2 | All-atom molecular dynamics study of hepatitis B virus
containing pregenome RNA in solution | Immature hepatitis B virus (HBV) captures nucleotides in its capsid for reverse transcription. The nucleotides and nucleotide analogue drugs, which are triphosphorylated and negatively charged in the cell, approach the capsid via diffusion and are absorbed into it. In this study, we performed a long-time molecular dynamics (MD) calculation of the entire HBV capsid containing pregenome RNA to investigate the interactions between the capsid and negatively charged substances. Electric field analysis demonstrated that negatively charged substances can approach the HBV capsid by thermal motion, avoiding spikes. The substances then migrate all over the floor of the HBV capsid. Finally, they find pores through which they can pass through the HBV capsid shell. Free energy profiles were calculated along these pores for small ions to understand their permeability through the pores. Anions (Cl-) showed higher free energy barriers than cations (Na+ and K+) through all pores, and the permeation rate of Cl- was eight times slower than that of K+ or Na+. Furthermore, the ions were more stable in the capsid than in the bulk water. Thus, the HBV capsid exerts ion selectivity for uptake and provides an environment for ions, such as nucleotides and nucleotide analogue drugs, to be stabilized within the capsid. | Kazushi Fujimoto; Youhei Yamaguchi; Ryo Urano; Wataru Shinoda; Tetsuya Ishikawa; Katsumi Omagari; Yasuhito Tanaka; Atsushi Nakagawa; Susumu Okazaki | Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Biophysics | CC BY NC 4.0 | CHEMRXIV | 2021-09-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/614145d7ac32195b5d7bf8b7/original/all-atom-molecular-dynamics-study-of-hepatitis-b-virus-containing-pregenome-rna-in-solution.pdf |
6706dbaa51558a15efa1e9bb | 10.26434/chemrxiv-2024-00f19 | Electric Field’s Dueling Effects through Dehydration and Ion Separation in Driving NaCl Nucleation at Charged Nanoconfined Interfaces | Investigating nucleation in charged nanoconfined environments is crucial for many scientific and engineering applications. Here we under electric fields is essential for the design of materials. We study the nucleation of NaCl from aqueous solution near charged surfaces using machine-learning-augmented enhanced sampling molecular dynamics simulations. Our simulations successfully drive phase transitions between liquid and solid phases of NaCl. The solid phase is stabilized under electric fields, particularly at an intermediate surface charge density. We examine which physical characteristics drive the nucleation of NaCl from aqueous solutions and find that the removal of solvent water from Cl- at the solid precursor surface plays a more critical role than the accumulation of ions. Our simulations reveal the competing effects of electric fields on nucleation processes: they facilitate the removal of water, promoting nucleation, but also promote the separation of ion pairs thereby hindering nucleation. This work provides a framework for studying nucleation processes in nanoconfined environments under electric fields and physical insights for the design of electrochemistry materials. | Ruiyu Wang; Pratyush Tiwary | Theoretical and Computational Chemistry; Physical Chemistry; Artificial Intelligence; Interfaces; Crystallography | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6706dbaa51558a15efa1e9bb/original/electric-field-s-dueling-effects-through-dehydration-and-ion-separation-in-driving-na-cl-nucleation-at-charged-nanoconfined-interfaces.pdf |
6381d4eb0146ef765e068596 | 10.26434/chemrxiv-2022-0d9cn | Tuning the competition between photoisomerization and photothermy in biomimetic cyclocurcumin analogues | We report the synthesis and photophysical characterization of biomimetic D-A-D’ cyclocurcumin derivatives, which can potentially be used in light activated chemotherapy. Particularly we highlight that both the donor (D) and acceptor (A) groups significantly influence the photophysical response of the chromophore inducing strong bathochromic shift with D/A strength increase and notable fluorescence quantum yield enhancement with donor strength increase. More important, the nature of the acceptor group (oxo or malonitrile) dramatically modifies the outcome in non-radiative deactivation channels. Indeed, while compounds functionalized with an oxo-moiety undergo ethylenic E→Z photoisomerization, the one bearing a malonitrile group leads exclusively to other non-adiabatic internal conversion channels which much favor photothermal conversion as no isomerization of the ethylenic double bond being observed. The tuning of the photophysical properties and the alteration of isomerization vs. photothermal conversion is rationalized through the analysis of the potential energy surfaces along the most relevant degrees of freedom and shows a competitive pathway over malonitrile rotation. Our results offer novel perspective in oxygen-independent light activated chemotherapy and in the control of photochemical processes in biomimetic chromophores.
| Jérémy Pecourneau; Raul Losantos; Axel Gansmuller; Stéphane Parant; Yann Bernhard; Maxime Mourer; Antonio Monari; Andreea Pasc | Physical Chemistry; Biological and Medicinal Chemistry | CC BY 4.0 | CHEMRXIV | 2022-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6381d4eb0146ef765e068596/original/tuning-the-competition-between-photoisomerization-and-photothermy-in-biomimetic-cyclocurcumin-analogues.pdf |
6735bc445a82cea2fa15eeb2 | 10.26434/chemrxiv-2024-zzjfs | Effective Cross-link Density: A Robust Metric for Structure-Property Relationship in Complex Polymer Networks | The structural complexities of polymer networks, i.e., multiple functional groups, diverse connection sites, and various defects, make it difficult to accurately describe their microstructure using theoretical models and traditional metrics such as cross-link density (XLD). This study uses multi-scale molecular dynamics simulations to construct complex network structures such as acrylic-melamine systems and establish correlations between their microstructure and thermo-mechanical properties. By accounting for the elastic contribution of each cross-link point within the network, we modified the XLD and introduced effective XLD (XLDeff). Our findings reveal strong linear correlations between XLDeff and both elastic modulus and Tg, relationships that conventional XLD could not establish. This demonstrates the robustness of XLDeff as a predictive metric for thermo-mechanical properties across diverse cross-linking conversions and prepolymer systems. XLDeff thus serves as a valuable metric for the in-silico design and optimization of thermoset polymers with tailored thermo-mechanical properties. | Amirhossein Gooranorimi; Seyed Mohammad Mousavifard; Mohsen Mohseni; Hossein Yahyaei; Hesam Makki | Polymer Science | CC BY 4.0 | CHEMRXIV | 2024-11-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6735bc445a82cea2fa15eeb2/original/effective-cross-link-density-a-robust-metric-for-structure-property-relationship-in-complex-polymer-networks.pdf |
67808dd781d2151a02899513 | 10.26434/chemrxiv-2024-sfk57-v2 | Nanoplastic-induced Disruption of DPPC and Palmitic Acid Monolayers: Implications for Membrane Integrity | Nanoplastics are generated from the fragmentation of microplastics under various environmental conditions in the atmosphere. These tiny pollutants are widespread and can enter the human body through the air we breathe and the food and water we consume. Understanding how nanoplastics interact with different membrane lipids is paramount to discerning the kind of threat they pose in terms of lung alveolar destabilization, impaired cell communication, cell wall disruption, diminished nutrient delivery, and neurotoxicity. In this research, we examined the interaction of polystyrene nanoplastics with palmitic acid and phosphatidylcholine at the air-aqueous interface to identify individual lipid response. Employing a comprehensive experimental approach that includes infrared-reflection absorption spectroscopy (IRRAS), Langmuir isotherms and Brewster angle microscopy (BAM), we investigated chemical and physical changes of lipid monolayer systems with nanoplastics dispersed within the water solution phase. Increasing concentration of the polystyrene nanoplastics in the solution phase led to enhanced interfacial activity; the nanoplastics were observed to incorporate into the monolayer driven by lipid adsorption/complexation to the nanoplastics. The findings in this research aid in understanding the physical mechanisms through which nanoplastics may alter and impact biophysical interfaces. | Shamma Jabeen Proma; Biswajit Biswas; Mohamed Yaseen Noor; Heather C. Allen | Physical Chemistry; Biophysical Chemistry; Interfaces; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67808dd781d2151a02899513/original/nanoplastic-induced-disruption-of-dppc-and-palmitic-acid-monolayers-implications-for-membrane-integrity.pdf |
67c179776dde43c908d6fedc | 10.26434/chemrxiv-2025-fnw1w | Soaring Chemical Space of Battery Electrolytes Using Universal Machine Learning Potential | Li-ion batteries, widely used in electronic devices, electric vehicles, and aviation, demand high energy density, fast charging capabilities, and broad operating temperature ranges. Computational approaches combined with experimental design have gained increasing attention for electrolyte development. However, the inherent complexity of electrolytes—arising from their diverse compositions and varying proportions—poses a significant challenge. Classical molecular dynamics often fails due to inaccuracies in force field parameters, while ab initio calculations are limited by prohibitive computational costs. Machine learning molecular dynamics (MLMD) offers a promising alternative, combining efficiency with ab initio accuracy. However, its potential has been hindered by the transferability limitations of machine learning potentials (MLPs). In this work, we develop a universal machine learning potential (uMLP) for electrolytes by generating randomly composed electrolytes and employing an iterative training approach to collect representative datasets, effectively overcoming these limitations. The uMLP enables accurate computation of key properties, including density, solvation structure, viscosity, ionic conductivity, and operating temperature range, for a broad range of electrolytes through MLMD simulations. Furthermore, coordination dynamics analysis of Li+ , by quantifying the coordination lifetime (¯τ), provides a direct, quantitative measure of solvation strength. Shorter ¯τ, indicative of weak solvation, correlates with faster ion transport and higher ionic conductivity. The uMLP for electrolytes facilitates the prediction and optimization of electrolyte properties, offering a powerful tool for electrolyte design. | Feng Wang; Yu-Hang Tang; Ze-Bing Ma; Yu-Cheng Jin; Jun Cheng | Theoretical and Computational Chemistry; Physical Chemistry; Energy; Electrochemistry - Mechanisms, Theory & Study | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c179776dde43c908d6fedc/original/soaring-chemical-space-of-battery-electrolytes-using-universal-machine-learning-potential.pdf |
60c74e6c842e65a73edb364e | 10.26434/chemrxiv.12685922.v2 | Rapid Detection of Strong Correlation with Machine Learning for Transition Metal Complex High-Throughput Screening | <p>Despite its widespread use in chemical discovery, approximate density functional theory (DFT) is poorly suited to many targets, such as those containing open-shell, 3<i>d</i> transition metals that can be expected to have strong multi-reference (MR) character. For discovery workflows to be predictive, we need automated, low-cost methods that can distinguish the regions of chemical space where DFT should be applied from those where it should not. We curate over 4,800 open-shell transition-metal complexes up to hundreds of atoms in size from prior high-throughput DFT studies and evaluate affordable, finite-temperature DFT evaluation of fractional occupation number (FON)-based MR diagnostics. We show that intuitive measures of strong correlation (i.e., the HOMO–LUMO gap) are not predictive of MR character as judged by FON-based diagnostics. Analysis of independently trained machine learning (ML) models to predict HOMO–LUMO gaps and FON-based diagnostics reveals differences in metal- and ligand-sensitivity of the two quantities. We use our trained ML models to rapidly evaluate MR character over a space of ca. 187,000 theoretical complexes, identifying large-scale trends in spin-state-dependent MR character and finding small HOMO–LUMO gap complexes while ensuring low MR character. </p> | Fang Liu; Chenru Duan; Heather Kulik | Organometallic Compounds; Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry; Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e6c842e65a73edb364e/original/rapid-detection-of-strong-correlation-with-machine-learning-for-transition-metal-complex-high-throughput-screening.pdf |
626b4afcef2ade2fc3414b26 | 10.26434/chemrxiv-2022-t74fg | Ligand Fluorination to Mitigate the Raman Relaxation of Dy(III) Single-Molecule Magnets: A Combined Terahertz, Far-IR and Vibronic Barrier Model Study | Engineering the local dynamic environment is currently the major approach for preventing fast magnetization loss for single-molecule magnets (SMMs). It is hypothesized that the presence of fewer −CH3 which results in fewer C−H bonds, would reduce excitation energy loss via vibrations, but thus far, no experimental evidence clearly elaborates this effect. Moreover, although Gu and Wu proposed a vibronic barrier model to interpret the Raman process, the relationship between the barriers (\hbar\omega) and the molecular structure has not been explicitly correlated. Here, we use the trifluoromethyl group to systematically substitute the methyl groups in the axial position of the parental bis-butoxide pentagonal-bipyramidal dysprosium(III) SMM - [Dy(OtBu)2(py)5][BPh4]. The resulting complexes - [Dy(OLA)2py5][BPh4] (LA = CH(CF3)2− 1, CH2CF3− 2, CMe2CF3− 3)- show progressively enhanced TBhys (@100 Oe/s) from 17 K (for 3), 20 K (for 2) to 23 K (for 1). As the gradually enhanced averaged vibration energy generated by different axial ligands from 230 cm−1 (for 3), 257 cm−1 (for 2) to 321 cm−1 (for 1) was identified experimentally and theoretically to be the only variant that leads to this improvement, this finding unambiguously reveals, for the first time, the correlation between structural change and the multi two-phonon (Raman) relaxation processes in lanthanide-based SMMs and highlights the importance of controlling the relevant vibrations in building SMMs with higher blocking temperatures. | Yan Ma; Yuan-Qi Zhai; Qian-Cheng Luo; You-Song Ding; Yan-Zhen Zheng | Theoretical and Computational Chemistry; Inorganic Chemistry; Lanthanides and Actinides; Magnetism; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2022-04-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/626b4afcef2ade2fc3414b26/original/ligand-fluorination-to-mitigate-the-raman-relaxation-of-dy-iii-single-molecule-magnets-a-combined-terahertz-far-ir-and-vibronic-barrier-model-study.pdf |
6516da28a69febde9eec8812 | 10.26434/chemrxiv-2023-k9lwz | Chiral bifunctional NHC/guanidine ligands for asymmetric hydrogenation | We report the synthesis of chiral N-heterocyclic carbene/guanidine bifunctional ligands from readily available amino alcohols. The resulting chiral bifunctional catalysts are active in an asymmetric hydrogenation of ketones, and stereoinduction by the chiral groups can be observed. We can show that the chiral linker unit can be employed for the transfer of stereoinformation. | Mahadeb Gorai; Teichert Johannes | Organic Chemistry; Catalysis; Stereochemistry; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6516da28a69febde9eec8812/original/chiral-bifunctional-nhc-guanidine-ligands-for-asymmetric-hydrogenation.pdf |
61447e60b1d4a605d589af2e | 10.26434/chemrxiv-2021-lk7rg-v2 | Stochastic Generalized Active Space Self-Consistent Field: Theory and Application | An algorithm to perform stochastic generalized active space
calculations, Stochastic-GAS, is presented, that
uses the Slater determinant based FCIQMC algorithm as configuration
interaction eigensolver.
Stochastic-GAS allows the construction and stochastic optimization
of preselected truncated configuration interaction wave functions,
either to reduce the computational costs of large active space wave
function optimizations, or to probe the role of specific electron
correlation pathways.
As for the conventional GAS procedure, the preselection of the
truncated wave function is based on the selection of multiple
active subspaces while imposing restrictions on the interspace excitations.
Both local and cumulative minimum and maximum occupation number
constraints are supported by Stochastic-GAS.
The occupation number constraints are efficiently encoded in precomputed
probability distributions, using the precomputed heat bath algorithm,
which removes nearly all runtime overheads of GAS.
This strategy effectively allows the FCIQMC dynamics to a priori exclude
electronic configurations that are not allowed by GAS restrictions.
Stochastic-GAS reduced density matrices are stochastically sampled,
allowing orbital relaxations via Stochastic-GASSCF, and direct evaluation
of properties that can be extracted from density matrices, such as the
spin expectation value.
Three test case applications have been chosen to demonstrate the
flexibility of Stochastic-GAS:
(a) the Stochastic-GASSCF optimization of a
stack of five benzene molecules, that shows the applicability of
Stochastic-GAS towards fragment-based chemical systems;
(b) an uncontracted stochastic MRCISD calculation
that correlates 96 electrons and 159 molecular orbitals, and uses a large
(32, 34) active space reference wave function for an Fe(II)-porphyrin
model system, showing how GAS can be applied to systematically
recover dynamic electron correlation, and how in the specific case
of the Fe(II)-porphyrin dynamic correlation further differentially stabilizes
the triplet over the quintet spin state;
(c) the study of an Fe4S4 cluster's spin-ladder energetics
via highly truncated stochastic-GAS wave functions, where we show
how GAS can be applied to understand the competing
spin-exchange and charge-transfer correlating mechanisms in
stabilizing different spin-states. | Oskar Weser; Kai Guther; Khaldoon Ghanem; Giovanni Li Manni | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61447e60b1d4a605d589af2e/original/stochastic-generalized-active-space-self-consistent-field-theory-and-application.pdf |
65baac919138d23161258963 | 10.26434/chemrxiv-2024-5fthz | An Expanded Palette of Fluorescent COS/H2S-Releasing Donors for H2S Delivery, Detection, and In Vivo Application | Hydrogen sulfide is an important reactive sulfur species that is involved in many biological functions, and H2S imbalances have been indicated as a potential biomarker for various diseases. Different H2S donors have been developed to deliver H2S directly to biological systems, but few reports include donors with optical responses that allow for tracking of H2S release. Moreover, donor systems that use the same chemistry to deliver H2S across a palette of fluorescent responses remain lacking. Here we report five thiol-activated fluorescence turn-on COS/H2S donors that utilize blue, yellow, orange, red, and near infrared-emitting dyes functionalized with an H2S-releasing sulfenyl thiocarbonate scaffold. Upon treatment with thiols, each donor provides a fluorescence turn-on response (3–310-fold) and high H2S release efficiencies (>60%). Using combined electrode and fluorescence experiments, we directly correlate the measured H2S release with the fluorescence response. All donors are biocompatible and release H2S in live cell environments. In addition, we demonstrate that the NIR donor allows for H2S release tracking after subcutaneous injection in live rats, which to the best of our knowledge is the first in vivo tracking of fluorogenic H2S release in non-transparent organisms. | Kaylin Fosnacht; Jonathan Dorogin; Payton Jefferis; Marian Hettiaratchi; Michael Pluth | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65baac919138d23161258963/original/an-expanded-palette-of-fluorescent-cos-h2s-releasing-donors-for-h2s-delivery-detection-and-in-vivo-application.pdf |
60c74f06469df41b59f445f4 | 10.26434/chemrxiv.12840776.v1 | Bovine Serum Albumin as A Superior “FP-Tag” for High-Throughput Glycosyltransferase Assay | <a></a>Here, we report the development of a high-throughput “FP-Tag” OGT assay with bovine serum albumin as a low-cost and superior “FP-Tag”. With this assay, 2-methyleurotinone was identified as a <a></a><a>low </a>M-range OGT inhibitor. This type of assay with BSA as “FP-Tag” would find more applications with other glycosyltransferases. | Xinjian Yin; Jiaxin Li; Senhua Chen; Yuping Wu; Zhigang She; Lan Liu; Yue Wang; Zhizeng Gao | Biochemical Analysis; Spectroscopy (Anal. Chem.); High-throughput Screening | CC BY NC ND 4.0 | CHEMRXIV | 2020-08-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f06469df41b59f445f4/original/bovine-serum-albumin-as-a-superior-fp-tag-for-high-throughput-glycosyltransferase-assay.pdf |
60c74ba84c89191d10ad34d7 | 10.26434/chemrxiv.12368963.v1 | MetIDfyR, an Open-Source R Package to Decipher Small-Molecule Drugs Metabolism Through High Resolution Mass Spectrometry | <div>After administration to humans or animals, small-molecule drugs most frequently undergo several biochemical transformations by the endogenous enzymatic machinery, called phase I and phase II metabolism. These molecular processes allow organisms to eliminate xenobiotics through modification of their chemical properties and generate metabolites. With recent advances in analytical chemistry, LC-HRMS/MS has become an essential tool for metabolite discovery and detection. Even if most common drug transformations have already been extensively described, manual search of drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology laboratories, disabling efficient metabolite discovery. Furthermore, the availability of free open-source software for metabolite discovery is still limited.</div><div><br /> </div>In this article, we present MetIDfyR, an open-source and cross-platform R package for in-silico drug phase I/II biotransformations prediction and mass-spectrometric data mining. MetIDfyR has proven efficacy for advanced metabolite identification in semi-complex and complex mixtures in in-vitro or in-vivo drug studies and is freely available at https://github.com/agnesblch/MetIDfyR.<br /> | Vivian Delcourt; Agnès Barnabé; Benoit Loup; Patrice Garcia; François André; Benjamin Chabot; Stéphane Trévisiol; Yves Moulard; Marie-Agnès Popot; Ludovic Bailly-Chouriberry | Analytical Chemistry - General; Chemoinformatics; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ba84c89191d10ad34d7/original/met-i-dfy-r-an-open-source-r-package-to-decipher-small-molecule-drugs-metabolism-through-high-resolution-mass-spectrometry.pdf |
617aa2c8ef38c0f8c65dfaae | 10.26434/chemrxiv-2021-p3h9s-v2 | Simultaneous enhancement of thermally activated delayed fluorescence and photoluminescence quantum yield via homoconjugation | A fundamental problem facing thermally activated delayed fluorescence (TADF) is to overcome the paradox of efficient electronic transitions and a narrow singlet-triplet energy gap (ΔEST) in a single luminophore. We present a quinoxaline-based TADF iptycene as the first clear example that homoconjugation can be harnessed as a viable design strategy toward this objective. Homoconjugation was introduced in an established TADF luminophore by trimerization through an iptycene core. This homoconjugation was confirmed by electrochemistry. As a direct consequence of homoconjugation we observed synergistic improvements to photoluminescence quantum yield (ΦPL), radiative rate of singlet decay (krS), delayed fluorescence lifetime (τTADF), and rate of reverse intersystem crossing (krISC), while narrowing the ΔEST. The cooperative enhancement is rationalised with TD-DFT calculations including spin-orbit coupling (SOC). A facile synthesis of this system, and the ubiquity of the pyrazine motif in state-of-the-art TADF materials across the electromagnetic spectrum, leads to a great potential for generality. | Stephanie Montanaro; Piotr Pander; Mark Elsegood; Simon Teat; Andrew Bond; Iain Wright; Daniel Congrave; Marc Etherington | Physical Chemistry; Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Physical Organic Chemistry; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2021-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/617aa2c8ef38c0f8c65dfaae/original/simultaneous-enhancement-of-thermally-activated-delayed-fluorescence-and-photoluminescence-quantum-yield-via-homoconjugation.pdf |
64dd2235dfabaf06ff624bee | 10.26434/chemrxiv-2021-dm90f-v5 | Using Photoluminescence Color Change in Cesium Lead Iodide Nanoparticles to Monitor the Kinetics of an External Organohalide Chemical Reaction by Halide Exchange
| In this work we demonstrate a photoluminescence-based method to monitor the kinetics of an organohalide reaction by way of detecting released bromide ions at cesium lead halide nanoparticles. Small aliquots of the reaction are added to an assay with known concentrations of CsPbI3, and the resulting Br-to-I halide exchange (HE) results in rapid and sensitive wavelength blue-shifts ( due to CsPbBrxI3-x intermediate concentrations, the wavelengths of which are proportional to concentrations. An assay response factor, C, relates to Br- concentration as a function of CsPbI3 concentration. The observed kinetics, as well as calculated rate constants, equilibrium, and activation energy of the solvolysis reaction tested correspond closely to synthetic literature values, validating the assay. Factors that influence the sensitivity and performance of the assay, such as CsPbI3 size and morphology, and concentration, are discussed. | Tennyson L. Doane; Kevin J. Cruz-Lopez; Tsung-Hsing Chiang; Mathew M. Maye | Analytical Chemistry; Nanoscience; Spectroscopy (Anal. Chem.); High-throughput Screening; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64dd2235dfabaf06ff624bee/original/using-photoluminescence-color-change-in-cesium-lead-iodide-nanoparticles-to-monitor-the-kinetics-of-an-external-organohalide-chemical-reaction-by-halide-exchange.pdf |
677bc4be81d2151a021200d6 | 10.26434/chemrxiv-2025-9hqwk | Substantial Magnetic Fields Arising from Ballistic Ring Currents in Single-molecule Junctions | When a small electric bias is applied to a single- molecule junction, current will flow through the molecule via a tunneling mechanism. In molecules with a cyclic or helical structure there may be circular currents, giving rise to a uni-directional magnetic field. Here, we implement the Biot-Savart law and calculate the magnetic field resulting from the ballistic current density for a selection of molecules. We find that three prerequisites are important for achieving a substantial magnetic field in a single-molecule junction. (1) The current must be high, (2) the ring current must be unidirectional within the bias window, and (3) the diameter of the ring current must be small. We identify both cyclic and linear molecules that potentially fulfill these requirements. In cyclic annulenes with bond-length alternation the current might induce a magnetic field in the mT-range whereas archetypical cyclic molecules, such as benzene, are not suitable candidates for the generation of a substantial magnetic field. Finally, we show that in linear carbon chains with circular current due to their helical π-orbital system, the magnetic field can potentially reach the tesla-range. Our results prove that a large magnetic field can, at least in theory, be induced in molecular wires even at low bias. | William Bro-Jørgensen; Stephan P. A. Sauer; Gemma C. Solomon; Marc H. Garner | Theoretical and Computational Chemistry; Physical Chemistry; Nanoscience; Nanodevices; Computational Chemistry and Modeling; Transport phenomena (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2025-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677bc4be81d2151a021200d6/original/substantial-magnetic-fields-arising-from-ballistic-ring-currents-in-single-molecule-junctions.pdf |
60c7495a842e6554fddb2d13 | 10.26434/chemrxiv.12044673.v1 | Driving Torsion Scans with Wavefront Propagation | <div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div> | Yudong Qiu; Daniel Smith; Chaya Stern; Mudong Feng; Lee-Ping Wang | Computational Chemistry and Modeling; Theory - Computational; Quantum Mechanics | CC BY 4.0 | CHEMRXIV | 2020-04-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7495a842e6554fddb2d13/original/driving-torsion-scans-with-wavefront-propagation.pdf |
60c74c4dbb8c1a38b73db3c8 | 10.26434/chemrxiv.12409451.v1 | “Green” Catalyst for the Oxygen Reduction Reaction in Ecological Metal-Air Systems | <p>Thermally treated caffeine doped active carbon
(Caffeine-Norit) is studied as a catalyst for the oxygen reduction reaction
(ORR) with application in metal-air systems and neutral aqueous electrolytes. Catalytic
activity is characterized by polarization curves and Tafel plots and the
results are compared with 5% Platinum (5% Pt-Norit) and 4% Silver (4% Ag-Norit)
catalysts. The Tafel slopes of all three catalysts are the same, the activity
of Ag-Norit being somewhat smaller then both Caffeine-Norit and Pt-Norit. The
polarization curves are also comparable, especially
in the low current density region. The increase of overpotential for the Caffeine-Norit
at current density higher than 50 mA cm<sup>-2</sup> is due to accumulation of
H<sub>2</sub>O<sub>2</sub> in the catalyst layer. This was demonstrated by
using a simple method for detection of peroxides in neutral electrolytes based
on indigo carmine indicator. </p> | Iliyan Popov; Krum Banov; Yovka Milusheva; Reneta Boukoureshtlieva; Toma Stankulov; Todor Petkov; Tanja Vidaković-Koch; Branimir Banov | Natural Products; Electrocatalysis; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74c4dbb8c1a38b73db3c8/original/green-catalyst-for-the-oxygen-reduction-reaction-in-ecological-metal-air-systems.pdf |
66d8413912ff75c3a15d972b | 10.26434/chemrxiv-2024-nlf00-v3 | Competitive co-diffusion as a route to enhanced step coverage in chemical vapor deposition | Molecules with a lower mass diffuse faster than heavier molecules in a mixture of gases at local thermodynamic equilibrium. We hypothesize that this phenomenon can be used to improve film uniformity and step coverage in chemical vapor deposition (CVD). Our concept is to add a heavy inert molecule as a diffusion additive to enhance the diffusion of the reactive gas species. We verify this by adding a co-flow of Xe in a thermal CVD process for boron carbide using a single source precursor. When adding a co-flow of Xe to the process we noted an increase in step coverage from 0.71 to 0.97 at 550 °C in 10:1 aspect ratio feature. The concept was further validated by depositing in lateral high aspect ratio chips with 500 nm gap height, rendering a penetration depth of about 25 μm with maintained material homogeneity into the structure. The results show that competitive co-diffusion with a heavy inert gas is a viable route to conformal CVD films. | Arun Haridas Choolakkal; Pentti Niiranen; Samira Dorri; Jens Birch; Henrik Pedersen | Physical Chemistry; Materials Science; Materials Processing; Thin Films; Transport phenomena (Physical Chem.); Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d8413912ff75c3a15d972b/original/competitive-co-diffusion-as-a-route-to-enhanced-step-coverage-in-chemical-vapor-deposition.pdf |
65b8717066c13817298ae4f2 | 10.26434/chemrxiv-2023-ps4h1-v2 | Drug–drug conjugates of MEK and Akt inhibitors for RAS-mutant cancers | Controlling RAS mutant cancer progression remains a significant challenge in developing anticancer drugs. Whereas Ras G12C-covalent binders have received clinical approval, the emergence of further mutations, along with the activation of Ras-related proteins and signals, has led to resistance to Ras binders. To discover novel compounds to overcome this bottleneck, we focused on the concurrent and sustained blocking of two major signaling pathways downstream of Ras. To this end, we synthesized 25 drug–drug conjugates (DDCs) by combining the MEK inhibitor trametinib with Akt inhibitors using seven types of linkers with structural diversity. These DDCs were evaluated for their cell permeability/accumulation and ability to inhibit proliferation in RAS-mutant cell lines. A representative DDC was further evaluated for its effects on signaling proteins, induction of apoptosis-related proteins, and the stability of hepatic metabolic enzymes. These in vitro studies identified a series of DDCs, especially those containing a furan-based linker, with promising properties as agents for treating RAS-mutant cancers. Additionally, in vivo experiments in mice using the two selected DDCs revealed prolonged half-lives and anticancer efficacies comparable to those of trametinib. The DDCs developed in this study have potential as drug candidates for the broad inhibition of RAS-mutant cancers. | Hikaru Fujita; Sachiko Arai; Hiroshi Arakawa; Kana Hamamoto; Toshiyuki Kato; Tsubasa Arai; Nanaka Nitta; Kazuki Hotta; Natsuko Hosokawa; Takako Ohbayashi; Chiaki Takahashi; Yasuhide Inokuma; Ikumi Tamai; Seiji Yano; Munetaka Kunishima; Yoshihiro Watanabe | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65b8717066c13817298ae4f2/original/drug-drug-conjugates-of-mek-and-akt-inhibitors-for-ras-mutant-cancers.pdf |
60c7457bbb8c1aa6c93da6c6 | 10.26434/chemrxiv.10028900.v1 | Lysine Acylation Using Conjugating Enzymes (LACE) for Site-Specific Modification and Ubiquitination of Native Proteins | <p>Enzymes are powerful tools for post-translational protein labeling due to their high sequence specificity and mild reaction conditions. Many existing protocols, however, are restricted to conjugations at terminal positions or rely on non-peptidic metabolites and large recognition domains. Here we introduce a chemoenzymatic method to functionalize proteins at internal lysine residues that are part of genetically encoded minimal recognition tags (four residues). We achieved this by employing the intrinsic sequence specificity of the E2 SUMO-conjugating enzyme Ubc9 and a short peptide thioester, which together obviate the need for E1 and E3 enzymes. Using a range of protein substrates, we apply this approach to the conjugation of biochemical probes, one-pot dual-labeling reactions in combination with sortase, and site-specific monoubiquitination and ISG15ylation. The small tag size and large substrate tolerance of Ubc9 will make this a method of choice for protein engineering by isopeptide formation and the preparation of ubiquitinated proteins. </p> | Raphael Hofmann; Gaku Akimoto; Thomas G. Wucherpfennig; Cathleen Zeymer; Jeffrey Bode | Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7457bbb8c1aa6c93da6c6/original/lysine-acylation-using-conjugating-enzymes-lace-for-site-specific-modification-and-ubiquitination-of-native-proteins.pdf |
63380aabba8a6d616863b9b9 | 10.26434/chemrxiv-2022-p43hn-v2 | On-Demand Release of Secondary Amine Bases for the Activation of Catalysts and Crosslinkers | We demonstrate that the species present in the equilibrium of DCv ureas can be employed in reaction cascades and as triggered organocatalysts. Easily controllable stimuli like heat or addition of water shift the equilibrium towards isocyanate and free base which can function as an in situ released reagent, both catalytically and in an equimolar fashion in different reactions. While applying heat to the system leads to a reversible liberation of amine base, addition of water makes this release irreversible. We demonstrate this application of DCv ureas with two examples. Firstly, we use the liberated base to activate a protected organocatalyst for acylhydrazone formation. Secondly, this base can be employed to trigger the release of nitrile-N-oxides from chlorooximes, which can react with 4-arm PEG-acrylates to form an isoxazoline polymer gel. These findings show the utility of DCv hindered ureas beyond their application in self-healing. | Benjamin Spitzbarth; Rienk Eelkema | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63380aabba8a6d616863b9b9/original/on-demand-release-of-secondary-amine-bases-for-the-activation-of-catalysts-and-crosslinkers.pdf |
66c925ee20ac769e5fa46744 | 10.26434/chemrxiv-2024-qdbrr | Autonomous Dissociation-type Selection for Glycoproteomics using a Real-Time Library Search | Tandem mass spectrometry (MS/MS) is the gold standard for intact glycopeptide identification, enabling peptide sequence elucidation and site-specific localization of glycan compositions. Beam-type collisional activation is generally sufficient for N-glycopeptides, while electron-driven dissociation is crucial for site localization in O-glycopeptides. Modern glycoproteomic methods often employ multiple dissociation techniques within a single LC-MS/MS analysis, but this approach frequently sacrifices sensitivity when analyzing multiple glycopeptide classes simultaneously. Here we explore the utility of intelligent data acquisition for glycoproteomics through real-time library searching (RTLS) to match oxonium ion patterns for on-the-fly selection of the appropriate dissociation method. By matching dissociation method with glycopeptide class, this autonomous dissociation-type selection (ADS) generates equivalent numbers of N-glycopeptide identifications relative to traditional beam-type collisional activation methods while also yielding comparable numbers of site-localized O-glycopeptide identifications relative to conventional electron transfer dissociation-based methods. The ADS approach represents a step forward in glycoproteomics throughput by enabling site-specific characterization of both N-and O-glycopeptides within the same LC-MS/MS acquisition. | Emmajay Sutherland; Tim S. Veth; William D. Barshop; Jacob H. Russell; Kathryn Kothlow; Jesse D. Canterbury; Christopher Mullen; David Bergen; Jingjing Huang; Vlad Zabrouskov; Romain Huguet; Graeme C. McAlister; Nicholas M. Riley | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c925ee20ac769e5fa46744/original/autonomous-dissociation-type-selection-for-glycoproteomics-using-a-real-time-library-search.pdf |
61001ad68f6bf65043715b0b | 10.26434/chemrxiv-2021-wr46c-v2 | Encapsulation of Paramagnetic Chelates in Perfluorocarbon-loaded Fractal Nanoparticles Enables Modulation of Fluorine-19 and Proton Magnetic Resonance Imaging Signal | 19F magnetic resonance imaging (19F MRI) is an emerging technique for quantitative imaging of novel therapies, such as cellular therapies and theranostic nanocarriers. A modification of perfluorocarbon (PFC)-loaded, nanocarrier-based 19F MRI probes with paramagnetic chelates can enhance probe’s functionality. Liquid PFC-loaded nanocarriers typically have a core-shell structure with PFC in the core due to the poor miscibility of PFC. However, paramagnetic relaxation enhancement acts only at a distance of a few angstroms. Thus, efficient modulation of 19F signal is possible only with fluorophilic PFC-soluble chelates. Such chelates, however, cannot interact with the surroundings of nanocarriers. Conversely, chelates on the surface typically affect only the aqueous environment but not the 19F signal.
We show that the confinement of PFC in biodegradable polymeric nanoparticles with fractal structure enables modulation of longitudinal and transverse 19F relaxation, as well as proton signal, using non-fluorophilic paramagnetic chelates. We compared nanoparticles with fractal multicore versus conventional core-shell structure, where the PFC is encapsulated in the core(s) and the chelate in the surrounding polymeric matrix. Importantly, paramagnetic chelates affected both longitudinal and transverse 19F relaxation in fractal multicore nanoparticles, but not in core-shell nanocapsules. Both relaxation rates of 19F nucleus increased with an increasing concentration of the paramagnetic chelate. Moreover, as the polymeric matrix remained water-permeable, proton enhancement additionally was observed in MRI. In the future, the effects of fractal confinement could be combined with more effective paramagnetic chelates to develop multifunctional imaging probes, for example, for high-sensitivity 19F MRI combined with sensing. | Margot Verbeelen; Paul White; Alexander H.J. Staal; Edyta Swider-Cios; Kimberly R.G. Cortenbach; N. Koen van Riessen; Cyril Cadiou; Françoise Chuburu; Mangala Srinivas; Olga Koshkina | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Aggregates and Assemblies; Core-Shell Materials; Imaging Agents | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61001ad68f6bf65043715b0b/original/encapsulation-of-paramagnetic-chelates-in-perfluorocarbon-loaded-fractal-nanoparticles-enables-modulation-of-fluorine-19-and-proton-magnetic-resonance-imaging-signal.pdf |
60c7490b702a9b264f18b0c9 | 10.26434/chemrxiv.11473080.v1 | A computational study of APTES surface functionalization of diatom-like amorphous SiO2 surfaces for heavy metal adsorption | The amorphous silica (SiO<sub>2</sub>) shell on diatom frustules is a highly attractive biomaterial for removing pollutants from aquatic ecosystems. The surface activity of silica can be enhanced by modification with organosilanes. In this work, we present an atomic-level theoretical study based on Molecular Dynamics (MD) and dispersion-corrected Density Functional Theory (DFT-D3BJ) calculations on the surface stability and adsorption of heavy metal compounds on silane and APTES covered SiO<sub>2</sub> surfaces. Our simulations show that at low APTES coverage, molecular adsorption of Cd(OH)<sub>2</sub> and HgCl<sub>2</sub> is more favourable near the modifier, compared to As(OH)<sub>3</sub> that binds at the hydroxylated region on silica. At higher coverages, the metallic compounds are preferentially adsorbed by the terminating amino group on the surface, whereas the adsorption in the region between APTES and the oxide surface is also spontaneous. The adsorption is strongly driven by van der Waals interactions at the highly-covered surface, where the consideration of dispersion corrections reduces the modifier-adsorbate interatomic distances and increases the adsorption energy by c.a. 0.4-0.7 eV. The adsorption of water is favourable, although it is generally weaker than for the heavy metal compounds. Based on our results, we conclude that the addition of APTES modifiers on silica increases the adsorption strength and provides extra binding sites for the adsorption of heavy metal pollutants. These outcomes can be used for the design more efficient biomaterials’ structures for heavy metals depollution. <br /> | Jose Julio Gutierrez Moreno; Ke Pan; Yu Wang; Wenjin Li | Biocompatible Materials; Biological Materials; Coating Materials; Nanostructured Materials - Materials; Computational Chemistry and Modeling; Theory - Computational; Water Purification; Interfaces; Self-Assembly; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7490b702a9b264f18b0c9/original/a-computational-study-of-aptes-surface-functionalization-of-diatom-like-amorphous-si-o2-surfaces-for-heavy-metal-adsorption.pdf |
63d49b891fe142081e5c6241 | 10.26434/chemrxiv-2023-2xb3b | Fluctuation-mediated orbital rotation of microparticles in non-coaxially counter-propagating optical tweezers | We have demonstrated in the present report that dielectric microparticles exhibited orbital rotation in the light field of non-coaxially configured two counter-propagating laser beams both in numerical simulations and experiments. A series of computational simulations indicated that when irradiated with two non-coaxially counter-propagating parallel laser beams with same intensity distributions in the absence of thermal (Brownian) motion, a microparticle did not exhibit orbital rotation due to the symmetry of the optical field. However, the computations predicted that a microparticle exhibited one directional orbital rotation in the presence of thermal motion because of the symmetry breaking of the optical force acting on the particle. This spontaneous orbital rotation was experimentally demonstrated for 1-µm dielectric particles in water at room temperature. | Kenji Setoura; Takayasu Kakimoto; Hiroshi Miyasaka; Syoji Ito | Physical Chemistry; Nanoscience; Plasmonic and Photonic Structures and Devices; Optics | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d49b891fe142081e5c6241/original/fluctuation-mediated-orbital-rotation-of-microparticles-in-non-coaxially-counter-propagating-optical-tweezers.pdf |
62c80e28252b21237adf588f | 10.26434/chemrxiv-2022-rjndn | Shedding light on the enigmatic TcO2·xH2O structure with density functional theory and EXAFS spectroscopy | The β-emitting 99Tc isotope is a high-yield fission product in 235U and 239Pu nuclear reactors, raising special concern in nuclear waste management due to its long half-life and the high mobility of pertechnetate (TcO4−). In the conditions of deep nuclear waste repositories, retention of Tc is achieved via biotic and abiotic reduction of TcO4− to compounds like amorphous TcO2·xH2O precipitates. It is generally accepted that these precipitates have linear (Tc(μ-O)2(H2O)2)n chains, with trans H2O. Although corresponding Tc Tc and Tc O distances have been obtained from Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy, this structure is largely based on analogy with other compounds. Here, we combine Density-Functional Theory with EXAFS measurements of fresh and aged samples to show that, instead, TcO2·xH2O forms zigzag chains that undergo a slow aging process whereby they combine to form longer chains and, later, a tridimensional structure that might lead to a new TcO2 polymorph. | Augusto F. Oliveira; Agnieszka Kuc; Thomas Heine; Ulrich Abram; Andreas C. Scheinost | Theoretical and Computational Chemistry; Inorganic Chemistry; Earth, Space, and Environmental Chemistry; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62c80e28252b21237adf588f/original/shedding-light-on-the-enigmatic-tc-o2-x-h2o-structure-with-density-functional-theory-and-exafs-spectroscopy.pdf |
60c75703842e65f0afdb45ec | 10.26434/chemrxiv.14333456.v1 | Triangular Boron Carbon Nitrides: An Unexplored Family of Chromophores with Unique Properties for Photocatalysis and Optoelectronics | In this work, we employed high-level ab initio electronic structure theory to devise and characterize a large family of novel heteroaromatic chromophores, the triangular boron carbon nitrides. These novel heterocycles inherit essential spectroscopic features from heptazine, in particular the inverted singlet-triplet gap, while their absorption and luminescence spectra and transition dipole moments are widely tuneable. For applications in photocatalysis, the wavelength of the absorption maximum can be tuned to improve the overlap with the solar spectrum at the surface of earth. For applications in OLEDs, the colour of emission can be adjusted and the fluorescence yield can be enhanced. <br /> | Sebastian Pios; Xiang Huang; Andrzej Sobolewski; Wolfgang Domcke | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75703842e65f0afdb45ec/original/triangular-boron-carbon-nitrides-an-unexplored-family-of-chromophores-with-unique-properties-for-photocatalysis-and-optoelectronics.pdf |
60c743690f50db55d3395ece | 10.26434/chemrxiv.9120017.v1 | Soft-Photoconversion Using Floating Self-Assembled Crystalline Films of Porphyrin Nanostructures | One of many evolved functions of biological cell membranes is to induce and regulate self-assembly of photoactive molecules into efficient light harvesting nanomaterials. Synthetic molecular assemblies at soft interfaces exhibit macroscale long-range order and so provide routes to biomimetic analogues that minimise concentration quenching. Here, we report the facile assembly of free-standing layered crystalline films of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrin nanostructures that exhibit significant photocurrents in situ at an electrified liquid | liquid interface. This methodology does not require acidic conditions, specialised amphiphilic porphyrins, or the use of additives or external stimuli. The assembly process is driven by an interplay between the hydrophobicity gradient at an immiscible aqueous | organic interface and optimised hydrogen bonding in the formed nanostructure. Highly-ordered interfacial nanostructures may provide a new paradigm for realisation of light-harvesting antennae in artificial photosynthetic technologies. | Andrés F. Molina-Osorio; David Cheung; Colm O'Dwyer; Andrew A. Stewart; Manuel Dossot; Grégoire Herzog; Micheal D. Scanlon | Photochemistry (Physical Chem.); Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743690f50db55d3395ece/original/soft-photoconversion-using-floating-self-assembled-crystalline-films-of-porphyrin-nanostructures.pdf |
63ef991b9da0bc6b33152e2b | 10.26434/chemrxiv-2023-bf6lv | Monolithically-stacked thin-film solid-state batteries | The power capability of Li-ion batteries has become increasingly limiting for the electrification of transport on land and in the air. The specific power of Li-ion batteries is restricted to a few thousand W/kg due to the required cathode thickness of a few tens of micrometers. We present a new design of monolithically-stacked thin-film cells that has the potential to increase the power ten-fold. We demonstrate an experimental proof-of-concept consisting of two monolithically stacked thin-film cells. Each cell consists of a silicon anode, a solid-oxide electrolyte, and a lithium cobalt oxide cathode. The battery can be cycled for more than 300 cycles between 6 and 8 V. Using a thermo-electric model, we predict that stacked thin-film batteries can achieve specific energies >250 Wh/kg at C-rates above 60, resulting in a specific power of tens of kW/kg needed for high-end mobile applications such as drones, robots, and eVTOLs. | Moritz H. Futscher; Luc Brinkman; André Müller; Abdessalem Aribia; Yaroslav Romanyuk | Physical Chemistry; Materials Science; Multilayers; Thin Films; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2023-02-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63ef991b9da0bc6b33152e2b/original/monolithically-stacked-thin-film-solid-state-batteries.pdf |
60c755cb0f50db5c36397f9f | 10.26434/chemrxiv.13027631.v2 | Elongation of Triplet Lifetime Caused by Intramolecular Energy Hopping in Diphenylanthracene Dyads Oriented to Undergo Efficient Triplet–Triplet Annihilation Upconversion | Triplet–triplet annihilation (TTA)-assisted photon upconversion (TTA-UC) in three dyads (DPA–Cn–DPA), comprised of two diphenylanthracene (DPA) moieties connected by nonconjugated C1, C2, and C3 linkages (Cn), has been investigated. The performance of these dyads as energy acceptors in the presence of the energy donor platinum octaethylporphyrin are characterized by longer triplet lifetimes (<i>τ</i><sub>T</sub>) and different TTA rate constants than those of the parent DPA. The larger <i>t</i><sub>T</sub> of the linked systems, caused by “Intramolecular Energy Hopping” in the triplet dyad <sup>3</sup>DPA*–Cn–DPA, results in a low threshold intensity, a key characteristic of efficient TTA-UC. | Masaya Kanoh; Yasunori Matsui; KIyomasa Honda; Yuto Kokita; Takuya Ogaki; Eisuke Ohta; Hiroshi Ikeda | Photochemistry (Physical Chem.); Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755cb0f50db5c36397f9f/original/elongation-of-triplet-lifetime-caused-by-intramolecular-energy-hopping-in-diphenylanthracene-dyads-oriented-to-undergo-efficient-triplet-triplet-annihilation-upconversion.pdf |
60c73e3ef96a003c04285e9b | 10.26434/chemrxiv.6726977.v1 | Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach | <p>The ranking of small molecule binders by their kinetic (kon and koff) and thermodynamic (delta G) properties can be a valuable metric for lead selection and optimization in a drug discovery campaign, as these quantities are often indicators of in vivo efficacy. Efficient and accurate predictions of these quantities can aid the in drug discovery effort, acting as a screening step. We have previously described a hybrid molecular dynamics, Brownian dynamics, and milestoning model, Simulation Enabled Estimation of Kinetic Rates (SEEKR), that can predict kon’s, koff’s, and G’s. Here we demonstrate the effectiveness of this approach for ranking a series of seven small molecule compounds for the model system, -cyclodextrin, based on predicted kon’s and koff’s. We compare our results using SEEKR to experimentally determined rates as well as rates calculated using long-timescale molecular dynamics simulations and show that SEEKR can effectively rank the compounds by koff and G with reduced computational cost. We also provide a discussion of convergence properties and sensitivities of calculations with SEEKR to establish “best practices” for its future use.</p> | Benjamin R. Jagger; Christoper T. Lee; Rommie Amaro | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e3ef96a003c04285e9b/original/quantitative-ranking-of-ligand-binding-kinetics-with-a-multiscale-milestoning-simulation-approach.pdf |
60c742ae4c89195b45ad24e3 | 10.26434/chemrxiv.8378345.v1 | A Simple Scheme for FInding Magnetic Aromatic Hydrocarbon Molecules | <div><div><div><div><p>The smallest magnetic aromatic hydrocarbons reported to date consist of at least six fused- azulene. In order to determine the magnetic state of a given molecule computationally- demanding state-of-the-art methods, such as DMRG or DFT, are required. We introduce a simple computational procedure to screen large sets of molecules and identify likely can- didates worthy of more sophisticated (and costly) analysis. We consider smaller molecules that combine azulene and naphtalene and find two new magnetic molecules.</p></div></div></div></div> | Alexandra Valentim; Gisela A. Bocan; Javier D. Fuhr; Daniel
J. Garcia; Manoranjan Kumar; Geetanjali Giri; Suryanarayanasastry Ramasesha | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c742ae4c89195b45ad24e3/original/a-simple-scheme-for-f-inding-magnetic-aromatic-hydrocarbon-molecules.pdf |
61975838a831ec4adbd5f139 | 10.26434/chemrxiv-2022-h2fqj | Synthesis of 5, 6, 11, 12-tetrahyroindolo[3,2-b]carbazole-based dicarboxylate acid for MOFs fabrication via in-situ oxidative dehydrogenation | The indolocarbazole derivatives has been shown great potentials as one of the key important compounds in the field of organic electronics owing to their attractive structural and electrical properties. However, studies that directly and systematically introduce indolocarbazole unit into MOFs are still lacking. Herein, we reported the synthesis of 6,12-di(hetero)aryl substituted 5,6,11,12-tetrahyroindolo[3,2-b]carbazole synthetic motifs in a facile way. The potential of these synthetic motifs as building block for porous materials fabrication is unveiled through the preparation of Zn-MOF-ICZ and UiO-68-ICZ by using 5,6,11,12-tetrahyroindolo[3,2-b]carbazole terminated with dicarboxylate acid. The resultant Zn-MOF-ICZ and UiO-68-ICZ feature 5,11-dihyroindolo[3,2-b]carbazole unit as a result of in-situ oxidative dehydrogenation, which was confirmed by 1H NMR and single crystal X-ray diffraction study. The successful construction of these MOFs indicated the powerful of 6,12-di(hetero)aryl substituted 5,6,11,12-tetrahyroindolo[3,2-b]carbazole unit for porous materials synthesis and this provides a broad platforms for potential applications investigation considering their fine optical properties. | Guoliang Liu; Chunqing Ji | Inorganic Chemistry; Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-01-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61975838a831ec4adbd5f139/original/synthesis-of-5-6-11-12-tetrahyroindolo-3-2-b-carbazole-based-dicarboxylate-acid-for-mo-fs-fabrication-via-in-situ-oxidative-dehydrogenation.pdf |
6286919d708767f657588c83 | 10.26434/chemrxiv-2022-dftzc | Visualizing Surface Phase Separation in PS PMMA Polymer Blends at the Nanoscale | Phase-separated polymer blend films are an important class of functional materials with numerous technological applications including solar cells, catalysis, and biotechnology. These technologies are underpinned by precise control of phase separation at the nanometer length-scales, which is highly challenging to visualize using conventional analytical tools. Herein, we introduce tip-enhanced Raman spectroscopy (TERS), in combination with AFM, confocal Raman spectroscopy, and XPS, as a sensitive nanoanalytical method to determine lateral and vertical phase-separation in polystyrene (PS)-poly(methyl methacrylate) (PMMA) polymer blend films. Correlative topographical, molecular, and elemental information reveals a vertical phase separation of the polymers within the top ca. 20 nm of the blend surface in addition to the lateral phase separation in the bulk. Furthermore, complementary TERS and XPS measurements reveal the presence of PMMA within 9.2 nm of the surface and PS at the sub-surface of the polymer blend. This fundamental work establishes TERS as an powerful analytical tool for surface characterization of this important class of polymers at nanometer length-scales. | Dušan Mrđenović; Daniel Abbot; Victor Mougel; Weitao Su; Naresh Kumar; Renato Zenobi | Analytical Chemistry; Polymer Science; Nanoscience; Polymer blends; Imaging; Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6286919d708767f657588c83/original/visualizing-surface-phase-separation-in-ps-pmma-polymer-blends-at-the-nanoscale.pdf |
60c75363469df4e320f44d6d | 10.26434/chemrxiv.13488120.v1 | A Plasmon-Based Nanoruler to Probe the Mechanical Properties of Synthetic and Biogenic Nanosized Lipid Vesicles | <p><b>Membrane-delimited
compartments, as lipid vesicles, are ubiquitous in natural and synthetic
systems. The mechanical properties of such vesicles are crucial for several
physical, chemical, and biological processes. However, their accurate
determination is still challenging and requires sophisticated instruments and
data analysis. Here we report the first evidence that the surface plasmon
resonance (SPR) of citrated gold nanoparticles (AuNPs) adsorbed on synthetic
vesicles is finely sensitive to the vesicles’ mechanical properties. We
leverage this finding to demonstrate that the spectrophotometric tracking of
the SPR provides quantitative access to the stiffness of vesicles of synthetic
and natural origin, such as extracellular vesicles (EVs). This plasmon-based
“stiffness nanoruler” paves the way for developing a facile, cost-effective,
and high-throughput method to assay the mechanical properties of vesicles of
nanometric size and unknown composition.</b></p> | Lucrezia Caselli; Andrea Ridolfi; Jacopo Cardellini; Lewis Sharpnack; Lucia Paolini; Marco Brucale; Francesco Valle; Costanza Montis; Paolo Bergese; Debora Berti | Nanostructured Materials - Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75363469df4e320f44d6d/original/a-plasmon-based-nanoruler-to-probe-the-mechanical-properties-of-synthetic-and-biogenic-nanosized-lipid-vesicles.pdf |
60c74ae59abda2493bf8cf7b | 10.26434/chemrxiv.12268325.v1 | Reconsidering XPS Quantification of Substitution Levels of Monolayers on Unoxidized Silicon Surfaces | In this preprint, we reevaluate the use of X-ray photoelectron spectroscopy (XPS) to determine substitution levels of reactions on non-oxidized silicon surfaces. XPS is the most commonly used method to determine the yields of reactions on surfaces. We go back to the most basic assumptions, and work through the calculations to provide a revised set of calculations that take into account (i) possible adventitious hydrocarbon contamination, (ii) the effect of choosing a different silicon crystal face [Si(100) versus Si(111)], and (iii) the utility of choosing a small heteroatom tag to enable a more accurate measure of substitution levels. We provide a simple algorithm and summary of the equations one can use to make it easy for the reader/researcher. | Minjia Hu; Erik Luber; Jillian Buriak | Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74ae59abda2493bf8cf7b/original/reconsidering-xps-quantification-of-substitution-levels-of-monolayers-on-unoxidized-silicon-surfaces.pdf |
657f8b1d66c13817296ff185 | 10.26434/chemrxiv-2023-x7sfr-v3 | Accelerating materials discovery by high-throughput GIWAXS characterization of quasi-2D formamidinium metal halide perovskites | The intriguing functionalities of emerging quasi-two-dimensional (2D) metal halide perovskites (MHPs) have led to further exploration of this material class for sustainable and scalable optoelectronic applications. However, the chemical complexities in precursors – primarily determined by the 2D:3D compositional ratio – result in uncontrolled phase heterogeneities in these materials, which compromises the optoelectronic performances. Yet, this phenomenon remains poorly understood due to the massive quasi-2D compositional space. To systematically explore the fundamental principles, herein, a high-throughput automated synthesis-characterization workflow is designed and implemented to formamidinium (FA)-based quasi-2D MHP system. It is revealed that the stable 3D-like phases, where the α-FAPbI3 surface is passivated by 2D spacer molecules, exclusively emerge at the compositional range (35-55% of FAPbI3), deviating from the stoichiometric considerations. A quantitative crystallographic study via high-throughput grazing-incidence wide-angle X-ray scattering (GIWAXS) experiments integrated with automated peak analysis function quickly reveals that the 3D-like phases are vertically aligned, facilitating vertical charge conduction that could be beneficial for optoelectronic applications. Together, this study uncovers the optimal 2D:3D compositional range for complex quasi-2D MHP systems, realizing desired optoelectronic performances and stability. The automated experimental workflow significantly accelerates materials discoveries and processing optimizations while providing fundamental insights into complex materials systems. | Jonghee Yang; Juanita Hidalgo; Donghoon Song; Sergei V. Kalinin; Juan-Pablo Correa-Baena; Mahshid Ahmadi | Materials Science; Energy; Hybrid Organic-Inorganic Materials; Materials Processing; Thin Films; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/657f8b1d66c13817296ff185/original/accelerating-materials-discovery-by-high-throughput-giwaxs-characterization-of-quasi-2d-formamidinium-metal-halide-perovskites.pdf |
60c74472bb8c1a5c943da4e7 | 10.26434/chemrxiv.7679798.v2 | A Machine Learning Based Intramolecular Potential for a Flexible Organic Molecule | <div><div><div><p>One limitation of the accuracy of computational predictions of protein–ligand binding free energies is the fixed functional form of the intramolecular component of the molecular mechanics force fields. Here, we employ the kernel regression machine learning technique to construct an analytical potential, using the Gaussian Approximation Potential software and framework, that reproduces the quantum mechanical potential energy surface of a small, flexible, drug-like molecule, 3-(benzyloxy)pyridin-2-amine. Challenges linked to the high dimensionality of the configurational space of the molecule are overcome by developing an iterative training protocol and employing a representation that separates short and long range interactions. The analytical model is connected to the MCPRO simulation software, which allows us to perform Monte Carlo simulations of the small molecule bound to two proteins, p38 MAP kinase and leukotriene A4 hydrolase, as well as in water. We demonstrate that the accuracy of our machine learning based intramolecular model is retained in the condensed phase, and that corrections to absolute protein–ligand binding free energies of up to 2 kcal/mol are obtained.</p></div></div></div> | Daniel Cole; Letif Mones; Gábor Csányi | Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY 4.0 | CHEMRXIV | 2019-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74472bb8c1a5c943da4e7/original/a-machine-learning-based-intramolecular-potential-for-a-flexible-organic-molecule.pdf |
67484261f9980725cf508cfd | 10.26434/chemrxiv-2024-tmtrx | Copper-mediated C–C Coupling of Alkenyl Boronates and Bromodifluoroacetates | The reaction of alkenyl boronates and bromo-difluoroacetates in the presence of copper powder and TMEDA as the catalytic system was developed. The corresponding C–C coupling products were obtained in 35–93% yield. The method tolerated a variety of functional groups, namely, phenol, (thio)ether, protected amino-, hydroxy-, ketone, and carboxylic acid moieties, as well as various saturated carbo- and heterocycles, and was compatible with multigram scale up (to 76 g). The diastereoselectivity of the process was typically low, so that ca. 1:1 E/Z isomeric mixtures were formed from pure E or Z alkenyl boronates. Further functional group transformations demonstrated the utility of the prepared compounds as valuable building blocks for synthetic and medicinal chemistry. Based on the obtained results and the literature data, a plausible reaction mechanism was proposed involving the formation of radical and organocopper intermediates. | Yevhen Yurov; Kamila Laniush; Oleksandr Hryschuk; Oleksandr Liashuk; Oleksandr Grygorenko | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67484261f9980725cf508cfd/original/copper-mediated-c-c-coupling-of-alkenyl-boronates-and-bromodifluoroacetates.pdf |
6399ca790fd9926dbf45fe59 | 10.26434/chemrxiv-2022-j2hqw | A Simple Method for Teaching Bragg’s Law in an Undergraduate Teaching Laboratory with the use of Metal–Organic Frameworks | Metal–organic frameworks (MOFs) are a class of porous materials that are often crystalline with high surface area and structural tunability. In this laboratory experiment designed for inorganic chemistry students at the undergraduate level, students complete a two-step experiment where they will first (i) synthesize two isostructural zirconium-based MOFs, UiO-66 and UiO-67, and then (ii) isolate and characterize the materials using powder X-ray diffraction (PXRD). A simple solvothermal procedure was developed for the synthesis of UiO-66 and UiO-67 using the air/moisture stable zirconyl chloride octahydrate as a starting reagent. Depending on the equipment available, the MOFs can be further characterized by nitrogen adsorption analysis for surface area determination using Brunauer–Emmett–Teller (BET) theory, diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS), thermogravimetric analysis (TGA), 1H nuclear magnetic resonance (NMR) spectroscopy, and scanning electron microscopy (SEM). Upon synthesizing the MOFs and collecting the characterization data, students analyze and describe their results by answering a series of questions included in the laboratory manual. This exercise will allow students to develop practical laboratory skills while expanding their knowledge on some fundamental concepts in inorganic chemistry, materials chemistry, MOFs, crystallography, and other characterization techniques as availability allows. | Zvart Ajoyan; Christopher Copeman; Hudson A. Bicalho; Jean-Louis Do; Tiffany Te; Jennifer Romero; Ashlee J. Howarth | Inorganic Chemistry; Chemical Education; Chemical Education - General; Coordination Chemistry (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6399ca790fd9926dbf45fe59/original/a-simple-method-for-teaching-bragg-s-law-in-an-undergraduate-teaching-laboratory-with-the-use-of-metal-organic-frameworks.pdf |
60c747d59abda285a2f8c9c0 | 10.26434/chemrxiv.11809128.v1 | Insights on Small Molecule Binding to the Hv1 Proton Channel from Free Energy Calculations with Molecular Dynamics Simulations | Hv1 is a voltage-gated proton channel whose main function is to facilitate extrusion of protons from the cell. The development
of effective channel blockers for Hv1 can lead to new therapeutics for the treatment of maladies related to Hv1 dysfunction.
Although the mechanism of proton permeation in Hv1 remains to be elucidated, a series of small molecules have been
discovered to inhibit Hv1. Here, we compute relative binding free energies of a prototypical Hv1 blocker on a model of
human Hv1 in an open state. We use alchemical free energy perturbation techniques based on atomistic molecular dynamics
simulations. The results support our proposed open state model, sheds light on the preferred tautomeric state of the blocker
that binds Hv1, and lays the groundwork for future studies on adapting the blocker molecule for more effective channel blocking. | Victoria T. Lim; Andrew D. Geragotelis; Nathan M. Lim; J. Alfredo Freites; Francesco Tombola; David Mobley; Doug Tobias | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c747d59abda285a2f8c9c0/original/insights-on-small-molecule-binding-to-the-hv1-proton-channel-from-free-energy-calculations-with-molecular-dynamics-simulations.pdf |
60c7579e9abda22716f8e789 | 10.26434/chemrxiv.14438801.v1 | Defining the Basis of Cyanine Phototruncation Enables a New Approach to Single Molecule Localization Microscopy | <p>The light-promoted conversion of extensively used cyanine dyes to blue-shifted emissive products has been observed in various contexts. However, both the underlying mechanism and the species involved in this photoconversion reaction have remained elusive. Here we report that irradiation of heptamethine cyanines provides pentamethine cyanines, which, in turn, are photoconverted to trimethine cyanines. We detail an examination of the mechanism and substrate scope of this remarkable two-carbon phototruncation reaction. Supported by computational analysis, we propose that this reaction involves a singlet oxygen-initiated multi-step sequence involving a key hydroperoxycyclobutanol intermediate. Building on this mechanistic framework, we identify conditions to improve the yield of photoconversion by over an order of magnitude. We then demonstrate that cyanine phototruncation can be applied to super-resolution single-molecule localization microscopy, leading to improved spatial resolution with shorter imaging times. We anticipate these insights will help transform a common, but previously mechanistically ill-defined, chemical transformation into a valuable optical tool.</p> | Siddharth Matikonda; Dominic Helmerich; Mara Meub; Gerti Beliu; Philip Kollmannsberger; Alec Greer; Markus Sauer; Martin Schnermann | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7579e9abda22716f8e789/original/defining-the-basis-of-cyanine-phototruncation-enables-a-new-approach-to-single-molecule-localization-microscopy.pdf |
60c748b54c8919e592ad2f7b | 10.26434/chemrxiv.11958969.v1 | Generation of N,N-Di(4-bromophenyl)nitrenium Ion Under Acidic Conditions: Search for a Nitrenium Dication | The behavior of the N,N-di(4-bromophenyl)nitrenium ion under acidic aqueous conditions was examined via laser flash photolysis experiments. A long-lived species forms and can be assigned as the cation radical or the dication. This species is unreactive towards nucleophiles and reactive towards strong electron donors, consistent with a cation radical. Mechanistic analysis indicates its formation is through a separate pathway than that of the nitrenium ion, suggestive of a triplet mechanism. | Andrea Zeppuhar; Daniel Falvey | Photochemistry (Org.); Physical Organic Chemistry; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748b54c8919e592ad2f7b/original/generation-of-n-n-di-4-bromophenyl-nitrenium-ion-under-acidic-conditions-search-for-a-nitrenium-dication.pdf |
665b5768418a5379b0d93af5 | 10.26434/chemrxiv-2024-46xnn | A Skeletally Diverse Library of Bioactive Natural Product-Like Compounds Enabled by Late-Stage P450-Catalyzed Oxyfunctionalization | The discovery of small-molecule agents for chemical biology and therapeutic applications depends upon the ability to access and explore new biologically relevant regions of chemical space, a goal often pursued through diversity-oriented synthesis (DOS). In this report, we describe the design and implementation of P450-mediated chemoenzymatic diversity-oriented synthesis (CeDOS), a strategy that leverages chemo- and regiodivergent P450-catalyzed oxyfunctionalizations as key steps for enabling the synthesis of complex molecules that resemble natural products, a major source of bioactive molecules and drugs. Using this strategy, a library of over 50 novel and structurally diverse natural product-like compounds was generated through skeletal rearrangement and diversification of a plant-derived terpene via divergent chemoenzymatic routes enabled by selective C–H hydroxylation and epoxidation reactions catalyzed by engineered P450s. This CeDOS library encompass many unique and unprecedented organic scaffolds, many of which were determined to exhibit notable cytotoxicity against human cancer cells as well as diversified anticancer activity profiles. This work demonstrates the power of the present chemoenzymatic diversity-oriented synthesis strategy for directing the construction and discovery of novel bioactive molecules and it offers a blueprint for the broader application of this approach toward the creation and exploration of natural product-like chemical libraries. | Rudi Fasan; Andrew Bortz; John Bennett | Organic Chemistry; Catalysis; Bioorganic Chemistry; Combinatorial Chemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665b5768418a5379b0d93af5/original/a-skeletally-diverse-library-of-bioactive-natural-product-like-compounds-enabled-by-late-stage-p450-catalyzed-oxyfunctionalization.pdf |
652042f145aaa5fdbb70b7c8 | 10.26434/chemrxiv-2023-4j6hd | Electrochemical characterization of electrolyte purity for CO2 reduction studies | In this work, we put forward a simple electrochemical approach to conveniently determine the purity of the electrolyte solution which improves the reproducibility and reliability of electrochemical CO2 reduction data such that experimental outcomes can be readily compared across research groups. The method uses a polycrystalline Au electrode as a probe to detect electrolyte impurities that can readily be adsorbed to surfaces even when ultrahigh-purity (99.999%) commercial chemicals are used as received. Herein, we show how the extent of trace contamination alters the measured activity during CO2 reduction and demonstrate electrochemical methods to capture these trace contaminants, such that CO2 reduction activity can be reproduced reliably. | Zhihao Cui; Melissa Marx; Modeste Tegomoh; Anne Co | Catalysis; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652042f145aaa5fdbb70b7c8/original/electrochemical-characterization-of-electrolyte-purity-for-co2-reduction-studies.pdf |
60c7582ff96a00e0bc288d9f | 10.26434/chemrxiv.14519445.v1 | Comparison of Numerical and Analytical Approaches for Simulating Purely Sinusoidal Voltammetry | In this paper we present a comparison of two mathematical techniques for simulating the behaviour of a surface-confined single-electron redox process when interrogated with a large amplitude sine-wave. The two simulation methods are an analytical approximation proposed by Bell and co-authors, and a numerical solution that we have previously used to analyse such single-electron processes. We show that the techniques are in good agreement, allowing for the limitations imposed by the construction of the analytical model. We also compare two different parameter inference approaches proposed for the respective simulation techniques. <br /> | Henry Lloyd-Laney; Martin Robinson; Alison Parkin; David Gavaghan | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7582ff96a00e0bc288d9f/original/comparison-of-numerical-and-analytical-approaches-for-simulating-purely-sinusoidal-voltammetry.pdf |
672114f4f9980725cf48495e | 10.26434/chemrxiv-2024-3b54n | Nickel - Titania Supported Catalysts for Direct Selective Hydrodeoxygenation of 5-Hydroxymethylfurfural to 5-Methylfurfural | The 5-Hydroxymethylfurfural (HMF) platform molecule can be derived from biomass feedstocks and catalytically hydrogenated into various added-value molecules. Its conversion to 5-methylfurfural (5-MF), a versatile synthetic intermediate and perfuming agent, is particularly challenging, the selective hydrodeoxygenation of the C–OH group in HMF being by far less favourable kinetically and thermodynamically than the hydrogenation of the C=O group that gives 2,5-bis-hydroxymethylfuran (BHMF). Herein, for the first time we showed that Ni/TiO2 catalysts can be tuned to promote the selective removal of a hydroxy group in the presence of an aldehyde moiety, and give high 5-MF yield. Among various synthesis approaches, the direct ion exchange incorporation of Ni into a TiO2 network prepared by an alginate synthesis route allowed the key-factors orientating the reaction selectivity towards 5-MF to be identified. The highest 5-MF selectivity (86%) at nearly full conversion was favoured by high acidity and ultra-high dispersion of Ni atoms at the surface, while the prime role of titania was discussed. By contrast, increasing the reduction temperature up to 700°C strongly lowered the acidity and formed larger Ni particles, which favour the C=O activation, and is thereby promoting the selectivity switch towards BHMF at 86% also at nearly full conversion. | Martyna Przydacz; Nathalie Tanchoux; Dris Ihiawakrim; David Kubička; Nicolas Keller; Agnieszka Ruppert | Catalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672114f4f9980725cf48495e/original/nickel-titania-supported-catalysts-for-direct-selective-hydrodeoxygenation-of-5-hydroxymethylfurfural-to-5-methylfurfural.pdf |
67d01bb1fa469535b9da6343 | 10.26434/chemrxiv-2024-s8zql-v3 | Altmetrics in Chemistry: Alternative Metrics for Research Impact in Chemistry | The research impact of published research is measured not only by citations in other academic research documents, but also by alternative metrics (altmetrics) indicators. They include news in newspapers, posts in social media, mentions in patents, policy documents, online encyclopedias, blogs, websites, and more. The findings of this study fifteen years after its introduction to complement citation-based metrics for assessing research im-pact may further benefit education on communication of gradu-ate student and young faculty in the chemical sciences. | Rosaria Ciriminna; Cristina Della Pina; Rafael Luque; Mario Pagliaro | Chemical Education | CC BY NC 4.0 | CHEMRXIV | 2025-03-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d01bb1fa469535b9da6343/original/altmetrics-in-chemistry-alternative-metrics-for-research-impact-in-chemistry.pdf |
6630e3ff418a5379b01893a4 | 10.26434/chemrxiv-2024-cflvv | Synthesis of β-(Hetero)aryl Ketones via Ligand-Enabled Nondirected C−H Alkylation | β-Aryl ketones are present in various natural products and bioactive molecules. Till now, -aryl
ketone has been synthesized through the directing group (DG) approach or Mizoroki-Heck
coupling. Herein, we reported a palladium(II) catalyzed dual ligand-enabled non-directed C−H
alkylation with arene and heteroarene as a limiting reagent for the synthesis of -(hetero)aryl
ketones. The combined influence of 2-methyl quinoxaline and N-acetyl phenylalanine ligands
imparts complementary selectivity, facilitating the diversification of drugs and natural products
through C−H alkylation. Integrated experimental and computational mechanistic studies
demonstrate the C−H activation as both the regio- and rate-determining step. Interestingly, while
the Pd−Ag heterobimetallic species is not directly involved in the 1,2-migratory insertion step, it is
proposed to play a vital role during the product release phase of the catalytic cycle. | Yogesh Bairagi; sandip porey; Sai V. C. Vummaleti; Xinglong Zhang; Goutam Kumar Lahiri; Debabrata Maiti | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Synthesis and Reactions; Homogeneous Catalysis; Bond Activation | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6630e3ff418a5379b01893a4/original/synthesis-of-hetero-aryl-ketones-via-ligand-enabled-nondirected-c-h-alkylation.pdf |
60c7410dee301c1ab8c78b6b | 10.26434/chemrxiv.7927166.v1 | Synthetic and Mechanistic Studies of a Versatile Heteroaryl Thioether Directing Group for Pd(II) Catalysis | A weakly coordinating monodentate heteroaryl thioether directing group has been developed for use in Pd(II) catalysis to orchestrate key elementary steps in the catalytic cycle that require conformational flexibility in a manner that is difficult to accomplish with traditional strongly coordinating directing groups. This benzothiazole thioether, (BT)S, directing group can be used to promote oxidative Heck reactivity of internal alkenes providing a wide range of products in moderate to high yields. To demonstrate the broad applicability of this directing group, arene C–H olefination was also successfully developed. Reaction progress kinetic analysis provides insights into the role of the directing group in each reaction, which is supplemented with computational data for the oxidative Heck reaction. Furthermore, this (BT)S directing group can be transformed into a number of synthetically useful functional groups, including a sulfone for Julia olefination, allowing it to serve as a “masked olefin” directing group in synthetic planning. In order to demonstrate this synthetic utility, natural products (+)-salvianolic acid A and salvianolic acid F are formally synthesized using the (BT)S directed C–H olefination as the key step. | Andrew Romine; Kin Yang; Malkanthi Karunananda; Jason Chen; Keary Engle | Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7410dee301c1ab8c78b6b/original/synthetic-and-mechanistic-studies-of-a-versatile-heteroaryl-thioether-directing-group-for-pd-ii-catalysis.pdf |
60c73f14337d6c8085e2648b | 10.26434/chemrxiv.7198559.v1 | Understanding Sequence Contributions to Peptoid–lipid Interactions: Using Peptoids as a Platform to Advance Multidisciplinary Research and Undergraduate Education in Parallel | <p>The synthesis and fluorescence spectroscopy studies of 21 peptoids,</p>
<p>including 19 new tripeptoids, are described. Insight into sequence features that influence biophysical properties in the presence and absence of unilamellar lipid vesicles is provided. Concomitantly, we highlight the educational value of training undergraduates in multidisciplinary research using peptoid science.</p> | Christian Jimenez; Jiacheng Tan; Kalli M. Dowell; Gillian Gadbois; Cameron Read; Nicole Burgess; Jesse Cervantes; Shannon Chan; Animal Jandaur; Tara Karanik; Jaenic Lee; Mikaela Ley; Molly McGeehan; Ann McMonigal; Kira Palazzo; Samantha Parker; Andre Payman; Maritza Soria; Lauren Verheyden; Vivian Vo; Jennifer Yin; Anna L. Calkins; Amelia A. Fuller; Grace Stokes | Organic Synthesis and Reactions; Biopolymers; Drug delivery systems; Chemical Education - General; Mass Spectrometry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f14337d6c8085e2648b/original/understanding-sequence-contributions-to-peptoid-lipid-interactions-using-peptoids-as-a-platform-to-advance-multidisciplinary-research-and-undergraduate-education-in-parallel.pdf |
61fdc8d37a054a945102f73f | 10.26434/chemrxiv-2022-bt3z4 | PdII-Catalyzed Site-selective β- and γ-C(sp3)−H Arylation of Primary Aldehydes Controlled by Transient Directing Groups | Pd(II)-catalyzed site-selective β- and γ-C(sp3)−H arylation of primary aldehydes is developed by rational design of L,X-type transient directing groups (TDG). External 2-pyridone ligands are identified to be crucial for the observed reactivity. By minimizing the loading of acid additives, the ligand effect is enhanced to achieve high reactivities of the challenging primary aldehyde substrates. Site-selectivity can be switched from the proximate to the relatively remote position by changing the bite angle of TDG to match the desired palladacycle size. Experimental and computational investigations support this rationale for designing TDG to potentially achieve remote site-selective C(sp3)−H functionalizations. | Yihao Li; Yuxin Ouyang; Nikita Chekshin; Jin-Quan Yu | Organic Chemistry; Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61fdc8d37a054a945102f73f/original/pd-ii-catalyzed-site-selective-and-c-sp3-h-arylation-of-primary-aldehydes-controlled-by-transient-directing-groups.pdf |
60c745df567dfe30bdec4522 | 10.26434/chemrxiv.10279283.v1 | Effect of Metabolic Constraints on the Observable Isotope Fractionation Associated with Aerobic Biodegradation of Hexachlorocyclohexanes | <div>Biodegradation of the highly persistent hexachlorocyclohexanes is difficult to assess in contaminated soils and sediments because this process occurs only slowly over timescales of years to decades. Recent instrumental advances for compound-specific isotope analysis (CSIA) now make it possible to monitor such processes based on the isotope fractionation of multiple elements as changes of 13C/12C, 37Cl/35Cl, and 2H/1H ratios in the residual HCH contamination. However, metabolic constraints from the expression of enzymes that can compete with the primary metabolic reactions leading to HCH biodegradation and thus alter the observable contaminant isotope fractionation through co metabolic side reactions have largely been overlooked. Here, we developed activity-based assays to assess the competitive behaviour of mixtures of lindane dehydrochlorinase LinA and haloalkane dehydrochlorinase LinB which catalyze the dehydrochlorination and hydrolytic dechlorination of several HCH isomers. Using X-HCH as model contaminant that can be transformed by both enzymes in mixtures of different LinA2/LinB activity, we observed preferential formation of products from hydrolytic dechlorination. This observation suggests that LinB was more reactive than predicted from the nominal enzyme activities. The C and H isotope fractionation of X-HCH in LinA2/LinB mixtures can be rationalized by a combination of isotope enrichment factors from independent dehydrochlorination and hydrolytic dechlorination reactions where LinA2 contributed more to H isotope fractionation than LinB, thus contrasting the assessment of competitive enzyme activity. Our study shows that metabolic constraints associated with the expression of multiple enzymes can potentially compromise inferences of extent and pathways of contaminant biodegradation from CSIA.</div> | Iris E. Schilling; Hans-Peter E. Kohler; Thomas Hofstetter | Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745df567dfe30bdec4522/original/effect-of-metabolic-constraints-on-the-observable-isotope-fractionation-associated-with-aerobic-biodegradation-of-hexachlorocyclohexanes.pdf |
60c748d9567dfed560ec4aa6 | 10.26434/chemrxiv.11877039.v2 | Solvent- and catalyst-free aza-Michael addition of imidazoles and related heterocycles | This work demonstrates the scope and limitations of the aza-Michael addition of imidazoles and related heterocycles with electron deficient olefins under solvent- and catalyst-free conditions. The reaction proceeds at 80°C within hours towards completion as long as the azole derivative is sufficiently soluble in the Michael acceptor, which has been used in small excess. Workup only comprises evaporation of surplus Michael-acceptor and no additional solvents are necessary for purifying the products.<br /> | Katharina Kodolitsch; Florian Gobec; Christian Slugovc | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748d9567dfed560ec4aa6/original/solvent-and-catalyst-free-aza-michael-addition-of-imidazoles-and-related-heterocycles.pdf |
60f4030135156b0448e264e5 | 10.26434/chemrxiv-2021-8gl92-v2 | Structural and Spectroscopic Characterization of Pyrene Derived Carbon Nano Dots: A Single Particle Level Analysis | The bottom-up approach has been widely used for large-scale synthesis of carbon nanodots (CNDs). However, the structure and origin of photoluminescence in CNDs synthesized by the bottom-up approach is still a subject of debate. Here, using a series of separation techniques like solvent extraction, column chromatography, gel electrophoresis and dialysis, we present three distinct fluorescent components in CNDs synthesized from pyrene, a well-known precursor molecule. The separated components have qualitative and quantitatively different absorption and emission spectral features including quantum yield (QY). Optical and vibrational spectroscopy techniques combined with electron microscopy indicate that a subtle balance between the extent of graphitization and the presence of molecular fluorophores determines the nature of fluorescence emission. Substantial difference in photons/cycle, single particle fluorescence blinking, on-off photoswitching strongly supports the distinct nature of the components. | Gayatri Batra; Shubham Sharma; Kush Kaushik; Chethana Rao; Pawan Kumar; Krishan Kumar; Subrata Ghosh; Deep Jariwala; Eric A. Stach; Aditya Yadav; Chayan Kanti Nandi | Physical Chemistry; Photochemistry (Physical Chem.); Physical and Chemical Properties; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f4030135156b0448e264e5/original/structural-and-spectroscopic-characterization-of-pyrene-derived-carbon-nano-dots-a-single-particle-level-analysis.pdf |
60c745fa567dfec557ec4549 | 10.26434/chemrxiv.10299416.v1 | Improving UV Curing in Lignin-Containing Photopolymers for Stereolithography by Chemical Reduction and Acetylation | Despite recent successes incorporating lignin into photoactive resins, lignin photo-properties can be detrimental to its application in UV-curable photopolymers, especially to customized, engineered resins for use in stereolithography printing. We report on chemical modification techniques employed to reduce UV absorption in lignin and the resulting mechanical, thermal, and cure properties in these lignin-containing materials. Pine lignin was modified using acetylation and reduction reactions and incorporated into a printable resin formulation. Modified lignin displayed enhanced printing properties because UV absorption at the 3D printable range was reduced in all acylated lignin from 25% up to greater than 60%. Resins made with the modified lignin showed increased stiffness and strength with lower thermal stability. Investigating these techniques is an important step in developing lignin for use in UV-curing applications and furthers the effort to valorize lignin toward commercial use. | Jordan T. Sutton; Kalavathy Rajan; David P. Harper; Stephen Chmely | Biological Materials; Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745fa567dfec557ec4549/original/improving-uv-curing-in-lignin-containing-photopolymers-for-stereolithography-by-chemical-reduction-and-acetylation.pdf |
637de4f89b5b80d591d2c7f1 | 10.26434/chemrxiv-2022-0tmtk | The origin of magnetization-caused increment in water oxidation | In recent years, using an external magnetic field to promote the oxygen evolution reaction (OER) on magnetic catalysts has attracted great attention. It is an appealing topic, but with a puzzle where the increment comes from. The early theoretical work has predicted that the production of triplet dioxygen in OER can be facilitated by the spin-polarization effect in a single domain of magnetic catalysts. Recent progress has revealed that the M-O radical species is the key for promoting the triplet dioxygen formation, which is evident by the pH-dependent enhancement by magnetization. However, magnetization of a ferromagnetic material only changes its magnetic domain structure in the case of bulk ferromagnetic catalytic structures. It does not directly change the spin orientation of unpaired electrons in the material. Thus, where would be the OER enhancement coming from? The confusion further lies in that each magnetic domain is a small magnet and theoretically the spin-polarization promoted OER already occurs on these magnetic domains, and thus the enhancement should have been achieved without magnetization. Here, we demonstrate that the enhancement comes from the disappeared domain wall between magnetic domains. The proportion of domain wall occupied surface before magnetization determines the degree of enhanced OER by magnetization. Due to the spin-facilitated promotion effect, the OER on surface occupied by magnetic domains are more favourable than that on surface occupied by domain walls. Magnetization leads to the evolution of the magnetic domain structure, from a multi-domain one to a single domain one, in which the domain wall disappears. Consequently, the occupied by the domain wall is reformatted into one by a single domain, on which the OER follows the spin-facilitated pathways and thus the overall increment on the electrode occurs. This study fills the missing gap for understanding the magnetic field enhanced OER and it further explains the type of ferromagnetic catalysts which can give increment by magnetization. | Xiao Ren; Tianze Wu; Zizhao Gong; Lulu Pan; Jianling Meng; Haitao Yang; FreyjaBjork Dagbjartsdottir; Adrian Fisher; Hongjun Gao; Zhichuan J. Xu | Physical Chemistry; Catalysis; Electrocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637de4f89b5b80d591d2c7f1/original/the-origin-of-magnetization-caused-increment-in-water-oxidation.pdf |
66c79d7cf3f4b05290c23d2f | 10.26434/chemrxiv-2024-8fdhv | Chemical Tagging of N-Alkylamine-Containing Natural Products and Pharmaceuticals through C(sp3)–H Functionalization | Development of efficient protocols for introducing handles into natural products and pharmaceutical agents that are suitable for bioconjugation is a compelling research objective. One attractive option would involve chemical tagging through late-stage C–H functionalization, but such strategies are uncommon. The primary challenge lies in the lack of catalyst systems that can chemo- and site-selectively cleave relatively inert C–H bonds. In this study, we demonstrate that bioactive N-alkylamine-based natural products and other small-molecule drugs can be modified in order to facilitate bioconjugation. Moreover, we show that under blue light irradiation, flavin analogues can promote oxidation of bioactive amines by sequential scission of α- and β-amino C–H bonds. Engagement of the resulting enamines in an inverse electron-demand Diels-Alder process with tetrazines can be used to achieve an array of structural modifications. Notably, the transformation occurs under mild, pH-neutral, and aerobic conditions. The utility of the approach is highlighted by a facile synthesis of antibody–drug conjugates involving anti-cancer agent irinotecan. | Cunyuan Zhao; Yuankai Wang; Andrew Steele; Soichiro Mori; Ben Shen; Masayuki Wasa | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Photocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c79d7cf3f4b05290c23d2f/original/chemical-tagging-of-n-alkylamine-containing-natural-products-and-pharmaceuticals-through-c-sp3-h-functionalization.pdf |
60c7437a337d6cdd25e26bfe | 10.26434/chemrxiv.9247694.v1 | Nanoribbons with Non-Alternant Topology from Fusion of Polyazulene: Carbon Allotropes Beyond Graphene | Various
two-dimensional (2D) carbon allotropes with non-alternant topologies, such as
pentaheptites and phagraphene, have been proposed. Predictions indicate that
these metastable carbon polymorphs, which contain odd-numbered rings, possess
unusual (opto)electronic properties. However, none of these materials has been
achieved experimentally due to synthetic challenges. In this work, by using
on-surface synthesis, nanoribbons of the non-alternant graphene allotropes,
phagraphene and tetra-penta-hepta(TPH)-graphene have been obtained by
dehydrogenative C-C coupling of 2,6-polyazulene chains. These chains were
formed in a preceding reaction step via on-surface Ullmann coupling of
2,6-dibromoazulene. Low-temperature scanning probe microscopies with
CO-functionalized tip and density functional theory calculations have been used
to elucidate their structural properties. <br /> | Qitang Fan; Daniel Martin-Jimenez; Daniel Ebeling; Claudio K. Krug; Lea Brechmann; Corinna Kohlmeyer; Gerhard Hilt; Wolfgang Hieringer; André Schirmeisen; Michael Gottfried | Carbon-based Materials | CC BY NC ND 4.0 | CHEMRXIV | 2019-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7437a337d6cdd25e26bfe/original/nanoribbons-with-non-alternant-topology-from-fusion-of-polyazulene-carbon-allotropes-beyond-graphene.pdf |
6685eb1e5101a2ffa8511b3c | 10.26434/chemrxiv-2024-dxd41-v3 | Correcting Implicit Solvation at Metal/Water Interfaces Through the Incorporation of Competitive Water Adsorption | Conventional continuum solvation models are ubiquitous in computational catalysis, including for describing metal/water interfaces which are relevant to both solution-phase heterogeneous catalysis and electrocatalysis. Nonetheless, we find that such continuum models qualitative fail to describe both the adsorption free energy and conformational preference for many organic molecules at such interfaces, largely due to the failure of continuum models to incorporate the role of competitive water adsorption. We develop a simple phenomenological model that accounts for competitive water adsorption and show that the model, when used in conjunction with continuum solvation, provides a dramatic improvement in the description of both adsorption and conformational preference. The model is also extended to additionally incorporate the influence of applied potential at the electrode surface, thus facilitating computationally efficient applications to scenarios including electrocatalysis. | Kwanpyung Lee; J. R. Schmidt | Theoretical and Computational Chemistry; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-07-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6685eb1e5101a2ffa8511b3c/original/correcting-implicit-solvation-at-metal-water-interfaces-through-the-incorporation-of-competitive-water-adsorption.pdf |
62d2e772581987160242abc0 | 10.26434/chemrxiv-2022-65k4h | Top-Down Mass Spectrometry and Assigning Internal Fragments for Determining Disulfide Bond Positions in Proteins | Disulfide bonds in proteins have a substantial impact on protein structure, stability, and biological activity. Localizing disulfide bonds is critical for understanding protein folding and higher-order structure. Conventional top-down mass spectrometry (TD-MS) where only terminal fragments are assigned, for disulfide intact proteins can access disulfide information, but suffers from low fragmentation efficiency, limiting sequence coverage. Here, we show that assigning internal fragments generated from TD-MS enhances the sequence coverage of disulfide intact proteins by 20-60% by returning information from the interior of the protein sequence, which cannot be obtained by terminal fragments alone. The inclusion of internal fragments can extend the sequence information of disulfide intact proteins to near complete sequence coverage. Importantly, the enhanced sequence information that arise from the assignment of internal fragments can be used to determine the relative position of disulfide bonds and the exact disulfide connectivity between cysteines. The data presented here demonstrates the benefits of incorporating internal fragment analysis into TD-MS workflow for analyzing disulfide intact proteins, which would be valuable for characterizing biotherapeutic proteins such as monoclonal antibodies and antibody-drug conjugates. | Benqian Wei; Muhammad Zenaidee; Carter Lantz; Brad Williams; Sarah Totten; Rachel Loo; Joseph Loo | Analytical Chemistry; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d2e772581987160242abc0/original/top-down-mass-spectrometry-and-assigning-internal-fragments-for-determining-disulfide-bond-positions-in-proteins.pdf |
60c73f1c0f50db08f839573b | 10.26434/chemrxiv.7246859.v1 | A Bifunctional Iron Nickel Catalyst for the Oxygen Evolution Reaction | The oxygen evolution reaction (OER) is a key process that enables the storage of renewable energies in the form of chemical fuels. Although numerous transition metal oxides have been explored as OER catalysts, the scaling relationship of the binding energies of various surface-bound intermediates imposes a limit on the maximum activity of these oxides. While previous computational studies have suggested bifunctional catalysts might be capable of overcoming this limit, stable and non-precious catalysts of this type remain elusive. Here, we describe a catalyst that exhibits activity significantly higher than current state-of-the-art catalysts that operate in alkaline solutions, including the benchmark nickel iron oxide. This new catalyst is both easy to prepare and stable for many hours. Operando X-ray absorption spectroscopic data reveal that the catalyst is made of nanoclusters of gamma-FeOOH covalently linked to the edge sites of a gamma-NiOOH support. According to density functional theory computations, this structure allows a reaction path involving iron as the oxygen evolving center and a nearby terrace O site on the gamma-NiOOH support oxide as a hydrogen acceptor. This bifunctional mechanism circumvents the aforementioned maximum activity limit associated with the scaling relationship and leads to superior OER activity.<br /> | fang song; Michael Busch; Benedikt Lassalle-Kaiser; Chia-Shuo Hsu; Elitsa Petkucheva; Michaël Bensimon; Hao Ming Chen; Clemence Corminboeuf; Xile Hu | Catalysts; Nanocatalysis - Catalysts & Materials; Electrocatalysis; Energy Storage; Spectroscopy (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2019-02-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73f1c0f50db08f839573b/original/a-bifunctional-iron-nickel-catalyst-for-the-oxygen-evolution-reaction.pdf |
60c75006567dfe6ac7ec57d4 | 10.26434/chemrxiv.12982001.v1 | Immobilising Giant Unilamellar Vesicles with Zirconium Metal-Organic Framework Anchors | Lipid bilayer vesicles have provided a window into the function and fundamental properties of cells.
Vesicles, however, do not remain still, requiring some microscopy experiments to include a
preparatory fixation step. Here, we describe a straightforward method to immobilise giant unilamellar
vesicles (GUVs) using a zirconium-based metal-organic framework (MOF) and demonstrate that they
stay in position on a timescale of minutes- to hours. Furthermore, immobilising GUVs in this way has
no discernible adverse effect on GUV stability and permeability. These findings indicate that this
strategy may be a powerful tool for future studies into lipid membrane function and dynamics. | Christopher Jennings; Jeremy S. Rossman; Ross Marshall; Ross Forgan; Barry Blight | Bioinorganic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75006567dfe6ac7ec57d4/original/immobilising-giant-unilamellar-vesicles-with-zirconium-metal-organic-framework-anchors.pdf |
660c78b766c13817298275ae | 10.26434/chemrxiv-2024-4s0f9 | Photoredox-Catalyzed Amidyl Radical Insertion to Bicyclo[1.1.0]butanes | Heteroaromatic rings play a prominent role in medicinal chemistry, featuring in numerous biologically relevant molecules. However, unlike benzene ring the saturated and structurally rigid bioisosteric mimetics of heteroaromatic rings are rarely known, mainly due to the inherent challenges associated with the stability and synthesis of heteroatom-substituted C(sp3)-rich polycyclic hydrocarbons. We envisioned that the strategic and highly selective insertion of different heteroatomic units to bicyclo[1.1.0]butanes (BCBs) could offer an ideal platform to access diverse heterobicyclo[n.1.1]alkanes. Herein, by circumventing the intrinsic challenges associated with the reaction of BCBs with heteroatomic radicals, we report a photoredox-catalyzed highly regio- and chemoselective insertion of amidyl radicals to BCBs, which provided direct access to 2-oxa-4-azabicyclo[3.1.1]hept-3-enes. Detailed experimental and computational studies have been carried out to underpin the mechanistic paradigm of this reaction. The newly synthesized heterobicyclic motifs are structurally rigid and exhibit well-defined exit vectors, the two important molecular properties in medicinal chemistry. Moreover, various downstream transformations were carried out with these compounds, highlighting their utility as versatile building blocks in synthetic chemistry. | Frank Glorius; Chetan Chintawar; Ranjini Laskar; Debanjan Rana; Felix Schäfer; Nele van Wyngaerden; Subhabrata Dutta; Constantin Daniliuc | Organic Chemistry; Catalysis | CC BY 4.0 | CHEMRXIV | 2024-04-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660c78b766c13817298275ae/original/photoredox-catalyzed-amidyl-radical-insertion-to-bicyclo-1-1-0-butanes.pdf |
6660db83418a5379b02abd41 | 10.26434/chemrxiv-2024-xs6f9 | Interfacial Ice Density Fluctuations Inform Surface Ice-philicity | The propensity of a surface to nucleate ice or bind to ice is governed by its ice-philicity — its relative preference for ice over liquid water. However, the relationship between the features of a surface and its ice-philicity is not well understood, and for surfaces with chemical or topographical heterogeneity, such as proteins, their ice-philicity is not even well-defined. In the analogous problem of surface hydrophobicity, it has been shown that hydrophobic surfaces display enhanced low water-density (vapor-like) fluctuations in their vicinity. To interrogate whether enhanced ice-like fluctuations are similarly observed near ice-philic surfaces, here we use molecular simulations and enhanced sampling techniques. Using a family of model surfaces for which the wetting coefficient, k, has previously been characterized, we show that the free energy of observing rare interfacial ice-density fluctuations decreases monotonically with increasing k. By utilizing this connection, we investigate a set of fcc systems and find that the (110) surface is more ice-philic than the (111) or (100) surfaces. By additionally analyzing the structure of interfacial ice, we find that all surfaces prefer to bind to the basal plane of ice, and the topographical complementarity of the (110) surface to the basal plane explains its higher ice-philicity. Using enhanced interfacial ice-like fluctuations as a measure of surface ice-philicity, we then characterize the ice-philicity of chemically heterogeneous and topologically complex systems. In particular, we study the spruce budworm anti-freeze protein (sbwAFP), which binds to ice using a known ice-binding site (IBS) and resists engulfment using non-binding sites of the protein (NBSs). We find that the IBS displays enhanced interfacial ice-density fluctuations and is therefore more ice-philic than the two NBSs studied. We also find the two NBSs are similarly ice-phobic. By establishing a connection between interfacial ice-like fluctuations and surface ice-philicity, our findings thus provide a way to characterize the ice-philicity of heterogeneous surfaces. | Zachariah Vicars; Jeongmoon Choi; Sean Marks; Richard Remsing; Amish Patel | Physical Chemistry; Materials Science; Nanoscience; Biological Materials; Interfaces; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6660db83418a5379b02abd41/original/interfacial-ice-density-fluctuations-inform-surface-ice-philicity.pdf |
656dc63929a13c4d47a02aa6 | 10.26434/chemrxiv-2023-jrpwm-v3 | Overlay databank unlocks data-driven analyses of biomolecules for all | Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank—a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution. | Anne Kiirikki; Hanne Antila; Lara Bort; Pavel Buslaev; Favela Fernando; Tiago Mendes Ferreira; Patrick Fuchs; Rebeca Garcia-Fandino; Ivan Gushchin; Batuhan Kav; Norbert Kučerka; Patrik Kula; Milla Kurki; Alexander Kuzmin; Anusha Lalitha; Fabio Lolicato; Jesper Madsen; Markus Miettinen; Cedric Mingham; Luca Monticelli; Ricky Nencini; Alexey Nesterenko; Thomas Piggot; Angel Pineiro; Nathalie Reuter; Suman Samantray; Fabian Suarez-Leston; Reza Talandashti; Samuli Ollila | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Bioinformatics and Computational Biology; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY 4.0 | CHEMRXIV | 2023-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/656dc63929a13c4d47a02aa6/original/overlay-databank-unlocks-data-driven-analyses-of-biomolecules-for-all.pdf |
665086a821291e5d1d299d0d | 10.26434/chemrxiv-2024-60lp4 | Amplification of Negative Gas Adsorption in a multivariate framework | The approach of multivariate MOFs was used to fine-tune the mechanical properties of the flexible framework DUT-49. In situ XRD, NMR and physisorption studies showed that the partial incorporation of a more rigid linker into DUT-49 framework enables a stabilization of the metastable open pore phase which led to a twofold amplification of ΔnNGA. | Francesco Walenszus; Volodymyr Bon; Ankita De; Stefan Kaskel | Physical Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Physical and Chemical Properties; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665086a821291e5d1d299d0d/original/amplification-of-negative-gas-adsorption-in-a-multivariate-framework.pdf |
60c74739337d6c4f9de272f0 | 10.26434/chemrxiv.11559531.v1 | Ultrafast Spin Crossover in a Room-Temperature Ferrimagnet: Element-Specific Spin Dynamics in Photoexcited Cobalt Ferrite | Transition metal complexes capable of photo - induced spin crossover have been widely investigated because of their potential to enable ultrafast optical control of information processing. However, any real application of photo-switchable molecules requires that spin crossover be paired with additional functionality such as long-range magnetic order. Important advances combining these functions are notably reported for a number of bimetallic Prussian Blue analogues; however, to date PBA-based magnetic photo-switches can only operate be-low 150 K due to loss of magnetic order. In contrast, cobalt ferrite is a ferrimagnetic semiconductor with a Curie temperature of 790 K and extremely favorable magnetic properties by comparison to state-of-the-art PBAs. The mixed valence electronic structure of cobalt ferrite is reminiscent of cobalt-iron PBA, which is a well-known photo-switch. To investigate the potential for photo-switching in this material, we employ transient XUV spectroscopy to probe charge and spin dynamics with element-speci fic resolution on the femtosecond time scale. Results show that 400 nm light excites a metal-to-metal charge transfer transition, which drives the crossover of high-spin Co2+ to low-spin Co3+ with a time constant of 405 ± 29 fs and an internal quantum efficiency of unity. This result establishes the existence of efficient photo-switching in a new class of robust ferrimagnetic spinel ferrites.<br /> | Stephen Londo; Somnath Biswas; Jakub Husek; Igor V. Pinchuk; Michael J. Newburger; Alexandra Boyadzhiev; Amanda H. Trout; David W. McComb; Roland Kawakami; L. Robert Baker | Physical and Chemical Properties; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74739337d6c4f9de272f0/original/ultrafast-spin-crossover-in-a-room-temperature-ferrimagnet-element-specific-spin-dynamics-in-photoexcited-cobalt-ferrite.pdf |
60c74124ee301c3aacc78ba9 | 10.26434/chemrxiv.7955831.v1 | New Class of Electrophiles in Palladium/Norbornene Cooperative Catalysis: Sulfenamide-Enabled Ortho Thiolation of Aryl Iodides | To expand the synthetic platform of the palladium-norbornene
cooperative catalysis, here we report a general <i>ortho</i> thiolation of aryl and heteroaryl iodides using sulfenamides
as a new class of electrophiles. The sulfenamides derived from a ε-<i><sup>t</sup></i>butyl-lactam
were found most efficient to introduce various aryl and methyl sulfur groups at
the arene <i>ortho</i> position. The<i> ipso</i> functionalization
is achieved through Heck or Suzuki termination. This reaction also provides a convenient
access to the corresponding aryl sulfoxides and sulfones via selective
oxidation of the <i>ortho</i> thiolation
products. | Renhe Li; Yun Zhou; Ki-Young Yoon; Zhe Dong; Guangbin Dong | Bioorganic Chemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74124ee301c3aacc78ba9/original/new-class-of-electrophiles-in-palladium-norbornene-cooperative-catalysis-sulfenamide-enabled-ortho-thiolation-of-aryl-iodides.pdf |
6625ff4591aefa6ce112662a | 10.26434/chemrxiv-2024-0sqdw | The Synthesis of Nucleotide Diphosphate Uronic Acids via the Coupling of Activated Nucleotides with Uronic Acid-1-Phosphates | The stereoselective synthesis of nucleotide diphosphate (NDP) uronic acids from simple sugar precursors, including gluco-, galacto-, and mannopyranoside derivatives, is described. Key to this convergent synthesis is the coupling of a uronic acid 1-phosphate with a nucleotide monophosphate activated as the phosphorimidazolide to form the NDP-uronic acid, of which 10 derivatives were prepared. The coupling is compatible with the carboxylic acid functionality present in uronic acid-1-phosphates with conversions above 95% and isolated yields typically above 60%. Key features of this work include (i) stereoselective synthesis of ⍺-phosphoglycosides from perbenzylated ⍺- and β-thioglycosides, (ii) selective and mild oxidation of galactose-, glucose-, and mannose-1-phosphates to the corresponding uronic acid-1-phosphate, and (iii) mild coupling conditions to directly provide nucleotide diphosphate uronic acids from unprotected uronic acid-1-phosphates and nucleotide phosphorimidazolides. | Austin Bargmann ; Marcelo Sousa; Tarek Sammakia | Organic Chemistry; Bioorganic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6625ff4591aefa6ce112662a/original/the-synthesis-of-nucleotide-diphosphate-uronic-acids-via-the-coupling-of-activated-nucleotides-with-uronic-acid-1-phosphates.pdf |
60c740df4c8919803bad21d8 | 10.26434/chemrxiv.7849151.v1 | Synthesis and Reactivity of Precolibactin 886 | <div>The clb gene cluster encodes the biosynthesis of metabolites known as precolibactins and colibactins. The clb pathway is found in gut commensal E. coli, and clb metabolites are thought to initiate colorectal cancer via DNA cross-linking. Precolibactin 886 (1) is one of the most complex isolated clb metabolites; it contains a 15-atom macrocycle and an unusual 5-hydroxy-3-oxazoline ring. Here we report confirmation of the structural assignment via a biomimetic synthesis of precolibactin 886 (1) proceeding through the amino alcohol 9. Double oxidation of 9 afforded the unstable α-ketoimine 2 which underwent macrocyclization to precolibactin 886 (1) upon HPLC purification (3% from 9). Studies of the putative precolibactin 886 (1) biosynthetic precursor 2, the model α-ketoimine 25, and the α-dicarbonyl 26 revealed that these compounds are susceptible to nucleophilic rupture of the C36–C37 bond. Moreover, cleavage of 2 produces other known clb metabolites or biosynthetic intermediates. This unexpected reactivity explains the difficulties in isolating full clb metabolites and accounts for the structure of a recently identified colibactin–adenine adduct. The colibactin peptidase ClbP deacylates synthetic precolibactin 886 (1) to form a non-genotoxic pyridone, suggesting precolibactin 886 (1) lies off-path of the major biosynthetic route.</div> | Seth Herzon; Alan R. Healy; kevin wernke; Chung Sub Kim; Nicholas Lees; Jason M. Crawford | Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-03-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740df4c8919803bad21d8/original/synthesis-and-reactivity-of-precolibactin-886.pdf |
66d96195cec5d6c1423026a6 | 10.26434/chemrxiv-2024-0x3xj-v2 | Borylative Desymmetrization of multifunctional haloarenes assisted by sodium dispersion | Multiply halogenated aromatic compounds were selectively borylated by a boron alkoxide in the presence of sodium dispersion when the reaction was carried out at a low temperature, while multi-functionalization took place at an elevated temperature. The reaction of 1,4-dichlorobenzene with sodium dispersion (200–1200 mol%) in the presence of isopropyloxyboron pinacolate (120–240 mol%) afforded (4-chlorophenyl)boron pinacolate in up to 84% yield. Formation of diborylated product hardly accompanied under the reaction conditions at –78 °C for 1 h. | Ukyo Ogi; Shuichi Ikeda; Kentaro Okano; Masaki Horie; Atsunori Mori | Organic Chemistry; Organometallic Chemistry; Organic Synthesis and Reactions; Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d96195cec5d6c1423026a6/original/borylative-desymmetrization-of-multifunctional-haloarenes-assisted-by-sodium-dispersion.pdf |
61703b210c04806f723b7fa0 | 10.26434/chemrxiv-2021-jfmqq | Tuning the Electrochemical and Photophysical Properties of Osmium Complexes for Application in Photoredox Catalysis | Photocatalysis driven by visible and ultraviolet irradiation is a fundamental tool for synthetic chemists. Recently, expansion of this tool to near-infrared (NIR) light has gained in popularity. Herein, we report the detailed photophysical characterization of a library of OsII polypyridyl photosensitizers that absorb NIR irradiation. By tuning ligand scaffold and electron density, we access a range of synthetically useful excited state energies and redox potentials. | Samantha Goldschmid; Eva Bednarova; Logan Beck; Katherine Xie; Nicholas Tay; Benjamin Ravetz; Jun Li; Candice Joe; Tomislav Rovis | Organic Chemistry; Catalysis; Photocatalysis | CC BY NC 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61703b210c04806f723b7fa0/original/tuning-the-electrochemical-and-photophysical-properties-of-osmium-complexes-for-application-in-photoredox-catalysis.pdf |
653a3c2348dad2312064a7ef | 10.26434/chemrxiv-2023-trnqm | Supported Erythrocyte Membranes on Piezoelectric Sensors for Studying the Interactions with Nanoparticles | Applications of nanoparticles (NPs) in nanodrugs, food additives, and cosmetics can result in the presence of nanomaterials in human circulatory system and their attachment to red blood cells (RBCs), which may lead to cytotoxic effects. To investigate the interactions of NPs with RBC membranes (RBCm), supported erythrocyte membranes (SRBCm) were developed on the piezoelectric sensors in a quartz crystal microbalance with dissipation (QCM-D) at 25 °C. A well dispersed RBCm suspension at 1 mM NaCl and 0.2 mM NaHCO3 was obtained from whole blood, and comprised of colloidal membrane fragments with the average hydrodynamic diameter and zeta potential as 390 nm and -0.53 mV, respectively, at pH 7.0. The thin and rigid SRBCm was formed mainly through the deposition of RBCm fragments on the poly-L-lysine modified crystal sensor, leading to the average frequency shift of -26.2 Hz and the low ratio of dissipation to frequency shift (7.2 × 10-8 Hz-1). The complete coverage of SRBCm was indicated by the plateau of frequency shift in the stage of SRBCm formation and no deposition of negatively charged 106 nm polystyrene nanoparticles (PSNPs) on the SRBCm. Atomic force microscopy and immunofluorescence microscopy images showed that RBCm aggregates with the average size of 420 nm and erythrocyte membrane proteins existed on SRBCm, respectively. The methods of determining attachment efficiencies of model positively charged NPs (i.e., hematite NPs or HemNPs) and model negatively charged NPs (i.e., PSNPs) on SRBCm were demonstrated in 1 mM NaCl solution at pH 5.1 and pH 7.0, respectively. HemNPs exhibited a favorable deposition with an attachment efficiency of 0.99 while PSNPs did not show any attachment propensity toward SRBCm. | Tanaz Islam; Olga N. Chesnokov; Andrew V. Oleinikov; Peng Yi | Biological and Medicinal Chemistry; Materials Science; Nanoscience; Biological Materials; Thin Films; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a3c2348dad2312064a7ef/original/supported-erythrocyte-membranes-on-piezoelectric-sensors-for-studying-the-interactions-with-nanoparticles.pdf |
65e0ce79e9ebbb4db993d6fe | 10.26434/chemrxiv-2024-fhn1k | Autonomous laboratories for accelerated materials discovery: a community survey and practical insights | What are researchers’ motivations and challenges related to automation and autonomy in materials science laboratories? Our survey on this topic received 102 responses from researchers across a variety of institutions and in a variety of roles. Accelerated discovery was a clear theme in the responses, and another theme was concern about the role of human researchers. Survey respondents shared a variety of use cases targeting accelerated materials discovery, including examples where partial automation is preferred over full self-driving laboratories. Building on the observed patterns of researcher priorities and needs, we propose a framework for levels of laboratory autonomy from non-automated (L0) to fully autonomous (L5). | Linda Hung; Joyce Yager; Danielle Monteverde; Dave Baiocchi; Ha-Kyung Kwon; Shijing Sun; Santosh Suram | Materials Science; Chemical Engineering and Industrial Chemistry; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65e0ce79e9ebbb4db993d6fe/original/autonomous-laboratories-for-accelerated-materials-discovery-a-community-survey-and-practical-insights.pdf |
631b8df203e27d3a49cf1a91 | 10.26434/chemrxiv-2022-kkgk0 | Exploring EPR Parameters of 187Re Complexes for Designing new MRI Probes: from the gas phase to solution and a model protein environment | Breast cancer is one of the major types of cancer around the world, and early diagnosis is essential for successful treatment. New contrast agents (CA), with reduced toxicology, are needed to improve diagnosis. One of the most promising Magnetic Resonance Imaging (MRI) CA is based on Rhenium conjugated with a benzothiazole derivate (ReABT). In this sense, DFT has been used to evaluate the best methodology for calculating the hyperfine coupling constant (Aiso) of ReABT. Then, a thermodynamic analysis was performed to confirm the stability of the complex. Furthermore, a docking study of ReABT at the enzyme PI3K active site and Aiso calculations of ReABT in the enzyme environment were carried out. The best methodology for the Aiso calculation of ReABT was using the M06L functional, SARC-ZORA-TZVP (for Re) and TZVP (for all other atoms) basis set, relativistic Hamiltonian, and the CPCM solvation model with water as the solvent, confirm that the relativistic effects are important for calculating the Aiso values. In addition, thermodynamic analysis indicates that ReABT presents a higher stability and a lower toxicity than Gd-based CAs. The docking studies point out that ReABT interacts with amino acids residues of alanine, aspartate, and lysine from the PI3K active site. Considering the enzyme environment, Aiso values decrease significantly. These findings indicate that the CA candidate ReABT could be a good candidate for a new contrast agent. | Gustavo A. Andolpho; Elaine F. F. da Cunha; Teodorico C. Ramalho | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631b8df203e27d3a49cf1a91/original/exploring-epr-parameters-of-187re-complexes-for-designing-new-mri-probes-from-the-gas-phase-to-solution-and-a-model-protein-environment.pdf |
65a54e529138d23161fa59d5 | 10.26434/chemrxiv-2024-53ckp | Transdermal hydrogen sulfide delivery enabled by open metal site metal-organic frameworks | Hydrogen sulfide (H2S) is an endogenously produced gasotransmitter involved in many physiological processes that are integral to proper cellular functioning, including chemical signaling, redox balancing, and modification of vital proteins. Due to its profound anti-inflammatory and antioxidant properties, H2S plays important roles in preventing inflammatory skin disorders and improving wound healing. Transdermal H2S delivery is a therapeutically viable option for the man-agement of such disorders. However, current small-molecule H2S donors are not optimally suited for transdermal deliv-ery and typically generate electrophilic byproducts that may lead to undesired toxicity. Here, we demonstrate that H2S release from metal-organic frameworks (MOFs) bearing coordinatively unsaturated metal centers is a promising alterna-tive for controlled transdermal delivery of gaseous H2S without the release of unwanted byproducts. In particular, exten-sive gas sorption measurements and powder X-ray diffraction (PXRD) studies of eleven MOFs support that the Mg-based framework Mg2(dobdc) (dobdc4− = 2,5-dioxidobenzene-1,4-dicarboxylate) is uniquely well-suited for transdermal H2S delivery due to its strong yet completely reversible binding of H2S, high capacity (14.7 mmol/g or 33.3 wt% at 1 bar and 25 °C), and lack of toxicity. In addition, Rietveld refinement of high-quality synchrotron PXRD data from a H2S-dosed mi-crocrystalline sample of Mg2(dobdc) supports that the high H2S capacity of this framework arises due to the presence of three distinct binding sites: at the Mg centers through a Mg⋅⋅⋅S interaction (primary site), through a short S⋅⋅⋅S interaction to the polarized H2S molecules at the primary sites (secondary site), and in the center of the pores (tertiary site). Last, we demonstrate that transdermal delivery of H2S from this framework is sustained over a 24 h period through porcine skin. Not only is this significantly longer than sodium sulfide (Na2S), but this represents the first example of controlled trans-dermal delivery of pure H2S gas. Overall, H2S-loaded Mg2(dobdc) is an easily accessible, solid-state source of H2S, ena-bling safe storage and transdermal delivery of this therapeutically relevant gas. | Ruth Mandel; Piyusha Lotlikar; Tomce Runcevski; Jung-Hoon Lee; Joshua Woods; Tristan Pitt; Justin Wilson; Phillip Milner | Biological and Medicinal Chemistry; Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65a54e529138d23161fa59d5/original/transdermal-hydrogen-sulfide-delivery-enabled-by-open-metal-site-metal-organic-frameworks.pdf |
61790b87913a7475706c7e34 | 10.26434/chemrxiv-2021-vj65l | Conduction Band Engineering of Half-Heusler Thermoelectrics Using Orbital Chemistry | Semiconducting half-Heusler (HH, XYZ) phases are promising thermoelectric materials owing to their versatile electronic properties. Because the valence band of half-Heusler phases benefit from the valence band extrema at several high-symmetry points in the Brillouin zone (BZ), it is possible to engineer better p-type HH materials through band convergence. However, the thermoelectric studies of n-type HH phases have been lagging behind since the conduction band minimum is always at the same high-symmetry point (X) in the BZ, giving the impression that there is little opportunity for band engineering. Here we study the n-type orbital diagram of 69 HHs, and show that there are two competing conduction bands with very different effective masses actually at the same X point in the BZ, which can be engineered to be converged. The two conduction bands are dominated by the d orbitals of X and Y atoms, respectively. The energy offset between the two bands depends on the difference in electron configuration and electronegativity of the X and Y atoms. Based on the orbital phase diagram, we provide the strategy to engineer the conduction band convergence by mixing the HH compounds with the reverse band offsets. We demonstrate the strategy by alloying VCoSn and TaCoSn. The V0.5Ta0.5CoSn mixture presents the high conduction band convergence and corresponding significantly larger density-of-states effective mass than either VCoSn or TaCoSn. Our work indicates that analyzing the orbital character of band edges provides new insight into engineering thermoelectric performance of HH compounds. | Shuping Guo; Shashwat Anand; Madison K. Brod; Yongsheng Zhang; G. Jeffrey Snyder | Materials Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61790b87913a7475706c7e34/original/conduction-band-engineering-of-half-heusler-thermoelectrics-using-orbital-chemistry.pdf |
6543ed7aa8b423585ad2b55a | 10.26434/chemrxiv-2023-wnm9n | TORO Indexer: A PyTorch-Based Indexing Algorithm for kHz Serial Crystallography | Serial Crystallography (SX) involves the processing of thousands of diffraction patterns coming from crystals in random orientations. To compile a complete dataset, these patterns must be indexed (i.e., determine orientation), integrated, and merged. We introduce the TORO (TOrch-powered Robust Optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO Indexer is capable of operating on GPUs, CPUs, and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In our tests, TORO outpaces existing solutions indexing thousands of frames per second when running on GPUs, positioning it as an attractive candidate to produce real-time indexing and user feedback. Our algorithm streamlines some of the ideas introduced by previous indexers like DIALS real grid search and XGandalf, and refines them using faster and principled robust optimization techniques which result in a concise codebase consisting of less than 500 lines. Based on our evaluations across four proteins, TORO consistently matches and, in certain instances, outperforms established algorithms such as XGandalf and MOSFLM, occasionally amplifying the quality of the consolidated data while achieving indexing rates that are orders of magnitude higher. The inherent modularity of TORO, and the versatility of Pytorch code bases, facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX. | Piero Gasparotto; Luis Barba; Hans-Christian Stadler; Greta Assmann; Henrique Mendonça; Alun Ashton; Markus Janousch; Filip Leonarski; Benjamı́n Béjar | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Artificial Intelligence; Crystallography | CC BY 4.0 | CHEMRXIV | 2023-11-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6543ed7aa8b423585ad2b55a/original/toro-indexer-a-py-torch-based-indexing-algorithm-for-k-hz-serial-crystallography.pdf |
638e0faa0a81272d05d47ada | 10.26434/chemrxiv-2022-0rvh2 | Giant Redox Entropy in the Intercalation Chemistry of MOF Nanocrystals with Confined Pores
| Redox intercalation involves coupled ion-electron motion within host materials, finding extensive application in energy storage, electrocatalysis, sensing, and optoelectronics. While metal-organic frameworks (MOFs) comprise a diverse class of porous electrochemical materials, the intercalation redox chemistry of MOFs remains poorly understood due to the presence of redox sites at the exterior of MOF particles and in the internal pores. Here, we report that Fe(1,2,3-triazolate)2 possesses an intercalation-based redox process shifted ca. 1.2 V from redox at the particle surface. Such distinct chemical environments do not appear in idealized MOF crystal structures but become magnified in MOF nanoparticles. Quartz crystal microbalance and time-of-flight secondary ion mass spectrometry combined with electrochemical studies identify the existence of a distinct and highly reversible Fe2+/Fe3+ redox event occurring within the MOF interior. Systematic manipulation of experimental parameters (e.g., film thickness, electrolyte species, solvent, and reaction temperature) reveals that this feature arises from the nanoconfined (4.54 Å) pores gating the entry of charge-compensating anions. Due to the requirement for full desolvation and reorganization of electrolyte outside the MOF particle, the anion-coupled oxidation of internal Fe2+ sites involves a giant redox entropy change (i.e., 164 J K-1 mol-1). Taken together, this study establishes a microscopic picture of ion intercalation redox chemistry in nanoconfined environments and demonstrates the synthetic possibility of tuning electrode potentials by over a volt, with profound implications for energy capture and storage technologies. | Jiawei Huang; Checkers Marshall; Kasinath Ojha; Meikun Shen; Stephen Golledge; Kentaro Kadota; Jacob McKenzie; Kevin Fabrizio; James Mitchell; Faiqa Khaliq; Carl Brozek | Inorganic Chemistry; Electrochemistry; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638e0faa0a81272d05d47ada/original/giant-redox-entropy-in-the-intercalation-chemistry-of-mof-nanocrystals-with-confined-pores.pdf |
660d17f0418a5379b0f48d77 | 10.26434/chemrxiv-2024-bgpz1 | Site-Selective Electrochemical C–H Silylations of Pyridines Enabled by Temporary Reductive Dearomatization | Site-selective pyridine C–H silylation chemistry is of significant value but remains underdeveloped. In this study, we demonstrated that electron-deficient pyridines are highly selectively reductively silylated at the C4-position under electrochemical reduction conditions. A diverse array of C4-silylated pyridines was synthesized in good-to-excellent yields using common chlorosilanes as activating agents. Additionally, the use of bulky chlorotriisopropylsilane led to the formation of the C5-silylated products, albeit in moderate yields. This method is noteworthy due to its mild reaction conditions, simplicity, and excellent site selectivity for a diverse range of pyridines. Mechanistic studies revealed that the reaction involves temporary dearomatization to yield a 1,4-disilylated compound, which is quickly converted into the final C4-silylated pyridine through hydrolysis and air-driven rearomatization. | Zhihao Yang; Xuan Liu; Tianyuan Zhang; Hirofumi Maekawa; Xin-Qi Hao; Mao-Ping Song | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660d17f0418a5379b0f48d77/original/site-selective-electrochemical-c-h-silylations-of-pyridines-enabled-by-temporary-reductive-dearomatization.pdf |
6565677acf8b3c3cd749091c | 10.26434/chemrxiv-2023-n1qx2 | Correlations in charged multi-pore systems: Implications for enhancing selectivity and permeability in nanoporous membranes | Nanoporous membranes have emerged as powerful tools for diverse applications, including gas separation and water desalination. Achieving high permeability for desired molecules alongside exceptional rejection of other species presents a significant design challenge. One potential strategy involves optimizing the chemistry and geometry of isolated nanopores to enhance permeability and selectivity, while maximizing their density within a membrane. However, the impact of pore proximity on membrane performance remains an open question. Through path sampling simulations of model graphitic membranes with multiple sub-nanometer pores, we reveal that nanoscale proximity between pores detrimentally affects water permeability and salt rejection. Specifically, counter-ion transport is decelerated, while co-ion transport is accelerated, due to direct interactions between water molecules, salt ions, and the dipoles within neighboring pores. Notably, the observed ionic transport timescales significantly deviate from established theories such as the access resistance model, but are well explained using the simple phenomenological model that we develop in this work. We use this model to pre-screen and optimize pore arrangements that elicit minimal correlations at a target pore density. These findings deepen our understanding of multi-pore systems, informing the rational design of nanoporous membranes for enhanced separation processes such as water desalination. They also shed light onto the physiology of biological cells that employ ion channel proteins to modulate ion transport and reversal potentials. | Brian A Shoemaker; Omar Khalifa; Amir Haji-Akbari | Theoretical and Computational Chemistry; Nanoscience; Chemical Engineering and Industrial Chemistry; Nanofluidics; Theory - Computational; Transport Phenomena (Chem. Eng.) | CC BY NC 4.0 | CHEMRXIV | 2023-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6565677acf8b3c3cd749091c/original/correlations-in-charged-multi-pore-systems-implications-for-enhancing-selectivity-and-permeability-in-nanoporous-membranes.pdf |
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