id
stringlengths 24
24
| doi
stringlengths 28
32
| title
stringlengths 8
495
| abstract
stringlengths 17
5.7k
| authors
stringlengths 5
2.65k
| categories
stringlengths 4
700
| license
stringclasses 3
values | origin
stringclasses 1
value | date
stringdate 1970-01-01 00:00:00
2025-03-24 00:00:00
| url
stringlengths 119
367
⌀ |
|---|---|---|---|---|---|---|---|---|---|
66386dbc21291e5d1d8acd92 | 10.26434/chemrxiv-2024-dp30s-v2 | Alignment and Actuation of Liquid Crystals via 3D Confinement and Two-Photon Laser Printing | Liquid crystalline (LC) materials are especially suited for the preparation of active 3D/4D microstructures using two-photon laser printing. To achieve the desired actuation, the alignment of the LCs must be controlled during the printing process. In most cases studied to date, the alignment relied on surface modifications and therefore, complex alignment patterns and concomitant actuation were not possible. Here, we introduce a strategy for spatially aligning LC domains in three-dimensional space by utilizing 3D-printed polydimethylsiloxane-based microscaffolds as confinement barriers, which induce the desired director field. The director field resulting from the boundary conditions is calculated with Landau de Gennes theory and validated by comparing experimentally measured and theoretically predicted birefringence patterns. We demonstrate our procedures for structures of varying complexity and then employed to fabricate 4D microstructures that show the desired actuation. Overall, we obtain excellent agreement between theory and experiment. This opens the door for rational design of functional materials for 4D (micro)printing in the future. | Li-Yun Hsu; Santiago Gomez Melo; Clara Vazquez-Martel; Christoph A. Spiegel; Falko Ziebert; Ulrich S. Schwarz; Eva Blasco | Polymer Science; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66386dbc21291e5d1d8acd92/original/alignment-and-actuation-of-liquid-crystals-via-3d-confinement-and-two-photon-laser-printing.pdf |
60c75271ee301c777ec7abd2 | 10.26434/chemrxiv.13296674.v1 | Planar Hexacoordinate Carbons: Half Covalent Half Ionic | <div>The global minima of thirteen combinations of atoms with formula CE<sub>3</sub>M<sub>3</sub><sup>+</sup> (E=S-Te and M=Li-Cs) adopt a planar structure with carbon covalently bonded to three chalcogens and ionically bonded to the three alkali-metals to stabilize the first global minima structures containing planar hexacoordinate carbon atoms.</div> | luis leyva-parra; Luz Diego; Osvaldo Yañez; Diego Inostroza; jorge barroso; alejandro vásquez-espinal; Gabriel Merino; William Tiznado | Theory - Computational; Clusters; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75271ee301c777ec7abd2/original/planar-hexacoordinate-carbons-half-covalent-half-ionic.pdf |
671ad58a1fb27ce124819f8e | 10.26434/chemrxiv-2024-j88pm | Label-Free Selection of Cancer Cells by Dielectrophoresis and Evaluation of Invasive Potential by Single-Cell Protease Secretion Assay | Enzymatic secretion in single tumor cells plays a pivotal role in cancer progression and metastasis. Matrix metalloproteinase 9 (MMP9) acts as a degradation agent for gelatin and collagen within the extracellular matrix and contributes to invasion and metastasis. Despite this established importance, the heterogeneous nature of enzyme secretion within the tumor microenvironment remains elusive at the single-cell level. Herein, we present an approach to investigate the secretion of MMP9 by individual tumor cells. Dielectrophoresis (DEP) is used to selectively capture individual cells at an array of bipolar electrodes (BPEs) each aligned to an overlying microchamber, which serves as a reaction volume for subsequent assay. The MMP9 activity of isolated cells is then assessed through use of a fluorogenic FRET-based substrate, which displays fluorescence upon cleavage of a peptide by MMP9. The reported workflow allows for the quantification of secretion behavior among cells, the acquisition of temporal secretion profiles, and the identification of highly invasive cells, which are critical for evaluating disease progression and treatment. The DEP-BPE platform's ability to isolate live, label-free cells enhances the potential for functional assays of complex cellular behaviors over time, in contrast to previously reported endpoint measurements on lysed cells. | Benjamin Schelske; Ethan Leung; Joseph Banovetz; Jared Anderson; Robbyn Anand | Analytical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ad58a1fb27ce124819f8e/original/label-free-selection-of-cancer-cells-by-dielectrophoresis-and-evaluation-of-invasive-potential-by-single-cell-protease-secretion-assay.pdf |
64f726583fdae147fa8bd02b | 10.26434/chemrxiv-2023-5b6k2-v2 | Exploiting locality in FCIQMC for fast excitation generation | In this paper we propose an improved excitation generation algorithm for the full configuration interaction quantum monte carlo (FCIQMC) method, which is particularly effective in systems described by localized orbitals. The method is an extension of the precomputed heat-bath (PCHB) strategy of Holmes et al., with more effective sampling of double excitations and a novel approach for non-uniform sampling of single excitations. We demonstrate the effectiveness of the algorithm for a chain of 30 hydrogen atoms with atom-localized orbitals, a stack of benzene molecules, an Fe-porphyrin model complex, whereby we show an overall efficiency gain by a factor of two to four, as measured by variance reduction per wall-clock time. | Oskar Weser; Ali Alavi; Giovanni Li Manni | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY 4.0 | CHEMRXIV | 2023-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f726583fdae147fa8bd02b/original/exploiting-locality-in-fciqmc-for-fast-excitation-generation.pdf |
63c89b2ef604d114815b2cca | 10.26434/chemrxiv-2023-wcpzh | Experimental and Theoretical Insights into Bienzymatic Cascade for Mediatorless Bioelectrochemical Ethanol Oxidation with Alcohol and Aldehyde Dehydrogenases | The efficient utilization of biomass fuels is a critical component of a sustainable energy economy. Via respiration, acetic acid bacteria can oxidize biomass ethanol into acetic acid using membrane-bound alcohol and aldehyde dehydrogenases (ADH and AlDH, respectively). Focusing on the ability of these enzymes to interact directly and electrically with electrode materials, we constructed a mediatorless bioanode for ethanol oxidation based on a direct electron transfer (DET)-type bienzymatic cascade by ADH and AlDH. The three-dimensional structural data of ADH and AlDH elucidated by cryo-electron microscopy were valuable for effectively designing electrode platforms with multi-walled carbon nanotubes (MWCNTs) and pyrene derivatives. DET-type bioelectrocatalysis by ADH and AlDH was improved by using 1-pyrene carboxylic acid-functionalized MWCNT. The catalytic current densities for bienzymatic ethanol oxidation were recorded at the bioanodes modified by various ADH/AlDH ratios. The reaction model was constructed by focusing on the competitive ad-sorption of two enzymes on the electrode surface and the collection efficiency of the intermediately produced acetaldehyde. The power output of an ethanol/air biofuel cell using the bienzymatic bioanode reached 0.48 ± 0.01 mW cm–2, which is the highest value reported for ethanol biofuel cells. In addition, the Faraday efficiency of acetate production by the cell reached 100 ± 4%. This study will lead to efficient conversion of biomass fuels based on a multi-catalytic cascade system. | Taiki Adachi; Tomoko Miyata; Fumiaki Makino; Hideaki Tanaka; Keiichi Namba; Kenji Kano; Keisei Sowa; Yuki Kitazumi; Osamu Shirai | Catalysis; Biocatalysis; Electrocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c89b2ef604d114815b2cca/original/experimental-and-theoretical-insights-into-bienzymatic-cascade-for-mediatorless-bioelectrochemical-ethanol-oxidation-with-alcohol-and-aldehyde-dehydrogenases.pdf |
66a2b14a5101a2ffa80c5f3d | 10.26434/chemrxiv-2024-x6q6d | Tuning the macroligand environment of a solid ruthenium phosphine catalyst for the hydrogenation of CO2 to formate | Advances in the essential direct hydrogenation of CO2 to formic acid are strongly linked to the development of suitable catalytic systems. Here, we have followed the molecular tailoring of macroligands that can be achieved by the crosslinking of aryl phosphine units or of entire transition metal phosphine complexes. Besides the systematic investigation of the reaction parameters, the metal uptake of these macroligands is studied. The versatile crosslinking strategy allows the incorporation of a series of common diphosphines into the frameworks, serving as fixed coordination sites for immobilized ruthenium species. The investigation described here is not restricted to one catalyst, but compares the characteristics and catalytic activities of a wide range of different materials, focusing on their stability over several recycling runs. In particular, catalysts derived from xantphos and BINAP show excellent catalytic performances after a certain induction period. Hence, this study highlights the advantageous properties of rigid bidentate macroligands with spatially close coordination sites for the design of an active and stable solid catalyst in the CO2 hydrogenation to formates. | Arne Nisters; Nils Heim; Marcus Rose | Catalysis; Chemical Engineering and Industrial Chemistry; Heterogeneous Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-07-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66a2b14a5101a2ffa80c5f3d/original/tuning-the-macroligand-environment-of-a-solid-ruthenium-phosphine-catalyst-for-the-hydrogenation-of-co2-to-formate.pdf |
60c744fe9abda2e39ef8c4b8 | 10.26434/chemrxiv.9947249.v1 | Density Driven Correlations in Ensemble Density Functional Theory: Insights from Simple Excitations in Atoms | Ensemble density functional theory extends the usual Kohn-Sham machinery to quantum state ensembles involving ground- and excited states. Recent work by the authors [<i>Phys. Rev. Lett.</i> 119, 243001 (2017); 123, 016401 (2019)] has shown that both the Hartree-exchange and correlation energies can attain unusual features in ensembles. Density-driven (DD) correlations -- which account for the fact that pure-state densities in Kohn-Sham ensembles do not necessarily reproduce those of interacting pure states -- are one such feature. Here we study atoms (specifically S--P and S--S transitions) and show that the magnitude and behaviour of DD correlations can vary greatly with the variation of the orbital angular momentum of the involved states. Such estimations are obtained through an approximation for DD correlations built from relevant exact conditions and plausible assumptions for weakly correlated systems.<br /> | Tim Gould; Stefano Pittalis | Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744fe9abda2e39ef8c4b8/original/density-driven-correlations-in-ensemble-density-functional-theory-insights-from-simple-excitations-in-atoms.pdf |
60c74abc9abda2465ef8ceef | 10.26434/chemrxiv.12249263.v1 | H2 as Fuel for Flavin- and H2O2-Dependent Biocatalytic Reactions | <div>
<p><a>Herein, we report a novel H<sub>2</sub>-driven regeneration system for
reduced flavin cofactors. Using an O<sub>2</sub>-tolerant hydrogenase, we
achieved </a>NAD(P)H-independent, highly
selective, ene-reductase-catalyzed
C=C-double bond reductions, monooxygenase-catalyzed epoxidations and
peroxygenase-catalyzed hydroxylations. The hydrogenase performed up to 46000
catalytic cycles and product titers of up to 22 mM have been accomplished.
Overall, this system bears the promise to power flavin-dependent
biocatalytic reactions with H<sub>2 </sub>in a highly atom efficient manner. </p>
</div> | Ammar Al-Shameri; Sebastian Willot; Caroline Paul; Frank Hollmann; Lars Lauterbach | Biocatalysis; Redox Catalysis | CC BY 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74abc9abda2465ef8ceef/original/h2-as-fuel-for-flavin-and-h2o2-dependent-biocatalytic-reactions.pdf |
63482bce86473a9d5711b191 | 10.26434/chemrxiv-2022-nw6f5-v5 | AIMSim: An Accessible Cheminformatics Platform for Similarity Operations on Chemicals Datasets | The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery applications to assess how new molecules differ from existing ones. Most tools target advanced users and lack general implementations accessible to the larger community. In this work, we introduce Artificial Intelligence Molecular Similarity (AIMSim), an accessible cheminformatics platform for performing similarity operations on collections of molecules called molecular datasets. AIMSim provides a unified platform to perform similarity-based tasks on molecular datasets, such as diversity quantification, outlier and novelty analysis, clustering, dimensionality reduction, and inter-molecular comparisons. AIMSim implements all major binary similarity metrics and molecular fingerprints and is provided as a Python package that includes support for command-line use as well as a fully functional Graphical User Interface for code-free utilization with fully interactive plots. | Himaghna Bhattacharjee; Jackson Burns; Dionisios Vlachos | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-10-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63482bce86473a9d5711b191/original/aim-sim-an-accessible-cheminformatics-platform-for-similarity-operations-on-chemicals-datasets.pdf |
6514b613ade1178b243eafc8 | 10.26434/chemrxiv-2023-d2ffl | Hsp40 Affinity Profiling Reveals Protein Destabilization Profiles Following Cellular Manganese and Vanadate Exposure
| Heavy metals such as arsenic, lead, and cadmium are well-characterized toxicants and heavily regulated in ground and surface waters. However, even metals that are essential nutrients can be hazardous at higher concentrations. These transition metals may be less aggressively regulated due to the perception that they do not pose health risks even in the ppm range. One such metal is manganese, which is highly abundant in many drinking water sources in the United States despite emerging evidence that these metals can pose a threat. Vanadium is more tightly regulated due to its phosphatase inhibition, but also is commonly present in drinking water at > 100 ppb. Herein, we evaluate the effects of 100 M (~5 ppm) manganese (II) and vanadium (V) exposure on cellular proteostasis, using HEK293T cells. We find that cellular manganese exposure destabilizes hundreds of proteins. These include NKRF, a repressor of NF-kB, explaining the known inflammation phenotype associated with manganese exposure. Vanadium, by contrast, stabilizes RNA-binding splicing factors, explaining its known perturbation of RNA splicing. These studies provide evidence that manganese and vanadium can strongly perturb cellular processes, and provide motivation for further study. | Guy Quanrud; Macon Abernathy; Ziqi Lyu; Samantha Ying; Joseph Genereux | Biological and Medicinal Chemistry; Analytical Chemistry; Earth, Space, and Environmental Chemistry; Environmental Science; Chemical Biology | CC BY NC 4.0 | CHEMRXIV | 2023-09-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6514b613ade1178b243eafc8/original/hsp40-affinity-profiling-reveals-protein-destabilization-profiles-following-cellular-manganese-and-vanadate-exposure.pdf |
676e9f59fa469535b9f9748b | 10.26434/chemrxiv-2024-gsprr | Precision labeling of proteins in live cells illustrated by in-cell 19F-NMR spectroscopy | Deciphering protein activity in living cells, especially at atomic resolution, remains a challenge. Nuclear magnetic resonance (NMR) spectroscopy is a unique tool to provide atomic-resolution information of proteins in live cells, but most currently modification methods for proteins are not suitable for in-cell NMR. Here we introduce a new strategy for site-precise labeling of proteins via a reversible Michael addition reaction-triggered neighbor group participation (RAT-NGP), where the NGP reaction stabilizes the reversible Michael addition product. The RAT-NGP labeling shows high performance in precision labeling of two engineered solvent-exposed cysteines without perturbations on the native cysteines in the target proteins. This labeling strategy causes no significant structural perturbations in the target proteins as examined by NMR and CD spectroscopy. In-cell 19F NMR shows that the RAT-NGP labeling method enables site-precise labeling of target proteins in live cells and effectively avoids the over consumption and interference of intracellular glutathione (GSH). | Xun-Cheng Su; Shu-Li Guo; Xing Zhang; Bin Li; Chao-Yu Cui; Mo-Han Li; Bin-Bin Pan; Jia-Long Zhao | Biological and Medicinal Chemistry; Organic Chemistry; Analytical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676e9f59fa469535b9f9748b/original/precision-labeling-of-proteins-in-live-cells-illustrated-by-in-cell-19f-nmr-spectroscopy.pdf |
60c751f3bb8c1ac4423dbdc3 | 10.26434/chemrxiv.13235342.v1 | Kinetics and Pathways of the Aqueous Photolysis of Pharmaceutical Pollutants: A Versatile Laboratory or Remote Learning Investigation | <p>In this laboratory experiment, students explore the aquatic photochemical fate of ranitidine and cimetidine, two common wastewater-derived pharmaceutical pollutants. It provides an engaging environmental context for students to develop knowledge of reaction kinetics and photochemistry, as well as skill using analytical instrumentation. This versatile experiment consists of two basic modules, three optional advanced modules, and additional add-ons that may be performed in various combinations to meet the unique learning objectives of general, analytical, physical, and environmental chemistry courses and science outreach activities. It may be performed as a traditional lab experiment or as an entirely remote exercise with an increased focus on data analysis and interpretation using provided example data sets. All photolysis experiments are carried out by preparing solutions of ranitidine or cimetidine in various matrices, irradiating the samples, and periodically removing subsamples for HPLC analysis of the compound of interest. Pseudo-first-order kinetic plots are then generated to determine rate constants that are used to draw conclusions about photolysis pathways or to calculate additional kinetic parameters. In the two basic modules, cimetidine is found to degrade appreciably only when irradiated in the presence natural organic matter (NOM), indicating an indirect, photosensitized degradation pathway. In contrast, ranitidine degrades in pure buffer and in the presence of NOM with comparable rate constants, highlighting the predominant role of direct photolysis. In the advanced modules, students calculate ranitidine direct photolysis quantum yields and examine the significance of singlet oxygen as a photochemically produced reactive intermediate. The two basic modules may be completed in two three- to five-hour lab periods while the advanced modules require additional time. This experiment requires only a HPLC, inexpensive chemicals, and common glassware and lab equipment if performed in person, and a personal computer if performed remotely.</p> | Jeffrey M. Buth; Rachele Ossola; Sarah
B. Partanen; Kristopher McNeill; William Arnold; Meghan O’Connor; Douglas E. Latch | Chemical Education - General; Environmental Science | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751f3bb8c1ac4423dbdc3/original/kinetics-and-pathways-of-the-aqueous-photolysis-of-pharmaceutical-pollutants-a-versatile-laboratory-or-remote-learning-investigation.pdf |
61a7055680299146acf8eaf5 | 10.26434/chemrxiv-2021-bj35s | Exploration of glassy state in Prussian blue analogues | Prussian blue analogues (PBAs), a class of microporous crystalline coordination frameworks, are long known for their diverse properties in porosity, magnetic, charge transport, catalysis, optics, and more. Versatile structural composition and the ability to control defect ordering through synthetic conditions offer opportunities to manipulate the functionality in the crystalline state. However, developments in Prussian blue analogues (PBAs) have primarily revolved around the ordered crystalline state, and the glassy state of PBAs has not yet been explored. Here we report the discovery of a disordered glassy state of the PBA via mechanically induced crystal–glass transformation. We found the preservation of metal–ligand–metal connectivity, confirming the short-range order and semiconductor behaviour, exhibiting an electronic conductivity value of 0.31 mS cm−1 at 50 ˚C. Mechanical-induced glass transformation also triggers changes in electronic states, where electroneutrality is compensated by introducing unconventional CN− vacancies. Partial disorders and ligand vacancies in recrystallized PBA give rise to an enhanced porosity, inaccessible in the crystalline parent. The present work also established a correlation between the mechanical stress required to initiate crystal–glass transformation and intrinsic mechanical properties, which are controlled by the vacancy/defect content, the presence of interstitial water, and the overall composition of PBAs. | Nattapol Ma; Ryo Ohtani; Hung M. Le; Ryuta Ishikawa; Satoshi Kawata; Sareeya Bureekaew; Soracha Kosasang; Yoshiyuki Kawazoe; Koji Ohara; Satoshi Horike | Inorganic Chemistry; Coordination Chemistry (Inorg.); Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61a7055680299146acf8eaf5/original/exploration-of-glassy-state-in-prussian-blue-analogues.pdf |
60c74e36469df43c6bf44414 | 10.26434/chemrxiv.12724724.v1 | Dynamic Ion Speciation During Hydrolysis of Aryltrifluoroborates | <p>Organotrifluoroborates serve as a coupling partner during
transmetallation in the Suzuki-Miyaura reaction but require hydrolysis prior to
the coupling reaction. Their anionic nature allows study of their hydrolysis by
electrospray ionization mass spectrometry (ESI-MS) by real-time monitoring,
complemented by pH analysis. Induction periods varied according to the borates
employed, and a dynamic series of equilibria for numerous ions was observed
during hydrolysis. We found that the induction periods and reaction rates were
sensitive to the R group of the borates, the shape of reaction vessel, and stir
rate, and that after complete decay of all of the aryltrifluoroborate ion the
solution contained a variety of partially hydrolyzed species.</p> | Isaac Omari; Lars Yunker; Johanne Penafiel; Darlene Gitaari; Atzin San Roman; J Scott McIndoe | Kinetics and Mechanism - Inorganic Reactions; Main Group Chemistry (Inorg.); Reaction (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74e36469df43c6bf44414/original/dynamic-ion-speciation-during-hydrolysis-of-aryltrifluoroborates.pdf |
60c74aafbb8c1ac6613db073 | 10.26434/chemrxiv.11888214.v2 | Towards Personalized Medicine: Photoacoustic Imaging of Glutathione Enables Companion Diagnosis and Targeted Treatment of Lung Cancer | <p>Companion diagnostics (CDx) represent a new frontier in personalized medicine that promises to improve treatment outcomes by matching therapies to patients. Currently, these tests are limited in scope and cannot report on real-time changes associated with disease progression and remediation. To address this, we have developed the first photoacoustic imaging-based CDx (PACDx) for the selective detection of elevated glutathione (GSH) in lung cancer. Since GSH is abundant in most cells, we utilized a physical organic approach to precisely tune the chemical reactivity to distinguish between normal and pathological states. In blinded studies, PACDx was applied to identify mice bearing lung tumors. Moreover, we designed a matching prodrug, PARx, that utilizes the same mechanism to release a chemotherapeutic with a PA readout. We demonstrate that PARx can inhibit tumor growth without off-target toxicity in a lung cancer xenograft model. We envision that this work will establish a new standard for personalized medicine by employing a unique imaging-based approach.<br /></p> | Melissa Lucero; Jefferson Chan | Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aafbb8c1ac6613db073/original/towards-personalized-medicine-photoacoustic-imaging-of-glutathione-enables-companion-diagnosis-and-targeted-treatment-of-lung-cancer.pdf |
639b3e0e16e9a8500f2947cc | 10.26434/chemrxiv-2022-fxnlc | Sustainable Fertilizers: Current Publication Landscape and Challenges | The ability of modern agriculture to meet future food demand imposed by accelerating growth of the world’s population is a major challenge, and fertilizers play a key role by replacing nutrients in agricultural soil. Given the need for fertilizer, its costs in nonrenewable resources and energy, and the consequences of the CO2 emissions required to make it, people have begun to explore ways to make fertilizer manufacture and use more sustainable. Using data from the CAS Content Collection™, this review examines and analyzes the academic and patent literature on sustainable fertilizers from 2001-2021. The breakdown of journal and patent literature publication over time on this topic, country or region of publications, the substances included in published research, among other things, allows us to understand the general progress in the field, as well as the classes of materials and concepts driving innovation. We hope that this bibliometric analysis and literary review will assist researchers in relevant industries to discover and implement ways to supplement conventional fertilizers and nutrient sources while improving the efficiency and sustainability of waste management and ammonia production. | Lisa Babcock-Jackson; Tatyana Konovalova; Jeremy Krogman; Robert Bird; Leilani Lotti Diaz | Earth, Space, and Environmental Chemistry; Agriculture and Food Chemistry; Environmental Science; Soil Science | CC BY 4.0 | CHEMRXIV | 2022-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/639b3e0e16e9a8500f2947cc/original/sustainable-fertilizers-current-publication-landscape-and-challenges.pdf |
60c73db89abda2552ef8b75b | 10.26434/chemrxiv.5807427.v2 | Directed Nickel-Catalyzed 1,2-Dialkylation of Alkenes | A nickel-catalyzed conjunctive cross-coupling of non-conjugated alkenes, alkyl halides, and alkylzinc reagents is reported. Regioselectivity is controlled by chelation of a removable bidentate 8-aminoquinoline directing group. Under optimized conditions, a wide range of 1,2-dialkylated products can be accessed in moderate to excellent yields. To the best of our knowledge, this report represents the first example of three-component 1,2-dialkylation of non-conjugated alkenes to introduce differentiated alkyl fragments. | Joseph Derosa; Vincent A. van der Puyl; Van T. Tran; Mingyu Liu; Keary Engle | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73db89abda2552ef8b75b/original/directed-nickel-catalyzed-1-2-dialkylation-of-alkenes.pdf |
64472667df78ec5015563fa7 | 10.26434/chemrxiv-2023-6g77r | How Effective Are Indicators for Individuals with Colour Vision Deficiency? | Coloured indicators, whether solution or paper based, are often used in laboratory courses and academic/industrial research as a qualitative method to test important experimental markers. While useful, these tools present challenges to those with colour vision deficiency (CVD), who are unable to interpret the same results as their peers. What’s more, some of these tools aren’t as useful in determining important reaction specifics. This commentary presents the perspective of four individuals, three with CVD and one with trichromatic (normal) vision, on how easily coloured indicators are interpreted and how we can address any difficulties in a laboratory setting. | Nicholas J. Roberts; Toren Hynes; Devon Stacey; Jennifer L. MacDonald | Chemical Education | CC BY 4.0 | CHEMRXIV | 2023-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64472667df78ec5015563fa7/original/how-effective-are-indicators-for-individuals-with-colour-vision-deficiency.pdf |
61012013d03b3d1cbd039825 | 10.26434/chemrxiv-2021-lkt60 | Exploring and Expanding the Fe-Terephthalate Metal-Organic Framework Phase Space by Coordination and Oxidation Modulation | The synthesis of phase pure metal-organic frameworks (MOFs) – network solids of metal clusters connected by organic linkers – is often complicated by the possibility of forming multiple diverse phases from one metal-ligand combination. For example, there are at least six Fe-terephthalate MOFs reported to date, with many examples of erroneous assignment of phase based on diffraction data alone. Herein, we show that modulated self-assembly can be used to influence the kinetics of self-assembly of Fe-terephthalate MOFs. We comprehensively assess the effect of addition of both coordinating modulators and pH modulators to the outcome of syntheses, as well as probing the influence of the oxidation state of the Fe precursor (oxidation modulation) and the role of the counteranion on the phase(s) formed. In doing so, we shed light on the thermodynamic landscape of this phase system, uncover mechanistics of modulation, provide robust routes to phase pure materials, often as single crystals, and introduce two new Fe-terephthalate MOFs to an already complex system. The results highlight the potential of modulated self-assembly to bring precision control and new structural diversity to systems that have already received significant study. | Dominic Bara; Emily Meekel; Ignas Pakamorė; Claire Wilson; Sanliang Ling; Ross Forgan | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Solid State Chemistry; Supramolecular Chemistry (Inorg.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61012013d03b3d1cbd039825/original/exploring-and-expanding-the-fe-terephthalate-metal-organic-framework-phase-space-by-coordination-and-oxidation-modulation.pdf |
618c8aeeda15060d229df281 | 10.26434/chemrxiv-2021-8vhcl | 1,2,3-Tri(9-anthryl)benzene. Photophysical Properties and Solid State Intermolecular Interactions of Radially Arranged, Congested Aromatic π-Planes | We report the Negishi coupling based synthesis of 1,2,3-tri(9-anthryl)benzene derivatives, containing three radially arranged anthracenes in a π-cluster. In the crystalline state of the unsubstituted derivative, intermolecular π-π and CH-π interactions between the anthracene units drive the formation of a two-dimensional packing structure. Owing to though-space π-conjugation between anthracene units, the substances have unique electronic properties. The excited state dynamic behavior occurring between the three radially arranged anthracene moieties, such as exciton localization/delocalization, was elucidated by means of transient absorption measurements and quantum chemical calculations. Interestingly, even though the three anthracenes are closely oriented with a ca. 3.0 Å distances between their C-9 positions, exciton localization on two anthracene units is energetically favorable because of the flexible nature of the radially arranged aromatic rings. | Tomohiko Nishiuchi; Hikaru Sotome; Kazuto Shimizu; Hiroshi Miyasaka; Takashi Kubo | Organic Chemistry; Materials Science; Organic Synthesis and Reactions; Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618c8aeeda15060d229df281/original/1-2-3-tri-9-anthryl-benzene-photophysical-properties-and-solid-state-intermolecular-interactions-of-radially-arranged-congested-aromatic-planes.pdf |
6573852729a13c4d4703a0fb | 10.26434/chemrxiv-2023-g72n5 | Cobalt(III) Halide Metal-Organic Frameworks Drive Catalytic Halogen Exchange | The selective halogenation of complex (hetero)aromatic systems is a critical yet challenging transformation relevant to medicinal chemistry, agriculture, and biomedical imaging. However, current methods are limited by toxic reagents, ex-pensive homogeneous second- and third-row transition metal catalysts, and/or poor substrate tolerance. Herein, we demonstrate that porous metal–organic frameworks (MOFs) containing terminal Co(III) halide sites represent a rare and general class of heterogeneous catalysts for the controlled installation of chlorine and fluorine centers into electron-deficient (hetero)aryl bromides using simple metal halide salts. Mechanistic studies support that these halogen exchange (halex) reactions proceed via redox-neutral nucleophilic aromatic substitution (SNAr) at the Co(III) sites. The MOF-based halex catalysts are recyclable, enable scalable halogenation with minimal waste generation, and facilitate halex in contin-uous flow. Our findings represent the first example of SNAr catalysis using MOFs, expanding the lexicon of synthetic trans-formations enabled by these materials. | Tyler Azbell; Phillip Milner | Organic Chemistry; Inorganic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6573852729a13c4d4703a0fb/original/cobalt-iii-halide-metal-organic-frameworks-drive-catalytic-halogen-exchange.pdf |
6392def20fd992e76f3e8573 | 10.26434/chemrxiv-2022-d7kn9 | Scaffold Remodelling of Diazaspirotricycles Enables Synthesis of Diverse sp3-Rich Compounds With Distinct Phenotypic Effects | A ‘top down’ scaffold remodelling approach to library synthesis was applied to spirotricyclic ureas prepared by a complexity-generating oxidative dearomatisation. Eighteen structurally-distinct, sp3-rich scaffolds were accessed from the parent tricycle through ring addition, cleavage and expansion strategies. Biological screening of a small compound library based on these scaffolds using the cell-painting assay demonstrated distinctive phenotypic responses engendered by different library members, illustrating the functional as well as structural diversity of the compounds. | Ephraim Okolo; Axel Pahl; Sonja Sievers; Christopher Pask; Adam Nelson; Stephen Marsden | Biological and Medicinal Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6392def20fd992e76f3e8573/original/scaffold-remodelling-of-diazaspirotricycles-enables-synthesis-of-diverse-sp3-rich-compounds-with-distinct-phenotypic-effects.pdf |
60c753960f50db78c7397bc1 | 10.26434/chemrxiv.13507596.v1 | Revisiting Relaxation Model towards Prediction of Longterm Mechanical Behavior of Semicrystalline Fibers? | <p>Tensile testing is a well-established method to assess the maximum strength of a material, while
relaxation tests are used to evaluate the viscoelastic behaviour of a polymer. Because of slow viscoelastic changes, significant measurement times are required for reliable descriptions. Therefore
the relaxation tests are usually combined with lifetime prediction models to reduce the experimental
load. Various traditional models use the time-temperature superposition principle while modificated
relaxation models are e.g. based on the time-strain superposition principle (TSSP). Both variations
require several measurement series to set up a relaxation master curve (RMC). The basic assumption
is that a higher strain corresponds to a higher temperature and a longer load duration, respectively.
The paper describes a new model approach which allows to predict the longterm behaviour by using
a reduced number of measurements as compared to widely models. The new model is based on the
well-known Maxwell model and assumes a mean relaxation time in combination with a relaxation
coecient. These parameters account for the inhomogeneity of the individual polymer chains. A
dimensionless number, similar to the relaxation coecient, has been successfully introduced for the
Weibull distribution and the particle size distribution. The new model allows to derive master curve
from one measurement series at a single strain by fitting the data to the model equation.<br /></p> | Christina Schippers; Thomas Bahners; Larisa Tsarkova; Jochen
S. Gutmann; Ernst Cleve | Biocompatible Materials; Biodegradable Materials; Fibers; Materials Processing; Polymer blends; Polymer morphology | CC BY NC ND 4.0 | CHEMRXIV | 2021-01-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c753960f50db78c7397bc1/original/revisiting-relaxation-model-towards-prediction-of-longterm-mechanical-behavior-of-semicrystalline-fibers.pdf |
63958949cfb5ff0045669ce0 | 10.26434/chemrxiv-2022-1hnt6-v2 | Near-infrared photon upconversion and solar synthesis using lead-free nanocrystals | Near-infrared to visible photon upconversion holds great promise for a diverse range of applications. Current photosensitizers for triplet-fusion upconversion across this spectral window often contain either precious or toxic elements, and have relatively low efficiencies. Although colloidal nanocrystals have emerged as versatile photosensitizers, the only family of nanocrystals discovered for near-infrared upconversion is the highly-toxic lead chalcogenides. Here we report zinc-doped CuInSe2 nanocrystals as a low-cost and lead-free alternate, allowing for near-infrared to yellow upconversion with an external quantum efficiency reaching 16.7%. When directly merged with photoredox catalysis, this system enables efficient near-infrared-driven organic synthesis and polymerization, which in turn solves the issue of reabsorption loss for nanocrystal-sensitized upconversion. Moreover, the broadband light capturing of these nanocrystals allows for very rapid reactions under indoor sunlight. Extending the reach of "solar synthesis" into the near-infrared may realize the century-long dream of conducting high added-value chemical transformations using sunlight. | Wenfei Liang; Chengming Nie; Jun Du; Yaoyao Han; Guohui Zhao; Fan Yang; Guijie Liang; Kaifeng Wu | Physical Chemistry; Nanoscience; Energy; Nanocatalysis - Catalysts & Materials; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63958949cfb5ff0045669ce0/original/near-infrared-photon-upconversion-and-solar-synthesis-using-lead-free-nanocrystals.pdf |
60c9e3b11fd5333ffc56ac80 | 10.26434/chemrxiv.14779089.v1 | Synthesis of Boroxine and Dioxaborole Covalent Organic Frameworks via Transesterification and Metathesis of Pinacol Boronates | Boroxine and dioxaborole are the first and some
of the most studied synthons of Covalent Organic Frameworks (COFs). Despite
their wide application in the design of functional COFs over the last 15 years,
their synthesis still relies on the original Yaghi’s condensation of boronic
acids (with itself or with polyfunctional catechols), some of which are
difficult to prepare, poorly soluble, or unstable in the presence of water.
Here we propose a new synthetic approach to boroxine COFs (based on
transesterification of pinacol aryl boronates (ArBpin) with methyl boronic acid
(MBA) and dioxaborole COFs (through the metathesis of pinacol boronates with methylboryl-protected
catechols). The ArBpin and MBA-protected catechols are easy to purify, highly
soluble, and bench-stable. Furthermore, kinetic analysis of the two model
reactions reveals high reversibility (Keq~1) and facile control over the
equilibrium. Unlike the conventional condensation which eliminates water by-products,
the by-product of the metathesis (MBA pinacolate) allows for easy kinetic
measurements of the COF formation by conventional <sup>1</sup>H NMR. We show
the generality of this approach by synthesis of seven known boroxine/dioxaborole
COFs whose crystallinity is better or equal to those reported by conventional
condensation. We also apply metathesis polymerization to obtain two new COFs, Py4THB
and B2HHTP, whose synthesis was previously precluded by their insolubility and
hydrolytic instability, respectively, of the boronic acid precursors.<br /> | Ehsan Hamzehpoor; Antranik Jonderian; eric mccalla; Dmitrii F. Perepichka | Physical Organic Chemistry; Solid State Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b11fd5333ffc56ac80/original/synthesis-of-boroxine-and-dioxaborole-covalent-organic-frameworks-via-transesterification-and-metathesis-of-pinacol-boronates.pdf |
60e111c2f7373f5a1544ccc0 | 10.26434/chemrxiv-2021-fr05w | Photo-triggered Aggregation-Induced Emission and Direct Generation of 4D Soft Patterns | The microscopic control of macroscopic phenomena is one of the core subjects in materials science. In particular, the spatio-temporal control of material behaviors through a non-contact way is of fundamental importance but different to accomplish. Herein, a strategy to realize remote spatio-temporal control of luminescence behaviors is reported. A multi-arm salicylaldehyde benzoylhydrazone-based aggregation-induced emission luminogen (AIEgen)/metal ion system was developed of which the fluorescence can be gated by the UV irradiation with time dependency. By changing metal ion species, the fluorescence can also be tuned. The mechanism of the UV-mediated fluorescence change behaivors was investigated and it was revealed that a photo-triggered aggregation-induced emission (PTAIE) process dominates the behaviors. The AIEgen was further covalently integrated into a polymeric network and the formed gel/metal ion system can achieve laser-mediated mask-free writing enabled by the PTAIE process. Moreover, by further taking advantage of the time-dependent self-healing property of hydrazone-based dynamic covalent bond, transformable four- dimensional (4D) soft patterns were generated. The findings and the strategy increase the choice of ways to manipulate molecules on the supramolecule or aggregate level. They also show opportunities for the development of controllable smart materials and expand the scope of the materials in advanced optoelectronic applications. | Huilin Xie; Zhao Li; Junyi Gong; Lianrui Hu; Parvej Alam; Xiaofan Ji; Yubing Hu; Joe, Hon Chung Chau; Jacky, Wing Yip Lam; Ryan, Tsz Kin Kwok; Ben Zhong Tang | Organic Chemistry; Materials Science; Aggregates and Assemblies; Dyes and Chromophores; Optical Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60e111c2f7373f5a1544ccc0/original/photo-triggered-aggregation-induced-emission-and-direct-generation-of-4d-soft-patterns.pdf |
625f8ad8bdc9c2dad4dbe8f8 | 10.26434/chemrxiv-2022-65067 | Unusual water-assisted NO adsorption over Pd/FER calcined at high temperatures: The effect of cation migration | Moisture contained in vehicle exhaust gas normally degrades the capacity and efficiency of Pd ion-exchanged zeolites as NOx adsorbents by competitive adsorption on active sites. Here, we report a counterexample to this general proposition, in which moisture facilitates the storage of NO as a nitrosyl complex on hydrated Pd ions in high temperature calcined FER-type zeolites. The divalent Pd2+ cations upon elevated temperature (>800 °C) calcination occupy sterically constrained cationic position that render them inactive for the adsorption of probe molecules such as NO. These ‘hidden’ Pd ions, however, are accessible by NO when the zeolite is hydrated, but readily release NO at around 200°C as dehydration proceeds. By combining systematic in situ infra-red data with X-ray diffraction Rietveld analyses, we revealed that the high temperature-induced relocation of Pd ions to more stable cationic positions located near 6-membered ring of the ferrierite cage is responsible for this anomalous behavior. This finding constitutes a notable advance in understanding coordination chemistry of cations in zeolites. | Inhak Song; Konstantin Khivantsev; Mark Bowden; Yiqing Wu; Yong Wang; Janos Szanyi | Physical Chemistry; Catalysis; Interfaces; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625f8ad8bdc9c2dad4dbe8f8/original/unusual-water-assisted-no-adsorption-over-pd-fer-calcined-at-high-temperatures-the-effect-of-cation-migration.pdf |
60c746bdbb8c1aa1073da918 | 10.26434/chemrxiv.11374260.v1 | A Low-Cost and Customizable TEER Meter for the Measurements of Cellular Barrier Integrity | <p>A
low-cost and translational TEER (trans-endothelial/epithelial electric
resistance) meter was designed, fabricated, validated, and applied in this
paper. TEER is a critical tool to quantitate the integrity of biological
barriers. Commercially available TEER meters are expensive (thousands of
dollars) with low customization capability. Using Arduino, an open-source
hardware and program that are used to control electronics, we fabricated the
TEER meter that costs ~$50 to purchase the parts and 2 hours to be constructed.
Robust characterization and validation shows that the meter can accurately measure
TEER values between 132 and 82,500 Ω·cm<sup>2</sup> with <3% errors, which
covers the reported TEER ranges based on a literature study we conducted. The
temporal resolution, the measurement duration, and the electrode configurations
of meter are also customizable. We successfully applied the meter to measure
TEERs of endothelial cell monolayers, finding that cells treated with histamine
have lower TEER values compared to untreated cells (793.4 ± 190.5 Ω·cm<sup>2 </sup>vs.
3027.5 ± 664.4 Ω∙cm<sup>2</sup>; p < 0.001), which is consistent with literature
results. We further validated the TEER measurement by showing that histamine
increased the intercellular gap from 2.34 ± 0.12 µm to 5.49 ± 0.17 µm, causing
leakier endothelial barriers and thus lower TEERs. In conclusion, we report for
the first time a low-cost Arduino-based TEER meter capable of accurately measuring
TEERs in the relevant range. We also include detailed tutorials in the supplementary
information to promote the translation of the technology. </p> | Curtis G. Jones; Chengpeng Chen | Analytical Apparatus; Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746bdbb8c1aa1073da918/original/a-low-cost-and-customizable-teer-meter-for-the-measurements-of-cellular-barrier-integrity.pdf |
62b0b9b85983a99577679995 | 10.26434/chemrxiv-2022-j3xfk | Conformal efficiency as a metric for comparative model
assessment befitting federated learning | As training volume increases predictive model quality, leveraging existing external data sources holds the promise of time- and cost-efficiency. In a drug discovery setting, pharmaceutical companies all own substantial but confidential datasets. The MELLODDY project develops a privacy-preserving federated machine learning solution and deploys it at an unprecedented scale (more than 100,000 tasks across ten major pharmaceutical companies), while ensuring the security and privacy of each partner’s sensitive data. Each partner builds models that benefit from a shared representation, for their own private assays. Established predictive performance metrics such as AUC ROC or AUC PR are constrained to unseen labelled chemical space. However, they cannot gauge performance gains in unlabelled chemical space. Federated learning indirectly extends labelled space, but in a privacy-preserving context, a partner cannot use this label extension for performance assessment. Metrics that estimate uncertainty on a prediction can be calculated even where no label is known. Practically, the chemical space covered with predictions of sufficient confidence, reflects the applicability domain of a model. After establishing a link to established performance metrics, we propose the efficiency from the conformal prediction framework (‘conformal efficiency’) as a proxy to the applicability domain size. A documented extension of the applicability domain would qualify as a tangible benefit from federated learning. In interim assessments, MELLODDY partners report a median increase in conformal efficiency of the federated over the single-partner model of 5.5% (with increases up to 9.7%). Subject to distributional conditions, that efficiency increase can be directly interpreted as the expected increase in conformal i.e. high confidence predictions. In conclusion, we present the first evidence that privacy-preserving federated machine learning across massive drug-discovery datasets from ten pharma partners indeed extends the applicability domain of property prediction models. | Wouter Heyndrickx; Adam Arany; Jaak Simm; Anastasia Pentina; Noe Sturm; Lina Humbeck; Lewis Mervin; Adam Zalewski; Martijn Oldenhof; Peter Schmidtke; Lukas Friedrich; Regis Loeb; Arina Afanasyeva; Yves Moreau; Hugo Ceulemans | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b0b9b85983a99577679995/original/conformal-efficiency-as-a-metric-for-comparative-model-assessment-befitting-federated-learning.pdf |
60c73dd7bdbb891bc1a37d2e | 10.26434/chemrxiv.6213950.v1 | Kinetically Guided Radical-Based Synthesis of C(sp3)-C(sp3) Linkages on DNA | <div><div><div><p>DNA-encoded libraries (DEL)-based discovery platforms have recently been widely adopted in pharmaceutical industry, mainly due to its powerful diversity and incredible number of molecules. In the past two decades since its disclosure, great strides have been made to expand the toolbox of reaction modes that are compatible with the idiosyncratic aqueous, dilute, and DNA-sensitive parameters of this system. However, construction of highly important C(sp3)-C(sp3) linkages on DNA through cross-coupling remains unexplored. In this article, we describe a systematic approach to translating standard organic reactions to a DEL-setting through the tactical combination of kinetic analysis and empirical screening with information captured from data mining. To exemplify this model, implementation of the Giese addition to forge high value C–C bonds on DNA was studied, which represents the first radical-based synthesis in DEL.</p></div></div></div> | Jie Wang; Helena Lundberg; Shota Asai; Pedro Martín-Acosta; Jason S. Chen; Stephen Brown; William Farrell; Russell Dushin; Christopher J. O’Donnell; Anohka S. Ratnayake; Paul Richardson; Zhiqing Liu; Tian Qin; Donna G. Blackmond; Phil Baran | Combinatorial Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73dd7bdbb891bc1a37d2e/original/kinetically-guided-radical-based-synthesis-of-c-sp3-c-sp3-linkages-on-dna.pdf |
623cafca202c0665a1dfb6ec | 10.26434/chemrxiv-2022-cg9lb | Strain Release [2p+2s]-Cycloadditions for the Synthesis of [2.1.1]-Bicyclohexanes Initiated by Energy Transfer | Saturated bicycles are becoming ever more important in the design and development of new pharmaceuticals. In this manuscript, a new strategy for the synthesis of [2.1.1]-bicyclohexanes is described. These bicycles are significant as they have defined exit vectors, yet many substitution patterns are underexplored as building blocks. The process involves sensitization of a [1.1.0]-bicyclobutane followed by cycloaddition with an alkene. The scope and mechanistic details of the methods are discussed. | Renyu Guo; Yu-Che Chang; Loic Herter; Christophe Salome; Sarah Braley; Thomas Fessard; Michael Brown | Organic Chemistry; Catalysis; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/623cafca202c0665a1dfb6ec/original/strain-release-2p-2s-cycloadditions-for-the-synthesis-of-2-1-1-bicyclohexanes-initiated-by-energy-transfer.pdf |
66600adc418a5379b01eb880 | 10.26434/chemrxiv-2024-q5zpn | Total Biosynthesis of Cotylenin Diterpene Glycosides | Cotylenins (CNs) are bioactive fungal diterpene glycosides that exhibits stabilizing activity on 14-3-3 protein-protein interactions (PPIs), which has significant therapeutic potential. Despite its importance, the biosynthetic pathway of CNs have remained unclear. Here, we report the identification of the biosynthetic gene cluster and elucidation of the biosynthetic pathway of CNs. Our investigation reveals the roles of glycosyltransferase, methyltransferase, and prenyltransferase enzymes in the assemble and modification of the glycoside moiety, as well as the multifunctional oxidation activity of the P450 enzyme CtyA. We also demonstrate the synthesis of an active unnatural CN derivative through combinatorial biosynthesis, showcasing the potential of pathway enzymes as catalytic tools to expand the structural diversity of the diterpene glycosides. Additionally, we highlight the stabilization effects of pathway intermediates on 14-3-3 PPIs, providing insights into the evolutionary optimization of bioactivity within the biosynthetic pathway. These findings pave the way for future efforts to achieve the production Cotylenin A and related compounds with enhanced bioactivity through synthetic biology or semisynthesis. | Zhenhua Guan; Nanyu Yao; Wenling Yuan; Fengli Li; Yang Xiao; Mewlude Rehmutulla; Chunmei Chen; Hucheng Zhu; Yuan Zhou; Qingyi Tong; Zheng Xiang; Ying Ye; Yonghui Zhang | Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Natural Products; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66600adc418a5379b01eb880/original/total-biosynthesis-of-cotylenin-diterpene-glycosides.pdf |
60c74530469df45164f4346f | 10.26434/chemrxiv.9807770.v2 | Changing the Static and Dynamic Lattice Effects for the Improvement of the Ionic Transport Properties Within the Argyrodite Li6PS5-xSexI | <p>The lithium argyrodites Li<sub>6</sub>PS<sub>5</sub>X (X = Cl, Br, I) have been gaining momentum as candidates for electrolytes in all-solid-state batteries. While these materials have been well-characterized structurally, the influences of the static and dynamic lattice properties are not fully understood. Recent improvements to the ionic conductivity of Li<sub>6</sub>PS<sub>5</sub>I (which as a parent compound is a poor ionic conductor) via elemental substitutions have shown that a multitude of influences affect the ionic transport in the lithium argyrodites, and that even poor conductors in this class have room left for improvement.</p><p>Here we explore the influence of isoelectronic substitution of sulfur with selenium in Li<sub>6</sub>PS<sub>5-<i>x</i></sub>Se<i><sub>x</sub></i>I. Using a combination of X-ray diffraction, impedance spectroscopy, Raman spectroscopy, and pulse-echo speed of sound measurements,we explore the influence of the static and dynamic lattice on the ionic transport. The substitution of S<sup>2-</sup>with Se<sup>2- </sup>broadens the diffusion pathways and structural bottlenecks, as well as leading to a softer more polarizable lattice, all of which lower the activation barrier and lead to an increase in the ionic conductivity. This work sheds light on ways to systematically understand and improve the functional properties of this exciting material family. </p> | Roman Schlem; Michael Ghidiu; Sean Culver; Anna-Lena Hansen; Wolfgang Zeier | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74530469df45164f4346f/original/changing-the-static-and-dynamic-lattice-effects-for-the-improvement-of-the-ionic-transport-properties-within-the-argyrodite-li6ps5-x-sex-i.pdf |
629a55d8a6101beab9da6648 | 10.26434/chemrxiv-2022-f72w5 | A Modified Electrostatic Complementary Score Function and Its Application Boundary Exploration in Drug Design | In recent years, machine learning (ML) models have been found to quickly predict various molecular properties with accuracy comparable to high level quantum chemistry methods. One such example is the calculation of electrostatic potential (ESP). Different ESP prediction ML models were proposed to generate surface molecular charge distribution. Electrostatic complementarity (EC) can quantitatively apply ESP data to scale the complementarity between a ligand and its binding pocket, leading to the potential to increase efficiency of drug design. However, there is not much research discussing EC score functions and its application boundary. We propose a new EC score function modified from the one originally developed by Bauer and Mackey, and confirmed its effectiveness against the available Pearson’s R correlation coefficient. Additionally, the application boundary of the EC score and two indices used to define the EC score application scope will be discussed.
| Liming Zhao; Huting Wang; yingsheng zhang | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-06-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629a55d8a6101beab9da6648/original/a-modified-electrostatic-complementary-score-function-and-its-application-boundary-exploration-in-drug-design.pdf |
60c74f689abda22686f8d846 | 10.26434/chemrxiv.12896501.v1 | Nano-3D-printed Photochromic Objects | A new class of photoresist is described for direct laser writing of photoswitchable 3D microstructures. The material comprising off-stoichiometric thiol-ene photo-clickable resins enables rapid two-photon laser processing of highly complex structures and facile post-modification with photoswitches. The microstructures were functionalized with a series of donor-acceptor Stenhouse adducts (DASAs) photoswitches with different excitation wavelength. The versatility of thiol–ene photo-click reaction enabled fine-tuning of the network structure and physical properties as well as the type and concentration of DASA photoswitches. When exposed to visible light, these microstructures exhibit excellent photo-responsiveness and undergo reversible color-changing via photoisomerization of DASA moieties. We describe that the weak fluorescence of DASAs can be used as a reporter of photoswitching, color changes, and thermal recovery, allowing the reading of DASA-containing sub-micrometric structures in 3D. This work delivers a new approach for custom microfabrication of 3D photochromic objects with molecularly engineered color and responsiveness. | Sebastian Ulrich; Xiaopu Wang; Markus Rottmar; René M. Rossi; Bradley
J. Nelson; Nico Bruns; Ralph Müller; Katharina Maniura-Weber; Xiao-Hua Qin; Luciano F. Boesel | Dyes and Chromophores; Materials Processing; Polymerization (Polymers) | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74f689abda22686f8d846/original/nano-3d-printed-photochromic-objects.pdf |
66e3d71a51558a15efd836f2 | 10.26434/chemrxiv-2024-hpbl9 | Atomic-Resolution Cinematography of Catalytic Intermediates over a Single-Site Heterogeneous Catalyst | Heterogeneous catalysts dominate the chemical industry but typically feature diverse, incompletely defined active sites. Thus, describing structure-activity relationships, unlike homogeneous catalysts, remains challenging. In contrast, molecularly defined single-site heterogeneous catalysts (SSHCs), using appropriate tools, are poised to address these challenges and provide new avenues for catalysis research and development. The present study explores eco-friendly H2 production mediated by discrete MO2 sites supported on carbon nanohorns (CNHs) and active for alcohol dehydrogenation. While informative, detailed ensemble EXAFS/XANES, XPS, kinetic measurements, and DFT analysis alone cannot provide a full molecular picture of the reaction pathway. Here, using single-molecule atomic-resolution time-resolved electron microscopy (SMART-EM), we identify four key catalytic intermediates anchored to the CNHs and uncover a new reaction pathway involving alkoxide/hemiacetal equilibration and acetal oligomerization. These intermediates are identified solely by theory and SMART-EM, and this advance highlights the potential of SMART-EM to establish and verify mechanistic hypotheses in catalysis. | Yosi Kratish; Yiqi Liu; Jiaqi Li; Anusheela Das; Leighton O. Jones; Amol Agarwal; Qing Ma; Michael J. Bedzyk; George C. Schatz; Takayuki Nakamuro; Eiichi Nakamura; Tobin J. Marks | Organic Chemistry; Catalysis; Organometallic Chemistry; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e3d71a51558a15efd836f2/original/atomic-resolution-cinematography-of-catalytic-intermediates-over-a-single-site-heterogeneous-catalyst.pdf |
648b8992e64f843f41d74785 | 10.26434/chemrxiv-2023-md5bq | Hybrid Vesicles Enable Mechano-Responsive Hydrogel Degradation | Stimuli-responsive hydrogels are intriguing biomimetic materials. Previous efforts to develop mechano-responsive hydrogels have mostly relied on chemical modifications of the hydrogel structures. Here, we present a simple, generalizable strategy that confers mechano-responsive behavior on hydrogels. Our approach involves embedding hybrid vesicles, composed of phospholipids and amphiphilic block copolymers, within the hydrogel matrix to act as signal transducers. Under mechanical stress, these vesicles undergo deformation and rupture, releasing encapsulated compounds that can control the hydrogel network. To demonstrate this concept, we embedded vesicles containing ethylene glycol tetraacetic acid (EGTA), a calcium chelator, into a calcium-crosslinked alginate hydrogel. When compressed, the released EGTA sequesters calcium ions and degrades the hydrogel. This study provides a novel method for engineering mechano-responsive hydrogels that may be useful in various biomedical applications. | Sung-Won Hwang; Chung-Man Lim; Cong Truc Huynh; Hossein Moghimianavval; Nicholas A. Kotov; Eben Alsberg; Allen P. Liu | Materials Science; Biocompatible Materials; Controlled-Release Systems | CC BY 4.0 | CHEMRXIV | 2023-06-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648b8992e64f843f41d74785/original/hybrid-vesicles-enable-mechano-responsive-hydrogel-degradation.pdf |
60c755d59abda22ee7f8e446 | 10.26434/chemrxiv.14171249.v1 | Peroxidase-Mimicking Nanozyme with Surface-Dispersed Pt Atoms as the Label for the Lateral Flow Immunoassay of C-Reactive Protein | We report a new approach to synthesize nanozyme with low consumption of precious Pt-precursor and high peroxidase-mimicking activity. The synthesis includes the formation of gold nanoparticles (Au NPs), the overgrowth of a silver layer over Au NPs (Au@Ag NPs), and the galvanic replacement of Ag with PtCl<sub>6</sub><sup>2-</sup> leading to the formation of Au@Ag–Pt NPs with uniformly deposited catalytic Pt sites. The reported approach facilitates up to 20-times lower consumption of Pt precursor. The use of Au@Ag-Pt NPs as the catalytic label in lateral flow immunoassay results in a 65-fold lower limit of detection (15 pg/mL in serum). | Vasily Panferov; Nadezhda
A. Byzova; Anatoly V. Zherdev; Boris B. Dzantiev | Core-Shell Materials; Nanostructured Materials - Materials; Biochemical Analysis; Nanocatalysis - Catalysts & Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755d59abda22ee7f8e446/original/peroxidase-mimicking-nanozyme-with-surface-dispersed-pt-atoms-as-the-label-for-the-lateral-flow-immunoassay-of-c-reactive-protein.pdf |
63376bc52984c98420731c28 | 10.26434/chemrxiv-2022-w6s0g | Self-Driving Laboratories: A Paradigm Shift in Nanomedicine Development | Nanomedicines have transformed promising therapeutic agents into clinically approved medicines with optimal safety and efficacy profiles. This is exemplified by the mRNA vaccines against COVID-19, which were made possible by lipid nanoparticle technology. Despite the success of nanomedicines to date, their design remains far from trivial in part due to the complexity associated with their preclinical development. Herein we propose a nanomedicine materials acceleration platform (NanoMAP) to streamline the preclinical development of these formulations. NanoMAP combines high-throughput experimentation with state-of-the-art advances in artificial intelligence (including active learning and few-shot learning) as well as a web-based application for data sharing. The deployment of NanoMAP requires interdisciplinary collaboration between leading figures in drug delivery and artificial intelligence to enable this data-driven design approach. The proposed approach will not only expedite the development of next generation nanomedicines, but also encourage participation of the pharmaceutical science community in a large data curation initiative.
| Riley Hickman; Pauric Bannigan; Zeqing Bao; Alán Aspuru-Guzik; Christine Allen | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Nanoscience; Bioengineering and Biotechnology; Drug Discovery and Drug Delivery Systems; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63376bc52984c98420731c28/original/self-driving-laboratories-a-paradigm-shift-in-nanomedicine-development.pdf |
67913b366dde43c908d63f49 | 10.26434/chemrxiv-2025-8fv73 | Nanotetrapods Promote Polymer Flow Through Confinement Induced Packing Frustration | Processing ultra-high molecular weight polymers presents significant experimental challenges due to their high viscosity, which requires elevated shear rates and consequently increases energy demands. Here, we explored the role of the geometry of nanoparticles – spheres, rods, and tetrapods – in controlling the effective viscosity of polymer nanocomposites. Intriguingly, our combined experiments and molecular dynamics simulations reveal a significant decrease in the viscosity of composites with tetrapod nanoparticles, without compromising mechanical or thermal integrity. On the other hand, the composites with spherical particles and rods exhibit an increase in its viscosity at the same level of loading. We show that the inner curvatures of the tetrapods impose strong physical confinement introducing an entropic cost for polymers to access this space. The inaccessible volume creates polymer packing frustration around tetrapod surfaces, which, in turn, increases their mobility and decreases the overall viscosity of the composite. Nanotetrapods prove to be effective flow promoters while preserving good dispersion within a polymer melt, offering significant potential for advanced polymer processing applications. | Jotypriya Sarkar; Sachin M B Gautham; Fariyad Ali; Mithun Madhusudanan; Harshit Yadav; Anindya Datta; Tarak K Patra; Sivasurender Chandran; Mithun Chowdhury | Physical Chemistry; Materials Science; Polymer Science | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67913b366dde43c908d63f49/original/nanotetrapods-promote-polymer-flow-through-confinement-induced-packing-frustration.pdf |
640936e06642bf8c8f32dcc4 | 10.26434/chemrxiv-2023-z0mqc-v2 | Carbohydrate-DNA Conjugation Enabled by Glycosyl Radicals Generated from Glycosyl Sulfinates
| Herein, we report a method that enables the synthesis of carbohydrate-DNA conjugates by radical addition, in which the gen-eration of glycosyl radicals from readily available and bench-stable unprotected glycosyl sulfinates is the key. These reactions were carried out under mild conditions and tolerate a broad substrate scope. | Hongxin Zeng; Yanjing Li; Yang Zhang; Shi-Yang Xu; Yingwei Wang; Dawen Niu | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640936e06642bf8c8f32dcc4/original/carbohydrate-dna-conjugation-enabled-by-glycosyl-radicals-generated-from-glycosyl-sulfinates.pdf |
6319dfe1173b5d5118f5dd65 | 10.26434/chemrxiv-2022-msgf8 | Systems Chemistry across Multiple Length Scales: Macroscopic Flow via Dissipative Co-Assemblies Featuring Transient Amides | Fueled chemical systems have considerable functional potential that is still largely unexplored. Here, we report a new approach to transient amide bond formation and use it to harness chemical energy and convert it to mechanical motion by integrating dissipative self-assembly and the Marangoni effect in a source-sink system. Droplets are formed through dissipative self-assembly following the reaction of octylamine with 2,3-dimethylmaleic anhydride. The resulting amides are hydrolytically labile making the droplets transient, which allows them to act as a source of octylamine. A sink for octylamine was created by placing a drop of oleic acid on the air-water interface. This source – sink system sets up a gradient in surface tension, which gives rise to a macroscopic Marangoni flow that can transport the droplets in solution with tunable speed. Carbodiimides can fuel this motion by converting diacid waste back to anhydride. This study shows how fueling at the molecular level can, via assembly at the supramolecular level, lead to liquid flow at the macroscopic level. | Kai Liu; Alex W. P. Blokhuis; Sietse J. Dijt; Shana Hamed; Armin Kiani; Bartosz M. Matysiak; Sijbren Otto | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6319dfe1173b5d5118f5dd65/original/systems-chemistry-across-multiple-length-scales-macroscopic-flow-via-dissipative-co-assemblies-featuring-transient-amides.pdf |
63cace53ae221a0b16373681 | 10.26434/chemrxiv-2023-t4mxc | Solar driven in-air plasma discharge for effective activation of water flow through self-suction mechanism | Plasma activated water(PAW) is water that is treated with cold plasma discharge. The dissolved reactive oxygen and nitrogen species in PAW are desirable for wastewater treatment, environment remediation, food processing and storage, enhanced plant growth in agriculture and many other applications. In this work, we develop microbubble-enhanced PAW production through a self-suction mechanism. Microbubbles form under the strong turbulence effect at the throat of a cavitation tube, transferring active species into a stream of water. As demonstrated by degradation rate of sulfathiazole, a model antibiotic compound in water, the main parameters identified from our experiments to be essential for the activation efficiency are the design of the cavitation tube, the flow rate of the water stream, and the distance from the discharge to the flow. Our three-dimensional numerical simulations reveal the impact of the tube dimensions on the multiphase flow characteristics. The simplicity of self-suction mechanism allowed us to set up a solar-driven, stand-alone cold plasma system to generate PAW outdoor. The as-prepared PAW can boost the growth rate of bean and peanut sprouts in hydroponics about 80% and 66%, respectively. The portable PAW production may open the door to even broader applications of field activated water for applications in sustainable agriculture and in environment remediation. | Yawen Gao; Hongbo Shi; Ziya Saedi; Binglin Zeng; Xuehua Zhang | Chemical Engineering and Industrial Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63cace53ae221a0b16373681/original/solar-driven-in-air-plasma-discharge-for-effective-activation-of-water-flow-through-self-suction-mechanism.pdf |
6794ffd281d2151a02f12662 | 10.26434/chemrxiv-2025-cdf0h | Nucleation rate and Gibbs free energy of nucleation of APIs in solution at different cooling rates | A new mathematical model that relies on the classical nucleation theory is proposed to predict the nucleation rate, nucleation rate kinetic constant and the Gibbs free energy of nucleation from the MSZW measured as a function of solubility temperatures. The model allows to calculate the nucleation rate at different cooling rates. The model seems to be universal as it well predicts the experimental data of 16 different combination of APIs and solvents that involves 10 APIs. According to the proposed model, the nucleation rate was found to be in the range of 1020 to 1024 molecules/m3s and the Gibbs free energy of nucleation was found to be in the range of 8 – 62 kJ/mol. The proposed model is also used to obtain the induction time based on MSZW obtained at different cooling rate. The proposed model is further exploited to obtain the thermodynamic parameters that includes the surface free energy, size of the critical nucleus and the number of unit cells that constitute the critical nucleus. | Mayank Vashishtha; Vasanth Kumar Kannuchamy | Physical Chemistry; Materials Science; Chemical Engineering and Industrial Chemistry; Pharmaceutical Industry; Crystallography | CC BY 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6794ffd281d2151a02f12662/original/nucleation-rate-and-gibbs-free-energy-of-nucleation-of-ap-is-in-solution-at-different-cooling-rates.pdf |
65f8225b9138d23161b25862 | 10.26434/chemrxiv-2024-wmmr7 | Silylium Ion-Catalyzed α-Arylation of Carboxylic Acids, Amides, and Esters: Efficient Synthesis of Anesthetic and Anti-inflammatory Drugs | A metal-free strategy has been developed for the α-arylation of carboxylic acids, secondary amides, and esters employing arenes as key reagents. This process entails the Lewis-acid catalyzed reductive Friedel–Crafts alkylation of aromatic and heterocyclic arenes with α-ketoacids, facilitated by silane as a reductant in HFIP solvent. The transformation is highly efficient and mild, providing significant advantages over existing protocols. Notably, the method exhibits exceptional tolerance towards various functional groups, enabling late-stage functionalization of pharmaceutical compounds and natural products such as Thymol, and Sesamol. The reaction mechanism has been studied through control experiments, providing valuable insight. This one-step reductive Friedel–Crafts type protocol has been successfully used in the synthesis of various commercially available drugs, such as Adiphenine, Piperidolate, derivatives of Ketoprofen, Ibuprofen, and Flurbiprofen, and Bromopropylate pesticide. Furthermore, after the gram-scale synthesis, the solvent (HFIP) was recovered, demonstrating the method's suitability for industrial applications. | Jabir Khan; Aparna Tyagi; chinmoy Kumar hazra | Organic Chemistry; Catalysis; Acid Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65f8225b9138d23161b25862/original/silylium-ion-catalyzed-arylation-of-carboxylic-acids-amides-and-esters-efficient-synthesis-of-anesthetic-and-anti-inflammatory-drugs.pdf |
60c7403d337d6c6807e26684 | 10.26434/chemrxiv.7670903.v1 | Accelerated Discovery of High-Refractive-Index Polyimides via First-Principles Molecular Modeling, Virtual High-Throughput Screening, and Data Mining | <div>We present a high-throughput computational study to identify novel polyimides (PIs) with exceptional refractive index (RI) values for use as optic or optoelectronic materials. Our study utilizes an RI prediction protocol based on a combination of first-principles and data modeling developed in previous work, which we employ on a large-scale PI candidate library generated with the ChemLG code. We deploy the virtual screening software ChemHTPS to automate the assessment of this extensive pool of PI structures in order to determine the performance potential of each candidate. This rapid and efficient approach yields a number of highly promising leads compounds. Using the data mining and machine learning program package ChemML, we analyze the top candidates with respect to prevalent structural features and feature combinations that distinguish them from less promising ones. In particular, we explore the utility of various strategies that introduce highly polarizable moieties into the PI backbone to increase its RI yield. The derived insights provide a foundation for rational and targeted design that goes beyond traditional trial-and-error searches.</div> | Mohammad Atif Faiz Afzal; Mojtaba Haghighatlari; Sai Prasad Ganesh; Chong Cheng; Johannes Hachmann | Oligomers; Optical Materials; Organic Polymers; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7403d337d6c6807e26684/original/accelerated-discovery-of-high-refractive-index-polyimides-via-first-principles-molecular-modeling-virtual-high-throughput-screening-and-data-mining.pdf |
60c74b559abda20118f8d021 | 10.26434/chemrxiv.12320273.v1 | Computational Screening of Phytochemicals from Medicinal plants as COVID-19 Inhibitors | <p>In this research a dataset of plant
based bioactive compound was developed. A total of 101 phytochemicals were selected,
virtually designed and its binding affinity with ACE enzyme was studied by
molecular docking. Human ACE related carboxypeptidase and complex (PDB ID: 1R42)
and (PDB ID: 6CS2) were selected for molecular docking studies as corona virus
binds to ACE2 to enter into the host cell. Docking score results revealed that almost
all selected phytochemicals binds to the pocket of the human ACE protein with
high binding affinity and the scores were compared with chloroquine and
hydroxychloroquine. The drug likeliness and ADMET analysis of all the screened
compounds were performed. Two potential compound 6-α-acetoxygedunin
and echitamine exhibited optimum binding with both the receptor.These
phytochemicals can serve as lead molecule for further optimization and drug
development against COVID-19. Therefore, it is predicted that the insights in
the present study could be regarded valuable towards development of natural
inhibitor of this virus.</p> | Alisha Khandelwal; Tripti Sharma | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b559abda20118f8d021/original/computational-screening-of-phytochemicals-from-medicinal-plants-as-covid-19-inhibitors.pdf |
676411df6dde43c9089de248 | 10.26434/chemrxiv-2024-6zg7f | Stereoselective Suzuki Reactions by
Overcoming Rh-Catalyst Memory Effects | Chiral non-racemic allylic species are key building blocks in the synthesis of a wide range of important
carbon-containing molecules, including pharmaceuticals and polymers. Metal-catalyzed asymmetric
additions of nucleophiles to allylic species undergo different reaction pathways depending on the
combination of metal and nucleophile used, which has hindered the development of broadly useful
addition reactions with aromatic nucleophiles. Here, we report an asymmetric cross-coupling method
between aryl boronic acids and linear allylic phosphates to give branched allylic products. This Suzukitype reaction overcomes the ‘memory effect’ in Rh-catalysis to allow an overall SN2’ transformation by
rate-determining reductive elimination and forms a new stereogenic centre adjacent to a terminal vinyl
moiety. The method tolerates pre-existing stereogenic centres allowing the development of synthetic
strategies where drugs and natural products are elaborated via diastereoselective allylic arylations. The
method is used, as the catalyst-controlled stereochemistry-setting step, in an iterative synthetic strategy
to give arrays of aryl substituted contiguous stereogenic centres, and we anticipate this approach will be
a useful compliment to existing catalyst controlled stereoselective methods for forming C-C bonds.
| Ke Liu; David Egea-Arrebola; Ruchuta Ardkhean; Laura Cunningham; Kirsten Christensen; Robert Paton; Stephen Fletcher | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Stereochemistry; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676411df6dde43c9089de248/original/stereoselective-suzuki-reactions-by-overcoming-rh-catalyst-memory-effects.pdf |
60c7596d702a9b0cf018cebc | 10.26434/chemrxiv.14692407.v1 | Analytical Gradients for Core-Excited States in the Algebraic Diagrammatic Construction (ADC) Framework | Here we present a derivation of the analytical expressions required to determine nuclear gradients for core-excited states at the core-valence separated algebraic diagrammatic construction (CVS-ADC) theory level. Analytical gradients up to and including the extended CVS-ADC(2)-x order have been derived and implemented into a Python module, adc_gradient. The gradients were used to determine core-excited state optimized geometries and relaxed potential energy surfaces for the water, formic acid, and benzne molecules. <br /> | Iulia Emilia Brumboiu; Dirk R. Rehn; Andreas Dreuw; Young Min Rhee; Patrick Norman | Computational Chemistry and Modeling; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7596d702a9b0cf018cebc/original/analytical-gradients-for-core-excited-states-in-the-algebraic-diagrammatic-construction-adc-framework.pdf |
659fc0279138d23161ac1121 | 10.26434/chemrxiv-2024-npb74 | Scalable and low-energy decoupled electrochemical CO2 capture | Electrochemical CO2 capture with renewable electricity provides a promising avenue for efficient decarbonization but faces challenges by instability, discontinuity, high energy consumption, and difficulties in scale-up. Here, we first propose a scalable electrochemical CO2 capture strategy by separating the traditional single electrochemical redox reaction process into a stepwise electrochemical-chemical redox reaction process. Hydrogen evolution reaction and redox carrier oxidation reaction swings the pH of electrolyte at the cathode and anode to capture CO2 efficiently which avoids side effects through decoupling of electrochemical-swing for CO2 capture and redox carrier regeneration in different times and spatial domains. We demonstrate a stable electrochemical CO2 capture process over 200 hours with low energy consumption (49.15 kJ mol-1 CO2 at 10 mA cm-2). Furthermore, the system is tunable and modular. Molecular design can be used to tailor the potential and allow scalability across various process sizes, making it a promising strategy for large-scale decarbonization. | Tao Liu; Yifan Wu; Yunpeng Wang; Wenchuan Jiang; Yuchao Deng; Qing Li; Cheng Lan; Zhiyu Zhao; Liangyu Zhu; Dongsheng Yang; Heping Xie | Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-01-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/659fc0279138d23161ac1121/original/scalable-and-low-energy-decoupled-electrochemical-co2-capture.pdf |
665e0020418a5379b001966b | 10.26434/chemrxiv-2023-rn9bj-v2 | Efficient Method for Achieving Electronic Coupling in TEMPO/TEMPO+ System | This research elucidates the intricate nature of electronic coupling in the redox- active (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO), commonly utilized in organic radical batteries (ORBs). The study employs a combination of classical molecular dynamics (MD) and various electronic coupling calculation schemes. Within the con- text of the generalized Mulliken-Hush (GMH) method, the electronic couplings are investigated via the complete active space self-consistent field (CASSCF) approach, in combination with n-eletron valence state perturbation theory (NEVPT2), to provide an accurate description of both static and dynamic electron correlation as well as using (time-dependent) density functional theory (TD–DFT) simulations. Furthermore, the electronic communication between redox-active sites is studied using the cost-efficient DFT–based frontier molecular orbital (FMO) approach. Our study reveals the de- pendence of the electronic coupling on the distance and the relative orientation of the redox pairs (TEMPO and TEMPO+ ). Apart from the expected exponential dis- tance dependence, we found a pronounced orientation dependence with coupling values varying up to 0.2 eV, especially at short distances. Our findings underline the signifi- cance of including dynamic correlation in the electronic coupling method, which, unlike CASSCF method, can be included via TDDFT–based GMH methods. Additionally, our study highlights the limitations of the DFT–based FMO method, in particular at short intermolecular distances between the redox-active sites which may lead to a mixing of the involved molecular orbitals. This comparison will provide us with the most cost–accuracy–effective method for calculating coupling in TEMPO–TEMPO+ systems. | Souvik Mitra; Clara Zens; Stephan Kupfer; Diddo Diddens | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/665e0020418a5379b001966b/original/efficient-method-for-achieving-electronic-coupling-in-tempo-tempo-system.pdf |
63a1d65e81e4bad3e2546f38 | 10.26434/chemrxiv-2022-rtzcx | Valorization of Kraft Lignin by mechanochemical processing with sodium percarbonate | Lignin is a highly underused resource. The complex and heterogeneous structure poses a challenge to industry and science. Problems are high polydispersity, high-molar-mass and insufficient functional groups. In this article, we present a mechanochemical one-pot reaction that depolymerises high-molecular-mass fractions by environmentally friendly hydrogen peroxide oxidation and introduces new carbonyl functionalities into the lignin framework. First, kraft lignin was ground using sodium percarbonate (SPC) and sodium hydroxide (NaOH) in a ball mill at different time intervals. After acidic work-up, the samples were analysed by infrared spectroscopy (IR), size exclusion chromatography (SEC), dynamic vapour sorption (DVS), and small angle X-ray scattering (SAXS). Already after 5 minutes, a reduction from the mass average molecular weight (Mw) of 47% and an increased carbonyl absorption by a factor of 2 can be observed. DVS data show a ~2.8-fold increase in water adsorption and provide information about the adsorption mechanism caused by the chemical modification. SAXS data show that there is no significant surface area increase of the lignin particles when additives are used, supporting the hypothesis that the increased adsorption performance is caused by chemical modification. A principal component analysis (PCA) gives additional insight into the IR spectra and SAXS parameter correlations. Refining of industrial lignin to produce homogeneous fractions with enhanced surface properties is essential for high-value applications | Friedrich Fink; Tomasz Stawski; Franziska Emmerling; Jana Falkenhagen | Analytical Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a1d65e81e4bad3e2546f38/original/valorization-of-kraft-lignin-by-mechanochemical-processing-with-sodium-percarbonate.pdf |
642be9c7a029a26b4ce3d48c | 10.26434/chemrxiv-2022-qxq56-v4 | Explaining compound activity predictions with
a substructure-aware loss for graph neural
networks | Explainable machine learning is increasingly used in drug discovery to help rationalize compound property predictions. Feature attribution techniques are popular choices to identify which molecular substructures are responsible for a predicted property change. However, established molecular feature attribution methods have so far displayed low performance for popular deep learning algorithms such as graph neural networks (GNNs), especially when compared with simpler modeling alternatives such as random forests coupled with atom masking. To mitigate this problem, in this work a modification of the regression objective for GNNs is proposed to specifically account for common core structures between pairs of molecules. The presented approach showed higher accuracy on a recently-proposed explainability benchmark. This methodology has the potential to assist with model explainability in drug discovery pipelines, particularly in lead optimization efforts where specific chemical series are investigated. | Kenza Amara; Raquel Rodriguez-Perez; José Jiménez Luna | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-04-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/642be9c7a029a26b4ce3d48c/original/explaining-compound-activity-predictions-with-a-substructure-aware-loss-for-graph-neural-networks.pdf |
60c74605702a9b756a18ab31 | 10.26434/chemrxiv.10320752.v1 | Can Metal Organic Frameworks Outperform Adsorptive Removal of Harmful Phenolic Compound 2-Chlorophenol by Activated Carbon? | <b>Abstract:</b> Removal of persistent organic compounds from aqueous solutions is generally achieved using adsorbent like activated carbon (AC) but it suffers from limited adsorption capacity due to low surface area. This paper describes a pioneering work on the adsorption of an organic pollutant, 2-chlorophenol (2-CP) by two MOFs with high surface area and water stability; MIL-101 and its amino-derivative, MIL-101-NH<sub>2</sub>. Although MOFs have higher surface area than AC, the latter was proven better having the highest equilibrium 2-CP uptake (345 mg.g<sup>-1</sup>), followed by MIL-101 (121 mg.g<sup>-1</sup>) and MIL-101-NH<sub>2</sub> (84 mg.g<sup>-1</sup>). Used MIL-101 could be easily regenerated multiple times by washing with ethanol and even showed improved adsorption capacity after each washing cycle. These results can open the doors to meticulous adsorbent selection for treating 2-CP-contaminated water | Luqman Hakim Mohd Azmi; Daryl R. Williams; Bradley P. Ladewig | Transport Phenomena (Chem. Eng.); Coordination Chemistry (Organomet.) | CC BY NC 4.0 | CHEMRXIV | 2019-11-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74605702a9b756a18ab31/original/can-metal-organic-frameworks-outperform-adsorptive-removal-of-harmful-phenolic-compound-2-chlorophenol-by-activated-carbon.pdf |
60c73cc0842e65bc1ddb169e | 10.26434/chemrxiv.14755380.v1 | New Materials Design Using Excitonic Quantum Effects: Applications for Fuel Cells, Catalysts, Superconductive and Bioactive Materials | <p>This manauscript begins with a theoretical substantiation of the possibility of thermal (dark) generation of electronically excited states (excitons) in the structure of oxides as a fundamental quantum-chemical property that ensures their continuous activity. For the first time, experimentally, a macro-scale process flow and its quantum nature are proven using a wide range of tools. The mechanism, features of the chemical structure of electron-hole components, and their role in the formation of catalytic properties have been extensively studied. The application of these new principles for the creation of highly efficient catalysts, energy generation and energy storage devices has been evaluated.</p> | Vladimir B. Kopylov; Paul Leonard | Electrocatalysis; Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Photocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc0842e65bc1ddb169e/original/new-materials-design-using-excitonic-quantum-effects-applications-for-fuel-cells-catalysts-superconductive-and-bioactive-materials.pdf |
60c745c7842e6517bcdb26c9 | 10.26434/chemrxiv.8325248.v2 | Chiral-Induced Spin Selectivity: A Symmetry Analysis of Electronic Transmission | The chiral-induced spin selectivity (CISS) effect, which describes the spin-filtering ability of diamagnetic structures like DNA or peptides having chiral symmetry, has emerged in the past years as the central mechanism behind a number of important phenomena, like long-range biological electron transfer, enantiospecific electrocatalysis, and molecular recognition. Also, CISS-induced spin polarization has a considerable promise for new spintronic devices and the design of quantum materials. The CISS effect is attributed to spin–orbit coupling, but a sound theoretical understanding of the surprising magnitude of this effect in molecules without heavy atoms is currently lacking. We are taking an essential step into this direction by analyzing the importance of imaginary terms in the Hamiltonian as a necessary condition for non-vanishing spin polarization in helical structures. Based on first-principles calculations and analytical considerations, we perform a symmetry analysis of the key quantities determining transport probabilities of electrons of different spin orientations. These imaginary terms originate from the spin–orbit coupling, and they preserve the Hermitian nature of the Hamiltonian. Hence, they are not related to the breaking of time-reversal symmetry resulting from the fact that molecules are open systems in a junction. Our symmetry analysis helps to identify essential constraints in the theoretical description of the CISS effect. We further draw an analogy with the appearance of imaginary terms in simple models of barrier scattering, which may help understanding the unusually effective long-range electron transfer in biological systems.<br /> | Martin Sebastian Zöllner; Solmar Varela; Ernesto Medina; Vladimiro Mujica; Carmen Herrmann | Nanodevices; Theory - Computational; Physical and Chemical Properties | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745c7842e6517bcdb26c9/original/chiral-induced-spin-selectivity-a-symmetry-analysis-of-electronic-transmission.pdf |
65fbb39de9ebbb4db926df54 | 10.26434/chemrxiv-2024-2h1nc | Bicyclic-ammonium-incorporated ylidic nitrogen groups for strong π-electron donation in push–pull benzene π-conjugated systems | Dialkylamino groups are electrically neutral π-electron-donating groups (πEDGs) typically used in push–pull benzene π-conjugated systems to shift their absorption toward longer wavelengths. To push the upper limit of the π-electron donation imposed by the dialkylamino groups while maintaining the neutral net electric charge, we developed novel ylidic nitrogen-based πEDGs, (quinuclidinio)amidyl (QA) and (1-azanorbornio)amidyl (ANA) groups, which were introduced to push–pull benzenes through nucleophilic aromatic substitution. The bicyclic ammonium structures incorporated in these groups enhanced their thermal stability and π-electron-donating ability. The QA and ANA groups donate more π-electrons than the pyrrolidinyl group, as demonstrated by comparing their σ+DCM values and conducting a competitive electrophilic bromination experiment. Changing the pyrrolidinyl group to the QA or ANA group achieved a bathochromic shift of 45–100 nm in the maximum absorption wavelength, depending on the push–pull π-conjugated system investigated (p-nitrobenzene, 1,8-naphthalimide, and an azo dye). | Hikaru Fujita; Takanari Arai; Naoto Kuchiki; Munetaka Kunishima | Organic Chemistry; Organic Compounds and Functional Groups; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65fbb39de9ebbb4db926df54/original/bicyclic-ammonium-incorporated-ylidic-nitrogen-groups-for-strong-electron-donation-in-push-pull-benzene-conjugated-systems.pdf |
60c7500b842e6550aedb3962 | 10.26434/chemrxiv.12917369.v2 | Predicting Carbonyl Excitation Energies Efficiently Using EOM-CC Trends | We approach the problem of predicting excitation energies of diverse, larger (5–6 carbons)
carbonyl species central to earth’s tropospheric
chemistry. Triples contributions are needed
for the vertical excitation energy (E<sup>vert</sup>), while
EOM-CCSD//TD-DFT calculations provide acceptable estimates for the S<sub>1</sub> relaxation energy (E<sup>relax</sup>), and (TD-)DFT suffices for the
S<sub>0</sub> → S<sub>1</sub> zero-point vibration energy correction
(∆E<sup>ZPVE</sup>). <div><br /></div><div>Perturbative triples corrections deliver E<sup>vert</sup>
values close in accuracy to full iterative triples
EOM-CC calculations. The error between EOM-CCSD and triples-corrected E
vert values appears
to be systematic and can be accounted for with
scaling factors. However, saturated and α,β-unsaturated carbonyls must be treated separately. Double-hybrid S<sub>0</sub> minima can be used to
calculate E<sup>vert</sup> with negligible loss in accuracy,
relegating the O(N<sup>5</sup>) expense of CCSD to only
single-point energy and excitation calculations. </div><div><br /></div><div>This affordable protocol can be applied to all
volatile carbonyl species.
E<sup>0−0</sup> predictions do overestimate measured
values by ∼8 kJ/mol due to a lack of triples
contribution in E
relax, but this overestimation
is systematic and the mean unsigned error is
within 4 kJ/mol once this is accounted for.</div> | Keiran Rowell; Scott Kable; Meredith J. T. Jordan | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7500b842e6550aedb3962/original/predicting-carbonyl-excitation-energies-efficiently-using-eom-cc-trends.pdf |
60c741e8ee301cbe75c78d53 | 10.26434/chemrxiv.8159576.v1 | Mechanical Adaptability of Artificial Muscles from Nanoscale Molecular Action | The cooperative operation of artificial molecular motors and switches has been amplified in polymer-based approaches that have led to versatile motion at the macroscale. As these active, shape-shifting polymers have become ever more sophisticated in their morphing capabilities, a major remaining challenge is to encode muscle-like mechanical adaptability during their operation and to explore its molecular origin. Here, we describe the mechanical adaptability of materials in which the light-induced action of molecular switches modifies the intrinsic interfacial tension, in a phase heterogeneous design featuring a liquid crystal polymer network swollen by a liquid crystal. When the swelling creates sufficient interfacial tension, light triggers an unprecedented and reversible photo-stiffening, analogous to myosin-powered muscle fibers. These mechanoadaptive materials adjust their stiffness to the task they must perform, also while they move, and display muscle-like behaviour that might contribute significantly to the development of human-friendly and soft robotics. | Federico Lancia; Alexander Ryabchun; Anne-Déborah Nguindjel; Supaporn Kwangmettatam; Nathalie Katsonis | Composites; Liquid Crystals; Polymer morphology; Photochemistry (Physical Chem.); Physical and Chemical Properties; Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2019-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741e8ee301cbe75c78d53/original/mechanical-adaptability-of-artificial-muscles-from-nanoscale-molecular-action.pdf |
6109836c171fc73926ba9775 | 10.26434/chemrxiv-2021-lrbts-v2 | Probing the Impact of Solvent on Lewis Acid Catalysis via Fluorescent Lewis Adducts | Over the years, various multiparameter methods have been developed to measure the strength of a Lewis acid. However, a major challenge for these measurements lies in the complexity that arises from variables such as solvent and other fundamental interactions, as well as perturbations of Lewis acids as their reaction environment changes. Herein, we evaluate the impact of solvent effects on the Fluorescent Lewis Adduct (FLA) method using a series of representative Lewis acids. The solution-state nature of the FLA method in particular, offers the ability to correlate Lewis Acid Units (LAUs) obtained from the FLA measurement with chemical reactivity. The binding of a Lewis acid in various solvents reveals a measurable dichotomy between both polarity and donor ability of the solvent. While not strictly separable, we observe that, as solvent polarity increases observed LAUs increase; however, as solvent donor ability increases, the observed LAUs decrease. This dichotomy was confirmed by titration data and catalytic Diels-Alder cycloaddition and hydrosilylation reactions, illustrating that solvation effects can be appropriately gauged by LAU values determined from the FLA method. | Amy Laturski; Jordan Bentley; Joshua Gaffen; Christopher Caputo; Thomas Baumgartner | Catalysis; Acid Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6109836c171fc73926ba9775/original/probing-the-impact-of-solvent-on-lewis-acid-catalysis-via-fluorescent-lewis-adducts.pdf |
60c752e0bdbb897f1ca3a389 | 10.26434/chemrxiv.13363694.v1 | One-Pot, Room-Temperature Conversion of CO2 into Porous Metal−Organic Frameworks | We demonstrate the one-pot synthesis of highly porous crystalline metal−organic frameworks, [Zn<sub>4</sub>O(piperazine dicarbamate)<sub>3</sub>], an analogue of [Zn<sub>4</sub>O(1,4-benzenedicarboxylate)<sub>3</sub>] (MOF-5), directly from atmospheric pressure CO<sub>2</sub> gas and piperazine derivatives at 25 °C. The structures showed high CO<sub>2</sub> contents over 30 wt% and surface areas of 1270−2366 m<sup>2</sup> g<sup>−1</sup>. We also show that the synthesis is feasible even by the use of 400 ppm of CO<sub>2</sub>. | Kentaro Kadota; You-Lee Hong; Yusuke Nishiyama; Easan Sivaniah; Daniel Packwood; Satoshi Horike | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752e0bdbb897f1ca3a389/original/one-pot-room-temperature-conversion-of-co2-into-porous-metal-organic-frameworks.pdf |
6230b05c5cf71943d1545ba8 | 10.26434/chemrxiv-2022-2bt1d | Silver-Catalyzed [4+3] Cycloaddition of 1,3-Dienes with Vinyl-N-triftosylhydrazones: A Practical Approach to 1,4-Cycloheptadienes | The first formal [4+3] cycloaddition of 1,3-dienes with vinyl-N-sulfonylhydrazones has been achieved by virtue of easily decomposable vinyl-N-triftosylhydrazones in the presence of silver catalysis. A series of acyclic and cyclic 1,3-dienes reacted effectively with silver(I) non-acceptor vinyl carbenes, including alkyl- and alkenyl-substituted carbenes, which are notoriously challenging, producing a broad spectrum of 1,4-cycloheptadienes with high yield and predictable stereochemistry. The products resulting from the herein described transformation include bridged and fused polycyclic systems, as well as the natural product dictyopterene C' and its isomer ectocarpene. The reaction mechanism and the origin of stereoselectivity were investigated via experimental work and density functional theory calculations. | Shaopeng Liu; Zhaohong Liu; Huricha Bai; Shuang Li; Zanoni Giuseppe; xihe bi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6230b05c5cf71943d1545ba8/original/silver-catalyzed-4-3-cycloaddition-of-1-3-dienes-with-vinyl-n-triftosylhydrazones-a-practical-approach-to-1-4-cycloheptadienes.pdf |
6796a2ddfa469535b9f6628d | 10.26434/chemrxiv-2025-tln5l | microPhotoGas reactor: High-throughput experimentation for photoinduced reactions under gas atmosphere | High-throughput experimentation has transformed the exploration of many catalytic processes, from a mechanistic and timeline point of view. However, some specific reactions remain impossible to transpose in HTE, mostly because of missing dedicated devices. With the development of photoinduced reactions involving gases as reactants, it is of importance to access HTE for such set-ups. We describe here the design and manufacture of a specific device for miniaturization and parallelization of photoinduced reactions under pressure of specific gas atmosphere. | Sylvain Foucquart; Taline Kerackian; Geraud Chacktas; Jean-Christophe Cintrat; Eugénie Romero | Organic Chemistry; Catalysis; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6796a2ddfa469535b9f6628d/original/micro-photo-gas-reactor-high-throughput-experimentation-for-photoinduced-reactions-under-gas-atmosphere.pdf |
60c7519ebb8c1a46f03dbd02 | 10.26434/chemrxiv.13193741.v1 | Upconversion in Molecular Hetero-Nonanuclear Lanthanide Clusters in Solution | <p>Up
until now restricted to solid state chemistry and nanoparticles, upconversion
(UC) phenomena by which low energy photons are piled up to engender higher
energy emission, are progressively entering the field of molecular probes with
a handful of molecular/supramolecular discrete complexes. Here we show that
nonanuclear lanthanide complexes respresent a new class of solution state UC
materials, and are straightforwardly crystalized from LnCl<sub>3</sub>.6H<sub>2</sub>O
salts, triethylamine and acetylacetone, retaining their structural integrity in
solution. For a composition of one Tb per eight Yb the nonanuclear clusters
display a very efficient upconversion phenomenon with Tb luminescence in the
visible region upon 980 nm NIR excitation of Yb. An unprecedented value of
1.0×10<sup>-7</sup> was obtained for the UC efficiency at only 2.86 W/cm<sup>2</sup>,
demonstrating these new molecular clusters to be up to 26 times more efficient
than the best current molecular systems, the UC being observed down to a
concentration of 10 nM.</p> | Richard Knighton; Lohona K. Soro; Alexandre Lecointre; Guillaume Pilet; Alexandra Fateeva; laurie pontille; Laura Laura Francés-Soriano; Niko Hildebrandt; Loïc J. Charbonnière | Coordination Chemistry (Inorg.); Spectroscopy (Inorg.); Supramolecular Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7519ebb8c1a46f03dbd02/original/upconversion-in-molecular-hetero-nonanuclear-lanthanide-clusters-in-solution.pdf |
62a3ca0bfe677d63714b9dc7 | 10.26434/chemrxiv-2022-52g7z-v2 | Continuous Addition Kinetic Elucidation: Catalyst and Reactant Order, Rate Constant, and Poisoning from a Single Experiment | Kinetic analysis of catalytic reactions is a powerful tool for mechanistic elucidation but is often challenging to perform. Establishing order in a catalyst is achieved by running several reactions at different loadings, which is complicated by the challenge of maintaining consistent run-to-run experimental conditions. We present Continuous Addition Kinetic Elucidation (CAKE), which involves steadily injecting catalyst into the reaction, and following reaction progress over time to generate a plot whose shape is dependent only on the order in reactant and in catalyst. Modelling the curve (using a convenient web tool) allows the catalyst and reactant order to be determined, as well as the rate constant and the amount of any catalyst poison present. | Peter Williams; Charles Killeen; Ian Chagunda; Brett Henderson; Sofia Donnecke; Wil Munro; Jaspreet Sidhu; Denaisha Kraft; David Harrington; Scott McIndoe | Physical Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62a3ca0bfe677d63714b9dc7/original/continuous-addition-kinetic-elucidation-catalyst-and-reactant-order-rate-constant-and-poisoning-from-a-single-experiment.pdf |
67544d35f9980725cf5701e7 | 10.26434/chemrxiv-2024-v2d9h | Molecular Simulation Study of Elasticity of Fluid-Saturated Zeolites | Zeolites are widely used for applications involving gas adsorption thanks to their crystalline porous structure, high surface area, and mechanical stability. Experiments using magnetoelastic sensors showed that gas adsorption can noticeably alter the elastic moduli of zeolites. Here we utilized a combination of the classical molecular dynamics and Monte Carlo simulations to explore this effect in silico, calculating the bulk moduli of the zeolites, of the fluids adsorbed in these zeolites, and of the zeolite-fluid composites. We considered two gases -- nitrogen and carbon dioxide, in two zeolite structures -- 13X and 4A. The moduli of the composite systems were calculated using two alternative approaches: from the moduli of the constituents (unsaturated zeolite and adsorbed fluid) using the Gassmann equation, and directly, using the Birch-Murnaghan equation of state. The direct approach showed better agreement with the experimental observations, raising a question on the applicability of the Gassmann equation for microporous zeolites. | Santiago Flores Roman; Alina Emelianova; Gennady Gor | Materials Science; Chemical Engineering and Industrial Chemistry; Composites; Elastic Materials; Thermodynamics (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67544d35f9980725cf5701e7/original/molecular-simulation-study-of-elasticity-of-fluid-saturated-zeolites.pdf |
65230001bda59ceb9a21af18 | 10.26434/chemrxiv-2023-twjpr-v2 | Experimental and Theoretical Studies on the Reactions of Aliphatic Imines with Isocyanates | In the context of a project aiming at the replacement of the 3-substituted β-lactam ring in classical β-lactam antibiotics by an N(3)-acyl-1,3-diazetidinone moiety, we have investigated the reaction of isocyanates with imines derived from allyl glycinate and differently substituted propionaldehydes. Imines of aromatic aldehydes with anilines have been reported to react with acyl isocyanates to give 1,3-azetidinones or 2,3-dihydro-4H-1,3,5-oxadiazin-4-ones, via [2+2] or [4+2] cycloaddition, respectively. However, neither of these products was formed with imines from allyl glycinate and 2-(mono)methyl propionaldehydes. α,α-Dimethylation of the imine enabled the [4+2] cycloaddition pathway, but the desired 1,3-diazetidinone products were not observed. Surprisingly, the imines obtained from thioesters of 2,2-dimethyl 3-oxo propionic acid reacted with aryl isocyanates or with benzyl isocyanate to give 2,2-dimethyl-2,4-dioxo-6-(aryl/akylthio)tetrahydropyrimidines, via thiol displacement and re-addition to a putative six-membered iminium intermediate. Such compounds have not been described in the literature so far. For aryl isocyanates, the reaction was insensitive to the nature of a para-substituent on the aromatic ring. The experimental results obtained for the reactions of acyl isocyanates with imines could be rationalized by DFT calculations. In addition, we have also shown that N(3)-acyl-1,3-azetidinone and 2,3-dihydro-4H-1,3,5-oxadiazin-4-one products can be distinguished based on experimental IR data in combination with theoretical reference spectra employing the IR spectra alignment (IRSA) algorithm. This discrimination was not possible by means of 1H, 13C, or 15N NMR spectroscopy. | Etienne Cotter; Felix Pultar; Sereina Riniker; Karl-Heinz Altmann | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65230001bda59ceb9a21af18/original/experimental-and-theoretical-studies-on-the-reactions-of-aliphatic-imines-with-isocyanates.pdf |
671ff4bf1fb27ce124dfb5eb | 10.26434/chemrxiv-2024-xb06z-v2 | Tetraperoxotitanates for High Capacity Direct Air Capture of Carbon Dioxide | Materials chemists play a strategic role towards achieving ambitious global climate goals, including removing legacy CO2 via direct air capture (DAC). Innovating diverse DAC materials will enable their effective use in varying conditions, and bring forth a better understanding of CO2 capture mechanisms. In our current contribution, we have synthesized a family of homoleptic alkali tetraperoxotitanate materials (generally formulated A4Ti(O2)4, A=Li, Na, K) and studied their DAC reactivity. Synthesis was achieved with inexpensive reagents, and >90% yields. We present the first single-crystal X-ray structures (five total) of A4Ti(O2)4 compounds, along with supplemental bulk characterization and computation. We compare their DAC behavior in simple ambient benchtop experiments, determining CO2 uptake by combustion analysis of post-capture materials. The K-analogue exhibited the most rapid and high capacity DAC, 8.17 mmol CO2/gram sorbent, translating to nearly 3 moles CO2 per mole Ti, and reaching near maximum capacity in under 10 days. The Li and Na analogues both exhibit delayed reactivity, but also with high DAC capacity (respectively 6.66 and 8.18 mmol CO2/gram sorbent). Characterization of the DAC products via scanning electron microscopy shows phase separation of alkali-rich and Ti-rich regions in core-shell morphologies for the Na and Li analogues, and this is discussed with respect to the role of the titanium vs the alkali in DAC. On the other hand, no phase separation was observed for the K-analogue. In situ monitoring detailed the early-stage CO2 capture behavior of the K-analogue, and it reaches ~50% of maximum capacity within one hour. The differentiating behavior of the K-analogue is attributed to its unique composition, containing four H2O2 lattice molecules in addition to the four O2- peroxide anions bonded to TiIV. While H2O2 (aq) alone does not exhibit CO2 chemisorption, the basic environment of the A4Ti(O2)4 lattice activates its rapid DAC, inspiring future exploration of peroxosolvate materials for DAC. | Karlie Bach; Eduard Garrido Ribo; Jacob Hirschi; Zhiwei Mao; Makenzie Nord; Lev Zakharov; Konstantinos Goulas; Tim Zuehlsdorff; May Nyman | Inorganic Chemistry; Reaction (Inorg.); Transition Metal Complexes (Inorg.); Materials Chemistry; Crystallography – Inorganic | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671ff4bf1fb27ce124dfb5eb/original/tetraperoxotitanates-for-high-capacity-direct-air-capture-of-carbon-dioxide.pdf |
64ae969f6e1c4c986b4328c8 | 10.26434/chemrxiv-2023-l1t9c | Fjord-Type AIEgens Based on Inherent Through-Space Conjugation | Through-space conjugation (TSC) is a noncovalently electronic interaction that is emerging as a potential complement to through-bond conjugation (TBC)-based strategies for constructing luminescent materials. However, the design of efficient luminogens based on TSC is currently challenging due to a lack of established structure-property understanding. This is particularly true in the case of luminogens displaying aggregation-induced emission (AIE) effects. In this work, three terphenyl derivatives were prepared, and their photophysical properties were systemically studied. It was found that relative to the corresponding m- and p-linked analogues, the electronic interaction of TBC is weakened while the strength of TSC is commensurately enhanced in the constitutional isomer containing an o-linked Fjord-type subunit. Within this set of luminogens, the presence of a Fjord-type arrangement promotes a transformation from aggregation-caused quenching (ACQ) to AIE. Further investigations involving congeneric quaterphenyl and pentphenyl isomers support the universality of the Fjord-type unit as a framework for synthesizing AIE-active luminogens (AIEgens) with inherent TSC. This work not only provides a novel set of AIEgens but also establishes the utility of TSC in controlling the photophysical properties of nonconventional and twisted luminogens. | Yeqiang Han; Yuan Xie; Jianyu Zhang; Shiyu Tan; Haoke Zhang; Ben Zhong Tang; Jonathan L. Sessler; Feihe Huang | Theoretical and Computational Chemistry; Organic Chemistry; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae969f6e1c4c986b4328c8/original/fjord-type-ai-egens-based-on-inherent-through-space-conjugation.pdf |
641c8a8962fecd2a8350bc43 | 10.26434/chemrxiv-2023-9dckb | Room-temperature stacking disorder in layered covalent-organic frameworks from machine-learning force fields | The local structures of layered covalent-organic frameworks (COFs) deviate from the average crystal structures assigned from X-ray diffraction experiments. For two prototype COFs of Tp-Azo and DAAQ-TFP, density functional theory calculations have shown that the eclipsed structure is not an energy minimum and that the internal energy is lowered for an inclined stacking arrangement. Here we explore the structural disorder of these frameworks at 300 K through molecular dynamics (MD) simulations using an on-the-fly machine learning force field (MLFF). We find that an initially eclipsed stacking mode spontaneously distorts to form a zigzag configuration that lowers the free energy of the crystal. The simulated diffraction patterns show good agreement with experimental observations. The dynamic disorder from the MLFF MD trajectories is found to persist in mesoscale MD simulations of 155 thousand atoms, giving further confidence in our conclusions. Our simulations show that the stacking behaviour of layered COFs is more complicated than previously understood. | Ju Huang; Seung-Jae Shin; Kasper Tolborg; Alex Ganose; Gabriel Krenzer; Aron Walsh | Theoretical and Computational Chemistry; Materials Science; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641c8a8962fecd2a8350bc43/original/room-temperature-stacking-disorder-in-layered-covalent-organic-frameworks-from-machine-learning-force-fields.pdf |
6142f60742198e8c31782e9e | 10.26434/chemrxiv-2021-5fwjd | Generative Pre-Training from Molecules | SMILES is a line notation for entering and representing molecules. Being inherently a language
construct, it allows estimating molecular data in a self-supervised fashion by employing machine
learning methods for natural language processing (NLP). The recent success of attention-based neural
networks in NLP has made large-corpora transformer pretraining a de facto standard for learning
representations and transferring knowledge to downstream tasks. In this work, we attempt to adapt
transformer capabilities to a large SMILES corpus by constructing a GPT-2-like language model. We
experimentally show that a pretrained causal transformer captures general knowledge that can be
successfully transferred to such downstream tasks as focused molecule generation and single-/multi-output molecular-property prediction. For each task, we freeze model parameters and attach trainable
lightweight networks between attention blocks—adapters—as alternative to fine-tuning. With a
relatively modest setup, our transformer outperforms the recently proposed ChemBERTa transformer
and approaches state-of-the-art MoleculeNet and Chemprop results. Overall, transformers pretrained
on SMILES corpora are promising alternatives that do not require handcrafted feature engineering,
make few assumptions about structure of data, and scale well with the pretraining data size. | Sanjar Adilov | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6142f60742198e8c31782e9e/original/generative-pre-training-from-molecules.pdf |
6781e1ac6dde43c908117cc4 | 10.26434/chemrxiv-2025-11wfv | ACES-GNN: Can Graph Neural Network Learn to Explain Activity Cliffs? | Graph Neural Networks (GNNs) have revolutionized molecular property prediction by leveraging graph-based representations, yet their opaque decision-making processes hinder broader adoption in drug discovery. This study introduces the Activity-Cliff-Explanation-Supervised GNN (ACES-GNN) framework, designed to simultaneously improve predictive accuracy and interpretability by integrating explanation supervision for activity cliffs (ACs) into GNN training. ACs, defined by structurally similar molecules with significant potency differences, pose challenges for traditional models due to their reliance on shared structural features. By aligning model attributions with chemist-friendly interpretations, the ACES-GNN framework bridges the gap between prediction and explanation. Validated across 30 pharmacological targets, ACES-GNN consistently enhances both predictive accuracy and attribution quality compared to baseline methods. Our results demonstrate a strong correlation between improved predictions and accurate explanations, offering a robust and adaptable framework for addressing the "intra-scaffold" generalization problem. This work underscores the potential of explanation-guided learning to advance interpretable artificial intelligence in molecular modeling and drug discovery. | Xu Chen; Dazhou Yu; Liang Zhao; Fang Liu | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry | CC BY NC 4.0 | CHEMRXIV | 2025-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6781e1ac6dde43c908117cc4/original/aces-gnn-can-graph-neural-network-learn-to-explain-activity-cliffs.pdf |
64c0e47fce23211b2092459b | 10.26434/chemrxiv-2023-wvxb2 | Comments on “The Transition Metal Catalyzed [.pi.2s + .pi.2s + .sigma.2s + .sigma.2s] Pericyclic Reaction: Woodward−Hoffmann Rules, Aromaticity, and Electron Flow" (J. Am. Chem. Soc. 2020, 142, 19033-19039.): An Orbital Phase Theory Approach | Recently, Goddard and Stoltz reported a theoretical investigation of the intramolecular coupling of two 1-allyl ligands on Pd atom (J. Am. Chem. Soc. 2020, 142, 19033-19039.). They proposed that the symmetry-allowed [.pi.2s + .pi.2s + .sigma.2s + .sigma.2s] orbital interaction is essential to achieve the reaction. However, there are four issues of misunderstanding: (i) Two .sigma.Pd-C orbitals, which are in phase combination of the hybrid orbitals, are always and unexeptionaly associated with two out-of-phase-combined .sigma.*Pd-C’s. Thus, total of four orbitals, two .sigma.Pd-C’s and .sigma.*Pd-C’s, are to be generated from only three orbitals, one dPd orbital and two nC’s; (ii) Two .pi.2s orbitals and .sigma.2s ones are all bonding and occupied orbitals so that interaction among them should lead to destabilization, not stabilization; (iii) Two .pi.2s orbitals are combined out of phase so that it is not appropriate to make a bond between them; (iv) Normally, two .eta.1-allyl ligands are regarded as two electron donors, while the Pd atom is an acceptor. From the orbital phase theory perspective, cyclic orbital interactions among d*Pd-.pi.2/allyl-.pi.2/allyl-, d*Pd-.pi.*3/allyl-.pi.2/allyl- and d*Pd-.pi.2/allyl-.pi.*3/allyl- are phase-continuous so that they can produce stabilization at the TS. The HOMO at the TS should consist of superimposition of these interactions. | Yuji Naruse | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Computational Chemistry and Modeling; Ligands (Organomet.); Theory - Organometallic | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c0e47fce23211b2092459b/original/comments-on-the-transition-metal-catalyzed-pi-2s-pi-2s-sigma-2s-sigma-2s-pericyclic-reaction-woodward-hoffmann-rules-aromaticity-and-electron-flow-j-am-chem-soc-2020-142-19033-19039-an-orbital-phase-theory-approach.pdf |
6717bb0d83f22e4214cdee8d | 10.26434/chemrxiv-2024-k3bxl | Prediction of Hydration energies of Adsorbates at Pt(111) and Liquid Water Interfaces using Machine Learning | Aqueous-phase heterogeneous catalysis has many applications, including biomass reforming, Fischer-Tropsch synthesis, and electrocatalysis. Developing accurate models for these systems is essential for gaining mechanistic understanding and making predictions of activity and selectivity under reaction conditions. However, molecular modeling of solid-liquid interfaces is computationally demanding. To address this, we carried out machine learning analysis on an existing dataset comprising energies and free energies of solvation for 90 adsorbates on a Pt(111) surface. These adsorbates include intermediates from the decomposition of methane, methanol, ethylene glycol, and glycerol. We investigated the structure-property relationship by combining molecular descriptors with machine learning models. Eight machine learning approaches were compared. In general, machine learning models outperform molecular dynamics for computing the same properties and achieve RMSE < 0.1 eV for predicting the energies and free energies of solvation, which is within the standard error within the original dataset. R2 for energies of solvation are in general above our threshold value of 0.8 but only 0.72 for free energies of solvation. To achieve better regression for free energies of solvation, the dataset should be expanded. However, our machine learning model still outperforms molecular dynamics for predicting free energies of solvation. Feature importance analysis shows that while hydrogen bonds between water and the adsorbates contribute most strongly to machine learning model performance, a combination of different types of features is important to achieve strong predictive performance. | Jiexin Shi; Rachel Getman | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis | CC BY NC 4.0 | CHEMRXIV | 2024-10-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6717bb0d83f22e4214cdee8d/original/prediction-of-hydration-energies-of-adsorbates-at-pt-111-and-liquid-water-interfaces-using-machine-learning.pdf |
60ec589a882582d677a770e5 | 10.26434/chemrxiv-2021-1dv37 | Jahn-Teller Effects in a Vanadate-Stabilized Manganese-Oxo Cubane Water Oxidation Catalyst | We report Jahn–Teller effects in different oxidation states of the water oxidation catalyst [(Mn4O4)(V4O13)(OAc)3]n-
and its activated form [(Mn4O4)(V4O13)(OAc)2(H2O)(OH)]n-. Based on all combinatorially possible Jahn–Teller axis arrangements of the Mn(III) atoms, the energetically stable minima are identified. We also derive five heuristic rules that associate a particular energetic cost with certain structural features, like crossings of multiple Jahn–Teller axes, the location of Jahn–Teller axes, or the ligand that is involved in a Jahn–Teller axis. It is found that the different
oxidation states seem to localize on different Mn centers, giving rise to clear Jahn–Teller distortions, unlike in previous crystallographic findings where an apparent valence delocalization was found. We conclude that the combination of cubane-vanadate bonds that are chemically inert, cubane-acetate/water bonds that can be activated through a Jahn–Teller axis, and low activation barriers for intramolecular rearrangement of the Jahn–Teller axes plays an important role in the reactivity of this and related compounds. | Sebastian Mai; Marcus Holzer; Anastasia Andreeva; Leticia González | Theoretical and Computational Chemistry; Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ec589a882582d677a770e5/original/jahn-teller-effects-in-a-vanadate-stabilized-manganese-oxo-cubane-water-oxidation-catalyst.pdf |
664e089c91aefa6ce1b21cf4 | 10.26434/chemrxiv-2024-sx1js | Diisopropyl Methylphosphonate and Sarin Decomposition on Pristine vs. Hydroxylated Alumina Surfaces: Mechanistic Predictions from Ab Initio Molecular Dynamics | Understanding the reactivity of chemical warfare agents on material surfaces is essential for mitigating and controlling their chemical/biological activity. Using \textit{ab initio} molecular dynamics, we compare the adsorption and decomposition of sarin and its simulant, diisopropyl methylphosphonate (DIMP), on both pristine and hydroxylated alumina surfaces at various temperatures. Our extensive calculations confirm that DIMP is a suitable simulant for sarin experimental studies on pristine alumina surfaces due to their similar adsorption configurations and reaction dynamics. Moreover, our ab initio molecular dynamics simulations predict C--O bond cleavage to be the initial decomposition step for both DIMP and sarin on the pristine surface. We also identify an additional potential decomposition route for sarin via cleavage of the P--F bond. While similarities exist on the pristine surface, differences between sarin and DIMP emerge on the hydroxylated surface at elevated temperatures. This work provides detailed insights into these atomistic decomposition mechanisms and highlights the utility of predictive quantum dynamics simulations for evaluating the suitability of simulants to guide future experimental investigations of these hazardous compounds. | Sohag Biswas; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Theory - Computational; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664e089c91aefa6ce1b21cf4/original/diisopropyl-methylphosphonate-and-sarin-decomposition-on-pristine-vs-hydroxylated-alumina-surfaces-mechanistic-predictions-from-ab-initio-molecular-dynamics.pdf |
6316a14149042ab863cd0481 | 10.26434/chemrxiv-2022-sgj8c | How good are AlphaFold models for docking-based virtual screening? | A crucial component in structure-based drug discovery is the availability of high-quality three-dimensional structures of the protein target. In molecular docking, whenever experimental structures were not available, in silico structural homology modeling has been the method of choice. However, using computationally predicted structures adds a further degree of uncertainty to the docking process. Recently, AlphaFold (AF), an artificial intelligence-based modeling tool, has shown impressive results in terms of model accuracy within the field of ab initio protein structure prediction. This outstanding success prompted us to evaluate how accurate AF models are from the perspective of docking-based drug discovery. We compared the performance of AF models in high-throughput docking (HTD) to their corresponding experimental PDB structures using a benchmark set of 16 targets spanning different protein families and binding site properties. Four docking programs and two consensus techniques were used to evaluate the HTD performance. The AF models showed consistently worse performance than their corresponding PDB structures, with zero enrichment factor values in several cases. While AlphaFold shows a remarkable ability to predict protein architecture and binding site anatomy, we conclude that this is not enough to guarantee that AF models can be reliably used for HTD purposes. Moreover, we show that very small variations at the side chain level of essential ligand-binding residues have a large impact on the outcome of HTD, what suggests that post-modeling refinement strategies might be key to increase the chance of success of AF models in prospective HTD campaigns. | Valeria Scardino; Juan I. Di Filippo; Claudio Cavasotto | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6316a14149042ab863cd0481/original/how-good-are-alpha-fold-models-for-docking-based-virtual-screening.pdf |
60c745bd337d6cfd06e27031 | 10.26434/chemrxiv.10250897.v1 | A Molecular Computing Approach to Solving Optimization Problems via Programmable Microdroplet Arrays | The search for novel
forms of computing that show advantages as alternatives to the dominant
von-Neuman model-based computing is important as it will enable different
classes of problems to be solved. By using droplets and room-temperature
processes, molecular computing is a promising research direction with potential
biocompatibility and cost advantages. In this work, we present a new approach
for computation using a network of chemical reactions taking place within an
array of spatially localized droplets whose contents represent bits of
information. Combinatorial optimization problems are mapped to an Ising
Hamiltonian and encoded in the form of intra- and inter- droplet interactions.
The problem is solved by initiating the chemical reactions within the droplets
and allowing the system to reach a steady-state; in effect, we are annealing
the effective spin system to its ground state. We propose two implementations
of the idea, which we ordered in terms of increasing complexity. First, we
introduce a hybrid classical-molecular computer where droplet properties are
measured and fed into a classical computer. Based on the given optimization
problem, the classical computer then directs further reactions via optical or
electrochemical inputs. A simulated model of the hybrid classical-molecular
computer is used to solve boolean satisfiability and a lattice protein model.
Second, we propose architectures for purely molecular computers that rely on
pre-programmed nearest-neighbour inter-droplet communication via energy or mass
transfer. | Si Yue Guo; Pascal Friederich; Yudong Cao; Tony Wu; Christopher Forman; Douglas Mendoza; Matthias Degroote; Andrew Cavell; Veronica Krasecki; Riley Hickman; Abhishek Sharma; Leroy Cronin; Nathan Gianneschi; Randall Goldsmith; Alan Aspuru-Guzik | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c745bd337d6cfd06e27031/original/a-molecular-computing-approach-to-solving-optimization-problems-via-programmable-microdroplet-arrays.pdf |
622412c997f2109450fec97a | 10.26434/chemrxiv-2022-d0zfn | Pd(II)-Catalyzed C(alkenyl)–H Activation Facilitated by a Transient Directing Group | Palladium(II)-catalyzed C(alkenyl)–H alkenylation enabled by a transient directing group (TDG) strategy is described. The dual catalytic process takes advantage of reversible condensation between an alkenyl aldehyde substrate and an amino acid TDG to facilitate coordination of the metal catalyst and subsequent C(alkenyl)–H activation by a tailored carboxylate base. The resulting palladacycle then engages an acceptor alkene, furnishing a 1,3-diene with high regio- and E/Z-selectivity. The reaction enables the synthesis of enantioenriched atropoisomeric 2-aryl-substituted 1,3-dienes, which have seldom been examined in previous literature. Catalytically relevant alkenyl palladacycles were synthesized and characterized by X-ray crystallography, and the energy profiles of the C(alkenyl)–H activation step and the stereoinduction model were elucidated by density functional theory (DFT) calculations. | Mingyu Liu; Juntao Sun; Tuğçe Erbay; Hui-Qi Ni; Raúl Martín-Montero; Peng Liu; Keary Engle | Organic Chemistry; Catalysis; Organometallic Chemistry; Organic Compounds and Functional Groups; Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/622412c997f2109450fec97a/original/pd-ii-catalyzed-c-alkenyl-h-activation-facilitated-by-a-transient-directing-group.pdf |
65ccf30666c1381729a56df4 | 10.26434/chemrxiv-2024-0s8c9 | How dynamics changes ammonia cracking on iron surfaces | Ammonia is a promising hydrogen carrier, being rich in hydrogen and ease of transport. However, a microscopic characterization of the ammonia cracking reaction is still lacking, hindered by extreme operando conditions. Leveraging state-of-the-art molecular dynamics, machine learning potentials, and enhanced sampling methods, we offer an atomistic view of the adsorption, diffusion, and dehydrogenation processes of NHx (x=1, 3) on two representative surfaces at operando temperature of 700 K. Dynamics pervasively affects all steps of decomposition, including on the stable (110) surface where the high mobility of reaction intermediates affects the reactivity. The role is even more dramatic on the (111) surface, where the mobility of Fe surface atoms introduces new adsorption sites and alters the dehydrogenation barriers. In both cases, a detailed analysis of reactive events shows that there is never a single transition state, but it is always an ensemble composed of at least two pathways. Notwithstanding, a unified mechanism can be identified by following the charge transfer along the different reaction pathways. | Simone Perego; Luigi Bonati; Shivam Tripathi; Michele Parrinello | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Computational Chemistry and Modeling; Machine Learning; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ccf30666c1381729a56df4/original/how-dynamics-changes-ammonia-cracking-on-iron-surfaces.pdf |
60c74130702a9b5f2318a1ff | 10.26434/chemrxiv.7988033.v1 | Synthesis of 3,3-Spirocyclic-2-Phosphono-Indolines via a Dearomative Addition of Phosphonyl Radicals to Indoles | We report the diastereoselective synthesis of alpha-aminophosphonates
derivatives embedded in a spirocyclic indolines. Our method proceeds via the
dearomative addition of phosphonyl radicals at the C2-position of the indole
nucleus in oxidative conditions followed by the intramolecular trapping of the
resulting carbocation before rearomatization.
trans-3,3-Spirocyclic-2-phosphonoindolines were thus obtained.<div><br /></div> | Dmytro Ryzakhov; Maxime Jarret; Jean Pierre Baltaze; Régis Guillot; Cyrille Kouklovsky; Guillaume Vincent | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74130702a9b5f2318a1ff/original/synthesis-of-3-3-spirocyclic-2-phosphono-indolines-via-a-dearomative-addition-of-phosphonyl-radicals-to-indoles.pdf |
615d3b1d35b40602430a53d6 | 10.26434/chemrxiv-2021-stw44 | Selective binding of small molecules to Vibrio cholerae DsbA offers a starting point for the design of novel antibacterials | DsbA enzymes catalyze oxidative folding of proteins that are secreted into the periplasm of Gram-negative bacteria, and they are indispensable for the virulence of human pathogens such as Vibrio cholerae and Escherichia coli. Therefore, targeting DsbA represents an attractive approach to control bacterial virulence. X-ray crystal structures reveal that DsbA enzymes share a similar fold, however, the hydrophobic groove adjacent to the active site, which is implicated in substrate binding, is shorter and flatter in the structure of V. cholerae DsbA (VcDsbA) compared to E. coli DsbA (EcDsbA). The flat and largely featureless nature of this hydrophobic groove is challenging for the development of small molecule inhibitors. Using fragment-based screening approaches, we have identified a novel small molecule, based on the benzimidazole scaffold, that binds to the hydrophobic groove of oxidized VcDsbA with a KD of 446 ± 10 µM. The same benzimidazole compound has ~8-fold selectivity for VcDsbA over EcDsbA and binds to oxidized EcDsbA, with KD > 3.5 mM. We generated a model of the benzimidazole complex with VcDsbA using NMR data but were unable to determine the structure of the benzimidazole bound EcDsbA using either NMR or X-ray crystallography. Therefore, a structural basis for the observed selectivity is unclear. To better understand ligand binding to these two enzymes we crystallized each of them in complex with a known ligand, the bile salt sodium taurocholate. The crystal structures show that taurocholate adopts different binding poses in complex with VcDsbA and EcDsbA, and reveals the protein-ligand interactions that stabilize the different modes of binding. This work highlights the capacity of fragment-based drug discovery to identify inhibitors of challenging protein targets. In addition, it provides a starting point for development of more potent and specific VcDsbA inhibitors that act through a novel anti-virulence mechanism. | Geqing Wang; Biswaranjan Mohanty; Martin Williams; Bradley Doak; Rabeb Dhouib; Makrina Totsika; Róisín Macmahon; Gaurav Sharma; Dan Zheng; Matthew Bentley; Yanni Ka-Yan Chin; James Horne; David Chalmers; Begona Heras; Martin Scanlon | Biological and Medicinal Chemistry; Biophysics; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/615d3b1d35b40602430a53d6/original/selective-binding-of-small-molecules-to-vibrio-cholerae-dsb-a-offers-a-starting-point-for-the-design-of-novel-antibacterials.pdf |
61479b91a7b249ac7030d823 | 10.26434/chemrxiv-2021-490hl-v2 | Protective Effect of Starch-stabilized Selenium Nanoparticles against Melamine-induced Hepato-renal Toxicity in Male Albino Rats | Melamine and its analogues are illegally added to raise the apparent protein content in foods. The elevated concentrations of these compounds cause adverse effects in humans and animals. In this contribution, the protective effects of the synthesized starch-stabilized selenium nanoparticles (Se-NPs@starch) on melamine-induced hepato-renal toxicity have been systematically investigated. The Se-NPs@starch were characterized by X-ray photoelectron spectroscopy (XPS) analysis, energy dispersive spectroscopy (EDS) mapping analysis, TEM, and FT-IR. Starch plays a crucial role in the stabilization and dispersion of Se NPs, as noticed from the TEM and EDS investigations. Furthermore, the atomic ratio of Se distribution over the starch surface is approximately 1.67%. The current study was conducted on four groups of adult male rats, and the oral daily treatments for 28 days were as follows: group I served as control, group II received Se-NPs@starch, group III was exposed to melamine, while group IV was treated with melamine and Se-NPs@starch. The results reveal a significant alteration in the histoarchitecture of both hepatic and renal tissues induced by melamine. Furthermore, elevated liver and kidney function markers, high malondialdehyde, and increased expression levels of apoptosis-related genes besides a reduction in GSH and expression levels of antioxidant genes were observed in the melamine-exposed group. Interestingly, the administration of the Se-NPs@starch resulted in remarkable protection of rats against melamine-induced toxicity through increasing the antioxidant capacity and inhibiting oxidative damage. Collectively, this study provides affordable starch-stabilized Se-NPs with potent biological activity, making them auspicious candidates for prospective biomedical applications. | Zainab Sabry Othman Ahmed; Mona K. Galal; Elsayed A. Drweesh; Khaled S. Abou-El-Sherbini; Eman A.M. Elzahany; Mohamed Elnagar; Noha A. E. Yasin | Biological and Medicinal Chemistry; Nanoscience; Biochemistry; Chemical Biology; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61479b91a7b249ac7030d823/original/protective-effect-of-starch-stabilized-selenium-nanoparticles-against-melamine-induced-hepato-renal-toxicity-in-male-albino-rats.pdf |
66f64408cec5d6c1425fc7e5 | 10.26434/chemrxiv-2024-qwpx7 | Highly selective Th2 and Th17 cytokine induction of nitrated lipid-modified ɑ-GalCer derivatives with their “anchoring effect” in the recognition of CD1d for NKT cell activation | On antigen-presenting cells, CD1d presents the glycolipids antigens to the TCRs of NKT cells, leading to immune responses via cytokine induction. Although various lipid antigens have been found, there are only limited numbers of glycolipid antigens having highly selective cytokine induction (Th2 and Th17 type) with very high binding affinity to CD1d. In this research, we discovered the glycolipids that express highly selective Th2 and Th17 type cytokine induction, with introducing natural nitro-modified fatty acyl groups to the ceramide moiety for the “anchoring effect” of polar functional groups at the CD1d binding site. | Kodai Sueyoshi; Junichiro Kishi; Shinsuke Inuki; Takanori Matsumaru; Yukari Fujimoto | Biological and Medicinal Chemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66f64408cec5d6c1425fc7e5/original/highly-selective-th2-and-th17-cytokine-induction-of-nitrated-lipid-modified-gal-cer-derivatives-with-their-anchoring-effect-in-the-recognition-of-cd1d-for-nkt-cell-activation.pdf |
66590232418a5379b0b49b42 | 10.26434/chemrxiv-2024-zp1zj | Divergent Syntheses of Near-Infrared Light Activated Molecular Jackhammers to Eradicate Cancer Cells | Aminocyanines involving Cy7 and Cy7.5 amines function as molecular jackhammers (MJH) by vibronic-driven action (VDA). That has been demonstrated through the coupling of the molecular vibrational and electronic modes, causing picosecond whole-molecule concerted stretching. If the molecules are cell-associated and then activated by near infrared light, the VDA mechanically disrupts the cell membranes resulting in the rapid death by necrosis. Distinct from photodynamic therapy and photothermal therapy, VDA with its ultrafast vibrational action is not slowed by high concentrations of reactive oxygen species (ROS) scavengers. With the importance of these MJH libraries, their efficient syntheses are here disclosed. We report a practical approach to access the key intermediate, facilitating the preparation of various Cy7 and Cy7.5 MJH in moderate and high yields with diverse side chains to study structure-¬activity relationships. | Bowen Li; Ciceron Ayala-Orozco; Tengda Si; Lixin Zhou; Zicheng Wang; Angel Martí; James Tour | Biological and Medicinal Chemistry; Organic Chemistry; Materials Science; Organic Compounds and Functional Groups; Physical Organic Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66590232418a5379b0b49b42/original/divergent-syntheses-of-near-infrared-light-activated-molecular-jackhammers-to-eradicate-cancer-cells.pdf |
641cb675647e3dca9966b102 | 10.26434/chemrxiv-2023-dxhft | Comparison of monophosphine and bisphosphine precatalysts for Ni-catalyzed Suzuki-Miyaura cross-coupling: understanding the role of ligation state in catalysis | Practical advances in Ni-catalyzed Suzuki-Miyaura cross-coupling (SMC) have been limited by a lack of mechanistic understanding of phosphine ligand effects. While bisphosphines are commonly used in these methodologies, we have observed instances where monophosphines can provide comparable or higher levels of reactivity. Seeking to understand the role of ligation state in catalysis, we performed a head-to-head comparison study of Ni SMCs catalyzed by mono and bisphosphine precatalysts using six distinct substrate pairings. Significant variation in optimal precatalyst was observed, with the monophosphine precatalyst tending to outperform the bisphosphines with electronically deactivated and sterically hindered substrates. Mechanistic experiments revealed a role for monoligated (P1Ni) species in accelerating the fundamental organometallic steps of the catalytic cycle, while highlighting the need for bisligated (P2Ni) species to avoid off-cycle reactivity and catalyst poisoning by heterocyclic motifs. These findings provide guidelines for ligand selection against challenging substrates and future ligand design tailored to the mechanistic demands of Ni-catalyzed SMCs. | Julia Borowski; Samuel Newman-Stonebraker; Abigail Doyle | Organic Chemistry; Catalysis; Organometallic Chemistry; Homogeneous Catalysis; Kinetics and Mechanism - Organometallic Reactions; Ligand Design | CC BY NC 4.0 | CHEMRXIV | 2023-03-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641cb675647e3dca9966b102/original/comparison-of-monophosphine-and-bisphosphine-precatalysts-for-ni-catalyzed-suzuki-miyaura-cross-coupling-understanding-the-role-of-ligation-state-in-catalysis.pdf |
61c35ae102c21409262e7843 | 10.26434/chemrxiv-2021-9gd5m | Workflow for Biocatalytic Reaction Performance Prediction and Analysis | The development of predictive tools to assess enzyme mutant performance and physical organic approaches to enzyme mechanistic interrogation are crucial to the field of biocatalysis. While many indispensable tools exist to address qualitative aspects of biocatalytic reaction design, they often require extensive experimental data sets or a priori knowledge of reaction mechanism. However, quantitative prediction of enzyme performance is lacking. Herein, we present a workflow that merges both computational and experimental data to produce statistical models that predict the performance of new substrates and enzyme mutants while also providing insight into reaction mechanism. As a validating case study, this platform was applied to investigate a non-native enantioselective photoenzymatic radical cyclization. Statistical models enabled interrogation of the reaction mechanism, and the predictive capabilities of these same models led to the quantitative prediction of the enantioselectivities of new substrates with several enzyme mutants. This platform was constructed for application to any biocatalytic system wherein mechanistic interrogation, prediction of reaction performance with new substrates, or quantitative performance of enzyme mutants would be desirable. Overall, this proof of concept study provides a new tool to complement existing protein engineering and reaction design strategies. | Hanna Clements; Autumn Flynn; Bryce Nicholls; Daria Grosheva; Todd Hyster; Matthew Sigman | Theoretical and Computational Chemistry; Organic Chemistry; Catalysis; Machine Learning; Chemoinformatics - Computational Chemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c35ae102c21409262e7843/original/workflow-for-biocatalytic-reaction-performance-prediction-and-analysis.pdf |
67d7e2c06dde43c90817d776 | 10.26434/chemrxiv-2025-2k7wc | Feshbach resonances in the H2(v=1)+OD→H+HOD reaction | Using the MRPD based time-dependent wave packet approach, we calculate the first fully converged state-to-state differential cross sections for the H2(v=1)+OD→H+HOD reaction on a highly accurate neural network PES. Two distinctive peaks are found in the J=0 reaction probabilities and the backward scattering differential cross sections. Detailed analysis reveals that these peaks originate from the Feshbach resonance states trapped in the peculiar well on the HOD(vOH=3) vibrationally adiabatic potential caused by chemical bond softening, and produces mainly HOD(vOH=2) product. | Shu Liu; Dong H. Zhang | Physical Chemistry | CC BY 4.0 | CHEMRXIV | 2025-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d7e2c06dde43c90817d776/original/feshbach-resonances-in-the-h2-v-1-od-h-hod-reaction.pdf |
6377f78974b7b66185035734 | 10.26434/chemrxiv-2022-1vmwv | Comprehensive exploration of graphically defined reaction spaces | Extant reaction transition state (TS) databases are comparatively small and lack chemical diversity. Here, this data gap has been addressed using the concept of a graphically-defined model reaction to comprehensively characterize a reaction space associated with C, H, O and N containing molecules with up to 10 heavy (non-hydrogen) atoms. The resulting dataset is composed of 176,992 organic reactions possessing at least one validated TS, activation energy, heat of reaction, reactant and product geometries, frequencies, and atom-mapping. For 33,032 reactions, more than one TS was discovered by conformational sampling, allowing conformational errors in TS prediction to be assessed. Data is supplied at the GFN2-xTB and B3LYP-D3/TZVP levels of theory. A subset of reactions were recalculated at the CCSD(T)-F12/cc-pVDZ-F12 and ωB97X- D2/TZVP levels to establish relative errors. The resulting collection of reactions and properties are called the Reaction Graph Depth 1 (RGD1) dataset. RGD1 represents the largest and most chemically diverse TS dataset published to date and should find immediate use in developing novel machine learning models for predicting reaction properties. | Qiyuan Zhao; Sai Mahit Vaddadi; Michael Woulfe; Lawal Ogunfowora; Sanjay Garimella; Olexandr Isayev; Brett Savoie | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377f78974b7b66185035734/original/comprehensive-exploration-of-graphically-defined-reaction-spaces.pdf |
6768f68481d2151a02a61733 | 10.26434/chemrxiv-2024-qvnls | Computational Design of the Molecules Exhibiting Non-Overlapping HOMO and LUMO in a Same Molecular Plane | The negative energy difference between singlet and triplet excited states (ΔEST) is currently attracting significant attention; however, molecular designs remain largely confined to azaphenalene structures, as reported by Leupin and Wirz in 1980. To show a negative ΔEST, a non-overlapping HOMO and LUMO arrangement is crucial to minimize the exchange interaction in the excited state. We revisited the electronic structure of cyclazine, consisting of cyclododecahexaene ([12]annulene) and a central nitrogen atom. The 12 π-electrons of the peripheral cyclic oligoene play an important role in achieving the non-overlapping HOMO and LUMO arrangement, and the bridging by the nitrogen atom inside produces the energy difference between HOMO and LUMO while maintaining a stable planar structure. Based on these insights, we designed a set of 10 molecules in which the number of π-electrons (N) in the peripheral cyclic oligoene is 16, 20, and 24, satisfying N = 4·n (n = 4, 5, 6), and a further set of 11 molecules in which N in the peripheral cyclic oligoene is extended to 14, 18, 22, and 26, satisfying N = 4·n + 2 (n = 3, 4, 5, 6). HOMO, LUMO, and ΔEST were calculated using CIS, TD-DFT, and EOM-CCSD with the structure optimized without any symmetry constraint. Among the molecular structures with N = 4·n, only the molecules without bond alternation exhibit a non-overlapping HOMO and LUMO and a small ΔEST. In contrast, among the molecular structures with N = 4·n + 2, none of the molecules exhibit a non-overlapping HOMO and LUMO arrangement. The molecules with both N = 4·n and no bond alternation show negative ΔEST in the EOM-CCSD calculation. The findings of this study will pave the way for broader molecular designs of molecules exhibiting negative ΔEST, where the non-overlap of HOMO and LUMO is essential. | Yong-Jin Pu | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6768f68481d2151a02a61733/original/computational-design-of-the-molecules-exhibiting-non-overlapping-homo-and-lumo-in-a-same-molecular-plane.pdf |
66e0aa4bcec5d6c142b4460d | 10.26434/chemrxiv-2024-j7c15 | Contrasteric glycosylations of cotylenol and 1,2-diols by virtual linker selection | Many terpene glycosides exhibit contrasteric patterns of 1,2-diol glycosylation in which the more hindered alcohol bears a sugar; protection of the less hindered alcohol only increases steric repulsion. Here we report a method for contrasteric glycosylation using a new sugar-linker that forms a cleavable, 10-membered ring with high efficiency, leading to syntheses of cotylenin E, J, and ISIR-050. Linker selection was aided by DFT calculations of side reactions and stereoselectivity, as well as conformational analysis using autoDFT, a Python script that converts SMILES strings to DFT-optimized conformational ensembles. | Dylan Snelson; Stephen Ting; Ryan Shenvi | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66e0aa4bcec5d6c142b4460d/original/contrasteric-glycosylations-of-cotylenol-and-1-2-diols-by-virtual-linker-selection.pdf |
6241bf1674104f94bdb57acf | 10.26434/chemrxiv-2022-qpvt0 | The (Not So) Simple Prediction of Enantioselectivity - A Pipeline for High-Fidelity Computations | The computation of reaction selectivity represents an appealing complementary route to experimental studies and a powerful mean to refine catalyst design strategies. Accurately establishing the selectivity of reactions facilitated by molecular catalysts, however, remains a challenging task for computational chemistry. The small free energy differences that lead to large variations in the enantiomeric ratio represent particularly tricky quantities to predict with sufficient accuracy to be helpful for prioritizing experi- ments. Further complicating this problem is the fact that standard approaches typically consider only one or a handful of conformers identified through human intuition as pars pro toto of the conformational space. Obviously, this assumption can potentially lead to dramatic failures should key energetic low-lying structures be missed. Here, we in- troduce a multi-level computational pipeline built upon the graph-based Molassembler library that combines conformer generation and tailored functionalization to facilitate high-throughput mechanistic investigations of chemical reactions. The capabilities of this approach are validated by examining a Rh(III) catalyzed asymmetric C-H activa- tion reaction and assessing the limitations associated with the underlying ligand design model. Specifically, the presence of remarkably flexible chiral Cp ligands, which induce the experimentally observed high level of selectivity, present a rich configurational landscape where multiple unexpected conformations contribute to the reported enan- tiomeric ratios (er). Using Molassembler, we show that considering about 20 transition state conformations per catalysts, which are generated with little human intervention and are not tied to “back of the envelope” models, accurately reproduces experimental er values with limited computational expense. | Rubén Laplaza; Jan-Grimo Sobez; Matthew Wodrich; Markus Reiher; Clémence Corminboeuf | Theoretical and Computational Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6241bf1674104f94bdb57acf/original/the-not-so-simple-prediction-of-enantioselectivity-a-pipeline-for-high-fidelity-computations.pdf |
65d6505a9138d23161a97fb3 | 10.26434/chemrxiv-2024-4gjgb | Pepticinnamins N, O and P, cytotoxic non-ribosomal peptides from a Soil-Derived Streptomyces mirabilis P8-A2 | Cinnamoyl moiety containing non-ribosomal peptides represented by pepticinnamin E, are a growing family of natural products isolated from different Streptomyces and possess diverse bioactivities. A soil bacterium Streptomyces mirabilis P8-A2 harbors a cryptic pepticinnamin biosynthetic gene cluster, producing azodyrecins as major products. Inactivation of the azodyrecin biosynthetic gene cluster by CRISPR-BEST base editing led to the activation and production of pepticinnamin E (1) and its analogues, pepticinnamins N, O and P (2-4), the structures of which were determined by detailed NMR spectroscopy, HRMS data, and Marfey´s reactions. These new compounds exerted modest growth inhibitory effect against the LNCaP and C4-2B prostate cancer lines, respectively, with pepticinnamin O being the most active. | Ling Ding; Manar Mahmoud; Maria Mahmoud Abboud; Matiss Maleckis; Luciano D. O. Souza; José M. A. Moreira; Charlotte H. Gotfredsen; Tilmann Weber | Organic Chemistry | CC BY 4.0 | CHEMRXIV | 2024-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d6505a9138d23161a97fb3/original/pepticinnamins-n-o-and-p-cytotoxic-non-ribosomal-peptides-from-a-soil-derived-streptomyces-mirabilis-p8-a2.pdf |
63f6a75c32cd591f1255bdd1 | 10.26434/chemrxiv-2023-cggfw | Enantioselective Total Synthesis of (+)-KB343 | A concise total synthesis of the complex guanidinium toxin KB343 is reported traversing through an unusual sequence of chemoselective transformations and strategic skeletal reorganization. The absolute configuration is confirmed through an enantioselective route and the structures of all key intermediates and the natural product itself are unassailably confirmed through X-ray crystallographic analysis. | phil baran; Cheng Bi; Yu Wang; Chi He | Organic Chemistry; Natural Products; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2023-02-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63f6a75c32cd591f1255bdd1/original/enantioselective-total-synthesis-of-kb343.pdf |
60c7562abdbb89d180a3a989 | 10.26434/chemrxiv.14199770.v1 | Kinetic Assessment of the Dry Reforming of Methane over a Solid Solution Ni–La Oxide Catalyst | The dry reforming of
methane is a promising technology for the abatement of CH<sub>4</sub> and CO<sub>2</sub>.
Solid solution Ni–La oxide catalysts are characterized by their long–term
stability (100h) when tested at full conversion. The kinetics of dry reforming
over this type of catalysts has been studied using both power law and Langmuir–Hinshelwood
based approaches. However, these studies typically deal with fitting the net CH<sub>4</sub>
rate hence disregarding competing and parallel surface processes and the different
possible configurations of the active surface. In this work, we synthesized a solid
solution Ni–La oxide catalyst and tested six Langmuir–Hinshelwood mechanisms considering
both single and dual active sites for assessing the kinetics of dry reforming and
the competing reverse water gas shift reaction and investigated the performance
of the derived kinetic models. In doing this, it was found that: (1) all the
net rates were better fitted by a single–site model that considered that the
first C–H bond cleavage
in methane occurred over a <a>metal−oxygen </a>pair
site; (2) this model predicted the existence of a
nearly saturated nickel surface with chemisorbed oxygen adatoms derived from
the dissociation of CO<sub>2</sub>; (3) the dissociation of CO<sub>2</sub> can
either be an inhibitory or an irrelevant step, and it can also modify the apparent
activation energy for CH<sub>4</sub> activation. These findings contribute to a
better understanding of the dry reforming reaction's kinetics and provide a
robust kinetic model for the design and scale–up of the process. | Victor Stivenson Sandoval-Bohorquez; Edgar M. Morales-Valencia; Carlos Omar Castillo-Araiza; Luz Marina Ballesteros Rueda; Víctor Gabriel Baldovino Medrano | Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7562abdbb89d180a3a989/original/kinetic-assessment-of-the-dry-reforming-of-methane-over-a-solid-solution-ni-la-oxide-catalyst.pdf |
618b7db02bf8a940d0d69a90 | 10.26434/chemrxiv-2021-xd440-v3 | Splitting chemical structure data sets for federated privacy-preserving machine learning | With the increase in applications of machine learning methods in drug design and related fields, the challenge of designing sound test sets becomes more and more prominent. The goal of this challenge is to have a realistic split of chemical structures (compounds) between training, validation and test set such that the performance on the test set is meaningful to infer the performance in a prospective application. This challenge is by its own very interesting and relevant,but is even more complex in a federated machine learning approach where multiple partners jointly train a model under privacy-preserving conditions where chemical structures must not be shared between the different participating parties in the federated learning. In this work we discuss three methods which provide a splitting of the data set and are applicable in a federated privacy-preserving setting, namely: a. locality-sensitive hashing (LSH), b. sphere exclusion clustering, c. scaffold-based binning (scaffold network). For evaluation of these splitting methods we consider the following quality criteria: bias in prediction performance, label and data imbalance, distance of the test set compounds to the training set and compare them to a random splitting. The main findings of the paper are a. both sphere exclusion clustering and scaffold-based binning result in high quality splitting of the data sets, b. in terms of compute costs sphere exclusion clustering is very expensive in the case of federated privacy-preserving setting. | Jaak Simm; Lina Humbeck; Adam Zalewski; Noe Sturm; Wouter Heyndrickx; Yves Moreau; Bernd Beck; Ansgar Schuffenhauer | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618b7db02bf8a940d0d69a90/original/splitting-chemical-structure-data-sets-for-federated-privacy-preserving-machine-learning.pdf |
67ae95b5fa469535b93ba2e9 | 10.26434/chemrxiv-2025-5bc2t-v2 | High Throughput Ligand Dissociation Kinetics Predictions using Site-Identification by Ligand Competitive Saturation | The dissociation or off rate, koff, of a drug molecule has been shown to be more relevant to efficacy than affinity for selected systems motivating the development of predictive computational methodologies. These are largely based on enhanced-sampling molecular dynamics (MD) simulations that come at a high computational cost limiting their utility for drug design where a large number of ligands needs to be evaluated. To overcome this, presented is a combined physics- and machine learning (ML)-based approach that uses the physics-based site-identification by ligand competitive saturation (SILCS) method to enumerate potential ligand dissociation pathways and calculate ligand dissociation free energy profiles along those pathways. The calculated free energy profiles along with molecular properties are used as features to train ML models, including tree- and neural network approaches, to predict koff values. The protocol is developed and validated using 329 ligands for thirteen proteins showing robustness of the ML workflows built upon the SILCS physics-based free energy profiles. The resulting SILCS-Kinetics workflow offers a highly efficient method to study ligand dissociation kinetics, providing a powerful tool to facilitate drug design including the ability to generate quantitative estimates of atomic and functional groups contributions to ligand dissociation. | Wenbo Yu; Shashi Kumar; Mingtian Zhao; David Weber; Alex MacKerell | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biophysics; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2025-02-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67ae95b5fa469535b93ba2e9/original/high-throughput-ligand-dissociation-kinetics-predictions-using-site-identification-by-ligand-competitive-saturation.pdf |
673651f45a82cea2fa255e9a | 10.26434/chemrxiv-2024-1t02z | Interactions of sucrose and trehalose with lysozyme in different media: a perspective from atomistic and coarse-grained molecular dynamics simulations | Disaccharides are promising additives for stabilizing proteins in, for example, pharmaceuticals and cryopreserved biomaterials. However, although many studies have shown that disaccharides exhibit such bioprotective and stabilizing properties, the underlying molecular mechanism is still elusive. In this study we have tried to reach such understanding by studying lysozyme in aqueous solutions of sucrose or trehalose and various ions (0.1 M of Cl− , NaCl, ZnCl2 and CaCl2 ) by classical atomistic molecular dynamics (MD) and coarse-grained simulations. The latter simulations were performed for more diluted systems for elucidating larger structures of protein and disaccharide molecules, and possible aggregations. The most important finding for understanding the mechanism of protein stabilization is that the disaccharides in general, and trehalose in particular, slow down the protein dynamics by reducing the number of internal hydrogen bonds (both with and without bridging water molecules) in the protein molecules. This reduction of internal protein interactions is caused by disaccharides binding to the protein hydration water, and trehalose forms more hydrogen bonds to water than sucrose. Although it is far from obvious that such a reduction of internal hydrogen bonding in the protein should lead to slower protein dynamics, and thereby also a stabilization of the protein, the results show that this is clearly the case. The presence of ions has also some effect on the protein dynamics and stability. Particularly, it is discovered that sucrose ability to prevent protein aggregation increases substantially if ZnCl2 is added to the solution. The disaccharide and the salt seem to exhibit a synergistic effect in this case. To summarize, we have obtained molecular understanding for protein stabilization by disaccharides, and why trehalose is more effective than sucrose for this particular system, and the finding is important for understanding how the protein stability in e.g. pharmaceuticals should be optimized. | Inna Ermilova; Jan Swenson | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Biophysics; Biophysical Chemistry; Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673651f45a82cea2fa255e9a/original/interactions-of-sucrose-and-trehalose-with-lysozyme-in-different-media-a-perspective-from-atomistic-and-coarse-grained-molecular-dynamics-simulations.pdf |
60c74440337d6c4b98e26d8a | 10.26434/chemrxiv.9771986.v1 | Photoredox-Catalyzed Intermolecular Radical Addition to Allenamides: A Complementary Approach to Conjugated N-Acyliminium Formation. | <div><div><div><p>An intermolecular radical addition, using photoredox catalysis, to allenamides is reported. This transformation synthesizes <i>N</i>-acyl-<i>N’</i>-aryl-<i>N</i>,<i>N’</i>-allylaminals, and proceeds by a conjugated <i>N</i>-acyliminium intermediate, that previously, has only been generated by electrophilic activation methods. The radical adds to the central carbon of the allene giving a conjugated <i>N</i>-acyliminium, that undergoes nucleophilic addition by arlyamines and alcohols.<b></b></p></div></div></div> | Kayode Koleoso; Matthew Turner; Felix Plasser; Marc Kimber | Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74440337d6c4b98e26d8a/original/photoredox-catalyzed-intermolecular-radical-addition-to-allenamides-a-complementary-approach-to-conjugated-n-acyliminium-formation.pdf |
60c74990702a9b089f18b158 | 10.26434/chemrxiv.12081768.v1 | Catalyst Deactivation Processes During 1-Hexene Polymerization | <p>The catalyst [Cp<sub>2</sub>Zr(<i>μ</i>-Me)<sub>2</sub>AlMe<sub>2</sub>]<sup>+</sup>[B(C<sub>6</sub>F<sub>5</sub>)<sub>4</sub>]<sup>−</sup>
(<b>1</b>) has been studied by electrospray
ionisation mass spectrometry (ESI-MS) in order to better understand the
complexities of catalyst deactivation in the polymerisation of 1-hexene. Using
offline, online and flow-based methods, we observe that zirconium π-allyl species
are unstable in solution and previously unobserved dimethylalane complexes are
more stable. The dimethylalane complexes are resistant to further 1-hexene
additions and their formation represent a new pathway for catalyst
deactivation.</p> | Anuj Joshi; Harmen S. Zijlstra; Scott Collins; J Scott McIndoe | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74990702a9b089f18b158/original/catalyst-deactivation-processes-during-1-hexene-polymerization.pdf |
Subsets and Splits
No saved queries yet
Save your SQL queries to embed, download, and access them later. Queries will appear here once saved.