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668eab6c01103d79c59cfc69 | 10.26434/chemrxiv-2024-7056b | A bridged azobenzene derivative exhibits fully-reversible
photocontrolled binding to a G-quadruplex DNA/duplex junction
| The ability to control G-quadruplex (G4) conformation using light as an external stimuli offers unique opportunities to control G4 in biological settings and for the development of
nucleotide-based nanodevices. We describe a novel G4-binding chemotype derived from a cyclic azobenzene core that reversibly photoisomerises between E- and Z- under physiological conditions. We demonstrate the selective binding of the E-ligand towards LTR-III G4 and show that binding and dissociation from the LTR-III G4 can be controlled reversibly by alternate irradiation with blue and green light. Interestingly, the different isomers exhibit very
distinct binding modes. Whilst the (E)-ligand preferentially binds at the G4/duplex junction of the LTR-III sequence, the (Z)-isomer favours the duplex region. | Javier Ramos-Soriano; Y. Jennifer Jiang; Bowen Deng; Michael O'Hagan; Susanta Haldar; Aditya Grao; Sofia Oliveira; Adrian Mulholland; M. Carmen Galan | Theoretical and Computational Chemistry; Organic Chemistry; Photochemistry (Org.); Supramolecular Chemistry (Org.); Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2024-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/668eab6c01103d79c59cfc69/original/a-bridged-azobenzene-derivative-exhibits-fully-reversible-photocontrolled-binding-to-a-g-quadruplex-dna-duplex-junction.pdf |
6740b578f9980725cf7756e3 | 10.26434/chemrxiv-2024-cm2t6 | Alternate InP Synthesis with Aminophosphines: Solution-Liquid-Solid Nanowire Growth | Indium phosphide nanowires are important components in high-speed electronics and optoelectronics, including photodetectors and photovoltaics. However, most syntheses either use high-temperature and costly vapor-phase methodology or highly toxic and pyrophoric tris(trimethylsilyl)phosphine. To expand on the success of the aminophosphine-based InP colloidal quantum dot synthesis, we developed a synthesis for thin (~13 nm) zincblende InP nanowires at 180 °C using indium tris(trifluoroacetate) and tris(diethylamino)phosphine. A flat nanoribbon morphology was identified by transmission electron and atomic force microscopy analysis, with the stoichiometric (110) lattice plane exposed. Nanowire growth proceeds through a solution-liquid-solid mechanism from in situ-formed indium metal nanoparticles. Molecular byproducts of tris(oleyl)aminophosphine oxide and N-oleyltrifluoroacetamide observed by 31P and 19F NMR spectroscopy inform a proposed mechanism of indium reduction by the aminophosphine. Morphological control over the nanowire product is achieved by varying the phosphorus injection to control the aspect ratio, the In:P ratio to toggle between nanowires and multipods, and the pre-hot injection evacuation step to favor a quantum dot product. Replacing the indium precursor with indium tris(trifluoromethanesulfonate) is found to make bulk zincblende InP nanowires with an average diameter of >250 nm and tens of microns in length. | Helen Larson; Zhixing Lin; Francois Baneyx; Brandi Cossairt | Nanoscience; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2024-11-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6740b578f9980725cf7756e3/original/alternate-in-p-synthesis-with-aminophosphines-solution-liquid-solid-nanowire-growth.pdf |
63a30fdc963bf345d9a1a891 | 10.26434/chemrxiv-2022-d6shx | Molecular Dynamics-Assisted Interaction of Vanadium Complex-AMPK: from the force field development to biological application for Alzheimer's treatment | Large part of the world population is affected by Alzheimer's disease (AD) and diabetes mellitus type 2, which causes both social and economic impacts. These two conditions are associated to one protein, AMPK. Studies have shown that vanadium complexes, such as bis(N',N'-dimethylbiguanidato)-oxovanadium (IV), VO(metf)2·H2O, are potential agents against AD. A crucial step on drug design studies is obtaining information about the structure and interaction of these complexes with the biological targets involved in the process through Molecular Dynamics (MD) simulations. However, MDs depend on the choice of a good force field that could present reliable results. Moreover, general force fields are not efficient for describing the properties of metal complexes, and a VO(metf)2·H2O-specific force field does not yet exist, thus the proper development of a parameter set is necessary. Furthermore, this investigation is essential and relevant given the importance for both the scientific community and the population that is affected by this neurodegenerative disease. Therefore, the present work aims to develop and validate the AMBER force field parameters for VO(metf)2·H2O, since the literature lacks such information on metal complexes, and investigate through classical molecular dynamics the interactions made by the complex with the protein. The proposed force field proved to be effective for describing the vanadium complex (VC), supported by different analysis and validation. Moreover, it had a great performance when compared to general AMBER force field. Beyond that, MD findings provided an in-depth perspective about vanadium complex-protein interactions that should be taken into consideration in future studies. | Camila Assis Tavares; Taináh Martins Resende Santos; Elaine Fontes Ferreira da Cunha; Teodorico de Castro Ramalho | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a30fdc963bf345d9a1a891/original/molecular-dynamics-assisted-interaction-of-vanadium-complex-ampk-from-the-force-field-development-to-biological-application-for-alzheimer-s-treatment.pdf |
60c758ae469df4e632f456eb | 10.26434/chemrxiv.13161359.v2 | Predicting Enzymatic Reactions with a Molecular Transformer | <p>The use of enzymes for organic synthesis allows for simplified, more economical
and selective synthetic routes not accessible to conventional reagents. However,
predicting whether a particular molecule might undergo a specific enzyme
transformation is very difficult. <a>Here we used
multi-task transfer learning to train the Molecular Transformer, a
sequence-to-sequence machine learning model, with one million reactions from
the US Patent Office (USPTO) database combined with 32,181 enzymatic
transformations annotated with a text description of the enzyme. The resulting Enzymatic
Transformer model predicts the structure and stereochemistry of
enzyme-catalyzed reaction products with remarkable accuracy. One of the key
novelties is that we combined the reaction SMILES language of only 405 atomic
tokens with thousands of human language tokens describing the enzymes, such
that our Enzymatic Transformer not only learned to interpret SMILES, but also the
natural language as used by human experts to describe enzymes and their
mutations.</a></p> | David Kreutter; Philippe Schwaller; Jean-Louis Reymond | Machine Learning; Artificial Intelligence; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758ae469df4e632f456eb/original/predicting-enzymatic-reactions-with-a-molecular-transformer.pdf |
60c750f7337d6c5697e28437 | 10.26434/chemrxiv.12866588.v2 | Breaking Simple Scaling Relations Through Metal-Oxide Interactions: Understanding Room Temperature Activation of Methane on M-CeO2 (M= Pt, Ni or Co) Interfaces | The clean activation of methane at low temperatures remains an eminent challenge and a field of competitive research. In particular, on late transition metal surfaces such as Pt(111) or Ni(111), elevated temperatures are necessary to activate the hydrocarbon molecule, but a massive deposition of carbon makes the metal surface useless for catalytic activity. However, on very low-loaded M/CeO2 (M= Pt, Ni, or Co) surfaces, the dissociation of methane occurs at room temperature, which is unexpected considering simple linear scaling relationships. This intriguing phenomenon has been studied using a combination of experimental techniques (ambient-pressure X-ray photoelectron spectroscopy, time-resolved X-ray diffraction and X-ray absorption spectroscopy) and density functional theory-based calculations. The experimental and theoretical studies show that the size and morphology of the supported nanoparticles together with strong metal-support interactions are behind the deviations from the scaling relations. These findings point toward a possible strategy to circumvent scaling relations, producing active and stable catalysts which can be employed for methane activation and conversion. <br /> | Pablo Lustemberg; Feng Zhang; Ramón A. Gutiérrez; Pedro J. Ramírez; Sanjaya D. Senanayake; José A. Rodriguez; M. V. Ganduglia-Pirovano | Catalysts; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-10-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c750f7337d6c5697e28437/original/breaking-simple-scaling-relations-through-metal-oxide-interactions-understanding-room-temperature-activation-of-methane-on-m-ce-o2-m-pt-ni-or-co-interfaces.pdf |
64da8a8969bfb8925aef5685 | 10.26434/chemrxiv-2023-n2g58 | Finite-Size Effects in Simulations of Chemical Reactions | To study macroscopic systems with coarse grained simulations one typically simulates a micro- scopic part of this macroscopic system. By reducing the size of the simulated system one introduces finite size effects. In this work we study the finite-size effects in the reaction ensemble, which is used to simulate reactive system. We calculate the finite-size effects in a non-interacting systems by explicitly calculating the partition function. This approach provides high precision data at low computational costs. For a grand canonical insertion/deletion of a pair of particles our results reproduces previously published results, validating our approach. Further, we show that a sim- ple isomerization reaction is not affected by finite size effects. For a decomposition reaction we show that previous estimates were overestimating the finite-size effects, and one can simulate much smaller systems while avoiding the finite-size effects. For previously studied acid-base equilibria the finite-size effects are only relevant at extreme conditions. The tool we provide allows to a priori estimate the finite-size effects and find the limits of the applicability of the reaction ensemble. | Pascal Hebbeker; Pablo Blanco; Filip Uhlík; Peter Kosovan | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da8a8969bfb8925aef5685/original/finite-size-effects-in-simulations-of-chemical-reactions.pdf |
6377ca2e082129e227fc6bcb | 10.26434/chemrxiv-2022-lk0g5 | Reactivity of trans-Resveratrol toward Electrogenerated Superoxide in N,N-Dimethylformamide | The reactivity of 5-[(E)-2-(4-hydroxyphenyl)ethen-1-yl]benzene-1,3-diol (trans-resveratrol) and related compounds toward electrogenerated superoxide radical anion (O2•−) was investigated using electrochemistry, in situ electrolytic electron spin resonance, and in situ electrolytic ultraviolet–visible spectral measurements, in N,N-dimethylformamide (DMF) with the aid of density functional theory (DFT) calculations. The quasi-reversible cyclic voltammogram of dioxygen/O2•− was modified by the presence of trans-resveratrol, suggesting that the electrogenerated O2•− was scavenged by trans-resveratrol through proton-coupled electron transfer (PCET) via three phenolic hydroxy groups (OH) on the stilbene moiety. The reactivity of trans-resveratrol toward O2•− characterized by the OHs was experimentally confirmed in comparative analyses using some related compounds in DMF. The electrochemical and DFT results suggested that a concerted PCET mechanism via 4’OH of trans-resveratrol proceeds, where the coplanarity of the two phenolic rings in the stilbene moiety linked by an ethylene bridge is essential for a successful O2•− scavenging. | tatsushi nakayama; bunji uno | Agriculture and Food Chemistry; Food | CC BY 4.0 | CHEMRXIV | 2022-11-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6377ca2e082129e227fc6bcb/original/reactivity-of-trans-resveratrol-toward-electrogenerated-superoxide-in-n-n-dimethylformamide.pdf |
64c276b39ed5166e93903605 | 10.26434/chemrxiv-2023-sv8wb | Combined Electrocatalytic Oxidation and Reduction to Selectively Cleave β-O-4 Linkage of Lignin over Platinum Electrode in Organic Solvent: Secondary treatment opportunity for CELF Process | Valorization of lignin is gaining popularity due to its ability to make industrial processes more sustainable. However, the currently prevalent catalytic technologies use large amounts of energy and harsh reaction conditions. As a result, bonds between lignin precursors are cleaved unselectively, and the selectivity of aromatic products is reduced. An electrocatalytic approach may allow improved control, and few studies have assessed electrocatalytic oxidation and reduction of lignin in organic solvents. Organic solvents like tetrahydrofuran (THF) are of interest for lignin electrocatalysis due to their use in the cosolvent enhanced lignocellulosic fractionation (CELF) process. The CELF process has the ability to overcome biomass recalcitrance by breaking β-O-4 aryl ether interunit linkages. Using electrocatalytic conversion processes, additional β-O-4 interunit linkages can be broken down selectively. As a result, if these two processes are integrated, a high amount of phenolic hydroxyl groups with low content aryl ether linkages will be produced, making the product suitable for development of biofuels and other chemicals. This study shows that by using controlled electrocatalytic oxidation and reduction in THF/aqueous acidic electrolytes in the ratio of 2:1, nonpolar β-O-4 linkages can be cleaved. This ratio was chosen to mimic the electrolyte composition environment of the CELF pretreatment. The results from both ATR-IR and NMR characterization are consistent and show that β-O-4 interlinkage bonds were broken. Quantitative calculations from NMR show that during oxidative potential holds, the presence of aromatic compounds increased by 28.67% and aliphatic compounds decreased by 32.73%. On the other hand, during reductive potential holds, the presence of aromatic compounds decreased by 33.50% and aliphatic compounds decreased by 78.43%. These results indicate that electrooxidation and electroreduction may be used strategically to cleave interunit linkages. Thus, if electrochemical degradation of lignin is used as a secondary treatment in conjunction with the CELF process, it will greatly increase the possibility of transforming lignin into value-added products. | Mahmudul Hasan; Amir Akbari; Lauren F. Greenlee | Organic Chemistry; Polymer Science; Chemical Engineering and Industrial Chemistry; Bioorganic Chemistry; Biopolymers; Cellulosic materials | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c276b39ed5166e93903605/original/combined-electrocatalytic-oxidation-and-reduction-to-selectively-cleave-o-4-linkage-of-lignin-over-platinum-electrode-in-organic-solvent-secondary-treatment-opportunity-for-celf-process.pdf |
6358f8f9ac45c7271898ca2e | 10.26434/chemrxiv-2022-5775s-v2 | Global Reactivity Models are Impactful in Industrial Synthesis Applications
| Artificial Intelligence is revolutionizing many aspects of the pharmaceutical industry. Deep learning models are now routinely applied to guide drug discovery projects leading to faster and improved findings, but there are still many tasks with enormous unrealized potential. One such task is the reaction yield prediction. Every year more than one fifth of all synthesis attempts result in product yields which are either zero or too low. This equates to chemical and human resources being spent on activities which ultimately do not progress the programs, leading to a triple loss when accounting for the cost of opportunity in time wasted. In this work we pre-train a BERT model on more than 16 million reactions from 4 different data sources, and fine tune it to achieve an uncertainty calibrated global yield prediction model. This model is an improvement upon state of the art not just from the increase in pre-train data but also by introducing a new embedding layer which solves a few limitations of SMILES and enables integration of additional information such as equivalents and molecule role into the reaction encoding, the model is called BERT Enriched Embedding (BEE). The model is benchmarked on an open-source dataset against a state-of-the-art synthesis focused BERT showing a near 20-point improvement in r2 score. The model is fine-tuned and tested on an internal company data benchmark, and a prospective study shows that the application of the model can reduce the total number of negative reactions (yield under 5%) ran in Janssen by at least 34%. Lastly, we corroborate the previous results through experimental validation, by directly deploying the model in an on-going drug discovery project and showing that it can also be used successfully as a reagent recommender due to its fast inference speed and reliable confidence estimation, a critical feature for industry application. | Paulo Neves; Kelly McClure; Jonas Verhoeven; Natalia Dyubankova; Ramil Nugmanov; Andrey Gedich; Sairam Menon; zhicai Shi; Jörg Wegner | Theoretical and Computational Chemistry; Organic Chemistry; Chemical Engineering and Industrial Chemistry; Organic Synthesis and Reactions; Artificial Intelligence; Pharmaceutical Industry | CC BY NC 4.0 | CHEMRXIV | 2022-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6358f8f9ac45c7271898ca2e/original/global-reactivity-models-are-impactful-in-industrial-synthesis-applications.pdf |
60c75244842e657f93db3cd5 | 10.26434/chemrxiv.13265618.v1 | Accessing Chemo- and Regioselective Benzylic and Aromatic Oxidations by Protein Engineering of an Unspecific Peroxygenase | Unspecific peroxygenases
(UPOs) enable oxyfunctionalisations of a broad substrate range with unparalleled
activities. Tailoring these enzymes for chemo- and regioselective
transformations represents a grand challenge due to the difficulties in their heterologous
productions. Herein, we performed a protein engineering in <i>S. cerevisiae</i> with the novel <i>Mth</i>UPO.
Experimental approaches were combined with computational modelling resulting in
the screening of more than 5,300 transformants. This protein engineering led to
a significant reshaping of the active site as elucidated by molecular dynamics.
The k<sub>cat</sub>/K<sub>m</sub> was improved by 16.5-fold. Variants were
identified with high chemo- and regioselectivities in the oxyfunctionalisation of
aromatic and benzylic carbons, respectively. The benzylic hydroxylation was demonstrated
to perform with excellent enantioselectivities of 95 % <i>ee</i>. Additionally, the first reported effective exchange of the
conserved catalytic Glu residue was observed. | Anja Knorrscheidt; Jordi Soler; Nicole Hünecke; Pascal Püllmann; Marc Garcia-Borràs; Martin Weissenborn | Bioorganic Chemistry; Biocatalysis | CC BY 4.0 | CHEMRXIV | 2020-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75244842e657f93db3cd5/original/accessing-chemo-and-regioselective-benzylic-and-aromatic-oxidations-by-protein-engineering-of-an-unspecific-peroxygenase.pdf |
60c756d30f50db05ad398164 | 10.26434/chemrxiv.14331578.v1 | Chemistry and Quantum Mechanics | Of quantum physics, quantum chemistry and quantum mechanics, the latter is least
useful for both chemical education and the practice of chemistry as a science concerned with the
reactions and properties of chemical substances. We show that quantum mechanics must be
viewed as a collection of methods, numbering at least thirteen, that one might apply for
calculations on a system of an atomic scale. Instead of quantum mechanics we advocate the
quantum laws or laws of discreteness, which have simple roots in laws of conservation and
which have practical applications in various areas of observations of chemical phenomena. We
conclude that quantum mechanics is largely irrelevant for the general practice of chemistry. <br /> | J. F. Ogilvie | Chemical Education - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756d30f50db05ad398164/original/chemistry-and-quantum-mechanics.pdf |
6150b0c24853d25f1fb39215 | 10.26434/chemrxiv-2021-49kpl-v3 | Using wide biological pores to cap and contain the COVID-19 spike protein
| Geometric analysis shows that the spike (S) protein in the COVID-19 virus (SARS-Cov-2) can fully or partially enter into the channel of a wide biological pore like perforin (PFN) or streptolysin (SLO) when the latter is anchored in a bilayer lipid membrane. The PFN channel is a β barrel formed from multiple monomers, for example a ~14 nm diameter channel is formed from 22 monomers. Coincidentally the wide canopy of S (which has three identical chains) has an enclosing diameter of ~14 nm. While inside the channel peripheral residues in the canopy may bind with residues on the pore side of the barrel. If there are no adverse cross-reactions this would effectively prevent S from interacting with a target cell. Calculations with data obtained from PDB and other sources show that there are ~12 peripheral residue triples in S within a circle of diameter ~14 nm that can potentially bind with 22 exposed residues in each barrel monomer. The revised Miyazawa-Jernighan matrix is used to calculate the binding energy of canopy-PFN barrel residue pairs. The results show a large number of binding pairs over distances of up to 38 Å into the pore. This geometric view of capture and containment points to the possibility of using biological pores to neutralize SARS-Cov-2 in its many variant forms. Some necessary conditions that must be satisfied for such neutralization to occur are noted. A wide pore (such as PFN or SLO) can also be used in an electrolytic cell to detect the presence of SARS-Cov-2, which would cause a large-sized blockade of the base current (the ionic current in a fully open pore). It can further be used to quantify the virus level in the sample. Solid-state pores, which have several advantages over biological ones, can be used instead; immune rejection is not an issue and there is no need for the spike or the virus to bind to the pore. | G Sampath | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6150b0c24853d25f1fb39215/original/using-wide-biological-pores-to-cap-and-contain-the-covid-19-spike-protein.pdf |
60c757db337d6cb6fde290d5 | 10.26434/chemrxiv.14483262.v1 | Synergistic Effect of a Mixed Culture in Solid-state Fermentation | This study determines the efficacy of a mixed culture in solid-state fermentation from the perspective of cooperative metabolism, in which comparisons with pure culture fermentations were made. Assays performed include Total Phenolic Content (TPC), Total Dietary Fibre (TDF), and Crude Protein Content via the Kjeldahl Method. | Adwin Ong; Ken Chi Lik Lee | Analytical Chemistry - General; Feed; Food | CC BY NC ND 4.0 | CHEMRXIV | 2021-04-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c757db337d6cb6fde290d5/original/synergistic-effect-of-a-mixed-culture-in-solid-state-fermentation.pdf |
67521e635a82cea2fa1e45bc | 10.26434/chemrxiv-2024-g2bt9 | Using Measurement-Informed Inventory to Assess Emissions in the Denver-Julesburg Basin | Aerial surveys, while effective in detecting emissions from upset conditions, face challenges in fully capturing CH4 emissions due to their temporal limitations, variability in measurements, and detection thresholds. Conversely, annual inventories submitted by operators likely don’t include emissions from failure events. This study introduces a novel methodology that utilizes the Mechanistic Air Emissions Simulator (MAES) to integrate two highly variable estimation methods: inventory and aerial methods. The proposed methodology identifies and characterizes failure events with site-specific information, thereby enhancing the accuracy of inventory programs through the so-called measurement-informed inventories (MIIs). Furthermore, it emphasizes the importance of carefully comparing instantaneous emission measurements from aerial surveys with annual average emissions reported in inventories, as they have distinct timeframes. Colorado State University
(CSU) collaborated with the Colorado Department of Public Health and Environment (CDPHE) to utilize this approach to enhance reported emissions from the upstream sector in Colorado Denver-Julesburg (DJ) basin. This initiative is part of the state’s efforts to reduce emissions under the Upstream greenhouse gas (GHG) Intensity Program. The goal was to incorporate measured emissions from failure events conducted by Carbon Mapper (CM) in the simulations to derive a multiplier that rectifies for potential omissions of emissions from abnormal conditions within the oil and gas (O&G) sector. To simplify the simulation process, prototypical sites were defined in conjunction with operators and are used to represent groups of O&G facilities
in the basin with similar configuration. The outcomes of this work indicate that inventories are likely underestimating total emissions, as an additional 16.4% of total emissions from abnormal events is estimated for the basin. | Arthur Santos; Winrose Mollel; Jerry Duggan; Anna Hodshire; Prajay Vora; Daniel Zimmerle | Earth, Space, and Environmental Chemistry; Atmospheric Chemistry | CC BY 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67521e635a82cea2fa1e45bc/original/using-measurement-informed-inventory-to-assess-emissions-in-the-denver-julesburg-basin.pdf |
65de00b8e9ebbb4db9642051 | 10.26434/chemrxiv-2024-1l0sn | Linear Amine-Linked Oligo-BODIPYs: Convergent Access via Buchwald-Hartwig Coupling | A convergent route towards nitrogen-bridged BODIPY oligomers has been developed. The synthetic key step is a Buchwald-Hartwig cross-coupling reaction of an alpha-amino-BODIPY and the respective halide. Not only does the selective synthesis provide control of the oligomer size, but the facile preparative procedure also enables easy access to this type of dyes. Furthermore, functionalized examples were accessible via brominated derivatives. | Sebastian H. Röttger; Lukas J. Patalag; Felix Hasenmaile; Lukas Milbrandt; Burkhard Butschke; Peter G. Jones; Daniel B. Werz | Organic Chemistry; Organic Compounds and Functional Groups | CC BY NC 4.0 | CHEMRXIV | 2024-02-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65de00b8e9ebbb4db9642051/original/linear-amine-linked-oligo-bodip-ys-convergent-access-via-buchwald-hartwig-coupling.pdf |
638da691836ceb0ed6743584 | 10.26434/chemrxiv-2022-tbq57 | One- and two- electron reductions in
miniSOG and their implication in catalysis | In the last years, the unconventional bioorthogonal catalytic activation of anticancer metal complexes by flavin and flavoproteins photocatalysis has been described [Alonso-de Castro et al., Angew. Chem.,Int. Ed., 2018, 57, 3143]. The reactivity is based on a two-electron redox reaction of the photoactivated flavin. Furthermore, when it comes to flavoproteins, we recently reported that site mutagenesis can modulate and improve this catalytic activity in miniSOG [Gurruchaga-Pereda et al., J. Phys. Chem. Lett., 2021, 12, 19, 4504]. In this paper, we analyze the reductive half-reaction in the different miniSOG environments by means of density functional theory. We observe that the redox properties of the flavin, and consequently, the reactivity of miniSOG changes upon selected mutations, unveiling the physico-
chemical fundamentals of this modulation: the competition between the single and double reduction of the flavin, and the electron transfer probability from the protein to the flavin, which are both ultimately related to the stability of the electron accepting orbitals of the flavin in the different coordination modes. Both factors alter the reactivity
of miniSOG, in line with the experimental results in the literature. | Oksana Azpitarte; Ane Zudaire; Xabier Lopez; Luca Salassa; Elena Formoso; Elixabete Rezabal | Theoretical and Computational Chemistry; Physical Chemistry; Catalysis; Organocatalysis; Redox Catalysis; Photochemistry (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638da691836ceb0ed6743584/original/one-and-two-electron-reductions-in-mini-sog-and-their-implication-in-catalysis.pdf |
61f85484537af82452ac1282 | 10.26434/chemrxiv-2022-596mc | Exploring Isovalent Substitution of Lead with Nickel in Methylammonium Lead Iodide Perovskites | We replaced lead ions with nickel ions in methylammonium lead triiodide (MAPbI3) perovskites and studied their electronic and photophysical properties. We synthesized thin films using solutions containing methylammonium iodide (MAI), PbI2, and NiI2 with varying Pb/Ni precursor ratios. We show that MAPbI3 retains its three-dimensional perovskite structure in the presence of Ni2+. We were able to incorporate up to 30% Ni2+ before we note the appearance of unconverted NiI2 via X-ray diffraction. Although the structures of NiI2 and PbI2 are isostructural and the metal ions have the same oxidation states, the bulk material did not behave as a solid solution. Furthermore, the addition of Ni2+ thoroughly quenched the emission of MAPbI3, suggesting that Ni2+ may act as a recombination center for excited charge carriers. Additionally, the materials displayed significant instability towards water. Thus, we conclude that there is a limited application for nickel and perhaps other transition metal ions as a replacement ion for lead in thin-film perovskite photovoltaic devices fabricated in these conditions. | Emily Smith; Hamza Javaid; Muhammad Abdullah; Kevin Kittilstved; D. Venkataraman | Materials Science; Inorganic Chemistry; Hybrid Organic-Inorganic Materials; Thin Films; Solid State Chemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2022-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61f85484537af82452ac1282/original/exploring-isovalent-substitution-of-lead-with-nickel-in-methylammonium-lead-iodide-perovskites.pdf |
649966a41dcbb92a5e95cad7 | 10.26434/chemrxiv-2023-lttnf | Limits to Hole Mobility and Doping in Copper Iodide | Over one hundred years have passed since the discovery of the p-type transparent conducting material copper iodide, pre-dating the concept of the ``electron-hole'' itself. Supercentenarian status notwithstanding, little is understood about the charge transport mechanisms in \ce{CuI}. Herein, a variety of modelling techniques are used to investigated the charge transport properties of \ce{CuI}, and limitations to the hole mobility over experimentally achievable carrier concentrations are discussed. Poor dielectric response is responsible for extensive scattering from ionised impurities at degenerately doped carrier concentrations, while phonon scattering is found to dominate at lower carrier concentrations. A phonon-limited hole mobility of \SI{162}{\centi\meter\squared\per\volt\per\second} is predicted at room temperature. The simulated charge transport properties for \ce{CuI} are compared to existing experimental data and the implications for future device performance are discussed. In addition to charge transport calculations, the defect chemistry of \ce{CuI} is investigated with hybrid functionals, revealing that reasonably localised holes from the copper vacancy are the predominant source of charge carriers. The chalcogens S and Se are investigated as extrinsic dopants, where it is found that despite relatively low defect formation energies, they are unlikely to act as efficient electron acceptors due to strong localisation of holes and subsequent deep transition levels. | Joe Willis; Romain Claes; Qi Zhou; Matteo Giantomassi; Gian-Marco Rignanese; Geoffroy Hautier; David O. Scanlon | Theoretical and Computational Chemistry; Materials Science; Optical Materials; Computational Chemistry and Modeling; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/649966a41dcbb92a5e95cad7/original/limits-to-hole-mobility-and-doping-in-copper-iodide.pdf |
60c755f70f50db75fd397fe1 | 10.26434/chemrxiv.14188895.v1 | Proton-Detected Solid-State NMR Spectroscopy of Spin-1/2 Nuclei with Large Chemical Shift Anisotropy | <p>Constant-time (CT) dipolar heteronuclear multiple quantum coherence (D-HMQC) has previously been demonstrated as a method for proton detection of high-resolution wideline NMR spectra of spin-1/2 nuclei with large chemical shift anisotropy (CSA). However, <sup>1</sup>H transverse relaxation and <i>t</i><sub>1</sub>-noise often reduce the sensitivity of D-HMQC experiments, preventing the theoretical gains in sensitivity provided by <sup>1</sup>H detection from being realized. Here we demonstrate a series of improved pulse sequences for <sup>1</sup>H detection of spin-1/2 nuclei under fast MAS, with <sup>195</sup>Pt SSNMR experiments on cisplatin as an example. First, a new <i>t</i><sub>1</sub>-incrementation protocol for D-HMQC dubbed Arbitrary Indirect Dwell (AID) is demonstrated. AID allows the use of arbitrary, rotor asynchronous <i>t</i><sub>1</sub>-increments, but removes the constant time period from CT D-HMQC, resulting in improved sensitivity by reducing transverse relaxation losses. Next, we show that short high-power adiabatic pulses (SHAPs), which efficiently invert broad MAS sideband manifolds, can be effectively incorporated into <sup>1</sup>H detected symmetry-based resonance echo double resonance (S-REDOR) and <i>t</i><sub>1</sub>-noise eliminated D-HMQC experiments. The S-REDOR experiments with SHAPs provide approximately double the dipolar dephasing, as compared to experiments with rectangular inversion pulses. We lastly show that sensitivity and resolution can be further enhanced with the use of swept excitation pulses as well as adiabatic magic angle turning.</p> | Amrit Venkatesh; Frédéric Perras; Aaron Rossini | Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c755f70f50db75fd397fe1/original/proton-detected-solid-state-nmr-spectroscopy-of-spin-1-2-nuclei-with-large-chemical-shift-anisotropy.pdf |
6752379df9980725cf31162e | 10.26434/chemrxiv-2024-lsp3k | Including physics-informed atomization constraints in neural networks for reactive chemistry | Machine learning interatomic potentials (MLIPs) have emerged as powerful tools for investigating atomistic systems with high accuracy and relatively low computational cost. However, a common challenge with current MLIPs is their limited ability to accurately predict the relative energies of systems containing isolated or nearly isolated atoms, which often appear in various chemical processes. To address this limitation, we present a technique for modifying existing neural network architectures in a minimal way which accounts for the energies of isolated atoms and the atomization energy (AE) of a system. Using this technique, we build a model architecture we call HIP-NN-AE, an enhanced version of the Hierarchically Interacting Particle Neural Network (HIP-NN). Our results demonstrate that the HIP-NN-AE model significantly outperforms the previous HIP-NN model in multiple scenarios involving isolated atoms, such as complete atomization and bond dissociation processes. We also show that this innovation does not compromise the model performance on other tasks, including barrier height and conformational energy variation. The HIP-NN-AE model thus offers a robust solution to the challenges posed by isolated atoms in energy prediction tasks. | Shuhao Zhang; Michael Chigaev; Olexandr Isayev; Richard Messerly; Nicholas Lubbers | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Machine Learning; Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6752379df9980725cf31162e/original/including-physics-informed-atomization-constraints-in-neural-networks-for-reactive-chemistry.pdf |
637e21c194ff60008c3c9870 | 10.26434/chemrxiv-2022-vhgsg | A π-Conjugated Covalent Organic Framework Enables Interlocked Nickel/Photoredox Catalysis for Light-Harvesting Cross-Coupling Reactions | Covalent organic frameworks (COF) is an outstanding manifesto for heterogeneous photocatalysis. Herein, we synthesized a pyrene-based two-dimensional C=C linked π-conjugated COF via Knoevenagel condensation and anchored Ni(II)-center through bipyridine moieties. Instead of traditional dual metallaphotoredox catalysis, the mono-metal decorated Ni@Bpy-sp2C-COF interlocked the catalysis mediated by light and the transition metal. Under light irradiation, enhanced energy and electron transfer in the COF backbone, as delineated by the photoluminescence, electrochemical, and control experiments, expedited the excitation of Ni centers to efficiently catalyzes diverse photocatalytic C–X (X = B, C, N, O, P, S) cross-coupling reactions with efficiencies orders of magnitude higher than its homogeneous controls. The COF catalyst tolerated a diverse range of coupling partners having various steric and electronic properties under these conditions delivering the products with up to 99% yields. A large number of functional groups were also accommodated for the model reaction. Some reactions were performed on a gram scale and were applied to diversify pharmaceuticals and complex molecules to demonstrate the synthetic utility. The Ni@Bpy-sp2C-COF catalyst could be recovered and reused for several cycles without significant loss in catalytic activities. | Ayan Jati; Suranjana Dam; Shekhar Kumar; Kundan Kumar; Biplab Maji | Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Heterogeneous Catalysis; Photocatalysis; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/637e21c194ff60008c3c9870/original/a-conjugated-covalent-organic-framework-enables-interlocked-nickel-photoredox-catalysis-for-light-harvesting-cross-coupling-reactions.pdf |
60c7462d842e65493adb274f | 10.26434/chemrxiv.11051315.v1 | Simulating Protein-Ligand Binding with Neural Network Potentials | Drug molecules adopt a range of conformations both in solution and in their protein-bound state. The strain and reduced flexibility of bound drugs can partially counter the intermolecular interactions that drive protein–ligand binding. To make accurate computational predictions of drug binding affinities, computational chemists have attempted to develop efficient empirical models of these interactions, although these methods are not always reliable. Machine learning has allowed the development of highly-accurate neural-network potentials (NNPs), which are capable of predicting the stability of molecular conformations with accuracy comparable to state-of-the-art quantum chemical calculations but at a billionth of the computational cost. Here, we demonstrate that these methods can be used to represent the intramolecular forces of protein-bound drugs within molecular dynamics simulations. These simulations are shown to be capable of predicting the protein–ligand binding pose and conformational component of the absolute Gibbs energy of binding for a set of drug molecules. Notably, the conformational energy for anti-cancer drug erlotinib binding to its target was found to considerably overestimated by a molecular mechanical model, while the NNP predicts a more moderate value. Although the ANI-1ccX NNP was not trained to describe ionic molecules, reasonable binding poses are predicted for charged ligands, although this method is not suitable for modeling the ligands in solution. | Shae-Lynn Lahey; Christopher Rowley | Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7462d842e65493adb274f/original/simulating-protein-ligand-binding-with-neural-network-potentials.pdf |
629fa138769c5e706247af32 | 10.26434/chemrxiv-2022-ql20q | Degradation Pathways and Complete Defluorination of Chlorinated Polyfluoroalkyl Substances (Clx−PFAS) | Chlorinated polyfluoroalkyl substances (Clx−PFAS) have been developed and applied for decades, but they have just been recognized as an emerging class of pollutants. This study systematically investigated the degradation of three types of Clx−PFAS structures, including omega-chloroperfluorocarboxylates (ω-ClPFCAs, n=1,2,4,8 Cl−CnF2nCOO−), 9-chlorohexadecafluoro-3-oxanonane-1-sulfonate (F-53B, Cl−(CF2)6−O−(CF2)2SO3−) and polychlorotrifluoroethylene oligomer acids (CTFEOAs, n=1,2,3 Cl−(CF2CFCl)nCF2COO−) under UV/sulfite treatment. The results lead to a series of transformative insights. After initial reductive dechlorination by hydrated electron (eaq–), multiple pathways occur, including hydrogenation, sulfonation, and dimerization. In particular, this study identified the unexpected hydroxylation pathway that convert the terminal ClCF2− into −OOC−, which is critical for the rapid and deep defluorination of F-53B. The hydroxylation of the middle carbons in CTFEOAs also triggers the cleavage of C−C bonds, yielding multiple −COO− groups to promote defluorination. Hence, the Cl atoms in Clx−PFAS enhance defluorination in comparison with the perfluorinated analogs. After UV/sulfite treatment, the HO• oxidation of the residue leads to ~100% defluorination of all ω-ClPFCAs and CTFEOAs, without generating toxic ClO3− from Cl−. This study renovates and further advances the mechanistic understanding of PFAS degradation in “advanced reduction” systems. It also suggests the synergy between “more degradable” molecular design and cost-effective degradation technology to achieve the balanced sustainability of fluorochemicals. | Jinyu Gao; Zekun Liu; Jun Huang; Jinyong Liu | Earth, Space, and Environmental Chemistry; Chemical Engineering and Industrial Chemistry; Environmental Science; Hydrology and Water Chemistry; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629fa138769c5e706247af32/original/degradation-pathways-and-complete-defluorination-of-chlorinated-polyfluoroalkyl-substances-clx-pfas.pdf |
60c74d59f96a00dfe128790c | 10.26434/chemrxiv.12456353.v2 | Chemical Compositions in Salinity Waterflooding of Carbonate Reservoirs: Theory | Higher oil recovery after waterflood in carbonate reservoirs is attributed to increasing water wettability of the rock that in turn relies on complicated surface chemistry. However, calcite mineral reacts with<br />aqueous solutions, and can alter substantially the composition of injected water by mineral dissolution. Care-<br />fully designed chemical and/or brine flood compositions in the laboratory may not remain intact while the<br />injected solutions pass through the reactive reservoir rock. This is especially true for a low-salinity waterflood<br />process, where some finely-tuned brine compositions can improve flood performances, whereas others cannot.<br />We present a 1D reactive transport numerical model that captures the changes in injected compositions dur-<br />ing water flow through porous carbonate rock. We include highly coupled bulk aqueous and surface carbonate-<br />reaction chemistry, detailed reaction and mass transfer kinetics, 2:1 calcium ion exchange, and axial dispersion.<br />At typical calcite reaction rates, local equilibrium is established immediately upon injection. Using an open-<br />source algorithm (Charlton and Parkhurst 2011), we present a design tool to specify chemical/brine flooding<br />packages that correct for composition alteration by carbonate rock.<br />Here, we present a comprehensive 1D reactive transport model and validate it against analytic solutions<br />for rock dissolution, ion exchange, and longitudinal dispersion, each considered separately. A companion paper<br />compares the proposed theory against experiments on core plugs of Indiana limestone that serve as high velocity<br />probes for reaction-controlled and mass-transfer-controlled dissolution. Finally, in another companion paper,<br />we give examples of how injected salinity compositions deviate from those designed in the laboratory for water-<br />wettability improvement based on contact angles, zeta potentials, surface charge densities, and ion exchange.<br />How to correct the design chemical packages for exposure to reactive rock is also discussed in there. | Maxim Yutkin; Clayton J. Radke; Tadeusz Patzek | Geochemistry; Hydrology and Water Chemistry; Natural Resource Recovery; Transport Phenomena (Chem. Eng.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-07-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d59f96a00dfe128790c/original/chemical-compositions-in-salinity-waterflooding-of-carbonate-reservoirs-theory.pdf |
60c74362bdbb890c7ca3862b | 10.26434/chemrxiv.9118343.v1 | Anisotropic Hydrolysis Susceptibility in Deformed Polydimethylsiloxanes | <div>Chemical reactions involving the polydimethylsiloxane (PDMS) backbone can induce significant network rearrangements and ultimately degrade macro-scale mechanical properties of silicone components. Using two levels of quantum chemical theory, we identify a possible electronic driver for chemical susceptibility in strained PDMS chains and explore the complicated interplay between hydrolytic chain scissioning reactions, mechanical deformations of the backbone, water attack vector, and chain mobility. Density functional theory (DFT) calculations reveal that susceptibility to hydrolysis varies significantly with the vector for water attacks on silicon backbone atoms, which matches strain-induced anisotropic changes in the backbone electronic structure. Efficient semiempirical density functional tight binding (DFTB) calculations are shown to reproduce DFT predictions for select reaction pathways and facilitate more exhaustive explorations of configuration space. We show that concerted strains of the backbone must occur over at least few monomer units to significantly increase hydrolysis susceptibility. In addition, we observe that sustaining tension across multiple monomer lengths by constraining molecular degrees of freedom further enhances hydrolysis susceptibility, leading to barrierless scission reactions for less substantial backbone deformations than otherwise. We then compute chain scission probabilities as functions of the backbone degrees of freedom, revealing complicated configurational inter-dependencies that impact the likelihood for hydrolytic degradation. The trends identified in our study suggest simple physical descriptions for the synergistic coupling between local mechanical deformation and environmental moisture in hydrolytic degradation of silicones.</div> | Matthew Kroonblawd; Nir Goldman; James Lewicki | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74362bdbb890c7ca3862b/original/anisotropic-hydrolysis-susceptibility-in-deformed-polydimethylsiloxanes.pdf |
64f8ed4279853bbd783eca1f | 10.26434/chemrxiv-2023-kmpmr | Microfluidically produced microcapsules with amphiphilic polymer conetwork shells | Microcapsules with aqueous core can be conveniently prepared by water-in-oil-in-water double emulsion microfluidics. However, conventional shell materials are either based on polymers or monomers that are soluble in the oil phase, or based on hydrophobic colloidal particles. As a result, microcapsules derived from double emulsions usually feature a hydrophobic shell that is not semipermeable for water-soluble compounds. While capsules with semipermeable hydrogel shells have been demonstrated, these may exhibit poor mechanical properties and lack the robustness required in many applications. In this study, amphiphilic polymer conetworks (APCNs) based on poly(2-hydroxyethyl acrylate)-linked by-polydimethylsiloxane (PHEA-l-PDMS) are introduced as a new class of wall materials in double emulsion microcapsules. These APCNs are mechanically robust silicone hydrogels that are swellable and permeable to water, and are soft and elastic in the dry and swollen states. Thus, the microcapsules can be dried and rehydrated multiple times or shrunken in sodium chloride salt solutions without getting damaged. Moreover, the APCNs are semipermeable for hydrophilic organic compounds, while being impermeable for macromolecules and colloids. Thus, they can be loaded with macromolecules or nanoparticles during microfluidic formation, and with organic molecules after capsule synthesis. Uptake into and release from the capsules were studied with the model compounds fluorescein and fluorescently labelled dextran. Moreover, the microcapsules served as microreactors for catalytically active platinum nanoparticles that decomposed hydrogen peroxide. Finally, the surface of APCN microcapsules can be selectively functionalized with a cholesterol-based linker that non-covalently binds to the hydrophobic domains of the APCN. Thus, APCN microcapsules represent versatile and broadly applicable capsules that could find application for the controlled delivery of drugs, as microreactors for synthesis, or even as scaffolds for synthetic cells. | Sara T. R. Velasquez; Andrea Belluati; Elena Tervoort; Iacopo Mattich; Brigitte Hertel; Sam Russell; Micael Gouveia; Clément Mugemana; André R. Studart; Nico Bruns | Catalysis; Polymer Science; Hydrogels; Organic Polymers; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-09-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64f8ed4279853bbd783eca1f/original/microfluidically-produced-microcapsules-with-amphiphilic-polymer-conetwork-shells.pdf |
611b760745805d4dcf893d72 | 10.26434/chemrxiv-2021-ltlpw | Precise Molecular Engineering of Type I Photosensitizers with Near-Infrared Aggregation-Induced Emission for Image-Guided Photodynamic Killing of Multidrug-Resistant Bacteria | Multidrug resistance (MDR) bacteria pose a serious threat to human health. The development of alternative treatment modalities and therapeutic agents for treating MDR bacteria-caused infections remains a global challenge. Herein, we rationally designed and successfully developed a series of near-infrared (NIR) anion-π+ photosensitizers featuring aggregation-induced emission (AIE-PSs) for broad-spectrum MDR bacteria eradication. Due to the strong intramolecular charge transfer (ICT) and enhanced highly efficient intersystem crossing (ISC), these electron-rich anion-π+ AIE-PSs showed boosted type I reactive oxygen species (ROS) generation capability involving hydroxyl radicals and superoxide anion radicals, and up to 99% photodynamic killing efficacy was achieved for both Methicillin-resistant Staphylococcus aureus (MRSA) and multi-drug resistant Escherichia coli (MDR E.coli) under a low dose white light irradiation (16 mW cm-2). In vivo experiments confirmed that one of these AIE-PSs exhibited excellent therapeutic performance in curing MRSA or MDR E.coli-infected wounds with negligible side-effects. The study would thus provide useful guidance for the rational design of high-performance type I AIE-PSs to overcome antibiotic resistance. | Peihong Xiao; Zipeng Shen; Deliang Wang; Yinzhen Pan; Ying Li; Junyi Gong; Lei Wang; Dong Wang; Ben Zhong Tang | Materials Science; Aggregates and Assemblies; Biocompatible Materials; Imaging Agents; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/611b760745805d4dcf893d72/original/precise-molecular-engineering-of-type-i-photosensitizers-with-near-infrared-aggregation-induced-emission-for-image-guided-photodynamic-killing-of-multidrug-resistant-bacteria.pdf |
60c74b74ee301ca952c79e81 | 10.26434/chemrxiv.12336704.v1 | Structure-Astringency Relationship of Anacardic Acids from Cashew Apple (Anacardium Occidentale L.) | <p>Cashew apple presents a characteristic astringency. However, the compounds responsible for this characteristic were not described yet. A cashew apple extract was added to a BSA solution and the compounds before and after precipitation were analyzed by UPLC-QTOF/MS<sup>E</sup>. The extract astringency was measured on a 5-point scale (0: non astringent and 4: extremely astringent). Among the phenolics detected anacardic acids were identified and evaluated for their astringent effect. In the sensorial tests the cashew apple extract was considered very astringent (average of 2.5). A mixture of anacardic acids, had an average of 1.76 (astringent). The three isolated anacardic acids were evaluated. The <i>in silico</i>experiments were performed to analyze mainly the steric factor associated to the binding. The sensory results were confirmed by <i>in silico</i> analysis, indicating that a higher unsaturation degree of the aliphatic chain leads to an astringency increase.</p> | Edy Brito; Liana Mendes; Deborah Garruti; Guilherme Zocolo; Marcelo Lima | Natural Products; Food; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b74ee301ca952c79e81/original/structure-astringency-relationship-of-anacardic-acids-from-cashew-apple-anacardium-occidentale-l.pdf |
60c7530e702a9bf16718c2db | 10.26434/chemrxiv.13382741.v1 | New High-Performance Porous Ionic Liquids for Low Pressure CO2 Capture | <div><div><div><p>Porous ionic liquids are non volatile, versatile materials that associate porosity and fluidity. New porous ionic liquids, based on the ZIF-8 metal-organic framework and on phosphonium acetate or levulinate salts, were prepared and show an increased capacity to absorb carbon dioxide at low pressures. Porous suspensions based on phosphonium levulinate ionic liquid absorb reversibly 103% more carbon dioxide per mass than pure ZIF-8 per mass at 1bar and 303K. We show how the rational combination of MOFs with ionic liquids can greatly enhance low pressure CO2 absorption, paving the way toward a new generation of high-performance, readily available liquid materials for effective low pressure carbon capture.</p></div></div></div> | Jocasta Avila; Luiz Fernando Lepre; Catherine Santini; Martin Tiano; Sandrine Denis-Quanquin; Kai Chung Szeto; Agilio Padua; Margarida Costa Gomes | Physical and Chemical Processes | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7530e702a9bf16718c2db/original/new-high-performance-porous-ionic-liquids-for-low-pressure-co2-capture.pdf |
60c758d9ee301ca9b0c7b7de | 10.26434/chemrxiv.14575992.v1 | Excited State Mechanisms in Crystalline Carbazole: The Role of Aggregation and Isomeric Defects | The molecule of Carbazole (Cz) is commonly used as a building block in organic materials for optoelectronic applications, acting as light-absorbing, electron donor and emitting moiety. Crystals from Cz and derivatives display ultralong phosphorescence at room temperature. However, different groups have reported inconsistent quantum efficiencies for the same compounds. In a recent experimental study by Liu et al. (<i>Nature Materials</i> <b>2021</b>, 20, 175-180), the ultralong phosphoresce properties of Cz have been associated with the presence of small fractions of isomeric impurities from commercially available Cz. In this paper, we use state-of-the-art computational approaches to investigate light-induced processes in crystalline and doped Cz. We revisit the role of aggregation and isomeric impurities on the excited state pathways and analyse the mechanisms for exciton, Dexter energy transfer and electron transport based on Marcus and Marcus-Levich-Jortner theories. Our excited state mechanisms provide a plausible interpretation for the experimental results and support the formation of charge-separated states at the defect/Cz molecular interface. These results contribute to a better understanding of the factors enhancing the excited state lifetimes in organic materials and the role of doping with organic molecules. | Federico J. Hernández; Rachel Crespo Otero | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c758d9ee301ca9b0c7b7de/original/excited-state-mechanisms-in-crystalline-carbazole-the-role-of-aggregation-and-isomeric-defects.pdf |
675011dcf9980725cf0047ce | 10.26434/chemrxiv-2024-sc8jv | Understanding the Nitrogen Reduction Reaction Mechanism on CuFeO2 Photocathodes | This study investigates the reaction pathways for the conversion of \ce{N2} to \ce{NH3} on \ce{CuFeO2} (CFO) by employing density functional theory (DFT) calculations. Concentrating on the most stable (012) surface orientation, two systems were examined: the pristine (012) surface and the corresponding oxygen defective surface. To find the thermodynamic stable pathway, the associative Heyrovsk{\'y} mechanism was considered, containing four different reaction pathways. The reaction intermediates predominantly interact with the iron sites on the surface, following the distal alternating reaction pathway via the formation of hydrazine. Introducing oxygen defects changes the reaction mechanism to a Mars--van--Krevelen--type mechanism, avoiding the formation of hydrazine, while the Gibbs free energy of the first hydrogenation step is lowered by 1.17~eV (from 2.17 to 1.00~eV). Analyzing the charge density distribution reveals that oxygen defective surface enables CFO to facilitate a $\pi$--backdonation between iron sites and the NRR intermediates, increasing the intermediate--surface interaction. This indicates an enhanced catalytic activity for the NRR by generating oxygen lattice defects in CFO. | Julian Beßner; Timo Jacob | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Photochemistry (Physical Chem.); Thermodynamics (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675011dcf9980725cf0047ce/original/understanding-the-nitrogen-reduction-reaction-mechanism-on-cu-fe-o2-photocathodes.pdf |
64ba35ffae3d1a7b0d16f871 | 10.26434/chemrxiv-2023-1zg89-v2 | High-throughput deconvolution of native protein mass spectrometry imaging datasets for mass domain analysis. | Protein mass spectrometry imaging (MSI) with electrospray-based ambient ionization techniques, such as nanospray-desorption electrospray ionization (nano-DESI), generates datasets in which each pixel corresponds to a mass spectrum populated by peaks corresponding to multiply-charged protein ions. Importantly, the signal associated with each protein is split among multiple charge states. These peaks can be transformed into the mass domain by spectral deconvolution. When proteins are imaged under native/non-denaturing conditions to retain non-covalent interactions, deconvolution is particularly valuable in helping interpret the data. To improve acquisition speed, signal-to-noise ratio, and sensitivity, native MSI is usually performed using mass resolving powers that do not provide isotopic resolution, and conventional algorithms for deconvolution of lower-resolution data are not suitable for these large data sets. UniDec was originally developed to enable rapid deconvolution of complex protein mass spectra. Here, we developed an updated feature set harnessing the high-throughput module, MetaUniDec, to deconvolve each pixel of native MSI datasets and transform m/z-domain image files to the mass domain. New tools enable reading, processing, and output of open format .imzML files for downstream analysis. Transformation of data into the mass domain also provides greater accessibility, with mass information readily interpretable by users of established protein biology tools such as SDS-PAGE. | Oliver Hale; Helen Cooper; Michael Marty | Analytical Chemistry; Biochemical Analysis; Imaging; Mass Spectrometry | CC BY NC ND 4.0 | CHEMRXIV | 2023-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ba35ffae3d1a7b0d16f871/original/high-throughput-deconvolution-of-native-protein-mass-spectrometry-imaging-datasets-for-mass-domain-analysis.pdf |
60c74bc5842e65f1e5db31f6 | 10.26434/chemrxiv.12376505.v1 | A Comprehensive Integrated Drug Similarity Resource for In-Silico Drug Repositioning and Beyond | <p><b>Drug similarity studies are driven by the hypothesis that similar drugs should display similar therapeutic actions and thus can potentially treat a similar constellation of diseases. Drug-drug similarity has been derived by variety of direct and indirect sources of evidence and frequently shown high predictive power in discovering validated repositioning candidates as well as other in-silico drug development applications. Yet, existing resources either have limited coverage or rely on an individual source of evidence, overlooking the wealth and diversity of drug-related data sources. Hence, there has been an unmet need for a comprehensive resource integrating diverse drug-related information to derive multi-evidenced drug-drug similarities. We addressed this resource gap by compiling heterogenous information for an exhaustive set of small-molecule drugs (total of 10,367 in the current version) and systematically integrated multiple sources of evidence to derive a multi-modal drug-drug similarity network. The resulting database, DrugSimDB currently includes 238,635 drug pairs with significant aggregated similarity, complemented with an interactive user-friendly web interface (http://vafaeelab.com/drugSimDB.html) which not only enables database ease of access, search, filtration and export, but also provides a variety of complementary information on queried drugs and interactions. The integration approach can flexibly incorporate further drug information into the similarity network, providing an easily extendable platform. The database compilation and construction source-code has been well-documented and semi-automated for any-time upgrade to account for new drugs and up-to-date drug information. </b></p><div><br /></div> | AKM Azad; Mojdeh Dinarvand; Alireza Nematollahi; Joshua Swift; Louise Lutze-Mann; Fatemeh Vafaee | Bioinformatics and Computational Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bc5842e65f1e5db31f6/original/a-comprehensive-integrated-drug-similarity-resource-for-in-silico-drug-repositioning-and-beyond.pdf |
653f89d9c573f893f16db894 | 10.26434/chemrxiv-2023-ffvmq | Exploring the substantial diversity of pesticide products | To understand the impacts of pesticides on non-targets, it is important to understand what pesticide products are authorised for use. Different pesticide formulations with the same active ingredient can pose different risks to non-target organisms due to the inclusion of co-formulants which can modify their toxicity. We collated datasets from the United Kingdom (UK) and Ireland containing information on all the authorised pesticide products (pesticide formulations and adjuvants). We reveal that there are 2,463 pesticide formulations authorised for use by professionals in the UK, representing 266 active ingredients. We also collated information on amateur pesticide formulations, finding 520 authorised in the UK, and adjuvants (separate products added to a tank mix to alter the spray action), finding 298 authorised in the UK. Although we focus on the UK dataset, the same overall trends are mirrored in the Irish data. For the first time we have brought together data on the diversity of pesticides on sale in the UK and Ireland. | Edward Straw; Dara Stanley | Agriculture and Food Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653f89d9c573f893f16db894/original/exploring-the-substantial-diversity-of-pesticide-products.pdf |
67815e5e81d2151a029d4905 | 10.26434/chemrxiv-2025-2q8vj | Tuning electrolyte composition subverts scaling relationships in molecular catalysis of electrochemical nitrate reduction | In molecular electrocatalysis, a log-linear tradeoff between turnover frequency (TOF) and overpotential (η) is frequently observed and limits catalytic performance. This scaling relationship is reflected in the molecularly catalyzed electrochemical nitrate reduction reaction (NO3RR), which generally requires large overpotentials for ammonia production (η > 1.5 V). Thus, strategies to lower η while increasing TOF are needed for more energy-efficient NO3RR. In this study, we investigate the molecular electrocatalyst [CoIII(DIM)Br2]ClO4 (DIM = 2,3-dimethyl-1,4,8,11-tetraazacyclotetradeca-1,3-diene), which selectivity catalyzes NO3RR to NH3. Through electroanalytical studies, we demonstrate that electrolyte pH and bromide concentration can be synergistically tuned to lower η (up to 0.50 V) while increasing TOF (up to 5.2x). We therefore tailor electrolyte composition to achieve a TOF of (5.3 ± 0.4) s−1 at −0.13 V vs. RHE (η ≈ 0.85 V), surpassing both the catalytic activities and overpotentials of state-of-the-art NO3RR molecular electrocatalysts. Our results reveal that tuning electrolyte composition can help overcome the TOF-η tradeoff in molecular electrocatalysis. | Matthew Liu; Dean Miller; Uran Iwata; William Tarpeh | Catalysis; Electrocatalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67815e5e81d2151a029d4905/original/tuning-electrolyte-composition-subverts-scaling-relationships-in-molecular-catalysis-of-electrochemical-nitrate-reduction.pdf |
60c73fe1842e65b7c9db1bbd | 10.26434/chemrxiv.7165468.v2 | Local Environment and Dynamic Behavior of Fluoride Anions in Silicogermanate Zeolites: A Computational Study of the AST Framework | <p>In
silicogermanate zeolites containing double four-ring (<i>d4r</i>) building units, the germanium atoms preferentially occupy the
corners of these cube-like units. While this general behaviour is well known, the
absence of long-range order precludes a determination of the preferred
arrangements of Si and Ge atoms at the corners of <i>d4r</i> cages by means of crystallographic methods. If fluoride anions
are present during the synthesis, these are incorporated into the <i>d4r</i> cages. Due to the sensitivity of the
<sup>19</sup>F chemical shift to the local environment, NMR experiments can
provide indirect insights into the predominant (Si,Ge) arrangements. However,
conflicting interpretations have been reported, both with regard to the
preference for, or avoidance of, Ge-O-Ge linkages, and concerning the
equilibrium position of fluorine inside the cage, where fluorine might either occupy
the cage centre or participate in a partly covalent Ge-F bond. In order to shed
light on the energetically preferred local arrangements, periodic electronic
structure calculations in the framework of dispersion-corrected density
functional theory (DFT) were performed. The AST framework was used as a suitable
model system, as this zeolite is synthetically accessible across the range of
(Si<sub>1-n</sub>,Ge<sub>n</sub>)O<sub>2</sub> compositions (0 ≤ <i>n</i> ≤ 1). DFT structure optimisations for (Si,Ge)-AST
systems containing fluoride anions and organic cations revealed that
arrangements of Si and Ge at the cage vertices which maximise the number of
Ge-O-Ge linkages are energetically preferred, and that fluorine tends to form
relatively short (~2.2 to 2.4 Å) bonds to Ge atoms that are surrounded by
Ge-O-Ge linkages. The preference for Ge-O-Ge linkages disappears in the absence
of fluorine, pointing to a “templating” effect of the anions. In addition to
the prediction of equilibrium structures, DFT-based Molecular Dynamics
calculations were performed for selected AST models in order to analyse the
dynamics of fluoride anions confined to <i>d4r</i>
cages. These calculations showed that the freedom of movement of fluorine
varies markedly depending on the local environment, and that it correlates with
the average Ge-F distance (short Ge-F bonds = restricted motion). An analysis
of the Ge-F radial distribution functions provided no evidence for a
coexistence of separate local energy minima at the cage centre and in the
proximity of a germanium atom for any of the systems considered. The
computational approach pursued in this work provides important new insights
into the local structure of silicogermanate zeolites with <i>d4r</i> units, enhancing the atomic-level understanding of these
materials. In particular, the findings presented here constitute valuable
complementary information that can aid the interpretation of experimental data.<i></i></p> | Michael Fischer | Catalysts; Solid State Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73fe1842e65b7c9db1bbd/original/local-environment-and-dynamic-behavior-of-fluoride-anions-in-silicogermanate-zeolites-a-computational-study-of-the-ast-framework.pdf |
62669452bdc9c2e04ae20bb6 | 10.26434/chemrxiv-2022-2g0j3-v2 | Impacts of orthophosphate-polyphosphate blends on the dissolution and transformation of lead (II) carbonate | Phosphate addition is a popular strategy to minimize lead release. Despite continuous research on orthophosphate for lead control, studies exploring the complexity of the interaction between lead and orthophosphate-polyphosphate blends in drinking water are scarce. Three model polyphosphates—tripoly-, trimeta- and hexametaphosphate— were used to examine the structural impacts of polyphosphate on lead release. We used a continuously-stirred tank reactor with a lead (II) carbonate solid to evaluate the impact of orthophosphate-polyphosphate blends compared to orthophosphate on lead solubility, speciation, and mineralogy under conditions relevant to drinking water. Tripolyphosphate was a stronger complexing agent for lead than trimetaphosphate (1 ± 0.01 vs 0.07 ± 0.01 molPb/molPolyphosphate), and hexametaphosphate was associated with greater lead solubility (1.6-2.1 ± 0.1 molPb/molPolyphosphate).
At equivalent orthophosphate and polyphosphate concentrations (as P), orthophosphate-trimetaphosphate had minimal impact on lead release, while orthophosphate-tripolyphosphate increased dissolved by 554 ± 29 and 213 ± 22 μg Pb0.2μm m-2 at 30-min and 24-hr reaction times, respectively. Meanwhile, orthophosphate-hexametaphosphate increased dissolved lead only at the 24-hr reaction time (by 256 ± 13 μg Pb0.2μm m-2). Both orthophosphate-tripolyphosphate and orthophosphate-hexametaphosphate increased small colloidal lead concentrations over a 24-hr stagnation. Except with orthophosphate-trimetaphosphate, having more polyphosphate than orthophosphate increased dissolved lead release.
All three polyphosphates inhibited the formation of hydroxypyromorphite and reduced the phosphorous content of the resulting lead solids. We attribute the impacts of orthophosphate-polyphosphates to a combination of complexation, adsorption, colloidal dispersion, polyphosphate hydrolysis, and lead mineral precipitation.
| Javier Locsin; Benjamin F. Trueman; Evelyne Doré; Aaron Bleasedale-Pollowy; Graham A. Gagnon | Earth, Space, and Environmental Chemistry; Environmental Science; Hydrology and Water Chemistry | CC BY NC 4.0 | CHEMRXIV | 2022-04-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62669452bdc9c2e04ae20bb6/original/impacts-of-orthophosphate-polyphosphate-blends-on-the-dissolution-and-transformation-of-lead-ii-carbonate.pdf |
64e4f55e79853bbd7837e9e9 | 10.26434/chemrxiv-2023-ppk9s | FLUID-GPT (Fast Learning to Understand and Investigate Dynamics with a Generative Pre-Trained Transformer): Efficient Predictions of Particle Trajectories and Erosion | The deleterious impact of erosion due to high-velocity particle impingement adversely affects a variety of engineering/industrial systems, resulting in irreversible mechanical wear of materials/components. Brute force computational fluid dynamics (CFD) calculations are commonly used to predict surface erosion by directly solving the Navier Stokes equations for the fluid and particle dynamics; however, these numerical approaches often require significant computational resources. In contrast, recent data-driven approaches using machine learning (ML) have shown immense promise for more efficient and accurate predictions to sidestep the computationally demanding CFD calculations. To this end, we have developed FLUID-GPT (Fast Learning to Understand and Investigate Dynamics with a Generative Pre-Trained Transformer), a new hybrid ML architecture for accurately predicting particle trajectories and erosion on an industrial-scale steam header geometry. Our FLUID-GPT approach utilizes a Generative Pre-Trained Transformer 2 (GPT-2) with a Convolutional Neural Network (CNN) for the first time to predict surface erosion using only information from five initial conditions: particle size, main-inlet speed, main-inlet pressure, sub-inlet speed, and sub-inlet pressure. Compared to the Long- and Short-Term Memory (LSTM) ML techniques used in previous work, our FLUID-GPT model is much more accurate (a 54% decrease in mean squared error) and efficient (70% less training time). Our work demonstrates that FLUID-GPT is an accurate and efficient ML approach for predicting time-series trajectories and their subsequent spatial erosion patterns in these complex dynamic systems. | Steve Yang; Zulfikhar Ali; Bryan Wong | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Machine Learning; Artificial Intelligence; Fluid Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64e4f55e79853bbd7837e9e9/original/fluid-gpt-fast-learning-to-understand-and-investigate-dynamics-with-a-generative-pre-trained-transformer-efficient-predictions-of-particle-trajectories-and-erosion.pdf |
60c74a9ebb8c1a6faa3db04b | 10.26434/chemrxiv.12129129.v2 | Computational Drug Simulation: A Step to the Possible Cure of COVID-19 | World Health Organization declared COVID-19 as a pandemic on 11th March,2020. Without any exact cure or vaccine, this disease has certainly taken a toll of humanity. Computer-aided Drug Design (CADD) is the modern era simulator for aiding in finding cure before starting actual clinical trials in patients. We have not indulged into making a new drug but analysing the existing drugs as approved by FDA to find the possible cure options. Based on the above data from our study, we find that anti-inflammatory drugs like prednisone and anti-psychotic drugs can be used for targeting the spike glycoprotein of the SARS-CoV2 virus. | Kumar Sharp; Dr. Shubhangi Dange | Bioinformatics and Computational Biology; Chemical Biology; Microbiology | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74a9ebb8c1a6faa3db04b/original/computational-drug-simulation-a-step-to-the-possible-cure-of-covid-19.pdf |
6532079087198ede07d915dd | 10.26434/chemrxiv-2023-qg51b | Chemometric guided isolation of new triterpenoid saponins as acetylcholinesterase inhibitors from Achyranthes bidentata Blume | Achyranthes bidentata Blume is an annual herb widely used as functional food and for ethnomedicinal purposes in Traditional Chinese medicine. Its seeds are widely used as cereal grain substitutes due to their excellent nutritional composition and health benefits. In current study, chemical profiling with chemometric guided approach was adopted for the tentative identification of fifty-six compounds based on UPLC-IM-Q-TOF-MS/MS analysis. Chemometric guided approach also led to the isolation of two previously undescribed triterpenoid saponins, named as, achyranosides A-B (1-2) along with three known compounds (3-5) from water fraction of A. bidentata seeds. The structure elucidation of isolated molecules was done by using NMR, HR-ESI-MS, FT-IR and GC-FID techniques. Chikusetsusaponin IVa (5) exhibited most promising inhibition (IC50 values of 63.72 µM) of acetylcholinesterase in vitro with mixed type of AChE inhibition in enzyme kinetic studies. Additionally, in-silico studies disclosed the underlying molecular interactions and binding free energy between ligands and the binding sites. The current study demonstrated the effectiveness of chemometric guided integrated approach for the phytochemical exploration and isolation of new oleanane-type triterpenoid saponins from A. bidentata seeds. | Shivani Puri; Prithvi Pal Singh; Prateek Singh Bora; Upendra Sharma | Organic Chemistry; Analytical Chemistry; Agriculture and Food Chemistry; Natural Products; Analytical Chemistry - General; Spectroscopy (Anal. Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532079087198ede07d915dd/original/chemometric-guided-isolation-of-new-triterpenoid-saponins-as-acetylcholinesterase-inhibitors-from-achyranthes-bidentata-blume.pdf |
60c73cc09abda2727df8b5d8 | 10.26434/chemrxiv.14770797.v1 | Visualizing Electron Beam-Capping Ligand Reactions for Controlled Nanoparticle Imaging with Liquid Phase Transmission Electron Microscopy | Liquid phase transmission electron microscopy (LP-TEM) enables real-time imaging of nanoparticle self-assembly, formation, and etching with single nanometer resolution. Despite the importance of organic nanoparticle capping ligands in these processes, the effect of electron beam irradiation on surface bound and soluble capping ligands during LP-TEM imaging has not been investigated. Here we use correlative LP-TEM and fluorescence microscopy (FM) to demonstrate that polymeric nanoparticle ligands undergo competing crosslinking and chain scission reactions that non-monotonically modify ligand coverage over time. Branched polyethylenimine (BPEI) coated silver nanoparticles were imaged with dose-controlled LP-TEM followed by labeling their primary amine groups with fluorophores to visualize the local thickness of adsorbed capping ligands. FM images showed that free ligands crosslinked in the LP-TEM image area over imaging times of tens of seconds, enhancing local capping ligand coverage on nanoparticles and silicon nitride membranes. Nanoparticle surface ligands underwent chain scission over irradiation times of minutes to tens of minutes, which depleted surface ligands from the nanoparticle and silicon nitride surface. Conversely, solutions of only soluble capping ligand underwent successive crosslinking reactions with no chain scission, suggesting nanoparticles enhanced the chain scission reactions by acting as radiolysis hotspots. The addition of a hydroxyl radical scavenger, tert-butanol, eliminated chain scission reactions and slowed the progression of crosslinking reactions. These experiments have important implications for performing controlled and reproducible LP-TEM nanoparticle imaging as they demonstrate the electron beam can significantly alter ligand coverage on nanoparticles in a non-intuitive manner. They emphasize the need to understand and control the electron beam radiation chemistry of a given sample to avoid significant perturbations to the nanoparticle capping ligand chemistry, which are invisible in electron micrographs.<br /> | Thilini Umesha Dissanayake; Mei Wang; Taylor Woehl | Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc09abda2727df8b5d8/original/visualizing-electron-beam-capping-ligand-reactions-for-controlled-nanoparticle-imaging-with-liquid-phase-transmission-electron-microscopy.pdf |
60c74fb1ee301c5ecec7a73b | 10.26434/chemrxiv.12928331.v1 | Hydroxo-Bridged Active Site of Flavodiiron NO Reductase Revealed by Spectroscopy and Computations | <p>NO
and O<sub>2</sub> are detoxified in many organisms using flavodiiron proteins
(FDPs). The exact coordination of the iron centre in the active site of these
enzymes remains unclear despite numerous structural studies. Here, we used <sup>57</sup>Fe
nuclear resonance vibrational spectroscopy (NRVS) to probe the iron-ligand
interactions in <i>Escherichia coli</i> FDP. This data combined with density
functional theory (DFT) and <sup>57</sup>Fe Mössbauer spectroscopy indicate
that the oxidised form of FDP contains a dihydroxo-diferric Fe(III)–(µOH<sup>–</sup>)<sub>2</sub>–Fe(III)
active site, while its reduction gives rise to a monohydroxo-diferrous
Fe(II)–(µOH<sup>–</sup>)–Fe(II) site upon elimination of one bridging OH<sup>–</sup>
ligand, thereby providing an open coordination site for NO binding. Prolonged
NRVS data collection of the oxidised FDP resulted in photoreduction and
formation of a partially reduced diiron center with two bridging hydroxyl
ligands. These results have crucial implications for studying and understanding
the mechanism of FDP as well as other non-haem diiron enzymes.</p> | Filipe Folgosa; Vladimir Pelmenschikov; Matthias Keck; Christian Lorent; Yoshitaka Yoda; James A. Birrell; Martin Kaupp; Miguel Teixeira; Kenji Tamasaku; Christian Limberg; Lars Lauterbach | Biochemistry; Biophysics; Chemical Biology; Biocatalysis; Redox Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74fb1ee301c5ecec7a73b/original/hydroxo-bridged-active-site-of-flavodiiron-no-reductase-revealed-by-spectroscopy-and-computations.pdf |
67556ae8f9980725cf6a9498 | 10.26434/chemrxiv-2024-0df8q | Enzyme Assisted Direct Air Capture of carbon dioxide | Direct removal of carbon dioxide from atmospheric air has been widely advocated as a key tool in the strive towards zero emissions. One class of technology for direct air capture (DAC) uses aqueous sorbents in air-liquid contactors to extract the CO2. Here we present the first systematic data on enzyme assisted DAC and show that even very low (sub µM) concentrations of carbonic anhydrase (CA) exert a strong acceleration on CO2 absorption. We also found that CA promoted the ability to retain a high capture efficiency as the flow rate was raised and we rationalized these observations based on molecular mechanism of enzyme assisted capture. We interpret that acceleration of carbon capture with CA is more efficient under DAC conditions (short contact times and diluted sources) than during capture from CO2 sources. These attributes may eventually pave the way for DAC in sorbents with low regeneration energies such as carbonate. | Agnese Zaghini; Silke Badino; Stefanie Neun; Peter Westh | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67556ae8f9980725cf6a9498/original/enzyme-assisted-direct-air-capture-of-carbon-dioxide.pdf |
66add5c601103d79c5a2e161 | 10.26434/chemrxiv-2024-qpt7p | A Comprehensive Review of Hydrogen Storage Methods | Lately, fossil fuels have been utilized to meet our energy requirements. However, due to their significant environmental impact, alternative fuels have become a major area of research. Among these, hydrogen stands out as a promising candidate. Despite its potential, hydrogen's lightweight and gaseous nature pose storage challenges. Hydrogen storage is an intriguing research area where significant advancements have been made. This review examines the methods and recent advancements in hydrogen storage. | Muhammad Raza; Ali Mehdi; Rida Zehra | Materials Science; Energy; Carbon-based Materials; Hydrogen Storage Materials; Energy Storage; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66add5c601103d79c5a2e161/original/a-comprehensive-review-of-hydrogen-storage-methods.pdf |
60c759d1f96a00697d2890b6 | 10.26434/chemrxiv.14161355.v2 | β-Zeolite Assisted Lignin-First Fractionation in a Flow-Through Reactor | <p>Lignin is one of the main constituents
of lignocellulosic biomass, whose valorization is essential for an economically
feasible biorefinery process scheme. In the present work, a
hydrogen-free one step catalytic fractionation of woody biomass using
commercial b-zeolite as catalyst in a
flow-through reactor was carried out, leading to a maximum aromatic monomer
yield of 20.5 wt.%. Birch, spruce and walnut shells were used
and compared as lignocellulosic feedstocks. Relevant insights in the
reaction mechanism were obtained through 2D HSQC NMR analysis, revealing that b-O-4 cleavage is catalyzed by the zeolite.
To optimize system operation, a rate limiting step analysis was performed by
using different reactor configurations. It was found that the system operated in
a mixed regime where the rates of both solvolytic delignification and
zeolite-based depolymerization/dehydration affect the net rate of aromatic
monomer
production. Oxalic acid addition was found to enhance monomer production at
moderate concentrations by improving solvolysis; however, it caused
structural changes to the zeolite leading to lower monomer
yields at higher concentrations. Zeolite stability was assessed through
catalyst recycling and characterization using NH<sub>3</sub>-TPD, XRD, N<sub>2</sub>
physisorption and TGA. Main catalyst deactivation mechanisms were found to be coking
and leaching, respectively leading to larger pore size and lower
concentration of acid sites.</p> | Alexei Kramarenko; Deniz Etit; G. Laudadio; Fernanda Neira Dangelo; Alexei Kramarenko Logvynenko | Reaction Engineering | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c759d1f96a00697d2890b6/original/zeolite-assisted-lignin-first-fractionation-in-a-flow-through-reactor.pdf |
64da9245dfabaf06ff483768 | 10.26434/chemrxiv-2023-s7fqx | Mingling Light, Oxygen, and Organometallics to Form Cobalt-Carbon Bonds in the Confines of a Metal-Organic Nanocage | First-row transition-metal complexes often show a propensity for forming reactive radical species, such as superoxide complexes (M–O2•) generated by the binding of O2 to the metal, or free alkyl-radicals formed via M–C homolysis. Such radicals are important intermediates in reactions catalyzed by synthetic metal complexes and metalloenzymes, but their high reactivity can lead to undesired side reactions such as quenching by solvent, oxygen, or other radicals. In this work, we show that confinement of a CoII porphyrin complex in a large porphyrin-walled M8L6 nanocage allows for the taming of radical reactivity to enable clean oxidative alkylation of the cobalt center with tetraalkyltin reagents via an unexpected process mediated by O2 and light, which usually promote homolytic decomposition of porphyrin-supported CoIII–alkyl bonds. Indeed, analogous CoIII–alkyl complexes in free solution degrade too quickly under the alkylating conditions to enable their clean formation. The nanocage also acts as a size-selective barrier for alkylating agents, allowing CoIII–alkyl formation using SnMe4 and SnEt4 but not SnBu4. Likewise, Co–C homolysis is facilitated by the persist radical reagent TEMPO but not by a bulky derivative of TEMPO. These results show that nanoconfinement is a promising strategy for guiding radical-based organometallic reactivity under otherwise prohibitive conditions. | Daniel A. Rothschild; Aaron Tran; Mark C. Lipke | Inorganic Chemistry; Organometallic Chemistry; Nanoscience | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64da9245dfabaf06ff483768/original/mingling-light-oxygen-and-organometallics-to-form-cobalt-carbon-bonds-in-the-confines-of-a-metal-organic-nanocage.pdf |
653772a2c3693ca993ffa04b | 10.26434/chemrxiv-2023-n2mmd-v2 | Understanding the Role of Electrode Thickness on Redox Flow Cell Performance | The electrode thickness is a critical design parameter to engineer high-performing flow cells by impacting the available surface area for reactions, current and potential distributions, and required pumping power. To date, redox flow cell assemblies employ repurposed off-the-shelf fibrous electrodes which feature a broad range of thicknesses. However, comprehensive guidelines to select the optimal electrode thickness for a given reactor architecture remain elusive. Here, we investigate the effect of the electrode thickness in the range of 200 - 1100 µm on the cell performance by stacking electrode layers in four different flow cell configurations – Freudenberg paper and ELAT cloth electrodes combined with flow-through and interdigitated flow fields. We employ a suite of polarization, electrochemical impedance spectroscopy and pressure drop measurements together with pore network modeling simulations to correlate the electrode thickness for various reactor designs to the electrochemical and hydraulic performance. We find that thicker electrodes (420 µm paper electrodes and 812 µm cloth electrodes) are beneficial in combination with flow-through flow fields, whereas when using interdigitated flow fields, thinner electrodes (210 µm paper electrodes and 406 µm cloth electrodes) result in a better current density and pressure drop trade-off. We hope our findings will aid researchers and technology practitioners in designing their electrochemical flow cells under convective operation. | Vanesa Muñoz-Perales; Maxime van der Heijden; Victor de Haas; Jacky Olinga; Marcos Vera; Antoni Forner-Cuenca | Energy; Chemical Engineering and Industrial Chemistry; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653772a2c3693ca993ffa04b/original/understanding-the-role-of-electrode-thickness-on-redox-flow-cell-performance.pdf |
624dada7739db1266024921b | 10.26434/chemrxiv-2022-8mnsh | To Chelate Thallium(I) - Synthesis and Evaluation of Kryptofix-based Chelators for 201Tl | While best known for its toxic properties, thallium has also been explored for applications in nuclear diagnostics and medicine. Indeed, [201Tl]TlCl has been used extensively for nuclear imaging in the past before it was superceded by other radionuclides such as 99mTc. One reason for this loss of interest is the severe lack of suitable organic chelators able to effectively coordinate ionic forms of Tl and deliver it to specific diseased tissue by means of attached biological vectors. Herein, we describe the synthesis and characterisation of a series of Kryptofix 222-based chelators that can be radiolabelled with 201Tl(I) in high radiochemical yields at ambient temperature. We demonstrate that from these simple chelators, targeted derivatives are readily accessible and describe the synthesis and preliminary biological evaluation of a PSMA-targeted 201Tl-labelled Kryptofix 222-peptide conjugate. While the Kryptofix system is demonstrably capable of binding the thallium cation, no PSMA-mediated cell-uptake could be detected with the PSMA conjugate, suggesting that this targeting moiety may not be ideal for use in conjunction with 201Tl. | Angelo Frei; Alex Rigby; Thomas T. C. Yue; George Firth; Michelle T. Ma; Nicholas J. Long | Biological and Medicinal Chemistry; Inorganic Chemistry; Coordination Chemistry (Inorg.); Nuclear Chemistry | CC BY 4.0 | CHEMRXIV | 2022-04-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/624dada7739db1266024921b/original/to-chelate-thallium-i-synthesis-and-evaluation-of-kryptofix-based-chelators-for-201tl.pdf |
60c75579f96a00ea0028889e | 10.26434/chemrxiv.14114210.v1 | Sunflower-like Fluorescent Self-Assembled Morphologies Formed by Pyridothiazole Based Aggregation Induced Emission (AIE) Dye and Its Cell Imaging Applications | <p>We
report for the very first-time <a>self-assembly of 4-(5-methoxythiazolo[4,5-b]pyridin-2-yl)-N,N-dimethylaniline<b>
(TPA)</b></a><b> </b>to fluorescent sunflower-like architectures<b>.</b> Interestingly,
<b>TPA </b>exhibits blue fluorescence in visible light at 385 nm and the fluorescence
is not affected by photo-induced quenching rather the fluorescence keeps on
increasing with time under broad day light. The morphologies of self-assembled
structures of <b>TPA </b>were studied at various concentrations in dimethyl
sulphoxide (DMSO) and Tetrahydrofuran (THF). The microscopic studies through
SEM and fluorescence microscopy reveal the formation of sunflower-like fluorescent
self-assemblies. Further, our study revealed that the sunflower shaped
assemblies formed by <b>TPA </b>exhibitfluorescence under blue, green, and red channels
that can be evinced by the fluorescence spectroscopy and microscopy. Hence <b>TPA</b>
exhibits panchromatic emission properties and it reveals tunable emission
properties under different excitation wavelengths. Further, AIE properties of <b>TPA</b>
were evinced by recording fluorescence in THF under varying concentrations of
water and doing solvent chromic studies.Finally,the utility of <b>TPA</b> as a cell imaging agent was studied
in human breast cancer cell lines (MDA-MB-231) which suggested
<b>TPA</b> can penetrate the cell membrane and can be effectively used as a cell
labeling dye.</p> | Vivekshinh Kshtriya; Bharti Koshti; Ashadul Haque; Ankit Gangrade; Ramesh, Singh; khashti Ballabh Joshi; Sujoy Bandyopadhyay; Dhiraj Bhatia; Nidhi Gour | Biochemistry; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75579f96a00ea0028889e/original/sunflower-like-fluorescent-self-assembled-morphologies-formed-by-pyridothiazole-based-aggregation-induced-emission-aie-dye-and-its-cell-imaging-applications.pdf |
6275e2d3d5555051e890c357 | 10.26434/chemrxiv-2022-svqft | A General Entry to Ganoderma Meroterpenoids: Synthesis of Lingzhiol via Photoredox Catalysis | Ganoderma meroterpenoids are a fungal-derived hybrid natural product class containing a 1,2,4-trisubstituted benzene ring and a polycyclic terpenoid part. The representatives applanatumol E, H and I, lingzhilactone B and meroapplanin B share the same bicyclic lactone moiety connected to the arene via a flexible C2-linker. This flexibility is lost for lingzhiol as the b-position of the lactone is fused to the arene to form a tetralone subunit. Employing a diastereoselective iodocarbocyclization and a photo-Fries rearrangement as the key-steps enabled a general entry to these natural products. For the synthesis of the tetracyclic framework of lingzhiol, we made use of a powerful photoredox oxidative decarboxylation/Friedel–Crafts sequence. | Thomas Magauer; Alexander Rode; Klaus Wurst | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2022-05-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6275e2d3d5555051e890c357/original/a-general-entry-to-ganoderma-meroterpenoids-synthesis-of-lingzhiol-via-photoredox-catalysis.pdf |
64829d774f8b1884b70a3327 | 10.26434/chemrxiv-2023-jz0pp | Highly Flexible Dielectric Films from Solution Processable Covalent Organic Frameworks | Covalent organic frameworks (COFs) are known to be a promising class of materials for a wide range of applications, yet their poor solution processability limits their utility in many areas. Here we report a pore engineering method using hydrophilic side chains to improve the processability of hydrazone and beta-ketoenamine-linked COFs and the production of flexible, crystalline films. Mechanical measurements of the free-standing COF films of COF-PEO-3 (hydrazone-linked) and TFP-PEO-3 (beta-ketoenamine-linked), revealed a Young’s modulus of 391.7 MPa and 1034.7 MPa, respectively. The solubility and excellent mechanical properties enabled the use of these COFs in dielectric devices. Specifically, the TFP-PEO-3 film-based dielectric capacitors display simultaneously high dielectric constant and breakdown strength, resulting in a discharged energy density of 11.22 J cm–3. This work offers a general approach for producing solution processable COFs and mechanically flexible COF-based films, which hold great potential for use in energy storage and flexible electronics applications. | Milinda Senarathna; He Li; Sachini Perera; Jose Torres-Correas; Shashini Diwakara; Samuel Boardman; Yi Liu; Ronald Smaldone | Polymer Science; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64829d774f8b1884b70a3327/original/highly-flexible-dielectric-films-from-solution-processable-covalent-organic-frameworks.pdf |
60c752a9bdbb897190a3a314 | 10.26434/chemrxiv.13239467.v3 | Modeling Variance: A Variance-Motivated Approach to Molecular Prediction | In this variance-motivated study, the variance of a multi-thousand molecular dataset of Coulomb matrices is analyzed. This paper presents novel statistical methods and models that can aide in molecular prediction and analysis. A blended statistical/ML model is introduced for classifying data as Normal as well as a model for visualizing variance. Linear regression is also used to show a potential simple and 1 dimensional molecular descriptor, for some molecules. Paper includes literature review. | na'il mitchell | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC 4.0 | CHEMRXIV | 2020-11-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752a9bdbb897190a3a314/original/modeling-variance-a-variance-motivated-approach-to-molecular-prediction.pdf |
60c752f19abda27084f8ded8 | 10.26434/chemrxiv.13369835.v1 | Arylphosphonate-Tethered Porphyrins: Fluorescence Silencing Speaks a Metal Language in Living Enterocyte | <p>We report the application of a highly versatile and</p>
<p>engineerable novel sensor platform to monitor biologically significant</p>
<p>and toxic metal ions in live human Caco-2 enterocytes. The extended</p>
<p>conjugation between the fluorescent porphyrin core and metal ions via</p>
<p>aromatic phenylphosphonic acid tethers generates a unique turn off</p>
<p>and turn on fluorescence and, in addition, shifts in absorption and</p>
<p>emission spectra for zinc, cobalt, cadmium and mercury. The reported</p>
<p>fluorescent probes p-H8TPPA and m-H8TPPA can monitor a wide</p>
<p>range of metal ion concentrations via fluorescence titration and also</p>
<p>via fluorescence decay curves. Cu and Zn-induced turn off</p>
<p>fluorescence can be differentially reversed by the addition of common</p>
<p>chelators. Both p-H8TPPA and m-H8TPPA readily pass the</p>
<p>mammalian cellular membrane due to their amphipathic character as</p>
<p>confirmed by confocal microscopic imaging of living enterocytes.</p> | Claudia Keil; Julia Klein; Franz-Josef Schmitt; Yunus Zorlu; Hajo Haase; Gündoğ Yücesan | Food; Bioinorganic Chemistry; Coordination Chemistry (Inorg.); Sensors; Spectroscopy (Inorg.); Transition Metal Complexes (Inorg.); Biochemistry; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752f19abda27084f8ded8/original/arylphosphonate-tethered-porphyrins-fluorescence-silencing-speaks-a-metal-language-in-living-enterocyte.pdf |
676586a86dde43c908cafe46 | 10.26434/chemrxiv-2024-fmdhf | Structural Characterization of Dimeric Perfluoroalkyl Carboxylic Acid Using Experimental and Theoretical Ion Mobility Spectrometry Analyses | Per- and polyfluoroalkyl substances (PFAS) are contaminants of increasing concern, with over seven million compounds currently inventoried in the PubChem PFAS Tree. Recently, ion mobility spectrometry has been combined with liquid chromatography and high-resolution mass spectrometry (LC-IMS-HRMS) to assess PFAS. Interestingly, using negative electrospray ionization, per-fluoroalkyl carboxylic acids (PFCAs) form homodimers ([2M-H]-), a phenomenon observed with trapped, traveling wave, and drift-tube IMS. In addition to the limited research on their effect on analytical performance, there is little information on the conformations these dimers can adopt. This study aimed to propose most probable conformations for PFCA dimers. Based on qualitative analysis of how collision cross section (CCS) values change with the mass-to-charge ratio (m/z) of PFCA ions, the PFCA dimers were hypothesized to likely adopt a V-shaped structure. To support this assumption, in silico geometry optimizations were performed to generate a set of conformers for each possible dimer. A CCS value was then calculated for each conformer using the trajectory method with Lennard-Jones and ion-quadrupole potentials. Among these conformers, at least one of the ten lowest-energy conformers identified for each dimer exhibited theoretical CCS values within a ±2% error margin compared to the experimental data, qualifying them as plausible structures for the dimers. Our findings revealed that the fluorinated alkyl chains in the dimers are close to each other due to a combination of C-F⸱⸱⸱O=C and C-F⸱⸱⸱F-C stabilizing interactions. These findings, together with supplementary investigations involving environmentally relevant cations, may offer valuable insights into the interactions and environmental behavior of PFAS. | Aurore Schneiders; Johann Far; Lidia Belova; Allison Fry; Adrian Covaci; Erin S. Baker; Edwin De Pauw; Gauthier Eppe | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Environmental Analysis; Mass Spectrometry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/676586a86dde43c908cafe46/original/structural-characterization-of-dimeric-perfluoroalkyl-carboxylic-acid-using-experimental-and-theoretical-ion-mobility-spectrometry-analyses.pdf |
60c73cc9842e65d2c8db169f | 10.26434/chemrxiv.14743116.v1 | Tailoring Long-Range Superlattice Chirality in the Molecular Selfassemblies via Weak Fluorine-Mediated Interactions | Controllable
fabrication of the enantiospecific molecular superlattices is a matter of
imminent scientific and technological interest. Herein, we demonstrate that long-range
superlattice chirality in molecular self-assemblies can be tailored by tuning the
interplay of weak intermolecular non-covalent interactions. Different chiral
recognition patterns are achieved in the two molecular self-assemblies comprised
by two molecular enantiomers with identical steric conformations, derived from the
hexaphenylbenzene – the smallest star-shaped polyphenylene. By means of high-resolution
scanning tunneling microscopy measurements, we demonstrate that functionalization
of star-shaped polyphenylene with fluorine (F) atoms leads to the formation of molecular
self-assemblies with the distinct long-range chiral recognition patterns. We employed
the density functional theory calculations to quantify F-mediated
lone pair F ···π, C-H··· F, F···F interactions attributed to the tunable enantiospecific
molecular self-organizations. Our findings underpin a viable route to tailor long-range chiral recognition
patterns in supramolecular assemblies by engineering the weak non-covalent intermolecular interactions. | Mykola Telychko; Lulu Wang; Chia-Hsiu Hsu; Guangwu Li; Xinnan Peng; Shaotang Song; Jie Su; Feng-Chuan Chuang; Jishan Wu; Richard Ming Wah Wong; Jiong Lu | Organic Compounds and Functional Groups; Supramolecular Chemistry (Org.); Physical and Chemical Properties; Self-Assembly; Structure; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cc9842e65d2c8db169f/original/tailoring-long-range-superlattice-chirality-in-the-molecular-selfassemblies-via-weak-fluorine-mediated-interactions.pdf |
60c7450a4c891905a8ad2902 | 10.26434/chemrxiv.9959807.v1 | Application of In Situ X-ray Absorption Spectroscopy to Study Dilute Chromium Ions in a Molten Chloride Salt | The local structure of dilute
CrCl<sub>3</sub> in a molten MgCl<sub>2</sub>:KCl salt was investigated by <i>in situ</i> x-ray absorption spectroscopy
(XAS) at temperatures from room temperature to 800<sup>o</sup>C. This
constitutes the first experiment where dilute Cr speciation is explored in a
molten chloride salt, ostensibly due to the compounding challenges arising from
a low Cr concentration in a matrix of heavy absorbers at extreme temperatures. CrCl<sub>3</sub> was confirmed to be the
stable species between 200 and 500<sup>o</sup>C, while mobility of metal ions
at higher temperature (>700<sup>o</sup>C) prevented confirmation of the
local structure. | Jisue Moon; Carter Abney; Dmitriy Dolzhnikov; James M. Kurley; Kevin
A. Beyer; Joshua Wright; Sheng Dai; Richard T. Mayes; Stephen S. Raiman | Coordination Chemistry (Inorg.); Main Group Chemistry (Inorg.); Nuclear Chemistry; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7450a4c891905a8ad2902/original/application-of-in-situ-x-ray-absorption-spectroscopy-to-study-dilute-chromium-ions-in-a-molten-chloride-salt.pdf |
644fc17b0d87b493e397756b | 10.26434/chemrxiv-2023-sfc7c | The Intrinsic Barrier Width and its Role in Chemical Reactivity | The Marcus dissection of the Gibbs activation energy (barrier height) into intrinsic and thermodynamic contributions, which successfully models the interplay of rate and driving force, has led to a crucial general phenomenological consequence: the well-known two reactivity paradigms of “kinetic versus thermodynamic control”. However, concepts analogous to the Marcus’ dissection for barrier widths are absent. Here we define and outline the barrier-width- counterpart of the Marcus dissection: the concept of intrinsic barrier width and driving force effect on the barrier width, and report experimental as well as theoretical studies to demonstrate their distinct roles. We present the idea of changing the barrier widths of conformational isomerizations of some simple aromatic carboxylic acids as models and use quantum mechanical tunneling (QMT) half-lives as a read-out for these changes. This sheds light on resolving conflicting trends in chemical reactivities where barrier widths are relevant, and allows us to draw some important conclusions about the general relevance of barrier widths, their qualitative definition, and the consequences for more complete descriptions of chemical reactions based on one-dimensional reaction coordinates. | Guanqi Qiu; Peter Richard Schreiner | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/644fc17b0d87b493e397756b/original/the-intrinsic-barrier-width-and-its-role-in-chemical-reactivity.pdf |
60c748de337d6c13fde27614 | 10.26434/chemrxiv.11991567.v1 | Structural Symmetry of DNA Nucleotides and Steroid Hormones | DNA is comprised of important structural characteristics, which include the complementary base pairs of adenine-thymine (A-T) and cytosine-guanine (C-G) that serve to initiate and code for transcription and translation into amino acids. Recently, structural analysis of DNA performed in this lab indicated that each DNA nucleotide complementary base pair is in perfect correspondence with the structure of the steroid molecule and steroid hormones. Here, detailed structural analysis and illustrations are presented to clearly support and extend this fundamental finding. The structural illustrations indicate that the DNA Nucleotide base pairs can achieve perfect alignment with steroid hormones, such that each of its functional groups can be assigned a purpose for binding, stabilization, and transcription regulation. The relation of the missing third hydrogen bond for A-T and T-A, relative to the three hydrogen bonds of C-G and G-C, is clearly shown to be found through its coupling with the class of corticosteroids like cortisol that have an oxygen group perfectly positioned for interaction with the available functional group of thymine. Thus the intermolecular coupling by hydrogen bonding of Cortisol-Thymine produces a strong complex. Moreover, the structural analysis of the end group couplings to an ionic linkage element, Ca2+ or Mg2+, demonstrate interaction with both the DNA phosphates as well as the oxygen element within the sugar. The relationships confirm a structural association of cortisol-like steroid hormones with A-T and T-A and a structural association of testosterone-like steroid hormones for G-C and C-G. Synthetic steroids are assessed, including prednisolone and dexamethasone, to indicate consistency of the functional group interactions with the DNA base pairs, phosphate, and sugar groups to support and confirm direct binding and structural correspondence of steroid hormones to DNA Nucleotides. | Charles Schaper | Biochemistry; Biophysics; Cell and Molecular Biology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748de337d6c13fde27614/original/structural-symmetry-of-dna-nucleotides-and-steroid-hormones.pdf |
65eb3868e9ebbb4db944c7f3 | 10.26434/chemrxiv-2024-7ch9f | Advancements in Hand-Drawn Chemical Structure Recognition through an Enhanced DECIMER Architecture | Accurate recognition of hand-drawn chemical structures is crucial for digitising hand-written chemical information found in traditional laboratory notebooks or for facilitating stylus-based structure entry on tablets or smartphones. However, the inherent variability in hand-drawn structures poses challenges for existing Optical Chemical Structure Recognition (OCSR) software. To address this, we present an enhanced Deep lEarning for Chemical ImagE Recognition (DECIMER) architecture that leverages a combination of Convolutional Neural Networks (CNNs) and Transformers to improve the recognition of hand-drawn chemical structures. The model incorporates an EfficientNetV2 CNN encoder that extracts features from hand-drawn images, followed by a Transformer decoder that converts the extracted features into Simplified Molecular Input Line Entry System (SMILES) strings. Our models were trained using synthetic hand-drawn images generated by RanDepict, a tool for depicting chemical structures with different style elements. To evaluate the model's performance, a benchmark was performed using a real-world dataset of hand-drawn chemical structures. The results indicate that our improved DECIMER architecture exhibits a significantly enhanced recognition accuracy compared to other approaches. | Kohulan Rajan; Henning Otto Brinkhaus; Achim Zielesny; Christoph Steinbeck | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2024-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65eb3868e9ebbb4db944c7f3/original/advancements-in-hand-drawn-chemical-structure-recognition-through-an-enhanced-decimer-architecture.pdf |
630f18ff1945ad7eb9eda06c | 10.26434/chemrxiv-2022-tqxb3 | Stair-Like Narrow Nanographene with Diradicaloid Character at the Topological Interface | π-magnetism of finite-sized nanoribbon occurring on the topological molecular interfaces remains largely unexplored due to limited experimental examples. Herein, we report rational design, solution synthesis and systematical characterization of a novel type of stair-like aza-nanographene (ANG) ANG-a~b with precise N-doping on the interfacial cove-edges. Within the same molecular π-backbone, ANG-a had a closed-shell structure due to the electronic perturbation of cove-edge substitution; while ANG-b hosted a spin-polarized interface state, and impressively its open-shell singlet diradicaloid structure produced a combined optoelectronic, magnetic and physicochemical characteristics. Besides, dicationic ANG-b was also synthesized and characterized as a ground-state diradicaloid, again closely associated with the interfacial spin-polarization in the charged π-system. Our studies might provide insights into future structural engineering of topological open-shell materials with robust yet exotic spin-polarized interface states. | Zuhao Li; Yue Tang; Jing Guo; Jun Zhang; Wang Xiao; Yifan Yao; Sheng Xie; Zebing Zeng | Organic Chemistry; Materials Science; Organic Compounds and Functional Groups; Organic Synthesis and Reactions; Carbon-based Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630f18ff1945ad7eb9eda06c/original/stair-like-narrow-nanographene-with-diradicaloid-character-at-the-topological-interface.pdf |
631479015351a3da7fee908b | 10.26434/chemrxiv-2022-g5nvr | D-Peptide and D-Protein technology: Recent advances, challenges, and opportunities | Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in D-enantiomers facilitating mirror-image replication and transcription of L-DNA. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery on non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities. | Louis Y.P. Luk; Yi Jin; Alexander J. Lander | Biological and Medicinal Chemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2022-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631479015351a3da7fee908b/original/d-peptide-and-d-protein-technology-recent-advances-challenges-and-opportunities.pdf |
653a77c048dad23120680ca9 | 10.26434/chemrxiv-2023-f47tv | Infrared Free Induction Decay (IR-FID) of Non-Interfacial Origin Observed in the Interfacial Sum-Frequency Generation Vibrational Spectroscopy (SFG-VS) | We report the observation of infrared free induction decay (IR-FID) signal of the anti-symmetric modes around ~ 2350 cm-1 of the gaseous CO2 molecules in the air in the sum-frequency generation vibrational spectroscopy (SFG-VS) measurement from the gold surface. These signals appeared with time-dependent interference pattern in the 15-73 ps range and beyond after the time-zero of the SFG-VS process. The interference pattern was found to reflect the rotational coherence of the gaseous CO2 molecules. Similar IR-FID and rotational coherence was also observed for the symmetric and asymmetric stretching modes of gaseous H2O molecules in air. The gold surface in this case serves as the up-conversion agent with the visible pulse as the time-gate for the ultrafast IR-FID emissions. We tested this hypothesis by replacing the gold surface with a β-BBO (beta-barium borate, β-BaB2O4) and found a five orders of magnitude increase of the signal in the reflecting geometry. The up-conversion of the IR-FID radiation of non-interfacial origin into the SFG-VS signal also provides the mechanistic understanding of the ‘abnormal spectral bands’ in broadband SFG-VS induced by bulk absorption and refraction reported in the literature. | Bojun Zhao; Xingxing Peng; Li Zhang; Jingming Cao; Shuyi Yang; An-An Liu; Hongfei Wang | Physical Chemistry; Interfaces; Radiation; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/653a77c048dad23120680ca9/original/infrared-free-induction-decay-ir-fid-of-non-interfacial-origin-observed-in-the-interfacial-sum-frequency-generation-vibrational-spectroscopy-sfg-vs.pdf |
60c74146567dfe2305ec3d40 | 10.26434/chemrxiv.8001473.v1 | Building Ferroelectric from the Bottom Up: The Machine Learning Analysis of the Atomic-Scale Ferroelectric Distortions | <div>Recent advances in scanning transmission electron microscopy (STEM) have enabled direct
visualization of the atomic structure of ferroic materials, enabling the determination of atomic
column positions with ~pm precision. This, in turn, enabled direct mapping of ferroelectric and
ferroelastic order parameter fields via the top-down approach, where the atomic coordinates are
directly mapped on the mesoscopic order parameters. Here, we explore the alternative bottom-up
approach, where the atomic coordinates derived from the STEM image are used to explore the
extant atomic displacement patterns in the material and build the collection of the building blocks
for the distorted lattice. This approach is illustrated for the La-doped BiFeO<sub>3</sub> system.</div><div>The full analysis procedure is available as an interactive paper in a form of a Google Colab (Jupyter) notebook where a classical paper organization is augmented with code cells that appear hidden by default (when viewed in Google Colab). This should allow a reader to retrace the analysis and, more importantly, it enables the readers to use the same codes for their data. The same paper is also available in a standard pdf format (without code).<br /></div> | Maxim Ziatdinov; Christopher Nelson; Rama Vasudevan; Deyang Chen; Sergei Kalinin | Microscopy; Nanostructured Materials - Nanoscience; Machine Learning; Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-04-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74146567dfe2305ec3d40/original/building-ferroelectric-from-the-bottom-up-the-machine-learning-analysis-of-the-atomic-scale-ferroelectric-distortions.pdf |
6686b96a5101a2ffa860eed1 | 10.26434/chemrxiv-2024-pk5vq-v2 | Prediction of the ground state for indenofluorene-type systems with Clar's π-sextet model | This study introduces the Ground State Stability (GSS) rule that allows predicting the nature of the ground state of indenofluorene (IF)-type systems from the simple counting of the Clar pi-sextets in the closed- and open-shell configurations. The IF-type system exhibits a triplet ground state when acquiring double or more the number of Clar pi-sextet in the open-shell form relative to the closed-shell form; otherwise, it assumes an open-shell singlet ground state. Performed state-of-the-art DFT calculations and analysis of aromaticity for the systems of interest validate the effectiveness of the proposed rule. We demonstrate that aromaticity plays the most crucial role in determining the ground electronic state for such polycyclic hydrocarbons. The simplicity of the GSS rule makes it a robust strategy for identifying promising systems in the development of indenofluorene-type materials. | Gibu George; Anton Stasyuk; Miquel Solà i Puig | Theoretical and Computational Chemistry; Theory - Computational | CC BY NC 4.0 | CHEMRXIV | 2024-07-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6686b96a5101a2ffa860eed1/original/prediction-of-the-ground-state-for-indenofluorene-type-systems-with-clar-s-sextet-model.pdf |
63d92e91ab681c2c9d242923 | 10.26434/chemrxiv-2023-3t227 | An Electrostatically Embedded QM/MM Scheme for Electrified Interfaces | Atomistic modelling of electrified interfaces remains a major issue for detailed insights in electrocatalysis, corrosion, electrodeposition, batteries and related devices such as pseudocapacitors. In these domains, the use of grand-canonical density functional theory (GC-DFT) in combination with implicit solvation models has become popular. GC-DFT can be conveniently applied not only to metallic surfaces, but also to semi-conducting oxides and sulfides and is, furthermore, sufficiently robust to achieve a consistent description of reaction pathways. However, the accuracy of implicit solvation models for solvation effects at interfaces is in general unknown. One promising way to overcome the limitations of implicit solvents is going towards hybrid quantum mechanical (QM)/molecular mechanics (MM) models. For capturing the electrochemical potential dependence, the key quantity is the capacitance, i.e., the relation between the surface charge and the electrochemical potential. In order to retrieve the electrochemical potential from a QM/MM hybrid scheme, an electrostatic embedding is required. Furthermore, the charge of the surface and of the solvent regions have to be strictly opposite in order to consistently simulate charge-neutral unit cells in MM and in QM. To achieve such a QM/MM scheme, we present the implementation of electrostatic embedding in the popular VASP code. This scheme is broadly applicable to any neutral or charged solid/liquid interface. Here, we demonstrate its use in the context of GC-DFT for the hydrogen evolution reaction (HER) over a noble-metal-free electrocatalyst, MoS2. We investigate the effect of electrostatic embedding compared to the implicit solvent model for three contrasting active sites on MoS2: (i) the sulfur vacancy defect which is rather apolar. (ii) an Mo anti-site defect, where the active site is a surface bound highly polar OH group and (iii) a reconstructed edge site which is generally believed to be responsible for most of the catalytic activity. Our results demonstrate that electrostatic embedding leads to almost indistinguishable results compared to the implicit solvent for apolar systems, but has a significant effect on polar sites. This demonstrates the reliability of the hybrid QM/MM, electrostatically embedded solvation model for electrified interfaces. | Nawras Abidi; Stephan Steinmann | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-02-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63d92e91ab681c2c9d242923/original/an-electrostatically-embedded-qm-mm-scheme-for-electrified-interfaces.pdf |
60c74d610f50db8cd739701a | 10.26434/chemrxiv.8003507.v4 | A novel sensor for sequential and cellular detection of copper and lactic acid | <div>
<p>We
report self assembling/aggregation properties of acyl-thiourea derivative,
N-((6-methoxy-pyridin-2-yl)carbamothioyl)benzamide<a>(<b>NG1</b>) </a><a>[i1]</a> and
the disaggregation induced emission which leads to its application as
fluorescence and colorimetric probe for the sensitive detection of Cu<sup>2+</sup>.
The microscopy analysis of <b>NG1</b>via
SEM, and AFM reveal that it self-assembles to give fiber-like morphologies.Interestingly,<b>NG1</b> also assembles to fluorescent
fibers which show tunable emission properties. Addition of Cu<sup>2+</sup>to
these fibers causedisruption/disaggregation of fibers and a golden yellow
fluorescence is produced due to disaggregation induced emission enhancement (DIEE).
The application of <b>NG1</b> as selective
sensor for copper was further assessed by UV visible and fluorescence
spectroscopy. Limit of Detection(LOD) of Cu<sup>2+ </sup>with colorimetry was 2.5ppm
while LOD of Cu<sup>2+</sup> with fluorescence was as low as 0.1ppm. This
yellow fluorescence is quenched after the addition of lactic acid and hence <b>NG1</b> could potentially be used for the sequential
detection of both Cu and lactate.Further, structural modification of the probe <b>NG1</b> suggest crucial role of both
pyridine and acyl-thiourea moiety in the binding of Cu<sup>2+</sup>. The
experimental results of interaction of <b>NG1</b>
with Cu<sup>2+</sup> and lactate were also validated theoretically by quantum chemical calculations based on
density functional theory (DFT). Finally, we explore the ability of <b>NG1</b>for the sequential detection of Cu<sup>2+</sup>
and lactate in cells, which suggests<b>NG1</b>
can be used effectively for the cellular imaging applications and to selectively
sense Cu<sup>2+</sup>. To, the best of our knowledge,</p></div>
<p>this
is the first report wherein a dual sensor for Cu<sup>2+</sup>and lactate ion is
synthesized and it may in allpossibilities pave the way for the diagnosis of Cu<sup>2+</sup>associated
disorders like Wilson’s disease and in the detection of elevated lactate levels
which are associated with the wide range of pathologies likemitochondrial diseases, cerebral ischemia
and cancer.<b></b></p>
<div>
</div><br /> | Nidhi Gour; Sumit Kharbanda; Deepak Kumar Pandey; Dheeraj K Singh; Dhiraj Bhatia; Vivek Shinh Kshtriya; chandra kanth P | Analytical Chemistry - General; Biochemical Analysis; Cell and Molecular Biology; Chemical Biology; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74d610f50db8cd739701a/original/a-novel-sensor-for-sequential-and-cellular-detection-of-copper-and-lactic-acid.pdf |
66b23d115101a2ffa842c13d | 10.26434/chemrxiv-2024-gmqrz | A Novel Ti12-based Metal-Organic Framework for Photocatalytic Hydrogen Evolution | Constructing titanium-based metal-organic frameworks (Ti-MOFs) is an effective way towards upgrading TiOx and the enhancement of their photocatalytic performance throughout higher accessibility to active sites and better tunability of photophysical properties. In this regard, Ti-MOFs have attracted much attention as photocatalyst candidates owing to their porosity and tunability in terms of chemical composition and pore engineering. However, Ti-MOFs remain still one of the least developed sub-class of MOF materials because of the complexity of titanium chemistry in solution hampering their rational design, despite recent progresses. Here, we present a new microporous Ti-MOFs with acs topology, labeled MIP-209(Ti) (MIP stands for Materials from Institute of Porous Materials of Paris) constructed by a nitro terephthalate ligand and Ti12O15 oxo-clusters, as revealed by continuous rotation electron diffraction (cRED). MIP-209(Ti) can be obtained using various terephthalate (1,4-BDC2-) derivatives such as NO2-BDC and 2Cl-BDC using an eco-friendly solvent, suggesting the ability of Ti12-MOFs for isostructural chemistry. Alternatively, it is also possible to tune the composition of its Ti-oxo-cluster, similarly to MIP-177(Ti)-LT bearing the same Ti12O15 sub-unit. Typically, low percentage Cr3+ doping (≤ 5 at%) in MIP-209(Ti) favorably enhances the water stability. Interestingly, photocatalytic hydrogen evolution from water splitting reaction (HER) were measured for MIP-209(Ti-Cr)-NO2 and a significant hydrogen production rate, with good reusability and stability under simulated solar light irradiation, were revealed. It showed enhanced photocatalytic hydrogen production performances under simulated solar light irradiation compared to the benchmark Ti-MOF IEF-11 with a fourfold enhanced hydrogen production in HER in 5h in presence of methanol (5812 µmol of H2/gcat against 1391 µmol of H2/gcat) as well as, without any noble metal co-catalyst, a 6-fold enhanced overall water splitting production (681 and 325 µmol/gcat of H2 and O2, respectively for MIP-209, against 94 and 53 µmol/gcat of H2 and O2, respectively, for IEF-11). This work represents a leap forward in the synthesis of Ti-MOFs and their practical photocatalytic applications. | Bingbing Chen; Asma Mansouri; Celia M. RUEDA-NAVARRO; Iurii Dovgaliuk; Philippe Boullay; Gilles Patriarche; Beibei Xiao; Dong Fan; Arianna Melillo; Lokuge Aravindani FERNANDO; Guillaume Maurin; Sergio Navalon; Hermenegildo Garcia; Georges Mouchaham; Christian Serre | Catalysis; Energy; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66b23d115101a2ffa842c13d/original/a-novel-ti12-based-metal-organic-framework-for-photocatalytic-hydrogen-evolution.pdf |
6532c5e42431cc1dac2d01aa | 10.26434/chemrxiv-2023-685z7 | Investigation of Dynamical flexibility of D5SIC-DNAM inside DNA duplex in Aqueous Solution: A Systematic Classical MD Approach | Incorporation of artificial 3rd base pairs (Unnatural base pairs, UBPs) has emerged as a fundamental technique in pursuit of expanding the genetic alphabet. 2,6-dimethyl-2H-isoquiniline-1-thione: D5SIC (DS) and 2-methoxy-3-methylnaphthalene: DNAM (DN), a potential unnatural base pair (UBP) developed by Romesberg and colleagues, has been shown to have remarkable capability for replication within DNA. Crystal structures of a Taq polymerase/double-stranded DNA (ds-DNA) complex containing a DS-DN pair in the 3’ terminus showed a parallelly stacked geometry for the pre-insertion, and an intercalated geometry for the post-insertion structure. Unconventional orientations of DS-DN inside a DNA duplex have inspired scientists to investigate the conformational orientations and structural properties of UBP-incorporated DNA. In recent years, computational simulations have been used to investigate the geometry of DS-DN within the DNA duplex; nevertheless, unresolved questions persist owing to inconclusive findings. In this work, we investigate the structural and dynamical properties of DS and DN inside a ds-DNA strand in aqueous solution considering both short and long DNA templates using polarizable, and non-polarizable classical MD simulations. Flexible conformational change of UBP with major populations of Watson-Crick-Franklin (WCF) and three distinct non-Watson-Crick-Franklin (nWCFP1, nWCFP2, nWCFO) conformations through intra and inter-strand flipping have been observed. Our results suggest that a dynamical conformational change leads to the production of random distribution of several intermediates. Simulations with a short ds-DNA duplex suggest nWCF (P1 and O) as the predominant structures, whereas long ds-DNA duplex simulations indicate almost equal populations of WCF, nWCFP1, nWCFO. DS-DN in the terminal position is found to be more flexible with occasional mispairing and fraying. Overall, these results suggest flexibility and random conformational distribution of the UBP as well as indicate varied conformational distribution with the increase of the length of the DNA strand. | Tanay Debnath; G. Andres Cisneros | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-10-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6532c5e42431cc1dac2d01aa/original/investigation-of-dynamical-flexibility-of-d5sic-dnam-inside-dna-duplex-in-aqueous-solution-a-systematic-classical-md-approach.pdf |
62b65d5fb7bbeda4e38fa7b1 | 10.26434/chemrxiv-2022-nhk2d | A computational mechanistic study of CH hydroxylation with mononuclear copper-oxygen complexes | We present a computational study of methane hydroxylation by oxygen-bound monocopper complexes with the twin goals of resolving the active site identity and preferred mechanism of CH activation. Oxyl ([Cu(II)O(Im)3]+) and superoxo ([Cu(II)OO(Im)3]+) monocopper centers coordinated to three imidazole N-donors are investigated. Constrained density functional theory (CDFT) is necessary to overcome delocalization errors inherent to DFT and generate catalyst geometries with physically meaningful charge and spin at the active site. A comparison of ground-state triplet and excited-state singlet potential energy profiles for CH hydroxylation shows that oxyl is the more likely active site. For oxyl, spin crossing from the triplet to singlet potential energy surface yields a lower energy hydroxylation pathway when compared to the pure triplet surface. The calculation of minimum energy crossing points is an essential next step towards determining whether CH hydroxylation proceeds via a two-step radical or single-step oxo-insertion mechanism. | Zhenzhuo Lan; Jacob Toney; Shaama Mallikarjun Sharada | Theoretical and Computational Chemistry; Inorganic Chemistry; Catalysis; Kinetics and Mechanism - Inorganic Reactions; Computational Chemistry and Modeling; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62b65d5fb7bbeda4e38fa7b1/original/a-computational-mechanistic-study-of-ch-hydroxylation-with-mononuclear-copper-oxygen-complexes.pdf |
60c7460f842e65784edb272b | 10.26434/chemrxiv.10593845.v1 | Incorporating Peptide Aptamers into Resistive Pulse Sensing | <p>The
use of nanocarriers within resistive pulse sensing, RPS, aids the detection and
quantification of analytes. In the absence of convection, the signal strength
and frequency can dependent upon the electrophoretic mobility of the nanocarrier/
analyte. Here we have developed a simple strategy to incorporate peptide
aptamers onto RPS assays with enhanced electrophoretic signals. Using a hybrid
DNA-Peptide nanocarrier an existing peptide was incorporated into a rapid assay
without having to engineer or modify the peptide sequence. The surface of a
nanocarrier is coated with a mixture of peptide aptamers and a nonbinding DNA.
The binding of the target to the peptide creates an “analyte corona” which
shields the phosphate groups of the underlying DNA. This results in a change in
electrophoretic mobility of the nanocarrier. The signal is concentration
dependent and is illustrated using a peptide to a key biomarker of infection, C-Reactive
Protein, CRP. As a comparison we also show the binding of the CRP to a DNA
aptamer. This universal approach can be easily adapted to other peptides
without the peptide itself to undergo any chemical modifications opening new
opportunities and applications in RPS strategies. </p> | Mark Platt; Rhushabh Maugi | Analytical Chemistry - General; Nanodevices | CC BY NC ND 4.0 | CHEMRXIV | 2019-11-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7460f842e65784edb272b/original/incorporating-peptide-aptamers-into-resistive-pulse-sensing.pdf |
60c74993ee301c046cc79a9a | 10.26434/chemrxiv.12084207.v1 | Elucidating Biophysical Basis of Binding of Inhibitors to SARS-CoV-2 Main Protease by Using Molecular Dynamics Simulations and Free Energy Calculations | <div>The recent outbreak of novel “coronavirus disease 2019” (COVID-19) has spread rapidly</div><div>worldwide, causing a global pandemic. In the absence of a vaccine or a suitable</div><div>chemotherapeutic intervention, it is an urgent need to develop a new antiviral drug to fight this</div><div>deadly respiratory disease. In the present work, we have elucidated the mechanism of binding</div><div>of two inhibitors, namely α-ketoamide and Z31792168 to SARS-CoV-2 main protease (Mpro</div><div>or 3CLpro) by using all-atom molecular dynamics simulations and free energy calculations. We</div><div>calculated the total binding free energy (ΔGbind) of both inhibitors and further decomposed</div><div>ΔGbind into various forces governing the complex formation using the Molecular</div><div>Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal</div><div>that α-ketoamide is more potent (ΔGbind= - 9.05 kcal/mol) compared to Z31792168 (ΔGbind= -</div><div>3.25 kcal/mol) against COVID-19 3CLpro. The increase in ΔGbind for α-ketoamide relative to</div><div>Z31792168 arises due to an increase in the favorable electrostatic and van der Waals</div><div>interactions between the inhibitor and 3CLpro. Further, we have identified important residues</div><div>controlling the 3CLpro-ligand binding from per-residue based decomposition of the binding free</div><div>energy. Finally, we have compared ΔGbind of these two inhibitors with the anti-HIV retroviral</div><div>drugs, such as lopinavir and darunavir. It is observed that α-ketoamide is more potent compared</div><div>to both lopinavir and darunavir. In the case of lopinavir, a decrease in the size of the van der</div><div>Waals interactions is responsible for the lower binding affinity compared to α-ketoamide. On</div><div>the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic</div><div>and van der Waals interactions contributes to lower affinity compared to α-ketoamide. Our</div><div>study might help in designing rational anticoronaviral drugs targeting the SARS-CoV-2 main</div><div>protease. </div> | Md Fulbabu Sk; Rajarshi Roy; Nisha Amarnath Jonniya; Sayan Poddar; Parimal Kar | Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74993ee301c046cc79a9a/original/elucidating-biophysical-basis-of-binding-of-inhibitors-to-sars-co-v-2-main-protease-by-using-molecular-dynamics-simulations-and-free-energy-calculations.pdf |
60c743739abda251dbf8c1da | 10.26434/chemrxiv.9176747.v1 | Potent Hemithioindigo-Based Antimitotics Photocontrol the Microtubule Cytoskeleton in Cellulo | <div>
<div>
<p>Hemithioindigo is a promising molecular photoswitch that has only recently been applied as a photoswitchable pharmacophore for control over bioactivity
in cellulo. Uniquely, in contrast to other photoswitches that have been applied to
biology, the pseudosymmetric hemithioindigo scaffold has allowed the creation of both
dark-active and lit-active photopharmaceuticals for the same binding site by a priori
design. However, the potency of previous hemithioindigo photopharmaceuticals has
not been optimal for their translation to other biological models.
</p>
<p>Inspired by the structure of tubulin-inhibiting indanones, we created
hemithioindigo-based indanone-like tubulin-inhibitors (HITubs) and optimised their
cellular potency as antimitotic photopharmaceuticals. These HITubs feature reliable
and robust visible light photoswitching and high fatigue resistance. The use of the
hemithioindigo scaffold also permitted us to employ a para-hydroxy hemistilbene motif
– a structural feature which is denied to most azobenzenes due to the negligibly short
lifetimes of their metastable Z isomers – which proved crucial to enhancing the potency
and photoswitchability. The HITubs are ten times more potent than previously reported
hemithioindigo photopharmaceutical antimitotics in a series of cell-free and cellular
assays, and allowed robust photocontrol over tubulin polymerisation, microtubule
network structure, cell cycle and cell survival.</p><div><div><div>
<p>We conclude that HITubs represent a powerful addition to the growing toolbox of
photopharmaceutical reagents for microtubule cytoskeleton research. Additionally, as
the hemithioindigo scaffold allows photoswitchable bioactivity for substituent patterns inaccessible to the majority of current photopharmaceuticals, wider adoption of the
hemithioindigo scaffold may significantly expand the scope cellular and in vivo targets
addressable by photopharmacology.
</p></div></div></div>
</div>
</div> | Alexander Sailer; Franziska Ermer; Yvonne Kraus; Rebekkah Bingham; Ferdinand H. Lutter; Julia Ahlfeld; Oliver Thorn-Seshold | Bioorganic Chemistry; Natural Products; Organic Synthesis and Reactions; Cell and Molecular Biology; Chemical Biology; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2019-07-31 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c743739abda251dbf8c1da/original/potent-hemithioindigo-based-antimitotics-photocontrol-the-microtubule-cytoskeleton-in-cellulo.pdf |
60c73edc702a9b75f2189e63 | 10.26434/chemrxiv.7166318.v1 | Isotopic Characterization (2H, 13C, 37Cl, 81Br) of the Abiotic Sinks of Methyl Bromide and Methyl Chloride in Water and Implications for Future Studies. | In this study we investigated the isotope fractionation of the abiotic sink (hydrolysis, halide exchange) of methyl halides in water.<br /> | Axel Horst; Magali Bonifacie; Gérard Bardoux; Hans-Hermann Richnow | Environmental Science; Hydrology and Water Chemistry; Environmental Analysis; Chemical Kinetics | CC BY NC ND 4.0 | CHEMRXIV | 2018-10-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73edc702a9b75f2189e63/original/isotopic-characterization-2h-13c-37cl-81br-of-the-abiotic-sinks-of-methyl-bromide-and-methyl-chloride-in-water-and-implications-for-future-studies.pdf |
678517fd81d2151a02ee033a | 10.26434/chemrxiv-2025-wp0nd | Coexistence of Metallocene Cations and Anions | We report the synthesis and structural characterization of the rhodocene anion [Rh(C5(CH3)5)(C5(CF3)5)]− [1]− as the [Co(C5(CH3)5)2]+ salt, representing an unprecedented coexistence of metallocene cations and anions in different oxidation states. [1]− was synthesized by the reduction of the rhodocenium cation [Rh(C5(CH3)5)(C5(CF3)5)][BF4] [1]+[BF4]− with two equivalents of decamethylcobaltocene [Co(C5(CH3)5)2], since the strongly electron-withdrawing effect of the [C5(CF3)5)]− ligand shifts the first and second reduction potentials of [1]+ to moderate values of −0.90 V and −1.46 V vs Fc+/Fc. The respective salt [Co(C5(CH3)5)2]+[1]− was characterized by single crystal X-ray diffraction (XRD), also providing the first example of an isolated and structurally characterized 4d metallocene anion. Whereas the Rh(III) cation has two η5- bound Cp ligands, the perfluorinated Cp* ligand is only η3-bound in the Rh(I) anion in order to obey the 18 electron rule. The reduction of the rhodocenium center is also accompanied by a significant shift of the 103Rh NMR signal from −9308 ppm [1]+ to −6895 ppm [1]− (referenced to Rh(acac)3), reflecting the change in coordination geometry. | Nico Gino Kub; Robin Sievers; Marc Reimann; Tim-Niclas Streit; Simon Steinhauer; Johanna Schlögl; Martin Kaupp; Moritz Malischewski | Theoretical and Computational Chemistry; Inorganic Chemistry; Organometallic Chemistry; Coordination Chemistry (Organomet.); Electrochemistry - Organometallic; Transition Metal Complexes (Organomet.) | CC BY 4.0 | CHEMRXIV | 2025-02-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/678517fd81d2151a02ee033a/original/coexistence-of-metallocene-cations-and-anions.pdf |
60c748950f50dbb96d3967bc | 10.26434/chemrxiv.11936175.v1 | Structural Contributions to Autocatalysis and Asymmetric Amplification in the Soai Reaction | Diisopropylzinc alkylation of pyrimidine aldehydes – the Soai reaction, with its astonishing attribute of amplifying asymmetric autocatalysis, occupies a unique position in organic chemistry and stands as an eminent challenge for mechanistic elucidation. A new paradigm of ‘mixed catalyst substrate’ experiments with pyrimidine and pyridine systems allows a disconnection of catalysis from autocatalysis, providing insights into the role played by reactant and alkoxide structure. The alkynyl substituent favorably tunes catalyst solubility, aggregation and conformation while modulating substrate reactivity and selectivity. The alkyl groups and the heteroaromatic core play further complementary roles in catalyst aggregation and substrate binding. In the study of these structure activity relationships, novel pyridine substrates demonstrating amplifying autocatalysis were identified. Comparison of three autocatalytic systems representing a continuum of nitrogen Lewis basicity strength suggests how the strength of N-Zn binding events is a predominant contributor towards the rate of autocatalytic progression.<br /><div>
</div> | Soumitra Athavale; Adam Simon; Kendall N Houk; Scott Denmark | Stereochemistry; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c748950f50dbb96d3967bc/original/structural-contributions-to-autocatalysis-and-asymmetric-amplification-in-the-soai-reaction.pdf |
60c73d92842e658f0adb17b9 | 10.26434/chemrxiv.5410918.v2 | Bond-length distributions for ions bonded to oxygen: Results for the non-metals and discussion of lone-pair stereoactivity and the polymerization of PO4 | Bond-length distributions are examined for three configurations of the H+ ion, sixteen configurations of the group 14-16 non-metal ions and seven configurations of the group 17 ions bonded to oxygen. Lone-pair stereoactivity for ions bonded to O<sup>2-</sup> is discussed, as well as the polymerization of the PO<sub>4</sub> group. | Olivier Charles Gagné; Frank Christopher Hawthorne | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2017-12-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d92842e658f0adb17b9/original/bond-length-distributions-for-ions-bonded-to-oxygen-results-for-the-non-metals-and-discussion-of-lone-pair-stereoactivity-and-the-polymerization-of-po4.pdf |
60ccb0c8a5b6af8d94757695 | 10.26434/chemrxiv-2021-ss23c | A system for the evolution of protein-protein interaction inducers | Molecules that induce interactions between proteins, often referred to as “molecular glues”, are increasingly recognized as important therapeutic modalities and as entry points for rewiring cellular signaling networks. Here, we report a new PACE-based method to rapidly select and evolve molecules that mediate interactions between otherwise non-interacting proteins: rapid evolution of Protein-Protein Interaction Glues (rePPI-G). Proof-of-concept evolutions demonstrated that rePPI-G reduces the “hook” effect of the engineered molecular glues, due at least in part to tuning the interaction affinities of each individual component of the bifunctional molecule. Altogether, this work validates rePPI-G as a continuous, phage-based evolutionary technology for optimizing molecular glues, providing a strategy for developing molecules that reprogram protein-protein interactions. | Jeffrey Dewey; Saara-Anne Azizi; Vivian Lu; Bryan Dickinson | Biological and Medicinal Chemistry; Biochemistry; Bioengineering and Biotechnology; Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60ccb0c8a5b6af8d94757695/original/a-system-for-the-evolution-of-protein-protein-interaction-inducers.pdf |
658c8cca66c13817292a7b09 | 10.26434/chemrxiv-2023-f7j1v-v2 | Merging Cobalt-Catalyzed C-H Activation with the
Mannich Reaction: An Efficient and Modular Approach
to a-Substituted Sulfonamides | A three-component synthesis of alpha-substituted sulfonamides from aryl aldehydes, primary sulfonamides and (hetero)arenes is described. This transformation enables a straightforward and modular synthesis of pharmaceutically relevant scaffolds in good yields. The direct functionalization of C(sp2)-H bonds via cobalt-catalyzed C-H-activation offers an appealing and atom-economical alternative to classical methods for the synthesis of alpha-arylated amines such as the Petasis or Mannich-type reactions. | Oluwaseun Olu-Igbiloba; Helmut Sitzmann; Georg Manolikakes | Biological and Medicinal Chemistry; Organic Chemistry; Catalysis; Organic Synthesis and Reactions; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/658c8cca66c13817292a7b09/original/merging-cobalt-catalyzed-c-h-activation-with-the-mannich-reaction-an-efficient-and-modular-approach-to-a-substituted-sulfonamides.pdf |
6720565583f22e42147ec556 | 10.26434/chemrxiv-2024-f1pw9 | Dearomative Selective Reduction of Structurally Diverse N-Heteroarenes Enabled by Titanium Catalysis | The reduction of aromatic compounds is a stalwart transformation in modern organic synthesis since it allows the generation of novel complex three-dimensional (3D) chemical entities from two-dimensional precursors (2D), linking readily available aro-matic feedstocks with unobtainable alicyclic structures. However, controlling the high level of selectivity of N-heteroarenes (quinolines and pyridines), particularly substituents positioned on the reducible quinoline ring, is both intriguing and challeng-ing, and methods for selective saturation of structurally complex derivatives (multiple aromatic rings) are rarely unaddressed and need some advances. Also, many approaches suffer from scalability problems as well as high cost and low availability of both catalysts and tailor-made ligands. To address this issue, we herein report the first example of commercially available ti-tanocene dichloride (Cp2TiCl2)-catalyzed dearomative selective reduction of structurally diverse nitrogen-based heteroarenes with ammonia borane as a reducing agent (>100 examples). The developed protocol features the advantage of chemoselectivity and wide functional group tolerance of quinolines. Meanwhile, the efficient reduction of challenging and unprotected functional-ized pyridines as well as pyrazines is also furnished with remarkable functional group preservation and also with an improved F(sp3) carbon fraction. Additionally, a few selected furans and benzofuran derivatives were also successfully demonstrated un-der synthetically relevant conditions, and gram-scale synthesis was effectively executed. The methodology can be extended to the saturation of complex N-heteroarenes with conserved selectivity. In addition, density functional theory (DFT) calculations were carried out to shed light on the mechanistic insights into the reduction of quinoline. | Kishore Natte; Tarun Bhatt; Suman Vadithya; Mridula Choudhary; Saurabh Kumar Singh | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY 4.0 | CHEMRXIV | 2024-11-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720565583f22e42147ec556/original/dearomative-selective-reduction-of-structurally-diverse-n-heteroarenes-enabled-by-titanium-catalysis.pdf |
66c7e8c2a4e53c48764d8a43 | 10.26434/chemrxiv-2024-g11ln | Local Order, Disorder, and Everything in Between: Using 91Zr Solid-State NMR Spectroscopy to Probe Zirconium-Based Metal-Organic Frameworks | Characterization of metal centers in metal-organic frameworks (MOFs) is critical for rational design and further understanding of structure-property relationships. The local structure of Zr atoms is challenging to properly elucidate in many Zr-MOFs, particularly when local disorder is present. Static 91Zr solid-state NMR spectra of the seven zirconium MOFs UiO-66, UiO-66-NH2, UiO-67, MOF-801, MOF-808, DUT-68 and DUT-69 have been acquired at high magnetic fields of 35.2 T and 19.6 T, yielding valuable information on the local structure, site symmetry, and order about Zr. 91Zr NMR is very sensitive to differences in MOF local structure caused by guest molecules, linker substitution, and post-synthetic treatment. Complementary density functional theory (DFT) calculations assist in the interpretation and assignment of 91Zr solid-state NMR spectra, lend insight into structural origins of 91Zr NMR parameters and enable determination of local Zr coordination environments. This approach can be extended to many other materials containing zirconium. | Wanli Zhang; Bryan Lucier; Vinicius Martins; Ivan Hung; Yijue Xu; Zhehong Gan; Amrit Venkatesh; Tian Wei Goh; Wenyu Huang; Aaron Rossini; Yining Huang | Physical Chemistry; Inorganic Chemistry; Organometallic Compounds; Spectroscopy (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66c7e8c2a4e53c48764d8a43/original/local-order-disorder-and-everything-in-between-using-91zr-solid-state-nmr-spectroscopy-to-probe-zirconium-based-metal-organic-frameworks.pdf |
60c7482d0f50dbd8a1396725 | 10.26434/chemrxiv.11803119.v2 | Targeting Productive Composition Space Through Machine-Learning Directed Inorganic Synthesis | This work presents an
approach to aid the discovery of novel inorganic solids by highlighting regions
of underexplored, yet likely productive composition space using machine
learning. A support vector regression (SVR) algorithm was constructed first to determine
a compound’s formation energy (∆𝐸𝑓,SVR) based solely on chemical
composition using data from 313,965 high-throughput density functional theory calculations.
The resulting predicted formation energies (r<sup>2</sup> = 0.94; MAE = 85 meV/atom)
were then used to construct zero-kelvin convex hull diagrams and identify compositions
immediately on the hull, as well as +50 meV above the convex hull to capture potential
compounds that are considered energetically unfavorable but that are still experimentally
accessible. Using this methodology, four ternary composition diagrams, Y−Ag−<i>Tr</i> (<i>Tr</i>
= B, Al, Ga, In), were explored owing to the diversity of chemistries as a
function of triel element to provide experimental validation for the
predictions. A particularly promising but unexplored region in the Y−Ag−In diagram
was identified, and the ensuing solid-state high-temperature synthesis produced
YAg<sub>0.65</sub>In<sub>1.35</sub>, which has not been reported. First-principle
calculations were finally used to determine the ordering of Ag and In as well
as confirm the crystal structure solution. Our combination of machine learning,
inorganic synthesis, and computational modeling describes a new avenue where data-centric
models and computation play a critical role in supporting the experimental
examination of unexplored phase diagrams. | Sogol Lotfi; Ziyan Zhang; Gayatri Viswanathan; Kaitlyn Fortenberry; Aria Mansouri Tehrani; Jakoah Brgoch | Solid State Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7482d0f50dbd8a1396725/original/targeting-productive-composition-space-through-machine-learning-directed-inorganic-synthesis.pdf |
67d42791fa469535b933c541 | 10.26434/chemrxiv-2024-k2k3l-v3 | Neural Mulliken Analysis: Molecular Graphs from Density Matrices for QSPR on Raw Quantum-Chemical Data | Here, molecular graphs derived from the one-electron density matrix are introduced within a more general effort to explore whether incorporating electronic structure awareness allows a single model to both better generalize from small data and better learn molecular encodings. Diagonal density matrix blocks serve as atomic node embeddings, while off-diagonal blocks provide embeddings for ''link'' nodes related to atomic pairs. In a minimal basis, these embeddings have dimensions of only 45 and 81, yet no information is lost, and the original density matrix can be fully reconstructed. Blocks from the basis set overlap matrix are used as edge embeddings to encode structural information and as weights for message aggregation operations. Additionally, element-wise multiplication performed during aggregating may provide access to electronic charges, analogous to Mulliken population analysis. The proposed concept was evaluated using data from the Solubility Challenge (2008, Llinàs et al.). A graph neural network (GNN) trained on 94 drug-like molecules achieved improved solubility prediction accuracy (RMSE 0.63, R^2 0.79). If combined with existing techniques for predicting electron density from molecular structures, this approach is promising for addressing a range of chemical machine-learning problems. | Oleg Gromov | Theoretical and Computational Chemistry; Physical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67d42791fa469535b933c541/original/neural-mulliken-analysis-molecular-graphs-from-density-matrices-for-qspr-on-raw-quantum-chemical-data.pdf |
664e0fee21291e5d1dfa1238 | 10.26434/chemrxiv-2024-4hxh4 | Metal-free Microwave-Assisted Azo-Povarov Reaction of N-Carbony Aryldiazenes with trans-Cyclooctene to access Ring-fused Cinnolines | A previously undescribed azo-Povarov reaction between N-carbonyl aryldiazenes with trans-cyclooctene is developed. The participation of these aryldiazenes in the uncatalysed [4 + 2] annulation reaction has been applied to the construction of a variety of appealing fused cinnoline derivatives in yields ranging from 34 to 91% for substrates over a broad scope. The starting materials are cost-effective and easily accessible, while the reaction conditions and procedures are simple, requiring no external catalysts. Moreover, the synthetic significance of this methodology has been evidenced by a gram-scale azo-Povarov reaction and further derivatizations of the resulting N-containing heterocycles. | Xabier Jiménez de Aberásturi; Gurutze Padrones; Javier Vicario; Jesús de los Santos | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/664e0fee21291e5d1dfa1238/original/metal-free-microwave-assisted-azo-povarov-reaction-of-n-carbony-aryldiazenes-with-trans-cyclooctene-to-access-ring-fused-cinnolines.pdf |
61c4e9ded6dcc2562f431175 | 10.26434/chemrxiv-2021-mgx03 | Leveraging the interplay between homogeneous and heterogeneous catalytic mechanisms: copper-iron nanoparticles working under chemically relevant tumor conditions | The present work sheds light on a generally overlooked issue in the emerging field of bio-orthogonal catalysis within tumor microenvironments (TMEs): the interplay between homogeneous and heterogeneous catalytic processes. In most cases, previous works dealing with nanoparticle-based catalysis in the TME, focus on the effects obtained (e.g. tumor cell death) and attribute the results to heterogeneous processes alone. The specific mechanisms are rarely substantiated and, furthermore, the possibility of a significant contribution of homogeneous processes by leached species –and the complexes that they may form with biomolecules- is neither contemplated nor pursued. Herein, we have designed a bimetallic catalyst nanoparticle containing Cu and Fe species and we have been able to describe the whole picture in a more complex scenario where both homogeneous and heterogeneous processes are coupled and fostered under TME relevant chemical conditions. We investigate the preferential leaching of Cu ions in the presence of a TME overexpressed biomolecule such as glutathione (GSH). We demonstrate that these homogeneous processes initiated by the released by Cu-GSH interactions are in fact responsible for the greater part of the cell death effects found (GSH, a scavenger of reactive oxygen species is depleted and highly active superoxide anions are generated in the same catalytic cycle). The remaining solid CuFe nanoparticle becomes an active catalase-mimicking surrogate able to supply oxygen from oxygen reduced species, such as superoxide anions (by-product from GSH oxidation) and hydrogen peroxide, another species that is enriched in the TME. This enzyme-like activity is essential to sustain the homogeneous catalytic cycle in the oxygen-deprived tumor microenvironment. The combined heterogeneous-homogeneous mechanisms revealed themselves as highly efficient in selectively killing cancer cells, due to their higher GSH levels compared to healthy cell lines. | Javier Bonet-Aleta; Miguel Encinas; Esteban Urriolabeitia; Pilar Martin-Duque; Jose L Hueso; Jesus Santamaria | Catalysis; Nanoscience; Heterogeneous Catalysis; Homogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c4e9ded6dcc2562f431175/original/leveraging-the-interplay-between-homogeneous-and-heterogeneous-catalytic-mechanisms-copper-iron-nanoparticles-working-under-chemically-relevant-tumor-conditions.pdf |
60c7584d567dfeb093ec6829 | 10.26434/chemrxiv.14527002.v1 | Room-Temperature Phosphorescence of a Supercooled Liquid: Kinetic Stabilization by Desymmetrization | <p><a>Metal-free
single component liquid, developed by desymmetrizing <i>C</i><sub>2</sub>-symmetrical diketone, exhibits room-temperature phosphorescence
(RTP) and phosphorescent thermochromism in air. The unsymmetrical flexible core
with as many as eight conformers kinetically stabilizes the supercooled liquid
state. The RTP is unique the liquid that benefits from external heavy atom
effect and suppresses oxygen diffusion, while produces an emissive conformer.</a></p> | Mao Komura; Takuji Ogawa; Yosuke Tani | Photochemistry (Org.); Physical Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7584d567dfeb093ec6829/original/room-temperature-phosphorescence-of-a-supercooled-liquid-kinetic-stabilization-by-desymmetrization.pdf |
65d34992e9ebbb4db9b09433 | 10.26434/chemrxiv-2024-90bjf | Total synthesis of cyclotripeptidic natural products anacine, aurantiomide C, polonimides A and C, and verrucine F | The total synthesis of cyclotripeptidic natural products possessing a central piperazino[2,1-b]quinazolin-3,6-dione core is described, through an original strategy involving the pivotal cyclocondensation of an electrophilic homoserine lactone intermediate. The alkylidene group was spontaneously installed by autooxidation during the cyclocondensa-tion process, while the propionamide side-chain was introduced through the nickel-catalyzed aminocarbonylation of a bromoethyl intermediate. This last reaction is unprecedented on such highly functionalized intermediates. Finally, we explored structural modifications and interconversions of the natural products. Overall, this work led to anacine, au-rantiomide C, polonimide A and C, and verrucine F. | Guanghui Han; Wei Zhang; Emmanuelle Acs; Alexis Paquin; Quentin Ronzon; Nicolas Casaretto; Bastien Nay | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-02-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d34992e9ebbb4db9b09433/original/total-synthesis-of-cyclotripeptidic-natural-products-anacine-aurantiomide-c-polonimides-a-and-c-and-verrucine-f.pdf |
66bc9d48a4e53c48765bc51e | 10.26434/chemrxiv-2024-zsf3n-v2 | From Generation to Collection – Impact of Deposition Temperature on Charge Carrier Dynamics of High-Performance Vacuum-Processed Organic Solar Cells | Vacuum-processed organic solar cells (VP-OSCs) possess many advantages for scalability. However, as the academic community focusses on high performing solution-processed OSCs, detailed studies about the relation between morphology and device characteristics in VP-OSCs are rare. Here, we present a study on a model donor/fullerene VP-OSC system deposited at different substrate temperatures. Substrate heating results in increases in current density and fill factor (FF). The changes in morphology are characterised by grazing-incidence wide-angle scattering (GIWAXS) and resonant soft X-ray scattering (RSoXS). The increase in the degree of crystallinity and preferential orientation of the donor molecule in heated samples results in enhanced absorption increasing current density. The exciton and charge separation efficiency studied by transient absorption and photoluminescence quenching show only minor differences. To study the FF differences, charge transport and non-geminate recombination are studied by optoelectronic measurements and device simulations. The charge carrier kinetics are governed by a large density of trap states. While the energetic disorder and non-geminate recombination under open circuit conditions remain largely unchanged, the increased effective mobility and lower transport disorder observed in photocurrent transients explain the increased collection efficiency for heated devices. We relate this to the increased donor phase purity. Our results suggest that charge recombination and transport are governed by different aspects of disorder related to amorphous and crystalline donor phases. Quantitative comparison with high FF solution-processed OSCs reveals that the low mobility limits FF. Finally, drift-diffusion simulations give an outlook for possible performance increases through further optimisation of the deposition control. | Richard Adam Pacalaj; Yifan Dong; Ivan Ramirez; Roderick MacKenzie; Seyed Mehrdad Hosseini; Eva Bittrich; Julian Eliah Heger; Pascal Kaienburg; Subhrangsu Mukherjee; Jiaying Wu; Moritz Riede; Harald Ade; Peter Müller-Buschbaum; Martin Pfeiffer; James Durrant | Physical Chemistry; Nanoscience; Energy; Nanofabrication; Photovoltaics; Spectroscopy (Physical Chem.) | CC BY NC ND 4.0 | CHEMRXIV | 2024-08-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66bc9d48a4e53c48765bc51e/original/from-generation-to-collection-impact-of-deposition-temperature-on-charge-carrier-dynamics-of-high-performance-vacuum-processed-organic-solar-cells.pdf |
60c741ea842e654a80db1fa6 | 10.26434/chemrxiv.8174525.v1 | Learning from the Ligand: Using Ligand-Based Features to Improve Binding Affinity Prediction | Machine learning scoring functions for protein-ligand binding affinity prediction have been found to consistently outperform classical scoring functions. Structure-based scoring functions for universal affinity prediction typically use features describing interactions derived from the protein-ligand complex, with limited information about the chemical or topological properties of the ligand itself. We demonstrate that the performance of machine learning scoring functions are consistently improved by the inclusion of diverse ligand-based features. For example, a Random Forest combining the features of RF-Score v3 with RDKit molecular descriptors achieved Pearson correlation coefficients of up to 0.831, 0.785, and 0.821 on the PDBbind 2007, 2013, and 2016 core sets respectively, compared to 0.790, 0.737, and 0.797 when using the features of RF-Score v3 alone. Excluding proteins and/or ligands that are similar to those in the test sets from the training set has a significant effect on scoring function performance, but does not remove the predictive power of ligand-based features. Furthermore a Random Forest using only ligand-based features is predictive at a level similar to classical scoring functions and it appears to be predicting the mean binding affinity of a ligand for its protein targets.<br /> | Fergus Boyles; Charlotte M Deane; Garrett Morris | Computational Chemistry and Modeling; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2019-05-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741ea842e654a80db1fa6/original/learning-from-the-ligand-using-ligand-based-features-to-improve-binding-affinity-prediction.pdf |
6400be8f37e01856dc06aa11 | 10.26434/chemrxiv-2023-r3r50 | High Throughput Determination of Stern Volmer Quenching Constants for Common Photocatalysts and Quenchers | Mechanistic information on reactions proceeding via photoredox catalysis has enabled rational optimizations of existing reactions and revealed new synthetic pathways. One essential step in any photoredox reaction is catalyst quenching via photoinduced electron transfer or energy transfer with either a substrate, additive, or co-catalyst. Identification of the correct quencher using Stern-Volmer studies is a necessary step mechanistic understanding; however, such studies are often cumbersome, low throughput and require specialized luminescence instruments. This report describes a high throughput method to rapidly acquire series of Stern-Volmer constants, employing readily available fluorescence plate readers and 96 well-plates. By leveraging multi-channel pipettors or liquid dispensing robots in combination with fast plate readers, the sampling frequency for quenching studies can be improved by several orders of magnitude. This new high-throughput method enabled the rapid collection of 220 quenching constants for a library of 20 common photocatalysts with 11 common quenchers. The extensive Stern-Volmer constants table generated greatly facilitates the systematic comparison between quenchers and can provide guidance to the synthetic community interested in designing and understanding catalytic photoredox reactions | Rachel Motz; Alexandra Sun; Dan Lehnherr; Serge Ruccolo | Physical Chemistry; Organic Chemistry; Catalysis; Photocatalysis; Photochemistry (Physical Chem.); Robotics | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6400be8f37e01856dc06aa11/original/high-throughput-determination-of-stern-volmer-quenching-constants-for-common-photocatalysts-and-quenchers.pdf |
641d888e647e3dca996f04e8 | 10.26434/chemrxiv-2023-ttqvd | Interchain Expanded Extra-Large Pore Zeolites | Stable aluminosilicate zeolites with extra-large pores open through rings of more than 12 tetrahedra are in demand to process molecules larger than those currently manageable. However, until very recently, they proved elusive. Here we report a new strategy based on an interchain expansion design concept that yields thermally and hydrothermally stable silicates by expansion of a one dimensional (1D) silicate chain with an intercalated silylating agent that separates and connects the chains. As a result, new types of zeolites zeolites with extra-large pores delimited by 20, 16, and 16 Si tetrahedra along the three crystallographic directions, respectively, are obtained. The as-made inter-chain expanded zeolite contains dangling Si-CH3 groups that by calcination connect to each other resulting in a true, fully connected 3D zeolite framework with a very low density, just slightly above that of water. Additionally, it features triple four ring units never seen before in any type of zeolite. Ti can be introduced in this zeolite to obtain a catalyst active in the liquid-phase oxidation of bulky alkenes that shows promise in the industrially relevant clean production of propylene oxide using cumene hydroperoxide as an oxidant. | Zihao Rei Gao; Huajian Yu; Fei-Jian Chen; Xintong Li; Alvaro Mayoral; Zijian Niu; Ziwen Niu; Hua Deng; Carlos Márquez-Álvarez; Hong He; Hao Xu; Wei Fan; Salvador R. G. Balestra ; Jian Li; Peng Wu; Jihong Yu; Miguel A. Camblor | Physical Chemistry; Materials Science; Catalysis; Heterogeneous Catalysis; Redox Catalysis; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2023-03-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641d888e647e3dca996f04e8/original/interchain-expanded-extra-large-pore-zeolites.pdf |
669e1efbc9c6a5c07a64116c | 10.26434/chemrxiv-2024-2fqn7 | Identification of deactivation mechanisms by periodic transient kinetic method | The understanding of deactivation processes in heterogeneous catalysis is key for the development of new materials and exploration of new operation windows. In this contribution, the periodic transient kinetic method (PTK) is used to identify and separate catalyst deactivation processes for the first time. The PTK-method is applied for a standard Ni/Al2O3 catalyst in CO and CO2 methanation for 24 h, and compared to steady-state experiments. For the example reactions, the study exhibits different deactivation behaviour for CO and CO2 methanation. The results show that the PTK method delivers an insight into the deactivation process and furthermore gives evidence for the underlying mechanism. | Max Gäßler; Robert Güttel; Jens Friedland | Chemical Engineering and Industrial Chemistry; Reaction Engineering | CC BY 4.0 | CHEMRXIV | 2024-07-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/669e1efbc9c6a5c07a64116c/original/identification-of-deactivation-mechanisms-by-periodic-transient-kinetic-method.pdf |
667315b601103d79c59a70fe | 10.26434/chemrxiv-2024-xnw4h | Identification of the dual roles of Al2O3 coatings on NMC811-cathodes via theory and experiment | Metal-oxide coatings are a favoured strategy for mitigating surface degradation problems in state-of-the-art lithium-ion battery Ni-rich layered positive electrode materials. Despite their extensive use, a full, fundamental understanding of the role of coatings in reducing degradation and extending cycling lifetimes is currently lacking. In this work, the interactions between an atomic layer deposited (ALD) alumina coating on polycrystalline LiNi0.8Mn0.1Co0.1O2 (NMC811) and a carbonate-based battery electrolyte are studied. Solid-state nuclear magnetic resonance (ssNMR) heteronuclear experiments show that the Al2O3 coating transforms by reacting with electrolyte species present before and during electrochemical cycling, scavenging protic and acidic species. Density-functional theory calculations highlight the additional chemical effect of the coating in locally stabilising the structure of the NMC811, limiting oxidation of the oxygen atoms coordinated to both Al and Ni, thereby limiting the surface reconstruction process and improving the electrochemical performance. Improved NMC811 surface stability is confirmed by monitoring gaseous degradation species by operando electrochemical mass-spectrometry and via X-ray spectroscopic analysis of the electrochemically aged samples to examine changes in Ni and O oxidation state and local structure. The combination of this experimental and theoretical analysis suggests that Al2O3 coatings have a dual role: as a protective barrier against attack from chemical species in the electrolyte, and as an artificial passivating layer hindering oxygen loss and surface phase transformations. This holistic approach, which provides a fundamental understanding of how the surface stability is improved by the coating, will aid the design of the state-of-the-art and future positive electrode materials. | Richard L.B. Chen; Farheen N. Sayed; Hrishit Banerjee; Israel Temprano; Andrew J. Morris; Clare P. Grey | Physical Chemistry; Energy; Energy Storage; Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-06-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/667315b601103d79c59a70fe/original/identification-of-the-dual-roles-of-al2o3-coatings-on-nmc811-cathodes-via-theory-and-experiment.pdf |
6386bccfe474bf5fed560d58 | 10.26434/chemrxiv-2022-glvkg-v2 | Halogen-bonding-promoted Photo-induced C–X Borylation of Aryl Halide using Phenol Derivatives | This study investigates the photo-induced C–X borylation reaction of aryl halides by forming a halogen-bonding complex. The method employs 2-naphthol as a halogen-bonding acceptor and proceeds under mild conditions without a photoredox catalyst under 420 nm blue light irradiation. The method is highly chemoselective, broadly functional group tolerant, and provides concise access to corresponding boronate esters. Mechanistic studies reveal that forming the halogen-bonding complex between aryl halide and naphthol acts as an electron donor-acceptor complex to furnish aryl radicals through photo-induced electron transfer. | Kazuki Matsuo; Eiji Yamaguchi; Akichika Itoh | Organic Chemistry; Photochemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-11-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6386bccfe474bf5fed560d58/original/halogen-bonding-promoted-photo-induced-c-x-borylation-of-aryl-halide-using-phenol-derivatives.pdf |
6435e3c3736114c963554651 | 10.26434/chemrxiv-2023-g5kwc | Antioxidant Activity via Free Radical Scavenging of Pitavastatin and Its Hydroxylated Metabolites. A Quantum Chemical Attempt Aiming to Assist Drug Development | Statins form a class of drugs often administered in a variety of cardiovascular diseases, for which their antioxidant capacity appears particularly relevant. Although experiments have long provided empirical evidence that statins can suppress various oxidation pathways, theoretical attempts to quantify the antioxidant activity of statins (read, atorvastatin ATV, because this is the only one studied so far) were not published until last year. Molecular and clinical differences of stains trace back to the ring attached to the statin’s active moiety. This can be, e.g., a pyrrole, as the case of the aforementioned ATV or a quinoline, as the case of pitavastatin (PVT), which represents the focus of the present work. Extensive results reported here for PVT and derivative include the thermodynamic antioxidant descriptors (bond dissociation enthalpy BDE, adiabatic ionization potential IP, proton dissociation enthalpy PDE, proton affinity PA, and electron transfer enthalpy ETE) related to the three antioxidant mechanisms (hydrogen atom transfer HAT, stepwise electron transfer proton transfer SETPT, sequential proton loss electron transfer SPLET). Our particular emphasis is on the PVT’s hydroxylated derivatives wherein a hydroxy group replaces a hydrogen atom either on the quinoline core (Q-hydroxylated metabolites) or on the fluorophenyl ring (F-hydroxylated metabolites). Our calculations indicate that both the Q- and F-hydroxylated metabolites possess antioxidant properties superior to the parent PVT molecule. Given the fact that, to the best of our knowledge, no experimental data for the antioxidant potency of PVT and its hydroxylated derivatives exist, this is a theoretical prediction, and we Given the fact that, to the best of our knowledge, no experimental data for the antioxidant potency of PVT and its hydroxylated derivatives exist, this is a theoretical prediction for the validation of which we aim hereby to stimulate companion experimental in vivo and in vitro investigations and inspire pharmacologists in further drug developments. | Ioan Baldea | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Theory - Computational; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-04-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6435e3c3736114c963554651/original/antioxidant-activity-via-free-radical-scavenging-of-pitavastatin-and-its-hydroxylated-metabolites-a-quantum-chemical-attempt-aiming-to-assist-drug-development.pdf |
65ef05f99138d2316135c712 | 10.26434/chemrxiv-2024-lmmd8 | Intramolecular Cyclization and a Retro-Ene Reaction Enable the Rapid Fragmentation of a Vitamin B1-derived Breslow Intermediate | In solution, analogues of the Breslow intermediate formed during catalysis by benzoylformate decarboxylase (BFDC) undergo rapid, irreversible fragmentation. The ability of BFDC to prevent this reaction and preserve its’ cofactor is a striking example of an enzyme ‘steering’ a reactive intermediate towards a productive pathway. To understand how BFDC suppresses the off-pathway reactivity of this Breslow intermediate, a clear mechanistic understanding of the fragmentation reaction is required. Here, DFT calculations reveal an unexpected mechanism for the solution-phase fragmentation that involves an intramolecular cyclization and a subsequent retro-ene reaction to release the final products. Free energy profiles demonstrate that this pathway is significantly more facile than the previously proposed mechanism that invoked Breslow intermediate enolates as intermediates. Additional computations have been performed to understand why related Breslow intermediates do not undergo analogous fragmentation reactions. Calculations performed with two closely related Breslow intermediates suggest that subtle differences in the relative values of ∆G‡ for protonation and fragmentation dictate whether a given intermediate will fragment or not. These differences and the fragmentation mechanism unveiled in this work have ramifications for the catalytic mechanism of BFDC and other thiamin-dependent enzymes and will provide general lessons related to the control of reactive intermediates by enzymes. | Neil Grenade; Graeme Howe | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Organic Chemistry; Bioorganic Chemistry; Physical Organic Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ef05f99138d2316135c712/original/intramolecular-cyclization-and-a-retro-ene-reaction-enable-the-rapid-fragmentation-of-a-vitamin-b1-derived-breslow-intermediate.pdf |
64ecab2fdd1a73847fb3eb97 | 10.26434/chemrxiv-2023-vlkr6 | Manufacturing free-standing porous layers with dynamic hydrogen bubble templating | The three-dimensional structure – i.e. microstructure – of porous electrodes governs the performance of emerging electrochemical technologies such as fuel cells, electrolysis and batteries. Sustaining electrochemical reactions and convective-diffusive mass transport at high efficiency is complex and motivates the search for sophisticated microstructures with multimodal pore size distributions and pore size gradients. Drawing inspiration from porous metallic foams, here we engineer a novel method to manufacture free-standing, thin, porous foams via dynamic hydrogen bubble templating in an electrochemical flow cell, through the introduction of an intermediate layer and optimization of synthesis parameters (i.e. voltage, concentration and charge). We create mechanically stable foams with thicknesses ranging from ~50 µm to ~200 µm comprising porous, dendritic structures, arranged to form a vascular network of larger pores with a gradient in radii from ~5 µm at the bottom and up to ~36 µm at the top of the material. Using segmented X-ray tomographic data, we simulate the diffusive transport through the material as function of liquid filling and compare it to carbon fiber-based material. For all ranges of saturation, the metallic foams outperforms the fibrous structure, showcasing the potential of bimodal pore size architectures to improve two phase transport by optimizing the distribution of phases. | Adrian Mularczyk; Daniel Niblett; Adam Wijpkema; Marc van Maris; Antoni Forner-Cuenca | Materials Science; Energy; Chemical Engineering and Industrial Chemistry; Nanostructured Materials - Materials; Transport Phenomena (Chem. Eng.); Fuel Cells | CC BY NC ND 4.0 | CHEMRXIV | 2023-08-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ecab2fdd1a73847fb3eb97/original/manufacturing-free-standing-porous-layers-with-dynamic-hydrogen-bubble-templating.pdf |
60c74aaa702a9b83ac18b2ed | 10.26434/chemrxiv.12237020.v1 | Comparing Zwitterionic and PEG Exteriors of Polyelectrolyte Complex Micelles | <p>A series of model polyelectrolyte complex micelles (PCMs) was prepared to investigate the consequences of neutral and zwitterionic chemistries and distinct charged cores on the size and stability of nanocarriers. Using aqueous reversible addition-fragmentation chain transfer (RAFT) polymerization, we synthesized a well-defined diblock polyelectrolyte system, poly(2-methacryloyloxyethyl phosphorylcholine methacrylate)-<i>block</i>-poly((vinylbenzyl) trimethylammonium) (PMPC-PVBTMA), at various neutral and charged block lengths to compare directly against PCM structure-property relationships centered on poly(ethylene glycol)-<i>block</i>-poly((vinylbenzyl) trimethylammonium) (PEG-PVBTMA) and poly(ethylene glycol)-<i>block</i>-poly(lysine) (PEG-PLK). After complexation with a common polyanion, poly(sodium acrylate), the resulting PCMs were characterized by dynamic light scattering (DLS) and small angle X-ray scattering (SAXS). We observed uniform assemblies of spherical micelles with a core diameter of ~40 nm when PMPC-PVBTMA was used, and smaller particles between 20-30 nm for PEG-PLK and PEG-PVBTMA via SAXS analysis. Additionally, PEG-PLK PCMs proved most resistant to dissolution by both monovalent and divalent salt, followed by PEG-PVBTMA then PMPC-PVBTMA. All micelle systems were serum stable in 100% fetal bovine serum over the course of 8 h by time-resolved DLS, demonstrating minimal interactions with serum proteins and potential as in vivo drug delivery vehicles. This thorough study of the synthesis, assembly, and characterization of zwitterionic polymers in PCMs advances the design space for charge-driven micelle assemblies.</p> | Jeffrey Ting; Alexander Marras; Joseph Mitchell; Trinity Campagna; Matthew Tirrell | Nanostructured Materials - Materials; Polyelectrolytes - Materials; Drug delivery systems; Polyelectrolytes - Polymers; Polymer chains; Polymer morphology; Nanostructured Materials - Nanoscience; Polymers; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74aaa702a9b83ac18b2ed/original/comparing-zwitterionic-and-peg-exteriors-of-polyelectrolyte-complex-micelles.pdf |
65206cac45aaa5fdbb72365d | 10.26434/chemrxiv-2023-lk2jl | Learning Intermolecular Electronic Coupling from a Molecular-Orbital-Pair-based Descriptor | In this work, we proposed a graphic molecular-orbital-pair-based descriptor to predict intermolecular electronic couplings (ECs).
We transform the numeric grid points data of the molecular orbitals (MOs) involved in the charge or energy transfer process by reducing the thousands of grid points to a few points based on the lobes of MO.
The simplified representation consists of two parts, the integral value over the space and the coordinates of centroid of each lobe.
To express the intermolecular interaction for a donor-acceptor pair, each simplified MO representation from the donor is paired to the one from the acceptor.
Then, the obtained MO-pair representation is the descriptor for learning the intermolecular ECs, including hole transfer (HT), electron transfer (ET) and Dexter energy transfer (DET) coupling, with a multi-layer perceptron (MLP) model.
The accuracy of our model reached at a promising level of 0.1~5 meV comparing with the quantum chemistry calculations.
The data size dependence tests shows that our model has exhibited good ability on low-shot learning.
Therefore, the graphic MO-pair-based descriptor has been proved to be capable to characterize MO interaction features. | Jingheng Deng; Shuming Bai | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2023-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65206cac45aaa5fdbb72365d/original/learning-intermolecular-electronic-coupling-from-a-molecular-orbital-pair-based-descriptor.pdf |
660d7e2691aefa6ce1b4bd3c | 10.26434/chemrxiv-2023-rhx7h-v2 | Non-Stereotypical Distribution and Effect of Ergosterol in Lipid Membranes | Sterols are an important class of lipids that regulate many biological processes. Among them, ergosterol in fungi and some protists is surprisingly understudied compared to cholesterol from animal membranes. Based on their similarity in chemical structure, ergosterol is assumed to modulate membrane in the similar fashion as cholesterol. In this study, however, we revealed very different interaction between ergosterol and lipid membranes. Using Neutron Membrane Diffraction, we found ergosterol is embedded much shallower than cholesterol in the bilayer. It doesn’t change the membrane thickness as much, indicating little condensation effect. From Neutron Spin Echo spectroscopy, we found ergosterol actually can both rigidify and soften membranes at different concentrations. The Quasi Elastic Neutron Scattering measurement of lateral lipid diffusion indicates that ergosterol promotes a jump diffusion of POPC, while cholesterol keeps the same continuous lateral diffusion mechanism as in the pure POPC membrane. All those results point to quite distinct interactions of ergosterol with membranes as compared to cholesterol. These structural and dynamical insights provide basic understandings for the properties of membranes containing ergosterol, as well as the implication for lipid rafts and drug interaction in those membranes. | Shuo Qian; Gergely Nagy; Piotr Zolnierczuk; Eugene Mamontov; Robert Standaert | Biological and Medicinal Chemistry; Biochemistry; Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660d7e2691aefa6ce1b4bd3c/original/non-stereotypical-distribution-and-effect-of-ergosterol-in-lipid-membranes.pdf |
677c0c1081d2151a0219e28e | 10.26434/chemrxiv-2025-mlb2w | The Future of Nanomaterials in Manufacturing | Nanomaterials have emerged as a transformative force in manufacturing, driving significant advancements in efficiency, sustainability, and precision. This chapter provides a comprehensive examination of the evolving role of nanomaterials in modern manufacturing, highlighting their profound impact across critical industries, including electronics, energy, aerospace, and pharmaceuticals. It delves into the unique physicochemical properties of metallic, carbon-based, polymeric, and composite nanomaterials, which confer superior performance across diverse manufacturing applications. These properties, such as enhanced durability, thermal stability, and conductivity, are pivotal in the development of next generation manufacturing processes. The chapter also addresses the major challenges hindering the widespread adoption of nanomaterials, including scalability, high production costs, and environmental sustainability concerns. It critically evaluates innovative strategies, including green nanotechnology, hybrid systems, and self-healing materials, as potential solutions to these challenges. Furthermore, the future prospects of nanomaterials are explored, particularly their integration with Industry 4.0 paradigms. This includes the incorporation of artificial intelligence, robotics, and smart manufacturing systems, which collectively contribute to the creation of a more sustainable and intelligent manufacturing ecosystem. A detailed case study on advanced nanomaterial systems is presented to demonstrate their potential in addressing complex industrial challenges, offering valuable insights into practical applications. This chapter serves as a comprehensive resource for researchers, industry practitioners, and policymakers, providing essential perspectives on the future trajectory of nanomaterials in manufacturing. | Marvellous Eyube; Courage Enuesueke; Marvellous Alimikhena | Materials Science; Nanostructured Materials - Materials; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-17 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/677c0c1081d2151a0219e28e/original/the-future-of-nanomaterials-in-manufacturing.pdf |
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