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67cf46c5fa469535b9c29273 | 10.26434/chemrxiv-2025-rdbs7 | Abiotic Transcription Factors by Strategic Insertion of Non-Proteinogenic Amino Acids | Nature employs proteins as molecular machines to orchestrate numerous intricate biological processes. Natural proteins are primarily synthesized from 22 proteinogenic amino acids. In principle, developing abiotic proteins with novel non-proteinogenic residues can expand their functional space, enabling the discovery of new reactivities not found in nature. Here, we combined a rational design with total synthesis to develop novel abiotic proteins derived from natural transcription factors (TFs). We synthesized a library of abiotic TFs using solid-phase synthesis and native chemical ligation to afford 27 novel analogs on a milligram scale. Systematic DNA binding analysis revealed that the mutation site plays a key role in the DNA binding activity of TFs. Remarkably, DNA binding and cellular studies enabled the discovery of the μMax20 analog, bearing two non-proteinogenic residues (Lys31/57 to hArg), which displayed potent DNA binding to the core E-box site and exceptional intrinsic cell permeability. Furthermore, the site-specific editing of μMax20 with staples led to an advanced analog, 2s-μMax20, which is amenable to cellular delivery at nanomolar concentrations. Collectively, our findings indicate that inserting non-natural transformations into strategic domains and residues is a powerful strategy for leveraging protein function to engineer novel analogs for basic research and biomedical applications. | Omer Harel; Ferran Nadal-Bufi; Raj Nithun; Yumi Minyi Yao; Ariel Afek; Marc Vendrell; Muhammad Jbara | Biological and Medicinal Chemistry; Biochemistry; Chemical Biology | CC BY 4.0 | CHEMRXIV | 2025-03-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cf46c5fa469535b9c29273/original/abiotic-transcription-factors-by-strategic-insertion-of-non-proteinogenic-amino-acids.pdf |
63dd09aaa8f79476ca64c70c | 10.26434/chemrxiv-2023-kmr9g | Determination of the Dissociation Constant for Polyvalent Receptors using ELISA: a Case of M13 Phages Displaying Troponin T-specific Peptides | Phage-derived affinity peptides have become widespread thanks to their easy selection via phage display. Interactions between a target protein and its specific peptide are similar to those between antibodies and antigens. The strength of these non-covalent complexes may be described by the dissociation constant (Kd). In this paper, protein-specific peptides are exposed on the pIII protein present in the M13 bacteriophage virion with up to 5 copies. Therefore, one phage particle can bind from one to five ligands. Here, we discuss the dependences between phage-displayed peptides and their ligands in solution using a model system based on troponin T (TnT) binding phages. Moreover, a method of calculating Kd values from ELISA experiments was developed and presented. Determined Kd values are in the picomolar range. | Sebastian Jan Machera; Joanna Niedziolka-Jonsson; Martin Jonsson-Niedziolka; Katarzyna Szot-Karpińska | Biological and Medicinal Chemistry; Analytical Chemistry; Biochemical Analysis; Biochemistry; Bioengineering and Biotechnology | CC BY 4.0 | CHEMRXIV | 2023-02-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63dd09aaa8f79476ca64c70c/original/determination-of-the-dissociation-constant-for-polyvalent-receptors-using-elisa-a-case-of-m13-phages-displaying-troponin-t-specific-peptides.pdf |
6166e003fb8619d5fcf6efb5 | 10.26434/chemrxiv-2021-knj2g | Lower Heating Value of Jet Fuel from Hydrocarbon Class Concentration Data and Thermo-Chemical Reference Data: An Uncertainty Quantification | A detailed assessment is presented on the calculation and uncertainty of the lower heating value (net heat of combustion) of conventional and sustainable aviation fuels, from hydrocarbon class concentration measurements, reference molecular heats of formation, and the uncertainties of these reference heats of formation. Calculations using this paper’s method and estimations using ASTM D3338 are reported for 17 fuels of diverse compositions and compared against reported ASTM D4809 measurements. All the calculations made by this method and the reported ASTM D4809 measurements agree (i.e., within 95% confidence intervals). The 95% confidence interval of the lower heating value of fuel candidates that are comprised entirely of normal- and iso-alkanes is less than 0.1 MJ/kg by the method described here, while high cyclo-alkane content leads to 95% confidence bands that approach 0.2 MJ/kg. Taking a possible bias into account, the accuracy and precision of the method described in this work could be as high as 0.23 MJ/kg for some samples. | Randall Boehm; Zhibin Yang; David Bell; John Feldhausen; Joshua Heyne | Energy; Chemical Engineering and Industrial Chemistry; Fuels - Energy Science | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6166e003fb8619d5fcf6efb5/original/lower-heating-value-of-jet-fuel-from-hydrocarbon-class-concentration-data-and-thermo-chemical-reference-data-an-uncertainty-quantification.pdf |
6102c3a1537d102a5a805693 | 10.26434/chemrxiv-2021-0nw8q | Ni-Catalyzed Arylbenzylation of Alkenylarenes. Kinetic Studies Reveal Autocatalysis by ZnX2 and 3-Fold Catalytic Rate Increase | We report a Ni-catalyzed regioselective arylbenzylation of alkenylarenes with benzyl halides and arylzinc reagents. The reaction furnishes differently substituted 1,1,3-triarylpropyl structures that are reminiscent of the cores of oligoresveratrol natural products. The reaction is also compatible for the coupling of internal alkenes, secondary benzyl halides and variously substituted arylzinc reagents. Kinetic studies reveal that the reaction proceeds with a rate-limiting single electron transfer process and is autocatalyzed by in situ-generated ZnX2. The reaction rate is amplified by three-fold through autocatalysis upon addition of ZnX2. | Roshan K. Dhungana; Rishi R. Sapkota; Laura M. Wickham; Doleshwar Niroula; Bijay Shrestha; Ramesh Giri | Organic Chemistry; Catalysis; Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6102c3a1537d102a5a805693/original/ni-catalyzed-arylbenzylation-of-alkenylarenes-kinetic-studies-reveal-autocatalysis-by-zn-x2-and-3-fold-catalytic-rate-increase.pdf |
671821eb83f22e4214d79774 | 10.26434/chemrxiv-2024-z29m3 | Generative Design of Functional Metal Complexes Utilizing the Internal Knowledge of Large Language Models | The design of functional transition metal complexes (TMCs) is hindered by the combinatorial explosion of the search space spanned by various metals and ligands, necessitating efficient multi- objective optimization strategies. Traditional genetic algorithms (GAs) are frequently employed in this domain, utilizing random mutations and crossovers steered by explicit mathematical objective formulations to navigate the search space. The transfer and sharing of knowledge across different GA optimization tasks, however, remain challenging. Here, we introduce the integration of large language models (LLMs) into the evolutionary optimization framework (LLM-EO) for TMCs. LLM- EO significantly outperforms traditional GAs due to the intrinsic chemical knowledge embedded within LLMs, acquired during their extensive pretraining. Notably, without the need for supervised fine-tuning, LLMs can leverage the entirety of historical data amassed during the optimization processes, demonstrating superior performance compared to LLMs that are limited to the best TMCs identified in the evolutionary cycle. Specifically, LLM-EO identifies eight out of the top 20 TMCs with the largest HOMO-LUMO gaps by interrogating merely 200 candidates within a vast search space of 1.37 million TMCs. Through prompt engineering using natural language, LLM-EO introduces unparalleled flexibility in multi-objective optimizations, especially when guided by seasoned researchers, thereby circumventing the necessity for intricate mathematical formulations. As generative models, LLMs possess the capability to propose novel ligands and TMCs with unique chemical properties by amalgamating both internal knowledge and external chemistry data, thus combining the benefits of efficient optimization and molecular generation. With the increasing potential of LLMs, both in their capacity as pretrained foundational models and new strategies in post-training inference, we anticipate broad applications of LLM-based evolutionary optimization in the fields of chemistry and materials design. | Jieyu Lu; Zhangde Song; Qiyuan Zhao; Yuanqi Du; Yirui Cao; Haojun Jia; Chenru Duan | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Artificial Intelligence | CC BY NC 4.0 | CHEMRXIV | 2024-10-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/671821eb83f22e4214d79774/original/generative-design-of-functional-metal-complexes-utilizing-the-internal-knowledge-of-large-language-models.pdf |
65d8f08c66c13817295cd2f6 | 10.26434/chemrxiv-2024-mdpw8 | What is the appropriate data representation of electrochemical impedance spectroscopy in machine-learning analysis? | Electrochemical impedance spectroscopy (EIS) is an important analytic technique for the understanding of electrochemical systems. With the recent advent and burgeoning deployment of machine learning (ML) in EIS analysis, a critical yet hitherto unanswered question emerges: what is the appropriate data representation of EIS for ML-based analysis? While the representation of a model’s input data is known to be critical for a successful deployment of ML model, EIS is known to possess multiple classical venues of data representation and it remains unclear how different EIS data should be compared following a proper data normalization protocol. Here we report the methodology and the outcomes that evaluate the efficacy of multiple data representation methods in ML-based EIS analysis. At least within our proof-of-concept parameter space, plotting the input training data’s impedance magnitude (|Z|) against phase angle (φ) while individually normalizing each EIS curve yields the highest accuracy and robustness in the correspondingly established residual neural network (ResNet) model. Rationalized by additional "importance" analysis of the input data, such a data representation method extracts information and hidden features more effectively. While Nyquist plot is more widely used in manual analysis, we found that ML-based analysis may require a different data representation and offered a clear guideline for future researchers to evaluate on a case-by-case basis. | Jingwen Sun; Weitong Zhang; Yuanzhou Chen; Benjamin Hoar; Hongyuan Sheng; Jenny Yang; Cyrille Costentin; Quanquan Gu; Chong Liu | Analytical Chemistry; Electrochemical Analysis | CC BY NC 4.0 | CHEMRXIV | 2024-02-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65d8f08c66c13817295cd2f6/original/what-is-the-appropriate-data-representation-of-electrochemical-impedance-spectroscopy-in-machine-learning-analysis.pdf |
67328daaf9980725cfe47d9b | 10.26434/chemrxiv-2024-fgz5m-v2 | Univariate Prediction of Hammett Parameters and Select Relative Reaction Rates Using Loewdin Atomic Charges | Loewdin charges from density functional theory calculations have been used here to obtain general, univariate linear correlations for the prediction of experimental Hammett parameters and relative reaction rates. While previous studies have established that Hirshfeld and CM5 charges perform strongly as univariate predictors, the near-ubiquitous Loewdin charges have not yet been evaluated. To this end, we assess the predictive capability of Loewdin charges for three chemical systems. First, we show that Loewdin charges outperform Hirshfeld and CM5 charges for Hammett parameter prediction. Second, we see Loewdin charges generally perform comparably to Hirshfeld charges for predicting the relative rates of olefin cleavage by photoexcited nitroarenes. The single case of poor correlation, between relative rates and the Loewdin charges on nitrogen sites, is ameliorated when considering the net charge on the NO2 group. Third, we show that Loewdin, Hirshfeld, and CM5 charges all perform very well for generating correlations for relative reaction rates for C-H activation of 9-(4-X-phenyl)-9H-fluorene substrates by a transition metal catalyst. The equations generated throughout the study enable the prediction of Hammett parameters and relative reaction rates. These tools can accelerate synthetic and experimental studies by enabling the in silico prediction of uncharacterized chemical properties. | Gautam Stroscio; Nir Goldman | Theoretical and Computational Chemistry; Physical Chemistry; Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67328daaf9980725cfe47d9b/original/univariate-prediction-of-hammett-parameters-and-select-relative-reaction-rates-using-loewdin-atomic-charges.pdf |
60c73e10842e6562cddb184b | 10.26434/chemrxiv.6272579.v1 | Conditioning–Free Electrolytes for Magnesium Batteries Using Sulfone–Ether Mixtures with Increased Thermal Stability | We report an investigation of electrochemical properties and speciation of electrolytes composed of magnesium bis(hexamethyldisilazide) (Mg(HMDS)<sub>2</sub>) and magnesium chloride in sulfone-ether mixtures. The inclusion of sulfones dramatically increased the thermal stability of the electrolytes to 80 °C. The addition of ether was necessary to form an electrochemically active species. Electrochemical reversibility was maintained above 90% for 50 cycles for equivolume mixtures of butyl sulfone and THF. Sulfolane based solutions demonstrated low reversibilities and mass spectrometry measurements showed the preferential formation of an MgCl<sup>+</sup> cation over the Mg<sub>2</sub>Cl<sub>3</sub><sup>+</sup> cation. Greater amounts of Mg<sub>2</sub>Cl<sub>3</sub><sup>+</sup> compared to MgCl<sup>+</sup> is linked with higher performing electrolytes. Spectroscopic measurements showed co-solvation of the active magnesium cation with both solvents. | Laura
C. Merrill; Jennifer Schaefer | Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2018-05-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73e10842e6562cddb184b/original/conditioning-free-electrolytes-for-magnesium-batteries-using-sulfone-ether-mixtures-with-increased-thermal-stability.pdf |
64809c1ebe16ad5c579b5572 | 10.26434/chemrxiv-2023-zbnfd | Electrochemical Nickel-Catalyzed Selective Arylation of Cysteine-Containing Peptides | Here we report a simple electrochemical route towards the synthesis of S-arylated peptides by a site selective coupling of peptides with aryl halides under base free conditions. This approach demonstrates the power of electrochemistry to access highly complex peptides conjugates under mild reaction conditions. We demonstrated also the utility of this appraoch to access to cyclic peptides. | Samir MESSAOUDI; Shen Linhua; Olivier Monasson; Elisa Peroni; Franck Le bideau | Organic Chemistry; Catalysis; Organometallic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64809c1ebe16ad5c579b5572/original/electrochemical-nickel-catalyzed-selective-arylation-of-cysteine-containing-peptides.pdf |
60c73d514c89195085ad1bd2 | 10.26434/chemrxiv.5772954.v1 | Melting of zeolitic imidazolate frameworks with different topologies: insight from first-principles molecular dynamics | Metal–organic frameworks are chemically versatile materials, and excellent candidates for many applications from carbon capture to drug delivery, through hydrogen storage. While most studies so far focus on the crystalline MOFs, there has been a recent shift to the study of their disordered states, such as defective structures, glasses, gels, and very recently liquid MOFs. Following the publication of the melting mechanism of zeolitic imidazolate framework ZIF-4, we use here molecular simulation in order to investigate the similarities and differences with two other zeolitic imidazolate frameworks, ZIF-8 and ZIF-zni. We perform first principles molecular dynamics simulations to study the melting phenomena and the nature of the liquids obtained, focusing on structural characterization at the molecular scale, dynamics of the species, and thermodynamics of the solid–liquid transition. We show how the retention of chemical configuration, the changes in the coordination network, and the variation of the porous volume in the liquid phase are influenced by the parent crystalline framework.<br /> | Romain Gaillac; Pluton Pullumbi; François-Xavier Coudert | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2018-06-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73d514c89195085ad1bd2/original/melting-of-zeolitic-imidazolate-frameworks-with-different-topologies-insight-from-first-principles-molecular-dynamics.pdf |
62d847c1724581802d9ff0dc | 10.26434/chemrxiv-2022-26vgr | One-Pot Synthesis of Aminated Bimodal Mesoporous Silica Nanoparticles as Antibacterial Nanocarrier and CO2 Capture Sorbent | Mesoporous silica nanoparticles have highly versatile structural properties that are suitable for a plethora of applications including catalysis, separation and nanotherapeutics. We report a one-pot synthesis strategy that generates bimodal mesoporous silica nanoparticles via co-assembly of a structure-directing Gemini surfactant (C16-3-16) with tetraethoxysilane/(3-aminopropyl)triethoxysilane-derived sol additive. Synthesis temperature enables control of the nanoparticle shape, structure and mesopore architecture. Variations of the aminosilane/alkylsilane molar ratio further enables programmable adjustments of hollow to dense nanoparticle morphologies, bimodal pore sizes and surface chemistry. The resultant Gemini-directed aminated mesoporous silica nanoparticles have excellent carbon dioxide adsorption capacities and antimicrobial properties against E. coli. Our results provide enhanced understandings in the structure formation of multiscale mesoporous inorganic materials that are desirable for numerous applications such as carbon sequestration, water remediation and biomedical-related applications. | Yun Li; Amit Kumar Tiwari; Jingyi Sandy Ng; Geok Leng Seah; Hong Kit Lim; Teeraporn Suteewong; Chor Yong Tay; Yeng Ming Lam; Kwan W. Tan | Materials Science; Nanoscience; Aggregates and Assemblies; Controlled-Release Systems; Nanostructured Materials - Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62d847c1724581802d9ff0dc/original/one-pot-synthesis-of-aminated-bimodal-mesoporous-silica-nanoparticles-as-antibacterial-nanocarrier-and-co2-capture-sorbent.pdf |
61307e56ac321936ea6f511f | 10.26434/chemrxiv-2021-951pq | Observation of the Ponderomotive Effect in Non-Valence Bound States of Polyatomic Molecular Anions | The ponderomotive effect in the non-valence bound states has been experimentally demonstrated for the first time, giving the great promise for the manipulation of the polyatomic molecules by the dynamic Stark effect. Entire quantum levels of the dipole-bound state (DBS) and quadruple-bound state (QBS) of the phenoxide (or 4-bromophenoxide) and 4-cyanophenoxide anions, respectively, show the clear-cut ponderomotive blue-shifts in the presence of the spatiotemporally overlapped non-resonant picosecond control laser pulse. The quasi-free electron in the QBS is found to be more vulnerable to the external oscillating electromagnetic field compared to that in the DBS, suggesting that the non-valence orbital of the former is more diffusive and thus more polarizable compared to that of the latter. | Do Hyung Kang; Jinwoo Kim; Heung-Ryoul Noh; Sang Kyu Kim | Physical Chemistry; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.) | CC BY NC 4.0 | CHEMRXIV | 2021-09-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61307e56ac321936ea6f511f/original/observation-of-the-ponderomotive-effect-in-non-valence-bound-states-of-polyatomic-molecular-anions.pdf |
63363657cf382949b5b72c4a | 10.26434/chemrxiv-2022-gt54q | Microsampling tools for collecting, processing, and storing blood at the point-of-care | In the wake of the COVID-19 global pandemic, self-administered microsampling tools have reemerged as an effective means to maintain routine healthcare assessments without inundating hospitals or clinics. Fingerstick collection of blood is easily performed at home, in the workplace, or at the point-of-care, obviating the need for a trained phlebotomist. While the initial collection of blood is facile, the diagnostic or clinical utility of the sample is dependent on how the sample is processed and stored prior to transport to an analytical laboratory. The past decade has seen incredible innovation for the development of new materials and technologies to collect low-volume samples of blood with excellent precision that operate independently of the hematocrit effect. The final application of that blood (i.e., the test to be performed) ultimately dictates the collection and storage approach as certain materials or chemical reagents can render a sample diagnostically useless. Consequently, there is not a single microsampling tool that is capable of addressing every clinical need at this time. In this review, we highlight technologies designed for patient-centric microsampling blood at the point-of-care and discuss their utility for quantitative sampling as a function of collection material and technique. In addition to surveying methods for collecting and storing whole blood, we emphasize the need for direct separation of the cellular and liquid components of blood to produce cell-free plasma to expand clinical utility. Integrating advanced functionality while maintaining simple user operation presents a viable means of revolutionizing self-administered microsampling, establishing new avenues for innovation in materials science, and expanding access to healthcare. | Keith Baillargeon; Charles Mace | Materials Science; Analytical Chemistry; Analytical Chemistry - General; Biochemical Analysis; Separation Science | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63363657cf382949b5b72c4a/original/microsampling-tools-for-collecting-processing-and-storing-blood-at-the-point-of-care.pdf |
629c48c1dd18093555f63f97 | 10.26434/chemrxiv-2022-2l7kj | An Oxygen-Insensitive Biosensor and a Biofuel Cell Device based on FMN L-lactate Dehydrogenase | Lactate sensing has high importance for metabolic diseases diagnostics, food spoilage, sports medicine, or the construction of biofuel cell devices. Therefore, continuous lactate sensing devices which enable accurate detection should be developed. Here we present the overexpression and utilization of FMN-lactate dehydrogenase from Saccharomyces cerevisiae for oxygen-insensitive, continuous amperometric lactate biosensing. The developed sensors exhibit a high signal-to-noise ratio, low interference effect, and a wide range of linear responses using both direct and mediated electron transfer configurations. The thionine-based mediated electron transfer configuration was stable for 8 hours of continuous activity and two weeks of periodic activity with storage at 4°C. We further grafted the redox mediators on multiwall carbon-nanotubes to lower the redox mediator leaching effect. The developed grafting technique improved the biosensor stability and allowed continuous operation for at least 20 hours. Both the mediator-entrapped and the grafted bioanodes were further coupled with a bilirubin oxidase-based biocathode to construct a biofuel cell device. The various biofuel cells have generated a maximal power output of 110µW/cm2 under atmospheric conditions. | Roy Cohen; Nidaa Herzallh; Matan Meirovich; Oren Bachar; Liora Frech; Yifat Cohen; Omer Yehezkeli | Physical Chemistry; Catalysis; Analytical Chemistry; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-06-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/629c48c1dd18093555f63f97/original/an-oxygen-insensitive-biosensor-and-a-biofuel-cell-device-based-on-fmn-l-lactate-dehydrogenase.pdf |
631e905249042ad61ed3ffd5 | 10.26434/chemrxiv-2022-hq85x | Stable bulk nanobubbles can be regarded as gaseous analogues of microemulsions | In our previous work [Phys. Chem. Chem. Phys. 2022, 24, 9685], we show with molecular dynamics simulations that bulk nanobubbles can be stabilized by forming a compressed amphiphile monolayer at bubble interfaces. This observation closely resembles the stability origin of microemulsions and inspires us to propose here that stable bulk nanobubbles can be regarded as gaseous analogues of microemulsions: the gas-in-water nanobubble phase coexisting with the external gas phase. The stability mechanism for bulk nanobubbles is then given: The formation of compressed amphiphilic monolayer because of microbubble shrinking leads to a vanishing surface tension, and consequently the curvature energy of the monolayer dominates the thermodynamic stability of bulk nanobubbles. With the monolayer model, we further interpret several strange behaviors of bulk nanobubbles: the gas supersaturation is not a prerequisite for nanobubble stability because of the vanishing surface tension, and the typical nanobubble size of 100nm is due to the small bending constant of the monolayer. Finally, through analyzing the compressed amphiphile monolayer model we propose that bulk nanobubbles can ubiquitously exist in aqueous solutions. | Changsheng Chen; Hongguang Zhang ; Xianren Zhang | Theoretical and Computational Chemistry; Physical Chemistry; Chemical Engineering and Industrial Chemistry; Interfaces; Physical and Chemical Properties; Thermodynamics (Physical Chem.) | CC BY 4.0 | CHEMRXIV | 2022-09-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/631e905249042ad61ed3ffd5/original/stable-bulk-nanobubbles-can-be-regarded-as-gaseous-analogues-of-microemulsions.pdf |
675060ea7be152b1d0ebd582 | 10.26434/chemrxiv-2024-pt4fp | Investigating whether alcohol is transformed to norepinephrine or dopamine in the mouse brain: preliminary findings | A number of studies in rodents have shown various effects of alcohol (ethanol) administration on the catecholaminergic neurotransmitters, norepinephrine (NE) and dopamine (DA). These studies suggest that presentation of alcohol to mice or rats can alter brain levels of NE and DA, in various subregions. Three previous publications (Fitzgerald 2012, 2020, 2022) have presented the hypothesis that there may be an unidentified pathway in rodents, and other organisms, that actually transforms ethanol to NE or DA. Here, this paper investigates the hypothesis in male CD-1 mice. Experimental mice were systemically injected with an intoxicating dose of stable isotope-labeled carbon 13 (C13) ethanol (ethanol-1-13C, 20% v/v, 1.5 g/kg, i.p.), and brain samples (hippocampus and brainstem) were collected two hours post-injection. Two other groups of mice received normal unlabeled carbon 12 (C12) ethanol or a water (Control) injection, respectively. Although we had difficulty detecting the two neurotransmitters (especially C13 NE) due to their very low concentrations, high resolution mass spectrometry analysis suggests that C12 ethanol selectively boosted hippocampal C12 NE, and C13 ethanol likewise boosted hippocampal C13 NE. We did not observe effects on DA. These data provide preliminary information on whether there is a novel biosynthetic pathway in mice that converts alcohol to catecholamines in select brain regions, where the ethanol molecule would presumably lead to formation of the ethanolamine side chain of NE. There are, however, alternative interpretations of these findings, including that acute alcohol administration modulates catecholamine release, reuptake, metabolism, or canonical biosynthesis. | Piotr Wlaź; Paul J. Fitzgerald ; Paweł Żmudzki; Katarzyna Socala | Biological and Medicinal Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/675060ea7be152b1d0ebd582/original/investigating-whether-alcohol-is-transformed-to-norepinephrine-or-dopamine-in-the-mouse-brain-preliminary-findings.pdf |
620beea9cbb4f465f3c2014c | 10.26434/chemrxiv-2022-tvkmj | First hyperpolarizability of water in the bulk phase:
long-range electrostatic effects included via the second
hyperpolarizability | The molecular first hyperpolarizability β contributes to second-order optical non-linear signals collected from molecular liquids. For the Second Harmonic Generation (SHG) response, the first hyperpolarizability β (2ω,ω,ω) often depends on the molecular electrostatic environment. This is especially true for water, due to its large second hyperpolarizability γ(2ω,ω,ω,0). In this study we compute the electronic γ(2ω,ω,ω,0) and β (2ω,ω,ω) for water molecules in their bulk phase using QM/MM calculations. The average value of γ(2ω,ω,ω,0) is smaller than the one for the gaz phase, and its standard deviation among the molecules is relatively small. In addition, we demonstrate that the average second hyperpolarizability ⟨γ(2ω,ω,ω,0)⟩ can be used to describe the electrostatic effects of the neighborhood on the β (2ω,ω,ω) ; but only the more distant neighbors can be accounted this way. This study paves the way towards QM/MM calculations of the first hyperpolarizability of molecules in complex environments, in which long-range electrostatic effects can be crucial, for example nearby charged interfaces. | Guillaume Le Breton; Oriane Bonhomme; Emmanuel Benichou; Claire Loison | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2022-02-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/620beea9cbb4f465f3c2014c/original/first-hyperpolarizability-of-water-in-the-bulk-phase-long-range-electrostatic-effects-included-via-the-second-hyperpolarizability.pdf |
60c740ee4c89194826ad221c | 10.26434/chemrxiv.7423175.v3 | Tetraurea macrocycles: aggregation-driven binding of chloride in aqueous solutions | <p>Artificial receptors that recognise anionic species <i>via</i>noncovalent interactions have a wide range of biomedical, industrial and environmental applications. A major challenge in this area of research is to achieve high affinity and selective anion binding in aqueous media. So far, only a few examples of receptors capable of strong (> 10<sup>5</sup>M<sup>-1</sup>) anion binding in solutions containing > 50% water are available and none show selectivity for chloride. We report here the discovery of a <i>D</i><sub>4h</sub>-symmetric fluorinated tetraurea macrocycle that fulfils this function owing to its unique self-assembly properties. The macrocycle has a strong tendency to self-associate into columnar aggregates <i>via</i>intermolecular hydrogen bonds and aromatic stacking. In aqueous solutions, macrocycle aggregation generates hydrophobic and size-selective binding pockets favourable for hydrogen bonding with chloride. As a result, micromolar affinity and highly selective chloride binding has been achieved with this simple small molecule (MW < 700) in <a>60 vol% water/</a>acetonitrile.</p> | Xin Wu; Patrick Wang; Peter Turner; William Lewis; Osman Catal; Donald Thomas; Philip Gale | Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2019-02-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740ee4c89194826ad221c/original/tetraurea-macrocycles-aggregation-driven-binding-of-chloride-in-aqueous-solutions.pdf |
60c74849337d6c84f5e27508 | 10.26434/chemrxiv.9633032.v2 | Use of an Asparaginyl Endopeptidase for Chemo-enzymatic Peptide and Protein Labeling | Transpeptidases are ideal biocatalysts for site-specific peptide and protein labeling, whereas reactions that target N-terminus cysteine with commercially available reagents have become common practice. However, a versatile approach that allows bioconjugation at the terminus of choice (N or C), while avoiding the use of backbone-modified substrates (<i>e.g.</i> depsipeptide) or large excess of reagent, is highly desirable. Aiming to meet these benchmarks, we have combined the advantages of asparaginyl endopeptidase (AEP) catalysis with a N-terminal cysteine trapping reaction and created a chemo-enzymatic labeling system. In this approach, polypeptide with a Asn-Cys-Leu recognition sequence are ligated with a counterpart possessing an N-terminal Gly-Leu by AEP; the byproduct Cys-Leu is subsequently trapped by a stable and inexpensive scavenger, 2-formyl phenylboronic acid (FPBA), to yield an inert thiazolidine derivative, thereby driving the reaction forward to product formation. By carefully screening the reaction conditions for optimal compatibility and minimal hydrolysis, conversion to the ligated product in the model reaction resulted in excellent yields. The versatility of this AEP ligation/FPBA coupling system was further demonstrated by site-specific labeling the N- or C-termini of various proteins. | Simon Tang; Davide Cardella; Alexander J. Lander; Xuefei Li; Yu-Hsuan Tsai; Louis YP Luk | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-02-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74849337d6c84f5e27508/original/use-of-an-asparaginyl-endopeptidase-for-chemo-enzymatic-peptide-and-protein-labeling.pdf |
60c75907f96a0086a0288f2b | 10.26434/chemrxiv.14635896.v1 | Machine Learning of Quasiparticle Energies in Molecules and Clusters | <div>
<div>
<div>
<p>We present a ∆-Machine Learning approach for the prediction of GW quasiparticle energies
(∆MLQP) and photoelectron spectra of molecules and clusters, using orbital-sensitive graph-based
representations in kernel ridge regression based supervised learning. Coulomb matrix, Bag-of-Bonds,
and Bonds-Angles-Torsions representations are made orbital-sensitive by augmenting them with
atom-centered orbital charges and Kohn–Sham orbital energies, which are both readily available
from baseline calculations on the level of density-functional theory (DFT). We first illustrate the
effects of different constructions of the orbital-sensitive representations (OSR) on the prediction
of frontier orbital energies of 22K molecules of the QM8 dataset, and show that is is possible to
predict the full photoelectron spectrum of molecules within the dataset using a single model with a
mean-absolute error below 0.1eV. We further demonstrate that the OSR-based ∆MLQP captures
the effects of intra- and intermolecular conformations in application to water monomers and dimers.
Finally, we show that the approach can be embedded in multiscale simulation workflows, by studying
the solvatochromic shifts of quasiparticle and electron-hole excitation energies of solvated acetone
in a setup combining Molecular Dynamics, DFT, the GW approximation and the Bethe–Salpeter
Equation. Our findings suggest that the ∆MLQP model allows to predict quasiparticle energies and
photoelectron spectra of molecules and clusters with GW accuracy at DFT cost.
</p>
</div>
</div>
</div> | Onur Çaylak; Björn Baumeier | Computational Chemistry and Modeling; Theory - Computational; Machine Learning; Artificial Intelligence | CC BY NC ND 4.0 | CHEMRXIV | 2021-05-24 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75907f96a0086a0288f2b/original/machine-learning-of-quasiparticle-energies-in-molecules-and-clusters.pdf |
60c749dcbb8c1a400b3daedf | 10.26434/chemrxiv.12118914.v1 | A Rapid and Quantitative Serum Test for SARS-CoV-2 Antibodies with Portable Surface Plasmon Resonance Sensing | We report a surface plasmon resonance (SPR) sensor detecting nucleocapsid antibodies specific against the novel coronavirus 2019 (SARS-CoV-2) in undiluted human serum. When exposed to SARS-CoV-2, the immune system responds by expressing antibodies at levels that can be detected and monitored to identify the patient population immunized against SARD-CoV-2 and support efforts to deploy a vaccine strategically. A SPR sensor coated with a peptide monolayer and functionalized with SARS-CoV-2 nucleocapsid recombinant protein detected anti-SARS-CoV-2 antibodies in the nanomolar range. This bioassay was performed on a portable SPR instrument in undiluted human serum and results were collected within 15 minutes of sample/sensor contact. This strategy paves the way to point-of-care and label-free rapid testing for antibodies. | Abdelhadi Djaileb; Benjamin Charron; Maryam Hojjat Jodaylami; Vincent Thibault; Julien Coutu; Keisean Stevenson; Simon Forest; Ludovic S. Live; Denis Boudreau; Joelle N. Pelletier; Jean-Francois Masson | Biochemical Analysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c749dcbb8c1a400b3daedf/original/a-rapid-and-quantitative-serum-test-for-sars-co-v-2-antibodies-with-portable-surface-plasmon-resonance-sensing.pdf |
60c74cfd4c89194764ad3742 | 10.26434/chemrxiv.12579611.v1 | Efficient Killing of Multidrug-Resistant Intracellular Bacteria by AIEgens in Vivo | <p><a>Bacteria infected cells
acting as “Trojan horses” not only protect bacteria from antibiotic therapies
and immune clearance, but also increase the dissemination of pathogens from the
initial sites of infection. Antibiotics are hard and insufficient to treat such
hidden intracellular bacteria, especially the multidrug</a>-resistant (MDR) bacteria. Herein, aggregation-induced
emission luminogens (AIEgens) such as TBPs showed potent broad-spectrum
bactericidal activity against both <a></a><a>extracellular and intracellular</a> Gram-positive
pathogens at low-dose levels. TBPs triggered
reactive oxygen species (ROS)-mediated membrane damage to kill bacteria, regardless of light
irradiation. Additionally, such AIEgens activated mitochondria dependent
autophagy to eliminate intracellular bacteria in host cells. Compared to the
routinely used vancomycin in clinics, TBPs showed comparable efficacy against
methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) <i>in vivo</i>. Our
studies demonstrate that AIEgens are promising new agents for the treatment of
MDR bacteria associated infections.</p> | Ying Li; Fei Liu; Jiangjiang Zhang; Xiaoye Liu; Peihong Xiao; Haotian Bai; Shang Chen; Dong Wang; Simon H. P. Sung; Ryan Tsz Kin Kwok; Kui Zhu; Ben Zhong Tang | Aggregates and Assemblies; Imaging Agents | CC BY NC ND 4.0 | CHEMRXIV | 2020-06-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74cfd4c89194764ad3742/original/efficient-killing-of-multidrug-resistant-intracellular-bacteria-by-ai-egens-in-vivo.pdf |
6171fa39d7e1ee2b432d5b46 | 10.26434/chemrxiv-2021-vwnpt-v2 | Visualizing reaction fronts and transport limitations in
solid-state Li-S batteries via operando neutron imaging | The exploitation of high-capacity conversion-type materials such as sulfur in solid-state secondary batteries is a dream combination for achieving improved battery safety and high energy density in the push towards a sustainable future. Yet, the exact rate-limiting step, bottlenecking further development of solid-state lithium-sulfur batteries, has not been determined. Here, we directly visualize the spatial distribution of lithium via neutron imaging during operation and show that sluggish macroscopic ion transport within the composite cathode is rate-limiting. Observing a reaction front propagating from the separator side towards the current collector confirms detrimental influences of a low effective ionic conductivity. Furthermore, irreversibly concentrated lithium in the vicinity of the current collector, revealed via state-of-charge-dependent tomography, highlights a hitherto-overlooked loss mechanism triggered by sluggish effective ionic transport within a composite cathode. This discovery will be a cornerstone for future research on solid-state batteries, irrespective of the type of active material. | Robert Bradbury; Georg F. Dewald; Marvin A. Kraft; Tobias Arlt; Nikolay Kardjilov; Jürgen Janek; Ingo Manke; Wolfgang G. Zeier; Saneyuki Ohno | Materials Science; Inorganic Chemistry; Energy; Composites; Kinetics and Mechanism - Inorganic Reactions; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-10-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6171fa39d7e1ee2b432d5b46/original/visualizing-reaction-fronts-and-transport-limitations-in-solid-state-li-s-batteries-via-operando-neutron-imaging.pdf |
661c350821291e5d1dd4887c | 10.26434/chemrxiv-2024-bdp43 | Predicting Reactivity and Passivation of Solid-State Battery Interfaces | In this work, we build a computationally inexpensive, data-driven model that utilizes only atomistic structure information to predict the reactivity of interfaces between any candidate solid-state electrolyte material and a Li metal anode. This model is trained on data from ab initio molecular dynamics (AIMD) simulations of the time evolution of the solid electrolyte-Li metal interface for 67 different materials. Predicting the reactivity of solid state interfaces with ab initio techniques remains an elusive challenge in materials discovery and informatics, and previous work on predicting interfacial compatibility of solid-state Li-ion electrolytes and Li metal anodes has focused mainly on thermodynamic convex hull calculations. Our framework involves training machine learning models on AIMD data, thereby capturing information on both kinetics and thermodynamics, and then leveraging these models to predict the reactivity of thousands of new candidates in the span of seconds, avoiding the need for additional weeks-long AIMD simulations. We identify over 300 new chemically stable and over 780 passivating solid-electrolytes that are predicted to be thermodynamically unfavored. Our results indicate many potential solid-state electrolyte candidates have been incorrectly labeled unstable via purely thermodynamic approaches using density functional theory (DFT) energetics, and that the pool of promising, Li-stable solid-state electrolyte materials may be much larger than previously thought from screening efforts. To showcase the value of our approach, we highlight two borate materials that were identified by our model and confirmed by further AIMD calculations to likely be highly conductive and chemically stable with Li: LiB13C2 and LiB12PC. | Eder G. Lomeli; Brandi Ransom; Akash Ramdas; Daniel Jost; Brian Moritz; Austin D. Sendek; Evan J. Reed; Thomas P. Devereaux | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Machine Learning; Electrochemistry - Mechanisms, Theory & Study; Physical and Chemical Properties | CC BY NC 4.0 | CHEMRXIV | 2024-04-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/661c350821291e5d1dd4887c/original/predicting-reactivity-and-passivation-of-solid-state-battery-interfaces.pdf |
60c73cbf4c8919566dad1ae4 | 10.26434/chemrxiv.14761839.v1 | A Simplified Procedures for Cellulase Filter Paper Assay | <p>A new procedures to minimize labor intensiveness and complexity that has long been recognized in cellulase filter paper activity measurement (FPAase) described by the international union of pure and applied chemistry (IUPAC)was developed. It follows the main idea of IUPAC with only exception finding at least two cellulase dilutions have optical densities slightly more and less than a reference optical density of an arbitrary fixed 2 mg absolute glucose amount after a red-ox color reaction and due to cellulase-filter paper hydrolysis. The yielding glucose amount difference as compared to this reference is expressed in terms of absorbance difference percent determined by 3,5-dinitrosalicylic acid (DNS), in case of cellulase is cellubiase rich. If not, an external supplemental portion should be added. The intersection of the line of these two cellulase dilutions with abscissa intersect a vertical at a hypothetical 0% absorbance difference percent corresponding to a critical cellulase dilution exactly release this fixed arbitrary 2 mg glucose amount value. The factor 0.37 of this critical cellulase dilution equals to its filter paper units expressed in FPU per ml.</p><br /> | Mohamed Abdelazim Abulela | Analytical Chemistry - General | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c73cbf4c8919566dad1ae4/original/a-simplified-procedures-for-cellulase-filter-paper-assay.pdf |
60c746aa4c89196967ad2ba1 | 10.26434/chemrxiv.11346962.v1 | Novel Protective Group Synthesis of Androgen Receptor Modulators with Steroidal and Nonsteroidal Scaffolds | Anabolic androgenic steroids (AAS) are frequently used either clinically, by athletes, or for body shaping due to their muscle building and performance enhancing properties. AAS misuse is associated with cardiovascular diseases, mood changes and endocrine issues. Despite the recognition of the severe adverse effects of AAS misuse, the underlying molecular mechanisms are insufficiently understood. Selective androgen receptor modulators (SARMs) are supposed to diminish the adverse androgenic AAS effects while maximizing anabolic effects. In order to obtain androgen receptor modulating compounds of high purity for mechanistic in vitro investigations, this study summarizes protocols of optimized chemical synthesis for five AAS and two SARMs. | Matthias Grill; Melanie Patt; Alex Odermatt | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746aa4c89196967ad2ba1/original/novel-protective-group-synthesis-of-androgen-receptor-modulators-with-steroidal-and-nonsteroidal-scaffolds.pdf |
6703551351558a15ef5007a9 | 10.26434/chemrxiv-2024-c8s16 | Towards Accurate and Efficient Anharmonic Vibrational Frequencies with the Universal Interatomic Potential ANI-1ccx-gelu and Its Fine-Tuning | Calculating anharmonic vibrational modes of molecules for interpreting experimental spectra is one of the most interesting challenges of contemporary computational chemistry. However, the traditional QM methods are costly for this application. Machine learning techniques have emerged as a powerful tool for substituting the traditional QM methods. Universal interatomic potentials (UIPs) hold a particular promise to deliver accurate results at a fraction of the cost of the traditional QM methods but the performance of UIPs for calculating anharmonic vibrational frequencies remains hitherto unknown. Here we show that despite a known excellent performance of the representative UIP ANI-1ccx for thermochemical properties, it fails for the anharmonic frequencies due to the original unfortunate choice of the activation function. Hence, we recommend evaluating new UIPs on anharmonic frequencies as an additional important quality test. To remedy the shortcomings of ANI-1ccx, we introduce its reformulation ANI-1ccx-gelu with the GELU activation function which is capable of calculating IR anharmonic frequencies with reasonable accuracy (close to B3LYP/6-31G*). We also show that our new UIP can be fine-tuned to obtain very accurate anharmonic frequencies for some specific molecules but more effort is needed to improve the overall quality of UIP and its capability for fine-tuning. The new UIP will be included as part of our universal and updatable AI-enhanced QM methods (UAIQM) platform and is available together with tutorials in open-source MLatom at https://github.com/dralgroup/mlatom. The calculations can also be performed via web browser at https://XACScloud.com. | Seyedeh Fatemeh Alavi; Yuxinxin Chen; Yi-Fan Hou; Fuchun Ge; Peikun Zheng; Pavlo O. Dral | Theoretical and Computational Chemistry; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6703551351558a15ef5007a9/original/towards-accurate-and-efficient-anharmonic-vibrational-frequencies-with-the-universal-interatomic-potential-ani-1ccx-gelu-and-its-fine-tuning.pdf |
630ddaaa1945ad0400ec350f | 10.26434/chemrxiv-2022-116hx | Influence of Wooden Flooring on the Indoor Air Quality - Influence of Flooring Type | Due to new environmental trends and restrictions and due to more interest in using renewable materials with circularity, wood has become an important group of building materials. In Scandinavia, wood is a preferred building material where wooden laminates and parquet flooring are extremely popular in housing.
Since wood contain terpene compounds and the flooring materials use a lot of adhesives to obtain different structures depending on if it is a parquet or a laminate flooring, it is of interest to investigate how such materials influence the indoor air quality (IAQ) and if the emitted compounds may contribute to health problems.
In this study, primary emissions from several commercially available wooden flooring materials such as parquet and laminated flooring are presented. Since indoor air climate is very much dependent on the emission of volatile organic compounds from the building materials, we investigated such materials from the point of view of emission of volatile organic compounds and aldehydes. Since aldehydes are more toxic, it is of interest to review some of such data for aldehydes in this paper, which are necessary to obtain good indoor air quality. Health risks may mainly arise from the emission of terpene compounds and aldehydes from such flooring materials. According to international Occupational Exposure Limit levels (OEL), aldehydes are very hazardous for health at relatively low concentrations. They are also classified as human carcinogens according to EPA. Aldehydes are mainly formed from the oxidation of terpenes and from urea formaldehyde (UF) adhesives that are mainly present as adhesives in the flooring materials. In this paper I shall also review the standards that are used to approve such flooring products and the mechanisms behind the emission of aldehydes from UF adhesives.
Our studies show that the levels of primary emissions are relatively high in such flooring materials and varies depending on if it is a parquet or laminate. These emissions may influence the indoor air quality and thereby may cause serious health problems. We have found that even an eco-labeled flooring material showed relatively high emission levels. This study reveals further that the standard used for the certification of building materials is not relevant to IAQ because they do not measure the total amount of free volatiles present in the flooring materials. The study reveals that to assure IAQ it is extremely important that the building materials are analyzed and specially when it concerns wooden materials.
| Swaraj Paul | Materials Science; Polymer Science; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-09-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/630ddaaa1945ad0400ec350f/original/influence-of-wooden-flooring-on-the-indoor-air-quality-influence-of-flooring-type.pdf |
67633e8a81d2151a02252a22 | 10.26434/chemrxiv-2024-gtmjd | Real-Time Optical Control of CB1 Receptor Signaling In Vitro with Tethered Photoswitchable THC Derivatives | Understanding the intricacies of the endocannabinoid system is hindered by the lack of tools to target specific pools of CB1 receptors (CB1Rs) across diverse neural circuits associated with mood, motor function, cognition, and other physiological processes. Herein we introduce the first photoswitchable, orthogonal remotely tethered cannabinoid ligand, PORTL-THC24, designed to achieve cell-specific and reversible control of CB1R signaling with high spatial and temporal resolution, thereby overcoming the limitations of conventional freely diffusible ligands. PORTL-THC24 was selectively tethered to membrane-anchored SNAP-tags expressed in live cells, providing reversible optical control of CB1R signaling when photoswitched by UV-A irradiation. We validated the functionality of PORTL-THC24 in live Neuro-2a cells using a novel real-time cAMP imaging assay, demonstrating light-dependent and reversible modulation of endogenously expressed CB1R activity. Additionally, we demonstrate that SNAP-tethered PORTL-THC24 does not induce CB1R internalization, distinguishing it from conventional, freely diffusible agonists. Our results establish PORTL-THC24 as a powerful tool for optical control of CB1R in a spatially-restricted manner, setting the stage for dissecting CB1R function in complex settings and advancing the study of cannabinoid signaling across various physiological and pathological contexts. | Sarahi Garza; Bilal Kicin; Roman Sarott; Patrick Pfaff; Miroslav Kosar; Tatum Weishaar; Paul Schnacke; Braden Lobingier; Erick Carreira; James Frank | Biological and Medicinal Chemistry; Organic Chemistry; Photochemistry (Org.); Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2024-12-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67633e8a81d2151a02252a22/original/real-time-optical-control-of-cb1-receptor-signaling-in-vitro-with-tethered-photoswitchable-thc-derivatives.pdf |
6450f3f727fccdb3ea5e49a2 | 10.26434/chemrxiv-2023-wdd1r-v2 | Modeling molecular ensembles with gradient-domain machine learning force fields | Gradient-domain machine learning (GDML) force fields have shown excellent accuracy, data efficiency, and applicability for molecules with hundreds of atoms, but the employed global descriptor limits transferability to ensembles of molecules. Many-body expansions (MBEs) should provide a rigorous procedure for size-transferable GDML by training models on fundamental n-body interactions. We developed many-body GDML (mbGDML) force fields for water, acetonitrile, and methanol by training 1-, 2-, and 3-body models on only 1000 MP2/def2-TZVP calculations each. Our mbGDML force field includes intramolecular flexibility and intermolecular interactions, providing that the reference data adequately describe these effects. Energy and force predictions of clusters containing up to 20 molecules are within 0.38 kcal/mol per monomer and 0.06 kcal/(mol Å) per atom of reference supersystem calculations. This deviation partially arises from the restriction of the mbGDML model to 3-body interactions. GAP and SchNet in this MBE framework achieved similar accuracies but occasionally had abnormally high errors up to 17 kcal/mol. NequIP trained on total energies and forces of trimers experienced much larger energy errors (at least 15 kcal/mol) as the number of monomers increased—demonstrating the effectiveness of size transferability with MBEs. Given these approximations, our automated mbGDML training schemes also resulted in fair agreement with reference radial distribution functions (RDFs) of bulk solvents. These results highlight mbGDML as valuable for modeling explicitly solvated systems with quantum-mechanical accuracy. | Alex M. Maldonado; Igor Poltavsky; Valentin Vassilev-Galindo; Alexandre Tkatchenko; John A. Keith | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning | CC BY 4.0 | CHEMRXIV | 2023-05-03 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6450f3f727fccdb3ea5e49a2/original/modeling-molecular-ensembles-with-gradient-domain-machine-learning-force-fields.pdf |
6257f8bf88636c6976110286 | 10.26434/chemrxiv-2022-0qh5w | The structural evolution of Mo2C and Mo2C/SiO2 under dry reforming of methane conditions: morphology and support effects | The thermal carburization of MoO3 nanobelts (nb) and SiO2-supported MoO3 nanosheets under a 1 : 4 mixture of CH4 : H2 yields Mo2C-nb and Mo2C/SiO2. Following this process by in situ Mo K-edge X-ray absorption spectroscopy (XAS) reveals different carburization pathways for unsupported and supported MoO3. In particular, the carburization of α-MoO3-nb proceeds via MoO2, and that of MoO3/SiO2 via the formation of highly dispersed MoOx species. Both Mo2C-nb and Mo2C/SiO2 catalyze the dry reforming of methane (DRM, 800 °C, 8 bar) but their catalytic stability differs. Mo2C-nb shows a stable performance when using a CH4-rich feed (CH4 : CO2 = 4 : 2), however deactivation due to the formation of MoO2 occurs for higher CO2 concentrations (CH4 : CO2 = 4 : 3). In contrast, Mo2C/SiO2 is notably more stable than Mo2C-nb under the CH4 : CO2 = 4 : 3 feed. The influence of the morphology of Mo2C and its dispersion on silica on the structural evolution of the catalysts under DRM is further studied by in situ Mo K-edge XAS. It is found that Mo2C/SiO2 features a higher resistance to oxidation under DRM than the highly crystalline unsupported Mo2C-nb and this correlates with an improved catalytic stability. Lastly, the oxidation of Mo in both Mo2C-nb and Mo2C/SiO2 under DRM conditions in the in situ XAS experiments leads to an increased activity of the competing reverse water gas shift reaction. | Alexey Kurlov ; Stoian Dragos ; Ali Baghi Zadeh; Evgenia Kountoupi; Evgeniya Deeva; Marc Willinger; Paula Abdala; Alexey Fedorov; Christoph Müller | Catalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6257f8bf88636c6976110286/original/the-structural-evolution-of-mo2c-and-mo2c-si-o2-under-dry-reforming-of-methane-conditions-morphology-and-support-effects.pdf |
641a9df5dab08ad68f81b34e | 10.26434/chemrxiv-2023-jn9ph | Molybdenum Carbonyl Assisted Reductive Tetramerization of CO by Activated Magnesium(I) Compounds: Squarate Dianion vs. Metallo-Ketene Formation | Reactions of a dimagnesium(I) compound, [{(DipNacnac)Mg}2] (DipNacnac = [HC(MeCNDip)2]-, Dip = 2,6-diisopropylphenyl), pre-activated by coordination with simple Lewis bases (4-dimethylaminopyridine, DMAP; or TMC, :C(MeNCMe)2), with 1 atmosphere of CO in the presence of one equivalent of Mo(CO)6 at room temperature, led to the reductive tetramerisation of the diatomic molecule. When the reactions were carried out at room temperature, there is an apparent competition between the formation of magnesium squarate, [{(DipNacnac)Mg}(C4O4){-Mg(DipNacnac)}]2, and magnesium metallo-ketene products, [{(DipNacnac)Mg}{-(C4O4)Mo(CO)5}{Mg(D)(DipNacnac)}], which are not inter-convertible. Repeating the reactions at 80 °C led to the selective formation of the magnesium squarate, implying that this is the thermodynamic product. In an analogous reaction, in which THF is the Lewis base, only the metallo-ketene complex, [{(DipNacnac)Mg}{-(C4O4)Mo(CO)5}{Mg(THF)(DipNacnac)}] is formed at room temperature, while a complex product mixture is obtained at elevated temperature. In contrast, treatment of a 1:1 mixture of the guanidinato magnesium(I) complex, [(Priso)Mg‒Mg(Priso)] (Priso = [Pri2NC(NDip)2]-), and Mo(CO)6, with CO gas in a benzene/THF solution, gave a low yield of the squarate complex, [{(Priso)(THF)Mg}(C4O4){-Mg(THF)(Priso)}]2, at 80 °C. Computational analyses of the electronic structure of squarate and metallo-ketene product types corroborate the bonding proposed, from experimental data, for the C4O4 fragments of these systems. | K Yuvaraj; Jeremy Mullins; Thayalan Rajeshkumar; Iskander Douair; Laurent Maron; Cameron Jones | Inorganic Chemistry; Organometallic Chemistry; Organometallic Compounds; Small Molecule Activation (Inorg.); Main Group Chemistry (Organomet.) | CC BY NC ND 4.0 | CHEMRXIV | 2023-03-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/641a9df5dab08ad68f81b34e/original/molybdenum-carbonyl-assisted-reductive-tetramerization-of-co-by-activated-magnesium-i-compounds-squarate-dianion-vs-metallo-ketene-formation.pdf |
650bd47ced7d0eccc3f02f7b | 10.26434/chemrxiv-2023-3rw6d | Autonomous Carcinogenic Potency Categorization Approach for Nitrosamine Drug Substance-related Impurities | Nitrosamine drug substance-related impurities (NDSRIs), which are compounds that can
form during certain drug manufacturing processes and have been shown to cause cancer,
assessing and mitigating their formation has become an important public health issue as
evidenced by recent guidelines from health authorities like the FDA and EMA that provide
acceptable intake limits for various N-nitrosamines. We have developed a web-based
application that can autonomously analyze the N-nitrosamine risk category of compounds
from their SMILES notation, providing instant screening to identify high-risk formations of N-nitrosamines. The accuracy of the tool was validated using an FDA dataset of compounds with known N-nitrosamine risks, as this algorithm rapidly and accurately categorized over 6000 chemicals' risks and comparison to the dataset labels showed high agreement, indicating it can quickly and reliably analyze large datasets. Further analysis revealing high parent amine pKaH correlates to low N-nitrosamine risk and more correlations with other descriptors is being discussed. Overall, the application integrates computational and regulatory knowledge to advance both environmental and human health priorities. | Jiazhou Zhu; Yang Qu; Ning Ye | Theoretical and Computational Chemistry; Organic Chemistry; Computational Chemistry and Modeling; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2023-09-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/650bd47ced7d0eccc3f02f7b/original/autonomous-carcinogenic-potency-categorization-approach-for-nitrosamine-drug-substance-related-impurities.pdf |
67929cc881d2151a02aa9d59 | 10.26434/chemrxiv-2024-wvqjd-v2 | Microcrystal electron diffraction-guided discovery of fungal metabolites | Nature remains a vast repository of complex and functional metabolites whose structural characterization continues to drive innovations in pharmaceuticals, agrochemicals, and materials science. The cryogenic electron microscopy (cryoEM) method, microcrystal electron diffraction (microED, a 3D ED technique) has emerged as a powerful tool to structurally characterize small molecules. Despite this emerging role in structural chemistry, the cost and throughput of microED have limited its application in the discovery of natural products (NPs). While recent advances in sample preparation (e.g. ArrayED) have provided a conceptual framework to address these challenges, they have remained unproven. Herein, we report the ArrayED-driven discovery of a structurally-unprecedented family of NPs (zopalide A-E), a muurolane-type sesquiterpene glycoside (rhytidoside A), aspergillicin analogs (aspergillicin H and aspergillicin I), and four crystal structures of previously reported fungal metabolites. We provide the first examples of absolute stereochemistry determination via microED for newly annotat-ed NPs. | David A. Delgadillo; Lin Wu; Caroline Wang; Yalong Zhang; Kunal Jha; Jessica Burch; Lygia Silva de Moraes; Isabel Hernandez Rodriguez; Melody Tang; Gerald Bills; Benjamin Tu; Yi Tang; Hosea Nelson | Organic Chemistry; Analytical Chemistry; Natural Products; Stereochemistry; Crystallography – Organic | CC BY NC ND 4.0 | CHEMRXIV | 2025-01-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67929cc881d2151a02aa9d59/original/microcrystal-electron-diffraction-guided-discovery-of-fungal-metabolites.pdf |
61ec92c7c18d671f5a8175d9 | 10.26434/chemrxiv-2022-bxlbr | Learning relationships between chemical and physical stability for drug development | Chemical and physical stabilities are two key features considered in pharmaceutical development. Chemical stability is typically reported as a combination of potency and degradation product. For peptide products, it is common to measure physical stability via aggregation or fibrillation using the fluorescent reporter Thioflavin T. Executing stability studies is a lengthy process and requires extensive resources. To reduce the resources and shorten the process for stability studies during the development of a product, we introduce a machine learning based model for predicting the chemical stability over time using both the formulation conditions as well as the aggregation curve. In this work, we explore the relationships between the formulation, stability time point, and the measurements of chemical stability and achieve a coefficient of determination on a random test set of 0.945 and a mean absolute error (MAE) of 0.421 when using a multilayer perceptron (MLP) neural network for total degradation. Similarly, we achieve a coefficient of determination of 0.908 and an MAE of 1.435 when predicting the potency using a random forest model. When measurements of physical stability are included into the model, the MAE in the prediction of TD decreases to 0.148 for the MLP model. Using a similar strategy for the prediction of potency, the MAE decreases to 0.705 for the random forest model. Therefore, we can conclude two important points: first, chemical stability can be modeled using machine learning techniques and second there is a relationship between the physical stability of a peptide and its chemical stability. | Jonathan Fine; Prageeth R Wijewardhane; Sheik Dawood Beer Mohideen; Katelyn Smith; Jameson Bothe; Yogita Krishnamachari; Alexandra Andrews; Peter Wuelfing; Yong Liu; Gaurav Chopra | Theoretical and Computational Chemistry; Physical Chemistry; Analytical Chemistry; Analytical Chemistry - General; Machine Learning; Physical and Chemical Processes | CC BY 4.0 | CHEMRXIV | 2022-01-25 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ec92c7c18d671f5a8175d9/original/learning-relationships-between-chemical-and-physical-stability-for-drug-development.pdf |
60c752fd842e659a2edb3e7b | 10.26434/chemrxiv.13373024.v1 | Computational Analysis of the Effect of [Tea][Ms] and [Tea][H2PO4] Ionic Liquids on the Structure and Stability of Aβ(17-42) Amyloid Protofibrils | <div>Experimental studies have reported the possibility of affecting the growth/dissolution of amyloid fibres by the addition of organic salts of the room-temperature ionic-liquids family, raising the tantalizing prospect of controlling these processes at physiological conditions. The effect of [Tea][Ms] and [Tea][H2PO4] at various concentrations on the structure and stability of a simple model of Aβ42 fibrils has been investigated by computational means. Free energy computations show that both [Tea][Ms] and [Tea][H2PO4] decrease the stability of fibrils with respect to isolated peptides in solution, and the effect is significantly stronger for [Tea][Ms]. The secondary structure of fibrils is not much affected, but single peptides in solution show a marked decr<br /></div>ease in their $\beta$-strand character, and an increase in <br />$\alpha$-propensity, again especially for [Tea][Ms]. These observations, consistent with the experimental picture, can be traced to two primary effects, i.e., the different ionicity of the [Tea][Ms] and [Tea][H2PO4] water solutions, and the remarkable affinity of peptides for [Ms]^- anions, due to a multiplicity of H-bonds. | Dorothea Gobbo; Andrea Cavalli; Pietro Ballone; Antonio Benedetto | Biophysics | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c752fd842e659a2edb3e7b/original/computational-analysis-of-the-effect-of-tea-ms-and-tea-h2po4-ionic-liquids-on-the-structure-and-stability-of-a-17-42-amyloid-protofibrils.pdf |
62cd788981efd0daeea66fc1 | 10.26434/chemrxiv-2022-6bp55-v2 | Phytochemical Drug Discovery for COVID-19 Using High-resolution Computational Docking and Machine Learning Assisted Binder Prediction | The COVID-19 pandemic has resulted in millions of deaths around the world. Multiple vaccines are in use, but there are many underserved locations that do not have adequate access to them. Variants may emerge that are highly resistant to existing vaccines, and therefore cheap and readily obtainable therapeutics are needed. Phytochemicals, or plant chemicals, can possibly be such therapeutics. Phytochemicals can be used in a polypharmacological approach, where multiple viral proteins are inhibited and escape mutations are made less likely. Finding the right phytochemicals for viral protein inhibition is challenging, but in-silico screening methods can make this a more tractable problem. In this study, we screen a wide range of natural drug products against a comprehensive set of SARS-CoV-2 proteins using a high-resolution computational workflow. This workflow consists of a structure-based virtual screening (SBVS), where an initial phytochemical library was docked against all selected protein structures. Subsequently, ligand-based virtual screening (LBVS) was employed, where chemical features of 34 lead compounds obtained from the SBVS were used to predict 53 lead compounds from a larger phytochemical library via supervised learning. A computational docking validation of the 53 predicted leads obtained from LBVS revealed that 28 of them elicit strong binding interactions with SARS-CoV-2 proteins. Thus, the inclusion of LBVS resulted in a 4-fold increase in the lead discovery rate. Of the total 62 leads, 18 showed promising pharmacokinetic properties in a computational ADME screening. Collectively, this study demonstrates the advantage of incorporating machine learning elements into a virtual screening workflow. | Zirui Wang; Theodore Belecciu; Joelle Eaves; Mark Reimers; Michael Bachmann; Daniel Woldring | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling; Machine Learning | CC BY NC ND 4.0 | CHEMRXIV | 2022-07-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/62cd788981efd0daeea66fc1/original/phytochemical-drug-discovery-for-covid-19-using-high-resolution-computational-docking-and-machine-learning-assisted-binder-prediction.pdf |
60c746c5567dfe0bbdec46e8 | 10.26434/chemrxiv.11401965.v1 | A Multifunctional Chemical Agent as an Attenuator of Amyloid and Tau Burden and Neuroinflammation in Alzheimer’s Disease | <div>Alzheimer’s disease (AD) is the most common neurodegenerative degenerative disease, and its main hallmark is the deposition of amyloid beta (Aβ) peptides. However, several clinical trials focusing on Aβ-targeting agents have failed recently, and thus new therapeutic leads are focusing on alternate targets such as tau protein pathology, Aβ-metal induced oxidative stress, and neuroinflammation. To address these different pathological aspects of AD, we have employed a multifunctional compound (MFC) L1 that integrates Aβ-interacting and metal-binding functional groups in a single molecular framework. By perturbing the interactions between the Aβ species and metal ions during the Aβ aggregation process, L1 alleviates the formation of neurotoxic Aβ oligomers and promotes the formation of nontoxic, amorphous Aβ aggregates. Furthermore, the significant antioxidant activity and strong metal chelating ability of L1 are operating cooperatively to rescue neuroblastoma N2A cells from Cu2+-induced Aβ neurotoxicity. Along with in vivo Aβ-binding and favorable BBB permeability properties, the treatment of transgenic 5xFAD mice with L1 significantly reduces the amount of both amyloid plaques and associated phosphorylated tau (p-tau) aggregates in the brain by 40–50% versus the vehicle-treated 5xFAD mice. Besides, L1 mitigates the neuroinflammatory response of the activated microglia during the Aβ-induced inflammation process. Overall, these results suggest that L1 not only efficiently attenuates the formation of amyloid plaques and p-tau aggregates in vivo, but also reduces the microgliamediated neuroinflammatory response, which is quite uncommon among the previously reported amyloid-targeting chemical agents, and thus L1 could be envisioned as a lead compound for the development of novel AD therapeutics.</div> | Hong-Jun Cho; Anuj K. Sharma; Ying Zhang; Michael L. Gross; Liviu M. Mirica | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-23 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746c5567dfe0bbdec46e8/original/a-multifunctional-chemical-agent-as-an-attenuator-of-amyloid-and-tau-burden-and-neuroinflammation-in-alzheimer-s-disease.pdf |
648abe714f8b1884b751fe9a | 10.26434/chemrxiv-2023-fc0gk-v2 | Polarizable Embedding without Artificial Boundary Polarization | We present a fully self-consistent polarizable embedding (PE) model that does not suffer from unphysical boundary polarization. This is achieved through the use of the minimum-image convention (MIC) in the induced electrostatics. It is a simple yet effective approach that includes a more physically accurate description of the polarization throughout the molecular system. Using PE with MIC (PE-MIC), we shed new light on the limitations of commonly employed cutoff models, such as the droplet model, when used in PE calculations. Specifically, we investigate the effects of the unphysical polarization at the outer boundary by comparing induced dipoles and the associated electrostatic potentials, as well as some optical properties of solute-solvent and biomolecular systems. We show that the magnitude of the inaccuracies caused by the unphysical polarization depends on multiple parameters: the nature of the quantum subsystem and of the environment, the cutoff model and distance, and the calculated property. | Sonata Kvedaravičiūtė; David Carrasco-Busturia; Klaus B. Møller; Jógvan Magnus Haugaard Olsen | Theoretical and Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/648abe714f8b1884b751fe9a/original/polarizable-embedding-without-artificial-boundary-polarization.pdf |
673390225a82cea2fae7c23e | 10.26434/chemrxiv-2024-jw9dx | Anomeric Selectivity of Glycosylations Through a Machine Learning Lens | Predicting the stereoselectivity of glycosylations is a major challenge in carbohydrate chemistry. Herein we show that it is possible to build machine learning models that can predict the major anomer of a glycosylation, whether the other anomer is observed as the minor product, and the anomeric ratio of the two anomers. The three models are integrated into a publicly available tool, GlycoPredictor. From a statistical analysis of literature data, we analyze glycosylation trends and compare them to known trends in the field of carbohydrate chemistry, making it possible to elucidate a hierarchy of rules governing the stereoselectivity of glycosylations and discover promising new trends that complement expert intuition. | Natasha Videcrantz Faurschou; Victor Friis; Priyanka Raghavan; Christian Marcus Pedersen; Connor W. Coley | Theoretical and Computational Chemistry; Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry; Machine Learning | CC BY 4.0 | CHEMRXIV | 2024-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/673390225a82cea2fae7c23e/original/anomeric-selectivity-of-glycosylations-through-a-machine-learning-lens.pdf |
60c7536d567dfe15a8ec5e72 | 10.26434/chemrxiv.13489398.v1 | Virus Inactivation in Water Using Laser-Induced Graphene Filters | Graphene in the form of laser-induced graphene (LIG) has antimicrobial
and antifouling surface effects due to its electrochemical properties and texture, and LIG-based
water filters were used for the inactivation of bacteria. However, the antiviral activity of LIGbased filters has not been explored. Here we showed that LIG filters also have antiviral effects
under application of electrical potential using the model prototypic poxvirus virus Vaccinia
lister. This antiviral activity of the LIG filters was compared with its antibacterial activity, which
showed that higher voltages are required for virus inactivation compared to bacteria. The
generation of reactive oxygen species, along with surface electrical effects, play a role in the
mechanism for the virus inactivation. | Najmul Haque Barbhuiya; Swatantra P. Singh; Arik Makovitzki; Pradnya Narkhede; Ziv Oren; Yaakov Adar; Edith Lupu; Lilach Cherry; Arik Monash; Christopher J. Arnusch | Environmental Science; Water Purification | CC BY NC ND 4.0 | CHEMRXIV | 2020-12-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7536d567dfe15a8ec5e72/original/virus-inactivation-in-water-using-laser-induced-graphene-filters.pdf |
672203137be152b1d04d55dc | 10.26434/chemrxiv-2024-vsnbb | Activation of I2 with aryl iodine(III) for the iodination of deactivated arenes | A highly effective method for iodinating deactivated aryl rings is reported, using organic solvents (CH2Cl2, CHCl3) where traditional methods typically require concentrated H2SO4. A new aryl iodine(III) system oxidizes I2 in the presence of trifluoroacetic anhydride as a water scavenger and catalytic H2SO4 in cases of very deactivated rings. The aryl iodine(III) oxidants, 4-nitrophenyliodine bis(trifluoroacetate) (NPIFA), 3-iodosylbenzoic acid (3-IBA), or 2,4-dichloro-5-iodosylbenzoic acid (3-IBACl2) are applied based on separability and reactivity of target substrates, and their reduced forms are recovered by simple acid/base extractions, demonstrating excellent reusability. Leveraging this, iodinated products are isolated without the need for chromatography. The method is suitable for use under benchtop conditions, and exhibits high atom efficiency, fully incorporating I2 into products. | Marcus Sceney; Jade Choi; Lachlan Barwise; Tania _; Juliette Phillips; Katerina Dostinoska; Jason Dutton | Organic Chemistry; Organic Synthesis and Reactions | CC BY NC ND 4.0 | CHEMRXIV | 2024-11-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/672203137be152b1d04d55dc/original/activation-of-i2-with-aryl-iodine-iii-for-the-iodination-of-deactivated-arenes.pdf |
60c741d99abda203b3f8bf0e | 10.26434/chemrxiv.8135288.v1 | Statistical Prediction of Donor-Acceptor Thiophene Copolymer Properties | This work illustrates some of the shortcomings of the standard donor-acceptor model as a tool for predicting polymer molecular orbital interactions. 8741 DFT calculations were performed for a series of co-oligomers of varying length from a diverse set of 91 thiophene monomers to explore statistical relationships between the frontier molecular orbital energies of oligomers and their degree of polymerization. These relationships were used to develop predictive models that allow for the calculation of polymer frontier molecular orbital energies. Polymer frontier molecular orbital energies have been shown to impact the device performances of many types of optoelectronic devices, including organic field effect transistors, organic photovoltaics and organic light emitting diodes. | Michael Cole; Ilana Kanal; Geoffrey Hutchison | Oligomers; Conducting polymers; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2019-05-20 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c741d99abda203b3f8bf0e/original/statistical-prediction-of-donor-acceptor-thiophene-copolymer-properties.pdf |
61ba07dc7f367eb2da547035 | 10.26434/chemrxiv-2021-xnjrt | Electrolyte reactivity at the charged Ni-rich cathode interface and degradation in Li-ion batteries | The chemical and electrochemical reactions at the positive electrode-electrolyte interface in Li-ion batteries are hugely influential on cycle life and safety. Ni-rich layered transition metal oxides exhibit higher interfacial reactivity than their lower Ni-content analogues, reacting via poorly understood mechanisms. Here, we study the role of the electrolyte solvent, specifically cyclic ethylene carbonate (EC) and linear ethyl methyl carbonate (EMC), in determining the interfacial reactivity at LiNi0.33Mn0.33Co0.33O2 (NMC111) and LiNi0.8Mn0.1Co0.1O2 (NMC811). Parasitic currents are measured during high voltage holds in NMC/Li4Ti5O12 (LTO) cells, LTO avoiding parasitic currents related to anode-cathode reduction species cross-over, and are found to be higher for EC-containing vs. EC-free electrolytes with NMC811. No difference between electrolytes are observed with NMC111. On-line gas analysis reveals this to be related to lattice oxygen release, and accompanying electrolyte decomposition, which increases substantially with greater Ni content, and for EC-containing electrolytes with NMC811. This is corroborated by electrochemical impedance spectroscopy (EIS) and transmission electron microscopy (TEM) of NMC811 after the voltage hold, which show a higher interfacial impedance and a thicker oxygen-deficient rock-salt surface reconstruction layer, respectively. Combined findings from solution NMR, ICP (of electrolytes) and XPS analysis (of electrodes) reveal that higher lattice oxygen release from NMC811 in EC-containing electrolytes is coupled with more electrolyte breakdown and higher amounts of transition metal dissolution compared to EC-free electrolyte. Finally, new mechanistic insights for the chemical oxidation pathways of electrolyte solvents and, critically, the knock-on chemical and electrochemical reactions that further degrade the electrolyte and electrodes curtailing battery lifetime are provided. | Wesley M. Dose; Israel Temprano; Jennifer P. Allen; Erik Björklund; Christopher A. O’Keefe; Weiqun Li; B. Layla Mehdi; Robert S. Weatherup; Michael F. L. De Volder; Clare P. Grey | Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2021-12-16 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61ba07dc7f367eb2da547035/original/electrolyte-reactivity-at-the-charged-ni-rich-cathode-interface-and-degradation-in-li-ion-batteries.pdf |
60f16a591053178e4d40f442 | 10.26434/chemrxiv-2021-5hvgc | Assembly of pH-Responsive Antibody-Inspired Protein-Drug Conjugates | With the advent of chemical strategies that allow the design of smart bioconjugates, peptide- and protein-drug conjugates are emerging as highly efficient therapeutics to overcome limitations of conventional treatment, as exemplified by antibody-drug conjugates. While targeting peptides serve similar roles as antibodies to recognize overexpressed receptors on diseased cell surfaces, peptide-drug conjugates suffer from poor stability and bioavailability due to their low molecular weights. Through a combination of a supramolecular protein-based assembly platform and a pH-responsive dynamic covalent linker, we devise herein the convenient assembly of a trivalent protein-drug conjugate. The conjugate mimics key features of antibody-drug conjugates such as (1) a multipartite structure, (2) peptide recognition sites arranged at distinct locations and at defined distances, (3) a high molecular weight protein scaffold, and (4) an attached drug molecule. These antibody-inspired protein-drug conjugates target cancer cells that overexpress somatostatin receptors, enable controlled release in the microenvironment of cancer cells through an entirely new dynamic covalent biotin linker and exhibit stability in biological media. | Marco Raabe; Astrid Heck; Michaela Pieszka ; Tao Wang; Maksymilian Marek Zegota; Lutz Nuhn; David Y. W. Ng; Seah Ling Kuan; Tanja Weil | Biological and Medicinal Chemistry; Organic Chemistry; Materials Science; Supramolecular Chemistry (Org.); Controlled-Release Systems; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60f16a591053178e4d40f442/original/assembly-of-p-h-responsive-antibody-inspired-protein-drug-conjugates.pdf |
6720fced5a82cea2fa363255 | 10.26434/chemrxiv-2022-hl0p1-v2 | Thermoresponsive redispersible polystyrene latexes | Polystyrene (PS) latexes prepared using low-molecular-weight amphiphilic thermoresponsive surfactants exhibited reversible coagulation. The prepared low molecular surfactant exhibited thermal transition at concentration above their critical micellar concentration (CMC). Latexes prepared with surfactant containing thermoresponsive segments, i.e., surfactants with poly(2-ethyloxazoline) resulted in white coagulant above its LCST at 85 oC and redispersed upon cooling to room temperature, while latexes prepared with non-responsive units remain unresponsive to change in temperature. Comparison of the particle sizes of the pristine and redispersed latex at 25 oC exhibited nearly identical size and shape, before and after heating up to 85 oC that effected coagulation. The re-dispersibility of the coagulated polystyrene latexes allows to mitigate energy consumption in the design and synthesis of such latexes used in many day-to-day applications. | Keerthika N; Jayalakshmi Arumugam; Ramkumar Santhanagopal | Polymer Science; Organic Polymers; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-30 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6720fced5a82cea2fa363255/original/thermoresponsive-redispersible-polystyrene-latexes.pdf |
6573204829a13c4d47fa0cf8 | 10.26434/chemrxiv-2023-1t89n | On the equivalence of grand-canonical and capacitor-based models in first-principle electrochemistry | First principles-based computational and theoretical methods are constantly evolving trying to overcome the many obstacles towards a comprehensive understanding of electrochemical processes on an atomistic level. One of the major challenges has been the determination of reaction energetics under a constant applied potential. Here, a theoretical framework was proposed applying standard electronic structure methods and extrapolating to the infinite-cell size limit where reactions do not alter the potential. More recently, grand-canonical modifications to electronic structure methods which hold the potential constant by varying the number of electrons in a finite simulation cell have gotten increasingly popular. In this perspective, we show that these two schemes are thermodynamically equivalent. Further, we link these methods to ones based on capacitive models of the interface, in the limit that the capacitance of the charging components (whether continuum or atomistic) are equal and invariant along the reaction pathway. We further benchmark the three approaches with an example of alkali cation adsorption on Pt(111) proving that all three approaches converge in the cases of Li, Na and K. For Cs, however, strong deviation from the ideal conditions leads to a spread in the respective results. We discuss the latter by highlighting the cases of broken equivalence and assumptions among the approaches. | Georg Kastlunger; Sudarshan Vijay; Shubham Sharma; Xi Chen; Andrew Peterson | Theoretical and Computational Chemistry; Materials Science; Catalysis; Computational Chemistry and Modeling; Electrocatalysis; Heterogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2023-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6573204829a13c4d47fa0cf8/original/on-the-equivalence-of-grand-canonical-and-capacitor-based-models-in-first-principle-electrochemistry.pdf |
66180af891aefa6ce15b48fd | 10.26434/chemrxiv-2024-bsjl4 | Top-down Fabrication of PEG-NHC Stabilized Gold Nanoparticles Bearing Azides Functional Groups | Swift and accurate biochemical marker detection is crucial for medical diagnosis. Gold nanoparticles (AuNPs) are promising for such diagnostic sensing due to their biocompatibility and unique physical properties. However, AuNPs bearing selective targeting vectors often lack prolonged stability in complex analytes. To enhance stability, (N)-heterocyclic carbene (NHC) ligands have been explored due to their strong binding to AuNP surfaces. This study presents an optimization path towards the general top-down synthesis of highly stable, azide-terminal PEGylated NHC (PEG-NHC) functionalized AuNPs using well-defined oleylamine-protected AuNPs and masked PEGylated NHC precursors. Furthermore, the activation and attachment mechanism of masked NHCs was elucidated by the identification of intermediate AuNPs obtained by insufficient ligand exchange. PEG-NHC@AuNPs retain colloidal stability in a range of biologically relevant media, showing no significant aggregation or ripening over a prolonged period and show greater stability when compared to the same particles synthesized via a bottom-up approach. Azide-functionalized PEG-NHC@AuNPs were further conjugated using a copper-catalyzed click- and a biorthogonal strain-promoted azide-alkyne cycloaddition reaction. The retained colloidal stability and the successful conjugation demonstrates the potential of azide-functionalized PEG-NHC@AuNP particles as a versatile platform for biomedical applications. | Constantin Eisen; Bernhard K. Keppler; Jia Min Chin; Xiaodi Su; Michael R. Reithofer | Inorganic Chemistry; Nanoscience; Nanostructured Materials - Nanoscience; Organometallic Compounds; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2024-04-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66180af891aefa6ce15b48fd/original/top-down-fabrication-of-peg-nhc-stabilized-gold-nanoparticles-bearing-azides-functional-groups.pdf |
618e3b9a2c7c0b4279d97467 | 10.26434/chemrxiv-2021-vgprq | Cell-free biosynthesis of ω-hydroxy acids boosted by a synergistic combination of alcohol dehydrogenases | The activity orchestration of an unprecedented cell-free enzyme system with self-sufficient cofactor recycling enables the step-wise transformation of aliphatic diols into -hydroxy acids at the expense of molecular oxygen as electron acceptor. The efficiency of the biosynthetic route was maximized when two compatible alcohol dehydrogenases were selected as specialist biocatalysts for each one of the oxidative steps required for the oxidative lactonization of diols. The cell-free system reached up to 100% conversion using 100 mM of linear C5 diols, and performed the dessymetrization of prochiral branched diols into the corresponding -hydroxy acids with an exquisite enantioselectivity (ee > 99%). Green metrics demostrate a superior sustanability of this system compared to traditional metal catalysts and even to whole cells for the synthesis of 5-hydroxy petanoic acid. Finally, the cell-free system was assembled into a consortium of heterogeneous biocatalysts that allowed the enzyme reutilization. This cascade illustrates the potential of systems biocatalysis to access new heterofunctional molecules such as -hydroxy acids. | Susana Velasco; Javier Santiago-Arcos; Maria Grazia; Fernando López-Gallego | Catalysis; Biocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-11-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/618e3b9a2c7c0b4279d97467/original/cell-free-biosynthesis-of-hydroxy-acids-boosted-by-a-synergistic-combination-of-alcohol-dehydrogenases.pdf |
610c8fc718911d6ef9dacee7 | 10.26434/chemrxiv-2021-x3p63-v2 | Maximizing TADF via Conformational Optimization | e investigate a new strategy to enhance thermally activated delayed fluorescence (TADF) in organic light-emitting diodes (OLEDs). Given that the TADF rate of a molecule depends on its conformation, we hypothesize that there exists a conformation that maximizes the TADF rate. In order to test this idea, we use time-dependent density functional theory (TDDFT) to simulate the TADF rates of several TADF emitters, while shifting their geometries towards higher TADF rates in a select subspace of internal coordinates. We find that geometric changes in this subspace can increase the TADF rate up to three orders of magnitude with respect to the minimum energy conformation, and the simulated TADF rate can even be brought into the submicrosecond timescales under the right conditions. Furthermore, the TADF rate enhancement can be maintained with a conformational energy that might be within the reach of modern synthetic chemistry. Analyzing the maximum TADF conformation, we extract a number of structural motifs that might provide a useful handle on the TADF rate of a donor-acceptor (DA) system. The incorporation of conformational engineering into the TADF technology could usher in a new paradigm of OLEDs. | Changhae Andrew Kim; Troy Van Voorhis | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2021-08-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610c8fc718911d6ef9dacee7/original/maximizing-tadf-via-conformational-optimization.pdf |
60c756b7567dfe8d2dec6537 | 10.26434/chemrxiv.14312780.v1 | Are All Single Atoms Created Equal? Surface Density Dependent Catalytic Activity of Single Pd Atoms Supported on Ceria | The analogy between single atom catalysts (SACs) and molecular catalysts predicts that the
specific catalytic activity of these systems is constant. We provide evidence that this prediction
is not necessarily true. As a case in point, we show that the specific activity over ceria5 supported single Pd atoms linearly increases with metal atom density, originating from the
cumulative enhancement of lattice oxygen mobility. The long-range electrostatic fingerprints
(~1.5 nm) around each Pd site overlap with each other as surface Pd density increases,
resulting in the observed deviation from constant specific activity. These cooperative effects
exhaust previously active O atoms above a certain Pd density, leading to their permanent
10 removal and consequent drop in reaction rate. The findings of our combined experimental and
computational study show that the specific catalytic activity of reducible oxide-supported single
atom catalysts can be tuned by varying the surface density of single metal atoms. | Yongseon Kim; Gregory Collinge; Mal Soon Lee; Konstantin Khivantsev; Sung June Cho; Vassiliki-Alexandra Glezakou; Roger Rousseau; Janos Szanyi; Ja Hun Kwak | Heterogeneous Catalysis; Nanocatalysis - Reactions & Mechanisms | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c756b7567dfe8d2dec6537/original/are-all-single-atoms-created-equal-surface-density-dependent-catalytic-activity-of-single-pd-atoms-supported-on-ceria.pdf |
6398abe1e6f9a1c645387e9f | 10.26434/chemrxiv-2022-96slq-v2 | Ground truth explanation dataset for chemical property prediction on molecular graphs | Interpretation of chemistry on an atomic scale improves with explainable artificial intelligence (XAI). The parts of the molecule with the most significant influence on the chemical property of interest can be visualized with atomwise and bondwise attributions. Nonetheless, the attributions from different XAI methods regularly disagree substantially, causing uncertainty about which explanation is correct. To determine a ground truth for attributions, we define chemical operations which avoid alchemical steps or approximations and allow extracting one attribution per atom or bond from existing datasets of chemical properties. This general procedure allows for generating large datasets of ground truth attributions. The approach allowed us to create a ground truth explanation dataset with more than 5 million data points for the HOMO-LUMO gap chemical property. This open-source dataset of atomistic ground truth explanations may serve as a reference for XAI approaches. | Eugen Hruska; Liang Zhao; Fang Liu | Theoretical and Computational Chemistry; Machine Learning; Artificial Intelligence; Chemoinformatics - Computational Chemistry | CC BY 4.0 | CHEMRXIV | 2022-12-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6398abe1e6f9a1c645387e9f/original/ground-truth-explanation-dataset-for-chemical-property-prediction-on-molecular-graphs.pdf |
638f43aa836ceb87a775ce88 | 10.26434/chemrxiv-2022-9vglj | Efficient radioactive gas detection
by porous metal-organic framework scintillating nanocrystals. | Natural radioactive gases and anthropogenic radionuclides such as radon, xenon, hydrogen and krypton isotopes, need to be carefully monitored to be properly managed as pathogenic agents, radioactive diagnostic agents or indicators of nuclear activity. State-of-the-art gas detectors based on liquid scintillators suffer from many drawbacks such as lengthy sample preparation procedures and limited solubility of gaseous radionuclides, which produces a detrimental effect on measurement sensitivity. A potential breakthrough solution to this problem is using solid porous scintillators that act as gas concentrators and, therefore, could increase detection sensitivity. Highly porous scintillating metal-organic frameworks (MOFs) stand out as relevant materials for the realization of these devices. We demonstrate the capability of porous hafnium-based MOF nanocrystals exploiting dicarboxy-9,10-diphenylanthracene (DPA) as a scintillating conjugated ligand to detect gas radionuclides. The nanocrystals show fast scintillation properties in the nanosecond domain, a fluorescence quantum yield of ~40% and an accessible porosity suitable to host noble gas atoms and ions. The adsorption and detection of radionuclides such as 85Kr, 222Rn and 3H have been explored for these MOFs utilising a newly developed device based on a time coincidence technique. MOF nanocrystals demonstrate an improved sensitivity for these radionuclides compared to a reference detector, showing an excellent linear response down to an activity value lower than 1 kBq·m-3 that outperforms commercial devices. These results strongly support the possible use of scintillating porous MOF nanocrystals as the building block of ultrasensitive sensors for detecting natural and anthropogenic radioactive gases. | Matteo Orfano; Jacopo Perego; Francesca Cova; Charl Bezuidenhout; Sergio Piva; Christophe Dujardin; Benoit Sabot; Sylvier Pierre; Pavlo Mai; Christophe Daniel; Silvia Bracco; Anna Vedda; Angiolina Comotti; Angelo Monguzzi | Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Materials; Optical Materials | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/638f43aa836ceb87a775ce88/original/efficient-radioactive-gas-detection-by-porous-metal-organic-framework-scintillating-nanocrystals.pdf |
66046c34e9ebbb4db9b4be98 | 10.26434/chemrxiv-2024-fvrc1 | Direct Benzylic C–H Etherification Enabled by Base-Promoted Halogen Transfer | We disclose a benzylic C–H oxidative coupling reaction with alcohols that proceeds through a synergistic deprotonation, halogenation and substitution sequence. The combination of tert-butoxide bases with 2-halothiophene halogen oxidants enables the first general protocol for generating and using benzyl halides through a deprotonative pathway. In contrast to existing radical-based pathways for C–H functionalization, this process is guided by C–H acidity trends. This gives rise to new synthetic capabilities, including the ability to functionalize diverse methyl(hetero)arenes, tolerance of oxidizable and nucleophilic functional groups, precision regioselectivity for polyalkylarenes and use of a double C–H etherification process to controllably oxidize methylarenes to benzaldehydes. | Kendelyn Bone; Thomas Puleo; Michael Delost; Yuka Shimizu; Jeffrey Bandar | Organic Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66046c34e9ebbb4db9b4be98/original/direct-benzylic-c-h-etherification-enabled-by-base-promoted-halogen-transfer.pdf |
60c75a08bdbb897c36a3b12e | 10.26434/chemrxiv.14629437.v2 | Photodoping and Fast Charge Extraction in Ionic Carbon Nitride Photoanodes | <p>Ionic carbon nitrides based on poly(heptazine
imides) (PHI) represent a vigorously studied class of materials with possible
applications in photocatalysis and energy storage. Herein, we study, for the
first time, the photogenerated charge dynamics in highly stable and binder-free
PHI photoanodes using <i>in operando</i> transient
photocurrents and spectroelectrochemical photoinduced absorption measurements.
We discover that light-induced accumulation of long-lived trapped electrons
within the PHI film leads to effective photodoping of the PHI film, resulting
in a significant improvement of photocurrent response due to more efficient
electron transport. While
photodoping has been previously reported for various semiconductors,
it has never been shown before for carbon nitride materials. Furthermore, we find that the extraction kinetics of
untrapped electrons are remarkably fast in these PHI photoanodes, with electron
extraction times (ms) comparable
to those measured for commonly employed metal oxide semiconductors. These results shed light
on the excellent performance of PHI photoanodes in alcohol photoreforming,
including very negative photocurrent onset, outstanding fill factor, and the
possibility to operate under zero-bias conditions. More generally, the here
reported photodoping effect and fast electron extraction in PHI photoanodes establish
a strong rationale for the use of PHI films in various applications, such as
bias-free photoelectrochemistry or photobatteries.<br /></p> | Christiane Adler; Shababa Selim; Igor Krivtsov; Chunyu Li; Dariusz Mitoraj; Benjamin Dietzek; James R Durrant; Radim Beranek | Carbon-based Materials; Fuels - Materials; Optical Materials; Heterogeneous Catalysis; Photocatalysis; Interfaces; Photochemistry (Physical Chem.); Spectroscopy (Physical Chem.); Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75a08bdbb897c36a3b12e/original/photodoping-and-fast-charge-extraction-in-ionic-carbon-nitride-photoanodes.pdf |
60c7566b702a9bb55e18c8e6 | 10.26434/chemrxiv.14237288.v1 | Amine-Catalysed Suzuki–Miyaura-Type Coupling? the Identification and Isolation of the Palladium Culprits. | A recent report in Nature Catalysis detailed the potentially paradigm-shifting organocatalysis of Suzuki cross-coupling of aryl halides with aryl boronic acids, catalysed by simple amine species. We have conducted a reinvestigation of key claims in this paper across multiple academic and industrial laboratories that shows that the observed catalytic activity cannot be due to the amine, but rather is due to tricyclohexylphosphine palladium complexes that are readily entrained during the purification of the amine<b>.</b> | Mickaël Avanthay; Robin Bedford; Callum Begg; Dietrich Böse; Jonathan Clayden; Sean Davis; Jean-Charles Eloi; Georgy P. Goryunov; Ingo V. Hartung; Joseph Heeley; Kirill A. Khaikin; Matthew Kitching; Johannes Krieger; Pavel S. Kulyabin; Alastair Lennox; Roberto Nolla-Saltiel; Natalie E. Pridmore; Benjamin J. S. Rowsell; Hazel A. Sparkes; Dmitry V. Uborsky; Alexander Z. Voskoboynikov; Mark Walsh; Harry J. Wilkinson | Homogeneous Catalysis; Organocatalysis | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7566b702a9bb55e18c8e6/original/amine-catalysed-suzuki-miyaura-type-coupling-the-identification-and-isolation-of-the-palladium-culprits.pdf |
660aa8e89138d23161e18381 | 10.26434/chemrxiv-2024-00hdq-v3 | A global view of T cell metabolism in Systemic Lupus Erythematosus | Impaired metabolism is recognized as an important contributor to pathogenicity of T cells in Systemic Lupus Erythematosus (SLE). Over the last two decades, we have acquired significant knowledge about the signaling and transcriptomic programs related to metabolic rewiring in healthy and SLE T cells. However, our understanding of metabolic network activity derives largely from studying metabolic pathways in isolation. Here, we argue that enzymatic activities are necessarily coupled through mass and energy balance constraints with in-built network-wide dependencies and compensation mechanisms. Therefore, metabolic rewiring of T cells in SLE must be understood in the context of the entire network, including changes in metabolic demands such as shifts in biomass composition and cytokine secretion rates as well as changes in uptake/excretion rates of multiple nutrients and waste products. As a way forward, we suggest cell physiology experiments and integration of orthogonal metabolic measurements through computational modeling towards a comprehensive understanding of T cell metabolism in lupus. | Andrew Goetz; Joy Cagmat; Maigan Brusko; Todd Brusko; Anna Rushin; Matthew Meritt; Timothy Garrett; Laurence Morel; Purushottam Dixit | Biological and Medicinal Chemistry; Biochemistry; Bioinformatics and Computational Biology; Cell and Molecular Biology | CC BY 4.0 | CHEMRXIV | 2024-04-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/660aa8e89138d23161e18381/original/a-global-view-of-t-cell-metabolism-in-systemic-lupus-erythematosus.pdf |
60c7426fee301cf349c78e38 | 10.26434/chemrxiv.8204159.v2 | Ab Initio Prediction of Metal-Organic Framework Structures | Metal-organic frameworks (MOFs) have emerged as highly versatile materials with applications in gas storage and separation, solar light energy harvesting and photocatalysis. The design of new MOFs, however, has been hampered by the lack of computational methods for <i>ab initio</i> crystal structure prediction, which could be used to direct experimental synthesis. Here we report the first <i>ab intio</i> method for MOF structure prediction, and test it against a diverse set of MOFs, with differences in topology, metal coordination geometry and ligand binding sites. In all cases our calculations produced structures which match experiment, proving the versatility of our procedure for MOF structure prediction. With our new methodology for <i>ab initio</i> structure prediction, current approaches to MOF design are set to change towards a more sustainable theory-driven materials development.<br /> | James P. Darby; Mihails Arhangelskis; Athanassios D. Katsenis; Joseph Marrett; Tomislav Friscic; Andrew
J. Morris | Hybrid Organic-Inorganic Materials; Computational Chemistry and Modeling; Theory - Computational; Ligands (Organomet.); Structure | CC BY NC ND 4.0 | CHEMRXIV | 2019-06-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7426fee301cf349c78e38/original/ab-initio-prediction-of-metal-organic-framework-structures.pdf |
65c34aab9138d231619a01b7 | 10.26434/chemrxiv-2024-4kkhd | Revisiting Hafner’s Azapentalenes: Some Old and New Chemistry of 1,3-Bis(dimethylamino)-2-azapentalene | Stable azaheterocyclic derivatives of pentalene have been reported by the group of Hafner in the 1970s, however, these structures remained of low interest until recently. Herein, we revisit the synthesis of stable azapentalene derivative 1,3-bis(dimethylamino)-2-azapentalene and further explore its properties both computationally and experimentally. Beyond the reproduction and optimiza-tion of some previously reported transformations, such as formylation and amine substitution, the available scope of reactions was expanded with azo-coupling, selective halogenations, and cross-coupling reactions. | Enikő Meiszter; Tamás Gazdag; Péter J. Mayer; Attila Kunfi; Tamás Holczbauer; Máté Sulyok-Eiler; Gábor London | Organic Chemistry; Organic Synthesis and Reactions | CC BY 4.0 | CHEMRXIV | 2024-02-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65c34aab9138d231619a01b7/original/revisiting-hafner-s-azapentalenes-some-old-and-new-chemistry-of-1-3-bis-dimethylamino-2-azapentalene.pdf |
652414ed8bab5d2055f394c5 | 10.26434/chemrxiv-2023-h5jnz | Triazenolysis of Alkenes: Aza-version of Ozonolysis | Numerous applications of alkenes exist due to their abundance and versatility in chemical transformations. In this study, we present a unique and novel chemical transformation of alkenes, the aza-version of canonical ozonolysis reaction, which we termed as triazenolysis. This process offers a non-trivial and previously unfeasible synthetic disconnection, allowing the cleavage of a C=C double bond into two new C-N bonds in a reductive manner. We carefully examined the applicability of the reaction, finding that diverse cyclic alkenes are suitable for the developed process. Furthermore, we present an example of an acyclic alkene, illustrating the potential for expanding triazenolysis to other acyclic counterparts. Through DFT calculations, we explored the mechanism of the key step and demonstrated the significance of Lewis acid catalysis in achieving the desired transformation. | Aleksandr Koronatov; Pavel Sakharov; Alexander Kaushansky; Natalia Fridman; Mark Gandelman | Organic Chemistry; Organic Compounds and Functional Groups; Organic Synthesis and Reactions | CC BY NC 4.0 | CHEMRXIV | 2023-10-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/652414ed8bab5d2055f394c5/original/triazenolysis-of-alkenes-aza-version-of-ozonolysis.pdf |
67348c715a82cea2fafb1a2a | 10.26434/chemrxiv-2024-35kds-v6 | Unified Mechanics on Thermodynamics, Classical Mechanics, Quantum Mechanics | Classical and quantum mechanics laws are rebuilt in the frame of new thermodynamics. Heat is the sum of kinetic energy, system work, and system potential of a system, while force is the heat gradients over distance. Hence, collision, temperature difference, and molar volume gradients are the sources of forces. The collision creates symmetric forces, i.e., mutual repulsion or attraction. The other sources produce asymmetric forces driving rotation and spin (self-rotation). Interaction doesn’t need a medium. As achievements, 1) a brief and general equation is derived to predict the equilibrium distance of molecular interaction: L_e=∛((3π^(α-1) m_A g)/(4N_A kT)), without using any assumption; 2) electrons and protons are electroneutral, while neutrons are the cold protons with ∆T≈6.01×〖10〗^9 K; thus, the heat of nuclear reaction, 4(_1^1)H→(_2^4)He, is ~9.18 MeV; 3) atom has isothermal and non-isothermal orbits. Each orbit accommodates 2 electrons with opposite spins; 4) the first ionization energies of elements reported in the references are close to the kinetic energies calculated in this paper; 5) the strengths of chemical bonds and H-bonds are calculated, comparable with the experimental data; 6) vibrations of chemical bonds are discussed which disclose the source of α in the system potential. It is suggested that transferring heat from the hot electrons and nuclei to the cold ones makes a network in the cosmos. Photons are the messengers on the way rather than the roaming travelers. | Henmei Ni | Theoretical and Computational Chemistry; Physical Chemistry; Quantum Mechanics; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY 4.0 | CHEMRXIV | 2024-11-14 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67348c715a82cea2fafb1a2a/original/unified-mechanics-on-thermodynamics-classical-mechanics-quantum-mechanics.pdf |
67c858e5fa469535b90c4f9a | 10.26434/chemrxiv-2025-8f0rq-v3 | CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13 | A critical assessment of computational hit finding experiments (CACHE) challenge was conducted to predict ligands for the SARS-CoV-2 Nsp13 helicase RNA binding site, a highly conserved COVID-19 target. Twenty-three participating teams comprised of computational chemists and data scientists used protein structure and data from fragment-screening paired with advanced computational and machine learning methods to each predict up to 100 inhibitory ligands. Across all teams, 1957 compounds were predicted and were subsequently procured from commercial catalogs for biophysical assays. Of these compounds, 0.7% were confirmed to bind to Nsp13 in a surface plasmon resonance assay. The six best performing computational workflows used fragment growing, active learning, or conventional virtual screening with and without complementary deep-learning scoring functions. Follow-up functional assays resulted in identification of two compound scaffolds that bound Nsp13 with a Kd below 10 µM and inhibited in vitro helicase activity. Overall, the CACHE #2 was successful in identifying hit compound scaffolds targeting Nsp13, a central component of the coronavirus replication-transcription complex. Computational design strategies recurrently successful across the first two CACHE challenges include linking or growing docked or crystallized fragments and docking small and diverse libraries to train ultra-fast machine-learning models. The CACHE#2 competition reveals how crowd-sourcing ligand prediction efforts using a distinct array of approaches followed with critical biophysical assays can result in novel lead compounds to advance drug discovery efforts. | Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz Abu-Saleh; Ayaz Ahmad; Jesus A. Alvarado-Huayhuaz; Oscar E. A. Arce; Roly J. Armstrong; Cheryl Arrowsmith; Kelly E. Bachta; Harmut Beck; Denes Berta; Mateusz K Bieniek; Vincent Blay; Albina Bolotokova; Philip E. Bourne; Marco Breznik; Peter J. Brown ; Aaron D. G. Campbell; Emanuele Carosati; Irene Chau; Daniel J. Cole ; Ben Cree; Wim Dehaen; Katrin Denzinger; Karina dos Santos Machado; Ian Dunn; Prasannavenkatesh Durai; Kristina Edfeldt; Aled Edwards; Darren Fayne; Kallie Friston; Pegah Ghiabi; Elisa Gibson; Judith Guenther; Anders Gunnarsson; Alexander Hillisch; Douglas R. Houston; Jan Halborg Jensen; Rachel J Harding; Kate S. Harris; Laurent Hoffer; Anders Hogner; Joshua T. Horton; Scott Houliston; Judd F. Hultquist; Ashley Hutchinson; John J. Irwin; Marko Jukič; Shubhangi Kandwal; Andrea Karlova; Vittorio L. Katis; Ryan P. Kich; Dmitri Kireev; David Koes; Nicole L. Inniss; Uta Lessel; Sijie Liu; Peter Loppnau; Wei Lu; Sam Martino; Miles McGibbon; Jens Meiler; Akhila Mettu; Sam Money-Kyrle; Rocco Moretti; Yurii S. Moroz; Charuvaka Muvva; Joseph A. Newman; Leon Obendorf; Brooks Paige; Amit Pandit; Keunwan Park; Sumera Perveen; Rachael Pirie; Gennady Poda; Mykola Protopopov; Vera Pütter; Federico Ricci; Natalie J. Roper; Edina Rosta; Margarita Rzhetskaya; Yogesh Sabnis; Karla J. F. Satchell; Frederico Schmitt Kremer; Thomas Scott; Almagul Seitova; Casper Steinmann; Valerij Talagayev; Olga O. Tarkhanova; Natalie J. Tatum; Dakota Treleaven; Adriano Velasque Werhli; W. Patrick Walters; Xiaowen Wang; Jude Wells; Geoffrey Wells; Yvonne Westermaier; Gerhard Wolber; Lars Wortmann; Jixian Zhang; Zheng Zhao; Shuangjia Zheng; Matthieu Schapira | Theoretical and Computational Chemistry; Biological and Medicinal Chemistry; Biochemistry; Drug Discovery and Drug Delivery Systems; Computational Chemistry and Modeling | CC BY 4.0 | CHEMRXIV | 2025-03-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67c858e5fa469535b90c4f9a/original/cache-challenge-2-targeting-the-rna-site-of-the-sars-co-v-2-helicase-nsp13.pdf |
6221dadbdaa4fb9b637f1c0c | 10.26434/chemrxiv-2022-dr88n | Modulating Noncovalent and Covalent Forces to Control Inverse Phosphocholine Lipid Self-Assembly on Inorganic Surfaces | While noncovalent forces typically drive lipid vesicle adsorption and rupture to form supported lipid bilayer (SLB) coatings on inorganic surfaces, this strategy only works on a few materials with suitable energetics such as SiO2. The use of coordination chemistry between inverse-phosphocholine (PC) lipid headgroups and surfaces has emerged as a promising strategy to enable SLB formation on other materials such as TiO2 based on covalent forces. However, until now, a cohesive picture of how noncovalent and covalent forces jointly contribute to the latter SLB formation process has been lacking. Herein, we investigated inverse-PC lipid vesicle adsorption onto TiO2 and SiO2 surfaces and discovered how adsorption pathways can be controlled by tuning the balance of noncovalent and covalent forces. On TiO2, SLB formation depended on two key factors: (1) favorable noncovalent forces to facilitate initial vesicle adsorption; and (2) a critical density of lipid-TiO2 coordinate bonds to enable sufficient vesicle deformation triggering fusion and rupture. In other cases, either no adsorption or intact vesicle adsorption without rupture occurred even when coordinate bonds were present. Conversely, on SiO2, conditions were identified to support inverse-PC lipid adsorption whereas vesicles were repelled otherwise. The experimental results were supported by interfacial force modeling and our findings demonstrate how a subtle interplay of noncovalent and covalent forces plays a deterministic role in modulating lipid self-assembly pathways. | Tun Naw Sut; Abdul Rahim Ferhan; Soohyun Park; Dong Jun Koo; Bo Kyeong Yoon; Joshua A. Jackman; Nam-Joon Cho | Physical Chemistry; Inorganic Chemistry; Nanoscience; Coordination Chemistry (Inorg.); Biophysical Chemistry; Self-Assembly | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-07 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6221dadbdaa4fb9b637f1c0c/original/modulating-noncovalent-and-covalent-forces-to-control-inverse-phosphocholine-lipid-self-assembly-on-inorganic-surfaces.pdf |
60c7488f4c89194148ad2f4d | 10.26434/chemrxiv.11908356.v1 | The MolSSI QCArchive Project: An Open-Source Platform to Compute, Organize, and Share Quantum Chemistry Data | <div>The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry results.</div><div>The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of quantum chemistry computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface.</div><div>Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at https://qcarchive.molssi.org.</div><div>The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of quantum chemistry computations for individuals or groups of researchers at any scale.</div><div>The QCArchive Infrastructure is open-source (BSD-3C), code repositories can be found at https://github.com/MolSSI, and releases can be downloaded via PyPI and Conda.</div> | Daniel Smith; Doaa Altarawy; Lori Burns; Matthew Welborn; Levi N. Naden; Logan Ward; Sam Ellis; Thomas Crawford | Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2020-03-05 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c7488f4c89194148ad2f4d/original/the-mol-ssi-qc-archive-project-an-open-source-platform-to-compute-organize-and-share-quantum-chemistry-data.pdf |
60c74bcf567dfe6b6aec5008 | 10.26434/chemrxiv.12380099.v1 | Selective CO2 Sorption Using a Compartmentalized Coordination Polymer with Discrete Voids | We report a novel Fe(II) compartmentalized coordination polymer (CCP) capable of physisorbing gas molecules in a selective manner. The crystal structure was modelled theoretically under the Density Functional Theory revealing the presence of discrete voids of 380 Å3, significantly larger than those reported for its predecesors. Adsorption isotherms of pure N2, CH4 and CO2 were measured, obtaining a loading capacity of 0.6, 1.7 and 2.2 molecules/void at 10 bar and at 298 K. Dynamic breakthrough gas experiments have been performed at different fluxes and temperatures, showing efficient adsorption and excellent selectivities for CO2 in gas mixtures with methane and nitrogen. | Eugenia Miguel-Casañ; Eduardo Andres-Garcia; Joaquin Calbo; Dr. Mónica Giménez Marqués; Guillermo Minguez Espallargas | Coordination Chemistry (Inorg.) | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74bcf567dfe6b6aec5008/original/selective-co2-sorption-using-a-compartmentalized-coordination-polymer-with-discrete-voids.pdf |
60c744bd337d6ca04de26e8a | 10.26434/chemrxiv.9905603.v1 | Synthesis of Hydroxyethyl Tetrathiatriarylmethyl Radicals OX063 and OX071 | <p>We report the synthesis of
hydroxyethyl tetrathiatriarylmethyl
radicals OX063 and its deuterated analogue OX071 for biomedical EPR
applications.<br /></p> | Martin Poncelet; Justin L. Huffman; Valery V. Khramtsov; Ilirian Dhimitruka; Benoit Driesschaert | Organic Synthesis and Reactions; Imaging Agents | CC BY NC ND 4.0 | CHEMRXIV | 2019-09-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c744bd337d6ca04de26e8a/original/synthesis-of-hydroxyethyl-tetrathiatriarylmethyl-radicals-ox063-and-ox071.pdf |
6130f79765db1e6b91aae4ab | 10.26434/chemrxiv-2021-d93gm | Structure and Surface Passivation of Ultrathin Cesium Lead-Halide Nanoplatelets Revealed by Multilayer Diffraction | The research on bidimensional colloidal semiconductors has received a boost from the emergence of ultrathin lead-halide perovskite nanoplatelets. While the optical properties of these materials have been widely investigated, their accurate structural and compositional characterization is still challenging. Here, we exploited the natural tendency of the platelets to stack into highly ordered films, which can be treated as single crystals made of alternating layers of organic ligands and inorganic nanoplatelets, to investigate their structure by Multilayer Diffraction. Using X-ray diffraction alone, this method allowed to refine the structure of ∼12 Å thick Cs-Pb-Br perovskite and ∼25 Å thick Cs-Pb-Cl-I Ruddlesden-Popper nanoplatelets by precisely measuring their thickness, stoichiometry, surface passivation type and coverage, as well as deviations from the crystal structures of the corresponding bulk materials. It is noteworthy that a single, readily available experimental technique, coupled with proper modeling, provides access to such detailed structural and composition information. | Stefano Toso; Dmitry Baranov; Cinzia Giannini; Liberato Manna | Materials Science; Inorganic Chemistry; Nanoscience; Aggregates and Assemblies; Hybrid Organic-Inorganic Materials; Crystallography – Inorganic | CC BY NC 4.0 | CHEMRXIV | 2021-09-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6130f79765db1e6b91aae4ab/original/structure-and-surface-passivation-of-ultrathin-cesium-lead-halide-nanoplatelets-revealed-by-multilayer-diffraction.pdf |
66db2c58cec5d6c14254fae3 | 10.26434/chemrxiv-2024-sqhw9-v2 | Modeling Ligand Binding Site Water Networks with Site-Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities | Appropriate treatment of water contributions to protein-ligand interactions is a very challenging problem in
the context of adequately determining the number of waters to investigate and undertaking the conformational
sampling of the ligands, the waters, and the surrounding protein. In the present study, an extension of the Site
Identification by Ligand Competitive Saturation-Monte Carlo (SILCS-MC) docking approach is presented that
enables determination of the location of water molecules in the binding pocket and their impact on the predicted
ligand binding orientation and affinities. The approach, termed SILCS-WATER, involves MC sampling of the
ligand along with explicit water molecules in a binding site followed by selection of a subset of waters within
specified energetic and distance cutoffs that contribute to ligand binding and orientation. To allow for
convergence of both the water and ligand orientations, SILCS-WATER is based on just the overlap of the
ligand and water with the SILCS FragMaps and the interaction energy between the waters and ligand. Results
show that the SILCS-WATER methodology is able to capture important waters and improve ligand binding
orientations. For 6 of 10 multiple-ligand protein systems the method improved relative binding affinity
prediction against experimental results, with substantial improvements in three systems, when compared to
standard SILCS-MC. Improved reproduction of crystallographic ligand binding orientations is shown to be an indicator of when SILCS-WATER will yield improved binding affinity correlations. The method also identifies
waters interacting with ligands that occupy unfavorable locations with respect to the protein whose
displacement through the appropriate ligands modifications should improve ligands binding affinity. Results
are consistent with the binding affinity being modeled as a ligand-water complex interacting with the protein.
The presented approach offers new possibilities in revealing water networks and their contributions to the
binding orientation and affinity of a ligand to a protein and is anticipated to be of utility for computer-aided
drug design. | Anmol Kumar; Himanshu Goel; Wenbo Yu; Mingtian Zhao; Alexander D. MacKerell | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66db2c58cec5d6c14254fae3/original/modeling-ligand-binding-site-water-networks-with-site-identification-by-ligand-competitive-saturation-impact-on-ligand-binding-orientations-and-relative-binding-affinities.pdf |
610133d91f990cf878a53b5a | 10.26434/chemrxiv-2021-4qn68-v2 | Quicksilver and Quick-thinking: Insight into the Alchemy of Mercury
A new interdisciplinary research to discover the chemical reality of ancient alchemical recipes
| Ancient alchemical recipes represent an invaluable source to understand how our ancestors described and conceptualised nature. Such recipes were often dismissed as nonsense, or even interpreted as mere allegories for spiritual practices of self-purification. Our research adopts a totally new interdisciplinary outlook through collaboration between chemists and historians of science, to investigate one of the most intriguing of elements, that is mercury. A corpus of ancient sources —in Greek, Latin and Syriac—was scoured in search of information on the extraction of mercury from cinnabar. Following the sources, we replicated the recipes and explored the viability and feasibility of the reactions, as well as the technical underpinnings of the texts, in order to disclose the practical dimensions of ancient alchemy and an unexpected variety of reactions. | Lucia Maini; Marianna Marchini; Massimo Gandolfi; Lucia Raggetti; Matteo Martelli | Inorganic Chemistry; Chemical Education; Minerals | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/610133d91f990cf878a53b5a/original/quicksilver-and-quick-thinking-insight-into-the-alchemy-of-mercury-a-new-interdisciplinary-research-to-discover-the-chemical-reality-of-ancient-alchemical-recipes.pdf |
60c74b18bb8c1a750b3db13e | 10.26434/chemrxiv.12284378.v1 | Iterative Supervised Principal Component Analysis-Driven Ligand Design for Regioselective Ti-Catalyzed Pyrrole Synthesis | <div>
<div>
<div>
<p>Herein, we describe the use of iterative supervised principal component analysis (ISPCA) in de novo catalyst design. The regioselective synthesis of 2,5-dimethyl-1,3,4-triphenyl-1H-
pyrrole (C) via Ti- catalyzed formal [2+2+1] cycloaddition of phenyl propyne and azobenzene was targeted as a proof of principle. The initial reaction conditions led to an unselective mixture of all possible pyrrole regioisomers. ISPCA was conducted on a
training set of catalysts, and their performance was regressed against the scores from the top three principal components. Component loadings from this PCA space along with k-means clustering were used to inform the design of new test catalysts. The
selectivity of a prospective test set was predicted in silico using the ISPCA model, and only optimal candidates were synthesized
and tested experimentally. This data-driven predictive-modeling workflow was iterated, and after only three generations the
catalytic selectivity was improved from 0.5 (statistical mixture of products) to over 11 (> 90% C) by incorporating 2,6-dimethyl-
4-(pyrrolidin-1-yl)pyridine as a ligand. The successful development of a highly selective catalyst without resorting to long, stochastic screening processes demonstrates the inherent power of ISPCA in de novo catalyst design and should motivate the general use of ISPCA in reaction development.
</p>
</div>
</div>
</div> | Xin Yi See; Benjamin Reiner; Xuelan Wen; T. Alexander Wheeler; Channing Klein; Jason Goodpaster; Ian Tonks | Homogeneous Catalysis | CC BY NC ND 4.0 | CHEMRXIV | 2020-05-13 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74b18bb8c1a750b3db13e/original/iterative-supervised-principal-component-analysis-driven-ligand-design-for-regioselective-ti-catalyzed-pyrrole-synthesis.pdf |
621f9e2b97f210882dfa9c90 | 10.26434/chemrxiv-2022-2znwc | Synthesis and styrene copolymerization of novel fluoro and iodomethoxy ring-disubstituted isobutyl phenylcyanoacrylates | Novel ring-disubstituted isobutyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH(CH3)2 (where R is 2-fluoro-3-methoxy, 2-fluoro-4-methoxy, 2-fluoro-5-methoxy, 2-fluoro-6-methoxy, 3-fluoro-4-methoxy, 4-fluoro-3-methoxy, 5-fluoro-2-methoxy, 3-iodo-4-methoxy,
5-iodo-2-methoxy) were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-disubstituted benzaldehydes and isobutyl cyanoacetate and characterized by CHN analysis, IR, 1H and 13C NMR. The acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis.
| Magen A. Higgs; Kelly C. Ho; Kristin N. Huffman; Alexis L. Johnson; Paulina Kapica; Melanie A. Knight; Ashley Lehan Lehan; Christina Guyn; Briana N. Hryhorysak; Sara M. Rocus; Gregory B. Kharas; William S. Schjerven | Organic Chemistry; Polymer Science; Organic Synthesis and Reactions; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/621f9e2b97f210882dfa9c90/original/synthesis-and-styrene-copolymerization-of-novel-fluoro-and-iodomethoxy-ring-disubstituted-isobutyl-phenylcyanoacrylates.pdf |
64c79ad19ed5166e93c7eab7 | 10.26434/chemrxiv-2023-945vj | Highly luminescent TCNQ in melamine | Optical properties of molecules change drastically as results of interactions with surrounding environments as observed in solutions, clusters and aggrergates. Here we make 7,7,8,8-tetracyanoquinodimethane (TCNQ) highly luminescent by encapsulating it in crystalline melamine. Coloured single crystals are synthesized by slow evaporation of a solution of melamine and TCNQ in water and tetrahydrofuran. Single crystal X-ray diffraction reveals the lattice structure of pure melamine, meaning that the colour is of impurities. Both mass spectrometry and UV-Vis spectroscopy combined with density-functional theory calculations elucidate that the impurity species are neutral TCNQ and its oxidation product, dicyano-$p$-toluoyl cyanide anion (DCTC$^-$), whose concentrations in a melamine crystal can be controlled by adjusting the molar ratio between melamine and TCNQ in the precursor solution. Fluorescence exciation-emission wavelength mappings on the precursor solutions illustrate dominant emissions from DCTC$^-$ while the emission from TCNQ is quenched by the resonance energy transfer to DCTC$^-$. On the contrary, TCNQ in crystalline melamine is a bright fluorophore whose emission wavelength centered at 450 nm and slow fluorescence lifetimes of about 2 ns. Our method of encapsulating molecules into transparent melamine would make many other molecules fluorescencent in solids. | Vipin Mishra; Arthur Mantel; Peter Kapusta; Alexander Prado-Roller; Hidetsugu Shiozawa | Materials Science; Optical Materials | CC BY 4.0 | CHEMRXIV | 2023-08-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64c79ad19ed5166e93c7eab7/original/highly-luminescent-tcnq-in-melamine.pdf |
60c9e3b27792a216fab2d46f | 10.26434/chemrxiv.14778270.v1 | A New Perspective for Nonphotochemical Quenching in Plant Antenna Complexes | <div>Light-harvesting complexes (LHCs) of plants exert a dual function of light-harvesting and photoprotection. While LH processes are relatively well characterized, those involved in photoprotection are less understood. The main mechanism involved in photoprotection is to dissipate the energy absorbed by chlorophylls into harmless heat through processes collectively called nonphotochemical quenching (NPQ). Here, we characterize the quenching mechanisms of CP29, a minor LHC of plants with an important role in photoprotection, through two complementary enhanced-sampling techniques, dimensionality reduction schemes, electronic calculations and the analysis of cryo-EM data in the light of the predicted conformational ensemble. Our analysis reveals that the mechanism is more complex than previously thought. Several conformations of the lumenal side of the protein occur and differently affect the pigments relative geometries and interactions. Moreover, we show that a quenching mechanism localized on a single pair of pigments is not sufficient but many pigments are simultaneously involved. In such a diffuse mechanism, short-range interactions between each carotenoid and different chlorophylls combined with a protein-mediated tuning of the carotenoid excitation energies, have to be considered in addition to the commonly suggested coulomb interactions.</div> | Edoardo Cignoni; Margherita Lapillo; Lorenzo Cupellini; Silvia Acosta Gutierrez; Francesco Luigi Gervasio; Benedetta Mennucci | Biophysics; Computational Chemistry and Modeling; Biophysical Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c9e3b27792a216fab2d46f/original/a-new-perspective-for-nonphotochemical-quenching-in-plant-antenna-complexes.pdf |
60c740e5469df45b9af42d1f | 10.26434/chemrxiv.7322237.v3 | Modelling of framework materials at multiple scales: current practices and open questions | The last decade has seen an explosion of the family of framework materials and their study, both from the experimental and computational point of view. We propose here a short highlight of the current state of methodologies for modelling framework materials at multiple scales, putting together a brief review of new methods and recent endeavours in this area, as well as outlining some of the open challenges in this field. We will detail advances in atomistic simulation methods, the development of materials databases, and the growing use of machine learning for properties prediction. | Guillaume Fraux; Siwar Chibani; François-Xavier Coudert | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 1970-01-01 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c740e5469df45b9af42d1f/original/modelling-of-framework-materials-at-multiple-scales-current-practices-and-open-questions.pdf |
6601c51166c1381729cbd562 | 10.26434/chemrxiv-2024-3b6vb | CO2 and Temperature Induced Switching of a Flexible Metal-Organic Framework with Surface-Mounted Nanoparticles | The stimuli responsiveness of a material defines its potential application. Within the class of metal-organic frameworks (MOFs) the subclass of flexible MOFs (flexMOFs) has attracted great attention, showing large structural flexibility as a response to external stimuli such as guest adsorption, temperature, and pressure. Derived hybrid composites like nanoparticle (NP) loaded flexible MOFs, which stand to potentially combine advantageous properties of both are yet largely unexplored. Here we report the synthesis of flexible MOFs with surface mounted nanoparticles, e. g. NP@Zn2(BME-bdc)2dabco composites (NP = Pt and SiO2 nanoparticles, BME-bdc2- = 2,5-bismethoxyethoxy-1,4-benzenedicarboxylate, dabco = 1,4-diazabicyclo[2.2.2]octane), studying the impact of nanoparticles on the stimulus-responsiveness of a flexible MOF. We show that CO2 physisorption triggered flexibility of the MOF is fully retained and reversible for all NP@flexMOF composites. Additionally, we observe that NPs stabilize the large pore state of the MOF, slightly increasing and shifting the switching pressure window. This effect is also observed during temperature-induced switching but Pt@flexMOF composites partially lose long-range order during the reversion to their narrow pore state, while attached SiO2 NPs allow for a fully reversible transition. These findings suggest that the total exerted material strain triggering the switching is heavily dependent on NP size and the applied stimulus and that guest-induced switchability can be fully realized in NP@flexMOF hybrid materials. | Jan Berger; Stephanie Terruzzi; Hana Bunzen; Marcello Marelli; Luca Braglia; Roland A. Fischer; Valentina Colombo; Gregor Kieslich | Materials Science; Nanoscience; Hybrid Organic-Inorganic Materials; Nanostructured Materials - Nanoscience; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6601c51166c1381729cbd562/original/co2-and-temperature-induced-switching-of-a-flexible-metal-organic-framework-with-surface-mounted-nanoparticles.pdf |
64ae5ed8ba3e99daeff43e52 | 10.26434/chemrxiv-2022-d1sj9-v3 | Quantifying the effect of Si/Al ratio on proton solvation and water diffusion in H-FAU using reactive neural network potential. | Acidic zeolites are one of the most important catalysts. In many of their catalytic applications, the mode of interaction with water heavily influences their activity, efficiency, and durability as a catalyst. Despite the recent (first principles) computational efforts to understand the mechanistic underpinning of the water-zeolite interactions, it is still prohibitively expensive to carry out comprehensive studies employing realistic zeolitic models. Therefore, we used a recently developed reactive neural network-based potential for aluminosilicate zeolites in the protonic form including their interaction with the aqueous solution that has a capacity to accelerate simulation by orders of magnitude while retaining the reference level of accuracy. We used it to determine how multiple factors (aluminum content, water loading and temperature) influence the proton solvation and water dynamics in one of the industrially most important acidic zeolites, the faujasite (FAU). We found that Si/Al ratio is a significant determinant of the water diffusivity, water capacity to solvate protons in the nanopores, and the zeolite hydrolytic stability. We expect that many of these findings are readily extendable to other acidic zeolites in interaction with water. | Indranil Saha; Andreas Erlebach; Petr Nachtigall; Christopher J. Heard; Lukáš Grajciar | Theoretical and Computational Chemistry; Physical Chemistry; Materials Science; Catalysts; Computational Chemistry and Modeling; Machine Learning | CC BY NC 4.0 | CHEMRXIV | 2023-07-12 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64ae5ed8ba3e99daeff43e52/original/quantifying-the-effect-of-si-al-ratio-on-proton-solvation-and-water-diffusion-in-h-fau-using-reactive-neural-network-potential.pdf |
60c75993bb8c1a2a1d3dcc46 | 10.26434/chemrxiv.14709477.v1 | Microfluidic Droplet Detection via Region-Based and Single-Pass Convolutional Neural Networks with Comparison to Conventional Image Analysis Methodologies | As the complexity of microfluidic experiments and the associated image data volumes scale, traditional feature extraction approaches begin to struggle at both detection and analysis pipeline throughput. Deep-neural networks trained to detect certain objects are rapidly emerging as data gathering tools that can either match or outperform the analysis capabilities of the conventional methods used in microfluidic emulsion science. We demonstrate that various convolutional neural networks can be trained and used as droplet detectors in a wide variety of microfluidic systems. A generalized microfluidic droplet training and validation dataset was developed and used to tune two versions of the You Only Look Once (YOLOv3/YOLOv5) model as well as Faster R-CNN. Each model was used to detect droplets in mono- and polydisperse flow cell systems. The detection accuracy of each model shows excellent statistical symmetry with an implementation of the Hough transform as well as relevant ImageJ plugins. The models were successfully used as droplet detectors in non-microfluidic micrograph observations, where these data were not included in the training set. The models outperformed the traditional methods in more complex, porous-media simulating chip architectures with a significant speedup to per-frame analysis times. Implementing these neural networks as the primary detectors in these microfluidic systems not only makes the data pipelining more efficient, but opens the door for live detection and development of autonomous microfluidic experimental platforms. <br /> | Gregory Rutkowski; Ilgar Azizov; Evan Unmann; Marcin Dudek; Brian Arthur Grimes | Imaging; Machine Learning; Fluid Mechanics; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2021-06-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75993bb8c1a2a1d3dcc46/original/microfluidic-droplet-detection-via-region-based-and-single-pass-convolutional-neural-networks-with-comparison-to-conventional-image-analysis-methodologies.pdf |
65ea3ebae9ebbb4db936cde9 | 10.26434/chemrxiv-2024-s86fr | HCl trimer: HCl-stretch excited intramolecular and intermolecular vibrational states from 12D fully coupled quantum calculations employing contracted intra- and intermolecular bases | We present fully coupled, full-dimensional quantum calculations of the inter- and intramolecular vibrational states of HCl trimer, a paradigmatic hydrogen-bonded molecular trimer. They are performed utilizing the recently developed methodology for rigorous 12D quantum treatment of the vibrations of the noncovalently bound trimers of flexible diatomic molecules [P. M. Felker and Z. Bačić, J. Chem. Phys. 158, 234109 (2023)], that was previously applied by us to HF trimer. In this work, the many-body 12D potential energy surface (PES) of (HCl)3 [J. S. Mancini and J. M. Bowman, J. Phys. Chem. A 118, 7367 (2014)] is employed. The calculations extend to the intramolecular HCl-stretch excited vibrational states of the trimer with one- and two-quanta, together with the low-energy intermolecular vibrational states in the two excited v = 1 intramolecular vibrational manifolds. They reveal significant coupling between the intra- and intermolecular vibrational modes. The 12D calculations also show that the frequencies of the v = 1 HCl stretching states of HCl trimer are significantly redshifted relative to those of the isolated HCl monomer. Detailed comparison is made between the results of the 12D calculations on the 2-body PES, obtained by removing the 3-body term from the original 2+3-body PES, and those computed on the 2+3-body PES. It demonstrates that the 3-body interactions have a strong effect on the trimer binding energy as well as on its intra- and intermolecular vibrational energy levels. Comparison with the available spectroscopic data shows that good agreement with experiment is achieved only if the 3-body interactions are included. Some low-energy vibrational states localized in a secondary minimum of the PES are characterized as well. | Irén Simkó; Peter M. Felker; Zlatko Bačić | Theoretical and Computational Chemistry; Physical Chemistry; Computational Chemistry and Modeling; Clusters; Quantum Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2024-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/65ea3ebae9ebbb4db936cde9/original/h-cl-trimer-h-cl-stretch-excited-intramolecular-and-intermolecular-vibrational-states-from-12d-fully-coupled-quantum-calculations-employing-contracted-intra-and-intermolecular-bases.pdf |
60c75662f96a006483288ab8 | 10.26434/chemrxiv.14236457.v1 | NP Navigator: a New Look at the Natural Product Chemical Space | NP Navigator – a freely available intuitive online tool for visualization and navigation through the chemical space of NPs and NP-like molecules. It is based on the hierarchical ensemble of generative topographic maps, featuring NPs from the COlleCtion of Open NatUral producTs (COCONUT), bioactive compounds from ChEMBL and commercially available molecules from ZINC. NP Navigator allows to efficiently analyze different aspects of NPs - chemotype distribution, physicochemical properties, biological activity and commercial availability of NPs. The latter concerns not only purchasable NPs but also their close analogs that can be considered as synthetic mimetics of NPs or pseudo-NPs.<br /> | Yuliana Zabolotna; Peter Ertl; Dragos Horvath; Fanny Bonachera; Gilles Marcou; Alexandre Varnek | Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2021-03-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c75662f96a006483288ab8/original/np-navigator-a-new-look-at-the-natural-product-chemical-space.pdf |
64692bf0f2112b41e9e0d7f4 | 10.26434/chemrxiv-2023-wltcr-v2 | Statistics and Bias-Free Sampling of Reaction Mechanisms from Reaction Network Models | Selection bias is inevitable in manually curated computational reaction databases but can have a significant impact on generalizability of quantum chemical methods and machine learning models derived from these data sets. Here, we propose quasireaction subgraphs as a discrete, graph-based representation of reaction mechanisms that has a well-defined associated probability space and admits a similarity function using graph kernels. Quasireaction subgraphs are thus well suited for constructing representative or diverse data sets of reactions. Quasireaction subgraphs are defined as subgraphs of a network of formal bond breaks and bond formations (transition network) composed of all shortest paths between reactant and product nodes. However, due to their purely geometric construction, they do not guarantee that the corresponding reaction mechanisms are thermodynamically and kinetically feasible. As a result, a binary classification of feasible (reaction subgraphs) and infeasible (non-reactive subgraphs) must be applied after sampling. In this paper, we describe the construction and properties of quasireaction subgraphs and characterize the statistics of quasireaction subgraphs from CHO transition networks with up to six nonhydrogen atoms. We explore their clustering using Weisfeiler--Lehman graph kernels. | Dmitrij Rappoport | Theoretical and Computational Chemistry; Computational Chemistry and Modeling | CC BY NC ND 4.0 | CHEMRXIV | 2023-05-22 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64692bf0f2112b41e9e0d7f4/original/statistics-and-bias-free-sampling-of-reaction-mechanisms-from-reaction-network-models.pdf |
61c534851e13eb63f803ec16 | 10.26434/chemrxiv-2021-1jz4m | Out with Acetonitrile: Water-assisted Accelerated-Aging Synthesis of CuI-Pyrazine Hybrid Materials | CuI and pyrazine form three hybrid materials, [(CuI)2(pyrazine)] (Yellow), [(CuI)2(pyrazine)2] (Orange), and [(CuI)(pyrazine)] (Red). In this work, Red was prepared using a green synthetic method, water-assisted accelerated-aging synthesis, for the first time. The syntheses were performed under ambient conditions with only water and no organic solvents. Depending on the reaction conditions, the other two hybrid materials can be formed as well: Orange was formed immediately after dry grinding CuI and pyrazine, while Yellow can be formed from Red and excess amount of CuI at mildly elevated temperatures. The impacts of temperature and types and amounts of liquid added to the aging mixture on the accelerated-aging synthesis were studied, and mechanisms of the synthesis and interconversions between the three CuI-pyrazine hybrid materials were proposed. | Will Lucas; Feier Hou | Physical Chemistry; Materials Science; Hybrid Organic-Inorganic Materials; Physical and Chemical Processes; Thermodynamics (Physical Chem.); Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2021-12-27 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/61c534851e13eb63f803ec16/original/out-with-acetonitrile-water-assisted-accelerated-aging-synthesis-of-cu-i-pyrazine-hybrid-materials.pdf |
6229163597f21030e903ee40 | 10.26434/chemrxiv-2022-49n7z | Ether cleavage and chemical removal of SU-8 | The high chemical stability of SU-8 makes it irreplaceable for a wide range of applica-
tions, most notably as a lithography photoresist for micro and nanotechnology. This
advantage becomes a problem when there is a need to remove SU-8 from the fabricated
devices. Researchers have been struggling for two decades with this problem, and al-
though a number of partial solutions have been found, this difficulty has limited the
applications of SU-8. Here we demonstrate a fast, reproducible, and comparatively gen-
tle method to chemically remove SU-8 photoresist. An ether cleavage mechanism for the
observed reaction is proposed, and the hypothesis is tested with ab initio quantum chem-
ical calculations. Also described are a polymer-metal adhesion treatment, and a comple-
mentary removal method, based on atomic hydrogen inductively coupled plasma. | Jose M. Ripalda; Raquel Alvaro; María Luisa Dotor | Polymer Science; Organic Polymers | CC BY 4.0 | CHEMRXIV | 2022-03-10 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6229163597f21030e903ee40/original/ether-cleavage-and-chemical-removal-of-su-8.pdf |
60c74795bdbb897f45a38e2a | 10.26434/chemrxiv.11734740.v1 | The Formation of the Solid-/Liquid Electrolyte Interphase (SLEI) on NASICON-Type Glass Ceramics and LiPON | Most electrochemical energy storages (battery cells) consist of solid electrodes separated by a liquid electrolyte (LE). If electrode materials are – at least partially – soluble in the electrolyte, detrimental mass transport between both electrodes (electrode cross-talk) occurs. The shuttle mechanism in lithium-sulfur batteries or leaching of Mn in high voltage cathode materials are important examples. Implementing a solid electrolyte (SE) membrane between the electrodes is a comprehensible approach to suppress undesired mass transport but additional resistances arise due to charge transport across the SE and charge transfer through the solid/liquid electrolyte interfaces. The latter contribution is often overlooked as its determination is challenging, however, these interface properties are crucial for practical application. In previous work a resistive solid-/liquid-electrolyte interphase “SLEI” was found at the interface between the SE lithium aluminum germanium phosphate (LAGP) in contact with a liquid ether-based electrolyte. Here we aim for deeper insight into this interphase formation, referring to a lithium ion conducting glass ceramic (NASICON-type) and the commonly used thin film ion conductor “LiPON” (lithium phosphorous oxide nitride). The growth of the SLEI is monitored by a combination of electrochemical characterization, XPS (x-ray photoelectron spectroscopy) and time-of flight secondary ion mass spectrometry (ToF-SIMS). | Martin R. Busche; Thomas Leichtweiss; Carsten Fiedler; Thomas Drossel; Matthias Geiss; Manuel Weiß; Achim Kronenberger; Dominik A. Weber; Jürgen Janek | Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-28 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74795bdbb897f45a38e2a/original/the-formation-of-the-solid-liquid-electrolyte-interphase-slei-on-nasicon-type-glass-ceramics-and-li-pon.pdf |
6480b011e64f843f417740bf | 10.26434/chemrxiv-2023-ls7mc-v2 | Quinone-functionalised carbons as new materials for electrochemical carbon dioxide capture | The need for cost-effective carbon dioxide capture technology is rapidly increasing. To limit the global temperature increase to 1.5 °C within the next century, the level of CO2 mitigation needs to increase drastically. Current capture technology, i.e., amine scrubbing, provides several challenges that limit widespread deployment: high regeneration energy, high operational costs and degradation issues. An emerging energy-efficient technology that can address some of the limitations of amines is electrochemically driven carbon dioxide capture. For example, redox-active quinone molecules are capable of capturing carbon dioxide following electrochemical reduction, and can then be regenerated upon electrochemical oxidation. Despite great advances in the chemistry of quinones for electrochemical CO2 capture, however, the integration of quinones in carbon capture devices remains an ongoing challenge. Here we present a new class of quinone-functionalized electrodes for electrochemical CO2 capture, using the diazonium radical reaction to graft quinone molecules to a porous carbon surface. By grafting redox-active molecules to this conductive surface, not only is carbon dioxide capture significantly enhanced when the bound quinone species are electrochemically reduced, but the functionalization process also improves the energy storage of the carbon material. Through constant current experiments in the presence of CO2, reversible carbon capture was observed with initial uptake capacities at 0.4 mmol g–1 which stabilizes to 0.2 mmol g–1 over 100 cycles with an energy consumption of 254 kJ mol–1 per cycle. Our facile low-cost synthesis of quinone-functionalised carbons is highly tunable since both the carbon and redox-active molecule can be modified, and our work therefore paves the way for the design and discovery of improved electrode materials for electrochemical CO2 capture. | Niamh A Hartley; Suzi M Pugh; Zhen Xu; Daniel CY Leong; Adam Jaffe; Alexander C Forse | Materials Science; Inorganic Chemistry; Carbon-based Materials; Electrochemistry; Materials Chemistry | CC BY 4.0 | CHEMRXIV | 2023-06-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6480b011e64f843f417740bf/original/quinone-functionalised-carbons-as-new-materials-for-electrochemical-carbon-dioxide-capture.pdf |
6242d4c661c5aa21ff7c5820 | 10.26434/chemrxiv-2022-4s2c7-v2 | Impact of Remdesivir Incorporation Along the Primer Strand on SARS-CoV-2 RNA-dependent RNA polymerase |
Remdesivir was the first antiviral drug that received emergency use authorization from the United States Food and Drug Administration and is now formally approved to treat COVID-19. Remdesivir is a nucleotide analogue that targets the RNA-dependent RNA polymerase (RdRp) of coronaviruses, including SARS-CoV-2. The solution of multiple RdRp structures has been one of the main axes of research in the race against the SARS-CoV-2 virus. Several hypotheses of the mechanism of inhibition of RdRp by remdesivir have been proposed, although open questions remain. This work uses molecular dynamics (MD) simulations to explore the impact of remdesivir and two analogues as incoming nucleotides, and of up to four incorporations of remdesivir along the primer strand on RdRp. The simulation results suggest that the overall structure and dynamical behavior of RdRp is destabilized by remdesivir and the two analogues in the incoming position. The incorporation of remdesivir along the primer strand im- pacts specific non-bonded interactions between the nascent RNA and the polymerase subunit, as well as overall dynamical networks on RdRp. The strongest impact on the structure and dynamics are observed after three incorporations, when remdesivir is located at position -A3, in agreement with previously reported experimental and computational results. Our results provide atomic-level detail on the role played by remdesivir on the disruption of RNA synthesis by RdRp, and the main drivers of these disruptions. | Sehr Naseem-Khan; Madison B. Berger; Emmett M. Leddin; Yazdan Maghsoud; G. Andrés Cisneros | Theoretical and Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-03-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6242d4c661c5aa21ff7c5820/original/impact-of-remdesivir-incorporation-along-the-primer-strand-on-sars-co-v-2-rna-dependent-rna-polymerase.pdf |
60c751ee567dfe3246ec5b5a | 10.26434/chemrxiv.13135532.v2 | Mapping the Electronic Structure of Polypyrrole with Image-Based Electrochemical Scanning Tunnelling Spectroscopy | Conducting
polymers are versatile semiconductors whose applications cover a wide range of
devices. Their versatility is due, in addition to other factors, to properties that
can be easily modulated according to the intended application. It is therefore important
to study and map the electronic structure of these materials to allow for a
better correlation between structure and properties. Electrochemical scanning
tunnelling spectroscopy (EC-STS) can be a powerful tool to characterize the electronic
structure of the semiconductor electrolyte interface. In this work we have used
image-based EC-STS (IB-EC-STS) to describe quantitatively the band structure of
an electrochemically deposited polypyrrole (PPy) film. IB-EC-STS located the
band edge of the polymer’s valence band (VB) at 0.95 V vs. RHE (-5.33 eV in the
absolute potential scale) and the intragap polaron states formed when the
polymer is oxidised (doped) at 0.46 V vs. RHE (-4.84 eV in the absolute
potential scale). The IB-EC-STS data were cross checked with electrochemical
impedance spectroscopy (EIS) and Mott-Schottky analysis of the interfacial
capacitance. The DOS spectrum obtained from EIS data is consistent with the
STS-deduced location of the VB and the polarons. | Roger Goncalves; Robert S. Paiva; Andres M R Ramirez; Jonathan A Mwanda; Ernesto C. Pereira; Angel Cuesta | Conducting polymers; Electrochemistry - Mechanisms, Theory & Study; Interfaces | CC BY NC ND 4.0 | CHEMRXIV | 2020-11-09 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751ee567dfe3246ec5b5a/original/mapping-the-electronic-structure-of-polypyrrole-with-image-based-electrochemical-scanning-tunnelling-spectroscopy.pdf |
60c746599abda23df1f8c72b | 10.26434/chemrxiv.11309480.v1 | Balancing DFT Interaction Energies in Charged Dimers Precursors to Organic Semiconductors | Accurately describing intermolecular interactions within the framework of Kohn-Sham density functional theory (KS-DFT) has resulted in numerous benchmark databases over the past two decades. By far, the largest efforts have been spent on closed-shell, neutral dimers for which today, the interaction energies and geometries can be accurately reproduced by various combinations of dispersion-corrected density functional approximations (DFAs). In sharp contrast, charged, open-shell dimers remain a challenge as illustrated by the analysis of the OREL26rad benchmark set consisting of pi-dimer radical cations. Aside from the methodological aspect, achieving a proper description of radical cationic complexes is appealing due to their role as models for charge carriers in organic semiconductors. In the interest of providing an assessment of more realistic dimer systems, we construct a dataset of large radical cationic dimers (CryOrel) and jointly train the 19 parameters of a dispersion corrected, range-separated hybrid density functional (wB97X-dDsC), with the objective of providing the maximum balance between the treatment of long-range London dispersion and reduction of the delocalization error. These conditions are essential to obtain accurate energy profiles and binding energies of charged, open-shell dimers. Comparisons with the performance of the parent wB97X functional series and state-of-the-art wavefunction based methods are provided. <br /> | Alberto Fabrizio; Riccardo Petraglia; Clemence Corminboeuf | Computational Chemistry and Modeling; Theory - Computational | CC BY NC ND 4.0 | CHEMRXIV | 2019-12-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c746599abda23df1f8c72b/original/balancing-dft-interaction-energies-in-charged-dimers-precursors-to-organic-semiconductors.pdf |
6710bbb912ff75c3a1ac8975 | 10.26434/chemrxiv-2024-4csd3 | Towards data-driven design of visible-light photoswitches using structural features | In this manuscript we present the strategy for modeling of the photoswitch properties (maximum absorption wavelength and thermal half-life of photoisomers) of visible-light azo-photoswitches using structural data. We compile a comprehensive data set from literature sources and perform a rigorous benchmark to select the best feature type and modeling approach. The fragment counts have demonstrated excellent performance in the benchmark for both properties. We validate the models in cross-validation and on an external set. The predictions for this set are highly accurate, despite the modest size of the data set related to thermal half-life of photoisomers, especially when consensus modeling approach is applied. We also provide the interpretation of the modeling results using ColorAtom approach and the insights into the chemical space covered by the data set. | Said Byadi; P.K. Hashim; Pavel Sidorov | Theoretical and Computational Chemistry; Machine Learning; Chemoinformatics - Computational Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2024-10-18 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/6710bbb912ff75c3a1ac8975/original/towards-data-driven-design-of-visible-light-photoswitches-using-structural-features.pdf |
66d6f62051558a15efe9023e | 10.26434/chemrxiv-2024-g6qcz | Stable Triphenolamine Radical Cathode with High Electron Conductivity for High-Rate Aqueous Zinc-ion Batteries | Comparing with conventional lithium-ion batteries with organic electrolyte, aqueous zinc-ion batteries with low cost, sustainable and environment-friendly organic cathodes exhibit promising potential to meet the continuously increasing demand on safe and large-scale energy storage. The representative organic cathodes, including quinoidal polycyclic aromatic hydrocarbons (PAHs) and 2,2,6,6-tetramethylpiperidinyl-N-oxyl (TEMPO) polymers, suffer from the challenging synthesis and limited theoretical specific capacity. Herein, different from PAHs and TEMPO polymers, a stable 4,4',4''-nitrilotriphenol (TPA-(OH)3) is explored as organic radical cathode material by extremely low-cost raw materials and two simple reactions. Furtherly, an open-shell TPA-O3 radical is obtained by a facile oxidation with air. Interestingly, TPA-O3 showed unexpected higher electron conductivity of 3.35×10-4 S cm-1 than the precursor (2.73×10-6 S cm-1 for TPA-(OMe)3). The nitro-like nitroxide resonance structures of TPA-O3 contribute to its high electrochemical stability during the 200-cycle cyclic voltammetry test in air and thus exhibits good reversibility when used as a cathode material. Moreover, TPA-O3 exhibit high reduction voltage of 1.02~1.33 V vs, Zn/Zn2+, stable capacities of 123.7 mAh g-1 and high-capacity retention of 95.87% after 2000 stable cycles at 5 A g−1, which is superior to previously reported organic radical cathodes. | Jiaxing Huang; Meilin Li; Cuiping Han; LI YUAN | Organic Chemistry; Energy; Energy Storage | CC BY NC ND 4.0 | CHEMRXIV | 2024-09-04 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/66d6f62051558a15efe9023e/original/stable-triphenolamine-radical-cathode-with-high-electron-conductivity-for-high-rate-aqueous-zinc-ion-batteries.pdf |
60c751530f50db8b9339776a | 10.26434/chemrxiv.13150679.v1 | Transient Colloid Assembly by Fuel-Driven Modulation of Depletion Interactions | In biology, energy stored in chemical fuels is used to drive processes energetically uphill, enabling the highly dynamic behavior of living organisms. The out-of-equilibrium behavior can propagate from molecular reaction networks to the micro- and macroscopic scale. These natural phenomena have sparked the design of man-made out of equilibrium chemical reaction networks (CRNs) and dissipative assembly systems with hydrogels, (supra)polymers, vesicles/micelles and colloids. In colloidal systems, the assembly process is typically controlled by balancing the interaction forces. Here, we use a polymeric depletant integrated in a fuel driven esterification CRN to induce transient colloidal assembly. The polymer undergoes a temporal coil-globule transition upon acetylation by the chemical fuel. In the random coil conformation it acts as depletant agent for the silica colloids, promoting colloidal aggregation. As compact globule, the polymer loses its<br />depletant characteristics. During the fuel cycle the polymer cyclically transitions from one form to the other, directly influencing colloidal aggregation and redispersion. Thus, a fuel-driven CRN on the molecular scale results in a microscopic response with a transient colloidal depletion cycle. Overall, the time-dependent propagation of out-of-equilibrium activity across length scales presented here, offers opportunities to design responsive materials with life like properties. | Michelle van der Helm; Chang-Lin Wang; Reece Lewis; Sarah Schyck; Laura Rossi; Rienk Eelkema | Aggregates and Assemblies; Granular Materials; Physical and Chemical Processes; Self-Assembly | CC BY 4.0 | CHEMRXIV | 2020-10-29 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c751530f50db8b9339776a/original/transient-colloid-assembly-by-fuel-driven-modulation-of-depletion-interactions.pdf |
63a15a65b9c5f6ff52d97d5d | 10.26434/chemrxiv-2022-5zs02 | Topological Impact of Delocalization on the Stability and Bandgap of Partially Oxidized Graphene | Strategic perturbations on graphene framework to inflict a tunable energy bandgap promises intelligent electronics that are smaller, faster, flexible, and much more efficient than silicon. Despite different chemical schemes, a clear scalable strategy for micromanaging the bandgap is lagging. Since conductivity arises from the delocalized π-electrons, chemical intuition suggests that selective saturation of some sp2 carbons will allow strategic control over the bandgap. However, the logical cognition of different 2D π-delocalization topologies is complex. Their impact on the thermodynamic stability and bandgap remains unknown. Using partially oxidized graphene with its facile and reversible epoxides, we show that delocalization overwhelmingly influences the nature of the frontier bands. Organic electronic effects like hyperconjugation, conjugation, aromaticity, etc., can be used effectively to understand the impact of delocalization. By keeping a constant C4O stoichiometry, the relative stability of various π-delocalization topologies is directly assessed without resorting to resonance energy concepts. Our results demonstrate that >C=C< and aromatic sextets are the two fundamental blocks resulting in a large bandgap in isolation. Extending the delocalization across these units will increase the stability at the expense of the band gap. The bandgap is directly related to the extent of bond alternation within the π-framework, with forced single/double bonds causing the large gap. Furthermore, it also establishes the ground rules for the thermodynamic stability associated with the π-delocalization in 2D systems. We anticipate our findings will provide the heuristic guidance for designing partially saturated graphene with desired bandgap and stability using chemical intuition. | Gaurav Jhaa; Pattath D. Pancharatna; Musiri M. Balakrishnarajan | Theoretical and Computational Chemistry; Materials Science; Carbon-based Materials; Computational Chemistry and Modeling; Theory - Computational; Materials Chemistry | CC BY NC ND 4.0 | CHEMRXIV | 2022-12-21 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63a15a65b9c5f6ff52d97d5d/original/topological-impact-of-delocalization-on-the-stability-and-bandgap-of-partially-oxidized-graphene.pdf |
60c74712bdbb891c82a38d20 | 10.26434/chemrxiv.11533506.v1 | Nongenetic Control of Receptor Signaling Dynamics with a DNA-based Optochemical Tool | Optochemical tools that can modulate activity of the target protein
provide an opportunity for studying and regulating the related biological
processes. Here we present a DNA-based nongenetic optochemical tool that can
control dynamics of growth factor signaling. A photo-caged DNA aptamer for a
growth factor receptor was designed to assemble into an active dimer form,
depending on UV irradiation, thereby enabling optical control of the
dimerization and subsequent activation of the receptor. This photo-caged
mimicry of growth factor can be a promising tool for elucidating a linkage
between dynamics of signaling and resulting biological outcomes, as well as for
manipulating cellular functions and the fate of living cells. | Ryosuke Ueki; Shota Hayashi; Masaya Tsunoda; Momoko Akiyama; Hanrui Liu; Tasuku Ueno; Yasuteru Urano; Shinsuke Sando | Chemical Biology | CC BY NC ND 4.0 | CHEMRXIV | 2020-01-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60c74712bdbb891c82a38d20/original/nongenetic-control-of-receptor-signaling-dynamics-with-a-dna-based-optochemical-tool.pdf |
633d1247f764e6b6670ec297 | 10.26434/chemrxiv-2022-qhzrp-v3 | Iteroselectivity, the missing sibling of chemo-, regio- and stereoselectivities | Iteroselectivity is the selectivity that governs the number of repeating chemical transformations that occur on a substrate bearing multiple identical reactive functions or when the reactive function is regenerated like in the case of polymerization. This new concept of selectivity is defined and compared with the classical chemo-, regio- and stereoselectivities encountered in chemical synthesis. Examples of iteroselective reactions are given ranging from very common reactions such as electrophilic aromatic substitutions to advanced methods involving large supramolecular complexes. | Roy Lavendomme; Ivan Jabin | Organic Chemistry; Organic Synthesis and Reactions; Supramolecular Chemistry (Org.) | CC BY 4.0 | CHEMRXIV | 2022-10-06 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/633d1247f764e6b6670ec297/original/iteroselectivity-the-missing-sibling-of-chemo-regio-and-stereoselectivities.pdf |
625f97936c989c53bfbec266 | 10.26434/chemrxiv-2022-bp028 | Temporal stimulus patterns drive differentiation of a synthetic coacervate | The fate of living cells often depends on their processing of temporally modulated information, such as the frequency and duration of various signals. Synthetic stimulus-responsive systems have been intensely studied for >50 y, but it is still challenging for chemists to create artificial systems that can decode dynamically oscillating stimuli and respond in the systems’ properties/functions, because of the lack of sophisticated reaction networks that are comparable with biological signal transduction. Here we report morphological differentiation of synthetic dipeptide-based coacervates in response to light pulse frequency. We designed a simple cationic diphenylalanine peptide derivative to enable formation of coacervates. The coacervates concentrated an anionic methacrylate monomer and a photo-initiator, which provided a unique reaction environment and facilitated light-triggered radical polymerisation—even in air. Pulsed light irradiation at 9.0 Hz (but not at 0.5 Hz) afforded anionic polymers. This frequency dependence is attributable to the competition of reactive radical intermediates between the methacrylate monomer and molecular oxygen. The frequency-dependent polymer formation enabled the coacervates to differentiate in terms of morphology and internal viscosity, with an ultrasensitive switch-like mode. Our achievements will facilitate rational design of smart supramolecular soft materials and are insightful regarding the origin of life. | Ryou Kubota; Shogo Torigoe; Itaru Hamachi | Organic Chemistry; Supramolecular Chemistry (Org.) | CC BY NC ND 4.0 | CHEMRXIV | 2022-04-26 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/625f97936c989c53bfbec266/original/temporal-stimulus-patterns-drive-differentiation-of-a-synthetic-coacervate.pdf |
60de5c1be92419755fe19d89 | 10.26434/chemrxiv-2021-9f5sv | The Ionic Atmosphere Effect on the Absorption Spectrum of a Flavoprotein: A Reminder to Consider the Importance of Solution Ions | Ionizable residues and monoatomic ions in solution modulate enzyme catalysis and the structural stability of proteins; however, the delicate interplay between these short-range charges and long-range charges, and their contributions to the electrostatic environment in a protein active site, is currently not fully understood. The study presented here utilizes the FMN-dependent NADH:quinone oxidoreductase from Pseudomonas aeruginosa PAO1 (NQO, EC 1.6.5.9, UniProtKB Q9I4V0) as a model system to study the effect of introducing an active site negative charge on the flavin absorption spectrum both in the absence and presence of a long-range electrostatic potential coming from solution ions. Using pH-dependent UV-visible spectroscopy, there were no observed changes in the flavin absorption spectrum when an active site tyrosine (Y277) deprotonated in vitro. These results could only be reproduced computationally using Average Solvent Electrostatic Configuration (ASEC) hybrid quantum mechanics / molecular mechanics (QM/MM) simulations that included both positive and negative solution ions. The same calculations performed with minimal ions to neutralize protein charges predicted that deprotonating Y277 would significantly affect the flavin absorption spectrum. Analyzing the distribution of solution ions from ASEC and radial distribution functions derived from molecular dynamics indicated that the solution ions reorganize around the protein surface upon Y277 deprotonation to cancel the effect of the tyrosinate on the flavin absorption spectrum. Biochemical experiments were performed to support this hypothesis. This work highlights the importance of salt ions, which are sometimes overlooked, since they can contribute a non-uniform and anisotropic long-range potential to the electrostatic environment of an active site. | Benjamin Dratch; Yoelvis Orozco-Gonzalez; Giovanni Gadda; Samer Gozem | Theoretical and Computational Chemistry; Physical Chemistry; Biological and Medicinal Chemistry; Computational Chemistry and Modeling; Spectroscopy (Physical Chem.); Statistical Mechanics | CC BY NC ND 4.0 | CHEMRXIV | 2021-07-02 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/60de5c1be92419755fe19d89/original/the-ionic-atmosphere-effect-on-the-absorption-spectrum-of-a-flavoprotein-a-reminder-to-consider-the-importance-of-solution-ions.pdf |
670a5a1bcec5d6c142eecb0b | 10.26434/chemrxiv-2024-4j7g2 | Molecular Aharonov-Bohm Interferometers Based on Porphyrin Nanorings | A goal of molecular electronics and spintronics is to create molecular devices that change their conductance in response to external stimuli. The Aharonov-Bohm (AB) effect implies that an electronic device formed from a quantum ring and metallic leads will exhibit such behavior under external magnetic fields. At first sight, it appears that unrealistically large fields would be required to significantly alter the conductance of a molecular ring. However, the sensitivity of a molecular AB interferometer to magnetic fields can be increased by weakening the coupling between the molecular ring and the metallic leads. An ideal molecular ring for an AB interferometer has a large radius (to access a larger portion of the full AB cycle), and a small effective mass (high electron mobility) to enhance its response to magnetic fields. Here, we use computational modelling to demonstrate that recently synthesized porphyrin nanorings, with radii of 2–9 nm, could behave as molecular AB interferometers at achievable magnetic field strengths (5–10 T), if weak ring-lead coupling is used. Building on our recently developed semi-empirical approach, which incorporates the effects of finite magnetic fields on the electronic structure, we develop a transport computational platform that allows us to identify sharp Fano resonances in the transmittance probability of porphyrin nanorings that could be exploited to control the current with an applied magnetic field. These resonances are rationalized in terms of a magnetic field-induced delocalization of the molecular orbitals. Our findings indicate that molecular AB interferometry should be feasible with current experimental capabilities. | Chi Cheng; Gil Harari; Igor Rončević; Juan Peralta; Harry Anderson; Andrew Wibowo-Teale; Oded Hod | Theoretical and Computational Chemistry; Organic Chemistry; Nanoscience; Supramolecular Chemistry (Org.); Nanodevices; Nanostructured Materials - Nanoscience | CC BY NC 4.0 | CHEMRXIV | 2024-10-15 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/670a5a1bcec5d6c142eecb0b/original/molecular-aharonov-bohm-interferometers-based-on-porphyrin-nanorings.pdf |
640695076642bf8c8f1684d4 | 10.26434/chemrxiv-2023-rvzmv | Rapid Estimation of the Intermolecular Electronic Couplings and Charge-Carrier Mobilities of Crystalline Molecular Organic Semiconductors through a Machine Learning Pipeline | Organic semiconductors offer tremendous potential across a wide range of (opto)electronic applications. However, the development of these materials is limited by trial-and-error design approaches, as well as computationally heavy modeling approaches to evaluate/screen candidates using a suite of materials descriptors. For the latter, for instance, density functional theory (DFT) methods are widely used to derive descriptors such as the oxidation and reduction potentials, molecular relaxation and reorganization energies, and intermolecular electronic couplings; these calculations are compute-intensive, often requiring hours to days to determine. Such bottlenecks slow the pace and limit the exploration of the vast chemical space that can comprise organic materials. Here, we introduce a machine learning (ML) model to predict intermolecular electronic couplings in organic, molecule-based crystalline materials that take a few seconds, as compared to hours by DFT. Further, we use the ML model in conjunction with mathematical formulations to rapidly screen the charge-carrier mobilities and associated anisotropies of over 60,000 molecular crystal structures. The ML models and pipeline are made fully available on the open-access OCELOT ML infrastructure. | Vinayak Bhat; Baskar Ganapathysubramanian; Chad Risko | Theoretical and Computational Chemistry; Computational Chemistry and Modeling; Machine Learning; Materials Chemistry | CC BY NC 4.0 | CHEMRXIV | 2023-03-08 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/640695076642bf8c8f1684d4/original/rapid-estimation-of-the-intermolecular-electronic-couplings-and-charge-carrier-mobilities-of-crystalline-molecular-organic-semiconductors-through-a-machine-learning-pipeline.pdf |
63c8257af604d133205ace45 | 10.26434/chemrxiv-2023-c1n52-v2 | Virtual screening of ultra-large chemical libraries identifies cell-permeable small-molecule inhibitors of a “non-druggable” target, STAT3 N-terminal domain | STAT3 N-terminal domain is a promising molecular target for cancer treatment and modulation of
immune responses. However, STAT3 is localized in the cytoplasm, mitochondria, and nuclei, and thus, is
inaccessible to therapeutic antibodies. Its N-terminal domain lacks deep pockets on the surface and
represents a typical "non-druggable" protein. In order to successfully identify potent and selective
inhibitors of the domain, we have used virtual screening of billion structure-sized virtual libraries of
make-on-demand screening samples. The results suggest that the expansion of accessible chemical space
by cutting-edge ultra-large virtual compound databases can lead to successful development of small
molecule drugs for hard-to-target intracellular proteins. | Pedro Andrade Bonilla; Cody Hoop; Karen Stefanisko; Sergey Tarasov; Sourav Sinha; Marc Nicklaus; Nadya Tarasova | Biological and Medicinal Chemistry; Drug Discovery and Drug Delivery Systems | CC BY NC ND 4.0 | CHEMRXIV | 2023-01-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/63c8257af604d133205ace45/original/virtual-screening-of-ultra-large-chemical-libraries-identifies-cell-permeable-small-molecule-inhibitors-of-a-non-druggable-target-stat3-n-terminal-domain.pdf |
64b79429ae3d1a7b0df97464 | 10.26434/chemrxiv-2023-64vxm-v2 | Multigram synthesis of stellane 1,5-dicarbonic acid as a key precursor for the ortho-benzene mimics | Herein we present previously unavailable C(sp3)-rich polycyclic hydrocarbon scaffolds which have a potential to become valuable tools in medicinal chemistry and crop science as saturated bioisosteres of benzenoids. We have developed a scalable protocol (up to 50 g from a single synthetic run) for the synthesis of tricyclo[3.3.0.03,7]octane (bisnoradamantane or stellane) 1,5-dicarbonic acid derivatives. X-ray crystallographic analysis of the stellane 1,5-dicarbonic acid dimethyl ester has revealed that this scaffold is an optimal saturated isostere for ortho-disubstituted benzene where substituents exhibit the in-plane topology. The synthetic protocol is based on the oxidative cyclization of dimethyl octahydropentalene-2,5-dicarboxylate (DMOD) through lithiation followed by I2 oxidation. The reaction outcome is determined by the stereochemistry of the substrate. While the endo,endo cis-DMOD, exclusively gives the "unwanted" Claisen cyclization product the exo,endo cis- and exo,exo cis- stereoisomers afford the desired stellane 1,5-dicarbonic acid dimethyl ester quantitatively. DFT computations have revealed that the reaction proceeds via the dianion of dimethyl octahydropentalene-2,5-dicarboxylate, which undergoes SET oxidation by I2 to form a radical anion. The subsequent cyclization followed by a second SET oxidation gives desired stellane derivative. | Oleh Smyrnov; Kostiantyn Melnykov; Eduard Rusanov; Sergey Suikov; Olexandr Pashenko; Andrey Fokin; Dmytro Volochnyuk; Serhiy Ryabukhin | Organic Chemistry; Organic Synthesis and Reactions; Stereochemistry | CC BY 4.0 | CHEMRXIV | 2023-07-19 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/64b79429ae3d1a7b0df97464/original/multigram-synthesis-of-stellane-1-5-dicarbonic-acid-as-a-key-precursor-for-the-ortho-benzene-mimics.pdf |
67cb6e7a6dde43c908fa6f65 | 10.26434/chemrxiv-2025-9w4ss | Expanding Cluster, Enhancing Adsorption: Investigating the Role of Electrostatic Configurations on Water Vapor Adsorption in Idealized Nanoporous Materials | The role of electrostatic configurations of adsorbents in water vapor adsorption and underlying mechanisms of adsorption are central to many established and emerging areas concerning the water-energy nexus, water security, etc. In this work, continuous fractional component grand-canonical Monte Carlo (CFC-GCMC) is applied to perform water adsorption simulations in idealized cylindrical nanopores for five different charge configurations with varying pore size (1, 1.1 and 1.2 nm) and charge magnitude (~ +/– 0.39-1.17). The alternating along (AA) configuration (positive charges in the inner ring and negative in the outer ring while alternating in z-direction) demonstrates higher water uptake at saturation and water adsorption starts at a much lower pressure than other configurations. Analysis of water clustering pattern in AA reveals radial as well axial expansion of water clusters which facilitates accommodation of extra water molecules. Increasing charge magnitude shifts the type-V isotherm inflexion point leftwards along the pressure axis, thereby increasing the hydrophilic nature of the cylinder. Probing different energetic interactions and electrostatic potentials of the configurations suggest unique relaxation of the water clusters in the AA patterned cylinders. Investigating the effect of charge magnitude and pore size provides more insight into their hydrophilic nature. Finally, analyzing the hydrogen bonding and adsorbed phase characteristic at saturation hints at strong ordering induced by the pore confinements and the electrostatic configurations compared to bulk liquid water. The simulations show that tailored charge arrangements can enhance adsorption by facilitating uptake at lower pressure as well as achieve higher water capacity at saturation. This study presents original insights into the interplay of electrostatics configuration, pore size, and charge strength in controlling water vapor adsorption within nanopores and the resulting confined water vapor structure. | Krishnendu Mukherjee; McKayla Zastrow; Yamil Colón | Physical Chemistry; Interfaces; Surface | CC BY NC ND 4.0 | CHEMRXIV | 2025-03-11 | https://chemrxiv.org/engage/api-gateway/chemrxiv/assets/orp/resource/item/67cb6e7a6dde43c908fa6f65/original/expanding-cluster-enhancing-adsorption-investigating-the-role-of-electrostatic-configurations-on-water-vapor-adsorption-in-idealized-nanoporous-materials.pdf |
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