化学•材料最新文献

{"title":"Kinetic Consequences of Quasi-Harmonic Entropies Calculated with Machine Learning Interatomic Potentials for Microkinetic Modeling","authors":"Geet Gupta, Brandon C. Bukowski","doi":"10.1021/acs.jpcc.4c05841","DOIUrl":"https://doi.org/10.1021/acs.jpcc.4c05841","url":null,"abstract":"Microporous catalysts are ubiquitous in chemical processes including sustainable transformations of biobased feedstocks into fuels and fine chemicals. The mechanistic insights needed to design next-generation microporous catalysts can be obtained with <i>ab initio</i> simulations coupled with microkinetic modeling, yet active site confinement complicates an accurate determination of adsorbate entropies, which, in turn, affect predictions of rate and equilibrium constants. In this study, we developed a machine learning force field (MLFF) strategy to rapidly predict temperature-dependent quasi-harmonic adsorbate entropies in zeolite Beta, reducing the number of compute-intensive <i>ab initio</i> molecular dynamics calculations needed to construct a microkinetic model. These entropies directly impacted the kinetics of a model parallel reaction mechanism. We chose lactic acid dehydration to acrylic acid on aluminosilicate zeolite Beta to explore the pathway dependence of unselective product formation and initial deactivation mechanisms using microkinetic modeling with our MLFF entropy strategy. The resulting quasi-harmonic entropy approximations led to shifts in steady-state coverages that impacted reaction orders and product selectivity. At low lactic acid partial pressures, concerted monomolecular decarbonylation is favored over Brønsted acid sites, which then shifts at high lactic acid partial pressures to concerted bimolecular condensations into lactic acid oligomers. Sequential pathways mediated by adsorbed alkoxide or carbonyl intermediates have no kinetic relevance at these conditions. These findings provide a strategy to integrate quasi-harmonic entropies into microkinetic modeling that is scalable with reaction temperature and applicable to a wide range of catalysts and catalytic cycles.","PeriodicalId":61,"journal":{"name":"The Journal of Physical Chemistry C","volume":null,"pages":null},"PeriodicalIF":4.126,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610043","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gold(I)-Catalyzed Synthesis of 2,2′-Biindoles via One-Pot Double Cycloisomerization Strategy","authors":"Jaime G. Ibarra-Gutiérrez, César R. Solorio-Alvarado, Luis Chacón-García, Jesús Adrián López, B. Yoaly Delgado-Piedra, Luis A. Segura-Quezada, Edson D. Hernández-Velázquez, Ana K. García-Dueñas","doi":"10.1021/acs.joc.4c01309","DOIUrl":"https://doi.org/10.1021/acs.joc.4c01309","url":null,"abstract":"The first systematic, concise and target-directed gold(I)-catalyzed synthesis of a family of 2,2′-biindoles containing different substitution patterns is described. The developed protocol involves the synthesis of 1,3-diyne-anilines followed by a one-pot gold(I)-catalyzed double cycloisomerization, giving rise to an efficient, broad and general protocol to get different 2,2′-biindoles under mild reaction conditions. Due to the methodological restriction of present methods for accessing this class of compounds, herein we present our synthetic proposal which allowed the preparation of several examples of 2,2′-biindoles. Their functionalization-guided us to the discovery that the chemical stability, is substitution structure-dependent.","PeriodicalId":57,"journal":{"name":"The Journal of Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":4.354,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142610384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"HF Trimer: A New Full-Dimensional Potential Energy Surface and Rigorous 12D Quantum Calculations of Vibrational States.","authors":"Jia Li, Patricia Vindel-Zandbergen, Jun Li, Peter M Felker, Zlatko Bačić","doi":"10.1021/acs.jpca.4c03771","DOIUrl":"10.1021/acs.jpca.4c03771","url":null,"abstract":"<p><p>HF trimer, as the smallest and the lightest cyclic hydrogen-bonded (HB) cluster, has long been a favorite prototype system for spectroscopic and theoretical investigations of the structure, energetics, spectroscopy, and dynamics of hydrogen-bond networks. Recently, rigorous quantum 12D calculations of the coupled intra- and intermolecular vibrations of this fundamental HB trimer (<i>J. Chem. Phys.</i> <b>2023</b>, <i>158</i>, 234109) were performed, employing an older ab initio-based many-body potential energy surface (PES). While the theoretical results were found to be in reasonably good agreement with the available spectroscopic data, it was also evident that it is highly desirable to develop a more accurate 12D PES of HF trimer. Motivated by this, here we report a new, and the first fully ab initio 12D PES of this paradigmatic system. Approximately 42,540 geometries were sampled and calculated at the level of CCSD(T)-F12a/AVTZ. The permutationally invariant polynomial-neural network based Δ-machine learning approach (<i>J. Phys. Chem. Lett.</i> <b>2022</b>, <i>13</i>, 4729) was employed to perform cost-efficient calculations of the basis-set-superposition error (BSSE) correction. By strategically selecting data points, this approach facilitated the construction of a high-precision PES with BSSE correction, while requiring only a minimal number of BSSE value computations. The fitting error of the final PES is only 0.035 kcal/mol. To assess its performance, the 12D fully coupled quantum calculations of excited intra- and intermolecular vibrational states of HF trimer are carried out using the rigorous methodology developed by us earlier. The results are found to be in a significantly better agreement with the available spectroscopic data than those obtained with the previously existing semiempirical 12D PES.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structure Determination of Zinc and Cadmium Dication Complexes with Intact and Deprotonated Histidyl Glycine and Glycyl Histidine Dipeptides.","authors":"Samantha K Walker, Brandon C Stevenson, Evan H Perez, Roland M Jones, David H Loertscher, Amanda R Bubas, Fan Yang, Talley A Fenn, Giel Berden, Jonathan Martens, Jos Oomens, P B Armentrout","doi":"10.1021/acs.jpcb.4c06308","DOIUrl":"10.1021/acs.jpcb.4c06308","url":null,"abstract":"<p><p>Metalated intact and deprotonated histidyl glycine and glycyl histidine dipeptides were investigated in the gas phase by using infrared multiple photon dissociation (IRMPD) spectroscopy with light from a free-electron laser (FEL). The dipeptides M²⁺(GlyHis), M²⁺(HisGly), [M(GlyHis-H)]⁺, and [M(HisGly-H)]⁺, where M = Zn and Cd, were probed to elucidate how the His position along the peptide chain and ligand charge state might influence the structures observed in the gas phase. Simulated annealing calculations were performed to determine energetically low-lying conformers and isomers of these structures. Quantum chemical calculations were used to optimize the structures at the B3LYP level of theory using the 6-311+G(d,p) and def2-TZVP basis sets for zinc and cadmium complexes, respectively. IRMPD and calculated linear absorption spectra were compared to evaluate which structures are present. Relative energies of the various species were evaluated using single-point energy calculations for low-lying structures at the B3LYP, B3LYP-GD3BJ, ωB97XD, and MP2(full) levels using the 6-311+G(2d,2p) and def2-TZVPP basis sets. For all species, structures for both metals mirror each other, and those that reproduce the experimental spectrum were determined to be iminol structures for the intact ligands or iminol-like structures for the deprotonated ligands. Additionally, when the spectra of the deprotonated dipeptides are compared to the intact dipeptides, the change in the spectra is correlated to the group that is deprotonated.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antiparallel G-Quadruplex Formation Hinders Conversion to a Parallel Topology.","authors":"Jianjun Xia, Jielin Chen, Jiahang Zhou, Mingpan Cheng, Xinzhe Zhuang, Chengfeng Cai, Huangxian Ju, Jean-Louis Mergny, Jun Zhou","doi":"10.1021/acs.jpcb.4c04570","DOIUrl":"10.1021/acs.jpcb.4c04570","url":null,"abstract":"<p><p>G-quadruplexes (G4s) are four-stranded structures formed by guanine-rich sequences. While their structures, properties, and applications have been extensively studied, an understanding of their folding processes remains limited. In this study, we investigated the folding of the sequence d[(G₃T₂)₃G₃] in potassium solutions, focusing on the impact of a folding intermediate on the overall folding process. Our results indicate that this sequence eventually folds into a parallel G4 structure, either directly or through an antiparallel conformation intermediate, suggesting the existence of a specific competitive folding process. Detailed kinetic analysis using stopped-flow techniques reveals that the antiparallel conformation forms much faster than the parallel one. This antiparallel G4 slowly converts to the thermodynamically favored parallel topology, thus slowing the overall folding rate. As a result, the formation of the parallel quadruplex via an antiparallel G4 intermediate is slower than the direct process, indicating that this antiparallel conformation negatively impacts the overall folding process in a temperature-dependent manner. Interestingly, sodium was shown to facilitate the conversion from antiparallel to parallel. These analyses highlight the complexity of the G4 folding process, which is crucial for most biological applications.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expanded Functionality and Portability for the Colvars Library.","authors":"Giacomo Fiorin, Fabrizio Marinelli, Lucy R Forrest, Haochuan Chen, Christophe Chipot, Axel Kohlmeyer, Hubert Santuz, Jérôme Hénin","doi":"10.1021/acs.jpcb.4c05604","DOIUrl":"10.1021/acs.jpcb.4c05604","url":null,"abstract":"<p><p>Colvars is an open-source C++ library that provides a modular toolkit for collective-variable-based molecular simulations. It allows practitioners to easily create and implement descriptors that best fit a process of interest and to apply a wide range of biasing algorithms in collective variable space. This paper reviews several features and improvements to Colvars that were added since its original introduction. Special attention is given to contributions that significantly expanded the capabilities of this software or its distribution with major MD simulation packages. Collective variables can now be optimized either manually or by machine-learning methods, and the space of descriptors can be explored interactively using the graphical interface included in VMD. Beyond the spatial coordinates of individual molecules, Colvars can now apply biasing forces to mesoscale structures and alchemical degrees of freedom and perform simulations guided by experimental data within ensemble averages or probability distributions. It also features advanced computational schemes to boost the accuracy, robustness, and general applicability of simulation methods, including extended-system and multiple-walker adaptive biasing force, boundary conditions for metadynamics, replica exchange with biasing potentials, and adiabatic bias molecular dynamics. The library is made available directly within the main distributions of the academic software GROMACS, LAMMPS, NAMD, Tinker-HP, and VMD. The robustness of the software and the reliability of the results are ensured through the use of continuous integration with a test suite within the source repository.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142580955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Paradox of Global Multireference Diagnostics.","authors":"Bun Chan","doi":"10.1021/acs.jpca.4c06148","DOIUrl":"10.1021/acs.jpca.4c06148","url":null,"abstract":"<p><p>Modern computational chemistry methods are a useful tool for modeling many chemical systems, but they are challenged by multireference species (e.g., transition metals). A variety of diagnostics have been formulated to identify such cases. They are typically developed by analyzing multireference characters of small molecules, and many provide an average picture of the entire system. We caution the use of such diagnostics for large systems because large systems may include parts with varying degrees of multireference characters. Specifically, a small but highly multireference component may yield a large error in absolute terms, which may be masked in an average value over the entire molecule. As the calculation of molecular relative energies often concerns errors in absolute terms, such a false sense of safety may be detrimental. A prospective means to tackle this challenge is to use fractional occupation density to identify potentially problematic components in a system and then examine this moiety with higher-level computations on appropriately constructed smaller models.</p>","PeriodicalId":59,"journal":{"name":"The Journal of Physical Chemistry A","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142542919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine-Learning Approach to Identify Potential Dengue Virus Protease Inhibitors: A Computational Perspective.","authors":"Jameel M Abduljalil, Abdo A Elfiky","doi":"10.1021/acs.jpcb.4c05388","DOIUrl":"10.1021/acs.jpcb.4c05388","url":null,"abstract":"<p><p>The global prevalence of dengue virus (DENV), a widespread flavivirus, has led to varied epidemiological impacts, economic burdens, and health consequences. The alarming increase in infections is exacerbated by the absence of approved antiviral agents against the DENV. Within flaviviruses, the NS3/NS2B serine protease plays a pivotal role in processing the viral polyprotein into distinct components, making it an attractive target for antiviral drug development. In this study, machine-learning (ML) techniques were employed to build predictive models for the screening of a library containing 32,000 protease inhibitors. Utilizing GNINA for structure-based virtual screening, the top potential candidates underwent a subsequent evaluation of their absorption, distribution, metabolism, excretion, and toxicity properties. Selected compounds were subjected to molecular dynamics simulations and binding free energy calculations via MM/GBSA. The results suggest that comp530 possesses binding potential to DENV protease as a noncovalent inhibitor with multiple positions for chemical substitutions, presenting opportunities for optimizing their selectivity and specificity. However, other compounds predicted via ML models may still provide a promising start for covalent inhibitors.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556668","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generation of Surface Ga-H Hydride and Reactivity toward CO₂.","authors":"Zhendong Feng, Qingnan Wang, Pengfei Zhang, Guanna Li, Jijie Wang, Zhaochi Feng, Can Li","doi":"10.1021/acs.jpclett.4c02854","DOIUrl":"10.1021/acs.jpclett.4c02854","url":null,"abstract":"<p><p>Hydrogen adsorption on gallium oxide was investigated by in situ infrared (IR) spectroscopy over a temperature range of 30-450 °C. Both hydroxyl groups and Ga-H hydrides with a pair of characteristic bands at 3685 (3532) cm^-1 and 2011 (1988) cm^-1 were detected on the surface gallium oxide. The formation and stability of surface Ga-H hydrides were found to be highly dependent on the temperature of H₂ dissociation. Through a combination of density functional theory (DFT) calculations and isotopic experiments, a mechanism involving both heterolytic and homolytic pathways for hydrogen dissociation was proposed for the generation of Ga-H hydrides. Furthermore, the reactivity of surface Ga-H hydrides was explored by their interactions with various probe molecules such as carbon dioxide, oxygen, and nitrogen. A potential reaction mechanism involving the attraction between nucleophilic hydrogen and positively charged intermediates was suggested during those hydrogenations.</p>","PeriodicalId":62,"journal":{"name":"The Journal of Physical Chemistry Letters","volume":null,"pages":null},"PeriodicalIF":4.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142556672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High Efficiency Shear-Driven Nanofluidic System for Energy Conversion/Harvesting.","authors":"Le Zhou, Yanguang Zhou, Zhigang Li","doi":"10.1021/acs.jpcb.4c06142","DOIUrl":"10.1021/acs.jpcb.4c06142","url":null,"abstract":"<p><p>In this work, we propose a shear-driven nanofluidic system for energy harvesting/conversion. The system consists of a nanochannel formed by two parallel walls, where the lower wall is negatively charged, while the upper wall is neutral. The motion of the upper wall caused by a shear force drives the solution in the fluidic system to move, which generates an ionic current due to the migration of excess cations in the system. Molecular dynamics simulations demonstrate that the efficiency of the system is affected by the wall charge density, shearing stress, channel height, and binding energy of the walls. The effects of these factors on the efficiency are studied. In particular, it is shown that a high binding energy for the upper wall (e.g., hydrophilic wall) can reduce the flow slip at the upper wall and effectively transfer energy from the wall to the fluid. For the lower wall, a low binding energy, which corresponds to a hydrophobic wall, can reduce the friction at the wall, enhance the flow velocity, and improve the energy conversion efficiency. By varying these parameters, it is found that the maximum energy conversion efficiency of the system reaches 65.8%, which is the highest compared with previous systems. The underlying mechanisms are explained using the slip length at the walls, wall velocity, and charge density profiles. The system proposed in this work provides insights into the design of nanofluidic systems for energy harvesting/conversion.</p>","PeriodicalId":60,"journal":{"name":"The Journal of Physical Chemistry B","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142566366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}