Journal of Chemical Theory and Computation最新文献

{"title":"","authors":"Anthony Val Canillas Camposano, Even Marius Nordhagen, Anders Malthe-So̷renssen and Henrik Andersen Sveinsson*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00722","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Zhenhao Zhou, Hongqiang Cui, Hongjun Fan*, Yuebin Zhang* and Guohui Li*, ","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00633","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/ctv021i014_1962183","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Benchmark of Approximate Quantum Chemical and Machine Learning Potentials for Biochemical Proton Transfer Reactions.","authors":"Guilherme M Arantes, Jan Řezáč","doi":"10.1021/acs.jctc.5c00690","DOIUrl":"10.1021/acs.jctc.5c00690","url":null,"abstract":"<p><p>Proton transfer reactions are among the most common chemical transformations and are central to enzymatic catalysis and bioenergetic processes. Their mechanisms are often investigated using DFT or approximate quantum chemical methods, whose accuracy directly impacts the reliability of the simulations. Here, a comprehensive set of semiempirical molecular orbital and tight-binding DFT approaches, along with recently developed machine learning (ML) potentials, are benchmarked against high-level MP2 reference data for a curated set of proton transfer reactions representative of biochemical systems. Relative energies, geometries, and dipole moments are evaluated for isolated reactions. Microsolvated reactions are also simulated using a hybrid QM/MM partition. Traditional DFT methods offer high accuracy in general but show markedly larger deviations for proton transfers involving nitrogen-containing groups. Among approximate models, RM1, PM6, PM7, DFTB2-NH, DFTB3, and GFN2-xTB show reasonable accuracy across properties, though their performance varies by chemical group. The ML-corrected (Δ-learning) model PM6-ML improves accuracy for all properties and chemical groups and transfers well to QM/MM simulations. Conversely, standalone ML potentials perform poorly for most reactions. These results provide a basis for evaluating approximate methods and selecting potentials for proton transfer simulations in complex environments.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"7149-7159"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12288007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144525460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Alberto Pacini*,&nbsp;Mauro Ferrario and Maria Clelia Righi*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00616","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Imran Chaudhry,&nbsp;Mark J. Bronson Jr. and Lasse Jensen*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00752","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Parisa Mollaei,&nbsp; and ,&nbsp;Amir Barati Farimani*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00483","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Zhenling Wang,&nbsp;Tianyi Shi,&nbsp;Weiliang Luo,&nbsp;Heather J. Kulik,&nbsp;Yang Liu,&nbsp;Xiaoye S. Li and Martin Head-Gordon*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00534","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"","authors":"Dulal Mondal,&nbsp; and ,&nbsp;Srabani Taraphder*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00529","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Real-Space Methods for Ab Initio Modeling of Surfaces and Interfaces under External Potential Bias.","authors":"Kartick Ramakrishnan, Gopalakrishnan Sai Gautam, Phani Motamarri","doi":"10.1021/acs.jctc.5c00513","DOIUrl":"10.1021/acs.jctc.5c00513","url":null,"abstract":"<p><p>Accurate ab initio modeling of surfaces and interfaces, especially under an applied external potential bias, is important for describing and characterizing various phenomena that occur in electronic, catalytic, and energy storage devices. Leveraging the ability of real-space density functional theory (DFT) codes to accommodate generic boundary conditions, we introduce two methods for applying an external potential bias that can be suitable for modeling surfaces and interfaces. In the first method, an external constant electric field is applied by modifying the DFT Hamiltonian via the introduction of an auxiliary linear potential while solving the electrostatic potential arising in DFT using a Poisson equation with zero-Neumann boundary conditions. The second method directly enforces the desired external potential bias by imposing constraints on the electrostatic potential, thereby naturally mimicking experimental conditions. We describe the underlying DFT governing equations for the two setups within the real-space formalism employing finite-element discretization. First, we validate the constant electric field setup within real-space finite-element DFT (DFT-FE) with an equivalent approach using plane-wave DFT (i.e., using periodic boundary conditions) on three representative benchmark systems, namely, La-terminated Li₇La₃Zr₂O₁₂, GaAs (111), and Al FCC (111) slabs. Subsequently, we present a comprehensive evaluation of the two setups in terms of the average ground-state properties, such as surface and adsorption energies. Also, we present an approach to constrain the electrostatic potential over a localised region, which is non-trivial to implement in periodic DFT codes. The methods developed in our work provide an attractive alternative to plane-wave DFT approaches in applying external potential bias that usually suffer from the periodic boundary conditions restrictions and poor scalability on parallel computing architectures. Our framework offers a robust approach for investigating surfaces and interfaces without any underlying assumptions or correction schemes while allowing for simulations of larger length scales than possible with plane-wave DFT.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"7087-7101"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}