Journal of Chemical Theory and Computation最新文献_第5页

Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials. 由混合机器学习和分子力学势驱动的多尺度模拟精确自由能计算。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-04 DOI: 10.1021/acs.jctc.5c00598

Xujian Wang, Xiongwu Wu, Bernard R Brooks, Junmei Wang

{"title":"Accurate Free Energy Calculation via Multiscale Simulations Driven by Hybrid Machine Learning and Molecular Mechanics Potentials.","authors":"Xujian Wang, Xiongwu Wu, Bernard R Brooks, Junmei Wang","doi":"10.1021/acs.jctc.5c00598","DOIUrl":"10.1021/acs.jctc.5c00598","url":null,"abstract":"This work develops a hybrid machine learning/molecular mechanics (ML/MM) interface integrated into the AMBER molecular simulation package. The resulting platform is highly versatile, accommodating several advanced machine learning interatomic potential (MLIP) models while providing stable simulation capabilities and supporting high-performance computations. Building upon this robust foundation, we developed new computational protocols to enable pathway-based and end point-based free energy calculation methods utilizing ML/MM hybrid potential. In particular, we proposed an ML/MM-compatible thermodynamic integration (TI) framework that adequately addressed the challenge of applying MLIPs in TI calculations due to its indivisible nature of energy and force. Our results demonstrated that the hydration free energies calculated using this framework achieved an accuracy of 1.0 kcal/mol, outperforming the traditional approaches. Moreover, ML/MM enables more precise sampling of conformational ensembles for improved end point-based free energy calculations. Overall, our efficient, stable, and highly compatible interface not only broadens the application of MLIPs in multiscale simulations but also enhances the accuracy of free energy calculations from multiple aspects. By introducing a novel ML/MM-compatible thermodynamic integration framework, we offered a novel foundation for combining advanced multiscale simulation methodologies with highly accurate free energy calculation techniques, thereby opening new avenues and providing a robust theoretical framework for future developments in this field.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6979-6987"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558462","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}

引用次数: 0

Toward Quantum-Centric Simulations of Extended Molecules: Sample-Based Quantum Diagonalization Enhanced with Density Matrix Embedding Theory. 扩展分子的量子中心模拟：密度矩阵嵌入理论增强的基于样品的量子对角化。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-08 DOI: 10.1021/acs.jctc.5c00114

Akhil Shajan, Danil Kaliakin, Abhishek Mitra, Javier Robledo Moreno, Zhen Li, Mario Motta, Caleb Johnson, Abdullah Ash Saki, Susanta Das, Iskandar Sitdikov, Antonio Mezzacapo, Kenneth M Merz

{"title":"Toward Quantum-Centric Simulations of Extended Molecules: Sample-Based Quantum Diagonalization Enhanced with Density Matrix Embedding Theory.","authors":"Akhil Shajan, Danil Kaliakin, Abhishek Mitra, Javier Robledo Moreno, Zhen Li, Mario Motta, Caleb Johnson, Abdullah Ash Saki, Susanta Das, Iskandar Sitdikov, Antonio Mezzacapo, Kenneth M Merz","doi":"10.1021/acs.jctc.5c00114","DOIUrl":"10.1021/acs.jctc.5c00114","url":null,"abstract":"Computing ground-state properties of molecules is a promising application for quantum computers operating in concert with classical high-performance computing resources. Quantum embedding methods are a family of algorithms particularly suited to these computational platforms: they combine high-level calculations on active regions of a molecule with low-level calculations on the surrounding environment, thereby avoiding expensive high-level full-molecule calculations and allowing the distribution of computational cost across multiple and heterogeneous computing units. Here, we present the first density matrix embedding theory (DMET) simulations performed in combination with a sample-based quantum diagonalization (SQD) method. We employ the DMET-SQD formalism to compute the ground-state energy of a ring of 18 hydrogen atoms and the relative energies of the chair, half-chair, twist-boat, and boat conformers of cyclohexane. The full-molecule 41- and 89-qubit simulations are decomposed into 27- and 32-qubit active-region simulations, which we carry out on the ibm_cleveland device, obtaining results in agreement with reference classical methods. Our DMET-SQD calculations mark tangible progress in the size of active regions that can be accurately tackled by near-term quantum computers and are an early demonstration of the potential for quantum-centric simulations to accurately treat the electronic structure of large molecules, with the ultimate goal of tackling systems such as peptides and proteins.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6801-6810"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590056","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}

引用次数: 0

Predicting Solid-Liquid Interfacial Free Energy with Realistic Interfacial Density Wave Amplitudes. 用实际界面密度波振幅预测固液界面自由能。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 DOI: 10.1021/acs.jctc.5c00656

Ya-Shen Wang,Zun Liang,Yang Yang

{"title":"Predicting Solid-Liquid Interfacial Free Energy with Realistic Interfacial Density Wave Amplitudes.","authors":"Ya-Shen Wang,Zun Liang,Yang Yang","doi":"10.1021/acs.jctc.5c00656","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00656","url":null,"abstract":"This study presents a theoretical framework for predicting the solid-liquid interfacial free energy (γ) of FCC systems using the two-mode Ginzburg-Landau (GL) model, refined with atomistic simulation data to generate more accurate density wave amplitude profiles. The analysis focuses on Lennard-Jones (LJ) systems along the p-T two-phase coexistence boundary. Equilibrium molecular dynamics simulations and the analytical minimization methods are employed to obtain the interfacial density wave amplitude profiles, which serve as inputs for the GL model to predict γ and its anisotropy. The predicted γ values strongly agree with previous benchmark computational studies, with a level of accuracy that surpasses prior predictions using either the GL or phase-field crystal models. The results demonstrate that the current two-mode GL model for FCC solid-liquid interfaces (SLIs) is computationally efficient and quantitatively reliable. It could provide valuable insight into the key factors governing the magnitude and anisotropy of γ and offer theoretical guidance for precisely tuning these properties. To further enhance predictive accuracy, refinements to the variational procedure used in the two-mode SLI free energy functionals are suggested, and potential extensions to the GL model are proposed.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"12 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684322","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}

引用次数: 0

IF 5.7 1区化学