Journal of Chemical Theory and Computation最新文献

A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding 在蛋白质与配体结合的炼金术自由能模拟中处理显著构象变化的方法

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-27 DOI: 10.1021/acs.jctc.4c00954

Junzhuo Liao, Alina P. Sergeeva, Edward D. Harder, Lingle Wang, Jared M. Sampson, Barry Honig, Richard A. Friesner

{"title":"A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding","authors":"Junzhuo Liao, Alina P. Sergeeva, Edward D. Harder, Lingle Wang, Jared M. Sampson, Barry Honig, Richard A. Friesner","doi":"10.1021/acs.jctc.4c00954","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00954","url":null,"abstract":"Relative binding free energy (RBFE) simulation is a rigorous approach to the calculation of quantitatively accurate binding free energy values for protein–ligand binding in which a reference binder is gradually converted to a target binder through alchemical transformation during the simulation. The success of such simulations relies on being able to accurately sample the correct conformational phase space for each alchemical state; however, this becomes a challenge when a significant conformation change occurs between the reference and target binder–receptor complexes. Increasing the simulation time and using enhanced sampling methods can be helpful, but effects can be limited, especially when the free energy barrier between conformations is high or when the correct target complex conformation is difficult to find and maintain. Current RBFE protocols seed the reference complex structure into every alchemical window of the simulation. In our study, we describe an improved protocol in which the reference structure is seeded into the first half of the alchemical windows, and the target structure is seeded into the second half of the alchemical windows. By applying information about the relevant correct end point conformations to different simulation windows from the beginning, the need for large barrier crossings or simulation prediction of the correct structures during an alchemical simulation is in many cases obviated. In the diverse cases we examine below, the simulations yielded free energy predictions that are satisfactory as compared to experiment and superior to running the simulations utilizing the conventional protocol. The method is straightforward to implement for publicly available FEP workflows.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325705","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

Massive Assessment of the Geometries of Atmospheric Molecular Clusters 大气分子簇几何学的大规模评估

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-27 DOI: 10.1021/acs.jctc.4c01046

Andreas Buchgraitz Jensen, Jonas Elm

{"title":"Massive Assessment of the Geometries of Atmospheric Molecular Clusters","authors":"Andreas Buchgraitz Jensen, Jonas Elm","doi":"10.1021/acs.jctc.4c01046","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01046","url":null,"abstract":"Atmospheric molecular clusters are important for the formation of new aerosol particles in the air. However, current experimental techniques are not able to yield direct insight into the cluster geometries. This implies that to date there is limited information about how accurately the applied computational methods depict the cluster structures. Here we massively benchmark the molecular geometries of atmospheric molecular clusters. We initially assessed how well different DF-MP2 approaches reproduce the geometries of 45 dimer clusters obtained at a high DF-CCSD(T)-F12b/cc-pVDZ-F12 level of theory. Based on the results, we find that the DF-MP2/aug-cc-pVQZ level of theory best resembles the DF-CCSD(T)-F12b/cc-pVDZ-F12 reference level. We subsequently optimized 1283 acid–base cluster structures (up to tetramers) at the DF-MP2/aug-cc-pVQZ level of theory and assessed how more approximate methods reproduce the geometries. Out of the tested semiempirical methods, we find that the newly parametrized atmospheric molecular cluster extended tight binding method (AMC-xTB) is most reliable for locating the correct lowest energy configuration and yields the lowest root mean square deviation (RMSD) compared to the reference level. In addition, we find that the DFT-3c methods show similar performance as the usually employed ωB97X-D/6-31++G(d,p) level of theory at a potentially reduced computational cost. This suggests that these methods could prove to be valuable for large-scale screening of cluster structures in the future.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325707","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

Adaptive Variational Quantum Computing Approaches for Green’s Functions and Nonlinear Susceptibilities 针对格林函数和非线性易感性的自适应变分量子计算方法

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-27 DOI: 10.1021/acs.jctc.4c00874

Martin Mootz, Thomas Iadecola, Yong-Xin Yao

{"title":"Adaptive Variational Quantum Computing Approaches for Green’s Functions and Nonlinear Susceptibilities","authors":"Martin Mootz, Thomas Iadecola, Yong-Xin Yao","doi":"10.1021/acs.jctc.4c00874","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00874","url":null,"abstract":"We present and benchmark quantum computing approaches for calculating real-time single-particle Green’s functions and nonlinear susceptibilities of Hamiltonian systems. The approaches leverage adaptive variational quantum algorithms for state preparation and propagation. Using automatically generated compact circuits, the dynamical evolution is performed over sufficiently long times to achieve adequate frequency resolution of the response functions. We showcase accurate Green’s function calculations using a statevector simulator on classical hardware for Fermi-Hubbard chains of 4 and 6 sites, with maximal ansatz circuit depths of 65 and 424 layers, respectively, and for the molecule LiH with a maximal ansatz circuit depth of 81 layers. Additionally, we consider an antiferromagnetic quantum spin-1 model that incorporates the Dzyaloshinskii-Moriya interaction to illustrate calculations of the third-order nonlinear susceptibilities, which can be measured in two-dimensional coherent spectroscopy experiments. These results demonstrate that real-time approaches using adaptive parametrized circuits to evaluate linear and nonlinear response functions can be feasible with near-term quantum processors.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142325717","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

Relativistic Correction from the Four-Body Nonadiabatic Exponential Wave Function 四体非绝热指数波函数的相对论修正

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-26 DOI: 10.1021/acs.jctc.4c00861

Krzysztof Pachucki, Jacek Komasa

引用次数: 0

Nutmeg and SPICE: Models and Data for Biomolecular Machine Learning 肉豆蔻和 SPICE：生物分子机器学习的模型和数据

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-25 DOI: 10.1021/acs.jctc.4c00794

Peter Eastman, Benjamin P. Pritchard, John D. Chodera, Thomas E. Markland

引用次数: 0

The Next Twenty Years of the Journal of Chemical Theory and Computation 化学理论与计算》杂志的下一个二十年

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-24 DOI: 10.1021/acs.jctc.4c0106710.1021/acs.jctc.4c01067

Qiang Cui, Marco De Vivo and Laura Gagliardi*,

引用次数: 0

The Beginnings of JCTC JCTC 成立之初

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-24 DOI: 10.1021/acs.jctc.4c0114610.1021/acs.jctc.4c01146

William L. Jorgensen*,

引用次数: 0

Structure of Multi-State Correlation in Electronic Systems. 电子系统中的多态相关结构。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-24 DOI: 10.1021/acs.jctc.4c00545

Yangyi Lu, Jiali Gao

{"title":"Structure of Multi-State Correlation in Electronic Systems.","authors":"Yangyi Lu, Jiali Gao","doi":"10.1021/acs.jctc.4c00545","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00545","url":null,"abstract":"Beyond the Hohenberg-Kohn density functional theory for the ground state, it has been established that the Hamiltonian matrix for a finite number (N) of lowest eigenstates is a matrix density functional. Its fundamental variable─the matrix density D(r)─can be represented by, or mapped to, a set of auxiliary, multiconfigurational wave functions expressed as a linear combination of no more than N2 determinant configurations. The latter defines a minimal active space (MAS), which naturally leads to the introduction of the correlation matrix functional, responsible for the electronic correlation effects outside the MAS. In this study, we report a set of rigorous conditions in the Hamiltonian matrix functional, derived by enforcing the symmetry of a Hilbert subspace, namely the subspace invariance property. We further establish a fundamental theorem on the correlation matrix functional. That is, given the correlation functional for a single state in the N-dimensional subspace, all elements of the correlation matrix functional for the entire subspace are uniquely determined. These findings reveal the intricate structure of electronic correlation within the Hilbert subspace of lowest eigenstates and suggest a promising direction for efficient simulation of excited states.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142306577","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

The Beginnings of JCTC. JCTC 成立之初。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-24 DOI: 10.1021/acs.jctc.4c01146

William L Jorgensen

引用次数: 0

The Next Twenty Years of the Journal of Chemical Theory and Computation. 化学理论与计算》杂志的下一个二十年。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2024-09-24 DOI: 10.1021/acs.jctc.4c01067

Qiang Cui, Marco De Vivo, Laura Gagliardi

引用次数: 0