Journal of Chemical Theory and Computation最新文献_第8页

Automated Microsolvation for Minimum Energy Path Construction in Solution. 溶液中最小能量路径构建的自动化微溶剂化。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10 Epub Date: 2025-05-28 DOI: 10.1021/acs.jctc.5c00245

Paul L Türtscher, Markus Reiher

{"title":"Automated Microsolvation for Minimum Energy Path Construction in Solution.","authors":"Paul L Türtscher, Markus Reiher","doi":"10.1021/acs.jctc.5c00245","DOIUrl":"10.1021/acs.jctc.5c00245","url":null,"abstract":"Describing chemical reactions in solution on a molecular level is a challenging task due to the high mobility of weakly interacting solvent molecules which requires configurational sampling. For instance, polar and protic solvents can interact strongly with solutes and may interfere in reactions. To define and identify representative arrangements of solvent molecules modulating a transition state is a nontrivial task. Here, we propose to monitor their active participation in the decaying normal mode at a transition state, which defines active solvent molecules. Moreover, it is desirable to prepare a low-dimensional microsolvation model in a well-defined, fully automated, high-throughput, and easy-to-deploy fashion, which we propose to derive in a stepwise protocol. First, transition state structures are optimized in a sufficiently solvated quantum-classical hybrid model, which are subjected to a redefinition of a then reduced quantum region. From the reduced model, minimally microsolvated structures are extracted that contain only active solvent molecules. Modeling the remaining solvation effects is deferred to a continuum model. To establish an easy-to-use free-energy model, we combine the standard thermochemical gas-phase model with a correction for the cavity entropy in solution. We assess our microsolvation and free-energy models for methanediol formation from formaldehyde; for the hydration of carbon dioxide (which we consider in a solvent mixture to demonstrate the versatility of our approach); and, finally, for the chlorination of phenol with hypochlorous acid.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5571-5587"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160001/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144155239","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}

引用次数: 0

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10

Jakub Pawelko*, Eric Furet, Gwenael Duplaix-Rata, Nicolas Perrin and Xavier Rocquefelte*,

引用次数: 0

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-10

Sayantan Mondal, Saumyak Mukherjee and Biman Bagchi*,

引用次数: 0

Comparison of QM Methods for the Evaluation of Halogen-π Interactions for Large-Scale Data Generation. 大规模数据生成中评估卤素-π相互作用的QM方法比较。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-09 DOI: 10.1021/acs.jctc.5c00456

Marc U Engelhardt, Markus O Zimmermann, Finn Mier, Frank M Boeckler

{"title":"Comparison of QM Methods for the Evaluation of Halogen-π Interactions for Large-Scale Data Generation.","authors":"Marc U Engelhardt, Markus O Zimmermann, Finn Mier, Frank M Boeckler","doi":"10.1021/acs.jctc.5c00456","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00456","url":null,"abstract":"Halogen-π interactions play a pivotal role in molecular recognition processes, drug design, and therapeutic strategies, providing unique opportunities for enhancing and fine-tuning the binding affinity and specificity of pharmaceutical agents. The present study systematically benchmarks various combinations of quantum mechanical (QM) methods and basis sets to characterize halogen-π interactions in model systems. We evaluate both density functional theory (DFT) methods and wave function-based post-HF methods in terms of accuracy to reference calculations at the CCSD(T)/CBS level of theory and runtime efficiency. By balancing these crucial aspects, we aim to identify an optimal configuration suitable for high-throughput applications. Our results indicate that MP2 using the reasonably large TZVPP basis set is in excellent agreement with reference calculations, striking a balance between accuracy and computational efficiency. This allows us to generate large, reliable data sets, which will serve as a basis to develop and train machine-learning models capable of accurately capturing the strength of halogen-π interactions, thereby providing a robust data-driven foundation for medicinal chemistry analysis.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256710","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 Simulations of Periodic Materials Using Qubit-Encoded Wave Functions. 使用量子比特编码波函数的周期性材料的自适应变分量子模拟。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-09 DOI: 10.1021/acs.jctc.5c00412

Xiaopeng Li, Yi Fan, Jie Liu, Zhenyu Li, Jinlong Yang

{"title":"Adaptive Variational Quantum Simulations of Periodic Materials Using Qubit-Encoded Wave Functions.","authors":"Xiaopeng Li, Yi Fan, Jie Liu, Zhenyu Li, Jinlong Yang","doi":"10.1021/acs.jctc.5c00412","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00412","url":null,"abstract":"Materials design stands to be one of the most promising applications of quantum computing. However, the presence of noise in near-term quantum devices restricts quantum simulations of materials to shallow circuits. In this work, we present circuit-efficient variational quantum eigensolver (VQE) simulations of periodic materials using qubit-encoded wave functions based on Adaptive Derivative-Assembled Pseudo-Trotter (ADAPT) VQE. To iteratively construct accurate wave functions for periodic systems, we introduce operator pools comprising a complete set of anti-Hermitian one- and two-body qubit excitation/flipping operators. Numerical results demonstrate that these qubit-encoded algorithms can accurately predict the ground-state energy of periodic systems while significantly reducing circuit depth compared to Fermion-encoded algorithms. Additionally, we integrate the variance extrapolation technique with ADAPT-VQE algorithms to enhance the accuracy of ground-state energy estimations. This strategy further reduces the required circuit depth, enabling scalable and precise simulations of periodic systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256709","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

Pair-Density Functional Theory Based on the Spin-Projected Unrestricted Hartree-Fock Method. 基于自旋投影不受限制Hartree-Fock方法的对密度泛函理论。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-09 DOI: 10.1021/acs.jctc.5c00392

Shirong Wang, Xin Xu

引用次数: 0

High-Resolution Tuning of Non-Natural and Cyclic Peptide Folding Landscapes against NMR Measurements Using Markov Models and Bayesian Inference of Conformational Populations. 利用马尔可夫模型和构象种群的贝叶斯推断对核磁共振测量进行非自然和循环肽折叠景观的高分辨率调谐。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-09 DOI: 10.1021/acs.jctc.5c00489

Thi Dung Nguyen, Robert M Raddi, Vincent A Voelz

{"title":"High-Resolution Tuning of Non-Natural and Cyclic Peptide Folding Landscapes against NMR Measurements Using Markov Models and Bayesian Inference of Conformational Populations.","authors":"Thi Dung Nguyen, Robert M Raddi, Vincent A Voelz","doi":"10.1021/acs.jctc.5c00489","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00489","url":null,"abstract":"The rational design of stable and highly preorganized non-native and/or cyclic peptides is a challenging task that requires atomically detailed insight into folded and unfolded conformational ensembles. In this work, we demonstrate how Markov models constructed from collections of simulated trajectories using general-purpose force fields can be reweighted against NMR measurements to produce accurate folding landscapes. Here, we model the folding landscapes of 12 linear and cyclic peptide β hairpin mimics studied by the Erdelyi group, with the goal of reproducing the effects of subtle chemical modifications on peptide folding stability. The Bayesian Inference of Conformational Populations (BICePs) algorithm was first used to refine Karplus parameters to obtain an optimal forward model for scalar coupling constants; then, BICePs was used to reweight conformational ensembles against experimental NMR observables (NOE distances, chemical shifts, and 3JHNHα scalar couplings). Before reweighting, Markov models of the folding dynamics reasonably capture the key features of the folding landscape. Only after reweighting, however, do we obtain folding landscapes that agree with experimental trends. Compared to previous estimates of folded populations made using the NAMFIS algorithm, BICePs-reweighted landscapes predict that the introduction of a side chain hydrogen- or halogen-bonding group changes the folding stability by no more than 2 kJ mol-1. The overall agreement between simulated and experimental NMR observables suggests that our approach is highly robust, offering a reliable pathway for designing foldable non-natural and cyclic peptides.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144256711","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

Force-Field Optimization by End-to-End Differentiable Atomistic Simulation. 基于端到端可微原子模拟的力场优化。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-05 DOI: 10.1021/acs.jctc.4c01784

Abhijeet Sadashiv Gangan, Ekin Dogus Cubuk, Samuel S Schoenholz, Mathieu Bauchy, N M Anoop Krishnan

{"title":"Force-Field Optimization by End-to-End Differentiable Atomistic Simulation.","authors":"Abhijeet Sadashiv Gangan, Ekin Dogus Cubuk, Samuel S Schoenholz, Mathieu Bauchy, N M Anoop Krishnan","doi":"10.1021/acs.jctc.4c01784","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01784","url":null,"abstract":"The accuracy of atomistic simulations depends on the precision of the force fields. Traditional numerical methods often struggle to optimize the empirical force-field parameters for reproducing the target properties. Recent approaches rely on training these force fields based on forces and energies from first-principle simulations. However, it is unclear whether these approaches will enable the capture of complex material responses such as vibrational or elastic properties. To this extent, we introduce a framework employing inner loop simulations and outer loop optimization that exploits automatic differentiation for both property prediction and force-field optimization by computing gradients of the simulation analytically. We demonstrate the approach by optimizing classical potentials such as Stillinger-Weber and EDIP for silicon and BKS for SiO2 to reproduce properties like the elastic constants, vibrational density of states, and phonon dispersion. We also demonstrate how a machine-learned potential can be fine-tuned using automatic differentiation to reproduce any target property such as radial distribution functions. Interestingly, the resulting force field exhibits improved accuracy and generalizability to unseen temperatures compared to those fine-tuned on energies and forces. Finally, we demonstrate the extension of the approach to optimize the force fields toward multiple target properties. Altogether, differentiable simulations, through the analytical computation of their gradients, offer a powerful tool for both theoretical exploration and practical applications toward understanding physical systems and materials.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144232675","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

Solute Tempered Adiabatic Free Energy Dynamics for Enhancing Conformational Space Sampling. 增强构象空间采样的溶质回火绝热自由能动力学。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-05 DOI: 10.1021/acs.jctc.5c00717

Shitanshu Bajpai, Charlles R A Abreu, Nisanth N Nair, Mark E Tuckerman

{"title":"Solute Tempered Adiabatic Free Energy Dynamics for Enhancing Conformational Space Sampling.","authors":"Shitanshu Bajpai, Charlles R A Abreu, Nisanth N Nair, Mark E Tuckerman","doi":"10.1021/acs.jctc.5c00717","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00717","url":null,"abstract":"Collective variable (CV) and generalized ensemble-based enhanced sampling methods are widely used for accelerating barrier-crossing events and enhancing conformational sampling in molecular dynamics simulations. Temperature-accelerated molecular dynamics (TAMD)/driven-adiabatic free energy dynamics (d-AFED) uses extended variables thermostated at high temperature to achieve better exploration of conformational space. Replica exchange with solute tempering (REST2) achieves improved sampling by scaling the solute-solute and solute-solvent interaction energies of different replicas and swapping conformations between them. It has been observed that a combination of CV-based enhanced sampling and global tempering is needed to boost the conformational sampling of large biomolecular systems due to the presence of large entropic basins. In this work, we propose a method called \"Solute Tempered d-AFED\" or \"STed-AFED\" that combines both d-AFED/TAMD and REST2. We implemented this approach in the OpenMM-UFEDMM interface and demonstrated the efficiency of this method by studying the conformational landscapes of small peptides and proteins, in particular, chignolin, Trp-cage, and villin.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144232676","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

High-Dimensional Operator Learning for Molecular Density Functional Theory. 分子密度泛函理论的高维算子学习。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-06-05 DOI: 10.1021/acs.jctc.5c00484

Jinni Yang, Runtong Pan, Jikai Sun, Jianzhong Wu

引用次数: 0