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

Further Refinement and Validation of the Drude Polarizable Force Field for Carboxylate and N-Acetyl amine Hexopyranose Derivatives 羧酸盐和n -乙酰胺己基糖衍生物德鲁德极化力场的进一步改进和验证。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-19 DOI: 10.1021/acs.jctc.5c00369

Chythra J. N., Takumi Yamaguchi and Sairam S. Mallajosyula*,

{"title":"Further Refinement and Validation of the Drude Polarizable Force Field for Carboxylate and N-Acetyl amine Hexopyranose Derivatives","authors":"Chythra J. N., Takumi Yamaguchi and Sairam S. Mallajosyula*, ","doi":"10.1021/acs.jctc.5c00369","DOIUrl":"10.1021/acs.jctc.5c00369","url":null,"abstract":"In this study, we present an improved parameter set for the Drude polarizable force field optimized to accurately capture the ring dynamics of four types of carboxylate- and N-acetyl amine-substituted aldohexoses and their anomers: α/β-d-glucuronate (AGLCA/BGLCA), α/β-l-iduronate (AIDOA/BIDOA), N-acetyl-α/β-d-galactosamine (AGALNA/BGALNA), and N-acetyl-α/β-d-glucosamine (AGLCNA/BGLCNA). This refinement builds on recent advances in the Drude polarizable force field, which previously demonstrated improved ring dynamics for unsubstituted monosaccharides. The new parameter set addresses discrepancies between calculated and experimental NMR 3J coupling constants, particularly in the description of ring and exocyclic torsional dynamics for hexopyranose derivatives. To evaluate its performance, we simulate multimicrosecond trajectories and compare the refined Drude parameter set with the CHARMM36 additive and GLYCAM06 additive force fields. Additionally, we used extended system adaptive biasing force (eABF) simulations to assess the conformational sampling efficiency of the different force fields. Our results show that polarization significantly enhances the sampling of ring conformations, resulting in better agreement with the ring based experimental NMR 3J coupling constants. Overall, the refined Drude polarizable force field, alongside the full set of Drude parameters, offers an improved tool for studying the conformational dynamics of carbohydrates and their conjugates in biomolecular systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 17","pages":"8533–8556"},"PeriodicalIF":5.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870269","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

Machine Learning Potential Analysis of Structural Transition in Cu and Ag Nanoparticles: From Icosahedral to Face-Centered Cubic Cu和Ag纳米颗粒结构转变的机器学习潜力分析：从二十面体到面心立方。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-19 DOI: 10.1021/acs.jctc.5c00791

Yongpeng Yang*, Jingli Han, Francesc Viñes and Francesc Illas*,

引用次数: 0

Systematic Embedding of All-Atom Reactive Molecular Dynamics into a Coarse-Grained Environment 全原子反应分子动力学在粗粒度环境中的系统嵌入。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-19 DOI: 10.1021/acs.jctc.5c00930

Kuntal Ghosh, Da Teng and Gregory A. Voth*,

{"title":"Systematic Embedding of All-Atom Reactive Molecular Dynamics into a Coarse-Grained Environment","authors":"Kuntal Ghosh, Da Teng and Gregory A. Voth*, ","doi":"10.1021/acs.jctc.5c00930","DOIUrl":"10.1021/acs.jctc.5c00930","url":null,"abstract":"Quantum mechanics/molecular mechanics (QM/MM) simulations are widely used for modeling chemical reactivity in complex environments. In the QM/MM method, the reactive center under study is typically treated using explicit quantum chemical calculations, while the nonreactive environment is treated using classical molecular mechanics. However, for large systems, even with the use of classical force fields for the MM part, QM/MM simulations are very computationally costly, particularly for systems with complex MM dynamics. In this work, we propose a much faster alternative method for studying reactivity denoted by multiscale reactive molecular dynamics/coarse-grained molecular mechanics (MS-RMD/CG-MM). MS-RMD has been shown to be a powerful method for modeling reactions involving proton transport and in principle other reactions. This all-atom reactive MD model, systematically parametrized from constrained DFT calculations, is embedded in a CG environment in this work, where the CG force fields are derived using the multiscale coarse-graining (MS-CG) method. We apply this scheme to organic SN2 reactions in a CG polar solvent (acetone) as examples.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 17","pages":"8456–8467"},"PeriodicalIF":5.5,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144881684","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

Light-Matter Entanglement in Real-Time Nuclear–Electronic Orbital Polariton Dynamics 实时核-电子轨道极化动力学中的光-物质纠缠。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-18 DOI: 10.1021/acs.jctc.5c00911

Millan F. Welman, Tao E. Li and Sharon Hammes-Schiffer*,

{"title":"Light-Matter Entanglement in Real-Time Nuclear–Electronic Orbital Polariton Dynamics","authors":"Millan F. Welman, Tao E. Li and Sharon Hammes-Schiffer*, ","doi":"10.1021/acs.jctc.5c00911","DOIUrl":"10.1021/acs.jctc.5c00911","url":null,"abstract":"Molecular polaritons are hybrid light-matter states that enable the exploration of potential cavity-modified chemistry. The development of dynamical, first-principles approaches for simulating molecular polaritons is important for understanding their origins and properties. Herein, we present a hierarchy of first-principles methods to simulate the real-time dynamics of molecular polaritons in the strong coupling regime. These methods are based on real-time time-dependent density functional theory (RT-TDDFT) and the corresponding real-time nuclear–electronic orbital (RT-NEO) approach, in which specified nuclei are treated quantum mechanically on the same level as the electrons. The hierarchy spans semiclassical, mean-field quantum, and full-quantum approaches to simulate polariton dynamics under both electronic strong coupling and vibrational strong coupling. In the semiclassical approaches, the cavity mode is treated classically, whereas in the full-quantum approaches, the cavity mode is treated quantum mechanically with propagation of a joint molecule-mode density matrix. The semiclassical and full-quantum approaches produce virtually identical Rabi splittings and polariton peak locations for the systems studied. However, the full-quantum approaches allow exploration of molecule-mode quantum entanglement in real-time dynamics. Although the degree of light-matter entanglement is relatively small in the systems considered, the oscillations of the von Neumann entropy reveal an entanglement Rabi splitting that differs from the Rabi splitting computed from the time-dependent dipole moment. These results suggest that a classical treatment of the cavity mode may provide an excellent description of polariton dynamics for macroscopic observables such as the Rabi splitting, but novel physics may be detectable by considering molecule-mode entanglement.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 17","pages":"8291–8307"},"PeriodicalIF":5.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870270","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

Surface Tension of Infinitely Planar Surfaces from Nucleation Free Energies: A Comparison of Monte Carlo Calculations and Classical Theories 从成核自由能看无限平面的表面张力：蒙特卡罗计算与经典理论的比较。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-18 DOI: 10.1021/acs.jctc.5c01122

Bin Chen*, and , Ngoc My Nhi Nguyen,

{"title":"Surface Tension of Infinitely Planar Surfaces from Nucleation Free Energies: A Comparison of Monte Carlo Calculations and Classical Theories","authors":"Bin Chen*,  and , Ngoc My Nhi Nguyen, ","doi":"10.1021/acs.jctc.5c01122","DOIUrl":"10.1021/acs.jctc.5c01122","url":null,"abstract":"A new approach for calculating the surface tension of an infinitely planar surface is presented, based on the thermodynamic relationship between clusters of different sizes. This method utilizes the aggregation-volume-bias Monte Carlo technique to compute the nucleation free energies of clusters of varying sizes. These free energy data are then compared with the predictions of conventional theories, such as classical nucleation theory and the Tolman equation, revealing that these theories accurately capture the size-dependency of the free energy for sufficiently large clusters. Key results from this analysis include the surface tension of an infinitely large cluster, corresponding to an infinitely planar surface, the Tolman length, and the chemical potential of the phases in equilibrium. The method is applied to two systems─Lennard–Jones and TIP4P/2005 water─and the calculated surface tension values for the infinitely large system (γ∞) show excellent agreement with results from other established approaches.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 16","pages":"8051–8059"},"PeriodicalIF":5.5,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870273","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

Machine Learning Model for Efficient Nonthermal Tuning of the Charge Density Wave in Monolayer NbSe2 单层NbSe2中电荷密度波有效非热调谐的机器学习模型。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-17 DOI: 10.1021/acs.jctc.5c00959

Luka Benić, Federico Grasselli, Chiheb Ben Mahmoud, Dino Novko* and Ivor Lončarić*,

{"title":"Machine Learning Model for Efficient Nonthermal Tuning of the Charge Density Wave in Monolayer NbSe2","authors":"Luka Benić, Federico Grasselli, Chiheb Ben Mahmoud, Dino Novko* and Ivor Lončarić*, ","doi":"10.1021/acs.jctc.5c00959","DOIUrl":"10.1021/acs.jctc.5c00959","url":null,"abstract":"Understanding and controlling the charge density wave (CDW) phase diagram of transition-metal dichalcogenides are long-studied problems in condensed matter physics. However, due to the complex involvement of electron and lattice degrees of freedom and pronounced anharmonicity, theoretical simulations of the CDW phase diagram at the density-functional-theory level are often numerically demanding. To reduce the computational cost of first-principles modeling by orders of magnitude, we have developed an electronic free-energy machine learning model for monolayer NbSe2 that allows us to control the electronic temperature as a parameter of the model. The ionic temperature is modeled via the stochastic self-consistent harmonic approximation. Our approach relies on a machine learning model of the electronic density of states and zero-temperature interatomic potential. This allows us to explore the CDW phase diagram of monolayer NbSe2 both under thermal and laser-induced nonthermal conditions. Our study provides an accurate estimate of the CDW transition temperature at low cost and can disentangle the role of hot electrons and phonons in the nonthermal ultrafast melting process of the CDW phase in NbSe2.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 16","pages":"8130–8141"},"PeriodicalIF":5.5,"publicationDate":"2025-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144870271","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 Switching and Potential Shifting Lead to Significant Cutoff Dependence in Alchemical Free Energies 力的转换和势的移动导致炼金术自由能的显著的切断依赖。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-16 DOI: 10.1021/acs.jctc.5c00646

Lindsey M. Whitmore, Yalda Ramezani, Sumit Sharma and Michael R. Shirts*,

引用次数: 0

Massively Parallel Free Energy Calculations for In Silico Affinity Maturation of Designed Miniproteins 设计的微型蛋白亲和成熟的大规模并行自由能计算。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-16 DOI: 10.1021/acs.jctc.5c00703

Dylan Novack, Si Zhang and Vincent A. Voelz*,

{"title":"Massively Parallel Free Energy Calculations for In Silico Affinity Maturation of Designed Miniproteins","authors":"Dylan Novack, Si Zhang and Vincent A. Voelz*, ","doi":"10.1021/acs.jctc.5c00703","DOIUrl":"10.1021/acs.jctc.5c00703","url":null,"abstract":"Computational protein design efforts continue to make remarkable advances, yet the discovery of high-affinity binders typically requires large-scale experimental screening of site-saturated mutant (SSM) libraries. Here, we explore how massively parallel free energy methods can be used for in silico affinity maturation of de novo designed binding proteins. Using an expanded ensemble (EE) approach, we perform exhaustive relative binding free energy calculations for SSM variants of three miniproteins designed to bind influenza A H1 hemagglutinin by Chevalier et al. [<contrib-group>Chevalier, A.</contrib-group>; <contrib-group>Silva, D. A.</contrib-group>; <contrib-group>Rocklin, G. J.</contrib-group>; <cite>Nature</cite> 2017, 550, 74–79]. We compare our predictions to experimental ΔΔG values inferred from a Bayesian analysis of the high-throughput sequencing data, and to state-of-the-art predictions made using the Flex ddG Rosetta protocol. A systematic comparison reveals prediction accuracies around 2 kcal/mol, and identifies net charge changes, large numbers of alchemical atoms, and slow side chain conformational dynamics as key contributors to the uncertainty of the EE predictions. Flex ddG predictions are more accurate on average, but highly conservative. In contrast, EE predictions can better classify stabilizing and destabilizing mutations. We also explored the ability of SSM scans to rationalize known affinity-matured variants containing multiple mutations, which are nonadditive due to epistatic effects. Simple electrostatic models fail to explain nonadditivity, but observed mutations are found at positions with higher Shannon entropies. Overall, this work suggests that simulation-based free energy methods can provide predictive information for in silico affinity maturation of designed miniproteins, with many feasible improvements to the efficiency and accuracy within reach.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 16","pages":"8034–8050"},"PeriodicalIF":5.5,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144858681","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

Development of an Exciton Model of Light-Harvesting Antenna LH2 Considering Charge Transfer States and Their Fluctuations 考虑电荷转移态及其波动的光收集天线LH2激子模型的建立。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-16 DOI: 10.1021/acs.jctc.5c00697

Shunsuke Yabu, Hirofumi Sato and Masahiro Higashi*,

{"title":"Development of an Exciton Model of Light-Harvesting Antenna LH2 Considering Charge Transfer States and Their Fluctuations","authors":"Shunsuke Yabu, Hirofumi Sato and Masahiro Higashi*, ","doi":"10.1021/acs.jctc.5c00697","DOIUrl":"10.1021/acs.jctc.5c00697","url":null,"abstract":"The light-harvesting complex 2 (LH2) of the purple bacteria absorbs sunlight and transfers energy to the RC with high efficiency. To achieve a microscopic understanding of the energy transfer process, theoretical analysis of the excited states of the bacteriochlorophyll a pigment aggregates is effective. In particular, not only the locally excited (LE) states of pigments but also the charge transfer (CT) states between pigments play a significant role in the excited states of the B850 ring, where the pigments are in close proximity to each other. We developed a new method to incorporate the fluctuations of such CT states into the exciton model of LH2, based on quantum chemical calculations and molecular dynamics (MD) simulations, with the aid of a machine learning model. The excitation energies to LE and CT states and the electronic couplings between these states were calculated from the MD trajectory with a low computational cost to obtain a time-dependent exciton Hamiltonian. The calculated absorption spectra of LH2 using the exciton Hamiltonian revealed that fluctuations of the CT states play an important role in the broadening of the B850 absorption band.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 16","pages":"8199–8212"},"PeriodicalIF":5.5,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144857811","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

Analytical Switching Algorithms for Global Trajectory Surface Hopping Molecular Dynamics Simulation 全局轨迹表面跳跃分子动力学模拟的解析切换算法。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-08-16 DOI: 10.1021/acs.jctc.5c00884

Chaoyuan Zhu*,

{"title":"Analytical Switching Algorithms for Global Trajectory Surface Hopping Molecular Dynamics Simulation","authors":"Chaoyuan Zhu*, ","doi":"10.1021/acs.jctc.5c00884","DOIUrl":"10.1021/acs.jctc.5c00884","url":null,"abstract":"The on-the-fly trajectory surface hopping molecular dynamics in which nuclear motions are based on the classical trajectory is a suitable method for simulating nonadiabatic dynamics in large and complex photochemical systems. However, the nonadiabatic switching probability that comes from a pure quantum effect must be formulated from quantum mechanics. The Landau–Zener and Zhu–Nakamura switching probabilities are analytically solved under a mixed quantum/classical method with T̂N = 0 and a semiclassical method with T̂N ≠ 0 (where T̂N is a quantum nuclear kinetic operator), respectively. Both switching probabilities are actually exact solutions under its T̂N assumption for the same two-state linear curve crossing model. Moreover, the global switching and fewest switching algorithms are extensively compared by on-the-fly trajectory surface hopping molecular dynamics simulation for cis-to-trans and trans-to-cis azobenzene photoisomerization. Both algorithms agree pretty well for quantum yields, lifetimes, hopping spot distributions, and population decay distributions.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 16","pages":"7729–7742"},"PeriodicalIF":5.5,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144857813","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