Journal of Chemical Theory and Computation最新文献_第2页

Assessment of RNA Force Fields for Dynamic Docking of Small Molecules Using Multicanonical MD Simulations. 基于多模态动力学模拟的小分子动态对接RNA力场评估。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-21 DOI: 10.1021/acs.jctc.5c01114

Gert-Jan Bekker,Yoshifumi Fukunishi,Junichi Higo,Narutoshi Kamiya

{"title":"Assessment of RNA Force Fields for Dynamic Docking of Small Molecules Using Multicanonical MD Simulations.","authors":"Gert-Jan Bekker,Yoshifumi Fukunishi,Junichi Higo,Narutoshi Kamiya","doi":"10.1021/acs.jctc.5c01114","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01114","url":null,"abstract":"Molecular dynamics (MD) simulations are increasingly important for analyzing RNA-ligand interactions, particularly in the context of therapeutic development. However, the accuracy of RNA force fields remains insufficiently assessed, partly due to the limited sampling efficiency of MD approaches and the lack of reliable docking protocols. To evaluate the performance of modern AMBER-based RNA force fields, we selected four small RNA-ligand complexes from the Protein Data Bank (PDB) and executed dynamic docking simulations using one of the generalized ensemble methods, multicanonical MD, across five different force fields. We analyzed a total of 600 μs of simulation data, each reweighted to the canonical ensemble at physiological temperature. The resulting conformational ensembles varied across force fields for three of the four targets. Among the tested force fields, the parm99χOL3-vdWbb yielded the most accurate results based on our R-value analysis that measures the ligand-RNA native contacts, assuming the PDB structures represent the correct native conformations. However, further analysis revealed that some metastable, non-native RNA conformations had smaller intercalation sites with a closed binding pocket, resulting in shrinkage of the RNA molecules. These findings suggest that current RNA force fields may overstabilize non-native, closed conformations. The present simulations, methodology, analyses, and data offer valuable insights to guide the development of next-generation RNA force fields to better assess non-native RNA conformations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"18 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145338611","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

O1NumHess: A Fast and Accurate Seminumerical Hessian Algorithm Using Only O(1) Gradients. 一种仅使用O(1)个梯度的快速、准确的半数值Hessian算法。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-21 DOI: 10.1021/acs.jctc.5c01354

Bo Wang, Shaohang Luo, Zikuan Wang, Wenjian Liu

{"title":"O1NumHess: A Fast and Accurate Seminumerical Hessian Algorithm Using Only O(1) Gradients.","authors":"Bo Wang, Shaohang Luo, Zikuan Wang, Wenjian Liu","doi":"10.1021/acs.jctc.5c01354","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01354","url":null,"abstract":"In this work, we describe a new algorithm, O1NumHess, to calculate the Hessian of a molecular system by finite differentiation of gradients calculated at O(1) displaced geometries, instead of O(Natom) displaced geometries (where Natom is the number of atoms) as in the conventional seminumerical Hessian algorithm. Key to the reduction of the number of gradients is the off-diagonal low-rank (ODLR) property of Hessians, namely the blocks of the Hessian that correspond to two distant groups of atoms having low rank. This property reduces the number of independent entries of the Hessian from O(Natom2) to O(Natom), such that O(1) gradients already contain enough information to uniquely determine the Hessian. Numerical results on model systems (long alkanes and polyenes), transition metal reactions (the WCCR10 set), and noncovalent complexes (the S30L-CI set) using the BDF program show that O1NumHess gives frequency, zero-point energy, enthalpy, and Gibbs free energy errors that are only about two times those of conventional double-sided seminumerical Hessians. Moreover, O1NumHess is always faster than the conventional numerical Hessian algorithm, frequently even faster than the analytic Hessian, and requires only about 100 gradients for sufficiently large systems. An open-source implementation of this method, which can also be applied to problems irrelevant to computational chemistry, is available on GitHub.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145342107","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

Correction to "Machine Learning Potential Analysis of Structural Transition in Cu and Ag Nanoparticles: From Icosahedral to Face-Centered Cubic". 修正“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 : 2025-10-20 DOI: 10.1021/acs.jctc.5c01651

Yongpeng Yang, Jingli Han, Francesc Viñes, Francesc Illas

引用次数: 0

FreeBird.jl: An Extensible Toolbox for Simulating Interfacial Phase Equilibria. 成为一只自由自在的飞鸟。模拟界面相平衡的可扩展工具箱。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-20 DOI: 10.1021/acs.jctc.5c01348

Ray Yang, Junchi Chen, Douglas Thibodeaux, Robert B Wexler

引用次数: 0

Force Field-Driven Backmapping for Multiscale Molecular Dynamics. 多尺度分子动力学的力场驱动反向映射。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-20 DOI: 10.1021/acs.jctc.5c00677

Xu Guo,Andrew Abi-Mansour,Peter Ortoleva

引用次数: 0

Modeling the Evolution of Laser-Induced Electronic Coherences with Trajectory Surface Hopping. 基于轨迹表面跳变的激光诱导电子相干演化建模。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-20 DOI: 10.1021/acs.jctc.5c00531

Gilbert Grell,Jesús González-Vázquez,Francisco Fernández-Villoria,Alicia Palacios,Fernando Martín

{"title":"Modeling the Evolution of Laser-Induced Electronic Coherences with Trajectory Surface Hopping.","authors":"Gilbert Grell,Jesús González-Vázquez,Francisco Fernández-Villoria,Alicia Palacios,Fernando Martín","doi":"10.1021/acs.jctc.5c00531","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00531","url":null,"abstract":"Current attosecond XUV/X-ray pulses and few-fs UV pulses, with bandwidths up to several eV, can excite molecules in a coherent superposition of electronic states. Theoretical modeling of the ensuing dynamics requires accounting for the coupled motion of electrons and nuclei to capture the subtle interplay between the initial electronic coherence, decoherence induced by nuclear motion, and additional coherences that may emerge at conical intersections. In this work, we introduce Trajectory Surface Hopping with Projected Forces and Momenta (TSH-PFM), which accounts for these effects in a numerically inexpensive way and, therefore, is particularly suited to describe molecular dynamics arising from an initial coherent superposition of electronic states. We demonstrate its performance by comparing with previously reported quantum mechanical results for the BMA[5,5], para-xylene, and fulvene molecules by working in full dimensionality. Application of the TSH-PFM method to the glycine molecule shows that the initial electronic coherences can have a dramatic impact in the charge distribution over the molecule at the very early stages of the dynamics.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"98 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145331829","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

FC2DES+HT: Including Herzberg-Teller Effects in the Simulation of 2D Electronic Spectra for Harmonic Hamiltonians. FC2DES+HT：含Herzberg-Teller效应的二维谐波哈密顿谱模拟。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-20 DOI: 10.1021/acs.jctc.5c01363

Lucas Allan, Tim J Zuehlsdorff

{"title":"FC2DES+HT: Including Herzberg-Teller Effects in the Simulation of 2D Electronic Spectra for Harmonic Hamiltonians.","authors":"Lucas Allan, Tim J Zuehlsdorff","doi":"10.1021/acs.jctc.5c01363","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c01363","url":null,"abstract":"Two-dimensional electronic spectroscopy (2DES) is a powerful experimental technique, as it directly probes the nonlinear (third-order) response function of the system, providing key insights into ultrafast energy transfer and relaxation processes. However, 2DES experiments are generally difficult to interpret, often relying on simulations in order to associate observed spectral features with specific underlying system dynamics. For this reason, the development of robust, computationally inexpensive theoretical methods for modeling these experiments remains an active area of research. We have recently derived such an approach for computing the exact finite-temperature nonlinear response function for harmonic Hamiltonians within the Condon approximation, assuming that the transition dipole moment is independent of nuclear coordinates. In this work, we extend our formalism to exactly account for non-Condon/Herzberg-Teller (HT) type contributions to the nonlinear response function, which are known to be crucial for accurately describing linear optical spectra in a wide range of molecular systems. We highlight the key insights that can be gained from our new method, named FC2DES+HT, by simulating the 2DES signals of two molecules with known non-Condon behavior, the phenolate anion and free-base porphyrin. The results demonstrate that Herzberg-Teller couplings substantially impact energy relaxation dynamics in these systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145336030","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

A Deep Learning-Based Framework for Valence Bond Structure Selection and Weight Prediction. 基于深度学习的价键结构选择和权重预测框架。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-20 DOI: 10.1021/acs.jctc.5c01220

Tao Xia,Tingzhen Chen,Wei Wu,Chen Zhou

引用次数: 0

Nonparametric Determination of the Committor in Multimolecular Systems. 多分子系统中提交者的非参数确定。

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-19 DOI: 10.1021/acs.jctc.5c01427

Lair F Trugilho,Stefan Auer,Leandro G Rizzi,Sergei V Krivov

引用次数: 0

A Binding Site Competition Model for Relative Sliding of Antiparallel Microtubules Mediated by Kinesin-4 Motors and PRC1 Proteins. 由Kinesin-4马达和PRC1蛋白介导的反平行微管相对滑动的结合位点竞争模型

IF 5.5 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-10-19 DOI: 10.1021/acs.jctc.5c00902

Yao Wang,Jie Wang,Yu-Ru Liu,Hui Li,Ping Xie

{"title":"A Binding Site Competition Model for Relative Sliding of Antiparallel Microtubules Mediated by Kinesin-4 Motors and PRC1 Proteins.","authors":"Yao Wang,Jie Wang,Yu-Ru Liu,Hui Li,Ping Xie","doi":"10.1021/acs.jctc.5c00902","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00902","url":null,"abstract":"The dynamic behaviors of the mitotic spindle composed of antiparallel microtubules (MTs) are critical for the successful completion of cell division. Motor proteins kinesin-4 and MT cross-linking proteins PRC1 can cooperatively regulate the length of antiparallel MT overlaps. However, the physical mechanism of relative sliding of the two MTs by the two types of proteins to regulate the overlap length is unclear. Here, using both the theoretical analysis and numerical simulation, we first study the clusters at MT plus ends formed by kinesin-4s alone and those formed by kinesin-4s and PRC1s, where a kinesin-4 and a PRC1 can form an unstable complex. The forward movement of the complex is proposed to be realized via a \"binding site competition\" mechanism; namely, the competition of the site bound by the kinesin-4 head with the PRC1 head makes the complex move forward. Furthermore, we study MT sliding mediated by the kinesin-4s and PRC1s. The theoretical/numerical results reproduce quantitatively the published experimental results and, in particular, the puzzling results showing that the initial MT sliding velocity increases with the initial MT overlap length. The study indicates that the MT sliding by the kinesin-4s and PRC1s occurs via the \"binding site competition\" mechanism, which is different from the well-known \"force-driving\" mechanism by kinesin-5 motors, where the forces generated by the kinesin-5s drive the MT sliding.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"56 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145319295","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