Journal of Chemical Theory and Computation最新文献

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Periodic Implementation of the Random Phase Approximation with Numerical Atomic Orbitals and Dual Reciprocal Space Grids 随机相位逼近的数值原子轨道和对偶互易空间网格的周期性实现。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-18 DOI: 10.1021/acs.jctc.5c00751
Edoardo Spadetto*, , , Pier Herman Theodoor Philipsen*, , , Arno Förster*, , and , Lucas Visscher*, 
{"title":"Periodic Implementation of the Random Phase Approximation with Numerical Atomic Orbitals and Dual Reciprocal Space Grids","authors":"Edoardo Spadetto*,&nbsp;, ,&nbsp;Pier Herman Theodoor Philipsen*,&nbsp;, ,&nbsp;Arno Förster*,&nbsp;, and ,&nbsp;Lucas Visscher*,&nbsp;","doi":"10.1021/acs.jctc.5c00751","DOIUrl":"10.1021/acs.jctc.5c00751","url":null,"abstract":"<p >The random phase approximation (RPA) has emerged as a prominent first-principles method in material science, particularly to study the adsorption and chemisorption of small molecules on surfaces. However, its widespread application is hampered by its relatively high computational cost. Here, we present a well-parallelised implementation of the RPA with localized atomic orbitals and pair-atomic density fitting, which is especially suitable for studying two-dimensional systems. Through a dual <b><i>k</i></b>-grid scheme, we achieve fast and reliable convergence of RPA correlation energies to the thermodynamic limit. We demonstrate the efficacy of our implementation through an application to the adsorption of CO on MgO(001) using PBE input orbitals (RPA@PBE). Our calculated adsorption energy is in excellent agreement with previously published RPA@PBE studies, but, as expected, overestimates the experimentally available adsorption energies as well as recent CCSD(T) results.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9347–9363"},"PeriodicalIF":5.5,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00751","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145084518","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
Understanding DFT Uncertainties for More Reliable Reactivity Predictions by Advancing the Analysis of Error Sources 通过推进误差源分析来理解DFT不确定性,以获得更可靠的反应性预测。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-18 DOI: 10.1021/acs.jctc.5c00985
Gergely Laczkó, , , Imre Pápai*, , and , Péter R. Nagy*, 
{"title":"Understanding DFT Uncertainties for More Reliable Reactivity Predictions by Advancing the Analysis of Error Sources","authors":"Gergely Laczkó,&nbsp;, ,&nbsp;Imre Pápai*,&nbsp;, and ,&nbsp;Péter R. Nagy*,&nbsp;","doi":"10.1021/acs.jctc.5c00985","DOIUrl":"10.1021/acs.jctc.5c00985","url":null,"abstract":"<p >Decades of advancements and thousands of successful applications have contributed to the reliability of density functional theory (DFT) methods. Especially in main group chemistry, DFT predictions tend to be increasingly more reliable. In this study, we deeply analyze unexpected (ca. 8–13 kcal/mol) DFT disagreements obtained for a few organic reactions using only widely adopted, modern, hybrid, and higher-rung DFT methods. To understand the underlying causes, we move beyond conventional statistics-based benchmarks by combining recent advances in DFT error decomposition with affordable gold-standard references. This approach helps to characterize and disentangle multiple functional and density-based error types and enables us to find functional(s) suitable for broad mechanistic studies in all studied examples. The proposed tools are cost-efficient, readily accessible, and easy to integrate into routine thermochemistry workflows. While the focus is on main group reactions, the approach is also applicable to transition metal, bio-, and surface chemistry to assist more predictive reactivity modeling.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9483–9497"},"PeriodicalIF":5.5,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00985","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079070","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
Recursive Linear Tensor Expansion with Natural Occupation Analysis 递归线性张量展开式的自然占用分析。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c01101
Zeynep Gündoğar*, , , Mads Greisen Ho̷jlund*, , , Kasper Green Larsen*, , and , Ove Christiansen*, 
{"title":"Recursive Linear Tensor Expansion with Natural Occupation Analysis","authors":"Zeynep Gündoğar*,&nbsp;, ,&nbsp;Mads Greisen Ho̷jlund*,&nbsp;, ,&nbsp;Kasper Green Larsen*,&nbsp;, and ,&nbsp;Ove Christiansen*,&nbsp;","doi":"10.1021/acs.jctc.5c01101","DOIUrl":"10.1021/acs.jctc.5c01101","url":null,"abstract":"<p >We introduce an innovative recursive tensor decomposition method that draws inspiration from quantum chemical theories. This approach integrates ideas such as natural occupation numbers and natural basis, much like natural orbitals, and employs truncations that parallel the excitation-level truncations in the linear expansions of configuration interaction theory. The framework features recursive algorithms that combine linear expansion with natural basis transformations at each step, ensuring convergence to the original tensor. Consequently, a numerical technique is developed that reconstructs the initial tensor with precision within a predetermined tolerance, using only subtensors of limited dimension and a series of matrix transformations. An initial Python implementation has been created for the 3D tensor scenario where 3D tensors are decomposed to be represented using vectors and matrices alone. We illustrate the behavior of the final Recursive Linear Tensor Expansion in Natural basis algorithm in processing random data sets, experimental data sets from diverse sources with both real and complex tensors, and data sets representing both time-independent and time-dependent anharmonic vibrational wave functions of water. Finally, the systematic accuracy control is illustrated for density fitting two-electron repulsion integrals and tested for the second-order correlation energy of molecular nitrogen and benzene.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9270–9289"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071789","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 Generalized Solid Solution Framework for the Gibbs Free Energy Calculation 吉布斯自由能计算的广义固解框架。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c00524
Yang Huang,  and , Jingrun Chen*, 
{"title":"A Generalized Solid Solution Framework for the Gibbs Free Energy Calculation","authors":"Yang Huang,&nbsp; and ,&nbsp;Jingrun Chen*,&nbsp;","doi":"10.1021/acs.jctc.5c00524","DOIUrl":"10.1021/acs.jctc.5c00524","url":null,"abstract":"<p >We propose a generalized solid solution model for calculating configurational contribution to the Gibbs free energy at finite temperatures, incorporating a crystal graph-based on-site energy approach. By leveraging linear graph neural networks, our method unifies pair-based and cluster expansion approaches, enabling broad applicability across crystal structures. Fractional occupation is physically interpreted via mean-field theory, while entropy is modeled using ideal mixing with extended site constraints. To resolve the constants of compositions, we implement three key strategies. First, we employ a softmax-based variable transformation. Second, we introduce a gradient projection method that preserves species composition throughout the optimization process by constraining updates within a subspace that maintains the desired elemental ratios. Finally, a renormalization step is incorporated to correct numerical deviations, ensuring strict adherence to the target composition. We then apply our model to the Mo–Nb–Ta-W quaternary system, achieving an energy model MAE of 1.24 meV. Predicted phase transition temperatures for equal atomic binary alloys align well with expectations, identifying phase separation in MoNb and order–disorder transitions in MoTa, MoW, TaW, NbTa, and NbW. At low temperatures, stable configurations lie below the convex hull of the training data set, demonstrating the model’s predictive accuracy. Further analysis of MoNbTaW reveals transition temperatures at 950 and 400 K, with observed asymmetry in Mo/W sublattices. Finally, we extend our approach to ternary phase diagram predictions using Gibbs free energy interpolation and second-derivative analysis, yielding phase diagrams in agreement with optimized atomic configurations.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9982–9992"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071791","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
Introducing the Coupled-Cluster Theory to the Amorphous World of Liquids and Their Thermodynamic Simulations 将耦合团簇理论引入非晶液体世界及其热力学模拟。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c01214
Ctirad Červinka*, 
{"title":"Introducing the Coupled-Cluster Theory to the Amorphous World of Liquids and Their Thermodynamic Simulations","authors":"Ctirad Červinka*,&nbsp;","doi":"10.1021/acs.jctc.5c01214","DOIUrl":"10.1021/acs.jctc.5c01214","url":null,"abstract":"<p >Amorphous molecular materials are ubiquitous, spanning drugs, semiconductors, or solvents. Large predictive capabilities of quantum-chemical simulations of structural and thermodynamic properties and phase transitions for such amorphous materials have remained out of reach for a long time due to the related immense computational costs. This work introduces a novel fragment-based ab initio Monte Carlo (FrAMonC) simulation technique to the amorphous realm of molecular liquids and glasses. It aims at enabling thermodynamic simulations for amorphous molecular materials based on direct ab initio sampling and at minimizing the amount of a priori required empirical inputs for such simulations. Focus on individual cohesive interactions within the bulk, and their sampling from multiple first-principles potentials with a many-body expansion scheme enables the use of very accurate electron-structure methods for the most important cohesive features within the material. Even the coupled-cluster theory, the direct use of which is unprecedented for molecular simulations of thermodynamic properties for liquids, then becomes applicable to the description of bulk amorphous materials. Its incorporation in the proposed Monte Carlo simulations promises very high computational accuracy. Bulk-phase equilibrium properties at finite temperatures and pressures, such as density and vaporization enthalpy, as well as response properties such as thermal expansivity and heat capacity that are particularly challenging to predict accurately, are the observables targeted in this work. Superior computational accuracy of the introduced FrAMonC simulations is demonstrated for most target properties (liquid-phase densities, thermal expansivities, and gas–liquid differences in the heat capacities) when compared with established classical or quantum-chemical models that are commonly used to model such properties of bulk liquids.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9868–9878"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c01214","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145079155","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
Geometric Direct Minimization for Low-Spin Restricted Open-Shell Hartree–Fock Theory 低自旋受限开壳Hartree-Fock理论的几何直接极小化。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c00898
Hugh G. A. Burton*, 
{"title":"Geometric Direct Minimization for Low-Spin Restricted Open-Shell Hartree–Fock Theory","authors":"Hugh G. A. Burton*,&nbsp;","doi":"10.1021/acs.jctc.5c00898","DOIUrl":"10.1021/acs.jctc.5c00898","url":null,"abstract":"<p >It has recently been shown that configuration state functions (CSFs) with local orbitals can provide a compact reference state for low-spin open-shell electronic structures, such as antiferromagnetic states. However, optimizing a low-spin configuration using self-consistent field (SCF) theory has been a long-standing challenge since each orbital must be an eigenfunction of a different Fock operator. We introduce a low-spin restricted open-shell Hartree–Fock (ROHF) algorithm to optimize any CSF at mean-field cost. This algorithm employs quasi-Newton Riemannian optimization on the orbital constraint manifold to provide robust convergence, extending the geometric direct minimization approach to open-shell electronic structures with arbitrary genealogical spin coupling. Numerical calculations on transition metal aquo complexes show improved convergence over existing methodology, while the possibility of local CSF energy minima is demonstrated for iron–sulfur complexes. Finally, open-shell CSFs with different spin coupling patterns are used to qualitatively study the singlet ground state in polyacenes, revealing the onset of polyradical character as the chain length increases.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9444–9458"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00898","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074087","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
Individual and Cooperative Superexchange Enhancement in Cuprates 铜的个体与合作超级交换增强。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c00755
Tonghuan Jiang, , , Nikolay A. Bogdanov*, , , Ali Alavi*, , and , Ji Chen*, 
{"title":"Individual and Cooperative Superexchange Enhancement in Cuprates","authors":"Tonghuan Jiang,&nbsp;, ,&nbsp;Nikolay A. Bogdanov*,&nbsp;, ,&nbsp;Ali Alavi*,&nbsp;, and ,&nbsp;Ji Chen*,&nbsp;","doi":"10.1021/acs.jctc.5c00755","DOIUrl":"10.1021/acs.jctc.5c00755","url":null,"abstract":"<p >It is now widely accepted that the antiferromagnetic coupling within high-temperature superconductors strongly exhibits a profound correlation with the upper limit of the superconducting transition temperature these materials can reach. Thus, accurately calculating the positive and negative mechanisms that influence magnetic coupling in specific materials is crucial for the exploration of superconductivity at higher temperatures. Nevertheless, it is notoriously difficult to establish a complete description of electron correlations employing ab initio theories because of the large number of orbitals involved. In this study, we tackle the challenge of achieving high-level ab initio wave function theory calculations that allow an explicit treatment of electron correlations associated with a large number of high-energy orbitals. We elucidate the atomic-shell-wise contributions to the superexchange coupling in the lanthanum cuprate, including individual effects of high-energy orbitals (Cu 4d, 5d, 4f, 5p) and cooperative effects between the core and these high-energy orbitals. Specifically, the prominent contributions from Cu 4d, 5d, 4f, and 5p give rise to a rich collection of previously unexamined superexchange channels. We propose a <i>p</i>-<i>d</i>-<i>f</i> model to universally account for the contributions of high-energy orbitals at copper sites. Our calculations and physical rationalizations offer a more robust theoretical foundation for investigating cuprate-type high-temperature superconductors.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9364–9375"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074152","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
Leveraging Transformer Models to Capture Multi-Scale Dynamics in Biomolecules by Nano-GPT 利用纳米gpt的变压器模型来捕获生物分子中的多尺度动力学。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c00180
Wenqi Zeng, , , Lu Zhang, , and , Yuan Yao*, 
{"title":"Leveraging Transformer Models to Capture Multi-Scale Dynamics in Biomolecules by Nano-GPT","authors":"Wenqi Zeng,&nbsp;, ,&nbsp;Lu Zhang,&nbsp;, and ,&nbsp;Yuan Yao*,&nbsp;","doi":"10.1021/acs.jctc.5c00180","DOIUrl":"10.1021/acs.jctc.5c00180","url":null,"abstract":"<p >Long-term biomolecular dynamics is critical for understanding key evolutionary transformations in molecular systems. However, capturing these processes requires extended simulation timescales that often exceed the practical limits of conventional models. To address this, shorter simulations, initialized with diverse perturbations, are commonly used to sample the phase space and explore a wide range of behaviors. Recent advances have leveraged language models to infer long-term behavior from short trajectories, but methods such as long short-term memory (LSTM) networks are constrained to low-dimensional reaction coordinates, limiting their applicability to complex systems. In this work, we present nano-GPT, a novel deep learning model inspired by the GPT architecture specifically designed to capture long-term dynamics in molecular systems with fine-grained conformational states and complex transitions. The model employs a two-pass training mechanism that incrementally replaces molecular dynamics (MD) tokens with model-generated predictions, effectively mitigating the accumulation errors inherent in the training window. We validate nano-GPT on three distinct systems: a four-state model potential, the alanine dipeptide, a well-studied simple molecule, and the Fip35 WW domain, a complex biomolecular system. Our results show that nano-GPT effectively captures long-time scale dynamics by learning high-order dependencies through an attention mechanism, offering a novel perspective for interpreting biomolecular processes.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9239–9248"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00180","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074090","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
Expressivity of Determinantal Ansatzes for Neural Network Wave Functions 神经网络波函数的行列式分析的表达性。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c01243
Ni Zhan, , , William A. Wheeler, , , Gil Goldshlager, , , Elif Ertekin, , , Ryan P. Adams, , and , Lucas K. Wagner*, 
{"title":"Expressivity of Determinantal Ansatzes for Neural Network Wave Functions","authors":"Ni Zhan,&nbsp;, ,&nbsp;William A. Wheeler,&nbsp;, ,&nbsp;Gil Goldshlager,&nbsp;, ,&nbsp;Elif Ertekin,&nbsp;, ,&nbsp;Ryan P. Adams,&nbsp;, and ,&nbsp;Lucas K. Wagner*,&nbsp;","doi":"10.1021/acs.jctc.5c01243","DOIUrl":"10.1021/acs.jctc.5c01243","url":null,"abstract":"<p >Neural network wave functions have shown promise as a way to achieve high accuracy in solving the many-body quantum problem. These wave functions most commonly use a determinant or a sum of determinants to antisymmetrize many-body orbitals, which are described by a neural network. In many cases, the wave function is projected onto a fixed-spin state. Such a treatment is allowed for spin-independent operators; however, it cannot be applied to spin-dependent problems, such as Hamiltonians containing spin–orbit interactions. We show that for spin-independent Hamiltonians, a strict upper bound property is obeyed between a traditional Hartree–Fock-like determinant, full spinor wave function, the full determinant wave function, and a generalized spinor wave function. The relationship between a spinor wave function and the full determinant arises because the full determinant wave function is the spinor wave function projected onto a fixed-spin, after which antisymmetry is implicitly restored in the spin-independent case. For spin-dependent Hamiltonians, the full determinant wave function is not applicable, because it is not antisymmetric. Numerical experiments on the H<sub>3</sub> molecule and two-dimensional homogeneous electron gas confirm these bounds.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9612–9619"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145074177","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
Navigating the Unknown: Discovering Minimum Free Energy Pathways without Predefined End States 导航未知:发现最小自由能路径没有预定义的结束状态。
IF 5.5 1区 化学
Journal of Chemical Theory and Computation Pub Date : 2025-09-17 DOI: 10.1021/acs.jctc.5c00946
Zhicheng Zhong,  and , Qian Wang*, 
{"title":"Navigating the Unknown: Discovering Minimum Free Energy Pathways without Predefined End States","authors":"Zhicheng Zhong,&nbsp; and ,&nbsp;Qian Wang*,&nbsp;","doi":"10.1021/acs.jctc.5c00946","DOIUrl":"10.1021/acs.jctc.5c00946","url":null,"abstract":"<p >Determining minimum free energy pathways (MFEPs) for protein conformational changes is essential for molecular-level mechanistic understanding. While many robust path-search algorithms have existed, most require end point conformations derived from experimental structures, creating a dependency on structural biology data that restricts their general applicability. To overcome this limitation, we present a new path-search algorithm based on local sampling. The process can initiate from any single state, while the search direction is automatically optimized without the information on other states. We demonstrate the effectiveness of this algorithm in several model systems by comparing with experimental data and conventional molecular dynamics simulations. This approach expands the methodological toolkit for investigating functional conformational transitions, particularly when experimental end point structures are unavailable.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 19","pages":"9943–9954"},"PeriodicalIF":5.5,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071790","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
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