Journal of Chemical Theory and Computation最新文献_第4页

Relevant, Hidden, and Frustrated Information in High-Dimensional Analyses of Complex Dynamical Systems with Internal Noise. 具有内噪声的复杂动力系统高维分析中的相关、隐藏和受挫信息。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-02 DOI: 10.1021/acs.jctc.5c00374

Chiara Lionello, Matteo Becchi, Simone Martino, Giovanni M Pavan

{"title":"Relevant, Hidden, and Frustrated Information in High-Dimensional Analyses of Complex Dynamical Systems with Internal Noise.","authors":"Chiara Lionello, Matteo Becchi, Simone Martino, Giovanni M Pavan","doi":"10.1021/acs.jctc.5c00374","DOIUrl":"10.1021/acs.jctc.5c00374","url":null,"abstract":"Extracting from trajectory data meaningful information to understand complex molecular systems might be nontrivial. High-dimensional analyses are typically assumed to be desirable, if not required, to prevent losing important information. But to what extent such high-dimensionality is really needed/beneficial often remains unclear. Here we challenge such a fundamental general problem. As a representative case of a system with internal dynamical complexity, we study atomistic molecular dynamics trajectories of liquid water and ice coexisting in dynamical equilibrium at the solid/liquid transition temperature. To attain an intrinsically high-dimensional analysis, we use as an example an abstract high-dimensional descriptor of local molecular environments (e.g., Smooth Overlap of Atomic Positions, SOAP), obtaining a large dataset containing 2.56 × 106 576-dimensional SOAP spectra that we analyze in various ways. Our results demonstrate how the time-series data contained in one single SOAP dimension accounting only <0.001% of the total dataset's variance (neglected and discarded in typical variance-based dimensionality reduction approaches) allows resolving a remarkable amount of information, classifying/discriminating the bulk of water and ice phases, as well as two solid-interface and liquid-interface layers as four statistically distinct dynamical molecular environments. Adding more dimensions to this one is found not only ineffective but even detrimental to the analysis due to recurrent negligible-information/non-negligible-noise additions and \"frustrated information\" phenomena leading to information loss. Such effects are proven general and are observed also in completely different systems and descriptors' combinations. This shows how high-dimensional analyses are not necessarily better than low-dimensional ones to elucidate the internal complexity of physical/chemical systems, especially when these are characterized by non-negligible internal noise.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6683-6697"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551442","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

Accurate Yet Affordable: An Integrated Tool for the Simulation of Criegee Intermediates via Pisa Composite Schemes and Localized Corrections. 准确而又负担得起：通过Pisa复合方案和局部校正模拟Criegee中间体的集成工具。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-03 DOI: 10.1021/acs.jctc.5c00797

Luigi Crisci, Federico Lazzari, Vincenzo Barone

{"title":"Accurate Yet Affordable: An Integrated Tool for the Simulation of Criegee Intermediates via Pisa Composite Schemes and Localized Corrections.","authors":"Luigi Crisci, Federico Lazzari, Vincenzo Barone","doi":"10.1021/acs.jctc.5c00797","DOIUrl":"10.1021/acs.jctc.5c00797","url":null,"abstract":"Criegee intermediates (CIs) are pivotal reactive species in atmospheric chemistry, playing a central role in alkene ozonolysis and secondary organic aerosol formation. However, their transient nature and unconventional electronic structure pose a serious challenge to both experimental characterization and theoretical modeling. In this work, we present an integrated and cost-effective computational platform for the accurate simulation of the structure and rotational constants of CIs, based on the Pisa Composite Schemes (PCSs) and localized correction strategies. Geometry optimizations on composite (including multilayer) potential energy surfaces are enabled by a newly developed interface that combines the strengths of different quantum chemistry codes. Benchmarking against the semiexperimental equilibrium structure of formaldehyde oxide allows the derivation of transferable corrections that extend the spectroscopic accuracy to larger Criegee systems. We also introduce a two-layer ONIOM scheme in which a DFT description of the full molecule is refined by higher-level corrections localized on the carbonyl oxide moiety. This approach, validated on cyclohexanone oxide, recovers high-level accuracy at a fraction of the computational cost of full high-level optimizations. Overall, our method provides a robust and automated framework for the spectroscopic characterization of Criegee intermediates, thereby broadening the reach of computational spectroscopy in atmospheric chemistry.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"7188-7197"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144558463","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

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22

Jian Cao, Zian Chen, Haichao Li, Chang Liu, Yutong He, Hongbin Zhang, Lina Xu*, Hongping Xiao, Xiao He* and Guoyong Fang*,

引用次数: 0

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22

Mike Pauls, Jan Kubelka, Francesca Plückhahn and Christoph Bannwarth*,

引用次数: 0

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22

Guilherme M. Arantes*, and , Jan Řezáč,

引用次数: 0

Benchmarking Selected Density Functionals and Dispersion Corrections for MOF-5 and Its Derivatives. MOF-5及其衍生物的选定密度泛函和色散校正的基准测试。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-13 DOI: 10.1021/acs.jctc.5c00399

Joshua Edzards, Julia Santana-Andreo, Holger-Dietrich Saßnick, Caterina Cocchi

引用次数: 0

A Deep Learning Framework for the Electronic Structure of Water: Toward a Universal Model. 水的电子结构的深度学习框架：迈向一个通用模型。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-06-30 DOI: 10.1021/acs.jctc.5c00496

Xinyuan Liang, Renxi Liu, Mohan Chen

引用次数: 0

Enhanced Krylov Methods for Molecular Hamiltonians: Reduced Memory Cost and Complexity Scaling via Tensor Hypercontraction. 分子哈密顿量的改进Krylov方法：通过张量超收缩降低内存开销和复杂度缩放。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-02 DOI: 10.1021/acs.jctc.5c00525

Yu Wang, Maxine Luo, Matthias Reumann, Christian B Mendl

引用次数: 0

clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling. clustertraj：一个基于溶剂的分子建模聚类工具。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-03 DOI: 10.1021/acs.jctc.5c00634

Rafael Bicudo Ribeiro, Henrique Musseli Cezar

{"title":"clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling.","authors":"Rafael Bicudo Ribeiro, Henrique Musseli Cezar","doi":"10.1021/acs.jctc.5c00634","DOIUrl":"10.1021/acs.jctc.5c00634","url":null,"abstract":"Clustering techniques are consolidated as a powerful strategy for analyzing the extensive data generated from molecular modeling. In particular, some tools have been developed to cluster configurations from classical simulations with a standard focus on individual units, ranging from small molecules to complex proteins. Since the standard approach includes computing the root mean square deviation (RMSD) of atomic positions, accounting for the permutation between atoms is crucial for optimizing the clustering procedure in the presence of identical molecules. To address this issue, we present the clusttraj program, a solvent-informed clustering package that fixes inflated RMSD values by finding the optimal pairing between configurations. The program combines reordering schemes with the Kabsch algorithm to minimize the RMSD of molecular configurations before running a hierarchical clustering protocol. By considering evaluation metrics, one can determine the ideal threshold in an automated fashion and compare the different linkage schemes available. The program capabilities are exemplified by considering solute-solvent systems ranging from pure water clusters to a solvated protein or a small solute in different solvents. As a result, we investigate the dependence on different parameters, such as the system size and reordering method, and also the representativeness of the cluster medoids for the characterization of optical properties. clusttraj is implemented as a Python library and can be employed to cluster generic ensembles of molecular configurations that go beyond solute-solvent systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6759-6768"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144551439","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 Complete Active Space Self-Consistent Field Approach for Molecules in QED Environments. QED环境中分子的完全主动空间自洽场方法。

IF 5.7 1区化学

Journal of Chemical Theory and Computation Pub Date : 2025-07-22 Epub Date: 2025-07-07 DOI: 10.1021/acs.jctc.5c00519

Riccardo Alessandro, Matteo Castagnola, Henrik Koch, Enrico Ronca

引用次数: 0