Journal of Chemical Theory and Computation最新文献

{"title":"Screening Fast-Mode Motion in Collective Variable Discovery for Biochemical Processes.","authors":"Donghui Shao, Zhiteng Zhang, Xuyang Liu, Haohao Fu, Xueguang Shao, Wensheng Cai","doi":"10.1021/acs.jctc.4c01282","DOIUrl":"10.1021/acs.jctc.4c01282","url":null,"abstract":"<p><p>Collective variables (CVs) describing slow degrees of freedom (DOFs) in biomolecular assemblies are crucial for analyzing molecular dynamics trajectories, creating Markov models and performing CV-based enhanced sampling simulations. While time-lagged independent component analysis (tICA) and its nonlinear successor, time-lagged autoencoder (tAE), are widely used, they often struggle to capture protein dynamics due to interference from random fluctuations along fast DOFs. To address this issue, we propose a novel approach integrating discrete wavelet transform (DWT) with dimensionality reduction techniques. DWT effectively separates fast and slow motion in protein simulation trajectories by decoupling high- and low-frequency signals. Based on the trajectory after filtering out high-frequency signals, which corresponds to fast motion, tICA and tAE can accurately extract CVs representing slow DOFs, providing reliable insights into protein dynamics. Our method demonstrates superior performance in identifying CVs that distinguish metastable states compared to standard tICA and tAE, as validated through analyses of conformational changes of alanine dipeptide and tripeptide and folding of CLN025. Moreover, we show that DWT can be used to improve the performance of a variety of CV-finding algorithms by combining it with Deep-tICA, a cutting-edge CV-finding algorithm, to extract CVs for enhanced-sampling calculations. Given its negligible computational cost and remarkable ability to screen fast motion, we propose DWT as a \"free lunch\" for CV extraction, applicable to a wide range of CV-finding algorithms.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10393-10405"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724534","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}

{"title":"A Refined Set of Universal Force Field Parameters for Some Metal Nodes in Metal-Organic Frameworks.","authors":"Yutao Li, Xin Jin, Elias Moubarak, Berend Smit","doi":"10.1021/acs.jctc.4c01113","DOIUrl":"10.1021/acs.jctc.4c01113","url":null,"abstract":"<p><p>Metal-organic frameworks (MOFs) exhibit promise as porous materials for carbon capture due to their design versatility and large pore sizes. The generic force fields (e.g., UFF and Dreiding) use one universal set of Lennard-Jones parameters for each element, while MOFs have a much richer local chemical environment than those chemical environments used to fit the UFF. When MOFs contain hard-Lewis acid metals, UFF systematically overestimates CO₂ uptakes. To address this, we developed a workflow to affordably and efficiently generate reliable force fields to predict CO₂ adsorption isotherms of MOFs containing metals from groups IIA (Mg, Ca, Sr, and Ba) and IIIA (Al, Ga, and In), connected to various carboxylate ligands. This method uses experimental isotherms as input. The optimal parameters are obtained by minimizing the loss function of the experimental and simulated isotherms, in which we use the Multistate Bennett Acceptance Ratio (MBAR) theory to derive the functionality relationship of loss functions in terms of force field parameters.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10540-10552"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142724530","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}

{"title":"Capturing Dichotomic Solvent Behavior in Solute-Solvent Reactions with Neural Network Potentials.","authors":"Frédéric Célerse, Veronika Juraskova, Shubhajit Das, Matthew D Wodrich, Clemence Corminboeuf","doi":"10.1021/acs.jctc.4c01201","DOIUrl":"10.1021/acs.jctc.4c01201","url":null,"abstract":"<p><p>Simulations of chemical reactivity in condensed phase systems represent an ongoing challenge in computational chemistry, where traditional quantum chemical approaches typically struggle with both the size of the system and the potential complexity of the reaction. Here, we introduce a workflow aimed at efficiently training neural network potentials (NNPs) to explore energy barriers in solution at the hybrid density functional theory level. The computational burden associated with training at the PBE0-D3(BJ) level is bypassed through the use of active and transfer learning techniques, whereas extensive sampling of the transition state region is accelerated by well-tempered metadynamics simulations using multiple time step integration. These NNPs serve to explore a puzzling solute-solvent reactivity route involving the ring opening of <i>N</i>-enoxyphthalimide experimentally observed in methanol but not in 2,2,2-trifluoroethanol (TFE). This reaction represents a challenging example characterized by intricate hydrogen bonding networks and structurally ambiguous solvent-sensitive transition states. The methodology successfully delivers detailed free energy surfaces and relative energy barriers in agreement with experiment. These barriers are associated with an ensemble of transition states involving the direct participation of up to five solvent molecules. While this picture contrasts with the single transition state structure assumed by current static models, no drastic qualitative difference is observed between the formed hydrogen bonding networks and the number of participating solvent molecules in methanol or TFE. The dichotomy between the two solvents thus essentially arises from an electronic effect (i.e., distinct nucleophilicity) and from the larger conformational entropy contributions in methanol. This example underscores the critical role that dynamic simulations at the ab initio levels play in capturing the full complexity of solute-solvent interactions.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10350-10361"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142685424","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}

{"title":"Bayesian Approach for Computing Free Energy on Perturbation Graphs with Cycles.","authors":"Xinqiang Ding, John Drohan","doi":"10.1021/acs.jctc.4c00948","DOIUrl":"10.1021/acs.jctc.4c00948","url":null,"abstract":"<p><p>A common approach for computing free energy differences among multiple states is to build a perturbation graph connecting the states and compute free energy differences on all edges of the graph. Such perturbation graphs are often designed to have cycles. Because free energy is a function of states, the free energy around any cycle is zero, which we refer to as the cycle consistency condition. Since the cycle consistency condition relates free energy differences on the edges of a cycle, it could be used to improve the accuracy of free energy estimates. Here, we propose a Bayesian method called the coupled Bayesian multistate Bennett acceptance ratio (CBayesMBAR) that can properly couple the calculations of free energy differences on the edges of cycles in a principled way. We apply the CBayesMBAR to compute free energy differences among harmonic oscillators and relative protein-ligand binding free energies. In both cases, the CBayesMBAR provides more accurate results compared to methods that do not consider the cycle consistency condition. Additionally, it outperforms the cycle closure correction method that also uses cycle consistency conditions.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10384-10392"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142666203","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}

{"title":"Creating Benchmarks for Lithium Clusters and Using Them for Testing and Validation.","authors":"Maryam Mansoori Kermani, Donald G Truhlar","doi":"10.1021/acs.jctc.4c01224","DOIUrl":"10.1021/acs.jctc.4c01224","url":null,"abstract":"<p><p>Metal clusters often have a variety of possible structures, and they are calculated by a wide range of methods; however, fully converged benchmarks on the energy differences of structures and spin states that could be used to test or validate these methods are rare or nonexistent. Small lithium clusters are good candidates for such benchmarks to test different methods against well-converged relative energetics for qualitatively different structures because they have a small number of electrons. The present study provides fully converged benchmarks for Li₄ and Li₅ clusters and uses them to test a diverse group of approximation methods. To create a dataset of well-converged single-point energies for Li₄ and Li₅, stationary structures were optimized by Kohn-Sham density functional theory (KS-DFT) and then single-point energy calculations at these structures were carried out by two quite different beyond-CCSD(T) methods. To test other methods single-point energy calculations at these structures were carried out by KS-DFT, Mo̷ller-Plesset (MP) theory, coupled cluster (CC) theory, five composite methods (Gaussian-4, the Wuhan-Minnesota (WM) composite method, and the W2X, W3X, and W3X-L composite methods of Radom and co-workers), multiconfiguration pair-density functional theory (MC-PDFT), complete active space second-order perturbation theory (CASPT2), and <i>n</i>-electron valence state second-order perturbation theory (NEVPT2). Our results show that rhomboid and trigonal bipyramid (TBP) geometries are the most stable structures for Li₄ and Li₅, respectively. Using the W3X-L method to obtain our best estimates, the mean unsigned deviations were calculated for other methods for several structures and spin states of both Li₄ and Li₅. Binding energies and <i>M</i> diagnostics were calculated for all structures. The data in this paper are valuable for assessing the reliability of current electronic structure theories and also developing new density functionals and machine learned models.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10491-10506"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142674425","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}

{"title":"Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck.","authors":"Dedi Wang, Pratyush Tiwary","doi":"10.1021/acs.jctc.4c00919","DOIUrl":"10.1021/acs.jctc.4c00919","url":null,"abstract":"<p><p>The weighted ensemble (WE) method stands out as a widely used segment-based sampling technique renowned for its rigorous treatment of kinetics. The WE framework typically involves initially mapping the configuration space onto a low-dimensional collective variable (CV) space and then partitioning it into bins. The efficacy of WE simulations heavily depends on the selection of CVs and binning schemes. The recently proposed state predictive information bottleneck (SPIB) method has emerged as a promising tool for automatically constructing CVs from data and guiding enhanced sampling through an iterative manner. In this work, we advance this data-driven pipeline by incorporating prior expert knowledge. Our hybrid approach combines SPIB-learned CVs to enhance sampling in explored regions with expert-based CVs to guide exploration in regions of interest, synergizing the strengths of both methods. Through benchmarking on alanine dipeptide and chignolin systems, we demonstrate that our hybrid approach effectively guides WE simulations to sample states of interest and reduces run-to-run variances. Moreover, our integration of the SPIB model also enhances the analysis and interpretation of WE simulation data by effectively identifying metastable states and pathways and offering direct visualization of dynamics.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"10371-10383"},"PeriodicalIF":5.7,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714848","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}

{"title":"B-Spline Solution of the Two-Center Dirac Equation in the Electronic Continuum for Relativistic Molecular Photoionization","authors":"Felipe Zapata*,&nbsp;Daniele Toffoli,&nbsp;Jan Marcus Dahlström,&nbsp;Eva Lindroth,&nbsp;Piero Decleva and Fernando Martín,&nbsp;","doi":"10.1021/acs.jctc.4c0123210.1021/acs.jctc.4c01232","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01232https://doi.org/10.1021/acs.jctc.4c01232","url":null,"abstract":"<p >In this work, the two-center Dirac equation is solved numerically using an extension of an adapted B-spline basis set method previously implemented in relativistic atomic calculations (Fischer, C. F.; Zatsarinny, O. <i>Comput. Phys. Commun.</i> <b>2009</b>, <i>180</i>, 879). The robustness of the chosen numerical method, which avoids the appearance of spurious states common in other approaches, allows us to investigate molecular photoionization within a relativistic framework by simply adapting those methods already available in the nonrelativistic case (Brosolo, M.; Decleva, P. <i>Chem. Phys.</i> <b>1992</b>, <i>159</i>, 185; Brosolo, M.; Decleva, P.; Lisini, A. <i>Mol. Opt. Phys.</i> <b>1992</b>, <i>25</i>, 3345). First, light diatomic molecules (i.e., H₂⁺ and HeH²⁺) are investigated with the purpose of testing the validity and efficiency of the method. Then, a series of one-electron molecular hydrides (i.e., HF⁹⁺, HCl¹⁷⁺ and HI⁵³⁺) is explored by computing the total photoionization cross sections, asymmetry β-parameters and partial phase shifts. The present methodology can be easily extended to treat <i>N</i>-electron molecules following previous approaches in nonrelativistic calculations (Plesiat, E.; Decleva, P.; Martin, F. <i>Phys. Chem. Chem. Phys.</i> <b>2012</b>, <i>14</i>, 10853). The inclusion of a second photon can be also accomplished just like in atomic investigations aiming at reproducing pump–probe experiments capable to extract the photoionization time-delays (Vinbladh, J.; Dahlstrom, J. M.; Lindroth, E. <i>Phys. Rev A</i> <b>2019</b>, <i>100</i>, 043424; Vinblach, J.; Dahlstrom, J. M.; Lindroth, E. <i>Atoms</i> <b>2022</b>, <i>10</i>, 80).</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"20 23","pages":"10507–10523 10507–10523"},"PeriodicalIF":5.7,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142842054","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}

{"title":"Automated Parametrization Approach for Coarse-Graining Soil Organic Matter Molecules","authors":"Lorenz F. Dettmann,&nbsp;Oliver Kühn and Ashour A. Ahmed*,&nbsp;","doi":"10.1021/acs.jctc.4c0133410.1021/acs.jctc.4c01334","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01334https://doi.org/10.1021/acs.jctc.4c01334","url":null,"abstract":"<p >Investigating the molecular structure of soil organic matter (SOM), along with its intramolecular interactions and interactions with other soil components and xenobiotics, is essential due to its ecological importance. However, the complexity and heterogeneity of SOM present significant challenges for systematic studies. While experimental methods are commonly employed, atomistic simulations provide a complementary approach to exploring molecular-level processes. The Vienna Soil Organic Matter Modeler 2 (VSOMM2) facilitates the construction of molecular models of SOM systems with various compositions at the atomistic scale, which can then be examined through molecular dynamics (MD) simulations. This study introduces a parametrization strategy that enables the conversion of VSOMM2-generated structures into a coarse-grained representation, thus allowing larger time and length scales to be explored. By employing a conformer search technique, direct construction and analysis of coarse-grained SOM models with diverse compositions were made possible, eliminating the need for atomistic MD simulations. To demonstrate this approach, coarse-grained SOM models were created based on selected samples from the International Humic Substances Society, considering different water content levels for each model. Comprehensive analyses, including density and potential energy profile calculations, revealed a partial correlation with the SOM compositions and demonstrated that electrostatic interactions govern the structural packing. Moreover, a local phase separation process, particularly the formation of SOM voids, was observed over several microseconds, underscoring the advantages of the coarse-graining technique.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"20 23","pages":"10684–10696 10684–10696"},"PeriodicalIF":5.7,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142843639","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}

{"title":"On the Performance of Second-Order Polarization Propagator Methods in the Calculation of 1JFC and nJFH NMR Spin–Spin Coupling Constants","authors":"Marinella de Giovanetti,&nbsp;Rodrigo A. Cormanich and Stephan P. A. Sauer*,&nbsp;","doi":"10.1021/acs.jctc.4c0104310.1021/acs.jctc.4c01043","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01043https://doi.org/10.1021/acs.jctc.4c01043","url":null,"abstract":"<p >This study evaluates the performance of doubles-corrected random phase approximation (RPA) and higher random phase approximation (HRPA) approaches in predicting nuclear magnetic resonance (NMR) coupling constants involving fluorine. Their performance is benchmarked against experimental data and compared with that of higher-level theoretical methods, specifically second-order polarization propagator (SOPPA) and SOPPA(CCSD). Additionally, we discuss their performance relative to density functional theory (DFT). We find that RPA(D) is severely constrained by (near) triplet instabilities, while HRPA(D) demonstrates markedly improved stability. Statistical analysis reveals stronger patterns for carbon–fluorine couplings across the methods and systems investigated compared with fluorine–hydrogen couplings. While SOPPA-based methodologies prove to be superior in accuracy, HRPA(D) shows promising performance in reducing the computational burden of these calculations, albeit with a tendency to underestimate the coupling strength. These findings highlight the potential of HRPA(D) as a practical alternative to SOPPA methods, even for such difficult properties as NMR spin–spin coupling constants involving fluorine, emphasizing its role in improving predictive accuracy and efficiency across diverse chemical environments.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"20 23","pages":"10453–10467 10453–10467"},"PeriodicalIF":5.7,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142843640","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}

{"title":"Real-Time TDDFT Using Noncollinear Functionals","authors":"Hao Li,&nbsp;Zhichen Pu,&nbsp;Yi Qin Gao and Yunlong Xiao*,&nbsp;","doi":"10.1021/acs.jctc.4c0121810.1021/acs.jctc.4c01218","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01218https://doi.org/10.1021/acs.jctc.4c01218","url":null,"abstract":"<p >Recently, we proposed a method to generalize collinear functionals to noncollinear functionals, called multicollinear approach, which has been applied in density functional theory (DFT) and linear-response time-dependent DFT (TDDFT) for the ground state and excited states calculations, respectively. In this work, we demonstrate the application of this method in real-time TDDFT by simulating electronic absorption spectra, Rabi resonance, and precession of a two-magnetic center system. Thanks to the nonvanishing local exchange-correlation torque provided by multicollinear functionals, research into the torques in the evolution of magnetization vector is carried out, which is useful for the exploration on spin dynamics.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"20 23","pages":"10477–10490 10477–10490"},"PeriodicalIF":5.7,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142843908","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}