Journal of Chemical Theory and Computation最新文献

{"title":"Correction to “BAT2: an Open-Source Tool for Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations”","authors":"Germano Heinzelmann, David J. Huggins, Michael K. Gilson","doi":"10.1021/acs.jctc.4c01153","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01153","url":null,"abstract":"The current published version did not include a few supporting files, namely, two tables containing detailed results of the calculations (Table S1 and Table S2) and also the input files needed to reproduce the paper results. The two tables are inside the tables.zip file, and the input files are inside input-files.zip, both uploaded as Supporting Information in this addition submission. The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jctc.4c01153. input-files.zip (ZIP) tables.zip (ZIP) Correction to “BAT2:\u0000an Open-Source Tool for\u0000Flexible, Automated, and Low Cost Absolute Binding Free Energy Calculations” <span> 0 </span><span> views </span> <span> 0 </span><span> shares </span> <span> 0 </span><span> downloads </span> Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html. The Article Processing Charge for the publication of this research was funded by the Coordination for the Improvement of Higher Education Personnel - CAPES (ROR identifier: 00x0ma614). This article has not yet been cited by other publications.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235390","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":"Exploring Ground and Excited States Via Single Reference Coupled-Cluster Theory and Algebraic Geometry","authors":"Svala Sverrisdóttir, Fabian M. Faulstich","doi":"10.1021/acs.jctc.4c00644","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00644","url":null,"abstract":"The exploration of the root structure of coupled cluster (CC) equations holds both foundational and practical significance for computational quantum chemistry. This study provides insight into the intricate root structures of these nonlinear equations at both the CCD and CCSD level of theory. We utilize computational techniques from algebraic geometry, specifically the monodromy and parametric homotopy continuation methods, to calculate the full solution set. We compare the computed CC roots against various established theoretical upper bounds, shedding light on the accuracy and efficiency of these bounds. We hereby focus on the dissociation processes of four-electron systems such as (H₂)₂ in both D_2h and D_<i>∞</i>h configurations, H₄ symmetrically distorted on a circle, and lithium hydride. We moreover investigate the ability of single-reference CC solutions to approximate excited state energies. We find that multiple CC roots describe energies of excited states with high accuracy. Our investigations reveal that for systems like lithium hydride, CC not only provides high-accuracy approximations to several excited state energies but also to the states themselves.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235566","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":"Capturing Correlation Effects in Positron Binding to Atoms and Molecules","authors":"Shiv Upadhyay, Anouar Benali, Kenneth D. Jordan","doi":"10.1021/acs.jctc.4c00727","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00727","url":null,"abstract":"A major challenge in contemporary electronic structure theory involves the development of methods to describe in a balanced manner the contribution of correlation effects to energy differences. This challenge can be even greater for multicomponent systems containing more than one type of quantum particle. In the present work, we describe a flexible code for carrying out self-consistent field and configuration interaction (CI) calculations on multicomponent systems and use it to generate trial wave functions for use in diffusion Monte Carlo (DMC) calculations of the positron affinity of Be, Be₂, Be₄, Mg, CS₂, and benzene. The resulting positron affinities (PAs) are in good agreement with the best values from the literature.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235294","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":"Completely Multipolar Model as a General Framework for Many-Body Interactions as Illustrated for Water","authors":"Joseph P. Heindel, Selim Sami, Teresa Head-Gordon","doi":"10.1021/acs.jctc.4c00812","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00812","url":null,"abstract":"We introduce a general framework for many-body force fields, the Completely Multipolar Model (CMM), that utilizes multipolar electrical moments modulated by exponential decay of electron density as a common functional form for all terms of an energy decomposition analysis of intermolecular interactions. With this common functional form, the CMM model establishes well-formulated damped tensors that reach the correct asymptotes at both long- and short-range while formally ensuring no short-range catastrophes. CMM describes the separable EDA terms of dispersion, exchange polarization, and Pauli repulsion with short-ranged anisotropy, polarization as intramolecular charge fluctuations and induced dipoles, while charge transfer describes explicit movement of charge between molecules, and naturally describes many-body charge transfer by coupling into the polarization equations. We also utilize a new one-body potential that accounts for intramolecular polarization by including an electric field-dependent correction to the Morse potential to ensure that CMM reproduces all physically relevant monomer properties including the dipole moment, molecular polarizability, and dipole and polarizability derivatives. The quality of CMM is illustrated through agreement of individual terms of the EDA and excellent extrapolation to energies and geometries of an extensive validation set of water cluster data.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235563","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 Mode Evolution Metric to Extract Reaction Coordinates for Biomolecular Conformational Transitions","authors":"Mitradip Das, Ravindra Venkatramani","doi":"10.1021/acs.jctc.4c00744","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00744","url":null,"abstract":"The complex, multidimensional energy landscape of biomolecules makes the extraction of suitable, nonintuitive collective variables (CVs) that describe their conformational transitions challenging. At present, dimensionality reduction approaches and machine learning (ML) schemes are employed to obtain CVs from molecular dynamics (MD)/Monte Carlo (MC) trajectories or structural databanks for biomolecules. However, minimum sampling conditions to generate reliable CVs that accurately describe the underlying energy landscape remain unclear. Here, we address this issue by developing a <u>M</u>ode <u>e</u>volution Metric (MeM) to extract CVs that can pinpoint new states and describe local transitions in the vicinity of a reference minimum from nonequilibrated MD/MC trajectories. We present a general mathematical formulation of MeM for both statistical dimensionality reduction and machine learning approaches. Application of MeM to MC trajectories of model potential energy landscapes and MD trajectories of solvated alanine dipeptide reveals that the principal components which locate new states in the vicinity of a reference minimum emerge well before the trajectories locally equilibrate between the associated states. Finally, we demonstrate a possible application of MeM in designing efficient biased sampling schemes to construct accurate energy landscape slices that link transitions between states. MeM can help speed up the search for new minima around a biomolecular conformational state and enable the accurate estimation of thermodynamics for states lying on the energy landscape and the description of associated transitions.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235339","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":"Reconciling Accuracy and Feasibility for Barrierless Reaction Steps by the PCS/DDCI/MC-PDFT Protocol: Methane and Ethylene Dissociations as Case Studies","authors":"Luigi Crisci, Vincenzo Barone","doi":"10.1021/acs.jctc.4c00911","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00911","url":null,"abstract":"Several enhancements have been introduced into state-of-the-art computational protocols for the treatment of barrierless reaction steps in the framework of variable reaction coordinate variational transition state theory. The first step is the synergistic integration of the Iterative Difference Dedicated Configuration Interaction (I-DDCI) and Pisa Composite Scheme, which defines a reduced cost, yet very accurate, computational workflow. This approach provides a near black box tool for obtaining 1D reference potentials. Then, a general strategy has been devised for tuning the level of theory used in Monte Carlo (MC) sampling, employing Multiconfiguration Pair Density Functional Theory (MC-PDFT) with dynamically adjusted Hartree–Fock exchange. Concurrently, partial geometry optimizations during the MC simulations account for the coupling between the reaction coordinates and conserved modes. The protocol closely approaches full size consistency and yields highly accurate results, with several test computations suggesting rapid convergence of the I-DDCI correction with the basis set dimensions. The capabilities of the new platform are illustrated by two case studies (the hydrogen dissociation from CH₄ and C₂H₄), which highlight its flexibility in handling different carbon hybridizations (sp³ and sp²). The remarkable accuracy of the computed rate constants confirms the robustness of the proposed method. Together with their intrinsic interest, these results pave the way for systematic investigations of complex gas-phase reactions through a reliable, user-friendly tool accessible to specialists and nonspecialists alike.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235564","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":"Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA","authors":"Egor S. Kolesnikov, Yeyue Xiong, Alexey V. Onufriev","doi":"10.1021/acs.jctc.4c00833","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00833","url":null,"abstract":"The ion atmosphere surrounding highly charged biomolecules, such as nucleic acids, is crucial for their dynamics, structure, and interactions. Here, we develop an approach for the explicit treatment of ions within an implicit solvent framework suitable for atomistic simulations of biomolecules. The proposed implicit solvent/explicit ions model, <span>GBION</span>, is based on a modified generalized Born (GB) model; it includes separate, modified GB terms for solute–ion and ion–ion interactions. The model is implemented in the AMBER package (version 24), and its performance is thoroughly investigated in atomistic molecular dynamics (MD) simulations of double-stranded DNA on a microsecond time scale. The aggregate characteristics of monovalent (Na⁺ and K⁺) and trivalent (Cobalt Hexammine, CoHex³⁺) counterion distributions around double-stranded DNA predicted by the model are in reasonable agreement with the experiment (where available), all-atom explicit water MD simulations, and the expectation from the Manning condensation theory. The radial distributions of monovalent cations around DNA are reasonably close to the ones obtained using the explicit water model: expressed in units of energy, the maximum deviations of local ion concentrations from the explicit solvent reference are within 1 <i>k</i>_B<i>T</i>, comparable to the corresponding deviations expected between different established explicit water models. The proposed <span>GBION</span> model is able to simulate DNA fragments in a large volume of solvent with explicit ions with little additional computational overhead compared with the fully implicit GB treatment of ions. Ions simulated using the developed model explore conformational space at least 2 orders of magnitude faster than in the explicit solvent. These advantages allowed us to observe and explore an unexpected “stacking” mode of DNA condensation in the presence of trivalent counterions (CoHex³⁺) that was revealed by recent experiments.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142234218","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":"Pursuing Extreme Descriptive Power and Generality in Chemical Bond Theories: A Method to Decipher “Interatomic Genomes” from Interatomic Electron Structures","authors":"Xinxu Zhang, Jiahao Wei, Hui Jia, Jiamin Liu, Guo Li, Ling Liu, Yulong Wu, Changlong Liu, Xiao-Dong Zhang, Yonghui Li","doi":"10.1021/acs.jctc.4c00557","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00557","url":null,"abstract":"The description and analysis of chemical bonds have been difficult following the popularization of electronic structure calculations. Although many attempts have been made from the perspective of electronic structure, the sheer volume of information in the electronic structure has left contemporary chemical bond analysis methods grappling with an inescapable “Trilemma” where the model briefness, generality, and descriptiveness (descriptive power) cannot be obtained simultaneously. To push the generality and descriptiveness to their extremes, herein a general machine learning-based framework is introduced to compact chemical bonds into a detailed residue-by-residue “genome” with matched encoding/decoding tools. The framework fuses the quantum mechanical aspects, auto feature extraction, nanostructures and/or simulations, and generative models. The encoded genomes are information-dense and decodable, where 100% generality is guaranteed. The descriptiveness of genomes appears to be broader than most known models. As a proof of concept, the realization presented in this work compacts the complete information regarding two critical chemical bonds in thiolate-protected gold nanoclusters, the S–Au and Au–Au bonds, from a Bosonic-Fermionic character perspective into 8-valued genomes. The machine learning component is trained based on 26,528 density functional theory simulated electron localization function images. With an exploration of the space span for the genome, bond polarization, hybridization, intrusion of other atoms, alignments, crystal orientation, atomic motions, and more details are observed. Furthermore, it has emerged from extensive generation tests that molecules and solids can be integrated in such a concise manner than is typically achieved with purely geometric representations. To showcase the intraclass complexity of S–Au and Au–Au bonds visually, a roadmap is plotted by summarizing and correlating the similarities of 8-value-genomes. Furthermore, genomes can be associated with realistic indices easily with a simple multilayer perception architecture as a simple calculating tool. Besides, there are 3 sets of applications, including a set of chemisorption, a set of molecular dynamical analysis, and a set of ultrafast processes, showcasing the interpretability potentials of interatomic genomes in the geometric structures, kinetic properties, and vibration characteristics of molecular systems. As the framework rose to the challenge of nanoclusters from a complicated mesoscopic family of material, the displayed generality and comprehensiveness indicate that the model may “understand” chemical bonds in a machine’s way.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142246155","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":"Excitonic Approach for Nonadiabatic Dynamics: Extending Beyond the Frenkel Exciton Model","authors":"Eduarda Sangiogo Gil, Andrea Giustini, Davide Accomasso, Giovanni Granucci","doi":"10.1021/acs.jctc.4c00886","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00886","url":null,"abstract":"We report the formulation and implementation of an extended Frenkel exciton model (EFEM) designed for simulating the dynamics of multichromophoric systems, taking into account the possible presence of interchromophore charge transfer states, as well as other states in which two chromophores are simultaneously excited. Our approach involves constructing a Hamiltonian based on calculations performed on monomers and selected dimers within the multichromophoric aggregate. Nonadiabatic molecular dynamics is addressed using a surface hopping approach, while the electronic wave functions and energies required for constructing the EFEM are computed utilizing the semiempirical floating occupation molecular orbitals-configuration interaction (FOMO-CI) electronic structure method. To validate our approach, we simulate the singlet fission process in a trimer of 2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene (ThBF) molecules, embedded in their crystal environment, comparing the results of the EFEM to the standard “supermolecule” approach.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142235565","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":"Particle–Particle Random Phase Approximation for Predicting Correlated Excited States of Point Defects","authors":"Jiachen Li*,&nbsp;Yu Jin,&nbsp;Jincheng Yu,&nbsp;Weitao Yang* and Tianyu Zhu*,&nbsp;","doi":"10.1021/acs.jctc.4c0082910.1021/acs.jctc.4c00829","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00829https://doi.org/10.1021/acs.jctc.4c00829","url":null,"abstract":"<p >The particle–particle random phase approximation (ppRPA) within the hole–hole channel was recently proposed as an efficient tool for computing excitation energies of point defects in solids [<i>J. Phys. Chem. Lett.</i> 2024, 15, 2757–2764]. In this work, we investigate the application of ppRPA within the particle–particle channel for predicting correlated excited states of point defects, including the carbon-vacancy (VC) in diamond, the oxygen-vacancy (VO) in magnesium oxide (MgO), and the carbon dimer defect (C_BC_N) in two-dimensional hexagonal boron nitride (h-BN). Starting from a density functional theory calculation of the (<i>N</i> – 2)-electron ground state, vertical excitation energies of the <i>N</i>-electron system are obtained as the differences between the two-electron addition energies. We show that active-space ppRPA with the B3LYP functional yields accurate excitation energies, with errors mostly smaller than 0.1 eV for tested systems compared to available experimental values. We further develop a natural transition orbital scheme within ppRPA, which provides insights into the multireference character of defect states. This study, together with our previous work, establishes ppRPA as a low-cost and accurate method for investigating excited-state properties of point defect systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310045","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}