Journal of Chemical Theory and Computation最新文献

{"title":"Role of Electron Correlation beyond the Active Space in Achieving Quantitative Predictions of Spin-Phonon Relaxation.","authors":"Soumi Haldar, Lorenzo A Mariano, Alessandro Lunghi, Laura Gagliardi","doi":"10.1021/acs.jctc.4c01696","DOIUrl":"10.1021/acs.jctc.4c01696","url":null,"abstract":"<p><p>Single-molecule magnets (SMMs) are promising candidates for molecular-scale data storage and processing due to their strong magnetic anisotropy and long spin relaxation times. However, as the temperature rises, interactions between electronic states and lattice vibrations accelerate spin relaxation, significantly limiting their practical applications. Recently, ab initio simulations have made it possible to advance our understanding of phonon-induced magnetic relaxation, but significant deviations from the experiments have often been observed. The description of molecules' electronic structure has been mostly based on complete active space self-consistent field (CASSCF) calculations, and the impact of electron correlation beyond the active space remains largely unexplored. In this study, we provide the first systematic investigation of spin-phonon relaxation in SMMs with post-CASSCF multiconfigurational methods, specifically CAS, followed by second-order perturbation theory and multiconfiguration pair-density functional theory. Taking Co(II)- and Dy(III)-based SMMs as case studies, we analyze how electron correlation influences spin-phonon relaxation rates across a range of temperatures by comparing theoretical predictions with experimental observations. Our findings demonstrate that post-CASSCF treatments make it possible to achieve quantitative predictions for Co(II)-based SMMs. For Dy(III)-based systems, however, accurate predictions require the consideration of additional effects, underscoring the urgent necessity of further advancing the study of the effects of electronic correlation in these complex systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11948317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143612823","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":"A Phase-Space View of Vibrational Energies without the Born–Oppenheimer Framework","authors":"Xuezhi Bian,&nbsp;Cameron Khan,&nbsp;Titouan Duston,&nbsp;Jonathan Rawlinson,&nbsp;Robert G. Littlejohn and Joseph E. Subotnik*,&nbsp;","doi":"10.1021/acs.jctc.4c0129410.1021/acs.jctc.4c01294","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01294https://doi.org/10.1021/acs.jctc.4c01294","url":null,"abstract":"<p >We show that following the standard mantra of quantum chemistry and diagonalizing the Born–Oppenheimer (BO) Hamiltonian <i>Ĥ</i>_BO(<b><i>R</i></b>) is not the optimal means to construct potential energy surfaces. A better approach is to diagonalize a phase-space electronic Hamiltonian, <i>Ĥ</i>_PS(<b><i>R</i></b>, <b><i>P</i></b>), which is parameterized by both nuclear position <b><i>R</i></b> and nuclear momentum <b><i>P</i></b>. Such a nonperturbative phase-space electronic Hamiltonian can be constructed using a partial Wigner transform and the method has exactly the same cost as BO for a semiclassical calculation (and only a slight increase in cost for a quantum nuclear calculation). For a three-particle system, with two heavy particles and one light particle, numerical results show that a phase-space electronic Hamiltonian produces not only meaningful electronic momenta (which are completely ignored by BO theory) but also far better vibrational energies. As such, for high level results and/or systems with degeneracies and spin degrees of freedom, we anticipate that future electronic structure and quantum chemistry packages will need to take as input not just the positions of the nuclei but also their momenta.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"2880–2893 2880–2893"},"PeriodicalIF":5.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678627","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":"Improved Free-Energy Estimates for the Permeation of Bulky Antibiotic Molecules through Porin Channels Using Temperature-Accelerated Sliced Sampling","authors":"Abhishek Acharya,&nbsp; and ,&nbsp;Ulrich Kleinekathöfer*,&nbsp;","doi":"10.1021/acs.jctc.4c0167910.1021/acs.jctc.4c01679","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01679https://doi.org/10.1021/acs.jctc.4c01679","url":null,"abstract":"<p >The estimation of accurate free energies for antibiotic permeation via the bacterial outer-membrane porins has proven to be challenging. Atomistic simulations of the process suffer from sampling issues that are typical of systems with complex and slow dynamics, even with the application of advanced sampling methods. Ultimately, the objective is to obtain accurate potential of mean force (PMF) for a large set of antibiotics and to predict permeation rates. Therefore, the computational expense becomes an important criterion as well. Simulation studies on the permeation process and similar complex processes have shown that both the sampling scheme employed and the procedure used for the generation of the initial states can critically affect the quality of the estimates obtained and the respective computational overhead. The temperature-accelerated sliced sampling method (TASS) has been shown to partly address the issues with efficient sampling of the important and slow degrees of freedom by enabling simultaneous biasing of a large number of collective variables. In this work, we investigate the effect of the procedure used for the generation of input conformations on the convergence of free-energy estimates obtained from TASS simulations. In particular, we compare the steered molecular dynamics (MD)-based procedure that has been used in previous TASS studies with the Monte Carlo pathway search method, which is used to obtain approximate permeation trajectories with minimum perturbation of the protein channel. We tested different input setups for enrofloxacin permeation through the porins OmpK35 and OmpE35. The best setup shows an improved agreement between independent PMFs in both cases at a much lower computational cost.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"3246–3259 3246–3259"},"PeriodicalIF":5.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c01679","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678629","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":"Role of Electron Correlation beyond the Active Space in Achieving Quantitative Predictions of Spin-Phonon Relaxation","authors":"Soumi Haldar,&nbsp;Lorenzo A. Mariano,&nbsp;Alessandro Lunghi* and Laura Gagliardi*,&nbsp;","doi":"10.1021/acs.jctc.4c0169610.1021/acs.jctc.4c01696","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01696https://doi.org/10.1021/acs.jctc.4c01696","url":null,"abstract":"<p >Single-molecule magnets (SMMs) are promising candidates for molecular-scale data storage and processing due to their strong magnetic anisotropy and long spin relaxation times. However, as the temperature rises, interactions between electronic states and lattice vibrations accelerate spin relaxation, significantly limiting their practical applications. Recently, ab initio simulations have made it possible to advance our understanding of phonon-induced magnetic relaxation, but significant deviations from the experiments have often been observed. The description of molecules’ electronic structure has been mostly based on complete active space self-consistent field (CASSCF) calculations, and the impact of electron correlation beyond the active space remains largely unexplored. In this study, we provide the first systematic investigation of spin-phonon relaxation in SMMs with post-CASSCF multiconfigurational methods, specifically CAS, followed by second-order perturbation theory and multiconfiguration pair-density functional theory. Taking Co(II)- and Dy(III)-based SMMs as case studies, we analyze how electron correlation influences spin-phonon relaxation rates across a range of temperatures by comparing theoretical predictions with experimental observations. Our findings demonstrate that post-CASSCF treatments make it possible to achieve quantitative predictions for Co(II)-based SMMs. For Dy(III)-based systems, however, accurate predictions require the consideration of additional effects, underscoring the urgent necessity of further advancing the study of the effects of electronic correlation in these complex systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"2829–2838 2829–2838"},"PeriodicalIF":5.7,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c01696","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678721","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":"Medium-Range Order in Iron Phosphate Glass Models Obtained Using Various Randomization Techniques: A Molecular Dynamics Study.","authors":"Shakti Singh, Manan Dholakia, Sharat Chandra","doi":"10.1021/acs.jctc.4c01372","DOIUrl":"10.1021/acs.jctc.4c01372","url":null,"abstract":"<p><p>Glasses are known to have medium-range order (MRO), but their link to any experimentally measurable quantity is still ambiguous. The first sharp diffraction peak (FSDP) in structure factor <i>S</i>(<i>q</i>) obtained from diffraction experiments on glasses has been associated with this MRO (∼7-15 Å), but understanding the fundamental origin of this universal peak is still an open problem. We have addressed this issue for a complex glass, i.e., iron phosphate glass (IPG), through atomistic models generated from a hybrid approach (our in-house-developed MC code + molecular dynamics simulation). IPG is a technologically important glass with applications in waste vitrification, bioactive glass, laser glass material, anode material for batteries, etc., and is seen as a strengthened substitute for borosilicate glasses. We performed a comparative study by generating glass models from different initial configurations and randomization techniques. The developed IPG models were first validated with existing data on short-range order (SRO) and MRO through the study of pair correlation functions, bond angle distributions, and coordination number for SRO and rings distribution, FSDP in structure factor, and void size distribution for MRO. The study of coordination environment of oxygen is specifically shown to aid in understanding glass formation through topological constraint theory. Thereafter, to understand the fundamental origin of FSDP in <i>S</i>(<i>q</i>), structure factors were calculated corresponding to the individual ring sizes present in the model. The relative contribution of these individual <i>S</i>(<i>q</i>)'s in the total experimental <i>S</i>(<i>q</i>) is estimated using an inverse fitting approach. The contributions thus obtained directly correlated with ring size percentages in the models for the considered q-range. In particular, the melt-quenched model obtained from the MC model as an initial structure is found to reproduce most experimental features seen in IPG. Through this exercise, we can connect the rings distribution of an atomistic glass model with an experimentally measurable quantity like FSDP in <i>S</i>(<i>q</i>) for a complex glass-like IPG. This gives physical meaning to the rings distribution while also proving that this structural descriptor is a useful tool for validation of MRO in simulation-produced models of glass.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2582-2597"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466520","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":"Efficient Energy Measurement of Chemical Systems via One-Particle Reduced Density Matrix: A NOF-VQE Approach for Optimized Sampling.","authors":"Juan Felipe Huan Lew-Yee, Mario Piris","doi":"10.1021/acs.jctc.4c01734","DOIUrl":"10.1021/acs.jctc.4c01734","url":null,"abstract":"<p><p>In this work, we explore the use of the one-particle reduced density matrix (1RDM) to streamline energy measurements of chemical systems on quantum computers, particularly within the variational quantum eigensolver (VQE) framework. This approach leverages the existence of an exact energy functional of the 1RDM, enabling a reduction in both the number of expectation values to measure and the number of circuits to execute, thereby optimizing quantum resource usage. Specifically, sampling the 1RDM involves measuring only [Formula: see text] elements, which is significantly fewer than the [Formula: see text] required for the Hamiltonian's expectation value ⟨<i>Ĥ</i>⟩. We demonstrate our approach by harnessing the well-established natural orbital functional (NOF) theory, using the natural orbitals and occupation numbers derived from the diagonalization of the 1RDM measured from the quantum computer. Starting with the H₂ system, we validate the accuracy of our method by comparing the energy derived from NOF approximations applied to the exact wave function with the value obtained from ⟨<i>Ĥ</i>⟩. This is followed by an optimization of the gate parameters by minimizing the energy using the NOF approximations as the objective function. The analysis is extended to larger systems, such as LiH, Li₂, OH^-, FH, NeH⁺, and F₂ using a wave function ansatz with single and double excitation gates. This NOF-based method reduces the scaling cost of circuit executions compared to standard VQE implementations, achieving around 90% savings in the systems used in this work. Overall, by using a well-performing NOF as the objective function, the proposed NOF-VQE demonstrates the viability of NOF approximations for obtaining accurate energies in the noisy intermediate-scale quantum era and underscores the potential for developing new functionals tailored to quantum computing applications.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2402-2413"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471992","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":"Structural Heterogeneity of Intermediate States Facilitates CRIPT Peptide Binding to the PDZ3 Domain: Insights from Molecular Dynamics and Markov State Model Analysis.","authors":"Xingyu Song, Dongdong Wang, Jie Ji, Jingwei Weng, Wenning Wang","doi":"10.1021/acs.jctc.4c01308","DOIUrl":"10.1021/acs.jctc.4c01308","url":null,"abstract":"<p><p>Intrinsically disordered proteins (IDPs), characterized by a lack of defined tertiary structure, are ubiquitous and indispensable components of cellular machinery. These proteins participate in a diverse array of biological processes, often undergoing conformational transitions upon binding to their target, a phenomenon termed \"folding-upon-binding.\" The finding raises the question of how to achieve rapid binding kinetics in the presence of intrinsic disorder, and the underlying molecular mechanism remains elusive. This study investigated the interaction between the C-terminal region of CRIPT and the third PDZ domain of PSD-95, a critical complex in neuronal development. Upon binding, the CRIPT peptide adopts a β-strand conformation, a process meticulously characterized through extensive molecular dynamics simulations totaling 67.7 μs. Our findings reveal a funnel-like binding landscape in which IDPs can adopt multiple conformations prior to binding, forming structurally heterogeneous intermediate complexes and leading to diverse binding pathways. The stabilization of these intermediate complexes necessitates a dynamic interplay of native and non-native interactions. Markov state model analysis underscores the important role of structural heterogeneity as it contributes to accelerated binding. These findings enrich the classical fly-casting mechanism and provide novel insights into the functional advantages conferred by intrinsic disorder.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2668-2682"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143471993","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":"Effective Electron-Vibration Coupling by Ab Initio Methods.","authors":"Maximilian F X Dorfner, Frank Ortmann","doi":"10.1021/acs.jctc.4c01608","DOIUrl":"10.1021/acs.jctc.4c01608","url":null,"abstract":"<p><p>The description of electron-phonon coupling in materials is complex, with varying definitions of coupling constants in the literature and different theoretical approaches available. This article analyzes different levels of theory to introduce and compute these coupling constants. Within the quasi-particle picture, we derive an effective linear-coupling Hamiltonian, describing the interaction of electronic quasi-particles with vibrations. This description allows a comparison between coupling constants computed using density functional theory and higher-level quasi-particle approaches by identifying the Kohn-Sham potential as an approximation to the frequency-independent part of the self-energy. We also investigate their dependence on the exchange-correlation (XC) functional. Despite significant deviations of the Kohn-Sham eigenvalues, which arise from different XC functionals, the resulting coupling constants are remarkably similar. A comparison to quasi-particle methods, such as the well-established G0W0 approach, reveals significant quasi-particle weight renormalization. Surprisingly, however, in nearly all the considered cases, the coupling constants computed in the DFT framework are excellent approximates of the ones in the quasi-particle framework, which is traced back to a significant cancellation of competing terms. Other quasi-particle methods, such as the Outer Valence Green's Function approach and the Δ<i>S</i>CF method, are also included in the comparison. Moreover, we investigate the coupling of vibrations to excitonic excitations and find, by comparison to time-dependent density functional theory and extended multiconfiguration quasi-degenerate second-order perturbation theory, that knowing the underlying electron- and hole-vibration couplings is sufficient to accurately determine the exciton-vibration coupling constants in the studied cases.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2371-2385"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481728","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":"Machine Learning Force Field for Optimization of Isolated and Supported Transition Metal Particles.","authors":"Alexandre Boucher, Cameron Beevers, Bertrand Gauthier, Alberto Roldan","doi":"10.1021/acs.jctc.4c01606","DOIUrl":"10.1021/acs.jctc.4c01606","url":null,"abstract":"<p><p>Computational modeling is an integral part of catalysis research. With it, new methodologies are being developed and implemented to improve the accuracy of simulations while reducing the computational cost. In particular, specific machine-learning techniques have been applied to build interatomic potential from ab initio results. Here, we report an energy-free machine-learning calculator that combines three individually trained neural networks to predict the energy and atomic forces of metallic particles. The investigated structures were a monometallic Pd nanoparticle, a bimetallic AuPd nanoalloy, and supported Pd metal crystallites on silica. Atomic energies were predicted via a graph neural network, leading to a mean absolute error (MAE) within 0.004 eV from density functional theory (DFT) calculations. The task of predicting atomic forces was split over two feed-forward networks, one predicting the force norm and another its direction. The force prediction resulted in a MAE within 0.080 eV/Å against DFT results. The interpretability of the graph neural network predictions was demonstrated by underlying the physics of the monometallic particle in the form of cohesion energy.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2626-2637"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912199/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490326","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":"Markov-Type State Models to Describe Non-Markovian Dynamics.","authors":"Sofia Sartore, Franziska Teichmann, Gerhard Stock","doi":"10.1021/acs.jctc.4c01630","DOIUrl":"10.1021/acs.jctc.4c01630","url":null,"abstract":"<p><p>When clustering molecular dynamics (MD) trajectories into a few metastable conformational states, the assumption of time scale separation between fast intrastate fluctuations and rarely occurring interstate transitions is often not valid. Hence, when we construct a Markov state model (MSM) from these states, the naive estimation of the macrostate transition matrix via simply counting transitions between the states may lead to significantly too-short implied time scales and thus to too-fast population decays. In this work, we discuss advanced approaches to estimate the transition matrix. Assuming that Markovianity is at least given at the microstate level, we consider the Laplace-transform-based method by Hummer and Szabo, as well as a direct microstate-to-macrostate projection, which by design yields correct macrostate population dynamics. Alternatively, we study the recently proposed quasi-MSM ansatz of Huang and co-workers to solve a generalized master equation, as well as a hybrid method that employs MD at short times and MSM at long times. Adopting a one-dimensional toy model and an all-atom folding trajectory of HP35, we discuss the virtues and shortcomings of the various approaches.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2757-2765"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912194/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514035","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}