Journal of Chemical Theory and Computation最新文献

{"title":"Algebraic Diagrammatic Construction Theory of Charged Excitations with Consistent Treatment of Spin-Orbit Coupling and Dynamic Correlation.","authors":"Rajat Majumder, Alexander Yu Sokolov","doi":"10.1021/acs.jctc.4c01762","DOIUrl":"10.1021/acs.jctc.4c01762","url":null,"abstract":"<p><p>We present algebraic diagrammatic construction theory for simulating spin-orbit coupling and electron correlation in charged electronic states and photoelectron spectra. Our implementation supports Hartree-Fock and multiconfigurational reference wave functions, enabling efficient correlated calculations of relativistic effects using single-reference (SR-) and multireference-algebraic diagrammatic construction (MR-ADC). We combine the SR- and MR-ADC methods with three flavors of spin-orbit two-component Hamiltonians and benchmark their performance for a variety of atoms and small molecules. When multireference effects are not important, the SR-ADC approximations are competitive in accuracy to MR-ADC, often showing closer agreement with experimental results. However, for electronic states with multiconfigurational character and in nonequilibrium regions of potential energy surfaces, the MR-ADC methods are more reliable, predicting accurate excitation energies and zero-field splittings. Our results demonstrate that the spin-orbit ADC methods are promising approaches for interpreting and predicting the results of modern spectroscopies.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2414-2431"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466489","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":"Low-Rank Algorithms for Ab Initio Valence Bond Approaches.","authors":"Chenru Ji, Yueyang Zhang, Fuming Ying, Chen Zhou, Wei Wu","doi":"10.1021/acs.jctc.4c01787","DOIUrl":"10.1021/acs.jctc.4c01787","url":null,"abstract":"<p><p>Valence bond (VB) theory is an ab initio approach that provides intuitive pictures and insights into chemical bonds and reaction mechanisms. This work integrates low-rank algorithms, including the resolution of the identity and the chain of spheres for exchange, into VB methods. These algorithms significantly improve the efficiency of VB calculations by reducing the computational expense and storage requirement of Fock matrix construction and integral transformations while preserving chemical accuracy. Historically, VB methods were limited to small or model systems due to these computational challenges. The adoption of low-rank techniques now enables efficient optimization of the full set of orbitals in ab initio VB theory, extending its applicability to molecular systems exceeding 100 atoms. The low-rank algorithm expands the scope of VB theory, allowing the study of larger and more realistic molecular systems from a VB perspective.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2462-2471"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143481729","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 Simulation of Surface-Enhanced Raman Scattering with a Simplified Damped Response Theory.","authors":"Gaohe Hu, Lasse Jensen","doi":"10.1021/acs.jctc.4c01567","DOIUrl":"10.1021/acs.jctc.4c01567","url":null,"abstract":"<p><p>Theoretical studies on enhancement mechanisms of surface-enhanced Raman scattering (SERS) are usually carried out with full quantum mechanical methods to capture the specific interactions between molecules and substrates. However, due to the computational costs of methods like time-dependent density functional theory (TDDFT), simplified model systems are commonly adopted. In the framework of TDDFT, the damped response theory is usually invoked to give a unified description of both on- and off-resonance Raman spectra based on the calculation of polarizability derivatives. However, the computational costs of full TDDFT allow for modeling SERS spectra only using small metal clusters. In this work, we demonstrate the implementation of an efficient method that simplifies the damped response calculations for the simulation of both on- and off-resonance SERS spectra. This simplified damped response method is named as TBAOResponse. We first compare the absorption spectra of a regular small system calculated with TBAOResponse and full TDDFT to benchmark the new method. Then, we demonstrate the efficiency and accuracy of the new method by comparing the on- and off-resonance SERS spectra calculated with different methods. Compared to full TDDFT, while significant improvement of efficiency is achieved, the simplified damped response maintains good accuracy for SERS calculation. We further showcase the efficiency of TBAOResponse by calculating the SERS spectra for a system that is computationally demanding with full TDDFT. This new method is promising for modeling SERS systems when a full quantum mechanical description of both the substrate and the molecule is necessary.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2546-2557"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447386","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":"Machine Learning Model to Predict Free-Energy Landscape and Position-Dependent Diffusion Constant to Extend the Scale of Dynamic Monte Carlo Simulations.","authors":"Tetsuro Nagai, Nobuaki Kikkawa, Ryosuke Jinnouchi, Masayuki Kimura, Susumu Okazaki","doi":"10.1021/acs.jctc.4c01552","DOIUrl":"10.1021/acs.jctc.4c01552","url":null,"abstract":"<p><p>We present a method to predict mass transport properties of large-scale heterogeneous media via coarse-grained dynamics using a dynamic Monte Carlo (MC) simulation aided by a machine learning (ML) surrogate model. The ML model was constructed to reproduce the free-energy landscape and local diffusion constant calculated by all-atom molecular dynamics (MD) simulations, aiming to efficiently evaluate these two local properties necessary for dynamic MC simulations. In this study, the ML model was built using kernel functions of descriptors representing local elemental distribution functions. The method was applied to the molecular diffusion of hydrogen in perfluorinated ionomer membranes for fuel cells, demonstrating that dynamic MC simulation using the ML model accurately reproduced the global diffusion constant across a wide range of humidity conditions, with a relative error of only 3% as compared with the original MC with the explicit position-dependent free energy and diffusion constant. On the basis of the learning curve of the ML model, even a relatively small training data set can reach a relative error of 5%. This approach is expected to be a valuable tool for elucidating mass transport mechanisms in various heterogeneous systems such as fuel cells, batteries, and biological systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2598-2611"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490327","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":"Multiscale Force Field Model Based on a Graph Neural Network for Complex Chemical Systems.","authors":"Zhaoxin Xie, Yanheng Li, Yijie Xia, Jun Zhang, Sihao Yuan, Cheng Fan, Yi Isaac Yang, Yi Qin Gao","doi":"10.1021/acs.jctc.4c01449","DOIUrl":"10.1021/acs.jctc.4c01449","url":null,"abstract":"<p><p>Inspired by the QM/MM methodology, the ML/MM approach introduces a new opportunity for multiscale simulation, improving the balance between accuracy and computational efficiency. Benefited from the rapid advancements in molecular embedding methods, density functional theory level quantum mechanical (QM) calculations within the QM/MM framework can be accelerated by several orders of magnitude through the application of machine learning (ML) potential energy surfaces. As a problem inherited from the QM/MM methodology, challenges exist in designing the interactions between machine learning and molecular mechanics (MM) regions. In this study, electrostatic interactions between machine learning and MM atoms are treated by using a graphical neural network based on stationary perturbation theory. In this protocol, we process coordinates and MM charges to yield electrostatic energy and forces, resulting in a high-performance electrostatic embedding ML/MM architecture. The accuracy of the ML/MM energy was validated in aqueous solutions of alanine dipeptide and allyl vinyl ether (AVE). We investigated the transferability of parameters trained from AVE in a single solvent to various other solvents, including water, methanol, dimethyl sulfoxide, toluene, ionic liquids, and water-toluene interface environments. We then established a solvent-free protocol for data set preparation. Comparison of the free energy landscapes of the Claisen rearrangement of AVE in different solvation environments showed the catalytic effect of aqueous solutions, consistent with experiments.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2501-2514"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514039","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":"Simulating Electronic Structure on Bosonic Quantum Computers.","authors":"Rishab Dutta, Nam P Vu, Chuzhi Xu, Delmar G A Cabral, Ningyi Lyu, Alexander V Soudackov, Xiaohan Dan, Haote Li, Chen Wang, Victor S Batista","doi":"10.1021/acs.jctc.4c01400","DOIUrl":"10.1021/acs.jctc.4c01400","url":null,"abstract":"<p><p>Quantum harmonic oscillators, or qumodes, provide a promising and versatile framework for quantum computing. Unlike qubits, which are limited to two discrete levels, qumodes have an infinite-dimensional Hilbert space, making them well-suited for a wide range of quantum simulations. In this work, we focus on the molecular electronic structure problem. We propose an approach to map the electronic Hamiltonian into a qumode bosonic problem that can be solved on bosonic quantum devices using the variational quantum eigensolver (VQE). Our approach is demonstrated through the computation of ground potential energy surfaces for benchmark model systems, including H₂ and the linear H₄ molecule. The preparation of trial qumode states and the computation of expectation values leverage universal ansatzes based on the echoed conditional displacement (ECD), or the selective number-dependent arbitrary phase (SNAP) operations. These techniques are compatible with circuit quantum electrodynamics (cQED) platforms, where microwave resonators coupled to superconducting transmon qubits can offer an efficient hardware realization. This work establishes a new pathway for simulating many-fermion systems, highlighting the potential of hybrid qubit-qumode quantum devices in advancing quantum computational chemistry.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2281-2300"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143539355","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":"Amber ff24EXP-GA, Based on Empirical Ramachandran Distributions of Glycine and Alanine Residues in Water.","authors":"Athul Suresh, Reinhard Schweitzer-Stenner, Brigita Urbanc","doi":"10.1021/acs.jctc.4c01450","DOIUrl":"10.1021/acs.jctc.4c01450","url":null,"abstract":"<p><p>Molecular dynamics (MD) offers important insights into intrinsically disordered peptides and proteins (IDPs) at a level of detail that often surpasses that available through experiments. Recent studies indicate that MD force fields do not reproduce intrinsic conformational ensembles of amino acid residues in water well, which limits their applicability to IDPs. We report a new MD force field, Amber ff24EXP-GA, derived from Amber ff14SB by optimizing the backbone dihedral potentials for guest glycine and alanine residues in cationic GGG and GAG peptides, respectively, to best match the guest residue-specific spectroscopic data. Amber ff24EXP-GA outperforms Amber ff14SB with respect to conformational ensembles of all 14 guest residues x (G, A, L, V, I, F, Y, D^p, E^p, R, C, N, S, T) in GxG peptides in water, for which complete sets of spectroscopic data are available. Amber ff24EXP-GA captures the spectroscopic data for at least 7 guest residues (G, A, V, F, C, T, E^p) better than CHARMM36m and exhibits more amino acid specificity than both the parent Amber ff14SB and CHARMM36m. Amber ff24EXP-GA reproduces the experimental data on three folded proteins and three longer IDPs well, while outperforming Amber ff14SB on short unfolded peptides.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2515-2534"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143466495","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":"Time-Reversible Implementation of MASH for Efficient Nonadiabatic Molecular Dynamics.","authors":"J Amira Geuther, Kasra Asnaashari, Jeremy O Richardson","doi":"10.1021/acs.jctc.4c01684","DOIUrl":"10.1021/acs.jctc.4c01684","url":null,"abstract":"<p><p>In this work, we describe various improved implementations of the mapping approach to surface hopping (MASH) for simulating nonadiabatic dynamics. These include time-reversible and piecewise-continuous integrators, which are only formally possible because of the deterministic nature of the underlying MASH equations of motion. The new algorithms allow for the use of either wave-function overlaps or nonadiabatic coupling vectors to propagate the spin, which encodes the electronic state. For a given time-step, Δ<i>t</i>, it is demonstrated that the global error for these methods is <math><mi>O</mi><mrow><mo>(</mo><mi>Δ</mi><msup><mrow><mi>t</mi></mrow><mrow><mn>2</mn></mrow></msup><mo>)</mo></mrow></math> compared to the <math><mi>O</mi><mrow><mo>(</mo><mi>Δ</mi><mi>t</mi><mo>)</mo></mrow></math> error of standard implementations. This allows larger time-steps to be used for a desired error tolerance, or conversely, more accurate observables given a fixed value of Δ<i>t</i>. The newly developed integrators thus provide further advantages for the MASH method, demonstrating that it can be implemented more efficiently than other surface-hopping approaches, which cannot construct time-reversible integrators due to their stochastic nature.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2179-2188"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912208/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143490329","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":"Fukui Function and Fukui Potential for Solid-State Chemistry: Application to Surface Reactivity","authors":"Nicolás F. Barrera,&nbsp;Javiera Cabezas-Escares,&nbsp;Francisco Muñoz,&nbsp;Wilver A. Muriel,&nbsp;Tatiana Gómez*,&nbsp;Mònica Calatayud and Carlos Cárdenas*,&nbsp;","doi":"10.1021/acs.jctc.5c0008610.1021/acs.jctc.5c00086","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00086https://doi.org/10.1021/acs.jctc.5c00086","url":null,"abstract":"<p >The Fukui function and its associated potential serve as essential descriptors of chemical reactivity within the framework of conceptual density functional theory (c-DFT). While c-DFT is well-established for molecular systems, it encounters formal and technical challenges when applied to extended systems. This comprehensive study addresses the complexities involved in calculating the Fukui function and its potential in systems with periodic boundary conditions (PBC). We specifically investigate the introduction of a fictitious potential associated with a compensating background of charge (CBC) in these calculations, examining its implications for the reliability of these reactivity descriptors. To explore this issue, we analyze a diverse range of metallic and semiconductor surfaces, including elemental metals such as Ti and Pt, metal oxides like TiO₂, SnO₂, and MgO, and transition metal carbides such as TiC and ZrC. By encompassing this varied selection, this work aims to uncover both the limitations and advantages of various computational approaches in accurately capturing the intrinsic chemical reactivity of extended systems. Our findings indicate that while certain methods yield reliable results, others introduce artifacts that can significantly distort interpretations of surface reactivity. We advocate for the calculation of the Fukui function and potential using finite differences with self-consistent potential correction whenever feasible. Interpolation methods may also be employed if delocalization errors are manageable. Furthermore, we demonstrate that a reliable method for computing the Fukui potential, in combination with perturbation theory, can predict the interaction energies of reducing agents such as sodium and oxidants like chlorine with TiO₂ surfaces, thus supporting the application of c-DFT in heterogeneous catalysis. This research contributes critical insights to the field, offering practical methodologies to address the inherent challenges in predicting surface reactivity. By elucidating the complexities of the Fukui function under PBC, we not only enhance theoretical frameworks but also equip researchers with robust tools for advancing materials science and surface chemistry.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 6","pages":"3187–3203 3187–3203"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143678570","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":"Discretization of Structured Bosonic Environments at Finite Temperature by Interpolative Decomposition: Theory and Application.","authors":"Hideaki Takahashi, Raffaele Borrelli","doi":"10.1021/acs.jctc.4c01728","DOIUrl":"10.1021/acs.jctc.4c01728","url":null,"abstract":"<p><p>We present a comprehensive theory for a novel method to discretize the spectral density of a bosonic heat bath, as introduced in [Takahashi, H.; Borrelli, R. <i>J. Chem. Phys.</i> 2024, 161, 151101]. The approach leverages a low-rank decomposition of the Fourier-transform relation connecting the bath correlation function to its spectral density. By capturing the time, frequency, and temperature dependencies encoded in the spectral density-autocorrelation function relation, our method significantly reduces the degrees of freedom required for simulating open quantum system dynamics. We benchmark our approach against existing methods and demonstrate its efficacy through applications to both simple models and a realistic electron transfer process in biological systems. Additionally, we show that this new approach can be effectively combined with the tensor-train formalism to investigate the quantum dynamics of systems interacting with complex non-Markovian environments. Finally, we provide a perspective on the selection and application of various spectral density discretization techniques.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"2206-2218"},"PeriodicalIF":5.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439346","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}