Journal of Chemical Theory and Computation最新文献

{"title":"Combining Optical Control and Geometrical Optimization for Efficient Control of Competing Molecular Photoinduced Processes Far from the Ground State.","authors":"David Veintemillas,Bo Y Chang,Ignacio R Sola","doi":"10.1021/acs.jctc.5c00609","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00609","url":null,"abstract":"The yield of a photochemical process can be maximized by optimizing the driving fields, such as in optical control, or the initial wave function, as in geometrical optimization. We combine both algorithms in an iterative process, showing very fast convergence and great improvement in the yields, as applied to driving population to the second excited state of the molecular hydrogen cation through the first excited dissociative state by a pump-pump scheme. The results reveal the impact of the initial vibrational coherences in photoinduced processes that occur at nuclear configurations very far from the ground state, or that are even mediated by processes in the continuum. On the other hand, depending on whether we maximize the total electronic population (that mainly dissociates) or the bound population, the initial wave functions change considerably, involving nodal patterns in the position or in the momentum representations, respectively, that lead to different dynamics.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"12 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329023","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":"Ab Initio Valence Bond Theory for Strongly Correlated Systems.","authors":"Chen Zhou,Xun Wu,Fuming Ying,Wei Wu","doi":"10.1021/acs.jctc.5c00596","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00596","url":null,"abstract":"Strongly correlated systems, characterized by significant multiconfigurational character, pose a persistent challenge in quantum chemistry. While molecular orbital (MO)-based multiconfigurational self-consistent field methods such as CASSCF and CASPT2 have become standard tools for treating such systems, valence bond (VB) theory offers a conceptually distinct and chemically intuitive alternative. Rooted in the classical Lewis structure framework, VB theory provides a compact and localized description of electron pairing, making it especially well-suited for strongly correlated systems. This review presents a comprehensive overview of the methodological development and practical applications of ab initio VB approaches, including VB self-consistent field (VBSCF), breathing orbital VB (BOVB), VB configuration interaction (VBCI), VB perturbation theory (VBPT2), and density functional VB (DFVB) methods. Particularly, the VBPT2 and DFVB methods enable accurate treatment of bond dissociation, excitation energies, and reaction barriers. Benchmark comparisons demonstrate that VB-based methods achieve performance comparable to established MO-based methods. The findings highlight the promise of VB theory as a powerful and interpretable framework for advancing the theoretical understanding of strongly correlated systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"45 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144335354","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":"Modulation of Electric Field and Interface on Competitive Reaction Mechanisms.","authors":"Pengchao Zhang,Xuefei Xu","doi":"10.1021/acs.jctc.5c00705","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00705","url":null,"abstract":"Recently, much evidence has accumulated, showing that electric fields and water interfaces influence the characteristics and alignment of biomolecules and greatly boost reaction rates. The prototropic tautomerism is a fundamental process in biological systems; however, a comprehensive understanding of the electric field effects and interfacial effects on it is still lacking. In this work, we performed a theoretical study of the modulation of the electric field and the interface on the tautomerism dynamics of solvated glycine by using deep potential molecular dynamics technology with enhanced sampling. The deep learning potentials used were trained to integrate long-range electrostatic interactions in order to better describe the electric field effect. We observed that an external electric field of 10 mV/Å barely changed the key structures involved in tautomerism reactions but significantly influenced their relative free energies and consequently made the transformation from zwitterionic ([Z]) to neutral ([N]) glycine more achievable both thermodynamically and dynamically and altered the optimal reaction mechanism from intramolecular proton transfer (Intra-PT) to intermolecular proton transfer (Inter-PT) involving a separate cationic-glycine-hydroxide ion pair. The detailed analysis revealed that the electric field increased the thermodynamical stability of [N] relative to [Z] by 7 kJ/mol due to the entropy effect and promoted the Inter-PT pathway by electrostatically facilitating the separation of ion pairs, causing the free-energy-barrier decrease of the rate-determined step by approximately 10 kJ/mol. Interestingly, in the air-water interface, due to the interfacial propensity of the glycine and water self-ions, the separation of ion pairs is restricted, slowing the Inter-PT pathways. Nevertheless, the interfacial interconversion between the [Z] and [N] forms of glycine is dynamically accelerated via the Intra-PT pathway due to partial solvation. These findings provide new insights into how the electric field and interfaces modulate thermodynamics, kinetics, and the mechanism of chemical reactions.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"237 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144329024","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":"Transfer Learning for Predictive Molecular Simulations: Data-Efficient Potential Energy Surfaces at CCSD(T) Accuracy.","authors":"Silvan Käser,Jeremy O Richardson,Markus Meuwly","doi":"10.1021/acs.jctc.5c00523","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00523","url":null,"abstract":"Accurate potential energy surfaces (PESs) are critical for predictive molecular simulations. However, obtaining a PES at the highest levels of quantum chemical accuracy, such as CCSD(T), becomes computationally infeasible as molecular size increases. This work presents CCSD(T)-quality PESs using data-efficient techniques based on transfer learning to obtain state-of-the-art accuracy at a fraction of the computational cost for systems that would otherwise be intractable. Most importantly, the framework for accurate molecular simulations pursued here extends beyond specific observables and follows a rational strategy to obtain highest-accuracy PESs, which can be used for applications to spectroscopy and other experiments. As rigorous tests of the PESs, semiclassical tunnelling splittings for tropolone and the (propiolic acid)-(formic acid) dimer (PFD) as well as anharmonic frequencies for tropolone were determined. For tropolone, all observables are in excellent agreement with the experiment using the high-level PES, whereas for PFD, the agreement is less good but still orders of magnitude better than previous calculations.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"15 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144335355","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":"General Quantum Alchemical Free Energy Simulations via Hamiltonian Interpolation.","authors":"Chenghan Li, Xing Zhang, Garnet Kin-Lic Chan","doi":"10.1021/acs.jctc.5c00682","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00682","url":null,"abstract":"<p><p>We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure theory and requires only one quantum calculation for each molecular dynamics step in contrast to multiple energy evaluations that would be needed when interpolating the ground-state energies. We demonstrate the correctness and applicability of the technique by computing alchemical free energy changes of gas-phase molecules, with both nuclear and electron creation/annihilation. We also show an initial application to first-principles p<i>K</i>_a calculation for solvated molecules where we quantum mechanically annihilate a bonded proton.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144332057","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 Chemical Space with Chemistry-Inspired Dynamic Quantum Circuits in the NISQ Era.","authors":"Lung-Yi Chen,Tai-Yue Li,Yi-Pei Li,Nan-Yow Chen,Fengqi You","doi":"10.1021/acs.jctc.5c00305","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00305","url":null,"abstract":"The generation of chemical molecular structures is crucial for advancements in drug design, materials science, and related fields. With the rise of artificial intelligence, numerous generative models have been developed to propose promising molecular structures to specific challenges. However, exploring the vast chemical space using classical generative models demands extensive chemical structure data, considerable computational resources, and a large number of model parameters, which hinders their efficiency. Quantum computing presents a promising alternative by exploiting quantum parallelism and entanglement, potentially reducing the computational overhead required for such tasks. In this study, we designed a quantum-based molecular generator (QMG) specifically tailored to generate small molecules containing carbon, nitrogen, and oxygen atoms. This model imposes strict constraints on the quantum circuit's output quantum states, significantly eliminating mathematically invalid connection graphs and enabling more efficient sampling of valid molecular structures. Remarkably, our quantum circuit, utilizing only 134 parameters, is capable of enumerating all molecular structures comprising up to nine heavy atoms, showcasing the parameter efficiency achievable through quantum superposition and entanglement. Our experimental results show that the output generated by this circuit exhibits a high degree of validity and uniqueness after Bayesian optimization, showing comparable performance to classical deep generative models. Furthermore, by fixing specific parameters in the quantum circuits, the quantum generator can constrain the chemical space and exclusively generate chemical molecules containing specified functional groups. This feature underscores its potential value for targeted applications in specific domains, especially in drug discovery. Overall, this compact design not only reduces parameter demands but also enables efficient exploration of a nontrivial portion of chemical space, demonstrating a key advantage of quantum-based generative models over larger classical counterparts.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320357","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 Computational Framework for Simulations of Dissipative Nonadiabatic Dynamics on Hybrid Oscillator-Qubit Quantum Devices.","authors":"Nam P Vu, Daniel Dong, Xiaohan Dan, Ningyi Lyu, Victor Batista, Yuan Liu","doi":"10.1021/acs.jctc.5c00315","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00315","url":null,"abstract":"<p><p>We introduce a computational framework for simulating nonadiabatic vibronic dynamics on circuit quantum electrodynamics (cQED) platforms. Our approach leverages hybrid oscillator-qubit quantum hardware with midcircuit measurements and resets, enabling the incorporation of environmental effects such as dissipation and dephasing. To demonstrate its capabilities, we simulate energy transfer dynamics in a triad model of photosynthetic chromophores inspired by natural antenna systems. We specifically investigate the role of dissipation during the relaxation dynamics following photoexcitation, where electronic transitions are coupled to the evolution of quantum vibrational modes. Our results indicate that hybrid oscillator-qubit devices, operating with noise levels below the intrinsic dissipation rates of typical molecular antenna systems, can achieve the simulation fidelity required for practical computations on near-term and early fault-tolerant quantum computing platforms.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144323846","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":"Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.","authors":"Andreas Hulm,Robert P Schiller,Christian Ochsenfeld","doi":"10.1021/acs.jctc.5c00395","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00395","url":null,"abstract":"On-the-fly probability enhanced sampling (OPES) has recently been introduced [Invernizzi, M.; Parrinello, M. J. Chem. Theory Comput. 2022, 18, 3988-3996], with important improvements over the highly popular metadynamics methods. In our work, we introduce a new combination of OPES with the extended-system adaptive biasing force (eABF) method. We show that the resulting OPES-eABF hybrid is highly robust to the choice of input parameters, while ensuring faster exploration of configuration space than the original OPES. The only critical parameter of OPES-eABF is the coupling width to the extended-system, for which we introduce an automatic algorithm based on a short initial unbiased simulation, such that OPES-eABF requires minimal user intervention. Additionally, we show that due to the decoupling of the physical system from the time-dependent potential, unbiased probabilities of visited configurations are recovered highly accurately.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"13 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144320250","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":"State-Interaction Approach for g-Matrix Calculations in TDDFT: Ground-Excited State Couplings and beyond First-Order Spin-Orbit Effects.","authors":"Antonio Cebreiro-Gallardo,David Casanova","doi":"10.1021/acs.jctc.5c00514","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00514","url":null,"abstract":"We introduce a state-interaction approach for computing g-matrices within time-dependent density functional theory (TDDFT) and the Tamm-Dancoff approximation (TDA), applied here for the first time. This method provides a detailed understanding of g-shifts by explicitly accounting for spin-orbit couplings (SOC) and excitation energies, enabling the analysis of different SOC orders and their contributions. To evaluate its accuracy and reliability, we compare state-interaction TDDFT and TDA with the widely used one-component coupled-perturbed Kohn-Sham approach. Applications to a diverse set of systems, including light and heavy atom molecules as well as transition-metal complexes, demonstrate that both methods yield comparable results in the absence of heavy elements, while the state-interaction approach offers improved insights into SOC effects and their impact on g-shifts.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"35 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144311599","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":"Graphically Defined Model Reactions Are Extensible, Accurate, and Systematically Improvable.","authors":"Qiyuan Zhao, Veerupaksh Singla, Hsuan-Hao Hsu, Brett M Savoie","doi":"10.1021/acs.jctc.5c00279","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00279","url":null,"abstract":"<p><p>Achieving fast and accurate reaction prediction is central to a suite of chemical applications. Nevertheless, classic approaches based on templates or simple models are typically fast but with limited scope or accuracy, while the emerging machine learning-based models are limited in their transferability due to the lack of large reaction databases. Here, we address these limitations by formalizing the model reaction concept based on fixed-depth condensed reaction graphs that are shown to achieve a cost and accuracy balance that is applicable to many problems. The model reaction concept can be utilized to provide reliable predictions of activation energies and transition state geometries for a large range of organic reactions. In addition, using an alkane pyrolysis system as a benchmarking example, we show that the accuracy of the activation energy prediction can be further improved by adding correction terms based on the empirical Brønsted-Evans-Polanyi (BEP) relationship. These successful applications demonstrate that the model reaction can serve as a general tool to reduce the cost associated with ab initio transition state searches.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144315558","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}