Journal of Chemical Theory and Computation最新文献

{"title":"Quantum Time Dynamics Mediated by the Yang-Baxter Equation and Artificial Neural Networks.","authors":"Sahil Gulania, Yuri Alexeev, Stephen K Gray, Bo Peng, Niranjan Govind","doi":"10.1021/acs.jctc.5c00353","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00353","url":null,"abstract":"<p><p>Quantum computing shows great potential, but errors pose a significant challenge. This study explores new strategies for mitigating quantum errors using artificial neural networks (ANNs) and the Yang-Baxter equation (YBE). Unlike traditional error mitigation methods, which are computationally intensive, we investigate artificial error mitigation. We developed a novel method that combines ANNs for noise mitigation combined with the YBE to generate noisy data. This approach effectively reduces noise in quantum simulations, enhancing the accuracy of the results. The YBE rigorously preserves quantum correlations and symmetries in spin chain simulations in certain classes of integrable lattice models, enabling effective compression of quantum circuits while retaining linear scalability with the number of qubits. This compression facilitates both full and partial implementations, allowing the generation of noisy quantum data on hardware alongside noiseless simulations using classical platforms. By introducing controlled noise through the YBE, we enhance the data set for error mitigation. We train an ANN model on partial data from quantum simulations, demonstrating its effectiveness in mitigating errors in time-evolving quantum states, providing a scalable framework to enhance quantum computation fidelity, particularly in noisy intermediate-scale quantum (NISQ) systems. We demonstrate the efficacy of this approach by performing quantum time dynamics simulations using the Heisenberg XY Hamiltonian on real quantum devices.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289341","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 Correlation Optimized Virtual Orbital Algorithm for Plane-Wave Full Configuration Interaction Calculations.","authors":"Mingyu Qiu, Zhenlin Zhang, Zhiyuan Zhang, Yexuan Lin, Yingzhou Li, Jinlong Yang, Wei Hu","doi":"10.1021/acs.jctc.5c00586","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00586","url":null,"abstract":"<p><p>Full configuration interaction (FCI) calculations have historically faced significant challenges in dealing with periodic systems. The plane-wave basis sets are valued for their efficiency and broad applicability in various computational physics and chemistry simulations. Because of their natural periodicity, the plane-wave basis sets offer a potential solution to this problem. Moreover, FCI can address the limitations of widely used methods, such as density functional theory (DFT) with plane-wave basis sets, in accurately describing strongly correlated systems. However, the large basis set nature of the plane-wave makes them unsuitable for direct application in FCI calculations. To address this challenge, we propose an improved algorithm based on the correlation-optimized virtual orbital (COVOS) framework. By incorporating rotational matrices to enhance the active space dimension and optimizing orbitals through iterative coupled processes, we successfully compress the extensive plane-wave basis set into a manageable number of virtual orbitals suitable for FCI calculations while retaining most of the original basis set characteristics. We apply this method to supercell calculations and potential energy curves of periodic metallic systems. To further validate our approach, we test it on nonperiodic small molecular systems and compare the results with those obtained from DFT, second-order Møller-Plesset perturbation theory (MP2), random phase approximation (RPA), FCI calculations using the 6-31G or cc-pVDZ basis sets, and the original COVOS algorithm. The improved COVOS framework demonstrates significant advantages in convergence and correlation description over the original method. Furthermore, we observe metal divergence issues in MP2 calculations for certain metallic systems and note that RPA may overestimate the correlation energy of such systems. These findings underscore the importance of achieving FCI calculations with plane-wave basis sets.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144289340","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":"Energy-Filtered Excited States and Real-Time Dynamics Served in a Contour Integral.","authors":"Ke Liao","doi":"10.1021/acs.jctc.4c01220","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01220","url":null,"abstract":"<p><p>It is observed that the Cauchy integral formula (CIF) can be used to represent holomorphic functions of diagonalizable operators on a finite domain. This forms the theoretical foundation for applying various operators in the form of a contour integral to a state, while filtering away eigen-components that are not included by the contour. As a special case, the identity operator in the integral form─the Riesz projector─is used to design an algorithm for finding a given number of eigen-pairs whose energies are close to a specified value in the equation-of-motion coupled cluster singles and doubles (EOM-CCSD) framework, with applications to calculate core excited states of molecules which is relevant for the X-ray absorption spectroscopy (XAS). As a generalization, I showcase a novel real-time electron dynamics (RT-EOM-CCSD) algorithm based on the CIF form of the exponential time-evolution operator, which admits extremely large time steps while preserving accurate spectral information.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281692","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":"Non-Hermitian State-to-State Analysis of Transport in Aggregates with Multiple Endpoints.","authors":"Devansh Sharma, Amartya Bose","doi":"10.1021/acs.jctc.5c00497","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00497","url":null,"abstract":"<p><p>Efficiency of quantum transport through aggregates with multiple endpoints or traps proves to be an emergent and a highly nonequilibrium phenomenon. We present an exact approach for computing the emergent time-scale and amount of extraction specific to particular traps, leveraging a non-Hermitian generalization of the recently introduced state-to-state transport analysis [Bose and Walters, J. Chem. Theory Comput. 2023, <b>19</b>, 15, 4828-4836]. This method is able to simultaneously account for the coupling between various sites, the many-body effects brought in by the vibrations and environment held at a nonzero temperature, and the local extraction processes described by non-Hermitian terms in the Hamiltonian. In fact, our non-Hermitian state-to-state analysis goes beyond merely providing an emergent loss time-scale. It can parse the entire dynamics into the constituent internal transport pathways and loss to the environment. We demonstrate this method using examples of exciton transport in a lossy polaritonic cavity. The loss at the cavity and the extraction of the exciton from a terminal molecule provide competing mechanisms that our method helps to unravel, revealing nonintuitive physics. This non-Hermitian state-to-state analysis technique contributes an important link to understanding and elucidating the routes of transport in open quantum systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281694","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":"Random Phase Approximation Correlation Energy Using Real-Space Density Functional Perturbation Theory.","authors":"Boqin Zhang, Shikhar Shah, John E Pask, Edmond Chow, Phanish Suryanarayana","doi":"10.1021/acs.jctc.5c00528","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00528","url":null,"abstract":"<p><p>We present a real-space method for computing the random phase approximation (RPA) correlation energy within Kohn-Sham density functional theory, leveraging the low-rank nature of the frequency-dependent density response operator. In particular, we employ a cubic-scaling formalism based on density functional perturbation theory that circumvents the calculation of the response function matrix, instead relying on the ability to compute its product with a vector through the solution of the associated Sternheimer linear systems. We develop a large-scale parallel implementation of this formalism using the subspace iteration method in conjunction with the spectral quadrature method while employing the Kronecker product-based method for the application of the Coulomb operator and the conjugate orthogonal conjugate gradient method for the solution of the linear systems. We demonstrate convergence with respect to key parameters and verify the method's accuracy by comparing with plane-wave results. We show that the framework achieves good strong scaling to many thousands of processors, reducing the time to solution for a lithium hydride system with 128 electrons to around 150 s on 4608 processors.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273666","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":"Charge-Induced Polarization in Dielectric Particle Systems: A Geometry-Dependent Effect.","authors":"Eric B Lindgren","doi":"10.1021/acs.jctc.5c00544","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00544","url":null,"abstract":"<p><p>Electrostatic interactions in systems composed of finite-sized dielectric materials extend well beyond simple point-charge approximations, particularly when many-body polarization effects become significant. This study shows that asymmetries in the size or net charge of spherical particles can trigger nontrivial phenomena, including like-charge attraction and intricate force balances involving neutral species. Through a rigorous boundary-integral framework, it is substantiated that induced surface charges propagate through iterative cascades, reflecting the full many-body, nonadditive character of polarization. Significantly, a geometry-based cutoff is adopted to discriminate whether long-range interactions can be approximated by monopoles, thereby retaining near-field multipole couplings without forfeiting computational efficiency. This approach provides significant computational gains without compromising the rigor of many-body treatment, underscoring the critical interplay between geometric factors─specifically, particle size (and its associated curvature) and interparticle separation─in determining local field intensities, which often exceed conventional Coulombic predictions. The findings can illuminate pathways for understanding and designing advanced materials and self-assembled architectures in which dielectric polarization governs or contributes to emergent behavior.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281691","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":"Investigating Non-Markovian Effects on Quantum Dynamics in Open Quantum Systems.","authors":"Mariia Ivanchenko, Peter L Walters, Fei Wang","doi":"10.1021/acs.jctc.4c01632","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01632","url":null,"abstract":"<p><p>The reduced description of the quantum dynamic processes in the condensed phase environment leads to the equation of motion with a memory kernel. Such a memory effect, termed non-Markovianity, presents more complex dynamics compared to its memoryless or Markovian counterpart, and many chemical systems have been demonstrated through numerical simulations to exhibit non-Markovian quantum dynamics. Explicitly how the memory impacts the dynamic process remains largely unexplored. In this work, we focus on ways to separate the non-Markovian contributions from the dynamics and study the non-Markovian effects. Specifically, we developed a rigorous procedure for mapping the exact non-Markovian quantum propagator to the Lindblad form. Consequently, it allows us to extract the negative decay rate from the Lindbladian that is the signature of the non-Markovianity. By including or excluding the negative rate in the time evolution, we can decisively pinpoint the influence of non-Markovianity on the system's properties such as coherence, entanglement, and equilibrium state distribution. The understanding of such memory effects on the dynamic process suggests the possibility of leveraging non-Markovianity for quantum control.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281693","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":"Liquid Phase Modeling in Porous Media: Adsorption of Methanol and Ethanol in H-MFI in Condensed Water.","authors":"Subrata Kumar Kundu, Muhammad Zeeshan, Panuwat Watthaisong, Andreas Heyden","doi":"10.1021/acs.jctc.5c00427","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00427","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Zeolites are used in the chemical and separation industries for their exceptional selectivity, adsorption capacity, regenerability, and stability in gas and liquid phase processing. Here, we developed an explicit solvation method for predicting solvent/condensed phase effects on adsorption free energies in microporous media such as zeolites based on the hybrid quantum mechanical/molecular mechanical free energy perturbation (QM/MM-FEP) technique. Our explicit solvation method for zeolite systems, called eSZS, aims to capture site-specific interactions during the adsorption process at the Brønsted acid sites of H-MFI zeolite while still considering the diverse configuration space of the solvent molecules. This strategy is ideal for chemical reactions or adsorbates that interact with the microporous medium in few distinct adsorbate/transition state configurations, i.e., the harmonic or similar approximations are acceptable for the adsorbate/transition state while such approximations break down for the solvent molecules that require extensive configuration space sampling. In this way, our approach effectively overcomes the limitations of implicit solvation models and classical force field methods for describing solvation effects on chemical reactions within porous materials such as zeolites. Specifically, in this study, we investigated various aspects of our hybrid QM/MM approach, including QM cluster size dependencies in a periodic electrostatically embedded cluster model (PEECM), rules for link atoms at the QM/MM boundary, and functional and basis set considerations for converged and reasonably accurate gas and aqueous phase methanol and ethanol adsorption free energy predictions in H-MFI. For gas phase adsorption of methanol and ethanol in H-MFI at a Brønsted acid site in T12 position, we compute adsorption free energies at 298 K of -0.61 and -0.75 eV, respectively, using a PEECM containing 50 Si and 1 Al atom with ωB97x-D/def2-TZVP level of theory. For solvent effect calculations, we sample the aqueous phase using grand canonical Monte Carlo (GCMC) simulations to (1) obtain a mean field of electrostatic interactions in the reaction system and (2) perform a rigorous free energy perturbation calculation. Similar to the experimentally and computationally observed endergonic solvation effects observed for hydrocarbon adsorption on metal surfaces, we also observe that a condensed aqueous environment destabilizes methanol and ethanol at these acid sites in H-MFI at 298 K. Specifically, the computed solvation free energies of adsorption (ΔΔ&lt;i&gt;G&lt;/i&gt;&lt;sub&gt;solv&lt;/sub&gt;) for methanol and ethanol are +0.44 and +0.54 eV, respectively. From this study, it is evident that adsorbates (methanol and ethanol) are competing with water for adsorption space inside the H-MFI zeolite, leading to an endergonic solvation effect. We expect that the endergonic, aqueous solvent effect during adsorption in microporous zeolites is highly tunable by changing the pore size a","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144264806","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":"Evaluating the Tamm-Dancoff Approximation for Two-Photon Absorption Properties.","authors":"Ismael A Elayan, Ryan Johannson, Alex Brown","doi":"10.1021/acs.jctc.5c00436","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00436","url":null,"abstract":"<p><p>Two-photon absorption (2PA) is a powerful tool in nonlinear optics, enabling advanced applications like high-resolution microscopy and photodynamic therapy. In this study, we explore the 2PA properties of 20 chromophores using time-dependent density-functional theory (TD-DFT), TD-DFT with the Tamm-Dancoff approximation (TDA), and the resolution-of-identity approximation in conjunction with the second-order approximate coupled-cluster (RI-CC2). TDA's performance in predicting 2PA properties remains insufficiently characterized compared to (full) TD-DFT, where the functionals CAM-B3LYP, MN15, and ωB97X are used, and their results are compared to RI-CC2. This comparison involves assessing key photophysical properties, including 2PA cross sections (σ^2PA) and dipole moments (μ₀₀, μ₁₁, μ₀₁, and Δμ). Among the tested functionals, MN15 demonstrated the lowest mean absolute errors (MAEs) for the computed photophysical properties for both TDA and TD-DFT. Our findings indicate that TDA captures qualitative trends and provides slightly more accurate quantitative predictions with generally lower MAEs than TD-DFT. These findings suggest that the use of TDA has significant potential as a cost-effective alternative to (full) TD-DFT for predicting 2PA properties.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144264805","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":"NepoIP/MM: Toward Accurate Biomolecular Simulation with a Machine Learning/Molecular Mechanics Model Incorporating Polarization Effects.","authors":"Ge Song, Weitao Yang","doi":"10.1021/acs.jctc.5c00372","DOIUrl":"10.1021/acs.jctc.5c00372","url":null,"abstract":"<p><p>Machine learning force fields offer the ability to simulate biomolecules with quantum mechanical accuracy while significantly reducing computational costs, attracting a growing amount of attention in biophysics. Meanwhile, by leveraging the efficiency of molecular mechanics in modeling solvent molecules and long-range interactions, a hybrid machine learning/molecular mechanics (ML/MM) model offers a more realistic approach to describing complex biomolecular systems in solution. However, multiscale models with electrostatic embedding require accounting for the polarization of the ML region induced by the MM environment. To address this, we adapt the state-of-the-art NequIP architecture into a polarizable ML force field, NepoIP, enabling the modeling of polarization effects based on the external electrostatic potential. We found that the nanosecond MD simulations based on NepoIP/MM are stable for the periodic solvated dipeptide system, and the converged sampling shows excellent agreement with the reference QM/MM level. Moreover, we show that a single NepoIP model can be transferable across different MM force fields, as well as an extremely different MM environment of water and proteins, laying the foundation for developing a general ML biomolecular force field to be used in ML/MM with electrostatic embedding.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5588-5598"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144118401","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}