Journal of Chemical Theory and Computation最新文献

{"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}

{"title":"FC2DES: Modeling 2D Electronic Spectroscopy for Harmonic Hamiltonians.","authors":"Lucas Allan, Tim J Zuehlsdorff","doi":"10.1021/acs.jctc.5c00349","DOIUrl":"10.1021/acs.jctc.5c00349","url":null,"abstract":"<p><p>Two-dimensional electronic spectroscopy (2DES) can provide detailed insight into the energy transfer and relaxation dynamics of chromophores by directly measuring the nonlinear response function of the system. However, experiments are often difficult to interpret, and the development of computationally affordable approaches to simulate experimental signals is desirable. For linear spectroscopy, optical spectra of small to medium-sized molecules can be efficiently calculated in the Franck-Condon approach. Approximating the nuclear degrees of freedom as harmonic around the ground- and excited-state minima, closed-form expressions for the exact finite-temperature linear response function can be derived using known solutions for the propagation operator between normal mode coordinate sets, fully accounting for Duschinsky mode-mixing effects. In the present work, we demonstrate that a similar approach can be utilized to yield analogous closed-form expression for the finite-temperature nonlinear (third-order) response function of harmonic nuclear Hamiltonians. The resulting approach, named FC2DES, is implemented on graphics processing units, allowing efficient computations of 2DES signals for medium-sized molecules containing hundreds of normal modes. Benchmark comparisons against the widely used cumulant method for computing 2DES signals are performed on small model systems, as well as the nile red molecule. We highlight the advantages of the FC2DES approach, especially in systems with moderate Duschinsky mode mixing and for long delay times in the nonlinear response function, where low-order cumulant approximations are shown to fail.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5625-5641"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180458","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":"Anharmonic Vibrational States of Double-Well Potentials in the Solid State from DFT Calculations.","authors":"Davide Mitoli, Maria Petrov, Jefferson Maul, William B Stoll, Michael T Ruggiero, Alessandro Erba","doi":"10.1021/acs.jctc.4c01394","DOIUrl":"10.1021/acs.jctc.4c01394","url":null,"abstract":"<p><p>We introduce a general approach for the simulation of quantum vibrational states of (symmetric and asymmetric) double-well potentials in molecules and materials for thermodynamic and spectroscopic applications. The method involves solving the nuclear Schrödinger equation associated with a one-mode potential of the type <i>V</i>(<i>Q</i>) = <i>aQ</i>² + <i>bQ</i>³ + <i>cQ</i>⁴ (with <i>a</i> < 0 and <i>c</i> > 0) and thus explicitly includes nuclear quantum effects. The potential, <i>V</i>(<i>Q</i>), is obtained from density functional theory (DFT) calculations performed at displaced nuclear configurations along the selected normal mode, <i>Q</i>. The strategy has been implemented into the Crystal electronic structure package and allows for (i) the use of many density functional approximations, including hybrid ones, and (ii) integration with a quasi-harmonic module. The method is applied to the spectroscopic characterization of soft lattice modes in two phases of the molecular crystal of thiourea: a low-temperature ferroelectric phase and a high-temperature paraelectric phase. Signature peaks associated with structural changes between the two phases are found in the terahertz region of the electromagnetic spectrum, which exhibit strong anharmonic character in their thermal evolution, as measured by temperature-dependent terahertz time-domain spectroscopy.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5365-5371"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12159970/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143595808","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 Quantum Computational Method for Corrosion Inhibition.","authors":"Naman Jain, Rosa Di Felice","doi":"10.1021/acs.jctc.5c00469","DOIUrl":"10.1021/acs.jctc.5c00469","url":null,"abstract":"<p><p>We present a hybrid classical-quantum computational pipeline for the determination of adsorption energies of a benzotriazole molecule on an aluminum alloy surface relevant for the transport industry, in particular to address the corrosion problem. The molecular adsorbate and substrate alloy were selected by interrogating molecular and materials databases, in search for desired criteria. The protocol can be generalized to other surfaces with arbitrary orientation and chemical composition, as well as to other molecular adsorbates. It includes three main steps based on mean-field electronic structure calculations, embedding theories and quantum algorithms. The quantum computing step demonstrated here with the variational quantum eigensolver is amenable to any other reliable quantum algorithm for ground-state energy estimation. Excited-state energies can also be taken into account in the quantum computing step, if the target reaction involves excited states.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"5697-5711"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12160000/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172209","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":"","authors":"Davide Mitoli,&nbsp;Maria Petrov,&nbsp;Jefferson Maul,&nbsp;William B. Stoll,&nbsp;Michael T. Ruggiero* and Alessandro Erba*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 11","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.4c01394","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144354531","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 11","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/ctv021i011_1943863","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144354536","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}