Journal of Chemical Theory and Computation最新文献

{"title":"Quasiclassical Doorway-Window Simulation of Femtosecond Transient-Absorption Pump-Probe Signals Beyond the Weak-Pump Limit.","authors":"Hefen Guan,Kewei Sun,Luis Vasquez,Lipeng Chen,Sebastian V Pios,Zhenggang Lan,Maxim F Gelin","doi":"10.1021/acs.jctc.5c00515","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00515","url":null,"abstract":"We developed an ab initio on-the-fly protocol for the simulation of transient-absorption strong-pump weak-probe signals by combining a trajectory surface hopping method with the classical doorway-window approximation. With this protocol, transient-absorption strong-pump weak-probe signals can be evaluated at about the same computational cost as weak-pulse transient-absorption pump-probe signals. The methodology is illustrated by the simulation of transient-absorption strong-pump weak-probe spectra of pyrazine, the weak-pulse pump-probe spectra of which were computed with the on-the-fly trajectory surface hopping─doorway-window method by Gelin et al., J. Chem. Theory Comput. 2021, 17, 2394. The effect of the intensity of the pump pulse on the transient-absorption strong-pump weak-probe spectra is investigated. In particular, it is demonstrated that the relative intensities of the ground-state bleach, stimulated emission, and excited-state absorption signals can be modified by variation of the strength of the pump pulse.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"124 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701377","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":"Long-Range Redox and Water Activation at Metal-Water Interfaces with Ferroelectric Ordering.","authors":"Arthur Hagopian,Jean-Sébastien Filhol,Tobias Binninger","doi":"10.1021/acs.jctc.5c00814","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00814","url":null,"abstract":"The molecular structure of water has profound influence on electron transfer and redox processes at metal-water interfaces. While ab initio molecular dynamics simulations provide an accurate description of the interfacial structure, the respective computational cost is often prohibitive. Static simulations using a few ordered water layers can serve as a pragmatic alternative maintaining an explicit description of molecular interactions at an affordable computational cost. We here study the coupling between electronic and structural degrees of freedom at ferroelectrically ordered metal-water interfaces. With increasing number of ice-like water layers, we observe a long-range transfer of electrons between the metal's Fermi level and HOMO/LUMO states of the outermost water molecules, mediated by ordered solvent dipole layers. Our findings reveal limitations of the applicability of the ordered interface model and reveal a strong coupling between ferroelectric ordering and long-range (auto)redox phenomena at dipolar solvent structures, shedding new light onto the long-standing question on the existence and stability of ferroelectric ice. Implications for the activation of water molecules in electrocatalytic reactions at charged metal-water interfaces are suggested.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"17 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693191","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":"Describing Excited States of Covalently Connected Crystals with Cluster and Embedded Cluster Approaches: Challenges and Solutions.","authors":"Michael Ingham,Marcus Brady,Rachel Crespo-Otero","doi":"10.1021/acs.jctc.5c00539","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00539","url":null,"abstract":"Understanding excited-state processes is essential for designing new functional organic materials. Modeling excited states in organic crystals is challenging due to the need to balance localized and delocalized processes and the competition between intramolecular and intermolecular interactions. Cluster models have proven highly effective for describing weakly interacting organic crystals; however, nonperiodic calculations on periodic systems must account for mechanical and electrostatic coupling to the crystal lattice, particularly in cases of extended coordination where covalent bonds are severed, such as in organic polymers and metal-organic frameworks (MOFs). Point charge embedding is a low-cost method for incorporating long-range electrostatics, enabling the consideration of long-range interactions using Ewald embedding. Small clusters have been effective for modeling excited-state processes in MOFs, yet embedding has rarely been included in such studies. In this work, we examine some of the challenges in describing excited states in covalently connected organic crystals using ONIOM(QM:QM') embedding techniques across systems with increasing coordination: diC4-BTBT (an organic molecular crystal), polythiophene (an organic polymer), and two MOFs (QMOF-d29cec2 and MOF-5). We analyze the effects of using different electronic structure methods, including TDHF, TDDFT, ADC(2), and CC(2). One of the main challenges is that embedded cluster models are susceptible to overpolarization near the QM:QM' boundary. To address this, we assess the impact of different charge redistribution schemes (Z-N (N = 0, 3), RC, and RCD) and implement them in fromage. Additionally, we compare cluster and periodic models. We find that localized models effectively reproduce excited states in both nonconnected systems (diC4-BTBT) and fully connected MOFs, whereas polythiophene remains the most challenging due to band conduction. The accuracy of vertical excitations, oscillator strengths, and simulated spectra is strongly influenced by model size, boundary charges, redistribution schemes, and level of theory. We further analyze the effect of vibrational broadening using the nuclear ensemble approach to predict the absorption and emission spectra of MOF-5. Our results provide a heuristic guide for nonperiodic studies of crystalline excited states, highlighting the remarkable relationship between molecular crystals and MOFs, which will be explored in the future work.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"93 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701108","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":"Reproducibility of QM/MM Calculations for the SARS-CoV-2 Main Protease.","authors":"Xiaoli Sun,Ulf Ryde","doi":"10.1021/acs.jctc.5c00841","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00841","url":null,"abstract":"Combined quantum mechanics and molecular mechanics (QM/MM) calculations are a popular approach to study reaction mechanisms of enzymes. However, recently, the reproducibility of such calculations has been questioned, comparing the results of two software: NWChem and Q-Chem. Here, we continue and extend this study by including three additional software─ComQum, ORCA, and AMBER─using the same test case, the covalent attachment of the carmofur inhibitor to the catalytic Cys-145 residue of the SARS-CoV-2 main protease, using a quantum region of 83 atoms. We confirm that the various software programs give varying results for the reaction (ΔE) and activation (ΔE‡) energies. The main reason for the variation is how charges around the cleaved bonds between the QM and MM regions are treated, i.e., the charge-redistribution scheme. However, there are still differences of ∼10 kJ/mol between different implementations of the same method in ComQum and ORCA. Some of these problems can be solved by calculating the final energies with larger QM systems. We show that energies calculated with the big-QM approach are reasonably converged if atoms within 8 Å of the minimal QM region are included (∼1400 atoms), solvent-exposed charged residues are neutralized, and the calculation is performed in a continuum solvent with a dielectric constant of 80. On the other hand, we show that different setups of the protein lead to even larger differences in the calculated energies, by up to 114 kJ/mol. Even if the same approach is used and the only difference is how water molecules are added (by random) to the crystal structure, energies differ by 18-57 kJ/mol. The results also strongly depend on how much of the surrounding protein and solvent are relaxed in the calculations. Therefore, it seems that for a solvent-exposed active site, QM/MM calculations with minimized structures cannot be recommended. Instead, methods that incorporate dynamic effects and calculate free energies seem preferable.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"189 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144701180","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":"Fermionic Free Energies from Ab Initio Path Integral Monte Carlo Simulations of Fictitious Identical Particles.","authors":"Tobias Dornheim, Zhandos Moldabekov, Sebastian Schwalbe, Panagiotis Tolias, Jan Vorberger","doi":"10.1021/acs.jctc.5c00301","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00301","url":null,"abstract":"<p><p>We combine the recent η-ensemble path integral Monte Carlo approach to the free energy [Dornheim et al. <i>Phys. Rev. B</i> <b>2025</b> <i>111</i>, L041114] with a recent fictitious partition function technique based on inserting a continuous variable that interpolates between the bosonic and Fermionic limits [Xiong and Xiong <i>J. Chem. Phys.</i> <b>2022</b> <i>157</i>, 094112] to deal with the Fermion sign problem. As a practical example, we apply our setup to the warm, dense, uniform electron gas over a broad range of densities and temperatures. We obtain accurate results for the exchange-correlation free energy down to half the Fermi temperature and find excellent agreement with the state-of-the-art parametrization by Groth et al. [<i>Phys. Rev. Lett.</i> <b>2017</b> <i>119</i>, 135001]. Our work opens up new avenues for the future study of a host of interacting Fermi systems, including warm dense matter, ultracold atoms, and electrons in quantum dots, and for Fermionic free energy calculations with unprecedented system size.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697094","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":"Chemtrain-Deploy: A Parallel and Scalable Framework for Machine Learning Potentials in Million-Atom MD Simulations.","authors":"Paul Fuchs, Weilong Chen, Stephan Thaler, Julija Zavadlav","doi":"10.1021/acs.jctc.5c00996","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00996","url":null,"abstract":"<p><p>Machine Learning Potentials (MLPs) have advanced rapidly and show great promise to transform Molecular Dynamics (MD) simulations. However, most existing software tools are tied to specific MLP architectures, lack integration with standard MD packages, or are not parallelizable across GPUs. To address these challenges, we present chemtrain-deploy, a framework that enables the model-agnostic deployment of MLPs in LAMMPS. chemtrain-deploy supports any JAX-defined semilocal potential, allowing users to exploit the functionality of LAMMPS and perform large-scale MLP-based MD simulations on multiple GPUs. It achieves state-of-the-art efficiency and scales to systems containing millions of atoms. We validate its performance and scalability using graph neural network architectures, including MACE, Allegro, and PaiNN, applied to a variety of systems such as liquid-vapor interfaces, crystalline materials, and solvated peptides. Our results highlight the practical utility of chemtrain-deploy for real-world, high-performance simulations and provide guidance for MLP architecture selection and future design.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697093","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":"An Extended Energy-Biased Aggregation-Volume-Bias Monte Carlo (EB-AVBMC) Method for Nucleation Simulation of a Reactive Water Potential.","authors":"Anthony Val Canillas Camposano, Even Marius Nordhagen, Anders Malthe-So̷renssen, Henrik Andersen Sveinsson","doi":"10.1021/acs.jctc.5c00722","DOIUrl":"10.1021/acs.jctc.5c00722","url":null,"abstract":"<p><p>The aggregation-volume-bias Monte Carlo (AVBMC) algorithm has been widely used with empirical water models like TIP3P, SPC/E, TIP4P, and TIP4<i>P</i>/2005 to study nucleation and vapor-liquid properties, but its application to reactive water models remains underexplored. Here, we present an extension of the energy-bias aggregation-volume-bias Monte Carlo (EB-AVBMC) method for calculating nucleation free energies and liquid-vapor properties, such as gas density and surface tension, using a three-body reactive force field based on the Vashishta potential functional form [<i>Phys. Rev. B</i> <b>1990</b>, <i>41</i>, 12197-12209]. Key modifications include revised acceptance rules that consider the intramolecular energy of the inserted/deleted molecule to prevent high acceptance probabilities that could bias the sampling and constraints to avoid the deletion of dissociated water molecules. These adjustments ensure valid bond topology modifications. We demonstrate the method's applicability by studying water nucleation at 298.15 K, with varying cluster sizes, and showing a free energy consistent with studies from rigid water models. This approach is generalizable to other reactive water force fields, offering a valuable tool for simulating reactive liquid-vapor properties.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":"6769-6776"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144564167","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":"","authors":"Chiara Lionello,&nbsp;Matteo Becchi,&nbsp;Simone Martino and Giovanni M. Pavan*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00374","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671697","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":"Bing Gu*,&nbsp;Jiajun Ren and Junzhe Zhang,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671699","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":"Jung-Hoon Lee*,&nbsp;Sang-Hoon Lee and Young-Woo Son*,&nbsp;","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"21 14","pages":"XXX-XXX XXX-XXX"},"PeriodicalIF":5.7,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.5c00818","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144671684","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}