Journal of Chemical Theory and Computation最新文献

{"title":"Accurate and Efficient Phonon Calculations in Molecular Crystals via Minimal Molecular Displacements.","authors":"Lorenzo Soprani, Andrea Giunchi, Marco Bardini, Quintin N Meier, Gabriele D'Avino","doi":"10.1021/acs.jctc.5c00494","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00494","url":null,"abstract":"<p><p>Vibrational dynamics governs the fundamental properties of molecular crystals, shaping their thermodynamics, mechanics, spectroscopy, and transport phenomena. However desirable, the accurate first-principles calculation of solid-state vibrations (i.e. phonons) stands as a major computational challenge in molecular crystals characterized by many atoms in the unit cell and by weak intermolecular interactions. Here, we propose a formulation of harmonic lattice dynamics based on a natural basis of molecular coordinates consisting of rigid-body displacements and intramolecular vibrations. This enables a sensible minimal molecular displacement approximation for the calculation of the dynamical matrix, combining isolated molecule calculations with only a small number of expensive crystal supercell calculations, ultimately reducing the computational cost by up to a factor of 10. The comparison with reference calculations demonstrates the quantitative accuracy of our method, especially for the challenging and dispersive low-frequency region for which it is designed. Our method provides an excellent description of the thermodynamic properties and offers a privileged molecular-level insight into the complex phonon band structure of molecular materials.</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":"144315557","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":"Optimization of the Qubit Coupled Cluster Ansatz on Classical Computers.","authors":"Ilya G Ryabinkin, Seyyed Mehdi Hosseini Jenab, Scott N Genin","doi":"10.1021/acs.jctc.5c00345","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00345","url":null,"abstract":"<p><p>Immense interest in quantum computing has prompted the development of electronic structure methods that are suitable for quantum hardware. However, the slow pace at which quantum hardware progresses forces researchers to implement their ideas on classical computers despite the obvious loss of any \"quantum advantage.\" As a result, the so-called <i>q</i>uantum-inspired methods emerge. They allow one to look at the electronic structure problem from a different angle, yet to fully exploit their capacity, efficient implementations are highly desirable. Here, we report two schemes for improving the amplitude optimization in the iterative qubit coupled cluster (iQCC) method: a variational quantum eigensolver-type approach, which is based on the qubit coupled cluster (QCC) Ansatz. Our first scheme approximates the QCC unitary as a sum of symmetrical polynomials of generators up to a given order. The resulting energy expression allows for flexible control of computational complexity via the order parameter. It also guarantees smoothness of trial energies and their derivatives, which is important for gradient-based optimization strategies. The second scheme limits the size of the expansion space in which the QCC unitary is generated. It provides better control of memory requirements but, in general, may lead to the nonsmooth variation of energy estimates upon changes in amplitudes. It can be used, however, to extrapolate energies for a given set of amplitudes toward the exact QCC value. Both schemes allow for a larger number of generators to be included in the QCC form compared to the exact formulation. This reduces the number of iterations in the iQCC method and/or leads to higher accuracy. We assess the capabilities of the new schemes to perform QCC amplitudes optimization for a few molecular systems: dinitrogen (N₂, 16 qubits), water (H₂O, 36 qubits), and tris(2-(2,4-difluorophenyl)pyridine) iridium(III), (Ir(F₂ppy)₃, 80 qubits).</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":"144315559","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":"Localized Active Space State Interaction Singles.","authors":"Matthew R Hermes, Bhavnesh Jangid, Valay Agarawal, Laura Gagliardi","doi":"10.1021/acs.jctc.5c00387","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00387","url":null,"abstract":"<p><p>We introduce localized active space state interaction singles (LASSIS), a multireference electronic structure method that uses two-step diagonalization to model low-energy electronic states of systems characterized by multiple distinct localized centers of strong electron correlation, with weaker but not negligible electron correlation between the centers. LASSIS is a specific variant of localized active space state interaction (LASSI), which restores interfragment interactions omitted by a LASSCF reference wave function by expanding the interacting wave function in a basis of model states characterized by various charge and spin distributions. These distributions, and the number of states of each type, are determined automatically, without any user input, in contrast to previous work with the LASSI formalism. LASSIS combined with multiconfiguration pair-density functional theory (MC-PDFT) energy calculation is shown in test calculations to qualitatively reproduce the results of converged DMRG-PDFT calculations on multimetallic transition metal compounds.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300633","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":"Elucidating Protein Dynamics through the Optimal Annealing of Variational Autoencoders.","authors":"Subinoy Adhikari, Jagannath Mondal","doi":"10.1021/acs.jctc.5c00365","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00365","url":null,"abstract":"<p><p>Proteins traverse intricate conformational landscapes with transitions and long-lived states that hold the key to their biological function. However, unraveling these dynamics remains a formidable challenge. An emerging approach has been to train the conformational ensemble via deep Variational autoencoders (VAEs) in a bid to machine learn the underlying reduced-dimensional representation. However, training VAEs typically involves a fixed β value of 1, where β acts as the crucial weighing factor between the reconstruction and regularization terms. This static setup can often lead to posterior collapse, which significantly hinders the model's ability to capture complex protein dynamics accurately. To mitigate this issue, annealing the β parameter offers a potential alternative. However, this approach frequently falls short in fully addressing the problem, mainly due to the arbitrary choice of the upper bound of β and the annealing schedule. In this work, we propose a new approach for selecting the β parameter by utilizing the Fraction of variation explained (FVE) score to identify its optimal value. We demonstrate that training annealed VAEs at their optimum β in a single cycle consistently outperformed their nonannealed counterparts, as evident from their higher variational approach for Markov processes-2 and generalized matrix Rayleigh quotient scores and distinct free energy surface minima on both folded and intrinsically disordered proteins. The improved latent space representations significantly improve state space discretization, thereby refining Markov State Models and providing more accurate insights into conformational landscapes, as reflected in distinct contact maps. Together, this development provides a systematic approach to optimizing the balance between reconstruction and regularization aspects of VAEs that would augment the potential of annealed VAEs in resolving complex conformational landscapes.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144300632","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":"\"Slim\" Benchmark Sets for Faster Method Development.","authors":"Tim Gould, Stefan Vuckovic","doi":"10.1021/acs.jctc.5c00512","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00512","url":null,"abstract":"<p><p>The construction of large benchmark sets has accelerated advancement of quantum chemistry methods, especially in density functional theory and lower-cost methods. However, these large benchmark sets can be unsuitable for cutting-edge method development, because research codes developed for fundamentally new approaches are often inefficient and may consequently struggle to handle large molecules. Here, we introduce Slim benchmark sets that are designed to 'summarize' the statistics of larger (in number and size of molecules) counterparts, but have the advantage that molecules are restricted in size (to 5, 16, and 20 atoms) and may therefore be treated by inefficient implementations. Remarkably, our 16 and 20 atom Slim sets effectively summarize reactions involving much larger numbers of atoms. They thereby allow data-driven methodologies to be exploited in the early stages of cutting-edge method development.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309264","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":"Adding the AMBER 14SB Force Field to the Stochastic Titration CpHMD Method.","authors":"João G N Sequeira, Adrian E Roitberg, Miguel Machuqueiro","doi":"10.1021/acs.jctc.5c00415","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00415","url":null,"abstract":"<p><p>Incorporating pH into molecular dynamics simulations is vital for accurately capturing the fully coupled conformational, energetic, and protonation landscape of many systems. The constant-pH molecular dynamics (CpHMD) methodologies represent state-of-the-art approaches to achieve this, with stochastic titration CpHMD (st-CpHMD) currently being one of the most well-developed and validated methods. St-CpHMD is already compatible with both the GROMOS 54A7 and CHARMM 36m force fields, and we extend it here to support the AMBER 14SB force field available in the GROMACS software package. We introduce and validate a minor modification to the official atomic partial charges of ff14SB (to achieve neutralization of the main chain) to render them compatible with st-CpHMD, and we benchmark the final implementation using lysozyme and Staphylococcal nuclease proteins. Although the root-mean-square error (RMSE) values of the predictions for p<i>K</i>_a versus experimental data align closely with those obtained using the other supported force fields, we also identified several challenging cases where the method requires further improvement. AMBER 14SB simulations showed a lower computational cost compared to CHARMM 36m, despite being slightly higher than the GROMOS 54A7 simulations. Our findings also indicate that to further enhance computational speed, future efforts should concentrate on accelerating the PB/MC step. With this extension, we have developed the first CpHMD method implementation compatible with the three most widely used protein force fields, enabling, for the first time, a direct performance comparison among them.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309265","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":"IR Spectra for the EMIM-TFSI Ion Pair Using Deep Potentials.","authors":"H Oliaei, N R Aluru","doi":"10.1021/acs.jctc.5c00187","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00187","url":null,"abstract":"<p><p>Despite advances in the characterization of ionic liquids (ILs), elucidating their infrared (IR) spectra remains challenging due to the computational demands of <i>ab initio</i> methods. In this study, we employ a framework that integrates deep potential (DP) and deep Wannier (DW) models to investigate the configuration, dipole moment, and IR spectra of a 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM]⁺-[TFSI]^-) pair. The accuracy and reliability of these models are evaluated by benchmarking against <i>ab initio</i> molecular dynamics (AIMD) across structural, dipolar, and spectral features. Our results demonstrate overall agreement while emphasizing the importance of achieving well-converged dipole distributions─typically requiring tens to hundreds of picoseconds of simulation─to enhance spectral resolution. Such convergence is essential for minimizing noise or bias arising from specific ionic configurations (referred to as \"on-top\" or \"in-front\" in the current study) and is enabled by the computational efficiency of DW- and DP-based molecular dynamics (DW/DPMD), which supports long simulation time scales. The DW/DPMD approach reproduces both the dipole moment range (7-16 D) and the average (∼10 D) observed in AIMD while yielding smoother and better-converged distributions. Furthermore, the IR spectrum obtained from DW/DPMD closely aligns with that of AIMD, faithfully capturing key vibrational features such as <i>v</i>_{<i>S</i> - <i>N</i> - <i>S</i>, <i>as</i>} < <i>v</i>_<i>CF</i>₃ < <i>v</i>_{<i>SO</i>₂, <i>as</i>}, consistent with experimental observations. In contrast, classical IR spectra tend to underestimate or overestimate the intensities of specific bands and fail to reproduce the correct relative wavenumbers compared to AIMD and experimental data. This study highlights the capability of deep learning potentials and dipole models─particularly DP and DW─to address systems involving charged species and complex ionic interactions while illustrating the limitations of classical approaches. Our findings pave the way for the development of more advanced surrogate models and their application to increasingly complex systems, including bulk materials and interfaces.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144309266","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":"Mixed Quantum/Classical Theory Approach to Rotationally Inelastic Molecular Collisions Implemented on a Quantum Computer.","authors":"Jonathan Andrade-Plascencia,Tamila Kuanysheva,Dulat Bostan,Brian K Kendrick,Dmitri Babikov","doi":"10.1021/acs.jctc.5c00504","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00504","url":null,"abstract":"All elements of a quantum algorithm for calculations of rotationally inelastic molecule + atom scattering within the framework of a mixed quantum/classical theory are outlined. In this approach, the rotational motion of the molecule is described quantum mechanically using the time-dependent Schrödinger equation, while the scattering process of two collision partners is treated classically. The matrix of potential coupling is precomputed on a classical processor, whereas the quantum hardware is used to propagate the system of coupled equations for the rotational state-to-state transitions. All quantum circuits needed for practical implementation of the algorithm are presented. First, the quantum codes written in Qiskit are rigorously tested by running calculations for a N2 + O collision on a classical emulator of quantum hardware using a realistic potential energy surface of this system and comparing these results against the results obtained by the MQCT code. Next, these codes are run on the actual quantum hardware, such as the publicly available IBM Brisbane, Kyiv, and Sherbrooke. A very good agreement with benchmark data was obtained. To the best of our knowledge, this is the first proof-of-principle calculation of inelastic scattering implemented successfully on a quantum computer using a case study within mixed quantum/classical framework.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":"598 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2025-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144295871","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":"Orbital Optimization of Large Active Spaces via AI-Accelerators.","authors":"Örs Legeza, Andor Menczer, Ádám Ganyecz, Miklós Antal Werner, Kornél Kapás, Jeff Hammond, Sotiris S Xantheas, Martin Ganahl, Frank Neese","doi":"10.1021/acs.jctc.5c00571","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00571","url":null,"abstract":"<p><p>We present an efficient orbital optimization procedure that combines the highly GPU accelerated, spin-adapted density matrix renormalization group (DMRG) method with the complete active space self-consistent field (CAS-SCF) approach for quantum chemistry implemented in the ORCA program package. Leveraging the computational power of the latest generation of Nvidia GPU hardware, we perform CAS-SCF based orbital optimizations for unprecedented CAS sizes of up to 82 electrons in 82 orbitals [CAS(82,82)] in molecular systems comprising active space sizes of hundreds of electrons in thousands of orbitals. For both the NVIDIA DGX-A100 and DGX-H100 hardware, we provide a detailed scaling and error analysis of our DMRG-SCF approach for benchmark systems consisting of polycyclic aromatic hydrocarbons and iron-sulfur complexes of varying sizes. Our efforts demonstrate for the first time that highly accurate DMRG calculations at large bond dimensions are critical for obtaining reliably converged CAS-SCF energies. For the more challenging iron-sulfur benchmark systems, we furthermore find the optimized orbitals of a converged CAS-SCF calculation to depend more sensitively on the DMRG parameters than those for the polycyclic aromatic hydrocarbons. The ability to obtain converged CAS-SCF energies and orbitals for active spaces of such large sizes within days reduces the challenges of including the appropriate orbitals into the CAS or selecting the correct minimal CAS, and may open up entirely new avenues for tackling strongly correlated molecular systems.</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":"144281695","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":"Accelerating Variable Cell Shape Molecular Dynamics with a Position-Dependent Mass Matrix.","authors":"Martin Sommer-Jörgensen, Marco Krummenacher, Stefan Goedecker","doi":"10.1021/acs.jctc.5c00237","DOIUrl":"https://doi.org/10.1021/acs.jctc.5c00237","url":null,"abstract":"<p><p>In molecular dynamics (MD), the accessible time scales are limited by the necessity to choose sufficiently small time steps so that the fastest vibrations of the system can still be modeled. Mass tensor molecular dynamics (MTMD) aims to increase the time step by augmenting the Hamiltonian with a position-dependent mass matrix. Higher masses are assigned to modes with fast vibrations. These modes are identified by using an approximate Hessian matrix. The approximate Hessian matrix presented in this paper is applicable to the simulation of molecular systems, where no changes in the bonding pattern occur. We have adapted the MTMD method to variable cell shape systems and present a suitable symplectic integrator. The efficiency of the method is demonstrated for a system of molecular crystals consisting of <i>N</i>-(4-Methylbenzylidene)-4-methylaniline, where we could sample transitions between two polymorphs and thereby increase the time step by a factor of 4.4 to speed up the simulation. We have also simulated liquid water at the density function theory level, where we have achieved an acceleration by a factor of 2.8.</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":"144281690","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}