Journal of Chemical Theory and Computation最新文献

{"title":"Correction to \"Comparing Self-Consistent <i>GW</i> and Vertex-Corrected <i>G</i>₀<i>W</i>₀ (<i>G</i>₀<i>W</i>₀Γ) Accuracy for Molecular Ionization Potentials\".","authors":"Ming Wen, Vibin Abraham, Gaurav Harsha, Avijit Shee, K Birgitta Whaley, Dominika Zgid","doi":"10.1021/acs.jctc.4c01577","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01577","url":null,"abstract":"","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447379","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":"Unveiling the Dance of Molecules: Rovibrational Dynamics of Molecules under Intense Illumination at Complex Plasmonic Interfaces.","authors":"Maxim Sukharev, Joseph E Subotnik, Abraham Nitzan","doi":"10.1021/acs.jctc.4c01652","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01652","url":null,"abstract":"<p><p>Understanding the quantum dynamics of strongly coupled molecule-cavity systems remains a significant challenge in molecular polaritonics. This work develops a comprehensive self-consistent model simulating electromagnetic interactions of diatomic molecules with quantum rovibrational degrees of freedom in resonant optical cavities. The approach employs an efficient numerical methodology to solve coupled Schrödinger-Maxwell equations in real spacetime, enabling three-dimensional simulations through a novel molecular mapping technique. The study investigates the relaxation dynamics of an ensemble of molecules following intense resonant pump excitation in Fabry-Perot cavities and at three-dimensional plasmonic metasurfaces. The simulations reveal dramatically modified relaxation pathways inside cavities compared to free space, characterized by persistent molecular alignment arising from cavity-induced rotational pumping. They also indicate the presence of a previously unreported relaxation stabilization mechanism driven by dephasing of the collective molecular-cavity mode. Additionally, the study demonstrates that strong molecular coupling significantly modifies the circular dichroism spectra of chiral metasurfaces, suggesting new opportunities for controlling light-matter interactions in quantum optical systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439384","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":"Computational Approach to Phosphor-Sensitized Fluorescence Based on Monomer Transition Densities.","authors":"Simon Metz, Christel M Marian","doi":"10.1021/acs.jctc.4c01688","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01688","url":null,"abstract":"<p><p>We present here an extension of the monomer transition density approach to spin multiplicity-altering excitation energy transfer (EET) processes. It builds upon complex-valued wave functions of the density functional theory-based multireference spin-orbit coupling configuration interaction method for generating the one-particle transition density matrices of the donor and acceptor molecules, which are then contracted with two-electron Coulomb and exchange integrals of the dimer. Due to the extensive use of symmetry relations between tensor components, the computation of triplet-singlet coupling remains technically feasible. As a proof-of-principle application, we have chosen an EET system, consisting of the phosphorescent platinum complex AG97 as the donor and the fluorescein derivative FITC as the acceptor. Taking experimental conditions into account, we estimate a Förster radius of about 35 Å. For intermolecular donor-acceptor separations close to the Förster radius and beyond, the error introduced by the ideal dipole approximation is rather small.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447354","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":"Discretization of Structured Bosonic Environments at Finite Temperature by Interpolative Decomposition: Theory and Application.","authors":"Hideaki Takahashi, Raffaele Borrelli","doi":"10.1021/acs.jctc.4c01728","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01728","url":null,"abstract":"<p><p>We present a comprehensive theory for a novel method to discretize the spectral density of a bosonic heat bath, as introduced in [Takahashi, H.; Borrelli, R. <i>J. Chem. Phys.</i> 2024, 161, 151101]. The approach leverages a low-rank decomposition of the Fourier-transform relation connecting the bath correlation function to its spectral density. By capturing the time, frequency, and temperature dependencies encoded in the spectral density-autocorrelation function relation, our method significantly reduces the degrees of freedom required for simulating open quantum system dynamics. We benchmark our approach against existing methods and demonstrate its efficacy through applications to both simple models and a realistic electron transfer process in biological systems. Additionally, we show that this new approach can be effectively combined with the tensor-train formalism to investigate the quantum dynamics of systems interacting with complex non-Markovian environments. Finally, we provide a perspective on the selection and application of various spectral density discretization techniques.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439346","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":"Multiscale Simulations of Membrane Adhesion Mediated by CD47-SIRPα Complexes.","authors":"Ruihan Hou, Shuanglong Ren, Rong Wang, Bartosz Różycki, Jinglei Hu","doi":"10.1021/acs.jctc.4c01337","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01337","url":null,"abstract":"<p><p>Adhesion of biological cells is essential for various processes, including tissue formation, immune responses, and signaling. It involves multiple length scales, ranging from nanometers to micrometers, which are characteristic of (a) the intercellular receptor-ligand binding that mediates the cell adhesion, (b) the spatial distribution of the receptor and ligand proteins in the membranes of adhering cells, (c) adhesion-induced deformations and thermal undulations of the membranes, (d) the overall size of the interface between adhering cells. Therefore, computer simulations of cell membrane adhesion require multiscale modeling and suitable approximations that capture the essential physics of the system under study. Here, we introduce such a multiscale approach to study membrane adhesion mediated by the CD47-SIRPα binding, which is an immunologically relevant process. The synergetic use of coarse-grained molecular dynamics simulations and mesoscale kinetic Monte Carlo simulations allows us to explore both equilibrium properties and dynamical behavior of adhering membranes on the relevant length scales between 1 nm and 1 μm on time scales ranging from 0.1 ns all the way up to about 20 s. The multiscale simulations not only reproduce available experimental data but also give quantitative predictions on binding-induced conformational changes of SIRPα and membrane-mediated cooperativity of the CD47-SIRPα binding as well as fluctuation-induced interactions between the CD47-SIRPα complexes. Our approach is applicable to various membrane proteins and provides invaluable data for comparison with experimental findings.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439295","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-iterative Triples for Transcorrelated Coupled Cluster Theory.","authors":"Maximilian Mörchen, Alberto Baiardi, Michał Lesiuk, Markus Reiher","doi":"10.1021/acs.jctc.4c01062","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01062","url":null,"abstract":"<p><p>We present an implementation of a perturbative triples correction for the coupled cluster ansatz including single and double excitations based on the transcorrelated Hamiltonian. Transcorrelation introduces explicit electron correlation in the electronic Hamiltonian through similarity transformation with a correlation factor. Due to this transformation, the transcorrelated Hamiltonian includes up to three-body couplings and becomes non-Hermitian. Since the conventional coupled cluster equations are solved by projection, it is well suited to harbor non-Hermitian Hamiltonians. The arising three-body operator, however, creates a huge memory bottleneck and increases the runtime scaling of the coupled cluster equations. As it has been shown that the three-body operator can be approximated, by expressing the Hamiltonian in the normal-ordered form, we investigate this approximation for the perturbative triples correction. Results are compared with a code-generation based transcorrelated coupled cluster implementation up to quadruple excitations.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439298","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":"Testing a Heterogeneous Polarizable Continuum Model against Exact Poisson Boundary Conditions.","authors":"Paige E Bowling, Montgomery Gray, Suranjan K Paul, John M Herbert","doi":"10.1021/acs.jctc.4c01665","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01665","url":null,"abstract":"<p><p>The polarizable continuum model (PCM) is a computationally efficient way to incorporate dielectric boundary conditions into electronic structure calculations, via a boundary-element reformulation of Poisson's equation. This transformation is only rigorously valid for an isotropic dielectric medium. To simulate anisotropic solvation, as encountered at an interface or when parts of a system are solvent-exposed while other parts are in a nonpolar environment, <i>ad hoc</i> modifications to the PCM formalism have been suggested, in which a dielectric constant is assigned separately to each atomic sphere that contributes to the solute cavity. The accuracy of this \"heterogeneous\" PCM (HetPCM) method is tested here for the first time, by comparison to results from a generalized Poisson equation solver. The latter is a more expensive and cumbersome approach to incorporate arbitrary dielectric boundary conditions, but one that corresponds to a well-defined scalar permittivity function, ε(<b>r</b>). We examine simple model systems for which a function ε(<b>r</b>) can be constructed in a manner that maps reasonably well onto a dielectric constant for each atomic sphere, using a solvent-exposed dielectric constant ε_solv = 78 and a range of smaller values to represent hydrophobic environments. For nonpolar dielectric constants ε_nonp ≤ 2, differences between the HetPCM and Poisson solvation energies are large compared to the effect of anisotropy on the solvation energy. For ε_nonp = 4 and ε_nonp = 10, however, HetPCM and anisotropic Poisson solvation energies agree to within 2 kcal/mol in most cases. As a realistic use case, we apply the HetPCM method to predict solvation energies and p<i>K</i>_a values for blue copper proteins. The HetPCM method affords p<i>K</i>_a values that are more in line with experimental results as compared to either gas-phase calculations or homogeneous (isotropic) PCM results.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439383","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":"Integrating Machine Learning and Quantum Circuits for Proton Affinity Predictions.","authors":"Hongni Jin, Kenneth M Merz","doi":"10.1021/acs.jctc.4c01609","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01609","url":null,"abstract":"<p><p>A key step in interpreting gas-phase ion mobility coupled with mass spectrometry (IM-MS) data for unknown structure prediction involves identifying the most favorable protonated structure. In the gas phase, the site of protonation is determined using proton affinity (PA) measurements. Currently, mass spectrometry and <i>ab initio</i> computation methods are widely used to evaluate PA; however, both methods are resource-intensive and time-consuming. Therefore, there is a critical need for efficient methods to estimate PA, enabling the rapid identification of the most favorable protonation site in complex organic molecules with multiple proton binding sites. In this work, we developed a fast and accurate method for PA prediction by using multiple descriptors in combination with machine learning (ML) models. Using a comprehensive set of 186 descriptors, our model demonstrated strong predictive performance, with an <i>R</i>² of 0.96 and a MAE of 2.47 kcal/mol, comparable to experimental uncertainty. Furthermore, we designed quantum circuits as feature encoders for a classical neural network. To evaluate the effectiveness of this hybrid quantum-classical model, we compared its performance with traditional ML models using a reduced feature set derived from the full set. A correlation analysis showed that the quantum-encoded representations have a stronger positive correlation with the target values than the original features do. As a result, the hybrid model outperformed its classical counterpart and achieved consistent performance comparable to traditional ML models with the same reduced feature set on both a noiseless simulator and real quantum hardware, highlighting the potential of quantum machine learning for accurate and efficient PA predictions.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439356","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 Landscapes for the Unitary Coupled Cluster Ansatz.","authors":"Choy Boy, Maria-Andreea Filip, David J Wales","doi":"10.1021/acs.jctc.4c01667","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01667","url":null,"abstract":"<p><p>The unitary coupled cluster (UCC) approach has been one of the most popular wavefunction parametrizations for the variational quantum eigensolver due to the relative ease of optimization compared to hardware-efficient ansätze. In this contribution, we explore the energy landscape of the unitary coupled cluster singles and doubles (UCCSD) wavefunction for two commonly employed benchmark systems, lithium hydride and the nitrogen dimer. We investigate the organization of the solution space in terms of local minima and show how it changes as the number and order of operators of the UCC ansatz are varied. Surprisingly, we find that in all cases, the UCCSD energy has numerous low-lying minima connected by high energy transition states. Additionally, the energy spread of the minima that lie in the same band as the global minimum may exceed chemical accuracy, making the location of the true global minimum especially challenging.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424621","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":"CHARMM-GUI <i>EnzyDocker</i> for Protein-Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes.","authors":"Donghyuk Suh, Renana Schwartz, Prashant Kumar Gupta, Shani Zev, Dan T Major, Wonpil Im","doi":"10.1021/acs.jctc.4c01691","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c01691","url":null,"abstract":"<p><p>Enzymes play crucial roles in all biological systems by catalyzing a myriad of chemical reactions. These reactions range from simple one-step processes to intricate multistep cascades. Predicting mechanistically appropriate binding modes along a reaction pathway for substrate, product, and all reaction intermediates and transition states is a daunting task. To address this challenge, special docking programs like EnzyDock have been developed. Yet, running such docking simulations is complicated due to the nature of multistep enzyme processes. This work presents CHARMM-GUI <i>EnzyDocker</i>, a web-based cyberinfrastructure designed to streamline the preparation and running of EnzyDock docking simulations. The development of <i>EnzyDocker</i> has been achieved through integration of existing CHARMM-GUI modules, such as <i>PDB Reader and Manipulator</i>, <i>Ligand Designer</i>, and <i>QM/MM Interfacer</i>. In addition, new functionalities have been developed to facilitate a one-stop preparation of multistate and multiscale docking systems and enable interactive and intuitive ligand modifications and flexible protein residues selections. A simple setup related to multiligand docking is automatized through intuitive user interfaces. <i>EnzyDocker</i> offers support for standard classical docking and QM/MM docking with CHARMM built-in semiempirical engines. Automated consensus restraints for incorporating experimental knowledge into the docking are facilitated via a maximum common substructure algorithm. To illustrate the robustness of <i>EnzyDocker</i>, we conducted docking simulations of three enzyme systems: dihydrofolate reductase, SARS-CoV-2 M^pro, and the diterpene synthase CotB2. In addition, we have created four tutorial videos about these systems, which can be found at https://www.charmm-gui.org/demo/enzydock. <i>EnzyDocker</i> is expected to be a valuable and accessible web-based tool that simplifies and accelerates the setup process for multistate docking for enzymes.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":" ","pages":""},"PeriodicalIF":5.7,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412359","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}