Journal of Chemical Theory and Computation最新文献

{"title":"Numerical Investigation of the Quantum Inverse Algorithm on Small Molecules","authors":"Mauro Cainelli*,&nbsp;Reo Baba and Yuki Kurashige*,&nbsp;","doi":"10.1021/acs.jctc.4c0048310.1021/acs.jctc.4c00483","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00483https://doi.org/10.1021/acs.jctc.4c00483","url":null,"abstract":"<p >We evaluate the accuracy of the quantum inverse (Q-Inv) algorithm, in which the multiplication of <i>Ĥ</i>^–<i>k</i> to the reference wave function is replaced by the Fourier transformed multiplication of e^{–iλ<i>Ĥ</i>}, as a function of the integration parameters and the iteration power <i>k</i> for various systems, including H₂, LiH, BeH₂ and the notorious H₄ molecule at square geometry. We further consider the possibility of employing the Gaussian-quadrature rule as an alternate integration method and compared it to the results employing trapezoidal integration. The Q-Inv algorithm is compared to the inverse iteration method using the <i>Ĥ</i>^–1 inverse (I-Iter) and the exact inverse by lower-upper decomposition. Energy values are evaluated as the expectation values of the Hamiltonian. Results suggest that the Q-Inv method provides lower energy results than the I-Iter method up to a certain <i>k</i>, after which the energy increases due to errors in the numerical integration that are dependent on the integration interval. A combined Gaussian-quadrature and trapezoidal integration method proved to be more effective at reaching convergence while decreasing the number of operations. For systems like H₄, in which the Q-Inv cannot reach the expected error threshold, we propose a combination of Q-Inv and I-Iter methods to further decrease the error with <i>k</i> at lower computational cost. Finally, we summarize the recommended procedure when treating unknown systems.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310037","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":"Internal Conversion Cascade in a Carbon Nanobelt: A Multiconfigurational Quantum Dynamical Study","authors":"James A. Green, Dominik Brey, Leyla P. Razgatlioglu, Badria Ali, Bartosz Błasiak, Irene Burghardt","doi":"10.1021/acs.jctc.4c00841","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00841","url":null,"abstract":"Carbon nanobelts feature intriguing photophysical properties, due to their high symmetry and structural rigidity. Here, we consider a (6,6) armchair carbon nanobelt, i.e., the very first carbon nanobelt to be synthesized [Povie et al., <i>Science</i> <b>2017</b>, 356, 172] and characterize the internal conversion dynamics using multiconfigurational quantum dynamics via the multi-layer multiconfiguration time-dependent Hartree (ML-MCTDH) method. A symmetry-adapted linear vibronic coupling Hamiltonian for 26 electronic states and 210 vibrational modes is employed. Electronic excitations are found to decay through a dense manifold of excited states, which interact via multiple conical intersections, while inducing minimal geometry change. It is shown that a rapid coherent decay, exhibiting a nonvanishing quantum flux on a time scale of less than 50 fs, transitions toward a slower, decoherent decay at longer times. As previously suggested in the literature, electronic relaxation is hindered by phonon bottlenecks such that a stepwise internal conversion cascade is observed. The computed vibronic absorption spectrum is shown to be in good agreement with the experimental spectrum.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142171429","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":"Is Quantum Above-Barrier Reflection Important for Molecular Barrier Crossing Rates?","authors":"Chiara Aieta, Michele Ceotto, Eli Pollak","doi":"10.1021/acs.jctc.4c00917","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00917","url":null,"abstract":"Understanding quantum tunneling and above-barrier reflection effects on unimolecular and bimolecular reaction rate constants remains challenging to this very day. In many applications, especially when considering moderate-to-high temperatures, the “standard” procedure is to use the parabolic barrier approximation. Recent work has shown though that this may be insufficient, and one cannot ignore anharmonicity. In this work, we study the analytic theory, including anharmonicity obtained when expanding the thermal rate up to order <i>ℏ</i>⁴. Such theories need high-order derivatives of the potential at the barrier top. We show that such derivatives are computed straightforwardly for six different reactions. We suggest a straightforward methodology for assessing whether the parabolic barrier approximation is valid and show that when the reaction asymmetry is large, this may lead to significant quantum above-barrier reflection and transmission coefficients, which are less than unity.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142171431","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":"Numerical Investigation of the Quantum Inverse Algorithm on Small Molecules","authors":"Mauro Cainelli, Reo Baba, Yuki Kurashige","doi":"10.1021/acs.jctc.4c00483","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00483","url":null,"abstract":"We evaluate the accuracy of the quantum inverse (Q-Inv) algorithm, in which the multiplication of <i>Ĥ</i>^–<i>k</i> to the reference wave function is replaced by the Fourier transformed multiplication of e^{–iλ<i>Ĥ</i>}, as a function of the integration parameters and the iteration power <i>k</i> for various systems, including H₂, LiH, BeH₂ and the notorious H₄ molecule at square geometry. We further consider the possibility of employing the Gaussian-quadrature rule as an alternate integration method and compared it to the results employing trapezoidal integration. The Q-Inv algorithm is compared to the inverse iteration method using the <i>Ĥ</i>^–1 inverse (I-Iter) and the exact inverse by lower-upper decomposition. Energy values are evaluated as the expectation values of the Hamiltonian. Results suggest that the Q-Inv method provides lower energy results than the I-Iter method up to a certain <i>k</i>, after which the energy increases due to errors in the numerical integration that are dependent on the integration interval. A combined Gaussian-quadrature and trapezoidal integration method proved to be more effective at reaching convergence while decreasing the number of operations. For systems like H₄, in which the Q-Inv cannot reach the expected error threshold, we propose a combination of Q-Inv and I-Iter methods to further decrease the error with <i>k</i> at lower computational cost. Finally, we summarize the recommended procedure when treating unknown systems.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142166676","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":"Production of Distinct Fibrillar, Oligomeric, and Other Aggregation States from Network Models of Multibody Interaction","authors":"Elizabeth M. Diessner,&nbsp;Loring J. Thomas and Carter T. Butts*,&nbsp;","doi":"10.1021/acs.jctc.4c0091610.1021/acs.jctc.4c00916","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00916https://doi.org/10.1021/acs.jctc.4c00916","url":null,"abstract":"<p >Protein aggregation can produce a wide range of states, ranging from fibrillar structures and oligomers to unstructured and semistructured gel phases. Recent work has shown that many of these states can be recapitulated by relatively simple, topological models specified in terms of multibody interaction energies, providing a direct connection between aggregate intermolecular forces and aggregation products. Here, we examine a low-dimensional network Hamiltonian model (NHM) based on four basic multibody interactions found in any aggregate system. We characterize the phase behavior of this NHM family, showing that fibrils arise from a balance between elongation-inducing and contact-inhibiting forces. Complex oligomers (including annular oligomers resembling those thought to be toxic species in Alzheimer’s disease) also form distinct phases in this regime, controlled in part by closure-inducing forces. We show that phase structure is largely independent of system size, and provide evidence of a rich structure of minor oligomeric phases that can arise from appropriate conditions. We characterize the phase behavior of this NHM family, demonstrating the range of ordered and disordered aggregation states possible with this set of interactions. As we show, fibrils arise from a balance between elongation-inducing and contact-inhibiting forces, existing in a regime bounded by gel-like and disaggregated phases; complex oligomers (including annular oligomers resembling those thought to be toxic species in Alzheimer’s disease) also form distinct phases in this regime, controlled in part by closure-inducing forces. We show that phase structure is largely independent of system size, allowing generalization to macroscopic systems, and provide evidence of a rich structure of minor oligomeric phases that can arise from appropriate conditions.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acs.jctc.4c00916","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309812","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":"Coarse-Graining Conformational Dynamics with Multidimensional Generalized Langevin Equation: How, When, and Why","authors":"Pinchen Xie*,&nbsp; and ,&nbsp;Weinan E*,&nbsp;","doi":"10.1021/acs.jctc.4c0072910.1021/acs.jctc.4c00729","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00729https://doi.org/10.1021/acs.jctc.4c00729","url":null,"abstract":"<p >A data-driven ab initio generalized Langevin equation (AIGLE) approach is developed to learn and simulate high-dimensional, heterogeneous, coarse-grained (CG) conformational dynamics. Constrained by the fluctuation–dissipation theorem, the approach can build CG models in dynamical consistency (DC) with all-atom molecular dynamics. We also propose practical criteria for AIGLE to enforce long-term DC. Case studies of a toy polymer, with 20 CG sites, and the alanine dipeptide, with two dihedral angles, elucidate why one should adopt AIGLE or its Markovian limit for modeling CG conformational dynamics in practice.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142309979","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":"Effect of Protein-Polarized Ligand Charges on Relative Protein Ligand Binding Affinities","authors":"Suliman Adam, Itamar Kass, Dana Krepel-Zussman, Gal Masarati, Dorit Shemesh, Avital Sharir-Ivry","doi":"10.1021/acs.jctc.3c01337","DOIUrl":"https://doi.org/10.1021/acs.jctc.3c01337","url":null,"abstract":"A major challenge in computer-aided drug design is predicting relative binding energies of different molecules to a target protein using fast and accurate free-energy calculation methods. Free-energy calculations are primarily computed by utilizing classical molecular dynamics simulations based on all-atom force fields (FF) to model the interactions in the system. The present standard classical all-atom FFs contain fixed partial charges on the atoms, and hence electrostatic interactions are modeled between them. The parametrization process to determine these partial charges usually relies on quantum mechanics or semiempirical calculations of the molecule in the gas phase or homogeneous water surrounding. These present standard parametrization schemes of the partial charges neglect, therefore, polarization effects from the protein surrounding. The absence of protein polarization effects can lead to significant errors in free-energy calculations in proteins. We present a parametrization scheme for the partial charges of ligands, named protein-induced polarization (PIP) charges, which account for the electrostatic polarization due to the protein surrounding. The scheme involves single-point quantum mechanics/molecular mechanics calculations of the ligand charges in the protein/water surrounding. Using PIP ligand partial charges, we have calculated the relative binding free energies (RBFEs) of well-studied protein−ligand systems. We show here that RBFEs computed with PIP charges are either significantly improved or at least comparable to those computed with nonpolarized standard GAFF charges. Overall, we present a simple-to-use parametrization scheme to include protein polarization in any type of binding free-energy calculations. The parametrization scheme increases the accuracy in RBFE calculations, while it does not add significant computation time to standard parametrization procedures.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142166675","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":"Direct Unconstrained Optimization of Molecular Orbital Coefficients in Density Functional Theory","authors":"Hanh D. M. Pham, Rustam Z. Khaliullin","doi":"10.1021/acs.jctc.4c00696","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00696","url":null,"abstract":"One-electron orbitals in Kohn–Sham density functional theory (DFT) are typically constrained to be orthogonal during their variational optimization, leading to elaborate parameterization of the orbitals and complicated optimization algorithms. This work shows that orbital optimization can be performed with nonorthogonal orbitals if the DFT energy functional is augmented with a term that penalizes linearly dependent states. This approach, called variable-metric self-consistent field (VM SCF) optimization, allows us to use molecular orbital coefficients, natural descriptors of one-electron orbitals, as independent variables in a direct, unconstrained minimization, leading to very simple closed-form expressions for the electronic gradient and Hessian. It is demonstrated that efficient convergence of the VM SCF procedure can be achieved with a basic preconditioned conjugate gradient algorithm for a variety of systems, including challenging narrow-gap systems and spin-pure two-determinant states of singlet diradicals. This simple reformulation of the variational procedure can be readily extended to electron correlation methods with multiconfiguration states and to the optimization of excited-state orbitals.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142171139","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":"Toward Reliable Conformational Energies of Amino Acids and Dipeptides─The DipCONFS Benchmark and DipCONL Datasets.","authors":"Christoph Plett,Stefan Grimme,Andreas Hansen","doi":"10.1021/acs.jctc.4c00801","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00801","url":null,"abstract":"Simulating peptides and proteins is becoming increasingly important, leading to a growing need for efficient computational methods. These are typically semiempirical quantum mechanical (SQM) methods, force fields (FFs), or machine-learned interatomic potentials (MLIPs), all of which require a large amount of accurate data for robust training and evaluation. To assess potential reference methods and complement the available data, we introduce two sets, DipCONFL and DipCONFS, which cover large parts of the conformational space of 17 amino acids and their 289 possible dipeptides in aqueous solution. The conformers were selected from the exhaustive PeptideCS dataset by Andris et al. [ J. Phys. Chem. B 2022, 126, 5949-5958]. The structures, originally generated with GFN2-xTB, were reoptimized using the accurate r2SCAN-3c density functional theory (DFT) composite method including the implicit CPCM water solvation model. The DipCONFS benchmark set contains 918 conformers and is one of the largest sets with highly accurate coupled cluster conformational energies so far. It is employed to evaluate various DFT and wave function theory (WFT) methods, especially regarding whether they are accurate enough to be used as reliable reference methods for larger datasets intended for training and testing more approximated SQM, FF, and MLIP methods. The results reveal that the originally provided BP86-D3(BJ)/DGauss-DZVP conformational energies are not sufficiently accurate. Among the DFT methods tested as an alternative reference level, the revDSD-PBEP86-D4 double hybrid performs best with a mean absolute error (MAD) of 0.2 kcal mol-1 compared with the PNO-LCCSD(T)-F12b reference. The very efficient r2SCAN-3c composite method also shows excellent results, with an MAD of 0.3 kcal mol-1, similar to the best-tested hybrid ωB97M-D4. With these findings, we compiled the large DipCONFL set, which includes over 29,000 realistic conformers in solution with reasonably accurate r2SCAN-3c reference conformational energies, gradients, and further properties potentially relevant for training MLIP methods. This set, also in comparison to DipCONFS, is used to assess the performance of various SQM, FF, and MLIP methods robustly and can complement training sets for those.","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.5,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142174471","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":"Is Quantum Above-Barrier Reflection Important for Molecular Barrier Crossing Rates?","authors":"Chiara Aieta*,&nbsp;Michele Ceotto* and Eli Pollak*,&nbsp;","doi":"10.1021/acs.jctc.4c0091710.1021/acs.jctc.4c00917","DOIUrl":"https://doi.org/10.1021/acs.jctc.4c00917https://doi.org/10.1021/acs.jctc.4c00917","url":null,"abstract":"<p >Understanding quantum tunneling and above-barrier reflection effects on unimolecular and bimolecular reaction rate constants remains challenging to this very day. In many applications, especially when considering moderate-to-high temperatures, the “standard” procedure is to use the parabolic barrier approximation. Recent work has shown though that this may be insufficient, and one cannot ignore anharmonicity. In this work, we study the analytic theory, including anharmonicity obtained when expanding the thermal rate up to order <i>ℏ</i>⁴. Such theories need high-order derivatives of the potential at the barrier top. We show that such derivatives are computed straightforwardly for six different reactions. We suggest a straightforward methodology for assessing whether the parabolic barrier approximation is valid and show that when the reaction asymmetry is large, this may lead to significant quantum above-barrier reflection and transmission coefficients, which are less than unity.</p>","PeriodicalId":45,"journal":{"name":"Journal of Chemical Theory and Computation","volume":null,"pages":null},"PeriodicalIF":5.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142310163","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}