1
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Sugisaki K, Nakano T, Mochizuki Y. Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme. J Comput Chem 2024; 45:2204-2213. [PMID: 38795375 DOI: 10.1002/jcc.27438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024]
Abstract
The fragment molecular orbital (FMO) scheme is one of the popular fragmentation-based methods and has the potential advantage of making the circuit shallow for quantum chemical calculations on quantum computers. In this study, we used a GPU-accelerated quantum simulator (cuQuantum) to perform the electron correlation part of the FMO calculation as unitary coupled-cluster singles and doubles (UCCSD) with the variational quantum eigensolver (VQE) for hydrogen-bonded (FH) 3 and (FH) 2 -H 2 O systems with the STO-3G basis set. VQE-UCCSD calculations were performed using both canonical and localized MO sets, and the results were examined from the point of view of size-consistency and orbital-invariance affected by the Trotter error. It was found that the use of localized MO leads to better results, especially for (FH) 2 -H 2 O. The GPU acceleration was substantial for the simulations with larger numbers of qubits, and was about a factor of 6.7-7.7 for 18 qubit systems.
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Affiliation(s)
- Kenji Sugisaki
- Graduate School of Science and Technology, Keio University, Kawasaki, Japan
- Quantum Computing Center, Keio University, Yokohama, Japan
- Centre for Quantum Engineering, Research and Education, TCG Centres for Research and Education in Science and Technology, Kolkata, India
| | - Tatsuya Nakano
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Toshima-ku, Japan
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Japan
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2
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Medrano Sandonas L, Van Rompaey D, Fallani A, Hilfiker M, Hahn D, Perez-Benito L, Verhoeven J, Tresadern G, Kurt Wegner J, Ceulemans H, Tkatchenko A. Dataset for quantum-mechanical exploration of conformers and solvent effects in large drug-like molecules. Sci Data 2024; 11:742. [PMID: 38972891 PMCID: PMC11228031 DOI: 10.1038/s41597-024-03521-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/13/2024] [Indexed: 07/09/2024] Open
Abstract
We here introduce the Aquamarine (AQM) dataset, an extensive quantum-mechanical (QM) dataset that contains the structural and electronic information of 59,783 low-and high-energy conformers of 1,653 molecules with a total number of atoms ranging from 2 to 92 (mean: 50.9), and containing up to 54 (mean: 28.2) non-hydrogen atoms. To gain insights into the solvent effects as well as collective dispersion interactions for drug-like molecules, we have performed QM calculations supplemented with a treatment of many-body dispersion (MBD) interactions of structures and properties in the gas phase and implicit water. Thus, AQM contains over 40 global and local physicochemical properties (including ground-state and response properties) per conformer computed at the tightly converged PBE0+MBD level of theory for gas-phase molecules, whereas PBE0+MBD with the modified Poisson-Boltzmann (MPB) model of water was used for solvated molecules. By addressing both molecule-solvent and dispersion interactions, AQM dataset can serve as a challenging benchmark for state-of-the-art machine learning methods for property modeling and de novo generation of large (solvated) molecules with pharmaceutical and biological relevance.
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Affiliation(s)
- Leonardo Medrano Sandonas
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
- Institute for Materials Science and Max Bergmann Center of Biomaterials, TU Dresden, 01062, Dresden, Germany.
| | - Dries Van Rompaey
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium.
| | - Alessio Fallani
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Mathias Hilfiker
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - David Hahn
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Laura Perez-Benito
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Jonas Verhoeven
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Gary Tresadern
- Computational Chemistry, Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Joerg Kurt Wegner
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
- Drug Discovery Data Sciences (D3S), Johnson & Johnson Innovative Medicine, 301 Binney Street, MA 02142, Cambridge, USA
| | - Hugo Ceulemans
- Drug Discovery Data Sciences (D3S), Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340, Beerse, Belgium
| | - Alexandre Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511, Luxembourg City, Luxembourg.
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3
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Spencer RJ, Zhanserkeev AA, Yang EL, Steele RP. The Near-Sightedness of Many-Body Interactions in Anharmonic Vibrational Couplings. J Am Chem Soc 2024; 146:15376-15392. [PMID: 38771156 DOI: 10.1021/jacs.4c03198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Couplings between vibrational motions are driven by electronic interactions, and these couplings carry special significance in vibrational energy transfer, multidimensional spectroscopy experiments, and simulations of vibrational spectra. In this investigation, the many-body contributions to these couplings are analyzed computationally in the context of clathrate-like alkali metal cation hydrates, including Cs+(H2O)20, Rb+(H2O)20, and K+(H2O)20, using both analytic and quantum-chemistry potential energy surfaces. Although the harmonic spectra and one-dimensional anharmonic spectra depend strongly on these many-body interactions, the mode-pair couplings were, perhaps surprisingly, found to be dominated by one-body effects, even in cases of couplings to low-frequency modes that involved the motion of multiple water molecules. The origin of this effect was traced mainly to geometric distortion within water monomers and cancellation of many-body effects in differential couplings, and the effect was also shown to be agnostic to the identity of the ion. These outcomes provide new understanding of vibrational couplings and suggest the possibility of improved computational methods for the simulation of infrared and Raman spectra.
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Affiliation(s)
- Ryan J Spencer
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Asylbek A Zhanserkeev
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Emily L Yang
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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4
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Khire SS, Nakajima T, Gadre SR. Cluster-in-Cluster Approach for Computing MP2-Level Vibrational Infrared Spectra of Large Molecular Clusters. J Phys Chem A 2024. [PMID: 38679884 DOI: 10.1021/acs.jpca.4c00952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Constructing the Hessian matrix (HM) for large molecules demands huge computational resources. Here, we report a cluster-in-cluster (CIC) procedure for efficiently evaluating HM and dipole derivatives for large molecular clusters by employing the second-order Møller-Plesset perturbation (MP2) theory. The highlight of the proposal is the separation of the estimations of Hartree-Fock (HF) and post-HF components. The parent cluster with n molecules is divided (virtually) into n subclusters centering each monomer and accommodating its near neighbors decided by a distance cutoff. The HF-level HM is obtained by doing full calculation (FC), while the correlation part is approximated by the respective subclusters. A software automating the procedure [followed by calculating infrared (IR) frequencies and intensities] is applied to deduce the IR spectrum for a variety of molecular clusters, particularly water clusters of various sizes, containing up to ∼2000 basis functions. The accuracy of the IR spectrum constructed using CIC is remarkable, with a substantial time advantage (with respect to its FC counterpart). The reduced computational resources and the tractability of the computations are other major benefits of the procedure.
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Affiliation(s)
- Subodh S Khire
- RIKEN Center for Computational Science, Kobe 6500047, Japan
| | | | - Shridhar R Gadre
- Department of Scientific Computing, Modelling, and Simulation, Savitribai Phule Pune University, Pune 411007, India
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India
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5
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Focke K, De Santis M, Wolter M, Martinez B JA, Vallet V, Pereira Gomes AS, Olejniczak M, Jacob CR. Interoperable workflows by exchanging grid-based data between quantum-chemical program packages. J Chem Phys 2024; 160:162503. [PMID: 38686818 DOI: 10.1063/5.0201701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
Quantum-chemical subsystem and embedding methods require complex workflows that may involve multiple quantum-chemical program packages. Moreover, such workflows require the exchange of voluminous data that go beyond simple quantities, such as molecular structures and energies. Here, we describe our approach for addressing this interoperability challenge by exchanging electron densities and embedding potentials as grid-based data. We describe the approach that we have implemented to this end in a dedicated code, PyEmbed, currently part of a Python scripting framework. We discuss how it has facilitated the development of quantum-chemical subsystem and embedding methods and highlight several applications that have been enabled by PyEmbed, including wave-function theory (WFT) in density-functional theory (DFT) embedding schemes mixing non-relativistic and relativistic electronic structure methods, real-time time-dependent DFT-in-DFT approaches, the density-based many-body expansion, and workflows including real-space data analysis and visualization. Our approach demonstrates, in particular, the merits of exchanging (complex) grid-based data and, in general, the potential of modular software development in quantum chemistry, which hinges upon libraries that facilitate interoperability.
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Affiliation(s)
- Kevin Focke
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Matteo De Santis
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Jessica A Martinez B
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, USA
| | - Valérie Vallet
- CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, Univ. Lille, F-59000 Lille, France
| | | | - Małgorzata Olejniczak
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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Gupta AK, Maier S, Thapa B, Raghavachari K. Toward Post-Hartree-Fock Accuracy for Protein-Ligand Affinities Using the Molecules-in-Molecules Fragmentation-Based Method. J Chem Theory Comput 2024; 20:2774-2785. [PMID: 38530869 DOI: 10.1021/acs.jctc.3c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The complexity and size of large molecular systems, such as protein-ligand complexes, pose computational challenges for accurate post-Hartree-Fock calculations. This study delivers a thorough benchmarking of the Molecules-in-Molecules (MIM) method, presenting a clear and accessible strategy for layer/theory selections in post-Hartree-Fock computations on substantial molecular systems, notably protein-ligand complexes. An approach is articulated, enabling augmented computational efficiency by strategically canceling out common subsystem energy terms between complexes and proteins within the supermolecular equation. Employing DLPNO-based post-Hartree-Fock methods in conjunction with the three-layer MIM method (MIM3), this study demonstrates the achievement of protein-ligand binding energies with remarkable accuracy (errors <1 kcal mol-1), while significantly reducing computational costs. Furthermore, noteworthy correlations between theoretically computed interaction energies and their experimental equivalents were observed, with R2 values of approximately 0.90 and 0.78 for CDK2 and BZT-ITK sets, respectively, thus validating the efficacy of the MIM method in calculating binding energies. By highlighting the crucial role of diffuse or small Pople-style basis sets in the middle layer for reducing energy errors, this work provides valuable insights and practical methodologies for interaction energy computations in large molecular complexes and opens avenues for their application across a diverse range of molecular systems.
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Affiliation(s)
- Ankur K Gupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sarah Maier
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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7
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Mamatkulov K, Zavatski S, Arynbek Y, Esawii HA, Burko A, Bandarenka H, Arzumanyan G. Conformational analysis of lipid membrane mimetics modified with A β42 peptide by Raman spectroscopy and computer simulations. J Biomol Struct Dyn 2024:1-14. [PMID: 38520152 DOI: 10.1080/07391102.2024.2330706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024]
Abstract
Peptide-lipid interactions play an important role in maintaining the integrity and function of the cell membrane. Even slight changes in these interactions can induce the development of various diseases. Specifically, peptide misfolding and aggregation in the membrane is considered to be one of the triggers of Alzheimer's disease (AD), however its exact mechanism is still unclear. To this end, an increase of amyloid-beta (Aβ) peptide concentration in the human brain is widely accepted to gradually produce cytotoxic Aβ aggregates (plaques). These plaques initiate a sequence of pathogenic events ending up in observable symptoms of dementia. Understanding the mechanism of the Aβ interaction with cells is crucial for early detection and prevention of Alzheimer's disease. Hence, in this work, a comprehensive Raman analysis of the Aβ42 conformational dynamics in water and in liposomes and lipodiscs that mimic the membrane system is presented. The obtained results show that the secondary structure of Aβ42 in liposomes is dominated by the α-helix conformation, which remains stable over time. However, it comes as a surprise to reveal that the lipodisc environment induces the transformation of the Aβ42 secondary structure to a β-turn/random coil. Our Raman spectroscopy findings are supported with molecular dynamics (MD) and density functional theory (DFT) simulations, showing their good agreement.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kahramon Mamatkulov
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
| | - Siarhei Zavatski
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Yersultan Arynbek
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Faculty of Physics and Technology, al-Farabi, Kazakh National University, Almaty, Kazakhstan
| | - Heba A Esawii
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Biophysics Department, Faculty of Science, Cairo University, Egypt
| | - Aliaksandr Burko
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Hanna Bandarenka
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Grigory Arzumanyan
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
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8
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Chodkiewicz M, Patrikeev L, Pawlędzio S, Woźniak K. Transferable Hirshfeld atom model for rapid evaluation of aspherical atomic form factors. IUCRJ 2024; 11:249-259. [PMID: 38446457 PMCID: PMC10916294 DOI: 10.1107/s2052252524001507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024]
Abstract
Form factors based on aspherical models of atomic electron density have brought great improvement in the accuracies of hydrogen atom parameters derived from X-ray crystal structure refinement. Today, two main groups of such models are available, the banks of transferable atomic densities parametrized using the Hansen-Coppens multipole model which allows for rapid evaluation of atomic form factors and Hirshfeld atom refinement (HAR)-related methods which are usually more accurate but also slower. In this work, a model that combines the ideas utilized in the two approaches is tested. It uses atomic electron densities based on Hirshfeld partitions of electron densities, which are precalculated and stored in a databank. This model was also applied during the refinement of the structures of five small molecules. A comparison of the resulting hydrogen atom parameters with those derived from neutron diffraction data indicates that they are more accurate than those obtained with the Hansen-Coppens based databank, and only slightly less accurate than those obtained with a version of HAR that neglects the crystal environment. The advantage of using HAR becomes more noticeable when the effects of the environment are included. To speed up calculations, atomic densities were represented by multipole expansion with spherical harmonics up to l = 7, which used numerical radial functions (a different approach to that applied in the Hansen-Coppens model). Calculations of atomic form factors for the small protein crambin (at 0.73 Å resolution) took only 68 s using 12 CPU cores.
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Affiliation(s)
- Michał Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Leonid Patrikeev
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
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9
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Xu H, Wang B, Liao L, Wang Y, Zhu Q, Ren H. High-Throughput Predictions of Accurate Enthalpies of Formation for Larger Molecules Utilizing the Bond Difference Correction Method. J Phys Chem Lett 2024; 15:998-1005. [PMID: 38252697 DOI: 10.1021/acs.jpclett.3c03390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The prediction of standard enthalpies of formation (EOFs) for larger molecules involves a trade-off between accuracy and cost, often resulting in non-negligible errors. The connectivity-based hierarchy (CBH) and simple bond additivity correction (BAC) are two promising means for evaluating EOFs, although they cannot achieve strict chemical accuracy. Calculated errors in the CBH are confirmed from accumulated systematic errors associated with bond differences in chemical environments. On the basis of a new set of bond descriptors, our developed bond difference correction (BDC) method effectively solves incremental errors with molecular size and inability applications for aromatic molecules. To balance the accuracy between non-aromatic and aromatic molecules, a more accurate BAC-based method with unpaired electrons and p hybrid orbitals (BAC-EP) is developed. With the incorporation of the two methods above, strict chemical accuracy by the largest deviation is achieved at low costs. These universal, ultrafast, and high-throughput methods greatly contribute to self-consistent thermodynamic parameters in combustion mechanisms.
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Affiliation(s)
- Huajie Xu
- Research Institute of Frontier Science, Southwest Jiao Tong University, Chengdu, Sichuan 610065, People's Republic of China
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Bo Wang
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Lingxian Liao
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Yang Wang
- Research Institute of Frontier Science, Southwest Jiao Tong University, Chengdu, Sichuan 610065, People's Republic of China
| | - Quan Zhu
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
| | - Haisheng Ren
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, People's Republic of China
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Beran GJO, Greenwell C, Cook C, Řezáč J. Improved Description of Intra- and Intermolecular Interactions through Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory. Acc Chem Res 2023; 56:3525-3534. [PMID: 37963266 DOI: 10.1021/acs.accounts.3c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods which can simultaneously describe intramolecular conformational energies and intermolecular interactions accurately. To achieve this, we have developed a spin-component-scaled, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D) model. SCS-MP2D augments canonical MP2 with a dispersion correction which removes the uncoupled Hartree-Fock dispersion energy present in canonical MP2 and replaces it with a more reliable coupled Kohn-Sham treatment, all evaluated within the framework of Grimme's D3 dispersion model. The spin-component scaling is then used to improve the description of the residual (nondispersion) portion of the correlation energy.The SCS-MP2D model improves upon earlier corrected MP2 models in a few ways. Compared to the highly successful dispersion-corrected MP2C model, which is based solely on intermolecular perturbation theory, the SCS-MP2D dispersion correction improves the description of both inter- and intramolecular interactions. The dispersion correction can also be evaluated with trivial computational cost, and nuclear analytic gradients are computed readily to enable geometry optimizations. In contrast to earlier spin-component scaling MP2 models, the optimal spin-component scaling coefficients are only mildly sensitive to the choice of training data, and a single global parametrization of the model can describe both thermochemistry and noncovalent interactions.The resulting dispersion-corrected, spin-component-scaled MP2 (SCS-MP2D) model predicts conformational energies and intermolecular interactions with accuracy comparable to or better than those of many range-separated and double-hybrid density functionals, as is demonstrated on a variety of benchmark tests. Among the functionals considered here, only the revDSD-PBEP86-D3(BJ) functional gives consistently smaller errors in benchmark tests. The results presented also hint that further improvements of SCS-MP2D may be possible through a more robust fitting procedure for the seven empirical parameters.To demonstrate the performance of SCS-MP2D further, several applications to molecular crystal problems are presented. The three chosen examples all represent cases where density-driven delocalization error causes GGA or hybrid density functionals to artificially stabilize crystals exhibiting more extended π-conjugation. Our pragmatic strategy addresses the delocalization error by combining a periodic density functional theory (DFT) treatment of the infinite lattice with intramolecular/conformational energy corrections computed with SCS-MP2D. For the anticancer drug axitinib, applying the SCS-MP2D conformational energy correction produces crystal polymorph stabilities that are consistent with experiment, in contrast to earlier studies. For the crystal structure prediction of the ROY molecule, so named for its colorful red, orange, and yellow crystals, this approach leads to the first plausible crystal energy landscape, and it reveals that the lowest-energy polymorphs have already been found experimentally. Finally, in the context of photomechanical crystals, which transform light into mechanical work, these techniques are used to predict the structural transformations and extract design principles for maximizing the work performed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Chandler Greenwell
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Cameron Cook
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 160 00 Prague, Czech Republic
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11
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Ricard TC, Zhu X, Iyengar SS. Capturing Weak Interactions in Surface Adsorbate Systems at Coupled Cluster Accuracy: A Graph-Theoretic Molecular Fragmentation Approach Improved through Machine Learning. J Chem Theory Comput 2023. [PMID: 38019639 DOI: 10.1021/acs.jctc.3c00955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The accurate and efficient study of the interactions of organic matter with the surface of water is critical to a wide range of applications. For example, environmental studies have found that acidic polyfluorinated alkyl substances, especially perfluorooctanoic acid (PFOA), have spread throughout the environment and bioaccumulate into human populations residing near contaminated watersheds, leading to many systemic maladies. Thus, the study of the interactions of PFOA with water surfaces became important for the mitigation of their activity as pollutants and threats to public health. However, theoretical study of the interactions of such organic adsorbates on the surface of water, and their bulk concerted properties, often necessitates the use of ab initio methods to properly incorporate the long-range electronic properties that govern these extended systems. Notable theoretical treatments of "on-water" reactions thus far have employed hybrid DFT and semilocal DFT, but the interactions involved are weak interactions that may be best described using post-Hartree-Fock theory. Here, we aim to demonstrate the utility of a graph-theoretic approach to molecular fragmentation that accurately captures the critical "weak" interactions while maintaining an efficient ab initio treatment of the long-range periodic interactions that underpin the physics of extended systems. We apply this graph-theoretical treatment to study PFOA on the surface of water as a model system for the study of weak interactions seen in the wide range of surface interactions and reactions. The approach divides a system into a set of vertices, that are then connected through edges, faces, and higher order graph theoretic objects known as simplexes, to represent a collection of locally interacting subsystems. These subsystems are then used to construct ab initio molecular dynamics simulations and for computing multidimensional potential energy surfaces. To further improve the computational efficiency of our graph theoretic fragmentation method, we use a recently developed transfer learning protocol to construct the full system potential energy from a family of neural networks each designed to accurately model the behavior of individual simplexes. We use a unique multidimensional clustering algorithm, based on the k-means clustering methodology, to define our training space for each separate simplex. These models are used to extrapolate the energies for molecular dynamics trajectories at PFOA water interfaces, at less than one-tenth the cost as compared to a regular molecular fragmentation-based dynamics calculation with excellent agreement with couple cluster level of full system potential energies.
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Affiliation(s)
- Timothy C Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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12
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Szabó PB, Csóka J, Kállay M, Nagy PR. Linear-Scaling Local Natural Orbital CCSD(T) Approach for Open-Shell Systems: Algorithms, Benchmarks, and Large-Scale Applications. J Chem Theory Comput 2023; 19:8166-8188. [PMID: 37921429 PMCID: PMC10687875 DOI: 10.1021/acs.jctc.3c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The extension of the highly optimized local natural orbital (LNO) coupled cluster (CC) with single-, double-, and perturbative triple excitations [LNO-CCSD(T)] method is presented for high-spin open-shell molecules based on restricted open-shell references. The techniques enabling the outstanding efficiency of the closed-shell LNO-CCSD(T) variant are adopted, including the iteration- and redundancy-free second-order Møller-Plesset and (T) formulations as well as the integral-direct, memory- and disk use-economic, and OpenMP-parallel algorithms. For large molecules, the efficiency of our open-shell LNO-CCSD(T) method approaches that of its closed-shell parent method due to the application of restricted orbital sets for demanding integral transformations and a novel approximation for higher-order long-range spin-polarization effects. The accuracy of open-shell LNO-CCSD(T) is extensively tested for radicals and reactions thereof, ionization processes, as well as spin-state splittings, and transition-metal compounds. At the size range where the canonical CCSD(T) reference is accessible (up to 20-30 atoms), the average open-shell LNO-CCSD(T) correlation energies are found to be 99.9 to 99.95% accurate, which translates into average absolute deviations of a few tenths of kcal/mol in the investigated energy differences already with the default settings. For more extensive molecules, the local errors may grow, but they can be estimated and decreased via affordable systematic convergence studies. This enables the accurate modeling of large systems with complex electronic structures, as illustrated on open-shell organic radicals and transition-metal complexes of up to 179 atoms as well as on challenging biochemical systems, including up to 601 atoms and 11,000 basis functions. While the protein models involve difficulties for local approximations, such as the spin states of a bounded iron ion or an extremely delocalized singly occupied orbital, the corresponding single-node LNO-CCSD(T) computations were feasible in a matter of days with 10s to 100 GB of memory use. Therefore, the new LNO-CCSD(T) implementation enables highly accurate computations for open-shell systems of unprecedented size and complexity with widely accessible hardware.
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Affiliation(s)
- P. Bernát Szabó
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - József Csóka
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
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13
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Hasan MN, Ray M, Saha A. Landscape of In Silico Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery. J Phys Chem B 2023; 127:9663-9684. [PMID: 37921534 DOI: 10.1021/acs.jpcb.3c04710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Covalent drug discovery has been a challenging research area given the struggle of finding a sweet balance between selectivity and reactivity for these drugs, the lack of which often leads to off-target activities and hence undesirable side effects. However, there has been a resurgence in covalent drug design following the success of several covalent drugs such as boceprevir (2011), ibrutinib (2013), neratinib (2017), dacomitinib (2018), zanubrutinib (2019), and many others. Design of covalent drugs includes many crucial factors, where "evaluation of the binding affinity" and "a detailed mechanistic understanding on covalent inhibition" are at the top of the list. Well-defined experimental techniques are available to elucidate these factors; however, often they are expensive and/or time-consuming and hence not suitable for high throughput screens. Recent developments in in silico methods provide promise in this direction. In this report, we review a set of recent publications that focused on developing and/or implementing novel in silico techniques in "Computational Covalent Drug Discovery (CCDD)". We also discuss the advantages and disadvantages of these approaches along with what improvements are required to make it a great tool in medicinal chemistry in the near future.
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Affiliation(s)
- Md Nazmul Hasan
- Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Manisha Ray
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Arjun Saha
- Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States
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14
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Khire SS, Nakajima T, Gadre SR. REAlgo: Rapid and efficient algorithm for estimating MP2/CCSD energy gradients for large molecular clusters. J Chem Phys 2023; 159:184109. [PMID: 37955321 DOI: 10.1063/5.0174726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
This work reports the development of an algorithm for rapid and efficient evaluation of energy gradients for large molecular clusters employing correlated methods viz. second-order Møller-Plesset perturbation theory (MP2) theory and couple cluster singles and doubles (CCSD). The procedure segregates the estimation of Hartree-Fock (HF) and correlation components. The HF energy and gradients are obtained by performing a full calculation. The correlation energy is approximated as the corresponding two-body interaction energy. Correlation gradients for each monomer are approximated from the respective monomer-centric fragments comprising its immediate neighbours. The programmed algorithm is explored for the geometry optimization of large molecular clusters using the BERNY optimizer as implemented in the Gaussian suite of software. The accuracy and efficacy of the method are critically probed for a variety of large molecular clusters containing up to 3000 basis functions, in particular large water clusters. The CCSD level geometry optimization of molecular clusters containing ∼800 basis functions employing a modest hardware is also reported.
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Affiliation(s)
- Subodh S Khire
- RIKEN Center for Computational Science, Kobe 6500047, Japan
| | | | - Shridhar R Gadre
- Department of Scientific Computing, Modelling and Simulation, Savitribai Phule Pune University, Pune 411007, India
- Department of Chemistry, Savitribai Phule Pune University, Pune 411007, India
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15
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Iyengar SS, Zhang JH, Saha D, Ricard TC. Graph-| Q⟩⟨ C|: A Quantum Algorithm with Reduced Quantum Circuit Depth for Electronic Structure. J Phys Chem A 2023; 127:9334-9345. [PMID: 37906738 DOI: 10.1021/acs.jpca.3c04261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The accurate determination of chemical properties is known to have a critical impact on multiple fundamental chemical problems but is deeply hindered by the steep algebraic scaling of electron correlation calculations and the exponential scaling of quantum nuclear dynamics. With the advent of new quantum computing hardware and associated developments in creating new paradigms for quantum software, this avenue has been recognized as perhaps one way to address exponentially complex challenges in quantum chemistry and molecular dynamics. In this paper, we discuss a new approach to drastically reduce the quantum circuit depth (by several orders of magnitude) and help improve the accuracy in the quantum computation of electron correlation energies for large molecular systems. The method is derived from a graph-theoretic approach to molecular fragmentation and enables us to create a family of projection operators that decompose quantum circuits into separate unitary processes. Some of these processes can be treated on quantum hardware and others on classical hardware in a completely asynchronous and parallel fashion. Numerical benchmarks are provided through the computation of unitary coupled-cluster singles and doubles (UCCSD) energies for medium-sized protonated and neutral water clusters using the new quantum algorithms presented here.
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Affiliation(s)
- Srinivasan S Iyengar
- Department of Chemistry, Department of Physics, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Juncheng Harry Zhang
- Department of Chemistry, Department of Physics, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Debadrita Saha
- Department of Chemistry, Department of Physics, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Timothy C Ricard
- Department of Chemistry, Department of Physics, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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16
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Focke K, Jacob CR. Coupled-Cluster Density-Based Many-Body Expansion. J Phys Chem A 2023; 127:9139-9148. [PMID: 37871170 PMCID: PMC10626589 DOI: 10.1021/acs.jpca.3c04591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
While CCSD(T) is often considered the "gold standard" of computational chemistry, the scaling of its computational cost as N7 limits its applicability for large and complex molecular systems. In this work, we apply the density-based many-body expansion [ Int. J. Quantum Chem. 2020, 120, e26228] in combination with CCSD(T). The accuracy of this approach is assessed for neutral, protonated, and deprotonated water hexamers, as well as (H2O)16 and (H2O)17 clusters. For the neutral water clusters, we find that already with a density-based two-body expansion, we are able to approximate the supermolecular CCSD(T) energies within chemical accuracy (4 kJ/mol). This surpasses the accuracy that is achieved with a conventional, energy-based three-body expansion. We show that this accuracy can be maintained even when approximating the electron densities using Hartree-Fock instead of using coupled-cluster densities. The density-based many-body expansion thus offers a simple, resource-efficient, and highly parallelizable approach that makes CCSD(T)-quality calculations feasible where they would otherwise be prohibitively expensive.
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Affiliation(s)
- Kevin Focke
- Institute of Physical and
Theoretical Chemistry, Technische Universität
Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Institute of Physical and
Theoretical Chemistry, Technische Universität
Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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17
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Olive LN, Dornshuld EV, Schaefer HF, Tschumper GS. Competition between Solvent···Solvent and Solvent···Solute Interactions in the Microhydration of the Tetrafluoroborate Anion, BF 4-(H 2O) n=1,2,3,4. J Phys Chem A 2023; 127:8806-8820. [PMID: 37774368 DOI: 10.1021/acs.jpca.3c04014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
This study systematically examines the interactions of the tetrafluoroborate anion (BF4-) with up to four water molecules (BF4-(H2O)n=1,2,3,4). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed using a variety of density functional theory (DFT) methods (B3LYP, B3LYP-D3BJ, and M06-2X) and the MP2 ab initio method with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for B, O, and F; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the CCSD(T) ab initio method and the haTZ basis set for the mono- and dihydrate (n = 1, 2) structures. The 2-body:Many-body (2b:Mb) technique, in which CCSD(T) computations capture the 1- and 2-body contributions to the interactions and MP2 computations recover all higher-order contributions, was used to extend these demanding computations to the tri- and tetrahydrate (n = 3, 4) systems. Four, five, and eight new stationary points have been identified for the di-, tri-, and tetrahydrate systems, respectively. The global minimum of the monohydrate adopts a symmetric double ionic hydrogen bond motif with C2v symmetry and an electronic dissociation energy of 13.17 kcal mol-1 at the CCSD(T)/haTZ level of theory. This strong solvent···solute interaction, however, competes with solute···solute interactions in the lowest-energy BF4-(H2O)n=2,3,4 minima that are not seen in the other di-, tri-, or tetrahydrate minima. The latter interactions help increase the 2b:Mb dissociation energies to more than 26, 41, and 51 kcal mol-1 for n = 2, 3, and 4, respectively. Structures that form hydrogen bonds between the solvating water molecules also exhibit the largest shifts in the harmonic OH stretching frequencies for the waters of hydration. These shifts can exceed -280 cm-1 relative to an isolated H2O molecule at the 2b:Mb/haTZ level of theory.
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Affiliation(s)
- Laura N Olive
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Eric V Dornshuld
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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18
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Fedorov R, Gryn’ova G. Unlocking the Potential: Predicting Redox Behavior of Organic Molecules, from Linear Fits to Neural Networks. J Chem Theory Comput 2023; 19:4796-4814. [PMID: 37463673 PMCID: PMC10414033 DOI: 10.1021/acs.jctc.3c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Indexed: 07/20/2023]
Abstract
Redox-active organic molecules, i.e., molecules that can relatively easily accept and/or donate electrons, are ubiquitous in biology, chemical synthesis, and electronic and spintronic devices, such as solar cells and rechargeable batteries, etc. Choosing the best candidates from an essentially infinite chemical space for experimental testing in a target application requires efficient screening approaches. In this Review, we discuss modern in silico techniques for predicting reduction and oxidation potentials of organic molecules that go beyond conventional first-principles computations and thermodynamic cycles. Approaches ranging from simple linear fits based on molecular orbital energy approximation and energy difference approximation to advanced regression and neural network machine learning algorithms employing complex descriptors of molecular compositions, geometries, and electronic structures are examined in conjunction with relevant literature examples. We discuss the interplay between ab initio data and machine learning (ML), i.e., whether it is better to base predictions on low-level quantum-chemical results corrected with ML or to bypass first-principles computations entirely and instead rely on elaborate deep learning architectures. Finally, we list currently available data sets of redox-active organic molecules and their experimental and/or computed properties to facilitate the development of screening platforms and rational design of redox-active organic molecules.
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Affiliation(s)
- Rostislav Fedorov
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing, Heidelberg
University, 69120 Heidelberg, Germany
| | - Ganna Gryn’ova
- Heidelberg
Institute for Theoretical Studies (HITS gGmbH), 69118 Heidelberg, Germany
- Interdisciplinary
Center for Scientific Computing, Heidelberg
University, 69120 Heidelberg, Germany
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19
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Zhang P, Yang W. Toward a general neural network force field for protein simulations: Refining the intramolecular interaction in protein. J Chem Phys 2023; 159:024118. [PMID: 37431910 PMCID: PMC10481389 DOI: 10.1063/5.0142280] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Molecular dynamics (MD) is an extremely powerful, highly effective, and widely used approach to understanding the nature of chemical processes in atomic details for proteins. The accuracy of results from MD simulations is highly dependent on force fields. Currently, molecular mechanical (MM) force fields are mainly utilized in MD simulations because of their low computational cost. Quantum mechanical (QM) calculation has high accuracy, but it is exceedingly time consuming for protein simulations. Machine learning (ML) provides the capability for generating accurate potential at the QM level without increasing much computational effort for specific systems that can be studied at the QM level. However, the construction of general machine learned force fields, needed for broad applications and large and complex systems, is still challenging. Here, general and transferable neural network (NN) force fields based on CHARMM force fields, named CHARMM-NN, are constructed for proteins by training NN models on 27 fragments partitioned from the residue-based systematic molecular fragmentation (rSMF) method. The NN for each fragment is based on atom types and uses new input features that are similar to MM inputs, including bonds, angles, dihedrals, and non-bonded terms, which enhance the compatibility of CHARMM-NN to MM MD and enable the implementation of CHARMM-NN force fields in different MD programs. While the main part of the energy of the protein is based on rSMF and NN, the nonbonded interactions between the fragments and with water are taken from the CHARMM force field through mechanical embedding. The validations of the method for dipeptides on geometric data, relative potential energies, and structural reorganization energies demonstrate that the CHARMM-NN local minima on the potential energy surface are very accurate approximations to QM, showing the success of CHARMM-NN for bonded interactions. However, the MD simulations on peptides and proteins indicate that more accurate methods to represent protein-water interactions in fragments and non-bonded interactions between fragments should be considered in the future improvement of CHARMM-NN, which can increase the accuracy of approximation beyond the current mechanical embedding QM/MM level.
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Affiliation(s)
- Pan Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
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20
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Mó O, Montero-Campillo MM, Yáñez M, Alkorta I, Elguero J. Dispersion, Rehybridization, and Pentacoordination: Keys to Understand Clustering of Boron and Aluminum Hydrides and Halides. J Phys Chem A 2023. [PMID: 37418427 PMCID: PMC10364081 DOI: 10.1021/acs.jpca.3c02747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
The structure, stability, and bonding characteristics of dimers and trimers involving BX3 and AlX3 (X = H, F, Cl) in the gas phase, many of them explored for the first time, were investigated using different DFT (B3LYP, B3LYP/D3BJ, and M06-2X) and ab initio (MP2 and G4) methods together with different energy decomposition formalisms, namely, many-body interaction-energy and localized molecular orbital energy decomposition analysis. The electron density of the clusters investigated was analyzed with QTAIM, electron localization function, NCIPLOT, and adaptive natural density partitioning approaches. Our results for triel hydride dimers and Al2X6 (X = F, Cl) clusters are in good agreement with previous studies in the literature, but in contrast with the general accepted idea that B2F6 and B2Cl6 do not exist, we have found that they are predicted to be weakly bound systems if dispersion interactions are conveniently accounted for in the theoretical schemes used. Dispersion interactions are also dominant in both homo- and heterotrimers involving boron halide monomers. Surprisingly, B3F9 and B3Cl9 C3v cyclic trimers, in spite of exhibiting rather strong B-X (X = F, Cl) interactions, were found to be unstable with respect to the isolated monomers due to the high energetic cost of the rehybridization of the B atom, which is larger than the two- and three-body stabilization contributions when the cyclic is formed. Another important feature is the enhanced stability of both homo- and heterotrimers in which Al is the central atom because Al is systematically pentacoordinated, whereas this is not the case when the central atom is B, which is only tri- or tetra-coordinated.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - M Merced Montero-Campillo
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias, and Institute of Advanced Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, IQM-CSIC, Juan de la Cierva, 3, 28006 Madrid, Spain
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21
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Raghavachari K, Maier S, Collins EM, Debnath S, Sengupta A. Approaching Coupled Cluster Accuracy with Density Functional Theory Using the Generalized Connectivity-Based Hierarchy. J Chem Theory Comput 2023. [PMID: 37338997 DOI: 10.1021/acs.jctc.3c00301] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
This Perspective reviews connectivity-based hierarchy (CBH), a systematic hierarchy of error-cancellation schemes developed in our group with the goal of achieving chemical accuracy using inexpensive computational techniques ("coupled cluster accuracy with DFT"). The hierarchy is a generalization of Pople's isodesmic bond separation scheme that is based only on the structure and connectivity and is applicable to any organic and biomolecule consisting of covalent bonds. It is formulated as a series of rungs involving increasing levels of error cancellation on progressively larger fragments of the parent molecule. The method and our implementation are discussed briefly. Examples are given for the applications of CBH involving (1) energies of complex organic rearrangement reactions, (2) bond energies of biofuel molecules, (3) redox potentials in solution, (4) pKa predictions in the aqueous medium, and (5) theoretical thermochemistry combining CBH with machine learning. They clearly show that near-chemical accuracy (1-2 kcal/mol) is achieved for a variety of applications with DFT methods irrespective of the underlying density functional used. They demonstrate conclusively that seemingly disparate results, often seen with different density functionals in many chemical applications, are due to an accumulation of systematic errors in the smaller local molecular fragments that can be easily corrected with higher-level calculations on those small units. This enables the method to achieve the accuracy of the high level of theory (e.g., coupled cluster) while the cost remains that of DFT. The advantages and limitations of the method are discussed along with areas of ongoing developments.
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Affiliation(s)
- Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sarah Maier
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Eric M Collins
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sibali Debnath
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Arkajyoti Sengupta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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22
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Chow M, Lambros E, Li X, Hammes-Schiffer S. Nuclear-Electronic Orbital QM/MM Approach: Geometry Optimizations and Molecular Dynamics. J Chem Theory Comput 2023. [PMID: 37329317 DOI: 10.1021/acs.jctc.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods allow simulations of chemical reactions in atomistic solvent and heterogeneous environments such as proteins. Herein, the nuclear-electronic orbital (NEO) QM/MM approach is introduced to enable the quantization of specified nuclei, typically protons, in the QM region using a method such as NEO-density functional theory (NEO-DFT). This approach includes proton delocalization, polarization, anharmonicity, and zero-point energy in geometry optimizations and dynamics. Expressions for the energies and analytical gradients associated with the NEO-QM/MM method, as well as the previously developed polarizable continuum model (NEO-PCM), are provided. Geometry optimizations of small organic molecules hydrogen bonded to water in either dielectric continuum solvent or explicit atomistic solvent illustrate that aqueous solvation can strengthen hydrogen-bonding interactions for the systems studied, as indicated by shorter intermolecular distances at the hydrogen-bond interface. We then performed a real-time direct dynamics simulation of a phenol molecule in explicit water using the NEO-QM/MM method. These developments and initial examples provide the foundation for future studies of nuclear-electronic quantum dynamics in complex chemical and biological environments.
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Affiliation(s)
- Mathew Chow
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Eleftherios Lambros
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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23
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Vornweg JR, Wolter M, Jacob CR. A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions. J Comput Chem 2023; 44:1634-1644. [PMID: 37171574 DOI: 10.1002/jcc.27114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/13/2023]
Abstract
The Molecular Fractionation with Conjugate Caps (MFCC) method is a popular fragmentation method for the quantum-chemical treatment of proteins. However, it does not account for interactions between the amino acid fragments, such as intramolecular hydrogen bonding. Here, we present a combination of the MFCC fragmentation scheme with a second-order many-body expansion (MBE) that consistently accounts for all fragment-fragment, fragment-cap, and cap-cap interactions, while retaining the overall simplicity of the MFCC scheme with its chemically meaningful fragments. We show that with the resulting MFCC-MBE(2) scheme, the errors in the total energies of selected polypeptides and proteins can be reduced by up to one order of magnitude and relative energies of different protein conformers can be predicted accurately.
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Affiliation(s)
- Johannes R Vornweg
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
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24
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Bowling PE, Broderick DR, Herbert JM. Fragment-Based Calculations of Enzymatic Thermochemistry Require Dielectric Boundary Conditions. J Phys Chem Lett 2023; 14:3826-3834. [PMID: 37061921 DOI: 10.1021/acs.jpclett.3c00533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Electronic structure calculations on enzymes require hundreds of atoms to obtain converged results, but fragment-based approximations offer a cost-effective solution. We present calculations on enzyme models containing 500-600 atoms using the many-body expansion, comparing to benchmarks in which the entire enzyme-substrate complex is described at the same level of density functional theory. When the amino acid fragments contain ionic side chains, the many-body expansion oscillates under vacuum boundary conditions but rapid convergence is restored using low-dielectric boundary conditions. This implies that full-system calculations in the gas phase are inappropriate benchmarks for assessing errors in fragment-based approximations. A three-body protocol retains sub-kilocalorie per mole fidelity with respect to a supersystem calculation, as does a two-body calculation combined with a full-system correction at a low-cost level of theory. These protocols pave the way for application of high-level quantum chemistry to large systems via rigorous, ab initio treatment of many-body polarization.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dustin R Broderick
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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25
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Witte JF, Wasternack J, Wei S, Schalley CA, Paulus B. The Interplay of Weakly Coordinating Anions and the Mechanical Bond: A Systematic Study of the Explicit Influence of Counterions on the Properties of (Pseudo)rotaxanes. Molecules 2023; 28:molecules28073077. [PMID: 37049840 PMCID: PMC10096450 DOI: 10.3390/molecules28073077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Weakly coordinating anions (WCAs) have attracted much attention in recent years due to their ability to stabilise highly reactive cations. It may well be argued, however, that a profound understanding of what truly defines a WCA is still lacking, and systematic studies to unravel counterion effects are scarce. In this work, we investigate a supramolecular pseudorotaxane formation reaction, subject to a selection of anions, ranging from strongly to weakly coordinating, which not only aids in fostering our knowledge about anion coordination properties, but also provides valuable theoretical insight into the nature of the mechanical bond. We employ state-of-the-art DFT-based methods and tools, combined with isothermal calorimetry and 1H NMR experiments, to compute anion-dependent Gibbs free association energies ΔGa, as well as to evaluate intermolecular interactions. We find correlations between ΔGa and the anions’ solvation energies, which are exploited to calculate physico-chemical reaction parameters in the context of coordinating anions. Furthermore, we show that the binding situation within the (pseudo)rotaxanes can be mostly understood by straight-forward electrostatic considerations. However, quantum-chemical effects such as dispersion and charge-transfer interactions become more and more relevant when WCAs are employed.
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Affiliation(s)
- J. Felix Witte
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
- Correspondence: (J.F.W.); (B.P.)
| | - Janos Wasternack
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Shenquan Wei
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie, Organische Chemie, Freie Universität Berlin, Arnimallee 20, 14195 Berlin, Germany
| | - Beate Paulus
- Institut für Chemie und Biochemie, Physikalische und Theoretische Chemie, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
- Correspondence: (J.F.W.); (B.P.)
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26
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Khire SS, Gattadahalli N, Gurav ND, Kumar A, Gadre SR. Constructing Potential Energy Surface with Correlated Theory for Dipeptides Using Molecular Tailoring Approach. Chemphyschem 2023; 24:e202200784. [PMID: 36735449 DOI: 10.1002/cphc.202200784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/04/2023]
Abstract
We demonstrate a cost-effective alternative employing the fragment-based molecular tailoring approach (MTA) for building the potential energy surface (PES) for two dipeptides viz. alanine-alanine and alanine-proline employing correlated theory, with augmented Dunning basis sets. About 1369 geometries are generated for each test dipeptide by systematically varying the dihedral angles Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . These conformational geometries are partially optimized by relaxing all the other Z-matrix parameters, fixing the values of Φ ${{\rm{\Phi }}}$ and Ψ ${{{\Psi }}}$ . The MP2 level PES is constructed from the MTA-energies of chemically intact geometries using minimal hardware. The fidelity of MP2/aug-cc-pVDZ level PES is brought out by comparing it with its full calculation counterpart. Further, we bring out the power of the method by reporting the MTA-based CCSD/aug-cc-pVDZ level PES for these two dipeptides containing 498 and 562 basis functions respectively.
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Affiliation(s)
- Subodh S Khire
- RIKEN Center for Computational Science, Kobe, 650-0047, Japan.,Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
| | - Nandini Gattadahalli
- Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
| | - Nalini D Gurav
- Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India.,Organisch-Chemisches Institut and Center for Multiscale Theory and Computation (CMTC), Westfälische Wilhelms-Universität Münster, Corrensstrasse 36, 48149, Münster, Germany
| | - Anmol Kumar
- School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, HSFII, Baltimore, Maryland, 21201, U.S.A
| | - Shridhar R Gadre
- Department of Scientific Computing Modelling and Simulation, Savitribai Phule Pune University, Pune, 411 007, India
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27
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Jia MX, Wang QD, Ren XF, Kang GJ. Benchmarking Composite Methods for Thermodynamic Properties of Nitro, Nitrite, and Nitrate Species Relevant to Energetic Materials. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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28
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Chen WK, Fang WH, Cui G. Extending multi-layer energy-based fragment method for excited-state calculations of large covalently bonded fragment systems. J Chem Phys 2023; 158:044110. [PMID: 36725521 DOI: 10.1063/5.0129458] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Recently, we developed a low-scaling Multi-Layer Energy-Based Fragment (MLEBF) method for accurate excited-state calculations and nonadiabatic dynamics simulations of nonbonded fragment systems. In this work, we extend the MLEBF method to treat covalently bonded fragment ones. The main idea is cutting a target system into many fragments according to chemical properties. Fragments with dangling bonds are first saturated by chemical groups; then, saturated fragments, together with the original fragments without dangling bonds, are grouped into different layers. The accurate total energy expression is formulated with the many-body energy expansion theory, in combination with the inclusion-exclusion principle that is used to delete the contribution of chemical groups introduced to saturate dangling bonds. Specifically, in a two-layer MLEBF model, the photochemically active and inert layers are calculated with high-level and efficient electronic structure methods, respectively. Intralayer and interlayer energies can be truncated at the two- or three-body interaction level. Subsequently, through several systems, including neutral and charged covalently bonded fragment systems, we demonstrate that MLEBF can provide accurate ground- and excited-state energies and gradients. Finally, we realize the structure, conical intersection, and path optimizations by combining our MLEBF program with commercial and free packages, e.g., ASE and SciPy. These developments make MLEBF a practical and reliable tool for studying complex photochemical and photophysical processes of large nonbonded and bonded fragment systems.
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Affiliation(s)
- Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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29
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Hong B, Fang T, Li W, Li S. Predicting the structures and vibrational spectra of molecular crystals containing large molecules with the generalized energy-based fragmentation approach. J Chem Phys 2023; 158:044117. [PMID: 36725497 DOI: 10.1063/5.0137072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The generalized energy-based fragmentation (GEBF) approach under periodic boundary conditions (PBCs) has been developed to facilitate calculations of molecular crystals containing large molecules. The PBC-GEBF approach can help predict structures and properties of molecular crystals at different theory levels by performing molecular quantum chemistry calculations on a series of non-periodic subsystems constructed from the studied systems. A more rigorous formula of the forces on translational vectors of molecular crystals was proposed and implemented, enabling more reliable predictions of crystal structures. Our benchmark results on several typical molecular crystals show that the PBC-GEBF approach could reproduce the forces on atoms and the translational vectors and the optimized crystal structures from the corresponding conventional periodic methods. The improved PBC-GEBF approach is then applied to predict the crystal structures and vibrational spectra of two molecular crystals containing large molecules. The PBC-GEBF approach can provide a satisfactory description on the crystal structure of a molecular crystal containing 312 atoms in a unit cell at density-fitting second-order Møller-Plesset perturbation theory and density functional theory (DFT) levels and the infrared vibrational spectra of another molecular crystal containing 864 atoms in a unit cell at the DFT level. The PBC-GEBF approach is expected to be a promising theoretical tool for electronic structure calculations on molecular crystals containing large molecules.
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Affiliation(s)
- Benkun Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
| | - Tao Fang
- Genesys Microelectronics (Shanghai) Co., Ltd., 6th Floor, 11th Building, No. 3000 LongDong Road, Pu Dong District, Shanghai, People's Republic of China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, People's Republic of China
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30
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Nakai H, Kobayashi M, Yoshikawa T, Seino J, Ikabata Y, Nishimura Y. Divide-and-Conquer Linear-Scaling Quantum Chemical Computations. J Phys Chem A 2023; 127:589-618. [PMID: 36630608 DOI: 10.1021/acs.jpca.2c06965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fragmentation and embedding schemes are of great importance when applying quantum-chemical calculations to more complex and attractive targets. The divide-and-conquer (DC)-based quantum-chemical model is a fragmentation scheme that can be connected to embedding schemes. This feature article explains several DC-based schemes developed by the authors over the last two decades, which was inspired by the pioneering study of DC self-consistent field (SCF) method by Yang and Lee (J. Chem. Phys. 1995, 103, 5674-5678). First, the theoretical aspects of the DC-based SCF, electron correlation, excited-state, and nuclear orbital methods are described, followed by the two-component relativistic theory, quantum-mechanical molecular dynamics simulation, and the introduction of three programs, including DC-based schemes. Illustrative applications confirmed the accuracy and feasibility of the DC-based schemes.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Masato Kobayashi
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido060-0810, Japan.,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Kita 21 Nishi 10, Kita-ku, Sapporo, Hokkaido001-0021, Japan
| | - Takeshi Yoshikawa
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba274-8510, Japan
| | - Junji Seino
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan.,Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
| | - Yasuhiro Ikabata
- Information and Media Center, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan.,Department of Computer Science and Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi441-8580, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo169-8555, Japan
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31
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Speake BT, Irons TJP, Wibowo M, Johnson AG, David G, Teale AM. An Embedded Fragment Method for Molecules in Strong Magnetic Fields. J Chem Theory Comput 2022; 18:7412-7427. [PMID: 36414537 DOI: 10.1021/acs.jctc.2c00865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An extension of the embedded fragment method for calculations on molecular clusters is presented, which includes strong external magnetic fields. The approach is flexible, allowing for calculations at the Hartree-Fock, current-density-functional theory, Møller-Plesset perturbation theory, and coupled-cluster levels using London atomic orbitals. For systems consisting of discrete molecular subunits, calculations using London atomic orbitals can be performed in a computationally tractable manner for systems beyond the reach of conventional calculations, even those accelerated by resolution-of-the-identity or Cholesky decomposition methods. To assess the applicability of the approach, applications to water clusters are presented, showing how strong magnetic fields enhance binding within the clusters. However, our calculations suggest that, contrary to previous suggestions in the literature, this enhanced binding may not be directly attributable to strengthening of hydrogen bonding. Instead, these results suggest that this arises for larger field strengths as a response of the system to the presence of the external field, which induces a charge density build up between the monomer units. The approach is embarrassingly parallel and its computational tractability is demonstrated for clusters of up to 103 water molecules in triple-ζ basis sets, which would correspond to conventional calculations with more than 12 000 basis functions.
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Affiliation(s)
- Benjamin T Speake
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Tom J P Irons
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Meilani Wibowo
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Andrew G Johnson
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom
| | - Grégoire David
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom.,Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, F-35000 Rennes, France
| | - Andrew M Teale
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United KIngdom.,Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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32
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Otten M, Hermes MR, Pandharkar R, Alexeev Y, Gray SK, Gagliardi L. Localized Quantum Chemistry on Quantum Computers. J Chem Theory Comput 2022; 18:7205-7217. [PMID: 36346785 DOI: 10.1021/acs.jctc.2c00388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantum chemistry calculations of large, strongly correlated systems are typically limited by the computation cost that scales exponentially with the size of the system. Quantum algorithms, designed specifically for quantum computers, can alleviate this, but the resources required are still too large for today's quantum devices. Here, we present a quantum algorithm that combines a localization of multireference wave functions of chemical systems with quantum phase estimation (QPE) and variational unitary coupled cluster singles and doubles (UCCSD) to compute their ground-state energy. Our algorithm, termed "local active space unitary coupled cluster" (LAS-UCC), scales linearly with the system size for certain geometries, providing a polynomial reduction in the total number of gates compared with QPE, while providing accuracy above that of the variational quantum eigensolver using the UCCSD ansatz and also above that of the classical local active space self-consistent field. The accuracy of LAS-UCC is demonstrated by dissociating (H2)2 into two H2 molecules and by breaking the two double bonds in trans-butadiene, and resource estimates are provided for linear chains of up to 20 H2 molecules.
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Affiliation(s)
- Matthew Otten
- HRL Laboratories, LLC, 3011 Malibu Canyon Road, Malibu, California90265, United States
| | - Matthew R Hermes
- Department of Chemistry, Pritzker School of Molecular Engineering, James Franck Institute, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois60637, United States
| | - Riddhish Pandharkar
- Department of Chemistry, Pritzker School of Molecular Engineering, James Franck Institute, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois60637, United States
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Stephen K Gray
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, Illinois60439, United States
| | - Laura Gagliardi
- Department of Chemistry, Pritzker School of Molecular Engineering, James Franck Institute, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois60637, United States.,Argonne National Laboratory, Lemont, Illinois60439, United States
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33
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Kumar A, DeGregorio N, Ricard T, Iyengar SS. Graph-Theoretic Molecular Fragmentation for Potential Surfaces Leads Naturally to a Tensor Network Form and Allows Accurate and Efficient Quantum Nuclear Dynamics. J Chem Theory Comput 2022; 18:7243-7259. [PMID: 36332133 DOI: 10.1021/acs.jctc.2c00484] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Molecular fragmentation methods have revolutionized quantum chemistry. Here, we use a graph-theoretically generated molecular fragmentation method, to obtain accurate and efficient representations for multidimensional potential energy surfaces and the quantum time-evolution operator, which plays a critical role in quantum chemical dynamics. In doing so, we find that the graph-theoretic fragmentation approach naturally reduces the potential portion of the time-evolution operator into a tensor network that contains a stream of coupled lower-dimensional propagation steps to potentially achieve quantum dynamics with reduced complexity. Furthermore, the fragmentation approach used here has previously been shown to allow accurate and efficient computation of post-Hartree-Fock electronic potential energy surfaces, which in many cases has been shown to be at density functional theory cost. Thus, by combining the advantages of molecular fragmentation with the tensor network formalism, the approach yields an on-the-fly quantum dynamics scheme where both the electronic potential calculation and nuclear propagation portion are enormously simplified through a single stroke. The method is demonstrated by computing approximations to the propagator and to potential surfaces for a set of coupled nuclear dimensions within a protonated water wire problem exhibiting the Grotthuss mechanism of proton transport. In all cases, our approach has been shown to reduce the complexity of representing the quantum propagator, and by extension action of the propagator on an initial wavepacket, by several orders, with minimal loss in accuracy.
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Affiliation(s)
- Anup Kumar
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
| | - Nicole DeGregorio
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
| | - Timothy Ricard
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
| | - Srinivasan S Iyengar
- Department of Chemistry, and the Indiana University Quantum Science and Engineering Center (IU-QSEC), Indiana University, Bloomington, Indiana 47405, United States
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34
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Liu J, He X. Recent advances in quantum fragmentation approaches to complex molecular and condensed‐phase systems. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jinfeng Liu
- Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing China
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Frontiers Science Center of Molecule Intelligent Syntheses, School of Chemistry and Molecular Engineering East China Normal University Shanghai China
- New York University‐East China Normal University Center for Computational Chemistry New York University Shanghai Shanghai China
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35
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Westheimer BM, Gordon MS. General, Rigorous Approach for the Treatment of Interfragment Covalent Bonds. J Phys Chem A 2022; 126:6995-7006. [PMID: 36166638 DOI: 10.1021/acs.jpca.2c04015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A generalized, projection-based transformation of the method-agnostic Fock operator in various ab initio fragment-based quantum chemistry methods has been developed for the treatment of interfragment covalent bonds. This transformation freezes the relevant localized molecular orbital associated with each interfragment bond, thereby restricting the variational subspace of the fragment wave functions, in order to maintain the proper physical characteristics of the involved covalent bonds. In addition, sets of orbitals that would lead to multiple occupancy of certain orbitals are explicitly removed from the variational space. The transformation is developed for the specific case of mutually orthonormal frozen and unfrozen orbitals within each fragment. The newly developed approach is then used to study model systems with two popular ab initio fragment-based methods, and the results of these calculations are compared to those obtained by existing methodologies. Analysis is focused on both quantitative and qualitative accuracy as well as computational scalability and stability. Other methods for which the developed formalisms are appropriate are outlined, and future extensions of the methods are discussed.
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Affiliation(s)
- Bryce M Westheimer
- Iowa State University, Ames, Iowa 50011, United States.,Ames Laboratory, Ames, Iowa 50011, United States
| | - Mark S Gordon
- Iowa State University, Ames, Iowa 50011, United States.,Ames Laboratory, Ames, Iowa 50011, United States
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36
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Förster A, Visscher L. Quasiparticle Self-Consistent GW-Bethe-Salpeter Equation Calculations for Large Chromophoric Systems. J Chem Theory Comput 2022; 18:6779-6793. [PMID: 36201788 PMCID: PMC9648197 DOI: 10.1021/acs.jctc.2c00531] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The GW-Bethe–Salpeter equation
(BSE) method
is promising for calculating the low-lying excitonic states of molecular
systems. However, so far it has only been applied to rather small
molecules and in the commonly implemented diagonal approximations
to the electronic self-energy, it depends on a mean-field starting
point. We describe here an implementation of the self-consistent and
starting-point-independent quasiparticle self-consistent (qsGW)-BSE approach, which is suitable for calculations on
large molecules. We herein show that eigenvalue-only self-consistency
can lead to an unfaithful description of some excitonic states for
chlorophyll dimers while the qsGW-BSE vertical excitation
energies (VEEs) are in excellent agreement with spectroscopic experiments
for chlorophyll monomers and dimers measured in the gas phase. Furthermore,
VEEs from time-dependent density functional theory calculations tend
to disagree with experimental values and using different range-separated
hybrid (RSH) kernels does change the VEEs by up to 0.5 eV. We use
the new qsGW-BSE implementation to calculate the
lowest excitation energies of the six chromophores of the photosystem
II (PSII) reaction center (RC) with nearly 2000 correlated electrons.
Using more than 11,000 (6000) basis functions, the calculation could
be completed in less than 5 (2) days on a single modern compute node.
In agreement with previous TD-DFT calculations using RSH kernels on
models that also do not include environmental effects, our qsGW-BSE calculations only yield states with local characters
in the low-energy spectrum of the hexameric complex. Earlier works
with RSH kernels have demonstrated that the protein environment facilitates
the experimentally observed interchromophoric charge transfer. Therefore,
future research will need to combine correlation effects beyond TD-DFT
with an explicit treatment of environmental electrostatics.
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Affiliation(s)
- Arno Förster
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
| | - Lucas Visscher
- Theoretical Chemistry, Vrije Universiteit, De Boelelaan 1083, NL-1081 HVAmsterdam, The Netherlands
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37
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Zhu X, Iyengar SS. Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol. J Chem Theory Comput 2022; 18:5125-5144. [PMID: 35994592 DOI: 10.1021/acs.jctc.1c01241] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over a series of publications we have introduced a graph-theoretic description for molecular fragmentation. Here, a system is divided into a set of nodes, or vertices, that are then connected through edges, faces, and higher-order simplexes to represent a collection of spatially overlapping and locally interacting subsystems. Each such subsystem is treated at two levels of electronic structure theory, and the result is used to construct many-body expansions that are then embedded within an ONIOM-scheme. These expansions converge rapidly with many-body order (or graphical rank) of subsystems and have been previously used for ab initio molecular dynamics (AIMD) calculations and for computing multidimensional potential energy surfaces. Specifically, in all these cases we have shown that CCSD and MP2 level AIMD trajectories and potential surfaces may be obtained at density functional theory cost. The approach has been demonstrated for gas-phase studies, for condensed phase electronic structure, and also for basis set extrapolation-based AIMD. Recently, this approach has also been used to derive new quantum-computing algorithms that enormously reduce the quantum circuit depth in a circuit-based computation of correlated electronic structure. In this publication, we introduce (a) a family of neural networks that act in parallel to represent, efficiently, the post-Hartree-Fock electronic structure energy contributions for all simplexes (fragments), and (b) a new k-means-based tessellation strategy to glean training data for high-dimensional molecular spaces and minimize the extent of training needed to construct this family of neural networks. The approach is particularly useful when coupled cluster accuracy is desired and when fragment sizes grow in order to capture nonlocal interactions accurately. The unique multidimensional k-means tessellation/clustering algorithm used to determine our training data for all fragments is shown to be extremely efficient and reduces the needed training to only 10% of data for all fragments to obtain accurate neural networks for each fragment. These fully connected dense neural networks are then used to extrapolate the potential energy surface for all molecular fragments, and these are then combined as per our graph-theoretic procedure to transfer the learning process to a full system energy for the entire AIMD trajectory at less than one-tenth the cost as compared to a regular fragmentation-based AIMD calculation.
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Affiliation(s)
- Xiao Zhu
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
| | - Srinivasan S Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States
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38
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Bozkaya U, Ermiş B. Linear-Scaling Systematic Molecular Fragmentation Approach for Perturbation Theory and Coupled-Cluster Methods. J Chem Theory Comput 2022; 18:5349-5359. [PMID: 35972734 PMCID: PMC9476663 DOI: 10.1021/acs.jctc.2c00587] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The coupled-cluster (CC) singles and doubles with perturbative
triples [CCSD(T)] method is frequently referred to as the “gold
standard” of modern computational chemistry. However, the high
computational cost of CCSD(T) [O(N7)], where N is the number of basis functions,
limits its applications to small-sized chemical systems. To address
this problem, efficient implementations of linear-scaling coupled-cluster
methods, which employ the systematic molecular fragmentation (SMF)
approach, are reported. In this study, we aim to do the following:
(1) To achieve exact linear scaling and to obtain a pure ab
initio approach, we revise the handling of nonbonded interactions
in the SMF approach, denoted by LSSMF. (2) A new fragmentation algorithm,
which yields smaller-sized fragments, that better fits high-level
CC methods is introduced. (3) A modified nonbonded fragmentation scheme
is proposed to enhance the existent algorithm. Performances of the
LSSMF-CC approaches, such as LSSMF-CCSD(T), are compared with their
canonical versions for a set of alkane molecules, CnH2n+2 (n = 6–10),
which includes 142 molecules. Our results demonstrate that the LSSMF
approach introduces negligible errors compared with the canonical
methods; mean absolute errors (MAEs) are between 0.20 and 0.59 kcal
mol–1 for LSSMF(3,1)-CCSD(T). For a larger alkanes
set (L12), CnH2n+2 (n = 50–70), the performance of
LSSMF for the second-order perturbation theory (MP2) is investigated.
For the L12 set, various bonded and nonbonded levels are considered.
Our results demonstrate that the combination of bonded level 6 with
nonbonded level 2, LSSMF(6,2), provides very accurate results for
the MP2 method with a MAE value of 0.32 kcal mol–1. The LSSMF(6,2) approach yields more than a 26-fold reduction in
errors compared with LSSMF(3,1). Hence, we obtain substantial improvements
over the original SMF approach. To illustrate the efficiency and applicability
of the LSSMF-CCSD(T) approach, we consider an alkane molecule with
10,004 atoms. For this molecule, the LSSMF(3,1)-CCSD(T)/cc-pVTZ energy
computation, on a Linux cluster with 100 nodes, 4 cores, and 5 GB
of memory provided to each node, is performed just in ∼24 h.
As a second test, we consider a biomolecular complex (PDB code: 1GLA), which includes
10,488 atoms, to assess the efficiency of the LSSMF approach. The
LSSMF(3,1)-FNO–CCSD(T)/cc-pVTZ energy computation is completed
in ∼7 days for the biomolecular complex. Hence, our results
demonstrate that the LSSMF-CC approaches are very efficient. Overall,
we conclude the following: (1) The LSSMF(m, n)-CCSD(T) methods can be reliably used for large-scale
chemical systems, where the canonical methods are not computationally
affordable. (2) The accuracy of bonded level 3 is not satisfactory
for large chemical systems. (3) For high-accuracy studies, bonded
level 5 (or higher) and nonbonded level 2 should be employed.
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Affiliation(s)
- Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Betül Ermiş
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
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39
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Hellmers J, Hedegård ED, König C. Fragmentation-Based Decomposition of a Metalloenzyme-Substrate Interaction: A Case Study for a Lytic Polysaccharide Monooxygenase. J Phys Chem B 2022; 126:5400-5412. [PMID: 35833656 DOI: 10.1021/acs.jpcb.2c02883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a novel decomposition scheme for electronic interaction energies based on the flexible formulation of fragmentation schemes through fragment combination ranges (FCRs; J. Chem. Phys., 2021, 155, 164105). We devise a clear additive decomposition with contribution of nondisjoint fragments and correction terms for overlapping fragments and apply this scheme to the metalloenzyme-substrate complex of a lytic polysaccharide monooxygenase (LPMO) with an oligosaccharide. By this, we further illustrate the straightforward adaptability of the FCR-based schemes to novel systems. Our calculations suggest that the description of the electronic structure is a larger error source than the fragmentation scheme. In particular, we find a large impact of the basis set size on the interaction energies. Still, the introduction of three-body interaction terms in the fragmentation setup improves the agreement to the supermolecular reference. Yet, the qualitative results for the decomposition scheme with two-body terms only largely agree within the investigated electronic-structure approaches and basis sets, which are B97-3c, DFT (TPSS and B3LYP), and MP2 methods. The overlap contributions are found to be small, allowing analysis of the interaction energy into individual amino acid residues: We find a particularly strong interaction between the substrate and the LPMO copper active site.
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Affiliation(s)
- Janine Hellmers
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, 30167 Hannover, Germany
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
| | - Carolin König
- Institute of Physical Chemistry and Electrochemistry, Leibniz University Hannover, 30167 Hannover, Germany
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40
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Chakraborty A, Tribedi S, Maitra R. A double exponential coupled cluster theory in the fragment molecular orbital framework. J Chem Phys 2022; 156:244117. [DOI: 10.1063/5.0090115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Fragmentation-based methods enable electronic structure calculations for large chemical systems through partitioning them into smaller fragments. Here, we have developed and benchmarked a dual exponential operator-based coupled cluster theory to account for high-rank electronic correlation of large chemical systems within the fragment molecular orbital (FMO) framework. Upon partitioning the molecular system into several fragments, the zeroth order reference determinants for each fragment and fragment pair are constructed in a self-consistent manner with two-body FMO expansion. The dynamical correlation is induced through a dual exponential ansatz with a set of fragment-specific rank-one and rank-two operators that act on the individual reference determinants. While the single and double excitations for each fragment are included through the conventional rank-one and rank-two cluster operators, the triple excitation space is spanned via the contraction between the cluster operators and a set of rank-two scattering operators over a few optimized fragment-specific occupied and virtual orbitals. Thus, the high-rank dynamical correlation effects within the FMO framework are computed with rank-one and rank-two parametrization of the wave operator, leading to significant reduction in the number of variables and associated computational scaling over the conventional methods. Through a series of pilot numerical applications on various covalent and non-covalently bonded systems, we have shown the quantitative accuracy of the proposed methodology compared to canonical, as well as FMO-based coupled-cluster single double triple. The accuracy of the proposed method is shown to be systematically improvable upon increasing the number of contractible occupied and virtual molecular orbitals employed to simulate triple excitations.
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Affiliation(s)
- Anish Chakraborty
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Soumi Tribedi
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Rahul Maitra
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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41
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Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating in vivo drug efficacy. More recently, the rise of deep-learning approaches has led to new tools for predicting RNA-small molecule binding. In this review, we present an overview of the recently developed computational methods for RNA-ligand docking and their advantages and disadvantages.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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42
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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43
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Chodkiewicz M, Pawlędzio S, Woińska M, Woźniak K. Fragmentation and transferability in Hirshfeld atom refinement. IUCRJ 2022; 9:298-315. [PMID: 35371499 PMCID: PMC8895009 DOI: 10.1107/s2052252522000690] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/19/2022] [Indexed: 05/06/2023]
Abstract
Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal-organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.
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Affiliation(s)
- Michał Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
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44
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Li Y, Wang D, Fu F, Xia Q, Li W, Li S. Structures and properties of ionic crystals and condensed phase ionic liquids predicted with the generalized energy-based fragmentation method. J Comput Chem 2022; 43:704-716. [PMID: 35213748 DOI: 10.1002/jcc.26828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/11/2022]
Abstract
The generalized energy-based fragmentation (GEBF) approach is extended to facilitate ab initio investigations of structures, lattice energies, vibrational spectra and 1 H NMR chemical shifts of ionic crystals and condensed-phase ionic liquids (ILs) with the periodic boundary conditions (PBC). For selected periodic systems, our results demonstrate that the so-called PBC-GEBF approach can provide satisfactory descriptions on ground-state energies, structures, and vibrational spectra of ionic crystals and IL crystals. The PBC-GEBF approach is then applied to three realistic condensed phase systems. For three ionic crystals (LiCl, NaCl, and KCl), we apply the PBC-GEBF approach with MP2 theory as well as some popular DFT methods to investigate their crystal structures and lattice energies. Our calculations indicate that the crystal structures obtained with PBC-GEBF-MP2/6-311 + G** are very close to the corresponding X-ray structures, while PBC-GEBF-ωB97X-D/6-311 + G** provides satisfactory prediction for crystal structures and lattice energies. For two polymorphs of [n-C4 mim][Cl] crystals, we find that the PBC-GEBF approach at the M06-2X/6-311 + G** level can give a satisfactory descriptions on structures and Raman spectra of these two crystals. Furthermore, for [C2 mim][BF4 ] ILs, we demonstrate that their 1 H NMR chemical shifts can be estimated from averaging over 5 typical snapshots (extracted from MD simulations) with the PBC-GEBF approach at the B97-2/pcSseg-2 level. The calculated results account for the observed experimental data quite well. Therefore, we expect that the PBC-GEBF approach, combined with various quantum chemistry methods, will become an effective tool in predicting structures and properties of ionic crystals and condensed-phase ILs.
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Affiliation(s)
- Yunzhi Li
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China.,School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, China
| | - Dong Wang
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Fangjia Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, China
| | - Qiying Xia
- School of Chemistry and Chemical Engineering, Linyi University, Linyi, China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing, China
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45
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Tölle J, Neugebauer J. The Seamless Connection of Local and Collective Excited States in Subsystem Time-Dependent Density Functional Theory. J Phys Chem Lett 2022; 13:1003-1018. [PMID: 35061387 DOI: 10.1021/acs.jpclett.1c04023] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The theoretical understanding of photoinduced processes in multichromophoric systems requires, as an essential ingredient, the possibility of accurately describing their electronically excited states. However, the size of these systems often prohibits the usage of conventional electronic-structure methods, so that often multiscale approaches based on phenomenologically motivated models are employed. In contrast, subsystem time-dependent density functional theory (sTDDFT) allows for a subsystem-based ab initio description of multichromophoric systems and therefore allows for, in principle, an exact description of photoinduced processes. This Perspective aims to outline the theoretical foundations and commonly used practical realizations as well as to illustrate benefits of recent developments and open issues in the field of sTDDFT. Prospective, potential future applications and possible methodological developments are discussed.
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Affiliation(s)
- Johannes Tölle
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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46
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Energy-based fragmentation contribution approach for calculating the fluorescence spectrum of biomacromolecules. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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47
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Decomposition of the interaction energy of several flavonoids with Escherichia coli DNA Gyr using the SAPT (DFT) method: The relation between the interaction energy components, ligand structure, and biological activity. Biochim Biophys Acta Gen Subj 2022; 1866:130111. [DOI: 10.1016/j.bbagen.2022.130111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/19/2022] [Accepted: 02/07/2022] [Indexed: 12/28/2022]
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48
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Bozkaya U, Ermiş B, Alagöz Y, Ünal A, Uyar AK. MacroQC 1.0: An electronic structure theory software for large-scale applications. J Chem Phys 2022; 156:044801. [DOI: 10.1063/5.0077823] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Uğur Bozkaya
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Betül Ermiş
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Yavuz Alagöz
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Aslı Ünal
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Ali Kaan Uyar
- Department of Chemistry, Hacettepe University, Ankara 06800, Turkey
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49
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Wang K, Xie Z, Luo Z, Ma H. Low-Scaling Excited State Calculation Using the Block Interaction Product State. J Phys Chem Lett 2022; 13:462-470. [PMID: 35015548 DOI: 10.1021/acs.jpclett.1c03445] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We develop an automatic and efficient scheme for the accurate construction of the bases for excitonic models, which can enable "black-box" excited state structure calculations for large molecular systems. These new and optimized bases, which are named the block interaction product state (BIPS), can be expressed as the direct products of the local states for each chromophore. Each chromophore's local states are selected by diagonalization of its reduced density matrix, which is obtained by quantum chemical calculation of the small subsystem composed of the chromophore and its nearest neighbors. We implemented the BIPS framework with fragment-based calculations considering two- and three-body interactions. Test calculations for eight different molecular aggregates demonstrate that this framework provides an accurate description of not only the excitation energies but also the first-order wave function properties (dipole moment and transition dipole moment) of the low-lying excited states at a low-scaling computational cost.
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Affiliation(s)
- Ke Wang
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhaoxuan Xie
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Zhen Luo
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
| | - Haibo Ma
- School of Chemistry and Chemical Engineering, Jiangsu Key Laboratory of Vehicle Emissions Control, Nanjing University, Nanjing 210023, China
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50
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Shen C, Wang X, He X. Fragment-Based Quantum Mechanical Calculation of Excited-State Properties of Fluorescent RNAs. Front Chem 2022; 9:801062. [PMID: 35004616 PMCID: PMC8727457 DOI: 10.3389/fchem.2021.801062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Fluorescent RNA aptamers have been successfully applied to track and tag RNA in a biological system. However, it is still challenging to predict the excited-state properties of the RNA aptamer–fluorophore complex with the traditional electronic structure methods due to expensive computational costs. In this study, an accurate and efficient fragmentation quantum mechanical (QM) approach of the electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) scheme was applied for calculations of excited-state properties of the RNA aptamer–fluorophore complex. In this method, the excited-state properties were first calculated with one-body fragment quantum mechanics/molecular mechanics (QM/MM) calculation (the excited-state properties of the fluorophore) and then corrected with a series of two-body fragment QM calculations for accounting for the QM effects from the RNA on the excited-state properties of the fluorophore. The performance of the EE-GMFCC on prediction of the absolute excitation energies, the corresponding transition electric dipole moment (TEDM), and atomic forces at both the TD-HF and TD-DFT levels was tested using the Mango-II RNA aptamer system as a model system. The results demonstrate that the calculated excited-state properties by EE-GMFCC are in excellent agreement with the traditional full-system time-dependent ab initio calculations. Moreover, the EE-GMFCC method is capable of providing an accurate prediction of the relative conformational excited-state energies for different configurations of the Mango-II RNA aptamer system extracted from the molecular dynamics (MD) simulations. The fragmentation method further provides a straightforward approach to decompose the excitation energy contribution per ribonucleotide around the fluorophore and then reveals the influence of the local chemical environment on the fluorophore. The applications of EE-GMFCC in calculations of excitation energies for other RNA aptamer–fluorophore complexes demonstrate that the EE-GMFCC method is a general approach for accurate and efficient calculations of excited-state properties of fluorescent RNAs.
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Affiliation(s)
- Chenfei Shen
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| | - Xianwei Wang
- College of Science, Zhejiang University of Technology, Hangzhou, China
| | - Xiao He
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.,New York University-East China Normal University Center for Computational Chemistry at New York University Shanghai, Shanghai, China
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