1
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Sun Y. Efficient acceleration of the convergence of the minimum free energy path via a path-planning generated initial guess. J Comput Chem 2024. [PMID: 39291721 DOI: 10.1002/jcc.27504] [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: 05/17/2024] [Revised: 07/25/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024]
Abstract
We demonstrate that combining a shifted clustering algorithm with a fast-marching-based algorithm can generate accurate approximations of the minimum energy path (MEP) given a free energy landscape (FEL). Using this approximation as the initial guess for the MEP, followed by further refinement with the string method (referred to as the fast marching tree (FMT)-string combined approach), significantly reduces the number of iterations required for MEP convergence. This approach saves substantial time compared to using linear interpolation (LI) for the initial guess. Our method offers a viable solution for obtaining an effective initial guess of the MEP when an approximate or converged FEL is available. This work highlights the potential of applying FMT-based approaches to extract the MEP in chemical reactions.
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Affiliation(s)
- Yi Sun
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
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2
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Plasencia Gutiérrez M, Argáez C, Jónsson H. Improved Minimum Mode Following Method for Finding First Order Saddle Points. J Chem Theory Comput 2016; 13:125-134. [DOI: 10.1021/acs.jctc.5b01216] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Carlos Argáez
- Science Institute of the University of Iceland, 107 Reykjavı́k, Iceland
| | - Hannes Jónsson
- Faculty
of Physical Sciences, University of Iceland, 107 Reykjavı́k, Iceland
- Applied
Physics Department, Aalto University, FIN-00076 Espoo, Finland
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3
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Ohno K. Study of Potential Energy Surfaces towards Global Reaction Route Mapping. CHEM REC 2016; 16:2198-2218. [PMID: 27059804 DOI: 10.1002/tcr.201500284] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Indexed: 11/11/2022]
Abstract
The potential energy surface (PES) is just a theoretical construct based on the Born-Oppenheimer approximation, but it underlies various phenomena, including molecular vibrations, collisional ionizations, and chemical reactions. This account describes how a new idea for global reaction route mapping (GRRM), which had seemed to be impossible for chemical systems with more than three atoms, was born and has been developed during the course of the study of the PES. GRRM has pioneered new fields of chemistry. Furthermore, techniques for GRRM are still developing, and GRRM is further extending its application to various areas of chemistry and chemical physics.
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Affiliation(s)
- Koichi Ohno
- Institute for Quantum Chemical Exploration, Minato-ku, Tokyo, 108-0022, Japan.
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4
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Satoh H, Oda T, Nakakoji K, Uno T, Tanaka H, Iwata S, Ohno K. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers. J Chem Theory Comput 2016; 12:5293-5308. [PMID: 27673598 DOI: 10.1021/acs.jctc.6b00439] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4 and 4C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1 conformations; that is, the potential energy of the global minimum of 4C1 is lower than that of 1C4 (thermodynamic predominance) and that the highest energy of those of all the TS structures along a route from 4C1 to 1C4 is lower than that of 1C4 to 4C1 (kinetic predominance).
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Affiliation(s)
- Hiroko Satoh
- Research Organization of Information and Systems (ROIS), Tokyo 105-0001, Japan.,Department of Chemistry, University of Zurich , 8057 Zurich, Switzerland.,National Institute of Informatics (NII), Tokyo 101-8430, Japan.,Institute for Quantum Chemical Exploration (IQCE), Tokyo 108-0022, Japan
| | - Tomohiro Oda
- Software Research Associates Inc., Tokyo 171-8513, Japan
| | - Kumiyo Nakakoji
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University , Kyoto 606-8501, Japan
| | - Takeaki Uno
- National Institute of Informatics (NII), Tokyo 101-8430, Japan
| | - Hiroaki Tanaka
- Department of Mathematical Informatics, University of Tokyo , Tokyo 113-8654, Japan
| | - Satoru Iwata
- Department of Mathematical Informatics, University of Tokyo , Tokyo 113-8654, Japan
| | - Koichi Ohno
- Institute for Quantum Chemical Exploration (IQCE), Tokyo 108-0022, Japan.,Department of Chemistry, Graduate School of Science, Tohoku University , Sendai 980-8578, Japan
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5
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Beć KB, Futami Y, Wójcik MJ, Nakajima T, Ozaki Y. Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region. J Phys Chem A 2016; 120:6170-83. [PMID: 27482762 DOI: 10.1021/acs.jpca.6b04470] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid was possible, with successful identification of numerous experimental bands, including those which originate from concentration effects. It was also found that the main spectral features observed in the NIR spectra of carboxylic acid upon the formation of hydrogen bond should be accounted for combination modes of the stretching and bending vibrations of double hydrogen-bonded bridge in the cyclic dimers of acetic acid.
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Affiliation(s)
- Krzysztof B Beć
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University , Sanda, Hyogo 669-1337, Japan.,RIKEN , 519-1399 Aramaki-Aoba, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Yoshisuke Futami
- Department of Biological and Chemical Systems Engineering, National Institute of Technology, Kumamoto College , Yatsushiro, Kumamoto 866-8501, Japan
| | - Marek J Wójcik
- Faculty of Chemistry, Jagiellonian University , Ingardena 3, 30-060 Kraków, Poland
| | - Takahito Nakajima
- RIKEN Advanced Institute for Computational Science , 7-1-26, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yukihiro Ozaki
- Department of Chemistry, School of Science and Technology, Kwansei Gakuin University , Sanda, Hyogo 669-1337, Japan
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6
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Czarnecki MA, Morisawa Y, Futami Y, Ozaki Y. Advances in Molecular Structure and Interaction Studies Using Near-Infrared Spectroscopy. Chem Rev 2015; 115:9707-44. [DOI: 10.1021/cr500013u] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Yusuke Morisawa
- Department
of Chemistry, School of Science and Engineering, Kinki University, Higashi-Osaka, Osaka 577-8502, Japan
| | - Yoshisuke Futami
- Department
of Biological and Chemical Systems Engineering, National Institute of Technology, Kumamoto College, Yatsushiro, Kumamoto 866-8501, Japan
| | - Yukihiro Ozaki
- Department
of Chemistry, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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7
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Maeda S, Taketsugu T, Morokuma K, Ohno K. Anharmonic Downward Distortion Following for Automated Exploration of Quantum Chemical Potential Energy Surfaces. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2014. [DOI: 10.1246/bcsj.20140189] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University
| | | | - Keiji Morokuma
- Fukui Institute for Fundamental Chemistry, Kyoto University
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University
| | - Koichi Ohno
- Graduate School of Science, Tohoku University
- Institute for Quantum Chemical Exploration
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8
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Nance J, Jakubikova E, Kelley CT. Reaction Path Following with Sparse Interpolation. J Chem Theory Comput 2014; 10:2942-9. [PMID: 26588269 DOI: 10.1021/ct5004669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Computing the potential energy of an N-atom molecule is an expensive optimization process of 3N - 6 molecular coordinates, so following reaction pathways as a function of all 3N - 6 coordinates is unfeasible for large molecules. In this paper, we present a method that isolates d < 3N - 6 molecular coordinates and continuously follows reaction paths on d-dimensional potential energy surfaces approximated by a Smolyak's sparse grid interpolation algorithm.1 Compared to dense grids, sparse grids efficiently improve the ratio of invested storage and computing time to approximation accuracy and thus allow one to increase the number of coordinates d in molecular reaction path following simulations. Furthermore, evaluation of the interpolant is much less expensive than the evaluation of the actual energy function, so our technique offers a computationally efficient way to simulate reaction paths on ground and excited state potential energy surfaces. To demonstrate the capabilities of our method, we present simulation results for the isomerization of 2-butene with two, three, and six degrees of freedom.
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Affiliation(s)
- James Nance
- Department of Mathematics and ‡Department of Chemsitry, North Carolina State University , Raleigh, North Carolina, United States
| | - Elena Jakubikova
- Department of Mathematics and ‡Department of Chemsitry, North Carolina State University , Raleigh, North Carolina, United States
| | - C T Kelley
- Department of Mathematics and ‡Department of Chemsitry, North Carolina State University , Raleigh, North Carolina, United States
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9
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Futami Y, Morisawa Y, Ozaki Y, Hamada Y, Wojcik MJ, Ozaki Y. The dielectric constant dependence of absorption intensities and wavenumbers of the fundamental and overtone transitions of stretching vibration of the hydrogen fluoride studied by quantum chemistry calculations. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.01.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Seidler P, Christiansen O. Automatic derivation and evaluation of vibrational coupled cluster theory equations. J Chem Phys 2009; 131:234109. [DOI: 10.1063/1.3272796] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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11
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Seidler P, Kaga T, Yagi K, Christiansen O, Hirao K. On the coupling strength in potential energy surfaces for vibrational calculations. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.10.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Cancès E, Legoll F, Marinica MC, Minoukadeh K, Willaime F. Some improvements of the activation-relaxation technique method for finding transition pathways on potential energy surfaces. J Chem Phys 2009; 130:114711. [DOI: 10.1063/1.3088532] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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14
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Watanabe Y, Maeda S, Ohno K. Intramolecular vibrational frequencies of water clusters (H2O)n (n=2–5): Anharmonic analyses using potential functions based on the scaled hypersphere search method. J Chem Phys 2008; 129:074315. [DOI: 10.1063/1.2973605] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Maeda S, Watanabe Y, Ohno K. Finding important anharmonic terms in the sixth-order potential energy function by the scaled hypersphere search method: An application to vibrational analyses of molecules and clusters. J Chem Phys 2008; 128:144111. [DOI: 10.1063/1.2884348] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Yagi K, Hirata S, Hirao K. Efficient configuration selection scheme for vibrational second-order perturbation theory. J Chem Phys 2007; 127:034111. [PMID: 17655435 DOI: 10.1063/1.2748774] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A fast algorithm of vibrational second-order Moller-Plesset perturbation theory is proposed, enabling a substantial reduction in the number of vibrational self-consistent-field (VSCF) configurations that need to be summed in the calculations. Important configurations are identified a priori by assuming that a reference VSCF wave function is approximated well by harmonic oscillator wave functions and that fifth- and higher-order anharmonicities are negligible. The proposed scheme has reduced the number of VSCF configurations by more than 100 times for formaldehyde, ethylene, and furazan with an error in computed frequencies being not more than a few cm(-1).
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Affiliation(s)
- Kiyoshi Yagi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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18
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Kongsted J, Christiansen O. Automatic generation of force fields and property surfaces for use in variational vibrational calculations of anharmonic vibrational energies and zero-point vibrational averaged properties. J Chem Phys 2006; 125:124108. [PMID: 17014167 DOI: 10.1063/1.2352734] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An automatic and general procedure for the calculation of geometrical derivatives of the energy and general property surfaces for molecular systems is developed and implemented. General expressions for an n-mode representation are derived, where the n-mode representation includes only the couplings between n or less degrees of freedom. The general expressions are specialized to derivative force fields and property surfaces, and a scheme for calculation of the numerical derivatives is implemented. The implementation is interfaced to electronic structure programs and may be used for both ground and excited electronic states. The implementation is done in the context of a vibrational structure program and can be used in combination with vibrational self-consistent field (VSCF), vibrational configuration interaction (VCI), vibrational Moller-Plesset, and vibrational coupled cluster calculations of anharmonic wave functions and calculation of vibrational averaged properties at the VSCF and VCI levels. Sample calculations are presented for fundamental vibrational energies and vibrationally averaged dipole moments and frequency dependent polarizabilities and hyperpolarizabilities of water and formaldehyde.
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Affiliation(s)
- Jacob Kongsted
- Department of Chemistry, University of Aarhus, DK-8000 Aarhus C, Denmark.
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