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Intrinsic molecular vibration and rigorous vibrational assignment of benzene by first-principles molecular dynamics. Sci Rep 2020; 10:17875. [PMID: 33087748 PMCID: PMC7578012 DOI: 10.1038/s41598-020-74872-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/07/2020] [Indexed: 11/08/2022] Open
Abstract
Vibrational assignment, which establishes the correspondence between vibrational modes and spectral frequencies, is a key step in any spectroscopic study. Due to the lack of experimental technique to directly observe the thermal vibration of atoms, the assignment is usually done by empirical trial-and-error method with considerable uncertainty. Here we demonstrate a successful study of intrinsic molecular vibration property based on first-principles molecular dynamics trajectory. A unified approach for calculating and assigning vibrational frequencies is developed and applied to solve some historical issues of benzene vibration. As a major achievement, the experimental frequencies of benzene a2g and b2u vibrations are reassigned, which breaks a deadlock in contemporary spectroscopic science and removes a cloud over the application of density-functional theory in organic chemistry. This work paves the way for the comprehensive realization of the first-principles spectroscopic research, and provides crucial clues to solve the century-old problems of Kekule resonance, π-deformation, and aromaticity.
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2
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Pandey A, Poirier B. Plumbing Potentials for Molecules with Up To Tens of Atoms: How to Find Saddle Points and Fix Leaky Holes. J Phys Chem Lett 2020; 11:6468-6474. [PMID: 32687368 DOI: 10.1021/acs.jpclett.0c01435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Potential energy surfaces (PESs) play an indispensable role in molecular dynamics but are notoriously difficult to flesh out properly in large-dimensional spaces. In particular, the undetected presence of PES holes, i.e., unphysical saddle points beyond which the potential energy drops arbitrarily, can have devastating effects on both classical and quantum dynamics calculations. In this study, the Crystal algorithm is developed as a tool for efficiently and accurately finding PES holes, as well as legitimate saddle points, even in very large-dimensional configuration spaces. The approach is applied to three large-dimensional PESs for molecular systems of current interest: uracil, naphthalene, and formic acid dimer. Low-lying PES holes are discovered and located for the first two systems-including naphthalene, for which no holes were previously suspected, to the best of our knowledge. Likewise, the double-well, double-proton-transfer isomerization saddle point for formic acid dimer is also located.
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Affiliation(s)
- Ankit Pandey
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Bill Poirier
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
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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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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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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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Alam MJ, Ahmad S. FTIR, FT-Raman, UV-Visible spectra and quantum chemical calculations of allantoin molecule and its hydrogen bonded dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:961-978. [PMID: 25459622 DOI: 10.1016/j.saa.2014.09.119] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/22/2014] [Accepted: 09/25/2014] [Indexed: 06/04/2023]
Abstract
FTIR, FT-Raman and electronic spectra of allantoin molecule are recorded and investigated using DFT and MP2 methods with 6-311++G(d,p) basis set. The molecular structure, anharmonic vibrational spectra, natural atomic charges, non-linear optical properties, etc. have been computed for the ground state of allantoin. The anharmonic vibrational frequencies are calculated using PT2 algorithm (Barone method) as well as VSCF and CC-VSCF methods. These methods yield results that are in remarkable agreement with the experiment. The coupling strengths between pairs of modes are also calculated using coupling integral based on 2MR-QFF approximation. The simulations on allantoin dimers have been also performed at B3LYP/6-311++G(d,p) level of theory to investigate the effect of the intermolecular interactions on the molecular structure and vibrational frequencies of the monomer. Vibrational assignments are made with the great accuracy using PED calculations and animated modes. The combination and overtone bands have been also identified in the FTIR spectrum with the help of anharmonic computations. The electronic spectra are simulated in gas and solution at TD-B3LYP/6-311++G(d,p) level of theory. The important global quantities such as electro-negativity, electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO, LUMO energy eigenvalues are also computed. NBO analysis has been performed for monomer and dimers of allantoin at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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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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Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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9
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Kupka T, Stachów M, Chełmecka E, Pasterny K, Stobińska M, Stobiński L, Kaminský J. Efficient Modeling of NMR Parameters in Carbon Nanosystems. J Chem Theory Comput 2013; 9:4275-86. [DOI: 10.1021/ct4002812] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Teobald Kupka
- University of Opole, Faculty of Chemistry,
48, Oleska Street, 45-052 Opole, Poland
| | - Michał Stachów
- University of Opole, Faculty of Chemistry,
48, Oleska Street, 45-052 Opole, Poland
| | - Elżbieta Chełmecka
- Division of Statistics, Department
of Instrumental Analysis, Medical University of Silesia, 30 Ostrogórska Street, 41-200 Sosnowiec, Poland
| | - Karol Pasterny
- A. Chełkowski Institute of
Physics, University of Silesia, 4 Uniwersytecka
Street, 40-007 Katowice, Poland
| | - Magdalena Stobińska
- Institute of Theoretical Physics and Astrophysics, University of Gdańsk, 57 Wita Stwosza Street, 80-952 Gdańsk,
Poland
- Institute of Physics, Polish Academy of Sciences, 32/46, al. Lotników,
02-668 Warsaw, Poland
| | - Leszek Stobiński
- Institute
of Physical Chemistry, Polish Academy of Sciences, 44/52 Kasprzaka Street, 01-224 Warsaw, Poland
| | - Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nam. 2., 166
10 Prague, Czech Republic
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Maeda S, Ohno K, Morokuma K. Systematic exploration of the mechanism of chemical reactions: the global reaction route mapping (GRRM) strategy using the ADDF and AFIR methods. Phys Chem Chem Phys 2013; 15:3683-701. [DOI: 10.1039/c3cp44063j] [Citation(s) in RCA: 358] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Alam MJ, Ahmad S. Anharmonic vibrational studies of L-aspartic acid using HF and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 96:992-1004. [PMID: 22939282 DOI: 10.1016/j.saa.2012.07.135] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/20/2012] [Accepted: 07/26/2012] [Indexed: 06/01/2023]
Abstract
The experimental and theoretical studies on the structure, molecular properties and vibrational spectra of L-aspartic acid are presented. The molecular structure, harmonic and anharmonic vibrational frequencies, molecular properties, MEP mapping, NBO analysis and electronic spectra of L-aspartic acid have been reported. Computed geometrical parameters and anharmonic frequencies of fundamental, combination and overtone transitions were found in satisfactory agreement with the experimental data. The UV-Vis spectrum of present molecule has been recorded and the electronic properties such as HOMO and LUMO energies and few low lying excited states were carried out by using time dependent density functional theory (TD-DFT) approach. Natural Bond Orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Molecular electrostatic potential map has also been used for quantitative measure of the chemical activities of various sites of the molecule.
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Affiliation(s)
- Mohammad Jane Alam
- Department of Physics, Aligarh Muslim University, Aligarh 202 002, India
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